Association of GTF2I gene polymorphisms with renal involvement of systemic lupus erythematosus in a Chinese population

Identification of GTF2I Polymorphisms as Potential Biomarkers for CKD in the Han Chinese Population : Multicentric Collaborative Cross-Sectional Cohort Study

Key Points

Genetic factors are key players in CKD, with two linked single-nucleotide polymorphisms in the GTF2I gene, associated with CKD susceptibility in the Taiwanese population. Individuals with specific GTF2I genotypes (CT/TT for rs117026326 and CT/CC for rs73366469) show higher CKD prevalence and earlier onset. Men with the specific genotypes of rs117026326 and rs73366469 face a heightened CKD risk compared with women, particularly at lower eGFR.

Background

CKD poses a global health challenge, but its molecular mechanisms are poorly understood. Genetic factors play a critical role, and phenome-wide association studies and genome-wide association studies shed light on CKD's genetic architecture, shared variants, and biological pathways.

Methods

Using data from the multicenter collaborative precision medicine cohort, we conducted a retrospective prospectively maintained cross-sectional study. Participants with comprehensive information and genotyping data were selected, and genome-wide association study and phenome-wide association study analyses were performed using the curated Taiwan Biobank version 2 array to identify CKD-associated genetic variants and explore their phenotypic associations.

Results

Among 58,091 volunteers, 8420 participants were enrolled. Individuals with CKD exhibited higher prevalence of metabolic, cardiovascular, autoimmune, and nephritic disorders. Genetic analysis unveiled two closely linked single-nucleotide polymorphisms, rs117026326 and rs73366469, both associated with GTF2I and CKD (r 2 = 0.64). Further examination revealed significant associations between these single-nucleotide polymorphisms and various kidney-related diseases. The CKD group showed a higher proportion of individuals with specific genotypes (CT/TT for rs117026326 and CT/CC for rs73366469), suggesting potential associations with CKD susceptibility (P < 0.001). Furthermore, individuals with these genotypes developed CKD at an earlier age. Multiple logistic regression confirmed the independent association of these genetic variants with CKD. Subgroup analysis based on eGFR demonstrated an increased risk of CKD among carriers of the rs117026326 CT/TT genotypes (odds ratio [OR], 1.15; 95% confidence interval [CI], 1.07 to 1.24; P < 0.001; OR, 1.32, 95% CI, 1.04 to 1.66; P = 0.02, respectively) and carriers of the rs73366469 CT/CC genotypes (OR, 1.13; 95% CI, 1.05 to 1.21; P < 0.001; OR, 1.31; 95% CI, 1.08 to 1.58; P = 0.0049, respectively). In addition, men had a higher CKD risk than women at lower eGFR levels (OR, 1.35; 95% CI, 1.13 to 1.61; P < 0.001).

Conclusions

Our study reveals important links between genetic variants GTF2I and susceptibility to CKD, advancing our understanding of CKD development in the Taiwanese population and suggesting potential for personalized prevention and management strategies. More research is needed to validate and explore these variants in diverse populations.

Neuronal Gtf2i deletion alters mitochondrial and autophagic properties

Gtf2i encodes the general transcription factor II-I (TFII-I), with peak expression during pre-natal and early post-natal brain development stages. Because these stages are critical for proper brain development, we studied at the single-cell level the consequences of Gtf2i's deletion from excitatory neurons, specifically on mitochondria. Here we show that Gtf2i's deletion resulted in abnormal morphology, disrupted mRNA related to mitochondrial fission and fusion, and altered autophagy/mitophagy protein expression. These changes align with elevated reactive oxygen species levels, illuminating Gtf2i's importance in neurons mitochondrial function. Similar mitochondrial issues were demonstrated by Gtf2i heterozygous model, mirroring the human condition in Williams syndrome (WS), and by hemizygous neuronal Gtf2i deletion model, indicating Gtf2i's dosage-sensitive role in mitochondrial regulation. Clinically relevant, we observed altered transcript levels related to mitochondria, hypoxia, and autophagy in frontal cortex tissue from WS individuals. Our study reveals mitochondrial and autophagy-related deficits shedding light on WS and other Gtf2i-related disorders.

Myelin oligodendrocyte glycoprotein-associated disease is associated with BANK1, RNASET2 and TNIP1 polymorphisms

AIM

Here we aimed to compare association of common immune-related genetic variants with three autoimmune central nervous system (CNS) demyelinating diseases, namely myelin oligodendrocyte glycoprotein-associated disease (MOGAD), multiple sclerosis (MS) and neuromyelitis optica spectrum disorder (NMOSD).

METHODS

In this retrospective cross-sectional study, 26 common immune-related single nucleotide polymorphisms were genotyped in 102 patients with MOGAD, 100 patients with MS, 198 patients with NMOSD and 541 healthy control subjects recruited from Guangzhou, China.

