Biology subjects

Wang, D.

Publications and source records attributed to Wang, D..

At least 145 records · Page 8Linked to original sources

bioRxiv2025

Microstructural functional coupling as a multimodal biomarker of emotional state transitions in bipolar disorder

Bipolar disorder (BD) is characterized by dynamic transitions between depressive and manic states, yet the neural mechanisms underlying these state shifts remain unclear. Here, we developed an integrative framework to quantify the microstructural-functional coupling (MFC) of the brain, which captures the distributional similarity between voxel-wise diffusion and functional features within each cortical region. Using multimodal MRI data from 72 BD patients and 65 matched healthy controls, we observed a global increase of MFC of BD, which indicates a de-similarity of brain microstructure and function. Partial least squares correlation (PLSC) analysis revealed that the principal latent component linking MFC to behavioral scores explained 67.2% of the variance, with the strongest contributions from the control and somatosensory networks. Mediation analysis demonstrated that regional MFC influenced anxiety indirectly through depressive symptoms, supporting a sequential affective transition from depression to anxiety. Moreover, macroscale gradient analysis showed that the principal MFC gradient was significantly correlated with neurotransmitter receptor distributions, including 4{beta}2, 5-HT1B, and H3. Together, these findings highlight MFC as a multimodal biomarker sensitive to emotional state transitions in BD and suggest its potential as a bridge between microstructural alterations, functional dynamics, and neurotransmitter systems.

neuroscience↗

bioRxiv2025

Rectal Transplantation of Fragmented Intestinal Organoids and Crypts Promotes Mucosal Regeneration in DSS-Induced Colitis

BackgroundUlcerative colitis (UC) represents a global health challenge characterized by relapsing inflammation and epithelial barrier disruption. Conventional immunosuppressive therapies have reached their therapeutic ceiling, with mucosal healing and long-term remission remaining unmet therapeutic goals for many patients. Organoid-based regenerative therapy offers a new paradigm by reconstructing damaged mucosa rather than merely controlling inflammation. MethodsWe hypothesized that fragmented intestinal organoids, building upon the foundational model established by Yui et al., whose use of immunodeficient Rag2-/- mice and surgical mucosal injury first demonstrated the feasibility of colon organoid transplantation. Our study advances this framework by introducing optimized transplantation timing and employing immunocompetent C57BL/6 mice to refine translational relevance and clinical feasibility, thereby extending the applicability of organoid therapy to more realistic physiological contexts., when transplanted rectally at an optimized time point, could integrate more efficiently into inflamed mucosa and accelerate epithelial regeneration even in an immunocompetent environment. A 2.5% dextran sulfate sodium (DSS)-induced colitis model was established in C57BL/6 mice. Intestinal organoids and crypts derived from EGFP-transgenic donors were cultured and transplanted rectally using a minimally invasive delivery system. Fluorescence microscopy, histological analysis, and clinical indices were used to evaluate engraftment and mucosal repair. ResultsEGFP+ organoid fragments and crypts successfully engrafted at ulcerated sites, reconstituting epithelial structures and restoring mucosal integrity. Mice receiving organoid or crypts transplantation exhibited rapid weight recovery and reduced bleeding compared to DSS-only controls. Histological and fluorescence analyses confirmed epithelial restitution exceeding 60% by day 7 post-administration versus 18% in controls. These results validate the regenerative potential of organoid transplantation within an immunocompetent host. ConclusionThis study demonstrates that rectal transplantation of fragmented intestinal organoids and crypts promotes robust mucosal regeneration in DSS-induced colitis. By optimizing transplantation timing and employing a clinically relevant model, our work establishes a translational foundation for organoid-based regenerative therapies targeting inflammatory bowel diseases.

