Biology subjects

Wilcox, J.

Publications and source records attributed to Wilcox, J..

9 recordsLinked to original sources

bioRxiv2026

Functional High Throughput Drug Screening Reveals Cyproheptadine as a Novel Treatment for LMNA -related Cardiomyopathy

ObjectivesTo define shared and variant-specific mechanisms underlying LMNA-associated dilated cardiomyopathy (DCM) and identify therapeutic candidates using human stem cell-based models. BackgroundVariants in the gene LMNA, encoding lamin A/C, cause 5-10% of dilated cardiomyopathies (DCM) and are strongly associated with heart failure and arrhythmias. Yet, the mechanisms by which LMNA variants drive disease and the distinction between shared and variant-specific phenotypes remain unclear. MethodsTo address this, we generated human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) from six LMNA-DCM patients carrying three pathogenic variants (T150A, E381Afs*39, R527H) and from five healthy control patients. ResultsLMNA hiPSC-CMs exhibited nuclear membrane deformation, reduced beat rate, arrhythmias, and prolonged calcium transients. Transcriptomic and electrophysiological analyses revealed downregulation of cardiac genes and ion channels, with abnormal Ca{superscript 2} handling emerging as a shared disease mechanism. Leveraging a high-throughput functional assay, we performed an unbiased drug screen and identified cyproheptadine, an FDA-approved antihistamine, as the only compound to alleviate abnormal function across all LMNA variants. ConclusionOur findings reveal a shared disease mechanism across multiple LMNA variants driven by dysregulated Ca{superscript 2} handling. This work establishes a patient-specific drug discovery platform and identifies cyproheptadine as a promising therapeutic candidate for LMNA-associated dilated cardiomyopathy. HighlightsO_LIPatient-specific LMNA hiPSC-cardiomyocytes robustly recapitulate disease phenotypes, including nuclear defects, arrhythmias, and contractile dysfunction. C_LIO_LIDysregulated calcium handling emerges as a unifying mechanism driving pathology across distinct LMNA variants. C_LIO_LIVariant-resolved analysis reveals both shared and mutation-specific molecular and functional signatures. C_LIO_LIHigh-throughput screening identifies cyproheptadine as a potent, broadly effective rescue agent across all tested LMNA variants. C_LIO_LIThis work establishes a scalable precision medicine platform for rapid therapeutic discovery in inherited cardiomyopathies. C_LI

Cell Biology↗

bioRxiv2025

Linked selection of insertions and deletions in coding regions of the great tit genome

Insertions and deletions (indels) are a ubiquitous form of genomic variation; yet, their contribution to adaptive evolution remains poorly understood. Technical challenges in identifying indels and integrating them into existing evolutionary models have limited their study, but previous work suggests that they may be subject to strong selective pressures. Here, we investigated selective signatures of indels in coding regions of the great tit (Parus major). We identified species-specific indels in protein-coding genes and analyzed the 300 bp flanking regions of indels using codeml to estimate dN, dS, and{omega} (dN/dS). Additionally, we performed enrichment analyses and protein structure modeling to assess functional consequences. We found that mutations in the flanking regions of indels are non-random and that selection strength varies with indel type and length. Genes including indels were enriched for functions related to protein and nucleic acid binding and linked to potentially adaptive traits such as vocal learning, migration, circadian rhythm, and environmental acclimation. Our results suggest that insertions and deletions may serve as hotspots of selection, influencing nearby sequences and contributing to adaptation in the great tit. Significance StatementSmall DNA changes called insertions and deletions (indels) are common in genomes, but their role in evolution is often overlooked because they are difficult to study. Using the genome of the great tit, a well-studied songbird, we identified thousands of indels in protein-coding regions and examined how they affect nearby DNA. We found that indels are not neutral accidents: they show signs of natural selection and may influence important traits. Some of the affected genes are linked to behaviors and adaptations that are crucial for survival, such as vocal learning, migration, and adaptation to new environments. These results suggest that indels can act as hotspots for evolutionary change and may help explain how species adapt to their surroundings. By high-lighting the evolutionary importance of these often-neglected mutations, our study opens new perspectives on the genetic basis of adaptation.

evolutionary biology↗

bioRxiv2024

Dysregulation of Nitrosylation Dynamics Promotes Nitrosative Stress and Contributes to Cardiometabolic Heart Failure with Preserved Ejection Fraction

