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Shah, S.

Publications and source records attributed to Shah, S..

At least 37 records · Page 2Linked to original sources

Drought tolerance of Aedes aegypti mosquito eggs is influenced by adaptation to local climate conditions and associations with humans

Urbanization is intensifying human interactions with mosquitoes, exacerbating public health challenges. Densely populated areas provide ideal conditions for container-dwelling mosquitoes, with increased host availability and the presence of artificial breeding sites. These anthropophilic mosquitoes often exhibit distinct ecological adaptations compared to their rural counterparts. Since mosquito eggs are immobile and remain at the site of oviposition, they provide a valuable lens for assessing how urbanization, climate-driven shifts in temperature, and drought affect mosquito reproductive success. This study examined Ae. aegypti egg viability under varying temperature and dry conditions over five months, focusing on lineages with distinct ancestries from West African populations. Mosquitoes collected from urban habitats with a high human preference demonstrated higher egg survival under prolonged arid conditions. Analysis of climatic factors revealed that dry season temperature and precipitation during wet periods are significant predictors of egg drought tolerance. Modeling future climate scenarios based on input from our egg viability results suggests a projected shift and expansion in the seasonal survival window for Ae. aegypti by the end of the century. This study highlights the importance of understanding environmental constraints on the drought tolerance of mosquito eggs to predict and mitigate future mosquito outbreaks.

physiology↗

Associations between amygdala connectivity and experienced discrimination in children

Discrimination is a chronic stressor linked to adverse health outcomes, particularly in racial and ethnic minorities. Understanding associations between early discrimination and the brain in childhood may help identify mechanisms through which discrimination impacts future health. Data from 4512 children (ages 9-11) and a subsample of Black, Indigenous, and People of Color (BIPOC; N = 1567) from the Adolescent Brain and Cognitive Development (ABCD) Study(R) was used to create linear mixed-effects models that evaluated associations between Perceived Discrimination (PD) and amygdala resting-state fMRI connectivity (AC) to the salience network (SN), default mode network (DMN), and thalamus. PD was measured using the youth self-reported PD Scale. Results indicated that greater PD significantly predicted greater AC to the right thalamus in our full sample. In secondary analyses, environmental and behavioral factors were evaluated as potential moderators for associations significant at least at a trend level in both our full sample and BIPOC subsample. In our BIPOC subsample, traumatic events experienced moderated the relationship between PD and AC to the anterior cingulate cortex (ACC; SN), such that greater traumatic experiences predicted stronger positive associations between PD and this connection. Results suggest PD impacts neural connections in early life, highlighting the need to consider the impact of discrimination on risk for psychopathology.

neuroscience↗

Viral transcriptional regulators extensively rewire host pathways through diverse mechanisms

Viral transcriptional regulators (vTRs) reprogram host gene regulatory networks to promote replication, persistence, and immune evasion. Despite the identification of hundreds of vTRs in human viruses, how they rewire host pathways remains unclear. Here, we systematically profiled 95 vTRs from diverse human viruses across multiple functional assays. vTRs perturb immune, cell proliferation/death, and signaling pathways through various mechanisms; some bind DNA directly, others cooperate or antagonize human transcription factors (hTFs), and some remodel chromatin. vTRs can act as activators or repressors and recruit similar but not identical repertoires of proteins as hTFs. These findings reveal vTRs as versatile transcriptional modulators that converge on conserved host "pressure points" while diversifying across pathways to promote viral replication and persistence. Notably, many vTR dysregulate genes within autoimmune, neurological, and cardiovascular risk loci, revealing mechanistic links to disease. Together, we provide a comprehensive resource for understanding and targeting viral control of human transcription.

genomics↗

Low Dose GLP-1 Therapy Attenuates Pathological Cardiac and Hepatic Remodelling in HFpEF Independent of Weight Loss

