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The soybean root system is complex. In addition to being composed of various cell types, the soybean root system is also composed of the nodule, an organ in which mutualistic symbiosis with the nitrogen-fixing bacterium Bradyrhizobium diazoefficiens occurs. Notably, the soybean root nodule is characterized by a central infection zone where the atmospheric nitrogen is fixed and assimilated by the symbiont, resulting from the close cooperation between the plant cell and the bacteria. To date, the cellular complexity of the soybean root and nodule has not been characterized. Applying single nucleus RNA-seq technology, we characterized the transcriptomic signature of the soybean root and nodule cell types and revealed the existence of different sub-populations of B. diazoefficiens-infected cells in the soybean nodule including those actively involved or not in nitrogen fixation. The mining of the single cell-resolution atlas also helped reevaluate the role of known and identified new genes controlling the nodulation process. For instance, we functionally characterized the role of a new microdomain-associated GmFWL3 protein in the soybean nodule. Our study reveals the unique cellular complexity of the soybean nodule and helps redefine the concept of cell types when focusing on the infection zone of the nodule.

RHOH/TFF, a member of the RAS GTPase super family, has important functions in lymphopoiesis and proximal T cell receptor signalling and has been implicated in a variety of leukaemias and lymphomas. RHOH was initially identified as a translocation partner with BCL-6 in non-Hodgkin lymphoma (NHL), and aberrant somatic hypermutation (SHM) in the 5ʹ untranslated region of the RHOH gene has also been detected in Diffuse Large B-Cell Lymphoma (DLBCL). Recent data suggest a correlation between RhoH expression and disease progression in Acute Myeloid Leukaemia (AML). However, the effects of RHOH mutations and translocations on RhoH expression and malignant transformation remain unknown. We found that aged Rhoh(−/−) (KO) mice had shortened lifespans and developed B cell derived splenomegaly with an increased Bcl-6 expression profile in splenocytes. We utilized a murine model of Bcl-6 driven DLBCL to further explore the role of RhoH in malignant behaviour by crossing Rhoh(KO) mice with Iµ-HABcl-6 transgenic (Bcl-6(Tg)) mice. The loss of Rhoh in Bcl-6(Tg) mice led to a more rapid disease progression. Mechanistically, we demonstrated that deletion of Rhoh in these murine lymphoma cells was associated with decreased levels of the RhoH binding partner KAISO, a dual-specific Zinc finger transcription factor, de-repression of KAISO target Bcl-6, and downregulation of the BCL-6 target Blimp-1. Re-expression of RhoH in Rhoh(KO)Bcl-6(Tg) lymphoma cell lines reversed these changes in expression profile and reduced proliferation of lymphoma cells in vitro. These findings suggest a previously unidentified regulatory role of RhoH in the proliferation of tumour cells via altered BCL-6 expression. (250)

Basal cell carcinoma (BCC) and squamous cell carcinoma (SCC) are both derived from epidermal keratinocytes but are phenotypically diverse. To improve the understanding of keratinocyte carcinogenesis, it is critical to understand epigenetic alterations, especially those that govern gene expression. We examined changes to the enhancer-associated histone acetylation mark H3K27ac by mapping matched tumor-normal pairs from 11 patients (five with BCC and six with SCC) undergoing Mohs surgery. Our analysis uncovered cancer-specific enhancers on the basis of differential H3K27ac peaks between matched tumor-normal pairs. We also uncovered biological pathways potentially altered in keratinocyte carcinoma, including enriched epidermal development and Wnt signaling pathways enriched in BCCs and enriched immune response and cell activation pathways in SCCs. We also observed enrichment of transcription factors that implicated SMAD and JDP2 in BCC pathogenesis and FOXP1 in SCC pathogenesis. On the basis of these findings, we prioritized three loci with putative regulation events (FGFR2 enhancer in BCC, intragenic regulation of FOXP1 in SCC, and WNT5A promoter in both subtypes) and validated our findings with published gene expression data. Our findings highlight unique and shared epigenetic alterations in histone modifications and potential regulators for BCCs and SCCs that likely impact the divergent oncogenic pathways, paving the way for targeted drug discoveries.

Known fetal hemoglobin (HbF) silencers have potential on-target liabilities for rational β-hemoglobinopathy therapeutic inhibition. Here, through transcription factor (TF) CRISPR screening, we identify zinc-finger protein (ZNF) 410 as an HbF repressor. ZNF410 does not bind directly to the genes encoding γ-globins, but rather its chromatin occupancy is concentrated solely at CHD4, encoding the NuRD nucleosome remodeler, which is itself required for HbF repression. CHD4 has two ZNF410-bound regulatory elements with 27 combined ZNF410 binding motifs constituting unparalleled genomic clusters. These elements completely account for the effects of ZNF410 on fetal globin repression. Knockout of ZNF410 or its mouse homolog Zfp410 reduces CHD4 levels by 60%, enough to substantially de-repress HbF while eluding cellular or organismal toxicity. These studies suggest a potential target for HbF induction for β-hemoglobin disorders with a wide therapeutic index. More broadly, ZNF410 represents a special class of gene regulator, a conserved TF with singular devotion to regulation of a chromatin subcomplex.

BCL11A, the major regulator of fetal hemoglobin (HbF, α2γ2) level, represses γ-globin expression through direct promoter binding in adult erythroid cells in a switch to adult hemoglobin (HbA, α2β2). To uncover how BCL11A initiates repression, we used CRISPR–Cas9, dCas9, dCas9-KRAB and dCas9-VP64 screens to dissect the γ-globin promoters and identified an activator element near the BCL11A-binding site. Using CUT&RUN and base editing, we demonstrate that a proximal CCAAT box is occupied by the activator NF-Y. BCL11A competes with NF-Y binding through steric hindrance to initiate repression. Occupancy of NF-Y is rapidly established following BCL11A depletion, and precedes γ-globin derepression and locus control region (LCR)–globin loop formation. Our findings reveal that the switch from fetal to adult globin gene expression within the >50-kb β-globin gene cluster is initiated by competition between a stage-selective repressor and a ubiquitous activating factor within a remarkably discrete region of the γ-globin promoters. CRISPR–Cas9 tiled screens of the β-globin gene cluster identify an NF-Y bound activator element at the γ-globin promoter. Binding competition by the transcriptional repressor BCL11A leads to NF-Y eviction and a switch from fetal to adult globin gene expression.

Background. Autoimmune thyroid disease (AITD), one of the most prevalent organ-specific autoimmune diseases, mainly includes Graves’ disease (GD) and Hashimoto’s thyroiditis (HT). This study was aimed at researching the association between AITD and single nucleotide polymorphisms (SNPs) of the HLA-DRA gene. Methods. Using Hi-SNP high-throughput sequencing technology, we detected the distribution of three SNPs (rs3177928, rs7197, and rs3129878) of HLA-DRA genotypes in 1033 AITD patients (634 GD and 399 HT ones) and 791 healthy volunteers in Chinese Han Population. Chi-square test, multivariate logistic regression, and haplotype analysis were performed by SPSS and Haploview software to analyze the relationship between HLA-DRA gene polymorphisms and AITD. Results. The results show that allele frequency and genotype distribution of rs3177928 and rs7197 were correlated with AITD and GD compared with the healthy control group, but not with HT. Rs3177928 and rs7197 were correlated with AITD and HT in the allele model, dominant model, and overdominant model before and after gender and age adjustment, but not with HT. In addition, we found that two loci (rs3177928 and rs7197) constituted a linkage disequilibrium (LD) region, and haplotype AA was associated with AITD and GD. However, we found no association between rs3129878 and AITD. Conclusion. Our study is the first to find that rs3177928 and rs7197 of HLA-DRA are significantly correlated with AITD and GD in the Chinese Han population. This will help further reveal the pathogenesis of AITD and provide new candidate genes for the prediction or treatment of AITD.

