Biology subjects

Young, M.

Publications and source records attributed to Young, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Tumor SETDB1 expression predicts worse overall survival for bladder cancer patients

Aberrant activity of histone methyltransferases promotes tumorigenesis across multiple cancer types, making this class of enzymes attractive therapeutic targets. The histone methyltransferase SETDB1 is frequently amplified in bladder cancer and has been implicated in chemotherapy resistance. We examine whether SETDB1 protein expression is associated with overall survival and tumor characteristics in bladder cancer. To assess SETDB1 protein expression in patients, we performed immunohistochemistry in tissue microarrays (TMAs) containing 350 bladder cancer cases with well-annotated clinical information. Digital image analysis was used to quantify SETDB1 protein expression to produce a SETDB1 H-score, from which patients were categorized as SETDB1-high or SETDB1-low. Using these categories, we compared tumor characteristics, clinical outcomes, and gene expression profiles between SETDB1-high and SETDB1-low patients. Patients with high SETDB1 expression (n=143) had significantly shorter overall survival compared to SETDB1-low (n=125) patients (median survival months: SETDB1-high, 30.09; SETDB1-low, 87.85; p = 0.0006), and SETDB1 expression was independently associated with overall survival upon multivariate cox regression analysis (HR = 1.93, 95% CI = 1.08 - 3.45, p = 0.026). SETDB1-high patients were more likely to present with squamous (35% vs 20%, p = 0.026) and sarcomatoid (11% vs 3.6%, p=0.049) differentiation features, which are associated with poorer prognosis. Exploratory analyses identified transcriptional differences associated with SETDB1 expression, providing rationale for further exploration of the mechanisms by which SETDB1 may promote bladder cancer.

cancer biology↗

bioRxiv2026

Hypoxia Disrupts Multiple Processes Supporting Spatial Navigation

Hypoxia impairs cognitive function, yet its effects on navigation and intrinsic brain activity remain poorly understood. This study investigated whether a continuous exposure to hypoxia (CH) or an intermittent exposure to hypoxia (IH) differentially influence navigation performance and resting-state electroencephalography (EEG) in healthy young adults. Seventy-two participants completed sham (FiO2 = .209) and hypoxia (FiO2 = .13) sessions during either a one hour of CH or IH intervention. Navigation was assessed using the Spatial Performance Assessment for Cognitive Evaluation (SPACE), while resting-state EEG was recorded before and after the intervention in a subset of participants (n = 40). EEG spectra were parameterised into periodic (alpha and beta power and central frequency) and aperiodic (exponent and offset) components. Aligned rank transform (ART) analyses of variance examined effects of hypoxia and intervention group, while linear regression determined whether reductions in peripheral oxygen saturation (SpO2) predicted changes in navigation or EEG. Hypoxia impaired multiple components of navigation, increasing path integration distance error and egocentric pointing angle error irrespective of intervention group, while mapping accuracy was preferentially impaired following IH and perspective taking performance following CH. Hypoxia also reduced alpha and beta power, beta central frequency, and aperiodic exponent, while aperiodic offset and alpha central frequency remained stable. The reduction in aperiodic exponent was primarily evident following IH, suggesting that the temporal pattern of oxygen delivery may influence specific neurophysiological responses. Contrary to our hypothesis, SpO2 reduction did not predict individual differences in navigation performance or EEG activity. These findings demonstrate that brief, moderate hypoxic exposure can disrupt allocentric and egocentric components of spatial navigation while selectively altering periodic and aperiodic features of intrinsic brain activity.

neuroscience↗

bioRxiv2026

Single-cell transcriptomics reveals life cycle and cell cycle gene expression dynamics during in vitro growth of two Leishmania species

