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Biology subjects

Hassan, A.

Publications and source records attributed to Hassan, A..

At least 19 recordsLinked to original sources

A mechanical time window for correct proprioceptor development

Proprioception requires the transduction of mechanical strain generated by muscle contractions into sensory neuron activity. Although mechanical forces are essential for the function of mechanosensory organs, their role in the development of these organs remains largely unknown. It was already shown that the fly chordotonal organ (ChO), a multicellular proprioceptor, must acquire correct mechanical properties for proper function. Here, using an in vivo approach, we identify a critical mechanical time window during which the ChOs must experience appropriate mechanical forces to acquire the mechanical properties required for sensory function. To define this developmental window, we downregulated Pericardin (Prc), a major component of the ChO extracellular matrix, at different time points during embryonic and larval development. We then measured in vivo the efficiency with which muscle-generated deformations are converted into compressive strain in the ChO cap cell, a key step in transmitting mechanical forces to the sensory neuron. The most severe effect on conversion efficiency was evident when prc was downregulated during late embryogenesis, a time window which coincides with the onset of embryonic muscle contractions. This observation suggests that muscle-generated forces provide developmental cues required for the development of ChOs with correct mechanical properties. Consistent with this hypothesis, reducing muscle-generated forces during the same embryonic period resulted in a similar phenotype of impaired ChO mechanics and sensory function. Together, our findings reveal a previously unknown role for muscle-generated forces in shaping the development of fully functional proprioceptors.

developmental biology↗

RecBCD Prevents Bacterial Autoimmunity by Clearing Self-DNA Ends Produced During Replication Termination

Viral-induced DNA damage triggers both eukaryotic and prokaryotic innate immunity. Here, we report that self-DNA ends generated routinely during normal termination of bacterial replication suffice to trigger the P2-encoded OLD antiphage system. Normally, these physiological triggers are cleared by the dual helicase-nuclease activities of the conserved RecBCD enzyme, which acts as an immune safeguard analogous to mammalian TREX1 exonuclease and plant DBR1 debranching enzyme. However, when this clearance fails, the transient self-DNA ends persist and are recognized by ATP-bound OLD dimers via a positively charged channel across their ATPase subunits. ATP hydrolysis then activates OLD to cleave tRNAs, causing cytotoxicity. Single-cell microscopy reveals that dozens of OLD molecules associate with kilobases of adjacent DNA, amplifying the sparse physiological DNA end signal. Our findings reveal how an endogenous byproduct poses a constant autoimmune threat in bacteria, highlighting a universal molecular conflict across kingdoms and the convergent solutions evolved to resolve it.

microbiology↗

Analysis of Rare Coding Variation Identifies New Genetic Contributors to Schizophrenia

In this study, we present the largest rare coding variant association study of schizophrenia to date, with 87,959 schizophrenia cases and 150,587 controls. We identify 16 genes at exome-wide significance: SETD1A, ZMYM2, HERC1, RB1CC1, SCAF1, XPO7, SP4, FYN, PPP3CA, CUL1, HDAC9, JARID2, ATP9A, PTK2, STAG1, and SCN2A, and an additional 24 at a 5% false discovery rate. Cases carrying ultra-rare, damaging variants, primarily protein-truncating and deleterious missense mutations, show strong enrichment in constrained genes with consistent effects across ancestries. Half of the 40 identified genes overlap with those implicated in developmental delay, autism, or bipolar disorder, underscoring shared neurodevelopmental risk. All 40 genes identified are highly expressed in excitatory and inhibitory neurons, and their expression patterns span diverse developmental stages. Functionally, the identified genes implicate chromatin regulation, protein degradation, and synaptic function. Overall, our results advance understanding of the genetic architecture of schizophrenia, provide a foundation for modeling risk genes in cellular and animal systems, and offer a framework for future work toward biologically informed patient stratification.

genetics↗

A CD109-SMURF2 Axis Diverts EGFR from Degradation to Sustain Oncogenic Signaling and Promote Squamous Cell Carcinoma Invasion and Stemness

