X-chromosome association study reveals genetic susceptibility loci of nasopharyngeal carcinoma

Background

The male predominance in the incidence of nasopharyngeal carcinoma (NPC) suggests the contribution of the X chromosome to the susceptibility of NPC. However, no X-linked susceptibility loci have been examined by genome-wide association studies (GWASs) for NPC by far.

Methods

To understand the contribution of the X chromosome in NPC susceptibility, we conducted an X chromosome-wide association analysis on 1615 NPC patients and 1025 healthy controls of Guangdong Chinese, followed by two validation analyses in Taiwan Chinese (n = 562) and Malaysian Chinese (n = 716).

Results

Firstly, the proportion of variance of X-linked loci over phenotypic variance was estimated in the discovery samples, which revealed that the phenotypic variance explained by X chromosome polymorphisms was estimated to be 12.63% (non-dosage compensation model) in males, as compared with 0.0001% in females. This suggested that the contribution of X chromosome to the genetic variance of NPC should not be neglected. Secondly, association analysis revealed that rs5927056 in DMD gene achieved X chromosome-wide association significance in the discovery sample (OR = 0.81, 95% CI 0.73–0.89, P = 1.49 × 10⁻⁵). Combined analysis revealed rs5927056 for DMD gene with suggestive significance (P = 9.44 × 10⁻⁵). Moreover, the female-specific association of rs5933886 in ARHGAP6 gene (OR = 0.62, 95%CI: 0.47–0.81, P = 4.37 × 10⁻⁴) was successfully replicated in Taiwan Chinese (P = 1.64 × 10⁻²). rs5933886 also showed nominally significant gender × SNP interaction in both Guangdong (P = 6.25 × 10⁻⁴) and Taiwan datasets (P = 2.99 × 10⁻²).

Conclusion

Our finding reveals new susceptibility loci at the X chromosome conferring risk of NPC and supports the value of including the X chromosome in large-scale association studies.

Electronic supplementary material

The online version of this article (10.1186/s13293-019-0227-9) contains supplementary material, which is available to authorized users.

SNP variants associated with non-Hodgkin lymphoma (NHL) correlate with human leukocyte antigen (HLA) class II expression

Large consortia efforts and genome-wide association studies (GWASs) have linked a number of genetic variants within the 6p21 chromosomal region to non-Hodgkin lymphoma (NHL). Complementing these efforts, we genotyped previously reported SNPs in the human leukocyte antigen (HLA) class I (rs6457327) and class II (rs9271100, rs2647012 and rs10484561) regions in a total of 1,145 subjects (567 NHL cases and 578 healthy controls) from two major ethnic groups in Malaysia, the Malays and the Chinese. We identified a NHL-associated (P_{NHL_add} = 0.0008; OR_{NHL_add} = 0.54; 95% CI = 0.37–0.77) and B-cell associated (P_{Bcell_add} = 0.0007; OR_{Bcell_add} = 0.51; 95% CI = 0.35–0.76) SNP rs2647012 in the Malaysian Malays. In silico cis-eQTL analysis of rs2647012 suggests potential regulatory function of nearby HLA class II molecules. Minor allele rs2647012-T is linked to higher expression of HLA-DQB1, rendering a protective effect to NHL risk. Our findings suggest that the HLA class II region plays an important role in NHL etiology.

Integrated pathway analysis of nasopharyngeal carcinoma implicates the axonemal dynein complex in the Malaysian cohort

Nasopharyngeal carcinoma (NPC) is an epithelial squamous cell carcinoma on the mucosal lining of the nasopharynx. The etiology of NPC remains elusive despite many reported studies. Most studies employ a single platform approach, neglecting the cumulative influence of both the genome and transcriptome toward NPC development. We aim to employ an integrated pathway approach to identify dysregulated pathways linked to NPC. Our approach combines imputation NPC GWAS data from a Malaysian cohort as well as published expression data GSE12452 from both NPC and non-NPC nasopharynx tissues. Pathway association for GWAS data was performed using MAGENTA while for expression data, GSA-SNP was used with gene p values derived from differential expression values from GEO2R. Our study identified NPC association in the gene ontology (GO) axonemal dynein complex pathway (pGWAS-GSEA  = 1.98 × 10(-2) ; pExpr-GSEA  = 1.27 × 10(-24) ; pBonf-Combined  = 4.15 × 10(-21) ). This association was replicated in a separate cohort using gene expression data from NPC and non-NPC nasopharynx tissues (pAmpliSeq-GSEA  = 6.56 × 10(-4) ). Loss of function in the axonemal dynein complex causes impaired cilia function, leading to poor mucociliary clearance and subsequently upper or lower respiratory tract infection, the former of which includes the nasopharynx. Our approach illustrates the potential use of integrated pathway analysis in detecting gene sets involved in the development of NPC in the Malaysian cohort.

