Gongqi Yu

Genomewide association study of leprosy.

BACKGROUND The narrow host range of Mycobacterium leprae and the fact that it is refractory to growth in culture has limited research on and the biologic understanding of leprosy. Host genetic factors are thought to influence susceptibility to infection as well as disease progression. METHODS We performed a two-stage genomewide association study by genotyping 706 patients and 1225 controls using the Human610-Quad BeadChip (Illumina). We then tested three independent replication sets for an association between the presence of leprosy and 93 single-nucleotide polymorphisms (SNPs) that were most strongly associated with the disease in the genomewide association study. Together, these replication sets comprised 3254 patients and 5955 controls. We also carried out tests of heterogeneity of the associations (or lack thereof) between these 93 SNPs and disease, stratified according to clinical subtype (multibacillary vs. paucibacillary). RESULTS We observed a significant association (P<1.00x10(-10)) between SNPs in the genes CCDC122, C13orf31, NOD2, TNFSF15, HLA-DR, and RIPK2 and a trend toward an association (P=5.10x10(-5)) with a SNP in LRRK2. The associations between the SNPs in C13orf31, LRRK2, NOD2, and RIPK2 and multibacillary leprosy were stronger than the associations between these SNPs and paucibacillary leprosy. CONCLUSIONS Variants of genes in the NOD2-mediated signaling pathway (which regulates the innate immune response) are associated with susceptibility to infection with M. leprae.

Identification of two new loci at IL23R and RAB32 that influence susceptibility to leprosy

We performed a genome-wide association study with 706 individuals with leprosy and 5,581 control individuals and replicated the top 24 SNPs in three independent replication samples, including a total of 3,301 individuals with leprosy and 5,299 control individuals from China. Two loci not previously associated with the disease were identified with genome-wide significance: rs2275606 (combined P = 3.94 × 10−14, OR = 1.30) on 6q24.3 and rs3762318 (combined P = 3.27 × 10−11, OR = 0.69) on 1p31.3. These associations implicate IL23R and RAB32 as new susceptibility genes for leprosy. Furthermore, we identified evidence of interaction between the NOD2 and RIPK2 loci, which is consistent with the biological association of the proteins encoded by these genes (NOD2-RIPK2 complex) in activating the NF-κB pathway as a part of the host defense response to infection. Our findings have expanded the biological functions of IL23R by uncovering its involvement in infectious disease susceptibility and suggest a potential involvement of autophagocytosis in leprosy pathogenesis. The IL23R association supports previous observations of the marked overlap of susceptibility genes for leprosy and Crohns disease, implying common pathogenesis mechanisms.

HLA-B*13:01 and the dapsone hypersensitivity syndrome.

BACKGROUND Dapsone is used in the treatment of infections and inflammatory diseases. The dapsone hypersensitivity syndrome, which is associated with a reported mortality of 9.9%, develops in about 0.5 to 3.6% of persons treated with the drug. Currently, no tests are available to predict the risk of the dapsone hypersensitivity syndrome. METHODS We performed a genomewide association study involving 872 participants who had received dapsone as part of multidrug therapy for leprosy (39 participants with the dapsone hypersensitivity syndrome and 833 controls), using log-additive tests of single-nucleotide polymorphisms (SNPs) and imputed HLA molecules. For a replication analysis, we genotyped 24 SNPs in an additional 31 participants with the dapsone hypersensitivity syndrome and 1089 controls and performed next-generation sequencing for HLA-B and HLA-C typing at four-digit resolution in an independent series of 37 participants with the dapsone hypersensitivity syndrome and 201 controls. RESULTS Genomewide association analysis showed that SNP rs2844573, located between the HLA-B and MICA loci, was significantly associated with the dapsone hypersensitivity syndrome among patients with leprosy (odds ratio, 6.18; P=3.84×10(-13)). HLA-B*13:01 was confirmed to be a risk factor for the dapsone hypersensitivity syndrome (odds ratio, 20.53; P=6.84×10(-25)). The presence of HLA-B*13:01 had a sensitivity of 85.5% and a specificity of 85.7% as a predictor of the dapsone hypersensitivity syndrome, and its absence was associated with a reduction in risk by a factor of 7 (from 1.4% to 0.2%). HLA-B*13:01 is present in about 2 to 20% of Chinese persons, 1.5% of Japanese persons, 1 to 12% of Indians, and 2 to 4% of Southeast Asians but is largely absent in Europeans and Africans. CONCLUSIONS HLA-B*13:01 was associated with the development of the dapsone hypersensitivity syndrome among patients with leprosy. (Funded by the National Natural Science Foundation of China and others.).

