NAR Molecular Medicine

Objective White smoke inhalation injury (WSI) causes severe acute lung damage with no specific therapy currently available. Sphingolipid metabolism is implicated in pulmonary inflammation, but its transcriptional regulatory landscape in WSI remains unexplored. This study aimed to identify key sphingolipid metabolism related genes and evaluate their regulatory roles and therapeutic potential in WSI. Methods We established a rat model of WSI and performed integrated bulk RNA sequencing, weighted gene coexpression network analysis (WGCNA), and single-cell RNA sequencing (scRNAseq) to screen for differentially expressed sphingolipid metabolism-related genes (DESRGs). Protein-protein interaction (PPI) network with four centrality algorithms was used to prioritize hub genes. In silico gene knockout and molecular docking were conducted to assess regulatory functions and identify potential drug candidates. Results We identified 22 DESRGs that were predominantly enriched in DNA replication and cell cycle pathways rather than canonical sphingolipid metabolic processes. PPI consensus prioritized three hub genes--Top2a, Ttk, and Ccna2--with Top2a exhibiting the highest expression in epithelial cells and significant downregulation after smoke exposure. ScRNAseq revealed immune cell infiltration and epithelial differentiation trajectories. Virtual knockout showed that Top2a depletion affected the largest transcriptomic fraction (~0.4%) and was enriched in lysosome biogenesis, innate immunity, phagocytosis, and lipid catabolism. Molecular docking identified thalidomide as a high affinity ligand for Top2a (Vina score: -8.5 kcal/mol). Conclusion Our multiomics integrative framework identifies Top2a as a central regulatory hub linking sphingolipid associated inflammation to epithelial responses in WSI, and nominates thalidomide as a potential drug repurposing candidate. These findings provide prioritized targets for future translational investigation.

Chemoradiotherapy (CRT) is the standard-of-care therapy for many solid malignancies, yet predictive biomarkers of treatment response remain limited. We identified a germline single nucleotide polymorphism (SNP) in an intrinsically disordered region of the lysine demethylase KDM3C/JMJD1C (p.S464T) that is associated with CRT outcomes in locally advanced rectal cancers (LARC) and head and neck squamous cell carcinoma (LA-HNSCC). In silico modeling with AlphaFold predicted S464T substitution influenced interaction between phosphorylated KDM3C and RNF8 FHA domain. In cellular models, conversion of S464 to T464 increased sensitivity to DNA-damaging agents. S464T substitution impaired damage-induced MDC1-RAP80 signaling and downstream RAP80-BRCA1 colocalization. SNP carrying cells impaired DNA repair causing genotoxic stress that is associated with increased cGAS-cGAMP innate immune signaling and increased apoptosis. Population analyses with the SNP highlighted an increase incidence of UV-induced skin and other cancers, linking inherited variation in the chromatin regulatory gene KDM3C to genome instability, cancer risk, and therapeutic vulnerability.

Metabolic dysfunction-associated steatotic liver disease (MASLD) is a major cause of chronic liver disease, with weight loss as the pivotal therapeutic strategy. However, the metabolic and molecular adaptations underlying rapid weight loss remain incompletely defined. In this pilot study, women with obesity and MASLD but without diabetes consumed a very low-calorie diet (VLCD) for 8 weeks. Clinical parameters, hepatic steatosis measured by controlled attenuation parameter (CAP), circulating metabolites, and microRNAs (miRs) were assessed before and after the dietary intervention. Integrated correlation and hierarchical clustering analyses were performed to identify molecular networks associated with clinical improvement. VLCD was well tolerated, resulting in significant weight loss (~11%) with ~80% adherence. Significant improvements in metabolic parameters were observed, including fat mass, waist circumference, blood pressure, insulinemia, HOMA-IR, HbA1c, and triglycerides, with unchanged liver enzymes. Hepatic steatosis decreased markedly, as indicated by a reduction in CAP, while stiffness remained unchanged. Metabolomic profiling revealed elevated ketone bodies and broad reductions in amino acid levels, consistent with enhanced fatty acid oxidation and a catabolic metabolic state. Correlation analysis identified distinct metabolite signatures associated with hepatic steatosis, with changes in CAP positively associated with changes in amino acids and inversely associated with changes in ketone bodies and tricarboxylic acid cycle intermediates. Circulating miRs underwent selective rather than global remodeling, with only a limited subset showing strong associations with clinical parameters, including CAP and HOMA-IR. Specifically, VLCD altered the circulating levels of miR-148a-3p, miR-140-3p, miR-10b-5p, and miR-345-5p. Integration of metabolomic and miR datasets identified coordinated metabolite-miR modules involving glucose metabolism, branched-chain amino acid catabolism, mitochondrial metabolism, purine metabolism, microbial metabolites, and cellular redox pathways. These findings demonstrate that improvement in hepatic steatosis during VLCD-induced weight loss is accompanied by coordinated remodeling of circulating metabolite-miR networks. Integrated multi-omics analysis identifies candidate molecular signatures associated with metabolic adaptation and highlights circulating miR-metabolite modules as potential biomarkers of therapeutic response in MASLD.

