Biology subjects

Humphrey, S. J.

Publications and source records attributed to Humphrey, S. J..

17 recordsLinked to original sources

bioRxiv2026

Personalized phosphoproteomics establish mTORC1 as a regulator of exercise-induced insulin sensitization in human skeletal muscle

Exercise enhances skeletal muscle insulin sensitivity, but the signaling mechanisms responsible are poorly understood. Understanding them may open new therapeutic avenues for individuals with limited exercise capacity. Here, we used rapamycin to inhibit mTORC1 in combination with exercise and insulin stimulation in healthy men. A single dose of rapamycin enhanced the insulin-sensitizing effect of exercise by 53% on average compared to placebo. Responses varied widely across individuals (-40% to 218%), and we leveraged this variance through personalized phosphoproteomics to map the mTORC1-dependent signaling network in skeletal muscle. This identified the protein kinase MKNK2 as a candidate downstream effector, which we then targeted for functional validation. Pharmacological inhibition of MKNK2 with eFT508 in insulin-clamped mice reduced both whole-body and skeletal muscle insulin sensitivity, confirming a functional role for MKNK2 activity in muscle glucose uptake. We then used eFT508 in ex vivo incubated human skeletal muscle to map the signaling network downstream of MKNK2, identifying the translational initiator eIF4G1 as a further regulatory node. Together, these findings indicate that exercise-induced insulin sensitization is actively constrained by a negative feedback pathway running from mTORC1 through the translational regulators MKNK2 and eIF4G1, raising the possibility that rapid translation of unidentified target proteins contributes to fine-tuning glucose uptake.

physiology↗

bioRxiv2026

High-throughput screening in hiPSC-cardiac models reveals cardiomyocyte-specific cell cycle regulatory mechanisms

Introductory ParagraphMultiple regulatory mechanisms govern cardiomyocyte proliferation including epigenetic modifications, metabolism and mechanical load. However, it is unclear whether such mechanisms can be pharmacologically targeted to induce cardiomyocyte proliferation without affecting other cell types. Here, we develop a dual-reporter (TNNT2eGFP; PCNAmScarlet-I) and a high-throughput image-based pipeline in human induced pluripotent stem cell (hiPSC)-derived cardiomyocytes, with counter screening in non-myocytes, to identify compounds that selectively promote cardiomyocyte proliferation without affecting other cell types. We identify the PIM kinase inhibitor GDC-0339 as a cardiomyocyte-selective pro-proliferative compound. GDC-0339 induced proliferation of hiPSC-derived cardiomyocytes without activity in non-myocytes, non-cardiac fibroblasts or epithelial cells. Phosphoproteomic profiling of GDC-0339 in cardiomyocytes and non-cardiac fibroblasts revealed a cardiomyocyte-specific mechanism of action involving sarcomere disassembly via remodelling of the F-actin cytoskeleton and metabolic reprogramming to anaerobic metabolism via Pyruvate Dehydrogenase Kinases (PDKs). Thus, we uncover cardiomyocyte-specific mechanisms governing the cell cycle that are potentially druggable.

cell biology↗

bioRxiv2026

Ageing blunts the phospho-proteomic response to resistance exercise in humans

Ageing blunts the adaptive growth response in human skeletal muscle. To define the molecular processes underlying this impairment, we performed unbiased analysis of the phosphoproteome and total proteome in healthy young and old human skeletal muscle following acute resistance exercise (ResEX) and essential amino acid (EAA) ingestion. Ageing led to global suppression of the growth-induced global phosphoproteome, despite intact mTORC1 activation in old muscle. Our results identify widespread effects of ageing on skeletal muscle growth and highlight novel pathways for therapeutic development in aged skeletal muscle.

physiology↗

bioRxiv2025

The functional maturation of mouse spermatozoa is underpinned by global remodeling of the cellular phosphoproteome

