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Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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bioRxiv2019

Altered dynamics may drift pathological fibrillization in membraneless organelles

Protein phase transition can generate non-membrane bound cellular compartments, which can convert from liquid-like to solid-like states. While the molecular driving forces of phase separation have been largely understood, much less is known about the mechanisms of material-state conversion. We apply a recently developed algorithm to describe the weak interaction network of multivalent motifs, and simulate the effect of pathological mutations. We demonstrate that linker dynamics is critical to the material-state of biomolecular condensates. We show that linker flexibility/mobility is a major regulator of the weak, heterogeneous meshwork of multivalent motifs, which promotes phase transition and maintains a liquid-like state. Decreasing linker dynamics increases the propensity of amyloid-like fragments via hampering the motif-exchange and reorganization of the weak interaction network. In contrast, increasing linker mobility may compensate rigidifying mutations, suggesting that the meshwork of weak, variable interactions may provide a rescue mechanism from aggregation. Motif affinity, on the other hand, has a moderate impact on fibrillization. Here we demonstrate that the fuzzy framework provides an efficient approach to handle the intricate organization of membraneless organelles, and could also be applicable to screen for pathological effects of mutations.

bioinformatics↗
bioRxiv2019

Pathologies of Between-Groups Principal Components Analysis in Geometric Morphometrics

Good empirical applications of geometric morphometrics (GMM) typically involve several times more variables than specimens, a situation the statistician refers to as \"high p/n,\" where p is the count of variables and n the count of specimens. This note calls your attention to two predictable catastrophic failures of one particular multivariate statistical technique, between-groups principal components analysis (bgPCA), in this high-p/n setting. The more obvious pathology is this: when applied to the patternless (null) model of p identically distributed Gaussians over groups of the same size, both bgPCA and its algebraic equivalent, partial least squares (PLS) analysis against group, necessarily generate the appearance of huge equilateral group separations that are actually fictitious (absent from the statistical model). When specimen counts by group vary greatly or when any group includes fewer than about ten specimens, an even worse failure of the technique obtains: the smaller the group, the more likely a bgPCA is to fictitiously identify that group as the end-member of one of its derived axes. For these two reasons, when used in GMM and other high-p/n settings the bgPCA method very often leads to invalid or insecure bioscientific inferences. This paper demonstrates and quantifies these and other pathological outcomes both for patternless models and for models with one or two valid factors, then offers suggestions for how GMM practitioners should protect themselves against the consequences for inference of these lamentably predictable misrepresentations. The bgPCA method should never be used unskeptically -- it is never authoritative -- and whenever it appears in partial support of any biological inference it must be accompanied by a wide range of diagnostic plots and other challenges, many of which are presented here for the first time.

evolutionary biology↗
bioRxiv2019

Amyloid pathology disrupts gliotransmitter release in astrocytes

Accumulation of amyloid-{beta} peptide (A{beta}), a hallmark of Alzheimers disease (AD), is associated with synchronous hyperactivity and dysregulated Ca2+ signaling in hippocampal astrocytes. However, the consequences of altered Ca2+ signaling on the temporal dynamics of Ca2+ and gliotransmitter release events at astrocytic microdomains are not known. We have developed a detailed biophysical model of microdomain signaling at a single astrocytic process that accurately describes key temporal features of Ca2+ events and Ca2+-mediated kiss-and-run and full fusion exocytosis. Using this model, we ask how aberrant plasma-membrane Ca2+ pumps and mGluR activity, molecular hallmarks of A{beta} toxicity that are also critically involved in Ca2+ signaling, modify astrocytic feedback at a tripartite synapse. We show that AD related molecular pathologies increase the rate and synchrony of Ca2+ and exocytotic events triggered by neuronal activity. Moreover, temporal precision between Ca2+ and release events, a mechanism indispensable for rapid modulation of synaptic transmission by astrocytes, is lost in AD astrocytic processes. Our results provide important evidence on the link between AD-related molecular pathology, dysregulated calcium signaling and gliotransmitter release at an astrocytic process.

