Grant Number:	2R01CA218668-06A1 Interpret this number
Primary Investigator:	Khurana, Ekta
Organization:	Weill Medical Coll Of Cornell Univ
Project Title:	Computational and Experimental Methods for Scalable Identification of Oncogenic Non-Coding Regions
Fiscal Year:	2024

Project Abstract In this project, we will identify context-specific enhancers, whose activity is essential for either the growth of primary tumors or for evolution of treatment-resistance in metastatic tumors by modulation of target gene expression. We will identify open chromatin sites in metastatic treatment-resistant breast tumors using whole-genome sequencing of cell-free DNA. Cell-free (cfDNA) enzymatic in plasma predominantly originates from nucleosome-protected parts of DNA after processing. We will develop innovative computational methods that will analyze the nucleosomal signal obtained from whole-genome sequencing of cfDNA from plasma of metastatic cancer patients. We will develop scalable methods to create catalogues of `oncogenic' enhancers that are essential for tumor growth, which may or may not be due to DNA sequence variants at these regions. We will decipher the impact of subtype specific enhancer perturbation on tumor initiation (using CRIPSRa) and continued growth (using CRISPRi) in primary breast cancers. We will test the impact of repressing ~15,000 accessible sites in breast cancer on tumor growth in pooled CRISPR screens in multiple cell lines for each major breast cancer subtype. Importantly, we will also study the impact of activation of the same enhancers on tumor initiation in normal (and malignant) breast cell lines, and we will identify `tumor-suppressive' enhancers that when silenced drive tumor growth. We will also identify oncogenic mutations by integration of 4,427 breast cancer whole-genomes and CRISPR base editing screens. We will focus on specific mutations at cis-regulatory elements, CREs (enhancers, promoters and untranslated regions). For the top 5000 putative noncoding drivers, we will first insert precise mutations via base editing and then, for the top 500 with the most dramatic impact on growth, we will use single-cell sequencing coupled with base editing to decipher their impact on gene expression in cis and in trans. We will also examine the interaction between the top noncoding drivers and aromatase inhibitors, which is a therapy prescribed in many breast cancers.




Discovery of therapeutic targets in cancer using chromatin accessibility and transcriptomic data.
Authors: Forbes A.N. , Xu D. , Cohen S. , Pancholi P. , Khurana E. .
Source: Cell Systems, 2024-09-18 00:00:00.0; 15(9), p. 824-837.e6.
EPub date: 2024-09-04 00:00:00.0.
PMID: 39236711
Related Citations

Genome-wide CRISPR screens in spheroid culture reveal that the tumor suppressor LKB1 inhibits growth via the PIKFYVE lipid kinase.
Authors: Ferrarone J.R. , Thomas J. , Unni A.M. , Zheng Y. , Nagiec M.J. , Gardner E.E. , Mashadova O. , Li K. , Koundouros N. , Montalbano A. , et al. .
Source: Proceedings Of The National Academy Of Sciences Of The United States Of America, 2024-05-21 00:00:00.0; 121(21), p. e2403685121.
EPub date: 2024-05-14 00:00:00.0.
PMID: 38743625
Related Citations

Next-generation forward genetic screens: uniting high-throughput perturbations with single-cell analysis.
Authors: Morris J.A. , Sun J.S. , Sanjana N.E. .
Source: Trends In Genetics : Tig, 2024 Feb; 40(2), p. 118-133.
EPub date: 2023-11-20 00:00:00.0.
PMID: 37989654
Related Citations

Essential transcription factors for induced neuron differentiation.
Authors: Lu C. , Garipler G. , Dai C. , Roush T. , Salome-Correa J. , Martin A. , Liscovitch-Brauer N. , Mazzoni E.O. , Sanjana N.E. .
Source: Nature Communications, 2023-12-15 00:00:00.0; 14(1), p. 8362.
EPub date: 2023-12-15 00:00:00.0.
PMID: 38102126
Related Citations

Recapitulation of patient-specific 3D chromatin conformation using machine learning.
Authors: Xu D. , Forbes A.N. , Cohen S. , Palladino A. , Karadimitriou T. , Khurana E. .
Source: Cell Reports Methods, 2023-09-25 00:00:00.0; 3(9), p. 100578.
EPub date: 2023-09-05 00:00:00.0.
PMID: 37673071
Related Citations