Seasonal influenza A viruses cause significant global morbidity each year. Although vaccination remains the primary preventive strategy, effectiveness is often reduced by antigenic drift. This challenge is particularly pronounced for influenza A(H3N2), which has required eight vaccine updates over the past decade. Here, we present a computational framework to engineer broadly reactive influenza A(H3N2) vaccines, using protein language models to generate novel hemagglutinin (HA) sequences and a machine learning model to predict antigenic distance from circulating strains. In a proof-of-concept study, seven HA candidates designed using sequence data from 2013-2018 were evaluated in mice against contemporary and subsequently circulating viruses. Two candidates elicited protective levels of reactive antibodies, robust H3-specific antibody-secreting cell responses, and cross-neutralization against contemporary clades and drifted 2019-2020 strains. These findings demonstrate that an integrated generation-selection strategy can enhance vaccine coverage across current and future A(H3N2) seasons and may be applicable to other influenza subtypes.

Haploinsufficiency in SYNGAP1 causes a severe neurodevelopmental syndrome. SYNGAP1 protein is mainly detected in neuronal synapses. However, SYNGAP1 RNA is more widely expressed and strongly regulated via alternative splicing: alternative 3' splice site (A3SS) inclusion leads to non-productive transcripts that are degraded through nonsense-mediated decay. Recently, splice-switching oligonucleotides (SSOs) that redirect SYNGAP1 splicing to increase SYNGAP1 protein levels were developed. However, we hypothesized that during neuronal maturation, non-productive splicing may decrease to enhance functional transcripts in mature neurons. This would reduce the abundance of the SSO target transcript, limiting the potential for SSO treatment to increase neuronal SYNGAP1 expression. Using neural differentiation of human induced pluripotent stem cells, we show that the A3SS transcript is abundant in neural progenitors, astrocytes, microglia and immature neurons, with minimal presence in mature neurons. These data imply that SSOs targeting A3SS might lack therapeutic efficacy to rescue the neuronal phenotypes associated with SYNGAP1 haploinsufficiency.

Infectious bronchitis virus (IBV) is a member of the Gammacoronavirus genus responsible for respiratory illness and weakened eggshells in infected chickens, adversely impacting the poultry industry. Escaping innate immune detection during infection is crucial for coronavirus proliferation in the host. The production of double-stranded RNA during coronavirus replication triggers innate immune sensors to create an antiviral state within infected cells. To counter this response, coronaviruses employ nonstructural protein 15 (nsp15) endoribonuclease to degrade double-stranded RNA. Here, we use cryo-electron microscopy and biochemistry to characterize IBV nsp15 interactions with RNA. While the overall structure and active site of IBV nsp15 strongly resemble previous studies of nsp15 from other coronaviral genera, we note that double-stranded RNA contacts several non-conserved residues peripheral to the enzyme active site. Our data show that these residue positions can have strong impacts on RNA cleavage suggesting unique solutions for RNA engagement across coronavirus species. We also demonstrate a preference for IBV nsp15 to cleave double-stranded RNA over single-stranded RNA and observe nsp15 hexamers with two double-stranded RNAs bound simultaneously. This study reinforces the need to study diverse coronavirus species to identify distinct viral enzyme characteristics.

