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Nair NU, Schäffer AA, Gertz EM, Cheng K, Zerbib J, Sahu AD, Leor G, Shulman ED, Aldape KD, Ben-David U, Ruppin E. Chromosome 7 to the rescue: overcoming chromosome 10 loss in gliomas. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.17.576103. [PMID: 38313282 PMCID: PMC10836086 DOI: 10.1101/2024.01.17.576103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
The co-occurrence of chromosome 10 loss and chromosome 7 gain in gliomas is the most frequent loss-gain co-aneuploidy pair in human cancers, a phenomenon that has been investigated without resolution since the late 1980s. Expanding beyond previous gene-centric studies, we investigate the co-occurrence in a genome-wide manner taking an evolutionary perspective. First, by mining large tumor aneuploidy data, we predict that the more likely order is 10 loss followed by 7 gain. Second, by analyzing extensive genomic and transcriptomic data from both patients and cell lines, we find that this co-occurrence can be explained by functional rescue interactions that are highly enriched on 7, which can possibly compensate for any detrimental consequences arising from the loss of 10. Finally, by analyzing transcriptomic data from normal, non-cancerous, human brain tissues, we provide a plausible reason why this co-occurrence happens preferentially in cancers originating in certain regions of the brain.
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Schäffer AA, Chung Y, Kammula AV, Ruppin E, Lee JS. A systematic analysis of the landscape of synthetic lethality-driven precision oncology. MED 2024; 5:73-89.e9. [PMID: 38218178 DOI: 10.1016/j.medj.2023.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 09/10/2023] [Accepted: 12/13/2023] [Indexed: 01/15/2024]
Abstract
BACKGROUND Synthetic lethality (SL) denotes a genetic interaction between two genes whose co-inactivation is detrimental to cells. Because more than 25 years have passed since SL was proposed as a promising way to selectively target cancer vulnerabilities, it is timely to comprehensively assess its impact so far and discuss its future. METHODS We systematically analyzed the literature and clinical trial data from the PubMed and Trialtrove databases to portray the preclinical and clinical landscape of SL oncology. FINDINGS We identified 235 preclinically validated SL pairs and found 1,207 pertinent clinical trials, and the number keeps increasing over time. About one-third of these SL clinical trials go beyond the typically studied DNA damage response (DDR) pathway, testifying to the recently broadening scope of SL applications in clinical oncology. We find that SL oncology trials have a greater success rate than non-SL-based trials. However, about 75% of the preclinically validated SL interactions have not yet been tested in clinical trials. CONCLUSIONS Dissecting the recent efforts harnessing SL to identify predictive biomarkers, novel therapeutic targets, and effective combination therapy, our systematic analysis reinforces the hope that SL may serve as a key driver of precision oncology going forward. FUNDING Funded by the Samsung Research Funding & Incubation Center of Samsung Electronics, the Institute of Information & Communications Technology Planning & Evaluation (IITP) grant funded by the Republic of Korea government (MSIT), the Kwanjeong Educational Foundation, the Intramural Research Program of the National Institutes of Health (NIH), National Cancer Institute (NCI), and Center for Cancer Research (CCR).
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Affiliation(s)
- Alejandro A Schäffer
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Youngmin Chung
- Department of Artificial Intelligence, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Ashwin V Kammula
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Eytan Ruppin
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Joo Sang Lee
- Department of Artificial Intelligence, Sungkyunkwan University, Suwon 16419, Republic of Korea; Department of Precision Medicine, School of Medicine, Sungkyunkwan University, Suwon 16419, Republic of Korea; Department of Digital Health & Health Sciences and Technology, Samsung Advanced Institute for Health Sciences & Technology, Samsung Medical Center, Sungkyunkwan University, Seoul 06351, Republic of Korea.
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3
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Liu M, Dong Q, Chen B, Liu K, Zhao Z, Wang Y, Zhuang S, Han H, Shi X, Jin Z, Hui Y, Gu Y. Synthetic viability induces resistance to immune checkpoint inhibitors in cancer cells. Br J Cancer 2023; 129:1339-1349. [PMID: 37620409 PMCID: PMC10575993 DOI: 10.1038/s41416-023-02404-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 08/05/2023] [Accepted: 08/11/2023] [Indexed: 08/26/2023] Open
Abstract
BACKGROUND Immune checkpoint inhibitors (ICI) have revolutionized the treatment for multiple cancers. However, most of patients encounter resistance. Synthetic viability (SV) between genes could induce resistance. In this study, we established SV signature to predict the efficacy of ICI treatment for melanoma. METHODS We collected features and predicted SV gene pairs by random forest classifier. This work prioritized SV gene pairs based on CRISPR/Cas9 screens. SV gene pairs signature were constructed to predict the response to ICI for melanoma patients. RESULTS This study predicted robust SV gene pairs based on 14 features. Filtered by CRISPR/Cas9 screens, we identified 1,861 SV gene pairs, which were also related with prognosis across multiple cancer types. Next, we constructed the six SV pairs signature to predict resistance to ICI for melanoma patients. This study applied the six SV pairs signature to divide melanoma patients into high-risk and low-risk. High-risk melanoma patients were associated with worse response after ICI treatment. Immune landscape analysis revealed that high-risk melanoma patients had lower natural killer cells and CD8+ T cells infiltration. CONCLUSIONS In summary, the 14 features classifier accurately predicted robust SV gene pairs for cancer. The six SV pairs signature could predict resistance to ICI.
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Affiliation(s)
- Mingyue Liu
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Qi Dong
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Bo Chen
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Kaidong Liu
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Zhangxiang Zhao
- The Sino-Russian Medical Research Center of Jinan University, The Institute of Chronic Disease of Jinan University, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Yuquan Wang
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Shuping Zhuang
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Huiming Han
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Xingyang Shi
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Zixin Jin
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yang Hui
- Department of Biochemistry and Molecular Biology, Harbin Medical University, Harbin, China.
| | - Yunyan Gu
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.
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4
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Wang X, Yang L, Yu C, Ling X, Guo C, Chen R, Li D, Liu Z. An integrated computational strategy to predict personalized cancer drug combinations by reversing drug resistance signatures. Comput Biol Med 2023; 163:107230. [PMID: 37418899 DOI: 10.1016/j.compbiomed.2023.107230] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 06/22/2023] [Accepted: 07/01/2023] [Indexed: 07/09/2023]
Abstract
Drug resistance currently poses the greatest barrier to cancer treatments. To overcome drug resistance, drug combination therapy has been proposed as a promising treatment strategy. Herein, we present Re-Sensitizing Drug Prediction (RSDP), a novel computational strategy, for predicting the personalized cancer drug combination A + B by reversing the resistance signature of drug A. The process integrates multiple biological features using a robust rank aggregation algorithm, including Connectivity Map, synthetic lethality, synthetic rescue, pathway, and drug target. Bioinformatics assessments revealed that RSDP achieved a relatively accurate prediction performance for identifying personalized combinational re-sensitizing drug B against cell line-specific intrinsic resistance, cell line-specific acquired resistance, and patient-specific intrinsic resistance to drug A. In addition, we developed the largest resource of cell line-specific cancer drug resistance signatures, including intrinsic and acquired resistance, as a byproduct of the proposed strategy. The findings indicate that personalized drug resistance signature reversal is a promising strategy for identifying personalized drug combinations, which may guide future clinical decisions regarding personalized medicine.