neuroscience↗
bioRxiv2019

EEG power spectra and subcortical pathology in chronic disorders of consciousness

ObjectiveTo determine (i) the association between long-term impairment of consciousness after severe brain injury, spontaneous brain oscillations, and underlying subcortical damage, and (ii) whether such data can be used to aid patient diagnosis, a process known to be susceptible to high error rates. MethodsCross-sectional observational sample of 116 patients with a disorder of consciousness secondary to brain injury, collected prospectively at a tertiary center between 2011 and 2013. Multimodal analyses relating clinical measures of impairment, electroencephalographic measures of spontaneous brain activity, and magnetic resonance imaging data of subcortical atrophy were conducted in 2018. ResultsIn the final analyzed sample of 61 patients, systematic associations were found between electroencephalographic power spectra and subcortical damage. Specifically, the ratio of beta-to-delta relative power was negatively associated with greater atrophy in regions of the bilateral thalamus and globus pallidus (both left > right) previously shown to be preferentially atrophied in chronic disorders of consciousness. Power spectrum total density was also negatively associated with widespread atrophy in regions of the left globus pallidus, right caudate, and in brainstem. Furthermore, we showed that the combination of demographics, encephalographic, and imaging data in an analytic framework can be employed to aid behavioral diagnosis. ConclusionsThese results ground, for the first time, electroencephalographic presentation detected with routine clinical techniques in the underlying brain pathology of disorders of consciousness and demonstrate how multimodal combination of clinical, electroencephalographic, and imaging data can be employed in potentially mitigating the high rates of misdiagnosis typical of this patient cohort. Search termsdisorders of consciousness, subcortical pathology, EEG, MRI.

neuroscience↗
bioRxiv2019

Neurons expressing pathological Tau protein trigger dramatic noninflammatory changes in microglial morphology and dynamics

Microglial cells, the resident macrophages of the brain, are important players in the pathological process of numerous neurodegenerative disorders, including tauopathies, a heterogeneous class of diseases characterized by intraneuronal Tau aggregates. However, microglia response in Tau pathologies remains poorly understood. Here we exploit a genetic zebrafish model of tauopathy, combined with live microglia imaging, to investigate the behaviour of microglia in vivo in the disease context. Results show that while microglia were almost immobile and displayed long and highly dynamic branches in a wild-type context, in presence of diseased neurons cells became highly mobile and displayed morphological changes, with highly mobile cell bodies together with fewer and shorter processes. We also imaged, for the first time to our knowledge, the phagocytosis of apoptotic tauopathic neurons by microglia in vivo and observed that microglia engulfed about as twice materials as in controls. Finally, genetic ablation of microglia in zebrafish tauopathy model significantly increased Tau hyperphosphorylation, suggesting that microglia provide neuroprotection to diseased neurons. Our findings demonstrate for the first time the dynamics of microglia in contact with tauopathic neurons in vivo and open perspectives for the real-time study of microglia in many neuronal diseases.

neuroscience↗
bioRxiv2019

Telomere Dysfunction Drives Chronic Lung Allograft Dysfunction Pathology

RationaleTelomere dysfunction is associated with multiple fibrotic lung processes, including chronic lung allograft dysfunction (CLAD) which is a major limitation to long-term survival following lung transplantation. Although shorter donor telomere lengths are associated with an increased risk of CLAD, it is unknown whether short telomeres are a cause or consequence of CLAD pathology.\n\nObjectiveOur objective was to test whether telomere dysfunction contributes to pathologic changes seen in CLAD.\n\nMethods and ResultsHistopathologic and molecular analysis of human CLAD lungs demonstrated shortened telomeres in lung epithelial cells quantified by teloFISH, increased numbers of surfactant protein C immunoreactive type II alveolar epithelial cells (AECs), and increased expression of senescence markers (beta-galactosidase, p16, p53 and p21) in lung epithelial cells. Telomere repeat binding factor 1 flox/flox (TRF1F/F) mice were crossed with tamoxifen inducible SCGB1a1-cre mice to generate SCGB1a1-creTRF1 F/F mice. Following 9 months of tamoxifen-induced deletion of TRF1 in club cells, mice developed mixed obstructive and restrictive lung physiology, small airway obliteration on micro-computed tomography, a 4-fold decrease in telomere length in airway epithelial cells, collagen deposition around bronchioles and adjacent lung parenchyma, increased type II AEC numbers, expression of senescence-associated beta-galactosidase in epithelial cells and decreased SCGB1a1 expression in airway epithelial cells.\n\nConclusionsThese findings demonstrate that telomere dysfunction isolated to club cells leads to airway-centric lung remodeling and fibrosis similar to that observed in patients with CLAD and suggest that lung epithelial cell telomere dysfunction may be a molecular driver of CLAD.

