Biology subjects

Kraft, M.

Publications and source records attributed to Kraft, M..

At least 19 recordsLinked to original sources

bioRxiv2026

A synthetic xeno-free extracellular matrix surrogate supports robust human induced pluripotent stem cell maintenance and multilineage differentiation

Animal-derived surface coatings present the gold standard in stem cell culture. However, they come with major drawbacks such as lot-to-lot inconsistency and an ethically problematic production. Approaches to develop synthetic coating alternatives have largely failed to recapitulate biological functions essential to PSC-self renewal and differentiation. In this study, we have investigated the suitability of a fully synthetic, chemically defined extracellular matrix-mimicking coating named BIOINSTRUCT for hiPSC culture. BIOINSTRUCT was employed during maintenance culture of IMR90-4 cells, as well as directed differentiation of HIHCNi008-A, ACTN2-GFP, and UKKI-011-A cells. BIOINSTRUCT preserved hiPSC characteristics over the experimental period of 10 passages similar to Matrigel. Spontaneous differentiation resulted in the formation of ectodermal, mesodermal and endodermal derivatives, confirming the retention of pluripotency. Directed differentiation on BIOINSTRUCT enabled the generation of neuronal, cardiac and pancreatic endocrine cells. Altogether, our data underscore BIOINSTRUCT as a promising alternative to animal-derived extracellular matrix coatings.

cell biology↗

bioRxiv2026

Deep axonal proteomics of human iPSC-derived neurons by microfluidic separation and DIA-MS

One of the defining features of neurons is their compartmentalisation into soma, dendrites and axon. Axons are highly specialised for the transmission of signals over long distances but also exhibit unique vulnerabilities in the context of neurodegeneration, implying a specialised axonal proteome. However, in-depth proteomic characterisation of axons has been limited by the difficulty of isolating pure axonal material in sufficient quantities for conventional mass spectrometry analysis. Here, we combine microfluidic-based axon-soma separation with data-independent acquisition mass spectrometry (DIA-MS) on an Orbitrap Astral mass spectrometer for deep profiling of compartment-resolved proteomes of human induced pluripotent stem cell (iPSC)-derived cortical neurons. We quantify over 9,000 proteins in the somatodendritic compartment and [~]6,000 proteins in the axonal compartment, to our knowledge, representing the deepest human axonal proteome reported to date. Differential abundance analysis identifies 1,250 axon-enriched proteins with strong enrichment of axon-related pathways including vesicle-mediated transport, synaptic vesicle dynamics, and cytoskeletal organisation. Extending this workflow to iPSC-derived lower motor neurons, we reveal a core set of 417 axon-enriched proteins shared between cortical and lower motor neurons, alongside subtype-specific axonal signatures whose functional differences become evident only through compartment-restricted analysis. We show broad coverage of genes for the neurodegenerative diseases hereditary spastic paraplegia and amyotrophic lateral sclerosis, establishing a quantitative reference for interpreting how disease-linked mutations may differentially affect axonal versus somatodendritic proteostasis. This workflow and resource are readily applicable to other neuronal subtypes and disease models, paving the way for studying axonal proteome dynamics in health and disease. HighlightsO_LIDeepest human axonal proteome with [~]6,000 proteins from iPSC-derived neurons C_LIO_LIMicrofluidic separation paired with DIA mass spectrometry C_LIO_LIAxon-specific signatures masked in whole-cell analyses are revealed C_LIO_LICore set of 417 axon-enriched proteins shared across neuron subtypes C_LIO_LIFramework for studying axon-selective vulnerability in neurodegeneration C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=74 SRC="FIGDIR/small/739061v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@191493dorg.highwire.dtl.DTLVardef@15f459forg.highwire.dtl.DTLVardef@1d3e61forg.highwire.dtl.DTLVardef@a9262a_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2026

