327 results on '"Ruano, D"'
Search Results
2. Causality and functional relevance of BRCA1 and BRCA2 pathogenic variants in non‐high‐grade serous ovarian carcinomas
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Kramer, CJH, primary, Lanjouw, L, additional, Ruano, D, additional, ter Elst, A, additional, Santandrea, G, additional, Solleveld‐Westerink, N, additional, Werner, N, additional, van der Hout, AH, additional, de Kroon, CD, additional, van Wezel, T, additional, Berger, LPV, additional, Jalving, M, additional, Wesseling, J, additional, Smit, VTHBM, additional, de Bock, GH, additional, van Asperen, CJ, additional, Mourits, MJE, additional, Vreeswijk, MPG, additional, Bart, J, additional, and Bosse, T, additional
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- 2023
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3. Practical guidance for mismatch repair-deficiency testing in endometrial cancer
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Stelloo, E., Jansen, A.M.L., Osse, E.M., Nout, R.A., Creutzberg, C.L., Ruano, D., Church, D.N., Morreau, H., Smit, V.T.H.B.M., van Wezel, T., and Bosse, T.
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- 2017
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4. Causality and functional relevance of BRCA1 and BRCA2 pathogenic variants in non‐high‐grade serous ovarian carcinomas.
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Kramer, CJH, Lanjouw, L, Ruano, D, ter Elst, A, Santandrea, G, Solleveld‐Westerink, N, Werner, N, van der Hout, AH, de Kroon, CD, van Wezel, T, Berger, LPV, Jalving, M, Wesseling, J, Smit, VTHBM, de Bock, GH, van Asperen, CJ, Mourits, MJE, Vreeswijk, MPG, Bart, J, and Bosse, T
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OVARIAN epithelial cancer ,HOMOLOGOUS recombination ,BRCA genes ,PATIENT selection ,CARCINOMA - Abstract
The identification of causal BRCA1/2 pathogenic variants (PVs) in epithelial ovarian carcinoma (EOC) aids the selection of patients for genetic counselling and treatment decision‐making. Current recommendations therefore stress sequencing of all EOCs, regardless of histotype. Although it is recognised that BRCA1/2 PVs cluster in high‐grade serous ovarian carcinomas (HGSOC), this view is largely unsubstantiated by detailed analysis. Here, we aimed to analyse the results of BRCA1/2 tumour sequencing in a centrally revised, consecutive, prospective series including all EOC histotypes. Sequencing of n = 946 EOCs revealed BRCA1/2 PVs in 125 samples (13%), only eight of which were found in non‐HGSOC histotypes. Specifically, BRCA1/2 PVs were identified in high‐grade endometrioid (3/20; 15%), low‐grade endometrioid (1/40; 2.5%), low‐grade serous (3/67; 4.5%), and clear cell (1/64; 1.6%) EOCs. No PVs were identified in any mucinous ovarian carcinomas tested. By re‐evaluation and using loss of heterozygosity and homologous recombination deficiency analyses, we then assessed: (1) whether the eight 'anomalous' cases were potentially histologically misclassified and (2) whether the identified variants were likely causal in carcinogenesis. The first 'anomalous' non‐HGSOC with a BRCA1/2 PV proved to be a misdiagnosed HGSOC. Next, germline BRCA2 variants, found in two p53‐abnormal high‐grade endometrioid tumours, showed substantial evidence supporting causality. One additional, likely causal variant, found in a p53‐wildtype low‐grade serous ovarian carcinoma, was of somatic origin. The remaining cases showed retention of the BRCA1/2 wildtype allele, suggestive of non‐causal secondary passenger variants. We conclude that likely causal BRCA1/2 variants are present in high‐grade endometrioid tumours but are absent from the other EOC histotypes tested. Although the findings require validation, these results seem to justify a transition from universal to histotype‐directed sequencing. Furthermore, in‐depth functional analysis of tumours harbouring BRCA1/2 variants combined with detailed revision of cancer histotypes can serve as a model in other BRCA1/2‐related cancers. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland. [ABSTRACT FROM AUTHOR]
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- 2024
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5. A clinically applicable molecular classification of oncocytic cell thyroid nodules.
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Koster, E.J. de, Corver, W.E., Geus-Oei, L.F. de, Oyen, W.J.G., Ruano, D., Schepers, A., Snel, M., Wezel, T. van, Vriens, D., Morreau, H., Koster, E.J. de, Corver, W.E., Geus-Oei, L.F. de, Oyen, W.J.G., Ruano, D., Schepers, A., Snel, M., Wezel, T. van, Vriens, D., and Morreau, H.
- Abstract
Item does not contain fulltext, Whole chromosome instability with near-whole genome haploidization (GH) and subsequent endoreduplication is considered a main genomic driver in the tumorigenesis of oncocytic cell thyroid neoplasms (OCN). These copy number alterations (CNA) occur less frequently in oncocytic thyroid adenoma (OA) than in oncocytic carcinoma (OCA), suggesting a continuous process. The current study described the CNA patterns in a cohort of 30 benign and malignant OCN, observed using a next-generation sequencing (NGS) panel that assesses genome-wide loss of heterozygosity (LOH) and chromosomal imbalances using 1500 single-nucleotide polymorphisms (SNPs) across all autosomes and the X chromosome in DNA derived from cytological and histological samples. Observed CNA patterns were verified using multiparameter DNA flow cytometry with or without whole-genome SNP array analysis and lesser-allele intensity-ratio (LAIR) analysis. On CNA-LOH analysis using the NGS panel, GH-type CNA were observed in 4 of 11 (36%) OA and in 14 of 16 OCA (88%). Endoreduplication was suspected in 8 of 16 (50%) OCA, all with more extensive GH-type CNA (P < 0.001). Reciprocal chromosomal imbalance type CNA, characterized by (imbalanced) chromosomal copy number gains and associated with benign disease, were observed in 6 of 11 (55%) OA and one equivocal case of OCA. CNA patterns were different between the histopathological subgroups (P < 0.001). By applying the structured interpretation and considerations provided by the current study, CNA-LOH analysis using an NGS panel that is feasible for daily practice may be of great added value to the widespread application of molecular diagnostics in the diagnosis and risk stratification of OCN.
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- 2023
6. Low-grade gliomas: Review of 10 years
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Pardal Souto, M.J., Hernández Marqués, C., Lassaletta Atienza, A., Ruano, D., Cormenzana, M., and Madero, L.
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- 2015
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7. Gliomas de bajo grado: revisión de 10 años
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Pardal Souto, M.J., Hernández Marqués, C., Lassaletta Atienza, A., Ruano, D., Cormenzana, M., and Madero, L.
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- 2015
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8. Gamma delta T cells are effectors of immunotherapy in cancers with HLA class I defects
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Vries, N.L. de, Haar, J. van de, Veninga, V., Chalabi, M., Ijsselsteijn, M.E., Ploeg, M. van der, Bulk, J. van den, Ruano, D., Berg, J.G. van den, Haanen, J.B., Zeverijn, L.J., Geurts, B.S., Wit, G.F. de, Battaglia, T.W., Gelderblom, H., Verheul, H.M.W., Schumacher, T.N., Wessels, L.F.A., Koning, F., Miranda, N.F.C.C. de, and Voest, E.E.
- Abstract
DNA mismatch repair-deficient (MMR-d) cancers present an abundance of neoantigens that is thought to explain their exceptional responsiveness to immune checkpoint blockade (ICB)(1,2). Here, in contrast to other cancer types(3-5), we observed that 20 out of 21 (95%) MMR-d cancers with genomic inactivation of beta 2-microglobulin (encoded by B2M) retained responsiveness to ICB, suggesting the involvement of immune effector cells other than CD8(+) T cells in this context. We next identified a strong association between B2M inactivation and increased infiltration by gamma delta T cells in MMR-d cancers. These gamma delta T cells mainly comprised the V delta 1 and V delta 3 subsets, and expressed high levels of PD-1, other activation markers, including cytotoxic molecules, and a broad repertoire of killer-cell immunoglobulin-like receptors. In vitro, PD-1(+) gamma delta T cells that were isolated from MMR-d colon cancers exhibited enhanced reactivity to human leukocyte antigen (HLA)-class-I-negative MMR-d colon cancer cell lines and B2M-knockout patient-derived tumour organoids compared with antigen-presentation-proficient cells. By comparing paired tumour samples from patients with MMR-d colon cancer that were obtained before and after dual PD-1 and CTLA-4 blockade, we found that immune checkpoint blockade substantially increased the frequency of gamma delta T cells in B2M-deficient cancers. Taken together, these data indicate that gamma delta T cells contribute to the response to immune checkpoint blockade in patients with HLA-class-I-negative MMR-d colon cancers, and underline the potential of gamma delta T cells in cancer immunotherapy.
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- 2023
9. Cancer-specific T helper shared and neo-epitopes uncovered by expression of the MHC class II master regulator CIITA
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Hos, B.J., Tondini, E., Camps, M.G.M., Rademaker, W., Bulk, J. van den, Ruano, D., Janssen, G.M.C., Ru, A.H. de, Elsen, P.J. van den, Miranda, N.F.C.C. de, Veelen, P.A. van, and Ossendorp, F.
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History ,Polymers and Plastics ,Histocompatibility Antigens Class II ,Epitopes, T-Lymphocyte ,Nuclear Proteins ,Cancer Vaccines ,Industrial and Manufacturing Engineering ,General Biochemistry, Genetics and Molecular Biology ,Mice ,HLA Antigens ,Neoplasms ,Vaccines, Subunit ,Trans-Activators ,Animals ,Humans ,Business and International Management ,Peptides - Abstract
We report an approach to identify tumor-specific CD4+ T cell neo-epitopes of both mouse and human cancer cells by analysis of major histocompatibility complex (MHC) class II-eluted natural peptides. MHC class II -presented peptide sequences are identified by introducing the MHC class II transactivator (CIITA) in tumor cells that were originally MHC class II negative. CIITA expression facilitates cell-surface expression of MHC class II molecules and the appropriate peptide-loading machinery. Peptide elution of purified MHC class II molecules and subsequent mass spectrometry reveals oncoviral-and neo-epitopes as well as shared epitopes. Immunological relevance of these epitopes is shown by natural presentation by dendritic cells and immunogenicity. Synthetic peptide vaccination induced functional CD4+ T cell responses, which helped tu-mor control in vivo. Thus, this CIITA transfection approach aids to identify relevant T helper epitopes pre-sented by any MHC class II allele that would be otherwise very difficult to predict and reveals important tar-gets for cancer immunotherapy.
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- 2022
10. 733MO γδT cells are effectors of immune checkpoint blockade in mismatch repair-deficient colon cancers with antigen presentation defects
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Van De Haar, J., primary, de Vries, N.L., additional, Veninga, V., additional, Chalabi, M., additional, Ijsselsteijn, M., additional, van der Ploeg, M., additional, van den Bulk, J., additional, Ruano, D., additional, Haanen, J.B.A.G., additional, Schumacher, T.N., additional, Wessels, L.F.A., additional, Koning, F., additional, de Miranda, N.F.C.C., additional, and Voest, E.E., additional
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- 2022
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11. Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)
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Klionsky, DJ, Abdel-Aziz, AK, Abdelfatah, S, Abdellatif, M, Abdoli, A, Abel, S, Abeliovich, H, Abildgaard, MH, Abudu, YP, Acevedo-Arozena, A, Adamopoulos, IE, Adeli, K, Adolph, TE, Adornetto, A, Aflaki, E, Agam, G, Agarwal, A, Aggarwal, BB, Agnello, M, Agostinis, P, Agrewala, JN, Agrotis, A, Aguilar, PV, Ahmad, ST, Ahmed, ZM, Ahumada-Castro, U, Aits, S, Aizawa, S, Akkoc, Y, Akoumianaki, T, Akpinar, HA, Al-Abd, AM, Al-Akra, L, Al-Gharaibeh, A, Alaoui-Jamali, MA, Alberti, S, Alcocer-Gómez, E, Alessandri, C, Ali, M, Alim Al-Bari, MA, Aliwaini, S, Alizadeh, J, Almacellas, E, Almasan, A, Alonso, A, Alonso, GD, Altan-Bonnet, N, Altieri, DC, Álvarez, ÉMC, Alves, S, Alves da Costa, C, Alzaharna, MM, Amadio, M, Amantini, C, Amaral, C, Ambrosio, S, Amer, AO, Ammanathan, V, An, Z, Andersen, SU, Andrabi, SA, Andrade-Silva, M, Andres, AM, Angelini, S, Ann, D, Anozie, UC, Ansari, MY, Antas, P, Antebi, A, Antón, Z, Anwar, T, Apetoh, L, Apostolova, N, Araki, T, Araki, Y, Arasaki, K, Araújo, WL, Araya, J, Arden, C, Arévalo, M-A, Arguelles, S, Arias, E, Arikkath, J, Arimoto, H, Ariosa, AR, Armstrong-James, D, Arnauné-Pelloquin, L, Aroca, A, Arroyo, DS, Arsov, I, Artero, R, Asaro, DML, Aschner, M, Ashrafizadeh, M, Ashur-Fabian, O, Atanasov, AG, Au, AK, Auberger, P, Auner, HW, Aurelian, L, Autelli, R, Avagliano, L, Ávalos, Y, Aveic, S, Aveleira, CA, Avin-Wittenberg, T, Aydin, Y, Ayton, S, Ayyadevara, S, Azzopardi, M, Baba, M, Backer, JM, Backues, SK, Bae, D-H, Bae, O-N, Bae, SH, Baehrecke, EH, Baek, A, Baek, S-H, Baek, SH, Bagetta, G, Bagniewska-Zadworna, A, Bai, H, Bai, J, Bai, X, Bai, Y, Bairagi, N, Baksi, S, Balbi, T, Baldari, CT, Balduini, W, Ballabio, A, Ballester, M, Balazadeh, S, Balzan, R, Bandopadhyay, R, Banerjee, S, Bánréti, Á, Bao, Y, Baptista, MS, Baracca, A, Barbati, C, Bargiela, A, Barilà, D, Barlow, PG, Barmada, SJ, Barreiro, E, Barreto, GE, Bartek, J, Bartel, B, Bartolome, A, Barve, GR, Basagoudanavar, SH, Bassham, DC, Bast, RC, Basu, A, Batoko, H, Batten, I, Baulieu, EE, Baumgarner, BL, Bayry, J, Beale, R, Beau, I, Beaumatin, F, Bechara, LRG, Beck, GR, Beers, MF, Begun, J, Behrends, C, Behrens, GMN, Bei, R, Bejarano, E, Bel, S, Behl, C, Belaid, A, Belgareh-Touzé, N, Bellarosa, C, Belleudi, F, Belló Pérez, M, Bello-Morales, R, Beltran, JSDO, Beltran, S, Benbrook, DM, Bendorius, M, Benitez, BA, Benito-Cuesta, I, Bensalem, J, Berchtold, MW, Berezowska, S, Bergamaschi, D, Bergami, M, Bergmann, A, Berliocchi, L, Berlioz-Torrent, C, Bernard, A, Berthoux, L, Besirli, CG, Besteiro, S, Betin, VM, Beyaert, R, Bezbradica, JS, Bhaskar, K, Bhatia-Kissova, I, Bhattacharya, R, Bhattacharya, S, Bhattacharyya, S, Bhuiyan, MS, Bhutia, SK, Bi, L, Bi, X, Biden, TJ, Bijian, K, Billes, VA, Binart, N, Bincoletto, C, Birgisdottir, AB, Bjorkoy, G, Blanco, G, Blas-Garcia, A, Blasiak, J, Blomgran, R, Blomgren, K, Blum, JS, Boada-Romero, E, Boban, M, Boesze-Battaglia, K, Boeuf, P, Boland, B, Bomont, P, Bonaldo, P, Bonam, SR, Bonfili, L, Bonifacino, JS, Boone, BA, Bootman, MD, Bordi, M, Borner, C, Bornhauser, BC, Borthakur, G, Bosch, J, Bose, S, Botana, LM, Botas, J, Boulanger, CM, Boulton, ME, Bourdenx, M, Bourgeois, B, Bourke, NM, Bousquet, G, Boya, P, Bozhkov, PV, Bozi, LHM, Bozkurt, TO, Brackney, DE, Brandts, CH, Braun, RJ, Braus, GH, Bravo-Sagua, R, Bravo-San Pedro, JM, Brest, P, Bringer, M-A, Briones-Herrera, A, Broaddus, VC, Brodersen, P, Brodsky, JL, Brody, SL, Bronson, PG, Bronstein, JM, Brown, CN, Brown, RE, Brum, PC, Brumell, JH, Brunetti-Pierri, N, Bruno, D, Bryson-Richardson, RJ, Bucci, C, Buchrieser, C, Bueno, M, Buitrago-Molina, LE, Buraschi, S, Buch, S, Buchan, JR, Buckingham, EM, Budak, H, Budini, M, Bultynck, G, Burada, F, Burgoyne, JR, Burón, MI, Bustos, V, Büttner, S, Butturini, E, Byrd, A, Cabas, I, Cabrera-Benitez, S, Cadwell, K, Cai, J, Cai, L, Cai, Q, Cairó, M, Calbet, JA, Caldwell, GA, Caldwell, KA, Call, JA, Calvani, R, Calvo, AC, Calvo-Rubio Barrera, M, Camara, NO, Camonis, JH, Camougrand, N, Campanella, M, Campbell, EM, Campbell-Valois, F-X, Campello, S, Campesi, I, Campos, JC, Camuzard, O, Cancino, J, Candido de Almeida, D, Canesi, L, Caniggia, I, Canonico, B, Cantí, C, Cao, B, Caraglia, M, Caramés, B, Carchman, EH, Cardenal-Muñoz, E, Cardenas, C, Cardenas, L, Cardoso, SM, Carew, JS, Carle, GF, Carleton, G, Carloni, S, Carmona-Gutierrez, D, Carneiro, LA, Carnevali, O, Carosi, JM, Carra, S, Carrier, A, Carrier, L, Carroll, B, Carter, AB, Carvalho, AN, Casanova, M, Casas, C, Casas, J, Cassioli, C, Castillo, EF, Castillo, K, Castillo-Lluva, S, Castoldi, F, Castori, M, Castro, AF, Castro-Caldas, M, Castro-Hernandez, J, Castro-Obregon, S, Catz, SD, Cavadas, C, Cavaliere, F, Cavallini, G, Cavinato, M, Cayuela, ML, Cebollada Rica, P, Cecarini, V, Cecconi, F, Cechowska-Pasko, M, Cenci, S, Ceperuelo-Mallafré, V, Cerqueira, JJ, Cerutti, JM, Cervia, D, Cetintas, VB, Cetrullo, S, Chae, H-J, Chagin, AS, Chai, C-Y, Chakrabarti, G, Chakrabarti, O, Chakraborty, T, Chami, M, Chamilos, G, Chan, DW, Chan, EYW, Chan, ED, Chan, HYE, Chan, HH, Chan, H, Chan, MTV, Chan, YS, Chandra, PK, Chang, C-P, Chang, C, Chang, H-C, Chang, K, Chao, J, Chapman, T, Charlet-Berguerand, N, Chatterjee, S, Chaube, SK, Chaudhary, A, Chauhan, S, Chaum, E, Checler, F, Cheetham, ME, Chen, C-S, Chen, G-C, Chen, J-F, Chen, LL, Chen, L, Chen, M, Chen, M-K, Chen, N, Chen, Q, Chen, R-H, Chen, S, Chen, W, Chen, X-M, Chen, X-W, Chen, X, Chen, Y, Chen, Y-G, Chen, Y-J, Chen, Y-Q, Chen, ZS, Chen, Z, Chen, Z-H, Chen, ZJ, Cheng, H, Cheng, J, Cheng, S-Y, Cheng, W, Cheng, X, Cheng, X-T, Cheng, Y, Cheng, Z, Cheong, H, Cheong, JK, Chernyak, BV, Cherry, S, Cheung, CFR, Cheung, CHA, Cheung, K-H, Chevet, E, Chi, RJ, Chiang, AKS, Chiaradonna, F, Chiarelli, R, Chiariello, M, Chica, N, Chiocca, S, Chiong, M, Chiou, S-H, Chiramel, AI, Chiurchiù, V, Cho, D-H, Choe, S-K, Choi, AMK, Choi, ME, Choudhury, KR, Chow, NS, Chu, CT, Chua, JP, Chua, JJE, Chung, H, Chung, KP, Chung, S, Chung, S-H, Chung, Y-L, Cianfanelli, V, Ciechomska, IA, Cifuentes, M, Cinque, L, Cirak, S, Cirone, M, Clague, MJ, Clarke, R, Clementi, E, Coccia, EM, Codogno, P, Cohen, E, Cohen, MM, Colasanti, T, Colasuonno, F, Colbert, RA, Colell, A, Čolić, M, Coll, NS, Collins, MO, Colombo, MI, Colón-Ramos, DA, Combaret, L, Comincini, S, Cominetti, MR, Consiglio, A, Conte, A, Conti, F, Contu, VR, Cookson, MR, Coombs, KM, Coppens, I, Corasaniti, MT, Corkery, DP, Cordes, N, Cortese, K, Costa, MDC, Costantino, S, Costelli, P, Coto-Montes, A, Crack, PJ, Crespo, JL, Criollo, A, Crippa, V, Cristofani, R, Csizmadia, T, Cuadrado, A, Cui, B, Cui, J, Cui, Y, Culetto, E, Cumino, AC, Cybulsky, AV, Czaja, MJ, Czuczwar, SJ, D'Adamo, S, D'Amelio, M, D'Arcangelo, D, D'Lugos, AC, D'Orazi, G, da Silva, JA, Dafsari, HS, Dagda, RK, Dagdas, Y, Daglia, M, Dai, X, Dai, Y, Dal Col, J, Dalhaimer, P, Dalla Valle, L, Dallenga, T, Dalmasso, G, Damme, M, Dando, I, Dantuma, NP, Darling, AL, Das, H, Dasarathy, S, Dasari, SK, Dash, S, Daumke, O, Dauphinee, AN, Davies, JS, Dávila, VA, Davis, RJ, Davis, T, Dayalan Naidu, S, De Amicis, F, De Bosscher, K, De Felice, F, De Franceschi, L, De Leonibus, C, de Mattos Barbosa, MG, De Meyer, GRY, De Milito, A, De Nunzio, C, De Palma, C, De Santi, M, De Virgilio, C, De Zio, D, Debnath, J, DeBosch, BJ, Decuypere, J-P, Deehan, MA, Deflorian, G, DeGregori, J, Dehay, B, Del Rio, G, Delaney, JR, Delbridge, LMD, Delorme-Axford, E, Delpino, MV, Demarchi, F, Dembitz, V, Demers, ND, Deng, H, Deng, Z, Dengjel, J, Dent, P, Denton, D, DePamphilis, ML, Der, CJ, Deretic, V, Descoteaux, A, Devis, L, Devkota, S, Devuyst, O, Dewson, G, Dharmasivam, M, Dhiman, R, di Bernardo, D, Di Cristina, M, Di Domenico, F, Di Fazio, P, Di Fonzo, A, Di Guardo, G, Di Guglielmo, GM, Di Leo, L, Di Malta, C, Di Nardo, A, Di Rienzo, M, Di Sano, F, Diallinas, G, Diao, J, Diaz-Araya, G, Díaz-Laviada, I, Dickinson, JM, Diederich, M, Dieudé, M, Dikic, I, Ding, S, Ding, W-X, Dini, L, Dinić, J, Dinic, M, Dinkova-Kostova, AT, Dionne, MS, Distler, JHW, Diwan, A, Dixon, IMC, 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- Abstract
In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.