BACKGROUND AND AIMSHeart failure with preserved ejection fraction (HFpEF) remains a therapeutic challenge. GLP-1 receptor agonists (GLP-1RAs) show clinical promise, and the prevailing hypothesis is that their benefits are primarily driven by weight loss and the downstream benefits of improved functional status. We investigated the weight loss-independent effects of low-dose GLP-1RA therapy in a clinically relevant rodent model of severe cardiometabolic HFpEF. METHODSTen-week-old male ZSF1 obese rats with spontaneous HFpEF were treated with low-dose semaglutide (30 nmol/kg twice weekly, n=6) or vehicle for 16 weeks. Comprehensive assessments included body weight, 2-D echocardiography, invasive hemodynamics, exercise capacity as well as cardiac and hepatic fibrosis and lipid deposition. The study utilized advanced multi-omics approaches, including single-cell RNA sequencing of the heart and liver, as well as cardiac, hepatic and plasma proteomics, to explore underlying mechanisms. RESULTSIn ZSF1 obese rats, low-dose semaglutide in the absence of weight loss, significantly improved cardiac function, exercise tolerance, and attenuated fibrosis in the heart and liver. Interestingly, semaglutide therapy reduced cardiac and hepatic lipid content as well as lipid droplets in cardiac myocytes and hepatocytes. Mechanistically, multi-omics analyses of cardiac and hepatic tissues revealed that semaglutide exerted these benefits by improving cardiac metabolism, interfering with pro-fibrotic and pro-hypertrophic signals, and by reducing systemic inflammation. CONCLUSIONSLow-dose semaglutide provides significant cardioprotective, hepatoprotective, and metabolic benefits in HFpEF independent of weight loss. Our findings support the investigation of lower GLP-1RA dosing in HFpEF and other cardiovascular conditions, including in non-obese patients, to expand the clinical utility of these potent drugs. Translational PerspectiveWe demonstrate that low-dose semaglutide attenuates HFpEF-mediated pathological cardiac and hepatic remodelling in HFpEF independently of the weight loss effects of GLP-1 receptor activation. Primary mechanisms are attenuated cardiac and hepatic fibrosis and reverse lipid transport. These findings provide a mechanistic basis for the direct cardiovascular actions of GLP-1RAs, revealing their potential to modulate key disease drivers like fibrosis and lipotoxicity. These data support the use of lower, better-tolerated doses of GLP-1RAs to treat HFpEF, potentially benefiting a wider range of patients, including those who are not obese or who suffer from side effects with current GLP-1 regimens.

pharmacology and toxicology↗

Deep Receptor Scanning Reveals General Sequence Constraints on GPCR Biosynthesis

G protein-coupled receptors (GPCRs) mediate a variety of signaling pathways and are the most common pharmacological targets. While advances in structural biochemistry have provided deep functional insights into key receptors, many of the 800+ human GPCRs remain understudied. We introduce a versatile "deep receptor scanning" platform that can be used to experimentally characterize 766 human GPCRs and 174 known GPCR splice variants in parallel. We use this platform to quantitatively characterize the relative abundance of canonical and alternative receptor transcripts, their translational efficiency, and the plasma membrane expression of each receptor in the context of a recombinant pool of HEK293T cells expressing individual GPCRs. We then employ machine learning to identify specific structural features that modulate GPCR expression. This experimental platform and informatic approach are compatible with a variety of assays and can be used to efficiently explore the biochemical and pharmacological properties of the GPCRome.

biochemistry↗

Combination Treatment with NCX 4040 and Napabucasin Triggers Enhanced Oxidative Stress, STAT3 Inhibition and Plausible Immunogenic Activation in Metastatic Prostate Cancer Cells