Disruption of RBM20 causes atrial electrophysiological disturbances

BackgroundDilated cardiomyopathy (DCM) is a leading cause of heart failure, with 30-50 % of cases attributed to familial inheritance. Mutations in RNA-binding motif protein 20 (RBM20) account for 3-5 % of cases and are associated with severe DCM and ventricular arrhythmias. However, the role of RBM20 mutations in atrial cardiomyopathy (AtCM) and atrial fibrillation (AF) remains underexplored. This study investigates the effects of the RBM20-R636Q mutation on atrial electrophysiology and evaluates sodium-glucose co-transporter (SGLT) inhibitors as potential therapeutics. ResultsRbm20-R636Q mice exhibited atrial remodeling, including hypertrophy, left atrial enlargement, and shortened action potential duration at 90% repolarization (APD90). Compared with RBM20-knockout and laminopathy models, RBM20-R636Q mice showed distinct reductions in Ito / IKur without changes in IK,sus or IK,tail currents, alongside TASK-1 potassium current upregulation and alterations of ICaL. SGLT inhibitors (sotagliflozin, empagliflozin, dapagliflozin) reduced AP inducibility and partially restored APD90, with effects comparable to lidocaine, suggesting a role in modulating peak sodium currents. ConclusionsRBM20 mutations contribute to atrial remodeling, promoting AtCM and AF. SGLT inhibitors demonstrate therapeutic potential by modulating atrial electrophysiology and reducing arrhythmogenesis, offering a promising strategy for managing RBM20-related cardiac disorders. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=156 SRC="FIGDIR/small/711772v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@7bcccaorg.highwire.dtl.DTLVardef@1c20b0dorg.highwire.dtl.DTLVardef@63bbcdorg.highwire.dtl.DTLVardef@1bea67f_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2026

Transcriptional regulation of the TASK-1 potassium channel by ETV1 -Implications for atrial excitability

BackgroundAtrial fibrillation (AF), the most common sustained arrhythmia, is driven by electrical and structural remodelling, including altered ion channel expression. The atrial-specific potassium channel TASK-1 regulates action potential duration (APD) and is differentially expressed in AF and left ventricular dysfunction, but the mechanisms controlling its expression are not well understood. ObjectiveThis study examines whether the transcription factor ETV1 regulates TASK-1 and contributes to atrial electrical remodelling. MethodsAtrial tissue from patients with and without AF was analysed to assess the relationship between ETV1 and TASK-1 (KCNK3) expression. In HL-1 cardiomyocyte-like cells and native fibroblasts, ETV1 activity was reduced using pharmacological inhibition or siRNA-mediated knockdown. TASK-1 expression, TASK-1 current, and APD at 90% repolarization were measured. Pacing experiments tested activity-dependent TASK-1 regulation. Direct transcriptional regulation was evaluated using ChIP-qPCR and ChIP-seq to detect ETV1 binding at the KCNK3 promoter. ResultsETV1 and TASK-1 levels were positively correlated in human atrial tissue. In HL-1 cells and fibroblasts, ETV1 inhibition or knockdown decreased TASK-1 expression and current and selectively prolonged APD90. Pacing-induced upregulation of TASK-1 was prevented by ETV1 inhibition, indicating a protective effect against pro-arrhythmic remodelling. ChIP-qPCR and ChIP-seq confirmed direct ETV1 binding to the KCNK3 promoter. ConclusionETV1 directly regulates TASK-1 expression and contributes to atrial electrical remodelling, identifying ETV1 as a potential upstream therapeutic target in AF. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=89 SRC="FIGDIR/small/711402v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@3e5b25org.highwire.dtl.DTLVardef@1d1f909org.highwire.dtl.DTLVardef@34cf37org.highwire.dtl.DTLVardef@1105539_HPS_FORMAT_FIGEXP M_FIG C_FIG Translational perspectiveAtrial fibrillation is sustained by maladaptive electrical remodelling that remains insufficiently addressed by current rhythm-control therapies. Direct inhibition of individual ion channels has shown efficacy but is limited by phenotype dependence and proarrhythmic risk. The present data identify ETV1 as an upstream transcriptional regulator of the atrial-specific potassium channel TASK-1. Modulation of ETV1 reduced TASK-1 expression, prolonged atrial repolarisation, and prevented tachycardia-induced electrical remodelling in vitro. Targeting ETV1 may therefore represent a disease-modifying strategy that intervenes earlier in the remodelling cascade than conventional antiarrhythmic drugs. This approach could enable phenotype-guided therapy in atrial cardiomyopathy, particularly in patients with preserved ventricular function, and warrants validation in translational large-animal and clinical studies.

molecular biology↗

bioRxiv2025

Advancing EEG Biosensing: Novel Scalable Production of Platinum-Silicon Microneedles