Base editing by nucleotide deaminases linked to programmable DNA-binding proteins represents a promising approach to permanently remedy blood disorders, although its application in engrafting hematopoietic stem cells (HSCs) remains unexplored. In this study, we purified A3A (N57Q)-BE3 base editor for ribonucleoprotein (RNP) electroporation of human-peripheral-blood-mobilized CD34+ hematopoietic stem and progenitor cells (HSPCs). We observed frequent on-target cytosine base edits at the BCL11A erythroid enhancer at +58 with few indels. Fetal hemoglobin (HbF) induction in erythroid progeny after base editing or nuclease editing was similar. A single therapeutic base edit of the BCL11A enhancer prevented sickling and ameliorated globin chain imbalance in erythroid progeny from sickle cell disease and β-thalassemia patient-derived HSPCs, respectively. Moreover, efficient multiplex editing could be achieved with combined disruption of the BCL11A erythroid enhancer and correction of the HBB −28A>G promoter mutation. Finally, base edits could be produced in multilineage-repopulating self-renewing human HSCs with high frequency as assayed in primary and secondary recipient animals resulting in potent HbF induction in vivo. Together, these results demonstrate the potential of RNP base editing of human HSPCs as a feasible alternative to nuclease editing for HSC-targeted therapeutic genome modification. A single therapeutic base edit of the BCL11A enhancer in human HSPCs can ameliorate cellular defects associated with sickle cell disease and β-thalassemia in vitro and efficiently induce fetal hemoglobin expression upon engraftment in mice in vivo.

Small proteins, encoded by small open reading frames, are only beginning to emerge with the current advancement of omics technology and bioinformatics. There is increasing evidence that small proteins play roles in diverse critical biological functions, such as adjusting cellular metabolism, regulating other protein activities, controlling cell cycles, and affecting disease physiology. In prokaryotes such as bacteria, the small proteins are largely unexplored for their sequence space and functional groups. For most bacterial species from a natural community, the sample cannot be easily isolated or cultured, and the bacterial peptides must be better characterized in a metagenomic manner. The bacterial peptides identified from metagenomic samples can not only enrich the pool of small proteins but can also reveal the community-specific microbe ecology information from a small protein perspective. In this study, metaBP (Bacterial Peptides for metagenomic sample) has been developed as a comprehensive toolkit to explore the small protein universe from metagenomic samples. It takes raw sequencing reads as input, performs protein-level meta-assembly, and computes bacterial peptide homolog groups with sample-specific mutations. The metaBP also integrates general protein annotation tools as well as our small protein-specific machine learning module metaBP-ML to construct a full landscape for bacterial peptides. The metaBP-ML shows advantages for discovering functions of bacterial peptides in a microbial community and increases the yields of annotations by up to five folds. The metaBP toolkit demonstrates its novelty in adopting the protein-level assembly to discover small proteins, integrating protein-clustering tool in a new and flexible environment of RBiotools, and presenting the first-time small protein landscape by metaBP-ML. Taken together, metaBP (and metaBP-ML) can profile functional bacterial peptides from metagenomic samples with potential diverse mutations, in order to depict a unique landscape of small proteins from a microbial community.

A major challenge of quantifying feedback between microbial communities and climate is the vast diversity of microbial communities and the intricacy of soil biogeochemical processes they mediate. We overcome this challenge by simplifying the representation of diverse enzyme functions from metagenomics data. We developed a dynamic allocation scheme for enzyme functional classes (EFCs) based on the premise that microbial communities act to maximize acquisition of limiting resources while minimizing energy expenditure for acquiring unlimited resources. We incorporated this scheme into a biogeochemical model to explicitly represent microbial functional diversity and simulate responses of microbially-mediated soil biogeochemical processes to varying environmental and nutrient conditions. Representing microbial functional diversity and environmental acclimation improved predictions of the stoichiometry of microbial biomass and mitigated the sensitivity of soil organic carbon to warming in nutrient-deficient regions. Our results indicate the importance of microbial functional diversity and environmental acclimation for projecting climate feedbacks of nutrient-limited soils.

A major challenge of quantifying feedback between microbial communities and climate is the vast diversity of microbial communities and the intricacy of soil biogeochemical processes they mediate. We overcome this challenge by simplifying the representation of diverse enzyme functions from metagenomics data. We developed a dynamic allocation scheme for enzyme functional classes (EFCs) based on the premise that microbial communities act to maximize acquisition of limiting resources while minimizing energy expenditure for acquiring unlimited resources. We incorporated this scheme into a biogeochemical model to explicitly represent microbial functional diversity and simulate responses of microbially-mediated soil biogeochemical processes to varying environmental and nutrient conditions. Representing microbial functional diversity and environmental acclimation improved predictions of the stoichiometry of microbial biomass and mitigated the sensitivity of soil organic carbon to warming in nutrient-deficient regions. Our results indicate the importance of microbial functional diversity and environmental acclimation for projecting climate feedbacks of nutrient-limited soils.

Background: The current study aimed at exploring the cytokine profile in the tears of patients with Graves’ ophthalmopathy (GO). Methods: Tears were sampled from the eyes of 7 patients with active GO and 7 healthy volunteers using filter paper. Then the levels of up to 34 cytokines in the tears of each subject were detected using high-throughput protein microarray technology in line with the introduction. Results: The results of cytokine protein microarray screening showed that 10 proteins, namely, CD40, CD40 Ligand, GITR, IL-12p70, IL-1 beta, IL-2, IL-21, IL-6, MIP-3 alpha and TRANCE, were overexpressed (with fold change >1.20) and 3 proteins, namely, GM-CSF, IL-1 sRI and IL-13 were downregulated (with fold change < 0.83) in GO patients. In addition, the protein levels of CD40 and CD40 ligand (CD40L) were significantly different between GO patients and healthy controls (P=0.028 and 0.011, respectively). Further Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of differently expressed proteins showed that these proteins were involved in biological functions including biological processes (positive regulation of cytokine production, JAK-STAT cascade and leukocyte proliferation), molecular functions (cytokine and growth factor receptors binding and cytokine activity), and other important pathways (cytokine-cytokine receptor interaction, JAK-STAT signaling pathway, IL-17 signaling pathway, NF-kappa B signaling pathway, Th17 cell differentiation, and intestinal immune network for IgA production), all of which might be involved in the pathology of GO. Conclusion: Our cytokine protein microarray analysis indicated that several proteins were differentially expressed in GO patients, which provides potential targets for GO prevention.

Transmembrane protein 39A (TMEM39A) gene polymorphisms have been related to various autoimmune diseases, but the relationship between TMEM39A polymorphisms and autoimmune thyroid disease (AITD) rem...