bioengineering↗

bioRxiv2025

Multimodal AI Decodes Extreme Environment Functional Dark Matter Beyond Homology

Functional annotation of proteins from extreme environments represents a major bottleneck for bioresource discovery, as a vast reservoir of functional dark matter defies existing homology-based methods. We demonstrate that environmental pressures impart conserved physicochemical energy signatures that co-determine protein function with sequence and structure. Here we developed ACCESS, a multimodal graph neural network employing hierarchical contrastive learning with a tailored label-sample co-embedding to fuse energy, sequence, and structural information and overcome homology scarcity. ACCESS surpasses state-of-the-art methods including BLASTp and CLEAN in annotating low-identity enzymes. Applied to extreme environmental metagenomics, we constructed a function map of extremophile enzymes to expand the biocatalyst library, pinpointed functionally critical residues to guide rational design, and enabled large-scale, function-based macro-evolutionary analyses. This paradigm transcends the limitations of homology, illuminating protein dark matter and accelerating the exploration of the biospheres functional diversity for applications in biotechnology and therapeutic development.

bioinformatics↗

bioRxiv2025

Predicting individual incubation of opioid craving by whole-brain functional connectivity

A high risk of relapse triggered by craving during abstinence remains a main challenge in opioid addiction treatment. Multiple brain regions have been implicated in opioid craving, but the brain-wide neural mechanisms underlying this process remain poorly understood. Using resting-state fMRI and connectome-based predictive modeling, we identified a whole-brain connectome that predicted the time-dependent increases (incubation) in oxycodone craving in individual rats after voluntary abstinence induced by exposure to an electric barrier. Incubation of oxycodone craving was operationally defined as the increase in non-reinforced lever pressing during relapse tests from early (day 1) to late (day 15) abstinence (incubation score). We found that changes in whole-brain functional connectivity during abstinence, but not during oxycodone self-administration, predicted the incubation score. Greater decreases in functional connectivity were associated with higher incubation scores. The predictive connectome involved complex interactions across multiple brain systems, including frontal-striatal, frontal-insula, insula-striatal, and hippocampal and sensorimotor circuits. To test causality of the predictive connectome, we examined the effect of pharmacological inactivation of dorsomedial striatum (DMS), which significantly decreased oxycodone seeking after electric barrier-induced abstinence. DMS inactivation increased connectivity strength within the predictive connectome, supporting a causal role of this connectome in incubation of oxycodone craving. The predictive connectome did not predict food-reward seeking after electric barrier-induced abstinence, indicating specificity to oxycodone craving. Our findings identify a brain-wide connectome marker that predicts individual differences in the incubation of opioid craving and provide potential targets for developing personalized interventions and monitoring therapeutic outcomes in opioid addiction treatment. Significance statementRelapse driven by craving remains a central challenge in treating opioid addiction. Using resting-state fMRI and connectome-based predictive modeling, we identified a whole-brain connectivity pattern that predicted incubation of oxycodone craving after voluntary abstinence in rats. Connectivity changes during abstinence predicted the magnitude of incubation, measured by increased oxycodone seeking from early to late abstinence. The predictive connectome involved interactions among cortical, basal ganglia, insular, hippocampal and sensorimotor systems. Pharmacological inactivation of the dorsomedial striatum modulated connectivity strength within this network, demonstrating a causal role of the connectome in incubation of craving. These findings identify a brain-wide marker of incubation of opioid craving and provide a translational framework for developing targeted interventions and monitoring therapeutic outcomes in opioid addiction treatment.

neuroscience↗

bioRxiv2025

Adaptive introgression from Pacific herring to Atlantic herring in the brackish Baltic Sea

The genomic era has revealed that interspecific gene flow can play an important role in adaptive evolution. Here, we report a striking case of adaptive introgression from Pacific into Atlantic herring following the colonization of the brackish Baltic Sea. Gene flow likely occurred in the Arctic, where the distributions of the two species overlap. Although introgression affected only 0.29% of the genome, these regions encompass about 10% of the loci showing strong differentiation between Atlantic and Baltic herring, indicating that natural selection has favored introgressed alleles in functionally important parts of the genome. Adaptive introgression may have been facilitated by shared spawning depths and salinity preferences between Pacific and Baltic herring, in contrast to Atlantic herring, which spawn in deeper, fully marine waters. Introgressed genes such as THRB and SEC16B may have enhanced visual acuity and lipid metabolism, respectively, promoting adaptation to the brackish Baltic environment.

