Biology subjects

Muthuswamy, S. K.

Publications and source records attributed to Muthuswamy, S. K..

6 recordsLinked to original sources

bioRxiv2026

Metabolic-epigenetic coupling between leucine catabolism and glycolysis drives CDK4/6 inhibitor resistance

Resistance to CDK4/6 inhibitors limits the durability of therapy for ER+ breast cancer. Despite the identification of mechanisms that regulate resistance, the metabolic adaptations that enable therapeutic escape remain poorly understood. Here, we identify a metabolic-epigenetic circuit that drives resistance by coordinately rewiring amino acid and glucose metabolism. CDK4/6 inhibitor-resistant ER+ tumor cells upregulate the leucine transporter SLC7A5, enhancing leucine uptake. SLC7A5 overexpression is sufficient to confer palbociclib resistance across ER+ cell lines, patient-derived organoids and xenografts. Stable isotope tracing in cell lines and in xenograft tumors revealed that leucine is catabolized through BCAT2 and HMGCL to increase acetyl-CoA levels, and elevated acetyl-CoA promotes H3K27 acetylation at the GLUT1 promoter, upregulating GLUT1 expression and glycolytic activity. Disrupting leucine transport, catabolism, or availability suppresses GLUT1 expression and restores therapeutic sensitivity in resistant models. In patients receiving palbociclib-based therapy, high SLC7A5 expression and coordinated SLC7A5-GLUT1 co-expression are associated with shorter progression-free survival. Together, these findings define a metabolic-epigenetic mechanism linking branched-chain amino acid catabolism to glycolysis and identify a biomarker-associated metabolic vulnerability in advanced ER+ breast cancer.

cancer biology↗

bioRxiv2023

Establishing conditions for the generation and maintenance of estrogen receptor-positive organoid models of breast cancer

Patient-derived organoid models of estrogen receptor-positive (ER+) breast cancer would provide a much-needed tool to better understand drug resistance and disease progression. However, the establishment and long-term maintenance of ER expression, function, and response in vitro remains a significant challenge. Here, we report the development of an ER+ breast tumor organoid medium (BTOM-ER) that conserves ER expression, estrogen responsiveness, and dependence, as well as sensitivity to endocrine therapy of ER+ patient-derived xenograft organoids (PDXO). Our findings demonstrate the utility of subtype-specific culture conditions that better mimic the characteristics of the breast epithelial biology and microenvironment, providing a powerful platform for investigating therapy response and disease progression of ER+ breast cancer.

cancer biology↗

bioRxiv2023

Oncogenic GNAS uses PKA-dependent and independent mechanisms to induce cell proliferation in human pancreatic ductal and acinar organoids

Ductal and acinar pancreatic organoids generated from human pluripotent stem cells (hPSCs) are promising models to study pancreatic diseases, including precursor lesions of pancreatic cancer. Genome sequencing studies have revealed that mutations in a G-protein (GNASR201C) are exclusively observed in intraductal papillary mucinous neoplasms (IPMNs), one of the most common cystic pancreatic precancerous lesions. GNASR201C cooperates with oncogenic KRASG12V/D to produce IPMN lesions in mice; however, the biological mechanisms by which oncogenic GNAS affects the ductal and acinar exocrine pancreas are not understood. In this study, we use pancreatic ductal and acinar organoids generated from human embryonic stem cells to investigate mechanisms by which GNASR201C functions. As expected, GNASR201C-induced cell proliferation in acinar organoids was PKA-dependent. Surprisingly, GNASR201C-induced cell proliferation independent of the canonical PKA signaling in short-term and stable, long-term cultures of GNAS-expressing ductal organoids and in an immortalized ductal epithelial cell line, demonstrating that GNASR201C uses PKA-dependent and independent mechanisms to induce cell proliferation in the exocrine pancreas. Co-expression of oncogenic KRASG12V and GNASR201C induced cell proliferation in ductal and acini organoids in a PKA-independent and dependent manner, respectively. Thus, we identify cell lineage-specific roles for PKA signaling driving pre-cancerous lesions and report the development of a human pancreatic ductal organoid model system to investigate mechanisms regulating GNASR201C-induced IPMNs.