- Published
- 2021
12. GEIS-SEHOP clinical practice guidelines for the treatment of rhabdomyosarcoma
- Author
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Gallego, S., Bernabeu, D., Garrido-Pontnou, M., Guillen, G., Hindi, N., Juan-Ribelles, A., Marquez, C., Mata, C., Orcajo, J., Ramirez, G., Ramos, M., Romagosa, C., Ruano, D., Rubio, P., Verges, R., Valverde, C., GEIS Grp Espanol Invest Sarcomas, and SEHOP Soc Espanola Hematologia Onc
- Subjects
Alveolar rhabdomyosarcoma, Embryonal rhabdomyosarcoma, Prognostic factors, Rhabdomyosarcoma - Abstract
Rhabdomyosarcoma (RMS) is the most frequent soft tissue sarcoma (STS) in children and adolescents. In Spain the annual incidence is 4.4 cases per million children < 14 years. It is an uncommon neoplasm in adults, but 40% of RMS are diagnosed in patients over 20 years of age, representing 1% of all STS in this age group. RMS can appear anywhere in the body, with some sites more frequently affected including head and neck, genitourinary system and limbs. Assessment of a patient with suspicion of RMS includes imaging studies (MRI, CT, PET-CT) and biopsy. All patients with RMS should receive chemotherapy, either at diagnosis in advanced or metastatic stages, or after initial resection in early local stages. Local control includes surgery and/or radiotherapy depending on site, stage, histology and response to chemotherapy. This guide provides recommendations for diagnosis, staging and treatment of this neoplasm.
- Published
- 2021
13. Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition).
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Quadrilatero J., Walker D.W., Walker M.J., Walker S.A., Walter J., Wandosell F.G., Wang B., Wang C., Wang C.-Y., Wang D., Wang F., Wang G., Wang H., Wang H.-G., Wang J., Wang K., Wang L., Wang M.H., Wang M., Wang N., Wang P., Wang Q.J., Wang Q., Wang Q.K., Wang Q.A., Wang W.-T., Wang W., Wang X., Wang Y.-Y., Wang Y., Wang Z., Warnes G., Warnsmann V., Watada H., Watanabe E., Watchon M., Wawrzynska A., Weaver T.E., Wegrzyn G., Wehman A.M., Wei H., Wei L., Wei T., Wei Y., Weiergraber O.H., Weihl C.C., Weindl G., Weiskirchen R., Wells A., Wen R.H., Wen X., Werner A., Weykopf B., Wheatley S.P., W... [Ovid has truncated this field to avoid Excel character limitations], Klionsky D.J., Abdel-Aziz A.K., Abdelfatah S., Abdellatif M., Abdoli A., Abel S., Abeliovich H., Abildgaard M.H., Abudu Y.P., Acevedo-Arozena A., Adamopoulos I.E., Adeli K., Adolph T.E., Adornetto A., Aflaki E., Agam G., Agarwal A., Aggarwal B.B., Agnello M., Agostinis P., Agrewala J.N., Agrotis A., Aguilar P.V., Ahmad S.T., Ahmed Z.M., Ahumada-Castro U., Aits S., Aizawa S., Akkoc Y., Akoumianaki T., Akpinar H.A., Al-Abd A.M., Al-Akra L., Al-Gharaibeh A., Alaoui-Jamali M.A., Alberti S., Alcocer-Gomez E., Alessandri C., Ali M., Alim Al-Bari M.A., Aliwaini S., Alizadeh J., Almacellas E., Almasan A., Alonso A., Alonso G.D., Altan-Bonnet N., Altieri D.C., Alvarez E.M.C., Alves S., Alves da Costa C., Alzaharna M.M., Amadio M., Amantini C., Amaral C., Ambrosio S., Amer A.O., Ammanathan V., An Z., Andersen S.U., Andrabi S.A., Andrade-Silva M., Andres A.M., Angelini S., Ann D., Anozie U.C., Ansari M.Y., Antas P., Antebi A., Anton Z., Anwar T., Apetoh L., Apostolova N., Araki T., Araki Y., Arasaki K., Araujo W.L., Araya J., Arden C., Arevalo M.-A., Arguelles S., Arias E., Arikkath J., Arimoto H., Ariosa A.R., Armstrong-James D., Arnaune-Pelloquin L., Aroca A., Arroyo D.S., Arsov I., Artero R., Asaro D.M.L., Aschner M., Ashrafizadeh M., Ashur-Fabian O., Atanasov A.G., Au A.K., Auberger P., Auner H.W., Aurelian L., Autelli R., Avagliano L., Avalos Y., Aveic S., Aveleira C.A., Avin-Wittenberg T., Aydin Y., Ayton S., Ayyadevara S., Azzopardi M., Baba M., Backer J.M., Backues S.K., Bae D.-H., Bae O.-N., Bae S.H., Baehrecke E.H., Baek A., Baek S.-H., Baek S.H., Bagetta G., Bagniewska-Zadworna A., Bai H., Bai J., Bai X., Bai Y., Bairagi N., Baksi S., Balbi T., Baldari C.T., Balduini W., Ballabio A., Ballester M., Balazadeh S., Balzan R., Bandopadhyay R., Banerjee S., Banreti A., Bao Y., Baptista M.S., Baracca A., Barbati C., Bargiela A., Barila D., Barlow P.G., Barmada S.J., Barreiro E., Barreto G.E., Bartek J., Bartel B., Bartolome A., Barve G.R., Basagoudanavar S.H., Bassham D.C., Bast R.C., Basu A., Batoko H., Batten I., Baulieu E.E., Baumgarner B.L., Bayry J., Beale R., Beau I., Beaumatin F., Bechara L.R.G., Beck G.R., Beers M.F., Begun J., Behrends C., Behrens G.M.N., Bei R., Bejarano E., Bel S., Behl C., Belaid A., Belgareh-Touze N., Bellarosa C., Belleudi F., Bello Perez M., Bello-Morales R., Beltran J.S.D.O., Beltran S., Benbrook D.M., Bendorius M., Benitez B.A., Benito-Cuesta I., Bensalem J., Berchtold M.W., Berezowska S., Bergamaschi D., Bergami M., Bergmann A., Berliocchi L., Berlioz-Torrent C., Bernard A., Berthoux L., Besirli C.G., Besteiro S., Betin V.M., Beyaert R., Bezbradica J.S., Bhaskar K., Bhatia-Kissova I., Bhattacharya R., Bhattacharya S., Bhattacharyya S., Bhuiyan M.S., Bhutia S.K., Bi L., Bi X., Biden T.J., Bijian K., Billes V.A., Binart N., Bincoletto C., Birgisdottir A.B., Bjorkoy G., Blanco G., Blas-Garcia A., Blasiak J., Blomgran R., Blomgren K., Blum J.S., Boada-Romero E., Boban M., Boesze-Battaglia K., Boeuf P., Boland B., Bomont P., Bonaldo P., Bonam S.R., Bonfili L., Bonifacino J.S., Boone B.A., Bootman M.D., Bordi M., Borner C., Bornhauser B.C., Borthakur G., Bosch J., Bose S., Botana L.M., Botas J., Boulanger C.M., Boulton M.E., Bourdenx M., Bourgeois B., Bourke N.M., Bousquet G., Boya P., Bozhkov P.V., Bozi L.H.M., Bozkurt T.O., Brackney D.E., Brandts C.H., Braun R.J., Braus G.H., Bravo-Sagua R., Bravo-San Pedro J.M., Brest P., Bringer M.-A., Briones-Herrera A., Broaddus V.C., Brodersen P., Brodsky J.L., Brody S.L., Bronson P.G., Bronstein J.M., Brown C.N., Brown R.E., Brum P.C., Brumell J.H., Brunetti-Pierri N., Bruno D., Bryson-Richardson R.J., Bucci C., Buchrieser C., Bueno M., Buitrago-Molina L.E., Buraschi S., Buch S., Buchan J.R., Buckingham E.M., Budak H., Budini M., Bultynck G., Burada F., Burgoyne J.R., Buron M.I., Bustos V., Buttner S., Butturini E., Byrd A., Cabas I., Cabrera-Benitez S., Cadwell K., Cai J., Cai L., Cai 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[Ovid has truncated this field to avoid Excel character limitations], Klionsky D.J., Abdel-Aziz A.K., Abdelfatah S., Abdellatif M., Abdoli A., Abel S., Abeliovich H., Abildgaard M.H., Abudu Y.P., Acevedo-Arozena A., Adamopoulos I.E., Adeli K., Adolph T.E., Adornetto A., Aflaki E., Agam G., Agarwal A., Aggarwal B.B., Agnello M., Agostinis P., Agrewala J.N., Agrotis A., Aguilar P.V., Ahmad S.T., Ahmed Z.M., Ahumada-Castro U., Aits S., Aizawa S., Akkoc Y., Akoumianaki T., Akpinar H.A., Al-Abd A.M., Al-Akra L., Al-Gharaibeh A., Alaoui-Jamali M.A., Alberti S., Alcocer-Gomez E., Alessandri C., Ali M., Alim Al-Bari M.A., Aliwaini S., Alizadeh J., Almacellas E., Almasan A., Alonso A., Alonso G.D., Altan-Bonnet N., Altieri D.C., Alvarez E.M.C., Alves S., Alves da Costa C., Alzaharna M.M., Amadio M., Amantini C., Amaral C., Ambrosio S., Amer A.O., Ammanathan V., An Z., Andersen S.U., Andrabi S.A., Andrade-Silva M., Andres A.M., Angelini S., Ann D., Anozie U.C., Ansari M.Y., Antas P., Antebi A., 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X., Qi Y., Qian W., Qiang L., Qiu Y., Quarleri J., Raben N., Rabinowich H., Ragona D., Ragusa M.J., Rahimi N., Rahmati M., Raia V., Raimundo N., Rajasekaran N.-S., Ramachandra Rao S., Rami A., Ramirez-Pardo I., Ramsden D.B., Randow F., Rangarajan P.N., Ranieri D., Rao H., Rao L., Rao R., Rathore S., Ratnayaka J.A., Ratovitski E.A., Ravanan P., Ravegnini G., Ray S.K., Razani B., Rebecca V., Reggiori F., Regnier-Vigouroux A., Reichert A.S., Reigada D., Reiling J.H., Rein T., Reipert S., Rekha R.S., Ren H., Ren J., Ren W., Renault T., Renga G., Reue K., Rewitz K., Ribeiro de Andrade Ramos B., Riazuddin S.A., Ribeiro-Rodrigues T.M., Ricci J.-E., Ricci R., Riccio V., Richardson D.R., Rikihisa Y., Risbud M.V., Risueno R.M., Ritis K., Rizza S., Rizzuto R., Roberts H.C., Roberts L.D., Robinson K.J., Roccheri M.C., Rocchi S., Rodney G.G., Rodrigues T., Rodrigues Silva V.R., Rodriguez A., Rodriguez-Barrueco R., Rodriguez-Henche N., Rodriguez-Rocha H., Roelofs J., Rogers R.S., Rogov V.V., Rojo 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Viret C., Viscomi M.T., Visnjic D., Vitale I., Vocadlo D.J., Voitsekhovskaja O.V., Volonte C., Volta M., Vomero M., Von Haefen C., Vooijs M.A., Voos W., Vucicevic L., Wade-Martins R., Waguri S., Waite K.A., and Wakatsuki S.
- Abstract
In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.Copyright © 2020 Informa UK Limited, trading as Taylor & Francis Group.
- Published
- 2021
14. Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1.
