Biology subjects

Sriram, V.

Publications and source records attributed to Sriram, V..

10 recordsLinked to original sources

bioRxiv2026

scRBP infers cell-specific RNA-binding protein regulons from single-cell transcriptomes at gene and isoform resolution

Single-cell regulatory network inference remains dominated by transcription factors, despite RNA-binding proteins (RBPs) orchestrating major aspects of transcriptional regulation. We present scRBP, a framework that infers motif-supported RBP regulons from short- and long-read single-cell transcriptomes at gene and isoform resolution, resolves targets by transcript region (5'UTR, CDS, intron, 3'UTR), scores regulon activity in individual cells, and tests common- and rare-variant association against matched empirical nulls. From 20,746 motifs for 616 RBPs, scRBP recovered experimentally defined targets across 223 ENCODE eCLIP datasets at gene and isoform level. Across 30 tissues, transcript-region preferences separated 3'UTR-associated stability factors from intron-dominant splicing regulators. In published genome-scale CRISPRi Perturb-seq data, scRBP-inferred targets were over-represented among genes responding to RBP knockdown (1.4-2.5-fold across 161 RBPs; FDR<2x10-4). Across 6.2 million cells and 50 traits, scRBP prioritized cell-specific post-transcriptional programs linking human genetic risk to development and disease.

genetics↗

bioRxiv2026

Myeloid STING restrains cardiac remodeling by suppressing macrophage amyloid precursor protein

Mitochondrial DNA (mtDNA) released into the cytosol activates innate immune signaling and promotes inflammation, yet its role in macrophages following sterile tissue injury remains poorly understood. Here, we show that cardiac macrophages from both patients and mice with myocardial infarction (MI) exhibit increased mitochondrial biogenesis, mitochondrial content, membrane potential, and expression of mitochondrial nucleases that facilitate mtDNA release. Consistently, macrophage-specific silencing of genes regulating mitochondrial biogenesis or mtDNA processing attenuated adverse cardiac remodeling after MI. Unexpectedly, despite the role of mtDNA in activating the cGAS-STING pathway, myeloid deletion or macrophage-specific silencing of Sting or cGas exacerbated ventricular dilation, fibrosis, and contractile dysfunction following MI. Single-cell transcriptomic and cell communication analyses identified amyloid precursor protein (APP) as a key downstream effector of STING in cardiac macrophages. Macrophage-specific in vivo App silencing rescued the detrimental effects of myeloid Sting deficiency, establishing APP as a critical mediator of adverse remodeling. Mechanistically, STING interacted with the transcriptional repressor MZF1, promoted its nuclear localization, facilitated its binding to the App promoter, and suppressed App transcription to restrain adverse cardiac remodeling. Together, our findings uncover an unexpected cardioprotective function of myeloid STING and identify the STING-MZF1-APP axis as a previously unrecognized mechanism governing cardiac repair after myocardial infarction.

cell biology↗

bioRxiv2026

Endosomal maturation is controlled by the trimeric Bulli-Mon1-Ccz1 GEF7 complex and Rab5-GTPase activating protein GAPsec

The endolysosomal system is crucial for the degradation of cellular waste in the lysosomal lumen. Within this pathway, endosomes mature prior to their fusion with lysosomes. This process relies on the sequential action of the CORVET and HOPS tethering complexes, guided by Rab5 and Rab7 GTPases, respectively. CORVET acts on early endosomes (EEs), transitioning to HOPS on maturing late endosomes/multivesicular bodies (LEs/MVBs) for lysosomal fusion. This process is finely tuned by the Rab activating guanine nucleotide exchange factor (GEF) and the inactivating GTPase activating protein (GAP). The BuMC1 GEF complex (Bulli-Mon1-Ccz1) uniquely activates Rab7 in metazoans and interacts with Rab5, which stimulates its activity. Here, we identified GAPsec as a novel GAP with activity for Rab5 required for endosomal maturation in fruit fly nephrocytes. Inactivation of GAPsec results in enlarged, dysfunctional endosomes that are unable to reach lysosomes for degradation. Our study highlights the importance of coordinated Rab regulation for efficient endosomal trafficking.