The functional maturation of mammalian spermatozoa is driven by modification of their intrinsic proteome as the cells transit the male (epididymal sperm maturation) and female reproductive tracts (capacitation). Here, high-resolution mass spectrometry was used to interrogate the central role that phosphoproteomic changes play in the functional remodeling of mouse spermatozoa. This strategy identified 14,586 site-specific phosphorylation events, including the phosphorylation of 573 proteins and dephosphorylation of 426 during epididymal maturation and additional phosphorylation changes in 211 proteins linked to capacitation. We identified over 300 kinases that putatively govern these events, including three novel kinases (STK33, HIPK4, and PAK1) implicated in acrosomal exocytosis. The functional relevance of these data was confirmed via the use of knockout mouse models, which demonstrated several phosphoproteins as being essential for sperm motility and fertilization capacity. These findings illustrate that large-scale phosphorylation remodeling occurs during sperm maturation with implications extending to novel means of fertility regulation. HIGHLIGHTSO_LISperm phosphoproteome is dramatically remodeled during post-testicular maturation C_LIO_LIIdentification of >14,000 site-specific phosphorylation events providing comprehensive insight into sperm cell signaling events associated with functional maturation C_LIO_LIMajor changes in the sperm phosphoproteome coincide with epididymal maturation whereas capacitation results in more modest changes C_LIO_LIIdentification of 343 novel kinases potentially important for conferring functional maturity to spermatozoa and demonstrated role for STK33, HIPK4 and PAK1 kinases C_LIO_LIKnockout mouse models of 23 genes provided in vivo validation, with loss of these proteins leading to pronounced defects in sperm motility and fertilization capacity C_LIO_LIAll data is available via our interactive ShinySpermPhospho application - https://reproproteomics.shinyapps.io/ShinySpermPhospho/ C_LI

cell biology↗

bioRxiv2025

Contractile function maintains cardiomyocyte differentiation and inhibits cell cycle activity

Numerous endotherm species lose cardiac regenerative capacity shortly after birth, which is in contrast to many ectotherm species who regenerate throughout life. Whether the enhanced contractile function required for endothermy contributes to the cell-cycle exit remains to be explored. Herein, we use human cardiac organoids with advanced maturation combined with direct targeting of contraction using mavacamten and aficamten to enable exquisite control of active contraction over brief time windows. We show that transient inhibition of contraction re-activates the cell cycle. Multi-omics analyses demonstrated the cell cycle response to be mediated through a dedifferentiation-like process, which was swiftly reversed upon removal of the myosin inhibitors. Together these findings reveal that active contraction maintains differentiation including cell cycle arrest in cardiomyocytes.

cell biology↗

bioRxiv2024

Adipose tissue protein kinase D (PKD): regulation of signalling networks and its sex-dependent effects on metabolism

The protein kinase D (PKD) family of three highly homologous isoforms (PKD1, PKD2, and PKD3) are implicated as nutrient sensing signalling kinases that regulate the response of adipose and other tissues to the nutrient environment. However, the physiological role of adipose tissue PKD and its downstream cellular signalling targets are not well characterised. Phosphoproteomics was performed to elucidate signalling events downstream of PKD activation in differentiated 3T3L1 adipocytes using a triple isoform siRNA knockdown model. This revealed PKD-regulated pathways including insulin and cAMP signalling, which control metabolic responses in adipose tissue. An adipose tissue-specific and inducible dominant negative PKD (atDNPKD) mouse model that achieves functional inhibition of all three PKD isoforms was generated to assess the function of adipose PKD on whole-body metabolism in vivo in both male and female mice. Insulin-stimulated suppression of lipolysis was blunted in male, but not female, atDNPKD mice compared to control mice. Female, but not male, atDNPKD mice had higher fasting insulin but normal insulin action. Male atDNPKD mice showed greater sensitivity to the {beta}3-adrenergic receptor agonist CL316,243 on measures of lipolysis and energy expenditure, and displayed greater fat oxidation during fasting. During refeeding, male atDNPKD mice consumed less food and took longer to regain body weight lost during fasting. These effects were not observed in female mice. These findings indicate that PKD provides sex-dependent fine-tuning control of cAMP signalling in adipose tissue that is important for the coordination of energy balance during fasting and refeeding. NEW & NOTEWORTHYThe protein kinase D (PKD) family is a target for the treatment of obesity-related disorders. However, the physiological role of PKD in adipose tissue remains to be resolved. Using phosphoproteomics and an adipose tissue PKD loss-of-function mouse model, results demonstrate that PKD provides fine tuning of metabolic signalling in adipose tissue and metabolic responses to fasting and refeeding challenges, via coordination of feeding behaviour and regulation of body weight.