evolutionary biology↗

bioRxiv2025

Integration of Nuclear Receptors into a Schwann cell Gene Regulatory Network

Peripheral nerve function depends on the proper formation and maintenance of Schwann cells. During development, large diameter axons are enveloped by single, myelinating Schwann cells whereas clusters of small diameter axons are surrounded by nonmyelinating Schwann cells in Remak bundles. The transcription factor SRY-box 10 (SOX10) is required for the development of Schwann cells, but its functions in different neural crest and glial lineages have shown that SOX10 commonly cooperates with other transcription factors to activate cell-specific gene programs. In a previous study, we compared SOX10-bound regulatory elements in Schwann cells and identified a specific enrichment for nuclear receptor motifs at SOX10 binding sites in Schwann cells. NR2F1 and NR2F2 (Coup-TFI/Coup-TFII) are expressed from neural crest through Schwann cell maturity, and knockdown of nuclear receptors Nr2f1 and Nr2f2 in primary Schwann cells downregulated several myelin genes. In this study, we have identified a NR2F-regulated target gene network in Schwann cells, which revealed enrichment for nonmyelinating Schwann cell genes. Cut&Run assays in S16 Schwann cells revealed novel, genome-wide binding sites of NR2F2 and two downstream transcription factors: 1) Retinoid X Receptor Gamma (RXRG), which is also expressed preferentially in nonmyelinating Schwann cells, and 2) TEA-Domain factor (TEAD1), which is an important HIPPO pathway component required for Remak bundle formation. Our study elucidates the transcriptional cooperation that programs the regulatory network in nonmyelinating Schwann cells.

neuroscience↗

bioRxiv2025

LRP8 is a Receptor for Yellow Fever Virus

Yellow fever virus (YFV), an arbovirus causing substantial human morbidity and mortality, was the first human virus discovered over a century ago. The live-attenuated 17D vaccine is among the most successful vaccines in medicine. Despite the importance of YFV, its receptor has remained unknown. Here, we performed a barcoded, genome-wide human ORF library screen and identified LRP8 (also named APOER2) as a receptor for YFV. We show that LRP8 expression specifically boosts YFV infection in cell lines by promoting entry. AAV-mediated expression of human LRP8 in mouse liver aggravates infection and pathology. LRP8 knockdown abolishes YFV infection in brain cells, primary human hepatocytes, and notably in mosquitoes. Biochemically, LRP8 directly interacts with YFV particles via the viral envelope protein. This function of LRP8 is conserved across species, particularly in mosquitoes and primates. A soluble LRP8 decoy protein can block YFV infection in vitro and in mice, providing a potential therapeutic or prophylactic strategy. Our findings provide groundwork for understanding YFV entry, tropism, and pathogenesis, and may enable development of novel therapeutics to treat YFV infection.

microbiology↗

bioRxiv2025

Adipose-mimetic granular hydrogels uncover biophysical cues driving breast cancer invasion

1.Breast cancer cells invade mammary adipose tissue during initial stages of metastasis but how the physical properties of adipose tissue regulate this process remains unclear. Here, we combined single cell mechanical characterization of primary adipocytes with microfluidic hydrogel fabrication, quantitative multiparametric imaging, Discrete Element Method (DEM) simulations, and in vivo experiments to elucidate these connections. First, we quantified the heterogeneous size and stiffness of primary adipocytes, and replicated these properties by fabricating adipocyte-sized polyacrylamide (PAAm) beads with tunable elasticity. Subsequently, we embedded these beads into type I collagen, the primary fibrillar extracellular matrix (ECM) component of breast adipose tissue, to form 3D granular hydrogels mimicking aspects of native adipose tissue architecture. Granular hydrogels embedded with beads demonstrated increased breast cancer cell invasion relative to bead-free controls, an effect that was more pronounced with soft versus stiff beads and correlated with increased collagen fiber alignment and hierarchical organization. In addition, live cell imaging and DEM simulations revealed that soft beads promoted invasion relative to stiff beads by deforming in response to confined cancer cell migration. Fiber alignment and adipocyte deformation trends were validated in vivo via intravital imaging of cancer cell migration in mammary fat pads of mice, and suggest that adipocyte mechanics regulate breast cancer invasion by coordinating both ECM architecture and cellular confinement. Ultimately, this work highlights the utility of tunable PAAm bead-collagen composites as micromechanical models to study the effect of adipose tissue structure on cancer cell invasion. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=106 SRC="FIGDIR/small/684224v1_ufig1.gif" ALT="Figure 1"> View larger version (56K): org.highwire.dtl.DTLVardef@d3ce0org.highwire.dtl.DTLVardef@117abb1org.highwire.dtl.DTLVardef@10917faorg.highwire.dtl.DTLVardef@55f3e_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical Abstract:C_FLOATNO Polyacrylamide bead granular hydrogels recapitulate adipose tissue structure and alter cancer cell invasion in a stiffness-dependent manner. The invasion of primary breast cancer cells through mammary adipose is influenced by the heterogeneous mechanical properties of native stromal components, namely adipocytes and extracellular matrix (left). Customizable granular hydrogels provide insight into the physical regulation of breast cancer progression by mimicking adipose tissue extracellular matrix structure (collagen I, i.) and stromal cell mechanics (polyacrylamide bead, ii.), whereby the inclusion of soft beads and/or dilute matrix promotes cancer cell migration compared to stiffer hydrogels (right). C_FIG

