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bioRxiv2026

T cells compete via reverse MHC class I signaling at the synapse with dendritic cells to secure Golgi recruitment for activation

Interleukin-12 (IL-12) is a key immunostimulatory cytokine produced by dendritic cells (DCs) upon infection that plays a central role in the activation and differentiation of cytotoxic T cells. Notably, IL-12 is secreted in a highly polarized manner from late endosomes or lysosomes at the contact interface between a DC and a T cell, known as the immunological synapse. However, the signaling mechanisms initiating this spatially restricted cytokine release remain poorly defined. Here, using artificial T cell mimics, beads coated with T cell surface ligands, we show that antigen recognition induces recruitment of the DCs microtubule organizing center (MTOC) and Golgi apparatus to the immunological synapse via reverse MHC class I signaling. Our results further indicate that the signaling pathways governing MTOC polarization are highly conserved in DCs, consistent with mechanisms described in other immune cell types. As newly synthesized IL-12 traffics through the Golgi, this intracellular reorientation facilitates localized release of IL-12 directly at the site of T cell engagement, likely enabling DCs to focus their stimulatory capacity on responsive T cells within the crowded environment of secondary lymphoid organs. Furthermore, by applying spatially patterned antibody arrays targeting MHC class I, we reveal that MTOC polarization is biased toward sites exhibiting the strongest reverse MHC class I signaling. This suggests that IL-12 is preferentially released at synapses formed with T cells displaying higher T cell receptor affinity, providing a mechanism for selection of the most potent T cell.

immunology↗

bioRxiv2026

A gavage-fomite based method to generate mouse models with natural microbiota

Laboratory-raised specific pathogen-free (SPF) mice have been indispensable for fundamental immunology research, yet their reliability in predicting human clinical outcomes has been questionable. A major factor contributing to this disconnect is the sanitized housing environment, which deprives laboratory mice of physiological microbial exposure critical for immune maturation. Various approaches have been developed to introduce microbes to SPF mice, aiming to mimic human-like microbial experiences and engender adult human-like immune traits. However, some of these methods, specifically the pet store mice cohousing approach suffer from significant variability in pathogen exposure driven by the uncontrolled nature of microbial exchange and is associated with heightened mortality. Here we present an alternative gavage-fomite (GaF) method that exposes mice to a similarly diverse array of pathogens and commensal as the pet store cohousing method while limiting mortality. GaF-treated mice exhibited consistent gut microbial composition, robust immune maturation characterized by mucosal T-cell distribution, elevated serum inflammatory cytokines, and a splenic immune transcriptional signature closely aligned with that of adult humans. Furthermore, these mice demonstrated enhanced protection against a virulent bacterial challenge. The simplicity, and effectiveness of the GaF method for generating mice with natural microbiota, may support broader use of these models in basic and translational immunological research across institutions.

immunology↗

bioRxiv2026

Chitin oligomers induce atypical NLRP3 inflammasome activation and innate immune training

Chitin is a highly abundant poly- N-acetyl-glucosamine (GlcNAc) and linked to immune recognition of fungal infections and asthma in humans. Ubiquitous in fungi and insects, in mammals and plants chitin represents a microbe-associated molecular pattern (MAMP) and whereas highly polymeric chitin is insoluble and immunologically inert, soluble chitin oligomers of 6 to 15 GlcNAc activate immediate pro-inflammatory cytokine release via TLR2 in human immune cells. However, TLR2 ligands do not the most typical activators of the NLRP3 inflammasome pathway or innate immune training, a phenomenon of long-term immunological remodeling. Here we show that especially 16-20 GlcNAc long chitin oligomers activate NLRP3-dependent IL-1{beta} and IL-18 release in human myeloid immune cells in an atypical, phagocytosis-dependent manner. Moreover, phagocytosis and methyl transferase activity were essential for innate immune training, by which the same chito-oligomer-training enhanced TNF release in primary murine and human immune cells. Collectively, this suggests that oligomer length impacts on the immune features of chitin which can be customized using glycan assembly.

