Biology subjects

Rathore, M.

Publications and source records attributed to Rathore, M..

10 recordsLinked to original sources

bioRxiv2025

Integrative plasma lipidomics and proteomics profiling to decipher potential biomarkers of dilated cardiomyopathy

BackgroundDilated cardiomyopathy (DCM), primarily characterised by left ventricular dilatation and systolic dysfunction, is one of the leading causes of heart failure and requires a critical clinical investigative strategy. However, conventional imaging techniques such as echocardiography and MRI, along with some classical CVD markers (NTproBNP, cTnT), fall short in diagnosing DCM-specific phenotypes. Thus, the need for biochemical markers with enhanced accuracy to DCM is of enormous importance. Lipids and proteins play essential roles in maintaining myocardial function. The homeostatic disruption of such biomolecules might contribute to DCM pathogenesis, thus offering to serve as potential biomarkers for DCM. Moreover, the lack of global lipidomics studies and specific protein markers in DCM patients prompted us to explore the disease pathophysiology through an integrative omics-based analysis coupled with an ML-derived approach. ObjectiveTo identify accurate, precise and specific circulatory lipidomic and proteomic biomarkers of DCM using high-resolution mass spectrometry and machine learning (ML)-based approaches. MethodsHigh-resolution-mass-spectrometry-based lipidomics and proteomics were applied to identify lipid and protein biomarkers in a cohort (n=360) of healthy and DCM patients. Top protein classifiers were further evaluated using single-cell transcriptomics on publicly available datasets from DCM myocardium and validated using ELISA. A biomarker panel was built by the integration of lipidomics and validated proteomics data using machine-learning-based approaches. ResultsA total of 125 lipids and 10 proteins have been primarily discovered with significant alterations in DCM (0.8 [≥] FC [≥] 1.2; padj < 0.05). Using a Boruta-based ML approach, we identified 39 lipids and 10 proteins as primary discriminators between DCM and controls. ELISA validation confirmed the potential of B2M (6.85 {+/-} 2.86 g/ml vs. 4.26 {+/-} 1.25 g/ml; p < 0.0001) and Tetranectin (CLEC3B) (1.99 {+/-} 0.88 g/ml vs. 2.49 {+/-} 0.90 g/ml; p = 0.0006) to emerge as protein biomarkers of DCM. In line with that, the single-cell transcriptomic analysis showed a similar trend of alteration of tetranectin (CLEC3B) in cardiomyocytes and {beta}2microglobulin (B2M) in varied cell types of the myocardium. Further, Integrated ROC analysis combining the top 8 lipid discriminators with B2M and CLEC3B achieved an AUC of 0.995, demonstrating enhanced diagnostic precision compared to the classical CVD marker NTproBNP (0.965). ConclusionThis study offers a system-omics-based perspective on first-global lipidomic and proteomic changes associated with DCM pathophysiology, with a high potential for diagnostic application.

systems biology↗

bioRxiv2024

Mitochondrial calcium uniporter regulates human fibroblast-like synoviocytes invasion via altering mitochondrial dynamics and dictates rheumatoid arthritis pathogenesis

Rheumatoid arthritis (RA) is characterized by the aggressive migration and invasion of fibroblast-like synoviocytes (FLS) into cartilage and bone, a process that is significantly influenced by mitochondrial calcium uptake. This study highlights the critical role of mitochondrial calcium uniporter (MCU) in regulating FLS migration and mitochondrial dynamics, and its potential as a therapeutic target in RA. Notably, RA-FLS exhibited increased MCU expression and mitochondrial dysfunction compared to controls. Treatment with Ru360, a potent MCU inhibitor significantly reduced RA-FLS migration, calcium influx, and mitochondrial reactive oxygen species (ROS) levels, while restoring mitochondrial morphology and enhancing ATP production. Further analysis of MCU complex expression revealed elevated levels of MCU and other regulatory subunits (EMRE, MICU1, MICU2) in RA-FLS compared to controls, indicating mitochondrial dysfunction in RA. Mechanistically, MCU inhibition altered gene expression related to cytoskeletal dynamics, focal adhesion, and metabolic pathways. In human RA-FLS, MCU inhibition suppressed migration and invasion both in vitro and in vivo. The interaction between MCU and Miro1, essential for mitochondrial transport, was validated, and its disruption impaired FLS migration. Our findings highlight MCU as a promising therapeutic target to inhibit FLS migration and ameliorate RA progression.

