Zhenwu Lin

Novel, Non-Radioactive, Simple and Multiplex PCR-cRFLP Methods for Genotyping Human SP-A and SP-D Marker Alleles

We have previously identified an allele of the human SP-A2 gene that occurs with greater frequency in an RDS population [12]. Because of the importance of SP-A in normal lung function and its newly emerging role in innate host defense and regu-lation of inflammatory processes, we wish to better characterize genotypes of both SP-A1 and SP-A2 genes. It has been determined that SP-D shares similar roles in immune response. Therefore, in this report we 1) describe a novel, non radioactive PCR based-cRFLP method for genotyping both SP-A and SP-D; 2) describe two previously unpublished biallelic polymorphisms within the SP-D gene; 3) present the partial sequence of one new SP-A1 allele (6A14) and describe other new SP-A1 and SP-A2 alleles; and 4) describe additional methodologies for SP-A genotype assessment. The ability to more accurately and efficiently genotype samples from individuals with various pulmonary diseases will facilitate population and family based association studies. Genetic poly-morphisms may be identified that partially explain individual disease susceptibility and/or treatment effectiveness.

Surfactant protein A, an innate immune factor, is expressed in the vaginal mucosa and is present in vaginal lavage fluid

Surfactant protein A (SP‐A), first identified as a component of the lung surfactant system, is now recognized to be an important contributor to host defence mechanisms. SP‐A can facilitate phagocytosis by opsonizing bacteria, fungi and viruses, stimulate the oxidative burst by phagocytes and modulate pro‐inflammatory cytokine production by phagocytic cells. SP‐A can also provide a link between innate and adaptive immune responses by promoting differentiation and chemotaxis of dendritic cells. Because of the obvious relevance of these mechanisms to the host defence and ‘gate keeping’ functions of the lower genital tract, we examined human vaginal mucosa for SP‐A protein and transcripts and analysed vaginal lavage fluid for SP‐A. By immunocytochemistry, SP‐A was identified in two layers of the vaginal epithelium: the deep intermediate layer (the site of newly differentiated epithelial cells); and the superficial layer (comprising dead epithelial cells), where SP‐A is probably extracellular and associated with a glycocalyx. Transcripts of SP‐A were identified by Northern blot analysis in RNA isolated from vaginal wall and shown, by sequencing of reverse transcription–polymerase chain reaction products, to be derived from each of the two closely related SP‐A genes, SP‐A1 and SP‐A2. SP‐A was identified in vaginal lavage fluid by two‐dimensional gel electrophoresis, and confirmed by mass spectrometry. This study provides evidence, for the first time, that SP‐A is produced in a squamous epithelium, namely the vaginal mucosa, and has a localization that would allow it to contribute to both the innate and adaptive immune response. The findings support the hypothesis that in the vagina, as in lung, SP‐A is an essential component of the host‐defence system. A corollary hypothesis is that qualitative and quantitative alterations of normal SP‐A may play a role in the pathogenesis of lower genital tract inflammatory conditions.

Identification of disease-associated DNA methylation in intestinal tissues from patients with inflammatory bowel disease

Lin Z, Hegarty JP, Cappel JA, Yu W, Chen X, Faber P, Wang Y, Kelly AA, Poritz LS, Peterson BZ, Schreiber S, Fan J‐B, Koltun WA. Identification of disease‐associated DNA methylation in intestinal tissues from patients with inflammatory bowel disease.

Pulmonary alveolar proteinosis: a review.

