Biology subjects

Thomas, R.

Publications and source records attributed to Thomas, R..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Epigenetically constrained astrocyte states underlie prefrontal cortex vulnerability in Down syndrome associated Alzheimer disease

Down syndrome (DS), caused by trisomy 21, confers a near-universal risk for Alzheimers disease (AD), yet individuals exhibit marked variability in cognitive decline, suggesting the presence of cellular mechanisms that modulate vulnerability and resilience. However, these mechanisms remain poorly defined in the human brain. Here, we integrate matched single-nucleus RNA-seq and ATAC-seq profiles from the prefrontal cortex (PFC) and amygdala (AMY) of age-matched individuals with DS with and without AD (DSAD), enabling direct comparison within a shared genetic background. We identify basal astrocytes in the PFC as a selectively vulnerable cell state in DSAD, characterized by both reduced abundance and coordinated transcriptional and regulatory reprogramming. This state exhibits a shift away from homeostatic support functions, with decreased cytokine signaling and lipid-handling programs, alongside increased steroid- and nuclear receptor-associated activity. Concomitantly, chromatin accessibility profiling reveals reduced engagement of immune- and stress-responsive transcription factor programs, including AP-1, STAT, and BACH families, with linked regulatory perturbations at loci such as ABCA1, DAB2IP, and IL1RAP. Together, these findings define a previously unrecognized astrocyte state marked by epigenetic constraint and diminished responsiveness to stress and inflammatory signals, distinguishing it from classical reactive astrocyte phenotypes. Our results nominate PFC basal astrocytes as a key locus of vulnerability in DSAD and suggest that failure to mount appropriate astrocyte responses, rather than overt activation alone, may contribute to neurodegenerative progression.

bioinformatics↗

bioRxiv2026

A targetable dependency on nonsense-mediated decay for proteostasis and immune control in small cell lung cancer

Small cell lung cancer (SCLC) is among the deadliest cancers with excessive somatic alterations, expectedly resulting in immunogenic epitopes. However, patient benefit from immunotherapy is limited. We found abundant frameshift mutations in SCLC, regarded as highly immunogenic, counterbalanced by a hyperactive nonsense-mediated decay (NMD) pathway, responsible for frameshift-mRNA degradation. NMD activity correlated with tumor mutational burden (TMB) across cancers, suggesting that SCLC depends on NMD for cellular homeostasis and immune evasion. NMD inhibition impaired SCLC proliferation and induced ER stress-dependent apoptosis in a TMB-dependent manner, thereby enabling pharmacological inhibition in vivo which effectively controlled tumor growth. By integrating genome and transcriptome sequencing with MHC-I immunopeptidomics and functional in vitro and in vivo assays, we identified that NMD inhibition boosted neoantigen expression and presentation by tumor cells and increased T cell recognition, thus enhancing overall tumor immunogenicity and further improving immunotherapy efficacy in vivo. Our work shows that SCLC - as a TMBhigh cancer - relies on NMD for survival and immune escape, uncovering a novel TMB-dependent tractable vulnerability for this devastating disease.

cancer biology↗

bioRxiv2025

Role of the SAF-A/HNRNPU ATPase and RGG domains in X chromosome inactivation, nuclear dynamics, transcription, splicing, and cell proliferation

The SAF-A/HNRNPU gene encodes an abundant nuclear protein conserved throughout vertebrates, and is mutated in individuals with HNRNPU syndrome, a neurological human disease. SAF-A is important for maintaining lncRNA localization, splicing, and gene expression state. The mechanistic role of SAF-A in each of these processes is coordinated by one or more of its functional domains, which include an N-terminal SAP domain, a central ATPase domain, and a series of C-terminal RGG repeats embedded in a low-complexity region. The SAP domain and RGG repeats define two nucleic acid interaction domains, with both capable of binding DNA or RNA. Here we use an allelic reconstitution strategy to investigate the role of the SAF-A ATPase domain and RGG repeats. We show that both the ATPase and RGG repeats control SAF-A nuclear dynamics, and present genetic evidence that SAF-A interacts with nascent transcripts through the RGG repeats. The SAF-A ATPase domain and RGG repeats were also required for maintaining XIST RNA and facultative heterochromatin marks on the inactive X chromosome, with distinct effects of mutations that block ATP binding and ATP hydrolysis. Analysis of transcriptome datasets revealed that the SAF-A ATPase domain and RGG repeats are both required for proper mRNA splicing, but not for gene expression. Importantly, we found that like the SAP domain, the SAF-A ATPase domain and RGG repeats are required for cell proliferation. Collectively, our findings highlight the importance of the SAF-A SAP, ATPase and RGG domains in essential functions of nuclear biology. These analyses will therefore inform our understanding of the disease state in HNRNPU syndrome.