RESULTS

Among all tested genetic variations, one polymorphism, B cell scaffold protein with ankyrin repeats 1 (BANK1) rs4522865 was associated with multiple disorders, namely MOGAD (OR = 1.94, 95% CI:1.19-3.17, P = 0.0059) and NMOSD (OR = 1.69, 95% CI:1.17-2.45). Besides BANK1 rs4522865, two other non-HLA loci, ribonuclease T2 (RNASET2) rs9355610 (OR = 0.47, 95% CI: 0.26-0.85) and TNFAIP3 interacting protein 1 (TNIP1) rs10036748 (OR = 1.76, 95% CI: 1.16-2.71), were associated with MOGAD. In addition, NMOSD was associated with signal transducer and activator of transcription 4 (STAT4) rs7574865 (OR = 1.58, 95% CI: 1.12-2.24) and general transcription factor Iii (GTF2I) rs73366469 (OR = 1.60, 95% CI:1.12-2.29), while MS was associated with a killer cell lectin like receptor G1 (KLRG1) rs1805673 (OR = 0.61, 95% CI: 0.40-0.94) and T-box transcription factor 21 (TBX21) rs17244587 (OR = 2.25, 95% CI: 1.25-4.06).

CONCLUSION

The current study suggests for the first time three non-HLA susceptibility loci for MOGAD. In addition, comparison of association of 26 immune-related polymorphisms with three autoimmune CNS demyelinating diseases demonstrates substantial difference in genetic basis of those disorders.

Meta-Analysis and Systematic Review of the Association between a Hypoactive NCF1 Variant and Various Autoimmune Diseases

Genetic association studies have discovered the GTF2I-NCF1 intergenic region as a strong susceptibility locus for multiple autoimmune disorders, with the missense mutation NCF1 rs201802880 as the causal polymorphism. In this work, we aimed to perform a comprehensive meta-analysis of the association of the GTF2I-NCF1 locus with various autoimmune diseases and to provide a systemic review on potential mechanisms underlying the effect of the causal NCF1 risk variants. The frequencies of the two most extensively investigated polymorphisms within the locus, GTF2I rs117026326 and NCF1 rs201802880, vary remarkably across the world, with the highest frequencies in East Asian populations. Meta-analysis showed that the GTF2I-NCF1 locus is significantly associated with primary Sjögren's syndrome, systemic lupus erythematosus, systemic sclerosis, and neuromyelitis optica spectrum disorder. The causal NCF1 rs201802880 polymorphism leads to an amino acid substitution of p.Arg90His in the p47phox subunit of the phagocyte NADPH oxidase. The autoimmune disease risk His90 variant results in a reduced ROS production in phagocytes. Clinical and experimental evidence shows that the hypoactive His90 variant might contribute to the development of autoimmune disorders via multiple mechanisms, including impairing the clearance of apoptotic cells, regulating the mitochondria ROS-associated formation of neutrophil extracellular traps, promoting the activation and differentiation of autoreactive T cells, and enhancing type I IFN responses. In conclusion, the identification of the association of NCF1 with autoimmune disorders demonstrates that ROS is an essential regulator of immune tolerance and autoimmunity mediated disease manifestations.

Thymic stroma and TFII-I: towards new targeted therapies

Thymic epithelial tumors (TETs) have been characterized at the molecular level through bioptic sections and cell lines. Despite these advances, there is a need for a more thorough characterization of the thymic stroma in thymoma, particularly because of the diversity of cell types that populate the tumor and the absence of a healthy thymic counterpart. Recent work on healthy pediatric thymi - both in vitro and at the single-cell level - now sets the stage for new studies on their neoplastic counterparts. Furthermore, general transcription factor IIi (GTF2I), a thymoma-specific oncogene, as well as some of its SNPs, are increasingly associated with autoimmune disease, a significant feature of thymomas. We summarize recent discoveries in the field and discuss the development of new targeted therapies.

Association of GTF2I, NFKB1, and TYK2 Regional Polymorphisms With Systemic Sclerosis in a Chinese Han Population

Objectives

Systemic sclerosis (SSc) is an uncommon autoimmune disease that varies with ethnicity. Single nucleotide polymorphisms (SNPs) in the GTFSI, NFKB1, and TYK2 genes have been reported to be associated with SSc in other populations and in individuals with various autoimmune diseases. This study aimed to investigate the association between these SNPs and susceptibility to SSc in a Chinese Han population.

Method

A case-control study was performed in 343 patients with SSc and 694 ethnically matched healthy controls. SNPs in GTF2I, NFKB1, and TYK2 were genotyped using a Sequenom MassArray iPLEX system. Association analyses were performed using PLINK v1.90 software.

Result

Our study demonstrated that the GTF2I rs117026326 T allele and the GTF2I rs73366469 C allele were strongly associated with patients with SSc (P = 6.97E-10 and P = 1.33E-08, respectively). Patients carrying the GTF2I rs117026326 TT genotype and the GTF2I rs73366469 CC genotype had a strongly increased risk of SSc (P = 6.25E-09 and P = 1.67E-08, respectively), and those carrying the NFKB1 rs1599961 AA genotype had a suggestively significantly increased risk of SSc (P = 0.014). Moreover, rs117026326 and rs73366469 were associated with SSc in different genetic models (additive model, dominant model, and recessive model) (P < 0.05) whereas rs1599961 was associated with SSc in the dominant genetic model but not in the addictive and recessive models (P = 0.0026). TYK2 rs2304256 was not significantly associated with SSc in this study.

