A-Mei Zhang

Targeted next-generation sequencing of candidate genes reveals novel mutations in patients with dilated cardiomyopathy

Dilated cardiomyopathy (DCM) is a major cause of sudden cardiac death and heart failure, and it is characterized by genetic and clinical heterogeneity, even for some patients with a very poor clinical prognosis; in the majority of cases, DCM necessitates a heart transplant. Genetic mutations have long been considered to be associated with this disease. At present, mutations in over 50 genes related to DCM have been documented. This study was carried out to elucidate the characteristics of gene mutations in patients with DCM. The candidate genes that may cause DCM include MYBPC3, MYH6, MYH7, LMNA, TNNT2, TNNI3, MYPN, MYL3, TPM1, SCN5A, DES, ACTC1 and RBM20. Using next-generation sequencing (NGS) and subsequent mutation confirmation with traditional capillary Sanger sequencing analysis, possible causative non-synonymous mutations were identified in ~57% (12/21) of patients with DCM. As a result, 7 novel mutations (MYPN, p.E630K; TNNT2, p.G180A; MYH6, p.R1047C; TNNC1, p.D3V; DES, p.R386H; MYBPC3, p.C1124F; and MYL3, p.D126G), 3 variants of uncertain significance (RBM20, p.R1182H; MYH6, p.T1253M; and VCL, p.M209L), and 2 known mutations (MYH7, p.A26V and MYBPC3, p.R160W) were revealed to be associated with DCM. The mutations were most frequently found in the sarcomere (MYH6, MYBPC3, MYH7, TNNC1, TNNT2 and MYL3) and cytoskeletal (MYPN, DES and VCL) genes. As genetic testing is a useful tool in the clinical management of disease, testing for pathogenic mutations is beneficial to the treatment of patients with DCM and may assist in predicting disease risk for their family members before the onset of symptoms.

Ethnic and geographic variations in HPV prevalence and genotype distribution in north-western Yunnan, China.

The prevalence and genotype distribution of human papillomavirus (HPV) vary throughout the world. To assess the prevalence and genotype distribution of HPV among three ethnic groups in two geographic locations in north‐western Yunnan, we recruited 522 women in Shangri‐le (n = 255) and Lijiang (n = 267). PCR amplification of HPV DNA was performed on cervical cells from these women using two consensus primer systems (MY09/11 and GP5/6). Amplified‐HPV DNA was genotyped using the HPV GenoArray test. Geographically, the HPV prevalence was significantly higher (P = 0.002) among Shangri‐le women than among Lijiang women. Infections with high‐risk (HR)‐HPV and with multiple HPV genotypes were also significantly more common (P = 0.001) among women in Shangri‐le than women in Lijiang. Additionally, the prevalence of overall, HR‐HPV, and single genotype HPV infections was significantly higher (P = 0.001) among Tibetan women than among Naxi and Han women. HPV‐16 and HPV‐33 were significantly more frequent in Shangri‐le women compared with Lijiang (P = 0.006) women. In addition, HPV‐16 (9.81%) and HPV‐33 (5.88%) were significantly more prevalent in Tibetan women than in Naxi and Han women. Here, for the first time, we highlight the significant variation in the prevalence and genotype distribution of HPV in various populations in the north‐western region of Yunnan Province. J. Med. Virol. 88:532–540, 2016.

GB Virus C infection in Patients With HIV/Hepatitis C Virus Coinfection: Improvement of the Liver Function in Chronic Hepatitis C

Background: Previous studies in patients with hepatitis C virus (HCV)/HIV coinfection have shown that the presence of GBV-C is associated with significantly less compensated and decompensated cirrhosis, and an improvement in cirrhosis-free survival. Objectives: This study aimed to describe the effect of GBV-C in patients with chronic hepatitis C and HIV coinfection. Patients and Methods: We retrospectively studied 105 injecting drug users with chronic hepatitis C and HIV coinfection and 72 patients with chronic HCV mono-infections. Plasma samples were tested for GBV-C RNA with primers to the 5’untranslated region gene. HIV and HCV viral load, CD4+ and CD8+ cell count, and the levels of alanine aminotransferase (ALT) and aspartate aminotransferase (AST) were tested in all patients. Results: GBV-C RNA was identified in 34 (32.38%) of the patients with HIV/HCV coinfection, and in 24 (33.33%) of the patients with HCV mono-infection. GBV-C infection was associated with significantly lower ALT and AST levels in patients with chronic hepatitis C and HIV coinfection, but not in those HCV mono-infections. The presence of GBV-C infection was not correlated with CD4+ and CD8+ cell count, gender, age, HIV load, HCV load, and HCV genotype. Conclusions: This study found that GBV-C infection has a high frequency among injecting drug users with HIV/HCV coinfection and HCV mono-infection in Yunnan, China. In patients with chronic hepatitis C and HIV coinfection, GBV-C RNA was associated with significantly lower ALT and AST levels, suggesting a beneficial effect of GBV-C infection on chronic hepatitis C.

