You are here

Home » Publications

Cancer Program

Phosphate dysregulation via the XPR1-KIDINS220 protein complex is a therapeutic vulnerability in ovarian cancer.
Bondeson DP, Paolella BR, Asfaw A, et al. Phosphate dysregulation via the XPR1-KIDINS220 protein complex is a therapeutic vulnerability in ovarian cancer. Nat Cancer. 2022. doi:10.1038/s43018-022-00360-7.
Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer.
Ouspenskaia T, Law T, Clauser KR, et al. Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer. Nat Biotechnol. 2022;40(2):209-217. doi:10.1038/s41587-021-01021-3.
PPM1D mutations are oncogenic drivers of de novo diffuse midline glioma formation.
Khadka P, Reitman ZJ, Lu S, et al. PPM1D mutations are oncogenic drivers of de novo diffuse midline glioma formation. Nat Commun. 2022;13(1):604. doi:10.1038/s41467-022-28198-8.
An In Vivo CRISPR Screening Platform for Prioritizing Therapeutic Targets in AML.
Lin S, Larrue C, Scheidegger NK, et al. An In Vivo CRISPR Screening Platform for Prioritizing Therapeutic Targets in AML. Cancer Discov. 2022;12(2):432-449. doi:10.1158/2159-8290.CD-20-1851.
Somatic and germline genomic alterations in very young women with breast cancer.
Waks AG, Kim D, Jain E, et al. Somatic and germline genomic alterations in very young women with breast cancer. Clin Cancer Res. 2022. doi:10.1158/1078-0432.CCR-21-2572.
Towards a Better Understanding of Antibody-Drug Conjugates in Urothelial Carcinoma.
Labaki C, Bakouny Z, Sonpavde G, Choueiri TK, Van Allen EM. Towards a Better Understanding of Antibody-Drug Conjugates in Urothelial Carcinoma. Eur Urol Oncol. 2022. doi:10.1016/j.euo.2022.01.004.
Implementation of a prostate cancer-specific targeted sequencing panel for credentialing of patient-derived cell lines and genomic characterization of patient samples.
Stover EH, Oh C, Keskula P, et al. Implementation of a prostate cancer-specific targeted sequencing panel for credentialing of patient-derived cell lines and genomic characterization of patient samples. Prostate. 2022. doi:10.1002/pros.24305.
Sparse dictionary learning recovers pleiotropy from human cell fitness screens.
Pan J, Kwon JJ, Talamas JA, et al. Sparse dictionary learning recovers pleiotropy from human cell fitness screens. Cell Syst. 2022. doi:10.1016/j.cels.2021.12.005.
Massively parallel phenotyping of coding variants in cancer with Perturb-seq.
Ursu O, Neal JT, Shea E, et al. Massively parallel phenotyping of coding variants in cancer with Perturb-seq. Nat Biotechnol. 2022. doi:10.1038/s41587-021-01160-7.
Single-cell profiling of tumour evolution in multiple myeloma - opportunities for precision medicine.
Dutta AK, Alberge J-B, Sklavenitis-Pistofidis R, Lightbody ED, Getz G, Ghobrial IM. Single-cell profiling of tumour evolution in multiple myeloma - opportunities for precision medicine. Nat Rev Clin Oncol. 2022. doi:10.1038/s41571-021-00593-y.
Liquid biopsy detection of genomic alterations in pediatric brain tumors from cell-free DNA in peripheral blood, CSF, and urine.
Pages M, Rotem D, Gydush G, et al. Liquid biopsy detection of genomic alterations in pediatric brain tumors from cell-free DNA in peripheral blood, CSF, and urine. Neuro Oncol. 2022. doi:10.1093/neuonc/noab299.
Understanding CLL biology through mouse models of human genetics.
Hacken ETen, Wu CJ. Understanding CLL biology through mouse models of human genetics. Blood. 2021;138(25):2621-2631. doi:10.1182/blood.2021011993.
Chronos: a cell population dynamics model of CRISPR experiments that improves inference of gene fitness effects.
Dempster JM, Boyle I, Vazquez F, et al. Chronos: a cell population dynamics model of CRISPR experiments that improves inference of gene fitness effects. Genome Biol. 2021;22(1):343. doi:10.1186/s13059-021-02540-7.
Analytical protocol to identify local ancestry-associated molecular features in cancer.
Carrot-Zhang J, Han S, Zhou W, et al. Analytical protocol to identify local ancestry-associated molecular features in cancer. STAR Protoc. 2021;2(4):100766. doi:10.1016/j.xpro.2021.100766.
Microenvironment drives cell state, plasticity, and drug response in pancreatic cancer.
Raghavan S, Winter PS, Navia AW, et al. Microenvironment drives cell state, plasticity, and drug response in pancreatic cancer. Cell. 2021;184(25):6119-6137.e26. doi:10.1016/j.cell.2021.11.017.
Age-related Diseases of Inflammation in Myelodysplastic Syndrome and Chronic Myelomonocytic Leukemia.
Weeks LDawn, Marinac CR, Redd RA, et al. Age-related Diseases of Inflammation in Myelodysplastic Syndrome and Chronic Myelomonocytic Leukemia. Blood. 2021. doi:10.1182/blood.2021014418.
Are CRISPR Screens Providing the Next Generation of Therapeutic Targets?
Vazquez F, Sellers WR. Are CRISPR Screens Providing the Next Generation of Therapeutic Targets?. Cancer Res. 2021;81(23):5806-5809. doi:10.1158/0008-5472.CAN-21-1784.
Paralog knockout profiling identifies DUSP4 and DUSP6 as a digenic dependence in MAPK pathway-driven cancers.
Ito T, Young MJ, Li R, et al. Paralog knockout profiling identifies DUSP4 and DUSP6 as a digenic dependence in MAPK pathway-driven cancers. Nat Genet. 2021;53(12):1664-1672. doi:10.1038/s41588-021-00967-z.
Racial, Ethnic, and Socioeconomic Disparities in Curative Treatment Receipt and Survival in Hepatocellular Carcinoma.
Wagle NSandeep, Park S, Washburn D, et al. Racial, Ethnic, and Socioeconomic Disparities in Curative Treatment Receipt and Survival in Hepatocellular Carcinoma. Hepatol Commun. 2021. doi:10.1002/hep4.1863.
Parallel Genomic Alterations of Antigen and Payload Targets Mediate Polyclonal Acquired Clinical Resistance to Sacituzumab Govitecan in Triple-Negative Breast Cancer.
Coates JT, Sun S, Leshchiner I, et al. Parallel Genomic Alterations of Antigen and Payload Targets Mediate Polyclonal Acquired Clinical Resistance to Sacituzumab Govitecan in Triple-Negative Breast Cancer. Cancer Discov. 2021;11(10):2436-2445. doi:10.1158/2159-8290.CD-21-0702.
Biologically informed deep neural network for prostate cancer discovery.
Elmarakeby HA, Hwang J, Arafeh R, et al. Biologically informed deep neural network for prostate cancer discovery. Nature. 2021;598(7880):348-352. doi:10.1038/s41586-021-03922-4.
Duplex-Repair enables highly accurate sequencing, despite DNA damage.
Xiong K, Shea D, Rhoades J, et al. Duplex-Repair enables highly accurate sequencing, despite DNA damage. Nucleic Acids Res. 2021. doi:10.1093/nar/gkab855.
Molecular Alterations in Pediatric Low-Grade Gliomas That Led to Death.
Ahrendsen JT, Sinai C, Meredith DM, et al. Molecular Alterations in Pediatric Low-Grade Gliomas That Led to Death. J Neuropathol Exp Neurol. 2021. doi:10.1093/jnen/nlab097.
TISMO: syngeneic mouse tumor database to model tumor immunity and immunotherapy response.
Zeng Z, Wong CJ, Yang L, et al. TISMO: syngeneic mouse tumor database to model tumor immunity and immunotherapy response. Nucleic Acids Res. 2021. doi:10.1093/nar/gkab804.
The challenges in treating Embryonal Tumors with Multilayered Rosettes (ETMR) and other infant brain tumors.
Bandopadhayay P, Chi SN. The challenges in treating Embryonal Tumors with Multilayered Rosettes (ETMR) and other infant brain tumors. Neuro Oncol. 2021. doi:10.1093/neuonc/noab206.