immunology↗

bioRxiv2024

A Ketogenic Diet Sensitizes Pancreatic Cancer to Inhibition of Glutamine Metabolism

Pancreatic cancer is the third leading cause of cancer death in the United States, and while conventional chemotherapy remains the standard treatment, responses are poor. Safe and alternative therapeutic strategies are urgently needed1. A ketogenic diet has been shown to have anti-tumor effects across diverse cancer types but will unlikely have a significant effect alone. However, the diet shifts metabolism in tumors to create new vulnerabilities that can be targeted (1). Modulators of glutamine metabolism have shown promise in pre-clinical models but have failed to have a marked impact against cancer in the clinic. We show that a ketogenic diet increases TCA and glutamine-associated metabolites in murine pancreatic cancer models and under metabolic conditions that simulate a ketogenic diet in vitro. The metabolic shift leads to increased reliance on glutamine-mediated anaplerosis to compensate for low glucose abundance associated with a ketogenic diet. As a result, glutamine metabolism inhibitors, such as DON and CB839 in combination with a ketogenic diet had robust anti-cancer effects. These findings provide rationale to study the use of a ketogenic diet with glutamine targeted therapies in a clinical context. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=186 SRC="FIGDIR/small/604377v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@1ebeefforg.highwire.dtl.DTLVardef@97e2ceorg.highwire.dtl.DTLVardef@1ab45c3org.highwire.dtl.DTLVardef@1713540_HPS_FORMAT_FIGEXP M_FIG C_FIG Graphical Abstract Description: Mechanistic rationale for combining a ketogenic diet and glutamine metabolism inhibitors. The combination of low glucose from a ketogenic diet and pharmacologic glutamine inhibition impairs nutrient input to mitochondria, reducing cancer growth.

cancer biology↗

bioRxiv2023

LRG1 is a novel ligand of HER3 and promotes metastatic colorectal cancer growth

Therapy failure for patients with metastatic colorectal cancer (mCRC) remains an overarching challenge in the clinic. We find that liver endothelial cells secrete soluble factor(s) to promote mCRC growth in vitro and in vivo. We identify LRG1 in ECs secretome, which promotes growth in tumor cells through binding and activation of HER3. Pharmacological blocking of the LRG1/HER3 axis using LRG1 antibody 15C4 completely attenuated LRG1-induced HER3 activation and in vitro and in vivo growth of the tumor. Moreover, LRG1-/- mice with CRC allografts in the liver had 2 times longer overall survival than tumor-bearing LRG1+/+ mice. Lastly, unbiased -omics analysis and target-specific inhibitors identified eIF4-protein synthesis is significantly activated by the LRG1/HER3/RSK1/2 axis. This work reveals a paracrine mechanism of mCRC growth in liver microenvironment and highlighted the potential of blocking LRG1-HER3 and involved downstream pathways for treating patients with mCRC. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=171 SRC="FIGDIR/small/529070v2_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@1a84299org.highwire.dtl.DTLVardef@1ac6654org.highwire.dtl.DTLVardef@1723260org.highwire.dtl.DTLVardef@4970a8_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2022

Liver Endothelium Microenvironment Promotes HER3-mediated Cell Growth in Pancreatic ductal adenocarcinoma

