Long COVID manifests with T cell dysregulation, inflammation and an uncoordinated adaptive immune response to SARS-CoV-2

Long COVID (LC) occurs after at least 10% of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections, yet its etiology remains poorly understood. We used 'omic" assays and serology to deeply characterize the global and SARS-CoV-2-specific immunity in the blood of individuals with clear LC and non-LC clinical trajectories, 8 months postinfection. We found that LC individuals exhibited systemic inflammation and immune dysregulation. This was evidenced by global differences in T cell subset distribution implying ongoing immune responses, as well as by sex-specific perturbations in cytolytic subsets. LC individuals displayed increased frequencies of CD4+ T cells poised to migrate to inflamed tissues and exhausted SARS-CoV-2-specific CD8+ T cells, higher levels of SARS-CoV-2 antibodies and a mis-coordination between their SARS-CoV-2-specific T and B cell responses. Our analysis suggested an improper crosstalk between the cellular and humoral adaptive immunity in LC, which can lead to immune dysregulation, inflammation and clinical symptoms associated with this debilitating condition.

Using published pathway figures in enrichment analysis and machine learning

Pathway Figure OCR (PFOCR) is a novel kind of pathway database approaching the breadth and depth of Gene Ontology while providing rich, mechanistic diagrams and direct literature support. Here, we highlight the utility of PFOCR in disease research in comparison with popular pathway databases through an assessment of disease coverage and analytical applications. In addition to common pathway analysis use cases, we present two advanced case studies demonstrating unique advantages of PFOCR in terms of cancer subtype and grade prediction analyses.

Long COVID manifests with T cell dysregulation, inflammation, and an uncoordinated adaptive immune response to SARS-CoV-2

Long COVID (LC), a type of post-acute sequelae of SARS-CoV-2 infection (PASC), occurs after at least 10% of SARS-CoV-2 infections, yet its etiology remains poorly understood. Here, we used multiple "omics" assays (CyTOF, RNAseq/scRNAseq, Olink) and serology to deeply characterize both global and SARS-CoV-2-specific immunity from blood of individuals with clear LC and non-LC clinical trajectories, 8 months following infection and prior to receipt of any SARS-CoV-2 vaccine. Our analysis focused on deep phenotyping of T cells, which play important roles in immunity against SARS-CoV-2 yet may also contribute to COVID-19 pathogenesis. Our findings demonstrate that individuals with LC exhibit systemic inflammation and immune dysregulation. This is evidenced by global differences in T cell subset distribution in ways that imply ongoing immune responses, as well as by sex-specific perturbations in cytolytic subsets. Individuals with LC harbored increased frequencies of CD4+ T cells poised to migrate to inflamed tissues, and exhausted SARS-CoV-2-specific CD8+ T cells. They also harbored significantly higher levels of SARS-CoV-2 antibodies, and in contrast to non-LC individuals, exhibited a mis-coordination between their SARS-CoV-2-specific T and B cell responses. RNAseq/scRNAseq and Olink analyses similarly revealed immune dysregulatory mechanisms, along with non-immune associated perturbations, in individuals with LC. Collectively, our data suggest that proper crosstalk between the humoral and cellular arms of adaptive immunity has broken down in LC, and that this, perhaps in the context of persistent virus, leads to the immune dysregulation, inflammation, and clinical symptoms associated with this debilitating condition.

Using Published Pathway Figures in Enrichment Analysis and Machine Learning

Pathway Figure OCR (PFOCR) is a novel kind of pathway database approaching the breadth and depth of Gene Ontology while providing rich, mechanistic diagrams and direct literature support. PFOCR content is extracted from published pathway figures currently emerging at a rate of 1000 new pathways each month. Here, we compare the pathway information contained in PFOCR against popular pathway databases with respect to overall and disease-specific coverage. In addition to common pathways analysis use cases, we present two advanced case studies demonstrating unique advantages of PFOCR in terms of cancer subtype and grade prediction analyses.

Defining blood-induced microglia functions in neurodegeneration through multiomic profiling

Blood protein extravasation through a disrupted blood-brain barrier and innate immune activation are hallmarks of neurological diseases and emerging therapeutic targets. However, how blood proteins polarize innate immune cells remains largely unknown. Here, we established an unbiased blood-innate immunity multiomic and genetic loss-of-function pipeline to define the transcriptome and global phosphoproteome of blood-induced innate immune polarization and its role in microglia neurotoxicity. Blood induced widespread microglial transcriptional changes, including changes involving oxidative stress and neurodegenerative genes. Comparative functional multiomics showed that blood proteins induce distinct receptor-mediated transcriptional programs in microglia and macrophages, such as redox, type I interferon and lymphocyte recruitment. Deletion of the blood coagulation factor fibrinogen largely reversed blood-induced microglia neurodegenerative signatures. Genetic elimination of the fibrinogen-binding motif to CD11b in Alzheimer's disease mice reduced microglial lipid metabolism and neurodegenerative signatures that were shared with autoimmune-driven neuroinflammation in multiple sclerosis mice. Our data provide an interactive resource for investigation of the immunology of blood proteins that could support therapeutic targeting of microglia activation by immune and vascular signals.

