Biology subjects

Ramachandran, P.

Publications and source records attributed to Ramachandran, P..

At least 19 recordsLinked to original sources

bioRxiv2025

Human hepatic stellate cells orchestrate the accumulation and function of CD103+ tissue-resident CD8+ T-cells in liver fibrosis

Tissue-resident memory cells (TRM) contribute to protective and pathogenic responses in the liver, yet precisely how hepatic TRM adapt and integrate cues from the underlying stroma and extracellular matrix (ECM) in chronic liver disease (CLD) has yet to be fully defined. Here we describe a role for activated myofibroblast-like hepatic stellate cells (HSCs) in the accumulation and in situ localisation of CD8+ TRM in the CLD liver. Activated HSCs drive a program of tissue residence in activated, tissue-infiltrating CD8+ T-cells in a TGF{beta}-dependent manner. We show upregulation of CD103, ECM-binding integrins and adhesion molecules driven by TGF{beta} which together contribute to the sequestration of TRM within the ECM-rich fibrotic niche. Ex vivo, hepatic CD103+ TRM correlate with the extent of ECM deposited, express an altered repertoire of co-stimulatory and co-inhibitory receptors, transcriptional regulators of cellular exhaustion and produce less proinflammatory mediators upon TCR engagement in CLD than in health. Through expression of several co-inhibitory ligands, we further demonstrate the potential for activated HSCs to acquire an immunomodulatory phenotype and limit the capacity of CD103+ TRM to produce anti-viral and anti-tumour mediators upon antigen encounter. Finally, we demonstrate that strategies to block such regulatory pathways, including the PD1:PD-L1/PD-L2 axis, have the potential to restore the antigen-specific effector function of tissue-compartmentalised CD103+ TRM and thus contribute to improving the effectiveness of local immunosurveillance in CLD. One Sentence Summary: Activated hepatic stellate cells characteristic of liver fibrosis orchestrate an accumulation of a CD103+ TRM population with a reduced capacity for antigen-specific effector function in human CLD.

immunology↗

bioRxiv2025

A Human Single-cell Atlas Identifies OLR1+ Scar-associated Macrophages as a Therapeutic Target for Chronic Liver Disease

Chronic liver disease (CLD) is a major global healthcare problem. Irrespective of cause, chronic damage to the liver results in fibrosis, which is associated with adverse clinical outcomes. Immune cells, in particular monocyte-derived macrophages (MDMs), are key regulators of fibrosis and represent an attractive therapeutic target for CLD. However, it has remained unclear which specific subpopulation of MDMs drives pro-inflammatory and pro-fibrotic functions in human CLD and how they might be selectively modulated. Here, we generate an annotated human liver single cell atlas from 42 healthy and 35 CLD patients, identifying 125 transcriptionally distinct cellular states. Leveraging large patient and cell numbers, our atlas resolves rare liver cell states and distinguishes two types of disease-expanded scar-associated macrophages (SAMac), including a specific subpopulation with a pro-inflammatory pro-fibrotic phenotype. The scavenger receptor OLR1 was enriched in pro-inflammatory SAMacs and high hepatic OLR1 expression was associated with increased mortality in CLD patients. A corresponding monocyte-derived OLR1+ SAMac subpopulation expanded in a mouse model of CLD and exhibited a pro-inflammatory phenotype based on single-cell RNA-seq, single-cell ATAC-seq, and flow cytometry analyses. Primary human OLR1+ MDMs promoted fibrogenic signalling in multilineage liver spheroid cultures, whilst specific targeting of OLR1 reduced IL-1{beta} production by human macrophages and attenuated myofibroblast activation. Overall, our annotated human liver single-cell atlas provides a valuable reference to study disease-associated cell states in CLD. We utilise this resource to identify a distinct pro-inflammatory subpopulation of SAMacs and highlight OLR1 as a potential therapeutic target to specifically modulate SAMac function and attenuate liver fibrosis.

immunology↗

bioRxiv2025

Regulatory T cell stability determines the efficiency of bile duct regeneration during cholangitis.