Telomerase as a therapeutic target in glioblastoma.
Aquilanti E, Kageler L, Wen PY, Meyerson M. Telomerase as a therapeutic target in glioblastoma. Neuro Oncol. 2021. doi:10.1093/neuonc/noab203.
Molecular basis for substrate recruitment to the PRMT5 methylosome.
Mulvaney KM, Blomquist C, Acharya N, et al. Molecular basis for substrate recruitment to the PRMT5 methylosome. Mol Cell. 2021;81(17):3481-3495.e7. doi:10.1016/j.molcel.2021.07.019.
60 Years Young: The Evolving Role of Allogeneic Hematopoietic Stem Cell Transplantation in Cancer Immunotherapy.
Cieri N, Maurer K, Wu CJ. 60 Years Young: The Evolving Role of Allogeneic Hematopoietic Stem Cell Transplantation in Cancer Immunotherapy. Cancer Res. 2021;81(17):4373-4384. doi:10.1158/0008-5472.CAN-21-0301.
Beyond the Front Line: Emerging Data for Maintenance Therapy in Pancreatic Cancer.
Singh H, Perez K, Wolpin BM, Aguirre AJ. Beyond the Front Line: Emerging Data for Maintenance Therapy in Pancreatic Cancer. J Clin Oncol. 2021:JCO2101510. doi:10.1200/JCO.21.01510.
Clonal hematopoiesis in patients receiving chimeric antigen receptor T-cell therapy.
Miller PG, Sperling AS, Brea EJ, et al. Clonal hematopoiesis in patients receiving chimeric antigen receptor T-cell therapy. Blood Adv. 2021;5(15):2982-2986. doi:10.1182/bloodadvances.2021004554.
Discovery of a First-in-Class Inhibitor of the PRMT5-Substrate Adaptor Interaction.
McKinney DC, McMillan BJ, Ranaghan MJ, et al. Discovery of a First-in-Class Inhibitor of the PRMT5-Substrate Adaptor Interaction. J Med Chem. 2021. doi:10.1021/acs.jmedchem.1c00507.
Targeting serine hydroxymethyltransferases 1 and 2 for T-cell acute lymphoblastic leukemia therapy.
Pikman Y, Ocasio-Martinez N, Alexe G, et al. Targeting serine hydroxymethyltransferases 1 and 2 for T-cell acute lymphoblastic leukemia therapy. Leukemia. 2021. doi:10.1038/s41375-021-01361-8.
Epigenetic scars of CD8 T cell exhaustion persist after cure of chronic infection in humans.
Yates KB, Tonnerre P, Martin GE, et al. Epigenetic scars of CD8 T cell exhaustion persist after cure of chronic infection in humans. Nat Immunol. 2021;22(8):1020-1029. doi:10.1038/s41590-021-00979-1.
Phenotype, specificity and avidity of antitumour CD8 T cells in melanoma.
Oliveira G, Stromhaug K, Klaeger S, et al. Phenotype, specificity and avidity of antitumour CD8 T cells in melanoma. Nature. 2021;596(7870):119-125. doi:10.1038/s41586-021-03704-y.
SMAD4 represses FOSL1 expression and pancreatic cancer metastatic colonization.
Dai C, Rennhack JP, Arnoff TE, et al. SMAD4 represses FOSL1 expression and pancreatic cancer metastatic colonization. Cell Rep. 2021;36(4):109443. doi:10.1016/j.celrep.2021.109443.
A phase II study of efficacy, toxicity, and the potential impact of genomic alterations on response to eribulin mesylate in combination with trastuzumab and pertuzumab in women with human epidermal growth factor receptor 2 (HER2)+ metastatic breast cancer
Balch SM, Vaz-Luis I, Li T, et al. A phase II study of efficacy, toxicity, and the potential impact of genomic alterations on response to eribulin mesylate in combination with trastuzumab and pertuzumab in women with human epidermal growth factor receptor 2 (HER2)+ metastatic breast cancer. Breast Cancer Res Treat. 2021. doi:10.1007/s10549-021-06329-x.
TRIM8 modulates the EWS/FLI oncoprotein to promote survival in Ewing sarcoma.
Seong BKyung A, Dharia NV, Lin S, et al. TRIM8 modulates the EWS/FLI oncoprotein to promote survival in Ewing sarcoma. Cancer Cell. 2021. doi:10.1016/j.ccell.2021.07.003.
Structure of PDE3A-SLFN12 complex reveals requirements for activation of SLFN12 RNase.
Garvie CW, Wu X, Papanastasiou M, et al. Structure of PDE3A-SLFN12 complex reveals requirements for activation of SLFN12 RNase. Nat Commun. 2021;12(1):4375. doi:10.1038/s41467-021-24495-w.
Multi-Center Immune Profiling Mass Cytometry Assay Harmonization.
Sahaf B, Pichavant M, Lee BH, et al. Multi-Center Immune Profiling Mass Cytometry Assay Harmonization. Clin Cancer Res. 2021. doi:10.1158/1078-0432.CCR-21-2052.
Synthetic Lethal Interaction between the ESCRT Paralog Enzymes VPS4A and VPS4B in Cancers Harboring Loss of Chromosome 18q or 16q.
Neggers JE, Paolella BR, Asfaw A, et al. Synthetic Lethal Interaction between the ESCRT Paralog Enzymes VPS4A and VPS4B in Cancers Harboring Loss of Chromosome 18q or 16q. Cell Rep. 2021;36(2):109367. doi:10.1016/j.celrep.2021.109367.
Cell line-specific network models of ER+ breast cancer identify potential PI3Kα inhibitor resistance mechanisms and drug combinations.
Zañudo JGómez Tej, Mao P, Alcon C, et al. Cell line-specific network models of ER+ breast cancer identify potential PI3Kα inhibitor resistance mechanisms and drug combinations. Cancer Res. 2021. doi:10.1158/0008-5472.CAN-21-1208.
Acquired Resistance to KRAS Inhibition in Cancer.
Awad MM, Liu S, Rybkin II, et al. Acquired Resistance to KRAS Inhibition in Cancer. N Engl J Med. 2021;384(25):2382-2393. doi:10.1056/NEJMoa2105281.
Gene fusions create partner and collateral dependencies essential to cancer cell survival.
Gillani R, Seong BKyung A, Crowdis J, et al. Gene fusions create partner and collateral dependencies essential to cancer cell survival. Cancer Res. 2021. doi:10.1158/0008-5472.CAN-21-0791.
Reprogramming of the esophageal squamous carcinoma epigenome by SOX2 promotes ADAR1 dependence.
Wu Z, Zhou J, Zhang X, et al. Reprogramming of the esophageal squamous carcinoma epigenome by SOX2 promotes ADAR1 dependence. Nat Genet. 2021;53(6):881-894. doi:10.1038/s41588-021-00859-2.
Advances in targeting 'undruggable' transcription factors with small molecules.
Henley MJ, Koehler AN. Advances in targeting 'undruggable' transcription factors with small molecules. Nat Rev Drug Discov. 2021. doi:10.1038/s41573-021-00199-0.
Extended-representation bisulfite sequencing of gene regulatory elements in multiplexed samples and single cells.
Shareef SJ, Bevill SM, Raman AT, et al. Extended-representation bisulfite sequencing of gene regulatory elements in multiplexed samples and single cells. Nat Biotechnol. 2021. doi:10.1038/s41587-021-00910-x.
Epigenetic silencing by SETDB1 suppresses tumour intrinsic immunogenicity.
Griffin GK, Wu J, Iracheta-Vellve A, et al. Epigenetic silencing by SETDB1 suppresses tumour intrinsic immunogenicity. Nature. 2021. doi:10.1038/s41586-021-03520-4.
The power of parent scientists.
Boehm JS. The power of parent scientists. Cell. 2021;184(9):2263-2270. doi:10.1016/j.cell.2021.03.049.
Selective modulation of a pan-essential protein as a therapeutic strategy in cancer.
Malone CF, Dharia NV, Kugener G, et al. Selective modulation of a pan-essential protein as a therapeutic strategy in cancer. Cancer Discov. 2021. doi:10.1158/2159-8290.CD-20-1213.
