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Targeted sequencing of untreated DLBCL and TLy

Targeted capture sequencing

targeted sequencing results of rrDLBCL

Purpose: Relapsed or refractory diffuse large B-cell lymphoma (rrDLBCL) is fatal in 90% of patients, and yet little is known about its biology.Experimental Design: Using exome sequencing, we characterized the mutation profiles of 38 rrDLBCL biopsies obtained at the time of progression after immunochemotherapy. To identify genes that may be associated with relapse, we compared the mutation frequency in samples obtained at relapse to an unrelated cohort of 138 diagnostic DLBCLs and separately amplified specific mutations in their matched diagnostic samples to identify clonal expansions.Results: On the basis of a higher frequency at relapse and evidence for clonal selection, TP53, FOXO1, MLL3 (KMT2C), CCND3, NFKBIZ, and STAT6 emerged as top candidate genes implicated in therapeutic resistance. We observed individual examples of clonal expansions affecting genes whose mutations had not been previously associated with DLBCL including two regulators of NF-κB: NFKBIE and NFKBIZ. We detected mutations that may be affect sensitivity to novel therapeutics, such as MYD88 and CD79B mutations, in 31% and 23% of patients with activated B-cell–type of rrDLBCL, respectively. We also identified recurrent STAT6 mutations affecting D419 in 36% of patients with the germinal center B (GCB) cell rrDLBCL. These were associated with activated JAK/STAT signaling, increased phospho-STAT6 protein expression and increased expression of STAT6 target genes.Conclusions: This work improves our understanding of therapeutic resistance in rrDLBCL and has identified novel therapeutic opportunities especially for the high-risk patients with GCB-type rrDLBCL. Clin Cancer Res; 22(9); 2290–300. ©2015 AACR.

Supplemental methods Supplemental Figures Supplemental Figure S1. Overview of somatic copy number alterations in rrDLBCLs. Supplemental Figure S2. Consistent low coverage in the first exon of FOXO1. Supplemental Figure S3. Overview of FOXO1 mutations in rrDLBCLs. Supplemental Figure S4. VAFs corrected using purity estimates. Supplemental Figure S5. Somatic copy number alterations affecting lymphoma-related genes. Supplemental Figure S6: Recurrent deletions in NFKBIE. Supplemental Tables Supplemental Table S1. Clinical details and sample processing of 38 patients with relapsed or refractory DLBCL and TLy Supplemental Table S2. Characteristics of samples used for exome sequencing and targeted sequencing of selected genes.

exome sequencing results of rrDLBCL

Background Therapeutic resistance is the main cause of death in metastatic colorectal cancer. To investigate genomic plasticity, most specifically of metastatic lesions, associated with response to first‐line systemic therapy, we collected longitudinal liver metastatic samples and characterized the copy number aberration (CNA) landscape and its effect on the transcriptome. Methods Liver metastatic biopsies were collected prior to treatment (pre, n = 97) and when clinical imaging demonstrated therapeutic resistance (post, n = 43). CNAs were inferred from whole exome sequencing and were correlated with both the status of the lesion and overall patient progression‐free survival (PFS). We used RNA sequencing data from the same sample set to validate aberrations as well as independent datasets to prioritize candidate genes. Results We identified a significantly increased frequency gain of a unique CN, in liver metastatic lesions after first‐line treatment, on chr18p11.32 harboring 10 genes, including TYMS, which has not been reported in primary tumors (GISTIC method and test of equal proportions, FDR‐adjusted p = 0.0023). CNA lesion profiles exhibiting different treatment responses were compared and we detected focal genomic divergences in post‐treatment resistant lesions but not in responder lesions (two‐tailed Fisher's Exact test, unadjusted p ≤ 0.005). The importance of examining metastatic lesions is highlighted by the fact that 15 out of 18 independently validated CNA regions found to be associated with PFS in this study were only identified in the metastatic lesions and not in the primary tumors. Conclusion This investigation of genomic‐phenotype associations in a large colorectal cancer liver metastases cohort identified novel molecular features associated with treatment response, supporting the clinical importance of collecting metastatic samples in a defined clinical setting., Graphical Abstract and Graphical Headlights Liver metastatic lesions from colorectal cancer patients were collected before and after first‐line standard chemotherapy and comprehensively profiled with the objective to assess the genomic impact of systemic therapy and investigate association with response and survival. This study allowed identification of novel CNAs having an impact on the transcriptome with a potential prognostic value in patients with colorectal cancer.