cell biology↗
bioRxiv2019

Disruption to NKCC1 impairs the response of myelinating Schwann cells to neuronal activity and leads to severe peripheral nerve pathology

Myelinating Schwann cells of the peripheral nervous system (PNS) express numerous ion channels and transporters, and have the capacity to respond to neuronal activity. However, it remains unknown how the response of Schwann cells to neuronal activity affects peripheral nerve formation, health or function in vivo. Through a genetic screen in zebrafish, we identified a mutant, ue58, with severe disruption to the morphology of myelin along peripheral nerves and associated nerve oedema. Molecular analyses indicated that this phenotype was caused by the loss of function of a previously uncharacterized gene, slc12a2b, which encodes a zebrafish paralog of the solute carrier NKCC1. NKCC1 is a co-transporter of Na+, K+, and Cl- ions and water, typically from the extracellular space into cells. Upon impairing slc12a2b function, constitutively, or specifically in neurons or myelinating Schwann cells, we observed disruption to myelin and nerve oedema. Strikingly, we found that treatment of slc12a2b mutants with TTX completely prevented the emergence of these pathologies. Furthermore, TTX treatment rescued pathology in animals with cell-type specific loss of slc12a2b from myelinating Schwann cells. Together our data indicate that NKCC1 regulates ion homeostasis following neuronal activity and that this is required to maintain myelinated axon and peripheral nerve integrity.

neuroscience↗
bioRxiv2019

Transcriptomic learning for digital pathology

Deep learning methods for digital pathology analysis have proved an effective way to address multiple clinical questions, from diagnosis to prognosis and even to prediction of treatment outcomes. They have also recently been used to predict gene mutations from pathology images, but no comprehensive evaluation of their potential for extracting molecular features from histology slides has yet been performed. We propose a novel approach based on the integration of multiple data modes, and show that our deep learning model, HE2RNA, can be trained to systematically predict RNA-Seq profiles from whole-slide images alone, without the need for expert annotation. HE2RNA is interpretable by design, opening up new opportunities for virtual staining. In fact, it provides virtual spatialization of gene expression, as validated by double-staining on an independent dataset. Moreover, the transcriptomic representation learned by HE2RNA can be transferred to improve predictive performance for other tasks, particularly for small datasets. As an example of a task with direct clinical impact, we studied the prediction of microsatellite instability from hematoxylin & eosin stained images and our results show that better performance can be achieved in this setting.

