Biology subjects

Ahmed, A.

Publications and source records attributed to Ahmed, A..

At least 19 recordsLinked to original sources

bioRxiv2026

The Human Gut Cell Atlas v1.0: A Unified, Community-BuiltReference of Cellular Diversity Across the Gut

Single-cell RNA-sequencing (scRNA-seq) studies have transformed our understanding of cellular diversity in the human intestine, but differences in anatomical sampling, experimental processing and cell-type nomenclature limit comparison across datasets. Here, we present the Human Gut Cell Atlas (HGCA) V1, a community-curated reference of 944,390 healthy and disease-adjacent intestinal cells from 502 samples, 265 donors and 24 landmark studies, linked to detailed anatomical, clinical, and technical metadata. As this metadata is of critical importance to human biology, we developed MetaManager, an open source data management framework for standardized metadata collection and tracking. A five-level consensus taxonomy resolves 94 homeostatic cell identities and enables transferrable, high-resolution annotation of new gut datasets. By assembling cell identity, sampling metadata, and independent spatial validation, intestinal segment and radial tissue depth were revealed to systematically shape cellular composition and transcriptional state, enabling inference of the presence of sampling-dependent tissue niches, including lymphoid follicles. Reference mapping accurately and rapidly recovered cohort-level Crohn's disease and treatment signatures without de novo annotation, while mapping human intestinal organoids quantified cell-type-specific identity, regional specification, maturation, and transcriptional fidelity to native tissue. The HGCA V1 provides a standardized cellular, anatomical coordinate, and metadata system for reproducible, high-quality analysis of intestinal biology across healthy tissue, disease-associated remodelling, and experimental models, providing a continuously evolving community reference for cumulative discovery in human intestinal biology.

systems biology↗

bioRxiv2026

Endothelial gain of PIEZO/TRPV mechanosensors drives cavernous malformations

Vascular disease often begins as a failure to read mechanical force. Cerebral cavernous malformations (CCMs) are leaky, brain-invading capillary clusters that cause stroke and seizures and arise from endothelial loss of the CCM complex. They form exclusively in low-flow vessels but existing models cannot explain this selectivity. We previously established that CCM-mutant endothelium inverts its adhesive balance, weakening cell-cell junctions while building matrix-degrading adhesions. The mechanosensors imposing this switch are unknown. Here we show that the mechanosensitive Ca2+ channels PIEZO1, TRPV2 and TRPV4 are overexpressed in the endothelium of CCM lesions in a 42-patient cohort, and that lesion volume scales with their expression level. Mechanistically, PIEZO1 partners with TRPV4 to destabilise cell-cell junctions and with TRPV2 to reinforce cell-matrix adhesions; silencing TRPV4 restores junctional integrity and abolishes KLF4 induction, whereas silencing TRPV2 or inhibition with tranilast abolishes matrix degradation and invasion. In vivo, trpv4 knockdown or inhibition with GSK2798745 restores atrioventricular canal morphogenesis in ccm2-mutant zebrafish. Gain of mechanosensory channel function is thus a causal step in CCM pathogenesis, upstream of the KLF program. Combined therapeutic targeting of TRPV2 and TRPV4 with inhibitors validated in humans offers a route to therapy.

cell biology↗

bioRxiv2026

Topoisomerase-mediated resolution of negative DNA supercoiling sustains human transcription and gene activation

Transcription generates DNA supercoiling that can influence gene expression, but how transcription-associated supercoiling shapes RNA polymerase II (RNAPII) dynamics in human cells remain poorly understood. Here, we show that topoisomerase-mediated resolution of negative DNA supercoiling is required for productive transcription. Acute topoisomerase perturbation causes negative supercoiling to accumulate around transcription start sites (TSS), with greater negative supercoiling accumulation associated with stronger transcription reduction. Elevated negative supercoiling behind the elongating RNAPII, but not positive supercoiling ahead, is associated with reduced RNAPII elongation rates. Using NOTE-seq2 to simultaneously profile newly synthesized and total RNA in single cells, we further demonstrate that acute TOP1 depletion increases gene expression noise by reducing both transcriptional burst size and frequency. Mechanistically, negative supercoiling accumulation at TSS increases RNAPII promoter occupancy and promoter-proximal pausing, providing a potential basis for reduced burst size. Micro-C analysis shows that TOP1 depletion largely preserves chromatin compartments and TADs but weakens short-range chromatin loops, including enhancer-promoter interactions, likely contributing to reduced burst frequency. Finally, during T-cell activation, impaired resolution of negative supercoiling compromises rapid gene upregulation and attenuates the transcriptional activation program. Together, these findings establish topoisomerase-mediated resolution of negative DNA supercoiling as a key mechanism linking DNA topological homeostasis to RNAPII dynamics, chromatin looping, and rapid gene activation.

