Biology subjects

Chatterjee, M.

Publications and source records attributed to Chatterjee, M..

At least 19 recordsLinked to original sources

bioRxiv2026

A single-cell transcriptomic atlas of paper wasp brains highlights Kenyon cells' role in social behavior

Social insects provide unique opportunities for studying social interactions, but the cellular and molecular mechanisms underlying these behaviors are poorly understood. Here, we performed single-cell sequencing to profile the transcriptomes of 96,310 cells across four phenotypes of Polistes fuscatus paper wasps: foundresses, workers, gynes, and males, to determine how social states and social interactions are encoded in the physiology of the central brain. We characterized the cellular diversity of the Polistes brain and demonstrate that a substantial portion of the brain is composed of diverse populations of Kenyon cell neurons. The composition and gene-expression profiles of these Kenyon cells, as well other neural and non-neural cell populations, vary across sex, caste, and season. We also demonstrate that social interactions, and even the mere observation of a social interaction, induce significant transcriptomic responses, including signatures of neural activation, across populations of Kenyon cell neurons. Notably, the transcriptional and activational signatures elicited by observing a social interaction frequently overlapped with those induced by direct social interaction, suggesting that a shared neural program underlies both direct social interactions and social observation.

genomics↗

bioRxiv2026

optix regulates abdominal melanin pigmentation in the tobacco hawkmoth Manduca sexta

Research on butterflies has uncovered a conserved "toolkit" of genes for color pattern development and evolution. One of these genes is optix, a homeobox transcription factor that regulates ommochrome and melanin pigmentation, as well as structural coloration, in nymphalid butterflies. It remains unclear, however, whether optix plays any roles in color patterning outside of the Nymphalidae. We used CRISPR-Cas9 to disrupt optix in the tobacco hornwormmoth Manduca sexta and observed a dramatic abdominal pigmentation phenotype, where orange pigmentation was replaced by black eumelanin. Chemical assays suggest that the orange pigment is not an ommochrome, indicating that optix modulates an alternative, uncharacterized pigment pathway in M. sexta. RNA-seq and chemical analyses of orange and black abdominal scales lead us to speculate that the orange pigment may be a type of melanin, perhaps N-{beta}-alanyldopamine (NBAD) sclerotin. Our results suggest that optix plays a deeply ancestral role in pigment regulation in Lepidoptera, and demonstrates evolutionary flexibility in how it interfaces with pigment chemistry across moths and butterflies.

genetics↗

bioRxiv2026

Cajal-Retzius fate specification is disrupted by constitutive activation of β-Catenin in hem progenitors

Cajal-Retzius cells (CR cells) are the earliest born neurons in the cerebral cortex, and have been implicated in regulating neuronal migration and development of circuitry. A major source of CR cells is the cortical hem, a signaling center at the dorsal telencephalic midline. The hem functions as the hippocampal organizer via canonical WNT signaling and hem progenitors are therefore exposed to high levels of WNT ligands. We tested whether constitutive stabilization of {beta}-Catenin (gain of function, GOF) in the mouse cortical hem progenitors supports CR cell production. We find that although neurons are produced from the hem, they do not acquire molecular features of CR cell identity. The trajectory of differentiation examined using single-cell transcriptomics reveals that immature CR cells normally display a Tbr2+ stage, which is absent upon {beta}-Catenin GOF. These data indicate that CR progenitors in the hem are sensitive to levels of stabilized {beta}-Catenin and that a Tbr2+ stage may be important for the acquisition of CR cell identity.

developmental biology↗

bioRxiv2026

AADAT-Driven Metabolic Control of Malate and CoQ10 Shapes Immune Evasion in Triple-Negative Breast Cancer

