p16 promoter hypermethylation:A useful serum marker for early detection of gastric cancer

AIM: To determine p16 promoter hypermethylation in gastric tumoral tissue and serum samples, its impact on p16-protein expression, and correlation with clinical and histological features. METHODS: Samples were obtained from 52 histologically confirmed cases of gastric adenocarcinoma. Gastric tissue and serum of 50 age- and sex-matched individuals with normal gastroscopy and biopsy were obtained as control samples. Methylation-specific polymerase chain reaction (MSP) was used to evaluate methylation status of p16 promoter. p16-protein expression was analyzed by immunohistochemical staining on paraffin-embedded sections. RESULTS: Methylation was detected in 44.2% (23/52) of tumoral tissues. 60.9% of them were also methylated in serum, i.e., 26.9% of all patients (14/52). Methylation was not detected in tissue and sera of control samples. p16-protein expression was decreased in 61.5% of cases (32/52), and was significantly associated with promoter hypermethylation (P < 0.001). Methylation was significantly more frequent in higher pathological grades (P < 0.05). Methylation was not associated with other clinicopathological features and environmental factors including H pylori infection and smoking. CONCLUSION: p16 promoter hypermethylation is an important event in gastric carcinogenesis. It is the principle mechanism of p16 gene silencing. It is related to malignant tumor behavior. Detection of DNA methylation in serum may be a biomarker for early detection of gastric cancer.

Association of p53/p21 expression with cigarette smoking and prognosis in esophageal squamous cell carcinoma patients

<Abstract>factors,such as cigarette smoking,in esophageal squamous cell carcinoma(ESCC)in northeastern Iran,a region with a high incidence of ESCC.METHODS:The expression of p53 and p21 proteins was investigated immunohistochemically in tumor tissue from 80 ESCC patients and in 60 available paraffinembedded blocks of adjacent normal specimens from the cases,along with normal esophageal tissue from 80 healthy subjects.RESULTS:Positive expression of p53 protein was detected in 56.2%(45/80)of ESCC cases,and in none of the normal esophageal tissue of the control group(P<0.001).Furthermore,73.8%(59/80)of ESCC cases and 43.8%(35/80)of controls had positive expression of p21 protein(P<0.001).Cigarette smoking was significantly associated with p53 over-expression in ESCC cases(P=0.010,OR=3.64;95%CI:1.32-10.02).p21 over-expression was associated with poorer clinical outcome among the ESCC patients(P=0.009).CONCLUSION:Over-expression of p53 in association with cigarette smoking may play a critical role in ESCC carcinogenesis among this high-risk population of northeastern Iran.Furthermore,p21 over-expression was found to be associated with poor prognosis,specifically in the operable ESCC patients.

Colonic manifestations of PTEN hamartoma tumor syndrome: Case series and systematic review

AIM:To investigate our clinical experience with the colonic manifestations of phosphatase and tensin homolog on chromosome ten(PTEN)hamartoma tumor syndrome(PHTS)and to perform a systematic literature review regarding the same.METHODS:This study was approved by the appropriate institutional review board prior to initiation.A clinical genetics database was searched for patients with PHTS or a component syndrome that received gastrointestinal endoscopy or pathology interpretation at our center.These patient’s records were retrospectively reviewed for clinical characteristics(including family history and genetic testing),endoscopy results and pathology findings.We also performed a systematic review of the literature for case series of PHTS or component syndromes that reported gastrointestinal manifestations and investigations published after consensus diagnostic criteria were established in 1996.These results were compiled and reported.RESULTS:Eight patients from our institution met initial inclusion criteria.Of these,5 patients underwent4.2 colonoscopies at mean age 45.8±10.8 years.All were found to have colon polyps during their clinical course and polyp histology included adenoma,hyperplastic,ganglioneuroma and juvenile.No malignant lesions were identified.Two had multiple histologic types.One patient underwent colectomy due to innumerable polyps and concern for future malignant potential.Systematic literature review of PHTS patients undergoing endoscopy revealed 107 patients receiving colonoscopy at mean age 37.4 years.Colon polyps were noted in92.5%and multiple colon polyp histologies were reported in 53.6%.Common polyp histologies included hyperplastic(43.6%),adenoma(40.4%),hamartoma(38.3%),ganglioneuroma(33%)and inflammatory(24.5%)polyps.Twelve(11.2%)patients had colorectal cancer at mean age 46.7 years(range 35-62).Clinical outcomes secondary to colon polyposis and malignancy were not commonly reported.CONCLUSION:PHTS has a high prevalence of colon polyposis with multiple histologic types.It should be considered a mixed polyposis syndrome.Systematic review found an increased prevalence of colorectal cancer and we recommend initiating colonoscopy for colorectal cancer surveillance at age 35 years.