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Affiliation(s)
- Xun Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Lele Yang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China; College of Chemistry and Environmental Science, Hebei University, Baoding, 071002, China
| | - Chuang Yu
- China Astronaut Research and Training Center, Beijing, 100094, China
| | - Xinping Ling
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Congcong Guo
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Ruzhen Chen
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Dong Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China; College of Chemistry and Environmental Science, Hebei University, Baoding, 071002, China.
| | - Zhongyang Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China; College of Chemistry and Environmental Science, Hebei University, Baoding, 071002, China.
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5
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Nair NU, Greninger P, Zhang X, Friedman AA, Amzallag A, Cortez E, Sahu AD, Lee JS, Dastur A, Egan RK, Murchie E, Ceribelli M, Crowther GS, Beck E, McClanaghan J, Klump-Thomas C, Boisvert JL, Damon LJ, Wilson KM, Ho J, Tam A, McKnight C, Michael S, Itkin Z, Garnett MJ, Engelman JA, Haber DA, Thomas CJ, Ruppin E, Benes CH. A landscape of response to drug combinations in non-small cell lung cancer. Nat Commun 2023; 14:3830. [PMID: 37380628 PMCID: PMC10307832 DOI: 10.1038/s41467-023-39528-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 06/14/2023] [Indexed: 06/30/2023] Open
Abstract
Combination of anti-cancer drugs is broadly seen as way to overcome the often-limited efficacy of single agents. The design and testing of combinations are however very challenging. Here we present a uniquely large dataset screening over 5000 targeted agent combinations across 81 non-small cell lung cancer cell lines. Our analysis reveals a profound heterogeneity of response across the tumor models. Notably, combinations very rarely result in a strong gain in efficacy over the range of response observable with single agents. Importantly, gain of activity over single agents is more often seen when co-targeting functionally proximal genes, offering a strategy for designing more efficient combinations. Because combinatorial effect is strongly context specific, tumor specificity should be achievable. The resource provided, together with an additional validation screen sheds light on major challenges and opportunities in building efficacious combinations against cancer and provides an opportunity for training computational models for synergy prediction.
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Affiliation(s)
- Nishanth Ulhas Nair
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Xiaohu Zhang
- Howard Hughes Medical Institute, Bethesda, MD, USA
| | - Adam A Friedman
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Arnaud Amzallag
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Eliane Cortez
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Avinash Das Sahu
- University of New Mexico, Comprehensive Cancer Center, Albuquerque, NM, USA
| | - Joo Sang Lee
- Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon, 16419, Republic of Korea
| | - Anahita Dastur
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Regina K Egan
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Ellen Murchie
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | - Erin Beck
- Howard Hughes Medical Institute, Bethesda, MD, USA
| | | | | | | | - Leah J Damon
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Jeffrey Ho
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Angela Tam
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Sam Michael
- Howard Hughes Medical Institute, Bethesda, MD, USA
| | - Zina Itkin
- Howard Hughes Medical Institute, Bethesda, MD, USA
| | - Mathew J Garnett
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK
| | | | - Daniel A Haber
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Bethesda, MD, USA
| | - Craig J Thomas
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institute of Health, Rockville, MD, 20850, USA
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Eytan Ruppin
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Cyril H Benes
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
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6
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Nair NU, Jiang Q, Wei JS, Misra VA, Morrow B, Kesserwan C, Hermida LC, Lee JS, Mian I, Zhang J, Lebensohn A, Miettinen M, Sengupta M, Khan J, Ruppin E, Hassan R. Genomic and transcriptomic analyses identify a prognostic gene signature and predict response to therapy in pleural and peritoneal mesothelioma. Cell Rep Med 2023; 4:100938. [PMID: 36773602 PMCID: PMC9975319 DOI: 10.1016/j.xcrm.2023.100938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 08/23/2022] [Accepted: 01/19/2023] [Indexed: 02/12/2023]
Abstract
Malignant mesothelioma is an aggressive cancer with limited treatment options and poor prognosis. A better understanding of mesothelioma genomics and transcriptomics could advance therapies. Here, we present a mesothelioma cohort of 122 patients along with their germline and tumor whole-exome and tumor RNA sequencing data as well as phenotypic and drug response information. We identify a 48-gene prognostic signature that is highly predictive of mesothelioma patient survival, including CCNB1, the expression of which is highly predictive of patient survival on its own. In addition, we analyze the transcriptomics data to study the tumor immune microenvironment and identify synthetic-lethality-based signatures predictive of response to therapy. This germline and somatic whole-exome sequencing as well as transcriptomics data from the same patient are a valuable resource to address important biological questions, including prognostic biomarkers and determinants of treatment response in mesothelioma.
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Affiliation(s)
- Nishanth Ulhas Nair
- Cancer Data Science Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Qun Jiang
- Thoracic and GI Malignancies Branch, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | | | | | - Betsy Morrow
- Thoracic and GI Malignancies Branch, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | | | - Leandro C Hermida
- Cancer Data Science Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA; Tumor Microenvironment Center, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Joo Sang Lee
- Cancer Data Science Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA; School of Medicine and Department of Artificial Intelligence, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Idrees Mian
- Thoracic and GI Malignancies Branch, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Jingli Zhang
- Thoracic and GI Malignancies Branch, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | | | | | - Manjistha Sengupta
- Thoracic and GI Malignancies Branch, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Javed Khan
- Genetics Branch, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Eytan Ruppin
- Cancer Data Science Laboratory, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA.
| | - Raffit Hassan
- Thoracic and GI Malignancies Branch, CCR, NCI, NIH, Bethesda, MD 20892, USA.