Mitochondrial DNAs decreased and correlated with clinical features in HCV patients from Yunnan, China

Abstract Hepatitis C was the most popular chronic infectious liver disease worldwide. It was identified that Hepatitis C virus (HCV) infection could lead to mitochondrial dysfunction, though the mechanism was not fully understood. To investigate whether mtDNA copy number could be affected by HCV infection and be associated with clinical features of HCV patients, mtDNA copy numbers were analyzed in 242 patients with HCV infection and 226 matched control samples. The results suggested that mtDNA copy numbers significantly decreased in HCV patients (68.80 ± 3.33) than in control samples (81.54 ± 4.50) (p = 0.022). When males/females were separated from total patients to compare mtDNA copy numbers with gender matched controls, mtDNA copy numbers still significantly decreased in male HCV patients (p = 0.002). Further analysis indicated that level of high-density lipoprotein cholesterol (HDL-C) was negatively correlated with mtDNA copy numbers in total HCV patients (r = −0.128, p = 0.047), and this correlation was more significant in male HCV patients (r = −0.266, p = 0.030). Intriguingly, aspartate amino-transferase (AST) showed positive correlation with mtDNA copy numbers (r = 0.260, p = 0.034) in male HCV patients. Our results indicated that mtDNA copy numbers depleted and correlated with clinical features in male HCV patients.

Screening mutations in drug-resistant Mycobacterium tuberculosis strains in Yunnan, China

Drug-resistant tuberculosis (DR-TB), especially multidrug-resistant tuberculosis (MDR-TB), is a serious medical and societal problem in China. The purpose of this study was to evaluate the mutation characteristics of drug-resistant Mycobacterium tuberculosis (M. tuberculosis) isolates in Yunnan, China. Drug susceptibility testing (DST) was performed in 523 clinical M. tuberculosis isolates. Six drug resistance genes (katG, inhA, rpoB, rpsL, embB, and pncA) were selected to screen for mutations. In total, 54 clinical M. tuberculosis strains were identified as drug-resistant by DST, including 18 single drug-resistant (SDR) strains and 36 multidrug-resistant (MDR) strains. Twenty-four types of mutations in five genes (excluding the inhA gene) were screened in forty-one strains. Six novel mutations were identified in this study, including three missense mutations (p.S302R in katG, p.D78G in embB, and p.M1I in pncA), two frameshift mutations (408 ins A and 538-580 del in pncA), and one mutation in a control region (-6 C>T located upstream of rpsL). The mutation frequencies in the hotspot mutation regions in the katG, rpoB, rpsL, embB, and pncA genes were 92.5%, 44.4%, 54.2%, 52.6%, and 37.5%, respectively. The mutation spectra and frequencies seemed somewhat unique in the Yunnan DR-TB strains.

Completely genomic and evolutionary characteristics of human-dominant G9P[8] group A rotavirus strains in Yunnan, China

G9P[8] rotavirus A (RVA) has been identified as the predominant genotype circulating in Yunnan, China. To elucidate the molecular characteristics of its genetic composition at the whole-genome level, the genomes of 12 strains isolated from paediatric patients with diarrhoea were fully sequenced and characterized. Eleven of the 12 strains were genotyped as G9-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1, which is closely related to the Wa-like genotype 1 constellation. In contrast, one strain was genotyped as G9-P[8]-I1-R1-C1-M1-A1-N2-T1-E1-H1, with the NSP2 gene characterized as a DS-1 like genotype. Bayesian phylogenetic analysis indicated that G9 strains had emerged in 1932 with an estimated average evolutionary rate of 1.63×10-3 substitutions/site/year. Considering the high prevalence and fast evolutionary rate of G9P[8] rotaviruses, our results suggest that G9P[8] RVA should be strictly monitored in China.

Molecular cloning and characterization of cystatin, a cysteine protease inhibitor, from bufo melanostictus.