Predicting cell health phenotypes using image-based morphology profiling.
Way GP, Kost-Alimova M, Shibue T, et al. Predicting cell health phenotypes using image-based morphology profiling. Mol Biol Cell. 2021;32(9):995-1005. doi:10.1091/mbc.E20-12-0784.
Splice it up: Atypical transcripts to boost leukemia immunotherapy.
Cieri N, Wu CJ. Splice it up: Atypical transcripts to boost leukemia immunotherapy. Immunity. 2021;54(4):608-610. doi:10.1016/j.immuni.2021.03.016.
A first-generation pediatric cancer dependency map.
Dharia NV, Kugener G, Guenther LM, et al. A first-generation pediatric cancer dependency map. Nat Genet. 2021;53(4):529-538. doi:10.1038/s41588-021-00819-w.
Bridging the gap between cancer cell line models and tumours using gene expression data.
Noorbakhsh J, Vazquez F, McFarland JM. Bridging the gap between cancer cell line models and tumours using gene expression data. Br J Cancer. 2021. doi:10.1038/s41416-021-01359-0.
A Leucine-Rich Repeat Protein Provides a SHOC2 the RAS Circuit: a Structure-Function Perspective.
Kwon JJ, Hahn WC. A Leucine-Rich Repeat Protein Provides a SHOC2 the RAS Circuit: a Structure-Function Perspective. Mol Cell Biol. 2021;41(4). doi:10.1128/MCB.00627-20.
Molecular and cellular features of CTLA-4 blockade for relapsed myeloid malignancies after transplantation.
Penter L, Zhang Y, Savell A, et al. Molecular and cellular features of CTLA-4 blockade for relapsed myeloid malignancies after transplantation. Blood. 2021. doi:10.1182/blood.2021010867.
Tumor and immune reprogramming during immunotherapy in advanced renal cell carcinoma.
Bi K, He MXiao, Bakouny Z, et al. Tumor and immune reprogramming during immunotherapy in advanced renal cell carcinoma. Cancer Cell. 2021. doi:10.1016/j.ccell.2021.02.015.
Progressive immune dysfunction with advancing disease stage in renal cell carcinoma.
Braun DA, Street K, Burke KP, et al. Progressive immune dysfunction with advancing disease stage in renal cell carcinoma. Cancer Cell. 2021. doi:10.1016/j.ccell.2021.02.013.
In vivo screens using a selective CRISPR antigen removal lentiviral vector system reveal immune dependencies in renal cell carcinoma.
Dubrot J, Lane-Reticker SKate, Kessler EA, et al. In vivo screens using a selective CRISPR antigen removal lentiviral vector system reveal immune dependencies in renal cell carcinoma. Immunity. 2021;54(3):571-585.e6. doi:10.1016/j.immuni.2021.01.001.
A hotspot mutation in transcription factor IKZF3 drives B cell neoplasia via transcriptional dysregulation.
Lazarian G, Yin S, Hacken ETen, et al. A hotspot mutation in transcription factor IKZF3 drives B cell neoplasia via transcriptional dysregulation. Cancer Cell. 2021;39(3):380-393.e8. doi:10.1016/j.ccell.2021.02.003.
An expanded universe of cancer targets.
Hahn WC, Bader JS, Braun TP, et al. An expanded universe of cancer targets. Cell. 2021;184(5):1142-1155. doi:10.1016/j.cell.2021.02.020.
Cancer therapies based on targeted protein degradation - lessons learned with lenalidomide.
Jan M, Sperling AS, Ebert BL. Cancer therapies based on targeted protein degradation - lessons learned with lenalidomide. Nat Rev Clin Oncol. 2021. doi:10.1038/s41571-021-00479-z.
RNA-SeQC 2: Efficient RNA-seq quality control and quantification for large cohorts.
Graubert A, Aguet F, Ravi A, Ardlie KG, Getz G. RNA-SeQC 2: Efficient RNA-seq quality control and quantification for large cohorts. Bioinformatics. 2021. doi:10.1093/bioinformatics/btab135.
Transcriptional mediators of treatment resistance in lethal prostate cancer.
He MXiao, Cuoco MS, Crowdis J, et al. Transcriptional mediators of treatment resistance in lethal prostate cancer. Nat Med. 2021;27(3):426-433. doi:10.1038/s41591-021-01244-6.
Dissecting the immunogenomic biology of cancer for biomarker development.
Van Allen EM, Choueiri TK. Dissecting the immunogenomic biology of cancer for biomarker development. Nat Rev Clin Oncol. 2021;18(3):133-134. doi:10.1038/s41571-020-00461-1.
Modulating Androgen Receptor-Driven Transcription in Prostate Cancer with Selective CDK9 Inhibitors.
Richters A, Doyle SK, Freeman DB, et al. Modulating Androgen Receptor-Driven Transcription in Prostate Cancer with Selective CDK9 Inhibitors. Cell Chem Biol. 2021;28(2):134-147.e14. doi:10.1016/j.chembiol.2020.10.001.
Matched Targeted Therapy for Pediatric Patients with Relapsed, Refractory or High-risk Leukemias: A Report from the LEAP Consortium.
Pikman Y, Tasian SK, Sulis MLuisa, et al. Matched Targeted Therapy for Pediatric Patients with Relapsed, Refractory or High-risk Leukemias: A Report from the LEAP Consortium. Cancer Discov. 2021. doi:10.1158/2159-8290.CD-20-0564.
Advances in the classification and treatment of pediatric brain tumors.
Fangusaro J, Bandopadhayay P. Advances in the classification and treatment of pediatric brain tumors. Curr Opin Pediatr. 2021;33(1):26-32. doi:10.1097/MOP.0000000000000975.
Noncanonical open reading frames encode functional proteins essential for cancer cell survival.
Prensner JR, Enache OM, Luria V, et al. Noncanonical open reading frames encode functional proteins essential for cancer cell survival. Nat Biotechnol. 2021. doi:10.1038/s41587-020-00806-2.
Antigen identification for HLA class I- and HLA class II-restricted T cell receptors using cytokine-capturing antigen-presenting cells.
Lee MN, Meyerson M. Antigen identification for HLA class I- and HLA class II-restricted T cell receptors using cytokine-capturing antigen-presenting cells. Sci Immunol. 2021;6(55). doi:10.1126/sciimmunol.abf4001.
Nailing Down a Notoriously Elusive Cancer Target: Direct Inhibition of MYC by a Covalent Small Molecule.
Henley MJ, Doyle SK, Koehler AN. Nailing Down a Notoriously Elusive Cancer Target: Direct Inhibition of MYC by a Covalent Small Molecule. Cell Chem Biol. 2021;28(1):1-3. doi:10.1016/j.chembiol.2020.12.014.
Targeting pan-essential genes in cancer: challenges and opportunities.
Chang L, Ruiz P, Ito T, Sellers WR. Targeting pan-essential genes in cancer: challenges and opportunities. Cancer Cell. 2021. doi:10.1016/j.ccell.2020.12.008.
CBL mutations drive PI3K/AKT signaling via increased interaction with LYN and PIK3R1.
Belizaire R, Koochaki SHassan Joh, Udeshi ND, et al. CBL mutations drive PI3K/AKT signaling via increased interaction with LYN and PIK3R1. Blood. 2021. doi:10.1182/blood.2020006528.
Cancer research needs a better map.
Boehm JS, Garnett MJ, Adams DJ, et al. Cancer research needs a better map. Nature. 2021;589(7843):514-516. doi:10.1038/d41586-021-00182-0.
Natural Barcodes for Longitudinal Single Cell Tracking of Leukemic and Immune Cell Dynamics.
Penter L, Gohil SH, Wu CJ. Natural Barcodes for Longitudinal Single Cell Tracking of Leukemic and Immune Cell Dynamics. Front Immunol. 2021;12:788891. doi:10.3389/fimmu.2021.788891.
Cohesin mutations alter DNA damage repair and chromatin structure and create therapeutic vulnerabilities in MDS/AML.
Tothova Z, Valton A-L, Gorelov R, et al. Cohesin mutations alter DNA damage repair and chromatin structure and create therapeutic vulnerabilities in MDS/AML. JCI Insight. 2020. doi:10.1172/jci.insight.142149.
