Patient-derived disease models have emerged as critical tools for biological research. Specifically, patient derived xenograft models (PDXs) generally provide higher fidelity representations of the underlying cancer than cell lines. The Jain T-cell lymphoma research team has expertise in generating PDX models and is continually expanding their repository of models representing diverse subtypes of T-cell lymphoma. Cancer cell lines are the most efficient and scalable systems for validating candidates and defining preclinical efficacy. Organoids are the miniature version of in vivo tissues and faithfully recapitulate their architectures. Their co-cultures with immune cells can be leveraged to screen immunotherapeutic compounds for personalized medicine. Through an ongoing collaboration with the Cancer Cell Line Factory at the Broad Institute, we are developing cell lines and organoids for rare types of T-cell lymphoma including hepatosplenic T-cell lymphoma, T-prolymphocytic leukemia, angioimmunoblastic T-cell lymphoma, and enteropathy associated T-cell lymphoma among others.

In aggressive lymphomas, such as diffuse large B-cell lymphoma (DLBCL), MRD could be prognostic of survival outcomes and predictive of emerging resistance to therapies. The assessment of MRD in plasma (where cell-free DNA and exosomes circulate) is easy to use and could be as informative as cellular DNA. In addition, NGS technologies are more useful than the classical "patient allele-specific PCR" because they can identify any possible clone evolving during the treatment or follow-up, even if different from that identified at diagnosis, thus forecasting relapse. We aim to use tissue and cfDNA based NGS approaches to interrogate clonal evolution and relapse in patients with T-cell lymphomas pre- and post-autologous stem cell consolidation.

The molecular mechanisms underlying resistance to chemotherapy in extranodal NK/T-cell lymphoma (ENKTCL) remain poorly understood. To elucidate these mechanisms, we have assembled a heterogeneous cohort of cases with varying responses to chemotherapy from multiple centers worldwide, aiming to dissect the genomic landscape of ENKTCL. To correlate structural variations with somatic mutations, we are conducting whole-genome, exome, and bulk-RNA sequencing on diagnostic formalin-fixed paraffin-embedded (FFPE) tumor tissues, using peripheral blood mononuclear cells (PBMCs) as healthy controls. In parallel, we have initiated studies to analyze the spatial transcriptomic and proteomic landscapes of these cases, employing a custom ENKTCL-specific gene panel with the Xenium high-throughput in situ analyzer from 10x Genomics. We aim to utilize this comprehensive multi-omic approach to gain insights into the unique cell states and pathways contributing to sensitivity or resistance to chemotherapy, determine spatial signatures of tumor and tumor-infiltrating immune cells, and identify biomarkers associated with response and resistance to therapy in patients with ENKTCL. The immunological components within tumors, termed the TME, have long been shown to be strongly related to tumor development, recurrence, and resistance to therapies. This remains poorly understood in T-cell lymphomas. We aim to utilize massively multiplexed single, bulk, and spatial technologies to untangle the complex relationships between tumor cells and TME.

Most NGS-based approaches to advance our knowledge of PTCL (peripheral T cell lymphoma) biology focus primarily on the coding regions of the genome, which represent only 2-3% of the genome. Emerging evidence indicates that non-coding regions of the genome like enhancers (E) and super-enhancers (SE) can be recurrently mutated, contributing to tumorigenesis in lymphomas. The full extent of mutational activity of these non- coding regions, their specific targets, and their consequent functional implications remain ill-defined in the most common PTCL subtypes. By defining these non-coding regions through multi-omics analysis that centralizes the investigation of 3D chromatin organization and post-translational histone modifications in primary tumor samples, cell lines, and patient- derived xenografts, we can fill the critical gap in our ability to appreciate the molecular underpinnings of these lymphomas and, ultimately, precision medicine.