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7
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Dinstag G, Shulman ED, Elis E, Ben-Zvi DS, Tirosh O, Maimon E, Meilijson I, Elalouf E, Temkin B, Vitkovsky P, Schiff E, Hoang DT, Sinha S, Nair NU, Lee JS, Schäffer AA, Ronai Z, Juric D, Apolo AB, Dahut WL, Lipkowitz S, Berger R, Kurzrock R, Papanicolau-Sengos A, Karzai F, Gilbert MR, Aldape K, Rajagopal PS, Beker T, Ruppin E, Aharonov R. Clinically oriented prediction of patient response to targeted and immunotherapies from the tumor transcriptome. MED 2023; 4:15-30.e8. [PMID: 36513065 PMCID: PMC10029756 DOI: 10.1016/j.medj.2022.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 08/30/2022] [Accepted: 10/31/2022] [Indexed: 12/14/2022]
Abstract
BACKGROUND Precision oncology is gradually advancing into mainstream clinical practice, demonstrating significant survival benefits. However, eligibility and response rates remain limited in many cases, calling for better predictive biomarkers. METHODS We present ENLIGHT, a transcriptomics-based computational approach that identifies clinically relevant genetic interactions and uses them to predict a patient's response to a variety of therapies in multiple cancer types without training on previous treatment response data. We study ENLIGHT in two translationally oriented scenarios: personalized oncology (PO), aimed at prioritizing treatments for a single patient, and clinical trial design (CTD), selecting the most likely responders in a patient cohort. FINDINGS Evaluating ENLIGHT's performance on 21 blinded clinical trial datasets in the PO setting, we show that it can effectively predict a patient's treatment response across multiple therapies and cancer types. Its prediction accuracy is better than previously published transcriptomics-based signatures and is comparable with that of supervised predictors developed for specific indications and drugs. In combination with the interferon-γ signature, ENLIGHT achieves an odds ratio larger than 4 in predicting response to immune checkpoint therapy. In the CTD scenario, ENLIGHT can potentially enhance clinical trial success for immunotherapies and other monoclonal antibodies by excluding non-responders while overall achieving more than 90% of the response rate attainable under an optimal exclusion strategy. CONCLUSIONS ENLIGHT demonstrably enhances the ability to predict therapeutic response across multiple cancer types from the bulk tumor transcriptome. FUNDING This research was supported in part by the Intramural Research Program, NIH and by the Israeli Innovation Authority.
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Affiliation(s)
| | | | | | | | | | | | - Isaac Meilijson
- Pangea Biomed Ltd., Tel Aviv, Israel; Tel Aviv University, Tel Aviv, Israel
| | | | | | | | | | - Danh-Tai Hoang
- Biological Data Science Institute, College of Science, The Australian National University, Canberra, ACT, Australia
| | - Sanju Sinha
- Cancer Data Science Laboratory (CDSL), National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Nishanth Ulhas Nair
- Cancer Data Science Laboratory (CDSL), National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Joo Sang Lee
- Department of Precision Medicine, School of Medicine & Department of Artificial Intelligence, Sungkyunkwan University, Suwon, Republic of Korea
| | - Alejandro A Schäffer
- Cancer Data Science Laboratory (CDSL), National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ze'ev Ronai
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Dejan Juric
- Department of Medicine, Massachusetts General Hospital Cancer Center, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Andrea B Apolo
- Genitourinary Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - William L Dahut
- Genitourinary Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stanley Lipkowitz
- Women's Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Raanan Berger
- Cancer Center, Chaim Sheba Medical Center, Tel Hashomer, Israel
| | - Razelle Kurzrock
- Worldwide Innovative Network (WIN) for Personalized Cancer Therapy, Chevilly-Larue, France
| | | | - Fatima Karzai
- Genitourinary Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mark R Gilbert
- Neuro-Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kenneth Aldape
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Padma S Rajagopal
- Cancer Data Science Laboratory (CDSL), National Cancer Institute, National Institutes of Health, Bethesda, MD, USA; Women's Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Eytan Ruppin
- Cancer Data Science Laboratory (CDSL), National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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8
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Jiang P, Sinha S, Aldape K, Hannenhalli S, Sahinalp C, Ruppin E. Big data in basic and translational cancer research. Nat Rev Cancer 2022; 22:625-639. [PMID: 36064595 PMCID: PMC9443637 DOI: 10.1038/s41568-022-00502-0] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/26/2022] [Indexed: 02/07/2023]
Abstract
Historically, the primary focus of cancer research has been molecular and clinical studies of a few essential pathways and genes. Recent years have seen the rapid accumulation of large-scale cancer omics data catalysed by breakthroughs in high-throughput technologies. This fast data growth has given rise to an evolving concept of 'big data' in cancer, whose analysis demands large computational resources and can potentially bring novel insights into essential questions. Indeed, the combination of big data, bioinformatics and artificial intelligence has led to notable advances in our basic understanding of cancer biology and to translational advancements. Further advances will require a concerted effort among data scientists, clinicians, biologists and policymakers. Here, we review the current state of the art and future challenges for harnessing big data to advance cancer research and treatment.
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Affiliation(s)
- Peng Jiang
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Sanju Sinha
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kenneth Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sridhar Hannenhalli
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Cenk Sahinalp
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Eytan Ruppin
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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9
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Olbryt M. Potential Biomarkers of Skin Melanoma Resistance to Targeted Therapy—Present State and Perspectives. Cancers (Basel) 2022; 14:cancers14092315. [PMID: 35565444 PMCID: PMC9102921 DOI: 10.3390/cancers14092315] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/02/2022] [Accepted: 05/04/2022] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Around 5–10% of advanced melanoma patients progress early on anti-BRAF targeted therapy and 20–30% respond only with the stabilization of the disease. Presumably, these patients could benefit more from first-line immunotherapy. Resistance to BRAF/MEK inhibitors is generated by genetic and non-genetic factors inherent to a tumor or acquired during therapy. Some of them are well documented as a cause of treatment failure. They are potential predictive markers that could improve patients’ selection for both standard and also alternative therapy as some of them have therapeutic potential. Here, a summary of the most promising predictive and therapeutic targets is presented. This up-to-date knowledge may be useful for further study on implementing more accurate genetic/molecular tests in melanoma treatment. Abstract Melanoma is the most aggressive skin cancer, the number of which is increasing worldwide every year. It is completely curable in its early stage and fatal when spread to distant organs. In addition to new therapeutic strategies, biomarkers are an important element in the successful fight against this cancer. At present, biomarkers are mainly used in diagnostics. Some biological indicators also allow the estimation of the patient’s prognosis. Still, predictive markers are underrepresented in clinics. Currently, the only such indicator is the presence of the V600E mutation in the BRAF gene in cancer cells, which qualifies the patient for therapy with inhibitors of the MAPK pathway. The identification of response markers is particularly important given primary and acquired resistance to targeted therapies. Reliable predictive tests would enable the selection of patients who would have the best chance of benefiting from treatment. Here, up-to-date knowledge about the most promising genetic and non-genetic resistance-related factors is described. These are alterations in MAPK, PI3K/AKT, and RB signaling pathways, e.g., due to mutations in NRAS, RAC1, MAP2K1, MAP2K2, and NF1, but also other changes activating these pathways, such as the overexpression of HGF or EGFR. Most of them are also potential therapeutic targets and this issue is also addressed here.
