Biology subjects

Fischer, M.

Publications and source records attributed to Fischer, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Digital pathological classification of peripheral neuroblastic tumors across multi-continent cohorts

Peripheral neuroblastic tumors (pNTs) are embryonal tumors of neural crest origin with highly variable clinical behaviors, ranging from spontaneous regression to aggressive and fatal disease. The International Neuroblastoma Pathology Classification (INPC) defines four diagnostic categories and stratifies tumors into Favorable Histology (FH) or Unfavorable Histology (UH) group based on age-linked assessment of tumor differentiation/maturation and the Mitosis-Karyorrhexis Index (MKI). Prognostic distinction according to INPC offers significant prediction of clinical outcomes, with patients harboring FH tumors demonstrating longer overall and event-free survival than those with UH tumor. Here, we assembled the largest multi-continental whole-slide histology imaging dataset of pNTs to date, comprising 2,030 tumors from the United States, Canada, Australia, New Zealand, Germany and Japan. Using this dataset, we developed NB-PathAssist, a computational pathology framework for automated INPC-based classification from digitized whole-slide images. NB-PathAssist integrates foundation-model-based feature extraction with an archetype-guided SummaryMixing architecture that compresses whole-slide morphology into representative histologic tokens for tumor-level classification. To automate MKI assessment, we manually annotated 14,049 nuclei, classifying them as mitotic-karyorrhectic (MK) tumor cells, non-MK tumor cells, or non-tumor cells. The resulting model was applied to phenotype cells in whole-slide images across 1,649 tissue sections. Across geographically and institutionally diverse cohorts, NB-PathAssist reproducibly assessed key diagnostic features and generated prognostic classifications concordant with reference INPC annotations. The average balanced accuracy for classifying tumor categories, grade of neuroblastic differentiation, MKI and prognostic groups achieved 0.84, 0.86, 0.89 and 0.96, respectively. We packaged the NB-PathAssist algorithms into an end-to-end online platform for scalable and standardized AI-assisted assessment of pNTs.

pathology↗

bioRxiv2026

Bivalent Inhibitor Development for a Dynamic Epigenetic Tandem Reader Protein Using a Combinatorial Histone Code

Epigenetic readers are a class of proteins that recognize specific chemical modifications on histones to differentially regulate gene expression. Aberrant expression of readers can drive the progression of many diseases and cancers, making this protein class viable therapeutic targets. Understanding the landscape of histone modifications recognized by reader domains, and the structural mechanisms that drive these molecular recognition events, is crucial for guiding the design of pharmaceutically relevant chemical probes. BPTF contains a plant homeodomain (PHD) finger and tandem bromodomain (BRD). Here, we expand upon previous studies that found the BPTF BRD can engage acetyllysine modifications on the N-terminus of histone H3. We uncover H3K4me3K14ac as the specific modifications recognized by the PHD BRD cassette, which is confirmed by crystallography. Using orthogonal methods, our work explores how these modifications can be read cooperatively, including in cis. We report the first experimental evidence proposing a ligand-induced conformational change between the two reader domains of BPTF, supporting previous computational approaches that have predicted a macromolecular rearrangement. We leverage these structural insights to rationally design a peptide-small molecule conjugate MJ-1 that inhibits both domains of BPTF and overcomes ligandability challenges associated with PHD-finger-containing proteins. The results presented here elucidate the molecular basis of the bivalent recognition of multiply modified histone H3 by BPTF and provide structural insight for developing compounds targeting the PHD finger of BPTF for therapeutic applications.

biochemistry↗

bioRxiv2026

Cerebral organoids recapitulate interneuron chain migration in the human cortex

The human brain is incomplete at birth, with streams of late-born interneurons migrating into the postnatal cortex. This process is absent in rodents, limiting mechanistic investigation to post-mortem tissue. Here, we show that human cerebral organoids cultured for over six months recapitulate postnatal interneuron migration, enabling its mechanistic and genetic dissection. Live imaging and mathematical modeling revealed that interneurons intrinsically migrate in chains, while astrocyte interactions promote stream organization. Spatial and single-cell transcriptomics identified a distinct molecular signature of human postnatal migratory streams enriched for neurodevelopmental disorder-associated genes. Perturbation of the autism-associated genes CNTN5 and FGF14 differentially disrupted chain organization and migration. Thus, long-term cerebral organoids enable mechanistic analysis of previously inaccessible aspects of postnatal human brain development and their contributions to neurodevelopmental disease.