Leishmania species are transmitted between mammals by sand flies, within which they undergo a complex developmental programme involving transitions between replicative and non-replicative life cycle forms. Recent work using single-cell transcriptomics has revealed the developmental pathways of Leishmania major in the sand fly, but it is unclear how faithfully such development is recapitulated during Leishmania culture in vitro. In addition, no work has revealed how gene expression changes across the cell cycle of replicative Leishmania forms. Using single-cell transcriptomics on unsynchronised cultures of L. major and L. mexicana, we addressed both questions. We show that in vitro L. mexicana promastigotes display the same two developmental endpoints seen in L. major cells recovered from sand flies, metacyclics and haptomonads. In contrast, L. major promastigote development in vitro does not predict the presence of leptomonads or haptomonads, although non-dividing late metacyclics form through an early metacyclic stage as parasites enter stationary phase. Using computational reconstruction of the cell cycle in procyclic promastigote forms of both Leishmania species identified hundreds of genes whose transcript levels vary as the cell cycle progresses, revealing core conserved processes between the two species and with the closely related Trypanosoma brucei. These genes allowed us to examine connections between life cycle and cell cycle progression, revealing that some developmental transitions are strongly linked to a cell cycle phase, whereas others occur asynchronously. This work provides a comprehensive atlas and marker gene list for the interlinked cell and life cycles of two laboratory-cultured Leishmania species.

microbiology↗

bioRxiv2026

A single bout of mistimed eating is sufficient to cause lasting disruptions in the daily rhythms of metabolism and behavior.

Synchrony between time-of-day and food intake is critical for maintaining homeostasis while desynchrony between these cues caused by repeated bouts of mistimed eating (ME) is profoundly disruptive to organismal health. However, it is unknown whether the same is true for a single bout of ME. While it is generally accepted that mammals recover quickly from acute alterations in feeding schedule and that chrono-disruption requires chronic, repeated changes, there have been no dedicated investigations of acute ME to suggest otherwise. Therefore, we exposed female and male C57Bl6/J mice to a single bout of ME or timed eating (TE) and continuously measured metabolic and behavioral responses for five days. A single bout of ME was sufficient to disrupt the daily rhythms of metabolic and behavioral outcomes for several days. Energy expenditure and wheel running activity were disrupted and light:dark variation in food intake and macronutrient utilization were altered for several days. Finally, ME changed the amount of time spent resting in for several days post-ME. The TE paradigm disrupted macronutrient utilization for two days but otherwise had no effect on metabolism or behavior. Our results demonstrate that one instance of ME alone has lasting impacts on daily rhythmicity and is an understudied source of circadian disruption.

physiology↗

bioRxiv2026

Architecture of the Gβγ-prefusion SNARE complex reveals the molecular mechanism of inhibition of vesicle fusion

Presynaptic inhibitory GPCR (Gi/o GPCR) signaling is an essential regulatory mechanism in vertebrate physiology. Near the presynaptic active zone, Gi/o GPCR activation releases G-protein {beta}{gamma} heterodimers (G{beta}{gamma}) which act to inhibit synaptic vesicle fusion through either modulation of Ca2+ entry via voltage-gated Ca2+ channels, or by direct interactions with the core exocytotic machinery comprised of the ternary SNARE complex downstream of Ca2+ influx. The precise molecular mechanism underlying G{beta}{gamma}-SNARE mediated inhibition has remained unclear due to lack of structural data for the G{beta}{gamma}-SNARE complex. We address this long-standing question here by stabilizing the interaction between G{beta}1{gamma}2 and a pre-fusion ternary SNARE mimetic and determining the structure using single-particle cryo-EM. We used our cryo-EM envelope to build an atomic level prediction of the interaction interface. We validated key interaction sites predicted by our model at the C-terminus of SNAP-25 using site directed mutagenesis and biochemical affinity measurements. Additionally, we found that G{beta}1{gamma}2 and a fragment of the regulatory protein complexin can engage the pre-fusion SNARE complex simultaneously. On the basis of these results, we propose a model in which G{beta}1{gamma}2 acts on the partially zipped SNARE complex at a late stage in the vesicle docking and priming cycle. In the model, the amino-terminal coiled-coil of G{beta}1{gamma}2 forms an interface with the C-terminus of the target membrane SNARE (t-SNARE) complex to prevent complete incorporation of the vesicle SNARE (v-SNARE) into the core SNARE helical bundle, thus blocking vesicle approach to the plasma membrane. The {beta}-propeller domain of G{beta}1 may also sterically hinder vesicle approach. Together these results provide crucial structural insights into the mechanism of binding of G{beta}{gamma} to the SNARE complex, and lends essential insights into the critical role of GPCR signaling to the SNARE complex in modulating synaptic vesicle fusion.