Pulmonary alveolar proteinosis (PAP) is a disorder that rapidly leads to respiratory failure, because the alveolar spaces fill with a lipid-rich, proteinaceous material that impedes gas exchange. The pathogenesis of this life-threatening process remained an enigma for decades. Recent analysis of the lung pathology and molecular genetics of affected families has provided a molecular basis for some cases of PAP—deficiency of surfactant protein SP-B. This lack results from mutations in the gene for SP-B. The common mutation, 121ins2, is present in about two-thirds of the patients with SP-B deficiency. Additional insights into the mechanism for this lipoproteinaceous accumulation within alveoli were contributed by serendipity in a granulocyte-macrophage – colony stimulating factor (GM–CSF) knock-out mouse model developed to study basal hematopoiesis. In this model, hematopoiesis was unaffected, but the animals developed pulmonary alveolar proteinosis. Subsequently, mutations in the genes for GM–CSF or its receptor were identified as the cause for pulmonary alveolar proteinosis in some patients. In our review, we discuss the known clinical, pathologic, and molecular genetic aspects of pediatric PAP and consider avenues for future research.

NOD2/CARD15 Mutations Correlate With Severe Pouchitis After Ileal Pouch-Anal Anastomosis

PURPOSE: Pouchitis and Crohns-like complications can plague patients after IPAA. NOD2 is an intracellular sensor for bacterial cell wall peptidoglycan. NOD2 mutations compromise host response to enteric bacteria and are increased in Crohns disease. We hypothesize that IPAA patients with complications (Crohns disease-like/pouchitis) have a higher rate of NOD2 mutations compared with asymptomatic IPAA patients. METHODS: Patients were retrospectively subclassified into the following groups: 1) IPAA with Crohns-like complications (n = 28, perianal fistula, pouch inlet stricture/upstream small-bowel disease, or biopsies showing granulomata) occurring at least 6 months after ileostomy closure; 2) IPAA with mild pouchitis (n = 33, ≤3 episodes/y for 2 consecutive years); 3) IPAA with severe pouchitis (n = 9, ≥4 episodes/y for 2 consecutive years or need for continuous antibiotics); 4) IPAA without complications or pouchitis (n = 37); 5) patients with Crohns disease with colitis undergoing total proctocolectomy/ileostomy (n = 11); and 6) healthy controls (n = 269). The 3 NOD2 single-nucleotide polymorphism mutations (rs2066844, rs2066845, and rs2066847) previously identified as associated with Crohns disease were genotyped using polymerase chain reaction. Groups were compared by use of &khgr;2 with Yates continuity correction. RESULTS: NOD2 mutations were found in 8.5% of healthy controls. NOD2 mutations were significantly higher in the severe pouchitis group (67%) compared with both asymptomatic IPAA (5.4%, P < .001) and IPAA with Crohns disease-like complications (14.3%, P = .008) groups. CONCLUSIONS: 1) Asymptomatic IPAA patients have a low incidence of NOD2 mutations not significantly different from patients with mild pouchitis or healthy controls. 2) Patients with severe pouchitis had the highest incidence of NOD2 mutations, suggesting that this group may have a compromised host defense mechanism to enteric bacteria. 3) Patients with Crohns-like complications after IPAA have a significantly lower incidence of NOD2 mutations than patients with severe pouchitis, suggesting a different genetic makeup in these 2 patient groups. Preoperative assessment of NOD2 in the equivocal IPAA candidate may predict severe pouchitis and might assist in preoperative surgical decision making.

Identification of Disease-Associated DNA Methylation in B Cells from Crohn’s Disease and Ulcerative Colitis Patients

BackgroundChanges in the methylation status of inflammatory bowel disease (IBD)-associated genes could significantly alter levels of gene expression, thereby contributing to disease onset and progression. We previously identified seven disease-associated DNA methylation loci from intestinal tissues of IBD patients using the Illumina GoldenGate BeadArray assay.AimsIn this study, we extended this approach to identify IBD-associated changes in DNA methylation in B cells from 18 IBD patients [9 Crohn’s disease (CD) and 9 ulcerative colitis (UC)]. B cell DNA methylation markers are particularly favorable for diagnosis due to the convenient access to peripheral blood.MethodsWe examined DNA methylation profiles of B cell lines using the Illumina GoldenGate BeadArray assay. Disease-associated CpGs/genes with changes in DNA methylation were identified by comparison of methylation profiles between B cell lines from IBD patients and their siblings without IBD. BeadArray data were validated using a bisulfite polymerase chain reaction (PCR)-based restriction fragment length polymorphism (RFLP) method. To verify that observed changes in DNA methylation were not due to virus transformation, we compared specific CpG DNA methylation levels of GADD45A and POMC between B cell lines and matching peripheral blood B lymphocytes from five individuals.ResultsUsing this approach with strict statistical analysis, we identified 11 IBD-associated CpG sites, 14 CD-specific CpG sites, and 24 UC-specific CpG sites with methylation changes in B cells.ConclusionsIBD- and subtype-specific changes in DNA methylation were identified in B cells from IBD patients. Many of these genes have important immune and inflammatory response functions including several loci within the interleukin (IL)-12/IL-23 pathway.