BackgroundRecent reports suggest increased myocardial iNOS expression leads to excessive protein s-nitrosylation, contributing to the pathophysiology of HFpEF. However, the relationship between NO bioavailability, dynamic regulation of protein s-nitrosylation by trans- and de-nitrosylases, and HFpEF pathophysiology has not been elucidated. Here, we provide novel insights into the delicate interplay between NO bioavailability and protein s-nitrosylation in HFpEF. MethodsPlasma nitrite, nitrosothiols (RsNO), and 3-nitrotyrosine (3-NT) were measured in HFpEF patients and in controls. Studies in WKY or ZSF1 obese rats were performed to evaluate HFpEF severity, NO signaling, and total nitroso-species (Rx(s)NO) levels. snRNA sequencing was performed to identify key genes involved in NO signaling and s-nitrosylation regulation. ResultsIn HFpEF patients, circulating RsNO and 3-NT were significantly elevated while nitrite, a biomarker for NO bioavailability, remained unchanged. In ZSF1 obese rats, NO bioavailability was significantly reduced while Rx(s)NO levels exhibited an age-dependent increase as HFpEF progressed. snRNA seq highlighted significant upregulation of a trans-nitrosylase, hemoglobin-beta subunit (HBb), which was corroborated in human HFpEF hearts1. Subsequent experiments confirmed HBb upregulation and revealed significant reductions in enzyme activity of two major de-nitrosylases, Trx2 and GSNOR in ZSF1 obese hearts. Further, elevated RxNO levels, increased HBb expression, and reduced activity of Trx2 and GSNOR were identified in the kidney and liver of the ZSF1 obese rats. ConclusionsOur data reveal circulating markers of nitrosative stress (RsNO and 3-NT) are significantly elevated in HFpEF patients. Data from the ZSF1 obese rat model mirror the results from HFpEF patients and reveal that pathological accumulation of RxNO/nitrosative stress in HFpEF may be in part, due to the upregulation of the trans-nitrosylase, HBb, and impaired activity of the de-nitrosylases, Trx2 and GSNOR. Our data suggest that dysregulated protein nitrosylation dynamics in the heart, liver, and kidney contribute to the pathogenesis of cardiometabolic HFpEF. Translational PerspectiveOur findings describe for the first time that circulating RsNO and 3-NT are significantly upregulated in HFpEF patients suggesting systemic nitrosative stress in HFpEF, and demonstrate a profound disconnect between insufficient physiological NO signaling and pathological nitrosative stress in HFpEF, which is in stark contrast to HFrEF in which both NO bioavailability and protein s-nitrosylation are attenuated. Further, this study provides novel mechanistic insights into a critical molecular feature of HFpEF in humans and animal models: nitrosative stress arises predominantly from imbalance of trans-nitrosylases and de-nitrosylases, thereby leading to impaired NO bioavailability concomitant with increased protein s-nitrosylation. Importantly, these perturbations extend beyond the heart to the kidney and liver, suggesting HFpEF is characterized by a systemic derangement in trans- and de-nitrosylase activity and providing a unifying molecular lesion for the systemic presentation of HFpEF pathophysiology. These findings have direct clinical implications for the modulation of NO levels in the HFpEF patient, and indicate that restoring the balance between trans- and denitrosylases may be novel therapeutic targets to ameliorate disease symptoms in HFpEF patients.

physiology↗

bioRxiv2024

Reduced Hydrogen Sulfide Bioavailability Contributes to Cardiometabolic Heart Failure with Preserved Ejection Fraction

BackgroundHeart failure with preserved ejection fraction (HFpEF) is a significant public health concern with limited treatment options. Dysregulated nitric oxide-mediated signaling has been implicated in HFpEF pathophysiology, however, little is known about the role of endogenous hydrogen sulfide (H2S) in HFpEF. ObjectivesThis study evaluated H2S bioavailability in patients and two animal models of cardiometabolic HFpEF and assessed the impact of H2S on HFpEF severity through alterations in endogenous H2S production and pharmacological supplementation. We also evaluated the effects of the H2S donor, diallyl trisulfide (DATS) in combination with the GLP-1/glucagon receptor agonist, survodutide, in HFpEF. MethodsHFpEF patients and two rodent models of HFpEF ("two-hit" L-NAME + HFD mouse and ZSF1 obese rat) were evaluated for H2S bioavailability. Two cohorts of two-hit mice were investigated for changes in HFpEF pathophysiology: (1) endothelial cell cystathionine-{gamma}-lyase (EC-CSE) knockout; (2) H2S donor, JK-1, supplementation. DATS and survodutide combination therapy was tested in ZSF1 obese rats. ResultsH2S levels were significantly reduced (i.e., 81%) in human HFpEF patients and in both preclinical HFpEF models. This depletion was associated with reduced CSE expression and activity, and increased SQR expression. Genetic knockout of H2S -generating enzyme, CSE, worsened HFpEF characteristics, including elevated E/e ratio and LVEDP, impaired aortic vasorelaxation and increased mortality. Pharmacologic H2S supplementation restored H2S bioavailability, improved diastolic function and attenuated cardiac fibrosis corroborating an improved HFpEF phenotype. DATS synergized with survodutide to attenuate obesity, improve diastolic function, exercise capacity, and reduce oxidative stress and cardiac fibrosis. ConclusionsH2S deficiency is evident in HFpEF patients and conserved across multiple preclinical HFpEF models. Increasing H2S bioavailability improved cardiovascular function, while knockout of endogenous H2S production exacerbated HFpEF pathology and mortality. These results suggest H2S dysregulation contributes to HFpEF and increasing H2S bioavailability may represent a novel therapeutic strategy for HFpEF. Furthermore, our data demonstrate that combining H2S supplementation with GLP-1/glucagon receptor agonist may provide synergistic benefits in improving HFpEF outcomes. HighlightsO_LIH2S deficiency is evident in both human HFpEF patients and two clinically relevant models. C_LIO_LIReduced H2S production by CSE and increased metabolism by SQR impair H2S bioavailability in HFpEF. C_LIO_LIPharmacological H2S supplementation improves diastolic function and reduces cardiac fibrosis in HFpEF models. C_LIO_LITargeting H2S dysregulation presents a novel therapeutic strategy for managing HFpEF. C_LIO_LIH2S synergizes with GLP-1/glucagon agonist and ameliorates HFpEF C_LI