- Author
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Klionsky D.J., Abdel-Aziz A.K., Abdelfatah S., Abdellatif M., Abdoli A., Abel S., Abeliovich H., Abildgaard M.H., Abudu Y.P., Acevedo-Arozena A., Adamopoulos I.E., Adeli K., Adolph T.E., Adornetto A., Aflaki E., Agam G., Agarwal A., Aggarwal B.B., Agnello M., Agostinis P., Agrewala J.N., Agrotis A., Aguilar P.V., Ahmad S.T., Ahmed Z.M., Ahumada-Castro U., Aits S., Aizawa S., Akkoc Y., Akoumianaki T., Akpinar H.A., Al-Abd A.M., Al-Akra L., Al-Gharaibeh A., Alaoui-Jamali M.A., Alberti S., Alcocer-Gomez E., Alessandri C., Ali M., Alim Al-Bari M.A., Aliwaini S., Alizadeh J., Almacellas E., Almasan A., Alonso A., Alonso G.D., Altan-Bonnet N., Altieri D.C., Alvarez E.M.C., Alves S., Alves da Costa C., Alzaharna M.M., Amadio M., Amantini C., Amaral C., Ambrosio S., Amer A.O., Ammanathan V., An Z., Andersen S.U., Andrabi S.A., Andrade-Silva M., Andres A.M., Angelini S., Ann D., Anozie U.C., Ansari M.Y., Antas P., Antebi A., Anton Z., Anwar T., Apetoh L., Apostolova N., Araki T., Araki Y., 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Pereira L.C., Pereira de Almeida L., Perera N.D., Perez-Lara A., Perez-Oliva A.B., Perez-Perez M.E., Periyasamy P., Perl A., Perrotta C., Perrotta I., Pestell R.G., Petersen M., Petrache I., Petrovski G., Pfirrmann T., Pfister A.S., Philips J.A., Pi H., Picca A., Pickrell A.M., Picot S., Pierantoni G.M., Pierdominici M., Pierre P., Pierrefite-Carle V., Pierzynowska K., Pietrocola F., Pietruczuk M., Pignata C., Pimentel-Muinos F.X., Pinar M., Pinheiro R.O., Pinkas-Kramarski R., Pinton P., Pircs K., Piya S., Pizzo P., Plantinga T.S., Platta H.W., Plaza-Zabala A., Plomann M., Plotnikov E.Y., Plun-Favreau H., Pluta R., Pocock R., Poggeler S., Pohl C., Poirot M., Poletti A., Ponpuak M., Popelka H., Popova B., Porta H., Porte Alcon S., Portilla-Fernandez E., Post M., Potts M.B., Poulton J., Powers T., Prahlad V., Prajsnar T.K., Pratico D., Prencipe R., Priault M., Proikas-Cezanne T., Promponas V.J., Proud C.G., Puertollano R., Puglielli L., Pulinilkunnil T., Puri D., Puri R., Puyal J., Qi X., Qi Y., Qian W., Qiang L., Qiu Y., Quadrilatero J., Quarleri J., Raben N., Rabinowich H., Ragona D., Ragusa M.J., Rahimi N., Rahmati M., Raia V., Raimundo N., Rajasekaran N.-S., Ramachandra Rao S., Rami A., Ramirez-Pardo I., Ramsden D.B., Randow F., Rangarajan P.N., Ranieri D., Rao H., Rao L., Rao R., Rathore S., Ratnayaka J.A., Ratovitski E.A., Ravanan P., Ravegnini G., Ray S.K., Razani B., Rebecca V., Reggiori F., Regnier-Vigouroux A., Reichert A.S., Reigada D., Reiling J.H., Rein T., Reipert S., Rekha R.S., Ren H., Ren J., Ren W., Renault T., Renga G., Reue K., Rewitz K., Ribeiro de Andrade Ramos B., Riazuddin S.A., Ribeiro-Rodrigues T.M., Ricci J.-E., Ricci R., Riccio V., Richardson D.R., Rikihisa Y., Risbud M.V., Risueno R.M., Ritis K., Rizza S., Rizzuto R., Roberts H.C., Roberts L.D., Robinson K.J., Roccheri M.C., Rocchi S., Rodney G.G., Rodrigues T., Rodrigues Silva V.R., Rodriguez A., Rodriguez-Barrueco R., Rodriguez-Henche N., Rodriguez-Rocha H., Roelofs J., Rogers R.S., Rogov V.V., Rojo A.I., Rolka K., Romanello V., Romani L., Romano A., Romano P.S., Romeo-Guitart D., Romero L.C., Romero M., Roney J.C., Rongo C., Roperto S., Rosenfeldt M.T., Rosenstiel P., Rosenwald A.G., Roth K.A., Roth L., Roth S., Rouschop K.M.A., Roussel B.D., Roux S., Rovere-Querini P., Roy A., Rozieres A., Ruano D., Rubinsztein D.C., Rubtsova M.P., Ruckdeschel K., Ruckenstuhl C., Rudolf E., Rudolf R., Ruggieri A., Ruparelia A.A., Rusmini P., Russell R.R., Russo G.L., Russo M., Russo R., Ryabaya O.O., Ryan K.M., Ryu K.-Y., Sabater-Arcis M., Sachdev U., Sacher M., Sachse C., Sadhu A., Sadoshima J., Safren N., Saftig P., Sagona A.P., Sahay G., Sahebkar A., Sahin M., Sahin O., Sahni S., Saito N., Saito S., Saito T., Sakai R., Sakai Y., Sakamaki J.-I., Saksela K., Salazar G., Salazar-Degracia A., Salekdeh G.H., Saluja A.K., Sampaio-Marques B., Sanchez M.C., Sanchez-Alcazar J.A., Sanchez-Vera V., Sancho-Shimizu V., Sanderson J.T., Sandri M., Santaguida S., Santambrogio L., Santana 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[Ovid has truncated this field to avoid Excel character limitations]
- Abstract
In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.Copyright © 2020 Informa UK Limited, trading as Taylor & Francis Group.
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- 2021
15. Prevalence and Prognosis of Lynch Syndrome and Sporadic Mismatch Repair Deficiency in Endometrial Cancer
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Post, CCB, Stelloo, E, Smit, VTHBM, Ruano, D, Tops, CM, Vermij, L, Rutten, TA, Jurgenliemk-Schulz, IM, Lutgens, LCHW, Jobsen, JJ, Nout, RA, Crosbie, EJ, Powell, ME, Mileshkin, L, Leary, A, Bessette, P, Putter, H, de Boer, SM, Horeweg, N, Nielsen, M, van Wezel, T, Bosse, T, Creutzberg, CL, Post, CCB, Stelloo, E, Smit, VTHBM, Ruano, D, Tops, CM, Vermij, L, Rutten, TA, Jurgenliemk-Schulz, IM, Lutgens, LCHW, Jobsen, JJ, Nout, RA, Crosbie, EJ, Powell, ME, Mileshkin, L, Leary, A, Bessette, P, Putter, H, de Boer, SM, Horeweg, N, Nielsen, M, van Wezel, T, Bosse, T, and Creutzberg, CL
- Abstract
BACKGROUND: Standard screening of endometrial cancer (EC) for Lynch syndrome (LS) is gaining traction; however, the prognostic impact of an underlying hereditary etiology is unknown. We established the prevalence, prognosis, and subsequent primary cancer incidence of patients with LS-associated EC in relation to sporadic mismatch repair deficient (MMRd)-EC in the large combined Post Operative Radiation Therapy in Endometrial Carcinoma-1, -2, and -3 trial cohort. METHODS: After MMR-immunohistochemistry, MLH1-promoter methylation testing, and next-generation sequencing, tumors were classified into 3 groups according to the molecular cause of their MMRd-EC. Kaplan-Meier method, log-rank test, and Cox model were used for survival analysis. Competing risk analysis was used to estimate the subsequent cancer probability. All statistical tests were 2-sided. RESULTS: Among the 1336 ECs, 410 (30.7%) were MMRd. A total of 380 (92.7%) were fully triaged: 275 (72.4%) were MLH1-hypermethylated MMRd-ECs; 36 (9.5%) LS MMRd-ECs, and 69 (18.2%) MMRd-ECs due to other causes. Limiting screening of EC patients to 60 years or younger or to 70 years or younger would have resulted in missing 18 (50.0%) and 6 (16.7%) LS diagnoses, respectively. Five-year recurrence-free survival was 91.7% (95% confidence interval [CI] = 83.1% to 100%; hazard ratio = 0.45, 95% CI = 0.16 to 1.24, P = .12) for LS, 95.5% (95% CI = 90.7% to 100%; hazard ratio = 0.17, 95% CI = 0.05 to 0.55, P = .003) for "other" vs 78.6% (95% CI = 73.8% to 83.7%) for MLH1-hypermethylated MMRd-EC. The probability of subsequent LS-associated cancer at 10 years was 11.6% (95% CI = 0.0% to 24.7%), 1.5% (95% CI = 0.0% to 4.3%), and 7.0% (95% CI = 3.0% to 10.9%) within the LS, "other," and MLH1-hypermethylated MMRd-EC groups, respectively. CONCLUSIONS: The LS prevalence in the Post Operative Radiation Therapy in Endometrial Carcinoma trial population was 2.8% and among MMRd-ECs was 9.5%. Patients with LS-associated ECs showed a trend t
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- 2021
16. Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)
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Klionsky, D, Abdel-Aziz, A, Abdelfatah, S, Abdellatif, M, Abdoli, A, Abel, S, Abeliovich, H, Abildgaard, M, Abudu, Y, Acevedo-Arozena, A, Adamopoulos, I, Adeli, K, Adolph, T, Adornetto, A, Aflaki, E, Agam, G, Agarwal, A, Aggarwal, B, Agnello, M, Agostinis, P, Agrewala, J, Agrotis, A, Aguilar, P, Ahmad, S, Ahmed, Z, Ahumada-Castro, U, Aits, S, Aizawa, S, Akkoc, Y, Akoumianaki, T, Akpinar, H, Al-Abd, A, Al-Akra, L, Al-Gharaibeh, A, Alaoui-Jamali, M, Alberti, S, Alcocer-Gómez, E, Alessandri, C, Ali, M, Alim Al-Bari, M, Aliwaini, S, Alizadeh, J, Almacellas, E, Almasan, A, Alonso, A, Alonso, G, Altan-Bonnet, N, Altieri, D, Álvarez, É, Alves, S, Alves da Costa, C, Alzaharna, M, Amadio, M, Amantini, C, Amaral, C, Ambrosio, S, Amer, A, Ammanathan, V, An, Z, Andersen, S, Andrabi, S, Andrade-Silva, M, Andres, A, Angelini, S, Ann, D, Anozie, U, Ansari, M, Antas, P, Antebi, A, Antón, Z, Anwar, T, Apetoh, L, Apostolova, N, Araki, T, Araki, Y, Arasaki, K, Araújo, W, Araya, J, Arden, C, Arévalo, M, 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Saftig, Paul, Sagona, Antonia P, Sahay, Gaurav, Sahebkar, Amirhossein, Sahin, Mustafa, Sahin, Ozgur, Sahni, Sumit, Saito, Nayuta, Saito, Shigeru, Saito, Tsunenori, Sakai, Ryohei, Sakai, Yasuyoshi, Sakamaki, Jun-Ichi, Saksela, Kalle, Salazar, Gloria, Salazar-Degracia, Anna, Salekdeh, Ghasem H, Saluja, Ashok K, Sampaio-Marques, Belém, Sanchez, Maria Cecilia, Sanchez-Alcazar, Jose A, Sanchez-Vera, Victoria, Sancho-Shimizu, Vanessa, Sanderson, J Thomas, Sandri, Marco, Santaguida, Stefano, Santambrogio, Laura, Santana, Magda M, Santoni, Giorgio, Sanz, Alberto, Sanz, Pascual, Saran, Shweta, Sardiello, Marco, Sargeant, Timothy J, Sarin, Apurva, Sarkar, Chinmoy, Sarkar, Sovan, Sarrias, Maria-Rosa, Sarkar, Surajit, Sarmah, Dipanka Tanu, Sarparanta, Jaakko, Sathyanarayan, Aishwarya, Sathyanarayanan, Ranganayaki, Scaglione, K Matthew, Scatozza, Francesca, Schaefer, Liliana, Schafer, Zachary T, Schaible, Ulrich E, Schapira, Anthony H V, Scharl, Michael, Schatzl, Hermann M, Schein, Catherine H, Scheper, Wiep, Scheuring, David, Schiaffino, Maria Vittoria, Schiappacassi, Monica, Schindl, Rainer, Schlattner, Uwe, Schmidt, Oliver, Schmitt, Roland, Schmidt, Stephen D, Schmitz, Ingo, Schmukler, Eran, Schneider, Anja, Schneider, Bianca E, Schober, Romana, Schoijet, Alejandra C, Schott, Micah B, Schramm, Michael, Schröder, Bernd, Schuh, Kai, Schüller, Christoph, Schulze, Ryan J, Schürmanns, Lea, Schwamborn, Jens C, Schwarten, Melanie, Scialo, Filippo, Sciarretta, Sebastiano, Scott, Melanie J, Scotto, Kathleen W, Scovassi, A Ivana, Scrima, Andrea, Scrivo, Aurora, Sebastian, David, Sebti, Salwa, Sedej, Simon, Segatori, Laura, Segev, Nava, Seglen, Per O, Seiliez, Iban, Seki, Ekihiro, Selleck, Scott B, Sellke, Frank W, Selsby, Joshua T, Sendtner, Michael, Senturk, Serif, Seranova, Elena, Sergi, Consolato, Serra-Moreno, Ruth, Sesaki, Hiromi, Settembre, Carmine, Setty, Subba Rao Gangi, Sgarbi, Gianluca, Sha, Ou, Shacka, John J, Shah, Javeed A, Shang, Dantong, Shao, Changshun, Shao, Feng, Sharbati, Soroush, Sharkey, Lisa M, Sharma, Dipali, Sharma, Gaurav, Sharma, Kulbhushan, Sharma, Pawan, Sharma, Surendra, Shen, Han-Ming, Shen, Hongtao, Shen, Jiangang, Shen, Ming, Shen, Weili, Shen, Zheni, Sheng, Rui, Sheng, Zhi, Sheng, Zu-Hang, Shi, Jianjian, Shi, Xiaobing, Shi, Ying-Hong, Shiba-Fukushima, Kahori, Shieh, Jeng-Jer, Shimada, Yohta, Shimizu, Shigeomi, Shimozawa, Makoto, Shintani, Takahiro, Shoemaker, Christopher J, Shojaei, Shahla, Shoji, Ikuo, Shravage, Bhupendra V, Shridhar, Viji, Shu, Chih-Wen, Shu, Hong-Bing, Shui, Ke, Shukla, Arvind K, Shutt, Timothy E, Sica, Valentina, Siddiqui, Aleem, Sierra, Amanda, Sierra-Torre, Virginia, Signorelli, Santiago, Sil, Payel, Silva, Bruno J de Andrade, Silva, Johnatas D, Silva-Pavez, Eduardo, Silvente-Poirot, Sandrine, Simmonds, Rachel E, Simon, Anna Katharina, Simon, Hans-Uwe, Simons, Matias, Singh, Anurag, Singh, Lalit P, Singh, Rajat, Singh, Shivendra V, Singh, Shrawan K, Singh, Sudha B, Singh, Sunaina, Singh, Surinder Pal, Sinha, Debasish, Sinha, Rohit Anthony, Sinha, Sangita, Sirko, Agnieszka, Sirohi, Kapil, Sivridis, Efthimios L, Skendros, Panagiotis, Skirycz, Aleksandra, Slaninová, Iva, Smaili, Soraya S, Smertenko, Andrei, Smith, Matthew D, Soenen, Stefaan J, Sohn, Eun Jung, Sok, Sophia P M, Solaini, Giancarlo, Soldati, Thierry, Soleimanpour, Scott A, Soler, Rosa M, Solovchenko, Alexei, Somarelli, Jason A, Sonawane, Avinash, Song, Fuyong, Song, Hyun Kyu, Song, Ju-Xian, Song, Kunhua, Song, Zhiyin, Soria, Leandro R, Sorice, Maurizio, Soukas, Alexander A, Soukup, Sandra-Fausia, Sousa, Diana, Sousa, Nadia, Spagnuolo, Paul A, Spector, Stephen A, Srinivas Bharath, M M, St Clair, Daret, Stagni, Venturina, Staiano, Leopoldo, Stalnecker, Clint A, Stankov, Metodi V, Stathopulos, Peter B, Stefan, Katja, Stefan, Sven Marcel, Stefanis, Leonidas, Steffan, Joan S, Steinkasserer, Alexander, Stenmark, Harald, Sterneckert, Jared, Stevens, Craig, Stoka, Veronika, Storch, Stephan, Stork, Björn, Strappazzon, Flavie, Strohecker, Anne Marie, Stupack, Dwayne G, Su, Huanxing, Su, Ling-Yan, Su, Longxiang, Suarez-Fontes, Ana M, Subauste, Carlos S, Subbian, Selvakumar, Subirada, Paula V, Sudhandiran, Ganapasam, Sue, Carolyn M, Sui, Xinbing, Summers, Corey, Sun, Guangchao, Sun, Jun, Sun, Kang, Sun, Meng-Xiang, Sun, Qiming, Sun, Yi, Sun, Zhongjie, Sunahara, Karen K S, Sundberg, Eva, Susztak, Katalin, Sutovsky, Peter, Suzuki, Hidekazu, Sweeney, Gary, Symons, J David, Sze, Stephen Cho Wing, Szewczyk, Nathaniel J, Tabęcka-Łonczynska, Anna, Tabolacci, Claudio, Tacke, Frank, Taegtmeyer, Heinrich, Tafani, Marco, Tagaya, Mitsuo, Tai, Haoran, Tait, Stephen W G, Takahashi, Yoshinori, Takats, Szabolcs, Talwar, Priti, Tam, Chit, Tam, Shing Yau, Tampellini, Davide, Tamura, Atsushi, Tan, Chong Teik, Tan, Eng-King, Tan, Ya-Qin, Tanaka, Masaki, Tanaka, Motomasa, Tang, Daolin, Tang, Jingfeng, Tang, Tie-Shan, Tanida, Isei, Tao, Zhipeng, Taouis, Mohammed, Tatenhorst, Lars, Tavernarakis, Nektarios, Taylor, Allen, Taylor, Gregory A, Taylor, Joan M, Tchetina, Elena, Tee, Andrew R, Tegeder, Irmgard, Teis, David, Teixeira, Natercia, Teixeira-Clerc, Fatima, Tekirdag, Kumsal A, Tencomnao, Tewin, Tenreiro, Sandra, Tepikin, Alexei V, Testillano, Pilar S, Tettamanti, Gianluca, Tharaux, Pierre-Louis, Thedieck, Kathrin, Thekkinghat, Arvind A, Thellung, Stefano, Thinwa, Josephine W, Thirumalaikumar, V P, Thomas, Sufi Mary, Thomes, Paul G, Thorburn, Andrew, Thukral, Lipi, Thum, Thomas, Thumm, Michael, Tian, Ling, Tichy, Ales, Till, Andreas, Timmerman, Vincent, Titorenko, Vladimir I, Todi, Sokol V, Todorova, Krassimira, Toivonen, Janne M, Tomaipitinca, Luana, Tomar, Dhanendra, Tomas-Zapico, Cristina, Tomić, Sergej, Tong, Benjamin Chun-Kit, Tong, Chao, Tong, Xin, Tooze, Sharon A, Torgersen, Maria L, Torii, Satoru, Torres-López, Liliana, Torriglia, Alicia, Towers, Christina G, Towns, Roberto, Toyokuni, Shinya, Trajkovic, Vladimir, Tramontano, Donatella, Tran, Quynh-Giao, Travassos, Leonardo H, Trelford, Charles B, Tremel, Shirley, Trougakos, Ioannis P, Tsao, Betty P, Tschan, Mario P, Tse, Hung-Fat, Tse, Tak Fu, Tsugawa, Hitoshi, Tsvetkov, Andrey S, Tumbarello, David A, Tumtas, Yasin, Tuñón, María J, Turcotte, Sandra, Turk, Boris, Turk, Vito, Turner, Bradley J, Tuxworth, Richard I, Tyler, Jessica K, Tyutereva, Elena V, Uchiyama, Yasuo, Ugun-Klusek, Aslihan, Uhlig, Holm H, Ułamek-Kozioł, Marzena, Ulasov, Ilya V, Umekawa, Midori, Ungermann, Christian, Unno, Rei, Urbe, Sylvie, Uribe-Carretero, Elisabet, Üstün, Suayib, Uversky, Vladimir N, Vaccari, Thomas, Vaccaro, Maria I, Vahsen, Björn F, Vakifahmetoglu-Norberg, Helin, Valdor, Rut, Valente, Maria J, Valko, Ayelén, Vallee, Richard B, Valverde, Angela M, Van den Berghe, Greet, van der Veen, Stijn, Van Kaer, Luc, van Loosdregt, Jorg, van Wijk, Sjoerd J L, Vandenberghe, Wim, Vanhorebeek, Ilse, Vannier-Santos, Marcos A, Vannini, Nicola, Vanrell, M Cristina, Vantaggiato, Chiara, Varano, Gabriele, Varela-Nieto, Isabel, Varga, Máté, Vasconcelos, M Helena, Vats, Somya, Vavvas, Demetrios G, Vega-Naredo, Ignacio, Vega-Rubin-de-Celis, Silvia, Velasco, Guillermo, Velázquez, Ariadna