The risk of thyroid autoimmunity and thyroid dysfunction among patients with gout and hyperuricemia has not been well defined. This study was undertaken to examine the impact of gout and hyperuricemia on risk of thyroid disorders including thyroid autoimmunity and thyroid dysfunction. A population-based cross-sectional study was conducted to assess the risk of thyroid autoimmunity and thyroid dysfunction related to gout and hyperuricemia, which included 115 gout patients, 439 hyperuricemic patients, and 2 254 individuals without gout and hyperuricemia. A systematic review and meta-analysis of 14 observational studies was also done to systematically evaluate the risk of thyroid dysfunction among patients with gout and hyperuricemia. Findings from the cross-sectional study suggested a significantly increased risk of hypothyroidism among female gout patients (OR=2.44, 95% CI 1.15–5.17, p=0.02). Besides, gout could also substantially increase risk of Hashimoto’s thyroiditis in women (OR=3.15, 95% CI 1.53–6.49, p=0.002). The meta-analysis proved a considerably increased risk of hypothyroidism among both gout patients (OR=1.51, 95% CI 1.23–1.85, p

Tropical ecosystems are an important sink for atmospheric CO2; however, plant growth is restricted by phosphorus (P) availability. Although soil microbiota facilitate organic P turnover and inorganic P mobilization, their role in carbon-phosphorus coupled processes remains poorly understood. To advance this topic, soils collected from four sites representing highly weathered tropical soils in the El Yunque National Forest, Puerto Rico were incubated with exogenous PO43− under controlled laboratory conditions. P amendment increased CO2 respiration by 14–23% relative to control incubations for soils sampled from all but the site with the greatest total and bioavailable soil P. Metatranscriptomics revealed an increase in the relative transcription of genes involved in cell growth and uptake of other nutrients in response to P amendment. A new methodology to normalize gene expression by population-level relative (DNA) abundance revealed that the pattern of increased transcription of cell growth and division genes with P amendment was community-wide. Soil communities responsive to P amendment possessed a greater relative abundance of α-glucosyl polysaccharide biosynthesis genes, suggestive of enhanced C storage under P-limiting conditions. Phosphorylase genes governing the degradation of α-glucosyl polysaccharides were also more abundant and increased in relative transcription with P amendment, indicating a shift from energy storage towards growth. Conversely, microbial communities in soils nonresponsive to P amendment were found to have metabolisms tuned for the phosphorolysis of labile plant-derived substrates, such as β-glucosyl polysaccharides. Collectively, our results provided quantitative estimates of increased soil respiration upon alleviation of P constraints and elucidated several underlying ecological and molecular mechanisms involved in this response.

Background: Graves’ disease (GD) is a common autoimmune disease, and its pathogenesis is unclear. Studies have found that the occurrence of GD is related to the immune disorder caused by the interaction of genetic susceptibility and environmental factors. The CD4+ T cell subset is closely related to the immune disorder of GD. LncRNAs are RNA molecules with a length of more than 200 nt and are involved in a variety of autoimmune diseases. However, the roles of lncRNAs in recurrent GD are still elusive. The purpose of this study is to identify lncRNA and mRNA expression profile in relapsed Graves’ disease.Method: CD4+ T cells from 12 recurrent GD and 8 healthy controls were collected for high-throughput sequencing. The gene-weighted co-expression network analysis (WGCNA) was used to construct the co-expression module relevant to recurrent GD, and the key genes in the module were verified by RT-PCR.Results: There are 602 upregulated lncRNAs and 734 downregulated lncRNAs in CD4+ T cells in recurrent GD patients compared with the healthy controls. The module most relevant to GD recurrence was constructed using WGCNA, and the key genes in the module were verified by RT-PCR. We found that the expression of RPL8, OAS2, NFAT5, DROSHA, NONHSAT093153.2, NONHSAT118924.2, and NONHSAT209004.1 was significantly decreased in GD group (p < 0.001, p < 0.001, p < 0.01, p < 0.05, p < 0.001, p < 0.05, and p < 0.01, respectively).Conclusion: LncRNAs are closely related to the recurrence of GD. For the first time, we constructed the expression profile of lncRNAs and mRNAs in CD4+ T cells in recurrent GD patients.

Objective. Rheumatoid arthritis (RA) is a complex disease with unknown pathogenesis. In recent years, fewer have paid attention to the broad spectrum of systemic markers of RA. The aim of this study was to identify exosomal candidate proteins in the pathogenesis of RA. Methods. Totally, 12 specimens of plasma from 6 RA patients and 6 age- and gender-matched controls from the Chinese population were obtained for nanoscale liquid chromatography coupled to tandem mass spectrometry (nano-LC-MS/MS) analysis to identify exosomal profiles. Results. A total of 278 exosomal proteins were detected. Among them, 32 proteins were significantly upregulated ( FC ≥ 2.0 and P < 0.05 ) and 5 proteins were downregulated ( FC ≤ 0.5 and P < 0.05 ). Bioinformatics analysis revealed that transthyretin (TTR), angiotensinogen (AGT), lipopolysaccharide-binding protein (LBP), monocyte differentiation antigen CD14 (CD14), cartilage oligomeric matrix protein (COMP), serum amyloid P (SAP/APCS), and tenascin (TNC) can interact with each other. Subsequently, these cross-linked proteins may be mainly involved in the inflammatory-related pathways to mediate the onset of RA. Noteworthy, the LBP/CD14 complex can promote the expression of IL-8 and TNF-α, eventually leading to the development of RA. Conclusions. Our findings suggest distinct plasmatic exosomal protein profiles in RA patients. These proteins not only take important parts in the vicious circle in the pathogenic process of RA but also serve as novel biomarkers in RA diagnosis and prognosis.

BackgroundRheumatoid arthritis (RA) is a heterogeneous and complex disease characterized by autoantibodies production and inflammation of the synovium. Its underlying mechanisms remain elusive. In recent years, exosomes have emerged as non-invasive biomarkers in diverse diseases. Due to its various inflammatory and immunological functions, some studies highlighted abnormalities of exosomes in RA, but fewer have paid attention to the broad spectrum of potential systemic markers of RA. The aim of this study was to identify exosomal candidate proteins in the pathogenesis of RA using systemic proteomic method. MethodsTotally 12 specimens of plasma from 6 RA patients and 6 age-and gender-matched controls from the Chinese population were obtained for nanoscale liquid chromatography coupled to tandem mass spectrometry (nano-LC-MS/MS) analysis to identify differentially expressed proteins (DEPs) in exosomes. Gene ontology (GO), protein interaction network (PPI) and KEGG pathway analyses were used in subcellular localization analysis. ResultsA total of 278 exosomal proteins were detected. Among them, 32 proteins were significantly upregulated (FC≥2.0 and PP

Epigenetic editing is an emerging technology that uses artificial transcription factors (aTFs) to regulate expression of a target gene. Although human genes can be robustly upregulated by targeting aTFs to promoters, the activation induced by directing aTFs to distal transcriptional enhancers is substantially less robust and consistent. Here we show that long-range activation using CRISPR-based aTFs in human cells can be made more efficient and reliable by concurrently targeting an aTF to the target gene promoter. We used this strategy to direct target gene choice for enhancers capable of regulating more than one promoter and to achieve allele-selective activation of human genes by targeting aTFs to single-nucleotide polymorphisms embedded in distally located sequences. Our results broaden the potential applications of the epigenetic editing toolbox for research and therapeutics. Long-range CRISPR activation can be enhanced by concurrent recruitment of artificial TFs to the enhancer and promoter of a target gene. This CRISPR activation system can be employed to achieve allele-selective gene upregulation by differentially targeting single-nucleotide polymorphisms embedded in enhancers or other distally located sequences.