pharmacology and toxicology↗

bioRxiv2023

The circulating immune cell landscape stratifies metastatic burden in breast cancer patients

Advanced breast cancers show varying degrees of metastasis; however, reliable biomarkers of metastatic disease progression remain unknown. In circulation, immune cells are the first line of defence against tumour cells. Herein, using >109,591 peripheral blood mononuclear cells from healthy individuals and breast cancer patients, we tested whether molecular traits of the circulating immune cells, probed with single-cell transcriptomics, can be used to segregate metastatic profiles. Our analyses revealed significant compositional and transcriptional differences in PBMCs of patients with restricted or high metastatic burden versus healthy subjects. The abundance of T cell and monocyte subtypes segregated cancer patients from healthy individuals, while memory and unconventional T cells were enriched in low metastatic burden disease. The cell communication axes were also found to be tightly associated with the extent of metastatic burden. Additionally, we identified a PBMC-derived metastatic gene signature capable of discerning metastatic condition from a healthy state. Our study provides unique molecular insights into the peripheral immune system operating in metastatic breast cancer, revealing potential new biomarkers of the extent of the metastatic state. Tracking such immune traits associated with metastatic spread could complement existing diagnostic tools.

cancer biology↗

bioRxiv2023

The expression profile and tumorigenic mechanisms of CD97 (ADGRE5) in glioblastoma render it a targetable vulnerability

Glioblastoma (GBM) is the most common and aggressive primary brain malignancy. Adhesion G protein-coupled receptors (aGPCRs) have attracted interest for their functional role in gliomagenesis and their potential as treatment targets. To identify therapeutically targetable opportunities among aGPCR family members in unbiased fashion, we analyzed expression levels of all aGPCRs in GBM and non-neoplastic brain tissue. Using bulk and single cell transcriptomic and proteomic data, we show that CD97 (ADGRE5), an aGPCR previously implicated in GBM pathogenesis, is the most promising aGPCR target in GBM, by virtue of its abundance in all GBM tumors and its de novo expression profile in GBM compared to normal brain tissue and neural progenitors. CD97 knockdown or knockout significantly reduces the tumor initiation capacity of patient-derived GBM cultures (PDGC) in vitro and in vivo. Transcriptomic and metabolomic data from PDGCs suggest that CD97 promotes glycolytic metabolism. The oncogenic and metabolic effects of CD97 are mediated by the MAPK pathway. Activation of MAPK signaling depends on phosphorylation of the cytosolic C-terminus of CD97 and recruitment of {beta}-arrestin. Using single-cell RNA-sequencing and biochemical assays, we demonstrate that THY1/CD90 is the most likely CD97 ligand in GBM. Lastly, we show that targeting of PDGCs with an anti-CD97 antibody-drug conjugate in vitro selectively kills tumor cells but not human astrocytes or neural stem cells. Our studies identify CD97 as an important regulator of tumor metabolism in GBM, elucidate mechanisms of receptor activation and signaling, and provide strong scientific rationale for developing biologics to target it for therapeutic purposes.