developmental biology↗

bioRxiv2026

Viral infection and virophage co-infection induce distinct remodeling of host lipidome

Virophages are small double-stranded DNA viruses that co-infect eukaryotic cells along with giant viruses. They are widespread in aquatic ecosystems and can influence microbial population dynamics by acting as an adaptive antiviral defense system, limiting production of giant virus progeny. Giant viruses extensively reprogram host metabolism to support their replication, yet little is known about how this process is altered by virophages. Characterizing these alterations may reveal the metabolic mechanisms underlying virophage-mediated changes in infection outcomes. Here, we used one of the few established host-giant virus-virophage experimental systems, consisting of the marine heterotrophic flagellate Cafeteria burkhardae, its giant virus CroV, and the virophage mavirus, to investigate lipid remodeling during viral infection and virophage co-infection. We found that infection by the giant virus strongly induced triacylglycerols containing furan fatty acids (FuFAs), a class of potent antioxidants that may protect infected cells and newly formed virions from oxidative damage. These lipids were also detected in purified giant virus particles, linking their accumulation to virus production. Co-infection with the virophage reduced the FuFA response and was instead characterized by pronounced accumulation of the betaine lipid diacylglyceryltrimethylhomoserine (DGTS). Most of the induced DGTS species were also present in the giant virus particles, suggesting that their accumulation during co-infection may be associated with altered giant virus production and lipid utilization. Together, these findings show that virophage co-infection reshapes giant virus-induced remodeling of the host lipidome, revealing a potential metabolic basis for their effects on virus production and infection outcomes.

microbiology↗

bioRxiv2026

Quantitative and sensitive neuroblastoma minimal residual disease detection using extrachromosomal DNA (ecDNA) breakpoints

Sensitive detection of minimal residual disease (MRD) remains a major unmet need in high-risk neuroblastoma. MYCN amplification, a hallmark of high-risk disease, typically occurs on extrachromosomal DNA (ecDNA), but the potential of ecDNA-associated genomic rearrangements for individualized MRD monitoring has not been fully exploited. Here, we applied neuroblastoma-specific hybrid capture-based panel sequencing to identify patient-unique breakpoints within MYCN amplicons, and used Circle-seq and Nanopore sequencing to resolve the extrachromosomal amplicon structure in representative samples. Analysis of 8 neuroblastoma cell lines and 22 primary tumors identified 69 tumor-specific breakpoints. Those selected for assay development were validated by breakpoint-specific PCR and Sanger sequencing. Breakpoints detected in primary tumors remained detectable at relapse, supporting their stability as MRD markers. Breakpoint-specific real-time quantitative PCR and droplet digital PCR detected these junctions in bone marrow aspirates with high specificity and reached sensitivities down to a tumor DNA fraction of 10^-6. We applied this approach to 53 serial bone marrow aspirates from 14 patients with high-risk neuroblastoma to monitor MRD dynamics, resolving treatment response and molecular persistence. In six samples, breakpoint-positive DNA was detected in bone marrow that was negative by conventional cytology and immunocytology, highlighting the added value of molecular monitoring. Together, these findings establish ecDNA breakpoint-based detection as a strategy for MRD assessment in neuroblastoma, that is, in principle, applicable to any ecDNA-amplified oncogene.

cancer biology↗

bioRxiv2026

Sediment depth-dependent trait expression controls species contributions to nutrient cycling

