Nidhi Sahni, Ph.D.
Department of Epigenetics and Molecular Carcinogenesis, Division of VP, Research
Present Title & Affiliation
Primary Appointment
Associate Professor, Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX
Dual/Joint/Adjunct Appointment
Regular Member, The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, TX
Faculty Member, Baylor College of Medicine, Houston, TX
Research Interests
Our laboratory is focused on systems biology of human cancer, integrating high-throughput experimental platforms with large-scale computational genomics to address fundamental problems in the modern era of personalized or precision medicine. The lab seeks a systems-level understanding of the underlying genetic and epigenetic aberrations in cancer heterogeneity and immunity. We aim to identify novel biomarkers and drug targets, and to have a major impact on cancer by translating into more effective prognosis and therapy for human cancer.
Education & Training
Degree-Granting Education
| 2010 | University of Iowa, Iowa City, IA, USA, PHD, Biology |
| 2005 | University of Delhi, New Delhi, IND, MS, Biotechnology |
| 2004 | University of Delhi, New Delhi, IND, BS, Microbiology |
Postgraduate Training
| 2010-2016 | Research Fellowship, Harvard Medical School and Dana-Farber Cancer Institute, Boston, MA |
Experience & Service
Academic Appointments
Assistant Professor, Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, 2018 - 2021
Assistant Professor, Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 2018 - 2021
Assistant Professor, Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 2016 - 2018
Postdoctoral Research Fellow, Harvard Medical School and Dana-Farber Cancer Institute, Boston, MA, 2010 - 2016
Honors & Awards
| 2020 | NextGen Star, American Association for Cancer Research |
| 2020 | Liz Tilberis Early Career Award, Ovarian Cancer Research Alliance |
| 2019 | Young Investigator Award, Breast Cancer Alliance |
| 2019 | Career Development Award, Department of Defense, PRCRP |
| 2018 | Sloan Scholar Research Fellowship, Alfred P. Sloan Foundation |
| 2017 | Pinnacle Research Award, AASLD |
| 2016 | CPRIT Scholar Award, Cancer Prevention and Research Institute of Texas |
| 2016 | The University of Texas Systems STARs Award |
| 2013 | Fanconi Anemia Research Fund Award |
| 2012 | NHGRI Center of Excellence in Genomic Science (CEGS) Travel Award |
| 2009 | Iowa Women of Innovation Finalist |
| 2008 | Eukaryotic Cell Outstanding Young Investigator Award |
| 2006 | Developmental Studies Hybridoma Bank Fellowship |
Professional Memberships
Selected Publications
Peer-Reviewed Articles
- Li Y, Burgman B, McGrail DJ, Sun M, Qi D, Shukla SA, Wu E, Capasso A, Lin SY, Wu CJ, Eckhardt SG, Mills GB, Li B#, Sahni N#, Yi SS#. Integrated Genomic Characterization of the Human Immunome in Cancer. Cancer Res 80(21):4854-4867, 2020. e-Pub 2020. PMID: 32855206 (#co-corresponding author).
- Liu XD, Kong W, Peterson CB, McGrail DJ, Hoang A, Zhang X, Lam T, Pilie PG, Zhu H, Beckermann KE, Haake SM, Isgandrova S, Martinez-Moczygemba M, Sahni N, Tannir NM, Lin SY, Rathmell WK, Jonasch E. PBRM1 loss defines a nonimmunogenic tumor phenotype associated with checkpoint inhibitor resistance in renal carcinoma. Nat Commun 11(1):2135, 2020. e-Pub 2020. PMID: 32358509.
- Daniels J, Doukas PG, Escala MEM, Ringbloom KG, Shih DJH, Yang J, Tegtmeyer K, Park J, Thomas JJ, Selli ME, Altunbulakli C, Gowthaman R, Mo SH, Jothishankar B, Pease DR, Pro B, Abdulla FR, Shea C, Sahni N, Gru AA, Pierce BG, Louissaint A, Guitart J, Choi J. Cellular origins and genetic landscape of cutaneous gamma delta T cell lymphomas. Nat Commun 11(1):1806, 2020. e-Pub 2020. PMID: 32286303.