Purpose: Relapsed or refractory diffuse large B-cell lymphoma (rrDLBCL) is fatal in 90% of patients, and yet little is known about its biology. Experimental Design: Using exome sequencing, we characterized the mutation profiles of 38 rrDLBCL biopsies obtained at the time of progression after immunochemotherapy. To identify genes that may be associated with relapse, we compared the mutation frequency in samples obtained at relapse to an unrelated cohort of 138 diagnostic DLBCLs and separately amplified specific mutations in their matched diagnostic samples to identify clonal expansions. Results: On the basis of a higher frequency at relapse and evidence for clonal selection, TP53, FOXO1, MLL3 (KMT2C), CCND3, NFKBIZ, and STAT6 emerged as top candidate genes implicated in therapeutic resistance. We observed individual examples of clonal expansions affecting genes whose mutations had not been previously associated with DLBCL including two regulators of NF-κB: NFKBIE and NFKBIZ. We detected mutations that may be affect sensitivity to novel therapeutics, such as MYD88 and CD79B mutations, in 31% and 23% of patients with activated B-cell–type of rrDLBCL, respectively. We also identified recurrent STAT6 mutations affecting D419 in 36% of patients with the germinal center B (GCB) cell rrDLBCL. These were associated with activated JAK/STAT signaling, increased phospho-STAT6 protein expression and increased expression of STAT6 target genes. Conclusions: This work improves our understanding of therapeutic resistance in rrDLBCL and has identified novel therapeutic opportunities especially for the high-risk patients with GCB-type rrDLBCL. Clin Cancer Res; 22(9); 2290–300. ©2015 AACR.

Chronic myeloid leukemia is characterized by the translocation t(9;22)(q34;q11) and expression of BCR-ABL1, a dysregulated tyrosine kinase. Pharmacologic inhibition of this kinase enables effective disease control in most patients. However, best management of patients with chronic myeloid leukemia with highly resistant BCR-ABL1mutation and feasibility of tyrosine kinase inhibitor (TKI) cessation for prolonged treatment-free remission (TFR) in this setting is challenging. The case reportedhere illustrates anunexpected success of a forced watch and wait strategy.

Increasingly, targeted therapies are being developed to treat malignancies. To define targets, determine mechanisms of response and resistance, and develop biomarkers for the successful investigation of novel therapeutics, high-quality tumor biospecimens are critical. We have developed standard operating procedures (SOPs) to acquire and process serial blood and tumor biopsies from patients with diffuse large B-cell lymphoma enrolled in multicenter clinical trials. These SOPs allow for collection and processing of materials suitable for multiple downstream applications, including immunohistochemistry, cDNA microarrays, exome sequencing, and metabolomics. By standardizing these methods, we control preanalytic variables that ensure high reproducibility of results and facilitate the integration of datasets from such trials. This will facilitate translational research, better treatment selection, and more rapid and efficient development of new drugs. See all the articles in this CEBP Focus section, “Biomarkers, Biospecimens, and New Technologies in Molecular Epidemiology.” Cancer Epidemiol Biomarkers Prev; 23(12); 2688–93. ©2014 AACR.