immunology↗

bioRxiv2026

Multi-Omics Clustering Differentiates the Total and Intact HIV Reservoirs and Related Host Immune Mechanisms

HIV reservoirs are heterogeneous across individuals, yet host determinants of this variability remain unclear. Applying multi-omics clustering to 1,230 people with HIV, integrating omics and functional data from circulating immune cells (transcriptomics, DNA methylation, immune phenotyping, ex-vivo cytokine production capacity), plasma proteomics, and CD4+ T-cell reservoir measurements (total and intact HIV-DNA copies), revealed three immunologically distinct endotypes: All Low (low total/low intact reservoir size), All High (high total/high intact reservoir size) and Mixed (high total/low intact reservoir size). Per endotype, distinct immune landscapes were noticed in single-layer analyses as well as differences in clinical signatures. Applying non-linear machine learning across all layers, key predictors not captured by linear single-layer approaches showed IFN-{gamma} production and TCF7/AK5 expression across T-cell and NK-cell populations as well as IL-1{beta}/MCP-1 production after 24h stimulation and MAN1C1/EDAR expression on T-cell populations, linked to intact and total reservoir size, respectively. This host-virus integrative multi-omics framework provides a systems-level resource that may help to personalize reservoir-reducing intervention studies aiming for HIV cure and/or comorbidity reductions. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/734029v4_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@16fded7org.highwire.dtl.DTLVardef@18f2e69org.highwire.dtl.DTLVardef@12ffc9borg.highwire.dtl.DTLVardef@17127cc_HPS_FORMAT_FIGEXP M_FIG a) Multi-omics clustering of 1,230 virally suppressed PLHIV identified three immunologically distinct endotypes: All Low (n=428), Mixed (n=483), and All High (n=280), with distinct total and intact HIV reservoir sizes. b) Single-layer analyses reveal characteristic immune landscapes: All Low Th1-skewed, naive T cells (immunophenotyping), high IFN-{gamma} production (7-day), downregulated Type I IFN pathways (bulk transcriptome); Mixed intermediate Th1/Th2, CD8 and CD4 effector memory T cells (immunophenotyping), IL-5 production (7-day), downregulated Type I IFN pathways (bulk transcriptome); All High Th2-skewed, CD4 effector memory T cells (immunophenotyping), high IL-5 production (7-day), upregulated Type I IFN pathways (bulk transcriptome). c) Endotypes carry distinct comorbidity burdens: All Low lower carotid plaque, AIDS-defining malignancies, and residual viremia; Mixed intermediate burden; All High highest carotid plaque, AIDS-defining malignancies, opportunistic infections, and residual viremia. d) Non-linear classification models (XGBoost) prioritize top host predictive markers: IFN-{gamma} response (7-day), TCF7 and AK5 expression in CD4/CD8 T-cells and NK-cells (characterize All Low; IL-1 response (24-hour), MAN1C1 and EDAR in CD4/CD8 T-cells, and MCP1 response (24-hour) characterize All High. Created in BioRender. C_FIG

immunology↗

bioRxiv2026

Microbial induction of MHC-II expression in colon cancer cells overcomes immunotherapy resistance and limits metastasis

Colorectal cancer remains a major cause of cancer mortality, and most microsatellite stable tumors derive little benefit from immune checkpoint blockade. Here, we identify a microbiome-dependent mechanism that converts immune-refractory colorectal cancer into a more immunologically responsive state. Using orthotopic mouse models spanning distinct genetic and immunologic contexts, we show that a Helicobacter-containing microbiome suppresses primary tumor growth and limits metastasis. This protective state is associated with increased intratumoral lymphocyte infiltration and stronger effector programs. Mechanistically, microbial exposure induces MHC class II expression in colon cancer cells to promote anti-tumor immunity. Tumor-intrinsic loss of CIITA abrogates microbial protection, whereas enforced CIITA expression is sufficient to increase intratumoral T cell accumulation, restrict progression and metastasis, and sensitize microsatellite-stable tumors to PD-1 and CTLA-4 blockade. In human microsatellite-stable patient-derived organoids, increased cancer-cell MHC-II enhanced interactions with autologous immune cells and increased tumor cell apoptosis. Together, these findings define a microbiome-cancer cell antigen presentation axis that restrains metastasis and overcomes immunotherapy resistance in colorectal cancer.

