Cancer Program
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. 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. Cancer Discov. 2020. doi:10.1158/2159-8290.CD-20-1165.
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. Nat Genet. 2020;52(12):1373-1383. doi:10.1038/s41588-020-00739-1.
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. Bioinformatics. 2020. doi:10.1093/bioinformatics/btaa980.
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. 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. Clin Cancer Res. 2020;26(22):5974-5989. doi:10.1158/1078-0432.CCR-19-3958.
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. Nat Genet. 2020;52(11):1208-1218. doi:10.1038/s41588-020-00726-6.
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. 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. Sci Transl Med. 2020;12(561). doi:10.1126/scitranslmed.abb7661.
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. 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. Nature. 2020. doi:10.1038/s41586-020-2374-x.
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. Nat Commun. 2020;11(1):2517. doi:10.1038/s41467-020-16399-y.
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. Cancer Discov. 2020. doi:10.1158/2159-8290.CD-19-1390.
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. 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. Genes Chromosomes Cancer. 2020. doi:10.1002/gcc.22850.
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. 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. Ann Oncol. 2020;31(3):387-394. doi:10.1016/j.annonc.2019.11.010.
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. 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. 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. Nat Med. 2020;26(2):181-187. doi:10.1038/s41591-019-0749-z.
Resistance Mechanisms to SYK Inhibition in Acute Myeloid Leukemia. Cancer Discov. 2020;10(2):214-231. doi:10.1158/2159-8290.CD-19-0209.
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. Elife. 2020;9. doi:10.7554/eLife.53003.
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. Nat Commun. 2019;10(1):5817. doi:10.1038/s41467-019-13805-y.
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. 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. 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. ACS Med Chem Lett. 2019;10(11):1537-1542. doi:10.1021/acsmedchemlett.9b00360.
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. Nat Commun. 2019;10(1):4346. doi:10.1038/s41467-019-12361-9.
Mitochondrial Reprogramming Underlies Resistance to BCL-2 Inhibition in Lymphoid Malignancies. Cancer Cell. 2019. doi:10.1016/j.ccell.2019.08.005.
Pooled Genomic Screens Identify Anti-apoptotic Genes as Targetable Mediators of Chemotherapy Resistance in Ovarian Cancer. Mol Cancer Res. 2019. doi:10.1158/1541-7786.MCR-18-1243.
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. 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. 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. Blood. 2019;134(2):160-170. doi:10.1182/blood.2019000789.
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. 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.
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. 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.
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. 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. Nat Commun. 2019;10(1):2400. doi:10.1038/s41467-019-10307-9.
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. Cancer Res. 2019;79(10):2564-2579. doi:10.1158/0008-5472.CAN-18-2674.
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. Cancer Res. 2019;79(9):2352-2366. doi:10.1158/0008-5472.CAN-18-2711.
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. Nat Commun. 2019;10(1):1617. doi:10.1038/s41467-019-09277-9.
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. 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. 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. 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. Elife. 2019;8. doi:10.7554/eLife.44161.
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. Mol Cancer Res. 2019. doi:10.1158/1541-7786.MCR-18-0963.
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. 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. Cancer Cell. 2019. doi:10.1016/j.ccell.2018.12.013.
Identification and characterization of oncogenic SOS1 mutations in lung adenocarcinoma. Mol Cancer Res. 2019. doi:10.1158/1541-7786.MCR-18-0316. .
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. 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. Nat Commun. 2018;9(1):5450. doi:10.1038/s41467-018-07824-4.
Genomic evolution of cancer models: perils and opportunities. Nat Rev Cancer. 2018. doi:10.1038/s41568-018-0095-3. .
Intron retention is a source of neoepitopes in cancer. Nat Biotechnol. 2018;36(11):1056-1058. doi:10.1038/nbt.4239.
Amplification Associates with Aggressive Phenotype but Not Markers of AKT-MTOR Signaling in Endometrial Carcinoma. Clin Cancer Res. 2018. doi:10.1158/1078-0432.CCR-18-0452.
KDM5 Histone Demethylase Activity Links Cellular Transcriptomic Heterogeneity to Therapeutic Resistance. Cancer Cell. 2018. doi:10.1016/j.ccell.2018.10.014.
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. Science. 2018;362(6414). doi:10.1126/science.aat0572.
Tumor fraction in cell-free DNA as a biomarker in prostate cancer. JCI Insight. 2018;3(21). doi:10.1172/jci.insight.122109.
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.
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.
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.
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. Nat Genet. 2018. doi:10.1038/s41588-018-0191-z.
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.
Author Correction: Targeting wild-type KRAS-amplified gastroesophageal cancer through combined MEK and SHP2 inhibition. Nat Med. 2018. doi:10.1038/s41591-018-0168-6.
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. Int J Cancer. 2018;143(3):679-685. doi:10.1002/ijc.31332. .
Genetic and transcriptional evolution alters cancer cell line drug response. Nature. 2018;560(7718):325-330. doi:10.1038/s41586-018-0409-3.
Crbn is sufficient to confer sensitivity to thalidomide and its derivatives in mice. Blood. 2018. doi:10.1182/blood-2018-05-852798.
Genome-wide screen identifies cullin-RING ligase machinery required for lenalidomide-dependent CRL4 activity. Blood. 2018. doi:10.1182/blood-2018-01-821769. .
GATK PathSeq: A customizable computational tool for the discovery and identification of microbial sequences in libraries from eukaryotic hosts. Bioinformatics. 2018. doi:10.1093/bioinformatics/bty501.
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. 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.
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.
PPM1D truncating mutations confer resistance to chemotherapy and sensitivity to PPM1D inhibition in hematopoietic cells. Blood. 2018. doi:10.1182/blood-2018-05-850339.
DeTiN: overcoming tumor-in-normal contamination. Nat Methods. 2018. doi:10.1038/s41592-018-0036-9.
Structural Alterations Driving Castration-Resistant Prostate Cancer Revealed by Linked-Read Genome Sequencing. Cell. 2018. doi:10.1016/j.cell.2018.05.036.
A Somatically Acquired Enhancer of the Androgen Receptor Is a Noncoding Driver in Advanced Prostate Cancer. Cell. 2018. doi:10.1016/j.cell.2018.05.037.
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. 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. Nat Med. 2018;24(5):679-690. doi:10.1038/s41591-018-0016-8.
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. 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. 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. Science. 2018;360(6386):331-335. doi:10.1126/science.aao4750.
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. 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. 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. Genome Res. 2018;28(4):581-591. doi:10.1101/gr.221028.117.
Landscapes of childhood tumours. Nature. 2018;555(7696):316-317. doi:10.1038/d41586-018-01648-4. .
Inherited DNA-Repair Defects in Colorectal Cancer. Am J Hum Genet. 2018;102(3):401-414. doi:10.1016/j.ajhg.2018.01.018.
Pooled in vivo screens for cancer immunotherapy target discovery. Immunotherapy. 2018;10(3):167-170. doi:10.2217/imt-2017-0164. .
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. Science. 2018;359(6377):801-806. doi:10.1126/science.aan5951.
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. Nat Methods. 2018;15(1):61-66. doi:10.1038/nmeth.4514.