Biology subjects

Hendy, J.

Publications and source records attributed to Hendy, J..

6 recordsLinked to original sources

bioRxiv2026

Latent Transforming Growth Factor Binding Protein ? 2 promotes microfibrillar TGF-? bioavailability to drive pathologic fibrosis in remote regions of infarcted hearts

Myocardial infarction (MI) initiates ventricular remodeling that extends beyond the infarct into remote, viable myocardium, where diffuse extracellular matrix (ECM) remodeling and stiffening contribute to progressive dysfunction and heart failure. Latent transforming growth factor binding protein 2 (LTBP2) is an injury-induced, microfibril-associated ECM glycoprotein that, among the LTBP family, does not covalently bind latent TGF-{beta}. We asked whether LTBP2 regulates remote remodeling after MI, and how a protein lacking latent TGF-{beta}-binding capacity could influence TGF-{beta}-dependent fibrosis. Wild-type and Ltbp2-null mice underwent permanent coronary ligation or sham surgery and were followed for 28 days by echocardiography and speckle-tracking strain analysis. Remote myocardium was assessed by histology, atomic force microscopy, and quantitative proteomics. Mechanism was interrogated in primary cardiac fibroblasts using a TGF-{beta} reporter assay. Sufficiency was tested with a fibrillin-1?binding module of LTBP2 delivered as purified protein or by lentiviral expression. LTBP2 was induced in injury-activated cardiac fibroblasts and localized to infarct and remote myocardium by 7 days post-MI. Ltbp2 deletion improved 28-day survival (P=0.0272) where Ltbp2-null hearts showed preserved ejection fraction and faster diastolic strain rates, with protection concentrated in segments remote from the infarct. Remote myocardium contained less interstitial collagen and was significantly less stiff. Proteomic profiling showed enrichment of ECM organization and TGF-{beta}-responsive programs in wild-type hearts that was attenuated in knockouts. In fibroblasts, loss of LTBP2 increased LTBP1 matrix incorporation and shifted TGF-{beta} from the soluble to the matrix-bound compartment; conversely, the minimal LTBP2 module bound fibrillin-1 directly and mobilized latent TGF-{beta} from established matrix within 20 minutes. LTBP2 drives maladaptive remodeling of remote myocardium after MI by limiting matrix sequestration of latent TGF-{beta} and expanding the activatable pool, resolving how an LTBP that does not bind latent TGF-{beta} amplifies TGF-{beta}- dependent fibrosis. LTBP2 and its fibrillin-1 interaction surface may be tractable targets.

physiology↗

bioRxiv2025

An unclean slate, discrepancies between food input and recovered protein signal from experimental foodcrusts

Organic residues are a rich source of biomolecular information on ancient diets. In particular, foodcrusts, charred residues on ceramics, are commonly analysed for their lipid content and to a lesser extent protein in order to identify foods, culinary practices and material culture use in past populations. However, the composition of foodcrusts and the factors behind their formation are not well understood. Here we analyse proteomic data (available via ProteomeXchange with identifier PXD059930) from foodcrusts made using a series of mixtures of protein- (salmon flesh), lipid- (beef fat) and carbohydrate-rich (beetroot) foods to investigate the relationship between the biomolecular composition of the input and the recovered signal using conventional methods applied to archaeological material. Additionally, using 3D modelling we quantify the volume of foodcrust generated by different ingredient combinations The results highlight biases in the data obtained in the analyses of organic residues both in terms of identified resources reflecting the cooked foodstuffs, e.g. an overrepresentation of fish proteins, as well as with regards to the abundance of foodcrust, for example mixtures of only salmon and beef fat resulted in relatively small amounts of foodcrust, and suggest caution in interpreting the composition of residues formed from complex mixtures of foodstuffs.

biochemistry↗

bioRxiv2024

An extensive archaeological dental calculus dataset spanning 5000 years for ancient human oral microbiome research

Archaeological dental calculus can provide detailed insights into the ancient human oral microbiome. We offer a multi-period, multi-site, ancient shotgun metagenomic dataset consisting of 174 samples obtained primarily from archaeological dental calculus derived from various skeletal collections in the United Kingdom. This article describes all the materials used including the skeletons historical period and burial location, biological sex, and age determination, data accessibility, and additional details associated with environmental and laboratory controls. In addition, this article describes the laboratory and bioinformatic methods associated with the dataset development and discusses the technical validity of the data following quality assessments, damage evaluations, and decontamination procedures. Our approach to collecting, making accessible, and evaluating bioarchaeological metadata in advance of metagenomic analysis aims to further enable the exploration of archaeological science topics such as diet, disease, and antimicrobial resistance (AMR).

