Biology subjects

White, C. H.

Publications and source records attributed to White, C. H..

9 recordsLinked to original sources

bioRxiv2026

Novel Plasma Proteomics and Phosphoproteomics Platform Captures Pleiotropic Cardiometabolic Spectrum Effects of Semaglutide in Patients with T2D and Atherosclerosis: A Companion Diagnostic Pilot Study from the STOP (Semaglutide Treatment On coronary atherosclerosis Progression) Randomized Trial

BACKGROUNDAs a GLP1 R agonist, semaglutide is known to exhibits pleiotropic health effects across the cardiometabolic spectrum in patients with type 2 Diabetes Mellitus (T2D). However, in depth and unbiased protein and phosphoprotein level evidence that reflects such effects of semaglutide in plasma remains elusive. OBJECTIVESThis pilot study applied an innovative plasma proteomics and phosphoproteomics technology to a sub-set of patients with T2D that participated in the Semaglutide Treatment effect on coronary atherosclerosis Progression (STOP) randomized trial. The aim of this study was to identify the systemic effects of semaglutide treatment in pathways that underpin its pleiotropic cardiometabolic spectrum health benefits. METHODSThe study applied a proprietary liquid biopsy discovery proteomics platform and its derivative cardiometabolic spectrum database (International patent PCT/US2021/063407) to 16 patients from the STOP randomized trial. Plasma samples from 8 patients in the active group and 8 patients in the placebo group at baseline and 52 weeks post treatment were analyzed. The methodology entailed the use of a unique liquid fixative chemistry to instantly solubilize and stabilize plasma proteins and phosphoproteins at room temperature followed by their direct microflow monolithic partition chromatography, dialysis purification, solution phase proteolysis, multiplex isobaric stable isotope labeling of proteotypic peptides, lab-on-chip TiO2/ZrO2 phosphopeptide enrichment and nanotechnology enhanced ultra-high resolution LC-MS analysis. To identify differentially abundant proteins (DAPs) and phosphoproteins (DApPs) in patients treated with semaglutide vs. placebo, the respective abundance ratio for each was considered repectively. Ratios were log2-transformed to normalize their distribution. A one-sample T-Test (paired) using the two-stage Benjamini Yekutieli Krieger step up method for multiple hypothesis testing FDR correction of the p-value was performed. The threshold of significance was set at q[less double equals]0.05. DAPs/DApPs were corrected for placebo. The expressed proteome and phosphoproteome were further interpreted with a multifactorial computational biology pipeline to deconvolute their underlying protein-level molecular pathways and their networks along with transcriptional factors and kinases that regulate them. RESULTSThis study achieved an extremely high depth-and-breadth in quantitative proteome and phosphoproteome coverage from only 20{micro}L whole plasma equivalent from each patient. Namely, a total of 13,173 proteins and 25,578 phosphopeptides were fully profiled (q[less double equals] 0.05). Of these, 1,040 were differentially abundant proteins (DAPs) and 1,064 were differentially abundant phosphoproteins (DApPs), in the semaglutide treated group after correcting for placebo, at an absolute log2-fold-change of [greater double equals] 0.5, CV [less double equals] 15%, q[less double equals] 0.05. Of interest, this study profiled over 85% of all proteins/phosphoproteins (6,700) reported to date based on the use of the well curated and up-to-date PaxDB database. Over 70% of these known proteins were of exosomal origin. Importantly, an additional [~]9000 plasma proteins and phosphoproteins of this study constituted entirely novel observations. Contextualization of the DAPS, DApPs, kinases and transcription factors for all statistically significant enriched canonical pathways (FDR-corrected q<0.001) revealed a wide array of pathophysiological processes attributed to semaglutide treatment. Furthermore, these pathways provided a molecular understanding to the reported imaging biomarkers against the same STOP trial patients. CONCLUSIONSThis feasibility study demonstrated how an effective plasma proteomics and phosphoproteomics platform can generate a treatment-adaptive companion diagnostic molecular signature that holistically captures the multiple cardiometabolic spectrum health effects of semaglutide in patients with atherosclerosis and T2D.

pharmacology and toxicology↗

bioRxiv2025

Dystrophin Dp71 is essential for the development and function of macrophages

Mutations in the DMD gene, encoding dystrophins, cause progressive muscle degeneration with severe sterile inflammation. While macrophages predominate amongst muscle-infiltrating cells, being central to both damage and regeneration, they were not known to express dystrophin. Yet, we recently demonstrated Dp71 dystrophin expression correlating with tumour infiltrating macrophages. Here we report physiological, developmentally regulated expression of Dp71 in human and mouse hematopoietic stem cells, which decreases with cell maturation into bone marrow macrophages (BMM). Proteomics with molecular and functional analyses in mouse dystrophin-null BMM and peritoneal macrophages reveal that absence of dystrophin disturbs their development. Alterations in over 300 proteins mapped to pathways and networks relating to reduced migration and phagocytosis and increased NLRP3 inflammasome functions. These defects are Dp71-dependent and not caused by the dystrophic environment, since Dmdmdx mouse macrophages, which express Dp71, are not affected. Thus, we identify an important new role for the DMD gene. Altered Dp71 expression in tumour microenvironment cells and in dystrophin-null patients should be investigated to understand the commonalities between DMD and tumours, and potentially identify new treatments.

