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311 results on '"Roehrl, Michael H. A."'

8. Genomic and transcriptomic analysis of a library of small cell lung cancer patient-derived xenografts

Author

Caeser, Rebecca, Egger, Jacklynn V., Chavan, Shweta, Socci, Nicholas D., Jones, Caitlin Byrne, Kombak, Faruk Erdem, Asher, Marina, Roehrl, Michael H., Shah, Nisargbhai S., Allaj, Viola, Manoj, Parvathy, Tischfield, Sam E., Kulick, Amanda, Meneses, Maximiliano, Iacobuzio-Donahue, Christine A., Lai, W. Victoria, Bhanot, Umeshkumar, Baine, Marina K., Rekhtman, Natasha, Hollmann, Travis J., de Stanchina, Elisa, Poirier, John T., Rudin, Charles M., and Sen, Triparna

Published
2022
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10. The 2023 Report on the Proteome from the HUPO Human Proteome Project

Author

Omenn, Gilbert S., Lane, Lydie, Overall, Christopher M., Lindskog, Cecilia, Pineau, Charles, Packer, Nicolle H., Cristea, Ileana M., Weintraub, Susan T., Orchard, Sandra, Roehrl, Michael H. A., Nice, Edouard, Guo, Tiannan, Van Eyk, Jennifer E., Liu, Siqi, Bandeira, Nuno, Aebersold, Ruedi, Moritz, Robert L., Deutsch, Eric W., Omenn, Gilbert S., Lane, Lydie, Overall, Christopher M., Lindskog, Cecilia, Pineau, Charles, Packer, Nicolle H., Cristea, Ileana M., Weintraub, Susan T., Orchard, Sandra, Roehrl, Michael H. A., Nice, Edouard, Guo, Tiannan, Van Eyk, Jennifer E., Liu, Siqi, Bandeira, Nuno, Aebersold, Ruedi, Moritz, Robert L., and Deutsch, Eric W.

Abstract

Since 2010, the Human Proteome Project (HPP), the flagship initiative of the Human Proteome Organization (HUPO), has pursued two goals: (1) to credibly identify the protein parts list and (2) to make proteomics an integral part of multiomics studies of human health and disease. The HPP relies on international collaboration, data sharing, standardized reanalysis of MS data sets by PeptideAtlas and MassIVE-KB using HPP Guidelines for quality assurance, integration and curation of MS and non-MS protein data by neXtProt, plus extensive use of antibody profiling carried out by the Human Protein Atlas. According to the neXtProt release 2023-04-18, protein expression has now been credibly detected (PE1) for 18,397 of the 19,778 neXtProt predicted proteins coded in the human genome (93%). Of these PE1 proteins, 17,453 were detected with mass spectrometry (MS) in accordance with HPP Guidelines and 944 by a variety of non-MS methods. The number of neXtProt PE2, PE3, and PE4 missing proteins now stands at 1381. Achieving the unambiguous identification of 93% of predicted proteins encoded from across all chromosomes represents remarkable experimental progress on the Human Proteome parts list. Meanwhile, there are several categories of predicted proteins that have proved resistant to detection regardless of protein-based methods used. Additionally there are some PE1–4 proteins that probably should be reclassified to PE5, specifically 21 LINC entries and ∼30 HERV entries; these are being addressed in the present year. Applying proteomics in a wide array of biological and clinical studies ensures integration with other omics platforms as reported by the Biology and Disease-driven HPP teams and the antibody and pathology resource pillars. Current progress has positioned the HPP to transition to its Grand Challenge Project focused on determining the primary function(s) of every protein itself and in networks and pathways within the context of human health and disease.

Published
2024
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11. The 2023 Report on the Proteome from the HUPO Human Proteome Project

Author

Omenn, Gilbert S., primary, Lane, Lydie, additional, Overall, Christopher M., additional, Lindskog, Cecilia, additional, Pineau, Charles, additional, Packer, Nicolle H., additional, Cristea, Ileana M., additional, Weintraub, Susan T., additional, Orchard, Sandra, additional, Roehrl, Michael H. A., additional, Nice, Edouard, additional, Guo, Tiannan, additional, Van Eyk, Jennifer E., additional, Liu, Siqi, additional, Bandeira, Nuno, additional, Aebersold, Ruedi, additional, Moritz, Robert L., additional, and Deutsch, Eric W., additional

Published
2024
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12. A renewed model of pancreatic cancer evolution based on genomic rearrangement patterns

Author

Notta, Faiyaz, Chan-Seng-Yue, Michelle, Lemire, Mathieu, Li, Yilong, Wilson, Gavin W, Connor, Ashton A, Denroche, Robert E, Liang, Sheng-Ben, Brown, Andrew MK, Kim, Jaeseung C, Wang, Tao, Simpson, Jared T, Beck, Timothy, Borgida, Ayelet, Buchner, Nicholas, Chadwick, Dianne, Hafezi-Bakhtiari, Sara, Dick, John E, Heisler, Lawrence, Hollingsworth, Michael A, Ibrahimov, Emin, Jang, Gun Ho, Johns, Jeremy, Jorgensen, Lars GT, Law, Calvin, Ludkovski, Olga, Lungu, Ilinca, Ng, Karen, Pasternack, Danielle, Petersen, Gloria M, Shlush, Liran I, Timms, Lee, Tsao, Ming-Sound, Wilson, Julie M, Yung, Christina K, Zogopoulos, George, Bartlett, John MS, Alexandrov, Ludmil B, Real, Francisco X, Cleary, Sean P, Roehrl, Michael H, McPherson, John D, Stein, Lincoln D, Hudson, Thomas J, Campbell, Peter J, and Gallinger, Steven

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Oncology and Carcinogenesis, Pancreatic Cancer, Human Genome, Cancer, Biotechnology, Digestive Diseases, Orphan Drug, Rare Diseases, Development of treatments and therapeutic interventions, 2.1 Biological and endogenous factors, 5.1 Pharmaceuticals, Aetiology, Carcinogenesis, Carcinoma in Situ, Chromothripsis, DNA Copy Number Variations, Disease Progression, Evolution, Molecular, Female, Gene Rearrangement, Genes, Neoplasm, Genome, Human, Humans, Male, Mitosis, Models, Biological, Mutagenesis, Mutation, Neoplasm Invasiveness, Neoplasm Metastasis, Pancreatic Neoplasms, Polyploidy, Precancerous Conditions, General Science & Technology
Abstract

Pancreatic cancer, a highly aggressive tumour type with uniformly poor prognosis, exemplifies the classically held view of stepwise cancer development. The current model of tumorigenesis, based on analyses of precursor lesions, termed pancreatic intraepithelial neoplasm (PanINs) lesions, makes two predictions: first, that pancreatic cancer develops through a particular sequence of genetic alterations (KRAS, followed by CDKN2A, then TP53 and SMAD4); and second, that the evolutionary trajectory of pancreatic cancer progression is gradual because each alteration is acquired independently. A shortcoming of this model is that clonally expanded precursor lesions do not always belong to the tumour lineage, indicating that the evolutionary trajectory of the tumour lineage and precursor lesions can be divergent. This prevailing model of tumorigenesis has contributed to the clinical notion that pancreatic cancer evolves slowly and presents at a late stage. However, the propensity for this disease to rapidly metastasize and the inability to improve patient outcomes, despite efforts aimed at early detection, suggest that pancreatic cancer progression is not gradual. Here, using newly developed informatics tools, we tracked changes in DNA copy number and their associated rearrangements in tumour-enriched genomes and found that pancreatic cancer tumorigenesis is neither gradual nor follows the accepted mutation order. Two-thirds of tumours harbour complex rearrangement patterns associated with mitotic errors, consistent with punctuated equilibrium as the principal evolutionary trajectory. In a subset of cases, the consequence of such errors is the simultaneous, rather than sequential, knockout of canonical preneoplastic genetic drivers that are likely to set-off invasive cancer growth. These findings challenge the current progression model of pancreatic cancer and provide insights into the mutational processes that give rise to these aggressive tumours.