biophysics↗

bioRxiv2025

Metagenomes and Metagenome-Assembled Genomes from Microbial Communities in a Biological Nutrient Removal Plant Operated at Hamptons Road Sanitation District (HRSD) with High and Low Dissolved Oxygen Conditions

Aeration in biological nutrient removal (BNR) systems constitutes one of the largest energy demands in water resource recovery facilities (WRRFs). Previous studies have shown that lowering dissolved oxygen (DO) concentrations can sustain effective nitrification and phosphorus removal while substantially reducing energy consumption. However, the microbial mechanisms enabling these low-DO processes remain poorly understood. In this study, we investigated microbial communities associated with reduced DO in a pilot-scale BNR system operated by the Hampton Roads Sanitation District (HRSD). DO was reduced over an 18-month period from 2.5 mg/L to 0.2 mg/L. Metagenomic DNA was obtained from samples from each DO condition then sequenced using PacBio HiFi technology. A total of 316 metagenome-assembled genomes were recovered and after dereplication, 207 were found to be unique. These data augment the metagenomic information related to wastewater treatment under low-DO conditions and provide valuable resources for understanding microbial adaptation to oxygen-limited BNR operation.

genomics↗

bioRxiv2025

Metagenomes and Metagenome-Assembled Genomes from Microbial Communities in a Biological Nutrient Removal Plant Operated at Los Angeles County Sanitation District (LACSD) with High and Low Dissolved Oxygen Conditions

Aeration represents one of the largest energy costs in water resource recovery facilities (WRRFs). Previous studies have shown that effective nitrification and phosphorus removal can be maintained in biological nutrient removal (BNR) systems operated under low dissolved oxygen (DO) conditions, significantly reducing energy use. To improve understanding of microbial community adaptation to reduced DO, we analyzed metagenomes and metagenome-assembled genomes (MAGs) from the Pomona WRRF (Los Angeles County Sanitation Districts) before and after a gradual decrease in operating DO from approximately 3.5 mg/L to 0.7 mg/L over 18 months. Metagenomic DNA was isolated from high and low DO samples, then sequenced using PacBio HiFi technology. A total of 492 MAGs were recovered of which 304 were unique after dereplication. These genomes expand current knowledge of microbial community dynamics in low-DO BNR systems and provide valuable genomic resources for understanding microbial adaptation to energy-efficient wastewater treatment processes.

genetics↗

bioRxiv2025

IgD-Expressing Mature B Cells Exhibit Enhanced Sensitivity to Glucocorticoid-Induced Cell Death

Glucocorticoids (GCs) regulate diverse physiological processes, comprising metabolism, immune responses, stress adaptation and inflammation. Synthetic GCs are widely used for their powerful anti-inflammatory and immunosuppressive effects, in the treatment of autoimmune diseases, allergies, and inflammation. Here, we investigated the role of the glucocorticoid receptor (GR) in B cell development and survival using both B cell-specific GR-deficient mice and continuous in vivo GR agonist treatments. Deletion of the GR in B cells altered splenic B cell subpopulations, increasing follicular and CD21lo B cells and leading to the accumulation of IgM-/IgD- B cells. In vivo treatment with GR agonists, such as Dexamethasone (Dex) and Prednisolone (Pred), selectively depleted IgDhigh follicular B cells while enriching IgDlow marginal zone B cells. IgDlow (IgMhigh) B cells, which were more resistant to glucocorticoid-induced cell death, showed increased expression of IL-10 and genes involved in survival, suggesting a potential regulatory function. In vitro, B cell activation via CpG or LPS altered IgM/IgD expression and B cell sensitivity to GR agonists, thereby leading to improved B cell survival and increased plasma cell differentiation. Together, these findings suggest that IgD downregulation and IgM upregulation are critical for B cell survival under GC exposure and that GR agonists promote the enrichment of IgDlow (IgMhigh) cells resistant to apoptosis.