bioinformatics↗
bioRxiv2019

Succinylation Links Metabolic Reductions to Amyloid and Tau Pathology

Abnormalities in glucose metabolism and misfolded protein deposits composed of the amyloid-{beta} peptide (A{beta}) and tau are the three most common neuropathological hallmarks of Alzheimers disease (AD), but their relationship(s) to the disease process or to each other largely remains unclear. In this report, the first human brain quantitative lysine succinylome together with a global proteome analysis from controls and patients reveals that lysine succinylation contributes to these three key AD-related pathologies. Succinylation, a newly discovered protein post-translational modification (PTM), of multiple proteins, particularly mitochondrial proteins, declines with the progression of AD. In contrast, amyloid precursor protein (APP) and tau consistently exhibit the largest AD-related increases in succinylation, occurring at specific sites in AD brains but never in controls. Transgenic mouse studies demonstrate that succinylated APP and succinylated tau are detectable in the hippocampus concurrent with A{beta} assemblies in the oligomer and insoluble fiber assembly states. Multiple biochemical approaches revealed that succinylation of APP alters APP processing so as to promote A{beta} accumulation, while succinylation of tau promotes its aggregation and impairs its microtubule binding ability. Succinylation, therefore, is the first single PTM that can be added in parallel to multiple substrates, thereby promoting amyloidosis, tauopathy, and glucose hypometabolism. These data raise the possibility that, in order to show meaningful clinical benefit, any therapeutic and/or preventative measures destined for success must have an activity to either prevent or reverse the molecular pathologies attributable to excess succinylation.

neuroscience↗
bioRxiv2019

Repurposing cell growth-regulating compounds identifies kenpaullone which ameliorates pathologic pain via normalization of inhibitory neurotransmission

Inhibitory GABA-ergic neurotransmission is fundamental for the adult vertebrate central nervous system and requires low chloride ion concentration in neurons. This basic ionic-homeostatic mechanism relies on expression and function of KCC2, a neuroprotective ionic transporter that extrudes neuronal chloride. Importantly, no other transporter can rescue KCC2 deficit, and attenuated expression of KCC2 is strongly associated with circuit malfunction in chronic pain, epilepsy, neuro-degeneration, neuro-trauma, and other neuro-psychiatric illnesses. To isolate Kcc2 gene expression-enhancing compounds, we screened 1057 cell growth-regulating compounds in cultured primary cortical neurons. We identified kenpaullone (KP), which enhanced Kcc2/KCC2 expression and function in cultured rodent and human neurons by inhibiting GSK3{beta}. KP effectively reduced pathologic pain in preclinical mouse models of nerve constriction injury and bone cancer. In nerve-injury pain, KP restored Kcc2 expression and GABA-evoked chloride reversal potential in the spinal cord dorsal horn. Delta-catenin, a phosphorylation-target of GSK3{beta} in neurons, activated the Kcc2 promoter via Kaiso transcription factor. Validating this new pathway in-vivo, transient spinal over-expression of delta-catenin mimicked KP analgesia. With relevance for pathologic pain, our discoveries of a newly repurposed compound and a novel genetically-encoded mechanism that each enhance Kcc2 gene expression enable us to re-normalize disrupted inhibitory neurotransmission through genetic re-programming.

neuroscience↗
bioRxiv2019

Coagulopathy signature precedes and predicts severity of end-organ heat stroke pathology in a mouse model

Heat stroke is a life-threatening condition characterized by loss of thermoregulation and severe elevation of core body temperature, which can cause organ failure and damage to the central nervous system. While no definitive test exists to measure heat stroke severity, immune challenge is known to increase heat stroke risk, although the mechanism of this increased risk is unclear. In this study, we used a mouse model of classic heat stroke to test the effect of immune challenge on pathology. Employing multivariate supervised machine learning to identify patterns of molecular and cellular markers associated with heat stroke, we found that prior viral infection simulated with poly I:C injection resulted in heat stroke presenting with high levels of factors indicating coagulopathy. Despite a decreased number of platelets in the blood, platelets are large and non-uniform in size, suggesting younger, more active platelets. Levels of D-dimer and soluble thrombomodulin were increased in more severe heat stroke, and in cases presenting with the highest level of organ damage markers D-dimer levels dropped, indicating potential fibrinolysis-resistant thrombosis. Genes corresponding to immune response, coagulation, hypoxia, and vessel repair were up-regulated in kidneys of heat-challenged animals, and these increases correlated with both viral treatment and distal organ damage while appearing before discernible tissue damage to the kidney itself. We conclude that heat stroke-induced coagulopathy may be a driving mechanistic force in heat stroke pathology, especially when exacerbated by prior infection, and that coagulation markers may serve as an accessible biomarker for heat stroke severity and therapeutic strategies.\n\nKey pointsO_LIA signature of pro-coagulation markers predicts circadian core body temperature and levels of organ damage in heat stroke\nC_LIO_LIChanges in coagulopathy-related gene expression are evidenced before histopathological organ damage\nC_LI

physiology↗
bioRxiv2019

The early life microbiota protects neonatal mice from pathological small intestinal epithelial cell shedding

