Resequencing Study Confirms That Host Defense and Cell Senescence Gene Variants Contribute to the Risk of Idiopathic Pulmonary Fibrosis

Rationale: Several common and rare genetic variants have been associated with idiopathic pulmonary fibrosis, a progressive fibrotic condition that is localized to the lung. Objectives: To develop an integrated understanding of the rare and common variants located in multiple loci that have been reported to contribute to the risk of disease. Methods: We performed deep targeted resequencing (3.69 Mb of DNA) in cases (n = 3,624) and control subjects (n = 4,442) across genes and regions previously associated with disease. We tested for associations between disease and 1) individual common variants via logistic regression and 2) groups of rare variants via sequence kernel association tests. Measurements and Main Results: Statistically significant common variant association signals occurred in all 10 of the regions chosen based on genome-wide association studies. The strongest risk variant is the MUC5B promoter variant rs35705950, with an odds ratio of 5.45 (95% confidence interval, 4.91-6.06) for one copy of the risk allele and 18.68 (95% confidence interval, 13.34-26.17) for two copies of the risk allele (P = 9.60 × 10-295). In addition to identifying for the first time that rare variation in FAM13A is associated with disease, we confirmed the role of rare variation in the TERT and RTEL1 gene regions in the risk of IPF, and found that the FAM13A and TERT regions have independent common and rare variant signals. Conclusions: A limited number of common and rare variants contribute to the risk of idiopathic pulmonary fibrosis in each of the resequencing regions, and these genetic variants focus on biological mechanisms of host defense and cell senescence.

Efficacy and safety of the Ahmed glaucoma valve implant in Chinese eyes with complicated glaucoma

AIMS

To evaluate the efficacy and safety of the Ahmed glaucoma valve implant in Chinese eyes with complicated glaucomas.

METHODS

This retrospective study reviewed the final intraocular pressure, visual outcome, and incidence of complications in all patients with the Ahmed glaucoma valve implant performed at the Prince of Wales Hospital, Hong Kong, between June 1996 and November 1998.

RESULTS

A total of 65 eyes from 60 patients were treated with the Ahmed glaucoma implant. At a mean follow up (SD, median) of 21.8 (9.2, 28. 0) months (range 6-37 months), the mean intraocular pressure was reduced from 37.0 (SD 12.1) mm Hg before the implant surgery to 16.1 (12.4) mm Hg at the last follow up after surgery. The success rate of intraocular pressure control of <22 mm Hg was achieved in 73.8% of operated eyes. Transient postoperative hypotony with shallow anterior chamber occurred in 10.8% of cases. The most common postoperative complication was the formation of encapsulated bleb (24.6%).

CONCLUSIONS

The Ahmed glaucoma valve implant appears to be effective and relatively safe for treating complicated glaucomas in Chinese eyes. The success rate is comparable with those reported in non-Asian eyes. Formation of postoperative encapsulated bleb is, however, more commonly encountered.

Inferior limbal-conjunctival autograft transplantation for recurrent pterygium

PURPOSE

To study the safety and efficacy of inferior limbal-conjunctival autograft (LCAT) transplantation in the surgical management of recurrent pterygium.

METHODS

Prospective non-comparative case series. Inferior limbal-conjunctival autografting was performed on 11 patients (11 eyes) with recurrent pterygium. Pterygium recurrence was considered a surgical failure.

RESULTS

Recurrence of pterygium was noted in two (18.2%) eyes, after a mean follow up of 16.2 +/- 0.9 months (range: 10-19 months). Neither recurrence required further surgical treatment. Nonprogressive pseudopterygium formation was noted at the donor site in five (45.5%) eyes.

CONCLUSION

Inferior LCAT appears to be a safe and effective option in the management of recurrent pterygium. In patients with suspected or proven glaucoma, this may be the procedure of choice, if mitomycin C is contraindicated.

Association of IgA nephropathy with T-cell receptor constant alpha chain gene polymorphism

T-cell receptor (TCR) proteins recognize a complex of an antigen-derived peptide bound to the cell surface products of the major histocompatibility complex (MHC) that could be of importance in the immunopathogenesis of IgA nephropathy (IgAN). Previous studies found no difference on TCR constant beta chain gene frequencies in IgAN compared with control. Yet no study on the TCR alpha gene in IgAN was reported. We studied the TCR C alpha gene polymorphisms by restriction fragment length polymorphism (RFLP) in 53 patients with IgAN and in comparison with 67 healthy controls. The patients were also classified into different histopathological grading (I, II, and III with increasing histological severity) and renal functions. The extracted DNA were digested with Taq I enzymes and probed with a full-length TCR-alpha cDNA clone p1.2alpha probe. A 7-kb C-alpha Taq 1 fragment is found in 32 of 53 patients (60.3%) compared with 26 of 67 controls (38.8%) (P < 0.05). There was no association of any polymorphic fragment, including the 7-kb fragment, with either the histological grading or renal function. It is concluded that the TCR C-alpha gene is associated with IgAN but not with the prognosis of the disease.

