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By inhibition of JAK-STAT signaling, SOCS1 acts as a master regulator of the cytokine response across numerous tissue types and cytokine pathways. Haploinsufficiency of SOCS1 has recently emerged as a monogenic immunodysregulatory disease with marked clinical variability. Here, we describe a patient with severe dermatitis, recurrent skin infections, and psoriatic arthritis that harbors a novel heterozygous mutation in SOCS1. The variant, c.202_203delAC, generates a frameshift in SOCS1, p.Thr68fsAla*49, which leads to complete loss of protein expression. Unlike WT SOCS1, Thr68fs SOCS1 fails to inhibit JAK-STAT signaling when expressed in vitro. The peripheral immune signature from this patient was marked by a redistribution of monocyte sub-populations and hyper-responsiveness to multiple cytokines. Despite this broad hyper-response across multiple cytokine pathways in SOCS1 haploinsufficiency, the patient’s clinical disease was markedly responsive to targeted IL4Rα- and IL17-blocking therapy. In accordance, the mutant allele was unable to regulate IL4Rα signaling. Further, patient cells were unresponsive to IL4/IL13 while on monoclonal antibody therapy. Together, this study reports a novel SOCS1 mutation and suggests that IL4Rα blockade may serve as an unexpected, but fruitful therapeutic target for some patients with SOCS1 haploinsufficiency.

Objective High serum interferon α (IFNα) activity is a heritable risk factor for systemic lupus erythematosus (SLE). Auto-antibodies found in SLE form immune complexes which can stimulate IFNα production by activating endosomal Toll-like receptors and interferon regulatory factors (IRFs), including IRF5. Genetic variation in IRF5 is associated with SLE susceptibility; however, it is unclear how IRF5 functional genetic elements contribute to human disease. Methods 1034 patients with SLE and 989 controls of European ancestry, 555 patients with SLE and 679 controls of African–American ancestry, and 73 patients with SLE of South African ancestry were genotyped at IRF5 polymorphisms, which define major haplotypes. Serum IFNα activity was measured using a functional assay. Results In European ancestry subjects, anti-double-stranded DNA (dsDNA) and anti-Ro antibodies were each associated with different haplotypes characterised by a different combination of functional genetic elements (OR>2.56, p<1.9×10−14 for both). These IRF5 haplotype-auto-antibody associations strongly predicted higher serum IFNα in patients with SLE and explained >70% of the genetic risk of SLE due to IRF5. In African–American patients with SLE a similar relationship between serology and IFNα was observed, although the previously described European ancestry-risk haplotype was present at admixture proportions in African–American subjects and absent in African patients with SLE. Conclusions The authors define a novel risk haplotype of IRF5 that is associated with anti-dsDNA antibodies and show that risk of SLE due to IRF5 genotype is largely dependent upon particular auto-antibodies. This suggests that auto-antibodies are directly pathogenic in human SLE, resulting in increased IFNα in cooperation with particular combinations of IRF5 functional genetic elements. SLE is a systemic autoimmune disorder affecting multiple organ systems including the skin, musculoskeletal, renal and haematopoietic systems. Humoral autoimmunity is a hallmark of SLE, and patients frequently have circulating auto-antibodies directed against dsDNA, as well as RNA binding proteins (RBP). Anti-RBP autoantibodies include antibodies which recognize Ro, La, Smith (anti-Sm), and ribonucleoprotein (anti-nRNP), collectively referred to as anti-retinol-binding protein). Anti-retinol-binding protein and anti-dsDNA auto-antibodies are rare in the healthy population.1 These auto-antibodies can be present in sera for years preceding the onset of clinical SLE illness2 and are likely pathogenic in SLE.3 4

The rate of raw sequence production through Next-Generation Sequencing (NGS) has been growing exponentially due to improved technology and reduced costs. This has enabled researchers to answer many biological questions through “multi-omics” data analyses. Even though such data promises new insights into how biological systems function and understanding disease mechanisms, computational analyses performed on such large datasets comes with its challenges and potential pitfalls. The aim of this study was to develop a robust portable and reproducible bioinformatic pipeline for the automation of RNA sequencing (RNA-seq) data analyses. Using Nextflow as a workflow management system and Singularity for application containerisation, the nf-rnaSeqCount pipeline was developed for mapping raw RNA-seq reads to a reference genome and quantifying abundance of identified genomic features for diferential gene expression analyses. The pipeline provides a quick and eficient way to obtain a matrix of read counts that can be used with tools such as DESeq2 and edgeR for diferential expression analysis. Robust and flexible bioinformatic and computational pipelines for RNA-seq data analysis, from QC to sequence alignment and comparative analyses, will reduce analysis time, and increase accuracy and reproducibility of findings to promote transcriptome research.