Mitochondrial variants may influence the phenotypic manifestation of Leber's hereditary optic neuropathy-associated ND4 G11778A mutation

We report here the characterization of a five-generation Han Chinese family with Leber＇s hereditary optic neuropathy （LHON）. Strik- ingly, this Chinese family displayed high penetrance and expressivity of visual loss. The average age-of-onset of vision loss was 18 years in this family. Nineteen （11 males/8 females） of 29 matrilineal relatives in this family developed visual loss with a wide range of severity, ranging from blindness to normal vision. Sequence analysis of mitochondrial genome in this pedigree revealed the presence of the ND4 G 11778A mutation and 44 other variants belonging to Asian haplogroup M7b. The G 11778A mutation is present at homoplasmy in matri- lineal relatives of this Chinese family. Of other variants, the C01 G6480A, ND5 T12811C and Cytb A15395G located at highly conserved residues of corresponding polypeptides. In fact, these variants were implicated to be involved in other clinical abnormalities. Here, these variants may act in synergy with the primary LHON-associated Gl1778A mutation. Thus, the mitochondrial dysfunction caused by the primary ND4 G11778A mutation may be worsened by these mitochondrial variants. The results imply that the G6480A, T12811C and A15395G variants might have a potential modifier role in increasing the penetrance and expressivity of the primary LHON-associated G11778A mutation in this Chinese family.

Application of computational methods in genetic study ofinflammatory bowel disease

Genetic factors play an important role in the etiology of inflammatory bowel disease(IBD). The launch of genome-wide association study(GWAS) represents a landmark in the genetic study of human complex disease. Concurrently, computational methods have undergone rapid development during the past a few years, which led to the identification of numerous disease susceptibility loci. IBD is one of the successful examples of GWAS and related analyses. A total of 163 genetic loci and multiple signaling pathways have been identified to be associated with IBD. Pleiotropic effects were found for many of these loci; and risk prediction models were built based on a broad spectrum of genetic variants. Important gene-gene, gene-environment interactions and key contributions of gut microbiome are being discovered. Here we will review the different types of analyses that have been applied to IBD genetic study, discuss the computational methods for each type of analysis, and summarize the discoveries made in IBD research with the application of these methods.

African origins and chronic kidney disease susceptibility in the human immunodeficiency virus era

Chronic kidney disease(CKD) is a major public health problem worldwide with the estimated incidence growing by approximately 6% annually. There are striking ethnic differences in the prevalence of CKD such that, in the United States, African Americans have the highest prevalence of CKD, four times the incidence of end stage renal disease when compared to Americans of European ancestry suggestive of genetic predisposition. Diabetes mel itus, hypertension and human immunodeficiency virus(HIV) infection are the major causes of CKD. HIV-associated nephropathy(HIVAN) is an irreversible form of CKD with considerable morbidity and mortality and is present predominantly in people of African ancestry. The APOL1 G1 and G2 alleles were more strongly associated with the risk for CKD than the previously examined MYH9 E1 risk haplotype in individuals of African ancestry. A strong association was reported in HIVAN, suggesting that 50% of African Americans with two APOL1 risk alleles, if untreated, would develop HIVAN. However these two variants are not enough to cause disease. The prevailing belief is that modifying factors or second hits(including genetic hits) underlie the pathogenesis of kidney disease. This work reviews the history of genetic susceptibility of CKD and outlines current theories regarding the role for APOL1 in CKD in the HIV era.

