Biology subjects

Fernando, S.

Publications and source records attributed to Fernando, S..

14 recordsLinked to original sources

bioRxiv2025

Metadomain and metaloop genome interactions in mammalian T cells

Recent studies have advanced our understanding of chromosomal organization and its principal role in gene regulation. However, most analyses have focused on short-range interactions (<2 Mb), limiting insight into broader regulatory architecture. In particular, the relationships between topologically associating domains (TADs), sub-TAD loops, long-range cross-TAD interactions, and higher-order chromosomal compartmentalization remain poorly understood. Here, we identify extensive multi-megabase and interchromosomal interactions (metaloops) in T lymphocytes, which organize into larger meta-TAD associations (metadomains). Metaloops bridge distal promoters and regulatory elements of key T cell-specific genes such as Ctla4, Ikzf2, Il2ra, Ets1, Lef1, Runx1, Bach2, Foxo1 and others, and are both shared and cell type-specific across functionally distinct T cell lineages. Reanalysis of published data confirms the reproducibility of these interactions in both mouse and human T cells and their dependence on superenhancers. Genome-wide clustering of metadomains reveals three interchromosomal hubs with distinct epigenomic profiles, including a superenhancer-enriched hub associated with T cell-specific gene activation. By integrating a compendium of new and public T cell epigenomic data, we infer distinct architectural factors associated with short-range loops and long-range metaloops. Altogether, our study reveals new features of T cell-specific 3D genome organization across scales, and our computational framework is broadly applicable to analyses of chromatin architecture across different cell types and experimental systems. Highlights- Ultra-long-range (>2 Mb) chromatin interactions linked to gene regulation in T cells - A new algorithm identifies distal and interchromosomal meta-TADs and metaloops - An interchromosomal T cell-specific active hub emerges from metadomain clustering - Epigenomic compendium implicates TFs associated with long-range interactions

genomics↗

bioRxiv2025

Stag2 dependent chromatin remodeling enforces the erythroid-specific Gata1 cistrome

The transcription factor GATA1 has pleiotropic hematopoietic functions, particularly in erythroid and megakaryocytic ontogeny. While mechanistic investigations have uncovered many facets of GATA1 biology, how GATA1 co-regulates divergent cell fates remains only partially characterized. We previously described that loss of Stag2, a member of the cohesin complex and a recurrent mutational target in myelodysplastic syndrome and Down Syndrome associated acute megakaryoblastic leukemia, results in altered chromatin accessibility, transcription factor function, and cell differentiation. Hence, we hypothesized that chromatin accessibility facilitates lineage specificity of GATA1, thereby permitting efficient cellular differentiation. To understand the connection between chromatin accessibility and GATA1, we performed comprehensive studies of erythropoiesis in Stag2{Delta} mice. Defects in Stag2-deficient hematopoiesis included reduced numbers of erythroid progenitors (EryPs), impaired terminal erythroid maturation, increased number of MkPs, and increased megakaryocytes. RNA- and ATAC-sequencing of EryPs revealed altered patterns of Gata1 target gene expression with altered accessibility in conjunction with loss of expression of erythroid targets and gain of megakaryocyte targets. Gata1 occupancy was lost at erythroid targets, while occupancy increased at megakaryocyte targets. Functionally, we observed that Stag2-deficient EryPs have diminished erythroid output and augmented megakaryocyte output in orthogonal differentiation assays. Human models and primary MDS patients recapitulated the essential phenotypic and molecular features of our in vivo murine MDS model. Collectively, this study advances the understanding of the interplay between TF function and chromatin accessibility. Moreover, these data suggest a novel conceptual paradigm of dyserythropoiesis in MDS. Key Pointsxxxxx

molecular biology↗

bioRxiv2025

Enhanced FLI1 accessibility mediates STAG2-mutant leukemogenesis

Chromatin architecture governs transcriptional output and cell identity; however, how its disruption promotes leukemic transformation remains incompletely understood. Here, we show that loss of the cohesin subunit STAG2 creates a hyper-accessible chromatin landscape that amplifies FLI1 activity and extends its binding to ectopic loci. Using multi-omic analyses in human AML samples, cell lines, and mouse models, we identify chromatin-dependent co-occupancy of FLI1 and Menin, accompanied by amplification of Menin occupancy at non-canonical loci beyond its HOXA/MEIS1 targets. Therapeutically, the aberrant expansion of Menin binding drives an altered response towards Revumenib and activates interferon response pathways, creating a therapeutic vulnerability to Menin inhibition. Functionally, STAG2/NPM1c co-mutation drives a stem cell-like immunophenotype and a fully penetrant leukemia in vivo. Collectively, these findings define a model in which cohesin loss rewires transcription factor occupancy to amplify oncogenic chromatin programs and expose context-specific therapeutic dependencies.