cell biology↗

bioRxiv2025

Inflammation modulates lymph node biomechanics in a sex-dependent manner

Lymph nodes are highly specialized immune organs that orchestrate the adaptive immune response. In the lymph nodes, naive B and T lymphocytes encounter cognate antigens, sparking their activation and response to foreign substances. Lymph nodes grow in response to an immune challenge, at least in part to accommodate increased numbers of infiltrating and proliferating B and T lymphocytes. This behavior is supported by a robust three-dimensional network of extracellular matrix (ECM) fibers and fibroblastic reticular cells (FRCs). ECM fibers and FRCs work synergistically to alternate stretching and contractile forces between them allowing the lymph node to maintain structural integrity during rapid tissue reconstruction. These changes ultimately alter the material properties of the lymph node, which can impact cell migration, proliferation, and differentiation. Recent work has investigated the physiological implications of the changing lymph node microenvironment; however, the biophysical properties of the lymph nodes during these changes remain largely unexplored. Here, we use multiple particle tracking microrheology (MPT), a minimally invasive nanoparticle-based technique to investigate the biophysical properties (elastic/loss moduli, microviscosity, pore size) of lymph nodes post inflammatory stimulus. Our results highlight mechanical changes both during the initial phases of the acute inflammatory response and upon resolution of inflammation, a topic that is relatively understudied. We show that B and T cell rich areas exhibit comparable changes in biomechanical properties over time, suggesting that they restructure in a similar fashion during acute inflammation. Additionally, for the first time, we show that biological sex modulates lymph node biomechanics in acute inflammation: Lymph nodes from female mice showed a [~]20-fold increase in elastic and loss moduli at peak inflammation, while lymph nodes from male mice had a [~]5-fold decrease in both moduli. Additionally, lymph nodes from female mice appeared to permanently remodel during the resolution of acute inflammation resulting in the maintenance of an overall higher elastic and loss modulus, while lymph nodes from male mice returned to the biomechanics of untreated lymph nodes. We also found that at least some of the changes in biomechanical properties were correlated with changes in ECM materials in the lymph nodes, suggesting a structure-function relationship. Overall, our studies provide key insights into how biomechanical properties in lymph nodes are altered during inflammation, a previously unstudied area, and lay the foundation for structure-function relationships involved in immune response. Additionally, we demonstrate a robust technique for the analysis of the lymph node interstitial tissue properties and how they vary with inflammatory stimuli.

bioengineering↗

bioRxiv2024

Deciphering the molecular mechanism associated with the interaction of TULP3 and Histone deacetylases, SIRT1 and SIRT2

Tubby-like protein-3 (TULP3), a member of the tubby family, is recognized for its role in ciliary trafficking, linking membrane-associated proteins to the intraflagellar transport complex A (IFT-A). Mammalian tubby family proteins (TULP1-4), featuring a C-terminal tubby domain, play crucial roles in intracellular transport, signaling, cell differentiation, and motility. TULP3 is also associated with renal and hepatic fibrocystic disease and liver, kidney, and heart degeneration. However, the modulation of TULP3 function and its interacting partners in the cell still need to be understood. Recent studies have indicated interactions between TULP3 and various proteins, including acetylating and deacetylating enzymes. In this study, we investigate the interaction of TULP3 with Sirtuins, SIRT1, and SIRT2 using biochemical and biophysical techniques. Our findings revealed that both the N- and C-terminal domains of TULP3 are necessary for the interaction with SIRT1 and SIRT2. Furthermore, we have identified that TULP3 is not a deacetylation substrate for SIRT1.

biochemistry↗

bioRxiv2024

Elongation of the nascent avian foregut requires coordination of intrinsic and extrinsic cell behaviors

The foregut tube gives rise to the lungs and upper gastrointestinal tract, enabling vital functions of respiration and digestion. How the foregut tube forms during embryonic development has historically received considerable attention, but over the past few decades this question has primarily been addressed indirectly through studies on morphogenesis of the primitive heart tube, a closely related process. As a result, many aspects of foregut development remain unresolved. Here, we exploit the accessibility of the chick embryo to study the initial formation of the foregut tube, combining embryology with fate mapping, live imaging, and biomechanical analyses. The present study reveals that the foregut forms and elongates over a narrower time window than previously thought, and displays marked dorso-ventral and left-right asymmetries early in its development. Through tissue-specific ablation of endoderm along the anterior intestinal portal, we confirm its central biomechanical role in driving foregut morphogenesis, despite not directly contributing cells to the elongating tube. We further confirm the important role of this cell population in formation of the heart tube, with evidence that this role extends to later stages of cardiac looping as well. Together, these data reveal the need for an intricate balance between intrinsic cell behaviors and extrinsic forces for normal foregut elongation, and set the stage for future studies aimed at understanding the underlying molecular cues that coordinate this balance. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=171 HEIGHT=200 SRC="FIGDIR/small/621372v1_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@374c2corg.highwire.dtl.DTLVardef@69ed3aorg.highwire.dtl.DTLVardef@55823aorg.highwire.dtl.DTLVardef@1d8d4fd_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2023

In search of the Goldilocks zone for hybrid speciation II: hard times for hybrid speciation.