cell biology↗

bioRxiv2022

Proteomic Mapping of Intercellular Synaptic Environments via Flavin-Dependent Photoredox Catalysis

Receptor-ligand interactions play essential signaling roles within intercellular contact regions. This is particularly important within the context of the immune synapse where protein communication at the surface of physically interacting T cells and antigen-presenting cells regulate downstream immune signaling responses. To identify protein microenvironments within immunological synapses, we combined a flavin-dependent photocatalytic labeling strategy with quantitative mass spectrometry-based proteomics. Using -PD-L1 or -PD-1 single-domain antibody (VHH)-based photocatalyst targeting modalities, we profiled protein microenvironments within the intercellular region of an immune synapse-forming co-culture system. In addition to enrichment of both PD-L1 and PD-1 with either targeting modality, we also observed enrichment of both known immune synapse residing receptor-ligand pairs and surface proteins, as well as previously unknown synapse residing proteins.

biochemistry↗

bioRxiv2022

High resolution photocatalytic mapping of SARS-CoV-2 Spike protein-host cell membrane interactions

Identifying protein environments at the virus-host cell interface can improve our understanding of viral entry and pathogenesis. SARS-CoV-2, the virus behind the ongoing COVID-19 pandemic, uses the cell surface ACE2 protein as a major receptor, but the contribution of other cellular proteins in the entry process is unknown. To probe the microenvironment of SARS-CoV-2 Spike-ACE2 protein interactomes on human cells, we developed a photocatalyst-based viral-host protein microenvironment mapping platform (ViraMap) employing iridium photocatalysts conjugated to Spike for visible-light driven proximity labelling on host cells. Application of ViraMap on ACE2-expressing cells captured ACE2, the established co-receptor NRP1, as well as other proteins implicated in host cell entry and immunomodulation. We further investigated these enriched proteins via loss-of-function and over-expression in pseudotype and authentic infection models and observed that the Ig receptor PTGFRN and tyrosine kinase ligand EFNB1 can serve as SARS-CoV-2 entry factors. Our results highlight additional host targets that participate infection and showcase ViraMap for interrogating virus-host cell surface interactomes.

biochemistry↗

bioRxiv2022

Novel neutrophil subsets associated with sepsis, vascular dysfunction and metabolic alterations identified using systems immunology

Sepsis is a life-threatening condition caused by a dysregulated host response to infection. Despite continued efforts to understand the pathophysiology of sepsis, no effective therapies are currently available. While singular components of the aberrant immune response have been investigated, comprehensive studies linking different data layers are lacking. Using an integrated systems immunology approach, we evaluated neutrophil phenotypes and concomitant changes in cytokines and metabolites in sepsis patients. Our findings identify novel differentially expressed immature neutrophil subsets in sepsis patients. These and other subsets correlate with various proteins, metabolites, and lipids, including pentraxin-3, angiopoietin-2 and lysophosphatidylcholines, in sepsis patients. These results enabled the construction of a predictive model based on weighted multi-omics linear regression analysis for patient classification. These findings could help inform earlier patient stratification and treatment options, as well as facilitate future mechanistic studies targeting the trifecta of surface marker expression, cytokines, and metabolites.

immunology↗

bioRxiv2021

Detection of Cell-Cell Interactions via Photocatalytic Cell Tagging

Cell-cell interactions drive essential biological processes critical to cell and tissue development, function, pathology, and disease outcome. The growing appreciation of immune cell interactions within disease environments has led to significant efforts to develop protein- and cell-based therapeutic strategies. A better understanding of these cell-cell interactions will enable the development of effective immunotherapies. However, characterizing these complex cellular interactions at molecular resolution in their native biological contexts remains challenging. To address this, we introduce photocatalytic cell tagging (PhoTag), a modality agnostic platform for profiling cell-cell interactions. Using photoactivatable flavin-based cofactors, we generate phenoxy radical tags for targeted labeling at the cell surface. Through various targeting modalities (e.g. MHC-Multimer, antibody, single domain antibody (VHH)) we deliver a flavin photocatalyst for cell tagging within monoculture, co-culture, and peripheral blood mononuclear cells. PhoTag enables highly selective tagging of the immune synapse between an immune cell and an antigen-presenting cell through targeted labeling at the cell-cell junction. This allowed for the ability to profile gene expression-level differences between interacting and bystander cell populations. Given the modality agnostic and spatio-temporal nature of PhoTag, we envision its broad utilization to detect and profile intercellular interactions within an immune synapse and other confined cellular regions for any biological system.