cell biology↗

bioRxiv2025

Crossmodal attention develops in the first year of life: Cortical signatures of tactile to visual exogenous spatial cuing at 8 but not 5 months of age

Adults are able to orient their attention between different (often fleeting) sensory cues that present to different senses ("crossmodal attention"), but we cannot assume that this is the case in early life. Here we report the findings of a study in which we probed the presence of tactile to visual crossmodal links in spatial attention using event related potentials (ERP) gathered from the scalp electroencephalograms (EEG) of 5-(n = 19) and 8-month-old (n = 19) infants. Whilst recording EEG, we presented 5- and 8month-old participants with vibrotactile stimuli on one of their hands, followed by visual stimuli on the same (Congruent) or the opposite (Incongruent) hand, or no touch at all (No probe). During the presentation of these stimuli the infants eyes were oriented centrally. We subtracted No probe trials from Congruent and Incongruent trials to yield visual evoked potentials (VEPs) free from the influence of prior somatosensory processing. Comparably to prior findings in adults, 8-month-olds first negative component of the VEP was enhanced in the hemisphere ipsilateral to the probe when the visual probe was spatially congruent with the tactile cue. No crossmodal effect was observed in the 5-month-olds, indicating developments in the crossmodal coordination of attention in the first year of life.

neuroscience↗

bioRxiv2025

Single nuclear RNA sequencing shows altered microglial and astrocytic functions in post-mortem Parkinson's disease tissue

BackgroundParkinsons disease (PD) is a neurodegenerative disease marked by a progressive loss of dopaminergic neurons in the substantia nigra pars compacta (SNpc) and formation of misfolded protein aggregates. A growing body of research has implicated glial cell dysfunction in PD etiology, including the concentration of activated glial cells around protein aggregates in post-mortem tissue. Disruptions in the balance of pro- and anti-inflammatory immune response functions of the microglia and astrocytes is believed to contribute towards neurons being lost as the disease progresses. However, the molecular mechanisms remain unclear. To shed light on the role of inflammation in PD, this study analyses two public single nuclear RNA sequencing datasets of the SNpc from patient and control postmortem brain to identify altered molecular pathways in PD-associated microglia and astrocytes. ResultsThe results show that both cell types have a significant upregulation in heat shock binding and misfolded protein response pathways, likely in response to the accumulation of protein aggregates. Microglia annotated with the MKI67 marker gene show a decreased expression in PD patient derived tissue. Markers associated with activated/reactive states in astrocytes and microglia are upregulated in PD samples. Notably, expression of genes associated with resting state microglia and non-inflammatory reactive state microglia are downregulated in PD microglia, including P2RY12, CSF1R, CSF2RA, CSF3R, and TGFBR1. Concurrently, genes associated with activated microglial states such as HSP90AB1 and GPNMB are upregulated. Among the top downregulated functions, genes associated with ion channel functions are downregulated in both astrocytes and microglia. ConclusionsTaken together, the findings imply that astrocytes and microglia respond to protein misfolding pathology in PD by upregulating chaperone protein folding functions. Additionally, the profile of upregulated genes implies that pathways responding to oxidative stress are also activated. The downregulation of inflammation-associated genes in PD microglia paired with the upregulation of misfolding protein response pathways, suggests a switch from immune receptor functions to protein aggregate clearance by the end of disease stages. Finally, GPNMB emerged as a potential target for therapeutic intervention, as the one primary non-HSP gene that is significantly increased in PD-associated microglia. AbbreviationsParkinsons disease (PD); neurodegenerative diseases (NDD); dopaminergic neurons (DNs); substantia nigra pars compacta (SNpc); microglia (Mg); Lewy body dementia (LBD); single nuclear RNA sequencing (snRNA-seq), single cell RNA sequencing (scRNA-seq); Gene Ontology (GO)

neuroscience↗

bioRxiv2025

APOE4-Aβ synergy drives brain network dysfunction and neuronal lysosomal-ER proteostasis dysregulation in preclinical Alzheimer's disease