[~]90% metastatic pancreatic ductal adenocarcinoma (mPDAC) occurs in the liver, and the 5-year survival rate for patients with mPDAC is only at 3%. We previously reported that liver endothelial cells (ECs) secreted soluble factors to promote colorectal cancer cell survival in a paracrine fashion. However, the effects of liver ECs on mPDAC have not been elucidated. In this study, we used primary ECs from non-neoplastic liver tissues. We treated PDAC cells with conditioned medium (CM) from liver ECs, with CM from PDAC as controls, and determined that liver EC-secreted factors increased PDAC cell growth. Using an unbiased receptor tyrosine kinase array, we identified human epidermal growth factor receptor 3 (HER3, also known as ErbB3) as a key mediator in EC-induced growth in PDAC cells that have HER3 expression (HER3 +ve). We found that EC-secreted neuregulins activated the HER3-AKT signaling axis, and that depleting neuregulins from EC CM or blocking HER3 with an antibody, seribantumab, attenuated EC-induced proliferation in HER3 +ve PDAC cells, but not in cells without HER3 expression. Furthermore, we determined that EC CM increased PDAC xenograft growth in vivo, and that seribantumab blocked EC-induced growth in xenografts with HER3 expression. These findings elucidated a paracrine role of liver ECs in promoting PDAC cell growth, and identified the HER3-AKT axis as a key mediator in EC-induced functions in PDAC cells with HER3 expression. Implicationsover 70% mPDAC express HER3. This study suggests the potential of using HER3-targeted therapies for treating patients with HER3 +ve mPDAC.

cancer biology↗

bioRxiv2022

Wild-type IDH1 inhibition enhances chemotherapy response in melanoma

Malignant melanoma is one of the most common types of cancer in the United States. Despite recent and well-described progress in melanoma treatment, advanced disease still carries a poor prognosis for many patients and chemotherapy has been appropriately abandoned as a front-line option. Wild-type isocitrate dehydrogenase 1 (wtIDH1) has recently been implicated as a metabolic dependency in cancer. The enzyme is protective to cancer cells under metabolic stress, including oxidative damage by conventional chemotherapy and nutrient limitation characteristic of the tumor microenvironment. Specifically, the cytosolic enzyme generates NADPH to maintain redox homeostasis. IDH1 also supports mitochondrial function through anaplerosis of its reaction product, -ketoglutarate. We show that melanoma patients express higher levels of the wtIDH1 enzyme compared to normal skin tissue, and elevated wtIDH1 expression portends poor patient survival. Knockdown of IDH1 by RNA interference inhibited cell proliferation and migration under low nutrient levels. Suppression of IDH1 expression in melanoma also decreased NADPH and glutathione levels, resulting in increased reactive oxygen species. An FDA-approved inhibitor of mutant IDH1, ivosidenib (AG-120), exhibited potent anti-wtIDH1 properties under low magnesium and nutrient levels, reflective of the tumor microenvironment in natura. Similarly, findings were replicated in murine models of melanoma. Further, wtIDH1 inhibition was synergistic to conventional anti-melanoma chemotherapy in pre-clinical models. This work points to a novel and readily available combination treatment strategy for patients with advanced and refractory melanoma.

cancer biology↗

bioRxiv2022

Increased glucose availability sensitizes pancreatic cancer to chemotherapy

Pancreatic cancer (Pancreatic Ductal Adenocarcinoma; PDAC) is highly resistant to chemotherapy. Effective alternative therapies have yet to emerge, leaving chemotherapy as the best available systematic treatment. The discovery of safe and available adjuncts that improve chemotherapeutic efficacy would potentially improve survival outcomes. We show that a hyperglycemic state enhances the efficacy of conventional single- and multi-agent chemotherapies against PDAC. Molecular analyses of tumors exposed to relatively high glucose levels revealed that a key metabolic pathway, glutathione biosynthesis, is diminished and underlies chemo-sensitization by enhancing oxidative injury to cancer cells. Inhibition of this pathway under normal conditions phenocopied a hyperglycemic state by enhancing chemotherapeutic efficacy in mouse PDAC, while rescuing the pathway under high glucose abrogated the anti-tumor effects observed with chemotherapy.

cancer biology↗

bioRxiv2021

Liver Endothelium Microenvironment Promotes HER3-mediated Cell Survival in KRAS Wild-type and Mutant Colorectal Cancer