Great advances in analytical technology coupled with accelerated new drug development and growing understanding of biological challenges, such as tumor heterogeneity, have required a change in the focus for biobanking. Most current banks contain samples of primary tumors, but linking molecular signatures to therapeutic questions requires serial biopsies in the setting of metastatic disease, next-generation of biobanking. Furthermore, an integration of multidimensional analysis of various molecular components, that is, RNA, DNA, methylome, microRNAome and post-translational modifications of the proteome, is necessary for a comprehensive view of a tumor's biology. While data using such biopsies are now regularly presented, the preanalytical variables in tissue procurement and processing in multicenter studies are seldom detailed and therefore are difficult to duplicate or standardize across sites and across studies. In the context of a biopsy-driven clinical trial, we generated a detailed protocol that includes morphological evaluation and isolation of high-quality nucleic acids from small needle core biopsies obtained from liver metastases. The protocol supports stable shipping of samples to a central laboratory, where biopsies are subsequently embedded in support media. Designated pathologists must evaluate all biopsies for tumor content and macrodissection can be performed if necessary to meet our criteria of >60% neoplastic cells and

Introduction: Colorectal cancer (CRC) is the third leading cause of cancer related deaths primarily due to its resistance to current treatments. Studies aiming at understanding mechanisms of resistance have largely investigated the genomic landscape of primary tumors at diagnosis. However, selective pressures during therapy can lead to the expansion of resistant clones and tumor heterogeneity. This highlights the need to characterize the molecular changes of metastasis over time of treatment and response to decipher tumor evolution and therapeutic resistance mechanisms. Methods: Metastatic liver tissue samples were collected at baseline (pre-biopsies) and at the time of resistance (post-biopsies) in responder and non-responder CRC patients undergoing the same first-line treatment. Paired pre/post biopsies were collected from 14 patients including 4 patients with multiple post-biopsies to assess temporal and spatio-temporal tumor heterogeneity following treatment exposure. Biopsies were profiled using exome and transcriptome sequencing as well as high-density Single-Nucleotide Polymorphism (SNP) array analysis to capture chromosomal anomalies, loss of heterozygosity and copy number (CN) variations. Results: Profiling of 45 samples with both high-density SNP array and exome sequencing revealed 97.4% similarity between both technologies in the identification of genes targeted by copy number changes. Using chemo-naïve biopsies, we identified 120 CN gains and 47 CN loss that were significantly associated with patient progression free survival. Integrative analysis with transcriptome data revealed that only 10% of the genomic CN gains and 17% of the CN loss correlated with their gene expression levels. Based on CN variants comparison between paired pre/post treatment samples, we found high temporal intra-patient heterogeneity over time of treatment. Interestingly, we observed a relationship between heterogeneity and tumor response; showing that acquired resistant tumors have the highest temporal variations. Conclusion: This study, using a multi-omic approach to profile serial liver metastatic samples in CRC patients, highlights the genomic changes in tumor composition after treatment exposure and constitutes an innovative approach to identify clinical biomarkers and molecular signatures of resistance. Citation Format: Mathilde Couetoux du Tertre, Maud Marques, Karen Gambaro, Michael Witcher, Benoit Samson, Bernard Lespérance, Yoo-Joung Ko, Richard Dalfen, Eve St-Hilaire, Lucas Sidéris, Félix Couture, Sabine Tejpar, Ronald Burkes, Mohammed Harb, Errol Camlioglu, Adrian Gologan, Vincent Pelsser, André Constantin, Suzan McNamara, Petr Kavan, Claudia Kleinman, Gerald Batist. Genomic profiling in serial metastatic colorectal tumors identifies copy number alterations and spatio temporal intra-patient heterogeneity profiles associated with clinical response. Q-CROC-01: NCT00984048 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr LB-231.