Identification of a high frequency of chromosomal rearrangements in the centromeric regions of prostate cancer patients

The aim of the present investigation was to study the major chromosomal aberrations (CA) like deletion, translocation, inversion and mosaic in prostate cancer patients of Tamilnadu, Southern India. Totally 45 blood samples were collected from various hospitals in Tamilnadu, Southern India. Equal numbers of normal healthy subjects were chosen after signing a consent form. Volunteers provided blood samples (5 ml) to establish leukocyte cultures. Cytogenetic studies were performed by using Giemsa-banding technique and finally the results were ensured by spectral karyotyping (SKY) technique. In the present investi-gation, major CA like deletion, translocation, inversion and mosaic were identified in experimental subjects. Results showed frequent CA in chromosomes 1, 3, 5, 6, 7, 9, 13, 16, 18 and X. In comparison with experimental subjects, the control subjects exhibited very low levels of major CA (P<0.05). In the present study, the high frequency of centromeric rearrangements indicates a potential role for mitotic irregularities associated with the centromere in prostate cancer tumorigenesis. Identification of chro-mosome alterations may be helpful in understanding the molecular basis of the disease in better manner.

Clinical lesson learned from genetic analysis in patients prior to surgical repair of hypospadias

In Indonesia,undervirilisation in 46,XY males is the most common form of difference of sex development(DSD).This can include hypospadias(misplacement of the urethra),micropenis,bifid scrotum,and undescended testis[1].Undervirilisation or 46,XY DSD can be associated with a number of congenital syndromes,including Smith-Lemli-Opitz Syndrome(OMIM 602858),caused by an inborn error of cholesterol synthesis,and characterised by growth delay,intellectual disability,microcephaly,distinctive facial features,cleft palate,limb anomalies,and hypospadias[2]or Opitz syndrome(also known as Opitz G/BBB syndrome).Opitz syndrome can be caused by variants in the X-linked midline 1(MID1)gene(Type I)or in an autosomal dominant manner by monoallelic variants in sperm antigen with calponin homology and coiled-coil domains 1-like(SPECC1L)on chromosome 22q11.2(Type II)[3].Opitz syndrome is characterised by hypospadias,hypertelorism,cleft lip/palate,and heart defects[4].The prevalence of X-linked Opitz syndrome is estimated to be from 1 in 50000 to 1 in 100000 males[5].Recognition of a syndrome informs appropriate clinical management and patient care.Therefore,although these syndromes are rare,hypospadias may be diagnosed before the emergence of other comorbidities meaning that it is crucial for clinicians to perform a thorough clinical evaluation with syndromic causes in mind.

Prevalence of fragile X syndrome in males and females in Indonesia

AIM: To investigate the prevalence of fragile X syndrome(FXS) in intellectually disabled male and female Indonesians.METHODS: This research is an extension of a previously reported study on the identification of chromosomal aberrations in a large cohort of 527 Indonesians with intellectual disability(ID). In this previous study,87 patients had a chromosomal abnormality, five of whom expressed fragile sites on Xq27.3. Since FXS cannot always be identified by cytogenetic analysis, molecular testing of the fragile X mental retardation 1 CGG repeat was performed in 440 samples. The testing was also conducted in the five previously identified samples to confirm the abnormality. In total, a molecular study was conducted in 445 samples(162 females and 283 males).RESULTS: In the cohort of Indonesian ID population, the prevalence of FXS is 9/527(1.7%). The prevalence in males and females is 1.5%(5/329) and 2%(4/198), respectively. Segregation analysis in the families and X-inactivation studies were performed. We performed the first comprehensive genetic survey of a representative sample of male and female ID individuals from institutions and special schools in Indonesia. Our findings show that a comprehensive study of FXS can be performed in a developing country like Indonesia where diagnostic facilities are limited.CONCLUSION: The prevalence of FXS is equal in females and males in our study, which suggests that the prevalence of FXS in females could be underestimated.

