Biology subjects

Cain, S. A.

Publications and source records attributed to Cain, S. A..

5 recordsLinked to original sources

bioRxiv2026

Manchester Proteome Profiler: A User-Friendly Platform for Quantitative Proteomic Analysis

Manchester Proteome Profiler (MPP) is an open-source R Shiny application that streamlines downstream analysis of quantitative proteomic data. Compatible with grouped protein intensities tables from MaxQuant, FragPipe, Proteome Discoverer and other custom layouts, MPP provides an integrated platform for filtering, normalisation, imputation, differential expression analysis and cluster analysis across user-chosen experimental conditions. MPP supports both single- and dual-dataset comparisons, incorporates SAINTexpress for affinity purification and proximity labelling experiments, and downstream analysis of the significant protein list clusters to functional enrichment and interaction networks via Gene Ontology, BioGRID and STRING. Benchmarking with a KRAS proximity biotinylation dataset demonstrated the ability of MPP to identify reproducible clusters of differentially expressed proteins and reveal biologically meaningful patterns, including enrichment of solute carrier transporters and adhesion molecules. With interactive visualisations, customisable reports, and support for complex experimental designs, MPP offers a novel, versatile and user-friendly environment for proteomic data exploration and hypothesis generation.

bioinformatics↗

bioRxiv2025

Inhibitory TIGIT signalling is dependent on T cell receptor activation

TIGIT is an immune checkpoint receptor that can signal via cytoplasmic ITT-like and ITIM motifs to regulate T cell function. The signalling molecules that mediate inhibitory TIGIT signalling in T cells remain poorly defined, and it is not clear how TIGIT activation is regulated. Here, proximity proteomics was employed in Jurkat T cells to identify TIGIT-associating proteins upon engagement with its ligand CD155. This identified several ligation-specific TIGIT interactors, including proteins involved in signalling (Grb2 and SOS1), cytoskeletal regulation (CD2AP and SdcBP), and endocytosis (IST1 and SNX3). A TIGIT mutant (Y225A/Y231A) incapable of signalling via its inhibitory motifs prevented the recruitment of these proteins, indicating inhibitory signalling-specific engagement of these pathways. Strikingly, T cell receptor (TCR) stimulation was also needed for TIGIT to engage with these pathways. Mechanistically, phosphorylation of TIGIT required both CD155 ligation and TCR activation, which resulted in signalling and internalisation. These findings demonstrate that TIGIT signalling is context-dependent and restricted to T cells receiving simultaneous TCR activation. This establishes a regulatory mechanism that limits checkpoint control to when functionally required.

immunology↗

bioRxiv2021

Proteolysis of fibrillin-2 microfibrils is essential for normal skeletal development

The embryonic extracellular matrix (ECM) undergoes transition to mature ECM as development progresses, yet specific transition mechanisms ensuring ECM proteostasis and their regulatory impact are poorly defined. Fibrillin microfibrils are macromolecular ECM complexes serving structural and regulatory roles. In mice, Fbn1 and Fbn2, encoding major microfibrillar components, are strongly expressed during embryogenesis, but fibrillin-1 is the major component observed in adult tissue microfibrils. Here, analysis of mouse Adamts6 and Adamts10 mutant embryos, lacking these homologous secreted metalloproteases individually and in combination, along with in vitro analysis of microfibrils, measurement of ADAMTS6-fibrillin affinities and N-terminomics identification of ADAMTS6-cleaved sites, demonstrates a transcriptionally adapted system for fibrillin-2 proteolysis that contributes to postnatal fibrillin-1 dominance. The lack of ADAMTS6, alone and in combination with ADAMTS10 led to excess fibrillin-2 in perichondrium, with impaired skeletal development resulting from a drastic reduction of aggrecan, cartilage link protein and impaired BMP, but not TGF{beta} signaling in cartilage. Although ADAMTS6 cleaves fibrillin-1 and fibrillin-2 as well as fibronectin, which provides the initial scaffold for microfibril assembly, primacy of the protease-substrate relationship between ADAMTS6 and fibrillin-2 was unequivocally established by reversal of these defects in Adamts6-/- embryos by genetic reduction of Fbn2, but not Fbn1.

developmental biology↗

bioRxiv2020

SIRT1 activity orchestrates ECM expression during hESC-chondrogenic differentiation through SOX5 and ARID5B

Epigenetic modification is a key driver of differentiation and the deacetylase Sirtuin1 (SIRT1) is an established regulator of cell function, ageing and articular cartilage homeostasis. Here we investigate the role of SIRT1 during development of chondrocytes by using human embryonic stem cells (hESCs). HESC-chondroprogenitors were treated with SIRT1 activator; SRT1720, or inhibitor; EX527, at different development stages. Activation of SIRT1 during 3D-pellet culture led to significant increases in expression of ECM genes for type-II collagen (COL2A1) and aggrecan (ACAN), and chondrogenic transcription factors SOX5 and ARID5B, with SOX5 ChIP analysis demonstrating enrichment on the ACAN -10 enhancer. Unexpectedly, while ACAN was enhanced, GAG retention in the matrix was reduced when SIRT1 was activated. Significantly, ARID5B and COL2A1 were positively correlated, with Co-IP indicating association of ARID5B with SIRT1 suggesting that COL2A1 expression is promoted by an ARID5B and SIRT1 interaction. In conclusion, SIRT1 activation positively impacts on the expression of the main ECM proteins, whilst altering ECM composition and suppressing GAG content during cartilage development. These results suggest that SIRT1 activity can be beneficial to cartilage development and matrix protein synthesis but tailored by addition of other positive GAG mediators.

developmental biology↗

bioRxiv2020

Optogenetic control of the Bone Morphogenetic Protein signalling pathway through engineered blue light-sensitive receptors

Bone Morphogenetic Proteins (BMPs) are members of the Transforming Growth Factor {beta} (TGF{beta}) superfamily and have crucial roles during development; including mesodermal patterning and specification of renal, hepatic and skeletal tissues. In vitro developmental models currently rely upon costly and unreliable recombinant BMP proteins that do not enable dynamic or precise perturbation of the BMP signalling pathway. Here, we develop a novel optogenetic BMP signalling system (optoBMP) that enables rapid induction of the canonical BMP signalling pathway through illumination with blue light. We demonstrate the utility of the optoBMP system in multiple human cell lines to initiate signal transduction through phosphorylation and nuclear translocation of SMAD1/5, leading to upregulation of BMP target genes including Inhibitors of DNA binding ID2 and ID4. Furthermore, we demonstrate how the optoBMP system can be used to fine-tune activation of the BMP signalling pathway through variable light stimulation. Optogenetic control of BMP signalling will enable dynamic and high-throughput intervention across a variety of applications in cellular and developmental systems.

molecular biology↗