cancer biology↗

bioRxiv2020

Clonal expansion of personalized anti-tumor T cells from circulation using tumor organoid-immune co-cultures

Tumor-specific cytotoxic T cells are effective tools for cancer immunotherapy, but the ability to generate them continues to be a challenge. Furthermore, there are no compelling approaches to empirically identify tumor-targeting T cells and T cell receptors by exploiting the multitude of antigens on tumor cell surfaces. Here, we use patients peripheral blood and autologous tumor organoids to enrich tumor-specific cytotoxic T cells with patient-specific killing mechanisms and a tissue-resident memory phenotype. We further demonstrate that these organoid-primed T (opT) cells undergo several orders of magnitude of clonal expansion and express T cells receptors and check-point proteins unique to each patient. Importantly, transferring the TCRs to heterologous T cells was sufficient to confer tumor recognition in a patient-specific manner. Thus, we report a patient-specific and antigen-agnostic platform for expansion of tumor-targeting T cells and identification of cancer-targeting TCRs from the peripheral blood of pancreatic cancer patients that can be exploited for immunotherapy applications.

cancer biology↗

bioRxiv2019

Differential functions of splicing factors in breast-cancer initiation and metastasis

Misregulation of alternative splicing is a hallmark of human tumors; yet to what extent and how it contributes to malignancy are only beginning to be unraveled. Here, we define which members of the splicing factor SR and SR-like families contribute to breast cancer, and uncover differences and redundancies in their targets and biological functions. We first identify splicing factors frequently altered in human breast tumors, and then assay their oncogenic functions using breast organoid models. Importantly we demonstrate that not all splicing factors affect mammary tumorigenesis. Specifically, upregulation of either SRSF4, SRSF6 or TRA2{beta} promotes cell transformation and invasion. By characterizing the targets of theses oncogenic factors, we identify a shared set of spliced genes associated with well-established cancer hallmarks. Finally, we demonstrate that the splicing factor TRA2{beta} is regulated by the MYC oncogene, plays a role in metastasis maintenance in vivo, and its levels correlate with breast-cancer-patient survival.

cancer biology↗

bioRxiv2018

Golgi stabilization, not its front-rear bias, is associated with EMT-enhanced fibrillar migration

Epithelial-to-mesenchymal transition (EMT) and maturation of collagen fibrils in the tumor microenvironment play a significant role in cancer cell invasion and metastasis. Confinement along fiber-like tracks enhances cell migration. To what extent and in what manner EMT further promotes migration in a microenvironment already conducive to migration is poorly understood. Here, we show that TGF{beta}-mediated EMT significantly enhances migration on fiber-like micropatterned tracks of collagen, doubling migration speed and quadrupling persistence relative to untreated mammary epithelial cells. Thus, cell-intrinsic EMT and extrinsic fibrillar tracks have non-redundant effects on motility. To better understand EMT-enhanced fibrillar migration, we investigated the regulation of Golgi positioning, which is involved in front-rear polarization and persistent cell migration. Confinement along fiber-like tracks has been reported to favor posterior Golgi positioning, whereas anterior positioning is observed during 2d wound healing. While EMT also regulates cell polarity, little is known about its effect on Golgi positioning. Here, we show that EMT induces a 2:1 rearward bias in Golgi positioning; however, positional bias explains less than 5% of single-cell variability in migration speed and persistence. Meanwhile, EMT significantly stabilizes Golgi positioning. Cells that enhance migration in response to TGF{beta} maintain Golgi position for 3-4 fold longer than untreated counterparts, irrespective of whether the Golgi is ahead or behind the nucleus. In fact, 35% of cells that respond to TGF{beta} exhibit a fully-committed Golgi phenotype with the organelle either in the anterior or posterior position for over 90% of the time. Furthermore, single-cell differences in Golgi stability capture up to 30% of variations in migration speed and persistence. These results lead us to propose that the Golgi is part of a core physical scaffold that distributes cell-generated forces necessary for migration. A stable scaffold more consistently, and therefore more productively, distributes forces over time, leading to efficient migration.

cell biology↗