Metabolic dysfunction-associated steatotic liver disease (MASLD), the leading cause of chronic liver pathologies worldwide, represents a growing clinical burden. Its diagnosis remains reliant on liver biopsy that limits early detection and the ability to capture molecular changes across disease progression. A systematic understanding of stage-dependent gene expression changes is essential to identify biomarkers and effectively characterize disease mechanisms. Therefore recent studies provided databases for searching genes as well as prediction of multi-gene signatures for disease progression. However, there is still a need for interactive and comprehensive meta-analysis of datasets of MASLD patients with available histological metadata. Herein, we performed a meta-analysis of RNA-seq datasets using NAFLD Activity Score (NAS; n = 897) and fibrosis stage (n = 856) upon conducting pairwise comparisons across histological stages and identified differentially expressed genes associated with disease progression. Most importantly, we provide our findings via a dedicated web server, the MASLD-META NETWORK (https://masld.scilicium.com), enabling users to interactively explore meta-analysis results across diverse network modalities. In addition, we characterized gene expression dynamics across increasing disease stages to identify consistent progression-associated pathways using Louvain clustering. Network-based parameters such as centrality in combination with meta-analysis scores further highlighted central genes and pathways implicated in disease mechanisms. Accordingly, MASLD-META NETWORK enabled an integrative reassessment of recently published gene signatures, identifying COL1A1, COL3A1, THBS2, FBLN5, and PDGFA as the most central genes, and SULF2, MMP14, IL32, GPNMB, and COL3A1 as candidate markers of earlier transcriptional alterations. Network analysis of MASLD associated biological modules further identified LAMA2 and LAMA3 as previously unrecognized central candidate targets.

The lack of effective anti-JEV therapy possesses significant challenge to control JEV. {beta}-catenin, a key mediator of Wnt signaling pathway regulates different viral replication and host immune responses. However, its role in JEV infection remains to be elucidated. Thus, the current study focused on evaluating iCRT-14, a specific {beta}-catenin inhibitor, against JEV. Treatment with iCRT-14 following JEV infection resulted efficient reduction in viral progeny release, viral RNA and protein levels in Huh7 and HEK293T cells. Further, active and total {beta}-catenin, Cyclin D-1 and GSK3-{beta}, the other key pathway players were also modulated in infected and inhibitor treated cells. Moreover, iCRT-14 showed an IC of 4.56 in Huh7 cell and maximal inhibition at the early stages of the JEV life cycle. Interestingly, the overexpression of {beta}-catenin in both the cells and siRNA-mediated {beta}-catenin knockdown (in Huh7 cells) significantly abrogated JEV replication, as evidenced by decreased viral titers, viral protein expression, and viral as well as total RNA levels. Moreover, the reduction in extracellular (84%) and intracellular (60%) viral titers following iCRT-14 treatment highlights its role in impairing JEV infection. Further, in silico molecular docking and co-immunoprecipitation studies demonstrated interactions between {beta}-catenin and the JEV NS5 and E proteins. Collectively, these findings suggest that optimum level of {beta}-catenin is required for efficient JEV infection, highlighting its potential as a target for designing host-directed control strategies to regulate viral infection.

Viral infections have long been proposed as environmental contributors to neurodegenerative diseases, including Parkinson's disease (PD), yet the molecular mechanisms linking infection and neurodegeneration are not well defined. Neuroinflammation and disruption of central nervous system (CNS) homeostasis have emerged as potential mediators. In this study, we used severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, as a model pathogen to investigate convergent molecular pathways between viral infection and PD. Single-nucleus RNA sequencing (snRNA-seq) was performed on post-mortem striatal tissue from 14 individuals stratified into four groups: COVID-19 only (COVID-19), PD only (PD), comorbid PD with COVID-19 (PD/COVID-19), and controls (Control). The PD/COVID-19 group exhibited an expanded astrocytic population and a pronounced interferon-associated molecular signature characterized by increased expression of canonical interferon-stimulated genes, including IFI44L (average log2FC= 3.9; adjusted p=2.3 x 10-373), IFI44 (average log2FC=2.9; adjusted p=8.0 x 10-266), ISG15 (average log2FC=3.1; adjusted p=1.2 x 10-197), and RSAD2 (average log2FC= 3.5; adjusted p=8.6 x 10-111). Pathway analyses demonstrated activation of innate immune and antiviral signaling pathways, particularly within microglia and astrocytes, including interferon signaling, pattern-recognition receptor pathways, and complement-associated responses. In parallel, genes involved in lipid metabolism, cholesterol homeostasis, synaptic maintenance, and neuronal signaling were reduced across disease groups. Proteomic analyses independently confirmed enrichment of antiviral and interferon-associated pathways and identified convergent suppression of sterol, cholesterol, and lipid metabolic processes. Our findings identify a convergent molecular signature linking PD and COVID-19, pronounced in comorbid individuals and characterized by interferon-driven innate immune activation, glial inflammatory responses, and dysregulation of lipid metabolic homeostasis. Collectively, the data support a model in which severe viral infection amplifies biological pathways already implicated in PD pathogenesis.