physiology↗

bioRxiv2023

The genetic and dietary landscape of the muscle insulin signalling network

Metabolic disease is caused by a combination of genetic and environmental factors, yet few studies have examined how these factors influence signal transduction, a key mediator of metabolism. Using mass spectrometry-based phosphoproteomics, we quantified 23,126 phosphosites in skeletal muscle of five genetically distinct mouse strains in two dietary environments, with and without acute in vivo insulin stimulation. Almost half of the insulin-regulated phosphoproteome was modified by genetic background on an ordinary diet, and high-fat high-sugar feeding affected insulin signalling in a strain-dependent manner. Our data revealed coregulated subnetworks within the insulin signalling pathway, expanding our understanding of the pathways organisation. Furthermore, associating diverse signalling responses with insulin-stimulated glucose uptake uncovered regulators of muscle insulin responsiveness, including the regulatory phosphosite S469 on Pfkfb2, a key activator of glycolysis. Finally, we confirmed the role of glycolysis in modulating insulin action in insulin resistance. Our results underscore the significance of genetics in shaping global signalling responses and their adaptability to environmental changes, emphasizing the utility of studying biological diversity with phosphoproteomics to discover key regulatory mechanisms of complex traits.

systems biology↗

bioRxiv2023

μPhos: a scalable and sensitive platform for functional phosphoproteomics

Mass spectrometry has revolutionized cell signaling research by vastly simplifying the identification and quantification of many thousands of phosphorylation sites in the human proteome. Defining the cellular response to internal or external perturbations in space and time is crucial for further illuminating functionality of the phosphoproteome. Here we describe {micro}Phos, an accessible phosphoproteomics platform that permits phosphopeptide enrichment from 96-well cell culture experiments in < 8 hours total processing time. By minimizing transfer steps and reducing liquid volumes to < 200 {micro}L, we demonstrate increased sensitivity, over 90% selectivity, and excellent quantitative reproducibility. Employing highly sensitive trapped ion mobility mass spectrometry, we quantify more than 20,000 unique phosphopeptides in a human cancer cell line using 20 {micro}g starting material, and confidently localize > 5,000 phosphorylation sites from 5 {micro}g. This depth covers key intracellular signaling pathways, rendering sample-limited applications and extensive perturbation experiments with hundreds of samples viable. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=199 SRC="FIGDIR/small/535617v1_ufig1.gif" ALT="Figure 1"> View larger version (87K): org.highwire.dtl.DTLVardef@43d3e9org.highwire.dtl.DTLVardef@10d975forg.highwire.dtl.DTLVardef@14ce090org.highwire.dtl.DTLVardef@2b2e67_HPS_FORMAT_FIGEXP M_FIG C_FIG

systems biology↗

bioRxiv2022

Parallel use of pluripotent human stem cell lung and heart models provide new insights for treatment of SARS-CoV-2

SARS-CoV-2 primarily infects the respiratory tract, but pulmonary and cardiac complications occur in severe COVID-19. To elucidate molecular mechanisms in the lung and heart, we conducted paired experiments in human stem cell-derived lung alveolar type II (AT2) epithelial cell and cardiac cultures infected with SARS-CoV-2. With CRISPR- Cas9 mediated knock-out of ACE2, we demonstrated that angiotensin converting enzyme 2 (ACE2) was essential for SARS-CoV-2 infection of both cell types but further processing in lung cells required TMPRSS2 while cardiac cells required the endosomal pathway. Host responses were significantly different; transcriptome profiling and phosphoproteomics responses depended strongly on the cell type. We identified several antiviral compounds with distinct antiviral and toxicity profiles in lung AT2 and cardiac cells, highlighting the importance of using several relevant cell types for evaluation of antiviral drugs. Our data provide new insights into rational drug combinations for effective treatment of a virus that affects multiple organ systems. One-sentence summaryRational treatment strategies for SARS-CoV-2 derived from human PSC models

microbiology↗

bioRxiv2022

Deep proteome profiling of white adipose tissue reveals marked conservation and distinct features between different anatomical depots

