Biology subjects

Sen, S.

Publications and source records attributed to Sen, S..

At least 73 records · Page 4Linked to original sources

bioRxiv2024

Two distinct integrin binding sites on MMP9 drive cancer invasion by mediating integrin membrane trafficking & stabilization

Matrix stiffening has been established to drive cancer progression through increased activity of matrix metalloproteases (MMPs) which degrade the matrix creating paths for migration. However, the non-proteolytic functions of MMPs in cancer invasion remain relatively less understood. Here we have probed the importance of proteolytic and non-proteolytic functions of MMP9, which exhibits robust stiffness dependent expression and secretion in highly invasive cancer cells. We show that while MMP9 sustains spreading and 2D migration non-proteolytically by stabilizing focal adhesions, MMP9 proteolytic activity is essential for 3D invasion. We then establish the function of two distinct integrin {beta}1 (ITG {beta}1) binding sites on MMP9, with the hemopexin domain mediating co-packaging and co-transport of ITG {beta}1/MMP9 to the cell periphery, and the RGD domain stabilizing ITG {beta}1 on the cell membrane prior to matrix degradation. Together, our results illustrate how MMP9 optimizes cancer invasion by spatiotemporally integrating matrix remodeling with adhesion formation.

cell biology↗

bioRxiv2024

Nuclear compression-mediated DNA damage drives ATR-dependent Lamin expression and mouse ESC differentiation

Embryonic stem cells (ESCs) which are susceptible to DNA damage depend on a robust and highly efficient DNA damage response (DDR) mechanism for their survival. However, the implications of physical force-mediated DNA damage on ESC fate remains unclear. We show that stiffness-dependent spreading of mouse ESCs (mESCs) induces DNA damage through nuclear compression, with DNA damage causing differentiation through early induction of Lamin A/C expression. Interestingly, differentiation is associated with rescue of DNA damage and activation of the DDR factor ATR. While ATR is typically known to play roles in DDR pathway, its role during stiffness-mediated nuclear compression and mESC differentiation is unknown. Nuclear enrichment of activated ATR on stiff substrates and reduction of Lamin A/C expression upon ATR inhibition suggests that mESC differentiation is driven by nuclear compression-mediated DNA damage and involves ATR-dependent modulation of Lamin A/C.

cell biology↗

bioRxiv2023

Prognostic relevance of correlated co-expression of coding and noncoding RNAs in cervical cancers

Human papillomavirus (HPV) drives cervical cancer (CaCx) pathogenesis and viral oncoproteins jeopardize global gene expression in such cancers. We aimed to identify differentially expressed coding (DEcGs) and long noncoding (sense intronic and Natural Antisense Transcripts) RNA genes (DElncGs) in HPV16-positive CaCx patients (N=44) compared to HPV-negative normal individuals (N=34). Thereby, employing strand-specific RNA-seq, we determined the relationships between DEcGs and DElncGs and their clinical implications. Gene set enrichment and protein-protein interaction analyses of DEcGs revealed enrichment of processes crucial for abortive virus life cycle and cancer progression. The DEcGs formed 16 gene clusters, portraying cancer-related functions. We recorded significantly correlated co-expression of 79 DElncGs with DEcGs at proximal genomic loci, and 24 such pairs portrayed significantly altered correlation coefficients among patients, compared to normal individuals. Of these, 6 DEcGs belonged to 5 gene clusters, one of which was survival-associated. Out of the 24 correlated DEcG: DElncG pairs, 3 pairs were identified, where expression of both members was significantly associated with patient overall survival. Besides being prognostically relevant, disruption of the significant correlative relationships of such gene pairs in CaCx bears immense potential for patient-targeted therapy. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=141 SRC="FIGDIR/small/573593v1_ufig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@19091c8org.highwire.dtl.DTLVardef@52fbeaorg.highwire.dtl.DTLVardef@18ecf3org.highwire.dtl.DTLVardef@6c5e30_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical Abstract:C_FLOATNO A schematic representation of the analyses undertaken to draw insights on the biological relevance of joint analysis of co-expressed and significantly correlated DElncGs and DEcGs considering the ncNATs and sense intronic DElncGs, in HPV16-positive CaCx patients compared with HPV-negative normal individuals. C_FIG

cancer biology↗

bioRxiv2023

BulkLMM: Real-time genome scans for multiple quantitative traits using linear mixed models