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Affiliation(s)
- Magdalena Olbryt
- Center for Translational Research and Molecular Biology of Cancer, Maria Sklodowska-Curie National Research Institute of Oncology, Gliwice Branch, 44-102 Gliwice, Poland
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10
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Harnessing Synthetic Lethal Interactions for Personalized Medicine. J Pers Med 2022; 12:jpm12010098. [PMID: 35055413 PMCID: PMC8779047 DOI: 10.3390/jpm12010098] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 01/07/2022] [Accepted: 01/09/2022] [Indexed: 02/01/2023] Open
Abstract
Two genes are said to have synthetic lethal (SL) interactions if the simultaneous mutations in a cell lead to lethality, but each individual mutation does not. Targeting SL partners of mutated cancer genes can kill cancer cells but leave normal cells intact. The applicability of translating this concept into clinics has been demonstrated by three drugs that have been approved by the FDA to target PARP for tumors bearing mutations in BRCA1/2. This article reviews applications of the SL concept to translational cancer medicine over the past five years. Topics are (1) exploiting the SL concept for drug combinations to circumvent tumor resistance, (2) using synthetic lethality to identify prognostic and predictive biomarkers, (3) applying SL interactions to stratify patients for targeted and immunotherapy, and (4) discussions on challenges and future directions.
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Deng Y, Zhou Y, Shi J, Yang J, Huang H, Zhang M, Wang S, Ma Q, Liu Y, Li B, Yan J, Yang H. Potential genetic biomarkers predict adverse pregnancy outcome during early and mid-pregnancy in women with systemic lupus erythematosus. Front Endocrinol (Lausanne) 2022; 13:957010. [PMID: 36465614 PMCID: PMC9708709 DOI: 10.3389/fendo.2022.957010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 11/01/2022] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Effectively predicting the risk of adverse pregnancy outcome (APO) in women with systemic lupus erythematosus (SLE) during early and mid-pregnancy is a challenge. This study was aimed to identify potential markers for early prediction of APO risk in women with SLE. METHODS The GSE108497 gene expression dataset containing 120 samples (36 patients, 84 controls) was downloaded from the Gene Expression Omnibus database. Weighted gene co-expression network analysis (WGCNA) was performed, and differentially expressed genes (DEGs) were screened to define candidate APO marker genes. Next, three individual machine learning methods, random forest, support vector machine-recursive feature elimination, and least absolute shrinkage and selection operator, were combined to identify feature genes from the APO candidate set. The predictive performance of feature genes for APO risk was assessed using area under the receiver operating characteristic curve (AUC) and calibration curves. The potential functions of these feature genes were finally analyzed by conventional gene set enrichment analysis and CIBERSORT algorithm analysis. RESULTS We identified 321 significantly up-regulated genes and 307 down-regulated genes between patients and controls, along with 181 potential functionally associated genes in the WGCNA analysis. By integrating these results, we revealed 70 APO candidate genes. Three feature genes, SEZ6, NRAD1, and LPAR4, were identified by machine learning methods. Of these, SEZ6 (AUC = 0.753) showed the highest in-sample predictive performance for APO risk in pregnant women with SLE, followed by NRAD1 (AUC = 0.694) and LPAR4 (AUC = 0.654). After performing leave-one-out cross validation, corresponding AUCs for SEZ6, NRAD1, and LPAR4 were 0.731, 0.668, and 0.626, respectively. Moreover, CIBERSORT analysis showed a positive correlation between regulatory T cell levels and SEZ6 expression (P < 0.01), along with a negative correlation between M2 macrophages levels and LPAR4 expression (P < 0.01). CONCLUSIONS Our preliminary findings suggested that SEZ6, NRAD1, and LPAR4 might represent the useful genetic biomarkers for predicting APO risk during early and mid-pregnancy in women with SLE, and enhanced our understanding of the origins of pregnancy complications in pregnant women with SLE. However, further validation was required.
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Affiliation(s)
- Yu Deng
- Department of Obstetrics and Gynecology, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Maternal Fetal Medicine of Gestational Diabetes Mellitus, Beijing, China
| | - Yiran Zhou
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Jiangcheng Shi
- School of Life Sciences, Tiangong University, Tianjin, China
| | - Junting Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Hong Huang
- Department of Rheumatology and Clinical Immunology, Peking University First Hospital, Beijing, China
| | - Muqiu Zhang
- Department of Obstetrics and Gynecology, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Maternal Fetal Medicine of Gestational Diabetes Mellitus, Beijing, China
| | - Shuxian Wang
- Department of Obstetrics and Gynecology, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Maternal Fetal Medicine of Gestational Diabetes Mellitus, Beijing, China
| | - Qian Ma
- Department of Clinical Laboratory, Peking University First Hospital, Beijing, China
| | - Yingnan Liu
- Department of Obstetrics and Gynecology, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Maternal Fetal Medicine of Gestational Diabetes Mellitus, Beijing, China
| | - Boya Li
- Department of Obstetrics and Gynecology, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Maternal Fetal Medicine of Gestational Diabetes Mellitus, Beijing, China
| | - Jie Yan
- Department of Obstetrics and Gynecology, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Maternal Fetal Medicine of Gestational Diabetes Mellitus, Beijing, China
| | - Huixia Yang
- Department of Obstetrics and Gynecology, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Maternal Fetal Medicine of Gestational Diabetes Mellitus, Beijing, China
- *Correspondence: Huixia Yang,
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12
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INCISOR: An Algorithm to Identify Synthetic Rescue Mediators of Resistance to Targeted and Immunotherapy. Methods Mol Biol 2021. [PMID: 34590278 DOI: 10.1007/978-1-0716-1740-3_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Despite the success of targeted therapies including immunotherapies in cancer treatments, tumor resistance to targeted therapies remains a fundamental challenge. Tumors can evolve resistance to a therapy that targets one gene by acquiring compensatory alterations in another gene, such compensatory interaction between two genes is referred to as synthetic rescue (SR) interactions. To identify SRs, here we describe an algorithm, INCISOR, that leverages tumor transcriptomics and clinical information from 10,000 patients as well as data from experimental screens. INCISOR can identify SRs that are common across several cancer-types in genome-wide fashion by sifting through half a billion possible gene-gene combinations and provide a framework to design therapies to tackle resistance.