A GWAS Meta-analysis and Replication Study Identifies a Novel Locus within CLPTM1L/TERT Associated with Nasopharyngeal Carcinoma in Individuals of Chinese Ancestry

BACKGROUND

Genetic loci within the major histocompatibility complex (MHC) have been associated with nasopharyngeal carcinoma (NPC), an Epstein-Barr virus (EBV)-associated cancer, in several GWAS. Results outside this region have varied.

METHODS

We conducted a meta-analysis of four NPC GWAS among Chinese individuals (2,152 cases; 3,740 controls). Forty-three noteworthy findings outside the MHC region were identified and targeted for replication in a pooled analysis of four independent case-control studies across three regions in Asia (4,716 cases; 5,379 controls). A meta-analysis that combined results from the initial GWA and replication studies was performed.

RESULTS

In the combined meta-analysis, rs31489, located within the CLPTM1L/TERT region on chromosome 5p15.33, was strongly associated with NPC (OR = 0.81; P value 6.3 × 10(-13)). Our results also provide support for associations reported from published NPC GWAS-rs6774494 (P = 1.5 × 10(-12); located in the MECOM gene region), rs9510787 (P = 5.0 × 10(-10); located in the TNFRSF19 gene region), and rs1412829/rs4977756/rs1063192 (P = 2.8 × 10(-8), P = 7.0 × 10(-7), and P = 8.4 × 10(-7), respectively; located in the CDKN2A/B gene region).

CONCLUSIONS

We have identified a novel association between genetic variation in the CLPTM1L/TERT region and NPC. Supporting our finding, rs31489 and other SNPs in this region have been reported to be associated with multiple cancer sites, candidate-based studies have reported associations between polymorphisms in this region and NPC, the TERT gene has been shown to be important for telomere maintenance and has been reported to be overexpressed in NPC, and an EBV protein expressed in NPC (LMP1) has been reported to modulate TERT expression/telomerase activity.

IMPACT

Our finding suggests that factors involved in telomere length maintenance are involved in NPC pathogenesis.

HLA-A SNPs and amino acid variants are associated with nasopharyngeal carcinoma in Malaysian Chinese

Nasopharyngeal carcinoma (NPC) arises from the mucosal epithelium of the nasopharynx and is constantly associated with Epstein-Barr virus type 1 (EBV-1) infection. We carried out a genome-wide association study (GWAS) of 575,247 autosomal SNPs in 184 NPC patients and 236 healthy controls of Malaysian Chinese ethnicity. Potential association signals were replicated in a separate cohort of 260 NPC patients and 245 healthy controls. We confirmed the association of HLA-A to NPC with the strongest signal detected in rs3869062 (p = 1.73 × 10(-9)). HLA-A fine mapping revealed associations in the amino acid variants as well as its corresponding SNPs in the antigen peptide binding groove (p(HLA-A-aa-site-99) = 3.79 × 10(-8), p(rs1136697) = 3.79 × 10(-8)) and T-cell receptor binding site (p(HLA-A-aa-site-145) = 1.41 × 10(-4), p(rs1059520) = 1.41 × 10(-4)) of the HLA-A. We also detected strong association signals in the 5'-UTR region with predicted active promoter states (p(rs41545520) = 7.91 × 10(-8)). SNP rs41545520 is a potential binding site for repressor ATF3, with increased binding affinity for rs41545520-G correlated with reduced HLA-A expression. Multivariate logistic regression diminished the effects of HLA-A amino acid variants and SNPs, indicating a correlation with the effects of HLA-A*11:01, and to a lesser extent HLA-A*02:07. We report the strong genetic influence of HLA-A on NPC susceptibility in the Malaysian Chinese.