Background and AimsCholangiopathies such as Primary Sclerosing Cholangitis (PSC) cause damage to the bile ducts and fibrosis with no effective cure. A reduction and impairment in the function of regulatory T cells (Tregs) occurs in PSC. Yet, it is currently unknown what consequence this has on bile duct regeneration. We investigate whether Tregs regulate bile duct regeneration and the dynamics of Tregs turnover during bile duct injury. Approach and ResultsWe used the transgenic Foxp3GFPDTR model to mimic reduced Tregs infiltration to the liver during bile duct injury and showed that reduced intrahepatic Tregs limits bile duct regeneration. Fate mapping of Tregs (Foxp3CreERTAi14) showed that Tregs acquire a pro-inflammatory phenotype within the inflammatory microenvironment, even after IL2 mediated Tregs expansion. Ox40L expression correlates with fibrosis in PSC patients. In the 3,5-Diethoxycarbonyl-1,4-Dihydrocollidine (DDC)-diet mouse model of experimental cholangiopathy, combining IL2-complex administration and blocking Ox40L decreases periportal fibrosis level, increases Treg number and reduces the pro-inflammatory phenotype of Tregs. ConclusionsThese results indicate that Tregs mediate cholangiocyte response to biliary injury, and Tregs downregulate Foxp3 and acquire an inflammatory phenotype in an inflammatory microenvironment. Enhancing Treg numbers through IL2 complex administration and blocking Ox40 signalling simultaneously suppress the inflammatory phenotype of Tregs and reduces bile duct damage and fibrosis.

immunology↗

bioRxiv2025

DNA data (genome skims and metabarcodes) paired with chemical data demonstrate utility for retrospective analysis of forage linked to fatal poisoning of cattle

Prepared and stored feeds, fodder, silage, and hay may be contaminated by toxic plants resulting in the loss of livestock. Several poisonous plants have played significant roles in livestock deaths from forage consumption in recent years in the Western United States including Salvia reflexa. Metagenomic data, genome skims and metabarcodes, have been used for identification and characterization of plants in complex matrices including diet composition of animals, mixed forages, and herbal products. Here, chemistry, genome skims, and metabarcoding were used to retrospectively describe the composition of contaminated alfalfa hay from a case of Salvia reflexa poisoning that killed 165 cattle. Genome skims and metabarcoding provided similar estimates of the relative abundance of the Salvia in the hay samples when compared to chemical methods. Additionally, genome skims and metabarcoding provided similar estimates of species composition in the contaminated hay and rumen contents of poisoned animals. The data demonstrate that genome skims and DNA metabarcoding may provide useful tools for plant poisoning investigations.

genomics↗

bioRxiv2024

Paired metagenomic and chemical evaluation of an aflatoxin contaminated dog kibble

Identification of chemical toxins from complex or highly processed foods can present needle in the haystack challenges for chemists. Metagenomic data can guide chemical toxicity evaluations with DNA-based description of the wholistic composition (bacterial, eukaryotic, protozoal, viral, and antimicrobial resistance) of any food suspected to harbor toxins, allergens, or pathogens. This approach can focus chemistry-based diagnostics, improve risk assessment, and address data gaps. There is increasing recognition that simultaneously co-occurring mycotoxins, either from single or multiple species, can impact dietary toxicity. Here we evaluate an aflatoxin contaminated kibble with known levels of specific mycotoxins and demonstrate that the abundance of DNA from putative aflatoxigenic Aspergillus spp. correlated with levels of aflatoxin quantified by Liquid Chromatography Mass Spectrometry (LCMS). Metagenomic data also identified an expansive range of co-occurring fungal taxa which may produce additional mycotoxins. Metagenomic data paired with chemical data provides a novel modality to address current data gaps pertaining to mycotoxin toxicity exposures, toxigenic fungal taxonomy, and mycotoxins of emerging concern.

microbiology↗

bioRxiv2023

Metagenomic survey of antimicrobial resistance (AMR) in Maryland surface waters differentiated by high and low human impact

In alignment with the One Health paradigm, surface waters are being evaluated as a modality to better understand baseline antimicrobial resistance (AMR) across the environment to supplement existing AMR monitoring in pathogens associated with humans, foods, and animals. Here, we use metagenomic and quasimetagenomic sequence data to describe AMR in Maryland surface waters from developed (high human impact) and natural (low human impact) classifications by the National Land Cover Database (NLCD). Critically important {beta}-lactamase genes were observed in twice as many high human impact zones. All data are available under BioProject PRJNA79347. https://www.ncbi.nlm.nih.gov/bioproject/794347

microbiology↗

bioRxiv2023

bettercallsal: better calling of Salmonella serotypes from enrichment cultures using shotgun metagenomic profiling and its application in an outbreak setting.