Squamous cell carcinoma (SCC) remains difficult to treat, particularly in recurrent or metastatic disease. Although EGFR signaling is a well-established driver of SCC pathogenesis, mechanisms regulating its activity remain incompletely understood. CD109, a GPI-anchored glycoprotein frequently overexpressed in SCC, has been implicated in EGFR signaling, but its mechanisms remain poorly defined. Here, we show that CD109 is elevated in head and neck SCC (HNSCC) in the TCGA PanCancer Atlas and significantly correlates with reduced disease-free survival. Integrative transcriptomic (TCGA PanCancer Atlas) and proteomic (LinkedOmics) analyses revealed strong positive correlations between CD109, EGFR, and SMURF2. These findings were further validated by immunohistochemistry in HNSCC patient samples. Mechanistically, CD109 overexpression impaired EGFR degradation, suppressed degradation-associated EGFR pY1045 phosphorylation, and enhanced signaling-associated pY1068 phosphorylation, resulting in increased STAT3, AKT, and ERK signaling. We identify SMURF2 as a mediator of these effects, with CD109 promoting EGFR-SMURF2 complex formation. SMURF2 gain- and loss-of-function studies in SCC cells, demonstrated that SMURF2 stabilizes EGFR by reducing EGFR interaction with the ubiquitin ligase c-Cbl, thereby limiting EGFR turnover in a CD109-dependent manner. Functionally, the CD109-SMURF2-EGFR axis promotes EGF-induced stemness, invasion, and proliferation in SCC cells. Together, these findings identify CD109 as a molecular switch controlling EGFR fate by redirecting EGFR from c-Cbl-mediated degradation toward SMURF2-dependent stabilization, sustaining oncogenic signaling. This previously unrecognized regulatory pathway reveals the CD109-SMURF2 axis as a vulnerability with potential for targeted intervention in EGFR-driven SCCs.

cancer biology↗

A developmental chimera: co-option of appendage, secretory and myogenic programs underlies spider venom gland evolution

The evolutionary emergence of complex organs requires the integration of distinct developmental modules, yet the mechanisms bridging divergent tissue programs into unified functional units remain poorly understood. Animal venom systems, combining high-output secretory epithelia with muscular delivery systems, a provide an exceptional model for studying this modular integration. Here, we show that the venom gland of the spider Parasteatoda tepidariorum is a developmental chimera built by the hierarchical co-option of three ancestral programs. The appendage-patterning gene Distal-less establishes the primary spatial coordinate system for gland development. Downstream, the transcription factor sage maintains secretory epithelium identity; its loss causes downregulation of key venom-processing enzymes and triggers a dramatic phenotypic reversion to a neuronal state. This neural upregulation, accompanied by the downregulation of Notch ligands (delta and jagged), reveals that sage actively represses a latent neural program to maintain secretory fate. Crucially, the myogenic factor sum-1 governs the surrounding muscle layer to drive paracrine crosstalk (Wnt) and sustain lipid metabolism. Knockdown of sum-1 downregulates wntless and fatty acid anabolism genes, alongside the abnormal accumulation of lipid droplets in the secretory epithelium. Ultimately, our findings demonstrate how a complex organ is assembled by fusing an appendicular address, a repressed neuroglandular program, and a myogenic metabolic driver. This modular architecture illustrates a fundamental principle in evolutionary developmental biology: novelty can arise by harnessing the physiological and metabolic capacities of adjacent tissues to fuel the physiological demands of a newly emerged organ. Significance statementHow novel organs evolve by integrating distinct developmental modules remains a fundamental question in biology. Using the spider venom gland as a model, we show that this complex organ is a developmental chimera built by recruiting three ancestral tissue programs. The appendage-selector gene Distal-less (Dll) establishes the glands primary proximal-distal structural axis. Downstream, the transcription factor sage maintains secretory epithelial identity by actively repressing a default neural program. Concurrently, the myogenic regulator sum-1 sustains epithelial lipid metabolism through paracrine Wnt signaling. These findings establish a mosaic model of organogenesis, demonstrating that radical evolutionary innovation can arise by forging morphogenetic and metabolic partnerships that harness adjacent tissues to fuel newly emerged structures.