Analysis of interleukin-10 promoter single nucleotide polymorphisms and risk of non-Hodgkin lymphoma in a Malaysian population

We evaluated the association of two IL10 single nucleotide polymorphisms (SNPs) (rs1800896 and rs1800871) with non-Hodgkin lymphoma (NHL) risk in the three major races of the Malaysian population (Malay, Chinese and Indian; 317 cases and 330 controls). Our initial screening demonstrated that rs1800871 but not rs1800896 was significantly associated with increased NHL risk in Malays (pMalay-Rec = 0.007) and Chinese only (pChinese-Rec = 0.039). Subsequent combined analysis of the Malay and Chinese revealed significant association of rs1800871 with all (ALL) NHL subtypes (pMeta-ALL-NHL-Rec = 0.001), ALL B-cell subtypes (pMeta-ALL-B-cell-Rec = 0.003), diffuse large B-cell lymphoma (DLBCL) subtype (pMeta-DLBCL-Rec = 0.002) and ALL T-cell subtypes (pMeta-ALL-T-cell-Rec = 0.031). SNP rs1800896 showed increased risk only in follicular lymphoma (FL) (pMeta-FL-Dom = 0.0004). We also detected a male-specific association of rs1800871 with increased NHL risk (pMeta-Male-ALL-NHL-Rec = 0.006) in the combined analysis. To our knowledge, this is the first report on the association of IL10 promoter SNPs with NHL susceptibility in the three major races of Malaysia.

Significant impact of gene polymorphisms on tacrolimus but not cyclosporine dosing in Asian renal transplant recipients

Calcineurin inhibitors (CNI) are metabolized by cytochrome-P4503A (CYP3A) enzymes and extruded into the intestinal lumen by the drug efflux pump, P-glycoprotein (P-gp). The impact of single nucleotide polymorphisms (SNPs) of genes encoding CYP3A5 and P-gp on CNI dosing was examined among Asian renal transplant recipients. Frequencies of CYP3A5*1 versus *3 and MDR1-C3435T were correlated with tacrolimus (TAC) and cyclosporine (CSA) concentration-to-dose (C/D) ratios. Among 82 recipients (49% male; 88% Chinese), the majority were CYP3A5 expressors (*1*1 and *1*3, 11% and 40%, respectively) and 49% were nonexpressors (*3/*3). The prevalence of MDR-1-C3435T variants was 3435CC (41%), 3435CT (46%), and 3435TT (13%). Among 18 TAC-treated recipients, all receiving Diltiazem (DTZ), the median C/D ratio was lower for CYP3A5 *1/*1 versus *1/*3 versus *3/*3 (1.9, 4.6, and 13.5 ng/mL per 0.1 mg/kg/d, respectively; P = .001). The median C/D ratio was higher for TAC-treated patients with MDR-1-3435CC (14.1, 7.3, and 2.2 ng/mL per 0.1 mg/kg/d for CC, CT, and TT, respectively; P = .023). Neither CYP3A5 nor MDR-1-C3435T variants had an impact on CSA C/D ratios. Thus, CYP3A5 SNP has a significant impact on TAC dosing in Asian renal transplant recipients, which was likely to facilitate TAC metabolism. Although MDR-1-3435CC with higher P-gp expression should experience more TAC efflux and, therefore, lower TAC C/D ratios, all MDR-1-3435CC carriers were CYP3A5 nonexpressors; the latter ultimately contributed to the observed higher TAC C/D ratios in this population. This study advocates starting with a higher TAC dose for CYP3A5 expressors. Coadministration of DTZ may further optimize the TAC level through preferential P-gp binding and CYP3A4 inhibition.

Clinical features and treatment outcome of children with myeloid antigen coexpression in B-lineage acute lymphoblastic leukemia: a study of 151 Malaysian children

The purpose of the study was to evaluate the incidence of myeloid antigen coexpression and its prognostic significance in childhood acute lymphoblastic leukemia (ALL) in Malaysia. A retrospective study was conducted of all ALL cases (< or = 12 years old) diagnosed and treated in University Hospital, Kuala Lumpur, Malaysia between 1 January 1992 and 30 May 1995, with available immunophenotype data. Presenting features and treatment outcome of 39 B-lineage ALL patients with myeloid antigen coexpression (My+B) were compared with 112 B-lineage ALL patients without myeloid antigen coexpression (My-B) for similarity in demographic, clinical and laboratory features and their treatment outcome. My+B and My-B patients were treated with a uniform treatment protocol. Myeloid antigen coexpression was defined as more than 30% isolated leukemic cells positive for CD13 and/or CD33. The ages at diagnoses ranged from 2 months to 12 years. Median age was 4 years. The incidence of myeloid antigen coexpression was 23 per cent. Univariate analyses showed that presenting features were similar between My+B and My-B with regard to age, sex, race, FAB morphology, white cell count, hemoglobin level, platelet count, liver/spleen size, central nervous system or mediastinal involvement, presence of lymphadenopathy, and proportion of blast cells detected in the marrow. Treatment outcome were not significant between the two groups. The 2-year event free survival was achieved in 44 per cent of My+B and 57 per cent of My-B (p = 0.11). The 2-year overall survival rates were 62 per cent for My+B vs. 77 per cent for My-B (p = 0.08). This study demonstrates that myeloid antigen coexpression is fairly common and constitutes 23 per cent of childhood ALL within the Malaysian population and that it is not an adverse risk factor in childhood ALL.