White adipose tissue is deposited mainly as subcutaneous adipose tissue (SAT), often associated with metabolic protection, and abdominal/visceral adipose tissue (VAT), which contributes to metabolic disease. To investigate the molecular underpinnings of these differences, we conducted comprehensive proteomics profiling of whole tissue and isolated adipocytes from these two depots across two diets from C57Bl/6J mice. The adipocyte proteomes from lean mice were highly conserved between depots, with the major depot-specific differences encoded by just 3% of the proteome. Adipocytes from SAT (SAdi) were enriched in pathways related to mitochondrial complex I and beiging, whereas visceral adipocytes (VAdi) were enriched in structural proteins and positive regulators of mTOR presumably to promote nutrient storage and cellular expansion. This indicates that SAdi are geared toward higher catabolic activity, while VAdi are more suited for lipid storage. By comparing adipocytes from mice fed chow or Western diet (WD), we define a core adaptive proteomics signature consisting of increased extracellular matrix proteins and decreased fatty acid metabolism and mitochondrial Coenzyme Q biosynthesis. Relative to SAdi, VAdi displayed greater changes with WD including a pronounced decrease in mitochondrial proteins concomitant with upregulation of apoptotic signaling and decreased mitophagy, indicating pervasive mitochondrial stress. Furthermore, WD caused reduction in lipid handling and glucose uptake pathways particularly in VAdi, consistent with adipocyte de-differentiation. By overlaying the proteomics changes with diet in whole adipose tissue and isolated adipocytes, we uncovered concordance between adipocytes and tissue only in the VAT, indicating a unique tissue-specific adaptation to sustained WD in SAT. Finally, an in-depth comparison of isolated adipocytes and 3T3-L1 proteomes revealed a high degree of overlap, supporting the utility of the 3T3-L1 adipocyte model. These deep proteomes provide an invaluable resource highlighting differences between white adipose depots that may fine-tune their unique functions and adaptation to an obesogenic environment.

molecular biology↗

bioRxiv2022

Phosphoproteomics reveals rewiring of the insulin signaling network and multi-nodal defects in insulin resistance

The failure of metabolic tissues to appropriately respond to insulin ("insulin resistance") is an early marker in the pathogenesis of type 2 diabetes. Protein phosphorylation is central to the adipocyte insulin response, but how adipocyte signaling networks are dysregulated upon insulin resistance is unknown. Here we employed phosphoproteomics to delineate insulin signal transduction in adipocyte cells and adipose tissue. Across a range of insults triggering insulin resistance, we observed marked rewiring of the insulin signaling network. This included both attenuated insulin-responsive phosphorylation, and the emergence of phosphorylation uniquely insulin-regulated in insulin resistance. Identifying signaling changes common to multiple insults revealed subnetworks likely containing causal drivers of insulin resistance. Focusing on defective GSK3 signaling initially observed in a relatively small subset of well-characterized substrates, we employed a pipeline for identifying context-specific kinase substrates. This facilitated robust identification of widespread dysregulated GSK3 signaling. Pharmacological inhibition of GSK3 partially reversed insulin resistance in cells and tissue explants. These data highlight that insulin resistance is a multi-nodal signaling defect that encompasses dysregulated GSK3 activity.

molecular biology↗

bioRxiv2021

SnapKin: a snapshot deep learning ensemble for kinase-substrate prediction from phosphoproteomics data