- McGrail DJ#, Garnett J, Yin J, Dai H, Shih DJH, Lam TNA, Li Y, Sun C, Li Y, Schmandt R, Wu JY, Hu L, Liang Y, Peng G, Jonasch E, Menter D, Yates MS, Kopetz S, Lu KH, Broaddus R, Mills GB, Sahni N#, Lin SY#. Proteome instability is a therapeutic vulnerability in mismatch repair-deficient cancer. Cancer Cell 37(3):371-386.e12, 2020. e-Pub 2020. PMID: 32109374 (#co-corresponding author).
- Li Y, McGrail DJ, Xu J, Li J, Liu NN, Sun M, Lin R, Pancsa R, Zhang J, Lee JS, Wang H, Mills GB, Li X#, Yi S#, Sahni N#. MERIT: Systematic analysis and characterization of mutational effect on RNA interactome topology. Hepatology 70(2):532-546, 2019. e-Pub 2019. PMID: 30153342 (#corresponding author).
- Fang Y, McGrail DJ, Sun C, Labrie M, Chen X, Zhang D, Ju Z, Vellano CP, Lu Y, Li Y, Jeong KJ, Ding Z, Liang J, Wang SW, Dai H, Lee S, Sahni N, Mercado-Uribe I, Kim TB, Chen K, Lin SY, Peng G, Westin SN, Liu J, O'Connor MJ, Yap TA, Mills GB. Sequential therapy with PARP and WEE1 inhibitors minimizes toxicity while maintaining efficacy. Cancer Cell 35(6):851-867.e7, 2019. PMID: 31185210.
- Lu J, Xu J, Li J, Pan T, Bai J, Wang L, Jin X, Lin X, Zhang Y#, Li Y#, Sahni N#, Li X#. FACER: Comprehensive molecular and functional characterization of epigenetic chromatin regulators. Nucleic Acids Res 46(19):10019-10033, 2018. PMID: 30102398 (#co-corresponding author).
- Ip CKM, Ng PKS, Jeong KJ, Shao SH, Ju Z, Leonard PG, Hua X, Vellano CP, Woessner R, Sahni N, Scott KL, Mills GB. Neomorphic PDGFRA extracellular domain driver mutations are resistant to PDGFRA targeted therapies. Nat Commun 9(1):4583, 2018. e-Pub 2018. PMID: 30389923.
- McGrail DJ, Federico L, Li Y, Dai H, Lu Y, Mills GB, Yi S#, Lin SY#, Sahni N#. Multi-omics analysis reveals neoantigen-independent immune cell infiltration in copy-number driven cancers. Nat Commun 9(1):1317, 2018. e-Pub 2018. PMID: 29615613 (#corresponding author).
- Ng PK, Li J, Jeong KJ, Shao S, Chen H, Tsang YH, Sengupta S, Wang Z, Bhavana VH, Tran R, Soewito S, Minussi DC, Moreno D, Kong K, Dogruluk T, Lu H, Gao J, Tokheim C, Zhou DC, Johnson AM, Zeng J, Ip CKM, Ju Z, Wester M, Yu S, Li Y, Vellano CP, Schultz N, Karchin R, Ding L, Lu Y, Cheung LWT, Chen K, Shaw KR, Meric-Bernstam F, Scott KL, Yi S#, Sahni N#, Liang H#, Mills GB. Systematic functional annotation of somatic mutations in cancer. Cancer Cell 33(3):450-462.e10, 2018. PMID: 29533785 (#co-corresponding author).
- Li Y, Li L, Wang Z, Pan T, Sahni N, Jin X, Wang G, Li J, Zheng X, Zhang Y, Xu J, Yi S, Li X. LncMAP: Pan-cancer atlas of long noncoding RNA-mediated transcriptional network perturbations. Nucleic Acids Res 46(3):1113-1123, 2018. PMID: 29325141.
- Yi S#, Liu NN, Hu L, Wang H, Sahni N#. Base-resolution stratification of cancer mutations using functional variomics. Nat Protoc 12(11):2323-2341, 2017. e-Pub 2017. PMID: 28981122 (#corresponding author).