This study presents the development and analysis of a silicon microneedle electrode array fabricated using a streamlined, two-step approach for enhanced bio-signal recording applications. Numerical simulations with COMSOL Multiphysics were employed to optimize the microneedle array design, focusing on mechanical stability and minimizing skin-electrode impedance. Structural analysis identified needle lengths between 500 m and 700 m as optimal for mechanical robustness, with critical load factors indicating a high resistance to buckling under applied forces. Optimal needle spacing was determined to prevent inter-needle interference and ensure effective skin penetration. Proof-of-concept electroencephalography testing confirmed that the microneedles achieved reliable bio-signal recording, comparable to traditional wet electrodes, while offering advantages such as reduced preparation time and improved user comfort. This work establishes a simple and cleanroom-compatible, scalable method for fabricating platinum-coated silicon microneedle arrays, advancing the development of wearable, user-friendly biopotential monitoring devices.

bioengineering↗

bioRxiv2025

Intracortical bipolar stimulation allows selective activation of neuronal populations in the cortex

BackgroundIntracortical electrical stimulation has emerged as a promising approach for sensory restoration, such as a cortical visual prosthesis, yet its effectiveness is limited by current spread and electrode density constraints. ObjectiveTo determine whether intracortical bipolar current steering--via modulation of the return electrode position--can enhance neural activation selectivity compared to traditional monopolar stimulation, with the aim of improving spatial precision in sensory restoration. MethodsWe applied intracortical stimulation and used two-photon calcium imaging on acute brain slices to directly visualize neural responses to bipolar stimulation. Biophysical computational modeling was used to complement the experimental results. The analysis included both cellular and population-level assessments to evaluate the impact of several stimulation patterns, such as current direction, electrode spacing and current amplitude, on recruitment patterns. ResultsBipolar stimulation selectively activated distinct neural populations based on the direction of the current flow. This approach decreased the overlap between activated groups and increased the number of independently addressable neural clusters by up to 9-fold relative to monopolar stimulation. Moreover, the electrode configuration and spacing critically influenced the spatial spread of activation. ConclusionsIntracortical bipolar current steering enhances neural activation selectivity by engaging independent neural populations through current directionality. These findings suggest that this strategy may improve the spatial precision of neural prosthetics and sensory restoration without the need for an increased electrode density.

neuroscience↗

bioRxiv2025

Identification of a multi-omics factor predictive of long COVID in the IMPACC study

Following SARS-CoV-2 infection, [~]10-35% of COVID-19 patients experience long COVID (LC), in which often debilitating symptoms persist for at least three months. Elucidating the biologic underpinnings of LC could identify therapeutic opportunities. We utilized machine learning methods on biologic analytes and patient reported outcome surveys provided over 12 months after hospital discharge from >500 hospitalized COVID-19 patients in the IMPACC cohort to identify a multi-omics "recovery factor". IMPACC participants who experienced LC had lower recovery factor scores compared to participants without LC. Biologic characterization revealed increased levels of plasma proteins associated with inflammation, elevated transcriptional signatures of heme metabolism, and decreased androgenic steroids in LC patients. The recovery factor was also associated with altered circulating immune cell frequencies. Notably, recovery factor scores were predictive of LC occurrence in patients as early as hospital admission, irrespective of acute disease severity. Thus, the recovery factor identifies patients at risk of LC early after SARS-CoV-2 infection and reveals LC biomarkers and potential treatment targets.

systems biology↗

bioRxiv2025

A wireless, scalable and modular EEG sensor network platform for unobtrusive brain recordings

This paper introduces a modular sensing platform for wearable electroencephalography (EEG) recordings. The platform is conceived as a wireless EEG sensor network (WESN), consisting of multiple miniaturized, wireless EEG sensor nodes that synchronously collect EEG data from different scalp locations. As there are no wires between the different sensors, the platform provides maximal flexibility and discreetness, combined with a reduced sensitivity to motion artefacts or electro-magnetic interference. By removing the driven right leg (DRL) electrode and reducing the within-node electrode spacing to 3cm, we obtain a compact design while maintaining a high signal integrity. The WESN system was validated through a series of experiments: achieving synchronization of EEG data transmission across multiple sensor nodes and the detection of actual neural responses in EEG experiments. These results demonstrate the effectiveness and robustness of the proposed WESN platform, establishing it as a promising research platform for scalable, flexible, and discreet multi-channel EEG monitoring in ambulatory settings.

bioengineering↗

bioRxiv2024

Unraveling SARS-CoV-2 Host-Response Heterogeneity through Longitudinal Molecular Subtyping