Published
2016

13. Comprehensive molecular characterization of lung tumors implicates AKT and MYC signaling in adenocarcinoma to squamous cell transdifferentiation

Author

Quintanal-Villalonga, Alvaro, Taniguchi, Hirokazu, Zhan, Yingqian A., Hasan, Maysun M., Chavan, Shweta S., Meng, Fanli, Uddin, Fathema, Allaj, Viola, Manoj, Parvathy, Shah, Nisargbhai S., Chan, Joseph M., Ciampricotti, Metamia, Chow, Andrew, Offin, Michael, Ray-Kirton, Jordana, Egger, Jacklynn D., Bhanot, Umesh K., Linkov, Irina, Asher, Marina, Roehrl, Michael H., Ventura, Katia, Qiu, Juan, de Stanchina, Elisa, Chang, Jason C., Rekhtman, Natasha, Houck-Loomis, Brian, Koche, Richard P., Yu, Helena A., Sen, Triparna, and Rudin, Charles M.

Published
2021
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14. Propensity score matching as an effective strategy for biomarker cohort design and omics data analysis.

Author

Maekawa, Masaki, Tanaka, Atsushi, Ogawa, Makiko, and Roehrl, Michael H.

Subjects
PROPENSITY score matching, DATA analysis, EXPERIMENTAL design, IMMUNOHISTOCHEMISTRY, COLORECTAL cancer, CONFOUNDING variables, BIOMARKERS, HISTOCHEMISTRY
Abstract

Background: Analysis of omics data that contain multidimensional biological and clinical information can be complex and make it difficult to deduce significance of specific biomarker factors. Methods: We explored the utility of propensity score matching (PSM), a statistical technique for minimizing confounding factors and simplifying the examination of specific factors. We tested two datasets generated from cohorts of colorectal cancer (CRC) patients, one comprised of immunohistochemical analysis of 12 protein markers in 544 CRC tissues and another consisting of RNA-seq profiles of 163 CRC cases. We examined the efficiency of PSM by comparing pre- and post-PSM analytical results. Results: Unlike conventional analysis which typically compares randomized cohorts of cancer and normal tissues, PSM enabled direct comparison between patient characteristics uncovering new prognostic biomarkers. By creating optimally matched groups to minimize confounding effects, our study demonstrates that PSM enables robust extraction of significant biomarkers while requiring fewer cancer cases and smaller overall patient cohorts. Conclusion: PSM may emerge as an efficient and cost-effective strategy for multiomic data analysis and clinical trial design for biomarker discovery. [ABSTRACT FROM AUTHOR]

Published
2024
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20. Latency and interval therapy affect the evolution in metastatic colorectal cancer

Author

Nikbakht, Hamid, Jessa, Selin, Sukhai, Mahadeo A., Arseneault, Madeleine, Zhang, Tong, Letourneau, Louis, Thomas, Mariam, Bourgey, Mathieu, Roehrl, Michael H. A., Eveleigh, Robert, Chen, Eric X., Krzyzanowska, Monika, Moore, Malcolm J., Giesler, Amanda, Yu, Celeste, Bedard, Philippe L., Kamel-Reid, Suzanne, Majewski, Jacek, Siu, Lillian L., Riazalhosseini, Yasser, and Graham, Donna M.

Published
2020
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21. Sensitive tumour detection and classification using plasma cell-free DNA methylomes

Author

Shen, Shu Yi, Singhania, Rajat, Fehringer, Gordon, Chakravarthy, Ankur, Roehrl, Michael H. A., Chadwick, Dianne, Zuzarte, Philip C., Borgida, Ayelet, Wang, Ting Ting, Li, Tiantian, Kis, Olena, Zhao, Zhen, Spreafico, Anna, Medina, Tiago da Silva, Wang, Yadon, Roulois, David, Ettayebi, Ilias, Chen, Zhuo, Chow, Signy, Murphy, Tracy, Arruda, Andrea, O’Kane, Grainne M., Liu, Jessica, Mansour, Mark, McPherson, John D., O’Brien, Catherine, Leighl, Natasha, Bedard, Philippe L., Fleshner, Neil, Liu, Geoffrey, Minden, Mark D., Gallinger, Steven, Goldenberg, Anna, Pugh, Trevor J., Hoffman, Michael M., Bratman, Scott V., Hung, Rayjean J., and De Carvalho, Daniel D.

Published
2018
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22. Data from Multiomic Analysis of Lung Tumors Defines Pathways Activated in Neuroendocrine Transformation

Author

Quintanal-Villalonga, Alvaro, primary, Taniguchi, Hirokazu, primary, Zhan, Yingqian A., primary, Hasan, Maysun M., primary, Chavan, Shweta S., primary, Meng, Fanli, primary, Uddin, Fathema, primary, Manoj, Parvathy, primary, Donoghue, Mark T.A., primary, Won, Helen H., primary, Chan, Joseph M., primary, Ciampricotti, Metamia, primary, Chow, Andrew, primary, Offin, Michael, primary, Chang, Jason C., primary, Ray-Kirton, Jordana, primary, Tischfield, Sam E., primary, Egger, Jacklynn, primary, Bhanot, Umesh K., primary, Linkov, Irina, primary, Asher, Marina, primary, Sinha, Sonali, primary, Silber, Joachim, primary, Iacobuzio-Donahue, Christine A., primary, Roehrl, Michael H., primary, Hollmann, Travis J., primary, Yu, Helena A., primary, Qiu, Juan, primary, de Stanchina, Elisa, primary, Baine, Marina K., primary, Rekhtman, Natasha, primary, Poirier, John T., primary, Loomis, Brian, primary, Koche, Richard P., primary, Rudin, Charles M., primary, and Sen, Triparna, primary

Published
2023
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23. Supplementary Figures from Multiomic Analysis of Lung Tumors Defines Pathways Activated in Neuroendocrine Transformation

Author

Quintanal-Villalonga, Alvaro, primary, Taniguchi, Hirokazu, primary, Zhan, Yingqian A., primary, Hasan, Maysun M., primary, Chavan, Shweta S., primary, Meng, Fanli, primary, Uddin, Fathema, primary, Manoj, Parvathy, primary, Donoghue, Mark T.A., primary, Won, Helen H., primary, Chan, Joseph M., primary, Ciampricotti, Metamia, primary, Chow, Andrew, primary, Offin, Michael, primary, Chang, Jason C., primary, Ray-Kirton, Jordana, primary, Tischfield, Sam E., primary, Egger, Jacklynn, primary, Bhanot, Umesh K., primary, Linkov, Irina, primary, Asher, Marina, primary, Sinha, Sonali, primary, Silber, Joachim, primary, Iacobuzio-Donahue, Christine A., primary, Roehrl, Michael H., primary, Hollmann, Travis J., primary, Yu, Helena A., primary, Qiu, Juan, primary, de Stanchina, Elisa, primary, Baine, Marina K., primary, Rekhtman, Natasha, primary, Poirier, John T., primary, Loomis, Brian, primary, Koche, Richard P., primary, Rudin, Charles M., primary, and Sen, Triparna, primary

Published
2023
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24. Supplementary Tables from Multiomic Analysis of Lung Tumors Defines Pathways Activated in Neuroendocrine Transformation