Deep immunophenotyping reveals endometriosis is marked by dysregulation of the mononuclear phagocytic system in endometrium and peripheral blood

BACKGROUND

Endometriosis is a chronic, estrogen-dependent disorder where inflammation contributes to disease-associated symptoms of pelvic pain and infertility. Immune dysfunction includes insufficient immune lesion clearance, a pro-inflammatory endometrial environment, and systemic inflammation. Comprehensive understanding of endometriosis immune pathophysiology in different hormonal milieu and disease severity has been hampered by limited direct characterization of immune populations in endometrium, blood, and lesions. Simultaneous deep phenotyping at single-cell resolution of complex tissues has transformed our understanding of the immune system and its role in many diseases. Herein, we report mass cytometry and high dimensional analyses to study immune cell phenotypes, abundance, activation states, and functions in endometrium and blood of women with and without endometriosis in different cycle phases and disease stages.

METHODS

A case-control study was designed. Endometrial biopsies and blood (n = 60 total) were obtained from women with (n = 20, n = 17, respectively) and without (n = 14, n = 9) endometriosis in the proliferative and secretory cycle phases of the menstrual cycle. Two mass cytometry panels were designed: one broad panel and one specific for mononuclear phagocytic cells (MPC), and all samples were multiplexed to characterize both endometrium and blood immune composition at unprecedented resolution. We combined supervised and unsupervised analyses to finely define the immune cell subsets with an emphasis on MPC. Then, association between cell types, protein expression, disease status, and cycle phase were performed.

RESULTS

The broad panel highlighted a significant modification of MPC in endometriosis; thus, they were studied in detail with an MPC-focused panel. Endometrial CD91+ macrophages overexpressed SIRPα (phagocytosis inhibitor) and CD64 (associated with inflammation) in endometriosis, and they were more abundant in mild versus severe disease. In blood, classical and intermediate monocytes were less abundant in endometriosis, whereas plasmacytoid dendritic cells and non-classical monocytes were more abundant. Non-classical monocytes were higher in severe versus mild disease.

CONCLUSIONS

A greater inflammatory phenotype and decreased phagocytic capacity of endometrial macrophages in endometriosis are consistent with defective clearance of endometrial cells shed during menses and in tissue homeostasis, with implications in endometriosis pathogenesis and pathophysiology. Different proportions of monocytes and plasmacytoid dendritic cells in blood from endometriosis suggest systemically aberrant functionality of the myeloid system opening new venues for the study of biomarkers and therapies for endometriosis.

Deep Phenotypic Analysis of Blood and Lymphoid T and NK Cells From HIV+ Controllers and ART-Suppressed Individuals

T and natural killer (NK) cells are effector cells with key roles in anti-HIV immunity, including in lymphoid tissues, the major site of HIV persistence. However, little is known about the features of these effector cells from people living with HIV (PLWH), particularly from those who initiated antiretroviral therapy (ART) during acute infection. Our study design was to use 42-parameter CyTOF to conduct deep phenotyping of paired blood- and lymph node (LN)-derived T and NK cells from three groups of HIV+ aviremic individuals: elite controllers (N = 5), and ART-suppressed individuals who had started therapy during chronic (N = 6) vs. acute infection (N = 8), the latter of which is associated with better outcomes. We found that acute-treated individuals are enriched for specific subsets of T and NK cells, including blood-derived CD56-CD16+ NK cells previously associated with HIV control, and LN-derived CD4+ T follicular helper cells with heightened expansion potential. An in-depth comparison of the features of the cells from blood vs. LNs of individuals from our cohort revealed that T cells from blood were more activated than those from LNs. By contrast, LNs were enriched for follicle-homing CXCR5+ CD8+ T cells, which expressed increased levels of inhibitory receptors and markers of survival and proliferation as compared to their CXCR5- counterparts. In addition, a subset of memory-like CD56^brightTCF1+ NK cells was enriched in LNs relative to blood. These results together suggest unique T and NK cell features in acute-treated individuals, and highlight the importance of examining effector cells not only in blood but also the lymphoid tissue compartment, where the reservoir mostly persists, and where these cells take on distinct phenotypic features.