Genetic studies often collect data using high-throughput phenotyping. That has led to the need for fast genomewide scans for large number of traits using linear mixed models (LMMs). Computing the scans one by one on each trait is time consuming. We have developed new algorithms for performing genome scans on a large number of quantitative traits using LMMs, BulkLMM, that speeds up the computation by orders of magnitude compared to one trait at a time scans. On a mouse BXD Liver Proteome data with more than 35,000 traits and 7,000 markers, BulkLMM completed in a few seconds. We use vectorized, multi-threaded operations and regularization to improve optimization, and numerical approximations to speed up the computations. Our soft-ware implementation in the Julia programming language also provides permutation testing for LMMs and is available at https://github.com/senresearch/BulkLMM.jl.

bioinformatics↗

bioRxiv2023

Matrix Linear Models for connecting metabolite composition to individual characteristics

AO_SCPLOWBSTRACTC_SCPLOWHigh-throughput metabolomics data provide a detailed molecular window into biological processes. We consider the problem of assessing how the association of metabolite levels with individual (sample) characteristics such as sex or treatment may depend on metabolite characteristics such as pathway. Typically this is one in a two-step process: In the first step we assess the association of each metabolite with individual characteristics. In the second step an enrichment analysis is performed by metabolite characteristics among significant associations. We combine the two steps using a bilinear model based on the matrix linear model (MLM) framework we have previously developed for high-throughput genetic screens. Our framework can estimate relationships in metabolites sharing known characteristics, whether categorical (such as type of lipid or pathway) or numerical (such as number of double bonds in triglycerides). We demonstrate how MLM offers flexibility and interpretability by applying our method to three metabolomic studies. We show that our approach can separate the contribution of the overlapping triglycerides characteristics, such as the number of double bonds and the number of carbon atoms. The proposed method have been implemented in the open-source Julia package, MatrixLM. Data analysis scripts with example data analyses are also available.

bioinformatics↗

bioRxiv2023

Tradeoffs in the Design of RNA Thermometers

The synthesis of RNA thermometers is aimed at achieving temperature responses with desired thresholds and sensitivities. Although previous works have generated thermometers with a variety of thresholds and sensitivities as well as guidelines for design, possible constraints in the achievable thresholds and sensitivities remain unclear. We addressed this issue using a two-state model and its variants, as well as melt profiles generated from thermodynamic computations. In the two-state model, we found that the threshold was inversely proportional to the sensitivity, in the case of a fixed energy difference between the two states. Notably, this constraint could persist in variations of the two-state model with sequentially unfolding states and branched parallel pathways. Furthermore, the melt profiles generated from a library of thermometers exhibited a similar constraint. These results should inform the design of RNA thermometers as well as other responses that are mediated in a similar fashion.

synthetic biology↗

bioRxiv2023

Fermented polyherbal formulation restored ricinoleic acid-induced diarrhea in Sprague Dawley rats and exhibited in vitro antibacterial effect on multiple antibiotics resistant gastric pathogens