Prostate cancer (PCa) remains a significant health concern, ranking as the second most common cancer after lung cancer, despite recent advances in diagnostics and therapeutics. Due to its heterogeneous nature, diverse etiology, and the limited efficacy of current treatments, developing a therapeutic approach that can address the multifaceted aspects of the disease is imperative. Combinatorial therapy has emerged as a promising strategy for addressing tumor heterogeneity and the limitations of current treatments across various cancer types. In our study, we investigated the potential of combining NCX 4040, a nitric oxide-releasing aspirin derivative, and Napabucasin, a STAT3 and cancer stemness inhibitor, as a novel PCa treatment strategy. We utilized two cellular models: BPH-Cd, a cadmium-transformed carcinogenic cell line, and DU145, a brain metastatic PCa cell line. Our findings demonstrate that the combination treatment exerted a synergistic and dose-dependent reduction in cell viability, tumorigenicity, and migratory capabilities in both BPH-Cd and DU145 cells, surpassing the effects observed with individual treatments. Furthermore, this combination treatment triggered a robust generation of cellular and mitochondrial reactive oxygen species (ROS), resulting in G2/M cell cycle arrest and late-stage apoptosis in both cell lines. Additionally, the combination treatment downregulated redox-sensitive transcription factors pSTAT3 Tyr705 and Ser727, as well as pro-survival proteins TRX1/2, TRXR1, and GPX4, while upregulating tumor suppressor proteins PRDX1 and TXNIP. This implies that inhibition of the pro-survival redox proteins leads to the accumulation of oxidized PRDX1 and TXNIP, thereby elevating oxidative stress and blocking STAT3-mediated transcription, ultimately impeding cell proliferation and survival. Moreover, increased expression of pH2AX protein, a DNA damage marker, indicated that the combination induced DNA damage, resulting in the activation of the cGAS-STING pathway, an anti-tumor immunogenic mechanism as confirmed with immunoblotting. Downregulation of various stem cell markers linked to Wnt/{beta}-catenin and Notch-1 signaling pathways highlight the combinations ability to also target cancer stemness. In summary, our study underscores the promise of combining NCX 4040 and Napabucasin as an innovative and multifaceted therapeutic approach for PCa. Abstract Figure O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=88 SRC="FIGDIR/small/675191v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@485f6dorg.highwire.dtl.DTLVardef@170f98forg.highwire.dtl.DTLVardef@1037b8org.highwire.dtl.DTLVardef@ba3f39_HPS_FORMAT_FIGEXP M_FIG C_FIG (A) The combination therapy modulates key markers of the redox signaling pathway, inducing excessive oxidative stress in PCa cells, which subsequently leads to DNA damage and late apoptotic cell death. DNA damage activates the cGAS-STING pathway, upregulating interferon regulatory factor 3 (IRF3), which may, in turn, trigger the activation of tumor-infiltrating lymphocytes, generating a potent anti-tumorigenic response. (B) The combination therapy inhibits stem-cell signaling pathways, including Wnt/{beta}-catenin, Notch-1, and STAT3, potentially suppressing cancer stemness and contributing to long-term disease control.

pharmacology and toxicology↗

Lipid Nanoparticles with Aptamers Enable Targeted mRNA Delivery to CD4⁺ T Cells

In vivo genetic engineering of T cells could overcome the logistical, biological, and safety challenges of ex vivo modification, but effective and safe delivery systems remain limited by a lack of cellular specificity. Here, we developed aptamer-functionalized lipid nanoparticles (LNPs) for targeted mRNA delivery to CD4+ T cells, employing both a validated CD4-binding aptamer (Apt62) and novel aptamers generated using our proprietary transformer-based AI language model, AptaBLE. LNPs formulated with ionizable lipid SM102 or MC3 and conjugated with aptamers at controlled densities were physiochemically characterized and assessed for binding, in vitro transfection, in vivo biodistribution, and safety evaluation. Aptamer-functionalized LNPs demonstrated selective nanomolar binding to recombinant CD4, achieved enhanced transfection of CD4+ versus CD4- T cells in vitro, and significantly enriched mRNA delivery to immune-rich tissues in vivo, achieving up to 70-fold spleen signal enhancement with SM102 formulations compared to non-targeted controls, while maintaining suitable safety profiles. Overall, these findings demonstrate aptamer-functionalized LNPs, augmented by AI-guided aptamer design, as a tunable, non-immunogenic platform for in vivo T cell engineering. HighlightsO_LIAptamer-functionalized LNPs enable selective mRNA delivery to CD4+ immune cells rich organs. C_LIO_LIAptamer-functionalized LNPs maintain a favorable systemic safety profile in vivo. C_LIO_LIAI-guided AptaBLE platform generated functional aptamers validated in nanoparticle delivery. C_LI

molecular biology↗

On-target toxicity limits the efficacy of CDK11 inhibition against cancers with 1p36 deletions