Global biodiversity loss is restructuring ecological communities and compromising ecosystem functioning. Yet, we still lack an empirical understanding of how specific trait combinations regulate ecosystem processes or how their functional expression is organised within the immediate environment. Here, we investigated trait-expression across 17 functionally contrasting sediment-dwelling marine invertebrate species. We show that while sediment reworking and burrow ventilation are depth dependent, their influence on nutrient concentrations are highly nutrient-specific. Our analyses reveal that nutrient concentrations are better explained by continuous, spatially explicit trait combinations than by categorical bioturbation modes. Surface modification was associated with higher ammonium concentrations, moderated by ventilation, while deeper sediment reworking and biomass were associated with higher nitrite concentrations. Phosphate relationships were weak, and nitrate was not explained by the measured traits. These results establish a mechanistic baseline for species-specific trait-nutrient relationships under controlled conditions. This shift from categorical trait assignments to a spatially explicit, empirically resolved trait-interaction framework provides a mechanistic foundation for predicting how changes in species composition may alter benthic nutrient cycling.

ecology↗

bioRxiv2026

MYC-MIZ1 Complexes at Enhancers Tune Neuroendocrine Identity of Small Cell Lung Cancer

MYC family members have been extensively studied as undruggable transcription factors regulating oncogenic signaling in highly aggressive tumors such as small cell lung cancer (SCLC), via promoter binding. Here, leveraging the previously described Myc-driven SCLC mouse model (RPM), we generated RPM-Miz1{Delta}POZ (RPMM) mice to uncover a Myc-dependent regulation of neuroendocrine (NE) differentiation, via enhancers. Our functional and genomic analyses reveal that Miz1 facilitates Myc binding to low-affinity E-boxes at distal chromosomal regions, thereby enabling Myc occupancy at sites with otherwise limited intrinsic affinity. We further show that SCLC patients and cellular models share an enrichment of low-affinity E-Box Myc binding motifs at enhancer regions that loop to genes of classic neuroendocrine differentiation. Integrated epigenetic and genomic analyses with AI-modeling implicate Myc/Miz1 binding at enhancers as the determinant for the expression of bona-fide neuroendocrine genes. In RPMM tumors, the suppression of neuroendocrine identity is paralleled by a redistribution of Myc protein towards promoter-proximal regions, hyper-activation of Myc transcriptional programs, apoptotic priming and enhanced sensitivity to etoposide. Together, these findings uncover Miz1/Myc-engaged enhancers as a central hub for neuroendocrine lineage programs and provide a mechanistic basis for a targeted inhibition of Miz1 to boost chemosensitivity in SCLC.

cancer biology↗

bioRxiv2026

Prevalent glutamyl-endopeptidases in the commensal skin microbiome have itch-relevant activity

Atopic dermatitis (AD) is frequently accompanied by pruritus, which has predominantly been attributed to skin colonization by Staphylococcus aureus, particularly through cleavage of protease-activated receptor 1 (PAR1) by the glutamyl endopeptidase (GEP) V8 protease. Whether related GEPs from other skin-associated staphylococci contribute to this process remains unclear. Here, we analyzed 273 staphylococcal isolates from skin swabs of 10 AD patients with pruritus, dominated by S. aureus and Staphylococcus epidermidis. Genome mining using a custom hidden Markov model identified 678 candidate GEPs, which were clustered and resolved into five structurally distinct protease architectures. Representative proteases (V8, Esp, SplB, Csp, and Hsp) were expressed and characterized. Esp displayed GEP activity and PAR1 tethered-ligand cleavage comparable to V8, generating noncanonical cleavage products, while Csp cleaved PAR1 with reduced but substantial efficiency. All representative proteases significantly disrupted barrier integrity in an epithelial barrier model. Analysis of isolate genomes and publicly available Staphylococcus genomes showed that V8 and Esp are highly conserved and largely species-restricted, whereas Csp is more broadly distributed across species. These findings identify Esp and Csp as functional GEP virulence factors in S. epidermidis and S. capitis, capable of activating itch signaling and compromising barrier function. Our study suggests that GEP-mediated pruritus and barrier dysfunction in AD may arise not only from pathogens like S. aureus, but also from commensals or opportunistic pathogens such as S. epidermidis and S. capitis. ImportanceStaphylococcus aureus colonization on the skin is closely associated with itch in atopic dermatitis (AD) through a secreted protease that cleaves PAR1 on sensory neurons. However, AD patients can experience pruritus without S. aureus colonization. This raises the question of whether other skin-colonizing staphylococci contribute to this process. We identify glutamyl endopeptidase homologs, including Esp from Staphylococcus epidermidis and Csp from Staphylococcus capitis, that cleave the same itch receptor and disrupt epithelial barrier integrity. These serine proteases are distributed across staphylococcal species that colonize human skin. Therefore, itch and barrier dysfunction in AD may not be restricted to S. aureus but instead arise from the proteolytic activity of multiple staphylococcal species. This functional redundancy means that other staphylococcal species can sustain GEP-driven itch and barrier dysfunction even in the absence of S. aureus, suggesting that therapeutic strategies targeting only S. aureus may overlook these alternative drivers of disease.