immunology↗

bioRxiv2026

Ensembles of in silico structures enable T cell peptide-MHC binding prediction

Adaptive immunity relies on T-cell receptor (TCR) recognition of peptides presented by the major histocompatibility complex (pMHC). Accurate prediction of TCR:pMHC binding pairs from sequence data remains a longstanding challenge in computational immunology, limiting the development of precision immunotherapies like cancer vaccines and adoptive cell therapies. Here, we present enFoldX (ensemble of Folded compleXes), a structure-based approach leveraging biophysical characterization of AlphaFold3-generated ensembles to classify TCR:pMHC sequence pairs as cognate versus non-cognate. Unlike previous methods reliant on only sequence data or a single, static predicted structure, enFoldX extracts features from an entire generated ensemble with a custom focus on the biophysical binding interface. Our model distinguishes T cell reactivity between peptides differing by a single amino acid substitution, the resolution required for cancer neoantigens, and generalizes to unseen peptides, MHCs, and TCRs, a major objective for artificial intelligence (AI) in immunology. Our performance on these crucial tasks demonstrates that diverse, structural sampling of biophysical interactions over an ensemble is fundamental for accurate AI-driven binding predictions and offers lessons for efficient future data generation to improve models. Our findings therefore offer a scalable framework to accelerate therapeutic binder design, and we provide access to a publicly available code repository.

immunology↗

bioRxiv2026

The lipid landscape shapes the immunomodulatory potential of fluoxetine in macrophages

Treatment-resistant depression (TRD) affects approximately one-third of depressed patients, yet the molecular mechanisms underlying this therapeutic non-responsiveness remain unclear. Pharmacological antidepressants, such as the selective serotonin reuptake inhibitor (SSRI) fluoxetine, exert immunomodulatory effects, partially by shifting macrophages towards an anti-inflammatory phenotype. Clinical aberrations in lipid metabolism have been associated with fluoxetine non-responsiveness in depressed populations. As macrophage polarization is highly sensitive to changes in lipid metabolism, pathological alterations in lipid metabolism may directly interfere with the therapeutic efficacy of SSRIs such as fluoxetine. However, how metabolic and immunomodulatory effects of antidepressants relate to each other in the context of TRD remains largely unexplored. We studied the interplay between immunomodulatory capacity of fluoxetine and the macrophage lipid landscape. Human monocyte-derived macrophages (MoDMs) and murine bone marrow-derived macrophages (BMDMs) were utilized as experimental models to evaluate these localized immunometabolic effects. Under baseline conditions in wild-type macrophages, the characteristic anti-inflammatory effect of fluoxetine coincided with distinct intracellular lipid accumulation. Conversely, disrupting this lipid environment yielded opposite immunological outcomes. BMDMs deficient in the low-density lipoprotein receptor (Ldlr-/-) or wild-type BMDMs exposed to inflammatory oxidized phosphocholine-containing phospholipids (OxPLs) failed to undergo anti-inflammatory polarization and exhibited a robust pro-inflammatory response upon fluoxetine treatment instead. Collectively, these data demonstrate a critical link between the macrophage lipid landscape and immunomodulatory efficacy of fluoxetine. These findings suggest that deficiencies in the endogenous LDLR pathway and exposure to circulating lipid peroxidation products can modulate the immunological response to fluoxetine. Our observations highlights microenvironmental lipid stress as a potential contributor to the underlying biology of antidepressant resistance in TRD.

immunology↗

bioRxiv2026

A 21-Color Spectral Flow Cytometry Panel for Comprehensive Immunophenotyping of Rat Tissues and a Companion 9-Color T-Cell Functional Assay