cancer biology↗

bioRxiv2022

Diversity, abundance, and host specificity of the human skin associated circular and single stranded DNA virome

The human skin is our point of contact with the microbial world, yet little is known about the diversity of the skin virome. Studies of the human skin virome have focused on bacteriophage and double-stranded DNA viral genomes, however, there have been few efforts to characterize circular single-stranded DNA viruses that populate human skin. Here, we evaluate the diversity of the circular single-stranded DNA virome collected across three anatomical skin locations from 60 human individuals with five time-point collections spanning six-months. Our analyses resulted in the identification of 272 novel and unique Rep-encoded single-stranded DNA viruses associated with human skin. Sequence similarity networks and maximum likelihood estimations of the Rep and Capsid protein amino acid sequences from our sequencing and public database references, reveal family level stability of the Cressdnaviricota across the study participants and a larger host-range than previously thought for these putative multi-host pathogens.

microbiology↗

bioRxiv2021

Novel Feline Papillomavirus Isolate P20 Assembled from Metagenomic Data Isolated from Human Skin of a House Cat Owner

A feline papillomavirus was assembled from metagenomic sequencing data collected from the human skin of a house cat owner. This circular papillomavirus strain P20 is 8069 bp in length, has a GC content of 54.38%, and displays genome organization typical of feline papillomaviruses with six annotated protein coding regions. The genome exhibits approximately 75% sequence similarity to other feline papillomavirus genomes.

microbiology↗

bioRxiv2021

Self-renewing tissue-resident endothelial-macrophage progenitor cells originate from yolk sac and are a local source of inflammation and neovascularization in postnatal aorta

Converging evidence indicates that extra-embryonic yolk sac is the source of both macrophages and endothelial cells in adult mouse tissues. Prevailing views are that these embryonically derived cells are maintained after birth by proliferative self-renewal in their differentiated states. Here we identify clonogenic endothelial-macrophage (EndoMac) progenitor cells in the adventitia of embryonic and postnatal mouse aorta, that are independent of Flt3-mediated bone marrow hematopoiesis and derive from an early embryonic CX3CR1+ and CSF1R+ source. These bipotent progenitors are proliferative and vasculogenic, contributing to adventitial neovascularization and forming perfused blood vessels after transfer into ischemic tissue. We establish a regulatory role for angiotensin II, which enhances their clonogenic and differentiation properties and rapidly stimulates their proliferative expansion in vivo. Our findings demonstrate that embryonically derived EndoMac progenitors participate in local vasculogenic responses in the aortic wall by contributing to the expansion of endothelial cells and macrophages postnatally.

cell biology↗

bioRxiv2021

The Application of The Skin Virome for Human Identification

The use of skin virome for human identification purposes offers a unique approach to instances where a viable and statistically relevant human DNA profile is unavailable. The human skin virome may act as an alternative DNA profile and/or an additional form of probative genetic material. To date, no study has attempted to investigate the human virome over a time series across various physical locations of the body to identify its potential as a tool for human identification. For this study, we set out to evaluate the stability, diversity, and individualization of the human skin virome. An additional goal was to identify viral signatures that can be used in conjunction with traditional forensic STR loci. In order to accomplish this, human virome metagenomes were collected and sequenced from 42 individuals at three anatomical locations (left hand, right hand, and scalp) across multiple collections periods over a 6-month window of time. Assembly dependent and independent bioinformatic approaches were employed, along with a database-based assessment, which resulted in three sets of stable putative viral markers. In total, with the three sets combined, 59 viral species and uncharacterized viral genome assemblies were identified as being significantly stable (P=5.3x10-15). Viral diversity, based on presence or absence, is significantly different across subjects (P<0.001). Here we demonstrate that not only is the human virome applicable to be used for human identification, but we have identified many viral signatures that can be used for forensic applications, thus providing a foundation to the novel field of forensic virology. HighlightsO_LIHere we provide the largest human skin virome study, to date. Our study revealed novel diversity findings of high abundance for certain viral taxa, for example, the Cress-like DNA phages, that have not previously been characterized in human skin viral ecology studies. C_LIO_LIThere were 59 putative human skin viral biomarkers suitable for human identification from the core stable human skin virome of 42 subjects. C_LIO_LIThe putative markers we identified were significantly stable over a 6-month period of time within individuals and across three autosomal locations of left hand, right hand, and scalp. C_LIO_LIDiversity of profiles, based on the presence and absence of our putative marker data set, were significantly different across test subjects. C_LI