evolutionary biology↗

Molecular mechanism of IF1- and IF2-driven translation initiation in bacteria

Bacterial translation initiation is a highly regulated process essential for accurate start codon selection and the assembly of an elongation-competent ribosome. Two initiation factors, 1 (IF1) and 3 (IF3), contribute to quality control for formation of 30S preinitiation complex (30S PIC), while the GTPase IF2 facilitates stable initiator tRNA binding and promotes subunit association. However, the molecular mechanism of IF1 action and the regulatory role of IF2-mediated GTP hydrolysis and inorganic phosphate (Pi) release remain poorly understood. Using ensemble cryo-EM integrated with fast-kinetics, we delineate the translation initiation pathway involving IF1 and IF2. We show that IF1 transiently associates with the 30S subunit and interferes with the formation of multiple inter-subunit bridges. IF2 promotes subunit association by stabilizing the 30S PIC through interactions mediated by its N-terminal domains. IF1 departure happens after or concomitant with GTP hydrolysis, following which the inter-subunit bridges establish. Then Pi release triggers remodeling of IF2 followed by its departure from the 70S initiation complex. These findings reveal how the coordinated interplay of IF1 and IF2 with the ribosome ensures translational fidelity and plays crucial role for formation of elongation-competent 70S.

biochemistry↗

Rewiring of EGFR oncogenic program by opposing actions of membrane versus soluble CD109 in HNSCC

The epidermal growth factor receptor (EGFR) expression is often dysregulated in head and neck squamous cell carcinoma (HNSCC), driving cancer cell proliferation, invasion, and metastasis through diverse pathways, thereby contributing to aggressive chemo- and radio-therapy resistance. A GPI-anchored protein, CD109 is upregulated in multiple cancers, including HNSCC. While membrane-anchored CD109 (mCD109) is pro-tumorigenic in SCC via EGFR/STAT3 activation, the role of protease-cleaved soluble CD109 (sCD109) is poorly understood. Our groundbreaking findings demonstrate that sCD109 antagonizes EGFR signaling by directly binding to the EGFR extracellular domain, preventing mCD109-EGFR stabilizing interactions on the cell surface, followed by inhibition of EGFR phosphorylation at Y1068 and downstream signaling cascades (AKT, MAPK, and STAT3) consequently suppressing cancer cell migration, invasion, 3D tumor spheroid formation and angiogenic tube formation. In addition, we found that sCD109 regulates EGFR fates by inhibiting nuclear localization of phosphorylated EGFR and promoting EGFR degradation. Additionally, sCD109 significantly reduces EGF-induced expression of cancer stem cell markers (CD44 and CD133) and embryonic stem cell markers (Nanog and Sox2), suggesting a suppressive role in cancer stemness. Taken together, these results underscore the opposing roles of mCD109 and sCD109: with sCD109 acting as an antagonist by inhibiting mCD109/EGFR-driven oncogenic signaling and phenotypes. Our current findings reveal a complex interplay among mCD109, sCD109, and EGFR, identifying a mechanism for targeting EGFRs degradation in HNSCC, and lay the groundwork for future research on investigating sCD109s modulatory role in preclinical models of HNSCC.

Cancer Biology↗

The essential molecular components for cellular CO2 sensing via connexins

CO2 opens a subset of connexin hemichannels by binding to a site in the cytoplasmic domain of the channel. From outside the cell, CO2 must cross at least one membrane to reach this site. We have used Neuro-2A cells, which exhibit very low expression of CO2 permeable aquaporins (AQPs) and do not express any of the connexins (Cxs) known to be CO2 sensitive, to evaluate the minimal complement of molecular components required to recapitulate whole cell CO2 sensitivity mediated by connexins (assayed by either whole cell patch clamp recordings or real time recordings of ATP release via a co-expressed genetically encoded ATP sensor). Neuro-2A cells that expressed either Cx26, Cx32 or Cx43 on their own did not exhibit CO2-dependent connexin hemichannel gating. Expression of AQP1 or AQP5 either with or without carbonic anhydrase 2 (CA2) did not reveal any endogenous CO2 sensitivity of Neuro-2A cells. Only by expressing one of Cx26, Cx32 or Cx43 with either AQP1 or AQP5, plus CA2 were we able to reconstitute whole cell CO2 sensitivity. We found that expression of Cx26 with either AQP1 or AQP5 resulted in high levels of cell death. This was prevented by co-expression of CA2. Simulations of the influx and diffusion of CO2 show that CA2 prevents accumulation of intracellular CO2 and excessive activation of Cx26, thus protecting the cells from death. Surveying the transcriptome of cells that express CO2 sensitive connexins shows that many also express CO2 permeable aquaporins and CA2. We suggest that connexins, aquaporins and carbonic anhydrases represent the minimal trifecta of components required for cellular CO2 sensing.