microbiology↗

bioRxiv2025

Dapagliflozin mitigates hypoxia-induced metabolic stress, kidney tubular cell death and fibrosis

Sodium-glucose co-transporter 2 inhibitors (SGLT2-i) slow progression of kidney disease but therapeutic mechanisms remain elusive. Here we report the beneficial effect of dapagliflozin on hypoxia-mediated kidney tubular epithelial cell injury, a contributing factor to kidney disease progression, using a human pluripotent stem cell (hPSC)-derived hypoxic kidney organoid model. Hypoxic organoids showed increased expression of Hypoxia Inducible Factor (HIF)-associated transcriptional targets, decreased tricarboxylic acid (TCA) cycle metabolites and mitochondrial {beta}-oxidation protein expression, and activated unfolded protein response. A transcriptional signature derived from hypoxic organoids 1) identified a subgroup of individuals whose kidney disease subsequently progressed, and 2) correlated with worse tubular injury. Dapagliflozin enhanced mitochondrial stress response resulting in reversed hypoxia-induced tubular epithelial cell apoptosis, reactive oxygen species (ROS) accumulation, and organoid fibrosis. These results indicate that dapagliflozin may contribute to improved kidney disease outcomes by attenuating hypoxia-induced metabolic stress-mediated tubular epithelial cell injury.

cell biology↗

bioRxiv2025

Genomic architecture of species-specific sex pheromone variation and mate choice

Speciation often begins with subtle changes in sexual communication and mate choice, yet the genetic basis of these early reproductive barriers remains largely unresolved. Here, we dissect the chemical and genomic architecture underlying species-specific female cuticular sex pheromones and their role in mate choice in two closely related parasitoid wasp species. Using high-resolution quantitative trait locus (QTL) mapping, fine-scale chemical profiling, and behavioral assays on hybrid populations, we identify three methyl-branched alkanes as key pheromonal compounds that strongly predict male mating preferences. QTL explaining their species-specific variation partially co-localize with genomic regions enriched for candidate genes involved in cuticular hydrocarbon biosynthesis, including cytochrome P450 enzymes and fatty acid synthases. These findings suggest a potential mechanistic link between the variation in these gene clusters and species-specific chemical signaling. Further comparative analyses reveal hitherto unrecognized sex-specific regulatory effects, cytoplasmic influences, and complex genomic interactions shaping the variation in these pheromonal profiles. This study is among the first to connect individual pheromone compounds with mate choice and their underlying genomic basis in a haplodiploid system, offering a rare glimpse into how chemical divergence can reinforce behavioral isolation and potentially drive early speciation.

evolutionary biology↗

bioRxiv2025

Breaking the ''one nucleus, one whole genome'' rule: Neurospora crassa separates its haploid chromosomes into different nuclei