The Prostate Outreach Project (POP) provided free prostate cancer (PCa) education and early detection to medically underserved communities. POP recruited participants in medically underserved communities. PCa education and detection events occurred in POP locations (static) or natural gathering places (mobile) within the community. PCa education was delivered by video and evaluated using a questionnaire. Screening consisted of serum prostate-specific antigen and digital rectal examination. A navigated follow-up strategy was utilized to provide medical care for participants with abnormal screening examinations (ASE). POP recruited 4,420 men, 62.8% (2,667) were African American (AA). Most participants had a high school education and no prior screening. Fifty-four percent (2,159) were uninsured and 41% (1,811) had no access to a physician. PCa knowledge increased following the educational video. Prostate-specific antigen levels were elevated in 9.8% (436), while 6.9% (233) had an abnormal digital rectal examination. Follow-up among 609 men with ASE was successful in 40% (244), despite a navigated approach. Overall, 3.3% (144) cancers were diagnosed among the POP with AA participants exhibiting a significantly higher incidence. Recruitment, education, and PCa testing among a medically underserved cohort was successful. However, failure to follow through on ASE could contribute to maintaining the disparity in PCa outcomes noted among AAs and the medically underserved if not addressed.

(1) Background: Understanding the function of circular RNAs (circRNAs), a class of noncoding RNA, in psoriatic skin can provide important insights into the complex regulation of genes contributing to the pathogenesis of psoriasis. (2) Methods: A novel method was applied to RNA-seq datasets from 93 skin biopsy samples to comprehensively identify circRNAs of all types, i.e., canonical circRNAs from the intron-exon junctions of mRNAs and interior circRNAs (i-circRNAs) from the interior regions of exons, introns, and intergenic regions. Selected circRNAs were experimentally validated by qRT-PCR and Sanger sequencing. CircRNAs with abundant and differential expression were identified and their putative function as competing endogenous RNAs (ceRNAs) was analyzed by an integrated analysis of circRNAs, microRNAs, and mRNAs. (3) Results: With a comprehensive search using no information of splicing signals, we systematically identified 179 highly abundant circRNAs in psoriatic skin. Many of these were reported for the first time and many were differentially expressed in involved versus normal or uninvolved skin. Validation based on three additional RNA-seq datasets confirmed most of the identified circRNAs in psoriatic skin. Experimental analyses confirmed the expression of the well-known circRNA CDR1as, a canonical circRNA, and a novel i-circRNA in psoriasis. We also identified many circRNAs that may act as ceRNAs to regulate the expression of mRNA genes in psoriasis-related signaling pathways in psoriasis. (4) Conclusions: The result of the study suggested that circRNAs are abundant in psoriatic skin, have distinct characteristics, and contribute to psoriatic pathogenesis.

The objective was to explore changes in gene expression in Wnt pathway genes in skin samples of black South Africans with diffuse cutaneous systemic sclerosis (dcSSc). Affected (forearm) and unaffected (upper back) skin samples of eight Black South Africans with active early dcSSc were compared to skin samples from seven ethnically matched control subjects. The Wnt Pathway Plus RT2 Profiler qPCR Array was used to determine gene expression and analyzed for differential expression between cases and controls. Selective validation was done using single-gene TaqMan assays. Several genes were similarly upregulated in both affected and unaffected skin of the dcSSc patients compared to controls. These included the Wnt ligands WNT7A and WNT10A, the frizzled receptors FZD8 and FZD9, intracellular signaling proteins AXIN1 and AXIN2, and the pathway target genes FGF4 and MMP7. Principal component analysis revealed patients clustering into two groups, which co-segregated with clinical features of interstitial lung disease and/or inflammatory myopathy, or the absence of an inflammation phenotype. These two groups showed paradoxical gene expression of the genes TCF7, SOX17, and FRZB in affected and unaffected skin. This study provides further evidence of dysregulation of gene expression at various levels of the Wnt signaling pathway in dcSSc. Moreover, principal component analysis showed two distinct patient clusters of gene expression, which co-segregated with the presence or absence of clinical inflammatory features, and may reflect different pathological pathways in dcSSc.