P, Vellai, Tibor, Vellenga, Edo, Velotti, Francesca, Verdier, Mireille, Verginis, Panayotis, Vergne, Isabelle, Verkade, Paul, Verma, Manish, Verstreken, Patrik, Vervliet, Tim, Vervoorts, Jörg, Vessoni, Alexandre T, Victor, Victor M, Vidal, Michel, Vidoni, Chiara, Vieira, Otilia V, Vierstra, Richard D, Viganó, Sonia, Vihinen, Helena, Vijayan, Vinoy, Vila, Miquel, Vilar, Marçal, Villalba, José M, Villalobo, Antonio, Villarejo-Zori, Beatriz, Villarroya, Francesc, Villarroya, Joan, Vincent, Olivier, Vindis, Cecile, Viret, Christophe, Viscomi, Maria Teresa, Visnjic, Dora, Vitale, Ilio, Vocadlo, David J, Voitsekhovskaja, Olga V, Volonté, Cinzia, Volta, Mattia, Vomero, Marta, Von Haefen, Clarissa, Vooijs, Marc A, Voos, Wolfgang, Vucicevic, Ljubica, Wade-Martins, Richard, Waguri, Satoshi, Waite, Kenrick A, Wakatsuki, Shuji, Walker, David W, Walker, Mark J, Walker, Simon A, Walter, Jochen, Wandosell, Francisco G, Wang, Bo, Wang, Chao-Yung, Wang, Chen, Wang, Chenran, Wang, Chenwei, Wang, Cun-Yu, Wang, Dong, Wang, Fangyang, Wang, Feng, Wang, Fengming, Wang, Guansong, Wang, Han, Wang, Hao, Wang, Hexiang, Wang, Hong-Gang, Wang, Jianrong, Wang, Jigang, Wang, Jiou, Wang, Jundong, Wang, Kui, Wang, Lianrong, Wang, Liming, Wang, Maggie Haitian, Wang, Meiqing, Wang, Nanbu, Wang, Pengwei, Wang, Peipei, Wang, Ping, Wang, Qing Jun, Wang, Qing, Wang, Qing Kenneth, Wang, Qiong A, Wang, Wen-Tao, Wang, Wuyang, Wang, Xinnan, Wang, Xuejun, Wang, Yan, Wang, Yanchang, Wang, Yanzhuang, Wang, Yen-Yun, Wang, Yihua, Wang, Yipeng, Wang, Yu, Wang, Yuqi, Wang, Zhe, Wang, Zhenyu, Wang, Zhouguang, Warnes, Gary, Warnsmann, Verena, Watada, Hirotaka, Watanabe, Eizo, Watchon, Maxinne, Wawrzyńska, Anna, Weaver, Timothy E, Wegrzyn, Grzegorz, Wehman, Ann M, Wei, Huafeng, Wei, Lei, Wei, Taotao, Wei, Yongjie, Weiergräber, Oliver H, Weihl, Conrad C, Weindl, Günther, Weiskirchen, Ralf, Wells, Alan, Wen, Runxia H, Wen, Xin, Werner, Antonia, Weykopf, Beatrice, Wheatley, Sally P, Whitton, J Lindsay, Whitworth, Alexander J, Wiktorska, Katarzyna, Wildenberg, Manon E, Wileman, Tom, Wilkinson, Simon, Willbold, Dieter, Williams, Brett, Williams, Robin S B, Williams, Roger L, Williamson, Peter R, Wilson, Richard A, Winner, Beate, Winsor, Nathaniel J, Witkin, Steven S, Wodrich, Harald, Woehlbier, Ute, Wollert, Thomas, Wong, Esther, Wong, Jack Ho, Wong, Richard W, Wong, Vincent Kam Wai, Wong, W Wei-Lynn, Wu, An-Guo, Wu, Chengbiao, Wu, Jian, Wu, Junfang, Wu, Kenneth K, Wu, Min, Wu, Shan-Ying, Wu, Shengzhou, Wu, Shu-Yan, Wu, Shufang, Wu, William K K, Wu, Xiaohong, Wu, Xiaoqing, Wu, Yao-Wen, Wu, Yihua, Xavier, Ramnik J, Xia, Hongguang, Xia, Lixin, Xia, Zhengyuan, Xiang, Ge, Xiang, Jin, Xiang, Mingliang, Xiang, Wei, Xiao, Bin, Xiao, Guozhi, Xiao, Hengyi, Xiao, Hong-Tao, Xiao, Jian, Xiao, Lan, Xiao, Shi, Xiao, Yin, Xie, Baoming, Xie, Chuan-Ming, Xie, Min, Xie, Yuxiang, Xie, Zhiping, Xie, Zhonglin, Xilouri, Maria, Xu, Congfeng, Xu, En, Xu, Haoxing, Xu, Jing, Xu, JinRong, Xu, Liang, Xu, Wen Wen, Xu, Xiulong, Xue, Yu, Yakhine-Diop, Sokhna M S, Yamaguchi, Masamitsu, Yamaguchi, Osamu, Yamamoto, Ai, Yamashina, Shunhei, Yan, Shengmin, Yan, Shian-Jang, Yan, Zhen, Yanagi, Yasuo, Yang, Chuanbin, Yang, Dun-Sheng, Yang, Huan, Yang, Huang-Tian, Yang, Hui, Yang, Jin-Ming, Yang, Jing, Yang, Jingyu, Yang, Ling, Yang, Liu, Yang, Ming, Yang, Pei-Ming, Yang, Qian, Yang, Seungwon, Yang, Shu, Yang, Shun-Fa, Yang, Wannian, Yang, Wei Yuan, Yang, Xiaoyong, Yang, Xuesong, Yang, Yi, Yang, Ying, Yao, Honghong, Yao, Shenggen, Yao, Xiaoqiang, Yao, Yong-Gang, Yao, Yong-Ming, Yasui, Takahiro, Yazdankhah, Meysam, Yen, Paul M, Yi, Cong, Yin, Xiao-Ming, Yin, Yanhai, Yin, Zhangyuan, Yin, Ziyi, Ying, Meidan, Ying, Zheng, Yip, Calvin K, Yiu, Stephanie Pei Tung, Yoo, Young H, Yoshida, Kiyotsugu, Yoshii, Saori R, Yoshimori, Tamotsu, Yousefi, Bahman, Yu, Boxuan, Yu, Haiyang, Yu, Jun, Yu, Li, Yu, Ming-Lung, Yu, Seong-Woon, Yu, Victor C, Yu, W Haung, Yu, Zhengping, Yu, Zhou, Yuan, Junying, Yuan, Ling-Qing, Yuan, Shilin, Yuan, Shyng-Shiou F, Yuan, Yanggang, Yuan, Zengqiang, Yue, Jianbo, Yue, Zhenyu, Yun, Jeanho, Yung, Raymond L, Zacks, David N, Zaffagnini, Gabriele, Zambelli, Vanessa O, Zanella, Isabella, Zang, Qun S, Zanivan, Sara, Zappavigna, Silvia, Zaragoza, Pilar, Zarbalis, Konstantinos S, Zarebkohan, Amir, Zarrouk, Amira, Zeitlin, Scott O, Zeng, Jialiu, Zeng, Ju-Deng, Žerovnik, Eva, Zhan, Lixuan, Zhang, Bin, Zhang, Donna D, Zhang, Hanlin, Zhang, Hong, Zhang, Honghe, Zhang, Huafeng, Zhang, Huaye, Zhang, Hui, Zhang, Hui-Ling, Zhang, Jianbin, Zhang, Jianhua, Zhang, Jing-Pu, Zhang, Kalin Y B, Zhang, Leshuai W, Zhang, Lin, Zhang, Lisheng, Zhang, Lu, Zhang, Luoying, Zhang, Menghuan, Zhang, Peng, Zhang, Sheng, Zhang, Wei, Zhang, Xiangnan, Zhang, Xiao-Wei, Zhang, Xiaolei, Zhang, Xiaoyan, Zhang, Xin, Zhang, Xinxin, Zhang, Xu Dong, Zhang, Yang, Zhang, Yanjin, Zhang, Yi, Zhang, Ying-Dong, Zhang, 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Werner, Brand-Saberi, Beate, Dong, X Charlie, Kenchappa, Chandra Shekar, Li, Zuguo, Lin, Yong, Oshima, Shigeru, Rong, Yueguang, Sluimer, Judith C, Stallings, Christina L, and Tong, Chun-Kit
- Abstract
In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.
- Published
- 2021
17. 219P Multicentric evaluation of amplicon-based next-generation sequencing solution for local comprehensive molecular tumor profiling
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Jantus Lewintre, E., Rappa, A., Ruano, D., Gallach Garcia, S., Camps Herrero, C.J.C., Lacroix, L., Kashofer, K., van Wezel, T., and Barberis, M.
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- 2023
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18. Increased frequency of 20q gain and copy-neutral loss of heterozygosity in mismatch repair proficient familial colorectal carcinomas
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Middeldorp, A., van Eijk, R., Oosting, J., Forte, G. I., van Puijenbroek, M., van Nieuwenhuizen, M., Corver, W. E., Ruano, D., Caldes, T., Wijnen, J., Morreau, H., and van Wezel, T.
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- 2012
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19. 28 Prevalence and prognosis of lynch syndrome and sporadic mismatch repair deficiency in the combined PORTEC-1,-2 and -3 endometrial cancer trials
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Post, C, primary, Stelloo, E, additional, Smit, V, additional, Ruano, D, additional, Tops, CM, additional, Vermij, L, additional, Rutten, TA, additional, Jürgenliemk-Schulz, IM, additional, Lutgens, LC, additional, Jobsen, JJ, additional, Nout, RA, additional, Crosbie, EJ, additional, Powell, ME, additional, Mileshkin, L, additional, Leary, A, additional, Bessette, P, additional, de Boer, SM, additional, Horeweg, N, additional, van Wezel, T, additional, Bosse, T, additional, and Creutzberg, CL, additional
- Published
- 2020
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20. Genome-wide prediction of functional gene-gene interactions in case-control association studies
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Bochdanovits, Z., Ruano, D., and Heutink, P.
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- 2008
21. #EUROmicroMOOC: using Twitter to share trends in Microbiology worldwide
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Natural Sciences and Engineering Research Council of Canada, López-Goñi, Ignacio, Giner-Lamia, Joaquín, Álvarez-Ordóñez, Avelino, Benítez-Páez, Alfonso, Claessen, David, Cortesao, M., Toro, María de, García-Ruano, D., Granato, E. T., Kovács, Á. T., Romalde, Jesús L., Sana, T. G., Sánchez-Angulo, M., Sangari, Félix J., Smits, W. K., Sturm, T., Thomassin, J. L., Valdehuesa, K. N. G., Zapotoczna, M., Natural Sciences and Engineering Research Council of Canada, López-Goñi, Ignacio, Giner-Lamia, Joaquín, Álvarez-Ordóñez, Avelino, Benítez-Páez, Alfonso, Claessen, David, Cortesao, M., Toro, María de, García-Ruano, D., Granato, E. T., Kovács, Á. T., Romalde, Jesús L., Sana, T. G., Sánchez-Angulo, M., Sangari, Félix J., Smits, W. K., Sturm, T., Thomassin, J. L., Valdehuesa, K. N. G., and Zapotoczna, M.
- Abstract
Twitter is one of the most popular social media networks that, in recent years, has been increasingly used by researchers as a platform to share science and discuss ongoing work. Despite its popularity, Twitter is not commonly used as a medium to teach science. Here, we summarize the results of #EUROmicroMOOC: the first worldwide Microbiology Massive Open Online Course taught in English using Twitter. Content analytics indicated that more than 3 million users saw posts with the hashtag #EUROmicroMOOC, which resulted in over 42 million Twitter impressions worldwide. These analyses demonstrate that free Microbiology MOOCs shared on Twitter are valuable educational tools that reach broad audiences throughout the world. We also describe our experience teaching an entire Microbiology course using Twitter and provide recommendations when using social media to communicate science to a broad audience.
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- 2019
22. Somatic mutation profiles in primary colorectal cancers and matching ovarian metastases: Identification of driver and passenger mutations
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Crobach, S., Ruano, D., Eijk, R. van, Schrumpf, M., Fleuren, G., Wezel, T. van, Morreau, H., and PALGA Grp
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0301 basic medicine ,Neuroblastoma RAS viral oncogene homolog ,Colorectal cancer ,Ovary ,Bioinformatics ,medicine.disease_cause ,Pathology and Forensic Medicine ,molecular diagnostics ,03 medical and health sciences ,0302 clinical medicine ,Germline mutation ,gene panel ,medicine ,cancer ,PTEN ,metastases ,neoplasms ,biology ,high‐throughput sequencing ,high-throughput sequencing ,Cancer ,Original Articles ,medicine.disease ,Molecular diagnostics ,digestive system diseases ,030104 developmental biology ,medicine.anatomical_structure ,colon cancer ,030220 oncology & carcinogenesis ,biology.protein ,Cancer research ,Original Article ,KRAS - Abstract
The mutational profiles of primary colorectal cancers (CRCs) and corresponding ovarian metastases were compared. Using a custom‐made next generation sequencing panel, 115 cancer‐driving genes were analyzed in a cohort of 26 primary CRCs and 30 matching ovarian metastases (four with bilateral metastases). To obtain a complete overview of the mutational profile, low thresholds were used in bioinformatics analysis to prevent low frequency passenger mutations from being filtered out. A subset of variants was validated using Sanger and/or hydrolysis probe assays. The mutational landscape of CRC that metastasized to the ovary was not strikingly different from CRC in consecutive series. When comparing primary CRCs and their matching ovarian metastases, there was considerable overlap in the mutations of early affected genes. A subset of mutations demonstrated less overlap, presumably being passenger mutations. In particular, primary CRCs showed a substantially high number of passenger mutations. We also compared the primary CRCs and matching metastases for stratifying variants of six genes (KRAS, NRAS, BRAF, FBXW7, PTEN and PIK3CA) that select for established (EGFR directed) or future targeted therapies. In a total of 31 variants 12 were not found in either of the two locations. Tumours thus differed in the number of discordant variants between the primary tumours and matching metastases. Half of these discordant variants were definitive class 4/5 pathogenic variants. However, in terms of temporal heterogeneity, no clear relationship was observed between the number of discordant variants and the time interval between primary CRCs and the detection of ovarian metastases. This suggests that dormant metastases may be present from the early days of the primary tumours.
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- 2016
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23. Evidence for genetic association between chromosome 1q loci and predisposition to colorectal neoplasia (vol 117, pg 1215, 2017)
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Schubert, S.A., Ruano, D., Elsayed, F.A., Boot, A., Crobach, S., Sarasqueta, A.F., Wolffenbuttel, B., Klauw, M.M. van der, Oosting, J., Tops, C.M., Eijk, R. van, Vasen, H.F.A., Vossen, R.H.A.M., Nielsen, M., Castellvi-Bel, S., Ruiz-Ponte, C., Tomlinson, I., Dunlop, M.G., Vodicka, P., Wijnen, J.T., Hes, F.J., Morreau, H., Miranda, N.F.C.C. de, Sijmons, R.H., and Wezel, T. van
- Published
- 2018
24. MOLECULAR ANALYSIS OF PRIMARY CUTANEOUS DIFFUSE LARGE B-CELL LYMPHOMA LEG TYPE AT DIAGNOSIS AND RELAPSE - IMPLICATIONS FOR TARGETED THERAPIES
- Author
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Schrader, A. M. R., primary, de Groen, R. A. L., additional, Willemze, R., additional, Jansen, P. M., additional, Quint, K. D., additional, Cleven, A. H. G., additional, van Wezel, T., additional, van Eijk, R., additional, Ruano, D., additional, Tensen, C. P., additional, Hauben, E., additional, Woei-A-Jin, S., additional, Busschots, A. M., additional, Vermeer, M. H., additional, and Vermaat, J. S. P., additional
- Published
- 2019
- Full Text
- View/download PDF
25. #EUROmicroMOOC: using Twitter to share trends in Microbiology worldwide
- Author
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López-Goñi, I, primary, Giner-Lamia, J, additional, Álvarez-Ordoñez, A, additional, Benitez-Páez, Alfonso, additional, Claessen, D, additional, Cortesao, M, additional, de Toro, M, additional, García-Ruano, D, additional, Granato, E T, additional, Kovács, Á T, additional, Romalde, J L, additional, Sana, T G, additional, Sánchez-Angulo, M, additional, Sangari, F J, additional, Smits, W K, additional, Sturm, T, additional, Thomassin, J L, additional, Valdehuesa, K N G, additional, and Zapotoczna, M, additional
- Published
- 2019
- Full Text
- View/download PDF
26. PF509 MOLECULAR ANALYSIS OF PRIMARY CUTANEOUS DIFFUSE LARGE B-CELL LYMPHOMA LEG TYPE AT DIAGNOSIS AND RELAPSE – IMPLICATIONS FOR TARGETED THERAPIES
- Author
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Schrader, A.M. R., primary, de Groen, R.A. L., additional, Willemze, R., additional, Jansen, P.M., additional, Quint, K.D., additional, Cleven, A.H. G., additional, van Wezel, T., additional, van Eijk, R., additional, Ruano, D., additional, Tensen, C.P., additional, Hauben, E., additional, Woei-A-Jin, S., additional, Busschots, A.M., additional, Vermeer, M.H., additional, and Vermaat, J.S. P., additional
- Published
- 2019
- Full Text
- View/download PDF
27. Validation and Implementation of BRCA1/2 Variant Screening in Ovarian Tumor Tissue
- Author
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de Jonge, M.M. (Marthe M.), Ruano, D. (Dina), Eijk, R. (Ronald) van, van der Stoep, N. (Nienke), Nielsen, M. (Maartje), Wijnen, J.T. (Juul), ter Haar, N.T. (Natalja T.), Baalbergen, A. (Astrid), Bos, M.E.M.M. (Monique E.M.M.), Kagie, M.J. (Marjolein ), Vreeswijk, M.P. (Maaike), Gaarenstroom, K.N. (Katja), Kroep, J.R. (Judith), Smit, V.T.H.B.M. (Vincent), Bosse, T. (Tjalling), Wezel, T. (Tom) van, van Asperen, C.J. (Christi J.), de Jonge, M.M. (Marthe M.), Ruano, D. (Dina), Eijk, R. (Ronald) van, van der Stoep, N. (Nienke), Nielsen, M. (Maartje), Wijnen, J.T. (Juul), ter Haar, N.T. (Natalja T.), Baalbergen, A. (Astrid), Bos, M.E.M.M. (Monique E.M.M.), Kagie, M.J. (Marjolein ), Vreeswijk, M.P. (Maaike), Gaarenstroom, K.N. (Katja), Kroep, J.R. (Judith), Smit, V.T.H.B.M. (Vincent), Bosse, T. (Tjalling), Wezel, T. (Tom) van, and van Asperen, C.J. (Christi J.)