Synthetic Lethal Interaction between the ESCRT Paralog Enzymes VPS4A and VPS4B in Cancers Harboring Loss of Chromosome 18q or 16q.
Neggers JE, Paolella BR, Asfaw A, et al. Synthetic Lethal Interaction between the ESCRT Paralog Enzymes VPS4A and VPS4B in Cancers Harboring Loss of Chromosome 18q or 16q. Cell Rep. 2020;33(11):108493. doi:10.1016/j.celrep.2020.108493.
Genetic ancestry contributes to somatic mutations in lung cancers from admixed Latin American populations.
Carrot-Zhang J, Soca-Chafre G, Patterson N, et al. Genetic ancestry contributes to somatic mutations in lung cancers from admixed Latin American populations. Cancer Discov. 2020. doi:10.1158/2159-8290.CD-20-1165.
Small-molecule-induced polymerization triggers degradation of BCL6.
Słabicki M, Yoon H, Koeppel J, et al. Small-molecule-induced polymerization triggers degradation of BCL6. Nature. 2020;588(7836):164-168. doi:10.1038/s41586-020-2925-1.
Integrated molecular drivers coordinate biological and clinical states in melanoma.
Conway JR, Dietlein F, Taylor-Weiner A, et al. Integrated molecular drivers coordinate biological and clinical states in melanoma. Nat Genet. 2020;52(12):1373-1383. doi:10.1038/s41588-020-00739-1.
A metastasis map of human cancer cell lines.
Jin X, Demere Z, Nair K, et al. A metastasis map of human cancer cell lines. Nature. 2020;588(7837):331-336. doi:10.1038/s41586-020-2969-2.
Quantification of aneuploidy in targeted sequencing data using ASCETS.
Spurr LF, Touat M, Taylor AM, et al. Quantification of aneuploidy in targeted sequencing data using ASCETS. Bioinformatics. 2020. doi:10.1093/bioinformatics/btaa980.
CloneSifter: enrichment of rare clones from heterogeneous cell populations.
Feldman D, Tsai FN, Garrity AJ, et al. CloneSifter: enrichment of rare clones from heterogeneous cell populations. BMC Biol. 2020;18(1):177. doi:10.1186/s12915-020-00911-3.
Detection of Pathogenic Variants With Germline Genetic Testing Using Deep Learning vs Standard Methods in Patients With Prostate Cancer and Melanoma.
AlDubayan SH, Conway JR, Camp SY, et al. Detection of Pathogenic Variants With Germline Genetic Testing Using Deep Learning vs Standard Methods in Patients With Prostate Cancer and Melanoma. JAMA. 2020;324(19):1957-1969. doi:10.1001/jama.2020.20457.
Acquired FGFR and FGF Alterations Confer Resistance to Estrogen Receptor (ER) Targeted Therapy in ER Metastatic Breast Cancer.
Mao P, Cohen O, Kowalski KJ, et al. Acquired FGFR and FGF Alterations Confer Resistance to Estrogen Receptor (ER) Targeted Therapy in ER Metastatic Breast Cancer. Clin Cancer Res. 2020;26(22):5974-5989. doi:10.1158/1078-0432.CCR-19-3958.
COVID-19 and Cancer: Current Challenges and Perspectives.
Bakouny Z, Hawley JE, Choueiri TK, et al. COVID-19 and Cancer: Current Challenges and Perspectives. Cancer Cell. 2020;38(5):629-646. doi:10.1016/j.ccell.2020.09.018.
Pan-cancer single-cell RNA-seq identifies recurring programs of cellular heterogeneity.
Kinker GS, Greenwald AC, Tal R, et al. Pan-cancer single-cell RNA-seq identifies recurring programs of cellular heterogeneity. Nat Genet. 2020;52(11):1208-1218. doi:10.1038/s41588-020-00726-6.
Contribution of Clonal Hematopoiesis to Adult-Onset Hemophagocytic Lymphohistiocytosis.
Miller P, Sperling AS, Gibson CJames, et al. Contribution of Clonal Hematopoiesis to Adult-Onset Hemophagocytic Lymphohistiocytosis. Blood. 2020. doi:10.1182/blood.2020008206.
Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples.
Bailey MH, Meyerson WU, Dursi LJonathan, et al. Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples. Nat Commun. 2020;11(1):4748. doi:10.1038/s41467-020-18151-y.
Distinct evolutionary paths in chronic lymphocytic leukemia during resistance to the graft-versus-leukemia effect.
Bachireddy P, Ennis C, Nguyen VN, et al. Distinct evolutionary paths in chronic lymphocytic leukemia during resistance to the graft-versus-leukemia effect. Sci Transl Med. 2020;12(561). doi:10.1126/scitranslmed.abb7661.
Genomic Profiling of Prostate Cancers from Men with African and European Ancestry.
Koga Y, Song H, Chalmers ZR, et al. Genomic Profiling of Prostate Cancers from Men with African and European Ancestry. Clin Cancer Res. 2020;26(17):4651-4660. doi:10.1158/1078-0432.CCR-19-4112.
Multiplexed single-cell transcriptional response profiling to define cancer vulnerabilities and therapeutic mechanism of action.
McFarland JM, Paolella BR, Warren A, et al. Multiplexed single-cell transcriptional response profiling to define cancer vulnerabilities and therapeutic mechanism of action. Nat Commun. 2020;11(1):4296. doi:10.1038/s41467-020-17440-w.
The CDK inhibitor CR8 acts as a molecular glue degrader that depletes cyclin K.
Słabicki M, Kozicka Z, Petzold G, et al. The CDK inhibitor CR8 acts as a molecular glue degrader that depletes cyclin K. Nature. 2020. doi:10.1038/s41586-020-2374-x.
Genomic Profiling of Smoldering Multiple Myeloma Identifies Patients at a High Risk of Disease Progression.
Bustoros M, Sklavenitis-Pistofidis R, Park J, et al. Genomic Profiling of Smoldering Multiple Myeloma Identifies Patients at a High Risk of Disease Progression. J Clin Oncol. 2020:JCO2000437. doi:10.1200/JCO.20.00437.
Loss of heterozygosity of essential genes represents a widespread class of potential cancer vulnerabilities.
Nichols CA, Gibson WJ, Brown MS, et al. Loss of heterozygosity of essential genes represents a widespread class of potential cancer vulnerabilities. Nat Commun. 2020;11(1):2517. doi:10.1038/s41467-020-16399-y.
Cas9 activates the p53 pathway and selects for p53-inactivating mutations.
Enache OM, Rendo V, Abdusamad M, et al. Cas9 activates the p53 pathway and selects for p53-inactivating mutations. Nat Genet. 2020. doi:10.1038/s41588-020-0623-4.
The genomic landscape of intrinsic and acquired resistance to cyclin-dependent kinase 4/6 inhibitors in patients with hormone receptor positive metastatic breast cancer.
Wander SA, Cohen O, Gong X, et al. The genomic landscape of intrinsic and acquired resistance to cyclin-dependent kinase 4/6 inhibitors in patients with hormone receptor positive metastatic breast cancer. Cancer Discov. 2020. doi:10.1158/2159-8290.CD-19-1390.
Comprehensive Analysis of Genetic Ancestry and Its Molecular Correlates in Cancer.
Carrot-Zhang J, Chambwe N, Damrauer JS, et al. Comprehensive Analysis of Genetic Ancestry and Its Molecular Correlates in Cancer. Cancer Cell. 2020;37(5):639-654.e6. doi:10.1016/j.ccell.2020.04.012.
Reversion and non-reversion mechanisms of resistance to PARP inhibitor or platinum chemotherapy in BRCA1/2-mutant metastatic breast cancer.
Waks AG, Cohen O, Kochupurakkal B, et al. Reversion and non-reversion mechanisms of resistance to PARP inhibitor or platinum chemotherapy in BRCA1/2-mutant metastatic breast cancer. Ann Oncol. 2020;31(5):590-598. doi:10.1016/j.annonc.2020.02.008.
Patterns of chromosome 18 loss of heterozygosity in multifocal ileal neuroendocrine tumors.
Zhang Z, Mäkinen N, Kasai Y, et al. Patterns of chromosome 18 loss of heterozygosity in multifocal ileal neuroendocrine tumors. Genes Chromosomes Cancer. 2020. doi:10.1002/gcc.22850.