Amyloid-{beta} (A{beta}) and APOE4 represent two of the strongest pathological and genetic risk factors for Alzheimers disease (AD), but how these co-pathogens interact during preclinical stages remains undefined. We addressed this question by developing a humanized knock-in model expressing physiological, endogenously regulated human A{beta} and APOE4. Aged AppNLF:APOE4 mice displayed incipient amyloidosis with subtle memory-related changes, consistent with preclinical AD. We found largely distinct, non-overlapping APOE4- and A{beta}-driven functional synaptic, sleep, and behavioral alterations. However, at the transcriptomic level, APOE4xA{beta} had a pronounced detrimental interaction in neuronal populations, whereas glial populations were primarily affected by either genotype. We found APOE4xA{beta} molecular interactions in neuronal populations, including excitatory and inhibitory cells, converged on a core lysosomal-ER proteostasis axis. We propose that APOE4xA{beta} interaction produces an early neuronal pathogenic signature, involving the lysosomal-ER proteostasis axis, preceding functional decline and driving disease progression. APOE4xA{beta}-KI models provide a physiologically relevant platform to study early pathogenesis. HighlightsO_LIEarly synergistic APOE4xA{beta} interaction emerges predominantly at the transcriptomic level in neurons, but not in glial cells. C_LIO_LIAPOE4 and A{beta} drive largely non-overlapping physiological changes in preclinical stages of disease, but converge at the level of network hyperexcitability. C_LIO_LIAPOE4xA{beta} neuronal synergy converges on a conserved lysosomal-ER proteostasis axis. C_LIO_LIHumanized APOE4xA{beta} KI mice provide a physiologically relevant model to dissect early AD pathogenesis in preclinical stages C_LI

neuroscience↗

bioRxiv2025

Taming the reference genome jungle: the refget sequence collection standard

Reference genomes are foundational to genomics but suffer from widespread ambiguity and incompatibility due to inconsistent naming, undocumented differences, and lack of formal mechanisms for comparison. To address this, we introduce the GA4GH refget Sequence Collections (seqcol) standard. Refget seqcol is a framework for unambiguous representation, retrieval, and comparison of sequence collections such as reference genomes and transcriptomes. The seqcol standard comprises four components: a structured data schema, a canonical encoding algorithm that produces content-based, globally unique identifiers, a retrieval API, and a comparison protocol. This standard enables precise identification of sequence collections, even across decentralized or private systems, and allows compatibility assessments beyond exact identity, such as order-relaxed matches or shared coordinate systems. We applied the refget seqcol standard to 60 human and 36 mouse reference genomes sourced from major providers. Using digest-based comparisons, we quantified levels of similarity across attributes including sequence names, lengths, coordinate systems, and actual sequence content. Our analysis revealed some consistent subsets of sequences or coordinate systems, as well as substantial incompatibility among references and duplicate references under different names. To support adoption of refget seqcol, we provide a Python package implementing the full standard, a web API, and a comparison interface allowing users to assess local references against a curated database. This work offers a scalable, reproducible solution to the reference genome compatibility crisis, enabling improved transparency, reuse, and integration in genomic analyses. Refget seqcol enhances interoperability across tools and datasets, making genomic research more robust and reproducible.

genomics↗

bioRxiv2025

PERM1 Gene Delivery via AAV Prevents Heart Failure in a Mouse Model of Pressure Overload