bioengineering↗

bioRxiv2025

Exacerbation of a Subset of Behavioral Phenotypes by Early Treatment with AAV FOXG1 Gene Replacement Therapy in a Mouse Model of FOXG1 Syndrome

FOXG1 syndrome is a severe neurodevelopmental disorder characterized by microcephaly, profound intellectual disability with communication deficits including lack of speech, impaired social interaction, increased anxiety, hyperkinetic/dyskinetic movements, seizures and abnormal sleep patterns. Mutations in a single allele of the FOXG1 gene cause disease, likely due to loss-of-function. However, current therapies do not target this root cause of FOXG1 syndrome and have little to modest therapeutic benefit on only a small subset of symptoms. Recently, we reported the beneficial effects of adeno-associated virus (AAV) human FOXG1 gene replacement therapy administered by intracerebroventricular (ICV) injection at postnatal day 6 (P6) on several behavioral deficits that are relevant to key features of human FOXG1 syndrome, in male FOXG1 mice that were engineered with a highly prevalent, patient-specific Q84P mutation. Here, we report the behavioral effects of AAV human FOXG1 gene replacement therapy administered by ICV injection in female as well as male mice and at an earlier age - postnatal day 2 (P2). Although the earlier studies had suggested that AAV FOXG1 gene replacement therapy is a promising approach for the treatment of a subset of functional deficits in human FOXG1 syndrome with no toxicity observations, our current study shows that certain motor behaviors can be negatively impacted or exacerbated by P2 treatment with AAV FOXG1 gene replacement therapy, in female but not male FOXG1 mice. Given these results, the risk-benefit balance of AAV FOXG1 gene replacement therapy in patients with FOXG1 syndrome should be carefully considered, especially in female patients.

neuroscience↗

bioRxiv2025

Neural Inflammation in Thoracic Dorsal Root Ganglia Mediates Cardiopulmonary Spinal Afferent Sensitization in Chronic Heart Failure