Hospitalized COVID-19 patients exhibit diverse immune responses during acute infection, which are associated with a wide range of clinical outcomes. However, understanding these immune heterogeneities and their links to various clinical complications, especially long COVID, remains a challenge. In this study, we performed unsupervised subtyping of longitudinal multi-omics immunophenotyping in over 1,000 hospitalized patients, identifying two critical subtypes linked to mortality or mechanical ventilation with prolonged hospital stay and three severe subtypes associated with timely acute recovery. We confirmed that unresolved systemic inflammation and T-cell dysfunctions were hallmarks of increased severity and further distinguished patients with similar acute respiratory severity by their distinct immune profiles, which correlated with differences in demographic and clinical complications. Notably, one critical subtype (SubF) was uniquely characterized by early excessive inflammation, insufficient anticoagulation, and fatty acid dysregulation, alongside higher incidences of hematologic, cardiac, and renal complications, and an elevated risk of long COVID. Among the severe subtypes, significant differences in viral clearance and early antiviral responses were observed, with one subtype (SubC) showing strong early T-cell cytotoxicity but a poor humoral response, slower viral clearance, and greater risks of chronic organ dysfunction and long COVID. These findings provide crucial insights into the complex and context-dependent nature of COVID-19 immune responses, highlighting the importance of personalized therapeutic strategies to improve both acute and long-term outcomes.

immunology↗

bioRxiv2024

Chronic Viral Reactivation and Associated Host Immune Response and Clinical Outcomes in Acute COVID-19 and Post-Acute Sequelae of COVID-19

Chronic viral infections are ubiquitous in humans, with individuals harboring multiple latent viruses that can reactivate during acute illnesses. Recent studies have suggested that SARS- CoV-2 infection can lead to reactivation of latent viruses such as Epstein-Barr Virus (EBV) and cytomegalovirus (CMV), yet, the extent and impact of viral reactivation in COVID-19 and its effect on the host immune system remain incompletely understood. Here we present a comprehensive multi-omic analysis of viral reactivation of all known chronically infecting viruses in 1,154 hospitalized COVID-19 patients, from the Immunophenotyping Assessment in a COVID-19 Cohort (IMPACC) study, who were followed prospectively for twelve months. We reveal significant reactivation of Herpesviridae, Enteroviridae, and Anelloviridae families during acute stage of COVID-19 (0-40 days post- hospitalization), each exhibiting distinct temporal dynamics. We also show that viral reactivation correlated with COVID-19 severity, demographic characteristics, and clinical outcomes, including mortality. Integration of cytokine profiling, cellular immunophenotyping, metabolomics, transcriptomics, and proteomics demonstrated virus-specific host responses, including elevated pro-inflammatory cytokines (e.g. IL-6, CXCL10, and TNF), increased activated CD4+ and CD8+ T-cells, and upregulation of cellular replication genes, independent of COVID-19 severity and SARS-CoV-2 viral load. Notably, persistent Anelloviridae reactivation during convalescence ([≥]3 months post-hospitalization) was associated with Post-Acute Sequelae of COVID-19 (PASC) symptoms, particularly physical function and fatigue. Our findings highlight a remarkable prevalence and potential impact of chronic viral reactivation on host responses and clinical outcomes during acute COVID-19 and long term PASC sequelae. Our data provide novel immune, transcriptomic, and metabolomic biomarkers of viral reactivation that may inform novel approaches to prognosticate, prevent, or treat acute COVID- 19 and PASC.

immunology↗

bioRxiv2024

The FAIR-Device - a non-lethal and generalist semi-automatic Malaise trap for insect biodiversity monitoring: Proof of concept

Field monitoring plays a crucial role in understanding insect dynamics within ecosystems. It facilitates pest distribution assessment, control measure evaluation, and prediction of pest outbreaks. Additionally, it provides important information on bioindicators with which the state of biodiversity and ecological integrity in specific habitats and ecosystems can be accurately assessed. However, traditional monitoring systems can present various difficulties, leading to a limited temporal and spatial resolution of the obtained information. Despite recent advancements in automatic insect monitoring traps, also called e-traps, most of these systems focus exclusively on studying agricultural pests, rendering them unsuitable for monitoring diverse insect populations. To address this issue, we introduce the Field Automatic Insect Recognition (FAIR)-Device, a novel non-lethal field tool that relies on semi-automatic image capture and species identification using artificial intelligence via the iNaturalist platform. Our objective was to develop an automatic, cost-effective, and non-specific monitoring solution capable of providing high-resolution data for assessing insect diversity. During a 26-day proof-of-concept evaluation, the FAIR-Device recorded 24.8 GB of video, identifying 431 individuals from 9 orders, 50 families, and 69 genera. While improvements are possible, our device demonstrated potential as a cost-effective, non-lethal tool for monitoring insect biodiversity. Looking ahead, we envision new monitoring systems such as e-traps as valuable tools for real-time insect monitoring, offering unprecedented insights for ecological research and agricultural practices.