Purpose Assess glomerular yield and safety profile of two different types of needles for percutaneous ultrasound-guided kidney biopsy. Materials and Methods Over 24 months, 121 ultrasonographic ultrasound-guided renal biopsies were performed on native kidneys of 121 adults: 66 with 16-gauge, 29-mm end-cut (BioPince) needles and 55 with 14-gauge, 1.9-mm side-notch (Tru-Cut) needles. Results The mean number of complete glomeruli harvested per biopsy was 21.0 and 19.3, respectively, and the mean number of core samples required to obtain a satisfactory biopsy was 1.8 and 2.6, respectively. The ratio of glomeruli harvested to core samples needed with the end-cut needle was 58% greater than that with the side-notch needles (11.7 vs 7.4, respectively; difference of 4.3; 95% confidence interval: 2.0, 6.8). Procedures performed with end-cut needles were associated with fewer major complications (1.5% vs 7.3% with side-notch needles). Conclusions Compared to the 14-g Tru-cut needle, the 16-g end-cut needle provided better glomerular yield per core sample, required fewer cores for satisfactory tissue specimen, and resulted in fewer major complications.

Félix Terrier was bom into a modest Paris bourgeois family. First, he followed courses at the Veterinary College of Alfort (1854-1858) where he did very well. But as he was drawn towards Hospiral surgery, he managed to get expelled, after a student riot. This brillant student made great strides in medical school and after qualifying in Surgery Agrégation was appointed Hospital Surgeon (1873). As a disciple of Pasteur, he used as a tribune his Surgery Department of Bichat Hospital in order to put into practice and to develop the rules of aseptic surgery still in use today. Thus, he was able to undertake operations considered impossible up until then., Félix Terrier naquit dans la petite bourgeoisie parisienne. Il suivit d’abord les cours de l’École Vétérinaire d’Alfort (1854-1858) où il se distingua. Mais, attiré par la grande chirurgie hospitalière, il fit en sorte de s’en faire exclure à l’occasion d’un chahut d’étudiants. Cet élève surdoué brûla les étapes de l’enseignement médical et après son Agrégation de chirurgie fut nommé chirurgien des Hôpitaux (1873). Pastorien convaincu, il usa de la tribune que lui offrait son service de chirurgie à l’Hôpital Bichat, pour mettre au point et faire connaître les règles de l’asepsie chirurgicale toujours en usage de nos jours. Il put ainsi réussir des opérations considérées comme impossibles., Constantin André. Félix Terrier, transfuge de l’École Vétérinaire d’Alfort et apôtre de la Chirurgie Aseptique Française (1837-1908). In: Bulletin de l'Académie Vétérinaire de France tome 149 n°2, 1996. pp. 237-243.

Oxytocin : recent data and prospects Pituitary posterior lobe extract was introduced in Pharmacopea at the beginning of this century, the major indication was lack of uterine contractions. Progressively, we understood that two peptides hormones composed the extract : oxytocin (1953) and vasopressin (1964). Neurosecretion was discovered in the same period (1956) specific neurophysins were associated to these two hormones. Analysis of hypothalamic hormones were performed in all animals populations and we found that these products were good markers of different stages of phylogenesis. Hypothalamus has not the exclusivity in oxytocin secretion. Luteal cells (granulosa) are able to elaborate this hormone but a low level. Now, research on rats has shown a negative action in memory and a positive action in maternal behaviour., L’extrait post-hypophysaire a été introduit dans la Pharmacopée au début du siècle, l’indication principale était le traitement des insuffisances de la contraction utérine. Peu à peu, on a compris qu’il y avait deux hormones peptidiques dans l’extrait : l’ocytocine (1953) et la vasopressine (1964). La notion de neuro-sécrétion est apparue en même temps (1956). Des neurophysines spécifiques sont couplées à ces deux hormones. On a également analysé les hormones hypothalamiques dans toute la série animale, et constaté qu’elles étaient de bons marqueurs des étapes de la phylogénèse. L’hypothalamus n’a pas l’exclusivité de la synthèse de l’ocytocine, des cellules lutéales (granulosa) en font de même, mais en quantité beaucoup plus faibles. Enfin, des recherches sur le rat ont permis de mettre en évidence une action négative sur la mémorisation et une action positive sur le comportement maternel., Constantin André. L’ocytocine : données nouvelles et perspectives. In: Bulletin de l'Académie Vétérinaire de France tome 145 n°1, 1992. pp. 93-106.