Although rats are crucial translational research models due to their immunological homology and surgical feasibility, the scarcity of conjugated antibodies has hampered high-dimensional immune profiling. To bridge this gap, we created a synergistic two-panel method that uses full-spectral flow cytometry: a 21-color comprehensive immunophenotyping panel and a 9-color intracellular cytokine staining (ICS) panel. The 21-color panel navigates the limited fluorophore pool and maps innate and adaptive lineages at high resolution. While it can be used to profile neutrophils and monocytes in peripheral blood it reaches its full potential in lymphoid organs, allowing for the simultaneous evaluation of tissue-resident macrophages, dendritic cells, T cell differentiation (including Tregs), and APC function. Based on this phenotypic paradigm, the 9-color ICS panel dissects effector T cell activation and Th1/Th2/Th17 cytokine production. Furthermore, we reserved the PE color during panel creation, allowing for the use of antibodies and probes with PE or comparable fluorophores in conjunction with this panel, hence increasing overall flexibility. This combination technique, designed for rat peripheral blood, spleen, and lymph nodes, combines panoramic phenotyping with functional analysis, offering an adaptable foundation for complicated tissue microenvironments in tumor immunology, rheumatology, and autoimmunity research.

immunology↗

bioRxiv2016

Toxicity Management in CAR T cell therapy for B-ALL: Mathematical modelling as a new avenue for improvement.

Advances in genetic engineering have made it possible to reprogram individual immune cells to express receptors that recognise markers on tumour cell surfaces. The process of re-engineering T cell lymphocytes to express Chimeric Antigen Receptors (CARs), and then re-infusing the CAR-modified T cells into patients to treat various cancers is referred to as CAR T cell therapy. This therapy is being explored in clinical trials - most prominently for B Cell Acute Lymphoblastic Leukaemia (B-ALL), a common B cell malignancy, for which CAR T cell therapy has led to remission in up to 90% of patients. Despite this extraordinary response rate, however, potentially fatal inflammatory side effects occur in up to 10% of patients who have positive responses. Further, approximately 50% of patients who initially respond to the therapy relapse. Significant improvement is thus necessary before the therapy can be made widely available for use in the clinic.\n\nTo inform future development, we develop a mathematical model to explore interactions between CAR T cells, inflammatory toxicity, and individual patients tumour burdens in silico. This paper outlines the underlying system of coupled ordinary differential equations designed based on well-known immunological principles and widely accepted views on the mechanism of toxicity development in CAR T cell therapy for B-ALL - and reports in silico outcomes in relationship to standard and recently conjectured predictors of toxicity in a heterogeneous, randomly generated patient population. Our initial results and analyses are consistent with and connect immunological mechanisms to the clinically observed, counterintuitive hypothesis that initial tumour burden is a stronger predictor of toxicity than is the dose of CAR T cells administered to patients.\n\nWe outline how the mechanism of action in CAR T cell therapy can give rise to such non-standard trends in toxicity development, and demonstrate the utility of mathematical modelling in understanding the relationship between predictors of toxicity, mechanism of action, and patient outcomes.

Cancer Biology↗

bioRxiv2016

A Zika virus-associated microcephaly case with background exposure to STORCH agents

We present a case of microcephaly associated with Zika virus (ZIKV) in a chronological, multimodal imaging approach, illustrating the hallmarks of this disease on intrauterine morphological ultrasound, transfontanelar ultrasound, computed tomography (CT) and magnetic resonance imaging (MRI). We also determined the serological e immunological status of the mother and newborn. Noticeably, there was evidence for maternal infection by ZIKV, cytomegalovirus (CMV), herpes simplex virus (HSV), dengue virus (DENV) and Toxoplasma gondii, which indicates a possible role of previous exposures to STORCH agents and possibly comorbidities in the severe fetal congenital manifestation.\n\nAuthor SummaryZika virus (ZIKV) is an emerging mosquito-borne arbovirus causing dengue-like symptoms. In humans the illness is characterized by malaise and cutaneous rash and absent or short-termed fever. Recently, the Brazilian Ministry of Health reported an outbreak of microcephaly in Brazil as a delayed effect of the 2014-2015 outbreak of ZIKV in the Northeast of Brazil. A 20-fold increase in the notifications of newborns with microcephaly was documented during the second semester of 2015. This increase was almost immediately found to be associated with ZIKV infections, both in Brazil and, retrospectively, in French Polynesia. Herein we report a case of microcephaly associated with ZIKV and we also present evidence of other maternal infections. Our results indicated that, both mother and microcephaly infant had immunologic status compatible with previous exposure (in the mother) by STORCH agents. These indicate a possible role of previous exposures and possibly comorbidities in the severe fetal congenital manifestation. {square}