genomics↗

bioRxiv2026

RNF213 M1-ubiquitinates damaged mitochondria to activate pro-inflammatory NF-κB signaling

Through mitochondrial outer membrane permeabilization (MOMP), mitochondria are central to apoptosis. MOMP is pro-inflammatory, impacting diverse processes including anti-tumor immunity and cellular senescence. Despite this, how damaged mitochondria activate inflammation remains unclear. Recent studies have shown that following MOMP, mitochondria are extensively ubiquitinated activating pro-inflammatory NF-{kappa}B signaling. We identify the E3 ligase, RNF213, as essential for pro-inflammatory mitochondrial ubiquitination following MOMP. RNF213 has an established role in pro- inflammatory, cell-autonomous immunity to bacteria and other pathogens. We discover that RNF213 is required for mitochondrial M1-linked (linear) ubiquitination. Interestingly, this was found to be independent of the canonical M1-ubiquitin ligase complex LUBAC. RNF213 can directly catalyze M1-linked ubiquitination. By promoting mitochondrial M1-linked ubiquitination, RNF213 initiates the recruitment of the essential NF{kappa}B adaptor molecule, NEMO, and subsequently activates pro-inflammatory NF-{kappa}B signaling. Collectively, our findings highlight striking similarities between how cells detect damaged mitochondria and intracellular pathogens, leading to inflammation.

cell biology↗

bioRxiv2026

Whole genome sequencing of endometrial cancer identifies novel subgroups, drivers, and actionable alterations

Endometrial cancer (EC) is the most common gynaecological malignancy in high income countries, and is increasing in incidence. While molecular stratification has improved its management, precision care is hampered by incomplete characterization of the EC genome. We address this by analysis of whole genome sequencing (WGS) of 665 ECs generated by the UK Genomics England 100,000 Genome Project (100kGP). 5% of cases were associated with germline pathogenic variants in cancer genes, including BRCA1 which we confirmed predisposes to EC. We identified 107 putative coding driver genes, 35% of which had no prior established role in EC. Novel structural variants included gains of MYCN and loss of its negative regulator NEDD4.1 which were significantly mutually exclusive in copy number (CN) high tumours. Immunogenomic analysis confirmed selection for driver alterations of low immunogenicity based on patient HLA haplotype, and pervasive immune escape through multiple mechanisms. Unsupervised clustering of mutational signatures and genomic alterations identified known and novel molecular subgroups, including a CN-high subset with mutational signatures of homologous recombination deficiency (HRD) and favourable outcome. Independent prognostic value of single nucleotide variant (SNV) burden, CN burden and multiple coding drivers, along with the identification of targetable molecular alterations in over one-third of cases, underscores the promise of WGS for precision medicine in EC.

genomics↗

bioRxiv2026

A Head and Neck Cancer Patient-Specific Microphysiological System for Predicting Response to Chemoradiation

Head and neck cancer (HNC) is the 6th most common malignancy worldwide. 60% of patients present with advanced disease and approximately 50% of patients recur following primary treatment. Chemoradiation remains a standard of care for most patients. However, clinicians lack functional tools to predict which patients will respond to chemoradiation prior to treatment and current models, including organoids and animal model systems, fail to capture either full complexity or patient-to-patient heterogeneity of the individual HNC tumor and microenvironment (TME). Here, we have developed, characterized, and tested a patient-specific microphysiological system (MPS) that reconstructs the HNC TME in a vascularized 3D environment. This MPS was constructed from malignant cells, fibroblasts, and immune cells from a patients surgically resected tumor, seeded within a 3D hydrogel with molded endothelial lumens. Single-cell RNA sequencing confirmed that the MPS preserved 12 transcriptionally distinct cell populations found in matched native tissue. The platform recapitulated tumor hypoxia, with a 12-fold increase in hypoxic marker expression that altered radiation response, consistent with clinical HNC biology. Compartment-resolved imaging revealed distinct treatment dynamics in tumor, stromal, and vascular regions, and individual patients exhibited divergent responses to chemoradiation in spheroid morphology, cell viability, and migration. We found the slope of spheroid area change with treatment tracked with tumor recurrence, suggesting this metric could serve as a functional predictor of therapeutic response.