immunology↗

bioRxiv2025

Population genomics of yellow-eyed penguins uncovers subspecies divergence and candidate genes linked to respiratory distress syndrome

Yellow-eyed penguins (hoiho/takaraka, Megadyptes antipodes) are among the worlds rarest penguins and are regarded as a taonga (treasured) species in Aotearoa New Zealand. Since 2019, chicks on the New Zealand mainland have been affected by a deadly neonatal disease called respiratory distress syndrome (RDS), contributing to a decline to fewer than 143 breeding pairs. To investigate the putative genetic basis of this disease, we generated high-quality whole-genome data from 249 individuals spanning the species range, including from the New Zealand mainland (Northern range) and subantarctic Enderby and Campbell Islands (Southern). Population genomic analyses unexpectedly revealed three deeply divergent lineages with negligible gene flow, consistent with recognition of three distinct subspecies. Phylogenetic divergence dating suggests that these splits predate human arrival by several millennia, with the Northern lineage diverging from the Southern populations 5-16 ka. Genome scans for local adaptation revealed regions of strong differentiation, and genome-wide association analyses identified candidate immune and respiratory genes linked to RDS. In partnership with Ng[a]i Tahu, who hold indigenous guardianship over yellow-eyed penguins, we recommend recognition of three subspecies, urgent conservation action for the critically small and rapidly declining Northern subspecies, and the need for immediate population size and trend assessments for Auckland and Campbell Island populations.

genomics↗

bioRxiv2025

Bat power-metabolic profiling of the Egyptian fruit bat Rousettus aegyptiacus reveals distinctive cardiac adaptations

AimThe present study aimed to elucidate which pathways contribute to cardiometabolic adaptation in Egyptian fruit bats. MethodsUtilising cardiac tissues from Egyptian fruit bats (Rousettus aegyptiacus) and C57BL/6J mice, we combined liquid chromatography-mass spectrometry metabolic profiling, non-targeted 1H NMR spectroscopy, and in silicocomputational modelling using the genome-scale mammalian network CardioNet. Main FindingsOur analyses revealed that bat hearts exhibit a distinct metabolic profile characterised by depleted glycogen reserves and increased reliance on lipid oxidation to meet energy demands. Notably, bat hearts displayed elevated fluxes in oxidative phosphorylation, {beta}-oxidation of long-chain fatty acids, and the Krebs cycle, alongside reduced amino acid catabolism. These findings suggest that bats have evolved unique metabolic strategies to support the high-energy demands of flight, maintaining cardiac function without succumbing to pathological remodelling. ConclusionsThis study provides the first comprehensive insight into the metabolic adaptations in the cardiac tissue of a bat species, contributing to our understanding of how these mammals endure extreme physiological stresses. Integrating metabolomics with computational modelling offers a powerful approach to studying metabolic adaptations in non-model species, potentially informing therapeutic strategies for human cardiac conditions.

systems biology↗

bioRxiv2024

Enhanced immunogenicity of a Clostridioides difficile TcdB vaccine adjuvanted with a synthetic dual-TLR ligand adjuvant.