Compared to other subtypes of breast cancer, triple-negative breast cancers (TNBC) have fewer treatment options and exhibit a worse prognosis. Through integrated transcriptomic, metabolomic, immunohistochemical, spatial, and clinical analyses, we identify the mitochondrial enzyme, -aminoadipate aminotransferase (AADAT) as a previously unrecognized metabolic immune checkpoint in TNBC. AADAT mRNA and protein were significantly upregulated in human TNBC, and high AADAT expression was associated with reduced intra-tumoral CD8 T-cell density and inferior survival. Genetic silencing of AADAT in orthotopic murine TNBC models curtailed primary tumor growth and distant metastasis in a CD8 T-cell-dependent manner, enhanced effector T-cell activation, and sensitized tumors to dual PD-1/CTLA-4 blockade. Mechanistically, unbiased metabolomics showed increased malate levels after AADAT knockdown. Additionally, 4-hydroxyphenylpyruvate, an essential precursor for coenzyme Q10(CoQ10) biosynthesis, decreased following AADAT knockdown, suggesting an impaired mitochondrial electron transport chain. CoQ10 supplementation restored metabolic balance and reversed malate accumulation caused by AADAT knockdown, indicating that AADAT helps maintain CoQ10-supported redox homeostasis, thereby preventing malate buildup and export. Notably, malate addition directly boosted CD8 T-cell oxidative metabolism, increased the NAD/NADH ratio and reactive oxygen species, and augmented TNF- and IFN-{gamma} production. In vivo, malate supplementation in drinking water phenocopied AADAT knockdown, restored the response to paclitaxel plus anti-PD-1 therapy in multiple independent syngeneic TNBC models with de novo or acquired resistance to immunotherapy, reduced tumor burden, and prolonged survival. In patient cohorts, higher spatially clustered intra-tumoral malate is associated with co-localization of functional CD8 T cells, decreased exhausted T-cell neighborhoods, and superior post-chemotherapy outcomes. These data position AADAT as a central metabolic orchestrator of immune escape in TNBC and nominate oral malate as a readily translatable adjuvant to reverse chemo-immunotherapy resistance in TNBC. Statement of SignificanceAADAT defines a metabolic-immune axis driving immune evasion and therapy resistance in triple-negative breast cancer. Blocking AADAT or administering oral malate reactivates CD8 T-cell immunity and sensitizes chemo-immunotherapy-resistant tumors to these agents. These findings uncover a readily translatable metabolic vulnerability with potential to improve outcomes for patients with aggressive breast cancer subtypes.

cancer biology↗

bioRxiv2025

CK2α phosphorylates CHIP for oncogenesis: A novel post-translational switch in cancer

The post-translational regulation of tumor suppressors by oncogenic kinases remains a critical yet underexplored determinant of proteostasis reprogramming in cancer. Here, we identified the E3 ubiquitin ligase CHIP (C-terminus of Hsc70-Interacting Protein) as a direct and functionally relevant substrate of the serine/threonine kinase CK2, which is frequently overexpressed in solid tumors. Using LC/MS analysis, in silico kinase prediction, and molecular interaction mapping, we demonstrated that CK2 phosphorylates CHIP at serine 19 (represented as S19), a conserved residue within its TPR domain, thereby promoting ubiquitination and subsequent proteasomal degradation of CHIP. This phosphorylation-dependent destabilization of CHIP impairs its ability to target oncogenic substrates, such as AKT, resulting in sustained AKT phosphorylation and activation, required for oncogenesis. Clinically, we observed a robust inverse correlation between CK2 and CHIP expressions across colorectal and breast cancer patient datasets, which was validated by immunofluorescence (IF) analyses in tumor samples. Multiple functional assays revealed that CK2 suppression, either by genetic ablation or pharmacological inhibition by TBCA, restores CHIP stability, reactivates apoptotic signalling cascades, and attenuates tumor cell proliferation, migration, and 3D spheroid integrity. Moreover, CK2 blockade in syngeneic murine models diminishes primary tumor burden and metastatic dissemination, concomitant with increased CHIP accumulation and reduced AKT signalling. Mechanistically, a phosphorylation-resistant mutant of CHIP at S19 (CHIP-S19A), is refractory to CK2- mediated degradation and preserves anti-tumor functions, delineating a phosphorylation-dependent proteolytic switch as a central node in the CK2-CHIP-AKT regulatory axis. These findings establish a novel paradigm wherein an oncogenic kinase hijacks protein quality control pathway to suppress tumor suppressive activity and facilitate malignancy. Our study positions CK2 as a druggable modulator of CHIP turnover, offering a translational framework for restoring proteostatic checkpoints and constraining oncogenic signalling in aggressive cancers. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC="FIGDIR/small/682604v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@8fad58org.highwire.dtl.DTLVardef@bd73dforg.highwire.dtl.DTLVardef@2746dorg.highwire.dtl.DTLVardef@129b6ad_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2025

