Biology subjects

Munshi, N. C.

Publications and source records attributed to Munshi, N. C..

7 recordsLinked to original sources

bioRxiv2026

Synthetic lethality of p97 inhibition and PSMC2-overexpressionovercomes bortezomib resistance in multiple myeloma

The aim of the present study was to analyze genomic profiles obtained from multiple myeloma (MM) patient tumors to identify prognostic classifiers of clinical response and survival following bortezomib monotherapy and then target key actionable classifiers that underly bortezomib resistance. We discovered higher levels of proteasome PSMC2 messenger RNA in myeloma cells from patients that did not respond to bortezomib and that higher PSMC2 expression correlated with inferior progression-free and overall survival. Pharmacologic screening revealed that CB-5339, an ATP-competitive inhibitor of the molecular chaperone p97/VCP that shuttles ubiquitin-conjugated substrates to proteasomes, was synthetic lethal in MM cells engineered to overexpress PSMC2. p97 co-immunoprecipitated with 26S proteasomes affinity-purified from PSMC2-overexpressing cells which exhibited greater activity and reduced bortezomib sensitivity relative to PSMC2-KO cells. Bortezomib treatment followed by in-situ cross-linking and western blotting revealed higher levels of K48- and K63-linkage-specific ubiquitin chains covalently bound to 26S proteasomes isolated from PSMC2-KO cells compared to proteasomes affinity-purified from PSMC2-overexpressing cells. Western blotting demonstrated higher levels of 19S RPs, 26S proteasomes, and a PSMC2-PSMC1-PSMD2 subcomplex in PSMC2-overexpressing cells relative to PSMC2-KO cells. CB-5339 and bortezomib co-treatment synergistically targeted tumor cells obtained from MM patients previously exposed to bortezomib therapy and reduced the in vivo growth of PSMC2-overexpressing myeloma xenografts in mice. Taken together, we have discovered a genetic vulnerability that provokes proteasome-intrinsic bortezomib resistance and validated the potential of synthetic lethality to guide therapeutic interventions. Our study reaffirms that transcriptomic heterogeneity in MM is a primary driver of prognostic variability.

cancer biology↗

bioRxiv2026

Mechanistically Defined Epoxide- and Aziridine-2-carboxamide Electrophiles Enable Stereoselective Covalent RNA Modulation

RNA remains a largely untapped target for covalent small-molecule intervention due to the lack of electrophiles with predictable reactivity and stability in biological settings. Here, a mechanistically defined and tunable class of epoxide- and aziridine-2-carboxamide electrophiles that enable structure-guided covalent targeting of RNA is described. These warheads arise from an unexpected hydrolytic rearrangement of 3-chloropivalamide precursors under physiological conditions and selectively react with guanine N7, with reactivity and stability controlled by substitution pattern, linkage chemistry, and stereochemistry. Application to two distinct RNA targets demonstrates generality: epoxide- and aziridine-based ligands covalently modify pathogenic r(CUG)exp repeat RNA and disrupt RNA-protein interactions in vitro and in cells, while structure-guided placement on a flavin scaffold yields stereoselective covalent modulators of the flavin mononucleotide (FMN) riboswitch with validated reaction site and cellular activity. Together, this work establishes epoxide- and aziridine-2-carboxamides as a versatile platform for covalent RNA targeting and provides a general framework for the rational design of stereochemically controlled RNA-reactive small molecules.

biochemistry↗

bioRxiv2025

Structure-Guided Design of a Bioactive Covalent Small Molecule Targeting a Riboswitch

Small molecule ligands targeting structured RNA elements hold promise for modulating RNA function, serving as chemical probes and potential therapeutics. In this study, the characterization of phenylglyoxal-based covalent probe designed to target unpaired guanine residues in structured RNAs is reported. A structure-guided design strategy was employed to modify covalently unpaired guanines critical for flavin mononucleotide (FMN) binding to the FMN riboswitch. Covalent modification occurs at the designed site and modulates riboswitch function in a cellular reporter system, highlighting the potential of covalent mechanisms of action for bioactive RNA ligands.

biochemistry↗

bioRxiv2022

Apurinic/apyrimidinic nuclease 1 drives genomic evolution contributing to chemoresistance and tumorigenesis in solid tumor

