Biology subjects

Basappa, J.

Publications and source records attributed to Basappa, J..

6 recordsLinked to original sources

bioRxiv2026

A Novel ACLY Inhibitor Induces Transcriptional and Metabolic Reprogramming to Overcome Tyrosine kinase inhibitor Resistance in Lymphoma

Background: Metabolic plasticity contributes to therapeutic resistance in T-cell lymphoma, but the metabolic dependencies underlying tyrosine kinase inhibitor (TKI) resistance remain poorly understood. ATP citrate lyase (ACLY), which converts citrate to cytosolic acetyl-CoA, links glucose metabolism to lipogenesis and acetylation-dependent regulation. We hypothesized that ACLY represents an actionable metabolic vulnerability in lymphoma. Methods: Structure-guided drug discovery and biochemical screening were used to identify the novel ACLY inhibitor VCB1. VCB1 was evaluated against recombinant human ACLY and in TKI-sensitive and TKI-resistant lymphoma models. Antitumor activity was assessed by proliferation, cell-cycle analysis, apoptosis, and immunoblotting, followed by integrated transcriptomic, metabolomic, and lipidomic profiling. Results: Our xenograft study showed that ACLY dependence in ALK+ALCL. We discovered novel ACLY inhibitor VCB1 directly inhibited recombinant ACLY with uM potency (IC, 0.9 uM) and strongly suppressed lymphoma cell growth. In ALK inhibitor-sensitive SUPM2, VCB1 showed an IC of 0.299 uM and retained potency in lorlatinib-resistant SUPM2-LR1000 cells (1.62 uM), whereas BMS-303141 was substantially less active (17.46 and 22.07 uM). VCB1 similarly inhibited BTK inhibitor sensitive and resistant mantle cell lymphoma cell growth (IC, 0.28 and 0.278 uM), compared with BMS-303141 (30.5 and 37.01 uM). Multi-omics profiling revealed suppression of de novo lipogenesis, including ACACA, FASN, and PPARGC1B, together with extensive remodeling of triglyceride, phospholipid, cardiolipin, ceramide, and acylcarnitine species and increased expression of fatty-acid oxidation genes. VCB1 activated the integrated stress response (ISR), inducing ATF4, PPP1R15A, DDIT3, DDIT4 and SESN2, while disrupting purine and pyrimidine metabolism and reducing nucleotide biosynthetic genes, including CAD, DHODH, UCK2, and ATIC. VCB1 further activated an ACLY/ISR/CHAC1 axis associated with reduced GCLC/GCLM expression, glutathione depletion, and a decreased GSH/GSSG ratio, indicating impaired redox homeostasis. TKI-resistant cells exhibited distinct lipid-metabolic remodeling consistent with metabolic plasticity. VCB1 also altered immune-regulatory programs involving PDCD1, TIGIT, CD247, CD226, NFATC2, and inflammatory cytokines. Functionally, VCB1 induced cell cycle arrest and apoptosis. Conclusions: ACLY represents an integrated metabolic and signaling vulnerability in lymphoma. VCB1 suppresses lymphoma growth across TKI-sensitive and resistant models by disrupting lipid and nucleotide metabolism, metabolic adaptation and ISR and redox homeostasis supporting ACLY inhibition as a therapeutic strategy for TKI-resistant lymphoma.

cancer biology↗

bioRxiv2026

Tyrosine phosphorylation and dimerization cooperatively activate NAMPT to enable NAD+ synthesis in cancer

Nicotinamide phosphoribosyltransferase (NAMPT), the rate-limiting enzyme in the NAD salvage pathway, is frequently upregulated in cancer, yet mechanisms regulating its catalytic activity remain undefined. We identify NAMPT as a direct substrate of multiple proto-oncogenic tyrosine kinases, including ALK, insulin receptor, IGF1R, and PDGFRA. Phosphoproteomics identified NAMPT Y188 as the major phosphorylation site, including the oncogenic fusion kinase NPM1::ALK. NAMPT interacted with NPM1::ALK in the cytoplasm, nucleus, and mitochondria, while Y188 phosphorylation enhanced catalytic activity, NMN/NAD biosynthesis, and downstream metabolism. Conversely, the Y188F mutant reduced enzymatic activity, proliferation, and clonogenicity, whereas disrupting dimerization similarly impaired phosphorylation and function. Interactome analyses showed phosphorylation and dimerization cooperatively remodel NAMPT-associated networks, enriching phosphorylated dimers for metabolic/redox regulators and monomeric NAMPT for ribosome biogenesis. NAMPT inhibition suppressed the growth of both ALK inhibitor-sensitive and -resistant lymphoma cells and enhanced the efficacy of ALK inhibition, revealing kinase-dependent NAMPT activation as a metabolic vulnerability in oncogene-driven cancers.