cell biology↗

Characterizing the Effects of Chronic Cannabis Vapour Exposure and Withdrawal on Cannabinoid Triad, Somatic Signs and Behavioural Network Reorganization Adult Male Rats

RationaleCannabis withdrawal contributes to relapse in individuals with cannabis use disorder, yet preclinical studies have largely focused on withdrawal induced by injected cannabinoids rather than inhaled cannabis, which remains the most common route in humans. The behavioural effects of chronic exposure to vapourized cannabis flower and resulting withdrawal after cessation of exposure remain poorly characterized. ObjectivesTo determine the behavioural effects of chronic vapourized high-THC cannabis flower exposure on cannabinoid tetrad, somatic withdrawal and behavioural transition networks in rats following both chronic vapour exposure and administration of the cannabinoid receptor 1 (CB1) receptor antagonist SR141716A (rimonabant). MethodsTwo studies were conducted using adult male Sprague Dawley rats. The first study (N = 16) exposed rats to either air or vapourized high-THC cannabis flower three times a day for seven days using a Volcano vapourizer, followed by intraperitoneal administration of the CB1 antagonist SR141716A (3 mg/kg). The second study (N = 24) included two air controls and two cannabis groups, with one of each receiving either saline or SR141716A. Behavioural assessments included triad measurements to confirm the cannabis effect, along with withdrawal assessment via a sucrose preference test and somatic signs 30 minutes following rimonabant administration. ResultsRepeated cannabis vapour exposure produced reduced locomotor activity, hypothermia, and increased tail-flick latency. Rimonabant administration precipitated withdrawal characterized by increased total withdrawal scores and somatic signs, including blinking, body shakes/tremors, and grooming-related behaviours. Behavioural network analyses revealed substantial reorganization of behavioural transition structure during both chronic cannabis exposure and withdrawal. Chronic cannabis exposure was associated with reduced network modularity, a condensed behavioural repertoire, and altered behavioural centrality measures. At the same time, precipitated withdrawal further increased the influence of exploratory behaviours, particularly sniffing, and reduced the network prominence of locomotor-associated behaviours, such as walking, beyond that detected using conventional behavioural measures alone. ConclusionChronic exposure to vapourized cannabis flower followed by CB1 receptor antagonism produces reliable withdrawal symptoms in rats. Behavioural network analyses further reveal that cannabis exposure and withdrawal are both associated with widespread reorganization of behavioural dynamics, suggesting that withdrawal alters not only individual behaviours but also the structure of behavioural transitions. These findings establish a translational model of cannabis withdrawal using inhaled cannabis flower vapour and identify behavioural network analysis as a sensitive approach for characterizing withdrawal-related behavioural states.

neuroscience↗

EGP1K: Whole-Genome Sequencing of 1,024 Egyptians Characterizes Population Structure and Genetic Diversity

Middle Eastern and North African populations remain underrepresented in genomic databases, comprising less than 1% of genome-wide association study participants despite representing approximately 6% of the global population. Here we present the Egypt Genome Project (EGP1K), in which we performed whole-genome sequencing on 1,024 unrelated Egyptian individuals originating from 21 of Egypts 27 governorates, recruited through eight clinical and research centers across Upper and Lower Egypt. We identified over 51.3 million variants, of which 17.1 million (33.4%) were absent from dbSNP. Allele frequency comparisons across 6.5 million shared variants showed the strongest concordance with Middle Eastern populations ({tau} = 0.977). Principal component analysis and ADMIXTURE modeling at K = 7 revealed that Egyptians share a dominant ancestry component (71.8%) with Middle Eastern populations and carry a smaller Egyptian-enriched component (18.5%) that distinguishes them from neighboring groups. Runs of homozygosity varied substantially across subregions, with Upper Egypt showing the highest burden, paralleling elevated consanguinity rates. Carrier frequency analysis identified MEFV (Familial Mediterranean Fever) at 9.1% as the most prevalent pathogenic carrier state; when adjusted for the national consanguinity rate, MEFV carrier status alone projects approximately 6,600 affected births per year. HLA class I typing identified allele frequencies placing Egyptians within the Levantine-Eastern Mediterranean cluster, providing baseline immunogenetic data currently absent from international databases. Analysis of polygenic risk score distributions revealed substantial differences in threshold-based risk stratification between Egyptians and European reference populations. When the Europeanderived 90th percentile threshold was applied, 83.3% of Egyptians were assigned to high-risk strata for stroke, 76.4% for chronic kidney disease, and 72.8% for gout, compared to the intended 10% high-risk proportion. These distributional shifts were observed across several cardiometabolic traits (Cohens d = 1.55-1.61), while other traits showed closer cross-population concordance, indicating that the degree of threshold miscalibration varies by trait. Together, these findings establish EGP1K as a genomic reference for Egypt and indicate that European-derived risk stratification thresholds may not be directly transferable to the Egyptian population, supporting the need for population-specific calibration of polygenic risk scores.