Hybridization opens a unique window for observing speciation mechanisms and is a potential engine of speciation. One controversially discussed outcome of hybridization is homoploid hybrid speciation by reciprocal sorting, where a hybrid population maintains a mixed combination of the parental genetic incompatibilities, preventing further gene exchange between the newly formed population and the two parental sources. Previous work showed that, for specific linkage architectures (i.e., the genomic location and order of hybrid incompatibilities), reciprocal sorting could reliably result in hybrid speciation. Yet, the sorting of incompatibilities creates a risk of population extinction. To understand how demographic consequences of the purging of incompatibilities interact with the formation of a hybrid species, we model an isolated hybrid population resulting from a single admixture event. We study how population size, linkage architecture and the strength of the incompatibility affect survival of the hybrid population, resolution/purging of the genetic incompatibilities and the probability of observing hybrid speciation. We demonstrate that the extinction risk is highest for intermediately strong hybrid incompatibilities. In addition, the linkage architecture displaying the highest hybrid speciation probabilities changes drastically with population size. Overall, this indicates that population dynamics can strongly affect the outcome of hybridization and the hybrid speciation probability.

evolutionary biology↗

bioRxiv2021

netCRS: Network-based comorbidity risk score for prediction of myocardial infarction using biobank-scaled PheWAS data

The polygenic risk score (PRS) can help to identify individuals genetic susceptibility for various diseases by combining patient genetic profiles and identified single-nucleotide polymorphisms (SNPs) from genome-wide association studies. Although multiple diseases will usually afflict patients at once or in succession, conventional PRSs fail to consider genetic relationships across multiple diseases. Even multi-trait PRSs, which take into account genetic effects for more than one disease at a time, fail to consider a sufficient number of phenotypes to accurately reflect the state of disease comorbidity in a patient, or are biased in terms of the traits that are selected. Thus, we developed novel network-based comorbidity risk scores to quantify associations among multiple phenotypes from phenome-wide association studies (PheWAS). We first constructed a disease-SNP heterogeneous multi-layered network (DS-Net), which consists of a disease network (disease-layer) and SNP network (SNP-layer). The disease-layer describes the population-level interactome from PheWAS data. The SNP-layer was constructed according to linkage disequilibrium. Both layers were attached to transform the information from a population-level interactome to individual-level inferences. Then, graph-based semi-supervised learning was applied to predict possible comorbidity scores on disease-layer for each subject. The SNP-layer serves as receiving individual genotyping data in the scoring process, and the disease-layer serves as the propagated output for an individuals multiple disease comorbidity scores. The possible comorbidity scores were combined by logistic regression, and it is denoted as netCRS. The DS-Net was constructed from UK Biobank PheWAS data, and the individual genetic profiles were collected from the Penn Medicine Biobank. As a proof-of-concept study, myocardial infarction (MI) was selected to compare netCRS with the PRS with pruning and thresholding (PRS-PT). The combined model (netCRS + PRS-PT + covariates) achieved an AUC improvement of 6.26% compared to the (PRS-PT + covariates) model. In terms of risk stratification, the combined model was able to capture the risk of MI up to approximately eight-fold higher than that of the low-risk group. The netCRS and PRS-PT complement each other in predicting high-risk groups of patients with MI. We expect that using these risk prediction models will allow for the development of prevention strategies and reduction of MI morbidity and mortality.

bioinformatics↗

bioRxiv2021

Imaging-guided fine tuning of CAR synapse dynamics and T cell triggering

T cells typically recognize their ligands using a defined cell biology - the scanning of their membrane microvilli to palpate their environment - while that same membrane scaffolds T cell receptors (TCRs) that can signal upon ligand binding. Chimeric antigen receptors (CARs) present both a therapeutic promise as well as a tractable means to study the interplay between receptor affinity, microvillar dynamics and T cell function. CARs are often built using single-chain variable fragments (scFvs) with far greater affinity than that of natural TCRs. We used high resolution lattice lightsheet (LLS) and total internal reflection fluorescence (TIRF) imaging to visualize microvillar scanning in the context of variations in CAR design. This demonstrated that conventional CARs hyper-stabilized microvillar contacts relative to TCRs. Reducing the affinity and/or avidity of binding brought synapse microvillar dynamics into natural ranges, normalized synapse resolution and improved downstream effector function. This work highlights the importance of understanding the underlying cell biology when designing receptors for optimal antigen engagement.

immunology↗

bioRxiv2020

NETMAGE: a humaN-disEase phenoType MAp GEnerator for the Visualization of PheWAS

SummaryGiven genetic associations from a PheWAS, a disease-disease network can be constructed where nodes represent phenotypes and edges represent shared genetic associations between phenotypes. To improve the accessibility of the visualization of shared genetic components across phenotypes, we developed the humaN-disEase phenoType MAp GEnerator (NETMAGE), a web-based tool that produces interactive phenotype network visualizations from summarized PheWAS results. Users can search the map by a variety of attributes, and they can select nodes to view information such as related phenotypes, associated SNPs, and other network statistics. As a test case, we constructed a network using UK BioBank PheWAS summary data. By examining the associations between phenotypes in our map, we can potentially identify novel instances of pleiotropy, where loci influence multiple phenotypic traits. Thus, our tool provides researchers with a means to identify prospective genetic targets for drug design, contributing to the exploration of personalized medicine. Availability and implementationOur service runs at https://hdpm.biomedinfolab.com. Source code can be downloaded at https://github.com/dokyoonkimlab/netmage. Contactdokyoon.kim@pennmedicine.upenn.edu Supplementary informationSupplementary data and user guide are available at Bioinformatics online.

genetics↗