The involvement of multiple antibiotics resistant gastric pathogens in diarrhea aggravates the disease condition uncontrollably. Current study was aimed at finding and developing a suitable formulation utilizing multiple natural components from known plant sources to augment current therapeutic outcomes. Hydro-ethanolic extraction method was applied through boiling and fermentation, on ancient observation based efficacious plant parts for developing antidiarrheal polyherbal formulation AP-01. Animal study model of diarrhea was used to evaluate safety and efficacy of the formulation. The formulation was tested in vitro on four different multiple antibiotics resistant gastric pathogens collected from national repository. The formulation depicted no cytotoxicity on normal gut cells and was efficacious at 10 ml/Kg single dose in relieving symptoms of diarrhea by 79.71%, in comparison with standard drug showing reduction of symptoms by 83.01%. AP-01 exhibited delaying the gastric motility. Symptoms of diarrhea ceased to occur within 321 minutes with AP-01, where the standard drug took 308 minutes. AP-01 was found successful at a viable dosage regimen of 75 to 100 microliter per ml, in inhibiting growth of different pathogens from Enterobacteriaceae family possessing resistance against several classes of antibiotics, in culture media. Chemical analysis revealed different alkaloids, flavonoids and polyphenols those probably work in unison through multiplex modes of action to arrest diarrhea and inhibit pathogens at the same time. These promising results shown by AP-01 should definitely evoke an effort to dive deep into research and development for better therapeutic formulations for infectious diarrhea by harvesting the arsenal of nature.

microbiology↗

bioRxiv2023

Fermented polyherbal formulation ameliorates the severity of acute multiple - antibiotics - resistant Pseudomonas aeruginosa infected burn wound in rat burn model

Pseudomonas aeruginosa, a Gram-negative opportunistic bacterium has emerged as a cause of life-threatening infections in topical burn wounds. Current therapeutic approaches thru wound dressings and systemic medicines are far from satisfactory; multiple-antibiotic-resistance shown by pathogens contribute to failures of therapy causing mortality. This animal study was conducted to check efficacy of one Ayurveda based fermented polyherbal preparation (AP 01) against multiple antibiotic resistant Pseudomonas aeruginosa HW01 infected rat burn wounds. AP-01 was applied on artificially inflected burn wound on rat model infected with Multiple Antibiotics Resistant Pseudomonas aeruginosa to register the healing effects in terms of reduction in residual wound area percentage, presence of C-reactive protein in blood, presence of viable bacteria colony while keeping conventional antibiotics as positive control. The polyherbal preparation had reduced the infected residual burn wound area at 40.63% {+/-} 0.69 from the initial burn wound area within two weeks after a single intervention; whereas residual burn wound area remained much higher in case of animals left untreated and in case of the animals treated with control drug. Restoration to normalcy of serum C-reactive protein level were also achieved earlier in case of polyherbal AP-01 treated groups than other groups. Fermented formulation using components of AP-01 singly or in different combinations were never been tested earlier for topical application in infected burn-wound. The formulation AP-01 was found superior in terms of rate of healing and control of infection by multiple-antibiotic-resistant P. aeruginosa strains in burn wounds in rat model.

microbiology↗

bioRxiv2023

PanEffect: A pan-genome visualization tool for variant effects in maize

Understanding the effects of genetic variants is crucial for accurately predicting traits and phenotypic outcomes. Recent advances have utilized protein language models to score all possible missense variant effects at the proteome level for a single genome, but a reliable tool is needed to explore these effects at the pan-genome level. To address this gap, we introduce a new tool called PanEffect. We implemented PanEffect at MaizeGDB to enable a comprehensive examination of the potential effects of coding variants across 51 maize genomes. The tool allows users to visualize over 550 million possible amino acid substitutions in the B73 maize reference genome and also to observe the effects of the 2.3 million natural variations in the maize pan-genome. Each variant effect score, calculated from the Evolutionary Scale Modeling (ESM) protein language model, shows the log-likelihood ratio difference between B73 and all variants in the pan-genome. These scores are shown using heatmaps spanning benign outcomes to strong phenotypic consequences. Additionally, PanEffect displays secondary structures and functional domains along with the variant effects, offering additional functional and structural context. Using PanEffect, researchers now have a platform to explore protein variants and identify genetic targets for crop enhancement. Availability and implementation: The PanEffect code is freely available on GitHub (https://github.com/Maize-Genetics-and-Genomics-Database/PanEffect). A maize implementation of PanEffect and underlying datasets are available at MaizeGDB (https://www.maizegdb.org/effect/maize/).