Mucus-associated microbiota consortia: Insights from the advanced TIM-2muc model

The mucus layer lining the epithelium of the colon contains a microbiome that is distinct from the luminal microbiome; this is referred to as the mucus-associated microbiome (MAM). Recently, research on the MAM has gained momentum due to its significant role in immune and metabolic health. However, the study of the MAM is limited by conventional experimental techniques, as sampling this microbiome often requires invasive procedures, making in vivo research challenging. Additionally, obtaining samples from the MAM can compromise the lumen, complicating simultaneous studies of both the MAM and the lumen. To address these limitations, we present the TIM-2muc, an advanced version of the colonic in vitro model TIM-2, which includes a mucus compartment comprising both colonic mucus beads - Gut3Beads and an electrospun sheet coated with Gut3Gel. To validate whether the integrated mucus compartment behaves like the in vivo MAM, we examined the bacterial composition, alpha and beta diversity, and the MAMs composition compared to the lumen compartment of both the TIM-2muc and the conventional TIM-2 model. Our findings suggest that the MAM in the TIM-2muc model closely resembles its in vivo counterpart, thereby enhancing the physiological relevance of the luminal microbiome. TIM-2muc, an advanced TIM-2 model, presents a novel, precise, standardized, and non-invasive method for studying the MAM and LM simultaneously.

microbiology↗

bioRxiv2025

Target the Heart: a new axis of Alzheimer's disease prevention

Cyclosporine A and other calcineurin inhibitors have been identified as prospective treatments for preventing Alzheimers disease. Utilizing a neural network model, Z-LaP Tracker, we previously found that calcineurin inhibitors elicit a unique behavioral profile in zebrafish larvae characterized by increased activity, acoustic hyperexcitability, and reduced visually guided behaviors. Screening a large library of FDA-approved drugs using Z-LaP Tracker revealed a cluster of 65 drugs demonstrating a cyclosporine A-like behavioral profile. 14 of these drugs were heart medications, including angiotensin receptor blockers, beta-blockers, alpha-adrenergic receptor antagonists, and a statin. This suggests some heart medications may be effective in preventing or ameliorating Alzheimers disease pathology. Other studies have shown that many of these 14 drugs directly or indirectly inhibit the calcineurin-NFAT pathway, alike cyclosporine A. Dual administration of the heart medications with cyclosporine A in Z-LaP Tracker revealed synergistic effects: lower doses of each heart medication could be delivered in conjunction with a lower dose of cyclosporine A to evoke a similar or larger behavioral effect than higher doses of each drug independently. This indicates that co-administering a low dose of cyclosporine A with select cardiac drugs could be a potentially effective treatment strategy for Alzheimers disease and cardiovascular dysfunction, while mitigating side effects associated with higher doses of cyclosporine A. Given that heart disease precedes Alzheimers disease in many patients, physicians may be able to create a treatment regimen that simultaneously addresses both conditions. Our results suggest that cyclosporine A combined with simvastatin, irbesartan, cilostazol, doxazosin, or nebivolol are the most promising candidates for future exploration.

animal behavior and cognition↗

bioRxiv2024

Single-nucleus transcriptomics of wing sexual dimorphism and scale cell specialization in sulphur butterflies

The evolution of sexual secondary characteristics necessitates regulatory factors that confer sexual identity to differentiating tissues and cells. In Colias eurytheme butterflies, males exhibit two specialized wing scale types -- UV-iridescent (UVI) and lanceolate scales -- absent in females and likely integral to male courtship behavior. This study investigates the regulatory mechanisms and single-nucleus transcriptomics underlying these two sexually dimorphic cell types during wing development. We show that Doublesex (Dsx) expression is itself dimorphic and required to repress the UVI cell state in females, while unexpectedly, UVI activation in males is independent from Dsx. In the melanic marginal band, Dsx is required in each sex to enforce the presence of lanceolate scales in males, and their absence in females. Single-nucleus RNAseq reveals that UV-iridescent and lanceolate scale cell precursors each show distinctive gene expression profiles at 40% of pupal development, with marker genes that include regulators of transcription, cell signaling, cytoskeletal patterning, and chitin secretion. Both male-specific cell types share a low expression of the Bric-a-brac (Bab) transcription factor, a key repressor of the UVI fate. Bab ChIP-seq profiling suggests that Bab binds the cis-regulatory regions of gene markers associated to UVI fate, including potential effector genes involved in the regulation of cytoskeletal processes and chitin secretion, and loci showing signatures of recent selective sweeps in an UVI-polymorphic population. These findings open new avenues for exploring wing patterning and scale development, shedding light on the mechanisms driving the specification of sex-specific cell states and the differentiation of specialized cell ultrastructures.

