bluuebunny/crossref_metadata_2025_split huggingface dataset:
DOCK8 mutations in COVID-19 and MIS-C Cytokine Storm Syndrome
Authors: Cron Randy Q , Zhang Mingce , Cron Remy R , Absher Devin , Bridges John M , Schnell Amanda , Bhatraju Pavan K , Vagrecha Anshul , Lozinsky Shannon , Acharya Suchitra , Levy Carolyn Fein , Chatham W. Winn 
Published: February 2023

Abstract

Background
We recently identified DOCK8 as a novel gene associated with cytokine storm syndrome (CSS). Heterozygous missense mutations in DOCK8 diminish NK cell lytic function and contribute to increased pro-inflammatory cytokine production (CSS). CSS is a potential complication of COVID-19 with severe consequences. Children are at risk of a SARS-CoV-2 post-infectious CSS, multisystem inflammatory syndrome in children (MIS-C). Host genetic factors associated with COVID-19 CSS and MIS-C CSS are unknown.

Methods
To date, 16 adult patients enrolled in a COVID-19 CSS clinical trial at UAB had whole genome sequencing. Four (25%) had rare heterozygous DOCK8 mutations (3 missense, 1 intronic). A COVID-19 CSS adult patient in Seattle also had a DOCK8 missense mutation. In addition, DOCK8 missense mutations were identified in 5 children (UAB & Northwell) hospitalized with MIS-C. DOCK8 mutations, or wild-type (WT) sequence controls, were introduced into human NK-92 cells by FOAMY virus transduction. WT and mutant DOCK8-expressing NK-92 cells were incubated with K562 target cells and compared for cytolysis and degranulation (CD107a).

Results
One COVID-19 patient DOCK8 mutation (Gly523Arg) reduced NK cell degranulation by 30% and cytolysis by 23% (n=3). Similar studies of 3 MIS-C patients with DOCK8 missense mutations revealed up to 31% reduced NK cell degranulation and 48% reduction in cytolysis by 3 mutations (n=3). Two-way ANOVA analysis revealed statistically significant (p&lt;0.05) differences in NK cell degranulation and lysis for 4 unique DOCK8 mutations.

Conclusion
Heterozygous DOCK8 missense mutations may contribute to severe COVID-19 and MIS-C CSS by partial dominant-negative effects yielding decreased NK cell cytolysis.
Activation-dependent post-transcriptional regulation of CD40L mediates B cell development and survival in germinal centers
Authors: De Maio Diego Javier Prado , Narayanan Bitha , La Porta James , Ganapathi Usha , Xie Ping , Covey Lori R 
Published: February 2023

Abstract
We have described a posttranscriptional pathway of induced mRNA stability that occurs at late times of T cell activation and is engaged by the binding of a polypyrimidine tract-binding protein (PTBP1) complex to the 3′UTR of the CD40L transcript. We explored the in vivo role of this pathway by generating a mouse bearing a deletion of the CD40L stability element (termed CD40LΔ5) and found that Tfh cells harboring the stability defect expressed approximately 60% of WT CD40L. Importantly, this decrease in CD40L corresponded to a poorly elaborated germinal center (GC) response which included significantly decreased levels of switched antibodies, antibody-secreting cells, GL7+ B cells and differentiated GC B cell subsets. In contrast, there was little difference in either somatic hypermutation or affinity maturation between B cells from WT compared to CD40LD5 mice. Notably, both the number and percentage of early memory B cells and plasmablasts were significantly decreased indicating that CD40L expression linked to mRNA stability was critical for B cell differentiation. To understand the impact of this stability pathway on gene expression, CD19+ B cells from CD40LD5 immunized mice were transcriptionally profiled using RNAseq and pathways associated with cell survival and proliferation were downregulated and apoptotic pathways upregulated compared to WT B cells. Importantly, the level of AID mRNA was unchanged whereas c-myc expression was significantly reduced in GL7+ B cells. Together these findings reveal that the CD40L stability element plays a critical role in regulating CD40L expression in Tfh cells, which in turn supports the optimal proliferation and cell survival of high affinity GC B cells and the differentiation of B cell subsets.
HIRA-dependent H3.3 deposition and its modification facilitate somatic hypermutation of immunoglobulin gene by maintaining the proper chromatin context and transcription
Authors: Yu GuoJun , Duan Zhi , Zhang Yongwei , Gupta Varun , MacCarthy Thomas , Scharff Matthew D 
Published: February 2023