Author

Quintanal-Villalonga, Alvaro, primary, Taniguchi, Hirokazu, primary, Zhan, Yingqian A., primary, Hasan, Maysun M., primary, Chavan, Shweta S., primary, Meng, Fanli, primary, Uddin, Fathema, primary, Manoj, Parvathy, primary, Donoghue, Mark T.A., primary, Won, Helen H., primary, Chan, Joseph M., primary, Ciampricotti, Metamia, primary, Chow, Andrew, primary, Offin, Michael, primary, Chang, Jason C., primary, Ray-Kirton, Jordana, primary, Tischfield, Sam E., primary, Egger, Jacklynn, primary, Bhanot, Umesh K., primary, Linkov, Irina, primary, Asher, Marina, primary, Sinha, Sonali, primary, Silber, Joachim, primary, Iacobuzio-Donahue, Christine A., primary, Roehrl, Michael H., primary, Hollmann, Travis J., primary, Yu, Helena A., primary, Qiu, Juan, primary, de Stanchina, Elisa, primary, Baine, Marina K., primary, Rekhtman, Natasha, primary, Poirier, John T., primary, Loomis, Brian, primary, Koche, Richard P., primary, Rudin, Charles M., primary, and Sen, Triparna, primary

Published
2023
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25. Table S2 from Inhibition of XPO1 Sensitizes Small Cell Lung Cancer to First- and Second-Line Chemotherapy

Author

Quintanal-Villalonga, Alvaro, primary, Taniguchi, Hirokazu, primary, Hao, Yuan, primary, Chow, Andrew, primary, Zhan, Yingqian A., primary, Chavan, Shweta S., primary, Uddin, Fathema, primary, Allaj, Viola, primary, Manoj, Parvathy, primary, Shah, Nisargbhai S., primary, Chan, Joseph M., primary, Offin, Michael, primary, Ciampricotti, Metamia, primary, Ray-Kirton, Jordana, primary, Egger, Jacklynn, primary, Bhanot, Umesh, primary, Linkov, Irina, primary, Asher, Marina, primary, Roehrl, Michael H., primary, Qiu, Juan, primary, de Stanchina, Elisa, primary, Hollmann, Travis J., primary, Koche, Richard P., primary, Sen, Triparna, primary, Poirier, John T., primary, and Rudin, Charles M., primary

Published
2023
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26. Data from Inhibition of XPO1 Sensitizes Small Cell Lung Cancer to First- and Second-Line Chemotherapy

Author

Quintanal-Villalonga, Alvaro, primary, Taniguchi, Hirokazu, primary, Hao, Yuan, primary, Chow, Andrew, primary, Zhan, Yingqian A., primary, Chavan, Shweta S., primary, Uddin, Fathema, primary, Allaj, Viola, primary, Manoj, Parvathy, primary, Shah, Nisargbhai S., primary, Chan, Joseph M., primary, Offin, Michael, primary, Ciampricotti, Metamia, primary, Ray-Kirton, Jordana, primary, Egger, Jacklynn, primary, Bhanot, Umesh, primary, Linkov, Irina, primary, Asher, Marina, primary, Roehrl, Michael H., primary, Qiu, Juan, primary, de Stanchina, Elisa, primary, Hollmann, Travis J., primary, Koche, Richard P., primary, Sen, Triparna, primary, Poirier, John T., primary, and Rudin, Charles M., primary

Published
2023
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27. Figures S1 - S5 from Inhibition of XPO1 Sensitizes Small Cell Lung Cancer to First- and Second-Line Chemotherapy

Author

Quintanal-Villalonga, Alvaro, primary, Taniguchi, Hirokazu, primary, Hao, Yuan, primary, Chow, Andrew, primary, Zhan, Yingqian A., primary, Chavan, Shweta S., primary, Uddin, Fathema, primary, Allaj, Viola, primary, Manoj, Parvathy, primary, Shah, Nisargbhai S., primary, Chan, Joseph M., primary, Offin, Michael, primary, Ciampricotti, Metamia, primary, Ray-Kirton, Jordana, primary, Egger, Jacklynn, primary, Bhanot, Umesh, primary, Linkov, Irina, primary, Asher, Marina, primary, Roehrl, Michael H., primary, Qiu, Juan, primary, de Stanchina, Elisa, primary, Hollmann, Travis J., primary, Koche, Richard P., primary, Sen, Triparna, primary, Poirier, John T., primary, and Rudin, Charles M., primary

Published
2023
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28. The 2022 Report on the Human Proteome from the HUPO Human Proteome Project

Author

Omenn, Gilbert S., Lane, Lydie, Overall, Christopher M., Pineau, Charles, Packer, Nicolle H., Cristea, Ileana M., Lindskog, Cecilia, Weintraub, Susan T., Orchard, Sandra, Roehrl, Michael H. A., Nice, Edouard, Liu, Siqi, Bandeira, Nuno, Chen, Yu-Ju, Guo, Tiannan, Aebersold, Ruedi, Moritz, Robert L., Deutsch, Eric W., Omenn, Gilbert S., Lane, Lydie, Overall, Christopher M., Pineau, Charles, Packer, Nicolle H., Cristea, Ileana M., Lindskog, Cecilia, Weintraub, Susan T., Orchard, Sandra, Roehrl, Michael H. A., Nice, Edouard, Liu, Siqi, Bandeira, Nuno, Chen, Yu-Ju, Guo, Tiannan, Aebersold, Ruedi, Moritz, Robert L., and Deutsch, Eric W.

Abstract

The 2022 Metrics of the Human Proteome from the HUPO Human Proteome Project (HPP) show that protein expression has now been credibly detected (neXtProt PE1 level) for 18 407 (93.2%) of the 19 750 predicted proteins coded in the human genome, a net gain of 50 since 2021 from data sets generated around the world and reanalyzed by the HPP. Conversely, the number of neXtProt PE2, PE3, and PE4 missing proteins has been reduced by 78 from 1421 to 1343. This represents continuing experimental progress on the human proteome parts list across all the chromosomes, as well as significant reclassifications. Meanwhile, applying proteomics in a vast array of biological and clinical studies continues to yield significant findings and growing integration with other omics platforms. We present highlights from the Chromosome-Centric HPP, Biology and Disease-driven HPP, and HPP Resource Pillars, compare features of mass spectrometry and Olink and Somalogic platforms, note the emergence of translation products from ribosome profiling of small open reading frames, and discuss the launch of the initial HPP Grand Challenge Project, “A Function for Each Protein”.

Published
2023
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30. An autoantigen profile from Jurkat T-Lymphoblasts provides a molecular guide for investigating autoimmune sequelae of COVID-19.

Author

Wang, Julia Y., Zhang, Wei, Roehrl, Michael W., Roehrl, Victor B., and Roehrl, Michael H.