Discovery of target genes and pathways at GWAS loci by pooled single-cell CRISPR screens.
Authors: Morris J.A. , Caragine C. , Daniloski Z. , Domingo J. , Barry T. , Lu L. , Davis K. , Ziosi M. , Glinos D.A. , Hao S. , et al. .
Source: Science (new York, N.y.), 2023-05-19 00:00:00.0; 380(6646), p. eadh7699.
EPub date: 2023-05-19 00:00:00.0.
PMID: 37141313
Related Citations

Efficient combinatorial targeting of RNA transcripts in single cells with Cas13 RNA Perturb-seq.
Authors: Wessels H.H. , Méndez-Mancilla A. , Hao Y. , Papalexi E. , Mauck W.M. , Lu L. , Morris J.A. , Mimitou E.P. , Smibert P. , Sanjana N.E. , et al. .
Source: Nature Methods, 2023 Jan; 20(1), p. 86-94.
EPub date: 2022-12-22 00:00:00.0.
PMID: 36550277
Related Citations

Modeling tissue-specific breakpoint proximity of structural variations from whole-genomes to identify cancer drivers.
Authors: Martinez-Fundichely A. , Dixon A. , Khurana E. .
Source: Nature Communications, 2022-09-26 00:00:00.0; 13(1), p. 5640.
EPub date: 2022-09-26 00:00:00.0.
PMID: 36163358
Related Citations

Cancer genes disfavoring T cell immunity identified via integrated systems approach.
Authors: Kishton R.J. , Patel S.J. , Decker A.E. , Vodnala S.K. , Cam M. , Yamamoto T.N. , Patel Y. , Sukumar M. , Yu Z. , Ji M. , et al. .
Source: Cell Reports, 2022-08-02 00:00:00.0; 40(5), p. 111153.
PMID: 35926468
Related Citations

Recurrent somatic mutations as predictors of immunotherapy response.
Authors: Gajic Z.Z. , Deshpande A. , Legut M. , Imieliński M. , Sanjana N.E. .
Source: Nature Communications, 2022-07-08 00:00:00.0; 13(1), p. 3938.
EPub date: 2022-07-08 00:00:00.0.
PMID: 35803911
Related Citations

Chromatin profiles classify castration-resistant prostate cancers suggesting therapeutic targets.
Authors: Tang F. , Xu D. , Wang S. , Wong C.K. , Martinez-Fundichely A. , Lee C.J. , Cohen S. , Park J. , Hill C.E. , Eng K. , et al. .
Source: Science (new York, N.y.), 2022-05-27 00:00:00.0; 376(6596), p. eabe1505.
EPub date: 2022-05-27 00:00:00.0.
PMID: 35617398
Related Citations

The BTB transcription factors ZBTB11 and ZFP131 maintain pluripotency by repressing pro-differentiation genes.
Authors: Garipler G. , Lu C. , Morrissey A. , Lopez-Zepeda L.S. , Pei Y. , Vidal S.E. , Zen Petisco Fiore A.P. , Aydin B. , Stadtfeld M. , Ohler U. , et al. .
Source: Cell Reports, 2022-03-15 00:00:00.0; 38(11), p. 110524.
PMID: 35294876
Related Citations

A genome-scale screen for synthetic drivers of T cell proliferation.
Authors: Legut M. , Gajic Z. , Guarino M. , Daniloski Z. , Rahman J.A. , Xue X. , Lu C. , Lu L. , Mimitou E.P. , Hao S. , et al. .
Source: Nature, 2022 03; 603(7902), p. 728-735.
EPub date: 2022-03-16 00:00:00.0.
PMID: 35296855
Related Citations

Transcriptome-wide Cas13 guide RNA design for model organisms and viral RNA pathogens.
Authors: Guo X. , Rahman J.A. , Wessels H.H. , Méndez-Mancilla A. , Haro D. , Chen X. , Sanjana N.E. .
Source: Cell Genomics, 2021-10-13 00:00:00.0; 1(1), .
EPub date: 2021-09-03 00:00:00.0.
PMID: 35664829
Related Citations

Integrative approach identifies SLC6A20 and CXCR6 as putative causal genes for the COVID-19 GWAS signal in the 3p21.31 locus.
Authors: Kasela S. , Daniloski Z. , Bollepalli S. , Jordan T.X. , tenOever B.R. , Sanjana N.E. , Lappalainen T. .
Source: Genome Biology, 2021-08-23 00:00:00.0; 22(1), p. 242.
EPub date: 2021-08-23 00:00:00.0.
PMID: 34425859
Related Citations