Abstract
The histone variant H3.3 and its chaperone HIRA are involved in active transcription but their detailed roles in regulating somatic hypermutation (SHM) in human B cells have not been fully elucidated. Here we found that the knockout (KO) of H3.3 HIRA chaperone significantly decreased SHM in the Ramos human germinal center like B cell line without changing the levels of AID and other major proteins known to be involved in SHM. The HIRA KO was associated with a decrease at the immunoglobulin (Ig) heavy chain locus of many factors related to transcription elongation including H3.3 and this was accompanied by decreased nascent transcription of the Ig heavy chain locus. However, H3K79me2/3 elongation modification was not affected. The abundance of ZMYND11 that specifically binds to H3.3K36me3 on the Ig locus was also reduced by the HIRA KO, suggesting that the HIRA loss decreased the level of H3.3K36me3. However, the chromatin accessibility of Ig locus was increased by the HIRA depletion. Furthermore, stable expression of ectopic H3.3G34V and H3.3G34R mutants that inhibit the trimethylation of H3.3K36 reduced SHM in Ramos cells, while the H3.3K79M mutant did not. Consistent with HIRA KO, H3.3G34V mutant also decreased the occupancy of various elongation factors and of ZMYND11 on Ig heavy chain variable and the downstream switching regions. These results reveal an unrecognized role of HIRA and the H3.3K36me3 modification in SHM and further confirm the central role of transcription-coupled chromatin accessibility in SHM in human B cells.
Downregulation of key B cell transcription factor Ets1 in response to antigen receptor signaling depends on IKK2 and unconventional downstream effectors.
Authors: Kearly Alyssa , Ottens Kristina , Satterthwaite Anne B , Garrett-Sinha Lee Ann 
Published: February 2023

Abstract
The transcription factor (TF) Ets1 plays a critical role in maintaining B cell quiescence. High Ets1 levels in resting B cells prevent premature plasma cell differentiation and suppress autoimmune responses, but Ets1 must be downregulated to allow for proper B cell responses. Despite this vital role, it remains unknown how the Ets1 expression pattern is coordinated. Upon activation of antigen receptors (ARs), Ets1 is downregulated and quantification of newly transcribed pre-mRNA indicates that a decrease in Ets1 gene transcription is responsible. New protein synthesis is shown to be dispensable for this downregulation, suggesting that it does not rely on upregulation of a repressor but rather changes in abundance or activity of existing TFs. NFκB is activated in response to AR signaling and its binding motifs are found in putative regulatory elements identified near the Ets1 gene. Inhibition of NFκB-activating kinase IKK2 prevents the decrease in Ets1 transcription in response to AR stimulation. However, neither RelA nor cRel downstream of IKK2 are required for proper control of Ets1 expression. Next, we examined potential roles for Foxo3 and Rictor, unconventional downstream effectors of IKK2. Foxo3 has a similar expression pattern to Ets1 and is downregulated upon BCR stimulation, but B cells lacking Foxo3 regulate Ets1 expression in a manner similar to WT B cells. Rictor is a component of the mTORC2 complex, but inhibition of mTOR signaling does not impact Ets1 downregulation in response to BCR stimulation. Overall, these data suggest that Ets1 expression is coordinated by unconventional, but as of yet unidentified, downstream effectors of IKK2 in response to AR signaling.
Funded by NIH R01 AI122720 and the Lupus Research Alliance.
H3K9 dimethyltransferase G9a deficiency modulates B-cell response to LPS
Authors: George-Alexander Lou-Ella , Kania Anna , Mi Tian , Scharer Christopher D. , Boss Jeremy M 
Published: February 2023

Abstract
B cell differentiation is a tightly regulated process coordinated by the timed expression of various transcription factors and chromatin accessibility changes mediated by histone modifying enzymes. The histone methyltransferase (HMT) G9a, dimethylates histone H3 lysine 9 (H3K9) at promoters and inhibits gene expression through recruitment of proteins that impair chromatin accessibility. HMTs are expressed ubiquitously but display distinct enzymatic activities and patterns of chromosomal localization. G9a is most known for co-localizing with Blimp-1 to silence genes associated with the B cell phenotype in plasma cells. However, our findings show a constitutive expression of G9a during B-cell division. In addition, B cell processes that are modulated by G9a mediated dimethylation remain to be elucidated. To study G9a’s involvement at various stages of B-cell differentiation, we crossed G9afl/fl mice onto the CD19Cre/+ background (G9aKO mice). Phenotypic characterization of these mice identified a skewing within the mature B cell population towards marginal zone (MZ) B cells in G9aKO mice. Upon challenge with LPS significantly elevated activated B-cell and plasmablast frequencies were observed in G9aKO mice. Regions with chromatin accessibility and expression changes identified by ATAC-Seq and RNA-Seq elucidated the B cell processes that are modulated in G9a deficient mice. B cell processes that are subject to direct modulation by G9a will be elucidated using CUT&Tag. Together, our data shows the importance of G9a in epigenetic modulation required for B cell function.
Integrative transcriptome and chromatin landscape analysis reveals distinct epigenetic regulations in human memory B cells
Authors: Casali Paolo , Moroney Justin B , Vasudev Anusha , Pertsemlidis Alexander , Zan Hong 
Published: February 2023