cancer biology↗

bioRxiv2025

Mitochondrial ACSS1 Links Acetate Metabolism to Pyrimidine Biosynthesis in Nutrient-Stressed B-Cell Lymphomas

Acetate serves as an alternative carbon source in nutrient-limited tumors, yet its role in supporting nucleotide biosynthesis remains poorly understood. Here, we identify the mitochondrial enzyme ACSS1 as a key metabolic driver in mantle cell lymphoma (MCL), diffuse large B-cell lymphoma (DLBCL), and chronic lymphocytic leukemia (CLL). ACSS1 is frequently overexpressed and catalyzes the conversion of acetate to mitochondrial acetyl-CoA, sustaining oxidative metabolism and biosynthesis under nutrient stress. Genetic silencing of ACSS1 impairs mitochondrial respiration and disrupts acetate incorporation into acetyl-CoA, TCA cycle intermediates, glutamate, and aspartate, while markedly reducing 13C-acetate labeling of dihydroorotate and orotate, intermediates in de novo pyrimidine synthesis. Untargeted metabolomics reveal enrichment of pyrimidine biosynthesis pathways in ACSS1-high cells. Notably, acetate or uridine supplementation rescues the growth of ACSS1-deficient cells, confirming a functional link between acetate metabolism and nucleotide synthesis. Importantly, in vivo studies using luciferase-labeled JeKo-1 and Maver mantle cell lymphoma xenografts demonstrate that ACSS1 knockdown significantly suppresses tumor growth. NSG mice injected with ACSS1-silenced cells exhibit a marked reduction in tumor burden, as measured by bioluminescence imaging and total photon flux, with significant differences observed at days 14 and 21 post-injection. These findings establish that ACSS1 is required not only for metabolic adaptation in vitro but also for lymphoma progression in vivo. Collectively, our results uncover an ACSS1-dependent mitochondrial acetate-pyrimidine axis that sustains lymphoma growth and represents a previously unrecognized therapeutic vulnerability. Statement of SignificanceThis study identifies ACSS1 as a critical metabolic vulnerability in mantle cell lymphoma (MCL), linking mitochondrial acetate metabolism to de novo pyrimidine biosynthesis and tumor progression. We demonstrate that ACSS1 is frequently overexpressed in MCL and is essential for converting acetate into mitochondrial acetyl-CoA, thereby sustaining TCA cycle activity, nucleotide production, and cell survival under nutrient stress. Loss of ACSS1 disrupts this acetate-pyrimidine axis, impairing oxidative metabolism and reducing lymphoma cell viability in vitro. Importantly, ACSS1 silencing significantly suppresses tumor growth in vivo, establishing its requirement for lymphoma progression. The ability of acetate or uridine supplementation to rescue ACSS1-deficient cells further highlights the functional coupling between mitochondrial acetate utilization and nucleotide synthesis. Together, these findings reveal a previously unrecognized mechanism of metabolic adaptation in aggressive lymphomas and offer ACSS1-mediated acetate metabolism as a promising therapeutic target.

cancer biology↗

bioRxiv2025

A Novel Allosteric Inhibitor Targeting IMPDH2 at Y233 Overcomes Resistance to Tyrosine Kinase Inhibitors in Lymphoma

Inosine monophosphate dehydrogenase-2 (IMPDH2) is a rate-limiting enzyme in the de novo biosynthesis of guanine nucleotides and is often overexpressed in hematologic malignancies and solid tumors. However, its regulatory mechanisms in cancer remain poorly understood. Here, we identify IMPDH2 as a direct substrate of the oncogenic kinases ALK and SRC, which phosphorylate tyrosine 233 (Y233) within the enzymes allosteric Bateman domain. Using peptide-based mutagenesis and enzymatic assays, we demonstrate that Y233 phosphorylation is essential for IMPDH2 activity. We found that phosphoinositide-3-phosphate (PI3P), a signaling phospholipid, selectively binds to and inhibits IMPDH2, but not its isoform IMPDH1, revealing a novel lipid-mediated, isoform-specific regulatory mechanism. Next, we conducted structure-based virtual screening and identified a potent allosteric inhibitor of IMPDH2, compound 10 (comp-10), with an IC of 260 nM. Comp-10 significantly impairs cell proliferation in ALK-positive anaplastic large cell lymphoma (ALCL) cell lines, including those resistant to the ALK inhibitors crizotinib and lorlatinib, and outperformed the FDA-approved IMPDH inhibitor mycophenolic acid. These findings reveal the dual regulation of IMPDH2 through tyrosine phosphorylation and binding to PI3P, and describe the discovery of a new IMPDH2 inhibitor, suggesting a potential therapeutic strategy to overcome resistance to tyrosine kinase inhibitors.