- Li Y, Sahni N*, Pancsa R, McGrail DJ, Xu J, Hua X, Coulombe-Huntington J, Ryan M, Tychhon B, Sudhakar D, Hu L, Tyers M, Jiang X, Lin SY, Babu MM#, Yi S#. Revealing the determinants of widespread alternative splicing perturbation in cancer. Cell Rep 21(3):798-812, 2017. PMID: 29045845 (*Lead contact and corresponding author; #co-corresponding author).
- Chung CY, Khurana V, Yi S, Sahni N, Loh KH, Auluck PK, Baru V, Udeshi ND, Freyzon Y, Carr SA, Hill DE, Vidal M, Ting AY, Lindquist S. In situ peroxidase labeling and mass-spectrometry connects alpha-synuclein directly to endocytic trafficking and mRNA metabolism in neurons. Cell Syst 4(2):242-250.e4, 2017. e-Pub 2017. PMID: 28131823.
- Karras GI, Yi S, Sahni N, Fischer M, Xie J, Vidal M, D'Andrea AD, Whitesell L, Lindquist S. HSP90 shapes the consequences of human genetic variation. Cell 168(5):856-866.e12, 2017. e-Pub 2017. PMID: 28215707.
- Sun S, Yang F, Tan G, Costanzo M, Oughtred R, Hirschman J, Theesfeld CL, Bansal P, Sahni N, Yi S, Yu A, Tyagi T, Tie C, Hill DE, Vidal M, Andrews BJ, Boone C, Dolinski K, Roth FP. An extended set of yeast-based functional assays accurately identifies human disease mutations. Genome Res 26(5):670-80, 2016. e-Pub 2016. PMID: 26975778.
- Barrera LA, Vedenko A, Kurland JV, Rogers JM, Gisselbrecht SS, Rossin EJ, Woodard J, Mariani L, Kock KH, Inukai S, Siggers T, Shokri L, Gordân R, Sahni N, Cotsapas C, Hao T, Yi S, Kellis M, Daly MJ, Vidal M, Hill DE, Bulyk ML. Survey of variation in human transcription factors reveals prevalent DNA binding changes. Science 351(6280):1450-4, 2016. e-Pub 2016. PMID: 27013732.
- Yang X, Coulombe-Huntington J, Kang S, Sheynkman GM, Hao T, Richardson A, Sun S, Yang F, Shen YA, Murray RR, Spirohn K, Begg BE, Duran-Frigola M, MacWilliams A, Pevzner SJ, Zhong Q, Trigg SA, Tam S, Ghamsari L, Sahni N, Yi S, Rodriguez MD, Balcha D, Tan G, Costanzo M, Andrews B, Boone C, Zhou XJ, Salehi-Ashtiani K, Charloteaux B, Chen AA, Calderwood MA, Aloy P, Roth FP, Hill DE, Iakoucheva LM, Xia Y, Vidal M. Widespread expansion of protein interaction capabilities by alternative splicing. Cell 164(4):805-17, 2016. PMID: 26871637.
- Sahni N, Yi S, Taipale M, Fuxman Bass JI, Coulombe-Huntington J, Yang F, Peng J, Weile J, Karras GI, Wang Y, Kovács IA, Kamburov A, Krykbaeva I, Lam MH, Tucker G, Khurana V, Sharma A, Liu YY, Yachie N, Zhong Q, Shen Y, Palagi A, San-Miguel A, Fan C, Balcha D, Dricot A, Jordan DM, Walsh JM, Shah AA, Yang X, Stoyanova AK, Leighton A, Calderwood MA, Jacob Y, Cusick ME, Salehi-Ashtiani K, Whitesell LJ, Sunyaev S, Berger B, Barabási AL, Charloteaux B, Hill DE, Hao T, Roth FP, Xia Y, Walhout AJM, Lindquist S, Vidal M. Widespread macromolecular interaction perturbations in human genetic disorders. Cell 161(3):647-60, 2015. PMID: 25910212.
- Fuxman Bass JI, Sahni N, Shrestha S, Garcia-Gonzalez A, Mori A, Bhat N, Yi S, Hill DE, Vidal M, Walhout AJM. Human gene-centered transcription factor networks for enhancers and disease variants. Cell 161(3):661-73, 2015. PMID: 25910213.