Therapeutic resistance remains a major obstacle in metastatic colorectal cancer (mCRC) and biomarkers to guide treatment are essential to improving survival and quality of life in mCRC patients. A biopsy-driven prospective study was designed to identify biomarkers and mechanisms of resistance to a standard first-line therapy in patients with mCRC which could be useful in guiding treatment selection (QCROC-01; NCT00984048). We also hoped to recognize molecular changes over time, or resulting from the selection pressure of treatment, which could have implications for subsequent therapy. This study is ongoing and approved at thirteen sites with one-hundred patients enrolled so far. Patients with mCRC receiving FOLFOX (5-fluorouracil, leucovorin and oxaliplatin) with bevacizumab consented to three needle core tumour biopsies at pre-treatment and at the time of resistance. The rate of both patient and physician acceptance of biopsies has steadily risen with time and experience. Serial bloods were also collected for proteomic analysis and circulating tumor DNA. Twenty-five biopsy samples were profiled using exome sequencing (tumor and germ line), RNAseq, low pass genome sequencing and miRNA analysis. Differential gene expression analysis revealed signatures associated with clinical response and resistance when comparing tumours obtained pre- and post-treatment. We detect changes in variant allele fraction including both depletion and enrichment of individual somatic mutations over the course of treatment, the latter of which may indicate subclonal and acquired “driver” mutations that confer therapeutic resistance. A small number of genes show recurrent evidence for changes in clonal enrichment at the time of relapse across multiple patients. These could also represent therapeutic targets for subsequent therapy for these patients, and as such, represent new treatment opportunities. Our findings provide insights into tumor evolution during first-line chemotherapy of mCRC that may hold clues to optimize current first-line therapeutic decision making and identifies potential target pathways for second-line stratification of patients. This study is part of the Canadian Colorectal Cancer Consortium which is a multi-site collaboration funded by the Terry Fox Research Institute and le fonds de recherche du québec - santé. Citation Format: Suzan McNamara, Ryan Morin, Mathilde Couëtoux du Tertre, Rosemary McCloskey, Rebecca Johnston, Daniel Fornika, Benoit Samson, Bernard Lespérance, Thierry Alcindor, Yoo-Joung Ko, Richard Dalfen, Eve St-Hilaire, Lucas Sideris, Felix Couture, Hans Prenen, Sabine Tejpar, Ronald Burkes, André Constantin, Errol Camlioglu, Adriana Aguilar, Adrian Gologan, Benoit Têtu, Celia M. Greenwood, Cyrla Hoffert, Samia Qureshi, Zuanel Diaz, Maud Marques, Micheal Witcher, Thérèse Gagnon-Kugler, Petr Kavan, Gerald Batist. Molecular profiling of sequential biopsies in patients with metastatic colorectal cancer identifies genomic alterations that evolve during first-line therapy and could have therapeutic implications: A prospective study to identify molecular mechanisms of clinical resistance (QCROC-01: NCT00984048). [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3888. doi:10.1158/1538-7445.AM2015-3888

