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MBio Aug 2021Meningitis and encephalitis are leading causes of central nervous system (CNS) disease and often result in severe neurological compromise or death. Traditional...
Meningitis and encephalitis are leading causes of central nervous system (CNS) disease and often result in severe neurological compromise or death. Traditional diagnostic workflows largely rely on pathogen-specific tests, sometimes over days to weeks, whereas metagenomic next-generation sequencing (mNGS) profiles all nucleic acid in a sample. In this single-center, prospective study, 68 hospitalized patients with known ( = 44) or suspected ( = 24) CNS infections underwent mNGS from RNA and DNA to identify potential pathogens and also targeted sequencing of viruses using hybrid capture. Using a computational metagenomic classification pipeline based on KrakenUniq and BLAST, we detected pathogen nucleic acid in cerebrospinal fluid (CSF) from 22 subjects, 3 of whom had no clinical diagnosis by routine workup. Among subjects diagnosed with infection by serology and/or peripheral samples, we demonstrated the utility of mNGS to detect pathogen nucleic acid in CSF, importantly for the Ixodes scapularis tick-borne pathogens Powassan virus, Borrelia burgdorferi, and Anaplasma phagocytophilum. We also evaluated two methods to enhance the detection of viral nucleic acid, hybrid capture and methylated DNA depletion. Hybrid capture nearly universally increased viral read recovery. Although results for methylated DNA depletion were mixed, it allowed the detection of varicella-zoster virus DNA in two samples that were negative by standard mNGS. Overall, mNGS is a promising approach that can test for multiple pathogens simultaneously, with efficacy similar to that of pathogen-specific tests, and can uncover geographically relevant infectious CNS disease, such as tick-borne infections in New England. With further laboratory and computational enhancements, mNGS may become a mainstay of workup for encephalitis and meningitis. Meningitis and encephalitis are leading global causes of central nervous system (CNS) disability and mortality. Current diagnostic workflows remain inefficient, requiring costly pathogen-specific assays and sometimes invasive surgical procedures. Despite intensive diagnostic efforts, 40 to 60% of people with meningitis or encephalitis have no clear cause of CNS disease identified. As diagnostic uncertainty often leads to costly inappropriate therapies, the need for novel pathogen detection methods is paramount. Metagenomic next-generation sequencing (mNGS) offers the unique opportunity to circumvent these challenges using unbiased laboratory and computational methods. Here, we performed comprehensive mNGS from 68 prospectively enrolled patients with known ( = 44) or suspected ( = 24) CNS viral infection from a single center in New England and evaluated enhanced methods to improve the detection of CNS pathogens, including those not traditionally identified in the CNS by nucleic acid detection. Overall, our work helps elucidate how mNGS can become integrated into the diagnostic toolkit for CNS infections.
Topics: Adult; Aged; Central Nervous System Viral Diseases; Encephalitis; Female; High-Throughput Nucleotide Sequencing; Humans; Male; Meningitis; Metagenome; Metagenomics; Middle Aged; Prospective Studies; Viruses
PubMed: 34465023
DOI: 10.1128/mBio.01143-21 -
Nature Immunology Nov 2022Naïve CD8 T cells can differentiate into effector (T), memory (T) or exhausted (T) T cells. These developmental pathways are associated with distinct transcriptional...
Naïve CD8 T cells can differentiate into effector (T), memory (T) or exhausted (T) T cells. These developmental pathways are associated with distinct transcriptional and epigenetic changes that endow cells with different functional capacities and therefore therapeutic potential. The molecular circuitry underlying these developmental trajectories and the extent of heterogeneity within T, T and T populations remain poorly understood. Here, we used the lymphocytic choriomeningitis virus model of acute-resolving and chronic infection to address these gaps by applying longitudinal single-cell RNA-sequencing (scRNA-seq) and single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) analyses. These analyses uncovered new subsets, including a subpopulation of T cells expressing natural killer cell-associated genes that is dependent on the transcription factor Zeb2, as well as multiple distinct TCF-1 stem/progenitor-like subsets in acute and chronic infection. These data also revealed insights into the reshaping of T subsets following programmed death 1 (PD-1) pathway blockade and identified a key role for the cell stress regulator, Btg1, in establishing the T population. Finally, these results highlighted how the same biological circuits such as cytotoxicity or stem/progenitor pathways can be used by CD8 T cell subsets with highly divergent underlying chromatin landscapes generated during different infections.
Topics: Humans; CD8-Positive T-Lymphocytes; Transcriptome; Lymphocytic choriomeningitis virus; Epigenesis, Genetic; Chromatin; Lymphocytic Choriomeningitis
PubMed: 36271148
DOI: 10.1038/s41590-022-01338-4 -
Neonatology 2021The diagnosis of neonatal meningitis often rests on microscopic and biochemical findings in the cerebrospinal fluid (CSF). There is ongoing uncertainty about age-related...