- Abstract
BRCA1/2 variant analysis in tumor tissue could streamline the referral of patients with epithelial ovarian, fallopian tube, or primary peritoneal cancer to genetic counselors and select patients who benefit most from targeted treatment. We investigated the sensitivity of BRCA1/2 variant analysis in formalin-fixed, paraffin-embedded tumor tissue using a combination of next-generation sequencing and copy number variant multiplex ligation-dependent probe amplification. After optimization using a training cohort of known BRCA1/2 mutation carriers, validation was performed in a prospective cohort in which screening of BRCA1/2 tumor DNA and leukocyte germline DNA was performed in parallel. BRCA1 promoter hypermethylation and pedigree analysis were also performed. In the training cohort, 45 of 46 germline BRCA1/2 variants were detected (sensitivity, 98%). In the prospective cohort (n = 62), all six germline variants were identified (sensitivity, 100%), together with five somatic BRCA1/2 variants and eight cases with BRCA1 promoter hypermethylation. In four BRCA1/2 variant–negative patients, surveillance or prophylactic management options were offered on the basis of positive family histories. We conclude that BRCA1/2 formalin-fixed, paraffin-embedded tumor tissue analysis reliably detects BRCA1/2 variants. When taking family history of BRCA1/2 variant–negative patients into account, tumor BRCA1/2 variant screening allows more efficient selection of epithelial ovarian cancer patients for genetic counseling and simultaneously selects patients who benefit most from targeted treatment.
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- 2018
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28. Validation and Implementation of BRCA1/2 Variant Screening in Ovarian Tumor Tissue
- Author
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de Jonge, MM, Ruano, D, Eijk, R, van der Stoep, N, Nielsen, M, Wijnen, JT, ter Haar, NT, Baalbergen, A, Bos, Monique, Kagie, MJ, Vreeswijk, MPG, Gaarenstroom, KN, Kroep, JR, Smit, V, Bosse, T, van Wezel, T, van Asperen, CJ, de Jonge, MM, Ruano, D, Eijk, R, van der Stoep, N, Nielsen, M, Wijnen, JT, ter Haar, NT, Baalbergen, A, Bos, Monique, Kagie, MJ, Vreeswijk, MPG, Gaarenstroom, KN, Kroep, JR, Smit, V, Bosse, T, van Wezel, T, and van Asperen, CJ
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- 2018
29. GENOMIC CHARACTERISATION OF VULVAR (PRE) CANCERS IDENTIFIES DISTINCT MOLECULAR SUBTYPES WITH PROGNOSTIC SIGNIFICANCE
- Author
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Nooij, L., Ter Haar, N., Ruano, D., Rakislova, N., Vincent THBM Smit, Trimbos, B., Ordi, J., Poelgeest, M., and Bosse, T.
- Published
- 2017
30. PO-059 Cancer-predisposing variants in alternatively spliced TP53 exons
- Author
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Schubert, S.A., primary, Miranda, N.F.C.C. De, additional, Ruano, D., additional, Barge-Schaapveld, D.Q.C.M., additional, Hes, F.J., additional, Tops, C.M., additional, Joruiz, S., additional, Diot, A., additional, Bourdon, J.C., additional, and Wezel, T. Van, additional
- Published
- 2018
- Full Text
- View/download PDF
31. PO-410 Discovery of immunogenic neoantigens for peptide vaccination approaches in murine colorectal cancer
- Author
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Hos, B., primary, Camps, M., additional, Tondini, E., additional, Ruano, D., additional, Van den Bulk, J., additional, Franken, K., additional, Janssen, G., additional, Van Veelen, P., additional, De Miranda, N., additional, and Ossendorp, F., additional
- Published
- 2018
- Full Text
- View/download PDF
32. BRCA1/2 mutational analysis on formalin fixed paraffin embedded (FFPE) ovarian tumour DNA
- Author
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Jonge, M., Eijk, R., Ruano, D., Wijnen, J., Stoep, N., Nielsen, M., Gaarenstroom, K., Kroep, J., Wezel, T., Tjalling Bosse, and Asperen, C.
- Published
- 2016
33. Comprehensive analysis of microsatellite instability and mismatch repair protein expression in nearly 700 endometrial cancers
- Author
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Stelloo, E., Jansen, A., Osse, E., Nout, R., Ruano, D., Wezel, T., Creutzberg, C., Vincent THBM Smit, Morreau, H., and Bosse, E.
- Published
- 2016
34. Erratum to: Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition) (Autophagy, 12, 1, 1-222, 10.1080/15548627.2015.1100356
- Author
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Klionsky, D.J. Abdelmohsen, K. Abe, A. Abedin, M.J. Abeliovich, H. Arozena, A.A. Adachi, H. Adams, C.M. Adams, P.D. Adeli, K. Adhihetty, P.J. Adler, S.G. Agam, G. Agarwal, R. Aghi, M.K. Agnello, M. Agostinis, P. Aguilar, P.V. Aguirre-Ghiso, J. Airoldi, E.M. Ait-Si-Ali, S. Akematsu, T. Akporiaye, E.T. Al-Rubeai, M. Albaiceta, G.M. Albanese, C. Albani, D. Albert, M.L. Aldudo, J. Algül, H. Alirezaei, M. Alloza, I. Almasan, A. Almonte-Beceril, M. Alnemri, E.S. Alonso, C. Altan-Bonnet, N. Altieri, D.C. Alvarez, S. Alvarez-Erviti, L. Alves, S. Amadoro, G. Amano, A. Amantini, C. Ambrosio, S. Amelio, I. Amer, A.O. Amessou, M. Amon, A. An, Z. Anania, F.A. Andersen, S.U. Andley, U.P. Andreadi, C.K. Andrieu-Abadie, N. Anel, A. Ann, D.K. Anoopkumar-Dukie, S. Antonioli, M. Aoki, H. Apostolova, N. Aquila, S. Aquilano, K. Araki, K. Arama, E. Aranda, A. Araya, J. Arcaro, A. Arias, E. Arimoto, H. Ariosa, A.R. Armstrong, J.L. Arnould, T. Arsov, I. Asanuma, K. Askanas, V. Asselin, E. Atarashi, R. Atherton, S.S. Atkin, J.D. Attardi, L.D. Auberger, P. Auburger, G. Aurelian, L. Autelli, R. Avagliano, L. Avantaggiati, M.L. Avrahami, L. Azad, N. Awale, S. Bachetti, T. Backer, J.M. Bae, D.-H. Bae, J.-S. Bae, O.-N. Bae, S.H. Baehrecke, E.H. Baek, S.-H. Baghdiguian, S. Bagniewska-Zadworna, A. Bai, H. Bai, J. Bai, X.-Y. Bailly, Y. Balaji, K.N. Balduini, W. Ballabio, A. Balzan, R. Banerjee, R. Bánhegyi, G. Bao, H. Barbeau, B. Barrachina, M.D. Barreiro, E. Bartel, B. Bartolomé, A. Bassham, D.C. Bassi, M.T. Bast, R.C., Jr. Basu, A. Batista, M.T. Batoko, H. Battino, M. Bauckman, K. Baumgarner, B.L. Bayer, K.U. Beale, R. Beaulieu, J.-F. Beck, G.R., Jr. Becker, C. Beckham, J.D. Bédard, P.-A. Bednarski, P.J. Begley, T.J. Behl, C. Behrends, C. Behrens, G.M.N. Behrns, K.E. Bejarano, E. Belaid, A. Belleudi, F. Bénard, G. Berchem, G. Bergamaschi, D. Bergami, M. Berkhout, B. Berliocchi, L. Bernard, A. Bernard, M. Bernassola, F. Bertolotti, A. Bess, A.S. Besteiro, S. Bettuzzi, S. Bhalla, S. Bhattacharyya, S. Bhutia, S.K. Biagosch, C. Bianchi, M.W. Biard-Piechaczyk, M. Billes, V. Bincoletto, C. Bingol, B. Bird, S.W. Bitoun, M. Bjedov, I. Blackstone, C. Blanc, L. Blanco, G.A. Blomhoff, H.K. Boada-Romero, E. Böckler, S. Boes, M. Boesze-Battaglia, K. Boise, L.H. Bolino, A. Boman, A. Bonaldo, P. Bordi, M. Bosch, J. Botana, L.M. Botti, J. Bou, G. Bouché, M. Bouchecareilh, M. Boucher, M.-J. Boulton, M.E. Bouret, S.G. Boya, P. Boyer-Guittaut, M. Bozhkov, P.V. Brady, N. Braga, V.M.M. Brancolini, C. Braus, G.H. Bravo-San-Pedro, J.M. Brennan, L.A. Bresnick, E.H. Brest, P. Bridges, D. Bringer, M.-A. Brini, M. Brito, G.C. Brodin, B. Brookes, P.S. Brown, E.J. Brown, K. Broxmeyer, H.E. Bruhat, A. Brum, P.C. Brumell, J.H. Brunetti-Pierri, N. Bryson-Richardson, R.J. Buch, S. Buchan, A.M. Budak, H. Bulavin, D.V. Bultman, S.J. Bultynck, G. Bumbasirevic, V. Burelle, Y. Burke, R.E. Burmeister, M. Bütikofer, P. Caberlotto, L. Cadwell, K. Cahova, M. Cai, D. Cai, J. Cai, Q. Calatayud, S. Camougrand, N. Campanella, M. Campbell, G.R. Campbell, M. Campello, S. Candau, R. Caniggia, I. Cantoni, L. Cao, L. Caplan, A.B. Caraglia, M. Cardinali, C. Cardoso, S.M. Carew, J.S. Carleton, L.A. Carlin, C.R. Carloni, S. Carlsson, S.R. Carmona-Gutierrez, D. Carneiro, L.A.M. Carnevali, O. Carra, S. Carrier, A. Carroll, B. Casas, C. Casas, J. Cassinelli, G. Castets, P. Castro-Obregon, S. Cavallini, G. Ceccherini, I. Cecconi, F. Cederbaum, A.I. Ceña, V. Cenci, S. Cerella, C. Cervia, D. Cetrullo, S. Chaachouay, H. Chae, H.-J. Chagin, A.S. Chai, C.-Y. Chakrabarti, G. Chamilos, G. Chan, E.Y.W. Chan, M.T.V. Chandra, D. Chandra, P. Chang, C.-P. Chang, R.C.-C. Chang, T.Y. Chatham, J.C. Chatterjee, S. Chauhan, S. Che, Y. Cheetham, M.E. Cheluvappa, R. Chen, C.-J. Chen, G. Chen, G.-C. Chen, G. Chen, H. Chen, J.W. Chen, J.-K. Chen, M. Chen, M. Chen, P. Chen, Q. Chen, Q. Chen, S.-D. Chen, S. Chen, S.S.-L. Chen, W. Chen, W.-J. Chen, W.Q. Chen, W. Chen, X. Chen, Y.-H. Chen, Y.-G. Chen, Y. Chen, Y. Chen, Y. Chen, Y.-J. Chen, Y.-Q. Chen, Y. Chen, Z. Chen, Z. Cheng, A. Cheng, C.H.K. Cheng, H. Cheong, H. Cherry, S. Chesney, J. Cheung, C.H.A. Chevet, E. Chi, H.C. Chi, S.-G. Chiacchiera, F. Chiang, H.-L. Chiarelli, R. Chiariello, M. Chieppa, M. Chin, L.-S. Chiong, M. Chiu, G.N.C. Cho, D.-H. Cho, S.-G. Cho, W.C. Cho, Y.-Y. Cho, Y.-S. Choi, A.M.K. Choi, E.-J. Choi, E.-K. Choi, J. Choi, M.E. Choi, S.-I. Chou, T.-F. Chouaib, S. Choubey, D. Choubey, V. Chow, K.-C. Chowdhury, K. Chu, C.T. Chuang, T.-H. Chun, T. Chung, H. Chung, T. Chung, Y.-L. Chwae, Y.-J. Cianfanelli, V. Ciarcia, R. Ciechomska, I.A. Ciriolo, M.R. Cirone, M. Claerhout, S. Clague, M.J. Cl� ria, J. Clarke, P.G.H. Clarke, R. Clementi, E. Cleyrat, C. Cnop, M. Coccia, E.M. Cocco, T. Codogno, P. Coers, J. Cohen, E.E.W. Colecchia, D. Coletto, L. Coll, N.S. Colucci-Guyon, E. Comincini, S. Condello, M. Cook, K.L. Coombs, G.H. Cooper, C.D. Cooper, J.M. Coppens, I. Corasaniti, M.T. Corazzari, M. Corbalan, R. Corcelle-Termeau, E. Cordero, M.D. Corral-Ramos, C. Corti, O. Cossarizza, A. Costelli, P. Costes, S. Cotman, S.L. Coto-Montes, A. Cottet, S. Couve, E. Covey, L.R. Cowart, L.A. Cox, J.S. Coxon, F.P. Coyne, C.B. Cragg, M.S. Craven, R.J. Crepaldi, T. Crespo, J.L. Criollo, A. Crippa, V. Cruz, M.T. Cuervo, A.M. Cuezva, J.M. Cui, T. Cutillas, P.R. Czaja, M.J. Czyzyk-Krzeska, M.F. Dagda, R.K. Dahmen, U. Dai, C. Dai, W. Dai, Y. Dalby, K.N. Valle, L.D. Dalmasso, G. D'amelio, M. Damme, M. Darfeuille-Michaud, A. Dargemont, C. Darley-Usmar, V.M. Dasarathy, S. Dasgupta, B. Dash, S. Dass, C.R. Davey, H.M. Davids, L.M. Dávila, D. Davis, R.J. Dawson, T.M. Dawson, V.L. Daza, P. de Belleroche, J. de Figueiredo, P. de Figueiredo, R.C.B.Q. de la Fuente, J. De Martino, L. De Matteis, A. De Meyer, G.R.Y. De Milito, A. De Santi, M. de Souza, W. De Tata, V. De Zio, D. Debnath, J. Dechant, R. Decuypere, J.-P. Deegan, S. Dehay, B. Del Bello, B. Del Re, D.P. Delage-Mourroux, R. Delbridge, L.M.D. Deldicque, L. Delorme-Axford, E. Deng, Y. Dengjel, J. Denizot, M. Dent, P. Der, C.J. Deretic, V. Derrien, B. Deutsch, E. Devarenne, T.P. Devenish, R.J. Di Bartolomeo, S. Di Daniele, N. Di Domenico, F. Di Nardo, A. Di Paola, S. Di Pietro, A. Di Renzo, L. Di Antonio, A. Díaz-Araya, G. Díaz-Laviada, I. Diaz-Meco, M.T. Diaz-Nido, J. Dickey, C.A. Dickson, R.C. Diederich, M. Digard, P. Dikic, I. Dinesh-Kumar, S.P. Ding, C. Ding, W.-X. Ding, Z. Dini, L. Distler, J.H.W. Diwan, A. Djavaheri-Mergny, M. Dmytruk, K. Dobson, R.C.J. Doetsch, V. Dokladny, K. Dokudovskaya, S. Donadelli, M. Dong, X.C. Dong, X. Dong, Z. Donohue, T.M., Jr. Donohue-Jr, T.M. Doran, K.S. D'orazi, G. Dorn, G.W., II Dosenko, V. Dridi, S. Drucker, L. Du, J. Du, L.-L. Du, L. du Toit, A. Dua, P. Duan, L. Duann, P. Dubey, V.K. Duchen, M.R. Duchosal, M.A. Duez, H. Dugail, I. Dumit, V.I. Duncan, M.C. Dunlop, E.A. Dunn, W.A., Jr. Dupont, N. Dupuis, L. Durán, R.V. Durcan, T.M. Duvezin-Caubet, S. Duvvuri, U. Eapen, V. Ebrahimi-Fakhari, D. Echard, A. Eckhart, L. Edelstein, C.L. Edinger, A.L. Eichinger, L. Eisenberg, T. Eisenberg-Lerner, A. Eissa, N.T. El-Deiry, W.S. El-Khoury, V. Elazar, Z. Eldar-Finkelman, H. Elliott, C.J.H. Emanuele, E. Emmenegger, U. Engedal, N. Engelbrecht, A.-M. Engelender, S. Enserink, J.M. Erdmann, R. Erenpreisa, J. Eri, R. Eriksen, J.L. Erman, A. Escalante, R. Eskelinen, E.-L. Espert, L. Esteban-Martínez, L. Evans, T.J. Fabri, M. Fabrias, G. Fabrizi, C. Facchiano, A. Færgeman, N.J. Faggioni, A. Fairlie, W.D. Fan, C. Fan, D. Fan, J. Fang, S. Fanto, M. Fanzani, A. Farkas, T. Faure, M. Favier, F.B. Fearnhead, H. Federici, M. Fei, E. Felizardo, T.C. Feng, H. Feng, Y. Feng, Y. Ferguson, T.A. Fernández, Á.F. Fernandez-Barrena, M.G. Fernandez-Checa, J.C. Fernández-López, A. Fernandez-Zapico, M.E. Feron, O. Ferraro, E. Ferreira-Halder, C.V. Fesus, L. Feuer, R. Fiesel, F.C. Filippi-Chiela, E.C. Filomeni, G. Fimia, G.M. Fingert, J.H. Finkbeiner, S. Finkel, T. Fiorito, F. Fisher, P.B. Flajolet, M. Flamigni, F. Florey, O. Florio, S. Floto, R.A. Folini, M. Follo, C. Fon, E.A. Fornai, F. Fortunato, F. Fraldi, A. Franco, R. Francois, A. François, A. Frankel, L.B. Fraser, I.D.C. Frey, N. Freyssenet, D.G. Frezza, C. Friedman, S.L. Frigo, D.E. Fu, D. Fuentes, J.M. Fueyo, J. Fujitani, Y. Fujiwara, Y. Fujiya, M. Fukuda, M. Fulda, S. Fusco, C. Gabryel, B. Gaestel, M. Gailly, P. Gajewska, M. Galadari, S. Galili, G. Galindo, I. Galindo, M.F. Galliciotti, G. Galluzzi, L. Galluzzi, L. Galy, V. Gammoh, N. Gandy, S. Ganesan, A.K. Ganesan, S. Ganley, I.G. Gannagé, M. Gao, F.-B. Gao, F. Gao, J.-X. Nannig, L.G. Véscovi, E.G. Garcia-Macía, M. Garcia-Ruiz, C. Garg, A.D. Garg, P.K. Gargini, R. Gassen, N.C. Gatica, D. Gatti, E. Gavard, J. Gavathiotis, E. Ge, L. Ge, P. Ge, S. Gean, P.-W. Gelmetti, V. Genazzani, A.A. Geng, J. Genschik, P. Gerner, L. Gestwicki, J.E. Gewirtz, D.A. Ghavami, S. Ghigo, E. Ghosh, D. Giammarioli, A.M. Giampieri, F. Giampietri, C. Giatromanolaki, A. Gibbings, D.J. Gibellini, L. Gibson, S.B. Ginet, V. 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- Published
- 2016
36. Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)
- Author
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- Published
- 2016
37. Erratum to: Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition) (Autophagy, 12, 1, 1-222, 10.1080/15548627.2015.1100356
- Author