Despite the well-known health risks of neutron exposures, key gaps remain in understanding neutron-induced molecular responses and identifying reliable biodosimetric markers that distinguish neutrons from photon exposure. We provide the first genome-wide analysis of the human blood transcriptional response to an accelerator-derived fission-like spectrum of neutrons versus photons, evaluating transcriptomic relative biological effectiveness (RBE) and radiation quality-discriminating gene signatures. Whole blood from healthy donors was irradiated ex vivo with X-rays (140 kV, 0-4 Gy, n = 3) or neutrons (0.1-8 MeV, 0-1 Gy, n = 2), incubated for 6 h or 24 h, and processed for RNA sequencing from peripheral blood mononuclear cells (PBMCs). Neutrons were markedly more potent than X-rays at inducing differentially expressed genes (DEGs) at equal doses, showing a peak response 6 h post-irradiation followed by a decline. In contrast, X-rays caused a continuous increase in DEGs up to 24 h (neutrons vs. X-rays at 1 Gy: 1,449 vs. 121 DEGs at 6 h; 996 vs. 621 DEGs at 24 h). A universal p53-centered 34-gene signature, including FDXR, EDA2R, GADD45A, and ZMAT3, showed highly monotonic dose responses (Spearman correlation coefficient {approx} 1) across donors, radiation qualities, and timepoints. Additionally, difference-in-differences analysis identified radiation quality-discriminating genes only at 6 h, with transcriptional convergence observed by 24 h, suggesting a very narrow time window for biodosimetric differentiation. We identified a neutron-specific gene signature driven by cGAS-STING-NF-{kappa}B signaling (RELB, NFKB1, C3, MALAT1) and suppression of B-cell and myeloid identity genes (IGHD, TCL1A, CLEC7A, TLR2), defining a biologically coherent neutron quality index with distinct immunomodulatory effects. For the first time, we assessed neutron RBEs at the gene, pathway, and global transcriptomic levels in a human blood model, reporting a global transcriptomic neutron RBE of 1.30 (95% CI: 1.14-1.49) at 6 h and 1.21 (95% CI: 1.14-1.28) at 24 h, providing a valuable basis for biodosimetry in mixed-field exposure scenarios. Our findings advance the mechanistic understanding of neutron radiation responses and support the development of biodosimetric approaches for mixed-field exposure scenarios.

Background: India has a rising incidence of chronic non-communicable diseases, making it a major healthcare burden today. Growing evidence suggests that chronic low-grade inflammation links ageing with cardiometabolic disorders, captured by the emerging concept of inflammaging. However, most evidence on biological ageing comes from Western populations, with no similar models developed for the Indian population. Given the country's distinctive genetic makeup, unique exposome, and heterogeneous NCD presentation, Western models may not capture inflammaging and its effects in the Indian population. Methods: We analysed baseline data from 4,240 adults in the Phenome India CSIR Health Cohort Knowledgebase (PI CheCK), a nationwide multi-centre cohort. Participants were stratified into eight cardiometabolic phenotype groups by BMI (Asian cut off), blood pressure and HbA1c status. We trained a Super Learner ensemble to predict chronological age in the lean normotensive-normoglycaemic reference group (n=615) using 44 plasma cytokines, sex, haemoglobin, and bioimpedance-derived visceral fat area, per cent body fat, and total body water. Performance was assessed by repeated five-fold cross-validation and in a held-out healthy test set. Calibrated biological age acceleration was then estimated in the remaining 3,625 participants. Results: Median age was 51.0 years (IQR 41.0 to 62.0) and 49.4% were female. The Super Learner outperformed elastic net and XGBoost comparators. Permutation importance identified visceral fat area, per cent body fat, CTACK, SDF1a, haemoglobin and sex as leading contributors, with body composition measures accounting for the largest share, indicating an immune-metabolic rather than cytokine-only signal. Biological age acceleration was concentrated in overweight/obese phenotypes. Lean phenotypes showed acceleration close to the reference (0.32 0.50 years). Conclusions: Cytokine and body composition measures capture a quantifiable immunometabolic ageing signal in a South Asian cohort, with acceleration driven predominantly by adiposity. External validation and longitudinal follow up are required.