Discovery of six new susceptibility loci and analysis of pleiotropic effects in leprosy

Genome-wide association studies (GWAS) have led to the discovery of several susceptibility loci for leprosy with robust evidence, providing biological insight into the role of host genetic factors in mycobacterial infection. However, the identified loci only partially explain disease heritability, and additional genetic risk factors remain to be discovered. We performed a 3-stage GWAS of leprosy in the Chinese population using 8,313 cases and 16,017 controls. Besides confirming all previously published loci, we discovered six new susceptibility loci, and further gene prioritization analysis of these loci implicated BATF3, CCDC88B and CIITA-SOCS1 as new susceptibility genes for leprosy. A systematic evaluation of pleiotropic effects demonstrated a high tendency for leprosy susceptibility loci to show association with autoimmunity and inflammatory diseases. Further analysis suggests that molecular sensing of infection might have a similar pathogenic role across these diseases, whereas immune responses have discordant roles in infectious and inflammatory diseases.

Genome-wide linkage, exome sequencing and functional analyses identify ABCB6 as the pathogenic gene of dyschromatosis universalis hereditaria

Background As a genetic disorder of abnormal pigmentation, the molecular basis of dyschromatosis universalis hereditaria (DUH) had remained unclear until recently when ABCB6 was reported as a causative gene of DUH. Methodology We performed genome-wide linkage scan using Illumina Human 660W-Quad BeadChip and exome sequencing analyses using Agilent SureSelect Human All Exon Kits in a multiplex Chinese DUH family to identify the pathogenic mutations and verified the candidate mutations using Sanger sequencing. Quantitative RT-PCR and Immunohistochemistry was performed to verify the expression of the pathogenic gene, Zebrafish was also used to confirm the functional role of ABCB6 in melanocytes and pigmentation. Results Genome-wide linkage (assuming autosomal dominant inheritance mode) and exome sequencing analyses identified ABCB6 as the disease candidate gene by discovering a coding mutation (c.1358C>T; p.Ala453Val) that co-segregates with the disease phenotype. Further mutation analysis of ABCB6 in four other DUH families and two sporadic cases by Sanger sequencing confirmed the mutation (c.1358C>T; p.Ala453Val) and discovered a second, co-segregating coding mutation (c.964A>C; p.Ser322Lys) in one of the four families. Both mutations were heterozygous in DUH patients and not present in the 1000 Genome Project and dbSNP database as well as 1,516 unrelated Chinese healthy controls. Expression analysis in human skin and mutagenesis interrogation in zebrafish confirmed the functional role of ABCB6 in melanocytes and pigmentation. Given the involvement of ABCB6 mutations in coloboma, we performed ophthalmological examination of the DUH carriers of ABCB6 mutations and found ocular abnormalities in them. Conclusion Our study has advanced our understanding of DUH pathogenesis and revealed the shared pathological mechanism between pigmentary DUH and ocular coloboma.

Investigation of 20 non-HLA (human leucocyte antigen) psoriasis susceptibility loci in Chinese patients with psoriatic arthritis and psoriasis vulgaris.

Background  Recently, a number of non‐HLA (human leucocyte antigen) psoriasis genetic susceptibility loci have been identified through genome‐wide association studies, but data on their association with psoriatic arthritis (PsA) are lacking.

Inferior vestibular neuritis: a novel subtype of vestibular neuritis.

OBJECTIVE To report eight cases of inferior vestibular neuritis, in order to raise awareness of this new subtype of vestibular neuritis. MATERIALS AND METHODS We retrospectively analysed 216 patients (104 males and 112 females; age range 10-64 years; mean age 38.4 years) with full clinical documentation who had attended our hospitals vertigo clinic between May 2007 and December 2008. All patients underwent systematic investigation, including hearing tests, radiology, caloric testing and vestibular evoked myogenic potential testing. RESULTS Of 216 patients with vestibular neuritis, eight cases were diagnosed as inferior vestibular neuritis, based on comprehensive analysis of test data. The clinical features of these eight patients were consistent with the characteristics of vestibular neuritis. The results of pure tone audiometry and caloric testing were normal, and the possibility of central lesions was excluded by cerebral computed tomography or magnetic resonance imaging on admission. Six cases had unilateral loss of vestibular evoked myogenic potentials, whereas two had a unilateral lower amplitude of vestibular evoked myogenic potentials. CONCLUSIONS Inferior vestibular neuritis is a novel subtype of vestibular neuritis, which involves the inferior vestibular nerve alone. Vestibular evoked myogenic potential testing is a useful aid to the diagnosis of inferior vestibular neuritis.