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Charlie, Dong, Xiaonan, Dong, Zheng, Donohue, Terrence M., Donohue-Jr, Terrence M., Doran, Kelly S., D'orazi, Gabriella, Dorn, Gerald W., Dosenko, Victor, Dridi, Sami, Drucker, Liat, Du, Jie, Du, Li-Lin, Du, Lihuan, du Toit, André, Dua, Priyamvada, Duan, Lei, Duann, Pu, Dubey, Vikash Kumar, Duchen, Michael R., Duchosal, Michel A., Duez, Helene, Dugail, Isabelle, Dumit, Verónica I., Duncan, Mara C., Dunlop, Elaine A., Dunn, William A., Dupont, Nicola, Dupuis, Luc, Durán, Raúl V., Durcan, Thomas M., Duvezin-Caubet, Stéphane, Duvvuri, Umamaheswar, Eapen, Vinay, Ebrahimi-Fakhari, Dariu, Echard, Arnaud, Eckhart, Leopold, Edelstein, Charles L., Edinger, Aimee L., Eichinger, Ludwig, Eisenberg, Tobia, Eisenberg-Lerner, Avital, Eissa, N. 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Dougla, Fan, Chunhai, Fan, Daping, Fan, Jie, Fang, Shengyun, Fanto, Manoli, Fanzani, Alessandro, Farkas, Thoma, Faure, Mathia, Favier, Francois B., Fearnhead, Howard, Federici, Massimo, Fei, Erkang, Felizardo, Tania C., Feng, Hua, Feng, Yibin, Feng, Yuchen, Ferguson, Thomas A., Fernández, Álvaro F., Fernandez-Barrena, Maite G., Fernandez-Checa, Jose C., Fernández-López, Arsenio, Fernandez-Zapico, Martin E., Feron, Olivier, Ferraro, Elisabetta, Ferreira-Halder, Carmen Veríssima, Fesus, Laszlo, Feuer, Ralph, Fiesel, Fabienne C., Filippi-Chiela, Eduardo C., Filomeni, Giuseppe, Fimia, Gian Maria, Fingert, John H., Finkbeiner, Steven, Finkel, Toren, Fiorito, Filomena, Fisher, Paul B., Flajolet, Marc, Flamigni, Flavio, Florey, Oliver, Florio, Salvatore, Floto, R. 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Robin, Higaki, Katsumi, Hilfiker, Sabine, Hill, Bradford G., Hill, Joseph A., Hill, William D., Hino, Keisuke, Hofius, Daniel, Hofman, Paul, Höglinger, Günter U., Höhfeld, Jörg, Holz, Marina K., Hong, Yonggeun, Hood, David A., Hoozemans, Jeroen J.M., Hoppe, Thorsten, Hsu, Chin, Hsu, Chin-Yuan, Hsu, Li-Chung, Hu, Dong, Hu, Guochang, Hu, Hong-Ming, Hu, Hongbo, Hu, Ming Chang, Hu, Yu-Chen, Hu, Zhuo-Wei, Hua, Fang, Hua, Ya, Huang, Canhua, Huang, Huey-Lan, Huang, Kuo-How, Huang, Kuo-Yang, Huang, Shile, Huang, Shiqian, Huang, Wei-Pang, Huang, Yi-Ran, Huang, Yong, Huang, Yunfei, Huber, Tobias B., Huebbe, Patricia, Huh, Won-Ki, Hulmi, Juha J., Hur, Gang Min, Hurley, James H., Husak, Zvenyslava, Hussain, Sabah N.A., Hussain, Salik, Hwang, Jung Jin, Hwang, Seungmin, Hwang, Thomas I.S., Ichihara, Atsuhiro, Imai, Yuzuru, Imbriano, Carol, Inomata, Megumi, Into, Takeshi, Iovane, Valentina, Iovanna, Juan L., Iozzo, Renato V., Ip, Nancy Y., Irazoqui, Javier E., Iribarren, Pablo, Isaka, Yoshitaka, Isakovic, Aleksandra J., Ischiropoulos, Harry, Isenberg, Jeffrey S., Ishaq, Mohammad, Ishida, Hiroyuki, Ishii, Isao, Ishmael, Jane E., Isidoro, Ciro, Isobe, Ken-Ichi, Isono, Erika, Issazadeh-Navikas, Shohreh, Itahana, Koji, Itakura, Eisuke, Ivanov, Andrei I., Iyer, Anand Krishnan V., Izquierdo, José M., Izumi, Yotaro, Izzo, Valentina, Jäättelä, Marja, Jaber, Nadia, Jackson, Daniel John, Jackson, William T., Jacob, Tony George, Jacques, Thomas S., Jagannath, Chinnaswamy, Jain, Ashish, Jana, Nihar Ranjan, Jang, Byoung Kuk, Jani, Alkesh, Janji, Bassam, Jannig, Paulo Roberto, Jansson, Patric J., Jean, Steve, Jendrach, Marina, Jeon, Ju-Hong, Jessen, Niel, Jeung, Eui-Bae, Jia, Kailiang, Jia, Lijun, Jiang, Hong, Jiang, Hongchi, Jiang, Liwen, Jiang, Teng, Jiang, Xiaoyan, Jiang, Xuejun, Jiang, Ying, Jiang, Yongjun, Jiménez, Alberto, Jin, Cheng, Jin, Hongchuan, Jin, Lei, Jin, Meiyan, Jin, Shengkan, Jinwal, Umesh Kumar, Jo, Eun-Kyeong, Johansen, Terje, Johnson, Daniel E., Johnson, Gail V.W., Johnson, James D., Jonasch, Eric, Jones, Chri, Joosten, Leo A.B., Jordan, Joaquin, Joseph, Anna-Maria, Joseph, Bertrand, Joubert, Annie M., Ju, Dianwen, Ju, Jingfang, Juan, Hsueh-Fen, Juenemann, Katrin, Juhász, Gábor, Jung, Hye Seung, Jung, Jae U., Jung, Yong-Keun, Jungbluth, Heinz, Justice, Matthew J., Jutten, Barry, Kaakoush, Nadeem O., Kaarniranta, Kai, Kaasik, Allen, Kabuta, Tomohiro, Kaeffer, Bertrand, Kågedal, Katarina, Kahana, Alon, Kajimura, Shingo, Kakhlon, Or, Kalia, Manjula, Kalvakolanu, Dhan V., Kamada, Yoshiaki, Kambas, Konstantino, Kaminskyy, Vitaliy O., Kampinga, Harm H., Kandouz, Mustapha, Kang, Chanhee, Kang, Rui, Kang, Tae-Cheon, Kanki, Tomotake, Kanneganti, Thirumala-Devi, Kanno, Haruo, Kanthasamy, Anumantha G., Kantorow, Marc, Kaparakis-Liaskos, Maria, Kapuy, Orsolya, Karantza, Vassiliki, Karim, Md Razaul, Karmakar, Parimal, Kaser, Arthur, Kaushik, Susmita, Kawula, Thoma, Kaynar, A. Murat, Ke, Po-Yuan, Ke, Zun-Ji, Kehrl, John H., Keller, Kate E., Kemper, Jongsook Kim, Kenworthy, Anne K., Kepp, Oliver, Kern, Andrea, Kesari, Santosh, Kessel, David, Ketteler, Robin, Kettelhut, Isis do Carmo, Khambu, Bilon, Khan, Muzamil Majid, Khandelwal, Vinoth K.M., Khare, Sangeeta, Kiang, Juliann G., Kiger, Amy A., Kihara, Akio, Kim, Arianna L., Kim, Cheol Hyeon, Kim, Deok Ryong, Kim, Do-Hyung, Kim, Eung Kweon, Kim, Hye Young, Kim, Hyung-Ryong, Kim, Jae-Sung, Kim, Jeong Hun, Kim, Jin Cheon, Kim, Jin Hyoung, Kim, Kwang Woon, Kim, Michael D., Kim, Moon-Moo, Kim, Peter K., Kim, Seong Who, Kim, Soo-Youl, Kim, Yong-Sun, Kim, Yonghyun, Kimchi, Adi, Kimmelman, Alec C., Kimura, Tomonori, King, Jason S., Kirkegaard, Karla, Kirkin, Vladimir, Kirshenbaum, Lorrie A., Kishi, Shuji, Kitajima, Yasuo, Kitamoto, Katsuhiko, Kitaoka, Yasushi, Kitazato, Kaio, Kley, Rudolf A., Klimecki, Walter T., Klinkenberg, Michael, Klucken, Jochen, Knævelsrud, Helene, Knecht, Erwin, Knuppertz, Laura, Ko, Jiunn-Liang, Kobayashi, Satoru, Koch, Jan C., Koechlin-Ramonatxo, Christelle, Koenig, Ulrich, Koh, Young Ho, Köhler, Katja, Kohlwein, Sepp D., Koike, Masato, Komatsu, Masaaki, Kominami, Eiki, Kong, Dexin, Kong, Hee Jeong, Konstantakou, Eumorphia G., Kopp, Benjamin T., Korcsmaros, Tama, Korhonen, Laura, Korolchuk, Viktor I., Koshkina, Nadya V., Kou, Yanjun, Koukourakis, Michael I., Koumenis, Constantino, Kovács, Attila L., Kovács, Tibor, Kovacs, Werner J., Koya, Daisuke, Kraft, Claudine, Krainc, Dimitri, Kramer, Helmut, Kravic-Stevovic, Tamara, Krek, Wilhelm, Kretz-Remy, Carole, Krick, Roswitha, Krishnamurthy, Malathi, Kriston-Vizi, Jano, Kroemer, Guido, Kruer, Michael C., Kruger, Rejko, Ktistakis, Nicholas T., Kuchitsu, Kazuyuki, Kuhn, Christian, Kumar, Addanki Pratap, Kumar, Anuj, Kumar, Ashok, Kumar, Deepak, Kumar, Dhiraj, Kumar, Rakesh, Kumar, Sharad, Kundu, Mondira, Kung, Hsing-Jien, Kuno, Atsushi, Kuo, Sheng-Han, Kuret, Jeff, Kurz, Tino, Kwok, Terry, Kwon, Taeg Kyu, Kwon, Yong Tae, Kyrmizi, Irene, La Spada, Albert R., Lafont, Frank, Lahm, Tim, Lakkaraju, Aparna, Lam, Truong, Lamark, Trond, Lancel, Steve, Landowski, Terry H., Lane, Darius J.R., Lane, Jon D., Lanzi, Cinzia, Lapaquette, Pierre, Lapierre, Louis R., Laporte, Jocelyn, Laukkarinen, Johanna, Laurie, Gordon W., Lavandero, Sergio, Lavie, Lena, Lavoie, Matthew J., Law, Betty Yuen Kwan, Law, Helen Ka-Wai, Law, Kelsey B., Layfield, Robert, Lazo, Pedro A., Le Cam, Laurent, Le Roch, Karine G., Le Stunff, Hervé, Leardkamolkarn, Vijittra, Lecuit, Marc, Lee, Byung-Hoon, Lee, Che-Hsin, Lee, Erinna F., Lee, Gyun Min, Lee, He-Jin, Lee, Hsinyu, Lee, Jae Keun, Lee, Jongdae, Lee, Ju-Hyun, Lee, Jun Hee, Lee, Michael, Lee, Myung-Shik, Lee, Patty J., Lee, Sam W., Lee, Seung-Jae, Lee, Shiow-Ju, Lee, Stella Y., Lee, Sug Hyung, Lee, Sung Sik, Lee, Sung-Joon, Lee, Sunhee, Lee, Ying-Ray, Lee, Yong J., Lee, Young H., Leeuwenburgh, Christiaan, Lefort, Sylvain, Legouis, Renaud, Lei, Jinzhi, Lei, Qun-Ying, Leib, David A., Leibowitz, Gil, Lekli, Istvan, Lemaire, Stéphane D., Lemasters, John J., Lemberg, Marius K., Lemoine, Antoinette, Leng, Shuilong, Lenz, Guido, Lenzi, Paola, Lerman, Lilach O., Barbato, Daniele Lettieri, Leu, Julia I. 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Sue, Menna-Barreto, Rubem F.S., Menon, Manoj B., Meraz-Ríos, Marco A., Merla, Giuseppe, Merlini, Luciano, Merlot, Angelica M., Meryk, Andrea, Meschini, Stefania, Meyer, Joel N., Mi, Man-Tian, Miao, Chao-Yu, Micale, Lucia, Michaeli, Simon, Michiels, Carine, Migliaccio, Anna Rita, Mihailidou, Anastasia Susie, Mijaljica, Dalibor, Mikoshiba, Katsuhiko, Milan, Enrico, Miller-Fleming, Leonor, Mills, Gordon B., Mills, Ian G., Minakaki, Georgia, Minassian, Berge A., Ming, Xiu-Fen, Minibayeva, Farida, Minina, Elena A., Mintern, Justine D., Minucci, Saverio, Miranda-Vizuete, Antonio, Mitchell, Claire H., Miyamoto, Shigeki, Miyazawa, Keisuke, Mizushima, Noboru, Mnich, Katarzyna, Mograbi, Baharia, Mohseni, Simin, Moita, Luis Ferreira, Molinari, Marco, Molinari, Maurizio, Møller, Andreas Buch, Mollereau, Bertrand, Mollinedo, Faustino, Mongillo, Marco, Monick, Martha M., Montagnaro, Serena, Montell, Craig, Moore, Darren J., Moore, Michael N., Mora-Rodriguez, Rodrigo, Moreira, Paula I., Morel, Etienne, Morelli, Maria Beatrice, Moreno, Sandra, Morgan, Michael J., Moris, Arnaud, Moriyasu, Yuji, Morrison, Janna L., Morrison, Lynda A., Morselli, Eugenia, Moscat, Jorge, Moseley, Pope L., Mostowy, Serge, Motori, Elisa, Mottet, Deni, Mottram, Jeremy C., Moussa, Charbel E.-H., Mpakou, Vassiliki E., Mukhtar, Hasan, Levy, Jean M. Mulcahy, Muller, Sylviane, Muñoz-Moreno, Raquel, Muñoz-Pinedo, Cristina, Münz, Christian, Murphy, Maureen E., Murray, James T., Murthy, Aditya, Mysorekar, Indira U., Nabi, Ivan R., Nabissi, Massimo, Nader, Gustavo A., Nagahara, Yukitoshi, Nagai, Yoshitaka, Nagata, Kazuhiro, Nagelkerke, Anika, Nagy, Péter, Naidu, Samisubbu R., Nair, Sreejayan, Nakano, Hiroyasu, Nakatogawa, Hitoshi, Nanjundan, Meera, Napolitano, Gennaro, Naqvi, Naweed I., Nardacci, Roberta, Narendra, Derek P., Narita, Masashi, Nascimbeni, Anna Chiara, Natarajan, Ramesh, Navegantes, Luiz C., Nawrocki, Steffan T., Nazarko, Taras Y., Nazarko, Volodymyr Y., Neill, Thoma, Neri, Luca M., Netea, Mihai G., Netea-Maier, Romana T., Neves, Bruno M., Ney, Paul A., Nezis, Ioannis P., Nguyen, Hang T.T., Nguyen, Huu Phuc, Nicot, Anne-Sophie, Nilsen, Hilde, Nilsson, Per, Nishimura, Mikio, Nishino, Ichizo, Niso-Santano, Mireia, Niu, Hua, Nixon, Ralph A., Njar, Vincent C.O., Noda, Takeshi, Noegel, Angelika A., Nolte, Elsie Magdalena, Norberg, Erik, Norga, Koenraad K., Noureini, Sakineh Kazemi, Notomi, Shoji, Notterpek, Lucia, Nowikovsky, Karin, Nukina, Nobuyuki, Nürnberger, Thorsten, O'donnell, Valerie B., O'donovan, Tracey, O'dwyer, Peter J., Oehme, Ina, Oeste, Clara L., Ogawa, Michinaga, Ogretmen, Besim, Ogura, Yuji, Oh, Young J., Ohmuraya, Masaki, Ohshima, Takayuki, Ojha, Rani, Okamoto, Koji, Okazaki, Toshiro, Oliver, F. Javier, Ollinger, Karin, Olsson, Stefan, Orban, Daniel P., Ordonez, Paulina, Orhon, Idil, Orosz, Laszlo, O'rourke, Eyleen J., Orozco, Helena, Ortega, Angel L., Ortona, Elena, Osellame, Laura D., Oshima, Junko, Oshima, Shigeru, Osiewacz, Heinz D., Otomo, Takanobu, Otsu, Kinya, Ou, Jing-Hsiung Jame, Outeiro, Tiago F., Ouyang, Dong-Yun, Ouyang, Hongjiao, Overholtzer, Michael, Ozbun, Michelle A., Ozdinler, P. Hande, Ozpolat, Bulent, Pacelli, Consiglia, Paganetti, Paolo, Page, Guyléne, Pages, Gille, Pagnini, Ugo, Pajak, Beata, Pak, Stephen C., Pakos-Zebrucka, Karolina, Pakpour, Nazzy, Palková, Zdena, Palladino, Francesca, Pallauf, Kathrin, Pallet, Nicola, Palmieri, Marta, Paludan, Søren R., Palumbo, Camilla, Palumbo, Silvia, Pampliega, Olatz, Pan, Hongming, Pan, Wei, Panaretakis, Theochari, Pandey, Aseem, Pantazopoulou, Areti, Papackova, Zuzana, Papademetrio, Daniela L., Papassideri, Issidora, Papini, Alessio, Parajuli, Nirmala, Pardo, Julian, Parekh, Vrajesh V., Parenti, Giancarlo, Park, Jong-In, Park, Junsoo, Park, Ohkmae K., Parker, Roy, Parlato, Rosanna, Parys, Jan B., Parzych, Katherine R., Pasquet, Jean-Max, Pasquier, Benoit, Pasumarthi, Kishore B.S., Patschan, Daniel, Pattingre, Sophie, Pattison, Scott, Pause, Arnim, Pavenstädt, Hermann, Pavone, Flaminia, Pedrozo, Zully, Peña, Fernando J., Peñalva, Miguel A., Pende, Mario, Peng, Jianxin, Penna, Fabio, Penninger, Josef M., Pensalfini, Anna, Pepe, Salvatore, Pereira, Gustavo J.S., Pereira, Paulo C., de la Cruz, Verónica Pérez, Pérez-Pérez, María Esther, Pérez-Rodríguez, Diego, Pérez-Sala, Dolore, Perier, Celine, Perl, Andra, Perlmutter, David H., Perrotta, Ida, Pervaiz, Shazib, Pesonen, Maija, Pessin, Jeffrey E., Peters, Godefridus J., Petersen, Morten, Petrache, Irina, Petrof, Basil J., Petrovski, Goran, Phang, James M., Piacentini, Mauro, Pierdominici, Marina, Pierre, Philippe, Pierrefite-Carle, Valérie, Pietrocola, Federico, Pimentel-Muiños, Felipe X., Pinar, Mario, Pineda, Benjamin, Pinkas-Kramarski, Ronit, Pinti, Marcello, Pinton, Paolo, Piperdi, Bilal, Piret, James M., Platanias, Leonidas C., Platta, Harald W., Plowey, Edward D., Pöggeler, Stefanie, Poirot, Marc, Polčic, Peter, Poletti, Angelo, Poon, Audrey H., Popelka, Hana, Popova, Blagovesta, Poprawa, Izabela, Poulose, Shibu M., Poulton, Joanna, Powers, Scott K., Powers, Ted, Pozuelo-Rubio, Mercede, Prak, Krisna, Prange, Reinhild, Prescott, Mark, Priault, Muriel, Prince, Sharon, Proia, Richard L., Proikas-Cezanne, Tassula, Prokisch, Holger, Promponas, Vasilis J., Przyklenk, Karin, Puertollano, Rosa, Pugazhenthi, Subbiah, Puglielli, Luigi, Pujol, Aurora, Puyal, Julien, Pyeon, Dohun, Qi, Xin, Qian, Wen-Bin, Qin, Zheng-Hong, Qiu, Yu, Qu, Ziwei, Quadrilatero, Joe, Quinn, Frederick, Raben, Nina, Rabinowich, Hannah, Radogna, Flavia, Ragusa, Michael J., Rahmani, Mohamed, Raina, Komal, Ramanadham, Sasanka, Ramesh, Rajagopal, Rami, Abdelhaq, Randall-Demllo, Sarron, Randow, Felix, Rao, Hai, Rao, V. Ashutosh, Rasmussen, Blake B., Rasse, Tobias M., Ratovitski, Edward A., Rautou, Pierre-Emmanuel, Ray, Swapan K., Razani, Babak, Reed, Bruce H., Reggiori, Fulvio, Rehm, Marku, Reichert, Andreas S., Rein, Theo, Reiner, David J., Reits, Eric, Ren, Jun, Ren, Xingcong, Renna, Maurizio, Reusch, Jane E.B., Revuelta, Jose L., Reyes, Leticia, Rezaie, Alireza R., Richards, Robert I., Richardson, Des R., Richetta, Clémence, Riehle, Michael A., Rihn, Bertrand H., Rikihisa, Yasuko, Riley, Brigit E., Rimbach, Gerald, Rippo, Maria Rita, Ritis, Konstantino, Rizzi, Federica, Rizzo, Elizete, Roach, Peter J., Robbins, Jeffrey, Roberge, Michel, Roca, Gabriela, Roccheri, Maria Carmela, Rocha, Sonia, Rodrigues, Cecilia M.P., Rodríguez, Clara I., de Cordoba, Santiago Rodriguez, Rodriguez-Muela, Natalia, Roelofs, Jeroen, Rogov, Vladimir V., Rohn, Troy T., Rohrer, Bärbel, Romanelli, Davide, Romani, Luigina, Romano, Patricia Silvia, Roncero, M. 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Molecular Biology ,Cell Biology ,Settore BIO/06 - Anatomia Comparata E Citologia - Abstract
non presente
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- 2016
38. Combined mismatch repair and POLE/POLD1 defects explain unresolved suspected Lynch syndrome cancers
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Jansen, A.M. (Anne Ml), Wezel, T. (Tom) van, Van Den Akker, B.E. (Brendy Ewm), Ventayol Garcia, M. (Marina), Ruano, D. (Dina), Tops, C. (Carli), Wagner, A. (Anja), Letteboer, T.G.W. (Tom), Gómez García, E.B. (Encarna), Devilee, P. (Peter), Wijnen, J.T. (Juul), Hes, F.J. (Frederik), Morreau, H. (Hans), Jansen, A.M. (Anne Ml), Wezel, T. (Tom) van, Van Den Akker, B.E. (Brendy Ewm), Ventayol Garcia, M. (Marina), Ruano, D. (Dina), Tops, C. (Carli), Wagner, A. (Anja), Letteboer, T.G.W. (Tom), Gómez García, E.B. (Encarna), Devilee, P. (Peter), Wijnen, J.T. (Juul), Hes, F.J. (Frederik), and Morreau, H. (Hans)
- Abstract
Many suspected Lynch Syndrome (sLS) patients who lack mismatch repair (MMR) germline gene variants and MLH1 or MSH2 hypermethylation are currently explained by somatic MMR gene variants or, occasionally, by germline POLE variants. To further investigate unexplained sLS patients, we analyzed leukocyte and tumor DNA of 62 sLS patients using gene panel sequencing including the POLE, POLD1 and MMR genes. Forty tumors showed either one, two or more somatic MMR variants predicted to affect function. Nine sLS tumors showed a likely ultramutated phenotype and were found to carry germline (n=2) or somatic variants (n=7) in the POLE/POLD1 exonuclease domain (EDM). Six of these POLE/POLD1-EDM mutated tumors also carried somatic MMR variants. Our findings suggest that faulty proofreading may result in loss of MMR and thereby in microsatellite instability.