The cyclin-dependent kinase CDK11 is an understudied kinase that has been the subject of conflicting reports regarding its function in cancer. Here, we combine genetic and pharmacological approaches to demonstrate that CDK11 is a critical regulator of cancer cell survival that is required for RNA splicing and the expression of homologous recombination genes. Inhibition of CDK11 disrupts genome stability, promotes the retention of intronic sequences in mature mRNAs, and induces synthetic lethality with PARP inhibitors. Through integrative analysis of functional genomics datasets, we identify heterozygous deletions of chromosome 1p36 - which encompasses CDK11 and its activating cyclin CCNL2 - as a recurrent and predictive biomarker of sensitivity to CDK11 inhibition. To assess the therapeutic potential of CDK11, we develop MEL-495R, a selective and orally bioavailable CDK11 inhibitor. Additionally, we establish a genetically-engineered mouse model that allows us to differentiate between the on-target and off-target effects of CDK11 inhibitors in vivo. Using this platform, we demonstrate that MEL-495R induces widespread on-target toxicity, revealing a narrow therapeutic index. Together, these findings define CDK11 as a core cancer dependency, uncover a chromosomal deletion that sensitizes tumors to CDK11 inhibition, and provide a generalizable strategy for deconvolving drug efficacy and toxicity in vivo for novel oncology targets.

cancer biology↗

Druggability of Phospholipase C-β Isoforms with Small Peptides Patterned after the Autoinhibitory XY Linker

The phospholipase C-{beta} (PLC{beta}) signaling pathway plays a pivotal role in peripheral nociception, particularly during inflammation and pain transduction. Despite their validation as important therapeutic targets, PLC{beta} isoforms are yet undruggable due to the difficulties to identify potent and selective modulators. Here, we addressed this question and used the autoinhibitory XY linker present in these enzymes as a source of peptide inhibitors of PLC{beta} activity. We report that peptides patterned after this motif inhibited PIP2 hydrolysis and the consequent calcium release from endoplasmic reticulum. In primary nociceptor cultures, active peptides notably attenuated bradykinin-induced electrogenesis and TRPV1 sensitization, thus reducing nociceptor hyperexcitability. Noteworthy, intraplantar administration of a lead peptide prevented inflammation and hypersensitivity in a mouse model of inflammatory pain. Collectively, our findings indicate that peptides patterned after the autoinhibitory XY linker act as selective PLC{beta} inhibitors with in vivo anti-inflammatory and antinociceptive activity, providing pharmacological tools for this enzyme family. SIGNIFICANCEPhospholipases C (PLC) are intracellular signaling proteins, with PLC{beta} isoforms crucial in somatosensory neuron signaling. These enzymes interact with G-protein coupled receptors for pro-inflammatory and algesic agents, sensitizing nociceptors by increasing their excitability. Despite their importance, selective PLC{beta} modulators remain limited; U73122 is widely used, though it lacks specificity and has off-target effects. Here, we introduce peptide inhibitors based on the XY autoinhibitory motif that selectively block PLC{beta} activity, reduce bradykinin-induced neuronal responses and TRPV1 sensitization, and do not affect other PLC isoforms. In a murine inflammatory pain model, local administration of our lead peptide showed both anti-inflammatory and antinociceptive effects, highlighting its therapeutic potential. This approach expands the toolkit of PLC-isoform selective modulators for drug development.

molecular biology↗

A gene regulatory element modulates myosin expression and controls cardiomyocyte response to stress

A hallmark of heart disease is gene dysregulation and reactivation of fetal gene programs. Reactivation of these fetal programs has compensatory effects during heart failure, depending on the type and stage of the underlying cardiomyopathy. Thousands of putative cardiac gene regulatory elements have been identified that may control these programs, but their functions are largely unknown. We profile genome-wide changes to gene expression and chromatin structure in cardiomyocytes derived from human pluripotent stem cells. We identify and characterize a gene regulatory element essential for the regulation of MYH6, which encodes human fetal myosin. Using chromatin conformation assays in combination with epigenome editing, we find that gene regulation is mediated by direct interaction between MYH6 and the enhancer. We also find that enhancer activation alters cardiomyocyte response to the hypertrophy-inducing peptide endothelin-1. Enhancer activation prevents polyploidization and changes in calcium dynamics following stress with endothelin-1. Collectively, these results identify regulatory mechanisms of cardiac gene expression programs that modulate cardiomyocyte maturation, cellular stress response, and could serve as potential therapeutic targets.