BACKGROUND
The diagnosis of neonatal meningitis often rests on microscopic and biochemical findings in the cerebrospinal fluid (CSF). There is ongoing uncertainty about age-related normal values for CSF findings in neonates, and many previous studies have included infants in whom antibiotics were administered before lumbar puncture or in whom viral meningitis was not excluded.
METHODS
A systematic search was done using MEDLINE and EMBASE to identify original studies which investigated CSF normal values in either healthy neonates or febrile neonates in whom bacterial and viral meningitis were reliably excluded.
RESULTS
We identified seven studies investigating 270 term and 96 preterm neonates. There were minimal differences between preterm and term neonates in the CSF white blood cell (WBC) count and glucose concentration. In contrast, the CSF neutrophil count and protein concentration were influenced by gestational and chronological age. In the four studies that reported individual patient data, in 95% of cases the CSF WBC count was <12 cells/μL in preterm and <10 cells/μL in term neonates, the neutrophil count was <16 and 8 cells/μL, and the protein concentration was <210 and 110 mg/dL, respectively.
CONCLUSION
The normal range for CSF parameters in neonates is different to that in older infants, and some parameters are influenced by gestational and chronological age. CSF parameters alone are not sufficiently reliable to exclude meningitis.
Topics: Aged; Humans; Infant; Infant, Newborn; Infant, Newborn, Diseases; Leukocyte Count; Meningitis; Reference Values; Retrospective Studies; Spinal Puncture
PubMed: 34818234
DOI: 10.1159/000517630 -
Trends in Immunology Apr 2023Reinvigorating the function of exhausted CD8 T cells during chronic viral infection and cancer is a major goal of current immunotherapy regimens. Here, we discuss recent... (Review)
Review
Reinvigorating the function of exhausted CD8 T cells during chronic viral infection and cancer is a major goal of current immunotherapy regimens. Here, we discuss recent advances in our understanding of exhausted CD8 T cell heterogeneity as well as the potential differentiation trajectories that exhausted T cells follow during chronic infection and/or cancer. We highlight surmounting evidence suggesting that some T cell clones are divergent in nature and can develop into either terminally differentiated effector or exhausted CD8 T cells. Lastly, we consider the potential therapeutic implications of such a bifurcation model of CD8 T cell differentiation, including the intriguing hypothesis that redirecting progenitor CD8 T cell differentiation along an effector pathway may serve as a novel approach to mitigate T cell exhaustion.
Topics: Humans; CD8-Positive T-Lymphocytes; Lymphocytic Choriomeningitis; Lymphocytic choriomeningitis virus; Cell Differentiation; Neoplasms
PubMed: 36907685
DOI: 10.1016/j.it.2023.02.006 -
Nature Jul 2020The mammalian immune system implements a remarkably effective set of mechanisms for fighting pathogens. Its main components are haematopoietic immune cells, including...
The mammalian immune system implements a remarkably effective set of mechanisms for fighting pathogens. Its main components are haematopoietic immune cells, including myeloid cells that control innate immunity, and lymphoid cells that constitute adaptive immunity. However, immune functions are not unique to haematopoietic cells, and many other cell types display basic mechanisms of pathogen defence. To advance our understanding of immunology outside the haematopoietic system, here we systematically investigate the regulation of immune genes in the three major types of structural cells: epithelium, endothelium and fibroblasts. We characterize these cell types across twelve organs in mice, using cellular phenotyping, transcriptome sequencing, chromatin accessibility profiling and epigenome mapping. This comprehensive dataset revealed complex immune gene activity and regulation in structural cells. The observed patterns were highly organ-specific and seem to modulate the extensive interactions between structural cells and haematopoietic immune cells. Moreover, we identified an epigenetically encoded immune potential in structural cells under tissue homeostasis, which was triggered in response to systemic viral infection. This study highlights the prevalence and organ-specific complexity of immune gene activity in non-haematopoietic structural cells, and it provides a high-resolution, multi-omics atlas of the epigenetic and transcriptional networks that regulate structural cells in the mouse.
Topics: Adaptive Immunity; Animals; Chromatin; Endothelium; Epigenesis, Genetic; Epigenome; Epithelial Cells; Female; Fibroblasts; Gene Expression Regulation; Gene Regulatory Networks; Hematopoietic Stem Cells; Immune System; Immunity, Innate; Lymphocytic Choriomeningitis; Lymphocytic choriomeningitis virus; Male; Mice; Organ Specificity; Transcription, Genetic; Transcriptome
PubMed: 32612232
DOI: 10.1038/s41586-020-2424-4 -
Molecular Cell Jun 2021CD8 T cells play an essential role in defense against viral and bacterial infections and in tumor immunity. Deciphering T cell loss of functionality is complicated by...