Introduction Personalized medicine in oncology relies on translational research efforts to identify biomarkers that will influence clinical management. This is a concerted effort requiring an organizational framework that is often underestimated. The Quebec Clinical Research Organization in Cancer (Q-CROC) consortium is a multi-disciplinary and multi-institutional group of scientists and clinicians devoted to integrating and enhancing translational and clinical research capacity in Quebec. We describe here the organizational framework driving a multicenter, prospective study to identify biomarkers of clinical resistance to first-line therapy in metastatic colorectal cancer (NCT00984048, Q-CROC-01). Results The Q-CROC consortium has put in place an organizational infrastructure to support the activities and operations of its translational projects. We identified and addressed several critical issues during the course of the Q-CROC-01 translational project that were also common to our subsequent biomarker-driven trial in lymphoma (Q-CROC-02, NCT01238692) and breast cancer (Q-CROC-03, NCT01276899). Examples of these issues include: (i) feasibility and burden of tissue collection at participating sites, (ii) limiting pre-analytical variability in blood and tissue specimens for functional downstream applications, (iii) verification of tumor content on biopsy specimens, (iv) tracking sample flow, (v) integration of clinical data with discovery platforms, and (vi) engaging participation throughout all steps of the project. A critical element in these projects was a scientific project management team to ensure that objectives were aligned and deliverables were met. This academic framework for translational research may be comparable to that of multicenter clinical trials undertaken by industry, but some challenges, including financial and time constraints, data sharing and IP agreements, and engagement of its members, may be more palpable in the academic setting. Conclusion Infrastructure science is underestimated and under-reported in translational cancer research and is crucial to the success of any large-scale biomarker discovery effort. Our experience with three multi-institutional biomarker-driven trials is that progress hinges upon the availability of an infrastructure that provides a concrete link between each component. The Q-CROC-01 project is funded by a Pfizer-FRSQ Innovation Fund award and by Sanofi-Aventis. Q-CROC-02 is funded by Novartis and Roche, and Q-CROC-03 is funded by a Genome Quebec grant.

Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL Introduction: The success of personalized medicine in oncology relies on translational research efforts to identify biomarkers that will influence clinical management. The discovery and validation of biomarkers is a concerted effort requiring an organizational framework that is often underestimated. The Quebec Clinical Research Organization in Cancer (Q-CROC) consortium is a multi-disciplinary and multi-institutional group of scientists and clinicians devoted to integrating and enhancing translational and clinical research capacity in Quebec. We describe here the organizational framework driving a multicenter, prospective study to identify biomarkers of clinical resistance to first-line therapy in metastatic colorectal cancer ([NCT00984048][1], Q-CROC-01). Results: The Q-CROC consortium has put in place an organizational infrastructure to support the activities and operations of its translational projects. We identified and addressed several critical issues during the course of the Q-CROC-01 translational project that were also common to our subsequent biomarker-driven trial in lymphoma (Q-CROC-02, [NCT01238692][2]) and breast cancer (Q-CROC-03, [NCT01276899][3]). Examples of these issues include: (i) feasibility and burden of tissue collection at participating sites, (ii) limiting pre-analytical variability in blood and tissue specimens for functional downstream applications, (iii) verification of tumor content on biopsy specimens, (iv) tracking sample flow, (v) integration of clinical data with discovery platforms, and (vi) engaging participation throughout all steps of the project. In part to address the above issues, we established five operational Cores: clinical, biobank, biospecimen processing, bioanalytical and bioinformatic. A further challenge was the integration between these Cores, who for the most part operated in silos. We observed that a critical element to unify all components of the consortium was a scientific project management team, consisting of dedicated individuals regularly interacting with each Core to ensure that objectives were aligned and deliverables were met. This academic framework for translational research may be comparable to that of multicenter clinical trials undertaken by industry, but some challenges, including financial and time constraints, data sharing and IP agreements, and engagement of its members, may be more palpable in the academic setting. Conclusion: Infrastructure science is underestimated and under-reported in translational cancer research and is crucial to the success of any large-scale biomarker discovery effort. Our experience with three multi-institutional biomarker-driven trials is that progress hinges upon the availability of an infrastructure that is not only the sum of its parts but that provides a concrete link between each component. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5534. doi:1538-7445.AM2012-5534 [1]: /lookup/external-ref?link_type=CLINTRIALGOV&access_num=NCT00984048&atom=%2Fcanres%2F72%2F8_Supplement%2F5534.atom [2]: /lookup/external-ref?link_type=CLINTRIALGOV&access_num=NCT01238692&atom=%2Fcanres%2F72%2F8_Supplement%2F5534.atom [3]: /lookup/external-ref?link_type=CLINTRIALGOV&access_num=NCT01276899&atom=%2Fcanres%2F72%2F8_Supplement%2F5534.atom

Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL Introduction: The biomarker discovery process requires patient tissue samples from which histology is verified and high-quality genomic material is isolated. Several methods have been developed to either preserve tissue morphology or extract sufficient quality and quantity of RNA and DNA for downstream discovery efforts. As clinical trials incorporate patient biopsies for biomarker discovery or validation, it is becoming increasingly important to ensure quality material and identify methods that allow for preservation of morphology and stabilization of molecular content concurrently. We assessed, in liver needle-core biopsies, different sampling, fixation, and genomic isolation methods to maintain morphology and obtain high-quality genomic material for a multi-center prospective study to identify biomarkers of clinical resistance to first-line therapy in metastatic colorectal cancer. Four sampling methods (snap freezing, RNAlater, frozen RNAlater, formalin), two different fixation protocols for histological studies (10% formalin, RNAlater followed by OCT embedding and freezing) and two RNA isolation procedures (Triazol and AllprepDNA/RNA isolation) were evaluated. Results: Keeping in mind site feasibility, we report that the ideal condition to both preserve morphology and obtain high-quality genomic material of patient liver biopsy samples is to collect biopsies in RNAlater for shipping to a Central Pathology core, followed by washing with cold PBS (on dry ice) to permit proper RNA preservation during OCT embedding and cryostat sectioning for histological verification. Simultaneous extraction of DNA and RNA from the same biopsy core yields nucleic acids of optimal concentration and quality for downstream genomic applications. Conclusion: The collection of biospecimens using pre-determined protocol-specific standard operating procedures (SOPs) is essential to control for pre-analytical variability inherent to multicenter trials. Furthermore, histological control of percent tumor cells in each biopsy is absolutely necessary to ensure optimal representation of tumor (>70%) in the specimen. The above conditions were used in the multicenter Q-CROC-01 study ([NCT00984048][1]), where three needle core biopsies are collected from liver metastases of patients with colorectal cancer. One biopsy is collected in formalin and is set aside for downstream immunohistochemistry experiments. Two biopsies are collected in RNAlater and verified for histology. If they pass quality control, both DNA and RNA are isolated concurrently and sent to discovery platforms (DNA: array comparative genomic hybridization (aCGH), methylation profiles, RNA: gene expression profiles, RT-PCR, microRNA profiles, alternative splicing profiles). Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3389. doi:1538-7445.AM2012-3389 [1]: /lookup/external-ref?link_type=CLINTRIALGOV&access_num=NCT00984048&atom=%2Fcanres%2F72%2F8_Supplement%2F3389.atom

Immuno-contraception : prospects in humain beings and animals. Immunological reactions may upset certain stages of reproduction and may be used in human and animal contraception. Today must be taken into account the possibilities offered by antisperm preparations which hinder the cervical migration of male gametes in women. An hormonal blockage is very promising when combined with an immunizing preparation against BHCG. Extensive research has been carried out in India, the U.S.A., in France and especially in Sweden where many important experiments have been done. With domestic animals, controlling cycles with progestatives gives satisfaction to ruminant owners. With dogs where progestagens do not always, Les réactions immunitaires peuvent contrarier certaines phases de la reproduction et être utilisées dans les contraceptions humaine et animale. Il faut retenir, à ce jour, chez la femme, les possibilités offertes par les préparations anti-spermatozoïdes empêchant la migration cervicale des gamètes mâles. Le blocage hormonal est riche d’espoir avec une préparation immunisante contre le 6HCG. De larges études ont été conduites en Inde, aux E.U., en France et surtout en Suède où se poursuivent d’importantes expérimentations. Chez les animaux d’élevage, la maîtrise des cycles avec les progestatifs satisfait les propriétaires de ruminants. Chez le chien, où les progestagènes ne donnent pas toujours les résultats escomptés, une préparation Anti-GnRH pourrait être utile. Affaire à suivre..., Constantin André. L’immuno-contraception : perspectives humaines et animales. In: Bulletin de l'Académie Vétérinaire de France tome 147 n°3, 1994. pp. 285-294.