The cardiac sympathetic afferent reflex (CSAR) and pulmonary spinal afferent reflex (PSAR) amplify sympathetic outflow, and their sensitization contributes to chronic heart failure (CHF). Using a myocardial infarction (MI) rat model, molecular profiling, imaging, and functional assays revealed that thoracic dorsal root ganglia (DRGs) undergo marked macrophage and glial activation and suppression of voltage-gated potassium (Kv) channels after MI. In vitro studies confirmed that pro-inflammatory cytokines and activated macrophages directly reduce Kv channel expression and activity in DRG neurons. Cardiac afferents mediated cytokine transport from the heart to DRGs, driving macrophage infiltration in a cytokine receptor-dependent manner. Anti-inflammatory strategies including systemic minocycline, liposomal clodronate-induced macrophage depletion, or local epidural dexamethasone prodrug delivery reduced neuroinflammation, restored Kv channel levels, attenuated the exaggerated CSAR and PSAR, and improved cardiac remodeling. These findings highlight a cytokine uptake-driven inflammatory pathway in cardiopulmonary spinal afferent sensitization and support targeted DRG anti-inflammatory therapy as a potential cardioprotective approach. AbstractThe cardiac sympathetic afferent reflex (CSAR) and pulmonary spinal afferent reflex (PSAR) amplify sympathetic activity and may contribute to chronic heart failure (CHF). We hypothesized that neural inflammation in thoracic dorsal root ganglia (DRGs) drives cardiopulmonary afferent sensitization through suppression of voltage-gated potassium (Kv) channels after myocardial infarction (MI). MI was induced in rats by coronary ligation. Molecular profiling, immunofluorescence, tissue clearing, and functional assays were used to assess neuroinflammation and reflex responses. Post-MI, thoracic DRGs showed macrophage infiltration, glial activation, cytokine upregulation, and reduced Kv channel expression. Bulk RNA-seq identified enrichment of macrophage activation-related genes, and in vitro studies confirmed that pro-inflammatory cytokines and activated macrophages suppressed Kv channels and increased DRG neuron excitability. Epicardial injection of biotinylated TNF- demonstrated cardiac afferent-mediated cytokine transport to DRGs, inducing macrophage infiltration via a cytokine receptor-dependent mechanism. Anti-inflammatory interventions including oral minocycline, systemic macrophage depletion, and local epidural delivery of thermo-responsive hydrogel-forming dexamethasone prodrug (ProGel-Dex) significantly reduced DRG neuroinflammation, restored Kv channel levels, and attenuated exaggerated CSAR and PSAR responses. ProGel-Dex also improved cardiac chamber dilation in the post-MI rats. These findings identify a cytokine uptake-glial activation- macrophage activation pathway as a driver of cardiopulmonary afferent sensitization after MI. Targeting DRG inflammation, particularly with sustained local dexamethasone delivery using ProGel-Dex, offers a precision medicine to dampen pathological sympathetic activation and improve cardiac outcomes in CHF. HighlightsO_LIBoth cardiac (CSAR) and pulmonary (PSAR) spinal afferent reflexes are sensitized after myocardial infarction, contributing to sympathetic overactivation. C_LIO_LIThoracic dorsal root ganglia (T1-T4) exhibit macrophage activation, glial responses, pro- inflammatory cytokine upregulation, and suppression of Kv channels following MI. C_LIO_LICardiac afferents mediate receptor-dependent uptake and transport of cytokines (e.g., TNF-) from the heart to DRGs, driving macrophage infiltration and inflammation. C_LIO_LIActivated macrophages and pro-inflammatory cytokines reduce Kv channel expression and Kv current density (Ito) in DRG neurons, enhancing excitability. C_LIO_LIAnti-inflammatory strategies including minocycline, liposomal clodronate-induced macrophage depletion, and local epidural dexamethasone prodrug attenuate neuroinflammation, restore Kv channel expression, and suppress exaggerated CSAR/PSAR. C_LIO_LITargeting DRG inflammation, particularly via sustained epidural dexamethasone delivery, represents a promising cardioprotective precise medicine. C_LI

neuroscience↗

bioRxiv2025

A Single-cell Spatiotemporal Manifold of Tissue Morphology and Dynamics

Complex tissues are now characterizable at single-cell resolution, but the spatial logic underlying tissue organization remains challenging to access without effective single-cell spatial descriptors. We present a learned single-cell manifold of cell positions over time, with which one can measure tissue morphology and trace dynamics. Learning co-processes pairs of cell point clouds sampled along time using a Transformer encoder with inter-sample attention, a strategy that promotes efficient joint spatiotemporal learning. The manifold shows desirable properties of a general descriptor, e.g. interpretable cell type clusters, preserved local distances, and a pseudo-time axis, and enables common but challenging spatial reasoning tasks such as annotation of anatomical landmarks at cellular resolution and detection of subtle, transient phenotypes in large screens. Our study demonstrates a widely applicable cell-based learning strategy and representation for studying tissue biology.

developmental biology↗

bioRxiv2025

New Quantitative Cost-Impact Effectiveness Indexes to Assist in Publication Decisions by Researchers in the Open Access Era