zoology↗

bioRxiv2024

Genetic polymorphisms of Leukocyte Immunoglobulin-Like Receptor B3 (LILRB3) gene in African American kidney transplant recipients are associated with post-transplant graft failure

BackgroundAfrican American (AA) kidney transplant recipients exhibit a higher rate of graft loss compared to other racial and ethnic populations, highlighting the need to identify causative factors underlying this disparity. MethodWe analyzed RNA sequences of pretransplant whole blood from subjects followed in three kidney transplant cohorts to identify single nucleotide polymorphisms (SNPs) associated with death censored graft loss (DCGL). We employed a meta-analysis to uncover key transcriptional signatures and pathways associated with the identified SNPs and used single cell RNA to define cellular specificity. We characterized SNP functions using in vitro immunological and survival assays and tested for associations between the identified SNPs and other immune-related diseases using a [~]30,100 subject, electronic health record (EHR)-linked database. ResultsWe uncovered a cluster of four consecutive missense SNPs in the Leukocyte Immunoglobulin-Like Receptor B3 (LILRB3, a negative immune response regulator) gene that strongly associated with DCGL. This LILRB3-4SNPs cluster encodes missense mutations at amino acids 617-618 proximal to a SHP-1/2 phosphatase-binding ITIM motif. LILRB3-4SNPs is specifically enriched within subjects of AA ancestry (8.6% prevalence vs 2.3% in Hispanic and 0.1% in European populations), is not linked to APOL1 G1/G2 alleles, and exhibited a strong association with DCGL. Analysis of PBMC and transplant biopsies from recipients with LILRB3-4SNPs showed evidence of enhanced adaptive immune responsiveness and ferroptosis-associated death in monocytes. Overexpression of the variant allele in THP-1 cells (macrophage line) induced augmented inflammation and ferroptosis, which were attenuated by a ferroptosis inhibitor, verifying a causal link. The LILRB3-4SNPs also associated with multiple systemic and organ-specific immune-related diseases in AAs, consistent with conferring a broadly relevant immune function. Conclusionthe LILRB3-4SNPs represent a functionally important, distinct genetic risk factor for kidney transplant outcome and development/severity of other immune-related diseases in patients of AA ancestry. Pharmacological targeting of ferroptosis should be tested to prevent or treat these disease processes in AA recipients carrying LILRB3-4SNPs.

genetics↗

bioRxiv2023

Integrated longitudinal multi-omics study identifies immune programs associated with COVID-19 severity and mortality in 1152 hospitalized participants

Hospitalized COVID-19 patients exhibit diverse clinical outcomes, with some individuals diverging over time even though their initial disease severity appears similar. A systematic evaluation of molecular and cellular profiles over the full disease course can link immune programs and their coordination with progression heterogeneity. In this study, we carried out deep immunophenotyping and conducted longitudinal multi-omics modeling integrating ten distinct assays on a total of 1,152 IMPACC participants and identified several immune cascades that were significant drivers of differential clinical outcomes. Increasing disease severity was driven by a temporal pattern that began with the early upregulation of immunosuppressive metabolites and then elevated levels of inflammatory cytokines, signatures of coagulation, NETosis, and T-cell functional dysregulation. A second immune cascade, predictive of 28-day mortality among critically ill patients, was characterized by reduced total plasma immunoglobulins and B cells, as well as dysregulated IFN responsiveness. We demonstrated that the balance disruption between IFN-stimulated genes and IFN inhibitors is a crucial biomarker of COVID-19 mortality, potentially contributing to the failure of viral clearance in patients with fatal illness. Our longitudinal multi-omics profiling study revealed novel temporal coordination across diverse omics that potentially explain disease progression, providing insights that inform the targeted development of therapies for hospitalized COVID-19 patients, especially those critically ill.