genomics↗

In vivo experimental model of β-glucan-induced innate immune memory

SUMMARYInnate immune memory is the ability of innate immune cells to develop a recallable, epigenetically imprinted response after an initial stimulus, enabling them to mount differential responses upon restimulation. Here, we present a detailed protocol of {beta}-glucan preparation, and its in vivo application to modulate innate immune memory in mice through repeated intraperitoneal (IP) injections. This approach results in enhanced hematopoiesis and bone marrow specific myeloid bias, key hallmarks of in vivo innate immune memory responses. For complete details on the use and execution of this protocol, please refer to Hassan et al. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=184 SRC="FIGDIR/small/705736v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@d41c3aorg.highwire.dtl.DTLVardef@18939cdorg.highwire.dtl.DTLVardef@31e879org.highwire.dtl.DTLVardef@956f6b_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIPreparation of {beta}-glucan for in vivo experiments. C_LIO_LIIn vivo modulation of innate immune memory through repeated intraperitoneal {beta}-glucan injections in mice. C_LIO_LIModulation of innate immune memory is assessed by enhanced bone marrow hematopoiesis and GMP production. C_LI

immunology↗

Transcriptomic profiling of human γδ T cells reveals non-linear immune aging characterized by childhood transitions and relative stability in adulthood

{gamma}{delta} T cells are one of the first T cell subsets developing in early ontogeny and show various effector functions in immune homeostasis and response in the young and the old. However, their maturation trajectories from infancy to children, adults and elderly have not been systematically defined. Here, we generated a single-cell transcriptome atlas of 106,711 {gamma}{delta} T cells from 223 individuals spanning infancy to old age. Our analysis reveals that {gamma}{delta} T cell aging is non-linear, characterized by pronounced childhood transitions followed by relative stability throughout adulthood despite marked inter-individual variability. In childhood, changes from developmental and mitochondrial programs toward cytotoxicity and inflammaging were evident. This includes maturation trajectories from GZMK intermediates to GZMB+Perforin+ effectors at both RNA and protein levels. Taken together, our study delineates the aging trajectories of human {gamma}{delta} T cells, establishes {gamma}{delta} T cells as a cellular paradigm of non-linear immune aging, and provides a comprehensive resource for investigating {gamma}{delta} T cell biology across the human lifespan.

immunology↗

Provirus induction diversifies adaptive variation in Pseudomonas aeruginosa lysogen populations

Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen that forms chronic infections in people with cystic fibrosis. Often P. aeruginosa strains are lysogens, infected with proviruses, that are induced by cellular stressors which include challenge with antibiotics such as ciprofloxacin. We asked how infection of P. aeruginosa with Mu-like provirus DMS3 would alter the evolution of antibiotic resistance through serial transfer of six replicates of four strain backgrounds, with and without sublethal doses of ciprofloxacin over 20 days. Through population metagenome sequencing we found that inducing lysogen populations had significantly higher diversity in adaptive mutations than non-lysogens after 20 days. Lysogen populations have more co-existing mutations within the population and a higher number of mutations in adaptive genes, including antibiotic efflux pump and gyrase alleles, and CRISPR-Cas loci. These data suggest that viral induction shifts the adaptive regime of a clonal population from one of stepwise periodic selective sweeps to recurrent competing mutations. Our results demonstrate the way that provirus infection can shape the evolutionary trajectory of their hosts in an environment-dependent manner. SignificanceMost long-term chronic infections of Pseudomonas aeruginosa in cystic fibrosis patients trace their origin to a single ancestor. During long-term chronic infection the evolution of each unique ancestor strain, defined by its starting genotype, can dramatically impact the success of future treatment efforts. Often the common ancestral Pseudomonas aeruginosa genotype is infected by a virus; this in turn shapes the evolution of bacterial cells within the human island of the lung. This work shows that when the nested virus infecting Pseudomonas aeruginosa is the very common transposable Mu-like virus, it can cause the bacterial population to diversify in response to antibiotic treatment in ways that may complicate future antibiotic treatment and phage therapy.