The gut microbiota plays a crucial role in regulating and maintaining the epithelial barrier, particularly during early life. Notably, patients with chronic intestinal inflammation have a dysregulated process of renewal and replenishment of the intestinal epithelial cell (IEC) barrier, which is linked to disturbances in the gut microbiota. To date, there are no studies focussed on understanding the impact of inflammatory cell shedding events during the early life developmental window, and which host and microbial factors mediate these responses. Here we sought to determine pathological cell shedding outcomes throughout the postnatal developmental period (day 14, 21, 29 and week 8). Surprisingly neonatal mice (day 14 and 21) were highly refractory to induction of cell shedding after intraperitoneal administration of LPS, with day 29 mice showing strong pathological responses, more similar to those observed in adult mice. These differential responses were not linked to defects in the cellular mechanisms and pathways known to regulate cell shedding responses, although we did observe that neonatal mice had elevated anti-inflammatory (IL-10) responses. Notably, when we profiled microbiota and metabolites from these mice, we observed significant alterations. Neonatal mice had high relative abundances of Streptococcus, Escherichia and Enterococcus and increased primary bile acids. In contrast, older mice were dominated by Candidatus Arthromitus, Alistipes and Lachnoclostridium, and had increased concentrations of SCFAs and methyamines. Faecal microbiota transplant (FMT) and antibiotic studies confirmed the importance of early life gut microbiota in cell shedding responses. In these studies, neonates treated with antibiotics restored LPS-induced small intestinal cell shedding, whereas adult FMT alone had no effect. Our findings further support the importance of the early life window for microbiota-epithelial interactions in the presence of inflammatory stimuli and highlight areas for further investigation to probe underlying mechanisms to drive therapeutic development within the context of chronic inflammatory intestinal diseases.

microbiology↗
bioRxiv2019

Mechanistic insights into NAD synthase NMNAT chaperoning phosphorylated Tau from pathological aggregation

Tau hyper-phosphorylation and deposition into neurofibrillary tangles have been found in brains of patients with Alzheimers disease (AD) and other tauopathies. Molecular chaperones are involved in regulating the pathological aggregation of phosphorylated Tau (pTau) and modulating disease progression. Here, we report that nicotinamide mononucleotide adenylyltransferase (NMNAT), a well-known NAD synthase, serves as a chaperone of pTau to prevent its amyloid aggregation in vitro as well as mitigate its pathology in a fly tauopathy model. By combining NMR spectroscopy, crystallography, single-molecule and computational approaches, we revealed that NMNAT adopts its enzymatic pocket to specifically bind the phosphorylated sites of pTau, which can be competitively disrupted by the enzymatic substrates of NMNAT. Moreover, we found that NMNAT serves as a co-chaperone of Hsp90 for the specific recognition of pTau over Tau. Our work uncovers a dedicated chaperone of pTau and suggests NMNAT as a key node between NAD metabolism and Tau homeostasis in aging and neurodegeneration.

biochemistry↗
bioRxiv2019

Dopamine and risky decision-making in pathological and problem gamblers.