Abstract

In order to understand autoimmune phenomena contributing to the pathophysiology of COVID-19 and post-COVID syndrome, we have been profiling autoantigens (autoAgs) from various cell types. Although cells share numerous autoAgs, each cell type gives rise to unique COVID-altered autoAg candidates, which may explain the wide range of symptoms experienced by patients with autoimmune sequelae of SARS-CoV-2 infection. Based on the unifying property of affinity between autoAgs and the glycosaminoglycan dermatan sulfate (DS), this paper reports 140 candidate autoAgs identified from proteome extracts of human Jurkat T-cells, of which at least 105 (75%) are known targets of autoantibodies. Comparison with currently available multi-omic COVID-19 data shows that 125 (89%) DS-affinity proteins are altered at protein and/or RNA levels in SARS-CoV-2-infected cells or patients, with at least 94 being known autoAgs in a wide spectrum of autoimmune diseases and cancer. Protein alterations by ubiquitination and phosphorylation during the viral infection are major contributors of autoAgs. The autoAg protein network is significantly associated with cellular response to stress, apoptosis, RNA metabolism, mRNA processing and translation, protein folding and processing, chromosome organization, cell cycle, and muscle contraction. The autoAgs include clusters of histones, CCT/TriC chaperonin, DNA replication licensing factors, proteasome and ribosome proteins, heat shock proteins, serine/arginine-rich splicing factors, 14-3-3 proteins, and cytoskeletal proteins. AutoAgs, such as LCP1 and NACA, that are altered in the T cells of COVID patients may provide insight into T-cell responses to viral infection and merit further study. The autoantigen-ome from this study contributes to a comprehensive molecular map for investigating acute, subacute, and chronic autoimmune disorders caused by SARS-CoV-2. Based on the unique affinity between autoantigens (autoAgs) and dermatan sulfate (DS), this paper reports 140 candidate autoAgs identified from proteome extracts of Jurkat T-cells, with at least 105 (75%) being known targets of autoantibodies in various autoimmune diseases and cancer. Comparison with currently available multi-omic COVID-19 data shows that 125 (89%) DS-affinity proteins are altered in SARS-CoV-2-infected cells or patients. AutoAgs, such as LCP1 and NACA, that are altered in the T cells of COVID-19 patients may provide insight into T-cell responses during viral infection. [ABSTRACT FROM AUTHOR]

Published
2023
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31. An autoantigen-ome from HS-Sultan B-Lymphoblasts offers a molecular map for investigating autoimmune sequelae of COVID-19.

Author

Wang, Julia Y., Zhang, Wei, Roehrl, Victor B., Roehrl, Michael W., and Roehrl, Michael H.

Abstract

To understand how COVID-19 may induce autoimmune diseases, we have been compiling an atlas of COVID autoantigens (autoAgs). Using dermatan sulfate (DS) affinity enrichment of autoantigenic proteins extracted from HS-Sultan lymphoblasts, we identified 362 DS-affinity proteins, of which at least 201 (56%) are confirmed autoAgs. Comparison with available multi-omic COVID data shows that 315 (87%) of the 362 proteins are affected in SARS-CoV-2 infection via altered expression, interaction with viral components, or modification by phosphorylation or ubiquitination, at least 186 (59%) of which are known autoAgs. These proteins are associated with gene expression, mRNA processing, mRNA splicing, translation, protein folding, vesicles, and chromosome organization. Numerous nuclear autoAgs were identified, including both classical antinuclear antibodies (ANAs) and extractable nuclear antigens (ENAs) of systemic autoimmune diseases and unique autoAgs involved in the DNA replication fork, mitotic cell cycle, or telomerase maintenance. We also identified many uncommon autoAgs involved in nucleic acid and peptide biosynthesis and nucleocytoplasmic transport, such as aminoacyl-tRNA synthetases. In addition, this study found autoAgs that potentially interact with multiple SARS-CoV-2 Nsp and Orf components, including CCT/TriC chaperonin, insulin degrading enzyme, platelet-activating factor acetylhydrolase, and the ezrin-moesin-radixin family. Furthermore, B-cell-specific IgM-associated endoplasmic reticulum (ER) complex (including MBZ1, BiP, heat shock proteins, and protein disulfide-isomerases) is enriched by DS-affinity and up-regulated in B-cells of COVID-19 patients, and a similar IgH-associated ER complex was also identified in autoreactive pre-B1 cells in our previous study, which suggests a role of autoreactive B1 cells in COVID-19 that merits further investigation. In summary, this study demonstrates that virally infected cells are characterized by alterations of proteins with propensity to become autoAgs, thereby providing a possible explanation for infection-induced autoimmunity. The COVID autoantigen-ome provides a valuable molecular resource and map for investigation of COVID-related autoimmune sequelae and considerations for vaccine design. This paper investigates the autoantigenic proteome ('autoantigen-ome') of human B cells and shows that a large fraction of these DS-binding autoantigens is affected during SARS-CoV-2 infection, giving rise to a diverse pool of autoAgs that may lead to infection-induced autoimmune diseases. The COVID autoantigen-ome provided in this paper may serve as a molecular map and resource for investigating autoimmune phenomena of SARS-CoV-2 infection and its long-term sequelae. Understanding immunogenic proteins of COVID may also enhance vaccine target design. [ABSTRACT FROM AUTHOR]

Published
2023
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32. Multicenter International Study of the Consensus Immunoscore for the Prediction of Relapse and Survival in Early-Stage Colon Cancer

Author

Mlecnik, Bernhard, primary, Lugli, Alessandro, additional, Bindea, Gabriela, additional, Marliot, Florence, additional, Bifulco, Carlo, additional, Lee, Jiun-Kae Jack, additional, Zlobec, Inti, additional, Rau, Tilman T., additional, Berger, Martin D., additional, Nagtegaal, Iris D., additional, Vink-Börger, Elisa, additional, Hartmann, Arndt, additional, Geppert, Carol I., additional, Kolwelter, Julie, additional, Merkel, Susanne, additional, Grützmann, Robert, additional, Van den Eynde, Marc, additional, Jouret-Mourin, Anne, additional, Kartheuser, Alex, additional, Léonard, Daniel, additional, Remue, Christophe, additional, Wang, Julia, additional, Bavi, Prashant, additional, Roehrl, Michael H. A., additional, Ohashi, Pamela S., additional, Nguyen, Linh T., additional, Han, SeongJun, additional, MacGregor, Heather L., additional, Hafezi-Bakhtiari, Sara, additional, Wouters, Bradly G., additional, Masucci, Giuseppe V., additional, Andersson, Emilia K., additional, Zavadova, Eva, additional, Vocka, Michal, additional, Spacek, Jan, additional, Petruzelka, Lubos, additional, Konopasek, Bohuslav, additional, Dundr, Pavel, additional, Skalova, Helena, additional, Nemejcova, Kristyna, additional, Botti, Gerardo, additional, Tatangelo, Fabiana, additional, Delrio, Paolo, additional, Ciliberto, Gennaro, additional, Maio, Michele, additional, Laghi, Luigi, additional, Grizzi, Fabio, additional, Fredriksen, Tessa, additional, Buttard, Bénédicte, additional, Lafontaine, Lucie, additional, Maby, Pauline, additional, Majdi, Amine, additional, Hijazi, Assia, additional, El Sissy, Carine, additional, Kirilovsky, Amos, additional, Berger, Anne, additional, Lagorce, Christine, additional, Paustian, Christopher, additional, Ballesteros-Merino, Carmen, additional, Dijkstra, Jeroen, additional, van de Water, Carlijn, additional, Vliet, Shannon van Lent-van, additional, Knijn, Nikki, additional, Mușină, Ana-Maria, additional, Scripcariu, Dragos-Viorel, additional, Popivanova, Boryana, additional, Xu, Mingli, additional, Fujita, Tomonobu, additional, Hazama, Shoichi, additional, Suzuki, Nobuaki, additional, Nagano, Hiroaki, additional, Okuno, Kiyotaka, additional, Torigoe, Toshihiko, additional, Sato, Noriyuki, additional, Furuhata, Tomohisa, additional, Takemasa, Ichiro, additional, Patel, Prabhu, additional, Vora, Hemangini H., additional, Shah, Birva, additional, Patel, Jayendrakumar B., additional, Rajvik, Kruti N., additional, Pandya, Shashank J., additional, Shukla, Shilin N., additional, Wang, Yili, additional, Zhang, Guanjun, additional, Kawakami, Yutaka, additional, Marincola, Francesco M., additional, Ascierto, Paolo A., additional, Fox, Bernard A., additional, Pagès, Franck, additional, and Galon, Jérôme, additional

