Biology subjects

Rahaman, S.

Publications and source records attributed to Rahaman, S..

5 recordsLinked to original sources

bioRxiv2026

Redistribution of codon-optimality effects: measurement strategy alters the division of labor between translation and mRNA decay

Codon optimality promotes efficient translation and, as recent research has shown, also extends mRNA lifetimes. However, how control is distributed between translation and mRNA degradation remains unclear. We show that this relative impact depends strongly on the measurement approach. Using fluorescent protein reporters can underestimate codon-optimality-dependent increases in translation efficiency. Conversely, analyses based on poly(A)-selected RNA overestimate the impact on translation, because stable transcripts undergoing poly(A) shortening are often inefficiently captured, leading to skewed protein-to-mRNA ratios. This technical bias is not offset by the marginal decline in ribosomal association observed as mRNAs age. Estimates based on total RNA measurements redistribute some of the control attributed to translation to mRNA stability, making the contributions comparable for mRNAs with shorter coding sequences. For longer mRNAs, codon optimality increasingly controls elongation speed, with a greater effect on translation efficiency than on degradation. These insights highlight the importance of measurement strategy for accurately quantifying the determinants of mRNA stability and protein synthesis.

biochemistry↗

bioRxiv2025

Heat shock induces silent ribosomes and reorganizes mRNA turnover

mRNAs associate with single or multiple ribosomes; these ribosomal assemblies -- monosomes and polysomes -- translate the mRNAs before degradation. The impact of heat stress on this mRNA turnover remains unclear. In heat-shocked yeast cells, the proportion of monosomes within the ribosomal assemblies rises without a corresponding increase in the number of mRNAs associated with them. As a result, most monosomes are devoid of mRNAs and silent, lacking translational initiation factors and proteins facilitating posttranslational folding. The accumulation of silent ribosomes generally reduces the rate of association of transcripts with the ribosomes. However, elevated temperatures enhance the ribosomal association of specific mRNAs, primarily those encoding heat-shock proteins, allowing them to balance their increased degradation rates. Additionally, reduced binding of the Xrn1 exonuclease to mRNAs diminishes the influence of codon optimality on mRNA stability. These mechanisms reorganize mRNA turnover to prioritize heat-shock protein synthesis over ribosome biogenesis.

genomics↗

bioRxiv2025

The Pdgfd-Pdgfrb axis orchestrates tumor-nerve crosstalk in pancreatic cancer

Nerves are an integral component of the tumor microenvironment, contributing to cancer progression, metastasis, morbidity, and mortality. In pancreatic ductal adenocarcinoma (PDAC), worse clinical outcomes are associated with perineural invasion (PNI), a process by which cancer cells surround and invade nerves. Here, we employed whole-transcriptome and single-cell spatial transcriptomics to identify candidate tumor-nerve interactions that promote PNI. We discovered that Pdgfd signaling promotes key features of nerve invasion. Mechanistically, Pdgfd stimulated cancer cell invasiveness, neurite outgrowth, and direct physical engagement with glia. Pharmacological blockade of this axis reduced each of these processes in vitro as well as PNI in vivo. Thus, Pdgfd-Pdgfrb signaling mediates PNI by coordinating multifaceted cancer-neuron-glia interactions and represents a promising therapeutic strategy aimed at disrupting harmful cancer-nerve crosstalk.

cancer biology↗

bioRxiv2024

TRPV4 calcium-permeable channel contributes to valve stiffening in aortic stenosis