Mutations in IRGM are associated with more frequent need for surgery in patients with ileocolonic Crohn's disease.

BACKGROUND: There are no clear criteria for judging the severity of disease in patients with Crohns disease. Yet classification of patients into low- and high-risk severity groups would benefit both medical and surgical management. At the time of this study, approximately 80 single-nucleotide polymorphisms within 55 genes had been associated with IBD. OBJECTIVE: The aim of this study was to identify genetic determinants (single-nucleotide polymorphisms) that could be markers of Crohns disease severity by the use of frequency of ileocolic surgery as a surrogate for disease severity. DESIGN: Sixty-six patients (30 male) with ileocolonic Crohns disease who previously underwent ileocolectomy were retrospectively studied. The severity of Crohns disease was quantified by dividing the total number of ileocolectomy procedures by the time between IBD diagnosis and the patients last clinic visit, the rationale being that more severe disease would be associated with a more frequent need for surgery. Genotyping for the 83 single-nucleotide polymorphisms associated with IBD was done on a customized Illumina Veracode genotyping platform. Three genetic models (general, additive, and dominant) were used to statistically quantify the genetic association of the studied single-nucleotide polymorphisms to the frequency of surgery after adjusting for covariates (age, smoking, family history, disease location, and disease behavior). RESULTS: For the entire group the average number of ileocolectomies per patient was 1.7 (range, 1–5) with an average duration of disease of 14.7 years. Single-nucleotide polymorphism rs4958847 in the IRGM gene (immunity-related GTPase family, M) was the most significant single-nucleotide polymorphism in all 3 models tested (p = 0.007) as being associated with ileocolectomy, and it remained significant even after a Benjamini-Hochberg false-discovery correction for multiple observations. Patients carrying the “at-risk” allele for this single-nucleotide polymorphism (n = 20) had an average of 1 surgery every 6.87 ± 1.33 years in comparison with patients carrying the wild-type genotype (n = 46) who averaged 1 surgery in 11.43 ± 1.21 years (p = 0.007, Mann-Whitney U test). CONCLUSIONS: Single-nucleotide polymorphism rs4958847 in the IRGM gene correlated very significantly with frequency of surgery in patients with ileocolonic Crohns disease. IRGM is a mediator of innate immune responses and is involved in autophagy. The presence of this IRGM SNP may be a marker for disease severity and/or early recurrence after ileocolectomy and may assist in surgical and medical decision making.

A General Model for Multilocus Epistatic Interactions in Case-Control Studies

Background Epistasis, i.e., the interaction of alleles at different loci, is thought to play a central role in the formation and progression of complex diseases. The complexity of disease expression should arise from a complex network of epistatic interactions involving multiple genes. Methodology We develop a general model for testing high-order epistatic interactions for a complex disease in a case-control study. We incorporate the quantitative genetic theory of high-order epistasis into the setting of cases and controls sampled from a natural population. The new model allows the identification and testing of epistasis and its various genetic components. Conclusions Simulation studies were used to examine the power and false positive rates of the model under different sampling strategies. The model was used to detect epistasis in a case-control study of inflammatory bowel disease, in which five SNPs at a candidate gene were typed, leading to the identification of a significant three-locus epistasis.