Published
2023
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33. Histopathologic and proteogenomic heterogeneity reveals features of clear cell renal cell carcinoma aggressiveness

Author

Li, Yize, primary, Lih, Tung-Shing M., additional, Dhanasekaran, Saravana M., additional, Mannan, Rahul, additional, Chen, Lijun, additional, Cieslik, Marcin, additional, Wu, Yige, additional, Lu, Rita Jiu-Hsien, additional, Clark, David J., additional, Kołodziejczak, Iga, additional, Hong, Runyu, additional, Chen, Siqi, additional, Zhao, Yanyan, additional, Chugh, Seema, additional, Caravan, Wagma, additional, Naser Al Deen, Nataly, additional, Hosseini, Noshad, additional, Newton, Chelsea J., additional, Krug, Karsten, additional, Xu, Yuanwei, additional, Cho, Kyung-Cho, additional, Hu, Yingwei, additional, Zhang, Yuping, additional, Kumar-Sinha, Chandan, additional, Ma, Weiping, additional, Calinawan, Anna, additional, Wyczalkowski, Matthew A., additional, Wendl, Michael C., additional, Wang, Yuefan, additional, Guo, Shenghao, additional, Zhang, Cissy, additional, Le, Anne, additional, Dagar, Aniket, additional, Hopkins, Alex, additional, Cho, Hanbyul, additional, Leprevost, Felipe da Veiga, additional, Jing, Xiaojun, additional, Teo, Guo Ci, additional, Liu, Wenke, additional, Reimers, Melissa A., additional, Pachynski, Russell, additional, Lazar, Alexander J., additional, Chinnaiyan, Arul M., additional, Van Tine, Brian A., additional, Zhang, Bing, additional, Rodland, Karin D., additional, Getz, Gad, additional, Mani, D.R., additional, Wang, Pei, additional, Chen, Feng, additional, Hostetter, Galen, additional, Thiagarajan, Mathangi, additional, Linehan, W. Marston, additional, Fenyö, David, additional, Jewell, Scott D., additional, Omenn, Gilbert S., additional, Mehra, Rohit, additional, Wiznerowicz, Maciej, additional, Robles, Ana I., additional, Mesri, Mehdi, additional, Hiltke, Tara, additional, An, Eunkyung, additional, Rodriguez, Henry, additional, Chan, Daniel W., additional, Ricketts, Christopher J., additional, Nesvizhskii, Alexey I., additional, Zhang, Hui, additional, Ding, Li, additional, Francis, Alicia, additional, Paulovich, Amanda G., additional, Antczak, Andrzej, additional, Green, Anthony, additional, Colaprico, Antonio, additional, Hakimi, Ari, additional, Pruetz, Barb, additional, Hindenach, Barbara, additional, Yadav, Birendra Kumar, additional, Reva, Boris, additional, Fevrier-Sullivan, Brenda, additional, Druker, Brian J., additional, Szczylik, Cezary, additional, Goldthwaite, Charles A., additional, Birger, Chet, additional, Jones, Corbin D., additional, Rohrer, Daniel C., additional, Tansil, Darlene, additional, Chesla, David, additional, Heiman, David, additional, Duffy, Elizabeth, additional, Schadt, Eri E., additional, Petralia, Francesca, additional, Bromiński, Gabriel, additional, Quiroga-Garza, Gabriela M., additional, Wilson, George D., additional, Li, Ginny Xiaohe, additional, Zhao, Grace, additional, Hsiao, Yi, additional, Hsieh, James, additional, Lubiński, Jan, additional, Bavarva, Jasmin, additional, Huang, Jasmine, additional, Hafron, Jason, additional, Eschbacher, Jennifer, additional, Hon, Jennifer, additional, Francis, Jesse, additional, Freymann, John, additional, Vo, Josh, additional, Wang, Joshua, additional, Kirby, Justin, additional, Zaalishvili, Kakhaber, additional, Ketchum, Karen A., additional, Hoadley, Katherine A., additional, Um, Ki Sung, additional, Qi, Liqun, additional, Domagalski, Marcin J., additional, Tobin, Matt, additional, Dyer, Maureen, additional, Anurag, Meenakshi, additional, Borucki, Melissa, additional, Gillette, Michael A., additional, Birrer, Michael J., additional, Ittmann, Michael M., additional, Roehrl, Michael H., additional, Schnaubelt, Michael, additional, Smith, Michael, additional, Fam, Mina, additional, Roche, Nancy, additional, Vatanian, Negin, additional, Maunganidze, Nicollette, additional, Potapova, Olga, additional, Paklina, Oxana V., additional, VanderKolk, Pamela, additional, Castro, Patricia, additional, Kurzawa, Paweł, additional, Hariharan, Pushpa, additional, Li, Qin, additional, Li, Qing Kay, additional, Dhir, Rajiv, additional, Thangudu, Ratna R., additional, Montgomery, Rebecca, additional, Smith, Richard D., additional, Mareedu, Sailaja, additional, Payne, Samuel H., additional, Cerda, Sandra, additional, Cottingham, Sandra, additional, Haynes, Sarah, additional, Satpathy, Shankha, additional, Richey, Shannon, additional, Singh, Shilpi, additional, Tsang, Shirley X., additional, Cai, Shuang, additional, Cao, Song, additional, Gabriel, Stacey, additional, Carr, Steven A., additional, Liu, Tao, additional, Bauer, Thomas, additional, Le, Toan, additional, Chen, Xi S., additional, Zhang, Xu, additional, Shutack, Yvonne, additional, and Zhang, Zhen, additional

Published
2023
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34. The 2022 Report on the Human Proteome from the HUPO Human Proteome Project

Author

Omenn, Gilbert S., primary, Lane, Lydie, additional, Overall, Christopher M., additional, Pineau, Charles, additional, Packer, Nicolle H., additional, Cristea, Ileana M., additional, Lindskog, Cecilia, additional, Weintraub, Susan T., additional, Orchard, Sandra, additional, Roehrl, Michael H. A., additional, Nice, Edouard, additional, Liu, Siqi, additional, Bandeira, Nuno, additional, Chen, Yu-Ju, additional, Guo, Tiannan, additional, Aebersold, Ruedi, additional, Moritz, Robert L., additional, and Deutsch, Eric W., additional

Published
2022
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35. Clinical Performance of the Consensus Immunoscore in Colon Cancer in the Asian Population from the Multicenter International SITC Study