Heart failure with reduced ejection fraction (HFrEF) remains a leading cause of mortality worldwide. A hallmark of HFrEF is impaired cardiomyocyte contractility accompanied by disrupted mitochondrial bioenergetics; however, no current therapy targets both pathologies simultaneously. PERM1, a striated muscle-specific regulator of mitochondrial bioenergetics, is downregulated in HFrEF patients. We recently demonstrated that overexpression of PERM1 via adeno-associated virus 9 (AAV9-PERM1) enhances both cardiac contractility and mitochondrial biogenesis in C57BL/6 mice. In this study, we evaluated the therapeutic potential of AAV9-PERM1 in a pressure overload-induced mouse model of HFrEF. C57BL/6 mice were treated with either AAV9-PERM1 or control AAV9-GFP (1x1012 GC/mouse), followed by transverse aortic constriction (TAC) surgery. At 4 weeks post-TAC, control mice receiving AAV-GFP exhibited reduced left ventricular ejection fraction (LVEF), whereas AAV-PERM1 preserved LVEF at baseline levels. This cardioprotective effect was sustained through 8 weeks. Notably, AAV9-PERM1 completely abrogated TAC-induced cardiac hypertrophy and fibrosis. Mitochondrial analysis revealed that AAV9-PERM1 preserved mitochondrial DNA copy number and TFAM protein levels, both of which were reduced by TAC in control hearts. AAV9-PERM1 also improved mitochondrial respiration using pyruvate and octanoylcarnitine as substrates and prevented TAC-induced impairments in oxidative capacity. While PGC-1 expression remained unchanged in control TAC hearts, it was modestly yet significantly upregulated by AAV9-PERM1 in both sham and TAC groups. In addition, AAV9-PERM1 suppressed TAC-induced increases in O-GlcNAcylation, a stress-related posttranslational modification of proteins. Co-immunoprecipitation further revealed interactions of PERM1 with creatine kinase and troponin C, key proteins in ATP transduction and contractility, suggesting a functional coupling between mitochondrial energetics and contractility. In conclusion, AAV-PERM1 gene therapy effectively preserves cardiac function under pressure overload by maintaining mitochondrial biogenesis, respiration capacity and contractility. This study further suggests AAV-PERM1 as a promising therapeutic strategy for HFrEF.

physiology↗

bioRxiv2025

Full-length next-generation sequencing of 11 HLA loci of more than 1000 individuals from clinical cohorts in East and West Africa

Human Leukocyte Antigen (HLA) loci have been implicated in several diseases from different world populations, including HIV-1. It is necessary to characterize HLA allele variation at the population level prior to investigating associations linked to human diseases. In global databases, limited high-resolution HLA allele types generated by next-generation sequencing (NGS) have been described for populations from African countries. We sought to expand our HLA NGS database to include a total of 1023 participants from multiple HIV clinical studies using full-length HLA genotyping by NGS. Collectively we describe HLA genotypes of individuals from Kenya (n=375), Uganda (n=338), Nigeria (n=139), Tanzania (n=89), and Mozambique (n=82). Overall, we identified 371 unique HLA alleles across 11 loci with the most frequent at each locus being A*02:01:01, B*53:01:01, C*04:01:01, C*06:02:01, DPA1*01:03:01, DPB1*01:01:01, DQA1*01:02:01, DQB1*06:02:01, DRB1*15:03:01, DRB3*02:02:01, DRB4*01:03:01, and DRB5*01:01:01. A total of 25 novel alleles were identified, including 4 with non-synonymous changes affecting the peptide binding groove of HLA molecules. This expansion of NGS based HLA data at the African population level will improve our understanding of human genetic variation and provide insights for vaccine development and targeted personalized therapies.

genetics↗

bioRxiv2025

Metal stress uncouples early pre-rRNA processing from ISR activation and reveals flexible checkpoints in human ribosome biogenesis

Ribosome synthesis is one of the most energy-intensive processes in a growing cell, consuming more than 60% of cellular energy reserves. As such, ribosome biogenesis is highly sensitive to stress to prevent costly expenditures under adverse conditions. Moreover, successful assembly requires precise stoichiometric balance between ribosomal proteins and ribosomal RNAs. Here, we define novel regulatory mechanisms of ribosome biogenesis under stress that reveal previously unrecognized aspects of rRNA maturation. We demonstrate that early pre-rRNA processing is particularly sensitive to stress induced by environmentally relevant heavy metals. Surprisingly, our analysis shows that 5' and 3' end processing can be uncoupled in human cells, with 3' end cleavage occurring independently of 5' end processing. We further show that classical inducers of endoplasmic reticulum stress suppress ribosomal protein synthesis without inhibiting rRNA transcription, leading to an imbalance between these essential components of ribosome assembly. This imbalance may exacerbate cellular stress and compromise proteostasis. Together, our findings uncover stress-specific checkpoints in ribosome biogenesis that link environmental exposures to disrupted nucleolar function and highlight new layers of regulation in human rRNA maturation.