Abstract
Memory B cells (MBCs) are long-lived and produce high-affinity, generally, class-switched antibodies. Here we use a multiparameter approach involving CD27 to segregate naïve B cells (NBCs), IgD+ unswitched (unsw) MBCs and IgG+ or IgA+ class-switched (sw) MBCs from humans of different age, sex and race. Conserved antibody variable gene expression indicates that MBCs emerge through unbiased selection from NBCs. Integrative analyses of mRNAs, miRNAs, lncRNAs, chromatin accessibility and cis-regulatory elements uncover a core mRNA-ncRNA transcriptional signature shared by IgG+ and IgA+ swMBCs and distinct from NBCs, while unswMBCs display a transitional transcriptome. Some swMBC transcriptional signature loci are accessible but not expressed in NBCs. Profiling miRNAs reveals downregulated MIR181 and concomitantly upregulated target-genes RASSF6, TOX, TRERF1, TRPV3 and RORa in swMBCs. Finally, lncRNAs differentially expressed in swMBCs cluster proximal to chromosome 14 IgH chain locus. Our findings provide new insights into MBC transcriptional programs and epigenetic regulation, opening new investigative avenues on these critical cell elements in human health and disease.
Deubiquitination of NLRP6 by Cyld critically regulates colonic inflammation
Authors: Poojary Venuprasad K , Mukherjee Sandip , Kumar Ritesh , Mosialos George , Theiss Arianne L , Flavell Richard A 
Published: February 2023

Abstract
The inflammasome NLRP6 plays a crucial role in regulating colonic inflammation and cancer. However, the molecular mechanisms by which NLRP6 function is inhibited to prevent excessive inflammation remain unclear. Here, we demonstrate that the deubiquitinase Cyld prevents excessive interleukin 18 (IL-18) production in the colonic mucosa by deubiquitinating NLRP6. We show that deubiquitination inhibited the NLRP6-ASC inflammasome complex and regulated the maturation of IL-18. Cyld deficiency in mice resulted in elevated levels of active IL-18 and severe colonic inflammation and increased colon cancer. Further, in patients with ulcerative colitis, the concentration of active IL-18 was inversely correlated with CYLD expression. Thus, we have identified a novel regulatory mechanism that inhibits the NLRP6-IL-18 pathway in colonic inflammation. (Nat Immunol. 2020. 21(6):626–635. PMID: 32424362)
MAPK regulates the immune responses in liver cirrhosis and hepatocellular carcinoma
Authors: Chang Chiung-Fang , Lu Ssu-Jung , Wang Chih-Hsuan , Jeng Kuo-Shyang 
Published: February 2023

Abstract
Liver diseases causes approximately 2 million death per year worldwide. Aberrant apoptosis is associated with the progression of liver fibrosis and cirrhosis, even for hepatocellular carcinoma (HCC). HCC is one of major causes of cancer death worldwide due to high heterogeneity and recurrence. Immune scores could be used to link HCC disease-free survival and to identify several microenvironment-related genes. MAPK signaling plays an important role in liver fibrogenesis and HCC. ERK activation is associated with aggressive HCC, resulting in short overall survival. In this study, the immune responses of liver fibrosis and HCC mediated by ERK signaling were investigated.
Both WT and Erk2 deficient mice were fed with choline-deficient diet to induce liver cirrhosis. Erk2 deficient livers have less degree of liver cirrhosis than WT livers. Our preliminary data suggested there was a significant increasement in the percentages of regulatory T cells in Erk2 deficient splenocytes. The percentages of follicular T cells were similar in WT and Erk2 deficient splenocytes. However, there was no significant differences in Erk2 deficient hepatic CD4 T cells for regulatory T cells and follicular T cells. In addition, Egr1 is one of ERK signaling downstream transcription factors. In HCC, there were about 10-fold differences in gene expression in the Egr1high and Egr1low group and the differential gene expression was identified. In hepatotoxicity, there was about more than 100 genes involved in HCC, 50~70 genes in liver cirrhosis, liver inflammation and liver necrosis/cell death. Therefore, MAPK signaling plays an important role in regulating the immune responses in the liver cirrhosis and HCC progression.
Downregulation of AW112010 upon treatment with 6-formylindolo[3,2-b] carbazole protects mice from fulminant Concanavalin-induced T cell-mediated liver injury
Authors: Cannon Alkeiver S , Wilson Kiesha , Miranda Kathryn , Nagarkatti Mitzi , Nagarkatti Prakash 
Published: February 2023