Major effectors of adult-stage fetal globin silencing include the transcription factors (TFs) BCL11A and ZBTB7A/LRF and the NuRD chromatin complex, although each has potential on-target liabilities for rational β-hemoglobinopathy therapeutic inhibition. Here through CRISPR screening we discover ZNF410 to be a novel fetal hemoglobin (HbF) repressing TF. ZNF410 does not bind directly to the γ-globin genes but rather its chromatin occupancy is solely concentrated at CHD4, encoding the NuRD nucleosome remodeler, itself required for HbF repression. CHD4 has two ZNF410-bound regulatory elements with 27 combined ZNF410 binding motifs constituting unparalleled genomic clusters. These elements completely account for ZNF410’s effects on γ-globin repression. Knockout of ZNF410 reduces CHD4 by 60%, enough to substantially de-repress HbF while avoiding the cellular toxicity of complete CHD4 loss. Mice with constitutive deficiency of the homolog Zfp410 are born at expected Mendelian ratios with unremarkable hematology. ZNF410 is dispensable for human hematopoietic engraftment potential and erythroid maturation unlike known HbF repressors. These studies identify a new rational target for HbF induction for the β-hemoglobin disorders with a wide therapeutic index. More broadly, ZNF410 represents a special class of gene regulator, a conserved transcription factor with singular devotion to regulation of a chromatin subcomplex.

Severe congenital neutropenia (SCN) is a life-threatening disorder most often caused by dominant mutations of ELANE that interfere with neutrophil maturation. We conducted a pooled CRISPR screen in human hematopoietic stem and progenitor cells (HSPCs) that correlated ELANE mutations with neutrophil maturation potential. Highly efficient gene editing of early exons elicited nonsense-mediated decay (NMD), overcame neutrophil maturation arrest in HSPCs from ELANE-mutant SCN patients, and produced normal hematopoietic engraftment function. Conversely, terminal exon frameshift alleles that mimic SCN-associated mutations escaped NMD, recapitulated neutrophil maturation arrest, and established an animal model of ELANE-mutant SCN. Surprisingly, only -1 frame insertions or deletions (indels) impeded neutrophil maturation, whereas -2 frame late exon indels repressed translation and supported neutrophil maturation. Gene editing of primary HSPCs allowed faithful identification of variant pathogenicity to clarify molecular mechanisms of disease and encourage a universal therapeutic approach to ELANE-mutant neutropenia, returning normal neutrophil production and preserving HSPC function.

Type 1 regulatory T (Tr1) cell is a special type of T regulatory cells with surface molecular markers such as lymphocyte-activation gene 3 and CD49b. A key property of Tr1 cells is the capability to produce high-level interleukin 10 (IL-10) upon activation, in a FOXP3-independent manner. The immunosuppressive function of IL-10 producing Tr1 cells has been extensively studied for many years. Autoimmune diseases (AIDs) are conditions in which the immune system breaks down and starts to attack the body. AIDs include inflammatory bowel disease, rheumatoid arthritis, multiple sclerosis (MS), type 1 diabetes mellitus, Greaves' disease, and so forth. In recent years, more and more studies have documented that the number of Tr1 cells is decreased and the function is inhibited in a variety of AIDs, among which MS is the most widely studied. The protocol for engineering Tr1 cell therapy has been established and is gradually being used in clinical practice in recent years. Tr1 cell therapy has been proven to be safe and effective, but it is mainly involved in myeloid leukemia, graft versus host disease currently. Its therapeutic role in AIDs still needs to be further explored. In this study, we will summarize the research advances of Tr1 cells in AIDs, which will provide useful information for treating AIDs through Tr1 cell therapy in the future.

BACKGROUND The adverse impact of thyroid dysfunction on cardiovascular system is well established, but the relationship between the level of thyroid stimulating hormone (TSH) and the risk of hypertension in euthyroid individuals is still inconclusive. METHODS We carried out a population-based, cross-sectional study to evaluate the relationship between TSH and hypertension risk in euthyroid individuals, and logistic regression analysis was utilized. In addition, a dose-response meta-analysis of relevant cohort or cross-sectional studies was carried out to further assess the impact of TSH on hypertension risk among euthyroid individuals. RESULTS A total of 2289 euthyroid individuals without thyroid diseases were recruited in our cross-sectional study. Serum TSH level within the upper reference range was associated with higher risk of hypertension [odds ratio (OR) = 1.29, 95% confidence interval (CI) 1.04-1.61, P = 0.023], and the OR for hypertension was still statistically significant after adjustment for confounding factors (OR = 1.32, 95% CI 1.01-1.72, P = 0.041). Moreover, meta-analysis suggested an obvious dose-response relationship between TSH and hypertension risk in euthyroid individuals, and the OR for hypertension associated with per 1 mIU/l increase in TSH level was 1.09 (95% CI 1.04-1.14, P

Motivation Genome-wide association studies (GWASs) have identified thousands of common trait-associated genetic variants but interpretation of their function remains challenging. These genetic variants can overlap the binding sites of transcription factors (TFs) and therefore could alter gene expression. However, we currently lack a systematic understanding on how this mechanism contributes to phenotype. Results We present Motif-Raptor, a TF-centric computational tool that integrates sequence-based predictive models, chromatin accessibility, gene expression datasets and GWAS summary statistics to systematically investigate how TF function is affected by genetic variants. Given trait-associated non-coding variants, Motif-Raptor can recover relevant cell types and critical TFs to drive hypotheses regarding their mechanism of action. We tested Motif-Raptor on complex traits such as rheumatoid arthritis and red blood cell count and demonstrated its ability to prioritize relevant cell types, potential regulatory TFs and non-coding SNPs which have been previously characterized and validated. Availability and implementation Motif-Raptor is freely available as a Python package at: https://github.com/pinellolab/MotifRaptor. Supplementary information Supplementary data are available at Bioinformatics online.

The present study was to explore whether the polymorphisms of FAM167 A-BLK region are associated with the susceptibility to autoimmune thyroid disease (AITD). The second sequencing technology was undertaken for seven tag loci mapping of the FAM167 A-BLK region, namely, rs11250144, rs2618431, rs4840568, rs13277113, rs2248932, rs2736340, and rs922483, in 999 AITD patients, including 624 Graves' disease (GD) and 375 Hashimoto's thyroiditis individuals, and 797 healthy cohorts. In contrast to those in controls, allele C of rs11250144 and allele G of rs2618431 both showed increased frequencies in GD patients. Consistent with this, the frequency of genotype GG in rs2618431 was increased in GD patients. Similarly, compared with that in female controls, allele G of rs2618431 was increased in the female AITD patients. Likewise, the frequency of allele G in rs2618431 obviously declined in the female GD patients. Allele A of rs4840568 linked to the susceptibility of the AITD teenagers. Besides, allele C in rs11250144 was correlated with thyroid-associated ophthalmopathy (TAO). Moreover, allele C in rs11250144 increased the risk to TAO by 56.3%. Genetic variants of FAM167 A-BLK region may contribute to the susceptibility to AITD, which can be added as the genetic candidates for this disease.

Immunometabolism is an emerging field that focuses on the role of cellular metabolism in the regulation of immune cells. Recent studies have revealed an intensive link between the metabolic state and the functions of immune cells. MicroRNAs (miRNAs) are small non-coding, single-stranded RNAs generally consisting of 18-25 nucleotides that exert crucial roles in regulating gene expression at the posttranscriptional level. Although the role of miRNAs in immune regulation has long been recognized, their roles in immunometabolism have not yet been well established. Over the past decade, increasing studies have proven that miRNAs are intensively involved in the metabolic control of immune cells including macrophages, T cells, B cells and dendritic cells. In this review, we highlight recent emerging findings in the miRNA-mediated metabolic control of immune cells.