microbiology↗

bioRxiv2020

Bcr-Abl tyrosine kinase inhibitor imatinib as a potential drug for COVID-19

The rapid geographic expansion of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the infectious agent of Coronavirus Disease 2019 (COVID-19) pandemic, poses an immediate need for potent drugs. Enveloped viruses infect the host cell by cellular membrane fusion, a crucial mechanism required for virus replication. The SARS-CoV-2 spike glycoprotein, due to its primary interaction with the human angiotensin-converting enzyme 2 (ACE2) cell-surface receptor, is considered as a potential target for drug development. Based on in silico screening followed by in vitro studies, here we report that the existing FDA-approved Bcr-Abl tyrosine kinase inhibitor, imatinib, inhibits SARS-CoV-2 with an IC50 of 130 nM. We provide evidence that although imatinib binds to the receptor-binding domain (RBD) of SARS-CoV-2 spike protein with an affinity at micromolar, i.e., 2.32 {+/-} 0.9 M levels, imatinib does not directly inhibit the spike RBD:ACE2 interaction - suggesting a Bcr-Abl kinase-mediated fusion inhibition mechanism is responsible for the inhibitory action. We also show that imatinib inhibits other coronaviruses, SARS-CoV, and MERS-CoV via fusion inhibition. Based on promising in vitro results, we propose the Abl tyrosine kinase inhibitor (ATKI), imatinib, to be a viable repurposable drug against COVID-19.

microbiology↗

bioRxiv2019

Metabolic Modeling Elucidates the Transactions in the Rumen Microbiome and the Shifts upon Virome Interactions

The complex microbial ecosystem within the bovine rumen plays a crucial role in host nutrition, health, and environmental impact. However, little is known about the interactions between the functional entities within the system, which dictates the community structure and functional dynamics and host physiology. With the advancements in high-throughput sequencing and mathematical modeling, in silico genome-scale metabolic analysis promises to expand our understanding of the metabolic interplay in the community. In an attempt to understand the interactions between microbial species and the phages inside rumen, a genome-scale metabolic modeling approach was utilized by using key members in the rumen microbiome (a bacteroidete, a firmicute, and an archaeon) and the viral phages associated with them. Individual microbial host models were integrated into a community model using multi-level mathematical frameworks. An elaborate and heuristics-based computational procedure was employed to predict previously-unknown interactions involving the transfer of fatty acids, vitamins, coenzymes, amino acids, and sugars among the community members. While some of these interactions could be inferred by the available multi-omic datasets, our proposed method provides a systemic understanding of why these occur and how these affect the dynamics in a complex microbial ecosystem. To elucidate the functional role of the virome on the microbiome, local alignment search was used to identify the metabolic functions of the viruses associated with the hosts. The incorporation these functions demonstrated the role of viral auxiliary metabolic genes in relaxing the metabolic bottlenecks in the microbial hosts and complementing the inter-species interactions. Finally, a comparative statistical analysis of different biologically significant community fitness criteria identified the variation in flux space and robustness of metabolic capacities of the community members. Our elucidation of metabolite exchange among three members of rumen microbiome shows how their genomic differences and interactions with the viral strains shape up a highly sophisticated metabolic interplay and explains how such interactions across kingdoms can cause metabolic and compositional shifts in the community and affect the health, nutrition, and pathophysiology of the ruminant animal.

systems biology↗

bioRxiv2018

The Relationship Between the Cervical Microbiome, HIV Status, and Pre-Cancerous Lesions