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13
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Brägelmann J, Lorenz C, Borchmann S, Nishii K, Wegner J, Meder L, Ostendorp J, Ast DF, Heimsoeth A, Nakasuka T, Hirabae A, Okawa S, Dammert MA, Plenker D, Klein S, Lohneis P, Gu J, Godfrey LK, Forster J, Trajkovic-Arsic M, Zillinger T, Haarmann M, Quaas A, Lennartz S, Schmiel M, D'Rozario J, Thomas ES, Li H, Schmitt CA, George J, Thomas RK, von Karstedt S, Hartmann G, Büttner R, Ullrich RT, Siveke JT, Ohashi K, Schlee M, Sos ML. MAPK-pathway inhibition mediates inflammatory reprogramming and sensitizes tumors to targeted activation of innate immunity sensor RIG-I. Nat Commun 2021; 12:5505. [PMID: 34535668 PMCID: PMC8448826 DOI: 10.1038/s41467-021-25728-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 08/23/2021] [Indexed: 12/29/2022] Open
Abstract
Kinase inhibitors suppress the growth of oncogene driven cancer but also enforce the selection of treatment resistant cells that are thought to promote tumor relapse in patients. Here, we report transcriptomic and functional genomics analyses of cells and tumors within their microenvironment across different genotypes that persist during kinase inhibitor treatment. We uncover a conserved, MAPK/IRF1-mediated inflammatory response in tumors that undergo stemness- and senescence-associated reprogramming. In these tumor cells, activation of the innate immunity sensor RIG-I via its agonist IVT4, triggers an interferon and a pro-apoptotic response that synergize with concomitant kinase inhibition. In humanized lung cancer xenografts and a syngeneic Egfr-driven lung cancer model these effects translate into reduction of exhausted CD8+ T cells and robust tumor shrinkage. Overall, the mechanistic understanding of MAPK/IRF1-mediated intratumoral reprogramming may ultimately prolong the efficacy of targeted drugs in genetically defined cancer patients.
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Affiliation(s)
- Johannes Brägelmann
- Molecular Pathology, Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany.
- Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany.
- Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany.
- Mildred Scheel School of Oncology Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany.
| | - Carina Lorenz
- Molecular Pathology, Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
| | - Sven Borchmann
- Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- Else-Kröner-Forschungskolleg Clonal Evolution in Cancer, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
| | - Kazuya Nishii
- Department of Hematology, Oncology and Respiratory Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Julia Wegner
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany
| | - Lydia Meder
- Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- Mildred Scheel School of Oncology Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
| | - Jenny Ostendorp
- Molecular Pathology, Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
| | - David F Ast
- Molecular Pathology, Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- Mildred Scheel School of Oncology Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
| | - Alena Heimsoeth
- Molecular Pathology, Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
| | - Takamasa Nakasuka
- Department of Hematology, Oncology and Respiratory Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Atsuko Hirabae
- Department of Hematology, Oncology and Respiratory Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Sachi Okawa
- Department of Hematology, Oncology and Respiratory Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Marcel A Dammert
- Molecular Pathology, Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
| | - Dennis Plenker
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
- Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Sebastian Klein
- Else-Kröner-Forschungskolleg Clonal Evolution in Cancer, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
| | - Philipp Lohneis
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
| | - Jianing Gu
- Institute for Developmental Cancer Therapeutics, West German Cancer Center, University Hospital Essen, Essen, Germany
- Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, partner site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany
| | - Laura K Godfrey
- Institute for Developmental Cancer Therapeutics, West German Cancer Center, University Hospital Essen, Essen, Germany
- Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, partner site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany
| | - Jan Forster
- Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, partner site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany
- Genome Informatics, Institute of Human Genetics, University Duisburg-Essen, Essen, Germany
| | - Marija Trajkovic-Arsic
- Institute for Developmental Cancer Therapeutics, West German Cancer Center, University Hospital Essen, Essen, Germany
- Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, partner site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany
| | - Thomas Zillinger
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany
| | - Mareike Haarmann
- Mildred Scheel School of Oncology Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
| | - Alexander Quaas
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
| | - Stefanie Lennartz
- Molecular Pathology, Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
| | - Marcel Schmiel
- Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
| | - Joshua D'Rozario
- Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
| | - Emily S Thomas
- Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases (CECAD), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- Imperial College London, London, UK
| | - Henry Li
- Crown Bioscience, San Diego, CA, USA
| | - Clemens A Schmitt
- Department of Hematology, Oncology and Tumor Immunology, Charité - University Medical Center, Virchow Campus, and Molekulares Krebsforschungszentrum, Berlin, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Department of Hematology and Oncology, Kepler University Hospital, Johannes Kepler University, Linz, Austria
| | - Julie George
- Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- Department of Head and Neck Surgery, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
| | - Roman K Thomas
- Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- German Cancer Research Center, German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Silvia von Karstedt
- Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases (CECAD), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
| | - Gunther Hartmann
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany
| | - Reinhard Büttner
- Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
| | - Roland T Ullrich
- Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
| | - Jens T Siveke
- Institute for Developmental Cancer Therapeutics, West German Cancer Center, University Hospital Essen, Essen, Germany
- Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, partner site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany
| | - Kadoaki Ohashi
- Department of Hematology, Oncology and Respiratory Medicine, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
- Department of Respiratory Medicine, Okayama University Hospital, Japan, 2-5-1 Shikata-cho, Kitaku, Okayama, 700-8558, Japan
| | - Martin Schlee
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany
| | - Martin L Sos
- Molecular Pathology, Institute of Pathology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany.
- Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany.
- Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany.
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14
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Synthetic lethality-mediated precision oncology via the tumor transcriptome. Cell 2021; 184:2487-2502.e13. [PMID: 33857424 DOI: 10.1016/j.cell.2021.03.030] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 10/29/2020] [Accepted: 03/12/2021] [Indexed: 01/27/2023]
Abstract
Precision oncology has made significant advances, mainly by targeting actionable mutations in cancer driver genes. Aiming to expand treatment opportunities, recent studies have begun to explore the utility of tumor transcriptome to guide patient treatment. Here, we introduce SELECT (synthetic lethality and rescue-mediated precision oncology via the transcriptome), a precision oncology framework harnessing genetic interactions to predict patient response to cancer therapy from the tumor transcriptome. SELECT is tested on a broad collection of 35 published targeted and immunotherapy clinical trials from 10 different cancer types. It is predictive of patients' response in 80% of these clinical trials and in the recent multi-arm WINTHER trial. The predictive signatures and the code are made publicly available for academic use, laying a basis for future prospective clinical studies.