bioengineering↗

bioRxiv2026

Increased utrophin expression in healthy and DMD patient derived myoblasts in response to ERK1/2 and EZH2 inhibitor treatment

BackgroundThe X-linked muscle wasting disorder Duchenne muscular dystrophy (DMD) is a progressive and ultimately fatal disease caused by loss of function mutations in the dystrophin (DMD) gene. Upregulation of utrophin (UTRN), an embryonic homologue of dystrophin, has been proposed as a therapeutic option that could ameliorate disease. We previously generated a bioluminescent screen for utrophin-upregulating compounds using a mouse reporter of endogenous utrophin expression and discovered that inhibition of ERK1/2 and EZH2, increases utrophin expression in myoblasts. MethodologyHere we extend this analysis to show that treatment of human myoblasts with the ERK1/2 inhibitor LY3214996 and the EZH2 inhibitor GSK503, increases UTRN expression in primary and immortalised myoblasts derived from healthy volunteers and DMD patients. ResultsShort-term (24 hours) inhibition of ERK1/2 and EZH2 resulted in increased expression of utrophin in proliferating myoblasts. Surprisingly, in patient-derived samples, but not healthy controls, increased UTRN expression was sustained following drug removal and in vitro differentiation. Furthermore, dystrophin deficient myoblasts have altered expression of myogenic transcription factors MYOD1 and MYOG and proliferation marker Ki67, signalling an altered regenerative capacity of these cells, while ERK1/2 inhibition, alone or combined with EZH2i, reversed this transcriptional signature. ConclusionsTreatment with ERK1/2 and EZH2 inhibitors could offer a therapeutic option for DMD by increasing UTRN and MYOD1 expression. We propose that this may compensate for DMD loss and help restore productive muscle differentiation and regeneration.

pharmacology and toxicology↗

bioRxiv2026

The transcription factor Vca0578 (DsvR) mediated expression of ZapC is required to promote cell division during lytic transglycosylase insufficiency in Vibrio cholerae

The bacterial peptidoglycan (PG) cell wall, a polymer made of amino-acid-bearing glycan strands, maintains cell shape, provides structural integrity, and protects against osmotic lysis. PG maintenance is an active process that requires regulated PG breakdown to make space for insertion of new PG strands. PG breakdown is accomplished by autolysins, i.e. endogenous enzymes with cell wall cleavage activity. The lytic transglycosylases (LTGs), a class of autolysins, for example, cleave glycan strands during PG remodelling. LTGs are broadly conserved and are highly redundant in bacteria, but their physiological role is poorly-defined. In this study, we interrogated physiological consequences of LTG insufficiency in Vibrio cholerae using TnSeq to gain insights about roles of these enzymes. We identify an uncharacterized transcription factor, Vca0578, which alleviates defects associated with the {Delta}6LTG mutant. We demonstrate that Vca0578 positively regulates the expression of zapC, a typically non-essential Z-ring associated protein. In the absence of zapC, cell division was impaired during perturbations of cell envelope homeostasis caused by absence of LTGs, or by exposure to antibiotics inhibiting cell elongation; either condition rendered zapC conditionally essential. This essentiality could be overcome by increasing FtsZ levels. Lastly, we found that ZapC also contributes to both width and length homeostasis during normal growth. This work thus uncovers a novel transcriptional circuit that contributes to effective cell division in{Delta} 6LTG cells, and suggests an essential role for ZapC in cell division under stress conditions that cause perturbation of cell width homeostasis. AUTHOR SUMMARYBacteria must maintain their outer shell (the cell envelope) in the face of changes in the environment. For this, they use elaborate systems that remodel the cell envelope. How some of these systems work is not well understood. In this study, we describe a new gene circuit that is required to keep cells dividing when the cell envelope is compromised. We found that Vca0578, a putative transcription factor, controls expression of the zapC gene. The protein ZapC then helps bacteria grow and divide when the cell envelope is under stress, for example, in the presence of certain antibiotics. Thus, we have discovered a regulatory circuit that promotes bacterial growth and antibiotic resistance under stress.