Molecular genetics of major histocompatibility complex class II genes in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is the most common malignant tumor of the liver with a possible genetic predisposition. We have studied the HLA-DQ and -DR regions of 57 unrelated HCC patients of southern Chinese origin using molecular DNA techniques and compared them with 104 normal controls. Seventy-six hepatitis B carriers (HBsAg) were also studied. Restriction fragment length polymorphism (RFLP) was used to genotype the MHC class II DR beta, DQ alpha and DQ beta loci of the subjects. Polymerase chain reaction (PCR) using sequence primer for DQ beta genes was also performed. No significant difference was found in the HLA-DQ and -DR loci between HCC patients and normal controls, HCC patients and HBsAg carriers, or HBsAg carriers and normal controls respectively. Forty-one HCC patients were HBsAg positive, and no difference was found in the HLA-DQ and -DR genotype between this group of patients compared with the group of normal controls or HBsAg carriers. Thirty-six HCC patients had elevated alpha-fetoprotein levels, and 15 HCC patients had normal levels. No difference in the HLA-DQ and -DR loci was detected between these two groups and the controls. The results suggest that HLA-DQ and -DR genotypes are not associated with hepatocellular carcinoma in southern Chinese.

Use of cultured permanent lines of intestinal epithelial cells for the assay of okadaic acid in mussel homogenates

Two non-transformed intestinal epithelial cell lines (RIE-1 and IEC-6) and three intestinal carcinoma cell lines (HT-29, T84 and MCA-38) were used to detect the toxic effects due to okadaic acid in the presence of mussel tissue homogenates. Cytotoxicity was assessed by measurement of the metabolic conversion of 3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyl tetrazolium bromide to its corresponding formazan dye. All of the cell lines were sensitive to okadaic acid, with HT-29, RIE-1 and IEC-6 showing the greatest response. Dilutions of whole mussel tissue homogenates caused some loss of viability in most of the cell lines but had no significant effect on the viability of RIE-1 cells. In no case did the mussel homogenate compromise the dose-response curve to okadaic acid when data were normalized to the appropriate control value. These intestinal epithelial cell lines may prove useful in the bioassay of okadaic acid and related toxins.

No association between HLA-DQ and -DR genotypes with nasopharyngeal carcinoma in southern Chinese

The pathogenesis of nasopharyngeal carcinoma (NPC) is multifactorial. Associations have been reported between HLA and NPC. We studied the HLA-DR and -DQ regions on the molecular level in 136 persons (51 NPC patients and 85 healthy controls) from southern China, a particularly high-prevalence area for NPC. Restriction fragment-length polymorphism (RFLP) was used to genotype the MHC class II DR beta, DQ alpha, and DQ beta regions of the subjects. Polymerase chain reaction (PCR) using sequence-specific primer (SSP) for DQ beta genes was also performed. By RFLP, no significant difference was observed with respect to DRB, DQA, and DQB genes. By PCR SSP typing, we confirmed that there was no significant difference between NPC patients and controls with respect to DQ beta alleles. Our study suggests that HLA-DQ and -DR genes are not associated with NPC in southern Chinese and there may be other gene loci that predispose them to have such a high prevalence of the disease.

Lack of association between HLA-DQ and -DR genotypes and asthma in southern Chinese patients

Asthma is an inflammatory disease with a strong genetic predisposition. We have studied a group of unrelated asthmatic patients of southern Chinese origin on their HLA-DR and -DQ regions using molecular techniques and compared them with 104 healthy controls of the same ethnic origin. Restriction fragment length polymorphism (RFLP) was used to genotype the MHC class II DR beta, DQ alpha and DQ beta loci of the subjects. Polymerase chain reaction (PCR) using sequence specific primer (SSP) for DQ beta genes was also performed. No significant difference was found in the HLA-DQ and -DR loci between the patients and the controls. All patients had their serum IgE antibody levels measured, bronchial reactivity assessed by histamine broncho-provocation and cutaneous reactivity to common allergens determined by skin-prick tests to Dermatophagoides pteronyssinus, Dermatophagoides farinae, mixed grass pollens, Aspergillus fumigatus, cat fur and dog dander and they were classified respectively. The HLA-DR and -DQ genotypes of these subgroups of patients were compared. There was no significant difference among these subgroups of patients according to their serum IgE levels, the degree of bronchial reactivity and whether they were positive for the skin tests for the various allergens respectively. The results suggest that HLA-DQ and -DR genotypes are not associated with asthma in southern Chinese people.