Nearly all cervical cancers are causally associated with Human Papillomavirus (HPV). The burden of HPV-associated dysplasias in Sub-Saharan Africa is influenced by HIV. To investigate the role of the bacterial microbiome in cervical dysplasia, cytobrush samples were collected directly from cervical lesions of 144 Tanzanian women. The V4 hypervariable region of the 16S rRNA gene was amplified and deep-sequenced. Alpha diversity metrics; Chao1, PD whole tree, and operational taxonomic Unit (OTU) estimates, displayed significantly higher bacterial richness in HIV positive patients (P = 0.01) than in HIV negative patients. Within HIV positive patients, there was higher bacterial richness in patients with high grade squamous intraepithelial lesions (HSIL; P = 0.13) than those without lesions. The most abundant OTUs associated with high-grade squamous intraepitheilal lesions (HSIL) were Mycoplasmatales, Pseudomonadales, and Staphylococcus. We suggest that a chronic mycoplasma infection of the cervix can contribute to HPV-dependent dysplasia by sustained inflammatory signals.

cancer biology↗

bioRxiv2018

Dietary Bovine Milk Exosomes Elicit Changes in Microbial Communities in C57BL/6 Mice

Exosomes and exosome-like vesicles participate in cell-to-cell communication in animals, plant and bacteria. Dietary exosomes in bovine milk are bioavailable in non-bovine species, but a fraction of milk exosomes reaches the large intestine. We hypothesized that milk exosomes alter the composition of the gut microbiome in mice. C57BL/6 mice were fed AIN-93G diets, defined by their content of bovine milk exosomes and RNA cargos: exosome/RNA depleted (ERD) versus exosome/RNA-sufficient (ERS) diets. Feeding was initiated at age three weeks and cecum content was collected at ages 7, 15 and 47 weeks. Microbial communities were identified by 16S rRNA gene sequencing. The dietary intake of exosomes and age had significant effects on the microbial communities in the cecum. At the phylum level, the abundance of Verrucomicrobia was greater in mice fed ERD compared to ERS, and the abundance of both Firmicutes and Tenericutes was smaller in mice fed ERD compared to ERS at age 47 weeks. At the family level, the abundance of Anaeroplasmataceae was greater in mice fed ERD compared to ERS, and the abundance of Bifidobacteriaceae, Lachnospiraceae, and Dehalobacteriaceae was significantly greater in mice fed ERS than mice fed ERD at age 15 weeks. Exosome feeding significantly altered the abundance of 52 operational taxonomic units; diet effects were particularly strong in the Lachnospiraceae, Ruminococcaceae and the Verrucomicrobiaceae families. We conclude that exosomes in bovine milk alter microbial communities in non-bovine species, suggesting that exosomes and their cargos participate in the crosstalk between bacterial and animal kingdoms.\n\nIMPORTANCEVirtually all living cells, including bacteria communicate through exosomes, which can be found in all body fluids. Exosomes and the RNA cargos have been implicated in all aspects of health and disease, e.g., metastasis of cancer, neuronal signaling and embryonic development. Previously, we reported that exosomes and their microRNA cargos are not solely derived from endogenous synthesis, but may also be obtained from dietary sources such as bovine milk in non-bovine mammals. Here, we report for the first time that bovine milk exosomes communicate with the intestinal microbiome and alters microbial communities in mice. This is the first report suggesting that the gut microbiome facilitates the signaling by dietary exosomes across kingdoms: animal (cow) [->] bacteria [->] animal (mouse).

microbiology↗

bioRxiv2018

Role of NS1 antibodies in the pathogenesis of acute dengue infection

The role of NS1-specific antibodies in the pathogenesis of dengue virus infection is of particular interest to the dengue field, yet remains poorly understood. We therefore investigated the immunoglobulin responses of patients with dengue fever (DF) and dengue hemorrhagic fever (DHF) to NS1. Antibody responses to recombinant-NS1 were assessed in serum samples obtained throughout illness of patients with acute secondary DENV1 and DENV2 infection by ELISA. NS1 antibody titres were significantly higher in patients with DHF compared to those with DF for both serotypes, during the critical phase of illness. Antibody responses were further assessed to NS1 peptides and showed that in both acute secondary DENV1 and DENV2 infection, the antibody repertoire of DF and DHF patients is directed towards distinct regions of the NS1 protein. Further experiments in healthy individuals, with either past severe dengue or past asymptomatic dengue infection revealed that individuals with past inapparent disease mounted antibody responses directed to the same NS1 epitope regions as those with mild acute infection (DF). Our results suggest that the specific epitope target of NS1-antibodies generated by patients could predict disease severity and be of potential therapeutic benefit in aiding vaccine and treatment design.