Precise and rapid identification of Salmonella serotypes from suspect food matrices is critical for successful source attribution of illness outbreaks (Scallan et al., 2011). Currently, close to 3% of U.S. foodborne Salmonella outbreaks have been attributed to multiple Salmonella serotypes (2.85%, 2000 - 2020) (CDC, 2022). Recent foodborne outbreaks that have been attributed to multiple Salmonella serotypes force us to question whether these are rare events or if previous methods simply did not have the throughput to provide an accurate picture of the complex ecology that is connected to outbreak etiologies. (Hassan et al., 2019; FDA, 2021; Whitney et al., 2021). An in-silico benchmark dataset, comprising 29 unique Salmonella, 46 non-Salmonella bacterial and 10 viral genomes, was generated with varying read depths. For outbreak samples, analysis was performed on previously sequenced pre-enrichments and selective enrichments of papayas and peaches (fruits and leaves) that led to the identification of multiple serovars. Data analyses was performed using a custom-built k-mer tool, SeqSero2, Kallisto and bettercallsal. The in-silico dataset analyzed with bettercallsal had accuracy, recall and specificity of 95%, 96% and 98 % respectively. In the papaya outbreak samples, bettercallsal identified multiple serovar presence in concordance with Bioplex assay results and the genome hits assigned to the samples are Salmonella isolates from the papaya outbreak as evident by NCBI SNP cluster information. In peach outbreak samples, bettercallsal identified both the serovars (Alachua and Gaminara) in concordance with k-mer analysis and the Luminex xMap assay. bettercallsal outperformed k-mer, Kallisto and Seqsero2 in identifying multiple serovars from enrichment cultures using shotgun metagenomics sequencing. Most Salmonella subtyping work has relied upon WGS methods which focuses on the high-resolution analysis of single genomes, or multiple single genomes picked from colonies on agar. Here we introduce laboratory and bioinformatics innovations for a metagenomic outbreak response workflow that accurately identifies multiple Salmonella serovars at the same time in a much higher throughput approach. bettercallsal is one of the first analysis tools that can potentially identify multiple Salmonella spp. serotypes from a metagenomic or quasi-metagenomic datasets with accuracy and can provide early insights into the etiology of the sample.

genomics↗

bioRxiv2023

Phenotypic and spatial heterogeneity of brain myeloid cells after stroke is associated with cell ontogeny, tissue damage, and brain connectivity

Acute stroke causes substantial mortality and morbidity and provokes extensive changes to myeloid immune cell populations in the brain that may be targets for limiting brain damage and enhancing brain repair. The most effective immunomodulatory approaches will require precise manipulation of discrete myeloid cell phenotypes in time and space to avoid harmful effects of indiscriminate neuroimmune perturbation. We sought to define how stroke alters the composition and phenotypes of mononuclear myeloid cells with particular attention to how cell ontogeny and spatial organisation combine to expand myeloid cell diversity across the brain after stroke. Multiple reactive microglial states and dual monocyte-derived populations contributed to an extensive repertoire of myeloid cells in post-stroke brain. We identified important overlap and distinctions among different cell types and states that involved ontogeny- and spatial-related properties. Notably, brain connectivity with infarcted tissue underpinned the pattern of local and remote altered cell accumulation and reactivity. Our discoveries suggest a global but anatomically-governed brain myeloid cell response to stroke that comprises diverse phenotypes arising through intrinsic cell ontogeny factors interacting with exposure to spatially-organised brain damage and neuroaxonal cues.

neuroscience↗

bioRxiv2023

Multimodal decoding of human liver regeneration

The liver has a unique ability to regenerate1,2, however in the setting of acute liver failure (ALF) this regenerative capacity is often overwhelmed and emergency liver transplantation is the only curative option3-5. To advance our understanding of human liver regeneration and to inform design of pro-regenerative therapies, we use paired single-nuclei RNA sequencing (snRNA-seq) combined with spatial profiling of healthy and ALF explant human livers to generate the first single-cell, pan-lineage atlas of human liver regeneration. We uncover a novel ANXA2+ migratory hepatocyte subpopulation which emerges during human liver regeneration, and a corollary migratory hepatocyte subpopulation in a mouse model of acetaminophen (APAP)-induced liver regeneration. Importantly, interrogation of necrotic wound closure and hepatocyte proliferation across multiple timepoints following APAP-induced liver injury in mice demonstrates that wound closure precedes hepatocyte proliferation. 4-D intravital imaging of APAP-induced mouse liver injury identifies motile hepatocytes at the edge of the necrotic area, enabling collective migration of the hepatocyte sheet to effect wound closure. Depletion of hepatocyte ANXA2 expression reduces HGF-induced human and mouse hepatocyte migration in vitro, and abrogates necrotic wound closure following APAP-induced mouse liver injury. Taken together, our work dissects unanticipated aspects of liver regeneration, demonstrating an uncoupling of wound closure and hepatocyte proliferation and uncovering a novel migratory hepatocyte subpopulation which mediates wound closure following liver injury. Therapies designed to promote rapid reconstitution of normal hepatic microarchitecture and reparation of the gut-liver barrier may open up new areas of therapeutic discovery in regenerative medicine.