developmental biology↗

bioRxiv2024

Integrative spatial omics reveals distinct tumor-promoting multicellular niches and immunosuppressive mechanisms in African American and European American patients with TNBC

Racial disparities in the clinical outcomes of triple-negative breast cancer (TNBC) have been well-documented, but the underlying biological mechanisms remain poorly understood. To investigate these disparities, we employed a multi-omic approach integrating imaging mass cytometry and spatial transcriptomics to characterize the tumor microenvironment (TME) in self-identified Black American (BA) and White American (WA) TNBC patients. Our analysis revealed that the TME in BA patients is marked by a network of endothelial cells, macrophages, and mesenchymal-like cells, which correlates with reduced patient survival. In contrast, the WA TNBC microenvironment is enriched in T-cells and neutrophils, indicative of T-cell exhaustion and suppressed immune responses. Ligand-receptor and pathway analyses further demonstrated that BA TNBC tumors exhibit a relatively "immune-cold" profile, while WA TNBC tumors display features of an "inflamed" TME, suggesting the evolution of a unique immunosuppressive mechanism. These findings provide insight into racially distinct tumor-promoting and immunosuppressive microenvironments, which may contribute to the observed differences in clinical outcomes among BA and WA TNBC patients. Statement of SignificanceThis study identifies distinct tumor microenvironment (TME) profiles in Black and White American TNBC patients, providing new insights into the biological mechanisms driving outcome disparities. Our findings highlight the role of the tumor-endothelial-macrophage niche in these disparities, offering a potential therapeutic target for race-inclusive strategies aimed at improving clinical outcomes. By revealing racial differences in treatment response profiles, this work underscores the necessity for tailored therapies in TNBC. These insights lay the groundwork for the development of inclusive, precision-driven treatment approaches that may help mitigate racial disparities and enhance patient outcomes.

cancer biology↗

bioRxiv2024

mirror determines the far posterior domain in butterfly wings

Insect wings, a key innovation that contributed to the explosive diversification of insects, are recognized for their remarkable variation and many splendid adaptations. Classical morphological work subdivides insect wings into several distinct domains along the antero-posterior (AP) axis, each of which can evolve relatively independently to produce the myriad forms we see in nature. Important insights into AP subdivision of insect wings comes from work in Drosophila melanogaster, however they do not fully explain the diversity of AP domains observed across broad winged insects. Here we show that the transcription factor mirror acts as a selector gene to differentiate a far posterior domain in the butterfly wing, classically defined as the vannus, and has effects on wing shape, scale morphology, and color pattern. Our results support models of how selector genes may facilitate evolutionarily individuation of distinct AP domains in insect wings outside of Drosophila, and suggest that the D. melanogaster wing blade has been reduced to represent only a portion of the archetypal insect wing.

