Biology subjects

Mody, N.

Publications and source records attributed to Mody, N..

3 recordsLinked to original sources

bioRxiv2025

Accelerating Antibody Development: Sequence and Structure-Based Models for Predicting Developability Properties through Size Exclusion Chromatography

Experimental screening for biopharmaceutical developability properties typically relies on resource-intensive, and time-consuming assays such as size exclusion chromatography (SEC). This study highlights the potential of in silico models to accelerate the screening process by exploring sequence and structure-based machine learning techniques. Specifically, we compared surrogate models based on pre-computed features extracted from sequence and predicted structure with sequence-based approaches using protein language models (PLMs) like ESM-2. In addition to different end-to-end fine-tuning strategies for PLM, we have also investigated the integration of the structural information of the antibodies into the prediction pipeline through graph neural networks (GNN). We applied these different methods for predicting protein aggregation propensity using a dataset of approximately 1200 Immunoglobulin G (IgG1) molecules. Through this empirical evaluation, our study identifies the most effective in silico approach for predicting developability properties for SEC assays, thereby adding insights to existing screening efforts for accelerating the antibody development process.

bioinformatics↗

bioRxiv2024

Hydroxysteroid 17-beta dehydrogenase 13 (Hsd17b13) knockdown attenuates liver steatosis in high-fat diet obese mice

Hydroxysteroid 17-beta dehydrogenase 13 (HSD17B13) loss-of-function gene variants are associated with decreased risk of metabolic dysfunction-associated steatotic liver disease (MASLD). Our RNA-seq analysis of steatotic liver from obese mice -/+ Fenretinide treatment identified major beneficial effects of Fenretinide on hepatic gene expression including Hsd17b13. We sought to determine the relationship between Hsd17b13 expression and MASLD and to validate it as a therapeutic target by liver-specific knockdown. Hsd17b13 expression, which is unique to hepatocytes and associated with the lipid-droplet, was elevated in multiple models of MASLD and normalised with prevention of obesity and steatotic liver. Direct, liver- specific, shRNA-mediated knockdown of Hsd17b13 (shHsd17b13) in high-fat diet (HFD)-obese mice, markedly improved hepatic steatosis with no effect on body weight, adiposity or glycaemia. shHsd17b13 decreased elevated serum ALT, serum FGF21 levels and markers of liver fibrosis e.g. Timp2. shHsd17b13 knockdown in HFD-obese mice and Hsd17b13 overexpression in cells reciprocally regulated expression of lipid metabolism genes e.g. Cd36. Global lipidomic analysis of liver tissue revealed a major decrease in diacylglycerols (e.g. DAG 34:3) with shHsd17b13 and an increase in phosphatidylcholines containing polyunsaturated fatty acids (PUFA) e.g. PC 34:3 and PC 42:10. Expression of key genes involved in phospholipid and PUFA metabolism e.g. Cept1, were also reciprocally regulated suggesting a potential mechanism of Hsd17b13 biological function and role in MASLD. In conclusion, Hsd17b13 knockdown in HFD-obese adult mice was able to alleviate MASLD via regulation of fatty acid and phospholipid metabolism, thereby confirming HSD17B13 as a genuine therapeutic target for MASLD and development of liver fibrosis. KEY POINTSO_LIHSD17B13 loss-of-function gene variants are associated with decreased risk of metabolic dysfunction-associated (MA) steatotic liver disease and steatohepatitis (MASLD and MASH). C_LIO_LIRNA-seq analysis of steatotic liver identified beneficial effects of Fenretinide on hepatic gene expression including downregulation of Hsd17b13. C_LIO_LILiver-specific shRNA knockdown of Hsd17b13 in obese mice markedly improved hepatic steatosis and markers of liver health e.g. serum ALT, serum Fgf21 levels. C_LIO_LIHsd17b13 influenced expression of lipid/phospholipid metabolism genes e.g. Cd36 and Cept1 and phosphatidylcholines PC 34:3 and PC 42:10. C_LIO_LIOur study suggests a mechanism of HSD17B13s biological function and the strong rationale behind targeting HSD17B13 for MASLD/MASH. C_LI

physiology↗

bioRxiv2022

Fenretinide inhibits obesity and fatty liver disease but induces Smpd3 to increase serum ceramides and worsen atherosclerosis in LDLR-/- mice.

Fenretinide is a synthetic retinoid that can prevent obesity and improve insulin sensitivity in mice by directly altering retinol/retinoic acid homeostasis and inhibiting excess ceramide biosynthesis. We determined the effects of Fenretinide on LDLR-/- mice fed high-fat/high-cholesterol diet +/- Fenretinide, a model of atherosclerosis and non-alcoholic fatty liver disease (NAFLD). Fenretinide prevented obesity, improved insulin sensitivity and completely inhibited hepatic triglyceride accumulation, ballooning and steatosis. Moreover, Fenretinide decreased the expression of hepatic genes driving NAFLD, inflammation and fibrosis e.g. Hsd17b13, Cd68 and Col1a1. The mechanisms of Fenretinides beneficial effects in association with decreased adiposity were mediated by inhibition of ceramide synthesis, via hepatic DES1 protein, leading to increased dihydroceramide precursors. However, Fenretinide treatment in LDLR-/- mice enhanced circulating triglycerides and worsened aortic plaque formation. Interestingly, Fenretinide led to a 4-fold increase in hepatic sphingomyelinase Smpd3 expression, via a retinoic acid-mediated mechanism and a further increase in circulating ceramide levels, linking induction of ceramide generation via sphingomyelin hydrolysis to a novel mechanism of increased atherosclerosis. Thus, despite beneficial metabolic effects, Fenretinide treatment may under certain circumstances enhance the development of atherosclerosis. However, targeting both DES1 and Smpd3 may be a novel, more potent therapeutic approach for the treatment of metabolic syndrome.

physiology↗