bioinformatics↗

bioRxiv2023

Bulky glycocalyx drives cancer invasiveness by modulating substrate-specific adhesion

Majority of the eukaryotic cell surface is decorated with a layer of membrane attached polysaccharides and glycoproteins collectively referred to as the glycocalyx. While formation of a bulky glycocalyx has been associated with cancer progression, the mechanisms by which the glycocalyx regulates cancer invasiveness is incompletely understood. We address this question by first documenting sub-type specific expression of the major glycocalyx glycoprotein Mucin-1 (MUC1) in breast cancer patient samples and breast cancer cell lines. Strikingly, glycocalyx disruption led to inhibition of 2D motility, loss of 3D invasion and reduction of clonal scattering of breast cancer cells at the population level. Tracking of 2D cell motility and 3D invasiveness of MUC1-based sorted sub-populations revealed fastest motility and invasiveness in intermediate MUC1-expressing cells, with glycocalyx disruption abolishing these effects. While differential sensitivity in 2D motility is attributed to a non-monotonic dependence of focal adhesion size on MUC1 levels, higher MUC1 levels enhance 3D invasiveness via increased traction generation. In contrast to inducing cell rounding on collagen-coated substrates, high MUC1 level promotes cell adhesion and confers resistance to shear flow on substrates coated with the endothelial surface protein E-selectin. Collectively, our findings illustrate how MUC1 drives cancer invasiveness by differentially regulating cell-substrate adhesion in a substrate-dependent manner.

cancer biology↗

bioRxiv2023

Measuring RBC deformability and its heterogeneity using a fast microfluidic device

We report a high-throughput microfluidic device to determine the Youngs modulus of single red blood cells (RBCs). Our device consists of a single channel opening into a funnel, with a semi-circular obstacle placed at the mouth of the funnel. As a RBC passes the obstacle, it deflects from its original path. Using populations of artificially-stiffened RBCs, we show that the stiffer RBCs deflect more compared to the healthy RBCs. We then generate a calibration curve that maps each RBC trajectory to its Youngs modulus obtained using an atomic force microscope. Finally, we sort a mixed population of RBCs based on their deformability alone. Our device could potentially be further miniaturized to sort and obtain the elastic constants of nanoscale objects, such exosomes, whose shape change is difficult to monitor by optical microscopy.

bioengineering↗

bioRxiv2023

Localized measurements of water potential reveal large loss of conductance in living tissues of maize leaves

The water status of the living tissue in leaves between the xylem and stomata (outside xylem zone - OXZ) play a critical role for plant function and global mass and energy balance but has remained largely inaccessible. We resolve the local water relations of OXZ tissue using a nanogel reporter of water potential ({psi}), AquaDust, that enables an in-situ, non-destructive measurement of both{psi} of xylem and highly localized{psi} at the terminus of transpiration in the OXZ. Working in maize, these localized measurements reveal gradients in the OXZ that are several fold larger than those based on conventional methods, and values of{psi} in the mesophyll apoplast well below the macroscopic turgor loss potential. We find a strong loss of hydraulic conductance in both the bundle sheath and the mesophyll with decreasing xylem potential but not with evaporative demand. Our measurements suggest an active role played by the OXZ in regulating the transpiration path and our methods provide novel means to study this phenomenon.