cell biology↗

bioRxiv2022

Application of Quasimetagenomics Methods to Define Microbial Diversity and Subtype Listeria monocytogenes in Dairy and Seafood Production Facilities

Microorganisms frequently colonize surfaces and equipment within food production facilities. Listeria monocytogenes is a ubiquitous foodborne pathogen widely distributed in food production environments and is the target of numerous control and prevention procedures. Detection of L. monocytogenes in a food production setting requires culture dependent methods, but the complex dynamics of bacterial interactions within these environments and their impact on pathogen detection remains largely unexplored. To address this challenge, we applied both 16S rRNA and shotgun quasimetagenomic (enriched microbiome) sequencing of swab culture enrichments from seafood and dairy production environments. Utilizing 16S rRNA amplicon sequencing, we observed variability between samples taken from different production facilities and a distinctive microbiome for each environment. With shotgun quasimetagenomic sequencing, we were able to assemble L. monocytogenes metagenome assembled genomes (MAGs) and compare these MAGSs to their previously sequenced whole genome sequencing (WGS) assemblies, which resulted in two polyphyletic clades (lineages I and II). Using these same datasets together with in silico downsampling to produce a titration series of proportional abundances of L. monocytogenes, we were able to begin to establish limits for Listeria detection and subtyping using shotgun quasimetagenomics. This study contributes to the understanding of microbial diversity within food production environments and presents insights into how many reads or relative abundance is needed in a metagenome sequencing dataset to detect, subtype, and source track at a SNP level, as well as providing an important foundation for utilizing metagenomics to mitigate unfavorable occurrences along the farm to fork continuum. IMPORTANCEIn developed countries, the human diet is predominantly food commodities, which have been manufactured, processed, and stored in a food production facility. It is well known that the pathogen Listeria monocytogenes is frequently isolated from food production facilities and can cause serious illness to susceptible populations. Multistate outbreaks of L. monocytogenes over the last 10 years have been attributed to food commodities manufactured and processed in production facilities, especially those dealing with dairy products such as cheese and ice cream. A myriad of recalls due to possible L. monocytogenes contamination have also been issued for seafood commodities originating from production facilities. It is critical to public health that the means of growth, survival and spread of Listeria in food production ecosystems is investigated with developing technologies, such as 16S rRNA and quasimetagenomic sequencing, to aid in the development of effective control methods.

microbiology↗

bioRxiv2022

Advancing antimicrobial resistance monitoring in surface waters with metagenomic and quasimetagenomic methods

Surface waters present a unique challenge for the monitoring of critically important antimicrobial resistance. Metagenomic approaches provide unbiased descriptions of taxonomy and antimicrobial resistance genes in many environments, but for surface water, culture independent data is insufficient to describe critically important resistance. To address this challenge and expand resistome reporting capacity of antimicrobial resistance in surface waters, we apply metagenomic and quasimetagenomic (enriched microbiome) data to examine and contrast water from two sites, a creek near a hospital, and a reservoir used for recreation and municipal water. Approximately 30% of the National Antimicrobial Resistance Monitoring Systems critically important resistance gene targets were identified in enriched data contrasted to only 1% in culture independent data. Four different analytical approaches consistently reported substantially more antimicrobial resistance genes in quasimetagenomic data compared to culture independent data across most classes of antimicrobial resistance. Statistically significant differential fold changes (p<0.05) of resistance determinants were used to infer microbiological differences in the waters. Important pathogens associated with critical antimicrobial resistance were described for each water source. While the single time-point for only two sites represents a small pilot project, the successful reporting of critically important resistance determinants is proof of concept that the quasimetagenomic approach is robust and can be expanded to multiple sites and timepoints for national and global monitoring and surveillance of antimicrobial resistance in surface waters.

microbiology↗

bioRxiv2022

Phase Separation of a Nodulin Sec14-like protein Maintains Auxin Efflux Carrier Polarity at Arabidopsis Plasma Membranes