Abstract
Upregulation of long noncoding RNA (lncRNA) AW112010 has been observed in multiple inflammatory disease models. In line with implication of this lncRNA as a regulator of inflammation, it has also been shown that AW112010 expression decreases upon treatment with anti-inflammatory compounds. Since lncRNAs show abnormal expression in many inflammatory diseases and reactions, elucidating their role in such ailments is necessary. Data from our lab has shown that treatment with aryl hydrocarbon receptor (AhR) ligands induce epigenetic pathway dysregulation, so this study aimed to determine inflammatory genes dysregulated upon treatment with the endogenous AhR ligand, 6-formylindolo[3,2-b] carbazole (FICZ). A murine model of immune cell-mediated liver injury was employed by intravenously injecting 12.5 mg/kg Concanavalin A (ConA). One hour after challenge, mice were treated with 50 μg/kg FICZ via an intraperitoneal injection. Interestingly, analysis of serum collected twenty-four hours after challenge showed that FICZ was able to reduce the level of alanine transaminase (ALT) suggesting a decrease in disease severity. Single cell RNA sequencing was conducted on infiltrating liver mononuclear cells enriched via a percoll gradient. We observed a reduced percentage of T cells upon FICZ treatment and an increase in the percentage of neutrophils. Overall, we observed downregulation of AW112010 in the FICZ-treated group. Specifically, AW112010 was identified as one of the top 20 genes dysregulated in the NK cell cluster and was downregulated in the B cell, CD8+ T cell, and Kupffer cell clusters. Together, these data suggest AW112010 downregulation as a potential mechanism through which FICZ protects mice from severe liver injury.
The type 1 diabetes-associated A946T single nucleotide polymorphism in IFIH1 results in increased type I interferon signaling
Authors: Taylor Jared P , Tse Hubert Ming 
Published: February 2023

Abstract
Single nucleotide polymorphisms (SNP) in the human IFIH1 gene are associated with autoimmunity and interferonopathies. The rs1990760 SNP, which results in an amino acid change from alanine to threonine at position 946 (A946T), is associated with several autoimmune diseases including rheumatoid arthritis, multiple sclerosis, and type 1 diabetes (T1D). IFIH1 encodes for melanoma differentiation-associated protein 5 (MDA5), a cytoplasmic dsRNA sensor. Viral infections have been implicated as environmental triggers in autoimmune diseases. In T1D, Coxsackievirus B (CVB) infections are associated with disease onset and an IFN gene signature is detected shortly before the development of autoantibodies. Interestingly, MDA5 is responsible for detecting dsRNA replication intermediates formed during CVB replication. The objective of this study is to determine the interplay of a genetic risk factor (A946T SNP) and an environmental factor (CVB infections) in the initiation of T1D. We hypothesize that the A946T SNP results in exacerbated signaling and increased production of type I IFNs and inflammatory cytokines during CVB infections. To test this, we infected peripheral blood mononuclear cells (PBMCs) from healthy donors that were genotyped for the A946T SNP and measured the subsequent IFN response. We found that the expression of type I IFNs was increased at baseline in cells homozygous for the A946T SNP in contrast to without the SNP. Overexpression of the A946T SNP also led to increased basal expression of type I IFNs and IFN-stimulated genes in βLox5 cells and a type I IFN reporter cell line. This increased basal expression of type I IFNs may lead to β-cell stress and hyperreactive immune cells and contribute to the initiation of T1D.
The role of the transcriptional repressor YY1 in immunoregulatory gp96-mediated immune responses
Authors: Sedlacek Abigail L , Binder Robert J 
Published: February 2023

