Microglia and infiltrating T-cells adopt long-term, age-specific, transcriptional changes after traumatic brain injury

Introduction: Traumatic brain injury (TBI) afflicts over 3 million Americans every year. Patients over 65 years of age suffer increased mortality as well as greater long-term neurocognitive and neuropsychiatric morbidity compared to younger adults. Microglia, the resident macrophages of the brain, are complicit in both. Our published and preliminary data have demonstrated a significant age-effect in which aged microglia are more prone to adopt a constitutively activated state associated with worse neurocognitive and neuropsychiatric outcomes. Therefore, we hypothesized that aged microglia would fail to return to a homeostatic state after TBI but instead adopt a long-term injury-associated state within the brain of aged mice as compared to young-adult mice after TBI. Methods: Young-adult (14-weeks) and aged (80-weeks) C57BL/6 mice underwent TBI via controlled cortical impact vs. sham injury. We utilized single-cell RNA sequencing to examine age-associated cellular responses after TBI. Four months post-TBI or sham injury, brains were harvested, and CD45+ cells (N=4,000 cells) were isolated via florescence-activated cell sorting. cDNA libraries were prepared via the 10x Genomics Chromium Single Cell 3' Reagent Kit, followed by sequencing on a HiSeq 4000 instrument. The raw data were processed using the Cell Ranger pipeline mapped to the mm10 mouse reference genome and Seurat following standard workflow. Seurat and GOrilla were used for downstream clustering, differential gene expression, and pathway analysis. All cell types were annotated using canonical markers and top expressed genes. ProjecTILs was additionally used to interpret T cell states. Results: Microglia from young-adult and aged mice have distinct transcriptional profiles pre-injury and markedly different transcriptional responses post-injury compared to young-adult mice. Pre-injury, aged mice demonstrated a disproportionate immune cell infiltration, including T cells, as compared to young-adult mice (aged versus young: 45.5% vs. 14.5%). Post-injury, the disparity was amplified with a proportional decrease in homeostatic microglia and greater increased infiltrating T cells compared to young-adult mice (Microglia: 27.5% vs. 71%; T cell: 45.5% vs. 4.5%). Of note, aged mice post-injury had a subpopulation of unique, age-specific, immune-inflammatory microglia resembling gene profiles of neurodegenerative disease-associated microglia (DAM) with enriched pathways involved in leukocyte recruitment and Alzheimer’s disease pathogenesis (FDR < 0.05). Contrastingly, post-injury, aged mice demonstrate a heterogenous T-cell infiltration with gene profiles corresponding to CD8 effector memory, CD8 native-like, CD4, and double-negative T cells (75.9%, 2.5%, 12.9%, and 8.6%, respectively) and enriched pathways including tau protein binding, macromolecule synthesis, and cytokine-mediated signaling pathways (FDR < 0.05). Conclusion: We hypothesized that aged microglia would fail to return to a homeostatic state after TBI and adopt a long-term, injury-associated state within the brain of aged mice as compared to young-adult mice after TBI. In particular, our data suggest an age-dependent reduction of homeostatic microglia post-injury yet an upregulation in a unique microglial subpopulation with a distinct immuno-inflammatory profile. Furthermore, aged subjects demonstrated a markedly disproportionate inflammatory infiltrate after TBI predominated by the presence of CD8+ T cells. In addition, post-injury, brain trauma reorganized the T cell milieu, especially CD8 effector memory T cells, via upregulating genes associated with macromolecule biosynthesis process and negative regulation of neuronal death, possibly linking TBI with its long-term sequelae and complications. Taken together, our data showed that age-specific gene signature changes in the T-cell infiltrates and the microglial subpopulation contributes to increased vulnerability of the aged brain to TBI. Age should be an a priori consideration in future TBI clinical trials.