immunology↗

bioRxiv2021

Assessing donor-to-donor variability in human intestinal organoid cultures

Donor-to-donor variability in primary human organoid cultures has not been well characterized. As these cultures contain multiple cell types, there is greater concern that variability could lead to increased noise. In this work we investigated donor-to-donor variability in human gut adult stem cell (ASC) organoids. We examined intestinal developmental pathways during culture differentiation in ileum- and colon-derived cultures established from multiple donors, showing that differentiation patterns were consistent among cultures. This finding indicates that donor-to-donor variability in this system remains at a manageable level. Intestinal metabolic activity was evaluated by targeted analysis of central carbon metabolites and by analyzing hormone production patterns. Both experiments demonstrated similar metabolic functions among donors. Importantly, this activity reflected intestinal biology, indicating that these ASC organoid cultures are appropriate for studying metabolic processes. This work establishes a framework for generating high confidence data using human primary cultures through thorough characterization of variability.

developmental biology↗

bioRxiv2021

Vaccine Hyporesponse Induced By Individual Antibiotic Treatment In Mice And Non-Human Primates Is Diminished Upon Recovery Of The Gut Microbiome

Emerging evidence demonstrates a connection between microbiome composition and suboptimal response to vaccines (vaccine hyporesponse). Harnessing the interaction between microbes and the immune system could provide novel therapeutic strategies for improving vaccine response. Currently we do not fully understand the mechanisms and dynamics by which the microbiome influences vaccine response. Using both mouse and non-human primate models, we report that short-term oral treatment with a single antibiotic (vancomycin) results in disruption of the gut microbiome and this correlates with a decrease in systemic levels of antigen-specific IgG upon subsequent parenteral vaccination. We further show that recovery of microbial diversity before vaccination prevents antibiotic-induced vaccine hyporesponse, and that the antigen specific IgG response correlates with the recovery of microbiome diversity. RNA-sequencing analysis of small intestine, spleen, whole blood, and secondary lymphoid organs from antibiotic treated mice revealed a dramatic impact on the immune system, and a muted inflammatory signature is correlated with loss of bacteria from Lachnospiraceae, Ruminococcaceae, and Clostridiaceae. These results suggest that microbially modulated immune pathways may be leveraged to promote vaccine response and will inform future vaccine design and development strategies. ImportanceAntibiotic-induced gut microbiome disruption has been linked to reduced vaccine efficacy. Despite these observations, there remains a knowledge gap in the specific mechanisms by which antibiotics and the gut microbiome influence vaccine efficacy. We aim to contribute to the fields growing mechanistic understanding by presenting a detailed analysis of antibiotic treatment and recovery as it relates to vaccine response and the microbiome. Using animal models, we show that short-term antibiotic treatment prior to vaccination results in diminished vaccine-specific immune responses, and that these are correlated with specific microbiome signatures. We also demonstrate the converse, in which gut microbiome recovery can result in improved vaccine response. We further reveal that antibiotics can significantly alter multiple relevant immune pathways and this alteration in immune tone may contribute to the vaccine hyporesponse. We expect our findings will enable the continued prosecution of the role of the microbiome in modulating the host immune system.

immunology↗

bioRxiv2021

Placental uptake and metabolism as determinants of pregnancy vitamin D status

Pregnancy 25-hydroxyvitamin D (25(OH)D) concentrations are associated with maternal and fetal health outcomes. Using physiological human placental perfusion and villous explants, we investigate the role of the placenta in regulating the relationships between maternal 25(OH)D and fetal physiology. We demonstrate active placental uptake of 25(OH)D3 by endocytosis, placental metabolism of 25(OH)D3 into 24,25-dihydroxyvitamin D3 and active 1,25-dihydroxyvitamin D [1,25(OH)2D3], with subsequent release of these metabolites into both the maternal and fetal circulations. Active placental transport of 25(OH)D3 and synthesis of 1,25(OH)2D3 demonstrate that fetal supply is dependent on placental function rather than simply the availability of maternal 25(OH)D3. We demonstrate that 25(OH)D3 exposure induces rapid effects on the placental transcriptome and proteome. These map to multiple pathways central to placental function and thereby fetal development, independent of vitamin D transfer. Our data suggest that the underlying epigenetic landscape helps dictate the transcriptional response to vitamin D treatment. This is the first quantitative study demonstrating vitamin D transfer and metabolism by the human placenta, with widespread effects on the placenta itself. These data demonstrate a complex interplay between vitamin D and the placenta and will inform future interventions using vitamin D to support fetal development and maternal adaptations to pregnancy.

physiology↗