genomics↗

A multi-omics analysis of human fibroblasts overexpressing an Alu transposon reveals widespread disruptions in aging-associated pathways

During aging and cellular senescence, repetitive elements are frequently transcriptionally derepressed across species and cell types. Among these, the most abundant repeats by copy number in the human genome are Alu retrotransposons. Though Alu elements are often studied for their mutagenic potential, there is increasing appreciation for their contributions to other biological functions, including pro-inflammatory signaling and mitochondrial dysfunction. However, a comprehensive analysis of Alu-driven molecular changes remains to be conducted, and Alus potential contributions to aging features remain incompletely characterized. Here, we show that overexpression of an AluJb transposon in human primary IMR-90 fibroblasts leads to large-scale alterations across the transcriptome, cellular proteome, and secretome. Functional genomics analyses reveal alterations in aging pathways, broadly, and mitochondrial metabolism, proteostasis, cell cycle, and extracellular matrix pathways, more specifically. Our results demonstrate that Alu transcriptional upregulation is sufficient to drive widespread disruptions to cellular homeostasis that mirror aging-associated alterations.

genomics↗

A Fibroblast State Choreographs an Epithelial YAP-dependent Regenerative Program Essential to (Pre)malignancy via ECM-mediated Mechanotransduction

Chronic lung injury generates metaplasia which occasionally, but ominously, progresses to squamous dysplasia and squamous lung cancer. To identify mechanisms through which disrupted tissue homeostasis contributes to malignant initiation and progression, we used in vivo and in vitro heterotypic recombinant models of human bronchial epithelial cells (hBECs) and fibroblasts. We demonstrate that injury-associated TGF-{beta} signaling creates a fibroblast state dependent upon HSP47 upregulation. These fibroblasts accumulated collagen, thus elevating tissue stiffness and activating mechanosignaling that sustained YAP-dependent embryonic-like, pro-malignant activities in adjacent hBECs. This Stress/Tension-Instructive Fibroblast (STIF) state, exhibited by stressed fibroblasts in premalignant and malignant lesions across multiple cancer types, was sufficient to reprogram disease-free hBECs to metaplasia and to drive hBECs with compromised tumor suppressor function to dysplasia, yet could be inhibited and reversed. STIFs suffice to activate epithelial phenotypes reminiscent of oncogene-mediated cell transformation and induce (pre)malignancy via increased force transmission, providing novel targets for prevention. Statement of significanceTissue injury creates a regenerative pro-tumorigenic Stress/Tension-Instructive Fibroblast (STIF) state which is sufficient to activate a YAP-dependent, pre-malignant program to induce or unmask pre-cancerous phenotypes in epithelial cells through mechanotransduction. Inhibition of STIF activity or mechanosignaling prevents metaplasia and progression to dysplasia. HighlightsO_LITissue injury creates a pro-tumorigenic Stress/Tension-Instructive Fibroblast (STIF) state in multiple organs that precedes and persists through cancer C_LIO_LISTIF signaling alone, working through fibroblasts and not epithelial cells, is sufficient to activate embryonic-like plasticity and induce epithelial pre-cancerous metaplastic lesions C_LIO_LISTIFs program (pre)malignant phenotypes in adjacent epithelial cells through mechanosignaling by activating YAP prior to tumor formation C_LIO_LIInhibiting STIFs or mechanosignaling prevents/reverts metaplasia and prevents progression to dysplasia C_LI

cancer biology↗

Unsupervised Variant Clustering Identifies Genetic Subtypes of Disease

Current approaches to identify disease subtypes rely on prior knowledge or external phenotypic references that limit their generalisability across traits. This study presents an unsupervised, phenotype- free framework that analyses the genetic co-occurrence of variants across individuals to identify variant clusters underpinning disease heterogeneity. The approach is developed and validated using simulated combinations of real phenotypes then applied to dissect disease subtypes of type 2 diabetes and asthma. The approach captures clinically established mechanistic profiles in type 2 diabetes and asthma without requiring any reference phenotype data and enables identification of plasma proteins for novel subtype- specific biomarkers and drug targets. Lastly, we demonstrate that variants with conflicting effects on disease-relevant traits are resolved into distinct clusters, identifying subtypes with opposing phenotypic profiles that are lost by the aggregated genetic risk. Co-occurrence-based clustering provides a scalable strategy for understanding disease heterogeneity across diverse populations by identifying biologically meaningful subtype structure from genotype data alone.