Toxin gene profiles and antimicrobial resistance of Clostridioides difficile infection: a single tertiary care center study in Iran

Background and Objectives: Due to the reduced susceptibility of clinical Clostridioides difficile strains in hospitals to var- ious antimicrobial agents, the importance of antimicrobial susceptibility testing (ASTs) has increased. This study aimed to investigate the toxin gene profiles and the antimicrobial resistance of C. difficile isolated from hospitalized patients suspected of having Clostridioides difficile infection (CDI) in Tehran, Iran. Materials and Methods: The stool samples were obtained from a hospitalized patients. The samples were shocked by al- cohol and the patients cultured on cycloserine-cefoxitin-fructose agar in anaerobic Conditions. Toxin assay was performed for detection of toxinogenic isolates. An antibiotic susceptibility test was done. Furthermore, their genome was extracted for PCR to confirm C. difficile and detect toxin gene profile. Results: Toxigenic C. difficile were identified in 21 of the 185 stool samples (11.3%). PCR detected seven toxin gene profiles; the highest prevalence was related to tcdA+B+, cdtA+B- toxin gene profile (57.1%). There were 14.3% and 28.6% resistant rates of the isolates towards vancomycin and metronidazole with the toxin gene profiles; tcdA+B+, cdtA±B+; and tc- dA+B-, cdtA-B+. All resistant isolates to moxifloxacin, clindamycin, and tetracycline were belonged to the toxin gene profiles; tcdA+B+, cdtA+B+; tcdA+B+, cdtA+B-, and tcdA-B+, cdtA+B-. Conclusion: Relative high resistance was detected towards metronidazole and vancomycin, although, still have acceptable activity for CDI treatment. However, a proper plan for the use of antibiotics and more regular screening of C. difficile anti- biotic resistance seems necessary.

The landscape of regulatory genes in brain-wide neuronal phenotypes of a vertebrate brain

Multidimensional landscapes of regulatory genes in neuronal phenotypes at whole-brain levels in the vertebrate remain elusive. We generated single-cell transcriptomes of ~67,000 region- and glutamatergic/neuromodulator-identifiable cells from larval zebrafish brains. Hierarchical clustering based on effector gene profiles ('terminal features') distinguished major brain cell types. Sister clusters at hierarchical termini displayed similar terminal features. It was further verified by a population-level statistical method. Intriguingly, glutamatergic/GABAergic sister clusters mostly expressed distinct transcriptional factor (TF) profiles ('convergent pattern'), whereas neuromodulator-type sister clusters predominantly expressed the same TF profiles ('matched pattern'). Interestingly, glutamatergic/GABAergic clusters with similar TF profiles could also display different terminal features ('divergent pattern'). It led us to identify a library of RNA-binding proteins that differentially marked divergent pair clusters, suggesting the post-transcriptional regulation of neuron diversification. Thus, our findings reveal multidimensional landscapes of transcriptional and post-transcriptional regulators in whole-brain neuronal phenotypes in the zebrafish brain.

Gene expression changes in mammalian hosts during schistosomiasis: a review

Schistosomiasis affects over 250 million people worldwide with an estimated mortality of more than 200,000 deaths per year in sub-Saharan Africa. Efforts to control schistosomiasis in the affected areas have mainly relied on mass administration of praziquantel, which kills adult but not immature worms of all Schistosoma species. Mammalian hosts respond differently to Schistosoma infection with some being more susceptible than others, which is associated with risk factors such as sociodemographic, epidemiological, immunological and/or genetic. Host genetic factors play a major role in influencing molecular processes in response to schistosomiasis as shown in gene expression studies. These studies highlight gene profiles expressed at different time points of infection using model animals. Immune function related genes; cytokines (Th1 and Th17) are upregulated earlier in infection and Th2 upregulated later indicating a mixed Th1/Th2 response. However, Th1 response has been shown to be sustained in S. japonicum infection. Immune mediators such as matrix metalloproteinases (Mmps) and tissue inhibitors of matrix metalloproteinases (Timps) are expressed later in the infection and these are linked to wound healing and fibrosis. Downregulation of metabolic associated genes is recorded in later stages of infection. Most mammalian host gene expression studies have been done using rodent models, with fewer in larger hosts such as bovines and humans. The majority of these studies have focused on S. japonicum infections and less on S. haematobium and S. mansoni infections (the two species that cause most global infections). The few human schistosomiasis gene expression studies so far have focused on S. japonicum and S. haematobium infections and none on S. mansoni, as far as we are aware. This highlights a paucity of gene expression data in humans, specifically with S. mansoni infection. This data is important to understand the disease pathology, identify biomarkers, diagnostics and possible drug targets.

