A. Rouf Banday, Ph.D.

Bladder cancer is the 10^th most common neoplasm worldwide for which treatment options remain limited both for muscle and non-muscle invasive disease. The central goal of our research is to elucidate mechanisms and map therapeutically actionable pathways underlying genetic and molecular alterations in bladder cancer. Specifically, our lab uses functional genomics and bioinformatics approaches to explore molecular mechanisms that drive and support tumor progression, weaken or inhibit tumor-immune surveillance, and impart resistance to therapies. Three areas of research focus are:

1) Mechanisms underlying genetic alterations in bladder cancer

Mechanisms underlying genetic alterations observed in bladder cancer are largely unknown, particularly in the non-coding regions of the genome that can perturb gene expression through gain/loss of enhancer or promoter activity (Fig. A). We seek to a) identify functional non-coding genomic alterations and their target genes; b) explore their tumorigenic effects and interaction with coding driver mutations; and c) evaluate the effects of these alterations in modulating response to cancer therapies. Our lab uses tumor multi-omics data including from clinical trials, and CRISPR-mediated DNA editing, activation, and interference tools for massively parallel genetic manipulations in cells both in vitro and in vivo setting to characterize effects of genomic alterations on malignant cell transformation, tumor subtype speciation, epithelial-to-mesenchymal transition, metastasis, and interaction with therapies. Through these studies we aim to map bladder cancer dependencies that can guide design of novel drug targets and improve the utility of existing therapeutic agents.

2) Role of APOBEC3s in tumor evolution and interactions with cancer therapies

APOBEC3 enzymes, specifically APOBEC3A and APOBEC3B, have been implicated to play a central role in driving tumor evolution by causing somatic mutations commonly referred to as APOBEC-associated mutations/APOBEC-mutational signature. The spectrum of this mutational signature — both occurrence and total burden — vary within tumors of the same class and of different cancer types. These differences can indicate the intensity and duration of exposure to a specific mutagen, likely determined by cell-intrinsic regulatory mechanisms. For example, our studies have shown germline variants identified by GWAS increase expression of APOBEC3B and APOBEC3A/B deletion variant, leading to APOBEC-mediated mutagenesis and increasing cancer risk (Nat Genet 2016). But on the other hand, higher mutation burden in tumors can also improve patient survival potentially by increasing neoantigen repertoire (Fig. B). Additionally, alternative splicing of APOBEC3A and APOBEC3B could restrict APOBEC-mediated mutagenesis (Commun Biol 2021). In all, we have just begun to unravel the role of APOBEC3s in cancer biology, and studies in this field will greatly expand our understanding of tumorigenesis and how to use this information for therapeutic and preventive strategies. Our long-term goals are a) to explore how the biological and environmental triggers influence APOBEC3 enzymes to cause tumor mutations and drive tumor evolution; b) what cell/tissue-specific co-factors regulate these enzymes to prevent or promote their mutational activity; c) how these enzymes modulate immune infiltration and tumor microenvironment and affect the efficacy of cancer therapies; and d) ultimately, whether modulating expression of these enzymes improves or worsens clinical outcomes. My future studies will specifically focus on bladder cancer where APOBEC-induced mutations account for >67% of all single nucleotide somatic variation.

3) Explore and exploit RNA splicing dependencies in tumors as druggable targets for cancer therapy

Tumors exhibit a high level of RNA splicing alterations driven by either direct mutations in splice cis-regulatory elements of genes including in tumor drivers or by mutations in trans-splicing factors SFRS2, SF3B1, U2AF1, RBM10, and ZRSR2. Mutations, including putative drivers, in these genes, are observed mutually exclusively in about ~ 15% of bladder tumors in TCGA (cbioportal.org). Conventionally, studies have focused on the role of aberrant splicing of single genes in cancer. High-throughput functional genomics approaches can be harnessed to systematically explore additive and synergistic effects of aberrant splicing modules in promoting carcinogenesis and resistance to therapies. We aim to explore data from large-scale bulk/single-cell RNA-seq projects, and lab-generated functional screens using CRISPR-mediated genome editing of splicing regulatory elements to identify splicing dependencies in tumors (Fig. C). Specifically, a) identify effects of recurrent intronic and synonymous mutations on splicing of tumor drivers; b) explore the role of mutated and dysregulated splicing factors such as SF3B1 in bladder tumorigenesis; and c) recreate systematically tumor-specific splicing dependencies and evaluate them for therapeutic purposes using nucleic acid-based strategies like antisense or splice switching oligos (SSOs).

Dr. Rouf Banday obtained his bachelor’s degree in science from the University of Kashmir in 2006 before earning his M.Sc. (2008) and Ph.D. (2012) degrees in biochemistry from Aligarh Muslim University in India. He was awarded a Junior Research Fellowship by the Indian Council of Scientific and Industrial Research for his doctoral training. His thesis focused on how alternative promoter usage and mRNA splicing spatiotemporally regulate protein kinase A complex subunit genes. During his Ph.D., Dr. Banday received a European Science Foundation summer school fellowship for training in bioinformatics at the University of Nottingham, United Kingdom (2009). As a postdoctoral fellow at the University of Connecticut, from 2012-2014, he studied gene regulation in mouse retinal development. Dr. Banday then joined the Laboratory of Translational Genomics in the Division of Cancer Epidemiology and Genetics (DCEG) as a postdoctoral fellow in 2014 and was promoted to research fellow in the laboratory of Ludmila Prokunina-Olsson, Ph.D., Senior Investigator, in 2016. He used computational and functional genomics approaches in studying cancer-associated genetic loci and mutational processes focusing on bladder cancer. His studies identified mechanisms that regulate APOBEC3A and APOBEC3B. These deaminase enzymes cause genomic mutations and drive tumor evolution. At NCI, Dr. Banday also studied the role of innate immunity in COVID-19. Specifically, regulation of ACE2, the SARS-CoV-2 receptor, by viruses, leading to the discovery of an interferon-inducible isoform of ACE2 (dACE2). More recently, he studied the role of genetic variation of OAS1 in COVID-19 severity. Dr. Banday ‘s work has been recognized with multiple awards, including American Association for Cancer Research Scholar-in-Training Award, the NCI Director’s Innovation Award (career development), Fellows Award for Research Excellence (FARE), DCEG-FARE, DCEG Intramural Research Award, John Quale Travel Award from the Bladder Cancer Advocacy Network, and Milstein Award from International Cytokine & Interferon Society. Dr. Banday joined Genitourinary Malignancies Branch, CCR NCI, as a Stadtman Investigator in March 2022.