physiology↗

bioRxiv2023

Pleiotropic Influence of DNA Methylation QTLs on physiological and aging traits

DNA methylation is influenced by genetic and non-genetic factors. Here, we chart quantitative trait loci (QTLs) that modulate levels of methylation at highly conserved CpGs using liver methylome data from mouse strains belonging to the BXD Family. A regulatory hotspot on chromosome 5 had the highest density of trans-acting methylation QTLs (trans-meQTLs) associated with multiple distant CpGs. We refer to this locus as meQTL.5a. The trans-modulated CpGs showed age-dependent changes, and were enriched in developmental genes, including several members of the MODY pathway (maturity onset diabetes of the young). The joint modulation by genotype and aging resulted in a more "aged methylome" for BXD strains that inherited the DBA/2J parental allele at meQTL.5a. Further, several gene expression traits, body weight, and lipid levels mapped to meQTL.5a, and there was a modest linkage with lifespan. DNA binding motif and protein-protein interaction enrichment analysis identified the hepatic nuclear factor, Hnf1a (MODY3 gene in humans), as a strong candidate. The pleiotropic effects of meQTL.5a could contribute to variation in body size and metabolic traits, and influence CpG methylation and epigenetic aging that could have an impact on lifespan.

genomics↗

bioRxiv2023

Adventitial macrophage accumulation impairs perivascular nerve function in mesenteric arteries with inflammatory bowel disease

1.Introduction: Inflammatory bowel disease (IBD) involves aberrant immune responses and is associated with both cardiovascular disease risk and altered intestinal blood flow. However, little is known about how IBD affects regulation of perivascular nerves that mediate blood flow. Previous work found perivascular nerve function is impaired in mesenteric arteries with IBD. The purpose of this study was to determine the mechanism of impaired perivascular nerve function. Methods: RNA sequencing was performed on mesenteric arteries from IL10-/- mice treated with H.hepaticus to induce disease (IBD) or left non-gavaged (Control). For all other studies, Control and IBD mice received either saline or clodronate liposome injections to study the effect of macrophage depletion. Perivascular nerve function was assessed using pressure myography and electrical field stimulation. Leukocyte populations, and perivascular nerves, and adventitial neurotransmitter receptors were labeled using fluorescent immunolabeling. Results: IBD was associated with increased in macrophage-associated gene expression, and immunolabeling showed accumulation of adventitial macrophages. Clodronate liposome injection eliminated adventitial macrophages, which reversed significant attenuation of sensory vasodilation, sympathetic vasoconstriction and sensory inhibition of sympathetic constriction in IBD. Acetylcholine-mediated dilation was impaired in IBD and restored after macrophage depletion, but sensory dilation remained nitric oxide independent regardless of disease and/or macrophage presence. Conclusion: Altered neuro-immune signaling between macrophages and perivascular nerves in the arterial adventitia contributes to impaired vasodilation, particularly via dilatory sensory nerves. Targeting the adventitial macrophage population may help preserve intestinal blood flow in IBD patients.

physiology↗

bioRxiv2023

Structure of alpha-synuclein fibrils derived from human Lewy body dementia tissue

The defining feature of Parkinson disease (PD) and Lewy body dementia (LBD) is the accumulation of alpha-synuclein (Asyn) fibrils in Lewy bodies and Lewy neurites. We developed and validated a novel method to amplify Asyn fibrils extracted from LBD postmortem tissue samples and used solid state nuclear magnetic resonance (SSNMR) studies to determine atomic resolution structure. Amplified LBD Asyn fibrils comprise two protofilaments with pseudo-21 helical screw symmetry, very low twist and an interface formed by antiparallel beta strands of residues 85-93. The fold is highly similar to the fold determined by a recent cryo-electron microscopy study for a minority population of twisted single protofilament fibrils extracted from LBD tissue. These results expand the structural landscape of LBD Asyn fibrils and inform further studies of disease mechanisms, imaging agents and therapeutics targeting Asyn.

neuroscience↗

bioRxiv2022

Differential transpiration between pods and leaves during stress combination in soybean