biochemistry↗

bioRxiv2025

AlphaGenome: advancing regulatory variant effect prediction with a unified DNA sequence model

Deep learning models that predict functional genomic measurements from DNA sequence are powerful tools for deciphering the genetic regulatory code. Existing methods trade off between input sequence length and prediction resolution, thereby limiting their modality scope and performance. We present AlphaGenome, which takes as input 1 megabase of DNA sequence and predicts thousands of functional genomic tracks up to single base pair resolution across diverse modalities - including gene expression, transcription initiation, chromatin accessibility, histone modifications, transcription factor binding, chro- matin contact maps, splice site usage, and splice junction coordinates and strength. Trained on human and mouse genomes, AlphaGenome matches or exceeds the strongest respective available external models on 24 out of 26 evaluations on variant effect prediction. AlphaGenomes ability to simultaneously score variant effects across all modalities accurately recapitulates the mechanisms of clinically-relevant variants near the TAL1 oncogene. To facilitate broader use, we provide tools for making genome track and variant effect predictions from sequence.

bioinformatics↗

bioRxiv2025

Cellular profiling identifies an early profibrotic alveolar type 2 cell signature in lung fibrosis

RationaleIdiopathic pulmonary fibrosis (IPF) is a progressive, age-associated, lung disease characterized by short telomeres in alveolar type 2 (AT2) cells, epithelial remodeling, and fibrosis. ObjectivesThis study investigated how telomere dysfunction in AT2 cells lacking Telomere Repeat Binding Factor 1 (TRF1) drives lung remodeling in SPC-creTRF1flox/flox mice and its relevance to IPF. MethodsMouse model of telomere dysfunction was used to conditionally delete TRF1 in AT2 cells. SPC-creTRF1flox/flox mouse lung epithelial cells were used to perform single cell RNA sequencing. AT2 cells from IPF lungs were analyzed by single cell RNA sequencing in an organoid model. Measurements and Main ResultsSingle cell RNA-sequencing revealed distinct pathological AT2 cells enriched in DNA damage, senescence, oxidative stress, and pro-fibrotic genes, along with fewer "normal" AT2 cells and increased club cells in SPC-creTRF1flox/flox mice. Pathological AT2 cells showed different early and late-stage gene signatures, with a prominent p53 signature at both time-points. Genetic deletion of p53 in SPC-creTRF1flox/flox AT2 cells improved survival and prevented lung fibrosis. p53 deletion or inhibition improved organoid formation, surfactant protein C expression, and reduced pro-fibrotic gene expression in AT2 cells isolated from SPC-creTRF1flox/flox mice or IPF lungs. ConclusionsThese data suggest that the DNA damage response to AT2 cell telomere dysfunction, driven by enhanced p53 activity, mediates early AT2 cell transdifferentiation and senescence, leading to epithelial cell remodeling and fibrosis and that reversing this reprogramming is a potential therapeutic approach for managing IPF.

cell biology↗

bioRxiv2025

Single cell transcriptional evolution of myeloid leukaemia of Down syndrome

Children with Down syndrome have a 150-fold increased risk of developing myeloid leukaemia (ML-DS). Unusually for a childhood leukaemia, ML-DS arises from a preleukaemic state, termed transient abnormal myelopoiesis (TAM), via a conserved sequence of mutations. Here, we examined the relationship between the genetic and transcriptional evolution of ML-DS from natural variation; a rich collection of primary patient samples and fetal tissues with a range of constitutional karyotypes. We distilled transcriptional consequences of each genetic step in ML-DS evolution, utilising single cell mRNA sequencing, complemented by phylogenetic analyses in progressive disease. We found that transcriptional changes induced by the TAM-defining GATA1 mutations are retained in, and account for most of the ML-DS transcriptome. The GATA1 transcriptome pervaded all stages of ML-DS, including progressive disease that had undergone genetic evolution. Our approach delineates the transcriptional evolution of ML-DS and provides an analytical blueprint for distilling consequences of mutations within their pathophysiological context.

cancer biology↗

bioRxiv2025

Spatial patterning of fibroblast TGFβ signaling underlies treatment resistance in rheumatoid arthritis