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- 2016
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39. Whole Gene Capture Analysis of 15 CRC Susceptibility Genes in Suspected Lynch Syndrome Patients
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Jansen, A.M.L. (Anne M. L.), Geilenkirchen, M.A. (Marije A.), Wezel, T. (Tom) van, Jagmohan-Changur, S.C. (Shantie), Ruano, D. (Dina), Klift, H.M. (Heleen) van der, Van Den Akker, B.E.W.M. (Brendy E. W. M.), Laros, J.F.J. (Jeroen F.), Van Galen, M. (Michiel), Wagner, A. (Anja), Letteboer, T.G.W. (Tom), Gómez García, E.B. (Encarna), Tops, C. (Carli), Vasen, H. (Hans), Devilee, P. (Peter), Hes, F.J. (Frederik), Morreau, H. (Hans), Wijnen, J.T. (Juul), Jansen, A.M.L. (Anne M. L.), Geilenkirchen, M.A. (Marije A.), Wezel, T. (Tom) van, Jagmohan-Changur, S.C. (Shantie), Ruano, D. (Dina), Klift, H.M. (Heleen) van der, Van Den Akker, B.E.W.M. (Brendy E. W. M.), Laros, J.F.J. (Jeroen F.), Van Galen, M. (Michiel), Wagner, A. (Anja), Letteboer, T.G.W. (Tom), Gómez García, E.B. (Encarna), Tops, C. (Carli), Vasen, H. (Hans), Devilee, P. (Peter), Hes, F.J. (Frederik), Morreau, H. (Hans), and Wijnen, J.T. (Juul)
- Abstract
Background and Aims Lynch Syndrome (LS) is caused by pathogenic germline variants in one of the mismatch repair (MMR) genes. However, up to 60% of MMR-deficient colorectal cancer cases are categorized as suspected Lynch Syndrome (sLS) because no pathogenic MMR germline variant can be identified, which leads to difficulties in clinical management. We therefore analyzed the genomic regions of 15 CRC susceptibility genes in leukocyte DNA of 34 unrelated sLS patients and 11 patients with MLH1 hypermethylated tumors with a clear family history. Methods Using targeted next-generation sequencing, we analyzed the entire non-repetitive genomic sequence, including intronic and regulatory sequences, of 15 CRC susceptibility genes. In addition, tumor DNA from 28 sLS patients was analyzed for somatic MMR variants. Results Of 1979 germline variants found in the leukocyte DNA of 34 sLS patients, one was a pathogenic variant (MLH1 c.1667+1delG). Leukocyte DNA of 11 patients with MLH1 hypermethylated tumors was negative for pathogenic germline variants in the tested CRC susceptibility genes and for germline MLH1 hypermethylation. Somatic DNA analysis of 28 sLS tumors identified eight (29%) cases with two pathogenic somatic variants, one with a VUS predicted to pathogenic and LOH, and nine cases (32%) with one pathogenic somatic variant (n = 8) or one VUS predicted to be pathogenic (n = 1). Conclusions This is the first study in sLS patients to include the entire genomic sequence of CRC susceptibility genes. An underlying somatic or germline MMR gene defect was identified in ten of 34 sLS patients (29%). In the remaining sLS patients, the underlying genetic defect explaining the MMRdeficiency in their tumors might be found outside the genomic regions harboring the MMR and other known CRC susceptibility genes.
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40. Combined mismatch repair and POLE/POLD1 defects explain unresolved suspected Lynch syndrome cancers
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Jansen, A M L, van Wezel, T, van den Akker, BEWM, Garcia, M V, Ruano, D, Tops, CMJ, Wagner, Anja, Letteboer, TGW, Gomez-Garcia, EB, Devilee, P, Wijnen, JT, Hes, FJ, Morreau, H, Jansen, A M L, van Wezel, T, van den Akker, BEWM, Garcia, M V, Ruano, D, Tops, CMJ, Wagner, Anja, Letteboer, TGW, Gomez-Garcia, EB, Devilee, P, Wijnen, JT, Hes, FJ, and Morreau, H
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- 2016
41. Whole Gene Capture Analysis of 15 CRC Susceptibility Genes in Suspected Lynch Syndrome Patients
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Jansen, A M L, Geilenkirchen, M A, van Wezel, T, Jagmohan-Changur, SC, Ruano, D, Van Der Klift, HM, van den Akker, BEWM, Laros, JFJ, van Galen, M, Wagner, Anja, Letteboer, TGW, Gomez-Garcia, EB, Tops, CMJ, Vasen, HF, Devilee, P, Hes, FJ, Morreau, H, Wijnen, JT, Jansen, A M L, Geilenkirchen, M A, van Wezel, T, Jagmohan-Changur, SC, Ruano, D, Van Der Klift, HM, van den Akker, BEWM, Laros, JFJ, van Galen, M, Wagner, Anja, Letteboer, TGW, Gomez-Garcia, EB, Tops, CMJ, Vasen, HF, Devilee, P, Hes, FJ, Morreau, H, and Wijnen, JT
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- 2016
42. Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition).
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P, Piperdi, B, Piret, Jm, Platanias, Lc, Platta, Hw, Plowey, Ed, Pöggeler, S, Poirot, M, Polčic, P, Poletti, A, Poon, Ah, Popelka, H, Popova, B, Poprawa, I, Poulose, Sm, Poulton, J, Powers, Sk, Powers, T, Pozuelo-Rubio, M, Prak, K, Prange, R, Prescott, M, Priault, M, Prince, S, Proia, Rl, Proikas-Cezanne, T, Prokisch, H, Promponas, Vj, Przyklenk, K, Puertollano, R, Pugazhenthi, S, Puglielli, L, Pujol, A, Puyal, J, Pyeon, D, Qi, X, Qian, Wb, Qin, Zh, Qiu, Y, Qu, Z, Quadrilatero, J, Quinn, F, Raben, N, Rabinowich, H, Radogna, F, Ragusa, Mj, Rahmani, M, Raina, K, Ramanadham, S, Ramesh, R, Rami, A, Randall-Demllo, S, Randow, F, Rao, H, Rao, Va, Rasmussen, Bb, Rasse, Tm, Ratovitski, Ea, Rautou, Pe, Ray, Sk, Razani, B, Reed, Bh, Reggiori, F, Rehm, M, Reichert, A, Rein, T, Reiner, Dj, Reits, E, Ren, J, Ren, X, Renna, M, Reusch, Je, Revuelta, Jl, Reyes, L, Rezaie, Ar, Richards, Ri, Richardson, Dr, Richetta, C, Riehle, Ma, Rihn, Bh, Rikihisa, Y, Riley, Be, Rimbach, G, Rippo, Mr, Ritis, K, 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Sardiello, M, Sargent, G, Sarkar, P, Sarkar, S, Sarrias, Mr, Sarwal, Mm, Sasakawa, C, Sasaki, M, Sass, M, Sato, K, Sato, M, Satriano, J, Savaraj, N, Saveljeva, S, Schaefer, L, Schaible, Ue, Scharl, M, Schatzl, Hm, Schekman, R, Scheper, W, Schiavi, A, Schipper, Hm, Schmeisser, H, Schmidt, J, Schmitz, I, Schneider, Be, Schneider, Em, Schneider, Jl, Schon, Ea, Schönenberger, Mj, Schönthal, Ah, Schorderet, Df, Schröder, B, Schuck, S, Schulze, Rj, Schwarten, M, Schwarz, Tl, Sciarretta, S, Scotto, K, Scovassi, Ai, Screaton, Ra, Screen, M, Seca, H, Sedej, S, Segatori, L, Segev, N, Seglen, Po, Seguí-Simarro, Jm, Segura-Aguilar, J, Seki, E, Sell, C, Seiliez, I, Semenkovich, Cf, Semenza, Gl, Sen, U, Serra, Al, Serrano-Puebla, A, Sesaki, H, Setoguchi, T, Settembre, C, Shacka, Jj, Shajahan-Haq, An, Shapiro, Im, Sharma, S, She, H, Shen, Ck, Shen, Cc, Shen, Hm, Shen, S, Shen, W, Sheng, R, Sheng, X, Sheng, Zh, Shepherd, Tg, Shi, J, Shi, Q, Shi, Y, Shibutani, S, Shibuya, K, Shidoji, Y, Shieh, Jj, Shih, Cm, Shimada, Y, Shimizu, S, Shin, Dw, Shinohara, Ml, Shintani, M, Shintani, T, Shioi, T, Shirabe, K, Shiri-Sverdlov, R, Shirihai, O, Shore, Gc, Shu, Cw, Shukla, D, Sibirny, Aa, Sica, V, Sigurdson, Cj, Sigurdsson, Em, Sijwali, P, Sikorska, B, Silveira, Wa, Silvente-Poirot, S, Silverman, Ga, Simak, J, Simmet, T, Simon, Ak, Simon, Hu, Simone, C, Simons, M, Simonsen, A, Singh, R, Singh, Sv, Singh, Sk, Sinha, D, Sinha, S, Sinicrope, Fa, Sirko, A, Sirohi, K, Sishi, Bj, Sittler, A, Siu, Pm, Sivridis, E, Skwarska, A, Slack, R, Slaninová, I, Slavov, N, Smaili, S, Smalley, K, Smith, Dr, Soenen, Sj, Soleimanpour, Sa, Solhaug, A, Somasundaram, K, Son, Jh, Sonawane, A, Song, C, Song, F, Song, Hk, Song, Jx, Song, W, Soo, Ky, Sood, Ak, Soong, Tw, Soontornniyomkij, V, Sorice, M, Sotgia, F, Soto-Pantoja, Dr, Sotthibundhu, A, Sousa, Mj, Spaink, Hp, Span, Pn, Spang, A, Sparks, Jd, Speck, Pg, Spector, Sa, Spies, Cd, Springer, W, Clair, D, Stacchiotti, A, Staels, B, Stang, Mt, Starczynowski, Dt, 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Taylor, Mj, Tchetina, Ev, Tee, Ar, Teixeira-Clerc, F, Telang, S, Tencomnao, T, Teng, Bb, Teng, Rj, Terro, F, Tettamanti, G, Theiss, Al, Theron, Ae, Thomas, Kj, Thomé, Mp, Thomes, Pg, Thorburn, A, Thorner, J, Thum, T, Thumm, M, Thurston, Tl, Tian, L, Till, A, Ting, Jp, Titorenko, Vi, Toker, L, Toldo, S, Tooze, Sa, Topisirovic, I, Torgersen, Ml, Torosantucci, L, Torriglia, A, Torrisi, Mr, Tournier, C, Towns, R, Trajkovic, V, Travassos, Lh, Triola, G, Tripathi, Dn, Trisciuoglio, D, Troncoso, R, Trougakos, Ip, Truttmann, Ac, Tsai, Kj, Tschan, Mp, Tseng, Yh, Tsukuba, T, Tsung, A, Tsvetkov, A, Tu, S, Tuan, Hy, Tucci, M, Tumbarello, Da, Turk, B, Turk, V, Turner, Rf, Tveita, Aa, Tyagi, Sc, Ubukata, M, Uchiyama, Y, Udelnow, A, Ueno, T, Umekawa, M, Umemiya-Shirafuji, R, Underwood, Br, Ungermann, C, Ureshino, Rp, Ushioda, R, Uversky, Vn, Uzcátegui, Nl, Vaccari, T, Vaccaro, Mi, Váchová, L, Vakifahmetoglu-Norberg, H, Valdor, R, Valente, Em, Vallette, F, Valverde, Am, Van den Berghe, G, Van Den Bosch, L, van den Brink, Gr, van der Goot, Fg, van der Klei, Ij, van der Laan, Lj, van Doorn, Wg, van Egmond, M, van Golen, Kl, Van Kaer, L, van Lookeren Campagne, M, Vandenabeele, P, Vandenberghe, W, Vanhorebeek, I, Varela-Nieto, I, Vasconcelos, Mh, Vasko, R, Vavvas, Dg, Vega-Naredo, I, Velasco, G, Velentzas, Ad, Velentzas, Pd, Vellai, T, Vellenga, E, Vendelbo, Mh, Venkatachalam, K, Ventura, N, Ventura, S, Veras, P, Verdier, M, Vertessy, Bg, Viale, A, Vidal, M, Vieira, Hl, Vierstra, Rd, Vigneswaran, N, Vij, N, Vila, M, Villar, M, Villar, Vh, Villarroya, J, Vindis, C, Viola, G, Viscomi, Maria Teresa, Vitale, G, Vogl, Dt, Voitsekhovskaja, Ov, von Haefen, C, von Schwarzenberg, K, Voth, De, Vouret-Craviari, V, Vuori, K, Vyas, Jm, Waeber, C, Walker, Cl, Walker, Mj, Walter, J, Wan, L, Wan, X, Wang, B, Wang, C, Wang, Cy, Wang, D, Wang, F, Wang, G, Wang, Hj, Wang, H, Wang, Hg, Wang, Hd, Wang, J, Wang, M, Wang, Mq, Wang, Py, Wang, P, Wang, Rc, Wang, S, Wang, Tf, Wang, X, Wang, Xj, Wang, Xw, Wang, Y, Wang, Yj, Wang, Yt, Wang, Zn, Wappner, P, Ward, C, Ward, Dm, Warnes, G, Watada, H, Watanabe, Y, Watase, K, Weaver, Te, Weekes, Cd, Wei, J, Weide, T, Weihl, Cc, Weindl, G, Weis, Sn, Wen, L, Wen, X, Wen, Y, Westermann, B, Weyand, Cm, White, Ar, White, E, Whitton, Jl, Whitworth, Aj, Wiels, J, Wild, F, Wildenberg, Me, Wileman, T, Wilkinson, D, Wilkinson, S, Willbold, D, Williams, C, Williams, K, Williamson, Pr, Winklhofer, Kf, Witkin, S, Wohlgemuth, Se, Wollert, T, Wolvetang, Ej, Wong, E, Wong, Gw, Wong, Rw, Wong, Vk, Woodcock, Ea, Wright, Kl, Wu, C, Wu, D, Wu, G, Wu, J, Wu, M, Wu, S, Wu, Wk, Wu, Y, Wu, Z, Xavier, Cp, Xavier, Rj, Xia, Gx, Xia, T, Xia, W, Xia, Y, Xiao, H, Xiao, J, Xiao, S, Xiao, W, Xie, Cm, Xie, Z, Xilouri, M, Xiong, Y, Xu, C, Xu, F, Xu, H, Xu, J, Xu, L, X, Xu, Xu, Y, Xu, Zx, Xu, Z, Xue, Y, Yamada, T, Yamamoto, A, Yamanaka, K, Yamashina, S, Yamashiro, S, Yan, B, Yan, X, Yan, Z, Yanagi, Y, Yang, D, Yang, Jm, Yang, L, Yang, M, Yang, Pm, Yang, P, Yang, Q, Yang, W, Yang, Wy, Yang, X, Yang, Y, Yang, Z, Yao, Mc, Yao, Pj, Yao, X, Yao, Z, Yasui, L, Ye, M, Yedvobnick, B, Yeganeh, B, Yeh, E, Yeyati, Pl, Yi, F, Yi, L, Yin, Xm, Yip, Ck, Yoo, Ym, Yoo, Yh, Yoon, Sy, Yoshida, K, Yoshimori, T, Young, Kh, Yu, H, Yu, Jj, Yu, Jt, Yu, J, Yu, L, Yu, Wh, Yu, Xf, Yu, Z, Yuan, J, Yuan, Zm, Yue, By, Yue, J, Yue, Z, Zacks, Dn, Zacksenhaus, E, Zaffaroni, N, Zaglia, T, Zakeri, Z, Zecchini, V, Zeng, J, Zeng, M, Zeng, Q, Zervos, A, Zhang, Dd, Zhang, F, Zhang, G, Zhang, Gc, Zhang, H, Zhang, J, Zhang, Jp, Zhang, L, Zhang, My, Zhang, X, Zhang, Xd, Zhang, Y, Zhao, M, Zhao, Wl, Zhao, X, Zhao, Yg, Zhao, Y, Zhao, Yx, Zhao, Z, Zhao, Zj, Zheng, D, Zheng, Xl, Zheng, X, Zhivotovsky, B, Zhong, Q, Zhou, Gz, Zhou, G, Zhou, H, Zhou, Sf, Zhou, Xj, Zhu, H, Zhu, Wg, Zhu, W, Zhu, Xf, Zhu, Y, Zhuang, Sm, Zhuang, X, Ziparo, E, Zois, Ce, Zoladek, T, Zong, Wx, Zorzano, A, Zughaier, Sm., Giordano A (ORCID:0000-0002-6978-0880), and Viscomi MT (ORCID:0000-0002-9096-4967)
- Abstract
In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure flux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we prese
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- 2016
43. Germline variants in POLE are associated with early onset mismatch repair deficient colorectal cancer
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Elsayed, F.A., Kets, C.M., Ruano, D., Akker, B. van den, Mensenkamp, A.R., Schrumpf, M., Nielsen, M., Wijnen, J.T., Tops, C.M., Ligtenberg, M.J., Vasen, H.F.A., Hes, F.J., Morreau, H., Wezel, T. van, Elsayed, F.A., Kets, C.M., Ruano, D., Akker, B. van den, Mensenkamp, A.R., Schrumpf, M., Nielsen, M., Wijnen, J.T., Tops, C.M., Ligtenberg, M.J., Vasen, H.F.A., Hes, F.J., Morreau, H., and Wezel, T. van
- Abstract
Item does not contain fulltext, Germline variants affecting the exonuclease domains of POLE and POLD1 predispose to multiple colorectal adenomas and/or colorectal cancer (CRC). The aim of this study was to estimate the prevalence of previously described heterozygous germline variants POLE c.1270C>G, p.(Leu424Val) and POLD1 c.1433G>A, p.(Ser478Asn) in a Dutch series of unexplained familial, early onset CRC and polyposis index cases. We examined 1188 familial CRC and polyposis index patients for POLE p.(Leu424Val) and POLD1 p.(Ser478Asn) variants using competitive allele-specific PCR. In addition, protein expression of the POLE and DNA mismatch repair genes was studied by immunohistochemistry in tumours from POLE carriers. Somatic mutations were screened using semiconductor sequencing. We detected three index patients (0.25%) with a POLE p.(Leu424Val) variant. In one patient, the variant was found to be de-novo. Tumours from three patients from two families were microsatellite instable, and immunohistochemistry showed MSH6/MSH2 deficiency suggestive of Lynch syndrome. Somatic mutations but no germline MSH6 and MSH2 variants were subsequently found, and one tumour displayed a hypermutator phenotype. None of the 1188 patients carried the POLD1 p.(Ser478Asn) variant. POLE germline variant carriers are also associated with a microsatellite instable CRC. POLE DNA analysis now seems warranted in microsatellite instable CRC, especially in the absence of a causative DNA mismatch repair gene germline variant.