Molecular Dynamics Simulations of DOPC Lipid Bilayers: The Effect of Lennard-Jones Parameters of Hydrocarbon Chains

The current Chemistry at Harvard Molecular Mechanics (CHARMM) force field cannot accurately describe the properties of unsaturated phospholipid membranes. In this paper, a series of simulations was performed in which the Lennard- Jones (L-J) parameters of lipid acyl chains of dioleoylphosphatidylcholine (DOPC) were systematically adjusted. The results showed that adjustment of the L-J parameters in lipid acyl chains can significantly improve the current CHARMM force field. It was found that the L-J parameters have different influences on the order parameters of the top half and bottom half of the chain, separated by the cis double bond. The order parameters of the top half and the bottom half of the chain are related to the area/lipid and the length of the chain, respectively.

The Genetic Variant c.553G>T in the Lipoprotein A5 Effects on Lipid Profile Parameters Levels

Abnormal levels of plasma lipid have been linked to atherosclerosis, strokes and heart conditions. Variations in high-density lipoprotein (HDL) and low-density lipoprotein (LDL) cholesterol levels are considered as risk factors for coronary artery disease (CAD). Furthermore, triglycerides are a leading cause of cardiovascular disease. Therefore, measurement of plasma lipid levels is an important mortality predictor. Several factors were associated with irregularity in plasma lipids such as genetic alterations. Recent researches have linked single nucleotides polymorphism (SNP) in ApoA5 gene with these deviations. In this study, we reported the effects of the genetic variant c.553G>T in ApoA5 on the levels of plasma lipids. To explore these effects, a case-control study including 280 male and female subjects (44 of them were assigned as CAD cases while the remaining subjects were categorized as control) was established. All patients in the study were recruited from the western region in KSA. The results have detected minor variations in LDL, HDL and cholesterol levels between CAD patients carrying T allele and CAD patients carrying the WT allele. However, there were no significant effects due to these variations. TG levels in the wild type carriers reached up to 291 mg/dl while T allele carriers, the cases, presented lower levels of TG (170 mg/dl and 71 mg/dl). Although, T allele showed no effects on plasma lipids with the exception of TG levels. We suggest by this study that T allele in this SNP might be considered as a valuable tool in the diagnosis of CAD.

闽浙地区香鱼线粒体Cytb基因和D-loop区序列多态性分析

对浙江瑞安、福建宁德、福建东张水库3个地理群体共31例香鱼(Plecoglossus altivelis)的线粒体细胞色素b(Cyt b)基因和线粒体D-loop区序列进行了PCR扩增、序列测定、核苷酸组成和多态性分析。Cytb基因中,A、T、C和G4种核苷酸的比例分别为19.72%、29.71%、32.25%和18.32%,A+T含量为49.43%,G+C含量为50.57%。D-loop区序列中,A、T、C和G4种核苷酸的比例分别为29.99%、29.29%、23.80%和16.92%,A+T含量为59.28%,G+C含量为40.72%。在长度为1141bp的Cytb基因序列中,仅存在1个变异位点,核苷酸多样性指数(π值)为0.00028,31个样本中仅出现两种单倍型;857 bp 长的D-loop区序列中,仅存在5个变异位点,核苷酸多样性指数(π值)为0.00199,仅出现5种单倍型。这表明闽浙地区香鱼的遗传多样性水平很低,应当加大对香鱼的保护力度。

与耳聋相关的线粒体tRNA突变

线粒体tRNA基因突变是导致感音神经性耳聋的原因之一.有些tRNA突变可直接造成耳聋的发生,称之为原发突变.如tRNALeu(UUR)A3243G等突变与综合征型耳聋相关,而tRNASer(UCN)T7511C等突变则与非综合征型耳聋相关.此外,继发突变如tRNAThr G15927A等突变则对原发突变起协同作用,影响耳聋的表型表达.这些突变可引起tRNA二级结构改变,从而影响线粒体蛋白质合成,降低细胞内ATP的产生,由此引起的线粒体功能障碍可导致耳聋的发生.主要讨论与耳聋相关的线粒体tRNA突变及其致聋机理.