microbiology↗

bioRxiv2026

Identification of disease-specific alleles and gene duplications from 1,600 Haemophilus influenzae genomes using predicted protein analyses from an unsupervised language model and clinical metadata

Haemophilus influenzae, a Gram-negative bacterium that is an obligate commensal of the human nasopharynx, is associated with both acute and chronic infections of the ears, adenoids, sinuses, and lungs, as well as pelvic inflammatory disease, sepsis, and meningitis. This diverse array of clinical disease phenotypes is due to H. influenzaes natural competence providing for frequent distributed gene exchange among strains during polyclonal colonizations. We performed whole genome sequencing (WGS) on [~]1000 H. influenzae strains and combined these data with [~]600 publicly available genomes. Clinical metadata including isolation site and disease were available for all strains. Our goal was to identify variations in protein sequences inferred from the WGS that correlate with the clinical metadata. We employed the alpha-fold unsupervised machine-learning model to all protein sequences. For each unique AA sequence, a numerical vector was generated reflecting the proteins biochemical properties. Multidimensional clustering was used to group variants into clusters by distance. For gene groups with two or more clusters, clinical metadata from the strain of origin was overlayed and subsequently tested for correlation with the clustering. This allowed identification of multiple gene groups with clusters of variants that correlated significantly with the patients disease. COG category analysis showed that many of the significant gene groups were associated with antibiotic targets. The TbpA gene group type was found to be significantly correlated with disease type with three of five variant clusters having a 95% prevalence among strains that were isolated from the lungs of COPD patients or other lower pulmonary tract infections.

genomics↗

bioRxiv2026

Side-necked turtle genomes reveal chromosomal dynamics, skeletal innovation and cancer resistance

Turtles exhibit a highly derived body plan, exceptional longevity, cancer resistance, and striking diversity in karyotypes and sex determination systems. However, the genomic basis of these innovations remains unresolved, largely because reference genomes were lacking for one of two extant turtle clades, the side-necked turtles (Pleurodira). As part of the Vertebrate Genomes Project, we generated seven reference-quality Pleurodira genomes and reconstructed the most comprehensive genome-wide turtle phylogeny. Combining demographic inference with historical climate and biome reconstructions indicates that ancient climate fluctuations shaped long-term population dynamics, while recent declines mainly reflect population structure. Ancestral genome reconstructions reveal that rare bursts of chromosome fusions and fissions, likely facilitated by repetitive elements, drove turtle karyotype diversity. By identifying sex chromosomes and tracing their evolutionary history, we resolve a long-standing debate and demonstrate a single origin of genetic sex determination in Chelidae on a microchromosome over 80 million years ago. Contrary to previous hypotheses, we find no evidence of coevolution between genetic sex determination and chromosome number in turtles. Comparative genomic analyses further identify gene losses and signatures of adaptive evolution associated with key turtle traits. Gene losses causing disproportionate dwarfism phenotypes may have contributed to skeletal adaptations underlying the compact turtle body plan. In addition, gene losses and adaptive changes in stress response and tumor suppressor pathways likely enhance oxidative stress tolerance and cancer resistance. Together, these findings illuminate turtle genome evolution, revealing chromosomal dynamics, sex chromosome evolution, molecular insights into skeletal innovation and cancer resistance, and implicate gene losses as a recurrent contributor to evolutionary novelty.