Treatment-refractory rheumatoid arthritis (RA) is a major unmet need, and the mechanisms driving treatment resistance are poorly understood. To identify molecular determinants of RA non-remission, we performed spatial transcriptomic profiling on pre- and post-treatment synovial tissue biopsies from treatment naive patients who received conventional DMARDs or adalimumab for 6 months. In the baseline biopsies of non-remission patients, we identified significant expansion of fibrogenic fibroblasts marked by high expression of COMP, a fibrosis-associated extracellular matrix protein. COMPhi fibroblasts localized to perivascular niches that, unexpectedly, served as transcriptional hubs for TGF{beta} activity. We identified endothelial-derived Notch signaling as an upstream regulator of fibroblast TGF{beta} signaling via its dual role in driving TGF{beta} isoform expression and suppressing TGF{beta} receptors, generating a proximal-distal gradient of TGF{beta} activity. Further, disruption of steady-state Notch signaling in vitro enabled fibrogenic fibroblast activation. Analysis of post-treatment biopsies revealed marked expansion of COMPhi fibroblasts in non-remission RA patients, despite evidence of successful immune cell depletion, suggesting a spatiotemporal process of fibrogenic remodeling linked to treatment resistance. Collectively, our data implicates targeting of TGF{beta} signaling to prevent exuberant synovial tissue fibrosis as a potential therapeutic strategy for refractory RA.

immunology↗

bioRxiv2025

Anti-tumor effects of a novel cell penetrating peptide-based therapeutic approach to target Lactate Dehydrogenase C (LDHC) in triple negative breast cancer.

BackgroundLactate Dehydrogenase C (LDHC) is a promising candidate for therapeutic targeting thanks to its highly tumor-specific expression, immunogenicity, and pro-tumorigenic functions. Aberrant LDHC expression is associated with poor clinical outcomes in multiple cancers, including breast cancer. However, no specific LDHC inhibitors are currently available, highlighting the need for novel strategies to selectively target LDHC in tumor cells. This study explores the anti-tumor potential of cell-penetrating peptides (CPPs) to target LDHC in triple negative breast cancer (TNBC). MethodsFour CPPs were evaluated for their ability to deliver LDHC siRNA to tumor cells, including the positively charged 10R peptide (10R) and three bifunctional peptides containing the integrin v{beta}3 recognition motif Arg-Gly-Asp (RGD): 10R-RGD, cyclicRGD-10R (cRGD-10R), and internalizing RGD-10R (iRGD-10R). We characterized the physicochemical properties of all CPP:siRNA complexes, and determined their serum stability, cytotoxicity, cellular uptake, and LDHC silencing efficiency in vitro. The anti-tumor effects and cytotoxicity of cRGD-10R:siRNA and iRGD-10R:siRNA complexes were further assessed in a TNBC xenograft zebrafish model. ResultsAll four CPPs formed stable nanocomplexes with favorable safety profiles. The 10R-RGD and cRGD-10R peptides demonstrated the most efficient LDHC knockdown, reduced the clonogenic ability of TNBC cells and enhanced their treatment response to the chemotherapeutic drug olaparib in vitro. Treatment of TNBC xenograft zebrafish with 10R-RGD:siRNA and cRGD-10R:siRNA complexes significantly reduced tumor burden without inducing major toxicity. Conclusion Our findings demonstrate that CPP-based siRNA delivery provides a novel and safe approach to target LDHC, either as a monotherapy or in combination with common anti-cancer drugs, to enhance treatment outcomes.

cancer biology↗

bioRxiv2025

Artificial intelligence-augmented drug discovery identifies gefitinib as a potential treatment for ALS

