Biology subjects

Kotecha, R. S.

Publications and source records attributed to Kotecha, R. S..

4 recordsLinked to original sources

bioRxiv2025

Profiling histone post-translational modifications to identify signatures of epigenetic drug response in T-cell acute lymphoblastic leukemia

Epigenetic modifications are dynamic and reversible, making them attractive targets for therapeutic intervention in cancer. Although several epigenetic drugs (epidrugs) have been clinically approved, their application in T-cell acute lymphoblastic leukemia (T-ALL) remains limited, and predictive biomarkers of response are lacking. Here, we present a mass spectrometry (MS)-based pharmacoepigenetic approach to profile histone post-translational modifications (hPTMs) to identify signatures associated with epidrug sensitivity in T-ALL. Baseline hPTM landscapes were previously established by our group for 21 T-ALL cell lines using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Here, we treated these cell lines with a panel of nine epidrugs including anthracyclines, histone deacetylase inhibitors, and DNA methyltransferase inhibitors. Correlation of cell viability data with hPTM levels revealed distinct hPTM signatures linked to sensitivity for each drug class. These signatures were subsequently evaluated in T-ALL patient-derived xenograft (PDX) models. However, we our analysis revealed substantial discepancies in hPTM sensitivity signatures compared to those observed in vitro. Co-variation network analysis highlighted divergence in hPTM-hPTM correlation between the two models, underscoring limitations of cell lines for modeling dynamic epigenetic regulation in vivo. Our findings establish a framework for MS-based hPTM profiling in T-ALL and emphasize the importance of model selection in developing predictive epigenetic biomarkers. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=134 SRC="FIGDIR/small/673463v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@1b15092org.highwire.dtl.DTLVardef@20bed5org.highwire.dtl.DTLVardef@1d0a687org.highwire.dtl.DTLVardef@1652999_HPS_FORMAT_FIGEXP M_FIG C_FIG Global hPTM profiling of 21 T-ALL cell lines was performed using LC-MS/MS, as previously published by Provez et al. In parallel, the 21 cell lines were treated with a dilution series of nine epidrugs, categorized into three distinct classes, to determine their IC50 values. Finally, Spearman correlation analysis was performed to assess the relationship between hPTM levels and drug sensitivity. Figure created with Biorender.com.

cancer biology↗

bioRxiv2025

Age-dependent tumor-immune interactions underlie immunotherapy response in pediatric cancer

Pediatric cancers originate in rapidly growing tissues within the context of a developing host. However, the interactions between cancer cells and the developing immune system are incompletely understood. Here, we established a suite of pediatric syngeneic mouse cancer models across diverse anatomical sites and compared their tumor immune microenvironment with that in adult mice. Tumors in pediatric mice exhibited significantly accelerated growth and diminished leukocyte infiltration, dominated by naive-like PD-1low/CD8+ T cells, and proliferative MHCIIlow/PD-L1hi/CD86low macrophages. Tumor-infiltrating leukocytes in pediatric mice were enriched for MYC targets, which was also observed in pediatric patient samples. Furthermore, pediatric mice displayed poor responses to anti-PD-1/PD-L1 or bispecific T cell engager antibodies, which could be reversed by inducing a proinflammatory microenvironment via MYC inhibition or inducing macrophage polarization to an MHCIIhi phenotype. These findings underscore the significant influence of young age on cancer immune responses and reveal potential new therapeutic opportunities for pediatric cancers. HIGHLIGHTSO_LIAllograft tumors exhibit markedly accelerated growth in pediatric hosts compared to adults. C_LIO_LITumors growing in pediatric mice have reduced leukocyte infiltration, dominated by naive-like PD-1low/CD8+ T cells, and MHCIIlow/M2-like macrophages. C_LIO_LIEnrichment of MYC target genes is observed in pediatric mouse tumors and confirmed in primary patient tumor samples. C_LIO_LIPediatric mice display reduced response to anti-PD-1/PD-L1 and BiTE immunotherapy, which can be reversed by remodeling the TIME, using either MYC inhibition or macrophage polarization. C_LI

cancer biology↗

bioRxiv2025

PRAME Epitopes are T-Cell Immunovulnerabilities in BRD4::NUTM1 Initiated NUT Carcinoma