immunology↗

bioRxiv2023

Penile cavernous sinusoids are Prox1-positive hybrid vessels

Endothelial cells (ECs) of blood and lymphatic vessels have distinct identity markers that define their specialized functions. Recently, specialized hybrid vasculatures with both blood and lymphatic vessel-specific features have been discovered in multiple tissues. Here, we identify the penile cavernous sinusoidal (pc-S) blood vasculature as a new hybrid vascular bed expressing key lymphatic EC identity genes Prox1, Vegfr3 and Lyve1. Using single cell transcriptome data of human corpus cavernosum tissue, we found heterogeneity within pc-S endothelia and observed distinct phenotypic alterations related to inflammation response in hybrid ECs in erectile dysfunction. Molecular, ultrastructural and functional studies further establish shared hybrid identity of pc-Ss in mouse, and reveal their morphological adaptations and ability to perform lymphatic-like function in draining high molecular weight tracers. Interestingly, we found that inhibition of the key lymphangiogenic growth factor VEGF-C did not block the development of pc-Ss in mice, distinguishing them from other lymphatic and hybrid vessels analyzed so far. Our findings provide a detailed molecular characterization of hybrid pc-Ss and pave the way for the identification of molecular targets for therapies in conditions of dysregulated penile vasculature, including erectile dysfunction.

cell biology↗

bioRxiv2022

A CDKN2C retroduplication in Bowhead whales is associated with the evolution of extremely long lifespans and alerted cell cycle dynamics

Among the constraints on the evolution of remarkably long lifespans is an increased risk of developing cancer because organisms with long lifespans have more time to accumulate cancer-causing mutations than organisms with shorter lifespans. Indeed, while there is a strong correlation between lifespan and cancer risk within species, there is no correlation between maximum lifespan and cancer risk across species ( Petos Paradox). Here we use evolutionary genomics and comparative experimental biology to explore the mechanisms by which Bowhead whales (Balaena mysticetus), which can live at least 211 years, evolved their extremely long lifespans. We found that the Bowhead whale genome encodes a species-specific retroduplicated CDKN2C (p18INK4C) gene (CDKN2CRTG). The CDKN2CRTG gene is embedded within a Cetacean-specific LINE L1 element, and is highly expressed in Bowhead whale tissues likely because it coopted an L1 promoter to drive constitutive expression. Furthermore we use a series of gain of function experiments to show how the duplicate CDKN2CRTG gene may influence cellular phenotypes such as cell cycle progression and DNA damage repair in ways that are beneficial for aging and cancer resistance. Remarkably, Bowhead and Right whales only diverged ~4-5 million years ago, suggesting the long lifespan of Bowheads may have evolved relatively recently and coincident with the origin of CDKN2CRTG. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=167 SRC="FIGDIR/small/506958v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@22cb1aorg.highwire.dtl.DTLVardef@444631org.highwire.dtl.DTLVardef@5c4c8aorg.highwire.dtl.DTLVardef@1a510d3_HPS_FORMAT_FIGEXP M_FIG C_FIG

evolutionary biology↗

bioRxiv2022

Parallel evolution of reduced cancer risk and tumor suppressor duplications in Xenarthra

The risk of developing cancer is correlated with body size and lifespan within species, but there is no correlation between cancer and either body size or lifespan between species indicating that large, long-lived species have evolved enhanced cancer protection mechanisms. Previously we showed that several large bodied Afrotherian lineages evolved reduced intrinsic cancer risk, particularly elephants and their extinct relatives (Proboscideans), coincident with pervasive duplication of tumor suppressor genes (Vazquez and Lynch 2021). Unexpectedly, we also found that Xenarthrans (sloths, armadillos, and anteaters) evolved very low intrinsic cancer risk. Here, we show that: 1) several Xenarthran lineages that independently evolved large bodies, long lifespans, and reduced intrinsic cancer risk; 2) reduced cancer risk in the stem lineages of Xenarthra and Pilosa occurred coincident with bursts of tumor suppressor gene duplications; 3) cells from sloths proliferate extremely slowly while Xenarthran cells induce apoptosis are very low levels of DNA damage; and 4) the prevalence of cancer is extremely low Xenarthrans, and cancer is nearly absent from armadillos. These data implicate the duplication of tumor suppressor genes in the evolution of remarkably large body sizes and decreased cancer risk in Xenarthrans and suggest they are a remarkably cancer resistant group of mammals. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=167 SRC="FIGDIR/small/502824v1_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@a98f15org.highwire.dtl.DTLVardef@1f0b859org.highwire.dtl.DTLVardef@d6ed7eorg.highwire.dtl.DTLVardef@81f3d5_HPS_FORMAT_FIGEXP M_FIG C_FIG

evolutionary biology↗

bioRxiv2022

Immunoregulatory subtype of dermal lymphatic endothelial cells at capillary terminals drives lymphatic malformations