Sensitive detection of minimal residual disease in patients treated for early-stage breast cancer.
Parsons HA, Rhoades J, Reed SC, et al. Sensitive detection of minimal residual disease in patients treated for early-stage breast cancer. Clin Cancer Res. 2020. doi:10.1158/1078-0432.CCR-19-3005.
Mechanistic insights into cancer cell killing through interaction of phosphodiesterase 3A and schlafen family member 12.
Wu X, Schnitzler GR, Gao GF, et al. Mechanistic insights into cancer cell killing through interaction of phosphodiesterase 3A and schlafen family member 12. J Biol Chem. 2020;295(11):3431-3446. doi:10.1074/jbc.RA119.011191.
Prevalence and mutational determinants of high tumor mutation burden in breast cancer.
Barroso-Sousa R, Jain E, Cohen O, et al. Prevalence and mutational determinants of high tumor mutation burden in breast cancer. Ann Oncol. 2020;31(3):387-394. doi:10.1016/j.annonc.2019.11.010.
Resistance Mechanisms to SYK Inhibition in Acute Myeloid Leukemia.
Cremer A, Ellegast JM, Alexe G, et al. Resistance Mechanisms to SYK Inhibition in Acute Myeloid Leukemia. Cancer Discov. 2020;10(2):214-231. doi:10.1158/2159-8290.CD-19-0209.
Gain-of-Function Mutations Promote Focal Adhesion Kinase Activation and Dependency in Diffuse Gastric Cancer.
Zhang H, Schaefer A, Wang Y, et al. Gain-of-Function Mutations Promote Focal Adhesion Kinase Activation and Dependency in Diffuse Gastric Cancer. Cancer Discov. 2020;10(2):288-305. doi:10.1158/2159-8290.CD-19-0811.
Early TP53 alterations engage environmental exposures to promote gastric premalignancy in an integrative mouse model.
Sethi NS, Kikuchi O, Duronio GN, et al. Early TP53 alterations engage environmental exposures to promote gastric premalignancy in an integrative mouse model. Nat Genet. 2020;52(2):219-230. doi:10.1038/s41588-019-0574-9.
Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.
Rheinbay E, Nielsen MMuhlig, Abascal F, et al. Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nature. 2020;578(7793):102-111. doi:10.1038/s41586-020-1965-x.
The Angiosarcoma Project: enabling genomic and clinical discoveries in a rare cancer through patient-partnered research.
Painter CA, Jain E, Tomson BN, et al. The Angiosarcoma Project: enabling genomic and clinical discoveries in a rare cancer through patient-partnered research. Nat Med. 2020;26(2):181-187. doi:10.1038/s41591-019-0749-z.
Quantitative Proteomics of the Cancer Cell Line Encyclopedia.
Nusinow DP, Szpyt J, Ghandi M, et al. Quantitative Proteomics of the Cancer Cell Line Encyclopedia. Cell. 2020;180(2):387-402.e16. doi:10.1016/j.cell.2019.12.023.
STRIPAK directs PP2A activity toward MAP4K4 to promote oncogenic transformation of human cells.
Kim JWook, Berrios C, Kim M, et al. STRIPAK directs PP2A activity toward MAP4K4 to promote oncogenic transformation of human cells. Elife. 2020;9. doi:10.7554/eLife.53003.
Targeted Covalent Inhibition of Plasmodium FK506 Binding Protein 35
Atack TC, Raymond DD, Blomquist CA, et al. Targeted Covalent Inhibition of Plasmodium FK506 Binding Protein 35. ACS Medicinal Chemistry Letters. 2020;11(11):2131-2138.
Targeted Covalent Inhibition of Plasmodium FK506 Binding Protein 35
Atack TC, Raymond DD, Blomquist CA, et al. Targeted Covalent Inhibition of Plasmodium FK506 Binding Protein 35. ACS Medicinal Chemistry Letters. 2020;11(11):2131-2138.
Genomic analyses of PMBL reveal new drivers and mechanisms of sensitivity to PD-1 blockade.
Chapuy B, Stewart C, Dunford AJ, et al. Genomic analyses of PMBL reveal new drivers and mechanisms of sensitivity to PD-1 blockade. Blood. 2019;134(26):2369-2382. doi:10.1182/blood.2019002067.
Agreement between two large pan-cancer CRISPR-Cas9 gene dependency data sets.
Dempster JM, Pacini C, Pantel S, et al. Agreement between two large pan-cancer CRISPR-Cas9 gene dependency data sets. Nat Commun. 2019;10(1):5817. doi:10.1038/s41467-019-13805-y.
Genomics and Targeted Therapies in Gastroesophageal Adenocarcinoma.
Nagaraja AK, Kikuchi O, Bass AJ. Genomics and Targeted Therapies in Gastroesophageal Adenocarcinoma. Cancer Discov. 2019;9(12):1656-1672. doi:10.1158/2159-8290.CD-19-0487.
Genomic and immune profiling of pre-invasive lung adenocarcinoma.
Chen H, Carrot-Zhang J, Zhao Y, et al. Genomic and immune profiling of pre-invasive lung adenocarcinoma. Nat Commun. 2019;10(1):5472. doi:10.1038/s41467-019-13460-3.
CREB5 Promotes Resistance to Androgen-Receptor Antagonists and Androgen Deprivation in Prostate Cancer.
Hwang JH, Seo J-H, Beshiri ML, et al. CREB5 Promotes Resistance to Androgen-Receptor Antagonists and Androgen Deprivation in Prostate Cancer. Cell Rep. 2019;29(8):2355-2370.e6. doi:10.1016/j.celrep.2019.10.068.
Optimization of PDE3A Modulators for SLFN12-Dependent Cancer Cell Killing.
Lewis TA, de Waal L, Wu X, et al. Optimization of PDE3A Modulators for SLFN12-Dependent Cancer Cell Killing. ACS Med Chem Lett. 2019;10(11):1537-1542. doi:10.1021/acsmedchemlett.9b00360.
Pooled Genomic Screens Identify Anti-apoptotic Genes as Targetable Mediators of Chemotherapy Resistance in Ovarian Cancer.
Stover EH, Baco MB, Cohen O, et al. Pooled Genomic Screens Identify Anti-apoptotic Genes as Targetable Mediators of Chemotherapy Resistance in Ovarian Cancer. Mol Cancer Res. 2019;17(11):2281-2293. doi:10.1158/1541-7786.MCR-18-1243.
A nuclease-polymerase chain reaction enables amplification of probes used for capture-based DNA target enrichment.
Leong KWai, Yu F, Adalsteinsson VA, et al. A nuclease-polymerase chain reaction enables amplification of probes used for capture-based DNA target enrichment. Nucleic Acids Res. 2019. doi:10.1093/nar/gkz870.
Metabolomic adaptations and correlates of survival to immune checkpoint blockade.
Li H, Bullock K, Gurjao C, et al. Metabolomic adaptations and correlates of survival to immune checkpoint blockade. Nat Commun. 2019;10(1):4346. doi:10.1038/s41467-019-12361-9.
Mitochondrial Reprogramming Underlies Resistance to BCL-2 Inhibition in Lymphoid Malignancies.
Guièze R, Liu VM, Rosebrock D, et al. Mitochondrial Reprogramming Underlies Resistance to BCL-2 Inhibition in Lymphoid Malignancies. Cancer Cell. 2019. doi:10.1016/j.ccell.2019.08.005.
Small-Molecule and CRISPR Screening Converge to Reveal Receptor Tyrosine Kinase Dependencies in Pediatric Rhabdoid Tumors.
Oberlick EM, Rees MG, Seashore-Ludlow B, et al. Small-Molecule and CRISPR Screening Converge to Reveal Receptor Tyrosine Kinase Dependencies in Pediatric Rhabdoid Tumors. Cell Rep. 2019;28(9):2331-2344.e8. doi:10.1016/j.celrep.2019.07.021.
Genomic Evolutionary Patterns of Leiomyosarcoma and Liposarcoma.
Amin-Mansour A, George S, Sioletic S, et al. Genomic Evolutionary Patterns of Leiomyosarcoma and Liposarcoma. Clin Cancer Res. 2019;25(16):5135-5142. doi:10.1158/1078-0432.CCR-19-0271.