BackgroundNUT carcinoma is a rare but highly lethal solid tumor without an effective standard of care. NUT carcinoma is caused by bromodomain-containing NUTM1 fusion oncogenes, most commonly BRD4::NUTM1. BRD4::NUTM1 recruits p300 to acetylate H3K27 forming expansive stretches of hyperacetylated chromatin called "megadomains" with the overexpression of corresponding oncogenes, including MYC. We hypothesized that transcriptional dysregulation caused by BRD4::NUTM1 would lead to the generation of cancer-specific antigens that could be therapeutically actionable. MethodsWe integrated genomics, computational antigen prediction software, targeted immunopeptidomics using single- and double-labeled peptide standards, and gain/loss-of-function genetic experiments on a panel of cell lines (N=5), a patient derived xenograft, a tissue microarray (N=77), and patient samples from the Tempus AI Sequencing Database harboring evidence of NUTM1 fusions (N=165). We created an PRAME425 T-cell receptor x SP34 CD3 bispecific molecule modeled after brenetafusp, an PRAME425 T-cell receptor bispecific T-cell engager, as well as PRAME425 TCR T-cells based on anzutresgene autoleucel and we applied these products to NUT carcinoma cells in vitro. ResultsWe identified PRAME as the most commonly expressed cancer/testis antigen in patient samples harboring the three canonical NUT carcinoma fusions (BRD4::NUTM1, BRD3::NUTM1, and NSD3::NUTM1). Additionally, 56% (43/77) of NUT carcinoma tissue microarray samples stained positive for PRAME. BRD4::NUTM1 expression in HEK 293T cells enhanced PRAME levels and BRD4::NUTM1 knockout in NUT carcinoma cells reduced PRAME levels. Immunopeptidomics detected more PRAME-derived HLA ligands (N=9) than all other cancer/testis antigens combined (N=5). Targeted mass spectrometry detected the HLA-A*02:01/SLLQHLIGL (PRAME425) epitope in 100% (4/4) of HLA-A*02+, PRAME+ NUT carcinoma samples at higher levels (>0.01 fM) than HLA-A*02:01/RLDQLLRHV (PRAME312) or HLA-A*02:01/YLHARLREL (PRAME462). The PRAME425 T-cell receptor x SP34 CD3 bispecific molecule and PRAME425 TCR T-cells each exhibited potent, T-cell mediated cytotoxicity against PRAME+ NUT carcinoma cells. ConclusionsPRAME is highly and frequently expressed in NUT carcinoma and the most common oncoprotein causing NUT carcinoma, BRD4::NUTM1, contributes to these high PRAME levels. PRAME epitopes presented by HLA Class I are a previously unrecognized therapeutic vulnerability for NUT carcinoma that warrant clinical trials testing PRAME targeted immunotherapies in this neglected patient population. What is already known on this topicNUT carcinoma is a devastating malignancy that is recalcitrant to cytotoxic chemotherapy, T-cell checkpoint blockade, and targeted therapies in the form of bromodomain inhibitors. What this study addsNUT carcinoma tumors are high in the cancer/testis gene PRAME. The oncogene most commonly causing NUT carcinoma, BRD4::NUTM1, contributes to these high levels. NUT carcinoma cells present PRAME epitopes on HLA Class I molecules and are susceptible to PRAME-directed, T-cell mediated cytotoxicity. How this study might affect research, practice or policyOur results argue for phase I/II clinical trials testing PRAME immunotherapies like brenetafusp or anzutresgene autoleucel in PRAME+ NUT carcinoma patients. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=149 SRC="FIGDIR/small/642090v3_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@495654org.highwire.dtl.DTLVardef@c2b975org.highwire.dtl.DTLVardef@1de507org.highwire.dtl.DTLVardef@a76d33_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2018

Recapitulation of human germline coding variation in an ultra-mutated infant leukemia

BackgroundMixed lineage leukemia/Histone-lysine N-methyltransferase 2A gene rearrangements occur in 80% of infant acute lymphoblastic leukemia, but the role of cooperating events is unknown. While infant leukemias typically carry few somatic lesions, we identified a case with over 100 somatic point mutations per megabase and here report unique genomic-features of this case.\n\nResultsThe patient presented at 82 days of age, one of the earliest manifestations of cancer hypermutation recorded. The transcriptional profile showed global similarities to canonical cases. Coding lesions were predominantly clonal and almost entirely targeting alleles reported in human genetic variation databases with a notable exception in the mismatch repair gene, MSH2. There were no rare germline alleles or somatic mutations affecting proof-reading polymerase genes POLE or POLD1, however there was a predicted damaging mutation in the error prone replicative polymerase, POLK. The patients diagnostic leukemia transcriptome was depleted of rare and low-frequency germline alleles due to loss-of-heterozygosity, while somatic point mutations targeted low-frequency and common human alleles in proportions that offset this discrepancy. Somatic signatures of ultra-mutations were highly correlated with germline single nucleotide polymorphic sites indicating a common role for 5-methylcytosine deamination, DNA mismatch repair and DNA adducts.\n\nConclusionsThese data suggest similar molecular processes shaping population-scale human genome variation also underlies the rapid evolution of an infant ultra-mutated leukemia.

cancer biology↗