genomics↗

ATP2B1 expression identifies human hematopoietic stem cells across ontogeny with superior repopulation and self-renewal capacity

Long-term hematopoietic stem cells (LT-HSC) maintain lifelong hematopoiesis while preserving the stem cell compartment through self-renewal. The human LT-HSC compartment is molecularly and functionally heterogeneous and also varies across ontogeny. Dissecting the molecular basis for this variation is impeded by the absence of immunophenotypic markers to resolve LT-HSC heterogeneity. Here, we identified ATPase plasma membrane Ca2+transporting 1 (ATP2B1/PMCA1) as a novel cell surface marker that is heterogeneously expressed by CD49f+ LT-HSC across ontogeny. ATP2B1 immunophenotypic expression stratified human CD49f+ LT-HSC from fetal liver (FL), neonatal cord blood (CB) and adult mobilized peripheral blood (mPB) sources into functionally distinct subpopulations in single-cell (sc) clonogenic assays. CD49f+ATP2B1+ LT-HSC exhibited superior long-term repopulation and self-renewal capacities in vivo compared to CD49f+ATP2B1- LT-HSC. Molecular profiling by scMultiome and immunofluorescence microscopy point to enrichment of an HSC self-renewal program that includes the TFEB-endolysosomal axis in CD49f+ATP2B1+ LT-HSC. Our study provides a new tool to dissect the heterogeneous molecular programs in LT-HSC across ontogeny.

cell biology↗

The Immunophenotype and Proviral Landscape of HIV-infected CD4 T Cells During Antiretroviral Therapy

In individuals on effective antiretroviral therapy, integrated HIV proviruses persist within CD4 T cells, forming a viral reservoir that rebounds if treatment is stopped. Identifying and targeting these rare, infected cells is critical for advancing therapies, but methods to study reservoir cells are limited and their unique properties remain largely unknown. We applied DAb-seq, a high-throughput method that combines single-cell DNA and surface protein sequencing, to profile over five hundred and twenty thousand CD4 T cells from the blood of six individuals on ART. Infected cells were unequally distributed in T cell subsets, and differential protein expression between infected and uninfected cells revealed significant heterogeneity across cell subsets. Attempts to identify surface markers that differentiate infected from uninfected cells found antigens that mirrored the enrichment of HIV in central memory subsets. However, while central memory T cells harbored the majority of HIV, cells with intact provirus were enriched relative to their defective counterparts in Naive and Regulatory T cell subsets, suggesting that they differentially maintain intact proviruses. In summary, we developed DAb-seq as an open-source platform for linking the proviral landscape to diverse cellular phenotypes, revealing heterogeneity in surface protein expression and provirus maintenance across infected subsets.

genomics↗

A high-throughput platform for biophysical antibody developability assessment to enable AI/ML model training

Antibodies must bind their targets with high affinity and specificity to achieve useful therapeutic activity. They must also possess suitable developability properties (e.g., thermostability, solubility, viscosity, polyreactivity) to ensure favorable manufacturing, formulation, and in vivo performance. Both binding and developability properties are inherent to a given antibody amino acid sequence. Identification or selection of antibodies possessing suitable binding characteristics is now routine, and de novo computational design models, trained on extensive complementarity-determining region sequence and structural data, are rapidly improving. Developability properties, however, remain difficult to predict largely due to insufficient training data, with empirical testing being heavily used to avoid challenges in late-stage antibody development. To fill this gap, we built a high-throughput antibody developability assay platform designed to generate the large datasets needed to train improved machine learning (ML) models. We optimized and automated known developability assays [Jain et al., 2017], and developed a robust integrated data analytics pipeline. Here we report data on 246 antibodies--representing 106 approved, 135 clinical-stage, and 5 preregistration/withdrawn molecules--across a panel of 10 developability assays, in a "tidy data" format suitable for AI/ML modeling. We used these data to develop an XGBoost [Chen et al., 2016] ML model that better predicts similarity to approved antibodies compared to conventional use of developability warning thresholds. Additionally, we confirm that preliminary predictive models do improve with more training data. Our high-throughput PROPHET-Ab platform enables data generation at the scale needed to develop improved ML models to predict antibody developability. SignificanceSuccessful antibody drugs exhibit important "developability" properties, beyond tight and specific binding to their target, including high expressibility, high stability and solubility, low aggregation propensity, low viscosity, low polyreactivity, and long in vivo half-life. Collectively, developability properties predict favorable manufacturing, storage, administration, and safety, and deficiencies in these properties increase risk for clinical failure. Despite progress in developing machine learning models to predict structure and binding, antibody developability models lag, largely due to a lack of sufficiently large training datasets. We have built a high-throughput platform, PROPHET-Ab, that enables data generation at the scale needed to train improved AI/ML models to predict antibody developability.