The changing pattern of glomerulonephritis in Singapore over the past two decades

This study reviews the pattern of glomerulonephritis (GN) in Singapore over the past 2 decades. In the earlier decade the pattern was typical of most Asian countries with mesangial proliferative GN (Mes GN) (56%) as the most common form of primary GN including the nephrotic syndrome (40%). In the 2nd decade the pattern undergoes a change. Though Mes GN is the commonest primary GN (42%), the commonest form of nephrotic syndrome is now minimal change disease (30%) with Mes GN decreasing to 25% among all primary nephrotic syndromes. Both minimal change and focal global sclerosis account for 50% of steroid/cyclophosphamide responsive GN today. Membranous GN though still uncommon, has increased from 3% (1st decade) to 6% (2nd decade) (p < 0.01). IgA nephritis is still the commonest primary GN occurring in Singapore (42% of all primary GN in the 1st decade and 45% in the 2nd decade). The present pattern of GN in Singapore, though, still predominantly Asian with the preponderance of mesangial proliferative GN with a relatively low incidence of membranous GN contrasts with the pattern in the West where membranous GN is the commonest form of primary GN. Even the incidence of FSGS has not increased as in the West where there is a rising incidence. The underlying basis for most GN in Singapore as in other Asian countries and elsewhere is antigen-driven: infective antigen as well as food or other allergens.

Concordant childhood acute lymphoblastic leukemia in monozygotic twins

Two 4-year-old monozygotic Chinese, female twins developed concordant childhood acute lymphoblastic leukemia (ALL) within an interval of about 2 weeks. Based on morphology and cytochemistry findings of the bone marrow blast cells, a diagnosis of ALL, L1 was made. Immunophenotyping showed the blast cells of both twins expressed similar antigens, i.e. HLA-DR, CD10, CD13, CD19, CD22 and CD34. Identical blood group, same HLA (human leucocyte antigen) genotype, sex and similar appearance suggest that the twins are monozygotic. Since the bone marrow leukemic cells of both twins were identical in morphology and expressed the same antigens with almost similar percentages of positivity, it is likely that the blast cells were derived from the same single clone. Based on the single clone hypothesis, the leukemogenic event must have arisen in utero in one twin and the cells from the abnormal clone then spread to the other twin via shared placental anastomoses.

Isoelectric focusing and selectivity index in IgA nephrotic syndrome

Proteinuria in 13 patients with IgA nephritis with nephrotic syndrome (IgANS) was analysed by isoelectric focusing (IEF) and compared with 12 patients with minimal change nephrotic syndrome (MCNS) (n = 8) or focal global sclerosis nephrotic syndrome (FGS) (n = 4) to determine the pattern of proteinuria on IEF and to assess the value of IEF and protein selectivity index (SI) as predictors of response to therapy with predisolone or cyclophosphamide. Steroid/cyclophosphamide responsive patients with IgANS had SC:UA (cationic serum albumin with anionic urine albumin) or SA:UC (anionic serum albumin with cationic urine albumin) IEF patterns and steroid/cyclophosphamide unresponsive patients with IgANS had an SC:UC (cationic serum albumin with cationic urine albumin) IEF pattern. The majority of patients with MCNS or FGS who had an SA:UC IEF pattern were steroid responsive. SI was a better predictor of steroid/cyclophosphamide responsiveness in patients with IgANS (r = 0.78, p < 0.002 compared to IEF, r = 0.64, p < 0.02).

The impact of percutaneous renal biopsies on clinical management

Percutaneous renal biopsy (PRB) is now standard practice in clinical nephrology. One hundred consecutive non-transplant PRBs performed on adult patients at the Department of Renal Medicine, Singapore General Hospital, between January and August 1990, were analysed to examine the impact and complications of PRBs in a single institution. The study population consisted of 37 male and 63 female patients with a mean age of 32 +/- 11.9 years. The most frequent indications for PRB were systemic lupus erythematosus with renal involvement (41 patients), haematuria and proteinuria (27 patients) and the nephrotic syndrome (26 patients). Histological diagnoses included lupus nephritis in 45 patients, IgA nephritis in 19 patients, minimal change/focal global sclerosis in 14, non-IgA mesangioproliferative glomerulonephritis in seven and other histologies in the remainder. Eighty-two of our patients received renal-specific therapy, including 72 who received prednisolone or other immunosuppression, and 11 who received persantin and warfarin, in contrast to only 18 patients who received non-specific therapy including diuretics, antihypertensive drugs or dialysis. PRB led to change in therapy in 54% of all our patients, including 42 who had immunosuppressive drugs added to their therapeutic regimen and 11 who were commenced on persantin and/or warfarin. Complications of the procedure were minimal with flank pain in 6% and gross haematuria in 4%. As the inherent risks of inappropriate immunosuppression are well established, these results suggest that PRBs have a major impact on clinical management.