B.S.E. and misfolded molecular chaperones. Research in Neurodegenerative Diseases in Vertebrates has changed the habits of Pathologists. The Prion, characterized by S. B. Prusiner has obtained progressively the leadership in Aetiology. But, we have still to explain how it works... J. P. Liautard developed the hypothesis of molecular chaperones which are in this case “auto chaperones”. And, we must note that such Proteins could be regarded as infectious organisms. Misfolding of Pr Pc can be considered as a “structural mutation” that propagates in the Target Cells (i.e. Neurons)., L’étude des maladies dégénératives du système nerveux des Vertébrés a modifié les habitudes des pathologistes. Le Prion de S. B. Prusiner s’impose progressivement. Reste à en définir le mode d’action. J. P. Liautard a étayé l’hypothèse des molécules chaperonnes qui, ici, sont devenues auto-chaperonnes et il faut bien constater que ces protéines se comportent comme des agents infectieux. Le mauvais repliement du Pr Pc doit être considéré comme une modification structurelle qui se propage dans les cellules cibles (les neurones)., Constantin André. L’Encéphalopathie Spongiforme Bovine. Une hypothèse étiologique séduisante : les molécules chaperonnes non repliées. In: Bulletin de l'Académie Vétérinaire de France tome 146 n°3, 1993. pp. 285-290.

In 50 piglets with weaning diarrhoea, the heat-labile fraction of the enterotoxin is detected by ELISA test, from 28 E. coli strains considered as containing only the heat-stable fraction. These results are confirmed by the rabbit cutaneous test. The comparative interest of the various diagnosis methods is discussed, and also the consequences in matter of piglets vaccination., Les auteurs, chez 50 porcelets atteints de colibacillose du sevrage, mettent en évidence, par le test ELISA (méthode immuno-enzymatique) la fraction thermolabile (LT) de l'entérotoxine à partir de 28 souches d’Escherichia coli, comme la 0141 : K 85 ac, considérées comme étant pourvues seulement de la fraction thermostable (ST). Ces résultats sont confirmés pour 26 d'entre elles par le test épicutané sur lapin. Les auteurs discutent ensuite de l’intérêt comparatif des méthodes de diagnostic ainsi que des conséquences à tirer de leurs résultats en matière de vaccination des porcelets., Renault Lucien, Storm P. K., Le Bourhis Elizabeth, Mathieu D., Constantin A. Mise en évidence chez les porcelets atteints de la colibacillose du sevrage de la fraction thermolabile de souches d’Escherichia coli réputées en être dépourvues. In: Bulletin de l'Académie Vétérinaire de France tome 134 n°4, 1981. pp. 451-457.

Histological examinations on the hypophysis of animals suffering from Hyena's disease revealed the existence of a lymphocytic hypophysitis. This fact, together with the presence of antibodies directed against the cells of the anterior hypophysis in the serum of the same animals, indicates that the disease may be of auto-immune origin. However, the necessity remains to perform additional epidemiological endocrinological, immunological and immunogenetic studies in order to reveal the cause of Hyena's disease., Les études histologiques réalisées sur des glandes hypophysaires d'animaux atteints de la maladie de la hyène ont permis de déceler l'existence d'une hypophysite lymphocytaire. Son association avec la présence, dans le sérum des mêmes animaux, d’anticorps dirigés contre des constituants cellulaires de l’antehypophyse permet d'envisager l'existence d'une atteinte autoimmune à l'origine des troubles. Néanmoins, de nombreuses études épidémiologiques, endocriniennes, immunologiques et immunogénétiques restent à faire pour mieux cerner l'origine de cette maladie., Pouplard A., Constantin André, Espinasse Jacques, Dubois Maurice P. Maladie de la hyène chez les bovins : une hypophysite d’origine autoimmune ? Résultats préliminaires d’une étude histologique et immunocytochimique . In: Bulletin de l'Académie Vétérinaire de France tome 135 n°2, 1982. pp. 327-334.