High-throughput Chemical Screening Identifies Focal Adhesion Kinase and Aurora Kinase B Inhibition as a Synergistic Treatment Combination in Ewing Sarcoma.
Wang S, Hwang EE, Guha R, et al. High-throughput Chemical Screening Identifies Focal Adhesion Kinase and Aurora Kinase B Inhibition as a Synergistic Treatment Combination in Ewing Sarcoma. Clin Cancer Res. 2019;25(14):4552-4566. doi:10.1158/1078-0432.CCR-17-0375.
Patterns of substrate affinity, competition, and degradation kinetics underlie biological activity of thalidomide analogs.
Sperling AS, Burgess M, Keshishian H, et al. Patterns of substrate affinity, competition, and degradation kinetics underlie biological activity of thalidomide analogs. Blood. 2019;134(2):160-170. doi:10.1182/blood.2019000789.
Publisher Correction: The long tail of oncogenic drivers in prostate cancer.
Armenia J, Wankowicz SAM, Liu D, et al. Publisher Correction: The long tail of oncogenic drivers in prostate cancer. Nat Genet. 2019;51(7):1194. doi:10.1038/s41588-019-0451-6.
Mitochondrial metabolism promotes adaptation to proteotoxic stress.
Tsvetkov P, Detappe A, Cai K, et al. Mitochondrial metabolism promotes adaptation to proteotoxic stress. Nat Chem Biol. 2019;15(7):681-689. doi:10.1038/s41589-019-0291-9.
Integrative molecular characterization of resistance to neoadjuvant chemoradiation in rectal cancer.
Kamran SC, Lennerz JK, Margolis CA, et al. Integrative molecular characterization of resistance to neoadjuvant chemoradiation in rectal cancer. Clin Cancer Res. 2019. doi:10.1158/1078-0432.CCR-19-0908.
A CRISPR Way to Identify Cancer Targets.
Hahn WC. A CRISPR Way to Identify Cancer Targets. N Engl J Med. 2019;380(25):2475-2477. doi:10.1056/NEJMcibr1905048.
Intrinsic Resistance to Immune Checkpoint Blockade in a Mismatch Repair-Deficient Colorectal Cancer.
Gurjao C, Liu D, Hofree M, et al. Intrinsic Resistance to Immune Checkpoint Blockade in a Mismatch Repair-Deficient Colorectal Cancer. Cancer Immunol Res. 2019. doi:10.1158/2326-6066.CIR-18-0683.
RNA sequence analysis reveals macroscopic somatic clonal expansion across normal tissues.
Yizhak K, Aguet F, Kim J, et al. RNA sequence analysis reveals macroscopic somatic clonal expansion across normal tissues. Science. 2019;364(6444). doi:10.1126/science.aaw0726.
Neuronal differentiation and cell-cycle programs mediate response to BET-bromodomain inhibition in MYC-driven medulloblastoma.
Bandopadhayay P, Piccioni F, O'Rourke R, et al. Neuronal differentiation and cell-cycle programs mediate response to BET-bromodomain inhibition in MYC-driven medulloblastoma. Nat Commun. 2019;10(1):2400. doi:10.1038/s41467-019-10307-9.
Growth dynamics in naturally progressing chronic lymphocytic leukaemia.
Gruber M, Bozic I, Leshchiner I, et al. Growth dynamics in naturally progressing chronic lymphocytic leukaemia. Nature. 2019;570(7762):474-479. doi:10.1038/s41586-019-1252-x.
Genome-Wide Interrogation of Human Cancers Identifies EGLN1 Dependency in Clear Cell Ovarian Cancers.
Price C, Gill S, Ho ZV, et al. Genome-Wide Interrogation of Human Cancers Identifies EGLN1 Dependency in Clear Cell Ovarian Cancers. Cancer Res. 2019;79(10):2564-2579. doi:10.1158/0008-5472.CAN-18-2674.
Next-generation characterization of the Cancer Cell Line Encyclopedia.
Ghandi M, Huang FW, Jané-Valbuena J, et al. Next-generation characterization of the Cancer Cell Line Encyclopedia. Nature. 2019. doi:10.1038/s41586-019-1186-3.
A Functional Landscape of Resistance to MEK1/2 and CDK4/6 Inhibition in NRAS-Mutant Melanoma.
Hayes TK, Luo F, Cohen O, et al. A Functional Landscape of Resistance to MEK1/2 and CDK4/6 Inhibition in NRAS-Mutant Melanoma. Cancer Res. 2019;79(9):2352-2366. doi:10.1158/0008-5472.CAN-18-2711.
The landscape of cancer cell line metabolism.
Li H, Ning S, Ghandi M, et al. The landscape of cancer cell line metabolism. Nat Med. 2019;25(5):850-860. doi:10.1038/s41591-019-0404-8.
A GPX4-dependent cancer cell state underlies the clear-cell morphology and confers sensitivity to ferroptosis.
Zou Y, Palte MJ, Deik AA, et al. A GPX4-dependent cancer cell state underlies the clear-cell morphology and confers sensitivity to ferroptosis. Nat Commun. 2019;10(1):1617. doi:10.1038/s41467-019-09277-9.
WRN helicase is a synthetic lethal target in microsatellite unstable cancers.
Chan EM, Shibue T, McFarland JM, et al. WRN helicase is a synthetic lethal target in microsatellite unstable cancers. Nature. 2019;568(7753):551-556. doi:10.1038/s41586-019-1102-x.
A (fire)cloud-based DNA methylation data preprocessing and quality control platform.
Kangeyan D, Dunford A, Iyer S, et al. A (fire)cloud-based DNA methylation data preprocessing and quality control platform. BMC Bioinformatics. 2019;20(1):160. doi:10.1186/s12859-019-2750-4.
From cell lines to living biosensors: new opportunities to prioritize cancer dependencies using ex vivo tumor cultures.
Tseng Y-Y, Boehm JS. From cell lines to living biosensors: new opportunities to prioritize cancer dependencies using ex vivo tumor cultures. Curr Opin Genet Dev. 2019;54:33-40. doi:10.1016/j.gde.2019.02.007.
Circulating Tumor DNA Provides a Sneak Peek into Treatment Responses in Non-Small Cell Lung Cancer.
Zou T, Meyerson M. Circulating Tumor DNA Provides a Sneak Peek into Treatment Responses in Non-Small Cell Lung Cancer. Cancer Res. 2019;79(6):1038-1040. doi:10.1158/0008-5472.CAN-19-0231.
Renal medullary carcinomas depend upon loss and are sensitive to proteasome inhibition.
Hong AL, Tseng Y-Y, Wala JA, et al. Renal medullary carcinomas depend upon loss and are sensitive to proteasome inhibition. Elife. 2019;8. doi:10.7554/eLife.44161.
Subsets of exhausted CD8 T cells differentially mediate tumor control and respond to checkpoint blockade.
Miller BC, Sen DR, Abosy RAl, et al. Subsets of exhausted CD8 T cells differentially mediate tumor control and respond to checkpoint blockade. Nat Immunol. 2019;20(3):326-336. doi:10.1038/s41590-019-0312-6.
MCL1 and DEDD Promote Urothelial Carcinoma Progression.
Hong AL, Guerriero JL, Doshi MB, et al. MCL1 and DEDD Promote Urothelial Carcinoma Progression. Mol Cancer Res. 2019. doi:10.1158/1541-7786.MCR-18-0963.
MDM2 and MDM4 are Therapeutic Vulnerabilities in Malignant Rhabdoid Tumors.
Howard TP, Arnoff TE, Song MR, et al. MDM2 and MDM4 are Therapeutic Vulnerabilities in Malignant Rhabdoid Tumors. Cancer Res. 2019. doi:10.1158/0008-5472.CAN-18-3066.
Acquired HER2 mutations in ER metastatic breast cancer confer resistance to estrogen receptor-directed therapies.
Nayar U, Cohen O, Kapstad C, et al. Acquired HER2 mutations in ER metastatic breast cancer confer resistance to estrogen receptor-directed therapies. Nat Genet. 2019;51(2):207-216. doi:10.1038/s41588-018-0287-5.