We report a comprehensive evaluation of the toxin B (TcdB) vaccine adjuvanted with a dual Toll-like receptor ligand liposome adjuvant for Clostridioides difficile infection (CDI). The vaccine completely protected mice from a lethal infection. Compared to alum adjuvanted TcdB, it generated functionally superior systemic antibodies and supported strong memory B cell and gut IgA responses. This pharmaceutically acceptable adjuvant platform holds promise for developing a next-generation CDI vaccine.

immunology↗

bioRxiv2024

IL-33 protects from recurrent C. difficile infection by restoration of humoral immunity

Clostridioides difficile infection (CDI) recurs in one of five patients. Monoclonal antibodies targeting the virulence factor TcdB reduce disease recurrence, suggesting that an inadequate anti-TcdB response to CDI leads to recurrence. In patients with CDI, we discovered that IL-33 measured at diagnosis predicts future recurrence, leading us to test the role of IL-33 signaling in the induction of humoral immunity during CDI. Using a mouse recurrence model, IL-33 was demonstrated to be integral for anti-TcdB antibody production. IL-33 acted via ST2+ ILC2 cells, facilitating germinal center T follicular helper (GC-Tfh) cell generation of antibodies. IL-33 protection from reinfection was antibody-dependent, as MT KO mice and mice treated with anti-CD20 mAb were not protected. These findings demonstrate the critical role of IL-33 in generating humoral immunity to prevent recurrent CDI. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=176 SRC="FIGDIR/small/623943v1_ufig1.gif" ALT="Figure 1"> View larger version (60K): org.highwire.dtl.DTLVardef@9ec4aeorg.highwire.dtl.DTLVardef@1827bd3org.highwire.dtl.DTLVardef@18f761dorg.highwire.dtl.DTLVardef@19396d4_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical Abstract:C_FLOATNO IL-33 restoration induces toxin-B-specific antibody production via the ILC2-TFH axis. In the left panel, IL-33 remediation increases ILC2s, subsequently inducing TFH directly or indirectly. TFH cell induction is pivotal for the production of antibodies. IL-33 also downregulates type 1 and type 3 immunity, favoring type 2 immunity to enhance host survival and reduce morbidity. The middle panel illustrates antibiotic-induced dysbiosis, resulting in decreased IL-33 levels and reduced antibody production. The right panel demonstrates the protective effect in reinfection, attributed to toxin-specific antibodie generated by IL-33 remediation. C_FIG

immunology↗

bioRxiv2024

A CONTRIBUTION TO THE ANATOMY OF TWO RARE CETACEAN SPECIES: THE HOURGLASS DOLPHIN (Lagenorhynchus cruciger) AND THE SPECTACLED PORPOISE (Phocoena dioptrica)

The anatomical description of the hourglass dolphin (Lagenorhynchus cruciger) and the spectacled porpoise (Phocoena dioptrica) remains largely unexplored, due to limited specimen availability and preservation challenges. This study employed digital imaging techniques, conventional histology and computed tomography to provide visualisation of anatomical structures for a detailed analysis. We present a comprehensive analysis of the gross macroscopical and microscopical morphology of two hourglass dolphins and four spectacled porpoises. The hourglass dolphins were characterised by their distinctive black and white pigmentation and a hooked dorsal fin, while the spectacled porpoises were defined by their large dorsal fin, lack of a visible rostrum and unique eye markings. Morphometric measurements and skeletal characteristics aligned with the literature, while internal anatomy (organs and systems) were similar to other odontocetes. Although precise lung measurements were challenging, qualitative assessments indicated relatively large lungs for their body size, supporting the "short dive, big lung" hypothesis and suggesting that these species are not deep divers. The spectacled porpoise dorsal fin was uniquely large with a well-developed blood supply; this is hypothesised to act as a thermoregulatory window, helping to manage body heat. Overall, this study provides new data on the anatomy of the hourglass dolphin and spectacled porpoise, contributing insights that may influence future research on these rare species. The findings highlight the importance of anatomical studies in explaining evolutionary relationships within cetaceans and their ecological roles in the Southern Ocean ecosystems.

evolutionary biology↗

bioRxiv2024

Altered systemic bioenergetic reserve in chronic kidney disease predisposes hearts to worse functional outcomes