Identification of three novel frameshift mutations of the MVK gene in four Chinese families with disseminated superficial actinic porokeratosis

MADAM, Porokeratosis is a group of hereditary disorders of epidermal keratinization, characterized by keratotic lesions with an atrophic centre and a prominent peripheral ridge, and a typical histological cornoid lamella. There are several clinical subtypes of porokeratosis, including disseminated superficial actinic porokeratosis (DSAP), disseminated superficial porokeratosis (DSP), classic porokeratosis of Mibelli (PM), porokeratosis palmar, plantar and disseminated, and linear porokeratosis (LP), all of which show typical pathological manifestations, i.e. cornoid lamella in the epidermis. Among these, DSAP is the most common clinical subtype of porokeratosis, and has been widely studied to identify the genetic variance. To date, four genetic loci have been mapped to be responsible for DSAP: 12q23.2-24.1 (DSAP1), 15q25.1-26.1 (DSAP2), 1p31.3-p31.1 (DSAP3) and 16q24.1-24.3 (DSAP4). The SSH1 and SART3 genes located in DSAP1 have been identified as the causal genes in two Chinese families, respectively. Recently, Zhang’s group performed exome sequencing in one family with DSAP and identified several mutations of the MVK gene in 33% of familial DSAP and 16% of sporadic cases. In this study, we conducted direct DNA sequencing of MVK, SSH1 and SART3 to investigate the causal variance in 10 families with DSAP and four sporadic cases. All the cases recruited manifested the multiple, small, annular, anhidrotic, keratotic lesions predominantly in sun-exposed areas of the skin (Fig. 1a). The lesions began to develop in adolescence with near complete penetrance by the third to fourth decades of life. Sunlight exposure to ultraviolet radiation can aggravate the lesions. All the clinical and histological characteristics of the cases supported the clinical diagnosis of DSAP. However, in the proband of family 2 and sporadic case 1, in addition to the typical manifestations of DSAP, there were also verrucous plaques in left gluteal region and thigh (Fig. 1b). Informed consent of the patients and approval from the human medical and ethics committee of Shandong Provincial Institute of Dermatology and Venereology were obtained. Genomic DNA was extracted from the peripheral blood of 14 affected individuals and two unaffected individuals from 10 families with DSAP, four sporadic cases and 100 healthy controls. All the exons of the MVK, SSH1 and SART3 genes and their flanking intronic sequences of 200 bp were amplified by polymerase chain reaction. After amplification, products were purified and directly sequenced on an ABI 3130xl Genetic Analyser (Applied Biosystems, Foster City, CA, U.S.A.). In total, three frameshift mutations (c.395delT, c.853insA and c.1057delTGGAGGCCACGAAG) of the MVK gene were identified in two families and two sporadic cases (Table 1; Fig. 2). None of these mutations was found in unaffected family members or the 100 controls.

A large-scale genome-wide association and meta-analysis identified four novel susceptibility loci for leprosy

Leprosy, a chronic infectious disease, results from the uncultivable pathogen Mycobacterium leprae (M. leprae), and usually progresses to peripheral neuropathy and permanent progressive deformity if not treated. Previously published genetic studies have identified 18 gene/loci significantly associated with leprosy at the genome-wide significant level. However as a complex disease, only a small proportion of leprosy risk could be explained by those gene/loci. To further identify more susceptibility gene/loci, we hereby performed a three-stage GWAS comprising 8,156 leprosy patients and 15,610 controls of Chinese ancestry. Four novel loci were identified including rs6807915 on 3p25.2 (P=1.94 × 10−8, OR=0.89), rs4720118 on 7p14.3 (P=3.85 × 10−10, OR=1.16), rs55894533 on 8p23.1 (P=5.07 × 10−11, OR=1.15) and rs10100465 on 8q24.11 (P=2.85 × 10−11, OR=0.85). Altogether, these findings have provided new insight and significantly expanded our understanding of the genetic basis of leprosy.

Mutation analysis of the IL36RN gene in Chinese patients with generalized pustular psoriasis with/without psoriasis vulgaris

BACKGROUND Generalized pustular psoriasis (GPP) is a rare type of psoriasis with potentially life-threatening implications. Mutations in IL36RN gene have been suggested to be causative or predisposing factors for GPP. OBJECTIVE To evaluate the genetic heterogeneity of GPP, PV and GPP alone, GPP with PV. METHODS We performed a sanger sequencing identify IL36RN mutations in 62 Chinese Han patients with sporadic GPP, including 17 GPP without psoriasis vulgaris (PV) (GPP alone) cases vs. 45 GPP with preceding, later or accompanied by PV (GPP with PV) cases; 16 patients with pediatric-onset GPP (PGPP) vs. 46 adult-onset GPP (AGPP). We included 96 healthy controls and 174 sporadic patients with PV. RESUTS We found 2 new variants and 4 known IL36RN variants in 29 GPP patients, 18 individuals carried recessive (homozygous/compound heterozygous) alleles and 11 cases harbored a single heterozygous change. Twelve PV patients and six controls harbored a single heterozygous for three out of the six variants. Significant differences were observed between GPP and PV groups, GPP alone and GPP with PV groups when compared frequencies of IL36RN variants, but we did not found association between PGPP and AGPP groups. CONCLUSION Our study provided more evidence that GPP and PV are distinct subtypes of psoriasis caused by different pathogenesis, and GPP alone could be regarded as an especial entities of GPP which is different from GPP with PV on the etiology.