microbiology↗

Integrative Network Meta-Analysis Reveals Estrogen-Mediated RUNX2PDLIM3microRNA Crosstalk via ERG Signaling: Implications for Bone and Tissue Regeneration

Estrogens govern the female reproductive cycle indefinitely. Estrogens, including estrone (E1), estradiol (E2), estriol (E3), and estetrol (E4), regulate the female life cycle since early embryonic stages and play a crucial role in development, metabolism, and cell function. Throughout evolution, estrogen has regulated reproduction by affecting reproductive organ development and behavior. Estrogen impacts all vertebrates, including fish, and has a role in physiological and pathological states in both genders. The RUNX-2 gene is a member of the RUNX family of transcription factors and encodes a nuclear protein with a Runt DNA-binding domain. This protein is essential for osteoblastic differentiation and skeletal morphogenesis and acts as a scaffold for nucleic acids and regulatory factors involved in skeletal gene expression. The protein can bind DNA both as a monomer or, with more affinity, as a subunit of a heterodimeric complex. In 2022, a study was conducted to characterize novel genes that are regulated by estrogen binding to its receptors ( or {beta}). The PDLIM3 gene, with a coefficient of variation (CV) of 0.083, received the most stable CV score among other genes. Our integrative research uncovers a unique regulatory cascade in which estrogen binding to ER/{beta} enhances PDLIM3 expression, then modulating the expression of miR-9, miR-10, and the newly identified miR-6769b, finally activating RUNX2 transcription.

genetics↗

Meningeal γδ T cells facilitate bacterial entry into the brain in neonatal meningitis and trigger long-term behavioural sequelae

Neonatal bacterial meningitis is a life-threatening condition and a leading cause of neurodevelopmental impairment among survivors. Despite its prevalence, the role of meningeal immunity on disease pathology during early life remains largely unexplored. Using a clinically relevant mouse model of neonatal group B streptococcal meningitis and single-cell RNA sequencing, we observed that IL-17A (IL-17)-producing {gamma}{delta} T cells ({gamma}{delta}17 T cells) accumulate in the meninges during the acute phase of infection and persist throughout the lifespan. Importantly, mice deficient in {gamma}{delta} T cells or in IL-17 show a significantly lower bacterial colonisation in the brain parenchyma, and IL-17 neutralisation in the cerebrospinal fluid leads to a similar phenotype. Reduced blood-brain barrier permeability in the absence of {gamma}{delta} T cells results in decreased bacterial invasion and diminished microglia activation. Wild-type but not {gamma}{delta} T cell-deficient mice surviving infection exhibit increased hyperactivity and open space anxiety during early adulthood, a behavioural profile that may reflect attention deficit and hyperactivity (ADHD)-like tendencies. Altogether, these findings establish a pathogenic role for meningeal {gamma}{delta}17 T cells in early life, uncovering a key mechanism that drives long-term sequelae in GBS neonatal meningitis.

immunology↗

Uniform processing and analysis of IGVF massively parallel reporter assay data with MPRAsnakeflow

