Sanju Sinha's Research Focus
Developing cancer preventive therapies using the power of AI.
At the heart of our research is the mission to develop cancer-preventive therapies using the power of artificial intelligence. Our current focus lies in dissecting the role of aging in cancer susceptibility, a crucial factor often overlooked in conventional research. We employ computational tools to analyze multi-omics data to understand the aging-induced alterations in the tissue microenvironment that increase cancer risk. But we don't stop at understanding these changes. We apply this knowledge in designing preventive therapy candidates that specifically target these alterations. Drawing on my experience in machine learning, drug discovery, and precision oncology, our lab is on a quest to reimagine the drug discovery pipeline.
As we aim to push the boundaries of cancer prevention research, we are hiring individuals eager to contribute to this mission at multiple levels including postdoctoral researchers, experienced computational biologists, and, Ph.D. students.
Sanju Sinha's Research Report
My key contributions to the field of computational oncology during my Ph.D. and postdoctoral tenure are outlined below:
DeepTarget: A Computational Tool for Decoding the Mechanism of Action for Cancer Drugs DeepTarget, our innovative computational tool, integrates data from genetic and drug screens to intricately understand the mechanism of action of cancer drugs. It identifies both primary and secondary drug targets, paving the way for a comprehensive understanding of drug function, its optimal indications, and clinical potential.
Revealing the Potential Cancer Risks associated with Genetic Editing Through computational analyses of vast genetic screens, we shed light on the inherent selection potential of specific cancer gene mutations associated with CRISPR-Knockout editing. This work has significantly enhanced our understanding of the risks associated with gene editing.
First Single-cell based Precision Oncology Framework: A Proof-of-concept Our innovative approach to precision oncology utilizes single-cell transcriptomics to predict patient treatment responses and detect resistance. We demonstrated its efficacy using patient-derived primary cells and three recent single-cell clinical cohorts, providing a powerful tool for the next generation of precision oncology approaches.
Why High Tumor Mutation Burden Biomarker of Immunotherapy is only effective for Certain Cancer Types? We unveiled the microenvironment context that can determine if the high-tumor mutation burden (TMB) biomarker will be effective in a certain cancer type - High M1 Macrophage levels and Low Resting Dendritic Cells. Based on this, we also predicted the rare tumor types with High-TMB where immunotherapy is most likely to be successful.
Uncovering Therapeutic Prospects for African Americans: A Step Forward in Inclusive Cancer Research Our work revealed distinct biological differences in tumors across African American and European American patients. Most notably, we identified a higher prevalence of homologous recombination deficiency in African American patients, pointing towards promising, personalized treatment options.
Sanju Sinha's Bio
Dr. Sanju Sinha earned his Bachelor of Technology in Bioengineering at the Indian Institute of Technology in Guwahati, India. He recently completed his postdoctoral research and Ph.D. in computational biology at the National Cancer Institute (NCI) with Dr. Eytan Ruppin with a co-mentorship of Dr. Brid Ryan during his Ph.D. His Ph.D. was earned in a joint University of Maryland and NCI program.
"At the core of my work is the desire to make a lasting impact on patient's lives, offering patients not just better treatment, but an opportunity to avoid the disease altogether. Sanford Burnham Prebys is renowned for its work in understanding aging and developing new drugs—two areas that are key to my research. This makes it the perfect place for what I'm hoping to achieve."
Education
2021: Ph.D., Computational Biology, University of Maryland and National Cancer Institute
2016: B.Tech., Bioengineering, Indian Institute of Technology, Guwahat
Honors and Recognition
2023: Top Five Outstanding NCI Postdoctoral Fellow
2023: Transition to Industry Fellowship
2021: Emerging Leaders of Computational Oncology by MSKCC.
2020: NCI Outstanding Ph.D. award
2020: NCI CCR milestone
2019: NCI Fellows Award for Research Excellence
Publications
Higher prevalence of homologous recombination deficiency in tumors from African Americans versus European Americans.
Sinha S, Mitchell KA, Zingone A, Bowman E, Sinha N, Schäffer AA, Lee JS, Ruppin E, Ryan BM
Nat Cancer 2020 Jan ;1(1):112-121
A systematic genome-wide mapping of oncogenic mutation selection during CRISPR-Cas9 genome editing.
Sinha S, Barbosa K, Cheng K, Leiserson MDM, Jain P, Deshpande A, Wilson DM 3rd, Ryan BM, Luo J, Ronai ZA, Lee JS, Deshpande AJ, Ruppin E
Nat Commun 2021 Nov 11 ;12(1):6512
Big data in basic and translational cancer research.
Jiang P, Sinha S, Aldape K, Hannenhalli S, Sahinalp C, Ruppin E
Nat Rev Cancer 2022 Nov ;22(11):625-639
The GPCR-Gα(s)-PKA signaling axis promotes T cell dysfunction and cancer immunotherapy failure.
Wu VH, Yung BS, Faraji F, Saddawi-Konefka R, Wang Z, Wenzel AT, Song MJ, Pagadala MS, Clubb LM, Chiou J, Sinha S, Matic M, Raimondi F, Hoang TS, Berdeaux R, Vignali DAA, Iglesias-Bartolome R, Carter H, Ruppin E, Mesirov JP, Gutkind JS
Nat Immunol 2023 Jun 12 ;
Clinically oriented prediction of patient response to targeted and immunotherapies from the tumor transcriptome.
Dinstag G, Shulman ED, Elis E, Ben-Zvi DS, Tirosh O, Maimon E, Meilijson I, Elalouf E, Temkin B, Vitkovsky P, Schiff E, Hoang DT, Sinha S, Nair NU, Lee JS, Schäffer AA, Ronai Z, Juric D, Apolo AB, Dahut WL, Lipkowitz S, Berger R, Kurzrock R, Papanicolau-Sengos A, Karzai F, Gilbert MR, Aldape K, Rajagopal PS, Beker T, Ruppin E, Aharonov R
Med 2023 Jan 13 ;4(1):15-30.e8
Sex Biases in Cancer and Autoimmune Disease Incidence Are Strongly Positively Correlated with Mitochondrial Gene Expression across Human Tissues.
Crawford DR, Sinha S, Nair NU, Ryan BM, Barnholtz-Sloan JS, Mount SM, Erez A, Aldape K, Castle PE, Rajagopal PS, Day CP, Schäffer AA, Ruppin E
Cancers (Basel) 2022 Nov 29 ;14(23)
Dysregulation of HNF1B/Clusterin axis enhances disease progression in a highly aggressive subset of pancreatic cancer patients.
Yang S, Tang W, Azizian A, Gaedcke J, Ströbel P, Wang L, Cawley H, Ohara Y, Valenzuela P, Zhang L, Lal T, Sinha S, Rupin E, Hanna N, Ghadimi BM, Hussain SP
Carcinogenesis 2022 Dec 31 ;43(12):1198-1210
Big data in basic and translational cancer research.
Jiang P, Sinha S, Aldape K, Hannenhalli S, Sahinalp C, Ruppin E
Nat Rev Cancer 2022 Nov ;22(11):625-639
MCP-1/CCR2 axis inhibition sensitizes the brain microenvironment against melanoma brain metastasis progression.
Pozzi S, Scomparin A, Ben-Shushan D, Yeini E, Ofek P, Nahmad AD, Soffer S, Ionescu A, Ruggiero A, Barzel A, Brem H, Hyde TM, Barshack I, Sinha S, Ruppin E, Weiss T, Madi A, Perlson E, Slutsky I, Florindo HF, Satchi-Fainaro R
JCI Insight 2022 Sep 8 ;7(17)