cancer biology↗

bioRxiv2024

Mitochondrial ACSS1 regulates the oncometabolite 2-hydroxyglutarate and De Novo Pyrimidine biosynthesis under nutrient-deprived conditions in lymphoma

The mitochondrial Acetyl-CoA synthetase short-chain family member 1 (ACSS1) converts acetate, an energy source in nutrient-deprived conditions, to mitochondrial acetyl-CoA. However, the specific mechanism behind this process remains unknown. Here, we show that ACSS1 is overexpressed in patients with mantle cell lymphoma (MCL), diffuse large B cell lymphoma (DLBCL), chronic lymphocytic leukemia (CLL), and Ibrutinib (IBR)-resistant cell lines. The mitochondrial stress test showed reduced oxygen consumption in ACSS1 knockdown (KD) cell lines. 13C-acetate stable isotope tracing revealed that ACSS1 knockdown (KD) in MCL cell lines attenuates the flux of mitochondrial acetate to acetyl-CoA, acetylcarnitine, and TCA cycle intermediates, including glutamine and aspartate, which are precursors for de novo pyrimidine synthesis. Consistently, there was a decrease in the labeling of glutamate, aspartate, dihydroorotate, and orotate pools in KD cell lines. Pathway analysis revealed the enrichment of de novo pyrimidine synthesis metabolites and depleting ACSS1 impaired cell growth and potential vulnerability of IBR-resistant MCL cells. Further, we discovered that acetate is used to synthesize 2-hydroxyglutarate in an ACSS1-dependent manner, and it is involved in histone methylation. These results highlight a metabolic phenotype in MCL cells, showing their ability to metabolize acetate in nutrient-deprived conditions and provide new insights into the role of ACSS1 in cancer metabolism. SignificanceThe enzyme ACSS1 catalyzes the conversion of acetate, an energy source in nutrient-deprived conditions, to mitochondrial acetyl-CoA. Our results show that ACSS1 may affect cancer metabolism, particularly in MCL. Studies using MCL cell lines showed that reducing ACSS1 activity affects acetate utilization for various metabolic pathways and influences the production of oncometabolite D-2-hydroxyglutarate. Additionally, reducing ACSS1 activity affects the expression of cyclin D1 and inhibits cell growth, highlighting the potential significance of ACSS1 in cancer metabolism.

cancer biology↗

bioRxiv2020

Tyrosine phosphorylation of ACLY regulates lipid metabolism and oncogenesis in ALK positive Anaplastic Large Cell Lymphoma

A fundamental requirement for growth of rapidly proliferating cells is metabolic adaptation to promote synthesis of biomass1. ATP citrate lyase (ACLY) is a critical enzyme responsible for synthesis of cytosolic acetyl-CoA, the key building component for de novo fatty acid synthesis and links vital pathways such as carbohydrate and lipid metabolism2. The mechanisms of ACLY regulation are not completely understood and the regulation of ACLY function by tyrosine phosphorylation is unknown. Here we show using mass-spectrometry-driven phosphoproteomics and metabolomics that ACLY is phosphorylated and functionally regulated at an evolutionary conserved residue, Y682. Physiologic signals promoting rapid cell growth such as epidermal growth factor stimulation in epithelial cells and T-cell receptor activation in primary human T-cells result in rapid phosphorylation of ACLY at Y682. In vitro kinase assays demonstrate that Y682 is directly phosphorylated by multiple tyrosine kinases, including ALK, ROS1, SRC, JAK2 and LTK. Oncogenically activating structural alterations such as gene-fusions, amplification or point mutations of ALK tyrosine kinase result in constitutive phosphorylation of ACLY in diverse forms of primary human cancer such as lung cancer, anaplastic large cell lymphoma (ALCL) and neuroblastoma. Expression of a phosphorylation-defective ACLY-Y682F mutant in NPM-ALK+ ALCL decreases ACLY activity and attenuates lipid synthesis. Metabolomic analyses reveal that ACLY-Y682F expression results in increased {beta}-oxidation of 13C-oleic acid-labeled fatty acid with increased labeling of +2-citrate (p<0.01) and +18-oleyol carnitine (p<0.001). Similarly, oxygen consumption rate (OCR) is significantly increased in cells expressing ACLY-Y682F (p<0.001). Moreover, expression of ACLY-Y682F dramatically decreases cell proliferation, impairs clonogenicity and abrogates tumor growth in vivo. Our results reveal a novel mechanism for direct ACLY regulation that is subverted by multiple oncogenically-activated tyrosine kinases in diverse human cancers. These findings have significant implications for novel therapies targeting ACLY in cancer and metabolism.

cancer biology↗