Protein function can be modulated by phase transitions in their material properties, which can range from liquid-to solid-like; yet the mechanisms that drive these transitions and whether they are important for physiology are still unknown. Using the model plant Arabidopsis, we show that developmental robustness is reinforced by phase transitions of the plasma membrane-bound lipid-binding protein SEC14-like. Using imaging, genetics, and in vitro reconstitution experiments, we show that SEC14-like undergoes liquid-like phase separation in the root stem cells. Outside the stem cell niche, SEC14-like associates with the caspase-like protease separase and conserved microtubule motors at unique polar plasma membrane interfaces. In these interfaces, SEC14-like undergoes abrupt processing by separase, which promotes its liquid-to-solid transition. The SEC14-like liquid-to-solid transition is important for root developmental robustness, as lines expressing an uncleavable SEC14-like variant or mutants of separase, and associated microtubule motors show similar developmental phenotypes. Furthermore, the processed and solidified but not the liquid form of SEC14-like interacts with the polar protein PINFORMED2 at the plasma membrane and perhaps other polar proteins of the PINFORMED family. This work demonstrates that robust development can involve abrupt liquid-to-solid transitions mediated by proteolysis at unique plasma membrane interfaces.

cell biology↗

bioRxiv2021

Serum glycoprotein markers in non-alcoholic steatohepatitis and hepatocellular carcinoma

Fatty liver disease progresses through stages of fat accumulation and inflammation to non-alcoholic steatohepatitis (NASH), fibrosis and cirrhosis and eventually hepatocellular carcinoma (HCC). Currently available diagnostic tools for HCC lack sensitivity and specificity and deliver little value to patients. In this study, we investigated the use of circulating serum glycoproteins to identify a panel of potential prognostic markers that may be indicative of progression from the healthy state to NASH and further to HCC. Serum samples were processed using a standard pre-analytical sample preparation protocol and were analyzed using a novel high throughput glycoproteomics platform. We analyzed 413 glycopeptides, representing 57 abundant serum proteins and compared among the three phenotypes. Our initial dataset contained healthy, NASH, and HCC serum samples. We analyzed normalized abundance of common glycoforms and found 40 glycopeptides with statistically significant differences in abundances in NASH and HCC compared to controls. Summary level relative abundance of core-fucosylated, sialylated and branched glycans containing glycopeptides were higher in NASH and HCC as compared to controls. We replicated some of our findings in an independent set of samples of individuals with benign liver conditions and HCC, respectively. Our results may be of value in the management of liver diseases. TOC only O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=95 SRC="FIGDIR/small/462486v2_ufig1.gif" ALT="Figure 1"> View larger version (14K): org.highwire.dtl.DTLVardef@91672corg.highwire.dtl.DTLVardef@cad49org.highwire.dtl.DTLVardef@4496b9org.highwire.dtl.DTLVardef@103615c_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2020

Divergence in a stress-associated gene regulatory network underlies differential growth control in the Brassicaceae family

The phytohormone abscisic acid (ABA) is a central regulator of acclimation during environmental stress. While some plants exhibit tremendous stress resilience, it has been unclear whether differences in ABA response underlie such adaptations. Here we establish a cross-species gene regulatory network (GRN) for ABA to identify broadly conserved, core components of the ABA signaling network and peripheral pathways exhibiting species-specific connectivity. Genes that are broadly conserved in the network share promoter architecture and patterns of gene expression. Networks associated with growth hormones exhibited highly divergent wiring of their ABA network leading to changes in the physiological outcome of signaling. Together our study provides a model for understanding how GRN subcircuits deploy different growth regulatory states across ecologically diverse species. One Sentence SummaryComparative studies reveal core and peripheral stress-mediated gene networks driving divergent growth control in plants.

plant biology↗

bioRxiv2020

Bipartite influence of abscisic acid on xylem differentiation trajectories is dependent on distinct VND transcription factors in Arabidopsis