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15
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Brockway S, Wang G, Jackson JM, Amici DR, Takagishi SR, Clutter MR, Bartom ET, Mendillo ML. Quantitative and multiplexed chemical-genetic phenotyping in mammalian cells with QMAP-Seq. Nat Commun 2020; 11:5722. [PMID: 33184288 PMCID: PMC7661543 DOI: 10.1038/s41467-020-19553-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 10/14/2020] [Indexed: 12/26/2022] Open
Abstract
Chemical-genetic interaction profiling in model organisms has proven powerful in providing insights into compound mechanism of action and gene function. However, identifying chemical-genetic interactions in mammalian systems has been limited to low-throughput or computational methods. Here, we develop Quantitative and Multiplexed Analysis of Phenotype by Sequencing (QMAP-Seq), which leverages next-generation sequencing for pooled high-throughput chemical-genetic profiling. We apply QMAP-Seq to investigate how cellular stress response factors affect therapeutic response in cancer. Using minimal automation, we treat pools of 60 cell types—comprising 12 genetic perturbations in five cell lines—with 1440 compound-dose combinations, generating 86,400 chemical-genetic measurements. QMAP-Seq produces precise and accurate quantitative measures of acute drug response comparable to gold standard assays, but with increased throughput at lower cost. Moreover, QMAP-Seq reveals clinically actionable drug vulnerabilities and functional relationships involving these stress response factors, many of which are activated in cancer. Thus, QMAP-Seq provides a broadly accessible and scalable strategy for chemical-genetic profiling in mammalian cells. Identifying chemical-genetic interactions in mammalian cells is limited to low-throughput or computational methods. Here, the authors present QMAP-Seq, a broadly accessible and scalable approach that uses NGS for pooled high-throughput chemical-genetic profiling in mammalian cells.
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Affiliation(s)
- Sonia Brockway
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.,Driskill Graduate Program in Life Sciences, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Geng Wang
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Jasen M Jackson
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - David R Amici
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.,Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Seesha R Takagishi
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Matthew R Clutter
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.,Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA.,Department of Molecular Biosciences, Northwestern University, Evanston, IL, 60208, USA
| | - Elizabeth T Bartom
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Marc L Mendillo
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA. .,Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA. .,Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
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16
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Tsyvina V, Zelikovsky A, Snir S, Skums P. Inference of mutability landscapes of tumors from single cell sequencing data. PLoS Comput Biol 2020; 16:e1008454. [PMID: 33253159 PMCID: PMC7728263 DOI: 10.1371/journal.pcbi.1008454] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 12/10/2020] [Accepted: 10/20/2020] [Indexed: 11/18/2022] Open
Abstract
One of the hallmarks of cancer is the extremely high mutability and genetic instability of tumor cells. Inherent heterogeneity of intra-tumor populations manifests itself in high variability of clone instability rates. Analogously to fitness landscapes, the instability rates of clonal populations form their mutability landscapes. Here, we present MULAN (MUtability LANdscape inference), a maximum-likelihood computational framework for inference of mutation rates of individual cancer subclones using single-cell sequencing data. It utilizes the partial information about the orders of mutation events provided by cancer mutation trees and extends it by inferring full evolutionary history and mutability landscape of a tumor. Evaluation of mutation rates on the level of subclones rather than individual genes allows to capture the effects of genomic interactions and epistasis. We estimate the accuracy of our approach and demonstrate that it can be used to study the evolution of genetic instability and infer tumor evolutionary history from experimental data. MULAN is available at https://github.com/compbel/MULAN.
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Affiliation(s)
- Viachaslau Tsyvina
- Department of Computer Science, Georgia State University, Atlanta, Georgia, United States of America
| | - Alex Zelikovsky
- Department of Computer Science, Georgia State University, Atlanta, Georgia, United States of America
| | - Sagi Snir
- Department of Evolutionary and Environmental Biology, University of Haifa, Haifa, Israel
| | - Pavel Skums
- Department of Computer Science, Georgia State University, Atlanta, Georgia, United States of America
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17
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Kobaisi F, Fayyad N, Sulpice E, Badran B, Fayyad-Kazan H, Rachidi W, Gidrol X. High-throughput synthetic rescue for exhaustive characterization of suppressor mutations in human genes. Cell Mol Life Sci 2020; 77:4209-4222. [PMID: 32270227 PMCID: PMC7588364 DOI: 10.1007/s00018-020-03519-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 03/21/2020] [Accepted: 03/30/2020] [Indexed: 02/06/2023]
Abstract
Inherited or acquired mutations can lead to pathological outcomes. However, in a process defined as synthetic rescue, phenotypic outcome created by primary mutation is alleviated by suppressor mutations. An exhaustive characterization of these mutations in humans is extremely valuable to better comprehend why patients carrying the same detrimental mutation exhibit different pathological outcomes or different responses to treatment. Here, we first review all known suppressor mutations' mechanisms characterized by genetic screens on model species like yeast or flies. However, human suppressor mutations are scarce, despite some being discovered based on orthologue genes. Because of recent advances in high-throughput screening, developing an inventory of human suppressor mutations for pathological processes seems achievable. In addition, we review several screening methods for suppressor mutations in cultured human cells through knock-out, knock-down or random mutagenesis screens on large scale. We provide examples of studies published over the past years that opened new therapeutic avenues, particularly in oncology.
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Affiliation(s)
- Farah Kobaisi
- University of Grenoble Alpes, CEA, INSERM, IRIG-BGE U1038, 38000, Grenoble, France
- Laboratory of Cancer Biology and Molecular Immunology, Faculty of Sciences I, Lebanese University, Hadath, Lebanon
- University of Grenoble Alpes, SYMMES/CIBEST UMR 5819 UGA-CNRS-CEA, IRIG/CEA-Grenoble, Grenoble, France
| | - Nour Fayyad
- University of Grenoble Alpes, SYMMES/CIBEST UMR 5819 UGA-CNRS-CEA, IRIG/CEA-Grenoble, Grenoble, France
| | - Eric Sulpice
- University of Grenoble Alpes, CEA, INSERM, IRIG-BGE U1038, 38000, Grenoble, France
| | - Bassam Badran
- Laboratory of Cancer Biology and Molecular Immunology, Faculty of Sciences I, Lebanese University, Hadath, Lebanon
| | - Hussein Fayyad-Kazan
- Laboratory of Cancer Biology and Molecular Immunology, Faculty of Sciences I, Lebanese University, Hadath, Lebanon
| | - Walid Rachidi
- University of Grenoble Alpes, SYMMES/CIBEST UMR 5819 UGA-CNRS-CEA, IRIG/CEA-Grenoble, Grenoble, France
| | - Xavier Gidrol
- University of Grenoble Alpes, CEA, INSERM, IRIG-BGE U1038, 38000, Grenoble, France.