线粒体tRNA^(Glu)A14693G可能是与Leber遗传性视神经病变相关的基因突变

收集了3个具有典型临床特征的中国汉族Leber遗传性视神经病变(Leber′s hereditary optic neuropathy,LHON)家系。通过对先证者和家系其他成员进行眼科临床(如视力损害程度和发病年龄)检查,发现这些家系成员中视力损害的外显率很低,经mtDNA测序分析,在tRNAGlu上发现了A14693G同质性突变位点,多态性位点分别属于东亚单体型Y1b、Y1和Y1,没有发现其他高度保守和有功能意义的突变位点。A14693G突变位于线粒体tRNAGlu高度保守区(通用位点为54位),可能导致tRNA空间结构和稳定性发生改变,继而影响tRNA的代谢,导致线粒体蛋白合成功能受损和ATP障碍,最终导致视力损害。所以,tRNAGluA14693G突变可能是与视神经病变相关的致病性线粒体突变位点。

线粒体DNA G7444A突变可能影响A1555G突变的表型表达

线粒体12S rRNA和tRNASer(UCN)基因是导致非综合征型听力损失的两个突变热点区域。作者收集了1个母系遗传感音神经性聋家系,该家系同时携带线粒体DNA(mtDNA)A1555G和G7444A突变。临床资料分析表明,该家系包括药物致聋的耳聋外显率(所有耳聋患者/所有母系成员)为58%,而非药物致聋的耳聋外显率(非药物性聋患者/所有母系成员)为25%,明显高于其他携带A1555G突变的耳聋家系。先证者的线粒体全序列分析表明,该线粒体基因组共有28个多态位点,属于东亚人群B4c1单体型。在这些多态位点中,除A1555G和G7444A突变外,未发现其他有功能意义的突变。这表明mtDNA G7444A突变可能加重由A1555G突变造成的线粒体功能缺失,从而增加耳聋的外显率。

线粒体ND1基因T3866C突变可能是Leber’s遗传性视神经病和四肢畸形跛行相关的突变

线粒体DNA(Mitochondrial DNA,mtDNA)突变与人类许多疾病的发病机制相关。现报道1个具有典型母系遗传特征的中国人Leber’s遗传性视神经病和四肢畸形跛行的家系。该家系共5代60人,共27名母系成员,其中4人只有Leber’s遗传性视神经病症状,1人呈现四肢畸形跛行症状,4人同时具有上述两种临床症状,而其他成员无临床症状。对先证者的mtDNA全序列进行分析,发现ND1基因T3866C突变位点和43个多态位点,经系统进化树分析属于东亚单体型D4a3。MtDNAND13866位点T-C碱基的改变使ND1亚基第187位进化高度保守的异亮氨酸转变为苏氨酸,从而改变该蛋白的结构,进而影响其功能。在135名正常对照中未发现该突变。因此,线粒体ND1T3866C可能是与Leber’s遗传性视神经病和四肢畸形跛行相关的线粒体基因突变。

线粒体T12338C突变可能是与Leber遗传性视神经病变相关的突变位点

Leber遗传性视神经病变变(Leber’s hereditary optic neuropathy,LHON)是一种与线粒体DNA(Mito-chondrial DNA,mtDNA)突变相关的母系遗传性眼科疾病。文章报道了两例具有典型LHON临床、分子遗传特征的中国汉族家系。首先通过对家系先证者和其他成员进行眼科相关检查,发现两个家系成员中视力都仅有先证者一人损害严重,即外显率很低。经常规的方法对母系成员进行mtDNA测序及相关软件分析,结果发现携带ND4 G11696A和ND5 T12338C同质性突变位点,多态性变异位点均属于东亚单体型F2。线粒体DNA ND4 G11696A是一个已知的与LHON相关的突变位点,而T12338C位于线粒体氧化磷酸化复合体I亚基ND5的第2个碱基,该突变使起始密码子由蛋氨酸转变成苏氨酸,并且紧连tRNALeu(CUN)的3′末端。这可能影响tRNA Leu(CUN)空间结构和稳定性发生改变,以及起始密码子改变导致线粒体ND5蛋白合成功能受损和ATP障碍,最终导致需求能量高的视神经受损和视力损害。因此,线粒体ND4 G11696A和ND5 T12338C突变可能协同作用Leber遗传性视神经病变的发生,是与LHON相关的mtDNA突变位点,但外显率很低说明突变本身不足以造成LHON的表型表达,提示其他修饰因子(核修饰基因、环境等)可能对这两个家系发病起协同作用。