Aortic valve stenosis (AVS) is a progressive disease marked by fibrosis, inflammation, calcification, and stiffening of the aortic valve leaflets, leading to disrupted blood flow and left ventricular pressure overload. AVS can result in heart failure and death within 2 to 5 years if left untreated, highlighting its high mortality rate. Understanding the molecular mechanisms of AVS is essential for developing noninvasive treatments. Emerging data suggest that extracellular and intracellular matrix stiffness influences gene expression, inflammation, and cell differentiation. Myofibroblast activation of valvular interstitial cells (VICs) along with excess extracellular matrix (ECM) accumulation and remodeling are primary drivers of AVS progression. Inflammation also plays a critical role, with macrophages accumulating in valve leaflets from AVS patients, promoting inflammation, activating VICs, and synthesizing and remodeling the ECM. Our lab and others have reported that macrophage and fibroblast activities, including migration, inflammatory gene expression, and myofibroblast activation, are sensitive to matrix stiffness, indicating that valve leaflet stiffening may regulate AVS progression via a cellular stiffness sensor. Our published work shows that mechanosensitive Ca2+-permeable transient receptor potential vanilloid 4 (TRPV4) channels regulate fibrosis in other organs and control macrophage and fibroblast activation, suggesting TRPV4 as the potential stiffness sensor in AVS. This implies that fibrosis and tissue stiffening may reinforce each other, creating a vicious cycle in AVS development, with VICs and macrophages playing central roles. Here, we identify the cellular stiffness sensor mediating the link between stiffness and AVS development using human aortic valve tissues, a murine model of aortic valve stenosis, and atomic force microscopy analysis.

pathology↗

bioRxiv2024

Thymidine Phosphorylase Promotes the Formation of Abdominal Aortic Aneurysm in Mice Fed a Western Diet

AimsThe precise molecular drivers of abdominal aortic aneurysm (AAA) remain unclear. Thymidine phosphorylase (TYMP) contributes to increased platelet activation, thrombosis, and inflammation, all of which are key factors in AAA development. Additionally, TYMP suppresses the proliferation of vascular smooth muscle cells (VSMCs), which are central to the development and progression of AAA. We hypothesize that TYMP plays a key role in AAA development. Methods and ResultsWe conducted a histological study using human AAA samples and normal abdominal aortas, revealing heightened levels of TYMP in human AAA vessel walls. To validate this observation, we utilized an Ang II perfusion-induced AAA model in wild-type C57BL/6J (WT) and Tymp-/-mice, feeding them a Western diet (TD.88137) starting from 4 weeks of age. We found that Tymp-/-mice were protected from Ang II perfusion-induced AAA formation. Furthermore, by using TYMP-expressing VSMCs as well as primarily cultured VSMCs from WT and Tymp-/- mice, we elucidated the essential role of TYMP in regulating MMP2 expression and activation. TYMP deficiency or inhibition by tipiracil, a selective TYMP inhibitor, led to reduced MMP2 production, release, and activation in VSMCs. Additionally, TYMP was found to promote pro-inflammatory cytokine expression systemically, and its absence attenuates TNF--stimulated activation of MMP2 and AKT. By co-culturing VSMCs and platelets, we observed that TYMP-deficient platelets had a reduced inhibitory effect on VSMC proliferation compared to WT platelets. Moreover, TYMP appeared to enhance the expression of activated TGF{beta}1 in cultured VSMCs in vitro and in human AAA vessel walls in vivo. TYMP also boosted the activation of thrombospondin-1 type 1 repeat domain-enhanced TGF{beta}1 signaling, resulting in increased connective tissue growth factor production. ConclusionOur findings collectively demonstrated that TYMP serves as a novel regulatory force in vascular biology, exerting influence over VSMC functionality and inflammatory responses that promote the development of AAA. Translational PerspectiveThymidine phosphorylase (TYMP) is increased in the vessel walls of patients with abdominal aortic aneurysm (AAA), and TYMP deficiency in mice reduces the incidence of AAA, suggesting that TYMP plays a crucial role in AAA development. This could be attributed to TYMPs role in enhancing systemic inflammation and thrombosis, inhibiting vascular smooth muscle cell function, increasing the activation of matrix metalloproteinase and AKT, as well as enhancing the expression of TGF{beta}1 and connective tissue growth factor. Tipiracil is an FDA-approved drug known to inhibit TYMP-enhanced thrombosis. Targeting TYMP with tipiracil could represent a promising new therapeutic strategy for AAA development.

cell biology↗