evolutionary biology↗

bioRxiv2024

The ivory lncRNA regulates seasonal color patterns in buckeye butterflies

Long non-coding RNAs (lncRNAs) are transcribed elements increasingly recognized for their roles in regulating gene expression. Thus far, however, we have little understanding of how lncRNAs contribute to evolution and adaptation. Here we show that a conserved lncRNA, ivory, is an important color patterning gene in the buckeye butterfly Junonia coenia. ivory overlaps with cortex, a locus linked to multiple cases of crypsis and mimicry in Lepidoptera. Along with a companion paper by Livraghi et. al., we argue that ivory, not cortex, is the color pattern gene of interest at this locus. In J. coenia a cluster of cis-regulatory elements (CREs) in the first intron of ivory are genetically associated with natural variation in seasonal color pattern plasticity, and targeted deletions of these CREs phenocopy seasonal phenotypes. Deletions of different ivory CREs produce other distinct phenotypes as well, including loss of melanic eyespot rings, and positive and negative changes in overall wing pigmentation. We show that the color pattern transcription factors Spineless, Bric-a-brac, and Ftz-f1 bind to the ivory promoter during wing pattern development, suggesting that they directly regulate ivory. This case study demonstrates how cis-regulation of a single non-coding RNA can exert diverse and nuanced effects on the evolution and development of color patterns, including modulating seasonally plastic color patterns. SignificanceThe genomic locus hosting the cortex gene has been linked to numerous cases of color pattern adaptation in moths and butterflies, including crypsis, mimicry, and seasonal polyphenism. Here we show in buckeye butterflies that the actual color pattern gene at the cortex locus is an evolutionarily conserved long non-coding RNA (lncRNA), dubbed ivory, that overlaps with cortex. Compared with other wing pattern genes, ivory stands out because of the highly nuanced, quantitative changes in pigmentation that can be achieved by manipulating adjacent cis-regulatory sequences. This study highlights how lncRNAs can be important factors underlying morphological evolution, and emphasizes the importance of considering non-coding transcripts in comparative genomics.

genetics↗

bioRxiv2023

Butterfly wing iridescence is regulated by araucan, a direct target of optix and spalt

Butterfly wings exhibit a remarkable diversity of structural iridescent colors, yet the genetic regulation of iridescence remains poorly understood. Here, we show that the Iroquois-complex transcription factor gene araucan plays a role in modulating wing scale iridescence in the common buckeye butterfly, Junonia coenia. Using CRISPR-Cas9 knockouts, we demonstrate that loss of araucan function causes dorsal wing scales to shift from golden-brown to blue iridescence, and eyespot center scales to shift from saturated purple-violet to dull grey-brown. These phenotypes are associated with changes in thickness of the lower lamina in scale cells, a structural feature known to influence thin-film interference, along with reduction of pigmentation in ground scales. Together, these results identify araucan as a single transcription factor that determines coloration by simultaneously regulating both photonic architecture and light-absorbing pigmentation, and show that these effects can be regulated in pattern-specific manner. Our findings provide a framework for linking gene regulation to the spatially coordinated evolution of structural and pigmentary components of color.

genetics↗

bioRxiv2023

Collagen receptor GPVI-mediated platelet activation and pro-coagulant activity aggravates inflammation and aortic wall remodelling in abdominal aortic aneurysm

Platelets play an important role in cardio- and cerebrovascular diseases. Abdominal aortic aneurysm (AAA) is a highly lethal, atherosclerotic-related disease with characteristic features of progressive dilatation of the abdominal aorta and degradation of the vessel wall accompanied by chronic inflammation. Platelet activation and pro-coagulant activity play a decisive role in the AAA pathology as they might trigger AAA development in both mice and men. The present study investigated the impact of the major platelet collagen receptor glycoprotein (GP)VI in cellular processes underlying AAA initiation and progression. Genetic deletion of GPVI offered protection of mice against aortic diameter expansion in experimental AAA. Mechanistically, GPVI deficiency resulted in decreased inflammation with reduced infiltration of neutrophils and platelets into the aortic wall. Further, remodelling of the aortic wall was improved in absence of GPVI, indicated by reduced MMP2/9 and OPN plasma levels and an enhanced -SMA content within the aortic wall, accompanied by reduced cell apoptosis. As a result, an elevation in intima/media thickness and elastin content were observed in GPVI-deficient PPE mice, coursing a significantly reduced aortic diameter expansion and reduced aneurysm incidence. In AAA patients, enhanced plasma levels of soluble GPVI and fibrin, besides fibrin accumulation within the intraluminal thrombus (ILT) suggested that GPVI might serve as a biomarker and mediator in fibrin-supported stabilization of the ILT. In conclusion, our results emphasize the potential need for a GPVI-targeted anti-platelet therapy to reduce AAA initiation and progression, as well as to protect AAA patients from aortic rupture. Translational perspectiveAbdominal aortic aneurysm (AAA) is an atherosclerotic-related, cardiovascular disease (CVD) with high mortality. The impact of platelets in different cellular processes underlying AAA initiation and progression remains unclear.Therefore, we analysed the role of the major platelet collagen receptor GPVI in the pathogenesis of AAA. Results from platelet depleted mice and patients with AAA revealed a significant contribution of GPVI to the inflammatory response and remodelling process of the aorta. Further, elevated accumulation of fibrin, a recently identified ligand of GPVI in the intraluminal thrombus (ILT) and in the plasma of AAA patients, suggests that GPVI binding to fibrin plays a role in ILT formation and probably stabilization of the abdominal aorta. Furthermore, increased levels of sGPVI suggest that GPVI might serve as a clinical biomarker for AAA. Thus, therapeutic targeting of GPVI-mediated platelet activation might be an effective anti-thrombotic strategy for AAA patients.