Mass spectrometry (MS)-based phosphoproteomics enables the quantification of proteome-wide phosphorylation in cells and tissues. A major challenge in MS-based phosphoproteomics lies in identifying the substrates of kinases, as currently only a small fraction of substrates identified can be confidently linked with a known kinase. By leveraging large-scale phosphoproteomics data, machine learning has become an increasingly popular approach for computationally predicting substrates of kinases. However, the small number of high-quality experimentally validated kinase substrates (true positive) and the high data noise in many phosphoproteomics datasets together impact the performance of existing approaches. Here, we aim to develop advanced kinase-substrate prediction methods to address these challenges. Using a collection of seven large phosphoproteomics datasets, including six published datasets and a new muscle differentiation dataset, and both traditional and deep learning models, we first demonstrate that a pseudo-positive learning strategy for alleviating small sample size is effective at improving model predictive performance. We next show that a data re-sampling based ensemble learning strategy is useful for improving model stability while further enhancing prediction. Lastly, we introduce an ensemble deep learning model ( SnapKin) incorporating the above two learning strategies into a snapshot ensemble learning algorithm. We demonstrate that the SnapKin model achieves overall the best performance in kinase-substrate prediction. Together, we propose SnapKin as a promising approach for predicting substrates of kinases from large-scale phosphoproteomics data. SnapKin is freely available at https://github.com/PYangLab/SnapKin.

bioinformatics↗

bioRxiv2021

TOR complex 2 promotes proteasome dependent Pub1 (NEDD4 family E3 ligase) turnover in fission yeast.

Cells respond to changing nutrient environments by adjusting the abundance of surface nutrient transporters and receptors. This can be achieved by modulating ubiquitin-dependent endocytosis, which in part is regulated by the NEDD4 family of E3 ligases. Here we report novel regulation of Pub1, a fission yeast Schizosaccharomyces pombe member of the NEDD4-family of E3 ligases. We show that nitrogen stress inhibits Pub1 function, thereby increasing the abundance of the amino acid transporter Aat1 at the plasma membrane and enhancing sensitivity to the toxic arginine analogue canavanine. We show that TOR complex 2 (TORC2) signalling negatively regulates Pub1, thus TORC2 mutants under nutrient stress have decreased Aat1 at the plasma membrane and are resistant to canavanine. Inhibition of TORC2 signalling increases Pub1 phosphorylation, and this is dependent on Gsk3 activity. Addition of the Tor inhibitor Torin1 increases phosphorylation of Pub1 at serine 199 (S199) by 2.5-fold, and Pub1 protein levels in S199A phospho-ablated mutants are reduced. S199 is conserved in NEDD4 and is located immediately upstream of a WW domain required for protein interaction. Together, we describe how the major TORC2 nutrient-sensing signalling network regulates environmental control of Pub1 to modulate the abundance of nutrient transporters.

cell biology↗

bioRxiv2020

Identifying a GSK3-TRARG1 signaling axis reveals BCL9L as a novel regulator of GLUT4 trafficking

Trafficking regulator of GLUT4-1, TRARG1, positively regulates insulin-stimulated GLUT4 trafficking and insulin sensitivity. However, the mechanism(s) by which this occurs remain(s) unclear. Using biochemical and mass spectrometry analyses we found that TRARG1 is dephosphorylated in response to insulin in a PI3K/Akt-dependent manner and is a novel substrate for GSK3. Priming phosphorylation of murine TRARG1 at serine 84 allows for GSK3-directed phosphorylation at serines 72, 76 and 80. A similar pattern of phosphorylation was observed in human TRARG1, suggesting that our findings are translatable to human TRARG1. Pharmacological inhibition of GSK3 increased cell surface GLUT4 in cells stimulated with a submaximal insulin dose, and this was impaired following Trarg1 knockdown, suggesting that TRARG1 acts as a GSK3-mediated regulator in GLUT4 trafficking. These data place TRARG1 within the insulin signaling network and provide insights into how GSK3 regulates GLUT4 trafficking in adipocytes.

cell biology↗

bioRxiv2020

TSC-Insensitive Rheb Mutations Induce Oncogenic Transformation Through a Combination of Hyperactive mTORC1 Signalling and Metabolic Reprogramming