Interspecific Sample Prioritization Can Improve QTL Detection With Tree-Based Predictive Models

Due to increasing demand for new advanced crops, considerable efforts have been made to explore the improvement of stress and disease resistance cultivar traits through the study of wild crops. When both wild and interspecific hybrid materials are available, a common approach has been to study two types of materials separately and simply compare the quantitative trait locus (QTL) regions. However, combining the two types of materials can potentially create a more efficient method of finding predictive QTLs. In this simulation study, we focused on scenarios involving causal marker expression suppressed by trans-regulatory mechanisms, where the otherwise easily lost associated signals benefit the most from combining the two types of data. A probabilistic sampling approach was used to prioritize consistent genotypic phenotypic patterns across both types of data sets. We chose random forest and gradient boosting to apply the prioritization scheme and found that both facilitated the investigation of predictive causal markers in most of the biological scenarios simulated.

Genomic diversity and genome-wide association analysis related to yield and fatty acid composition of wild American oil palm

Existing Elaeis guineensis cultivars lack sufficient genetic diversity due to extensive breeding. Harnessing variation in wild crop relatives is necessary to expand the breadth of agronomically valuable traits. Using RAD sequencing, we examine the natural diversity of wild American oil palm populations (Elaeis oleifera), a sister species of the cultivated Elaeis guineensis oil palm. We genotyped 192 wild E. oleifera palms collected from seven Latin American countries along with four cultivated E. guineensis palms. Honduras, Costa Rica, Panama and Colombia palms are panmictic and genetically similar. Genomic patterns of diversity suggest that these populations likely originated from the Amazon Basin. Despite evidence of a genetic bottleneck and high inbreeding observed in these populations, there is considerable genetic and phenotypic variation for agronomically valuable traits. Genome-wide association revealed several candidate genes associated with fatty acid composition along with vegetative and yield-related traits. These observations provide valuable insight into the geographic distribution of diversity, phenotypic variation and its genetic architecture that will guide choices of wild genotypes for crop improvement.

Multi-trait analysis of domestication genes in Cicer arietinum - Cicer reticulatum hybrids with a multidimensional approach: Modeling wide crosses for crop improvement

Domestication and subsequent breeding have eroded genetic diversity in the modern chickpea crop by ˜100-fold. Corresponding reductions to trait variation create the need, and an opportunity, to identify and harness the genetic capacity of wild species for crop improvement. Here we analyze trait segregation in a series of wild x cultivated hybrid populations to delineate the genetic underpinnings of domestication traits. Two species of wild chickpea, C. reticulatum and C. echinospermum, were crossed with the elite, early flowering C. arietinum cultivar ICCV96029. KASP genotyping of F2 parents with an FT-linked molecular marker enabled selection of 284 F3 families with reduced phenological variation: 255 F3 families of C. arietinum x reticulatum (AR) derived from 17 diverse wild parents and 29 F3 families of C. arietinum x echinospermum (AE) from 3 wild parents. The combined 284 lineages were genotyped using a genotyping-by-sequencing strategy and phenotyped for agronomic traits. 50 QTLs in 11 traits were detected from AR and 35 QTLs in 10 traits from the combined data. Using hierarchical clustering to assign traits to six correlated groups and mixed model based multi-trait mapping, four pleiotropic loci were identified. Bayesian analysis further identified four inter-trait relationships controlling the duration of vegetative growth and seed maturation, for which the underlying pleiotropic genes were mapped. A random forest approach was used to explore the most extreme trait differences between AR and AE progenies, identifying traits most characteristic of wild species origin. Knowledge of the genomic basis of traits that segregate in wild-cultivated hybrid populations will facilitate chickpea improvement by linking genetic and phenotypic variation in a quantitative genetic framework.

WhoGEM: an admixture-based prediction machine accurately predicts quantitative functional traits in plants

The explosive growth of genomic data provides an opportunity to make increased use of sequence variations for phenotype prediction. We have developed a prediction machine for quantitative phenotypes (WhoGEM) that overcomes some of the bottlenecks limiting the current methods. We demonstrated its performance by predicting quantitative disease resistance and quantitative functional traits in the wild model plant species, Medicago truncatula, using geographical locations as covariates for admixture analysis. The method's prediction reliability equals or outperforms all existing algorithms for quantitative phenotype prediction. WhoGEM analysis produces evidence that variation in genome admixture proportions explains most of the phenotypic variation for quantitative phenotypes.