This study analyzed data from a community-based prostate cancer (PCa) education and screening program (Prostate Outreach Project; POP) to enhance PCa-related knowledge among medically underserved Asian American men. It also examined PCa screening history, clinical abnormalities based on prostate-specific antigen (PSA) tests and digital rectal examination (DRE) results, and follow-up and PCa diagnosis rates. Participants—521 Asian men (251 Vietnamese, 142 Chinese, and 128 South Asians)—were offered PCa screening using PSA tests and/or DRE and an educational session on PCa. Of these men, 277 completed PCa-related knowledge surveys before and after viewing an educational video. Significant between-group differences in PCa-related knowledge were found at pre-assessment (p < 0.001) but not at post-assessment (p = 0.11), at which time all groups showed improved PCa-related knowledge. Most participants (77.9%) had never received PCa screening, but Vietnamese men had the lowest previous screening rate (17.3%). Chinese men had elevated PSA values and the highest abnormal DRE rates. Of the 125 men with abnormal screening outcomes, only 15.2% had adequate follow-up. Of the 144 men diagnosed with PCa in POP, 11.1% were Asians (seven Chinese, six Vietnamese, and three South Asian). Despite the ethnic heterogeneity among Asian men, a community outreach program may successfully enhance their PCa-related knowledge.

We are currently seeing an unprecedented growth in the number of nonreligious people in the United States. However, our sociological understandings of this growing demographic have been limited by dominant cultural and social science narratives that presume the loss of religion comes with a detrimental loss of certainty, meaning, and community. Much of the social scientific theorizing about the consequences of modernization and secularization is based in a “subtraction story” – a story of moving away from stable social identities, communities, and religious beliefs, and moving toward a hollow and meaningless secular modernity that leaves individuals feeling uncertain, anomic, and socially isolated. In this dissertation, I draw on three years of ethnographic research with a network of atheist churches called The Sunday Assembly to disrupt this narrative of loss, revealing the meaningful cultures and communities that nonreligious people are constructing without religion. Rather than simply the absence of religious beliefs and practices, atheist churches signal the presence of substantive nonreligious beliefs and practices. And I show how practice-oriented investigations of these nonreligious cultures and communities can shed new light on core sociological questions about social change and meaning-making in contemporary social life. Instead of a demographic burdened by a detrimental loss of certainty, community, and meaning, I found a rich nonreligious field full of politicized certainty and meaningful uncertainty, contested conceptions and practices of community, and a meaning-filled discourse of “scientific spirituality” that combines the language of spirituality and transcendence with commitments to secular worldviews and scientific rationalism. I use the case of the Sunday Assembly to show how these nonreligious meaning systems are constructed, contextual, and contested.

The aim of this study was to identify genetic variants associated with rheumatoid arthritis (RA) risk in black South Africans. Black South African RA patients (n = 263) were compared with healthy controls (n = 374). Genotyping was performed using the Immunochip, and four-digit high-resolution human leukocyte antigen (HLA) typing was performed by DNA sequencing of exon 2. Standard quality control measures were implemented on the data. The strongest associations were in the intergenic region between the HLA-DRB1 and HLA-DQA1 loci. After conditioning on HLA-DRB1 alleles, the effect in the rest of the extended major histocompatibility (MHC) diminished. Non-HLA single nucleotide polymorphisms (SNPs) in the intergenic regions LOC389203IRBPJ, LOC100131131|IL1R1, KIAA1919|REV3L, LOC643749|TRAF3IP2 , and SNPs in the intron and untranslated regions (UTR) of IRF1 and the intronic region of ICOS and KIAA1542 showed association with RA ( p < 5 × 10 −5 ). Of the SNPs previously associated with RA in Caucasians, one SNP rs874040, locating to the intergenic region LOC389203|RBPJ was replicated in this study. None of the variants in the PTPN22 gene was significantly associated. The seropositive subgroups showed similar results to the overall cohort. The effects observed across the HLA region are most likely due to HLA-DRB1 , and secondary effects in the extended MHC cannot be detected. Seven non-HLA loci are associated with RA in black South Africans. Similar to Caucasians, the intergenic region between LOC38920 and RBPJ is associated with RA in this population. The strong association of the R620W variant of the PTPN22 gene with RA in Caucasians was not replicated since this variant was monomorphic in our study, but other SNP variants of the PTPN22 gene were also not associated with RA in black South Africans, suggesting that this locus does not play a major role in RA in this population.