Conclusion

GTF2I rs117026326 and rs73366469 SNPs were strongly associated with SSc in this Chinese Han population. NFKB1 rs1599961 showed a suggestive association with SSc, and no significant association was found between TYK2 rs2304256 and SSc in this Chinese Han population.

Novel partners of USP6 gene in a spectrum of bone and soft tissue lesions

Nodular fasciitis, primary aneurysmal bone cyst, myositis ossificans, and their related lesions are benign tumors that share common histological features and a chromosomal rearrangement involving the ubiquitin-specific peptidase 6 (USP6) gene. The identification of an increasing number of new partners implicated in USP6 rearrangements demonstrates a complex tumorogenesis of this tumor spectrum. In this study on a series of 77 tumors (28 nodular fasciitis, 42 aneurysmal bone cysts, and 7 myositis ossificans) from the database of the French Sarcoma Group, we describe 7 new partners of the USP6 gene. For this purpose, rearrangements were first researched by multiplexed RT-qPCRs in the entire population. A targeted RNA sequencing was then used on samples selected according to a high USP6-transcription level expression estimated by RT-qPCR. Thanks to this multistep approach, besides the common USP6 fusions observed, we detected novel USP6 partners: PDLIM7 and MYL12A in nodular fasciitis and TPM4, DDX17, GTF2I, KLF3, and MEF2A in aneurysmal bone cysts. In order to try to bring to light the role played by the recently identified USP6 partners in this lesional spectrum, their functions are discussed. Taking into account that a traumatic participation has long been mentioned in the histogenesis of most of these lesions and because of their morphological resemblance to organizing granulation reparative tissue or callus, a focus is placed on their relationship with tissue remodeling and, to a lesser extent, with bone metabolism.

Gene of the month: GTF2I

The GTF2I is a general transcription factor and its mutations have been reported to be recurrent in thymic epithelial tumours and are rare in other malignancies. Apart from thymic epithelial tumours, these mutations have also been reported in a subgroup of T cell lymphomas, angioimmunoblastic T cell lymphomas. Soft tissue angiofibroma has been reported to harbour GTF2I-NCOA2 fusion, whereas GTF2I partners with Retinoic acid receptor alpha (RARA) in acute promyelocytic leukaemia as GTF2I-RARA GTF2I has also been implicated in immune disorders and two neuropsychiatric genetic disorders, namely autism and Williams-Beuren syndrome. The various structural, biochemical and functional properties of GTF2I suggest towards the oncogenic nature of this gene. Studies involving patients are presently few and the availability of biospecimens amenable to molecular diagnostic studies is limited. Future studies involving biospecimens and transformed cell lines shall provide a clear understanding of the GTF2I mechanistic to eventually lead to targeted treatment.

Meta-analysis of genome-wide association study identifies FBN2 as a novel locus associated with systemic lupus erythematosus in Thai population

BACKGROUND

Differences in the expression of variants across ethnic groups in the systemic lupus erythematosus (SLE) patients have been well documented. However, the genetic architecture in the Thai population has not been thoroughly examined. In this study, we carried out genome-wide association study (GWAS) in the Thai population.

METHODS

Two GWAS cohorts were independently collected and genotyped: discovery dataset (487 SLE cases and 1606 healthy controls) and replication dataset (405 SLE cases and 1590 unrelated disease controls). Data were imputed to the density of the 1000 Genomes Project Phase 3. Association studies were performed based on different genetic models, and pathway enrichment analysis was further examined. In addition, the performance of disease risk estimation for individuals in Thai GWAS was assessed based on the polygenic risk score (PRS) model trained by other Asian populations.

RESULTS

Previous findings on SLE susceptible alleles were well replicated in the two GWAS. The SNPs on HLA class II (rs9270970, A>G, OR = 1.82, p value = 3.61E-26), STAT4 (rs7582694, C>G, OR = 1.57, p value = 8.21E-16), GTF2I (rs73366469, A>G, OR = 1.73, p value = 2.42E-11), and FAM167A-BLK allele (rs13277113, A>G, OR = 0.68, p value = 1.58E-09) were significantly associated with SLE in Thai population. Meta-analysis of the two GWAS identified a novel locus at the FBN2 that was specifically associated with SLE in the Thai population (rs74989671, A>G, OR = 1.54, p value = 1.61E-08). Functional analysis showed that rs74989671 resided in a peak of H3K36me3 derived from CD14+ monocytes and H3K4me1 from T lymphocytes. In addition, we showed that the PRS model trained from the Chinese population could be applied in individuals of Thai ancestry, with the area under the receiver-operator curve (AUC) achieving 0.76 for this predictor.

CONCLUSIONS

We demonstrated the genetic architecture of SLE in the Thai population and identified a novel locus associated with SLE. Also, our study suggested a potential use of the PRS model from the Chinese population to estimate the disease risk for individuals of Thai ancestry.