Microbiology↗

bioRxiv2016

PhysiCell: an Open Source Physics-Based Cell Simulator for 3-D Multicellular Systems

Many multicellular systems problems can only be understood by studying how cells move, grow, divide, interact, and die. Tissue-scale dynamics emerge from systems of many interacting cells as they respond to and influence their microenvironment. The ideal \"virtual laboratory\" for such multicellular systems simulates both the biochemical microenvironment (the \"stage\") and many mechanically and biochemically interacting cells (the \"players\" upon the stage).\n\nPhysiCell--physics-based multicellular simulator--is an open source agent-based simulator that provides both the stage and the players for studying many interacting cells in dynamic tissue microenvironments. It builds upon a multi-substrate biotransport solver to link cell phenotype to multiple diffusing substrates and signaling factors. It includes biologically-driven sub-models for cell cycling, apoptosis, necrosis, solid and fluid volume changes, mechanics, and motility \"out of the box.\" The C++ code has minimal dependencies, making it simple to maintain and deploy across platforms. PhysiCell has been parallelized with OpenMP, and its performance scales linearly with the number of cells. Simulations up to 105-106 cells are feasible on quad-core desktop workstations; larger simulations are attainable on single HPC compute nodes.\n\nWe demonstrate PhysiCell by simulating the impact of necrotic core biomechanics, 3-D geometry, and stochasticity on the dynamics of hanging drop tumor spheroids and ductal carcinoma in situ (DCIS) of the breast. We demonstrate stochastic motility, chemical and contact-based interaction of multiple cell types, and the extensibility of PhysiCell with examples in synthetic multicellular systems (a \"cellular cargo delivery\" system, with application to anti-cancer treatments), cancer heterogeneity, and cancer immunology. PhysiCell is a powerful multicellular systems simulator that will be continually improved with new capabilities and performance improvements. It also represents a significant independent code base for replicating results from other simulation platforms. The PhysiCell source code, examples, documentation, and support are available under the BSD license at http://PhysiCell.MathCancer.org and http://PhysiCell.sf.net.\n\nAuthor SummaryThis paper introduces PhysiCell: an open source, agent-based modeling framework for 3-D multicellular simulations. It includes a standard library of sub-models for cell fluid and solid volume changes, cycle progression, apoptosis, necrosis, mechanics, and motility. PhysiCell is directly coupled to a biotransport solver to simulate many diffusing substrates and cell-secreted signals. Each cell can dynamically update its phenotype based on its microenvironmental conditions. Users can customize or replace the included sub-models.\n\nPhysiCell runs on a variety of platforms (Linux, OSX, and Windows) with few software dependencies. Its computational cost scales linearly in the number of cells. It is feasible to simulate 500,000 cells on quad-core desktop workstations, and millions of cells on single HPC compute nodes. We demonstrate PhysiCell by simulating the impact of necrotic core biomechanics, 3-D geometry, and stochasticity on hanging drop tumor spheroids (HDS) and ductal carcinoma in situ (DCIS) of the breast. We demonstrate contact- and chemokine-based interactions among multiple cell types with examples in synthetic multicellular bioengineering, cancer heterogeneity, and cancer immunology.\n\nWe developed PhysiCell to help the scientific community tackle multicellular systems biology problems involving many interacting cells in multi-substrate microenvironments. PhysiCell is also an independent, cross-platform codebase for replicating results from other simulators.