cell biology↗

bioRxiv2023

Chiral flows in the separating wall during cell division

Material flow in the acto-myosin cortex of a cell, during cell division, has been found to be chiral in nature. Here we look for possible signature of such chirality during the growth of the intra-cellular membrane partition which physically divides the cell into two compartments. Many groups have recorded this partition formation phenomenon in C. elegans embryo, in real time, using fluorescent microscopy. We analyze some of these movies using PIV technique in order to search for signatures of chirality in the acto-myosin flow field on this partition. Further, we use standard hydrodynamic theory of active gell to predict possible chiral flow structures in the growing partition. While the flows in the growing annular shaped membrane partition is mainly radially inward, it can also develop non zero azimuthal velocity components due to chirality.

biophysics↗

bioRxiv2023

Interaction Between HCN and Slack Channels Regulates mPFC Pyramidal Cell Excitability and Working Memory

The ability of monkeys and rats to carry out spatial working memory tasks has been shown to depend on the persistent firing of pyramidal cells in the prefrontal cortex (PFC), arising from recurrent excitatory connections on dendritic spines. These spines express hyperpolarization-activated cyclic nucleotide-gated (HCN) channels whose open state is increased by cAMP signaling, and which markedly alter PFC network connectivity and neuronal firing. In traditional neural circuits, activation of these non-selective cation channels leads to neuronal depolarization and increased firing rate. Paradoxically, cAMP activation of HCN channels in PFC pyramidal cells reduces working memory-related neuronal firing. This suggests that activation of HCN channels may hyperpolarize rather than depolarize these neurons. The current study tested the hypothesis that Na+ influx through HCN channels activates Na+-activated K+ (KNa or Slack) channels to hyperpolarize the membrane. We have found that HCN and Slack KNa channels co-immunoprecipitate in cortical extracts and that, by immunoelectron microscopy, they colocalize at postsynaptic spines of PFC pyramidal neurons. A specific blocker of HCN channels, ZD7288, reduces KNa current in pyramidal cells that express both HCN and Slack channels, indicating that blockade of HCN channels reduced K+ current indirectly by lowering Na+ influx. In contrast, ZD7288 has no effect on KNa currents in an HEK cell line stably expressing this Slack channels but no HCN channels, demonstrating that ZD7288 does not block Slack channels directly. Activation of HCN channels by cAMP in a cell line expressing a Ca2+ reporter results in elevation of cytoplasmic Ca2+, but the effect of cAMP is completely reversed if the HCN channels are co-expressed with Slack channels. Finally, we have used a novel pharmacological blocker of Slack channels to show that inhibition of either Slack or HCN channels in rat PFC improves working memory performance, and that the actions of Slack and HCN channel blockers occlude each other in the memory task. Our results suggest that the regulation of working memory by HCN channels in PFC pyramidal neurons is mediated by an HCN-Slack channel complex that links activation HCN channels to suppression of neuronal excitability.