genomics↗

bioRxiv2026

Astrocytes mediate a positive feedback loop for oxytocin

Social interactions are critical for well-being and survival. Oxytocin neurons in the paraventricular nucleus of the hypothalamus help regulate social behaviors in many species, and respond to social stimuli to promote pro-social interactions. Here, we show that chronic social isolation reduced production of oxytocin peptide, and led to a delay in the onset of huddling behavior upon resocialization in male mice. Exogenous oxytocin treatment prevented both the behavioral and molecular effects of social deprivation. Using conditional knockouts, we found that oxytocin-induced oxytocin expression was mediated by local hypothalamic astrocytes. Oxytocin signaling in astrocytes upregulated the expression of a retinoic acid-synthesizing enzyme Aldh1a1, and retinoic acid increased oxytocin expression. These findings reveal a mechanism in which astrocytes can sense and control neuropeptide levels to influence social behaviors.

neuroscience↗

bioRxiv2026

Ongoing lymphoid HIV production drives pyroptosis and GLP-1 counter-regulation in ART-suppressed infection

Despite effective antiretroviral therapy (ART), many people with HIV (PWH) exhibit persistent immune activation (IA) and suffer metabolic comorbidities. We investigated whether residual HIV production in lymphoid tissues drives IA. Among 20 ART-suppressed PWH, HIV RNA+ cells were detected in lymph nodes and correlated directly with markers of pyroptosis, assessed via cleaved gasdermin D positivity, but not with most plasma cytokines or IA markers. Notably, glucagon-like peptide 1 (GLP-1), an enteroendocrine hormone with anti-inflammatory roles, was upregulated in the ileum of PWH and correlated directly with systemic cytokines but inversely with lymph node pyroptosis. These findings suggest that chronic occult inflammation in people with successfully suppressed HIV infection is mediated by persistent virus production in lymph nodes leading to pyroptosis, which may trigger compensatory anti-inflammatory enteroendocrine activation that may dampen pyroptosis. Targeting pyroptosis or enhancing GLP-1 signaling represent potential therapeutic strategies for modulating IA and managing metabolic comorbidities in PWH. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=140 SRC="FIGDIR/small/698696v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@af8909org.highwire.dtl.DTLVardef@4dbc95org.highwire.dtl.DTLVardef@197ff48org.highwire.dtl.DTLVardef@1f9051a_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2025

Fission yeast histone chaperone Rtt106 regulates histone levels, prevents early division, and promotes genome stability

Chromatin packaging influences gene expression and is linked to genome stability through the establishment and maintenance of histone modifications. Histone chaperone proteins regulate chromatin assembly and thus packaging. We tested how loss of the histone chaperone Rtt106 affects genome stability through cell cycle checkpoint stability in response to cellular stress. We tested how double mutants lacking DNA replication or DNA damage checkpoint kinases are impacted by the absence of histone chaperone rtt106. Rtt106 brings histone H3 and histone H4 together into complexes. We found that rtt106{Delta} cells with loss of the DNA replication checkpoint (cds1{Delta}, rad3{Delta}) were more sensitive to hydroxyurea. However, DNA damage kinase chk1{Delta} rtt106{Delta} cells became less sensitive to DNA damaging drugs. The effects of Rtt106 on growth are observed in division timing, where rtt106{Delta} cells show early division in the presence of drug. Coupled to a decrease in histone H3 levels and increased mutation rate, our work shows how non-essential Rtt106 activities contribute to genome stability. By regulating histone levels and use, Rtt106 regulates the cell division and may function in chromatin arm coherence and segregation.

genetics↗

bioRxiv2025

Dual-Channel Event Microscopy for Ultrafast Biological Imaging

Many fundamental biological processes--spanning immune-tumor interactions, neuronal signaling, and microvascular flow--exhibit fast, multiscale dynamics among diverse cell types within three-dimensional tissue environments. Capturing such activity requires imaging systems that simultaneously achieve high temporal resolution, multicolor capability, and volumetric coverage over large fields of view (FOVs). However, existing modalities remain limited by trade-offs among imaging speed, spectral capacity, depth of field (DOF), and spatial resolution. Here, we present Dual-Channel Event Microscopy (DEM), which integrates digital micromirror device (DMD)-based pulsed illumination, extended-DOF optics, and event-based sensing for ultrafast, dual-channel volumetric imaging across a 2.3 x 1.3 mm2 FOV with an effective 200 {micro}m DOF. Using dual-color fluorescent phantoms and microsphere flow assays, DEM achieves accurate spectral separation and reconstruction of rapid motion at kilohertz frame rates. In vivo, DEM enables simultaneous visualization of neutrophils and premalignant tumors in freely swimming zebrafish. In immobilized specimens, it provides robust, sensor-level optical sectioning near the heart, suppressing diffuse background to reveal fine vascular networks and active blood circulation into and out of the cardiac chambers. DEM further enables quantitative mapping of blood-flow dynamics in the zebrafish tail, resolving arterial-venous differences and capturing heartbeat-driven oscillations that reflect cardiac pumping with high temporal fidelity. By uniting ultrafast acquisition, dual-channel capability, volumetric coverage, and intrinsic optical sectioning within a single event-driven architecture, DEM offers a powerful platform for visualizing rapid multicellular interactions and physiological dynamics in living systems.