Climate change is causing an increase in the frequency and intensity of droughts, heat waves, and their combinations, diminishing agricultural productivity and destabilizing societies worldwide. We recently reported that during a combination of water deficit (WD) and heat stress (HS) stomata on leaves of soybean plants are closed, while stomata on flowers are open. This unique stomatal response was accompanied by differential transpiration (higher in flowers, while lower in leaves) that cooled flowers during a combination of WD+HS. Here we reveal that developing pods of soybean plants subjected to a combination of WD+HS use a similar acclimation strategy of differential transpiration to reduce internal pod temperature by about 4{degrees}C. We further show that enhanced expression of transcripts involved in abscisic acid degradation accompanies this response, and that preventing pod transpiration by sealing stomata causes a significant increase in internal pod temperature. Using an RNA-Seq analysis of pods developing on plants subjected to WD+HS, we also show that the response of pods to WD, HS, or WD+HS is distinct from that of leaves or flowers. Interestingly, we report that although flower, pod and seed numbers per plant are decreased under conditions of WD+HS, seed mass of plants subjected to WD+HS is larger than that of plants subjected to HS, and number of seeds with suppressed/aborted development is lower in WD+HS compared to HS. Taken together our findings reveal that differential transpiration occurs in pods of soybean plants subjected to WD+HS and that this process limits heat-induced damage to seed production. One sentence summaryDifferential transpiration between pods and leaves of soybean plants subjected to a combination of water deficit and heat stress buffers internal pod temperature.

plant biology↗

bioRxiv2022

Global Endometrial DNA Multi-omics Analysis Reveals Insights into mQTL Regulation and Associated Endometriosis Disease Risk

Endometriosis is a leading cause of pain and infertility affecting millions of women globally. Identifying biologic and genetic effects on DNA methylation (DNAm) in endometrium increases understanding of mechanisms that influence gene regulation predisposing to endometriosis and offers an opportunity for novel therapeutic target discovery. Herein, we characterize variation in endometrial DNAm and its association with menstrual cycle phase, endometriosis, and genetic variants through analysis of genome-wide genotype data and methylation at 759,345 DNAm sites in endometrial samples from 984 deeply-phenotyped participants. We identify significant differences in DNAm profiles between menstrual cycle phases and at four DNAm sites between stage III/IV endometriosis and controls. We estimate that 15.4% of the variation in endometriosis is captured by DNAm, and identify DNAm networks associated with endometriosis. DNAm quantitative trait locus (mQTL) analysis identified 118,185 independent cis-mQTL including some tissue-specific effects. We find significant differences in DNAm profiles between endometriosis sub- phenotypes and a significant association between genetic regulation of methylation in endometrium and disease risk, providing functional evidence for genomic targets contributing to endometriosis risk and pathogenesis.

systems biology↗

bioRxiv2022

FASSO: An AlphaFold based method to assign functional annotations by combining sequence and structure orthology

Methods to predict orthology play an important role in bioinformatics for phylogenetic analysis by identifying orthologs within or across any level of biological classification. Sequence-based reciprocal best hit approaches are commonly used in functional annotation since orthologous genes are expected to share functions. The process is limited as it relies solely on sequence data and does not consider structural information and its role in function. Previously, determining protein structure was highly time-consuming, inaccurate, and limited to the size of the protein, all of which resulted in a structural biology bottleneck. With the release of AlphaFold, there are now over 200 million predicted protein structures, including full proteomes for dozens of key organisms. The reciprocal best structural hit approach uses protein structure alignments to identify structural orthologs. We propose combining both sequence- and structure-based reciprocal best hit approaches to obtain a more accurate and complete set of orthologs across diverse species, called Functional Annotations using Sequence and Structure Orthology (FASSO). Using FASSO, we annotated orthologs between five plant species (maize, sorghum, rice, soybean, Arabidopsis) and three distance outgroups (human, budding yeast, and fission yeast). We inferred over 270,000 functional annotations across the eight proteomes including annotations for over 5,600 uncharacterized proteins. FASSO provides confidence labels on ortholog predictions and flags potential misannotations in existing proteomes. We further demonstrate the utility of the approach by exploring the annotation of the maize proteome.

bioinformatics↗