Gambling disorder is a behavioral addiction that is associated with impairments in value-based decision-making such as increased temporal discounting and reduced risk-aversion. Dopamine regulates learning and decision-making by modulating information processing throughout fronto-striatal circuits. Although the role of alterations in dopamine neurotransmission in the etiology of gambling disorder is controversial, preliminary evidence suggests that specifically increasing frontal dopamine levels might improve cognitive functioning in pathological and problem gamblers. We therefore examined whether increasing frontal dopamine levels via the catechol-O-methyltransferase (COMT) inhibitor tolcapone would reduce risky choice in a group of pathological and problem gamblers (n=14) in a repeated-measures counter-balanced placebo-controlled double-blind study. Choice data were fit using hierarchical Bayesian parameter estimation and a modeling scheme that combined a risky choice model with the drift diffusion model to account for both choices and response time distributions. Model comparison revealed that the data were best accounted for by a variant of the drift diffusion model with a non-linear modulation of trial-wise drift rates by value differences, confirming recent findings. Contrary to our hypothesis, risk-taking was slightly increased under tolcapone vs. placebo (Cohens d = -.281). Examination of drug effects on diffusion model parameters revealed an increase in the value-dependency of the drift rate (Cohens d = .932) with a simultaneous reduction in the maximum drift rate (Cohens d = -1.84). These results add to previous work on the potential role of COMT inhibitors in behavioral addictions, and show no consistent beneficial effect of tolcapone on risky choice in gambling disorder. Modeling results add to mounting evidence for the applicability of diffusion models in value-based decision-making. Future work should focus on individual genetic, clinical and cognitive factors that might account for the heterogeneity in the effects of COMT inhibition.

neuroscience↗
bioRxiv2019

Pathological modeling of TBEV infection reveals differential innate immune responses in human neurons and astrocytes that correlate with their susceptibility to infection.

Tick-borne encephalitis virus (TBEV) is a member of the Flaviviridae family, Flavivirus genus, which includes several important human pathogens. It is responsible for neurological symptoms that may cause permanent disability or death, and, from a medical point of view, is the major arbovirus in Central/Northern Europe and North-eastern Asia. TBEV tropism is critical for neuropathogenesis, yet, little is known about the molecular mechanisms that govern the susceptibility of human brain cells to the virus. In this study, we sought to establish and characterize a new in vitro model of TBEV infection in the human brain and to decipher cell type-specific innate immunity and its relation to TBEV tropism and neuropathogenesis. We showed that infection of neuronal/glial cultures derived from human fetal neural progenitor cells (hNPCs) mimicked three major hallmarks of TBEV infection in the human brain, namely, preferential neuronal tropism, neuronal death and astrogliosis. We also showed that these cells had conserved their capacity to build an antiviral response against TBEV. TBEV-infected neuronal/glial cells, therefore, represented a highly relevant pathological model. By enriching the cultures in either human neurons or astrocytes, we further demonstrated qualitative and quantitative differential innate immune responses in the two cell types that correlated with their particular susceptibility to TBEV. Our results thus reveal that cell type-specific innate immunity is likely to contribute to shaping TBEV tropism for human brain cells. They offer a new in vitro model to further study TBEV-induced neuropathogenesis and improve our understanding of the mechanisms by which neurotropic viruses target and damage human brain cells.\n\nAuthor summaryTick-borne encephalitis virus (TBEV), a neurotropic Flavivirus that is responsible for encephalitis in humans, is of growing concern in Europe. Indeed, over the last two decades the number of reported cases has continuously increased and the virus has spread into new geographical areas. Whereas it is well established that neurons are the main target of TBEV in the human brain, the mechanisms that underlie this preferential tropism have not yet been elucidated. Here, we used neuronal/glial cells derived from human fetal neural progenitors to establish and characterize a new in vitro pathological model that mimics major hallmarks of TBEV infection in vivo; namely, neuronal tropism, neuronal death and astrogliosis. Using this highly relevant model, we showed that human neurons and astrocytes were both capable of developing an innate immune response against TBEV, but with dissimilar magnitudes that correlated with differential susceptibility to TBEV. Our results thus revealed that TBEV tropism for subsets of human brain cells is likely to depend on cell-type specific innate immunity. This improves our understanding of the mechanisms by which neurotropic viruses target and damage human brain cells and may help guide development of future therapies.

microbiology↗
bioRxiv2019

Identification of distinct pathological signatures induced by patient-derived α-synuclein structures in non-human primates