biophysics↗

Learning and language in the unconscious human hippocampus

Consciousness is a fundamental component of cognition,1 but the degree to which higher-order pattern recognition relies on it remains disputed.2,3 Here we demonstrate the persistence of oddball discrimination, semantic processing, and online prediction in individuals under general anesthesia-induced loss of consciousness.4,5 Using high-density Neuropixels microelectrodes6 to record both single unit and local field potential neural activity in the human hippocampus while playing a series of tones to anesthetized patients, we found that hippocampal neurons and local oscillations retained some detection of oddball tones. This effect size grew over the course of the experiment ([~]10 minutes), demonstrating representational plasticity. A biologically plausible recurrent neural network model showed that learning and oddball representation are an emergent property of flexible tone discrimination. Moreover, when we played language stimuli, single units and local field potentials carried information about the semantic and grammatical features of natural speech, even predicting semantic information about upcoming words. Together these results indicate that in the hippocampus, which is anatomically and functionally distant from primary sensory cortices,7 complex processing of sensory stimuli occurs even in the unconscious state.

neuroscience↗

Longitudinal multimodal neuroimaging after traumatic brain injury

Traumatic brain injury is a major cause of long-term cognitive impairment, yet the mechanisms underlying recovery remain poorly understood. Neuroimaging methods such as diffusion MRI, functional MRI, and positron emission tomography (PET) provide insight into micro- and macro-scale changes post-TBI, but the relationships between regional cellular and functional alterations remain unclear. In this study, we conducted a longitudinal, multimodal neuroimaging analysis quantifying TBI-related pathologies in four biomarkers, namely flumazenil PET derived binding potential, dMRI-derived structural connectivity, and resting-state fMRI-derived functional connectivity and fractional amplitude of low-frequency fluctuations in individuals with mild-to-severe brain injury at the subacute (4-6 months post-injury) and chronic (1-year postinjury) stages. Brain injury related regional pathologies, and their changes over time, were correlated across the four biomarkers. Our results reveal complex, dynamic changes over time. We found that flumazenil-PET binding potential was significantly reduced in frontal and thalamic regions in brain injured subjects, consistent with neuronal loss, with partial recovery over time. Functional hyperconnectivity was observed in brain injured subjects initially but declined while remaining elevated compared to non-injured controls, whereas cortical structural hypoconnectivity persisted. Importantly, we observed that brain injury related alterations across MRI modalities became more strongly correlated with flumazenil-PET at the chronic stage. Regions with chronic reductions in flumazenil-PET binding also showed weaker structural node strength and lower amplitude of low frequency fluctuations, a relationship that was not found at the subacute stage. This observation could suggest a progressive convergence of structural and functional disruptions with neuronal loss over time. Additionally, regions with declining structural node strength also exhibited decreases in functional node strength, while these same regions showed increased amplitude of low frequency fluctuations over time. This pattern suggests that heightened intrinsic regional activity may serve as a compensatory mechanism in regions increasingly disconnected due to progressive axonal degradation. Altogether, these findings advance our understanding of how multimodal neuroimaging captures the evolving interplay between neuronal integrity, structural connectivity, and functional dynamics after brain injury. Clarifying these interrelationships could inform prognostic models and enhance knowledge of degenerative, compensatory, and recovery mechanisms in traumatic brain injury.

neuroscience↗