A Murine Model of Chronic Lymphocytic Leukemia Based on B Cell-Restricted Expression of Sf3b1 Mutation and Atm Deletion.
Yin S, Gambe RG, Sun J, et al. A Murine Model of Chronic Lymphocytic Leukemia Based on B Cell-Restricted Expression of Sf3b1 Mutation and Atm Deletion. Cancer Cell. 2019. doi:10.1016/j.ccell.2018.12.013.
Identification and characterization of oncogenic SOS1 mutations in lung adenocarcinoma.
Cai D, Choi PS, Gelbard M, Meyerson M. Identification and characterization of oncogenic SOS1 mutations in lung adenocarcinoma. Mol Cancer Res. 2019. doi:10.1158/1541-7786.MCR-18-0316.
Amplification Associates with Aggressive Phenotype but Not Markers of AKT-MTOR Signaling in Endometrial Carcinoma.
Holst F, Werner HMJ, Mjøs, iv S, et al. Amplification Associates with Aggressive Phenotype but Not Markers of AKT-MTOR Signaling in Endometrial Carcinoma. Clin Cancer Res. 2019;25(1):334-345. doi:10.1158/1078-0432.CCR-18-0452.
Loss of ADAR1 in tumours overcomes resistance to immune checkpoint blockade.
Ishizuka JJ, Manguso RT, Cheruiyot CK, et al. Loss of ADAR1 in tumours overcomes resistance to immune checkpoint blockade. Nature. 2019;565(7737):43-48. doi:10.1038/s41586-018-0768-9.
Neoantigen vaccine generates intratumoral T cell responses in phase Ib glioblastoma trial.
Keskin DB, Anandappa AJ, Sun J, et al. Neoantigen vaccine generates intratumoral T cell responses in phase Ib glioblastoma trial. Nature. 2019;565(7738):234-239. doi:10.1038/s41586-018-0792-9.
Identification of ADAR1 adenosine deaminase dependency in a subset of cancer cells.
Gannon HS, Zou T, Kiessling MK, et al. Identification of ADAR1 adenosine deaminase dependency in a subset of cancer cells. Nat Commun. 2018;9(1):5450. doi:10.1038/s41467-018-07824-4.
Genomic evolution of cancer models: perils and opportunities.
Ben-David U, Beroukhim R, Golub TR. Genomic evolution of cancer models: perils and opportunities. Nat Rev Cancer. 2018. doi:10.1038/s41568-018-0095-3.
GATK PathSeq: a customizable computational tool for the discovery and identification of microbial sequences in libraries from eukaryotic hosts.
Walker MA, Pedamallu CSekhar, Ojesina AI, et al. GATK PathSeq: a customizable computational tool for the discovery and identification of microbial sequences in libraries from eukaryotic hosts. Bioinformatics. 2018;34(24):4287-4289. doi:10.1093/bioinformatics/bty501.
KDM5 Histone Demethylase Activity Links Cellular Transcriptomic Heterogeneity to Therapeutic Resistance.
Hinohara K, Wu H-J, Vigneau S, et al. KDM5 Histone Demethylase Activity Links Cellular Transcriptomic Heterogeneity to Therapeutic Resistance. Cancer Cell. 2018;34(6):939-953.e9. doi:10.1016/j.ccell.2018.10.014.
Intron retention is a source of neoepitopes in cancer.
Smart AC, Margolis CA, Pimentel H, et al. Intron retention is a source of neoepitopes in cancer. Nat Biotechnol. 2018;36(11):1056-1058. doi:10.1038/nbt.4239.
A combination CDK4/6 and IGF1R inhibitor strategy for Ewing sarcoma.
Guenther LM, Dharia NV, Ross L, et al. A combination CDK4/6 and IGF1R inhibitor strategy for Ewing sarcoma. Clin Cancer Res. 2018. doi:10.1158/1078-0432.CCR-18-0372.
Defining the human C2H2 zinc finger degrome targeted by thalidomide analogs through CRBN.
Sievers QL, Petzold G, Bunker RD, et al. Defining the human C2H2 zinc finger degrome targeted by thalidomide analogs through CRBN. Science. 2018;362(6414). doi:10.1126/science.aat0572.
Tumor fraction in cell-free DNA as a biomarker in prostate cancer.
Choudhury AD, Werner L, Francini E, et al. Tumor fraction in cell-free DNA as a biomarker in prostate cancer. JCI Insight. 2018;3(21). doi:10.1172/jci.insight.122109.
A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade.
Jerby-Arnon L, Shah P, Cuoco MS, et al. A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade. Cell. 2018;175(4):984-997.e24. doi:10.1016/j.cell.2018.09.006.
Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma.
Sade-Feldman M, Yizhak K, Bjorgaard SL, et al. Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma. Cell. 2018;175(4):998-1013.e20. doi:10.1016/j.cell.2018.10.038.
is sufficient to confer in vivo sensitivity to thalidomide and its derivatives in mice.
Fink EC, McConkey M, Adams DN, et al. is sufficient to confer in vivo sensitivity to thalidomide and its derivatives in mice. Blood. 2018;132(14):1535-1544. doi:10.1182/blood-2018-05-852798.
Author Correction: Targeting wild-type KRAS-amplified gastroesophageal cancer through combined MEK and SHP2 inhibition.
Wong GS, Zhou J, Bin Liu J, et al. Author Correction: Targeting wild-type KRAS-amplified gastroesophageal cancer through combined MEK and SHP2 inhibition. Nat Med. 2018;24(10):1627. doi:10.1038/s41591-018-0168-6.
Mutational processes shape the landscape of TP53 mutations in human cancer.
Giacomelli AO, Yang X, Lintner RE, et al. Mutational processes shape the landscape of TP53 mutations in human cancer. Nat Genet. 2018;50(10):1381-1387. doi:10.1038/s41588-018-0204-y.
Genome-wide screen identifies cullin-RING ligase machinery required for lenalidomide-dependent CRL4 activity.
Sievers QL, Gasser JA, Cowley GS, Fischer ES, Ebert BL. Genome-wide screen identifies cullin-RING ligase machinery required for lenalidomide-dependent CRL4 activity. Blood. 2018;132(12):1293-1303. doi:10.1182/blood-2018-01-821769.
-truncating mutations confer resistance to chemotherapy and sensitivity to PPM1D inhibition in hematopoietic cells.
Kahn JD, Miller PG, Silver AJ, et al. -truncating mutations confer resistance to chemotherapy and sensitivity to PPM1D inhibition in hematopoietic cells. Blood. 2018;132(11):1095-1105. doi:10.1182/blood-2018-05-850339.
Genomic correlates of response to immune checkpoint blockade in microsatellite-stable solid tumors.
Miao D, Margolis CA, Vokes NI, et al. Genomic correlates of response to immune checkpoint blockade in microsatellite-stable solid tumors. Nat Genet. 2018;50(9):1271-1281. doi:10.1038/s41588-018-0200-2.
Selective gene dependencies in MYCN-amplified neuroblastoma include the core transcriptional regulatory circuitry.
Durbin AD, Zimmerman MW, Dharia NV, et al. Selective gene dependencies in MYCN-amplified neuroblastoma include the core transcriptional regulatory circuitry. Nat Genet. 2018;50(9):1240-1246. doi:10.1038/s41588-018-0191-z.
Widespread Chromosomal Losses and Mitochondrial DNA Alterations as Genetic Drivers in Hürthle Cell Carcinoma.
Gopal RK, Kübler K, Calvo SE, et al. Widespread Chromosomal Losses and Mitochondrial DNA Alterations as Genetic Drivers in Hürthle Cell Carcinoma. Cancer Cell. 2018;34(2):242-255.e5. doi:10.1016/j.ccell.2018.06.013.
Genome-scale CRISPR-Cas9 screen identifies druggable dependencies in wild-type Ewing sarcoma.
Stolte B, Iniguez ABalboni, Dharia NV, et al. Genome-scale CRISPR-Cas9 screen identifies druggable dependencies in wild-type Ewing sarcoma. J Exp Med. 2018;215(8):2137-2155. doi:10.1084/jem.20171066.
Autophosphorylation of the carboxyl-terminal domain is not required for oncogenic transformation by lung-cancer derived EGFR mutants.