BackgroundCardiovascular mortality in chronic kidney disease (CKD) remains disproportionately high, yet the mechanisms linking renal dysfunction to cardiac vulnerability are incompletely understood. Uraemic cardiomyopathy is increasingly recognised as a systemic metabolic disease, but the contribution of multi-organ bioenergetic failure in cardiac dysfunction is poorly defined. HypothesisCKD induces metabolic remodelling across peripheral organs (liver, skeletal muscle, and kidneys) depleting systemic bioenergetic reserve, compromising cardiometabolic flexibility and stress resilience. MethodsUsing CKD models of different aetiologies in rats (glomerulosclerosis by partial nephrectomy and interstitial fibrosis by adenine diet) we investigated cardiac and systemic metabolic remodelling. ResultsIrrespective of aetiology, renal insufficiency resulted in cardiac dysfunction including impaired functional recovery after 25-minutes ischaemia. 1H NMR metabolomic analysis revealed perturbations of systemic metabolism in CKD were more severe than cardiometabolic changes with alterations of skeletal muscle, liver, and kidney metabolism indicating reduced systemic bioenergetic reserve. This pre-clinical observation was recapitulated in human CKD patients where phosphorus magnetic resonance spectroscopy assessment of exercising lower leg muscle identified bioenergetic deficiencies preventing maximal force generation. Thus, both heart and skeletal muscles in CKD have impaired response to metabolic stress. ConclusionsCKD induces multi-organ metabolic failure that limits the hearts ability to meet energetic demands under stress. This study identifies systemic bioenergetic collapse as a contributing factor to uraemic cardiomyopathy, thus targeting peripheral organ metabolism may represent a novel therapeutic strategy to improve cardiac outcomes in CKD. Key learning pointsO_ST_ABSWhat Was KnownC_ST_ABSCKD significantly increases cardiovascular risk, but the cause of heart failure in these patients is largely attributed to cardiac pathology alone whilst the potential contribution of systemic metabolic dysfunction remains unexplored. What This Study AddsUtilising clinical and pre-clinical approach we show that CKD triggers widespread metabolic dysfunction in the liver, skeletal muscle, and kidney, depleting the systemic bioenergetic reserve and impairing the hearts ability to handle metabolic stress. Potential ImpactThese findings show uraemic cardiomyopathy is a multi-organ metabolic disease and targeting peripheral metabolic dysfunction could offer a new therapeutic strategy to enhance cardiac resilience by restoring systemic energy balance.

physiology↗

bioRxiv2024

Phosphorylation of CRYAB Induces a Condensatopathy to Worsen Post-Myocardial Infarction Left Ventricular Remodeling.

Protein aggregates are emerging therapeutic targets in rare monogenic causes of cardiomyopathy and amyloid heart disease, but their role in more prevalent heart failure syndromes remains mechanistically unexamined. We observed mis-localization of desmin and sarcomeric proteins to aggregates in human myocardium with ischemic cardiomyopathy and in mouse hearts with post-myocardial infarction ventricular remodeling, mimicking findings of autosomal-dominant cardiomyopathy induced by R120G mutation in the cognate chaperone protein, CRYAB. In both syndromes, we demonstrate increased partitioning of CRYAB phosphorylated on serine-59 to NP40-insoluble aggregate-rich biochemical fraction. While CRYAB undergoes phase separation to form condensates, the phospho-mimetic mutation of serine-59 to aspartate (S59D) in CRYAB mimics R120G-CRYAB mutants with reduced condensate fluidity, formation of protein aggregates and increased cell death. Conversely, changing serine to alanine (phosphorylation-deficient mutation) at position 59 (S59A) restored condensate fluidity, and reduced both R120G-CRYAB aggregates and cell death. In mice, S59D CRYAB knock-in was sufficient to induce desmin mis-localization and myocardial protein aggregates, while S59A CRYAB knock-in rescued left ventricular systolic dysfunction post-myocardial infarction and preserved desmin localization with reduced myocardial protein aggregates. 25-Hydroxycholesterol attenuated CRYAB serine-59 phosphorylation and rescued post-myocardial infarction adverse remodeling. Thus, targeting CRYAB phosphorylation-induced condensatopathy is an attractive strategy to counter ischemic cardiomyopathy.