cancer biology↗

bioRxiv2022

PTK7 is a positive allosteric modulator of GPR133 (ADGRD1) signaling in GBM

GPR133 (ADGRD1), an adhesion G protein-coupled receptor, supports growth of glioblastoma, a brain malignancy. We demonstrated that GPR133 is intramolecularly cleaved, and that dissociation of its N-terminal and C-terminal fragments (NTF and CTF) at the plasma membrane correlates with increased receptor signaling. However, how the extracellular interactome of GPR133 in glioblastoma modulates signaling remains unknown. Here, we use affinity purification and mass spectrometry to identify extracellular binding partners of GPR133 in patient-derived glioblastoma cells. We show that the transmembrane protein PTK7 binds the GPR133 NTF and its expression in trans increases GPR133 signaling. This effect requires the intramolecular cleavage of GPR133 and PTK7s anchoring in the plasma membrane. The GPR133-PTK7 interaction facilitates orthosteric activation of GPR133 by soluble peptide mimicking the endogenous tethered Stachel agonist, suggesting PTK7 binding allosterically enhances accessibility of GPR133s orthosteric Stachel binding pocket. GPR133 and PTK7 are expressed in adjacent cells in glioblastoma, where their knockdown phenocopies each other. We propose that this novel ligand-receptor interaction is relevant to the pathogenesis of glioblastoma, as well as physiological processes in several tissues.

cell biology↗

bioRxiv2022

Linked-Read Sequencing of Eight Falcons Reveals a Unique Genomic Architecture in Flux

Falcons are diverse birds of cultural and economic importance. They have undergone major lineage-specific chromosomal rearrangements, resulting in greatly-reduced chromosome counts relative to other birds. Here, we use 10X Genomics linked reads to provide new high-contiguity genomes for two gyrfalcons, a saker falcon, a lanner falcon, three subspecies of peregrine falcons, and the common kestrel. Assisted by a transcriptome sequenced from 22 gyrfalcon tissues, we annotate these genomes for a variety of genomic features, estimate historical demography, and then investigate genomic equilibrium in the context of falcon-specific chromosomal rearrangements. We find that falcon genomes are not in AT-GC equilibrium with a bias in mutations towards higher AT content; this bias is predominantly driven by--but not dependent on--hypermutability of CpG sites. Small indels and large structural variants were also biased towards insertions rather than deletions. Patterns of disequilibrium were linked to chromosomal rearrangements: falcons have lost GC content in regions that have fused to larger chromosomes from microchromosomes and gained GC content in regions of macrochromosomes that have translocated to microchromosomes. Inserted bases have accumulated on regions ancestrally belonging to microchromosomes, consistent with insertion-biased gene conversion. We also find an excess of interspersed repeats on regions of microchromosomes that have fused to macrochromosomes. Our results reveal that falcon genomes are in a state of flux. They further suggest that many of the key differences between microchromosomes and macrochromosomes are driven by differences in chromosome size, and indicate a clear role for recombination and biased-gene-conversion in determining genomic equilibrium. SignificanceFalcons are a particularly diverse and widespread genus of birds of particular cultural and economic importance. Falcons have also undergone recent large-scale chromosomal rearrangements to arrive at atypically low chromosome counts relative to other birds. We produced eight new high-quality falcon genomes to support general research on falcons, and we analyze these genomes to assess how chromosome loss has influenced specific aspects of genomic architecture.

genomics↗

bioRxiv2020

Dissociation of the intramolecularly cleaved N- and C-terminal fragments of the adhesion G protein-coupled receptor GPR133 (ADGRD1) increases canonical signaling

GPR133 (ADGRD1), an adhesion G protein-coupled receptor (GPCR), is necessary for growth of glioblastoma (GBM), a brain malignancy. The extracellular N-terminus of GPR133 is thought to be autoproteolytically cleaved into an N-terminal and a C-terminal fragment (NTF and CTF). Nevertheless, the role of this cleavage in receptor activation remains unclear. Here, we show that the wild-type (WT) receptor is cleaved after protein synthesis and generates significantly more canonical signaling than an uncleavable point mutant (H543R) in patient-derived GBM cultures and HEK293T cells. However, the resulting NTF and CTF remain non-covalently bound until the receptor is trafficked to the plasma membrane, where we find NTF-CTF dissociation. Using a fusion of the hPAR1 receptor N-terminus and the CTF of GPR133, we demonstrate that thrombin-induced cleavage and shedding of the hPAR1 NTF increases receptor signaling. This study supports a model where dissociation of the NTF at the plasma membrane promotes GPR133 activation. Highlights- GPR133 is intramolecularly cleaved in patient-derived GBM cultures - Cleaved GPR133 signals at higher efficacy than the uncleavable GPR133 H543R mutant - The N- and C-terminal fragments (NTF and CTF) of GPR133 dissociate at the plasma membrane - Acute thrombin-induced cleavage of the human PAR1 NTF from the GPR133 CTF increases signaling eTOC BlurbFrenster et al. demonstrate intramolecular cleavage of the adhesion GPCR GPR133 in glioblastoma and HEK293T cells. The resulting N- and C-terminal fragments dissociate at the plasma membrane to increase canonical signaling. The findings suggest dissociation of GPR133s N-terminus at the plasma membrane represents a major mechanism of receptor activation.

cell biology↗