Author

Mlecnik, Bernhard, primary, Torigoe, Toshihiko, additional, Bindea, Gabriela, additional, Popivanova, Boryana, additional, Xu, Mingli, additional, Fujita, Tomonobu, additional, Hazama, Shoichi, additional, Suzuki, Nobuaki, additional, Nagano, Hiroaki, additional, Okuno, Kiyotaka, additional, Hirohashi, Yoshihiko, additional, Furuhata, Tomohisa, additional, Takemasa, Ichiro, additional, Patel, Prabhudas, additional, Vora, Hemangini, additional, Shah, Birva, additional, Patel, Jayendrakumar B., additional, Rajvik, Kruti N., additional, Pandya, Shashank J., additional, Shukla, Shilin N., additional, Wang, Yili, additional, Zhang, Guanjun, additional, Yoshino, Takayuki, additional, Taniguchi, Hiroya, additional, Bifulco, Carlo, additional, Lugli, Alessandro, additional, Lee, Jiun-Kae Jack, additional, Zlobec, Inti, additional, Rau, Tilman T., additional, Berger, Martin D., additional, Nagtegaal, Iris D., additional, Vink-Börger, Elisa, additional, Hartmann, Arndt, additional, Geppert, Carol I., additional, Kolwelter, Julie, additional, Merkel, Susanne, additional, Grützmann, Robert, additional, Van den Eynde, Marc, additional, Jouret-Mourin, Anne, additional, Kartheuser, Alex, additional, Léonard, Daniel, additional, Remue, Christophe, additional, Wang, Julia, additional, Bavi, Prashant, additional, Roehrl, Michael H. A., additional, Ohashi, Pamela S., additional, Nguyen, Linh T., additional, Han, SeongJun, additional, MacGregor, Heather L., additional, Hafezi-Bakhtiari, Sara, additional, Wouters, Bradly G., additional, Masucci, Giuseppe V., additional, Andersson, Emilia, additional, Zavadova, Eva, additional, Vocka, Michal, additional, Spacek, Jan, additional, Petruzelka, Lubos, additional, Konopasek, Bohuslav, additional, Dundr, Pavel, additional, Skalova, Helena, additional, Nemejcova, Kristyna, additional, Botti, Gerardo, additional, Tatangelo, Fabiana, additional, Delrio, Paolo, additional, Ciliberto, Gennaro, additional, Maio, Michele, additional, Laghi, Luigi, additional, Grizzi, Fabio, additional, Marliot, Florence, additional, Fredriksen, Tessa, additional, Buttard, Bénédicte, additional, Lafontaine, Lucie, additional, Maby, Pauline, additional, Majdi, Amine, additional, Hijazi, Assia, additional, El Sissy, Carine, additional, Kirilovsky, Amos, additional, Berger, Anne, additional, Lagorce, Christine, additional, Paustian, Christopher, additional, Ballesteros-Merino, Carmen, additional, Dijkstra, Jeroen, additional, Van de Water, Carlijn, additional, van Lent-van Vliet, Shannon, additional, Knijn, Nikki, additional, Mușină, Ana-Maria, additional, Scripcariu, Dragos-Viorel, additional, Marincola, Francesco M., additional, Ascierto, Paolo A., additional, Fox, Bernard A., additional, Pagès, Franck, additional, Kawakami, Yutaka, additional, and Galon, Jérôme, additional

Published
2022
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36. Molecular Profiling of Patients With Advanced Colorectal Cancer: Princess Margaret Cancer Centre Experience

Author

Chiu, Joanne W., Krzyzanowska, Monika K., Serra, Stefano, Knox, Jennifer J., Dhani, Neesha C., Mackay, Helen, Hedley, David, Moore, Malcolm, Liu, Geoffrey, Burkes, Ronald L., Brezden-Masley, Christine, Roehrl, Michael H., Craddock, Kenneth J., Tsao, Ming-Sound, Zhang, Tong, Yu, Celeste, Kamel-Reid, Suzanne, Siu, Lillian L., Bedard, Philippe L., and Chen, Eric X.

Published
2018
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38. Abstract 704: Development of a patient-derived xenograft (PDX) modeling program to enable pediatric precision medicine

Author

Dela Cruz, Filemon S., primary, McCarter, Joseph G., additional, You, Daoqi, additional, Bouvier, Nancy, additional, Wang, Xinyi, additional, Guillan, Kristina C., additional, Siddiquee, Armaan H., additional, Souto, Katie B., additional, Li, Hongyan, additional, Gao, Teng, additional, Glodzik, Dominik, additional, Diolaiti, Daniel, additional, Shukla, Neerav N., additional, Silber, Joachim, additional, Bhanot, Umeshkumar K., additional, Kombak, Faruk Erdem, additional, Coutinho, Diego F., additional, Li, Shanita, additional, Ossa, Juan E. Arango, additional, Medina-Martinez, Juan S., additional, Ortiz, Michael V., additional, Slotkin, Emily K., additional, Kinnaman, Michael D., additional, Sait, Sameer F., additional, O'Donohue, Tara J., additional, Mattar, Marissa, additional, Meneses, Maximiliano, additional, LaQuaglia, Michael P., additional, Heaton, Todd E., additional, Gerstle, Justin T., additional, Fabbri, Nicola, additional, Burke, Chelsey M., additional, Rodriquez-Sanchez, Irene M., additional, Iacobuzio-Donahue, Christine A., additional, Bender, Julia L. Glade, additional, Roberts, Ryan D., additional, Yustein, Jason T., additional, Rainusso, Nino C., additional, Crompton, Brian D., additional, Stewart, Elizabeth, additional, Sweet-Cordero, Alejandro, additional, Sayles, Leanne C., additional, Thomas, Andrika D., additional, Roehrl, Michael H., additional, de Stanchina, Elisa, additional, Papaemmanuil, Elli, additional, and Kung, Andrew L., additional

Published
2022
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39. Clinical Performance of the Consensus Immunoscore in Colon Cancer in the Asian Population from the Multicenter International SITC Study.