cell biology↗

bioRxiv2024

Automatic parameter estimation and detection of Saimaa ringed seal knocking vocalizations

Passive acoustic monitoring (PAM) offers a non-invasive method for monitoring elusive pinnipeds, but manual analysis of large recording datasets limits its scalability. For the endangered Saimaa ringed seal ( Pusa saimensis ), PAM provides a rare opportunity to study breeding-season behavior beneath seasonal ice cover. We evaluated automated methods for detecting and characterizing the species' distinctive knocking vocalizations using recordings from Lake Saimaa. Annotated data ( n = 12 565 calls) were used to develop pulse repetition rate (PRR) estimation and call-detection systems. The best-performing PRR estimator matched manual measurements with a mean absolute error of 1.50 Hz, while a spectrogram-based convolutional neural network detected knocking calls with a mean F1-score of up to 99.28%. These results show close agreement with manual approaches, indicating that automated detection and characterization are achievable at a standard that could substantially reduce PAM analysis effort. This represents an important step toward scalable, long-term acoustic monitoring of this endangered seal.

ecology↗

bioRxiv2024

High-Resolution Epitope Mapping for Glycosylated Antigens: Pembrolizumab-PD1 as a Case Study

High-resolution binding site mapping is important for in-depth activity assessment of new therapeutics including AI-designed antibodies. However, complex protein targets such as glycosylated antigens are challenging for many methods including crystallography. PD1 is a highly glycosylated antigen, and with the traditional HDX-MS method, only 51% sequence coverage could be obtained with multiple epitope residues undetected for Pembrolizumab. By implementing glyco-peptide detection, subzero temperature LC-MS and electron based MSMS fragmentation, the new HDX FineMapping methodology enabled 100% sequence coverage and complete epitope characterization for the Pembrolizumab-PD1 system, with amino acid level resolution. Furthermore, HDX FineMapping detects binding epitopes directly in solution, without any mutation or modification to either the antigen or the antibody. The amino acid level resolution combined with low cost, minimal sample consumption, fast turnaround time, and no need of mutant library or crystallization makes it a competitive methodology for binding mode validation of AI-designed therapeutics.

biophysics↗

bioRxiv2024

Transcriptional regulation in the absence of inositol trisphosphate receptor calcium signaling

The activation of IP3 receptor (IP3R) Ca2+ channels generates agonist-mediated Ca2+ signals that regulate a wide range of biological processes. It is therefore surprising that CRISPR induced loss of all three IP3R isoforms (TKO) in HEK293 and HeLa cell lines yields cells that can survive, grow and divide, albeit more slowly than wild-type cells. In an effort to understand the adaptive mechanisms involved, we have examined the activity of key Ca2+ dependent transcription factors (NFAT, CREB, AP-1 and NF{kappa}b) and signaling pathways using luciferase-reporter assays, phosphoprotein immunoblots and whole genome transcriptomic studies. In addition the role of protein kinase C (PKC) was investigated with inhibitors and siRNA knockdown. The data showed that agonist-mediated NFAT activation was lost but CREB activation was maintained in IP3R TKO cells. Under base-line conditions transcriptome analysis indicated the differential expression (DEG) of 828 and 311 genes in IP3R TKO HEK293 or HeLa cells, respectively, with only 18 genes being in common. In summary three main adaptations in TKO cells are identified in this study: 1) increased basal activity of NFAT, CREB, AP-1 and NF{kappa}b; 2) an increased reliance on Ca2+-insensitive PKC isoforms; and 3) increased production of reactive oxygen species and upregulation of antioxidant defense enzymes. We suggest that whereas wild-type cells rely on a Ca2+ and DAG signal to respond to stimuli, the TKO cells utilize the adaptations to allow key signaling pathways (e.g. PKC, Ras/MAPK, CREB) to transition to the activated state using a DAG signal alone.

cell biology↗