Botulinum neurotoxins (BoNTs) comprise a highly diverse group of seven serotypes (from A-G) and over 40 subtypes worldwide. Previous primer- and probe-based nucleic acid amplification tests (NAATs) for detection of BoNT encoding genes are challenged by high levels of nucleotide polymorphism both across and within subtypes. In this study, multiple BoNT gene sequences were aligned to identify highly conserved regions for the design of new primers that enable the detection of all seven serotypes under the same conditions. Specific primer sets were designed and validated using in silico, conventional and real-time PCR with constructed plasmids carrying the target fragments and spiked food matrices. The established procedure achieved highly specific and sensitive detection of BoNT serotypes A-G with sensitivity of 10 copies/reaction and a total turnaround time of approximately 1.5 hours. The procedure also eliminated the carryover PCR product by using uracil-N-glycosylase in combination with dUTP in the assay reaction mix. This study provides an alternative NAAT with higher coverage and compliments the traditional mouse bioassays in enhancing global botulism surveillance capabilities.

Autosomal dominant retinitis pigmentosa (adRP) caused by RHO mutations is a leading form of inherited retinal degeneration. Extensive allelic heterogeneity of RHO pathogenic variants limits the translational applicability of mutation-specific gene therapies. To address this, we developed SNARE (SNP-guided Silencing of Aberrant RHO Expression), a mutation-independent, allele-specific antisense oligonucleotide (ASO) strategy. SNARE selectively suppresses mutant RHO transcripts by targeting the common, benign c.-26A/G single-nucleotide polymorphism (SNP) as an allelic discriminator. Candidate gapmer ASOs were screened in engineered reporter lines and validated in patient-derived retinal organoids, identifying RHOligo-A as the lead c.-26A-targeting candidate. In vitro, RHOligo-A achieved robust, preferential knockdown of the target allele, improving RHO localization in retinal organoids, and demonstrated a favorable safety profile with minimal transcriptomic off-target effects and no detectable immunostimulatory activity. Subsequent validation in a novel, humanized RHOP347L/WT mouse model, achieved sustained c.-26A-linked allele-selective suppression, retinal structure preservation, and significantly restored visual function, upon a single intravitreal administration. These findings establish RHOligo-A and SNARE as a scalable, mutation-independent therapeutic platform with strong translational potential and substantial clinical reach for RHO-associated adRP.

Hyperglycaemia disrupts mitochondrial homeostasis, leading to oxidative stress, ATP depletion, lysosomal dysfunction, impaired stress signalling, and proteostasis collapse. Although static magnetic fields (SMFs) have shown therapeutic potential in diabetic models, the optimal field strength for restoring subcellular organelle integrity post high glucose associated dysfunction remains unknown. Here, using Caenorhabditis elegans exposed to 40 mM glucose, we systematically evaluated SMFs ranging from 20 to 100 mT. Hyperglycaemia induced mitochondrial fragmentation, elevated reactive oxygen species, lysosomal abnormalities, reduced ATP levels, caused developmental delay, suppression of cytoprotective stress reporters, and increased polyglutamine aggregation. Among all field strengths tested, 70 mT produced the most robust recovery, restoring mitochondrial network architecture, reducing oxidative stress, normalizing lysosomal morphology, recovering ATP homeostasis, improving developmental progression, enhancing stress-responsive signalling, reducing proteotoxic aggregates, and increasing mitochondrial resilience to secondary hypoxic stress. These findings identify an optimal therapeutic SMF window and provide the first whole-organism demonstration that appropriately tuned static magnetic fields restore mitochondrial homeostasis and reverse multiple downstream consequences of hyperglycaemic stress.