Breakpoint cluster region (BCR) gene rearrangement studies in chronic myeloid and acute lymphoblastic leukemias

Deoxyribonucleic acid (DNA) of twenty chronic myeloid leukemia (CML) and thirty acute lymphoblastic leukemia (ALL) patients were analysed by Southern hybridization. The DNA was digested with BglII and hybridized with a 4.5-kilobase (kb) ph1/bcr-3 DNA probe. All the 20 CML patients showed gene rearrangement within a 5.8-kb segment (the major breakpoint cluster region, M-bcr) of the breakpoint cluster region (bcr) gene of chromosome 22, indicating the presence of the Philadelphia chromosome. M-bcr rearrangement at the bcr gene of chromosome twenty-two was not detected in all the thirty ALL patients (nine adults and twenty-one children) and two normal controls.

Biphenotypic hybrid acute leukaemia detected by two colour flow cytometry

Immunophenotypic studies using immunofluorescent flow cytometry were performed on the blast cells of 36 patients with acute leukaemia using a panel of eight monoclonal antibodies. Six patients had blasts which co-expressed markers for lymphoid and myeloid differentiation, and which were therefore defined as biphenotypic hybrid acute leukaemia. Of the six, three patients were in the paediatric age group (below 12 years old) while the other three were more than 12 years old. Peripheral blood counts were variable; however, bone marrow infiltration was extensive (blasts > or = 75% in all). At the time of study, remission was achieved in only two patients. The authors' data show that biphenotypic hybrid acute leukaemia is not rare in Malaysia. This represents a subgroup of acute leukaemia identifiable by immunophenotyping but not by the French-American-British classification based on morphological and basic cytochemical studies alone. The recognition of this subgroup is important for both practical and theoretical reasons. There are implications for treatment of the individual patient because treatment directed at a single lineage may not be effective. The two colour flow cytometry proved to be a useful tool for diagnosis and classification of acute leukaemia.

Analysis of ras gene mutations in acute myeloid leukemia by the polymerase chain reaction and oligonucleotide probes

In vitro deoxyribonucleic acid (DNA) amplification by the polymerase chain reaction (PCR) followed by hybridization with oligonucleotide probes were used to study ras gene mutations in acute myeloid leukemia (AML). The DNA of 30 AML patients at presentation of the disease at the University of Malaya Hospital, Kuala Lumpur were screened for ras gene mutations in codons 12, 13 and 61 of the N-ras, K-ras and H-ras genes. Four patients (13.3%) had ras gene mutations. They were all below their early thirties in age. Of the four patients with ras gene mutations, three were M3 and one was M4 according to the French American British (FAB) classification of AML.

Cytogenetic studies in women with primary amenorrhea

Cytogenetic investigations were carried out on 117 women with primary amenorrhea who had been referred to our Genetics Laboratory by clinicians throughout Malaysia, after exclusion of other causes of the disorder. Thirty-six cases (31%) showed numerical or structural abnormalities of the sex chromosomes. These can be broadly classified into 4 main types, namely, presence of a Y chromosome (14%), X-chromosome aneuploidies (8%), structural anomalies of the X-chromosome (7%) and lastly, presence of a marker chromosome (2%). Mosaics constituted 17% of the abnormalities observed, always in association with a 45,X cell line. There was no observable correlation between the phenotype of the patients and their respective abnormal karyotypes. The aetiological role of sex chromosomal abnormalities in these amenorrheic women is discussed.

Three cases of partial trisomy 9q in one generation due to maternal reciprocal t(6;8;9) translocation

A family is described in which three siblings had congenital abnormalities consistent with partial trisomy 9q syndrome. Karyotyping indicated that the mother was a carrier of two separate balanced reciprocal translocations involving three chromosomes (46,XX,t (6;8;9)(6q27;8p23;9q32;9q13] resulting from four breakpoints. The three siblings had inherited the der(8) from their mother and hence were partially trisomic for 9q32----9qter and partially monosomic for 8p23----8pter (46,XX,der(8),t(8;9)(p23;q32)mat). The clinical features of the three cases were comparable to those reported in the literature.