neuroscience↗

bioRxiv2023

Proteome encoded determinants of protein sorting into extracellular vesicles

Extracellular vesicles (EVs) are membranous structures released by cells into the extracellular space and are thought to be involved in cell-to-cell communication. While EVs and their cargo are promising biomarker candidates, protein sorting mechanisms of proteins to EVs remain unclear. In this study, we ask if it is possible to determine EV association based on the protein sequence. Additionally, we ask what the most important determinants are for EV association. We answer these questions with explainable AI models, using human proteome data from EV databases to train and validate the model. It is essential to correct the datasets for contaminants introduced by coarse EV isolation workflows and for experimental bias caused by mass spectrometry. In this study, we show that it is indeed possible to predict EV association from the protein sequence: a simple sequence-based model for predicting EV proteins achieved an area under the curve of 0.77{+/-}0.01, which increased further to 0.84{+/-}0.00 when incorporating curated post-translational modification (PTM) annotations. Feature analysis shows that EV associated proteins are stable, polar, and structured with low isoelectric point compared to non-EV proteins. PTM annotations emerged as the most important features for correct classification; specifically palmitoylation is one of the most prevalent EV sorting mechanisms for unique proteins. Palmitoylation and nitrosylation sites are especially prevalent in EV proteins that are determined by very strict isolation protocols, indicating they could potentially serve as quality control criteria for future studies. This computational study offers an effective sequence-based predictor of EV associated proteins with extensive characterisation of the human EV proteome that can explain for individual proteins which factors contribute to their EV association.

bioinformatics↗

bioRxiv2023

UVB modifies skin immune-stroma cross-talk and promotes effector T cell recruitment during cryptic Leishmania donovani infection

Many parasites of significant public health importance assume skin residency without causing overt pathlogy. How immune and stromal cells respond to such "cryptic" infections and how exposure to UVB alters such responses in poorly understood. We combined scRNA-seq, spatial transcriptomics and inferential network analysis to address these questions in a model of cryptic skin infection by Leishmania donovani. In infected C57BL/6 mice, p-selectin and CXCL12 interactions dominate intercellular communication between leucocytes, fibroblast and endothelial cells, but effector T cell function remains muted. Following UVB exposure, increased numbers of IFN{gamma}+ CD4+ Th1 cells and NK cells enter the skin, communicating with stromal cells via CCL5-CCR5 and LFA-1-ICAM1/2. However, spatial mapping indicated that Th1 cells and macrophages occupied distinct niches after UVB exposure, likely limiting effector function. Our data provide the first holistic view of the immune landscape during cryptic L. donovani infection and demonstrate how UVB exposure fundamentally reshapes this response. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=141 SRC="FIGDIR/small/526940v1_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@1238cbaorg.highwire.dtl.DTLVardef@ec350eorg.highwire.dtl.DTLVardef@18f412corg.highwire.dtl.DTLVardef@1ffd468_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2022

Platelets modulate inflammation and matrix remodeling in abdominal aortic aneurysm

Abdominal aortic aneurysm (AAA) is a highly lethal disease with progressive dilatation of the abdominal aorta accompanied by degradation and remodelling of the vessel wall due to chronic inflammation. Platelets play an important role in cardiovascular diseases but their role in AAA is poorly understood. The present study revealed that platelets play a crucial role in promoting AAA through modulation of inflammation and degradation of the ECM. They are responsible for the up-regulation of SPP1 (osteopontin, OPN) gene expression in macrophages and aortic tissue, which triggers inflammation and remodeling but also platelet adhesion and migration into the abdominal aortic wall and the intraluminal thrombus (ILT). Further, enhanced platelet activation and pro-coagulant activity results in elevated gene expression of various cytokines, Mmp9 and Col1a1 in macrophages and Il-6 and Mmp9 in fibroblasts. Enhanced platelet activation and pro-coagulant activity was also detected in AAA patients. Further, we detected platelets and OPN in the vessel wall and in the ILT of patients who underwent open repair of AAA. Platelet depletion in experimental murine AAA reduced inflammation and ECM remodeling, with reduced elastin fragmentation and aortic diameter expansion. Of note, OPN co-localized with platelets, suggesting a potential role of OPN for the recruitment of platelets into the ILT and the aortic wall. In conclusion, our data strongly supports the potential relevance of anti-platelet therapy to reduce AAA progression and rupture in AAA patients. Translational perspectiveAbdominal aortic aneurysm (AAA) is a severe cardiovascular disease (CVD) with high mortality. Since the role of platelets is unclear, we explored platelet-mediated processes in the pathogenesis of AAA. Results from platelet depleted mice and patients with AAA revealed that platelets modulate inflammatory and stiffness-related gene expression of macrophages and fibroblasts. Further, platelets induce the release of osteopontin important for the recruitment of platelets to the aortic wall and to the intraluminal thrombus (ILT). Consequently, platelet depletion significantly reduced aneurysm growth. Thus, therapeutic targeting of platelet activation might be crucial for the treatment of patients to reduce AAA formation and progression.

molecular biology↗