Biology subjects

Martin, S. D.

Publications and source records attributed to Martin, S. D..

6 recordsLinked to original sources

bioRxiv2026

Single-cell spatial multi-omic characterization of the tumour microenvironment in transformed follicular lymphoma

Histological examination of follicular lymphoma (FL) biopsies remains the cornerstone for diagnostic grading of FL. Single-cell sequencing approaches, while transcriptomically rich, require tissue dissociation and lose the native spatial context that underpins FL transformation to diffuse large B-cell lymphoma (DLBCL). To investigate the spatial interplay between malignant B-cells and the tumour microenvironment (TME) across disease states, we performed subcellular single-cell spatial transcriptomics and spatial proteomics on 12 paired pre/post-transformation samples and 10 non-transforming FL controls, integrated with matched single-cell whole genome sequencing (scWGS). Our analysis reveals that transformation is accompanied by a shift toward B-cell-predominant stromal and immunosuppressive cellular neighbourhoods, where the magnitude of expansion correlates with time to transformation. Prior to transformation, immunomodulatory Galectin-9 interactions move from the intra-follicular core to the extra-follicular space. Integration with scWGS demonstrates that high copy-number instability in malignant B-cells is associated with reduced supportive T-cell niches and intensified immunoregulatory crosstalk at the transformed state. Collectively, our multi-omic analysis characterizes TME remodeling during FL transformation, contributing to a refined disease evolution model.

bioinformatics↗

bioRxiv2024

Adipose tissue protein kinase D (PKD): regulation of signalling networks and its sex-dependent effects on metabolism

The protein kinase D (PKD) family of three highly homologous isoforms (PKD1, PKD2, and PKD3) are implicated as nutrient sensing signalling kinases that regulate the response of adipose and other tissues to the nutrient environment. However, the physiological role of adipose tissue PKD and its downstream cellular signalling targets are not well characterised. Phosphoproteomics was performed to elucidate signalling events downstream of PKD activation in differentiated 3T3L1 adipocytes using a triple isoform siRNA knockdown model. This revealed PKD-regulated pathways including insulin and cAMP signalling, which control metabolic responses in adipose tissue. An adipose tissue-specific and inducible dominant negative PKD (atDNPKD) mouse model that achieves functional inhibition of all three PKD isoforms was generated to assess the function of adipose PKD on whole-body metabolism in vivo in both male and female mice. Insulin-stimulated suppression of lipolysis was blunted in male, but not female, atDNPKD mice compared to control mice. Female, but not male, atDNPKD mice had higher fasting insulin but normal insulin action. Male atDNPKD mice showed greater sensitivity to the {beta}3-adrenergic receptor agonist CL316,243 on measures of lipolysis and energy expenditure, and displayed greater fat oxidation during fasting. During refeeding, male atDNPKD mice consumed less food and took longer to regain body weight lost during fasting. These effects were not observed in female mice. These findings indicate that PKD provides sex-dependent fine-tuning control of cAMP signalling in adipose tissue that is important for the coordination of energy balance during fasting and refeeding. NEW & NOTEWORTHYThe protein kinase D (PKD) family is a target for the treatment of obesity-related disorders. However, the physiological role of PKD in adipose tissue remains to be resolved. Using phosphoproteomics and an adipose tissue PKD loss-of-function mouse model, results demonstrate that PKD provides fine tuning of metabolic signalling in adipose tissue and metabolic responses to fasting and refeeding challenges, via coordination of feeding behaviour and regulation of body weight.

physiology↗

bioRxiv2022

Class IIa HDACs reprogram mitochondrial metabolism to inhibit apoptosis and ferroptosis in response to lipotoxicity

Lipotoxicity, the accumulation of lipids in non-adipose tissues, alters the metabolic transcriptome and mitochondrial metabolism in skeletal muscle. The mechanisms involved remain poorly understood. Here we show that lipotoxicity increased histone deacetylase 4 (HDAC4) and histone deacetylase 5 (HDAC5), which reduced the expression of metabolic genes and oxidative metabolism in skeletal muscle, resulting in increased non-oxidative glucose metabolism. This metabolic reprogramming was also associated with impaired apoptosis and ferroptosis responses, and preserved muscle cell viability in response to lipotoxicity. Mechanistically, increased HDAC4 and 5 decreased acetylation of p53 at K120, a modification required for transcriptional activation of apoptosis. Redox drivers of ferroptosis derived from oxidative metabolism were also reduced. The relevance of this pathway was demonstrated by overexpression of loss-of-function HDAC4 and HDAC5 mutants in skeletal muscle of obese db/db mice, which enhanced oxidative metabolic capacity, increased apoptosis and ferroptosis and reduced muscle mass. This study identifies HDAC4 and HDAC5 as repressors of skeletal muscle oxidative metabolism, which is linked to inhibition of cell death pathways and preservation of muscle integrity in response to lipotoxicity.