Graves' disease (GD) is a common autoimmune thyroid disease characterized by positive thyroid stimulating hormone receptor antibody. To better understand its molecular pathogenesis, we adopted the weighted gene co-expression network analysis to reveal co-expression modules of key genes involved in the pathogenesis of GD, protein-protein interaction network analysis to identify the hub genes related to GD development and functional analyses to explore their possible functions. Our results showed that 1) a total of 2667 differentially expressed genes in our microarray study and 16 different gene co-expression modules were associated with GD, and 2) the most significant module was associated with the percentage of macrophages, T follicular helper cells and CD4+ memory T cells and mainly enriched in immune regulation and immune response. Overall, our study reveals several key gene co-expression modules and functional pathways involved in GD, which provides some novel insights into the pathogenesis of GD.

Heparanase degrades heparan sulfate in glomerular basement membrane (GBM) and plays an important role in diabetic nephropathy (DN). However, its regulating mechanisms remain to be deciphered. Our present study showed that the major advanced glycation endproducts (AGEs), CML-BSA, significantly increased heparanase expression in cultured podocytes and the effect was blocked by the receptor for advanced glycation endproducts (RAGE) knockdown, antibody and antagonist. In addition, NF-κB p65 phosphorylation was elevated and the increased heparanase expression and secretion upon CML-BSA could be attenuated by NF-κB inhibitor PDTC. Mechanistically, CML-BSA activated heparanase promoter through p65 directly binding to its promoter. Furthermore, the in vivo study showed that serum and renal cortex AGEs levels, glomerular p65 phosphorylation and heparanase expression were significantly increased in DN mice. Taken together, our data suggest that AGEs and RAGE interaction increases podocyte heparanase expression by activating NF-κB signal pathway, which is involved in GBM damages of DN.

Phosphorus is a scarce nutrient in many tropical ecosystems, yet how soil microbial communities cope with growth-limiting phosphorus deficiency at the gene and protein levels remains unknown. Here, we report a metagenomic and metaproteomic comparison of microbial communities in phosphorus-deficient and phosphorus-rich soils in a 17-year fertilization experiment in a tropical forest. The large-scale proteogenomics analyses provided extensive coverage of many microbial functions and taxa in the complex soil communities. A greater than fourfold increase in the gene abundance of 3-phytase was the strongest response of soil communities to phosphorus deficiency. Phytase catalyses the release of phosphate from phytate, the most recalcitrant phosphorus-containing compound in soil organic matter. Genes and proteins for the degradation of phosphorus-containing nucleic acids and phospholipids, as well as the decomposition of labile carbon and nitrogen, were also enhanced in the phosphorus-deficient soils. In contrast, microbial communities in the phosphorus-rich soils showed increased gene abundances for the degradation of recalcitrant aromatic compounds, transformation of nitrogenous compounds and assimilation of sulfur. Overall, these results demonstrate the adaptive allocation of genes and proteins in soil microbial communities in response to shifting nutrient constraints.

Motivation Complex microbial communities can be characterized by metagenomics and metaproteomics. However, metagenome assemblies often generate enormous, and yet incomplete, protein databases, which undermines the identification of peptides and proteins in metaproteomics. This challenge calls for increased discrimination of true identifications from false identifications by database searching and filtering algorithms in metaproteomics. Results Sipros Ensemble was developed here for metaproteomics using an ensemble approach. Three diverse scoring functions from MyriMatch, Comet and the original Sipros were incorporated within a single database searching engine. Supervised classification with logistic regression was used to filter database searching results. Benchmarking with soil and marine microbial communities demonstrated a higher number of peptide and protein identifications by Sipros Ensemble than MyriMatch/Percolator, Comet/Percolator, MS-GF+/Percolator, Comet & MyriMatch/iProphet and Comet & MyriMatch & MS-GF+/iProphet. Sipros Ensemble was computationally efficient and scalable on supercomputers. Availability and implementation Freely available under the GNU GPL license at http://sipros.omicsbio.org. Supplementary information Supplementary data are available at Bioinformatics online.

Glomerular basement membrane (GBM) damage plays a pivotal role in pathogenesis of albuminuria in diabetic nephropathy (DN). Heparan sulfate (HS) degradation induced by podocyte heparanase is the major cause of GBM thickening and abnormal perm-selectivity. In the present study, we aimed to examine the prophylactic effect of hyperoside on proteinuria development and GBM damage in DN mouse model and the cultured mouse podocytes. Pre-treatment with hyperoside (30 mg/kg/d) for four weeks could significantly decrease albuminuria, prevent GBM damage and oxidative stress in diabetes mellitus (DM) mice. Immunofluorescence staining, Real time PCR and Western blot analysis showed that decreased HS contents and increased heparanase expression in DN mice were also significantly improved by hyperoside pre-treatment. Meanwhile, transmission electron microscope imaging showed that hyperoside significantly alleviated GBM thickening in DN mice. In addition, hyperoside pre-treatment inhibited the increased heparanase gene (HPR1) promoter activity and heparanase expression induced by high glucose or reactive oxidative species (ROS) in cultured podocytes. Our data suggested that hyperoside has a prophylactic effect on proteinuria development and GBM damage in DM mice by decreasing podocyte heparanase expression.

Soybean is a widely grown grain legume and one of the most important economic crop species. Brassinosteroids play a crucial role in plant vegetative growth and reproductive development. However, it remains unclear how BRs regulate the developmental processes in soybean, and the molecular mechanism underlying soybean early development is largely unexplored. In this study, we first characterized how soybean early vegetative growth was specifically regulated by the BR biosynthesis inhibitor propiconazole; this characterization included shortened root and shoot lengths, reduced leaf area, and decreased chlorophyll content. In addition, the growth inhibition induced by Pcz could be rescued by exogenous brassinolide application. The RNA-seq technique was employed to investigate the BR regulatory networks during soybean early vegetative development. Identification and analysis of differentially expressed genes indicated that BRs orchestrate a wide range of cellular activities and biological processes in soybean under various BR concentrations. The regulatory networks between BRs and multiple hormones or stress-related pathways were investigated. The results provide a comprehensive view of the physiological functions of BRs and new insights into the molecular mechanisms at the transcriptional level of BR regulation of soybean early development.

Purpose: Sjogren's syndrome (SS) is an autoimmune disease characterized by dry mouth and eyes. To date, the exact molecular mechanisms of its etiology are still largely unknown. The aim of this study was to identify SS related key genes and functionally enriched pathways using the weighted gene co-expression network analysis (WGCNA). Materials and Methods: We downloaded the microarray data of 190 SS patients and 32 controls from Gene Expression Omnibus (GEO). Gene network was constructed and genes were classified into different modules using WGCNA. In addition, for the hub genes in the most related module to SS, gene ontology analysis was applied. The expression profile and diagnostic capacity (ROC curve) of interested hub genes were verified using a dataset from the GEO. Moreover, gene set enrichment analysis (GSEA) was also performed. Results: A total of 1483 differentially expressed genes were filtered. Weighted gene coexpression network was constructed and genes were classified into 17 modules. Among them, the turquoise module was most closely associated with SS, which contained 278 genes. These genes were significantly enriched in 10 Gene Ontology terms, such as response to virus, immune response, defense response, response to cytokine stimulus, and the inflammatory response. A total of 19 hub genes (GBP1, PARP9, EPSTI1, LOC400759, STAT1, STAT2, IFIH1, EIF2AK2, TDRD7, IFI44, PARP12, FLJ20035, PARP14, ISGF3G, XAF1, RSAD2,LY6E, IFI44L, and DDX58) were identified. The expression levels of the five interested genes including EIF2AK2, GBP1, PARP12, PARP14, and TDRD7 were also confirmed. ROC curve analysis determined that the above five genes' expression can distinguish SS from controls (the area under the curve is all greater than 0.7). GSEA suggests that the SS samples with highly expressed EIF2AK2 or TDRD7 genes are correlated with inflammatory response, interferon α response, and interferon γ response. Conclusion: The present study applied WGCNA to generate a holistic view of SS and provide a basis for the identification of potential pathways and hub genes that may be involved in the development of SS.