As researchers and clinicians seek to identify human genomic alterations relevant to traits and disorders, identifying and aggregating evidence providing mechanistic support for associations between alterations and phenotypes remains challenging. In particular, the study of non-coding genomic variation remains a major challenge due to the lack of accurate functional annotation for activity in a given context and across alleles. Experimental evidence is critical for prioritizing and interpreting functional effects of genetic alterations. Massively Parallel Reporter Assays (MPRAs) have emerged as a powerful high-throughput approach, enabling quantification of regulatory element activity and allelic effects, and systematic dissection of gene regulatory logic and variant effects across different contexts. However, the diversity of MPRA designs, lack of standardized formats, and many potential processing parameters hamper data integration, reproducibility, and meta-analyses across studies. To address these challenges, the Impact of Genomic Variation on Function (IGVF) Consortium established an MPRA focus group to develop community standards, including harmonized file formats, and robust analysis pipelines for a wide range of library types and experimental designs. Here, we present these formats and comprehensive computational tools, MPRAlib and MPRAsnakeflow, for uniform processing from raw sequencing reads to counts, processing and visualization. Using diverse MPRA datasets, we characterize technical variability sources including barcode sequence bias, outlier barcodes, and delivery method (episomal vs. lentiviral). Our results establish best practices for MPRA data generation and analysis, facilitating robust, reproducible research and large-scale integration. The presented tools and standards are publicly available, providing a foundation for future collaborative efforts in regulatory genomics.

genomics↗

RNase H1 counteracts DNA damage and ameliorates SMN-dependent phenotypes in a Drosophila model of Spinal Muscular Atrophy

Spinal Muscular Atrophy (SMA) is caused by a deficiency of the Survival Motor Neuron (SMN) protein. Mutations in SMN disrupt mRNA splicing and translation, leading to maladaptive changes in transcriptomes, proteomes, neuroinflammation, and metabolism, which drive motor neuron degeneration in SMA patients. Using a Drosophila SMA model, we found that systemic depletion of Smn leads to accumulation of RNA:DNA hybrids (R-loops), increased DNA damage, dysregulation of amino acids and sugar metabolism and activation of the innate immune response, recapitulating key pathological features reported in mammalian models and severe SMA patients. Persistent DNA damage in Smn-deficient flies alters cell proliferation rates in larval brains and induces extensive cell death in the developing eye. Importantly here, we show that stimulating the resolution of RNA:DNA hybrids with transgenic human RNAse H1 prevents the accumulation of DNA damage and attenuates the transcriptome and amino acid alterations induced by Smn depletion, mitigating the Smn-dependent cellular and developmental abnormalities, in Smn-deficient flies. Our data suggest that depletion of Smn causes an accumulation of aberrant transcripts and chronic DNA damage, which--along with the altered metabolomic profiles associated with Smn deficiency--trigger systemic inflammatory responses, ultimately affecting neuronal function and survival.

genetics↗

An early functional adaptive NK cell signature drives optimal CD8+ T-cell activation and predicts sustained HIV-1 viral control.

A better understanding of the immune responses associated with future viral control in humans during acute HIV-1 infection (AHI) is critical to inform vaccines and immune-based therapeutics. Natural killer (NK) cells and CD8+ T-cells are pivotal in antiviral defence, yet the dynamics and complementary roles of these effector subsets during AHI with different HIV-1 subtypes remain poorly understood. Access to a unique patient cohort recruited during and post-peak HIV-1 viral load with different HIV-1 subtypes and followed up longitudinally in the absence of antiretroviral therapy up to six years post estimated date of infection (EDI) provided a rare opportunity to fill this knowledge gap. Our data show an early expansion of Fc{varepsilon}R{gamma}-CD57+ NK cells with classical adaptive traits concomitant with an enhanced capacity for antibody-dependent cellular cytotoxicity (ADCC) and reactivity against HIV-1 antigens. This distinctive NK cell profile was more abundant in donors with subtype A infection compared to non-subtype A, partially driven by elevated pro-inflammatory cytokine levels and changes in the epigenetic landscape. The accumulation of adaptive NK cells during the first month of infection contributed to the optimal activation of CD8+ T-cells, promoting virus-specific responses. Notably, individuals with higher levels of Fc{varepsilon}R{gamma}-CD57+ adaptive NK cells during the first month of infection were more likely to exhibit long-term viral control in the absence of ART. These findings underscore the critical role of early, high-magnitude adaptive NK cell responses in CD8+ T-cell activation and subsequent immune control. This work provides novel insights into the correlates of protective immunity against HIV-1 infection, with implications for preventative or therapeutic vaccine strategies aimed at promoting adaptive NK cell responses. One Sentence SummaryEarly expansion of adaptive NK cells during acute HIV-1 infection promotes long-term viral control.

immunology↗