immunology↗

bioRxiv2018

Emergence of a Dengue virus serotype 2 causing the largest ever dengue epidemic in Sri Lanka

BackgroundSri Lanka experienced the largest ever dengue outbreak in year 2017, which coincided with the shift of the predominant circulating dengue virus (DENV) 1 to DENV2 after 9 years. As it was felt that more patients appeared to develop complications and severe dengue, we compared clinical features of patients with acute dengue, with the previous circulating serotype (DENV1) and also sequenced the new virus, to determine the lineage of the virus.\n\nMethodology/Principal findingsWe studied the clinical and laboratory features of 172 adult patients with acute DENV1 (n=79) and DENV2 (n=93) infection. 65 (82.3%) of those with DENV1 and 86 (92.4%) of those with DENV2 were experiencing a secondary infection. The risk of developing dengue haemorrhagic fever (DHF) was significantly higher (=0.005, odds ratio=2.5) in those infected with DENV2 (54.8%) when compared to DENV1(32.9%), even though similar proportions of patients had a secondary dengue infection. Patients with DENV2 infection developed leakage significantly earlier (p<0.0001, median= 3, days) when compared to those with a DENV1 infection (median 5 days) and were more likely to develop significant bleeding and to require blood transfusions. Furthermore, patients with DENV2 were more likely to have significantly lower platelet counts during day 3, 4 and 5 since onset of illness.\n\nWhole genome sequencing showed that these DENV-2 isolates belonged to a cosmopolitan strain and was genetically more distant than the DENV-2 strains that circulated from 1981 to 2004 in Sri Lanka.\n\nConclusions/significanceSince this DENV2 strain appears to cause more severe forms of clinical disease, it would be important to determine variations in the virus genome or other factors that could have contributed to severe disease.\n\nAuthor summarySri Lanka experienced the largest ever dengue outbreak in year 2017, which coincided with the shift of the predominant circulating dengue virus (DENV) 1 to DENV2 after 9 years. We studied the clinical and laboratory features of 172 adult patients with acute DENV1 (n=79) and DENV2 (n=93) infection. The risk of developing dengue haemorrhagic fever was significantly higher (=0.005, odds ratio=2.5) in those infected with DENV2 (54.8%) when compared to DENV1(32.9%), even though similar proportions of patients had a secondary dengue infection. Patients with DENV2 infection developed leakage significantly earlier (p<0.0001, median= 3, days) when compared to those with a DENV1 infection (median 5 days) and were more likely to develop significant bleeding. Whole genome sequencing showed that these DENV-2 isolates belonged to cosmopolitan strain and was genetically more distant to the DENV-2 strains that circulated from 1981 to 2004 in Sri Lanka.

epidemiology↗

bioRxiv2018

Quantification of dengue virus specific T cell responses and correlation with viral load and clinical disease severity in acute dengue infection

BackgroundIn order to understand the role of dengue virus (DENV) specific T cell responses that associate with protection, we studied their frequency and phenotype in relation to clinical disease severity and resolution of viraemia in a large cohort of patients with varying severity of acute dengue infection.\n\nMethodology/Principal findingsUsing ex vivo IFN{gamma} ELISpot assays we determined the frequency of dengue viral peptide (DENV)-NS3, NS1 and NS5 responsive T cells in 74 adult patients with acute dengue infection and examined the association of responsive T cell frequency with the extent of viraemia and clinical disease severity. We found that total DENV-specific and DENV-NS3-specific T cell responses, were higher in patients with dengue fever (DF), when compared to those with dengue haemorrhagic fever (DHF). In addition, early appearance of DENV-specific T cell responses was significantly associated with milder clinical disease (p=0.02). DENV peptide specific T cell responses inversely correlated with the degree of viraemia, which was most significant for DENV-NS3 specific T cell responses (Spearmans r = -0.47, p=0.0003). The frequency of T cell responses to NS1, NS5 and pooled DENV peptides, correlated with the degree of thrombocytopenia but had no association with levels of liver transaminases. In contrast, DENV-IgG inversely correlated with the degree of thrombocytopenia and levels of liver transaminases.\n\nConclusions/significanceEarly appearance of DENV-specific T cell IFN{gamma} responses appears to associate with milder clinical disease and resolution of viraemia, suggesting a protective role in acute dengue infection.

immunology↗