Molecular genetics of MHC class II alleles in Chinese patients with IgA nephropathy

We have studied the restriction fragment length polymorphism (RFLP) of the major histocompatibility complex (MHC) class II DQ and DR regions of 79 Chinese patients with IgA nephropathy (IgAN) and compared it with 104 normal Chinese controls. The DR and DQ alleles were confirmed by polymerase chain reaction using sequence specific primers. There was a significantly higher frequency of homozygous DQ beta 3b (DQ7) in patients with IgAN (16.4%) compared with controls (5.7%). Seventy-one IgAN patients had their renal biopsies graded according to histopathological severity: grades I, II or III. There was no statistical difference in the DR and DQ alleles among the three grades. Seventy-three patients were classified into group A with normal and stable renal function (serum creatinine < or = 150 mumol/liter) and group B with chronic renal failure (serum creatinine > 150 mumol/liter). There was a significant increase in frequency of DQA2 U (DX alpha U) allele in group B (66.9%) compared with group A (26.9%). Also, there was an increased frequency of DQ alpha 2 allele in the group A (40.4%) compared with group B (14.3%). Out of the 24 patients carrying the DQ alpha 2 allele, 17 were DQA2 U allele-negative and they all had normal renal function, suggesting that DQA2 U allele is associated with a poor prognostic factor in IgAN. The study shows that DQ alleles are probably the important genetic loci or are close markers for the disease susceptibility and prognostic index for IgAN in Chinese people.

Charge distribution of IgA-lambda in IgA nephropathy

The finding that eluted mesangial IgA and serum IgA from patients with IgA nephropathy had a restricted anionic charge contrasting with normal serum IgA prompted us to study the charge of the kappa and lambda subclasses of IgA. Serum IgA from 11 patients with IgA nephropathy and 11 controls was purified by affinity chromatography by binding to jacalin. The charges of IgA were studied by a novel method. The spectrotype of total IgA was first studied by isoelectric focusing and immunoblotting. IgA lambda and IgA kappa was further analyzed by reacting with specific monoclonal antibodies. The amount of IgA with different pIs was analyzed by computerized densitometry. The anionic:cationic (A:C) ratio of IgA using pI 5.6 as the dividing point was greater in patients (at clinical quiescence and during exacerbation) than in controls (1.67 +/- 0.31 versus 1.36 +/- 0.27, p < 0.025). IgA lambda in both groups was anionic (A:C ratio 2.22 +/- 0.77 versus 2.36 +/- 0.36) and IgA kappa was cationic (A:C ratio 1.15 +/- 0.36 versus 1.04 +/- 0.39) but no difference in the A:C ratio was demonstrated. The increased A:C ratio in total IgA in patients was due to raised serum IgA lambda (kappa/lambda ratio 1.11 +/- 0.14 in patients and 1.51 +/- 0.16 in controls, p < 0.01). We had previously shown a predominant mesangial deposition of IgA lambda in IgA nephropathy. Animal experiments have revealed the preferential mesangial deposition of immune complexes is related to their anionic charges. Our data of raised anionic IgA lambda in IgA nephropathy may be important in determining its selective mesangial binding that could contribute to the immunopathogenesis.

Restriction fragment length polymorphism of HLA-DQ and -DR allogenotypes in normal southern Chinese

We have examined the Taq I restriction fragment length polymorphism (RFLP) of the MHC class II regions of 96 normal Southern Chinese with respect to the HLA-DRB, -DQA, and -DQB genes. The data were compared with the DR and DQ serotyping. RFLP correlates well with the serological typing of the DR types of Chinese. Variants are seen in DR2 and DR12. The variant in DR12 with a 10 kb at the upper band (DR12b) is not found in Caucasoids and is more frequent in Chinese (19.4% of the alleles). With the help of DQA and DQB RFLP the assignment of genotyping of DRB types is facilitated. Some of the linkage disequilibrium patterns among DRB, DQA and DQB are different from Caucasoids. This is particularly obvious in the DR2 and DR5 haplotypes. In the 96 Southern Chinese, the 3 commonest haplotype frequencies are: DR12b, DQ alpha 1b, DQ beta 3b (18.3%); DR9, DQ alpha 3, DQ beta 3a (15.7%); DR4, DQ alpha 3, DQ beta 3a (14.2%). The various DR beta, DQ alpha. DQ beta genes can be accurately defined in Chinese by RFLP. Polymerase chain reactions using sequence-specific primers were performed to confirm the various HLA-DRB and -DQB alleles. The use of RFLP is important in the study of HLA matching and HLA-disease association in Southern Chinese.