Author

UCL - SSS/IREC/MIRO - Pôle d'imagerie moléculaire, radiothérapie et oncologie, UCL - (SLuc) Unité d'oncologie médicale, UCL - (SLuc) Service d'anatomie pathologique, UCL - SSS/IREC/CHEX - Pôle de chirgurgie expérimentale et transplantation, UCL - (SLuc) Service de chirurgie et transplantation abdominale, Mlecnik, Bernhard, Torigoe, Toshihiko, Bindea, Gabriela, Popivanova, Boryana, Xu, Mingli, Fujita, Tomonobu, Hazama, Shoichi, Suzuki, Nobuaki, Nagano, Hiroaki, Okuno, Kiyotaka, Hirohashi, Yoshihiko, Furuhata, Tomohisa, Takemasa, Ichiro, Patel, Prabhudas, Vora, Hemangini, Shah, Birva, Patel, Jayendrakumar B, Rajvik, Kruti N, Pandya, Shashank J, Shukla, Shilin N, Wang, Yili, Zhang, Guanjun, Yoshino, Takayuki, Taniguchi, Hiroya, Bifulco, Carlo, Lugli, Alessandro, Lee, Jiun-Kae Jack, Zlobec, Inti, Rau, Tilman T, Berger, Martin D, Nagtegaal, Iris D, Vink-Börger, Elisa, Hartmann, Arndt, Geppert, Carol I, Kolwelter, Julie, Merkel, Susanne, Grützmann, Robert, Van den Eynde, Marc, Jouret-Mourin, Anne, Kartheuser, Alex, Léonard, Daniel, Remue, Christophe, Wang, Julia, Bavi, Prashant, Roehrl, Michael H A, Ohashi, Pamela S, Nguyen, Linh T, Han, SeongJun, MacGregor, Heather L, Hafezi-Bakhtiari, Sara, Wouters, Bradly G, Masucci, Giuseppe V, Andersson, Emilia, Zavadova, Eva, Vocka, Michal, Spacek, Jan, Petruzelka, Lubos, Konopasek, Bohuslav, Dundr, Pavel, Skalova, Helena, Nemejcova, Kristyna, Botti, Gerardo, Tatangelo, Fabiana, Delrio, Paolo, Ciliberto, Gennaro, Maio, Michele, Laghi, Luigi, Grizzi, Fabio, Marliot, Florence, Fredriksen, Tessa, Buttard, Bénédicte, Lafontaine, Lucie, Maby, Pauline, Majdi, Amine, Hijazi, Assia, El Sissy, Carine, Kirilovsky, Amos, Berger, Anne, Lagorce, Christine, Paustian, Christopher, Ballesteros-Merino, Carmen, Dijkstra, Jeroen, Van de Water, Carlijn, van Lent-van Vliet, Shannon, Knijn, Nikki, Mușină, Ana-Maria, Scripcariu, Dragos-Viorel, Marincola, Francesco M, Ascierto, Paolo A, Fox, Bernard A, Pagès, Franck, Kawakami, Yutaka, Galon, Jérôme, UCL - SSS/IREC/MIRO - Pôle d'imagerie moléculaire, radiothérapie et oncologie, UCL - (SLuc) Unité d'oncologie médicale, UCL - (SLuc) Service d'anatomie pathologique, UCL - SSS/IREC/CHEX - Pôle de chirgurgie expérimentale et transplantation, UCL - (SLuc) Service de chirurgie et transplantation abdominale, Mlecnik, Bernhard, Torigoe, Toshihiko, Bindea, Gabriela, Popivanova, Boryana, Xu, Mingli, Fujita, Tomonobu, Hazama, Shoichi, Suzuki, Nobuaki, Nagano, Hiroaki, Okuno, Kiyotaka, Hirohashi, Yoshihiko, Furuhata, Tomohisa, Takemasa, Ichiro, Patel, Prabhudas, Vora, Hemangini, Shah, Birva, Patel, Jayendrakumar B, Rajvik, Kruti N, Pandya, Shashank J, Shukla, Shilin N, Wang, Yili, Zhang, Guanjun, Yoshino, Takayuki, Taniguchi, Hiroya, Bifulco, Carlo, Lugli, Alessandro, Lee, Jiun-Kae Jack, Zlobec, Inti, Rau, Tilman T, Berger, Martin D, Nagtegaal, Iris D, Vink-Börger, Elisa, Hartmann, Arndt, Geppert, Carol I, Kolwelter, Julie, Merkel, Susanne, Grützmann, Robert, Van den Eynde, Marc, Jouret-Mourin, Anne, Kartheuser, Alex, Léonard, Daniel, Remue, Christophe, Wang, Julia, Bavi, Prashant, Roehrl, Michael H A, Ohashi, Pamela S, Nguyen, Linh T, Han, SeongJun, MacGregor, Heather L, Hafezi-Bakhtiari, Sara, Wouters, Bradly G, Masucci, Giuseppe V, Andersson, Emilia, Zavadova, Eva, Vocka, Michal, Spacek, Jan, Petruzelka, Lubos, Konopasek, Bohuslav, Dundr, Pavel, Skalova, Helena, Nemejcova, Kristyna, Botti, Gerardo, Tatangelo, Fabiana, Delrio, Paolo, Ciliberto, Gennaro, Maio, Michele, Laghi, Luigi, Grizzi, Fabio, Marliot, Florence, Fredriksen, Tessa, Buttard, Bénédicte, Lafontaine, Lucie, Maby, Pauline, Majdi, Amine, Hijazi, Assia, El Sissy, Carine, Kirilovsky, Amos, Berger, Anne, Lagorce, Christine, Paustian, Christopher, Ballesteros-Merino, Carmen, Dijkstra, Jeroen, Van de Water, Carlijn, van Lent-van Vliet, Shannon, Knijn, Nikki, Mușină, Ana-Maria, Scripcariu, Dragos-Viorel, Marincola, Francesco M, Ascierto, Paolo A, Fox, Bernard A, Pagès, Franck, Kawakami, Yutaka, and Galon, Jérôme

Abstract

In this study, we evaluated the prognostic value of Immunoscore in patients with stage I-III colon cancer (CC) in the Asian population. These patients were originally included in an international study led by the Society for Immunotherapy of Cancer (SITC) on 2681 patients with AJCC/UICC-TNM stages I-III CC. CD3+ and cytotoxic CD8+ T-lymphocyte densities were quantified in the tumor and invasive margin by digital pathology. The association of Immunoscore with prognosis was evaluated for time to recurrence (TTR), disease-free survival (DFS), and overall survival (OS). Immunoscore stratified Asian patients (n = 423) into different risk categories and was not impacted by age. Recurrence-free rates at 3 years were 78.5%, 85.2%, and 98.3% for a Low, Intermediate, and High Immunoscore, respectively (HR[Low-vs-High] = 7.26 (95% CI 1.75-30.19); = 0.0064). A High Immunoscore showed a significant association with prolonged TTR, OS, and DFS ( < 0.05). In Cox multivariable analysis stratified by center, Immunoscore association with TTR was independent (HR[Low-vs-Int+High] = 2.22 (95% CI 1.10-4.55) = 0.0269) of the patient's gender, T-stage, N-stage, sidedness, and MSI status. A significant association of a High Immunoscore with prolonged TTR was also found among MSS (HR[Low-vs-Int+High] = 4.58 (95% CI 2.27-9.23); ≤ 0.0001), stage II (HR[Low-vs-Int+High] = 2.72 (95% CI 1.35-5.51); = 0.0052), low-risk stage-II (HR[Low-vs-Int+High] = 2.62 (95% CI 1.21-5.68); = 0.0146), and high-risk stage II patients (HR[Low-vs-Int+High] = 3.11 (95% CI 1.39-6.91); = 0.0055). A High Immunoscore is significantly associated with the prolonged survival of CC patients within the Asian population.

Published
2022

40. Erratum: A renewed model of pancreatic cancer evolution based on genomic rearrangement patterns

Author

Notta, Faiyaz, Chan-Seng-Yue, Michelle, Lemire, Mathieu, Li, Yilong, Wilson, Gavin W., Connor, Ashton A., Denroche, Robert E., Liang, Sheng-Ben, Brown, Andrew M. K., Kim, Jaeseung C., Wang, Tao, Simpson, Jared T., Beck, Timothy, Borgida, Ayelet, Buchner, Nicholas, Chadwick, Dianne, Hafezi-Bakhtiari, Sara, Dick, John E., Heisler, Lawrence, Hollingsworth, Michael A., Ibrahimov, Emin, Jang, Gun Ho, Johns, Jeremy, Jorgensen, Lars G. T., Law, Calvin, Ludkovski, Olga, Lungu, Ilinca, Ng, Karen, Pasternack, Danielle, Petersen, Gloria M., Shlush, Liran I., Timms, Lee, Tsao, Ming-Sound, Wilson, Julie M., Yung, Christina K., Zogopoulos, George, Bartlett, John M. S., Alexandrov, Ludmil B., Real, Francisco X., Cleary, Sean P., Roehrl, Michael H., McPherson, John D., Stein, Lincoln D., Hudson, Thomas J., Campbell, Peter J., and Gallinger, Steven

Published
2017
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44. Inhibition of XPO1 Sensitizes Small Cell Lung Cancer to First- and Second-Line Chemotherapy

Author

Quintanal-Villalonga, Alvaro, primary, Taniguchi, Hirokazu, additional, Hao, Yuan, additional, Chow, Andrew, additional, Zhan, Yingqian A., additional, Chavan, Shweta S., additional, Uddin, Fathema, additional, Allaj, Viola, additional, Manoj, Parvathy, additional, Shah, Nisargbhai S., additional, Chan, Joseph M., additional, Offin, Michael, additional, Ciampricotti, Metamia, additional, Ray-Kirton, Jordana, additional, Egger, Jacklynn, additional, Bhanot, Umesh, additional, Linkov, Irina, additional, Asher, Marina, additional, Roehrl, Michael H., additional, Qiu, Juan, additional, de Stanchina, Elisa, additional, Hollmann, Travis J., additional, Koche, Richard P., additional, Sen, Triparna, additional, Poirier, John T., additional, and Rudin, Charles M., additional

Published
2022
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46. Multiomic Analysis of Lung Tumors Defines Pathways Activated in Neuroendocrine Transformation