- Rolland T*, Tasan M*, Charloteaux B*, Pevzner SJ*, Zhong Q*, Sahni N*, Yi S*, Lemmens I, Fontanillo C, Mosca R, Kamburov A, Ghiassian SD, Yang X, Ghamsari L, Balcha D, Begg BE, Braun P, Brehme M, Broly MP, Carvunis AR, Convery-Zupan D, Corominas R, Coulombe-Huntington J, Dann E, Dreze M, Dricot A, Fan C, Franzosa E, Gebreab F, Gutierrez BJ, Hardy MF, Jin M, Kang S, Kiros R, Lin GN, Luck K, MacWilliams A, Menche J, Murray RR, Palagi A, Poulin MM, Rambout X, Rasla J, Reichert P, Romero V, Ruyssinck E, Sahalie JM, Scholz A, Shah AA, Sharma A, Shen Y, Spirohn K, Tam S, Tejeda AO, Trigg SA, Twizere JC, Vega K, Walsh J, Cusick ME, Xia Y, Barabási AL, Iakoucheva LM, Aloy P, De Las Rivas J, Tavernier J, Calderwood MA, Hill DE, Hao T, Roth FP, Vidal M. A proteome-scale map of the human interactome network. Cell 159(5):1212-1226, 2014. PMID: 25416956 (*co-first author).
- Hill SJ, Rolland T, Adelmant G, Xia X, Owen MS, Dricot A, Zack TI, Sahni N, Jacob Y, Hao T, McKinney KM, Clark AP, Reyon D, Tsai SQ, Joung JK, Beroukhim R, Marto JA, Vidal M, Gaudet S, Hill DE, Livingston DM. Systematic screening reveals a role for BRCA1 in the response to transcription-associated DNA damage. Genes Dev 28(17):1957-75, 2014. PMID: 25184681.
Invited Articles
- Li Y, McGrail DJ, Latysheva N, Yi S#, Babu MM#, Sahni N#. Pathway perturbations in signaling networks: Linking genotype to phenotype. Semin Cell Dev Biol 99:3-11, 2020. e-Pub 2018. PMID: 29738884 (#corresponding author).
- Li Y, McGrail DJ, Xu J, Mills GB, Sahni N#, Yi S#. Gene Regulatory Network Perturbation by Genetic and Epigenetic Variation. Trends Biochem Sci 43(8):576-592, 2018. e-Pub 2018. PMID: 29941230 (#co-corresponding author).
- Yi S#, Lin S, Li Y, Zhao W, Mills GB, Sahni N#. Functional variomics and network perturbation: connecting genotype to phenotype in cancer. Nat Rev Genet 18(7):395-410, 2017. e-Pub 2017. PMID: 28344341 (#corresponding author).
Editorials
- Yi S#, Sahni N#. Regulome networks and mutational landscape in liver cancer: An informative path to precision medicine. Hepatology 66(1):280-282, 2017. PMID: 28422313 (#corresponding author).
- Yi S, Chen S, Zhang L, Sahni N. Signal Transduction and Regulation: Insights into Evolution. Biomed Res Int 2016:8604245, 2016. PMID: 27525280.
Grant & Contract Support
| Title: | Systematic functional variomics of cancer genomes |
| Funding Source: | Cancer Prevention & Research Institute of Texas (CPRIT) |
| Role: | Principal Investigator |
| Title: | Functional analysis and characterization of cancer genomic mutations |
| Funding Source: | Alfred P. Sloan Foundation |
| Role: | Principal Investigator |
| Title: | Role of altered enhancer-mediated signaling in liver carcinogenesis |
| Funding Source: | American Association for The Study of Liver Diseases |
| Role: | Principal Investigator |
| Title: | Novel systems biology approach to decoding actionable targets to overcome resistance in GI cancer monotherapies |
| Funding Source: | Department of Defense (DOD) |
| Role: | Principal Investigator |
| Title: | Systems approach for PARP-based novel combination therapy in ovarian cancer |
| Funding Source: | Ovarian Cancer Research Alliance |
| Role: | Principal Investigator |
| Title: | Integrative bioinformatics and functional characterization of oncogenic driver aberrations in cancer |
| Funding Source: | NIH/NCI |
| Role: | Co-Investigator |