The nucleus is a defining feature of eukaryotic cells, compartmentalizing the genome to enable precise regulation of diverse cellular processes. The long-standing paradigm in textbooks states that each nucleus carries at least a complete haploid genome --the "one nucleus, one whole genome" rule. A striking exception was recently uncovered: in two sclerotia-forming plant pathogenic fungi in the Sclerotiniaceae family, Sclerotinia sclerotiorum and Botrytis cinerea, haploid chromosomes are irregularly distributed across multiple nuclei. However, whether such phenomenon occurs in other eukaryotes, particularly in non-pathogenic fungi, is unclear. Through a literature survey, we identified many fungi that can potentially also separate their haploid chromosomes across different nuclei. Interestingly, Neurospora crassa, a foundational fungal genetics model, came out as a candidate. Its conidia, typically containing two or three nuclei, were believed to harbor a complete haploid genome within each nucleus. However, using approaches including chromosome counting, flow cytometry, and fluorescence in situ hybridization, we found that haploid chromosomes in N. crassa can be unevenly distributed among multiple nuclei. These findings challenge longstanding assumptions in fungal genetics and provide new directions for investigating genome organization. Our results indicate that the organisms violating the "one nucleus, one whole genome" rule are beyond sclerotia-forming pathogenic fungi. Since over 90% of fungi have not even been described, we propose that many more of them may likewise partition their genomes non-uniformly across nuclei, a process that could facilitate their adaptation and evolution.

microbiology↗

bioRxiv2025

Dynamic neutrophil lipidome remodeling during induction of NETosis

Neutrophil Extracellular Trap formation (NETosis) affects a wide variety of clinically relevant human diseases. Although lipid remodeling is essential for neutrophil function and membrane rupture during NETosis, the neutrophil lipidome and its dynamics have not been characterized. Thus, we establish the first quantitative lipidome of human neutrophils comprising 1,039 species across nine orders of magnitude and map its remodeling during NETosis. NET formation caused profound alterations in the phosphatidylinositol, phosphatidic acid, diacylglycerol and lysoglycerophospholipid levels. Calcium- and reactive oxygen species-dependent NETosis pathways displayed distinct lipidomic trajectories, yet converged on the significance of phospholipid lipase networks. Pharmacological inhibition of this networks altered lipid composition and markedly impaired NETosis, while diacylglycerol (DG) treatment revoked the effect. Altogether our findings reveal lipid remodeling as a fundamental determinant of NETosis and identify interconnected and dependent phospholipid lipase networks with downstream DG-dependent signaling as a potential therapeutic target in NET-associated diseases.

molecular biology↗

bioRxiv2025

Voxel-accurate MRI-microscopy correlation enables AI-powered prediction of brain disease states

Magnetic resonance imaging (MRI) is essential for visualizing the healthy and diseased brain, yet the cellular basis of MRI signal and how it changes over time remain poorly understood. Here, we present BRIDGE (Brain Radiological Imaging with Deep-learning based Ground-Truth Exploration), a platform integrating in vivo MRI with in vivo two-photon (2P) and ex vivo super-resolution microscopy using a multi-step, iterative co-registration pipeline. It enables in vivo, longitudinal, and voxel-precise mapping of MRI signals to their cellular origins for the first time. The registered overlay reveals the cellular and anatomical origins of MRI signals and enables training of convolutional neural networks to enhance the effective resolution of MRI. Using BRIDGE, we identified a microenvironmental vessel biomarker for early metastatic colonization in patient-derived xenograft models of brain metastasis. In particular we found that distinct T2*-weighted hypointense lesions correspond to reduced blood flow and erythrostasis in perimetastatic capillaries. In glioma, longitudinal intravital studies further demonstrated direct correlations between non-vasogenic T2-weighted signal changes and patient-dependent tumor growth dynamics. Taken together, BRIDGE advances radiological interpretation by establishing a microscopic ground truth for MRI signatures over time, enabling deep learning-based predictive histology, and providing cellular-level insights into tumor microenvironment features with direct clinical imaging implications. Graphical abstractBRIDGE enables longitudinal voxel-to-voxel correlation and ground truth based automatic segmentation of MR images O_FIG O_LINKSMALLFIG WIDTH=177 HEIGHT=200 SRC="FIGDIR/small/680637v1_ufig1.gif" ALT="Figure 1"> View larger version (73K): org.highwire.dtl.DTLVardef@f1f64eorg.highwire.dtl.DTLVardef@1619e3eorg.highwire.dtl.DTLVardef@1dc2e7forg.highwire.dtl.DTLVardef@7097e1_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2025

LCK-targeting molecular glues overcome resistance to inhibitor-based therapy in T-cell acute lymphoblastic leukemia