Scientific publications have become the backbone of scientific communication since their foundation in 1665. The three main models for publishing are Traditional (or subscription-based), Open Access (OA), and Hybrid. As of July 1, 2025, the NIH requires that Author Accepted Manuscripts resulting from NIH-funded research be immediately publicly available. To comply with this new requirement, authors may be forced to pay an Article Processing Charge (APC) to publish Open Access, ranging from [~]$2000 to [~]$13,000 per article. With this change to the scientific publishing landscape, publishing costs shift from subscribers to authors causing authors to re-evaluate how they choose which journal to publish in. Here we analyze 75 popular biomedical journals to evaluate the publishing costs compared to the scientific impact (i.e. Impact Factor, CiteScore, SNIP) illustrated by three different Cost-Impact Effectiveness (CIE) metrics (APC/IF, APC/CS and APC/SNIP). To complement the new open access policy, our goal is to provide a resource to help the scientific community evaluate the impact-based cost effectiveness of different Open Access options during their journal selection process.

scientific communication and education↗

bioRxiv2025

Single-cell lineage tracing identifies hemogenic endothelial cells in the adult mouse bone marrow

During mouse development, hematopoietic stem and progenitor cells (HSPC) originate from hemogenic endothelial cells (ECs) through a process of endothelial-to-hematopoietic transition. These HSPC are thought to fully sustain adult hematopoiesis. However, it remains unknown whether adult ECs retain hemogenic potential. Here we used in vivo genetic lineage tracking at population and single-cell (sc) levels, scRNA sequencing, and bone marrow transplantation to detect hemogenic ECs in adult mice. We identify and characterize bone marrow-resident, adult Cdh5/VE-Cadherin+ ECs that produce hematopoietic cell-progeny in vitro and in mice. These adult hemogenic ECs and their hematopoietic cell progeny give rise to hematopoietic cells following adoptive transfer into adult mice. Furthermore, blood cells generated from adult and developmental ECs comparably home to peripheral tissues, where they similarly contribute to inflammatory responses. Thus, our results identify previously unrecognized bone marrow-derived adult hemogenic ECs that generate HSPC and functional mature blood cells.

cell biology↗

bioRxiv2025

Pharmacological Induction of Irreversible Senescence in Drug-Tolerant Persister Cells Prevents Tumor Relapse

Despite substantial advances in targeted therapies, most patients with advanced cancers ultimately relapse. This relapse is frequently seeded by drug-tolerant persister cells (DTPs), which persist as minimal residual disease (MRD) by adopting a reversible quiescent state and later reacquire proliferative capacity under ongoing treatment. To address this, we sought to convert quiescent DTPs into an irreversible, non-proliferative state by pharmacologically inducing senescence. Through large-scale chemical screening and combination optimization, we identified SAHA plus tilorone dihydrochloride (SIC) as a regimen that robustly induces senescence in melanoma DTPs and abolishes their proliferative potential in vitro. Mechanistically, SAHA relieves HDAC1-mediated repression of HMGA2, a key senescence driver, while tilorone synergistically inhibits autophagy to promote a fully senescent state. In a melanoma xenograft mouse model receiving MAPK-targeted therapy, SIC treatment significantly suppressed MRD progression. Importantly, SIC also induced robust senescence across diverse DTP models irrespective of tumor origin, mutational background, or prior treatment. Collectively, these findings provide proof-of-concept that converting DTPs from reversible quiescence to permanent senescence represents an effective strategy to prevent relapse under targeted therapy and position SIC as a broadly applicable pharmacological approach for durable control of residual disease in advanced cancers.

cancer biology↗

bioRxiv2025

Dynamic landscapes of gene regulatory networks in early mammalian neurogenesis: Insights into brain evolution and disorder risk

Neurogenesis--the process of generating neurons--is governed by dynamic transcriptional programs that vary across time, brain regions, and cell types, forming regionally specialized neuronal circuits. To understand these dynamics, we constructed a comprehensive gene regulatory network (GRN) resource encompassing 22 neurogenic lineages from human, macaque, and mouse, enabling cross-species and cross-regional comparisons. Leveraging state-of-the-art trajectory analysis and GRN inference, we characterized temporal regulatory dynamics and introduced a "dynamic score" to identify key subnetworks with lineage-specific dynamics, including hundreds of regulons and co-regulatory modules. Our analysis uncovered both known and novel candidate regulators driving neuronal differentiation and regional identity, spanning the entire human brain, as well as evolutionary divergence in neurogenic GRNs distinguishing human brains. Mapping risk genes to the resource helped understand associated early gene regulatory dynamics with 35 neurodevelopmental disorders and traits including autism, schizophrenia, severe intellectual disability, and microcephaly. This resource is publicly available as an interactive online platform.