Transmembrane protein 39A (

Stable isotope probing (SIP) enables tracking the nutrient flows from isotopically labeled substrates to specific microorganisms in microbial communities. In proteomic SIP, labeled proteins synthesized by the microbial consumers of labeled substrates are identified with a shotgun proteomics approach. Here, proteomic SIP was combined with targeted metagenomic binning to reconstruct metagenome-assembled genomes (MAGs) of the microorganisms producing labeled proteins. This approach was used to track carbon flows from 13CO2 to the rhizosphere communities of Zea mays, Triticum aestivum, and Arabidopsis thaliana. Rhizosphere microorganisms that assimilated plant-derived 13C were capable of metabolic and signaling interactions with their plant hosts, as shown by their MAGs containing genes for phytohormone modulation, quorum sensing, and transport and metabolism of nutrients typical of those found in root exudates. XoxF-type methanol dehydrogenases were among the most abundant proteins identified in the rhizosphere metaproteomes. 13C-methanol proteomic SIP was used to test the hypothesis that XoxF was used to metabolize and assimilate methanol in the rhizosphere. We detected 7 13C-labeled XoxF proteins and identified methylotrophic pathways in the MAGs of 8 13C-labeled microorganisms, which supported the hypothesis. These two studies demonstrated the capability of proteomic SIP for functional characterization of active microorganisms in complex microbial communities.

Background Our purpose was to determine the prevalence of thyroid disorders in myasthenia gravis (MG) or whether MG was associated with an increased risk of thyroid disorders. Methods Pubmed, Embase, Web of Science, Cochrane database, Google Scholar and the Chinese Biomedical Databases were searched about the relationship between thyroid disorders and myasthenia gravis up to November 30, 2018, without language restrictions. The prevalence and relative risk (RR) for thyroid disorders were pooled by the R and STATA software. Results 39 papers with 24,927 MG patients were ultimately included for analysis in this meta-analysis. The pooled estimate of thyroid autoimmunity prevalence in MG patients was 10.1% (95%CI 6.7%–15.1%). Subgroups in patients with thyroid autoimmunity showed the prevalence of positive TGAb was the highest in MG patients (12.6%, 95%CI 8.1%–19.1%), followed by GD (6.0%, 95%CI 4.2%–8.5%), HT (4.6%, 95%CI 1.9%–10.5%). Moreover, the pooled estimated prevalence of thyroid dysfunction in MG patients was 6.8% (95%CI 4.6%–9.8%). After stratification, the results showed the prevalence of hyperthyroidism and hypothyroidism in MG cases were 5.6% (95%CI 3.9%–8.0%) and 2.6% (95%CI 1.7%–4.1%), respectively. In addition, meta-analysis of 2 studies showed that MG was significantly associated with the increased risk of thyroid autoimmunity (OR = 2.86; 95%CI 1.54–5.28, P = .001). Conclusions This systemic review and meta-analysis provides reliable evidence that thyroid disorders are prevalent in MG, especially TGAb positivity, GD, hyperthyroidism, and HT, and MG is associated with increased risk for thyroid autoimmunity.

Background Iodine status has long been regarded as an environmental determinant for thyroid dysfunction, but its relationship with thyroid autoimmunity (TAI) is still controversial. Our study aimed to elucidate the relationship between iodine status and TAI through both a population-based study and a dose–response meta-analysis of eligible epidemiological studies. Methods A population-based, cross-sectional study was firstly carried out, which enrolled a total of 2808 Chinese adults. Odds ratio (OR) with 95% confidence interval (95% CI) was calculated through logistic regression analysis. A dose–response meta-analysis of eligible epidemiological studies was also carried out. Results The cross-sectional study showed an U-shaped relationship between iodine intake and TAI in adults. Compared with those with more than adequate iodine status, individuals with iodine deficiency, adequate iodine status and iodine excess all had higher risk of TAI, and the adjusted ORs were 1.50 (95% CI 1.03–2.17, P = 0.032), 1.50 (95% CI 1.09–2.07, P = 0.013) and 1.68 (95% CI 1.11–2.53, P = 0.014), respectively. The dose–response meta-analysis included 22 epidemiological studies with a total of 69,987 participants and further validated the U-shaped relationship between iodine intake and TAI in adults, which proved the significantly increased risk of TAI among individuals with either iodine deficiency or iodine excess. Stratified analysis of studies with low risk of confounding bias also identified similar findings. Conclusion The study suggests an U-shaped relationship between iodine intake and TAI in adults, and both iodine deficiency and iodine excess are risk factors of TAI in adults. The underlying mechanisms need to be elucidated in future studies.

Many plant-associated fungi host endosymbiotic endobacteria with reduced genomes. While endobacteria play important roles in these tri-partite plant-fungal-endobacterial systems, the active physiology of fungal endobacteria has not been characterized extensively by systems biology approaches. Here, we use integrated proteomics and metabolomics to characterize the relationship between the endobacterium Mycoavidus sp. and the root-associated fungus Mortierella elongata. In nitrogen-poor media, M. elongata had decreased growth but hosted a large and growing endobacterial population. The active endobacterium likely extracted malate from the fungal host as the primary carbon substrate for energy production and biosynthesis of phospho-sugars, nucleobases, peptidoglycan and some amino acids. The endobacterium obtained nitrogen by importing a variety of nitrogen-containing compounds. Further, nitrogen limitation significantly perturbed the carbon and nitrogen flows in the fungal metabolic network. M. elongata regulated many pathways by concordant changes on enzyme abundances, post-translational modifications, reactant concentrations and allosteric effectors. Such multimodal regulations may be a general mechanism for metabolic modulation.

Non-thyroidal illness syndrome (NTIS) is characterized by decreased serum triiodothyronine level without increased thyroid-stimulating hormone level during critical illness. The summary data on the prevalence of NTIS in cardiovascular patients are lacking, and its prognostic role in cardiovascular patients is also unclear.We performed a systematic review and meta-analysis to comprehensively determine the prevalence and the prognostic role of NTIS in cardiovascular patients. The prevalence of NTIS was pooled using random-effect meta-analysis and the hazard ratios (HRs) for all-cause mortality, cardiac mortality and major adverse cardiovascular events (MACE) were also pooled.Forty-one studies were finally included. The pooled prevalence of NTIS in cardiovascular patients was 21.7% (95% CI 18.4%-25.3%). Subgroup by the types of cardiovascular diseases showed the prevalence of NTIS was highest in patients with heart failure (24.5%), followed by acute myocardial infarction (18.9%) and acute coronary syndrome (17.1%). Meta-analysis of studies using strict diagnostic criteria of NITS showed that the pooled prevalence of NTIS in cardiovascular patients was 17.6% (95% CI 14.5%-21.2%). NTIS was independently associated with increased risks of all-cause mortality (HR=2.52, 95% CI 1.87-3.40, P0.001) and cardiac mortality (HR=2.06, 95% CI 1.58-2.69, P0.001) in cardiovascular patients. NTIS was also an independent predictor of MACE in cardiovascular patients (HR=1.73, 95% CI 1.32-2.26, P0.001).NTIS is very common in patients with cardiovascular diseases. NTIS is an independent prognostic factor in cardiovascular patients and is associated with increased risks of all-cause mortality, cardiac mortality and MACE.