bioengineering↗

bioRxiv2025

A multicenter spatial transcriptomics atlas of human tuberculosis and non-tuberculous mycobacterial disease

Granulomas are the hallmark of mycobacterial (MB) infections, forming structured immune environments that contain bacteria but also drive disease persistence. However, their spatial and functional organization remains unclear. Using spatial RNA sequencing on 38 patient samples, we identified five distinct granuloma niches: a necrotic core, an immune-activated inner niche, an inflammatory and an extracellular matrix (ECM)-remodeling middle niche, an outer structural niche, and a tertiary lymphoid structure niche supporting antigen presentation. Immune activity peaks in the inner niche, transitioning to fibrosis at the periphery. Lymph node granulomas display reduced fibroblast involvement but stronger JAK-STAT activation. Mycobacterium tuberculosis (MTB) granulomas exhibit heightened JAK-STAT and IFN-{gamma} signaling, while non-tuberculous mycobacteria (NTM) granulomas show increased hypoxia signatures. Compared to sarcoidosis, MB granulomas feature a structured adaptive immune response, marked by the clustering of plasma cells. Our findings, accessible via https://lab-li.ciim-hannover.de/mb-granuloma/, define key disease signatures, guiding biomarker discovery and therapeutic targeting in granuloma-related diseases.

bioinformatics↗

bioRxiv2025

Saturation mutagenesis map of generalist versus specialist adaptations of β-lactamase to novel antibiotics

The evolution of {beta}-lactamase proteins is shaped by the need to maintain enzymatic activity against previously prevalent {beta}-lactam antibiotics while expanding substrate range against new classes of antibiotics. Using saturation mutagenesis and sequence-barcoding-based quantification, we comprehensively mapped the response of the fitness landscape of TEM-1 {beta}-lactamase, which evolved against penicillin-class antibiotics, to mutational perturbations against six diverse {beta}-lactam antibiotics. This systematic panel of antibiotic substrates, including representatives from penicillin, cephalosporin, and monobactam classes, allowed us to classify resistance mutations into two categories. Generalist mutations conferred resistance to multiple antibiotics and were consistently restricted to three positions critical for substrate recognition and catalytic function R164, G238, and E240. These substitutions produced broad spectrum resistance through mechanisms such as expansion of the active site and improved substrate accommodation. In contrast, specialist mutations conferred resistance to only a single antibiotic and exhibited much wider positional diversity. Ceftazidime selection yielded the greatest number of distinct specialist mutations, which were frequently found in flexible or peripheral regions including the omega loop. One especially unexpected finding was the identification of the E166P variant. E166 is a catalytic residue required for deacylation during hydrolysis, and substitutions at this site are generally assumed to abolish function. However, E166P conferred a significant increase in ceftazidime resistance despite eliminating activity against penicillins. Molecular dynamics simulations and mutational analysis revealed that the E166P mutant employs an alternative catalytic mechanism, involving residue N132, rather than the canonical pathway. Together, our findings reveal, at the molecular level, how specialist mutations open up a wide range of diverse and idiosyncratic solutions at the expense of generalizability. These insights may inform strategic design of antibiotic administration protocols to systematically lower pathogenic evolvability.