基于16S rRNA和recA香鱼鳗利斯顿氏菌的分离鉴定

为研究引起香鱼(Plecoglossus altivelis)出血溃烂症病因及致病菌系统发育地位,本研究从患病香鱼的肝脏、肾脏及体表分离到11株病原菌(编号:X0901-X0911),运用常规细菌生理生化方法鉴定致病菌所属种类;运用16SrRNA基因、recA基因序列分析方法研究致病菌的系统发育地位。细菌生理生化鉴定结果表明:致病菌为鳗利斯顿氏菌,11株细菌生理生化结果相同,均为革兰氏阴性杆菌、氧化酶阳性、接触酶阳性、吲哚阳性、精氨酸脱羧酶阳性、精氨酸双水解酶阳性、硝酸盐还原阳性、甘露醇阳性、MR测定阳性;H2S阴性、V-P测定阴性等。根据16SrRNA基因、recA基因序列分别构建弧菌科常见细菌系统进化树,结果表明:致病菌与鳗利斯顿氏菌(Listonella anguillarum)均聚为一枝,聚类结果与细菌生理生化鉴定结果相符。致病菌与鳗利斯顿氏菌16SrRNA基因、recA基因的同源性分别为99.9%、99.8%。以recA基因构建的系统进化树的拓扑学结构与16SrRNA基因建树结果相类似。此外,与16SrRNA基因相比,recA基因在不同物种之间具有更高的鉴别能力,本研究表明recA基因适合作为弧菌科常见细菌物种间进化关系研究的标记。

高血压相关的线粒体DNA突变

线粒体DNA(mtDNA)突变是高血压发病的分子机制之一。已经报道的与原发性高血压相关的mtDNA突变包括:tRNAMet A4435G,tRNAMet/tRNAGln A4401G,tRNAIle A4263G,T4291C和A4295G突变。这些高血压相关的mtDNA突变改变了相应的线粒体tRNA的结构,导致线粒体tRNA的代谢障碍。而线粒体tRNAs的代谢缺陷则影响蛋白质合成,造成氧化磷酸化缺陷,降低ATP的合成,增加活性氧的产生。因此,线粒体的功能缺陷可能在高血压的发生发展中起一定的作用。mtDNA突变发病的组织特异性则可能与线粒体tRNAs的代谢以及核修饰基因相关。目前发现的这些高血压相关的mtDNA突变则应该作为今后高血压诊断的遗传风险因子。高血压相关的线粒体功能缺陷的深入研究也将进一步诠释母系遗传高血压的分子致病机制,为高血压的预防、控制和治疗提供依据。文章对高血压相关的mtDNA突变进行了综述。

人工耳蜗植入聋儿术前基因检测及家系分析

国内外研究表明GJB2、SLC26A4(PDS)和线粒体DNA(Mitochondrial DNA,mtDNA)的病理性突变导致了大部分的遗传性聋。文章收集了2006年4月～2007年9月接受人工耳蜗(Cochlearimplant,CI)植入的14例患儿及其父母的外周血,应用基因诊断方法进行GJB2、SLC26A4(PDS)和mtDNA1555位点突变检测。结果显示,35.7%的患儿检测到致病突变,其中28.6%为GJB2基因突变,类型均为235delC纯和突变,其父母为携带GJB2 235delC的杂和子;7.1%为mtDNA A1555G突变,其母亲亦携带mtDNA A1555G突变。这表明CI植入聋儿最常见的基因突变是GJB2 235delC突变,其次是mtDNA A1555G突变,通过对耳聋家系常见致病基因的检测和家系分析,可以对优生优育及减少耳聋发病率提供科学准确的遗传信息。