Mutations in the E3 Ubiquitin (Ub) ligase RNF216 cause Gordon Holmes syndrome (GHS), a neurodegenerative disorder accompanied by neuroendocrine disruption. We developed an orthogonal ubiquitin transfer (OUT) platform to capture RNF216 substrates in neuronal cells and identified OTUD4, a deubiquitinating enzyme (DUB) mutated in GHS, and FMRP, a neuronal-enriched translational repressor. RNF216 predominantly synthesizes K6-linked Ub chains on OTUD4 to induce its degradation, forming donut-shaped structures in neurons. In return, OTUD4 removes the ubiquitination of RNF216 and FMRP. Analysis of RNF216 substrates revealed biological functions regulating protein synthesis, a shared function of the OTUD4-RNF216 substrate interaction network. Indeed, RNF216 expression increased protein synthesis rates in different cell types while Rnf216 deletion decreased dendritic development in neurons. Overall, our findings show that RNF216 and OTUD4 balance rates of protein synthesis and degradation and suggest GHS-related mutations in RNF216 or OTUD4 may offset this balance, triggering neurodegeneration.

We present the solution structures of HIV-1 proteins NC(p7)1-55 corresponding to the full-length NC(p7) and mature p6. The studies were carried in water and, to mimic the membrane, in micellar DPC (Dodecylphosphocholine) conditions. Our results unravel for the first time the structure adopted by the N-terminal amino acids of the free NC(p7)1-55, with the formation of a small helix spanning residues F6 to R10. Our NMR and Fluorescence Anisotropy data disclose an interaction between NC(p7)1-55 and p6 both in water and DPC, with respective Kd of 2.5mM and 370 mM at 23{degrees}C. The interaction is thus strengthened in lipidic conditions. Protein p6 stabilizes the N-terminus of NC(p7)1-55 while increasing at the same time the dynamic of the first zinc finger. Although the entire p6 sequence is involved in the interaction, we show that its C-terminal region is particularly sensitive to the presence of NC(p7)1-55, with a propensity of forming a a helix ranging from amino acids S111 to F116. This study brings experimental evidence of a direct protein-protein interaction between p6 and the N-terminal region of NC(p7)1-55. We further show that such interaction is readily accommodated within the NC(p15) framework and hypothesize that it may facilitate the selective assembly of assembly of the viral genomic RNA (gRNA) in the cell.

We report the generation and characterization of a human induced pluripotent stem cell (iPSC) line derived from dermal fibroblasts of a patient with Skogholt disease, a rare maternally inherited neurodegenerative syndrome associated with choroid plexus dysfunction and impaired cerebrospinal fluid (CSF) homeostasis. Patient fibroblasts were reprogrammed using the non-integrating Repro-OSKGM kit. The resulting iPSC line exhibited typical pluripotent morphology, expressed canonical pluripotency markers, maintained a normal karyotype, retained the disease-associated genetic variant, was mycoplasma-free, and demonstrated trilineage differentiation potential. We also made choroid plexus (ChP) like organoids from the generated iPSCs. This patient-specific iPSC line provides a valuable resource for generating choroid plexus organoids and neurons to investigate disease mechanisms and develop therapeutic strategies.

Amyotrophic lateral sclerosis (ALS) is a motor neuron disease, leading to progressive muscle weakness and motor impairment. Growing evidence indicates that cerebellar Purkinje cells, which play a central role in motor coordination, are also affected in ALS. However, it is unclear whether the molecular events that initiate neurodegeneration in these ALS-relevant motor-controlling neurons are shared or distinct. Here, we used a MATR3 S85C knock-in (KI) mouse model of early-stage ALS with stage-specific motor phenotypes and selective vulnerability of motor neurons and Purkinje cells to decipher the molecular events underlying neurodegeneration in these two neuronal populations. We found that a profound reduction in detectable MATR3 S85C immunoreactivity (hereafter referred to as MATR3 loss) in both motor neurons and Purkinje cells precedes the onset of motor dysfunction and neuropathology, implicating MATR3 loss as the earliest detectable molecular event. Our bulk cerebellar RNA profiling and motor neuron-specific RNA profiling data at the onset of MATR3 loss revealed distinct molecular signatures. In the cerebellum, Ngfr expression emerged in Purkinje cells before the onset of neuronal loss and remained elevated throughout the disease course. This increase was accompanied by activation of the JNK-mediated cell death pathway. In the motor neurons, elevated Fgf21 and integrated stress response (ISR) gene expression were the first to be observed and persisted throughout disease progression, consistent with previous findings in SOD1 mouse models. Our findings provide mechanistic insights into the initiation of neurodegeneration in ALS-relevant motor-controlling neurons and implicate potential neuron type-specific targets for future therapeutics.