microbiology↗

bioRxiv2024

The impact of cooking and burial on proteins: a characterisation of experimental foodcrusts and ceramics

Foodcrusts have received relatively little attention in the burgeoning field of proteomic analysis of ancient cuisine. We remain ignorant of how cooking and burial impacts protein survival, and crucially, the extent to which the extractome reflects the composition of input ingredients. Therefore, through experimental analogues we explore the extent of protein survival in unburied and buried foodcrusts and ceramics using typical Mesolithic ingredients (red deer, Atlantic salmon and sweet chestnut). We then explore a number of physiochemical properties theorised to aid protein preservation. The results reveal that proteins were much more likely to be detected in foodcrusts than ceramics using the methodology employed, input ingredient strongly influences protein preservation, and that degradation is not universal nor linear between proteins, indicating that multiple protein physiochemical properties are at play. While certain properties such as hydrophobicity apparently aid protein preservation, none single-handedly explain why particular proteins/peptides survive in buried foodcrusts: this complex interplay requires further investigation. The findings demonstrate that proteins indicative of the input ingredient can be identifiable in foodcrust, but that the full proteome is unlikely to preserve. While this shows promise for the survival of proteins in archaeological foodcrust, further research is needed to accurately interpret foodcrust extractomes.

biochemistry↗

bioRxiv2023

Dysregulated expression of Hoxa1 isoforms in hematopoietic stem and progenitor cells causes myelodysplastic syndromes.

The homeobox gene, Hoxa1, has two different isoforms generated by alternative splicing: a full-length homeodomain-containing Hoxa1 (Hoxa1-FL), and a truncated Hoxa1 (Hoxa1-T), that lacks the homeodomain. The effects of the distinct Hoxa1 isoforms in hematopoiesis have not been investigated. Oncoretroviral studies revealed that Hoxa1-T acts in a dominant negative manner, regulating transcriptionally active Hoxa1. Oncoretroviral overexpression of wildtype Hoxa1 (WT-Hoxa1), which generates both Hoxa1 isoforms, in murine hematopoietic stem and progenitor cells (HSPCs) perturbed hematopoiesis, resulting in transplantable myelodysplastic syndromes (MDS) in mice. Overexpression of a mutated Hoxa1 cDNA (MUT-Hoxa1) that generates Hoxa1-FL, but not Hoxa1-T, led to a more severe MDS that transformed to secondary acute myeloid leukemia (sAML). DNA damage repair pathways were downregulated in Hoxa1-overexpressing hematopoietic progenitor cells, accompanied by increased {gamma}H2AX foci. In silico analyses revealed that CD34+ cells from approximately 50% of patients with MDS had elevated HOXA1-FL expression. Conditional knock-in WT-Hoxa1 and MUT-Hoxa1 mice were generated and had features of pre-MDS, developing altered hematopoiesis within 4 months of Hoxa1 isoform overexpression in HSPCs. HSPCs were significantly reduced in all knock-in mice, accompanied by significantly increased apoptosis in WT-Hoxa1 HSPCs. Healthy wildtype recipients transplanted with bone marrow cells from Hoxa1 knock-in mice developed trilineage MDS, with Hoxa1 isoform and gene dosage dependent phenotypes. Collectively our data identify a role for HOXA1 in the pathogenesis of MDS. Our Hoxa1 mouse models capture different stages of progression of disease from pre-MDS to MDS to sAML and provide novel, clinically relevant tools to study MDS. Key pointsHOXA1 is upregulated in approximately 50% of MDS patient CD34+ BM cells, highlighting a potential role for HOXA1 in the pathogenesis of MDS. Dysregulated expression of Hoxa1 isoforms in murine hematopoietic stem and progenitor cells predisposes mice to pre-MDS and MDS.

cancer biology↗

bioRxiv2020

A dynamic 6,000-year genetic history of Eurasia's Eastern Steppe

The Eastern Eurasian Steppe was home to historic empires of nomadic pastoralists, including the Xiongnu and the Mongols. However, little is known about the regions population history. Here we reveal its dynamic genetic history by analyzing new genome-wide data for 214 ancient individuals spanning 6,000 years. We identify a pastoralist expansion into Mongolia ca. 3000 BCE, and by the Late Bronze Age, Mongolian populations were biogeographically structured into three distinct groups, all practicing dairy pastoralism regardless of ancestry. The Xiongnu emerged from the mixing of these populations and those from surrounding regions. By comparison, the Mongols exhibit much higher Eastern Eurasian ancestry, resembling present-day Mongolic-speaking populations. Our results illuminate the complex interplay between genetic, sociopolitical, and cultural changes on the Eastern Steppe.

genomics↗