Drug resistance is a major challenge in cancer therapy, especially in the context of kinase inhibitors. While targeted protein degradation (TPD) was a distinct mode of action compared to inhibition-based therapeutic targeting, the potential value of TPD in drug-resistant cancer remains unclear. Here, we report the discovery of cereblon-recruiting molecular glue degraders (MGDs) targeting LCK, an oncogenic kinase in T-cell acute lymphoblastic leukemia (T-ALL). By high-throughput screening and medicinal chemistry optimization, we developed a series of MGDs that induced CRBN-dependent degradation of LCK as well as potent cytotoxicity in T-ALL in vitro. Structure-activity relationship analysis and ternary complex modeling revealed a non-canonical degron at the LCK-CRBN interface involving the G-loop, whose mutation disrupts this interaction. Unlike inhibitors and inhibitor-based PROTACs, these MGDs engage LCK in regions distal to the ATP binding site and thus their activities in T-ALL are not affected by gate-keeper LCK mutations that drive resistance to inhibitor-based therapeutics. Taken together, our data underscore the potential of LCK-targeting MGDs as a strategy to overcome kinase inhibitor resistance in T-ALL, highlighting a potentially generalizable strategy in cancer therapy.

cancer biology↗

bioRxiv2025

Accurate Prediction of ecDNA in Interphase Cancer Cells using Deep Neural Networks

Oncogene amplification is a key driver of cancer pathogenesis and is often mediated by extrachromosomal DNA (ecDNA). EcDNA amplifications are associated with increased pathogenicity of cancer and poorer outcomes for patients. EcDNA can be detected accurately using fluorescence in situ hybridization (FISH) when cells are arrested in metaphase. However, the majority of cancer cells are non-mitotic and must be analyzed in interphase, where it is difficult to discern extrachromosomal amplifications from chromosomal amplifications. Thus, there is a need for methods that accurately predict oncogene amplification status from interphase cells. Here, we present interSeg, a deep learning-based tool to cytogenetically determine the amplification status as EC-amp, HSR-amp, or not amplified from interphase FISH images. We trained and validated interSeg on 652 images (40,446 nuclei). Tests on 215 cultured cell and tissue model images (9,733 nuclei) showed 89% and 97% accuracy at the nuclear and sample levels, respectively. The neuroblastoma patient tissue hold-out set (67 samples and 1,937 nuclei) also revealed 97% accuracy at the sample level in detecting the presence of focal amplification. In experimentally and computationally mixed images, interSeg accurately predicted the level of heterogeneity. The results showcase interSeg as an important method for analyzing oncogene amplifications.

cancer biology↗

bioRxiv2025

UV laser crosslinking uncovers novel DNA-binding pattern of CTCF

Eukaryotic genomes are spatially organized to regulate gene expression, and CTCF is a key architectural protein that links chromatin topology to transcriptional control. Accurate mapping of CTCF-DNA interactions is critical for understanding gene regulation. However, conventional formaldehyde-based crosslinking in ChIP-seq biases towards long-lived protein-DNA interactions. We substituted chemical crosslinking with ultraviolet (UV) laser crosslinking (UV ChIP-seq) to capture both stable and dynamic CTCF-DNA interactions in living K-562 cells. UV ChIP-seq identified 38,706 CTCF binding sites, 70% of which were previously undetected by standard formaldehyde (FA) ChIP-seq. These UV-specific sites were enriched in active promoters, enhancers, and short-range chromatin loops, whereas formaldehyde ChIP-seq preferentially detected CTCF at topologically associated domain (TAD) boundaries and long-range loops. CTCF was detected at 85% of active transcription start sites, and when uniquely FA-identified sites were included, over 90% of active promoters were detected. De novo motif analysis also revealed noncanonical CTCF motifs at UV-specific sites, suggesting alternative binding configurations. These results expand the CTCF cistrome, redefine its role in active chromatin, and underscore the need for complementary crosslinking strategies to characterize the full spectrum of transcription factor-DNA interactions.

genomics↗

bioRxiv2025

Single-Stranded nucleic acid binding enhances the in vitro catalytic activity of Chikungunya virus nsP2 protease

