Biology subjects

Itan, Y.

Publications and source records attributed to Itan, Y..

5 recordsLinked to original sources

bioRxiv2025

Acute cold exposure in humans shifts the circulating proteome to a cardioprotective and anti-aging profile

Cold exposure has been proposed to provide a constellation of salutary effects, yet its molecular correlates remain largely unknown. Brown adipose tissue (BAT) is the main site of adaptive thermogenesis, and its prevalence is linked with cardiometabolic health. Since the benefits of BAT activation and cold exposure more generally may be mediated through blood-borne factors, we conducted an extensive analysis of the circulating proteome linked with an acute cold challenge in healthy adults. Our goal was to uncover early molecular changes triggered by cooling and establish their specific relationships with the human brown adipocyte secretome as well as various phenotypic traits. Based on comprehensive inter-cohort validations, we provide the first reproducible proteomic signature of cold exposure in humans. Our data demonstrate that cooling favorably modulates circulating mediators linked with chronological aging, as well as metabolic and cardiovascular diseases, providing new potential biochemical transducers of the benefits associated with cold therapy. HighlightsO_LICooling alters the plasma proteome with striking concordance in independent human cohorts. C_LIO_LICooling represses circulating proteins linked with type 2 diabetes, hypercholesterolemia, hypertension, coronary heart disease and heart failure. C_LIO_LIThe circulating signature of cooling resembles a cardioprotective and anti-aging profile. C_LI

physiology↗

bioRxiv2025

Ablation of Prdm16 and beige fat causes vascular remodeling and elevated blood pressure

While excess adiposity is a major risk factor for hypertension and cardiovascular disease, brown fat is associated with protection from these pathologies. Whether brown fat has a causal role in this process and the underlying molecular mechanisms remain unknown. Here we investigate the role of murine beige fat, as a model of inducible brown fat in humans, in adipocyte-vascular crosstalk. Using mice with an adipocyte-specific deletion of PRDM16, resulting in a loss of beige adipocyte identity, we discover a dramatic remodeling of perivascular adipose tissue, increased vascular reactivity and elevated blood pressure. We further show that the circulating enzyme Qsox1 is de-repressed in Prdm16-deficient adipocytes, and deletion of Qsox1 in PRDM16cKO mice rescues vascular fibrosis and reactivity. These results demonstrate a key new role for beige adipocytes in blood pressure regulation and identify Qsox1 as an important mediator of adipocyte-vascular crosstalk.

physiology↗

bioRxiv2022

Genome-wide prediction of pathogenic gain- and loss-of-function variants from ensemble learning of diverse feature set

Gain-of-function (GOF) variants give rise to increased or novel protein functions whereas loss-of-function (LOF) variants lead to diminished protein function. GOF and LOF variants can result in markedly varying phenotypes, even when occurring in the same gene. However, experimental approaches for identifying GOF and LOF are generally slow and costly, whilst currently available computational methods have not been optimized to discriminate between GOF and LOF variants. We have developed LoGoFunc, an ensemble machine learning method for predicting pathogenic GOF, pathogenic LOF, and neutral genetic variants. LoGoFunc was trained on a broad range of gene-, protein-, and variant-level features describing diverse biological characteristics, as well as network features summarizing the protein-protein interactome and structural features calculated from AlphaFold2 protein models. We analyzed GOF, LOF, and neutral variants in terms of local protein structure and function, splicing disruption, and phenotypic associations, thereby revealing previously unreported relationships between various biological phenomena and variant functional outcomes. For example, GOF and LOF variants exhibit contrasting enrichments in protein structural and functional regions, whilst LOF variants are more likely to disrupt canonical splicing as indicated by splicing-related features employed by the model. Further, by performing phenome-wide association studies (PheWAS), we identified strong associations between relevant phenotypes and high-confidence predicted GOF and LOF variants. LoGoFunc outperforms other tools trained solely to predict pathogenicity or general variant impact for the identification of pathogenic GOF and LOF variants.

genetics↗

bioRxiv2021

Identification of Discriminative Gene-level and Protein-level Features Associated with Gain-of-Function and Loss-of-Function Mutations

Identifying whether a given genetic mutation results in a gene product with increased (gain-of-function; GOF) or diminished (loss-of-function; LOF) activity is an important step toward understanding disease mechanisms as they may result in markedly different clinical phenotypes. Here, we generated the first extensive database of all currently known germline GOF and LOF pathogenic mutations by employing natural language processing (NLP) on the available abstracts in the Human Gene Mutation Database. We then investigated various gene- and protein-level features of GOF and LOF mutations by applying machine learning and statistical analyses to identify discriminative features. We found that GOF mutations were enriched in essential genes, autosomal dominant inheritance, protein binding and interaction domains, whereas LOF mutations were enriched in singleton genes, protein-truncating variants, and protein core regions. We developed a user-friendly web-based interface that enables the extraction of selected subsets from the GOF/LOF database by a comprehensive set of annotated features, and downloading up-to-date versions (https://itanlab.shinyapps.io/goflof/). These results could ultimately improve our understanding of how mutations affect gene/protein function thereby guiding future treatment options.

genetics↗

bioRxiv2018

SeqTailor: a user-friendly webserver for the extraction of DNA or protein sequences from next-generation sequencing data

Human whole-genome sequencing generally reveals about 4,000,000 genetic variants, including 20,000 coding variants, in each individual studied. These data are mostly stored as VCF-format files. Although many variant analysis methods accept VCF files as input, many other tools require DNA or protein sequences, particularly for splicing prediction, sequence alignment, phylogenetic analysis, and structure prediction. However, there is currently no existing online tool for extracting DNA or protein sequences for genomic variants from VCF files with user-defined parameters in a user-friendly, efficient, and standardized manner. We developed the SeqTailor webserver to bridge this gap. It can be used for the rapid extraction of (1) DNA sequences around genetic variants, with customizable window sizes, from the hg19 or hg38 human reference genomes; and (2) protein sequences encoded by the DNA sequences around genetic variants, with built-in SnpEff annotation and customizable window sizes, from human canonical transcripts. The SeqTailor webserver streamlines the sequence extraction process, and accelerates the analysis of genetic variant data with software requiring DNA or protein sequences. SeqTailor will facilitate the study of human genomic variation, by increasing the feasibility of sequence-based analysis and prediction. The SeqTailor webserver is freely available from http://shiva.rockefeller.edu/SeqTailor/.

bioinformatics↗