Research

Telomeres are nucleotide sequences composed of 5'-TTAGGG-3' tandem repeats that play an important role in maintaining genomic integrity by protecting the ends of chromosomes from DNA damage by means of the telomere-shelterin complex. Replication of telomeres is carried out by telomerase. To achieve replicative immortality, approximately 85% of cancers reactivate TERT expression. The remaining 15% cancers maintain telomere length via a telomerase-independent mechanism termed alternative lengthening of telomeres (ALT). Our previous work (Chudasama et al.2018) and that of others has established ALT as a frequent feature in sarcomas that contributes to tumor progression. Being a cancer cell-specific process, ALT represents an attractive therapeutic target. The interrogation of genes involved in ALT may reveal new biomarkers for targeted treatment of these aggressive tumors. We are employing integrative omics analysis, CRISPR/Cas9 based genome-editing and drug sensitivity screens to investigate ALT occurrence and ALT-associated aberrations in tumors and relevant model systems for functional and mechanistic study of ALT process to nominate compounds that selectively target ALT positive sarcomas.

Epigenetic mechanisms, such as DNA methylation, histone modifications, formation of superenhancers and enhancer hijacking can deregulate gene expression. Epigenetic changes have been shown to drive tumorigenesis and epigenetics-based drugs are being investigated to expand the therapeutic armamentarium against many cancers, including sarcoma. Our previous work (Chudasama et al. 2017) has unveiled the aberrant expression of sarcoma drivers, e.g. Fibroblast growth factor receptor 1 in multiple sarcoma subtypes. We are employing comprehensive epigenetic profiling methods such as ATAC-seq (chromatin accessibility), ACT-seq (histone modifications), EPIC-array (DNA methylation) and 4C-seq (three dimensional chromosomal confirmation) in sarcoma tumors and cell lines. Integrative analysis of these datasets coupled with genome and transcriptomes of sarcomas will reveal candidate aberrations, which will be pursued by in-depth functional investigations to identify mechanisms underlying overexpression of sarcoma drivers. These inquiries will identify entry points for targeted "epi-drugs" that may serve as single or combinatorial treatment options for sarcoma patients.

One third of sarcomas are characterized by recurrent genetic changes known as chromosomal translocations created by breakpoints within two cellular genes that result in generation of a chimeric fusion gene. In majority of cases, fusion genes in sarcoma involve chromatin remodeling factors or transcription factors. Gene fusion results in alteration in pattern of gene expression regulation, which results in – in majority of cases – enhanced proliferation, resistance to apoptosis, increased migration and invasion. As the fusion genes are the oncogenic drivers that are expressed only in tumor cells, they represent attractive molecular targets. However, fusion genes derived from transcription factors do not exhibit enzymatic activity and are hence not amenable to small-molecule inhibition. A promising approach towards that end is small molecules which induce proximity between E3 ubiquitin ligases and oncogenic substrates thereby targeting the substrates for degradation by the ubiquitin proteasome system (UPS). Success of this approach is exemplified by of compounds such as lenalidomide analogs, also known as immunomodulatory drugs (IMiDs) and proteolysis-targeting chimeras (PROTACs). By means of reporter-based functional genomic screens coupled with protein biochemistry and structural biology approaches, we are investigating protein degradation pathways of sarcoma fusion genes to lay groundwork for IMiD and/PROTAC design, pushing the development of new therapeutic for the "undruggable" sarcoma fusion oncoproteins.

Immunotherapy has emerged as a promising modality for the treatment of cancer and is designed to tip the balance from tumor immune evasion to an effective anti-tumor immune response. Major immunotherapeutic approaches are immune checkpoint inhibition, neoantigen-based peptide vaccination as well as adoptive cell transfer (ACT) based on T-cell receptors (TCRs; MHC-restricted) or chimeric antigen receptors (CARs; non-MHC-restricted) that target tumor-associated antigens (TAA) derived from cancer testis antigens (CTA), neoantigens or cancer germline antigens. Studying tumor-intrinsic pathways and immunoregulatory proteins expressed on tumors and their interactions with tumor immune microenvironment can unveil disease mechanisms and inform the choice of effective immunotherapeutic strategy. Our group is combining multi-omics-based immune profiling of tumors with multiplex immunohistochemistry, mass spectrometry and in vitro immune-assays to uncover the immune evasion strategies of tumors and enable systematic discovery of immunotherapeutic targets.