Discordance between different bioinformatic methods for identifying resistance genes from short-read genomic data, with a focus on Escherichia coli

Several bioinformatics genotyping algorithms are now commonly used to characterise antimicrobial resistance (AMR) gene profiles in whole genome sequencing (WGS) data, with a view to understanding AMR epidemiology and developing resistance prediction workflows using WGS in clinical settings. Accurately evaluating AMR in Enterobacterales, particularly Escherichia coli, is of major importance, because this is a common pathogen. However, robust comparisons of different genotyping approaches on relevant simulated and large real-life WGS datasets are lacking. Here, we used both simulated datasets and a large set of real E. coli WGS data (n=1818 isolates) to systematically investigate genotyping methods in greater detail. Simulated constructs and real sequences were processed using four different bioinformatic programs (ABRicate, ARIBA, KmerResistance, and SRST2, run with the ResFinder database) and their outputs compared. For simulations tests where 3,092 AMR gene variants were inserted into random sequence constructs, KmerResistance was correct for all 3,092 simulations, ABRicate for 3,082 (99.7%), ARIBA for 2,927 (94.7%) and SRST2 for 2,120 (68.6%). For simulations tests where two closely related gene variants were inserted into random sequence constructs, ABRicate identified the correct alleles in 11,382/46,279 (25%) of simulations, ARIBA in 2494/46,279 (5%), SRST in 2539/46,279 (5%) and KmerResistance in 38,826/46,279 (84%). In real data, across all methods, 1392/1818 (76%) isolates had discrepant allele calls for at least one gene. Our evaluations revealed poor performance in scenarios that would be expected to be challenging (e.g. identification of AMR genes at <10x coverage, discriminating between closely related AMR gene sequences), but also identified systematic sequence classification (i.e. naming) errors even in straightforward circumstances, which contributed to 1081/3092 (35%) errors in our most simple simulations and at least 2530/4321 (59%) discrepancies in real data. Further, many of the remaining discrepancies were likely artefactual, with reporting cut-off differences accounted for at least 1430/4321 (33%) discrepants. Comparing outputs generated by running multiple algorithms on the same dataset can help identify and resolve these artefacts, but ideally new and more robust genotyping algorithms are needed.

Universal features shaping organelle gene retention

Almost all eukaryotes contain mitochondria, and many contain plastids, playing vital roles in the bioenergetic and metabolic processes that power complex life. Since their endosymbiotic origins, the genomes of both organelles have been reduced, with genes being lost or transferred to the host cell nucleus from organelle DNA (oDNA) to different extents in different species. Why some genes are retained in oDNA and some lost remains a debated question. Long-standing hypotheses include the preferential retention of genes encoding hydrophobic products and those most central to redox regulation , but quantitative testing of these and other ideas remains absent. Here we harness over 15k oDNA sequences and over 300 whole genome sequences with tools from structural biology, bioinformatics, machine learning, and Bayesian model selection to reveal the properties of protein-coding genes that shape oDNA evolution. We find striking symmetry in the features predicting mitochondrial (mtDNA) and plastid (ptDNA) gene retention. Striking symmetry exists between the two organelle types: gene retention patterns in both are predicted by the hydrophobicity of a protein product and its energetic centrality within its protein complex, with additional influences of nucleic acid and amino acid biochemistry. Supporting this generality, models trained with one organelle type successfully predict gene retention in the other, and these features also distinguish gene profiles in independent endosymbiotic relationships. The identification of these features both provide quantitative support for several existing evolutionary hypotheses, and suggest new biochemical and biophysical mechanisms influencing organelle genome evolution.

