Biology subjects

Coulombe, B.

Publications and source records attributed to Coulombe, B..

5 recordsLinked to original sources

bioRxiv2025

Discovery and characterization of a pancreatic β cell subpopulation expressing an unknown surface epitope through single cell proteomics

The pancreatic {beta} cell surface proteome is essential for supporting cell communication, as it contributes to their secretory identity and maintains {beta} cell responsiveness to any extra- and intracellular variations. Therefore, studies are actively looking to identify specific surface biomarkers that not only can differentiate dysfunctional cell populations, particularly in the context of diabetes, but also can be used to develop therapeutic targets. While {beta} cell heterogeneity has been explored at the single-cell genomic and transcriptomic levels, in this study we aimed to demonstrate that even when a new plasma membrane epitope is identified, characterization of the proteome of cells expressing the same surface protein confirms that different subpopulations do exist. Using single-cell proteomic approach, we analyzed the proteome of MIN6 and Tc1 cells expressing Cd71, Cd99, and P538, which binds to a Fab-phage-538 identified in our previous study. Our findings suggest that the MIN6 (P538+) subpopulation may hold a more specialized functional identity compared to the other MIN6 (Cd71+), MIN6 (Cd99+), and control subpopulations. Moreover, we demonstrate that cell lines derived from the same tissue and expressing the same surface epitope can exhibit heterogeneity in their proteome. Indeed, while the specific expression of 17 protein groups confers to the MIN6 (P538+) subpopulation an insulin production and secretion-oriented identity, Tc1 (P538+), on the other hand, was characterized by only two proteins with no established involvement in glucagon production or secretion. Also, while the MIN6 (Cd99+) subpopulation may be predisposed to the development of insulin deficiency compared to MIN6 (Cd71+) and MIN6 (P538+), the proteomic profile of the Tc1 (Cd99+) subpopulation suggests that this subpopulation may hold an ability to adapt to stressful environmental conditions. Finally, when comparing MIN6 (Cd71+) to Tc1 (Cd71+), our findings suggest that the MIN6 subpopulation has probably a lesser role in Type 2 Diabetes Mellitus (T2DM) genesis in the context of iron homeostasis disruption than Tc1 (Cd71+).

molecular biology↗

bioRxiv2025

Investigating pancreatic beta cell membrane epitopes using unbiased cell-based Fab-phage display

The phenotypic and functional changes of cells in response to physiological and pathological conditions are strongly influenced by the roles of plasma membrane proteins. Recombinant Fab antibody-based phage display for an unbiased antigen-driven affinity selection is a suitable approach for identifying novel membrane proteins. Alterations in the function and distribution of cell membrane proteins in pancreatic {beta} cells have been observed in pathological conditions like diabetes. In this study, we integrated an unbiased cell-based Fab-phage display screening method with bioinformatics tools to identify and characterize Fabs that selectively bind to pancreatic {beta} cells in conditions simulated by a hyperglycemic environment. We isolated three Fab-phages, namely Fab_53, 538, and 54.68, that have binding properties matching specific epitopes on the MIN6 membrane. These Fabs are part of the immunoglobulin G groups that contain Kappa light chains. Bioinformatics analysis of the variable domains of their light and heavy chains (VL and VH) revealed that the potential epitope binding sites on the {beta} cell membrane are associated with pathways involved in insulin activity. Through FACS and IF analysis, we found that, of the three Fabs, Fab_538 exhibited the strongest binding to MIN6 cells. The use of InterProScan software resulted in the generation of 344 potential Fab_538 binding epitopes, and from these, AF2Complex predicted 10 interacting antigens. Our goal in combining Fab-phage display with bioinformatic tools is to develop a more effective, specific, and streamlined method for identifying disease-modifying membrane epitopes for monoclonal antibodies (mAbs).

molecular biology↗

bioRxiv2023

High-accuracy mapping of human and viral direct physical protein-protein interactions using the novel computational system AlphaFold-pairs