Author

Quintanal-Villalonga, Alvaro, primary, Taniguchi, Hirokazu, additional, Zhan, Yingqian A., additional, Hasan, Maysun M., additional, Chavan, Shweta S., additional, Meng, Fanli, additional, Uddin, Fathema, additional, Manoj, Parvathy, additional, Donoghue, Mark T.A., additional, Won, Helen H., additional, Chan, Joseph M., additional, Ciampricotti, Metamia, additional, Chow, Andrew, additional, Offin, Michael, additional, Chang, Jason C., additional, Ray-Kirton, Jordana, additional, Tischfield, Sam E., additional, Egger, Jacklynn, additional, Bhanot, Umesh K., additional, Linkov, Irina, additional, Asher, Marina, additional, Sinha, Sonali, additional, Silber, Joachim, additional, Iacobuzio-Donahue, Christine A., additional, Roehrl, Michael H., additional, Hollmann, Travis J., additional, Yu, Helena A., additional, Qiu, Juan, additional, de Stanchina, Elisa, additional, Baine, Marina K., additional, Rekhtman, Natasha, additional, Poirier, John T., additional, Loomis, Brian, additional, Koche, Richard P., additional, Rudin, Charles M., additional, and Sen, Triparna, additional

Published
2021
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47. Progress Identifying and Analyzing the Human Proteome: 2021 Metrics from the HUPO Human Proteome Project

Author

Omenn, Gilbert S., primary, Lane, Lydie, additional, Overall, Christopher M., additional, Paik, Young-Ki, additional, Cristea, Ileana M., additional, Corrales, Fernando J., additional, Lindskog, Cecilia, additional, Weintraub, Susan, additional, Roehrl, Michael H. A., additional, Liu, Siqi, additional, Bandeira, Nuno, additional, Srivastava, Sudhir, additional, Chen, Yu-Ju, additional, Aebersold, Ruedi, additional, Moritz, Robert L., additional, and Deutsch, Eric W., additional

Published
2021
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48. Proteogenomic characterization of pancreatic ductal adenocarcinoma

Author

Cao, Liwei, primary, Huang, Chen, additional, Cui Zhou, Daniel, additional, Hu, Yingwei, additional, Lih, T. Mamie, additional, Savage, Sara R., additional, Krug, Karsten, additional, Clark, David J., additional, Schnaubelt, Michael, additional, Chen, Lijun, additional, da Veiga Leprevost, Felipe, additional, Eguez, Rodrigo Vargas, additional, Yang, Weiming, additional, Pan, Jianbo, additional, Wen, Bo, additional, Dou, Yongchao, additional, Jiang, Wen, additional, Liao, Yuxing, additional, Shi, Zhiao, additional, Terekhanova, Nadezhda V., additional, Cao, Song, additional, Lu, Rita Jui-Hsien, additional, Li, Yize, additional, Liu, Ruiyang, additional, Zhu, Houxiang, additional, Ronning, Peter, additional, Wu, Yige, additional, Wyczalkowski, Matthew A., additional, Easwaran, Hariharan, additional, Danilova, Ludmila, additional, Mer, Arvind Singh, additional, Yoo, Seungyeul, additional, Wang, Joshua M., additional, Liu, Wenke, additional, Haibe-Kains, Benjamin, additional, Thiagarajan, Mathangi, additional, Jewell, Scott D., additional, Hostetter, Galen, additional, Newton, Chelsea J., additional, Li, Qing Kay, additional, Roehrl, Michael H., additional, Fenyö, David, additional, Wang, Pei, additional, Nesvizhskii, Alexey I., additional, Mani, D.R., additional, Omenn, Gilbert S., additional, Boja, Emily S., additional, Mesri, Mehdi, additional, Robles, Ana I., additional, Rodriguez, Henry, additional, Bathe, Oliver F., additional, Chan, Daniel W., additional, Hruban, Ralph H., additional, Ding, Li, additional, Zhang, Bing, additional, Zhang, Hui, additional, Amin, Mitual, additional, An, Eunkyung, additional, Ayad, Christina, additional, Bauer, Thomas, additional, Birger, Chet, additional, Birrer, Michael J., additional, Boca, Simina M., additional, Bocik, William, additional, Borucki, Melissa, additional, Cai, Shuang, additional, Carr, Steven A., additional, Cerda, Sandra, additional, Chen, Huan, additional, Chen, Steven, additional, Chesla, David, additional, Chinnaiyan, Arul M., additional, Colaprico, Antonio, additional, Cottingham, Sandra, additional, Derejska, Magdalena, additional, Dhanasekaran, Saravana M., additional, Domagalski, Marcin J., additional, Druker, Brian J., additional, Duffy, Elizabeth, additional, Dyer, Maureen A., additional, Edwards, Nathan J., additional, Ellis, Matthew J., additional, Eschbacher, Jennifer, additional, Francis, Alicia, additional, Francis, Jesse, additional, Gabriel, Stacey, additional, Gabrovski, Nikolay, additional, Gardner, Johanna, additional, Getz, Gad, additional, Gillette, Michael A., additional, Goldthwaite, Charles A., additional, Grady, Pamela, additional, Guo, Shuai, additional, Hariharan, Pushpa, additional, Hiltke, Tara, additional, Hindenach, Barbara, additional, Hoadley, Katherine A., additional, Huang, Jasmine, additional, Jones, Corbin D., additional, Ketchum, Karen A., additional, Kinsinger, Christopher R., additional, Koziak, Jennifer M., additional, Kusnierz, Katarzyna, additional, Liu, Tao, additional, Long, Jiang, additional, Mallery, David, additional, Mareedu, Sailaja, additional, Matteotti, Ronald, additional, Maunganidze, Nicollette, additional, McGarvey, Peter B., additional, Minoo, Parham, additional, Paklina, Oxana V., additional, Paulovich, Amanda G., additional, Payne, Samuel H., additional, Potapova, Olga, additional, Pruetz, Barbara, additional, Qi, Liqun, additional, Roche, Nancy, additional, Rodland, Karin D., additional, Rohrer, Daniel C., additional, Schadt, Eric E., additional, Shabunin, Alexey V., additional, Shelton, Troy, additional, Shutack, Yvonne, additional, Singh, Shilpi, additional, Smith, Michael, additional, Smith, Richard D., additional, Sokoll, Lori J., additional, Suh, James, additional, Thangudu, Ratna R., additional, Tsang, Shirley X., additional, Um, Ki Sung, additional, Valley, Dana R., additional, Vatanian, Negin, additional, Wang, Wenyi, additional, Wilson, George D., additional, Wiznerowicz, Maciej, additional, Zhang, Zhen, additional, and Zhao, Grace, additional

Published
2021
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50. Integrated digital pathology at scale: A solution for clinical diagnostics and cancer research at a large academic medical center

Author

Schüffler, Peter J, primary, Geneslaw, Luke, additional, Yarlagadda, D Vijay K, additional, Hanna, Matthew G, additional, Samboy, Jennifer, additional, Stamelos, Evangelos, additional, Vanderbilt, Chad, additional, Philip, John, additional, Jean, Marc-Henri, additional, Corsale, Lorraine, additional, Manzo, Allyne, additional, Paramasivam, Neeraj H G, additional, Ziegler, John S, additional, Gao, Jianjiong, additional, Perin, Juan C, additional, Kim, Young Suk, additional, Bhanot, Umeshkumar K, additional, Roehrl, Michael H A, additional, Ardon, Orly, additional, Chiang, Sarah, additional, Giri, Dilip D, additional, Sigel, Carlie S, additional, Tan, Lee K, additional, Murray, Melissa, additional, Virgo, Christina, additional, England, Christine, additional, Yagi, Yukako, additional, Sirintrapun, S Joseph, additional, Klimstra, David, additional, Hameed, Meera, additional, Reuter, Victor E, additional, and Fuchs, Thomas J, additional

Published
2021
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