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterized by progressive dysfunction and loss of upper and lower motor neurons. Although motor neuron degeneration ultimately drives paralysis, neuronal dysfunction may precede cell death by a prolonged interval, suggesting that vulnerable neurons engage stress-adaptive programs that permit survival despite impaired function. Cellular senescence represents one such persistent stress response and has increasingly been implicated in neurodegenerative disease, including disorders associated with TDP-43 pathology. Here, we investigated whether senescence-associated molecular states are present in vulnerable motor neurons in ALS and whether they differ according to anatomical region and phosphorylated TDP-43 (pTDP-43) pathology. Postmortem primary motor cortex, cervical spinal cord, and lumbar spinal cord were obtained from the Department of Veterans Affairs Biorepository Brain Bank from individuals with ALS classified as pTDP-43-positive or pTDP-43-negative, together with non-ALS controls. Targeted bulk transcriptomic profiling was combined with GeoMx Digital Spatial Profiling of individual motor neurons to characterize disease-, region-, and pathology-associated molecular phenotypes while preserving anatomical context. Across ALS cases, we identified alterations in pathways related to cell-cycle regulation, RNA processing, mitochondrial function, proteostasis, inflammation, and synaptic signaling. These signatures varied by anatomical region and pTDP-43 status, indicating substantial heterogeneity in the molecular response to ALS pathology. Despite these differences, both ALS groups exhibited convergent proteomic and transcriptomic features associated with cellular senescence. These findings identify senescence-associated molecular states within vulnerable neuronal populations in ALS and support a model in which persistent stress adaptation may permit neuronal survival while contributing to progressive cellular dysfunction. This spatially resolved analysis links neuronal phenotype to anatomical and pathological context and supports further evaluation of senescence-associated pathways as therapeutic vulnerabilities in ALS.

People with HIV (PWH) on long-term antiretroviral therapy (ART) continue to experience elevated rates of morbidities and mortality driven by persistent immune activation despite viral suppression. Known contributors include low-level HIV provirus activity, microbial translocation in part from epithelial barrier dysfunction, microbiome dysfunction, and co-infections. However, how these interact and where they predominate across tissue compartments remains incompletely defined. Here, we applied spatial transcriptomics to characterize compartment-specific transcriptional programs in ileum (epithelium, Peyer's patches, lamina propria) and inguinal lymph nodes (B Cell follicles and T cell zone) from ten PWH on long-term ART, stratified by CD4/CD8 ratio into low-ratio and high-ratio groups, with low-ratio as a proxy for immune activation and increased risk for non-AIDS related serious event. Comparison of global expression found significant differences between groups in four of five compartments. Differential expression analysis identified 483 differentially expressed genes across four of five compartments, with the greatest burden in the T-cell zone and none in the lamina propria. Gene set enrichment analysis identified 116 enriched pathways predominantly in the low-ratio group, spanning immune activation, infection-associated, and metabolic programs, with Peyer's patches showing the broadest transcriptional divergence of any compartment. Cross-compartment signals included higher expression of ORMDL3 and ARL17B in the low-ratio group implicating mitochondrial stress and inflammasome activation, lower expression of CCL3L3 and FCMR in the low-ratio group suggesting impaired immune execution, and divergent ribosomal protein programs between B-cell follicles and the T-cell zone. Cell deconvolution identified compartment-specific differences in estimated immune cell proportions, and T-cell zone gene expression showed significant associations with HIV reservoir measures and plasma markers of microbial translocation and immune activation. Together these findings support spatially heterogeneous immune activation as a feature of persistent immune dysregulation in treated HIV infection and provide compartment-resolved, hypothesis-generating evidence for the tissue-specific mechanisms driving inflammation in this population.