cell biology↗

bioRxiv2022

Amyloid beta 42 alters cardiac metabolism and impairs cardiac function in obesity

There are epidemiological associations between obesity and type 2 diabetes, cardiovascular disease and Alzheimers disease. While some common aetiological mechanisms are known, the role of amyloid beta 42 (A{beta}42) in these diverse chronic diseases is obscure. Here we show that adipose tissue releases A{beta}42, which is increased from adipose tissue of obese mice and is associated with higher plasma A{beta}42. Increasing circulating A{beta}42 levels in non-obese mice had no effect on systemic glucose homeostasis but had obesity-like effects on the heart, including reduced cardiac glucose clearance and impaired cardiac function. These effects on cardiac function were not observed when circulating levels of the closely related A{beta}40 isoform were increased. Administration of an A{beta} neutralising antibody prevented obesity-induced cardiac dysfunction and hypertrophy. Furthermore, A{beta} neutralising antibody administration in established obesity prevented further deterioration of cardiac function. Multi-contrast transcriptomic analyses revealed that A{beta}42 impacted pathways of mitochondrial metabolism and exposure of cardiomyocytes to A{beta}42 inhibited mitochondrial function. These data reveal a role for systemic A{beta}42 in the development of cardiac disease in obesity and suggest that therapeutics designed for Alzheimers disease could be effective in combating obesity-induced heart failure.

physiology↗

bioRxiv2020

Integrated analysis of a compendium of RNA-Seq datasets for splicing factors

A vast amount of public RNA-sequencing datasets have been generated and used widely to study transcriptome mechanisms. These data offer precious opportunity for advancing biological research in transcriptome studies such as alternative splicing. We report the first large-scale integrated analysis of RNA-Seq data of splicing factors for systematically identifying key factors in diseases and biological processes. We analyzed 1,321 RNA-Seq libraries of various mouse tissues and cell lines, comprising more than 6.6 TB sequences from 75 independent studies that experimentally manipulated 56 splicing factors. Using these data, RNA splicing signatures and gene expression signatures were computed, and signature comparison analysis identified a list of key splicing factors in Rett syndrome and cold-induced thermogenesis. We show that cold-induced RNA-binding proteins rescue the neurite outgrowth defects in Rett syndrome using neuronal morphology analysis, and we also reveal that SRSF1 and PTBP1 are required for energy expenditure in adipocytes using metabolic flux analysis. Our study provides an integrated analysis for identifying key factors in diseases and biological processes and highlights the importance of public data resources for identifying hypotheses for experimental testing.

bioinformatics↗

bioRxiv2018

A physiological drop in pH decreases mitochondrial respiration, and AMPK and Akt signalling, in L6 myocytes

Exercise stimulates mitochondrial biogenesis and increases mitochondrial respiratory function and content. However, during high-intensity exercise muscle pH can decrease below pH 6.8 with a concomitant increase in lactate concentration. This drop in muscle pH is associated with reduced exercise-induced mitochondrial biogenesis, whilst increased lactate may act as a signaling molecule to affect mitochondrial biogenesis. Therefore, in this study we wished to determine the impact of altering pH and lactate concentration in L6 myotubes on genes and proteins known to be involved in mitochondrial biogenesis. We also examined mitochondrial respiration in response to these perturbations. Differentiated L6 myotubes were exposed to normal (pH 7.5), low (pH 7.0) or high pH (pH 8.0) media with and without 20 mM sodium L-lactate for 1 and 6 h. Low pH and 20 mM Sodium L-Lactate resulted in decreased Akt (Ser473) and AMPK (T172) phosphorylation at 1 h compared to controls, whilst at 6 h the nuclear localisation of HDAC5 was decreased. When the pH was increased both Akt (Ser473) and AMPK (T172) phosphorylation was increased at 1 h. Overall increased lactate decreased the nuclear content of HDAC5 at 6 h. Exposure to both high and low pH media significantly decreased basal mitochondrial respiration, ATP turnover, and maximum mitochondrial respiratory capacity. These data indicate that muscle pH affects several metabolic signalling pathways, including those required for mitochondrial function.

cell biology↗