The mechanistic target of rapamycin complex 1 (mTORC1) is an important regulator of cellular metabolism that is commonly hyperactivated in cancer. Recent cancer genome screens have identified multiple mutations in Ras-homolog enriched in brain (Rheb), the primary activator of mTORC1, that might act as driver oncogenes by causing hyperactivation of mTORC1. Here, we show that a number of recurrently occurring Rheb mutants drive hyperactive mTORC1 signalling through differing levels of insensitivity to the primary inactivator of Rheb, Tuberous Sclerosis Complex. We show that two activated mutants, Rheb-T23M and E40K, strongly drive increased cell growth, proliferation and anchorage-independent growth resulting in enhanced tumour growth in vivo. Proteomic analysis of cells expressing the mutations revealed, surprisingly, that these two mutants promote distinct oncogenic pathways with Rheb-T23M driving metabolic reprogramming and an increased rate of glycolysis, while Rheb-E40K regulates the translation factor eEF2 and autophagy, likely through a differential interaction with AMPK. Our findings suggest that unique bespoke combination therapies may be utilised to treat cancers according to which Rheb mutant they harbour.

cell biology↗

bioRxiv2020

Discovery of drugs to treat cytokine storm-induced cardiac dysfunction using human cardiac organoids

Cardiac injury and dysfunction occur in COVID-19 patients and increase the risk of mortality. Causes are ill defined, but could be direct cardiac infection and/or inflammation-induced dysfunction. To identify mechanisms and cardio-protective drugs, we use a state-of-the-art pipeline combining human cardiac organoids with phosphoproteomics and single nuclei RNA sequencing. We identify an inflammatory cytokine-storm, a cocktail of interferon gamma, interleukin 1{beta} and poly(I:C), induced diastolic dysfunction. Bromodomain-containing protein 4 is activated along with a viral response that is consistent in both human cardiac organoids and hearts of SARS-CoV-2 infected K18-hACE2 mice. Bromodomain and extraterminal family inhibitors (BETi) recover dysfunction in hCO and completely prevent cardiac dysfunction and death in a mouse cytokine-storm model. Additionally, BETi decreases transcription of genes in the viral response, decreases ACE2 expression and reduces SARS-CoV-2 infection of cardiomyocytes. Together, BETi, including the FDA breakthrough designated drug apabetalone, are promising candidates to prevent COVID-19 mediated cardiac damage.

cell biology↗

bioRxiv2018

Multi-Omic Profiling Reveals Dynamics of the Phased Progression of Pluripotency

Pluripotency is highly dynamic and progresses through a continuum of pluripotent stem-cell states. The two states that bookend the pluripotency continuum, naive and primed, are well characterized, but our understanding of the intermediate states and transitions between them remain incomplete. Here, we dissect the dynamics of pluripotent state transitions underlying pre-to post-implantation epiblast differentiation. Through comprehensive mapping of the proteome, phosphoproteome, transcriptome, and epigenome of mouse embryonic stem cells transitioning from naive to primed pluripotency, we find that rapid, acute, and widespread changes to the phosphoproteome precede ordered changes to the epigenome, transcriptome, and proteome. Reconstruction of kinase-substrate networks reveals signaling cascades, dynamics, and crosstalk. Distinct waves of global proteomic changes demarcate discrete phases of pluripotency, characterized by cell-state-specific surface marker expression. Our data provide new insights into the multi-layered control of the phased progression of pluripotency and a foundation for modeling mechanisms underlying pre-to post-implantation epiblast differentiation.\n\nHIGHLIGHTSO_LIMulti-ome maps of cells transitioning from naive to primed pluripotency\nC_LIO_LIPhosphoproteome dynamics precede changes to epigenome, transcriptome, and proteome\nC_LIO_LIKinase-substrate network reconstruction uncovers signaling dynamics and crosstalk\nC_LIO_LIProteins and cell surface markers that track pluripotent state transitions\nC_LIO_LIComparative analysis of mouse and human pluripotent states\nC_LI

genomics↗