Protein-protein interactions are central, highly flexible components of regulatory mechanisms in all living cells. Over the years, diverse methods have been developed to map protein-protein interactions. These methods have revealed the organization of protein complexes and networks in numerous cells and conditions. However, these methods are also time consuming, costly and sensitive to various experimental artifacts. To avoid these caveats, we have taken advantage of the AlphaFold-Multimer software, which succeeded in predicting the structure of many protein complexes. We designed a relatively simple algorithm based on assessing the physical proximity of a test protein with other AlphaFold structures. Using this method, named AlphaFold-pairs, we have successfully defined the probability of a protein-protein interaction forming. AlphaFold-pairs was validated using well-defined protein-protein interactions found in the literature and specialized databases. All pairwise interactions forming within the 12-subunit transcription machinery RNA Polymerase II, according to available structures, have been identified. Out of 66 possible interactions (excluding homodimers), 19 specific interactions have been found, and an additional previously unknown interaction has been unveiled. The SARS-CoV-2 surface glycoprotein Spike (or S) was confirmed to interact with high preference with the human ACE2 receptor when compared to other human receptors. Notably, two additional receptors, INSR and FLT4, were found to interact with S. For the first time, we have successfully identified protein-protein interactions that are likely to form within the reassortant Eurasian avian-like (EA) H1N1 swine G4 genotype Influenza A virus, which poses a potential zoonotic threat. Testing G4 proteins against human transcription factors and molecular chaperones (a total of 100 proteins) revealed strong specific interactions between the G4 HA and HSP90B1, the G4 NS and the PAQosome subunit RPAP3, as well as the G4 PA and the POLR2A subunit. We predict that AlphaFold-pairs will revolutionize the study of protein-protein interactions in a large number of healthy and diseased systems in the years to come.

bioinformatics↗

bioRxiv2021

Recurrent chromosomal translocations in sarcomas create a mega-complex that mislocalizes NuA4/TIP60 to Polycomb target loci

Chromosomal translocations frequently promote carcinogenesis by producing gain-of-function fusion proteins. Recent studies have identified highly recurrent chromosomal translocations in patients with Endometrial Stromal Sarcomas (ESS) and Ossifying FibroMyxoid Tumors (OFMT) leading to an in-frame fusion of PHF1 (PCL1) to six different subunits of the NuA4/TIP60 complex. While NuA4/TIP60 is a co-activator that acetylates chromatin and loads the H2A.Z histone variant, PHF1 is part of the Polycomb repressive complex 2 (PRC2) linked to transcriptional repression of key developmental genes through methylation of histone H3 on lysine 27. In this study, we characterize the fusion protein produced by the EPC1-PHF1 translocation. The chimeric protein assembles a mega-complex harboring both NuA4/TIP60 and PRC2 activities and leads to mislocalization of chromatin marks in the genome, in particular over an entire topologically- associating domain including part of the HOXD cluster. This is linked to aberrant gene expression, most notably increased expression of PRC2 target genes. Furthermore, we show that JAZF1, implicated with a PRC2 component in the most frequent translocation in ESS, JAZF1-SUZ12, is a potent transcription activator that physically associates with NuA4/TIP60, its fusion creating similar outcomes as EPC1-PHF1. Importantly, the specific increased expression of PRC2 targets/HOX genes was also confirmed with ESS patient samples. Altogether, these results indicate that most chromosomal translocations linked to these sarcomas employ the same molecular oncogenic mechanism through a physical merge of NuA4/TIP60 and PRC2 complexes leading to mislocalization of histone marks and aberrant polycomb target gene expression.

molecular biology↗

bioRxiv2021

The unphosphorylated form of the PAQosome core subunit RPAP3 binds ribosomal preassembly complexes to modulate ribosome biogenesis.

The PAQosome (Particle for Arrangement of Quaternary structure) is a twelve-subunit HSP90 co-chaperone involved in the biogenesis of several human protein complexes. Two mechanisms of client selection have previously been identified, namely the selective recruitment of specific adaptors and the differential use of homologous core subunits. Here, we describe a third client selection mechanism by showing that RPAP3, one of the core PAQosome subunits, is phosphorylated at several Ser residues in HEK293 cells. Affinity purification coupled with mass spectrometry (AP-MS) using expression of tagged RPAP3 with single phospho-null mutations at Ser116, Ser119 or Ser121 reveals binding of the unphosphorylated form to several proteins involved in ribosome biogenesis. In vitro phosphorylation assays indicate that the kinase CK2 phosphorylates these RPAP3 residues. This finding is supported by data showing that pharmacological inhibition of CK2 enhances binding of RPAP3 to ribosome preassembly factors in AP-MS experiments. Moreover, silencing of PAQosome subunits interferes with ribosomal assembly factors interactome. Altogether, these results indicate that RPAP3 phosphate group addition/removal at specific residues modulates binding to subunits of preribosomal complexes and allows speculating that PAQosome posttranslational modifications is a mechanism of client selection.

biochemistry↗