Identification of the novel HLA-B*15:18:01:04 in a Korean individual

HLA-B*15:18:01:04 differs from HLA-B*15:18:01:02 by single nucleotide substitution at position 2176 (G > A).

HLA-DPB1*519:01, a new allele identified by sequence-based typing in a Korean individual

The new allele DPB1*519:01 showed one nucleotide difference with DPB1*13:01:01 at codon 234 (GTG/ATG).

HLA-A*24:02:01:09, a new allele identified by sequence-based typing in a Korean individual

One nucleotide insertion between residues 1804 and 1805 of HLA-A*24:02:01:01 results in a new allele, HLA-A*24:02:01:09.

A new HLA-C*07:244 allele identified by sequence-based typing in a Korean individual

The C*07:244 changes single nucleotide of C*07:02:01 at codon 75 (CGA → CAA), Arg to Gln.

Cooperative activation of PI3K by Ras and Rho family small GTPases

Phosphoinositide 3-kinases (PI3Ks) and Ras and Rho family small GTPases are key regulators of cell polarization, motility, and chemotaxis. They influence each other's activities by direct and indirect feedback processes that are only partially understood. Here, we show that 21 small GTPase homologs activate PI3K. Using a microscopy-based binding assay, we show that K-Ras, H-Ras, and five homologous Ras family small GTPases function upstream of PI3K by directly binding the PI3K catalytic subunit, p110. In contrast, several Rho family small GTPases activated PI3K by an indirect cooperative positive feedback that required a combination of Rac, CDC42, and RhoG small GTPase activities. Thus, a distributed network of Ras and Rho family small GTPases induces and reinforces PI3K activity, explaining past challenges to elucidate the specific relevance of different small GTPases in regulating PI3K and controlling cell polarization and chemotaxis.

Chimerism and mosaicism are important causes of ABO phenotype and genotype discrepancies

Discrepancies between blood group genotype and RBC phenotype are important to recognize when implementing DNA-based blood grouping techniques. This report describes two such cases involving the ABO blood group in the Korean population. Propositus #1 was a 22-year-old healthy man undergoing pretransfusion testing for minor surgery. Propositus #2 was a 23- year-old male blood donor. RBCs from both propositi were determined to be group AB and demonstrated unusual agglutination patterns on forward typing, which were inconsistent with their ABO genotype determined by allele-specific (AS) PCR. RBCs from propositus #1 demonstrated mixed field agglutination with both anti-A and -B, while RBCs from propositus #2 demonstrated mixed field only with anti-A reagents. Both had B/O genotypes by AS-PCR. Cloning and sequencing of ABO exons 6 and 7 revealed three alleles in both propositi: propositus #1: A102/B101/O04; propositus #2: A102/B101/O01. A panel of nine short-tandem repeat (STR) loci was tested on DNA extracted from blood, buccal mucosal cells, and hair from the propositi and on DNA isolated from their parents' blood. In all tissues tested from propositus #1, three loci demonstrated a double paternal and a single maternal DNA contribution, indicating that he was a chimera or a mosaic; in those from propositus # 2, one STR locus demonstrated a double paternal DNA contribution, indicating that he was a tetragametic chimera. Chimerism and mosaicism are uncommon but important causes of ABO genotype and phenotype discrepancies. The evaluation of patients and donors with unusual or unexpected serology in pretransfusion testing and consensus ABO alleles may include the evaluation of STR loci to detect these phenomena.

The genetic and phenotypic basis of blood group A subtypes in Koreans

A serological and genetic study of Korean blood donors with phenotypic group A subtypes was performed. There were 176 donors with phenotypic A subtypes identified. Exons 6 and 7 from 57 representative donors were sequenced. The A(var) allele (784 G > A) was cloned and sequenced, and a family study demonstrating its inheritance and unusual serological characteristics was performed. The A102 allele was the most frequently identified allele in phenotypically A2 (58%, 11/19) and A2B (68%, 17/25) donors. Anti-A1 was rarely present amongst A2 and A2B donors. The family study revealed that the A(var) allele was expressed as phenotype A(weak)B in A(var)/B heterozygote members, but as phenotype O in A(var)/O heterozygotes. The most frequent allele in Korean donors with the A2 phenotype differs from its Caucasian counterpart, as does the frequency of anti-A1. The A(var) allele demonstrates allelic enhancement in A(var)/B heterozygotes.