AO_SCPLOWBSTRACTC_SCPLOWDopaminergic neuronal cell death, associated with intracellular -synuclein (-syn)-rich protein aggregates (termed Lewy bodies), is a well-established characteristic of Parkinsons disease. Much evidence, accumulated from multiple experimental models has suggested that -syn plays a role in PD pathogenesis, not only as a trigger of pathology but also as a mediator of disease progression through pathological spreading. Here we have used a machine learning-based approach to identify unique signatures of neurodegeneration in monkeys induced by distinct -syn pathogenic structures derived from PD patients. Unexpectedly, our results show that, in non-human primates, a small amount of singular -syn aggregates is as toxic as larger amyloid fibrils present in the LBs, thus reinforcing the need for preclinical research in this species. Furthermore, our results provide evidence supporting the true multifactorial nature of PD as multiple causes can induce similar outcome regarding dopaminergic neurodegeneration.

neuroscience↗
bioRxiv2019

Human-specific regulatory features of brain development manifest staggering breadth of associations with physiological processes and pathological conditions of H. sapiens

Recent advances in identification and characterization of human-specific regulatory DNA sequences set the stage for the assessment of their global impact on physiology and pathology of Modern Humans. Gene set enrichment analyses (GSEA) of 8,405 genes linked with 35,074 human-specific neuro-regulatory single-nucleotide changes (hsSNCs) revealed a staggering breadth of significant associations with morphological structures, physiological processes, and pathological conditions of Modern Humans. Significantly enriched traits include more than 1,000 anatomically-distinct regions of the adult human brain, many different types of cells and tissues, more than 200 common human disorders and more than 1,000 records of rare diseases. Thousands of genes connected with neuro-regulatory hsSNCs have been identified, which represent essential genetic elements of the autosomal inheritance and offspring survival phenotypes. A total of 1,494 hsSNC- linked genes are associated with either autosomal dominant or recessive inheritance and 2,273 hsSNC-linked genes have been associated with premature death, embryonic lethality, as well as pre-, peri-, neo-, and post-natal lethality phenotypes of both complete and incomplete penetrance. Differential GSEA implemented on hsSNC-linked loci and associated genes identify 7,990 genes linked to evolutionary distinct classes of human-specific regulatory sequences (HSRS), expression of a majority of which (5,389 genes; 67%) is regulated by stem cell-associated retroviral sequences (SCARS). Interrogations of the MGI database revealed readily available mouse models tailored for precise experimental definitions of functional effects of hsSNCs and SCARS on genes causally affecting thousands of mammalian phenotypes and implicated in hundreds of common and rare human disorders. These observations suggest that a preponderance of human-specific traits evolved under a combinatorial regulatory control of HSRS and neuro-regulatory loci harboring hsSNCs that are fixed in humans, distinct from other primates, and located in differentially-accessible chromatin regions during brain development.

genomics↗
bioRxiv2025

SP140 limits type I interferon-driven pathology, preserving T cell motility and promoting resistance in tuberculosis

CD8+ T cells are elicited during tuberculosis yet how susceptible lung environments shape their maintenance and behavior is unclear. We examined pulmonary T cell responses to Mycobacterium tuberculosis in resistant control and Sp140-/- mice, a model of type I interferon (IFN-I)-driven susceptibility. Resistant mice generated diverse CD8+ effector- and memory-like subsets producing TNF and IFN{gamma}, whereas Sp140-/- mice showed a broad loss of pulmonary CD8+ T cells. Single-cell RNA sequencing revealed altered states in CD8+ T cells from susceptible mice with exhaustion and IFN-I transcriptional programs. IFNAR blockade rescued CD8+ T cell numbers, diversity, cytokine production, reduced bacterial burden and lung pathology, with comparable benefits also valid for CD4+ T cells. Intravital microscopy of infected lungs further showed that T cell dynamics and motility within lesions were restricted under exuberant IFN-I signaling but fully restored by IFNAR blockade. Thus, IFN-I-driven tissue pathology restricts T cell accumulation and motility during tuberculosis. TeaserIn tuberculosis, excessive type I interferon signaling reshapes the lung environment, limiting T cell accumulation and motility within infected lesions.

immunology↗