Diabetes self-management education is an essential part of diabetes care, but its impact on all-cause mortality risk of type 2 diabetes patients is unclear. A systematic review and meta-analysis aiming to elucidate the impact of diabetes self-management education on all-cause mortality risk of type 2 diabetes patients was performed. Randomised controlled trials were identified though literature search in Medline, Embase, CENTRAL, conference abstracts, and reference lists. Only randomised controlled trials comparing diabetes self-management education with usual care in type 2 diabetes patients and reporting outcomes after a follow-up of at least 12 months were considered eligible. Risk ratios with 95 %CIs were pooled. This study was registered at PROSPERO with the number of CRD42016043911. 42 randomised controlled trials containing 13,017 participants were included. The mean time of follow-up was 1.5 years. There was no heterogeneity among those included studies (I 2 = 0 %). Mortality occurred in 159 participants (2.3 %) in the diabetes self-management education group and in 187 (3.1 %) in the usual care group, and diabetes self-management education significantly reduced risk of all-cause mortality in type 2 diabetes patients (pooled risk ratios : 0.74, 95 %CI 0.60–0.90, P = 0.003; absolute risk difference: −0.8 %, 95 %CI −1.4 to −0.3). Both multidisciplinary team education and nurse-led education could significantly reduce mortality risk in type 2 diabetes patients, and the pooled risk ratios were 0.66 (95 %CI 0.46–0.96, P = 0.02; I 2 = 0 %) and 0.64 (95 % CI 0.47– 0.88, P = 0.005; I 2 = 0 %), respectively. Subgroup analyses of studies with longer duration of follow-up (≥1.5 years) or larger sample size (≥300) also found a significant effect of diabetes self-management education in reducing mortality risk among type 2 diabetes. Significant effect of diabetes self-management education in reducing mortality risk was also found in those patients receiving diabetes self-management education with contact hours more than 10 h (pooled risk ratio: 0.60, 95 %CI 0.44–0.82, P = 0.001; I 2 = 0 %), those receiving repeated diabetes self-management education (pooled RR: 0.71, P = 0.001; I 2 = 0 %), those receiving diabetes self-management education using structured curriculum (pooled risk ratio: 0.72, P = 0.01; I 2 = 0 %) and those receiving diabetes self-management education using in-person communication (pooled risk ratio: 0.75, P = 0.02; I 2 = 0 %). The quality of evidence for the effect of diabetes self-management education in reducing all-cause mortality risk among type 2 diabetes patients was rated as moderate according to the Grading of Recommendations Assessment, Development, and Evaluation method, and the absolute risk reduction of all-cause mortality of type 2 diabetic patients by diabetes self-management education was estimated to be 4 fewer per 1000 person-years (from 1 fewer to 6 fewer). The available evidence suggests that diabetes self-management education can reduce all-cause mortality risk in type 2 diabetes patients. Further clinical trials with longer time of follow-up are needed to validate the finding above.

Over four hundred different microRNAs (miRNAs) have been identified in the genome of the model organism the nematode Caenorhabditis elegans. As the germline is dedicated to the preservation of each species, and almost half of all the cells in an adult nematode are germline, it is likely that regulatory miRNAs are important for germline development and maintenance. In C. elegans the miR35 family has strong maternal effects, contributing to normal embryogenesis and to adult fecundity. To determine whether any particular miRNAs are greatly enriched in the C. elegans germline we used RNA-seq to compare the miRNA populations in several germline-defective strains of adult C. elegans worms, including glp-4(germline proliferation-4), glh-1(germline helicase-1) and dcr-1(dicer-1). Statistical analyses of RNA-seq comparisons identified 13 miRNAs that are germline-enriched, including seven members of the well-studied miR35 family that were reduced as much as 1000-fold in TaqMan qRT PCR miRNA assays. Along with the miR35s, six others: miR-56 (a member of the miR51 family),-70, -244, -260 , -788 and -4813, none of which previously considered as such, were also identified by RNA-seq as germline-enriched candidates. We went on to develop a successful miRNA in situ hybridization protocol for C. elegans, revealing miR35s specifically concentrate during oogenesis in the pachytene region of the gonad, and persist throughout early embryogenesis, while in adult animals neither let-7 nor miR-228 has a germline-bias.

Several major effectors of adult-stage fetal globin silencing have been identified, including the transcription factors (TFs) BCL11A and ZBTB7A/LRF and the NuRD chromatin complex, although each has potential on-target liabilities for rational β-hemoglobinopathy therapeutic inhibition. Here through CRISPR screening of 1591 transcription factors, we discover ZNF410 to be a novel fetal hemoglobin (HbF) repressing TF. ZNF410 does not bind directly to the γ-globin genes but rather its chromatin occupancy is solely concentrated at CHD4, encoding the NuRD nucleosome remodeler, itself required for HbF repression. CHD4 has two ZNF410-bound regulatory elements, one at its promoter and the other at an enhancer 6 kb upstream, with 27 combined ZNF410 binding motifs constituting unparalleled genomic clusters. Peaks at these clusters display up to 57- and 77-fold enrichment respectively for ZNF410 binding compared to controls. Footprint analysis shows that the ZNF410 motifs are protected from nuclease cleavage. No other bona fide peaks could be detected across the genome in HUDEP-2 cells or primary CD34+ HSPC-derived erythroid precursors. We demonstrate that the ZNF410-bound elements at CHD4 completely account for ZNF410's effects on γ-globin repression. Knockout of ZNF410 reduces CHD4 by 60%, enough to substantially de-repress HbF while avoiding the cellular toxicity of complete CHD4 loss. Mice with constitutive deficiency of the homolog Zfp410 are born at expected Mendelian ratios (6 homozygous Zfp410Gt/Gt gene-trap allele mice out of 20 live births) with unremarkable hematology. ZNF410 is dispensable for human hematopoietic engraftment potential and erythroid maturation unlike known HbF repressors. Engrafting human erythrocytes induce HbF from ~2.5% in controls to ~17% in ZNF410 edited recipients, by hemoglobin HPLC. These studies identify a new rational target for HbF induction for the β-hemoglobin disorders with a wide therapeutic index. More broadly, ZNF410 represents a special class of gene regulator, a conserved transcription factor with singular devotion to regulation of a chromatin subcomplex. FIGURE LEGEND: ZNF410 chromatin occupancy is restricted to CHD4. (A) Dense mutagenesis of ZNF410 shows its five C2H2 zinc-finger domains (red rectangles) are especially critical for HbF repression. (B) Genome-wide ZNF410 binding was identified by CUT&RUN in HUDEP-2 cells. Enrichment for ZNF410 binding was concentrated at just two sites in the genome - at the promoter and at an enhancer ~6 kb upstream of CHD4. (C) Genome-wide ZNF410 motif occurrences (JASPAR motif shown in center) were mapped using a 3 kb sliding window. Clusters of ZNF410 motifs were found only at three locations in the genome, including the CHD4 promoter and CHD4 -6 kb enhancer. (D) CHD4 locus showing ZNF410 binding (red peaks) at the CHD4 promoter and CHD4 -6 kb enhancer regions with anti-HA antibody recognizing epitope-tagged ZNF410 and anti-ZNF410 antibody recognizing endogenous ZNF410 in both HUDEP-2 cells and CD34+ HSPC derived erythroid precursors. CUT&RUN footprints demonstrate ZNF410 motif protection, ATAC-seq chromatin accessibility and phyloP DNA sequence conservation. Disclosures Bauer: Pfizer: Consultancy; Syros Pharmaceuticals: Consultancy; Fulcrum Therapeutics: Consultancy; Sanofi: Research Funding.