Abstract
Heat shock protein (HSP)-mediated immune responses encompass both antigen-specific pro-inflammatory responses as well as non-antigen specific regulatory responses. The type of immune response primed depends on antigen presenting cell engaged by the HSP. Classical dendritic cells (cDCs) and macrophages elicit inflammatory responses in response to immunogenic HSPs such as gp96, whereas plasmacytoid dendritic cells (pDCs) induce regulatory responses. We have previously shown that NRP1 is in part responsible for the difference between these subsets. Gp96 signaling increases NRP1 expression on pDCs but not cDCs. This increased expression drives pDC-Treg interactions and results in activated Tregs. Increased NRP1 expression in pDCs is dependent on DNA methylation and an area of differential methylation has been identified in intron 2 of NRP1. Within this region of intron 2, bisulfite sequencing was used to look for specific sites of methylation. Intron 2 includes 2 CpG sites which show increased methylation in pDCs following stimulation with gp96. In the same region of these CpG sites, there is a consensus sequence for the transcriptional repressor YY1. We are investigating the role of YY1 as an inhibitor of NRP1 transcription, whose binding is blocked by methylation at intron 2. Using ChIP assays, siRNA knockdowns and cell imaging studies we will determine the role of YY1 in gp96-mediated immunoregulatory responses.
Bystander CD8 T cell memory responses partially protect mice against lethal vaginal HSV-2 challenge
Authors: Arkatkar Tanvi , Dave Veronica , Prlic Martin , Lund Jennifer M 
Published: February 2023

Abstract
Herpes Simplex Virus type-2 (HSV-2) infection is one of the most prevalent sexually transmitted diseases, yet no vaccine is currently available. Detailed analysis of HSV-infected human tissue revealed tissue-resident CD8 T cells (TRM) limit the duration and severity of HSV-2 episodes. Interestingly, recent studies reveal that the sensing and alarming function of CD8 TRMs is not restricted to cognate antigen interaction, but CD8 TRM can mediate protection against antigenically unrelated pathogens, termed “bystander activation.” Here, we extended our findings to determine if antigen non-specific CD8 T cells could provide some degree of protection in a bystander fashion in the context of HSV infection. To test this, we created antigen non-specific memory compartments through immunization of mice with Listeria expressing ovalbumin (OVA) (LM-OVA). Mice were then challenged with wild-type HSV-2 to assess the degree of vaccine-mediated protection. Immunization with LM- OVA-induced intermediate protection from lethal viral challenge, suggesting that bystander CD8 T cells (BA-CTL) may mediate protection despite the absence of antigen-specificity. The bystander functionality could be context-dependent, and the unregulated expansion of these cells can be damaging to the host. A potential explanation of BA-CTL regulation is via the involvement of regulatory T cells (Tregs), in the absence of Treg-mediated regulation, massive expansion of BA-CTLs can be predicted. On the contrary, we found depletion of Tregs resulted in significantly fewer BA- CTLs in the vaginal tract on days 2 and 6 post-HSV-2 challenge. Hence how these cells maintain the delicate balance of protection against pathology necessitates further investigation.
Filling the innate myeloid niche in a 3D human tissue-engineered lung model to study age-dependent immune response to respiratory syncytial virus
Authors: Roe Mandi M , Do Taylor , Turner Sean , Gappa-Fahlenkamp Heather , Kovats Susan 
Published: February 2023

Abstract
The immune response to respiratory syncytial virus (RSV) is vastly influenced by age. RSV can lead to severe disease in neonates and the elderly. To study human age-dependent innate immune responses, we utilized a 3D Human Tissue-Engineered Lung Model (3D-HTLM) consisting of multiple layers that mimic alveoli, including vascular endothelium, stromal cells, and small airway epithelial cells at air-liquid interface. Our goal is to determine if blood monocytes (Mo) added to the 3D-HTLM will fill the myeloid niche and acquire characteristics of tissue resident cells, including alveolar macrophages (AM), and respond to RSV infection. Based on CD1c and CD14 expression, freshly enriched Mo included small populations of cDC2s, Mo-DCs, and non-classical CD14− Mo, all of which lacked CD206 and CD169 markers typical of innate lung resident cells. The 3D-HTLM was harvested 4 days after Mo addition and 1 day after RSV infection (MOI 10). Independent of RSV, all CD45+ Mo, cDC2s, Mo-DCs, and CD14− Mo had significantly increased expression of CD206, CD169, and HLA-DR, including a minor population resembling AM, identified as CD1c−CD14loHLA-DR+CD169+CD206+CD71+. After seeding the 3D-HTLM, cDC2s had increased expression of activation markers CD86, CD83, and CD40. Mo populations showed few phenotypic changes after RSV infection of the 3D-HTLM, yet cDC2s and Mo-DCs had increased production of IL-12 and TNFα, respectively. These data suggest Mo populations adapt to the 3D-HTLM environment and respond to RSV, but transcriptional profiles will better indicate whether the AM niche is being filled. The 3D-HTLM seeded with myeloid cells from neonates or the elderly will be a significant tool to study age-dependent innate immune responses to RSV.