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Beyond Synthetic Lethality: Charting the Landscape of Pairwise Gene Expression States Associated with Survival in Cancer. Cell Rep 2020; 28:938-948.e6. [PMID: 31340155 DOI: 10.1016/j.celrep.2019.06.067] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 04/01/2019] [Accepted: 06/18/2019] [Indexed: 12/14/2022] Open
Abstract
The phenotypic effect of perturbing a gene's activity depends on the activity level of other genes, reflecting the notion that phenotypes are emergent properties of a network of functionally interacting genes. In the context of cancer, contemporary investigations have primarily focused on just one type of functional relationship between two genes-synthetic lethality (SL). Here, we define the more general concept of "survival-associated pairwise gene expression states" (SPAGEs) as gene pairs whose joint expression levels are associated with survival. We describe a data-driven approach called SPAGE-finder that when applied to The Cancer Genome Atlas (TCGA) data identified 71,946 SPAGEs spanning 12 distinct types, only a minority of which are SLs. The detected SPAGEs explain cancer driver genes' tissue specificity and differences in patients' response to drugs and stratify breast cancer tumors into refined subtypes. These results expand the scope of cancer SPAGEs and lay a conceptual basis for future studies of SPAGEs and their translational applications.
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19
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Kagan J, Moritz RL, Mazurchuk R, Lee JH, Kharchenko PV, Rozenblatt-Rosen O, Ruppin E, Edfors F, Ginty F, Goltsev Y, Wells JA, LaCava J, Riesterer JL, Germain RN, Shi T, Chee MS, Budnik BA, Yates JR, Chait BT, Moffitt JR, Smith RD, Srivastava S. National Cancer Institute Think-Tank Meeting Report on Proteomic Cartography and Biomarkers at the Single-Cell Level: Interrogation of Premalignant Lesions. J Proteome Res 2020; 19:1900-1912. [PMID: 32163288 DOI: 10.1021/acs.jproteome.0c00021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A Think-Tank Meeting was convened by the National Cancer Institute (NCI) to solicit experts' opinion on the development and application of multiomic single-cell analyses, and especially single-cell proteomics, to improve the development of a new generation of biomarkers for cancer risk, early detection, diagnosis, and prognosis as well as to discuss the discovery of new targets for prevention and therapy. It is anticipated that such markers and targets will be based on cellular, subcellular, molecular, and functional aberrations within the lesion and within individual cells. Single-cell proteomic data will be essential for the establishment of new tools with searchable and scalable features that include spatial and temporal cartographies of premalignant and malignant lesions. Challenges and potential solutions that were discussed included (i) The best way/s to analyze single-cells from fresh and preserved tissue; (ii) Detection and analysis of secreted molecules and from single cells, especially from a tissue slice; (iii) Detection of new, previously undocumented cell type/s in the premalignant and early stage cancer tissue microenvironment; (iv) Multiomic integration of data to support and inform proteomic measurements; (v) Subcellular organelles-identifying abnormal structure, function, distribution, and location within individual premalignant and malignant cells; (vi) How to improve the dynamic range of single-cell proteomic measurements for discovery of differentially expressed proteins and their post-translational modifications (PTM); (vii) The depth of coverage measured concurrently using single-cell techniques; (viii) Quantitation - absolute or semiquantitative? (ix) Single methodology or multiplexed combinations? (x) Application of analytical methods for identification of biologically significant subsets; (xi) Data visualization of N-dimensional data sets; (xii) How to construct intercellular signaling networks in individual cells within premalignant tumor microenvironments (TME); (xiii) Associations between intrinsic cellular processes and extrinsic stimuli; (xiv) How to predict cellular responses to stress-inducing stimuli; (xv) Identification of new markers for prediction of progression from precursor, benign, and localized lesions to invasive cancer, based on spatial and temporal changes within individual cells; (xvi) Identification of new targets for immunoprevention or immunotherapy-identification of neoantigens and surfactome of individual cells within a lesion.
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Affiliation(s)
- Jacob Kagan
- Cancer Biomarkers Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, Maryland, United States
| | - Robert L Moritz
- Institute for Systems Biology, Seattle, Washington, United States
| | - Richard Mazurchuk
- Cancer Biomarkers Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, Maryland, United States
| | - Je Hyuk Lee
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States
| | - Peter Vasili Kharchenko
- Blavatnik Institute for Biomedical Information, Harvard Medical School, Boston, Massachusetts, United States
| | | | - Eytan Ruppin
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States
| | - Fredrik Edfors
- Science for Life Laboratory, KTH - Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Fiona Ginty
- Life Sciences and Molecular Diagnostics Laboratory, GE Global Research Center, Niskayuna, New York, United States
| | - Yury Goltsev
- Department of Microbiology and Immunology, Baxter Laboratory in Stem Cell Biology, Stanford University, Stanford Medical School, Stanford, California, United States
| | - James A Wells
- Department of Pharmaceutical Sciences, University of California, San Francisco, California, United States
| | - John LaCava
- Laboratory of Cellular and Structural Biology, Rockefeller University, New York, New York, United States
| | - Jessica L Riesterer
- Center for Spatial Systems Biomedicine, Oregon Health and Science University, Portland, Oregon, United States
| | - Ronald N Germain
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, United States
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States
| | - Mark S Chee
- Encodia, Inc., San Diego, California, United States
| | - Bogdan A Budnik
- Faculty of Arts & Sciences, Division of Science. Harvard University, Boston, Massachusetts, United States
| | - John R Yates
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, California, United States
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York, United States
| | - Jeffery R Moffitt
- Boston Children's Hospital and Harvard University Medical School, Boston, Massachusetts, United States
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States
| | - Sudhir Srivastava
- Cancer Biomarkers Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, Maryland, United States
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20
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Pathria G, Lee JS, Hasnis E, Tandoc K, Scott DA, Verma S, Feng Y, Larue L, Sahu AD, Topisirovic I, Ruppin E, Ronai ZA. Translational reprogramming marks adaptation to asparagine restriction in cancer. Nat Cell Biol 2019; 21:1590-1603. [PMID: 31740775 PMCID: PMC7307327 DOI: 10.1038/s41556-019-0415-1] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Accepted: 09/25/2019] [Indexed: 01/24/2023]
Abstract
While amino acid restriction remains an attractive strategy for cancer therapy, metabolic adaptations limit its effectiveness. Here we demonstrate a role of translational reprogramming in the survival of asparagine-restricted cancer cells. Asparagine limitation in melanoma and pancreatic cancer cells activates RTK-MAPK as part of a feedforward mechanism involving mTORC1-dependent increase in MNK1 and eIF4E, resulting in enhanced translation of ATF4 mRNA. MAPK inhibition attenuates translational induction of ATF4 and the expression of its target asparagine biosynthesis enzyme ASNS, sensitizing melanoma and pancreatic tumors to asparagine restriction, reflected in their growth inhibition. Correspondingly, low ASNS expression is among the top predictors of response to MAPK signaling inhibitors in melanoma patients and is associated with favorable prognosis, when combined with low MAPK signaling activity. While unveiling a previously unknown axis of adaptation to asparagine deprivation, these studies offer the rationale for clinical evaluation of MAPK inhibitors in combination with asparagine restriction approaches.