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- 2015
44. Recurrent Coding Sequence Variation Explains only A Small Fraction of the Genetic Architecture of Colorectal Cancer
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Timofeeva, M.N. (Maria N.), Kinnersley, B. (Ben), Farrington, S.M. (Susan M.), Whiffin, N. (Nicola), Palles, C. (Claire), Svinti, V. (Victoria), Lloyd, A. (Amy), Gorman, M. (Maggie), Ooi, L.-Y. (Li-Yin), Hosking, F. (Fay), Barclay, E. (Ella), Zgaga, L. (Lina), Dobbins, S.E. (Sara E.), Martin, L. (Lynn), Theodoratou, E. (Evropi), Broderick, P. (Peter), Tenesa, A. (Albert), Smillie, C. (Claire), Grimes, G. (Graeme), Hayward, C. (Caroline), Campbell, A. (Archie), Porteous, D. (David), Deary, I.J. (Ian), Harris, S.E. (Sarah), Northwood, J.B. (John Blackman), Barrett, J.H. (Jennifer H.), Smith, G. (Gillian), Wolf, R. (Roland), Forman, D. (David), Morreau, H. (Hans), Ruano, D. (Dina), Tops, C. (Carli), Wijnen, J.T. (Juul), Schrumpf, M. (Melanie), Boot, A. (Arnoud), Vasen, H. (Hans), Hes, F.J. (Frederik), Wezel, T. (Tom) van, Franke, A. (Andre), Lieb, W. (Wolgang), Schafmayer, C. (Clemens), Hampe, J. (Jochen), Buch, T. (Thorsten), Propping, P. (Peter), Hemminki, K. (Kari), Försti, A. (Asta), Westers, H. (Helga), Hofstra, R.M.W. (Robert), Pinheiro, M. (Manuela), Pinto, C. (Carla), Teixeira, P.J., Ruiz-Ponte, C. (Clara), Fernández-Rozadilla, C. (Ceres), Carracedo, A. (Angel), Castells, A., Castellví-Bel, S., Campbell, H. (Harry), Bishop, D.T. (David Timothy), Tomlinson, I. (Ian), Dunlop, M.G. (Malcolm), Houlston, R. (Richard), Timofeeva, M.N. (Maria N.), Kinnersley, B. (Ben), Farrington, S.M. (Susan M.), Whiffin, N. (Nicola), Palles, C. (Claire), Svinti, V. (Victoria), Lloyd, A. (Amy), Gorman, M. (Maggie), Ooi, L.-Y. (Li-Yin), Hosking, F. (Fay), Barclay, E. (Ella), Zgaga, L. (Lina), Dobbins, S.E. (Sara E.), Martin, L. (Lynn), Theodoratou, E. (Evropi), Broderick, P. (Peter), Tenesa, A. (Albert), Smillie, C. (Claire), Grimes, G. (Graeme), Hayward, C. (Caroline), Campbell, A. (Archie), Porteous, D. (David), Deary, I.J. (Ian), Harris, S.E. (Sarah), Northwood, J.B. (John Blackman), Barrett, J.H. (Jennifer H.), Smith, G. (Gillian), Wolf, R. (Roland), Forman, D. (David), Morreau, H. (Hans), Ruano, D. (Dina), Tops, C. (Carli), Wijnen, J.T. (Juul), Schrumpf, M. (Melanie), Boot, A. (Arnoud), Vasen, H. (Hans), Hes, F.J. (Frederik), Wezel, T. (Tom) van, Franke, A. (Andre), Lieb, W. (Wolgang), Schafmayer, C. (Clemens), Hampe, J. (Jochen), Buch, T. (Thorsten), Propping, P. (Peter), Hemminki, K. (Kari), Försti, A. (Asta), Westers, H. (Helga), Hofstra, R.M.W. (Robert), Pinheiro, M. (Manuela), Pinto, C. (Carla), Teixeira, P.J., Ruiz-Ponte, C. (Clara), Fernández-Rozadilla, C. (Ceres), Carracedo, A. (Angel), Castells, A., Castellví-Bel, S., Campbell, H. (Harry), Bishop, D.T. (David Timothy), Tomlinson, I. (Ian), Dunlop, M.G. (Malcolm), and Houlston, R. (Richard)
- Abstract
Whilst common genetic variation in many non-coding genomic regulatory regions are known to impart risk of colorectal cancer (CRC), much of the heritability of CRC remains unexplained. To examine the role of recurrent coding sequence variation in CRC aetiology, we genotyped 12,638 CRCs cases and 29,045 controls from six European populations. Single-variant analysis identified a coding variant (rs3184504) in SH2B3 (12q24) associated with CRC risk (OR = 1.08, P = 3.9 × 10-7), and novel damaging coding variants in 3 genes previously tagged by GWAS efforts; rs16888728 (8q24) in UTP23 (OR = 1.15, P = 1.4 × 10-7); rs6580742 and rs12303082 (12q13) in FAM186A (OR = 1.11, P = 1.2 × 10-7
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- 2015
- Full Text
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45. Recurrent Coding Sequence Variation Explains Only A Small Fraction of the Genetic Architecture of Colorectal Cancer
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Timofeeva, MN, Ben Kinnersley, Farrington, SM, Whiffin, N, Palles, C, Svinti, V, Lloyd, A, Gorman, M, Ooi, LY, Hosking, F, Barclay, E, Zgaga, L, Dobbins, S, Martin, L, Theodoratou, E, Broderick, P, Tenesa, A, Smillie, C, Grimes, G, Hayward, C, Campbell, A (Archie), Porteous, D, Deary, IJ, Harris, SE, Northwood, EL, Barrett, JH, Smith, G, de Wolf, R, Forman, D, Morreau, H, Ruano, D, Tops, C, van Wijnen, J (Juul), Schrumpf, M, Boot, A (Arnoud), Vasen, HFA, Hes, FJ, van Wezel, T, Franke, A, Lieb, W, Schafmayer, C, Hampe, J, Buch, S, Propping, P, Hemminki, K, Forsti, A, Westers, H, Hofstra, R, Pinheiro, M, Pinto, C, Teixeira, M, Ruiz-Ponte, C, Fernandez-Rozadilla, C, Carracedo, A, Castells, A, Castellvi-Bel, S, Campbell, H, Bishop, DT, Tomlinson, IPM, Dunlop, MG, Houlston, RS, Timofeeva, MN, Ben Kinnersley, Farrington, SM, Whiffin, N, Palles, C, Svinti, V, Lloyd, A, Gorman, M, Ooi, LY, Hosking, F, Barclay, E, Zgaga, L, Dobbins, S, Martin, L, Theodoratou, E, Broderick, P, Tenesa, A, Smillie, C, Grimes, G, Hayward, C, Campbell, A (Archie), Porteous, D, Deary, IJ, Harris, SE, Northwood, EL, Barrett, JH, Smith, G, de Wolf, R, Forman, D, Morreau, H, Ruano, D, Tops, C, van Wijnen, J (Juul), Schrumpf, M, Boot, A (Arnoud), Vasen, HFA, Hes, FJ, van Wezel, T, Franke, A, Lieb, W, Schafmayer, C, Hampe, J, Buch, S, Propping, P, Hemminki, K, Forsti, A, Westers, H, Hofstra, R, Pinheiro, M, Pinto, C, Teixeira, M, Ruiz-Ponte, C, Fernandez-Rozadilla, C, Carracedo, A, Castells, A, Castellvi-Bel, S, Campbell, H, Bishop, DT, Tomlinson, IPM, Dunlop, MG, and Houlston, RS
- Abstract
Whilst common genetic variation in many non-coding genomic regulatory regions are known to impart risk of colorectal cancer (CRC), much of the heritability of CRC remains unexplained. To examine the role of recurrent coding sequence variation in CRC aetiology, we genotyped 12,638 CRCs cases and 29,045 controls from six European populations. Single-variant analysis identified a coding variant (rs3184504) in SH2B3 (12q24) associated with CRC risk (OR = 1.08, P = 3.9 x 10(-7)), and novel damaging coding variants in 3 genes previously tagged by GWAS efforts; rs16888728 (8q24) in UTP23 (OR = 1.15, P = 1.4 x 10(-7)); rs6580742 and rs12303082 (12q13) in FAM186A (OR = 1.11, P = 1.2 x 10(-7) and OR = 1.09, P = 7.4 x 10(-8)); rs1129406 (12q13) in ATF1 (OR = 1.11, P = 8.3 x 10(-9)), all reaching exome-wide significance levels. Gene based tests identified associations between CRC and PCDHGA genes (P < 2.90 x 10(-6)). We found an excess of rare, damaging variants in base-excision (P = 2.4 x 10(-4)) and DNA mismatch repair genes (P = 6.1 x 10(-4)) consistent with a recessive mode of inheritance. This study comprehensively explores the contribution of coding sequence variation to CRC risk, identifying associations with coding variation in 4 genes and PCDHG gene cluster and several candidate recessive alleles. However, these findings suggest that recurrent, low-frequency coding variants account for a minority of the unexplained heritability of CRC.
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- 2015
46. Distinct chromosomal alterations in oncocytic follicular thyroid carcinoma
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Corver, W.E., Ruano, D., Weijers, K., Nieuwenhuizen, M.P. van, Miranda, N. de, Eijk, R. van, Middeldorp, A., Jordanova, E.S., Oosting, J., Kapiteijn, E., Hovens, G., Smit, J., Wezel, T. van, and Morreau, H.
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- 2012
47. Anti-inflammatory activity of a honey flavonoid extract on N13 microglial cells
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Candiracci, M., Piatti, Elena, Domínguez, M., García Antras, D., Morgado, B., Ruano, D., Gutiérrez, J. F., Parrado, J., and Castaño, A.
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- 2012
48. Colorectal cancer risk variants on 11q23 and 15q13 are associated with unexplained adenomatous polyposis
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Hes, F.J., Ruano, D., Nieuwenhuis, M., Tops, C.M., Schrumpf, M., Nielsen, M., Huijts, P.E., Wijnen, J.T., Wagner, A., Garcia, E.B., Sijmons, R.H., Menko, F.H., Letteboer, T.G., Hoogerbrugge, N., Harryvan, J., Kampman, E., Morreau, H., Vasen, H.F., Wezel, T. van, Hes, F.J., Ruano, D., Nieuwenhuis, M., Tops, C.M., Schrumpf, M., Nielsen, M., Huijts, P.E., Wijnen, J.T., Wagner, A., Garcia, E.B., Sijmons, R.H., Menko, F.H., Letteboer, T.G., Hoogerbrugge, N., Harryvan, J., Kampman, E., Morreau, H., Vasen, H.F., and Wezel, T. van
- Abstract
Item does not contain fulltext, BACKGROUND: Colorectal adenomatous polyposis is associated with a high risk of colorectal cancer (CRC) and is frequently caused by germline mutations in APC or MUTYH. However, in about 20-30% of patients no underlying gene defect can be identified. In this study, we tested if recently identified CRC risk variants play a role in patients with >10 adenomas. METHODS: We analysed a total of 16 SNPs with a reported association with CRC in a cohort of 252 genetically unexplained index patients with >10 colorectal adenomas and 745 controls. In addition, we collected detailed clinical information from index patients and their first-degree relatives (FDRs). RESULTS: We found a statistically significant association with two of the variants tested: rs3802842 (at chromosome 11q23, OR=1.60, 95% CI 1.3 to 2.0) and rs4779584 (at chromosome 15q13, OR=1.50, 95% CI 1.2 to 1.9). The majority of index patients (84%) had between 10 and 100 adenomas and 15% had >100 adenomas. Only two index patients (1%), both with >100 adenomas, had FDRs with polyposis. Forty-one per cent of the index patients had one or more FDRs with CRC. CONCLUSIONS: These SNPs are the first common, low-penetrant variants reported to be associated with adenomatous polyposis not caused by a defect in the APC, MUTYH, POLD1 and POLE genes. Even though familial occurrence of polyposis was very rare, CRC was over-represented in FDRs of polyposis patients and, if confirmed, these relatives will therefore benefit from surveillance.
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- 2014
49. Colorectal cancer risk variants on 11q23 and 15q13 are associated with unexplained adenomatous polyposis
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Hes, F.J. (Frederik), Ruano, D. (Dina), Nieuwenhuis, M.H. (Mary), Tops, C. (Carli), Schrumpf, M. (Melanie), Nielsen, M. (Maartje), Huijts, P. (Petra), Wijnen, J.T. (Juul), Wagner, A. (Anja), Gómez García, E.B. (Encarna), Sijmons, R.H. (Rolf), Menko, F. (Fred), Letteboer, T.G.W. (Tom), Hoogerbrugge, N. (Nicoline), Harryvan, J. (Jan), Kampman, E. (Ellen), Morreau, H. (Hans), Vasen, H. (Hans), Wezel, T. (Tom) van, Hes, F.J. (Frederik), Ruano, D. (Dina), Nieuwenhuis, M.H. (Mary), Tops, C. (Carli), Schrumpf, M. (Melanie), Nielsen, M. (Maartje), Huijts, P. (Petra), Wijnen, J.T. (Juul), Wagner, A. (Anja), Gómez García, E.B. (Encarna), Sijmons, R.H. (Rolf), Menko, F. (Fred), Letteboer, T.G.W. (Tom), Hoogerbrugge, N. (Nicoline), Harryvan, J. (Jan), Kampman, E. (Ellen), Morreau, H. (Hans), Vasen, H. (Hans), and Wezel, T. (Tom) van
- Abstract
Background: Colorectal adenomatous polyposis is associated with a high risk of colorectal cancer (CRC) and is frequently caused by germline mutations in APC or MUTYH. However, in about 20-30% of patients no underlying gene defect can be identified. In this study, we tested if recently identified CRC risk variants play a role in patients with >10 adenomas. Methods We analysed a total of 16 SNPs with a reported association with CR
- Published
- 2014
- Full Text
- View/download PDF
50. 659: Somatic mutation profiles in primary colorectal cancers and matching ovarian metastases: Identification of driver and passenger mutations
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Crobach, S., primary, Ruano, D., additional, van Eijk, R., additional, Schrumpf, M., additional, Fleuren, G., additional, Wezel, T., additional, and Morreau, H., additional
- Published
- 2014
- Full Text
- View/download PDF
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