Plants display a remarkable ability to adjust their growth and development to changes in environmental conditions, such as reduction in water availability. This high degree of plasticity is apparent not only as altered root and shoot growth rates, but also as changes to tissue patterning and cell morphology [1,2]. We have previously shown that Arabidopsis thaliana root xylem displays plastic developmental responses to limited water availability, mediated by non-cell autonomous action of abscisic acid, ABA [2]. Here, we show through analyses of ABA response reporters and tissue specific suppression of ABA signalling that xylem cells act as primary signalling centres for mediation of changes to both xylem cell fate and differentiation rate revealing a cell autonomous control of xylem development by ABA. Transcriptomic changes in response to ABA showed that members of the VASCULAR RELATED NAC DOMAIN (VND) transcription factor family are rapidly activated. Molecular and genetic analyses revealed that the two aspects of xylem developmental changes, cell fate and differentiation rate, are dependent on distinct members of this transcription factor family. Thus, this study provides insights into how different aspects of developmental plasticity can be interlinked, yet genetically independent of each other. Moreover, similarities in phenotypic and molecular responses to ABA in diverse species indicate an evolutionary conservation of the ABA-xylem development regulatory network among eudicots. Hence, this study gives molecular insights on how environmental stress promotes anatomical plasticity to key plant traits with potential relevance for water use optimization and adaptation to drought conditions.

plant biology↗

bioRxiv2020

Kidney single-cell atlas reveals myeloid heterogeneity in progression and regression of kidney disease.

The kidney has a limited capacity to repair following injury, however, the endogenous reparative pathways are not well understood. Here we employ integrated droplet- and plate-based scRNA-seq in the murine reversible unilateral ureteric obstruction model to dissect the transcriptomic landscape at the single cell level during renal injury and resolution of fibrosis. We generate a comprehensive catalogue of the changes induced during injury and repair, revealing significant myeloid cell heterogeneity, which would not have been identifiable by conventional flow cytometry. We identify new markers for the myeloid populations within the kidney as well as identification of novel subsets including an Arg1+ monocyte population specific to early injury and a Mmp12+ macrophage subset exclusive to repair. Finally, using paired blood exchange to track circulating immune cells, we confirm that monocytes are recruited to the kidney early after injury and are the source of Ccr2+ macrophages that accumulate in late injury. Our data demonstrate the utility of complementary technologies to identify novel myeloid subtypes that may represent therapeutic targets to inhibit progression or promote regression of kidney disease.

immunology↗

bioRxiv2019

Single-cell RNA-seq reveals CD16- monocytes as key regulators of human monocyte transcriptional response to Toxoplasma

Monocytes are among the major myeloid cells that respond to Toxoplasma, a ubiquitous foodborne that infects [≥]1 billion people worldwide, in human peripheral blood. As such, a molecular understanding of human monocyte-Toxoplasma interactions can expedite the development of novel human toxoplasmosis control strategies. Current molecular studies on monocyte-Toxoplasma interactions are based on average cell or parasite responses across bulk cell populations. Although informative, population-level averages of monocyte responses to Toxoplasma have sometimes produced contradictory results, such as whether CCL2 or IL12 define effective monocyte response to the parasite. Here, we used single-cell dual RNA sequencing (scDual-Seq) to comprehensively define, for the first time, the monocyte and parasite transcriptional responses that underpin human monocyte-Toxoplasma encounters at the single cell level. We report extreme transcriptional variability between individual monocytes. Furthermore, we report that Toxoplasma-exposed and unexposed monocytes are transcriptionally distinguished by a reactive subset of CD14++CD16- monocytes. Functional cytokine assays on sorted monocyte populations show that the infection-distinguishing monocytes secrete high levels of chemokines, such as CCL2 and CXCL5. These findings uncover the Toxoplasma-induced monocyte transcriptional heterogeneity and shed new light on the cell populations that largely define cytokine and chemokine secretion in human monocytes exposed to Toxoplasma.

genomics↗

bioRxiv2019

Resolving the fibrotic niche of human liver cirrhosis using single-cell transcriptomics

Currently there are no effective antifibrotic therapies for liver cirrhosis, a major killer worldwide. To obtain a cellular resolution of directly-relevant pathogenesis and to inform therapeutic design, we profile the transcriptomes of over 100,000 primary human single cells, yielding molecular definitions for the major non-parenchymal cell types present in healthy and cirrhotic human liver. We uncover a novel scar-associated TREM2+CD9+ macrophage subpopulation with a fibrogenic phenotype, that has a distinct differentiation trajectory from circulating monocytes. In the endothelial compartment, we show that newly-defined ACKR1+ and PLVAP+ endothelial cells expand in cirrhosis and are topographically located in the fibrotic septae. Multi-lineage ligand-receptor modelling of specific interactions between the novel scar-associated macrophages, endothelial cells and collagen-producing myofibroblasts in the fibrotic niche, reveals intra-scar activity of several major pathways which promote hepatic fibrosis. Our work dissects unanticipated aspects of the cellular and molecular basis of human organ fibrosis at a single-cell level, and provides the conceptual framework required to discover rational therapeutic targets in liver cirrhosis.

immunology↗