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Affiliation(s)
- Gaurav Pathria
- Tumor Initiation and Maintenance Program, Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.
| | - Joo Sang Lee
- Cancer Data Science Lab (CDSL), National Cancer Institute, National Institute of Health, Bethesda, MD, USA.,Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Erez Hasnis
- Tumor Initiation and Maintenance Program, Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Kristofferson Tandoc
- Gerald Bronfman Department of Oncology, Lady Davis Institute, SMBD Jewish General Hospital, and Departments of Experimental Medicine and Biochemistry, McGill University, Montreal, Quebec, Canada
| | - David A Scott
- Tumor Initiation and Maintenance Program, Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Sachin Verma
- Tumor Initiation and Maintenance Program, Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Yongmei Feng
- Tumor Initiation and Maintenance Program, Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Lionel Larue
- Normal and Pathological Development of Melanocytes, Institut Curie, PSL Research University, INSERM U1021, Orsay, France.,Universitê Paris-Sud and Université Paris-Saclay, CNRS UMR 3347, Orsay, France.,Equipe Labellisée Ligue Contre le Cancer, Orsay, France
| | - Avinash D Sahu
- Harvard School of Public Health and Massachusetts General Hospital, Boston, MA, USA
| | - Ivan Topisirovic
- Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Eytan Ruppin
- Cancer Data Science Lab (CDSL), National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Ze'ev A Ronai
- Tumor Initiation and Maintenance Program, Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.
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21
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Sahu AD, S Lee J, Wang Z, Zhang G, Iglesias-Bartolome R, Tian T, Wei Z, Miao B, Nair NU, Ponomarova O, Friedman AA, Amzallag A, Moll T, Kasumova G, Greninger P, Egan RK, Damon LJ, Frederick DT, Jerby-Arnon L, Wagner A, Cheng K, Park SG, Robinson W, Gardner K, Boland G, Hannenhalli S, Herlyn M, Benes C, Flaherty K, Luo J, Gutkind JS, Ruppin E. Genome-wide prediction of synthetic rescue mediators of resistance to targeted and immunotherapy. Mol Syst Biol 2019; 15:e8323. [PMID: 30858180 PMCID: PMC6413886 DOI: 10.15252/msb.20188323] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 12/31/2018] [Accepted: 01/21/2019] [Indexed: 01/09/2023] Open
Abstract
Most patients with advanced cancer eventually acquire resistance to targeted therapies, spurring extensive efforts to identify molecular events mediating therapy resistance. Many of these events involve synthetic rescue (SR) interactions, where the reduction in cancer cell viability caused by targeted gene inactivation is rescued by an adaptive alteration of another gene (the rescuer). Here, we perform a genome-wide in silico prediction of SR rescuer genes by analyzing tumor transcriptomics and survival data of 10,000 TCGA cancer patients. Predicted SR interactions are validated in new experimental screens. We show that SR interactions can successfully predict cancer patients' response and emerging resistance. Inhibiting predicted rescuer genes sensitizes resistant cancer cells to therapies synergistically, providing initial leads for developing combinatorial approaches to overcome resistance proactively. Finally, we show that the SR analysis of melanoma patients successfully identifies known mediators of resistance to immunotherapy and predicts novel rescuers.
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Affiliation(s)
- Avinash Das Sahu
- Department of Biostatistics and Computational Biology, Harvard School of Public Health, Boston, MA, USA
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, MA, USA
- University of Maryland Institute of Advanced Computer Science (UMIACS), University of Maryland, College Park, MD, USA
| | - Joo S Lee
- University of Maryland Institute of Advanced Computer Science (UMIACS), University of Maryland, College Park, MD, USA
- Cancer Data Science Lab, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Zhiyong Wang
- Department of Pharmacology & Moores Cancer Center, University of California, San Diego La Jolla, CA, USA
| | - Gao Zhang
- Molecular and Cellular Oncogenesis Program and Melanoma Research Center, The Wistar Institute, Philadelphia, PA, USA
- Department of Neurosurgery and The Preston Robert Tisch Brain Tumor Center, Duke University, Durham, NC, USA
| | | | - Tian Tian
- New Jersey Institute of Technology, Newark, NJ, USA
| | - Zhi Wei
- New Jersey Institute of Technology, Newark, NJ, USA
| | - Benchun Miao
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Nishanth Ulhas Nair
- University of Maryland Institute of Advanced Computer Science (UMIACS), University of Maryland, College Park, MD, USA
- Cancer Data Science Lab, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Olga Ponomarova
- University of Massachusetts Medical School, Worcester, MA, USA
| | - Adam A Friedman
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Arnaud Amzallag
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Tabea Moll
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Gyulnara Kasumova
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Patricia Greninger
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Regina K Egan
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Leah J Damon
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Dennie T Frederick
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Livnat Jerby-Arnon
- Schools of Computer Science & Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Allon Wagner
- Department of Electrical Engineering and Computer Science, the Center for Computational Biology, University of California, Berkeley, CA, USA
| | - Kuoyuan Cheng
- University of Maryland Institute of Advanced Computer Science (UMIACS), University of Maryland, College Park, MD, USA
| | - Seung Gu Park
- Department of Biostatistics and Computational Biology, Harvard School of Public Health, Boston, MA, USA
| | - Welles Robinson
- University of Maryland Institute of Advanced Computer Science (UMIACS), University of Maryland, College Park, MD, USA
| | - Kevin Gardner
- Cancer Data Science Lab, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Genevieve Boland
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Sridhar Hannenhalli
- University of Maryland Institute of Advanced Computer Science (UMIACS), University of Maryland, College Park, MD, USA
| | - Meenhard Herlyn
- Molecular and Cellular Oncogenesis Program and Melanoma Research Center, The Wistar Institute, Philadelphia, PA, USA
| | - Cyril Benes
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Keith Flaherty
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Ji Luo
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - J Silvio Gutkind
- Department of Pharmacology & Moores Cancer Center, University of California, San Diego La Jolla, CA, USA
| | - Eytan Ruppin
- University of Maryland Institute of Advanced Computer Science (UMIACS), University of Maryland, College Park, MD, USA
- Cancer Data Science Lab, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Schools of Computer Science & Medicine, Tel-Aviv University, Tel-Aviv, Israel
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