Amyotrophic lateral sclerosis (ALS) is characterised by motor neuron (MN) death; however, astrocytes play a key role in disease pathogenesis. Developments in the field of artificial intelligence (AI) have the potential to impact drug discovery in multiple ways, including the rapid identification of drug repurposing candidates. A combination of natural language processing and deep learning algorithms was used to generate a knowledge graph based on scientific literature, omics and chemical databases, and other public sources with the aim to identify drug repurposing candidates for ALS. The aim of the study was to determine the effect of a cancer compound identified by AI, gefitinib, on MN survival, and to decipher its mode of action inin vitroandin vivomodels of ALS. We used co-cultures of healthy motor neurons with ALS patient-derived astrocytes (iAstrocytes), obtained through a semi-direct conversion protocol, to assess the neuroprotective properties of gefitinib. Compound treatment led to a significant rescue of MNs cultured with ALS iAstrocytes and a significant reduction in the levels of cleaved TDP-43 fragments in ALS iAstrocytes. Our data suggest that gefitinib-mediated activation of autophagy decreased the 35 kDa fragments of TDP-43. In a proof-of-conceptin vivostudy in SOD1G93Amice, gefitinib treatment significantly delayed the onset of neurological symptoms, thus showing the potential of AI-augmented drug discovery for neurodegenerative disorders.Significance StatementThis study presents an AI-augmented method of identifying potential repurposing candidates for disease with an unprecedented speed. The AI’s results were validatedin vitrousing iAstrocytes differentiated from induced neuronal progenitor cells (iNPCs), which are pathophysiologically relevant models suitable for studying neurodegeneration. iNPCs recapitulate many pathological hallmarks of the disease and they retain the ageing phenotype of the patient that they are obtained from. TDP-43 proteinopathy is one of the disease hallmarks observed in patients and is present in 97% of ALS patients. Here, we show gefitinib, a repurposing candidate identified by AI, improves survival of MNs in a co-culture with patient-derived astrocytes and can modulate TDP-43 proteinopathy.

neuroscience↗

bioRxiv2025

Bi-specific CAR-iNKT cell immunotherapy for high-risk KMT2A-rearranged leukemia outperforms CAR-T in an NKG2D-dependent manner and eradicates leptomeningeal disease

Current therapies, including autologous CAR-T immunotherapy, fail to cure half of infants with KMT2A-rearranged acute lymphoblastic leukemia (KMT2Ar-ALL). Here we deploy allogeneic iNKT cells, innately more powerful effectors than T cells, and equip them with CD19- and/or CD133-targeting CARs. Compared to mono-specific counterparts and bi-specific CAR-T, CD19-CD133 bi-specific CAR-iNKT have more potent anti-leukemia activity, they effectively target CAR antigen-low leukemia, eradicate medullary and leptomeningeal leukemia and induce sustained remissions without discernible hematologic toxicity. Mechanistically, dynamic CAR- and CAR antigen-dependent upregulation of the activating innate receptor NKG2D and its engagement by corresponding ligands on KMT2Ar-ALL cells lead to more potent anti-leukemia effect of CAR-iNKT over CAR-T cells, including against CAR antigen-negative leukemia. Thus, by engaging with two different types of leukemia-associated targets, CAR-iNKT provide a powerful platform for the treatment of KMT2Ar-ALL. This approach can be readily adapted for other high-risk malignancies, including those with otherwise difficult to target leptomeningeal involvement.

cancer biology↗

bioRxiv2024

HIV-SEQ REVEALS GLOBAL HOST GENE EXPRESSION DIFFERENCES BETWEEN HIV-TRANSCRIBING CELLS FROM VIREMIC AND SUPPRESSED PEOPLE WITH HIV

"Active" reservoir cells transcribing HIV can perpetuate chronic inflammation in virally suppressed people with HIV (PWH) and likely contribute to viral rebound after antiretroviral therapy (ART) interruption, so they represent an important target for new therapies. These cells, however, are difficult to study using single-cell RNA-seq (scRNA-seq) due to their low frequency and low levels of HIV transcripts, which are usually not polyadenylated. Here, we developed "HIV-seq" to enable more efficient capture of HIV transcripts - including non-polyadenylated ones - for scRNA-seq analysis of cells from PWH. By spiking in a set of custom-designed capture sequences targeting conserved regions of the HIV genome during scRNA-seq, we increased our ability to find HIV RNA+ cells from PWH by up to 44%. Implementing HIV-seq in conjunction with surface phenotyping by CITE-seq on paired blood specimens from PWH before vs. after ART suppression, we found that HIV RNA+ cells were enriched among T effector memory (Tem) cells during both viremia and ART suppression, but exhibited a cytotoxic signature during viremia only. By contrast, HIV RNA+ cells from the ART-suppressed timepoints exhibited a distinct anti-inflammatory signature involving elevated TGF-{beta} and diminished IFN signaling. Overall, these findings demonstrate that active reservoir cells exhibit transcriptional features distinct from HIV RNA+ cells during viremia, and underscore HIV-seq as a useful tool to better understand the mechanisms by which HIV-transcribing cells can persist during ART.

immunology↗