Chemically modified guide RNAs enhance CRISPR-Cas13 knockdown in human cells.
Authors: Méndez-Mancilla A. , Wessels H.H. , Legut M. , Kadina A. , Mabuchi M. , Walker J. , Robb G.B. , Holden K. , Sanjana N.E. .
Source: Cell Chemical Biology, 2021-07-27 00:00:00.0; , .
EPub date: 2021-07-27 00:00:00.0.
PMID: 34343484
Related Citations

Tracking cell lineages to improve research reproducibility.
Authors: Zaaijer S. , Groen S.C. , Sanjana N.E. .
Source: Nature Biotechnology, 2021 06; 39(6), p. 666-670.
PMID: 34012093
Related Citations

Profiling the genetic determinants of chromatin accessibility with scalable single-cell CRISPR screens.
Authors: Liscovitch-Brauer N. , Montalbano A. , Deng J. , Méndez-Mancilla A. , Wessels H.H. , Moss N.G. , Kung C.Y. , Sookdeo A. , Guo X. , Geller E. , et al. .
Source: Nature Biotechnology, 2021-04-29 00:00:00.0; , .
EPub date: 2021-04-29 00:00:00.0.
PMID: 33927415
Related Citations

Integrative approach identifies SLC6A20 and CXCR6 as putative causal genes for the COVID-19 GWAS signal in the 3p21.31 locus.
Authors: Kasela S. , Daniloski Z. , Jordan T.X. , tenOever B.R. , Sanjana N.E. , Lappalainen T. .
Source: Medrxiv : The Preprint Server For Health Sciences, 2021-04-13 00:00:00.0; , .
EPub date: 2021-04-13 00:00:00.0.
PMID: 33880488
Related Citations

Pluripotent stem cell-derived models of neurological diseases reveal early transcriptional heterogeneity.
Authors: Sorek M. , Oweis W. , Nissim-Rafinia M. , Maman M. , Simon S. , Hession C.C. , Adiconis X. , Simmons S.K. , Sanjana N.E. , Shi X. , et al. .
Source: Genome Biology, 2021-03-04 00:00:00.0; 22(1), p. 73.
EPub date: 2021-03-04 00:00:00.0.
PMID: 33663567
Related Citations

The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types.
Authors: Daniloski Z. , Jordan T.X. , Ilmain J.K. , Guo X. , Bhabha G. , tenOever B.R. , Sanjana N.E. .
Source: Elife, 2021-02-11 00:00:00.0; 10, .
EPub date: 2021-02-11 00:00:00.0.
PMID: 33570490
Related Citations

Whole-genome characterization of lung adenocarcinomas lacking the RTK/RAS/RAF pathway.
Authors: Carrot-Zhang J. , Yao X. , Devarakonda S. , Deshpande A. , Damrauer J.S. , Silva T.C. , Wong C.K. , Choi H.Y. , Felau I. , Robertson A.G. , et al. .
Source: Cell Reports, 2021-02-02 00:00:00.0; 34(5), p. 108707.
PMID: 33535033
Related Citations

CNCDatabase: a database of non-coding cancer drivers.
Authors: Liu E.M. , Martinez-Fundichely A. , Bollapragada R. , Spiewack M. , Khurana E. .
Source: Nucleic Acids Research, 2021-01-08 00:00:00.0; 49(D1), p. D1094-D1101.
PMID: 33095860
Related Citations

Identification of Required Host Factors for SARS-CoV-2 Infection in Human Cells.
Authors: Daniloski Z. , Jordan T.X. , Wessels H.H. , Hoagland D.A. , Kasela S. , Legut M. , Maniatis S. , Mimitou E.P. , Lu L. , Geller E. , et al. .
Source: Cell, 2021-01-07 00:00:00.0; 184(1), p. 92-105.e16.
EPub date: 2020-10-24 00:00:00.0.
PMID: 33147445
Related Citations

Massively parallel Cas13 screens reveal principles for guide RNA design.
Authors: Wessels H.H. , Méndez-Mancilla A. , Guo X. , Legut M. , Daniloski Z. , Sanjana N.E. .
Source: Nature Biotechnology, 2020 06; 38(6), p. 722-727.
EPub date: 2020-03-16 00:00:00.0.
PMID: 32518401
Related Citations