Vascular malformations are congenital, chronically debilitating diseases. Somatic oncogenic mutations in PIK3CA, encoding p110-PI3K, specifically cause venous and lymphatic malformations (LM), yet the basis of vessel type-restricted disease manifestation is unknown. Here we report endothelial subtype-specific responses to the common causative Pik3caH1047R mutation, and reveal a new immunoregulatory subtype of dermal lymphatic capillary endothelial cells (iLECs) as a driver of LM pathology. Mouse model of Pik3caH1047R-driven vascular malformations showed that cell proliferation was a common early response of venous and lymphatic ECs to oncogenic Pik3ca, but sustained selectively in LECs of advanced lesions. Lymphatic overgrowth was associated with increased pro-inflammatory cytokine levels and pro-lymphangiogenic myeloid cell infiltrate. Single-cell transcriptomics revealed a new LEC subtype at capillary terminals, characterized by the expression of immunoregulatory genes. Selective expansion and activation of iLECs in the Pik3caH1047R mice was evidenced by proliferation and upregulation of pro-inflammatory genes. Importantly, macrophage depletion or anti-inflammatory COX-2 inhibition limited Pik3caH1047R-driven lymphangiogenesis. This provides a therapeutic target for LM and suggests a paracrine crosstalk in which LEC-autonomous oncogenic Pik3ca signaling induces immune activation that in turn sustains pathological lymphangiogenesis. Identification of iLECs indicates that peripheral lymphatic vessels not only respond to inflammation but also actively orchestrate the immune response.

cell biology↗

bioRxiv2020

Paradoxical effects of cigarette smoke and COPD on SARS-CoV2 infection and disease

IntroductionHow cigarette smoke (CS) and chronic obstructive pulmonary disease (COPD) affect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and severity is controversial. We investigated the protein and mRNA expression of SARS-CoV-2 entry receptor ACE2 and proteinase TMPRSS2 in lungs from COPD patients and controls, and lung tissue from mice exposed acutely and chronically to CS. Also, we investigated the effects of CS exposure on SARS-CoV-2 infection in human bronchial epithelial cells. MethodsIn Cohort 1, ACE2-positive cells were quantified by immunostaining in FFPE sections from both central and peripheral airways. In Cohort 2, we quantified pulmonary ACE2 protein levels by immunostaining and ELISA, and both ACE2 and TMPRSS2 mRNA levels by RT-qPCR. In C57BL/6 WT mice exposed to air or CS for up to 6 months, pulmonary ACE2 protein levels were quantified by triple immunofluorescence staining and ELISA. The effects of CS exposure on SARS-CoV-2 infection were evaluated after 72hr in vitro infection of Calu-3 cells. After SARS-CoV-2 infection, the cells were fixed for IF staining with dsRNA-specific J2 monoclonal Ab, and cell lysates were harvested for WB of viral nucleocapsid (N) protein. Supernatants (SN) and cytoplasmic lysates were obtained to measure ACE2 levels by ELISA. ResultsIn both human cohorts, ACE2 protein and mRNA levels were decreased in peripheral airways from COPD patients versus both smoker and NS controls, but similar in central airways. TMPRSS2 levels were similar across groups. Mice exposed to CS had decreased ACE2 protein levels in their bronchial and alveolar epithelia versus air-exposed mice exposed to 3 and 6 months of CS. In Calu3 cells in vitro, CS-treatment abrogated infection to levels below the limit of detection. Similar results were seen with WB for viral N protein, showing peak viral protein synthesis at 72hr. ConclusionsACE2 levels were decreased in both bronchial and alveolar epithelial cells from uninfected COPD patients versus controls, and from CS-exposed versus air-exposed mice. CS-pre-treatment did not affect ACE2 levels but potently inhibited SARS-CoV-2 replication in this in vitro model. These findings urge to further investigate the controversial effects of CS and COPD on SARS-CoV2 infection.

immunology↗