CD8 T cells play an essential role in defense against viral and bacterial infections and in tumor immunity. Deciphering T cell loss of functionality is complicated by the conspicuous heterogeneity of CD8 T cell states described across experimental and clinical settings. By carrying out a unified analysis of over 300 assay for transposase-accessible chromatin sequencing (ATAC-seq) and RNA sequencing (RNA-seq) experiments from 12 studies of CD8 T cells in cancer and infection, we defined a shared differentiation trajectory toward dysfunction and its underlying transcriptional drivers and revealed a universal early bifurcation of functional and dysfunctional T cell states across models. Experimental dissection of acute and chronic viral infection using single-cell ATAC (scATAC)-seq and allele-specific single-cell RNA (scRNA)-seq identified state-specific drivers and captured the emergence of similar TCF1 progenitor-like populations at an early branch point, at which functional and dysfunctional T cells diverge. Our atlas of CD8 T cell states will facilitate mechanistic studies of T cell immunity and translational efforts.
Topics: Acute Disease; Atlases as Topic; CD8-Positive T-Lymphocytes; Chromatin; Chronic Disease; Epigenesis, Genetic; Gene Expression Profiling; Gene Regulatory Networks; High-Throughput Nucleotide Sequencing; Humans; Immunity, Cellular; Lymphocyte Activation; Lymphocytic Choriomeningitis; Lymphocytic choriomeningitis virus; Neoplasms; Principal Component Analysis; Single-Cell Analysis; Transcription Factors; Transcription, Genetic; Transposases
PubMed: 33891860
DOI: 10.1016/j.molcel.2021.03.045 -
Proceedings of the National Academy of... Oct 2023CD8 T cells play an essential role in antitumor immunity and chronic viral infections. Recent findings have delineated the differentiation pathway of CD8 T cells in...
CD8 T cells play an essential role in antitumor immunity and chronic viral infections. Recent findings have delineated the differentiation pathway of CD8 T cells in accordance with the progenitor-progeny relationship of TCF1 stem-like and Tim-3TCF1 more differentiated T cells. Here, we investigated the characteristics of stem-like and differentiated CD8 T cells isolated from several murine tumor models and human lung cancer samples in terms of phenotypic and transcriptional features as well as their location compared to virus-specific CD8 T cells in the chronically lymphocytic choriomeningitis virus (LCMV)-infected mice. We found that CD8 tumor-infiltrating lymphocytes (TILs) in both murine and human tumors exhibited overall similar phenotypic and transcriptional characteristics compared to corresponding subsets in the spleen of chronically infected mice. Moreover, stem-like CD8 TILs exclusively responded and produced effector-like progeny CD8 T cells in vivo after antigenic restimulation, confirming their lineage relationship and the proliferative potential of stem-like CD8 TILs. Most importantly, similar to the preferential localization of PD-1 stem-like CD8 T cells in T cell zones of the spleen during chronic LCMV infection, we found that the PD-1 stem-like CD8 TILs in lung cancer samples are preferentially located not in the tumor parenchyma but in tertiary lymphoid structures (TLSs). The stem-like CD8 T cells are present in TLSs located within and at the periphery of the tumor, as well as in TLSs closely adjacent to the tumor parenchyma. These findings suggest that TLSs provide a protective niche to support the quiescence and maintenance of stem-like CD8 T cells in the tumor.
Topics: Humans; Animals; Mice; Lymphocytic Choriomeningitis; Programmed Cell Death 1 Receptor; CD8-Positive T-Lymphocytes; Lymphocytic choriomeningitis virus; Persistent Infection; Lung Neoplasms; Mice, Inbred C57BL
PubMed: 37782797
DOI: 10.1073/pnas.2221985120 -
Ugeskrift For Laeger Jun 2024Ramsay Hunt syndrome (RHS) is an infection with the Varicella Zoster virus in the geniculate ganglion of the facial nerve. The syndrome consists of a triad of peripheral...
Ramsay Hunt syndrome (RHS) is an infection with the Varicella Zoster virus in the geniculate ganglion of the facial nerve. The syndrome consists of a triad of peripheral facial nerve palsy, ear pain and concurrent zoster rash in the ear canal. However, vesicles in the mouth can be seen. A rare complication of RHS is viral meningitis. This is a case report of a patient with orally manifested RHS and concurrent asymptomatic viral meningitis. This case aims to raise awareness of RHS with atypical presentation and concurrent viral meningitis and, thereby, the importance of a thorough neurological examination.
Topics: Humans; Herpes Zoster Oticus; Meningitis, Viral; Male; Female; Middle Aged
PubMed: 38903036
DOI: 10.61409/V02240092