systems biology↗

bioRxiv2016

Recent evolution of cestode growth suppression by threespine stickleback

Parasites can be a major cause of natural selection on hosts, which consequently evolve a variety of strategies to avoid, eliminate, or tolerate infection. When ecologically similar host populations present disparate infection loads, this natural variation can reveal immunological strategies underlying adaptation to infection and population divergence. For instance, the tapeworm Schistocephalus solidus persistently infects between 0% to 80% of threespine stickleback (Gasterosteus aculeatus) in lakes on Vancouver Island. To test whether these heterogeneous infection rates are due to evolved differences in immunity, we experimentally exposed lab-reared fish from high-and low-infection populations, which are not known to differ in natural exposure risk, to controlled doses of Schistocephalus. We observed heritable between-population differences in several immune traits: fish from the naturally uninfected population initiated a stronger granulocyte response to Schistocephalus infection, and their granulocytes constitutively generated threefold more reactive oxygen species (ROS). Despite these immunological differences, Schistocephalus was equally successful at establishing initial infections in both host populations. However, the low-infection fish dramatically suppressed tapeworm growth relative to high-infection fish, and parasite size was intermediate in F1 hybrid hosts. Our results show that stickleback recently evolved heritable variation in their capacity to suppress helminth growth. Comparative data from many from natural populations indicate that growth suppression is widespread but not universal and, when present, is associated with reduced infection prevalence. Host suppression of helminth somatic growth may be an important immune strategy that aids in parasite clearance, or in mitigating the fitness costs of persistent infection.\n\nSignificanceLarge parasites remain a persistent source of morbidity and mortality in humans, domesticated animals, and wildlife. Hosts are subject to strong natural selection to eliminate or tolerate these parasite infections. Here, we document the recent evolution of a striking form of resistance by a vertebrate host (threespine stickleback) against its cestode parasite (Schistocephalus solidus). After Pleistocene glacial retreat, marine stickleback colonized freshwater lakes, encountered Schistocephalus, and evolved varying levels of resistance to it. We show that a heavily-and a rarely-infected population of stickleback have similar resistance to Schistocephalus colonization, but rarely-infected fish suppress parasite growth by orders of magnitude. These populations represent ends of a natural continuum of cestode growth suppression, which is associated with reduced infection prevalence.

evolutionary biology↗

bioRxiv2017

Immuno-phenotypes of Pancreatic Ductal Adenocarcinoma: Metaanalysis of transcriptional subtypes

Pancreatic ductal adenocarcinoma (PDAC) is the most common malignancy of the pancreas and has one of the highest mortality rates of any cancer type with a 5-year survival rate of < 5% and median overall survival of typically six months from diagnosis. Recent transcriptional studies of PDAC have provided several competing stratifications of the disease. However, the development of therapeutic strategies will depend on a unique and coherent classification of PDAC. Here, we use an integrative meta-analysis of four different PDAC gene expression studies to derive the consensus PDAC classification. Despite the fact that immunotherapies have yet to have an impact in treatment of PDAC, the gene expression signatures that stratify PDAC across studies are immunologic. We define these as \"adaptive\", \"innate\" and \"immune-exclusion\" immunologic signatures, which are prognostic across independent cohorts. An appreciation of the immune composition of PDAC with prognostic significance is an opportunity to understand distinct immune escape mechanisms in development of the disease and design novel immune-oncology therapeutic strategies to overcome current barriers.