Background Brassinosteroids (BRs) play a crucial role in plant vegetative growth and reproductive development. The transcription factors BZR1 and BES1/BZR2 are well characterized as downstream regulators of the BR signaling pathway in Arabidopsis and rice. Soybean contains four BZR1-like proteins (GmBZLs), and it was reported that GmBZL2 plays a conserved role in BR signaling regulation. However, the roles of other GmBZLs have not been thoroughly studied, and the targets of GmBZLs in soybean remain unclear. Results In this study, we first characterized GmBZL3 in soybean from gene expression patterns, conserved domains in coding sequences, and genomic replication times of four GmBZL orthologous. The results indicated that GmBZL3 might play conserved roles during soybean development. The overexpression of GmBZL3P219L in the Arabidopsis BR-insensitive mutant bri1–5 partially rescued the phenotypic defects including BR-insensitivity, which provides further evidence that GmBZL3 functions are conserved between soybean and the homologous Arabidopsis genes. In addition, the identification of the GmBZL3 target genes through ChIP-seq technology revealed that BR has broad roles in soybean and regulates multiple pathways, including other hormone signaling, disease-related, and immunity response pathways. Moreover, the BR-regulated GmBZL3 target genes were further identified, and the results demonstrate that GmBZL3 is a major transcription factor responsible for BR-regulated gene expression and soybean growth. A comparison of GmBZL3 and AtBZR1/BES1 targets demonstrated that GmBZL3 might play conserved as well as specific roles in the soybean BR signaling network. Finally, the identification of two natural soybean varieties of the GmBZL3 mutantion by SNP analysis could facilitate the understanding of gene function during soybean development in the future. Conclusions We illustrate here that GmBZL3 orchestrates a genome-wide transcriptional response that underlies BR-mediated soybean early vegetative growth, and our results support that BRs play crucial regulatory roles in soybean morphology and gene expression levels. Electronic supplementary material The online version of this article (10.1186/s12870-019-1677-2) contains supplementary material, which is available to authorized users.

Co-signaling molecules include co-stimulatory and co-inhibitory molecules and play important roles in modulating immune responses. The roles of co-signaling molecules in autoimmune diseases have not been clearly defined. We assessed the expressions of co-stimulatory and co-inhibitory molecules in autoimmune diseases through a bioinformatics-based study. By using datasets of whole-genome transcriptome, the expressions of 54 co-stimulatory or co-inhibitory genes in common autoimmune diseases were analyzed using Robust rank aggregation (RRA) method. Nineteen array datasets and 6 RNA-seq datasets were included in the RRA discovery study and RRA validation study, respectively. Significant genes were further validated in several autoimmune diseases including Graves' disease (GD). RRA discovery study suggested that CD160 was the most significant gene aberrantly expressed in autoimmune diseases (Adjusted P = 5.9E-12), followed by CD58 (Adjusted P = 5.7E-06) and CD244 (Adjusted P = 9.5E-05). RRA validation study also identified CD160 as the most significant gene aberrantly expressed in autoimmune diseases (Adjusted P = 5.9E-09). We further found that the aberrant expression of CD160 was statistically significant in multiple autoimmune diseases including GD (P < 0.05), and CD160 had a moderate role in diagnosing those autoimmune diseases. Flow cytometry confirmed that CD160 was differentially expressed on the surface of CD8+ T cells between GD patients and healthy controls (P = 0.002), which proved the aberrant expression of CD160 in GD at the protein level. This study suggests that CD160 is the most significant co-signaling gene aberrantly expressed in autoimmune diseases. Treatment strategy targeting CD160-related pathway may be promising for the therapy of autoimmune diseases.

Autoimmune thyroid diseases (AITDs) are chronic organ-specific autoimmune diseases and mainly include Graves' disease (GD) and Hashimoto's thyroiditis (HT). CD14 is an important component of the immune system as a receptor for gram-negative lipopolysaccharide (LPS). The genetic polymorphisms of CD14 have been confirmed to be associated with a variety of autoimmune diseases. However, its relationship with AITDs is still unclear. The study was aimed to determine whether four single nucleotide polymorphisms (rs2915863, rs2569190, rs2569192, and rs2563298) of CD14 are associated with AITDs and its subgroups of GD and HT. The results showed significant association of rs2915863 and rs2569190 with GD. The frequencies of rs2915863 genotypes and T allele in patients with GD differed significantly from their controls (P = 0.007 and P = 0.021, respectively). For rs2569190, frequencies of genotypes and G allele in GD patients also showed positive P-values (P = 0.038 and P = 0.027, respectively). The correlations between these two loci and GD are more pronounced in female GD patients and patients with a family history. In genetic model analysis, the allele model, recessive model, and homozygous model of rs2569190 and rs2915863 embodied strong correlations with GD after the adjusting of age and gender (P = 0.014, P = 0.015, P = 0.009, and P = 0.014, P = 0.001, P = 0.006, respectively). However, these four sites are not related to HT. We firstly discovered the relationship between CD14 gene polymorphism and GD, and the results indicate that CD14 is an important risk locus for AITD and its SNPs may contribute to host's genetic predisposition to GD.

The thalassemias are compelling targets for therapeutic genome editing in part because monoallelic correction of a subset of hematopoietic stem cells (HSCs) would be sufficient for enduring disease amelioration. A primary challenge is the development of efficient repair strategies that are effective in HSCs. Here, we demonstrate that allelic disruption of aberrant splice sites, one of the major classes of thalassemia mutations, is a robust approach to restore gene function. We target the IVS1-110G>A mutation using Cas9 ribonucleoprotein (RNP) and the IVS2-654C>T mutation by Cas12a/Cpf1 RNP in primary CD34+ hematopoietic stem and progenitor cells (HSPCs) from β-thalassemia patients. Each of these nuclease complexes achieves high efficiency and penetrance of therapeutic edits. Erythroid progeny of edited patient HSPCs show reversal of aberrant splicing and restoration of β-globin expression. This strategy could enable correction of a substantial fraction of transfusion-dependent β-thalassemia genotypes with currently available gene-editing technology.

The objective of this study was to investigate whether IRF7 polymorphisms are associated with autoimmune thyroid diseases (AITDs). We selected three single nucleotide polymorphisms (SNPs) of IRF7, namely, rs1061501, rs1131665, and rs1061502 for genotyping using PCR-based ligase detection reaction (LDR) method in a total of 1659 participants (592 with Graves’ disease, 297 with Hashimoto’s thyroiditis, and 770 healthy controls). Gene-disease and genotype-clinical phenotype associations were evaluated for the three SNPs. Our results showed that the AG genotype and the minor allele G frequency of rs1131665 and rs1061502 in AITD patients were both higher than those of the controls (rs1131665: AG genotype: P=0.017, OR=1.968; allele G: P=0.018, OR=1.946; rs1061502: AG genotype: P=0.029, OR=1.866; allele G: P=0.031, OR=1.847). Subgroup analysis also showed that the AG genotype and the minor allele G frequency of rs1131665 and rs1061502 in Graves’ disease patients were both higher than those of the controls (rs1131665: AG genotype: P=0.015, OR=2.074; allele G: P=0.016, OR=2.048; rs1061502: AG genotype: P=0.034, OR=1.919; allele G: P=0.035, OR=1.898). Furthermore, the allele G frequency of rs1061501 was associated with Graves’ ophthalmopathy (P=0.035, OR=1.396). No significant difference in IRF7 polymorphisms was found between Hashimoto’s thyroiditis patients and controls. Our study has revealed for the first time that IRF7 is a susceptibility gene for AITD, especially for Graves’ disease and Graves’ ophthalmopathy.