Loss-of-function tolerance of enhancers in the human genome.
Authors: Xu D. , Gokcumen O. , Khurana E. .
Source: Plos Genetics, 2020 Apr; 16(4), p. e1008663.
EPub date: 2020-04-03 00:00:00.0.
PMID: 32243438
Related Citations

DeepMILO: a deep learning approach to predict the impact of non-coding sequence variants on 3D chromatin structure.
Authors: Trieu T. , Martinez-Fundichely A. , Khurana E. .
Source: Genome Biology, 2020-03-26 00:00:00.0; 21(1), p. 79.
EPub date: 2020-03-26 00:00:00.0.
PMID: 32216817
Related Citations

Applying genome-wide CRISPR-Cas9 screens for therapeutic discovery in facioscapulohumeral muscular dystrophy.
Authors: Lek A. , Zhang Y. , Woodman K.G. , Huang S. , DeSimone A.M. , Cohen J. , Ho V. , Conner J. , Mead L. , Kodani A. , et al. .
Source: Science Translational Medicine, 2020-03-25 00:00:00.0; 12(536), .
PMID: 32213627
Related Citations

Passenger Mutations in More Than 2,500 Cancer Genomes: Overall Molecular Functional Impact and Consequences.
Authors: Kumar S. , Warrell J. , Li S. , McGillivray P.D. , Meyerson W. , Salichos L. , Harmanci A. , Martinez-Fundichely A. , Chan C.W.Y. , Nielsen M.M. , et al. .
Source: Cell, 2020-03-05 00:00:00.0; 180(5), p. 915-927.e16.
EPub date: 2020-02-20 00:00:00.0.
PMID: 32084333
Related Citations

High-Throughput Screens of PAM-Flexible Cas9 Variants for Gene Knockout and Transcriptional Modulation.
Authors: Legut M. , Daniloski Z. , Xue X. , McKenzie D. , Guo X. , Wessels H.H. , Sanjana N.E. .
Source: Cell Reports, 2020-03-03 00:00:00.0; 30(9), p. 2859-2868.e5.
PMID: 32130891
Related Citations

Pathway and network analysis of more than 2500 whole cancer genomes.
Authors: Reyna M.A. , Haan D. , Paczkowska M. , Verbeke L.P.C. , Vazquez M. , Kahraman A. , Pulido-Tamayo S. , Barenboim J. , Wadi L. , Dhingra P. , et al. .
Source: Nature Communications, 2020-02-05 00:00:00.0; 11(1), p. 729.
EPub date: 2020-02-05 00:00:00.0.
PMID: 32024854
Related Citations

Pan-cancer analysis of whole genomes.
Authors: ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium .
Source: Nature, 2020 02; 578(7793), p. 82-93.
EPub date: 2020-02-05 00:00:00.0.
PMID: 32025007
Related Citations

Patterns of somatic structural variation in human cancer genomes.
Authors: Li Y. , Roberts N.D. , Wala J.A. , Shapira O. , Schumacher S.E. , Kumar K. , Khurana E. , Waszak S. , Korbel J.O. , Haber J.E. , et al. .
Source: Nature, 2020 02; 578(7793), p. 112-121.
EPub date: 2020-02-05 00:00:00.0.
PMID: 32025012
Related Citations

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes.
Authors: Rheinbay E. , Nielsen M.M. , Abascal F. , Wala J.A. , Shapira O. , Tiao G. , Hornshøj H. , Hess J.M. , Juul R.I. , Lin Z. , et al. .
Source: Nature, 2020 02; 578(7793), p. 102-111.
EPub date: 2020-02-05 00:00:00.0.
PMID: 32025015
Related Citations

Generation of a knock-in MAP2-tdTomato reporter human embryonic stem cell line with inducible expression of NEUROG2/1 (NYGCe001-A).
Authors: Lu C. , Sanjana N.E. .
Source: Stem Cell Research, 2019 12; 41, p. 101643.
EPub date: 2019-11-01 00:00:00.0.
PMID: 31707212
Related Citations

Identification of Cancer Drivers at CTCF Insulators in 1,962 Whole Genomes.
Authors: Liu E.M. , Martinez-Fundichely A. , Diaz B.J. , Aronson B. , Cuykendall T. , MacKay M. , Dhingra P. , Wong E.W.P. , Chi P. , Apostolou E. , et al. .
Source: Cell Systems, 2019-05-22 00:00:00.0; 8(5), p. 446-455.e8.
EPub date: 2019-05-08 00:00:00.0.
PMID: 31078526
Related Citations