cancer biology↗

bioRxiv2020

Chronic hM3Dq signaling in microglia ameliorates neuroinflammation in male mice

Microglia express muscarinic G protein-coupled receptors (GPCRs) that sense cholinergic activity and are activated by acetylcholine to potentially regulate microglial functions. Knowledge about how distinct types of muscarinic GPCR signaling regulate microglia function in vitro and in vivo is still poor, partly due to the fact that some of these receptors are also present in astrocytes and neurons. We generated mice expressing the hM3Dq Designer Receptor Exclusively Activated by Designer Drugs (DREADD) selectively in microglia to investigate the role of muscarinic M3Gq-linked signaling. We show that activation of hM3Dq using clozapine N-oxide (CNO) elevated intracellular calcium levels and increased phagocytosis of FluoSpheres in vitro. Acute treatment with CNO in vivo did not affect male mouse behavior, however chronic CNO treatment decreased sickness behavior triggered by lipopolysaccharide (LPS) treatment. Interestingly, whereas acute treatment with CNO increased synthesis of cytokine mRNA, chronic treatment attenuated LPS-induced cytokine mRNA changes in the brain, likely explaining the improvement in sickness behavior by chronic hM3Dq activation. No effect of CNO was observed in DREADD-negative mice. These results suggest that chronic activation of M3 muscarinic receptors (the hM3Dq progenitor) in microglia, and potentially other Gq-coupled GPCRs, preconditions microglia to decrease their response to further immunological challenges. Our results indicate that hM3Dq can be a useful tool to modulate neuroinflammation and study microglial immunological memory in vivo, which may be applicable for manipulations of neuroinflammation in neurodegenerative and psychiatric diseases. HighlightsO_LIMicroglial function was manipulated by specific activation of hM3Dq signaling. C_LIO_LIChronic hM3Dq activation prevented LPS-induced sickness behavior in mice. C_LIO_LIMicroglial hM3Dq signaling modulated expression of pro-inflammatory cytokines. C_LI

neuroscience↗

bioRxiv2020

Parental investment and immune dynamics in sex-role reversed pipefishes

Parental care elevates reproductive success by allocating resources into the upbringing of the offspring. However, it also imposes strong costs for the care giving parent and can foster sexual dimorphism. Trade-offs between the reproductive system and the immune system may result in differential immunological capacities between the care-providing and the non-care-providing parent. Usually, providing care is restricted to the female sex making it impossible to study a sex-independent influence of parental investment on sexual immune dimorphism. The decoupling of sex-dependent parental investment and their influences on the parental immunological capacity, however, is possible in syngnathids, which evolved the unique male pregnancy on a gradient ranging from a simple carrying of eggs on the trunk (Nerophinae, low paternal investment) to full internal pregnancy (Syngnathus, high paternal investment). In this study, we compared candidate gene expression between females and males of different gravity stages in three species of syngnathids (Syngnathus typhle, Syngnathus rostellatus and Nerophis ophidion) with different male pregnancy intensities to determine how parental investment influences sexual immune dimorphism. While our data failed to detect sexual immune dimorphism in the subset of candidate genes assessed, we show a parental care specific resource-allocation trade-off between investment into pregnancy and immune defense when parental care is provided.

evolutionary biology↗

bioRxiv2020

Activator protein-1 transactivation of the major immediate early locus is a determinant of cytomegalovirus reactivation from latency

Human cytomegalovirus (HCMV) is a ubiquitous pathogen that latently infects hematopoietic cells and has the ability to reactivate when triggered by immunological stress. This reactivation causes significant morbidity and mortality in immune-deficient patients, who are unable to control viral dissemination. While a competent immune system helps prevent clinically detectable viremia, a portrait of the factors that induce reactivation following the proper cues remains incomplete. Our understanding of the complex molecular mechanisms underlying latency and reactivation continue to evolve. We previously showed the HCMV-encoded G-protein coupled receptor US28 is expressed during latency and facilitates latent infection by attenuating the activator protein-1 (AP-1) transcription factor subunit, c-fos, expression and activity. We now show AP-1 is a critical component for HCMV reactivation. Pharmacological inhibition of c-fos significantly attenuates viral reactivation. In agreement, infection with a virus in which we disrupted the proximal AP-1 binding site in the major immediate early (MIE) enhancer results in inefficient reactivation compared to wild type. Concomitantly, AP-1 recruitment to the MIE enhancer is significantly decreased following reactivation of the mutant virus. Further, AP-1 is critical for de-repression of MIE-driven transcripts and downstream early and late genes, while immediate early genes from other loci remain unaffected. Our data also reveal MIE transcripts driven from the MIE promoter, the distal promoter, and the internal promoter, iP2, are dependent upon AP-1 recruitment, while iP1-driven transcripts are AP-1-independent. Collectively, our data demonstrate AP-1 binding to and activation of the MIE enhancer is a key molecular process controlling reactivation from latency. Significance StatementHuman cytomegalovirus (HCMV) is a common pathogen that infects the majority of the population for life. This infection poses little threat in immunologically healthy individuals, but can be fatal in people with compromised immune systems. Our understanding of the mechanisms underlying latency and reactivation remains incomplete. Here, we show the cellular transcription factor, AP-1, is a key to regulating HCMV reactivation. Our findings reveal AP-1 binding to the major immediate early enhancer/promoter is critical for switching this locus from one that is repressed during latency to one that is highly active following reactivation. Our work provides a novel mechanism HCMV exploits to reactivate, highlighting AP-1 as a potential target to prevent HCMV reactivation.