Aberrant SP-B mRNA in lung tissue of patients with congenital alveolar proteinosis (CAP).

Mutations in the surfactant protein (SP)‐B gene are responsible for SP‐B deficiency in congenital alveolar proteinosis (CAP) (Nogee et al. J Clin Invest 1994: 93: 1860–1883; Lin et al. Mol Genet Metab 1998: 64: 25–35; Klein et al. Pediatrics 1998: 132: 244–248; Ballard et al. Pediatrics 1995: 96: 1046–1052). The multigenerational consanguineous pedigree under study does not carry any of the known mutations, although this pedigree had 14 infant deaths following respiratory distress at birth. Immunostaining of the lungs from three such infants revealed decreased or absent SP‐B. By sequencing of SP‐B exons, exon–intron junctions, and the 5′ and 3′ flanking regions, nine polymorphisms were found in this pedigree, but none of them could explain the observed SP‐B deficiency. Further analysis of SP‐B mRNA by reverse transcription‐polymerase chain reaction from paraffin‐embedded lung tissue of CAP patients showed that SP‐B mRNA is not intact. Although the sequence of mRNA from exon 1–exon 7 and from exon 8–exon 10 could be amplified, the region between exons 7 and 8 could not. From fluorescence in situ hybridization of the short arm of chromosome 2p, only 2 signals were identified, eliminating the possibility of translocation as the cause of the SP‐B mRNA aberrance. Although the nature of the genetic basis of SP‐B deficiency in this family is currently unknown, the existence of aberrant SP‐B mRNA may, at least in part, be responsible for the SP‐B deficiency in this pedigree.

Genetic risk profiling and gene signature modeling to predict risk of complications after IPAA.

BACKGROUND: Severe pouchitis and Crohns disease-like complications are 2 adverse postoperative complications that confound the success of the IPAA in patients with ulcerative colitis. To date, approximately 83 single nucleotide polymorphisms within 55 genes have been associated with IBD. OBJECTIVE: The aim of this study was to identify single-nucleotide polymorphisms that correlate with complications after IPAA that could be utilized in a gene signature fashion to predict postoperative complications and aid in preoperative surgical decision making. DESIGN: One hundred forty-two IPAA patients were retrospectively classified as “asymptomatic” (n = 104, defined as no Crohns disease-like complications or severe pouchitis for at least 2 years after IPAA) and compared with a “severe pouchitis” group (n = 12, ≥4 episodes pouchitis per year for 2 years including the need for long-term therapy to maintain remission) and a “Crohns disease-like” group (n = 26, presence of fistulae, pouch inlet stricture, proximal small-bowel disease, or pouch granulomata, occurring at least 6 months after surgery). Genotyping for 83 single-nucleotide polymorphisms previously associated with Crohns disease and/or ulcerative colitis was performed on a customized Illumina genotyping platform. The top 2 single-nucleotide polymorphisms statistically identified as being independently associated with each of Crohns disease-like and severe pouchitis were used in a multivariate logistic regression model. These single-nucleotide polymorphisms were then used to create probability equations to predict overall chance of a positive or negative outcome for that complication. RESULTS: The top 2 single-nucleotide polymorphisms for Crohns disease-like complications were in the 10q21 locus and the gene for PTGER4 (p = 0.006 and 0.007), whereas for severe pouchitis it was NOD2 and TNFSF15 (p = 0.003 and 0.011). Probability equations suggested that the risk of these 2 complications greatly increased with increasing number of risk alleles, going as high as 92% for severe pouchitis and 65% for Crohns disease-like complications. CONCLUSION: In this IPAA patient cohort, mutations in the 10q21 locus and the PTGER4 gene were associated with Crohns disease-like complications, whereas mutations in NOD2 and TNFSF15 correlated with severe pouchitis. Preoperative genetic analysis and use of such gene signatures hold promise for improved preoperative surgical patient selection to minimize these IPAA complications.