Molecular typing of vibrio vulnificus isolated from clinical specimens by pulsed-field gel electrophoresis and random amplified polymorphic DNA analysis

Primary V. vulnificus septicemia has been continuously reported in Korea. We analyzed the molecular diversity of V. vulnificus strains isolated from clinical specimens using pulsed-field gel electrophoresis (PFGE) and random amplified polymorphic DNA (RAPD) analysis. We analyzed a total of 23 V. vulnificus strains isolated from 22 patients between 1992 and 1997. RAPD analysis was performed using five random primers, and we obtained chromosomal DNA restriction patterns with NotI and SfiI by PFGE. Two isolates from one patient disclosed similarity value 1.0 by RAPD and had an indistinguishable pattern when analyzed with PFGE, which indicated that they were the same strains. The remaining 22 isolates from 22 patients could be separated into 5 different molecular types in RAPD analysis. The range of similarity values among the isolates was wide (0.29-0.81). Of 22 strains, four strains could not be typed in repeated trials by PFGE with NotI and SfiI. The PFGE patterns of 18 strains showed a remarkable polymorphism consisting 12-19 fragments (20-870 kb). These results show that V. vulnificus strains isolated from Korea are genetically diversified for the most part.

Molecular typing of Vibrio vulnificus isolates by random amplified polymorphic DNA (RAPD) analysis

This study was undertaken to determine molecular types and genetic similarity among V. vulnificus isolates by RAPD analysis. We compared these results with serotypes of V. vulnificus. Ninety-seven V. vulnificus strains including 69 strains from Chonnam University Hospital (CUH; Kwangju, Korea), 13 from Wonkwang University Hospital (WUH; Iksan, Korea), 13 from the Japanese National Institute of Health (JNIH) and two reference strains (ATCC 33815 and ATCC 27562) were analyzed. Four molecular types comprising all the strains were obtained by RAPD analysis. Type I was the most common (60/95) and included 58 strains from CUH. Type I showed a further subdivision into seven subtypes. Type II (23/95) composed of 11 strains from CUH, nine from WUH, three from JNIH and two reference strains. Six type III strains comprised four WUH strains and two JNIH strains. All six strains of type IV were from JNIH. The range of genetic similarity values among V. vulnificus isolates was 0.24 to 1.00. The serotypes of 95 strains were 04 (84.2%), 014 (3.2%), 01 (2.1%), 013 (2.1%), and R (2.1%). The most common 04 serotype strains were distributed among types I (60 strains), II (23 strains), III and IV (six strains). Although the V. vulnificus isolates showed a wide range of genetic similarity values, RAPD analysis could separate V. vulnificus strains into four molecular types, and the isolates from the same hospitals tended to belong to the same molecular type. There was no specific correlation between molecular types and serotypes of V. vulnificus.

Alternative use of polymerase chain reaction instead of rho-nitro-alpha-acetylamino-beta-hydroxypropiophenone test for the early detection of Mycobacterium tuberculosis in BACTEC 12B cultures

Compared with conventional culture media, the TB BACTEC system has demonstrated improved isolation rates as well as an earlier detection time for mycobacterial species. However, the identification of M. tuberculosis by the rho-nitro-alpha-acetylamino-beta-hydroxypropiophenone (NAP) test in the TB BACTEC 460 system may require 6 days for interpretable results. We evaluated the usefulness of a polymerase chain reaction (PCR) assay for earlier identification of M. tuberculosis in positive BACTEC 12B cultures. A total of 262 TB BACTEC culture specimens with GIs > or = 10 were assayed by PCR, and the results were compared with those of the NAP test. The aliquot from BACTEC 12B vials was boiled for 10 min, and 2 microliters of the boiled suspension was used for the PCR assay. One set of primers based on the IS 6110 sequence of M. tuberculosis was used to amplify a 457 bp fragment of DNA. Of the 173 TB BACTEC culture specimens which were identified as M. tuberculosis by the NAP test. 171 were PCR positive. Of the 21 TB BACTEC cultures identified as MOTT by the NAP test. 19 were PCR negative, but 2 were PCR positive: these two cultures were shown to grow both M. tuberculosis and MOTT in BACTEC 12B vials. Of the remaining 68 cultures which were contaminated with AFB-negative bacteria, the PCR identified M. tuberculosis in 13, in agreement with the NAP results in the reprocessed specimens. Overall, the PCR results in the 262 BACTEC culture specimens with GIs > or = 10 were sensitive in 99.5% (186/187) and specific in 100% (68/68). The mean time for the identification of M. tuberculosis in TB BACTEC cultures with GIs > or = 10 was 7 h by the PCR compared to 5.9 days by the NAP test. These results suggest that the PCR could be used as an alternative to the NAP test for the rapid identification of M. tuberculosis in BACTEC 12B cultures, particularly in those which contained both M. tuberculosis and MOTT or M. tuberculosis and AFB-negative bacteria.