microbiology↗

bioRxiv2020

Engineering an RNA-based tissue-specific platform for genetic editing through use of a miRNA-enabled Cas12a

The capacity to edit genomes using CRISPR-Cas systems holds immense potential for countless genetic-based diseases. However, one significant impediment preventing broad therapeutic utilization is in vivo delivery. While genetic editing at a single cell level in vitro can be achieved with high efficiency, the capacity to utilize these same biologic tools in a desired tissue in vivo remains challenging. Non-integrating RNA virus-based vectors constitute efficient platforms for transgene expression and surpass several barriers to in vivo delivery. However, the broad tissue tropism of viral vectors raises the concern for off-target effects. Moreover, prolonged expression of the Cas proteins, regardless of delivery method, can accumulate aberrant RNAs leading to unwanted immunological responses. In an effort to circumvent these shortcomings, here we describe a versatile RNA virus-based technology that can achieve cell-specific activity and self-inactivation by combining host microRNA (miRNA) biology with the CRISPR-Cas12a RNA-guided nuclease. Exploiting the RNase activity of Cas12a, we generated a vector that self-inactivates upon delivery of Cas12a and an accompanying CRISPR RNA (crRNA). Furthermore, we show that maturation of the crRNA can be made dependent on cell-specific miRNAs, which confers cell-specificity. We demonstrate that this genetic editing circuit delivers diminished yet sufficient levels of Cas12a to achieve effective genome editing whilst inducing a minimal immunological response. It can also function in a cell-specific manner thereby facilitating in vivo editing and mitigating the risk of unwanted, off-target effects.

bioengineering↗

bioRxiv2020

Rapid community-driven development of a SARS-CoV-2 tissue simulator

The 2019 novel coronavirus, SARS-CoV-2, is a pathogen of critical significance to international public health. Knowledge of the interplay between molecular-scale virus-receptor interactions, single-cell viral replication, intracellular-scale viral transport, and emergent tissue-scale viral propagation is limited. Moreover, little is known about immune system-virus-tissue interactions and how these can result in low-level (asymptomatic) infections in some cases and acute respiratory distress syndrome (ARDS) in others, particularly with respect to presentation in different age groups or pre-existing inflammatory risk factors. Given the nonlinear interactions within and among each of these processes, multiscale simulation models can shed light on the emergent dynamics that lead to divergent outcomes, identify actionable "choke points" for pharmacologic interventions, screen potential therapies, and identify potential biomarkers that differentiate patient outcomes. Given the complexity of the problem and the acute need for an actionable model to guide therapy discovery and optimization, we introduce and iteratively refine a prototype of a multiscale model of SARS-CoV-2 dynamics in lung tissue. The first prototype model was built and shared internationally as open source code and an online interactive model in under 12 hours, and community domain expertise is driving regular refinements. In a sustained community effort, this consortium is integrating data and expertise across virology, immunology, mathematical biology, quantitative systems physiology, cloud and high performance computing, and other domains to accelerate our response to this critical threat to international health. More broadly, this effort is creating a reusable, modular framework for studying viral replication and immune response in tissues, which can also potentially be adapted to related problems in immunology and immunotherapy.

systems biology↗