Chikungunya virus (CHIKV) is an emerging arbovirus whose replication relies on the multifunctional nonstructural protein 2 (nsP2), particularly its viral protease (nsP2pro), which is essential for polyprotein processing. In this study, we investigated how interactions with nucleic acids influence nsP2pro activity. Using high-throughput sequencing-fluorescent ligand interaction profiling, we identified specific single-stranded DNA aptamers that enhanced nsP2pro activity. Additionally, both random single-stranded DNA and single-stranded RNA were found to stimulate protease activity, whereas double-stranded DNA showed no such effect. Circular dichroism spectroscopy and secondary structure predictions confirmed that the identified aptamers adopt stable folded conformations. Similarly, structured RNA sequences were also capable of promoting protease activity. The observed stimulatory effect depended on the nucleic acid strand type, length, and buffer conditions, suggesting the involvement of electrostatic interactions. Molecular docking analyses further let us assume that these nucleic acids interact specifically with the nsP2pro methyltransferase domain. Our findings provide novel insights into the regulation of nsP2pro, enhancing our understanding of CHIKV replication mechanisms, and may guide future antiviral development strategies.

biochemistry↗

bioRxiv2025

Liver biopsies obtained throughout SIV infection reveal evolving interferon stimulated protein expression within distinct monocyte/macrophage subsets

ABSTRACTLiver dysfunction is more common and more severe among people with HIV than in the general population. Our previous transcriptomic analysis identified an increased hepatic type-1 interferon (IFN-1) response in simian immunodeficiency virus (SIV) infected rhesus macaques, including pronounced upregulation of the IFN-1 stimulated gene product MX1. Here, we interrogated the role of different cell types in the IFN-1 response, focusing on macrophage subsets. During the acute phase of SIV infection, the expression of MX1 in liver biopsies was elevated in the resident macrophage Kupffer cells (KCs, CD163+ CD206+) as well as liver sinusoidal endothelial cells (LSECs, CD163- CD206+). Chronic infection was associated with increased MX1 expression both within KCs and the recruited monocyte-derived macrophages (MdMs, CD163+ CD206-) although the KCs were associated with the highest MX1 expression levels. We explored factors in the liver potentially associated with the macrophage IFN-1 response: 1) SIV DNA load, 2) bacterial DNA load (assessed via SIV DNA and 16S bacterial DNA qPCR, respectively), and 3) acute-phase hepatocyte lipid accumulation (steatosis). Both SIV and bacteria were elevated during chronic infection and directly correlated with MdM frequency. KC frequency did not correlate with SIV load but inversely correlated with bacterial load and also correlated directly with hepatocyte microvesicular steatosis in acute infection. Hepatocytes expressed variable levels of MX1 during acute and chronic infection. Overall, our data identify MdMs, LSECs and KCs as contributors to the heightened expression of MX1 in the liver during SIV infection. KCs express the highest levels of MX1 and therefore represent a potential target to reduce liver inflammation in people with HIV. AUTHOR SUMMARYLiver disease disproportionately affects people with HIV (PWH). However, liver biopsies are generally not indicated in humans, making the immune mechanisms underlying HIV-driven liver dysfunction difficult to study. Using a model of HIV infection in which rhesus macaques are infected with SIV, we previously found a strong upregulation of type 1 interferon (IFN-1) signaling as well as an increased number of CD68+ monocyte/macrophage cells in the liver during chronic infection. Here we used longitudinally collected liver biopsies from SIV-infected macaques to describe the kinetics of the IFN-1 response, focusing on MX1, which was a top differentially expressed gene in our previous transcriptomic screen. We also defined two populations of liver macrophages - resident Kupffer cells and recruited monocyte-derived macrophages - to identify which cells produce MX1, what stimuli the cells respond to, and where the cells accumulate within the liver. Our results indicate that Kupffer cells are the major producers of MX1 during acute and chronic infection and that their frequency in the liver correlates with lipid accumulation (steatosis) during acute infection. These data provide insights into how Kupffer cells may promote inflammation and fibrosis and identify Kupffer cells as an important target to limit liver disease in PWH.

immunology↗