developmental biology↗

bioRxiv2025

Age- and Sex- Driven Transcriptional and Metabolic Diversity in Myeloid-Derived Suppressor Cells After Mouse Sepsis

Sepsis induces profound immune dysregulation, often resulting in chronic critical illness characterized by persistent immunosuppression and poor outcomes. Myeloid-derived suppressor cells (MDSCs) are central mediators of this immunosuppressive phenotype, yet the influence of age and sex on their transcriptional and metabolic states remain poorly understood. Here, we employed single-cell RNA sequencing of splenic leukocytes from young (3-4 months) and older (18-24 months) adult male and female mice subjected to a clinically relevant murine sepsis model to define age- and sex-specific MDSC phenotypes. We identified significant differences regarding age and sex in MDSC expansion, transcriptome, canonical pathway activation, RNA velocity, mitochondrial metabolism, and predicted cell-cell communication after sepsis. Using drug2cell analysis of total leukocytes we also identified cohort-specific drug target profiles. These findings underscore the importance of age and sex in shaping sepsis-induced MDSC biology and suggest that personalized immunomodulatory strategies targeting MDSCs could improve sepsis outcomes.

immunology↗

bioRxiv2025

Widespread genomic heterogeneity at the type II NAD(P)H dehydrogenase locus predisposes Cryptosporidium to clofazimine resistance

The parasite Cryptosporidium is a leading cause of life-threatening diarrheal disease, and effective treatment is not available. The discovery of potent anti-Cryptosporidium activity of clofazimine, offered the opportunity to repurpose a drug already used to treat leprosy and tuberculosis. However, clofazimine failed in a human trial, which was attributed to poor bioavailability. Here, we observed differential susceptibility among parasite isolates which we exploit to map the mode of action to type II NADH dehydrogenase (NDH2) in an unbiased genetic cross. Targeted genetic ablation of NDH2 resulted in profound clofazimine resistance, and biochemical studies demonstrated NDH2 mediated electron transfer to clofazimine. Through genomic analyses we uncovered heterogeneity at the NDH2 locus for C. parvum and C. hominis and widespread carriage of a conserved attenuated allele across multiple continents. This heterogeneity allows parasites genomically linked through frequent sexual recombination to adjust to changing NDH2 requirements and predisposes Cryptosporidium to evade clofazimine treatment.

microbiology↗

bioRxiv2025

A deep learning and co-conservation framework enable discovery of non-canonical Cas proteins

CRISPR-Cas systems are central to prokaryotic adaptive immunity, widely harnessed for biotechnology. Yet, their vast and uncharacterized diversity, especially non-canonical variants, impedes full exploitation. Here we present BioPrinCRISPR, a class-agnostic computational framework leveraging gene co-conservation, protein domain co-occurrence, and embedding similarity to identify and characterize CRISPR-Cas systems across prokaryotic genomes. Applying BioPrinCRISPR to over one million bacterial genomes, we uncovered extensive canonical and uncharacterized systems, revealing a rich landscape of atypical Cas proteins and novel domain architectures. Notably, we identified recurrent fusion proteins with unique enzymatic combinations, suggesting roles in regulatory control or nucleic acid remodeling. Experimental validation of two divergent Cas13an-like effectors demonstrated RNA knockdown capacity in human cells, confirming our frameworks predictive power. These findings expand the functional repertoire of CRISPR-associated proteins and highlight unexplored modes of microbial immunity. BioPrinCRISPR thus stands as a powerful tool for comprehensively mapping CRISPR-Cas diversity, offering new insights into prokaryotic defense and facilitating discovery of novel candidates for next-generation genome engineering. An accompanying interactive web platform was also developed to facilitate data exploration.

synthetic biology↗