We previously showed that liver endothelial cells (ECs) secreted soluble factors in a paracrine fashion and activated human epidermal growth factor receptor 3 (HER3, also known as ERBB3) for promoting colorectal cancer (CRC) growth and chemoresistance. However, RAS proteins play a critical role in receptor tyrosine kinase signaling pathways, and KRAS mutations mediate CRC resistance to therapies targeting EGFR, another HER protein. Therefore, the role of KRAS mutation status in EC-induced HER3 activation and CRC survival was investigated as it has therapeutic implications. We used CRC cell lines and patient-derived xenografts harboring KRAS wild-type or mutant genes and demonstrated that liver EC-secreted factors promoted HER3-mediated CRC cell growth independent of KRAS mutation status. Also, blocking HER3 in CRC cells by siRNAs or a HER3 antibody seribantumab blocked EC-induced CRC survival. Our findings highlight the potential of utilizing HER3 targeted therapies for treating patients with mCRC independent of RAS mutational status.

cancer biology↗

bioRxiv2021

Identification of oxalyl-CoA synthetase gene (LsAAE3) and its regulatory role in β-ODAP biosynthesis in grasspea (Lathyrus sativus L.)

Grasspea is a popular pulse crop due to its hardiness and low cost of production. Presence of anti-nutritive factor {beta}-ODAP in its seeds and other plant parts hinder its widespread cultivation and usage. Oxalyl-CoA synthetase is one of the key enzyme of {beta}-ODAP biosynthesis pathway, catalyses the conversion of oxalate to oxalyl-CoA. ACYL ACTIVATING ENZYME 3 (AAE3) gene has been characterised to encode an oxalyl-CoA synthetase enzyme in many plant species. We report here the isolation of full length AAE3 homolog in grasspea with a combination of PCR based strategy and in silico analysis. We first identified AAE3 homolog by PCR using degenerate primers. The partial LsAAE3 sequence showed 88% amino acids sequence identity with the characterised AAE3 gene of M. truncatula. We then predicted the full length AAE3 sequence using the publically available transcriptome datasets of grasspea. Determination of LsAAE3 gene and protein structure and phylogenetic relationship analysis strongly suggested that LsAAE3 is a true homolog of AAE3 gene. Expression profiling of LsAAE3 in grasspea varieties with contrast in {beta}-ODAP content revealed its inverse relationship with the {beta}-ODAP content, LsAAE3 thus negatively regulates the synthesis of {beta}-ODAP. Involvement of AAE3 encoded oxalyl-CoA synthetase in a CoA-dependent pathway of oxalate degradation is well proven in many plant species. We also identified the CoA-dependent pathway of oxalate degradation in grasspea. Based on these observations, we hypothesized that LsAAE3 may regulate {beta}-ODAP content, possibly, by CoA-dependent pathway of oxalate degradation in grasspea. If this hypothesis is substantiated, genetic manipulation of LsAAE3 presents viable option for reducing {beta}-ODAP content in grass pea.

molecular biology↗

bioRxiv2018

Development of an on-chip detection of Zika virus and antibodies simultaneously using array of nanowells

Zika virus (ZIKV) infections are an emerging health pandemic of significant medical importance. ZIKV appeared recently in the Americas from Africa via the South Pacific. The current outbreak has garnered attention by exhibiting unique characteristics of devastating neurodevelopmental defects in newborns of infected pregnant women. Current guidelines for ZIKV diagnostics developed by the Center of Diseases Control and Prevention (CDC) consist of nucleic acid testing, plaque reduction neutralization test (PRNT), and a serologic test for IgM detection. To better accommodate and comply with these guidelines, we developed a simultaneous on-chip detection of ZIKV and anti-ZIKV antibodies using an array of nanowells. Using on-chip microengraving, we were able to detect anti-ZIKV antibodies and their immunoglobulin isotypes. In parallel, applying on-chip real-time PCR with epifluorescence microscopy, we were able to quantify ZIKV viral load as low as one copy. To test clinical samples of patients at the postconvalescent stage, we analyzed samples from 8 patients. The on-chip nanowells could effectively identify antibodies that reacted against ZIKV envelope protein and their isotypes with high sensitivity and specificity. The small sample requirement with high specificity and sensitivity and combined molecular and serological tests could potentially be very advantageous and beneficial in accurate detection of Zika infection for better disease monitoring and management.

bioengineering↗