Cho J, Kim S, Du J, Meyerson M. Autophosphorylation of the carboxyl-terminal domain is not required for oncogenic transformation by lung-cancer derived EGFR mutants. Int J Cancer. 2018;143(3):679-685. doi:10.1002/ijc.31332.
Genetic and transcriptional evolution alters cancer cell line drug response.
Ben-David U, Siranosian B, Ha G, et al. Genetic and transcriptional evolution alters cancer cell line drug response. Nature. 2018;560(7718):325-330. doi:10.1038/s41586-018-0409-3.
Structural Alterations Driving Castration-Resistant Prostate Cancer Revealed by Linked-Read Genome Sequencing.
Viswanathan SR, Ha G, Hoff AM, et al. Structural Alterations Driving Castration-Resistant Prostate Cancer Revealed by Linked-Read Genome Sequencing. Cell. 2018;174(2):433-447.e19. doi:10.1016/j.cell.2018.05.036.
A Somatically Acquired Enhancer of the Androgen Receptor Is a Noncoding Driver in Advanced Prostate Cancer.
Takeda DY, Spisák S, Seo J-H, et al. A Somatically Acquired Enhancer of the Androgen Receptor Is a Noncoding Driver in Advanced Prostate Cancer. Cell. 2018;174(2):422-432.e13. doi:10.1016/j.cell.2018.05.037.
DeTiN: overcoming tumor-in-normal contamination.
Taylor-Weiner A, Stewart C, Giordano T, et al. DeTiN: overcoming tumor-in-normal contamination. Nat Methods. 2018;15(7):531-534. doi:10.1038/s41592-018-0036-9.
Genome-scale analysis identifies paralog lethality as a vulnerability of chromosome 1p loss in cancer.
Viswanathan SR, Nogueira MF, Buss CG, et al. Genome-scale analysis identifies paralog lethality as a vulnerability of chromosome 1p loss in cancer. Nat Genet. 2018;50(7):937-943. doi:10.1038/s41588-018-0155-3.
GeNets: a unified web platform for network-based genomic analyses.
Li T, Kim A, Rosenbluh J, et al. GeNets: a unified web platform for network-based genomic analyses. Nat Methods. 2018;15(7):543-546. doi:10.1038/s41592-018-0039-6.
Targeting wild-type KRAS-amplified gastroesophageal cancer through combined MEK and SHP2 inhibition.
Wong GS, Zhou J, Bin Liu J, et al. Targeting wild-type KRAS-amplified gastroesophageal cancer through combined MEK and SHP2 inhibition. Nat Med. 2018;24(7):968-977. doi:10.1038/s41591-018-0022-x.
Targetable vulnerabilities in T- and NK-cell lymphomas identified through preclinical models.
Ng SY, Yoshida N, Christie AL, et al. Targetable vulnerabilities in T- and NK-cell lymphomas identified through preclinical models. Nat Commun. 2018;9(1):2024. doi:10.1038/s41467-018-04356-9.
A Convergence-Based Framework for Cancer Drug Resistance.
Konieczkowski DJ, Johannessen CM, Garraway LA. A Convergence-Based Framework for Cancer Drug Resistance. Cancer Cell. 2018;33(5):801-815. doi:10.1016/j.ccell.2018.03.025.
Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes.
Chapuy B, Stewart C, Dunford AJ, et al. Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes. Nat Med. 2018;24(5):679-690. doi:10.1038/s41591-018-0016-8.
The long tail of oncogenic drivers in prostate cancer.
Armenia J, Wankowicz SAM, Liu D, et al. The long tail of oncogenic drivers in prostate cancer. Nat Genet. 2018;50(5):645-651. doi:10.1038/s41588-018-0078-z.
Distinct mutational signatures characterize concurrent loss of polymerase proofreading and mismatch repair.
Haradhvala NJ, Kim J, Maruvka YE, et al. Distinct mutational signatures characterize concurrent loss of polymerase proofreading and mismatch repair. Nat Commun. 2018;9(1):1746. doi:10.1038/s41467-018-04002-4.
Whole-exome sequencing of cell-free DNA and circulating tumor cells in multiple myeloma.
Manier S, Park J, Capelletti M, et al. Whole-exome sequencing of cell-free DNA and circulating tumor cells in multiple myeloma. Nat Commun. 2018;9(1):1691. doi:10.1038/s41467-018-04001-5.
Developmental and oncogenic programs in H3K27M gliomas dissected by single-cell RNA-seq.
Filbin MG, Tirosh I, Hovestadt V, et al. Developmental and oncogenic programs in H3K27M gliomas dissected by single-cell RNA-seq. Science. 2018;360(6386):331-335. doi:10.1126/science.aao4750.
Cancer-Germline Antigen Expression Discriminates Clinical Outcome to CTLA-4 Blockade.
Shukla SA, Bachireddy P, Schilling B, et al. Cancer-Germline Antigen Expression Discriminates Clinical Outcome to CTLA-4 Blockade. Cell. 2018;173(3):624-633.e8. doi:10.1016/j.cell.2018.03.026.
Genomic and Functional Approaches to Understanding Cancer Aneuploidy.
Taylor AM, Shih J, Ha G, et al. Genomic and Functional Approaches to Understanding Cancer Aneuploidy. Cancer Cell. 2018;33(4):676-689.e3. doi:10.1016/j.ccell.2018.03.007.
Convergent Therapeutic Strategies to Overcome the Heterogeneity of Acquired Resistance in Colorectal Cancer.
Hazar-Rethinam M, Kleyman M, G Han C, et al. Convergent Therapeutic Strategies to Overcome the Heterogeneity of Acquired Resistance in Colorectal Cancer. Cancer Discov. 2018;8(4):417-427. doi:10.1158/2159-8290.CD-17-1227.
SvABA: genome-wide detection of structural variants and indels by local assembly.
Wala JA, Bandopadhayay P, Greenwald NF, et al. SvABA: genome-wide detection of structural variants and indels by local assembly. Genome Res. 2018;28(4):581-591. doi:10.1101/gr.221028.117.
Landscapes of childhood tumours.
Bandopadhayay P, Meyerson M. Landscapes of childhood tumours. Nature. 2018;555(7696):316-317. doi:10.1038/d41586-018-01648-4.
Pooled in vivo screens for cancer immunotherapy target discovery.
Lane-Reticker SK, Manguso RT, W Haining N. Pooled in vivo screens for cancer immunotherapy target discovery. Immunotherapy. 2018;10(3):167-170. doi:10.2217/imt-2017-0164.
Inherited DNA-Repair Defects in Colorectal Cancer.
AlDubayan SH, Giannakis M, Moore ND, et al. Inherited DNA-Repair Defects in Colorectal Cancer. Am J Hum Genet. 2018;102(3):401-414. doi:10.1016/j.ajhg.2018.01.018.
Association of Cell-Free DNA Tumor Fraction and Somatic Copy Number Alterations With Survival in Metastatic Triple-Negative Breast Cancer.
Stover DG, Parsons HA, Ha G, et al. Association of Cell-Free DNA Tumor Fraction and Somatic Copy Number Alterations With Survival in Metastatic Triple-Negative Breast Cancer. J Clin Oncol. 2018;36(6):543-553. doi:10.1200/JCO.2017.76.0033.
Genomic correlates of response to immune checkpoint therapies in clear cell renal cell carcinoma.
Miao D, Margolis CA, Gao W, et al. Genomic correlates of response to immune checkpoint therapies in clear cell renal cell carcinoma. Science. 2018;359(6377):801-806. doi:10.1126/science.aan5951.
EWS/FLI Confers Tumor Cell Synthetic Lethality to CDK12 Inhibition in Ewing Sarcoma.
Iniguez ABalboni, Stolte B, Wang EJue, et al. EWS/FLI Confers Tumor Cell Synthetic Lethality to CDK12 Inhibition in Ewing Sarcoma. Cancer Cell. 2018;33(2):202-216.e6. doi:10.1016/j.ccell.2017.12.009.
NetSig: network-based discovery from cancer genomes.
Horn H, Lawrence MS, Chouinard CR, et al. NetSig: network-based discovery from cancer genomes. Nat Methods. 2018;15(1):61-66. doi:10.1038/nmeth.4514.