evolutionary biology↗

bioRxiv2025

The Long Non-coding RNA Landscape of Endurance Exercise Training

Long non-coding RNAs (lncRNAs) regulate multiple cellular processes. However, knowledge of the responses and regulatory functions of lncRNAs in physical exercise and training remains limited. As part of the Molecular Transducers of Physical Activity Consortium (MoTrPAC), we conducted a comprehensive analysis of lncRNA expression patterns in 18 tissues after an 8-week progressive endurance training program in rats. The lncRNA expression pattern was largely tissue-specific. In total, 759 unique lncRNAs were found to be differentially expressed across all tissues, generally displaying lower abundance, shorter transcript length, and reduced GC content compared with protein-coding genes. The most pronounced changes were observed in white and brown adipose tissues, the hypothalamus, and the adrenal gland. In the two skeletal muscle tissues investigated, only two lncRNAs were commonly differentially expressed. White and brown adipose tissues revealed a correlation between upregulated differentially expressed lncRNAs and coding genes associated with immune regulation. We identified substantial sex differences in the lncRNA regulatory landscape in response to exercise training. This comprehensive tissue-specific characterization of exercise-responsive lncRNAs opens new avenues for understanding exercise as molecular medicine and may inform the development of lncRNA-targeted therapeutics that harness the beneficial effects of exercise.

physiology↗

bioRxiv2025

Partially-functional exhausted CD8+ T cells can contribute to short-term viral suppression: a computational prediction for children with perinatal HIV

We and others have reported evidence of T cell exhaustion in children with perinatal HIV with increased expression of inhibitory receptors PD-1, CD160, and TIM-3, but there is limited data on the virologic functional consequences of this immune exhaustion. We address this by using an immune database from Kenyan children with perinatal HIV and unexposed controls. We computationally integrate T cell profiles of differentiation, activation and exhaustion in an agent-based model (ABM) to predict how T cell exhaustion impacts viral control following HIV exposure in vitro. Our ABM includes macrophages, CD4 and CD8 T cells, cytokines, and HIV. Model mechanisms include viral dynamics, macrophage activation, T cell activation and proliferation, cytotoxic T cell killing, and cytokine/HIV diffusion and degradation. Participants are grouped by HIV plasma viremia and by age, less than 5 years or 5-18 years. Our findings indicate that cells from virally active participants, who have the highest levels of exhaustion, have lower predicted viral concentrations and infected cells compared to other participant groups during new infection. However, this coincides with higher cell death, suggesting that short-term viral control is associated with excessive inflammation, which could be detrimental long-term. Cells from virally suppressed participants older than 5 years can maintain lower viral concentrations while limiting cell death, reflecting a more sustainable short-term immune response. In virally suppressed children younger than 5 years, immune response patterns strongly resemble the age-matched healthy control group, suggesting early viral suppression may preserve antiviral immune responses. Our model predicts unique patterns of cell death for each participant group, with CD8 T cell death being dominant in virally active groups and CD4 T cell and macrophage death being dominant in healthy and virally suppressed groups. Finally, exhausted CD8 T cells are predicted to contribute significantly to CD8 T cell killing, proliferation, and activation in the virally active group, indicating partially functional CD8 T cells can still contribute to short-term viral control. Our analysis functionally integrates participant-specific immunophenotypic data to allow quantification of the extent, mechanisms, and impact of immune dysfunction in perinatal HIV and could inform pediatric HIV remission and cure strategies. Author SummaryCytotoxic CD8+ T cells are vital for our ability to kill infected cells. However, chronic stimulation of CD8+ T cells can result in T cell exhaustion, leading to cellular dysfunction and reduced ability to fight infections. Here we ask: What impact does CD8+ T cell exhaustion have on the ability to control HIV replication over the short term? We answer this using a computational model, anchored in experimental data from children with perinatal HIV. We use participant-specific data on dozens of immune markers that characterize the state of their immune system. We carefully map these markers to known immune cell functions and use our model to predict how immune cells with these participant-specific markers would respond to HIV infection. Our results suggest that earlier viral suppression can lead to better immune function in children with perinatal HIV. Our findings also suggest that exhausted CD8+ T cells could still contribute to fighting HIV infection, but only if there are enough of them to compensate for their reduced functionality. Our work uses computational models to put valuable participant-specific data into context, allowing us to predict short-term infection outcomes and better understand immune function in children with perinatal HIV.

systems biology↗