Genomic instability fuels genomic alterations that befit cancer cells with necessary adaptations to keep proliferating and overcome the impact of host anti-tumor immunity and cytotoxic therapy. Since DNA breaks are required for genomic rearrangements to take place, we hypothesized that dysregulated nuclease activity mediates genomic instability in cancer. Using an integrated genomics protocol, we identified a four gene deoxyribonuclease signature correlating with genomic instability in six human cancers which included adenocarcinomas of esophagus (EAC), lung, prostate, stomach, pancreas and triple negative breast cancer. Functional screens confirmed the role of these nucleases in genomic instability and growth of cancer cells. Apurinic/apyrimidinic nuclease 1 (APE1), identified as top nuclease in functional screen, was further investigated in five cell lines representing four solid tumors (EAC, lung, prostate and breast cancer). We demonstrate that chemical as well as transgenic suppression of APE1 impaired growth/colony formation and increased cytotoxicity of chemotherapeutic agent, whereas inhibited spontaneous as well as chemotherapy-induced DNA breaks, homologous recombination (HR) activity and genomic instability in all cancer cell types tested. Treatment with APE1 inhibitor also impaired tumor growth and significantly increased efficacy of a chemotherapeutic agent in a subcutaneous mouse model of EAC. Overexpression of APE1 in normal esophageal epithelial cells increased DNA breaks and HR activity, leading to massive mutational, copy number as well as karyotypic instability. Evaluation of by whole genome sequencing identified HR as the top mutational process activated by APE1. Normal cells overexpressing APE1 grew as tumors in mice and tumors removed from mice displayed additional karyotypic changes, providing evidence of genomic instability in vivo. Overall, our data demonstrate that elevated APE1 dysregulates HR activity, G2/M checkpoint and genome stability thus contributing to tumorigenesis and chemoresistance in cancer. Therefore, inhibitors of APE1 have potential to inhibit growth and increase cytotoxicity of chemotherapeutic agents while minimizing spontaneous as well as chemotherapy-induced genomic damage and instability in EAC and other solid tumors.

cancer biology↗

bioRxiv2021

Long Noncoding RNA RROL Provides Chromatin Scaffold for MYC-WDR82 Interaction to Impact Lipid Metabolism and Tumor Cell Growth in Multiple Myeloma

Long noncoding RNAs (lncRNA) can drive the tumorigenesis and be susceptible to therapeutic intervention. To define the landscape of therapeutically actionable lncRNA dependencies in multiple myeloma (MM), we coupled our extensive lncRNA transcriptomic profile with lncRNA targeted CRISPR interference viability screen and identified RNA Regulator of Lipogenesis (RROL) as a leading lncRNA dependency in MM. RROL shares its origin with the microRNA locus MIR17HG, however supports the proliferation and survival of MM cells in a microRNA- and DROSHA- independent manner. We found that RROL provides a chromatin scaffold for the functional interaction between c-MYC and WDR82 to promote the regulation of the lipogenic pathways via the transcriptional control of the rate-limiting enzyme ACC1 in MM cells. Inhibition of RROL with clinically applicable antisense molecules disrupts its transcriptional and functional activities causing potent anti-tumor effects both in vitro and in vivo in two pre-clinical animal models. This study establishes lncRNA RROL as a therapeutically actionable dependency with a unique mechanism of action in support of myeloma cell growth.

cancer biology↗

bioRxiv2020

The DNA methylation landscape of multiple myeloma shows extensive inter- and intrapatient heterogeneity that fuels transcriptomic variability

BackgroundCancer evolution depends on epigenetic and genetic diversity. Historically, in multiple myeloma (MM), subclonal diversity and tumor evolution have been investigated mostly from a genetic perspective. ResultsHere, we combined the notions of epipolymorphism and epiallele switching to analyze DNA methylation heterogeneity in MM patients. We show that MM is characterized by the continuous accumulation of stochastic methylation at the promoters of development-related genes. High entropy change is associated with poor outcomes and depends predominantly on partially methylated domains (PMDs). These PMDs, which represent the major source of inter- and intrapatient DNA methylation heterogeneity in MM, are linked to other key epigenetic aberrations, such as CpG island (CGI)/transcription start site (TSS) hypermethylation and H3K27me3 redistribution as well as 3D organization alterations. In addition, transcriptome analysis revealed that intratumor methylation heterogeneity was associated with low-level expression and high variability. ConclusionWe propose that disordered methylation in MM is responsible for high epigenetic and transcriptomic instability allowing tumor cells to adapt to environmental changes by tapping into a pool of evolutionary trajectories.

cancer biology↗

bioRxiv2020

Integrated genomics and comprehensive validation reveal novel drivers of genomic evolution in esophageal adenocarcinoma

Identification of genes driving genomic evolution can provide novel targets for cancer treatment and prevention. Here we show identification of a genomic instability gene signature, using an integrated genomics approach. Elevated expression of this signature correlated with poor survival in esophageal adenocarcinoma (EAC) as well as three other human cancers. Knockout and overexpression screens confirmed the relevance of this signature to genomic instability. Indepth evaluation of TTK (a kinase), TPX2 (spindle assembly factor) and RAD54B (recombination protein) further confirmed their role in genomic instability and tumor growth. Mutational signatures identified by whole genome sequencing and functional studies demonstrated that DNA damage and homologous recombination were common mechanisms of genomic instability induced by these genes. Consistently, a TTK inhibitor impaired EAC cell growth in vivo, and increased chemotherapy-induced cytotoxicity while inhibiting genomic instability in surviving cells. Thus inhibitors of TTK and other genes identified in this study have potential to inhibit/delay genomic evolution and tumor growth. Such inhibitors also have potential to increase chemotherapy-induced cytotoxicity while reducing its harmful genomic impact in EAC and possibly other cancers.

cancer biology↗