Rapid changes in nasopharyngeal antibiotic resistance gene profiles after short courses of antibiotics in a pilot study of ambulatory young children

We quantified antibiotic resistance genes before and after short antibiotic courses in nasopharyngeal specimens from ambulatory children. Carriage of certain bacteria and resistance genes was common before antibiotics. After antibiotics, we observed substantial reductions in pneumococcal and Staphylococcus aureus carriage and rapid expansion in the abundance of certain resistance genes.

The Persistence of Hepatitis C Virus Infection in Hepatocytes Promotes Hepatocellular Carcinoma Progression by Pro-Inflammatory Interluekin-8 Expression

Background: A large amount of epidemiological evidence indicates that persistent HCV infection is the main risk factor for HCC. We aimed to study the effects of persistent HCV infection on the interaction of the virus and host cell to identify cancer gene profiles. Methods: Next-generation sequencing (NGS) was used to identify differentially expressed genes between uninfected Huh7.5.1 control cells, short-term HCV (S-HCV), early long-term HCV (eL-HCV), and long-term HCV (L-HCV) infections, which were analyzed using different dynamic bioinformatics and analytic tools. mRNA expression was validated and quantified using q-PCR. One hundred ninety-six serum samples of HCV patients with IFN/RBV treatment were used to study chemokine levels. Results: S-HCV activates an inflammatory response and drives cell death and apoptosis through cell cycle arrest via MAPK signaling. L-HCV promotes cell growth and alters cell adhesion and chemokine signaling via CXCL8-mediated-SRC regulation. A total of 196 serum samples from the HCV and HCV-HCC cohorts demonstrated significantly upregulated pro-inflammatory CXCL8 in non-SVR (persistent HCV infection) patients in the HCV-HCC group. Conclusions: Persistent infection with HCV induced pro-inflammatory CXCL8 and the oncogene SRC, thereby triggering and promoting hepatocarcinogenesis. CXCL8 may be a potential biomarker for monitoring HCV-related HCC progression.

IKK2/NF-κB Activation in Astrocytes Reduces Amyloid β Deposition: A Process Associated with Specific Microglia Polarization

Alzheimer’s disease (AD) is a common neurodegenerative disease that is accompanied by pronounced neuroinflammatory responses mainly characterized by marked microgliosis and astrogliosis. However, it remains open as to how different aspects of astrocytic and microglial activation affect disease progression. Previously, we found that microglia expansion in the spinal cord, initiated by IKK2/NF-κB activation in astrocytes, exhibits stage-dependent beneficial effects on the progression of amyotrophic lateral sclerosis. Here, we investigated the impact of NF-κB-initiated neuroinflammation on AD pathogenesis using the APP23 mouse model of AD in combination with conditional activation of IKK2/NF-κB signaling in astrocytes. We show that NF-κB activation in astrocytes triggers a distinct neuroinflammatory response characterized by striking astrogliosis as well as prominent microglial reactivity. Immunohistochemistry and Congo red staining revealed an overall reduction in the size and number of amyloid plaques in the cerebral cortex and hippocampus. Interestingly, isolated primary astrocytes and microglia cells exhibit specific marker gene profiles which, in the case of microglia, point to an enhanced plaque clearance capacity. In contrast, direct IKK2/NF-κB activation in microglia results in a pro-inflammatory polarization program. Our findings suggest that IKK2/NF-κB signaling in astrocytes may activate paracrine mechanisms acting on microglia function but also on APP processing in neurons.