Cystatins are efficient inhibitors of papain-like cysteine proteinases, and they serve various important physiological functions. In this study, a novel cystatin, Cystatin-X, was cloned from a cDNA library of the skin of Bufo melanostictus. The single nonglycosylated polypeptide chain of Cystatin-X consisted of 102 amino acid residues, including seven cysteines. Evolutionary analysis indicated that Cystatin-X can be grouped with family 1 cystatins. It contains cystatin-conserved motifs known to interact with the active site of cysteine proteinases. Recombinant Cystatin-X expressed and purified from Escherichia coli exhibited obvious inhibitory activity against cathepsin B. rCystatin-X at a concentration of 8 µM inhibited nearly 80% of cathepsin B activity within 15 s, and about 90% of cathepsin B activity within 15 min. The Cystatin-X identified in this study can play an important role in host immunity and in the medical effect of B. melanostictus.

Analysis of Biochemical Features of Hepatitis B Virus Infected Patients in Southwest China

BACKGROUND Hepatitis B is one of the most common infectious diseases in China, and it is necessary to study biochemical indicators of HBV infected patients. METHODS Biochemical and basic features of 1765 HBV infected patients and 840 general controls were collected and analyzed from Southwest China. RESULTS A total of 23.5% of the patients were children or young persons (less than 40 years old). The co-infected rate was only 0.3% for those who were co-infected with Hepatitis C virus (HCV) or Treponema pallidum (TPa). Most of patients (1081 individuals) were under convalescent condition, and 4.2% and 34.6% HBV patients were at acute and chronic phase, respectively. The indicators of liver function were significantly different between HBV patients and normal controls. In order to further study the variation of biochemical features in HBV patients in different phase, they were divided into three groups (sample #1: patients in acute infected phase; sample #2: patients in chronic infected phase; and sample #3: patients in convalescent condition). Excluding total protein and globin, all other indicators of liver function were statically different among the three groups. Total protein and albumin gradually decreased from convalescent patients, chronic HBV-infected patients, to acute HBV-infected patients. CONCLUSIONS Biochemical features could be used to evaluate the progress and therapeutic effects of HBV-infection. Our analysis firstly reported basic and biochemical information of HBV patients in Southwest China.

High prevalence of HIV-1 transmitted drug resistance among therapy-naïve Burmese entering travelers at Dehong ports in Yunnan, China

BackgroundThe overall success of Human immunodeficiency virus type 1 (HIV-1) antiretroviral therapy (ART) was heavily challenged upon the occurrence of drug resistance. Dehong Prefecture witnessed not only the first report of HIV-1 infection but also the experimental adoption of antiviral treatment in China. The transmission and epidemic of HIV-1 in Dehong is impacted by cross-border activities. The characteristics of HIV-1 drug resistance among therapy-naïve Burmese entering travelers in Yunnan and their speculated origin are still not clarified.MethodsTwo hundred ninety-eight HIV-1 infected Burmese entering travelers at Dehong ports were recruited between 2003 and 2012. The partial HIV-1 pol gene fragments were amplified and sequenced for the analysis of drug-resistance mutations (DRMs). Phylogenetic analysis on gag-pol gene was conducted to elucidate phylogenetic and evolutionary characteristics of these drug resistant strains.ResultsIt was figured out that the occurrence ratio of HIV-1 drug resistance among HIV-1 infected entering travelers from Myanmar was up to 12.8%. The resistant mutations covered several types, including one type of PI mutations (L33F), six types of NRTI mutations and seven types of NNRTI. Close genetic relationship was observed in the phylogenetic analysis on gag-pol gene among the drug resistant strains respectively from Dehong, other Yunnan areas, neighboring provinces (Guangxi) and neighboring countries (Thailand and Myanmar).ConclusionsThe findings in this study revealed that HIV drug resistant locus is spreading from the population who is receiving drug-resistance treatment to the new infectors, which indicates the urgency of surveillance work on drug resistance among the migrant population with high risks of HIV infection.

Association between genetic polymorphisms of the IL28B gene and leukomonocyte in Chinese hepatitis B virus-infected individuals

Background Hepatitis B infection is one of the most severe hepatic diseases in China. Thus, understanding the genetic pathogenesis of hepatitis B virus (HBV)-infected individuals is important. Although no consistent result is obtained in different populations, HBV treatment effect is reportedly associated with the IL28B gene. Methods To investigate the role of the IL28B gene in HBV-infected individuals in Yunnan, China, we screened genotypes of three single nucleotide polymorphisms (SNPs, rs12979860, rs8099917, and rs12980275) in HBV-infected individuals and general controls by using SnapShot and sequencing. Results Results showed no significant difference was found in genotypes, alleles, and haplotypes frequency between the HBV-infected individuals and controls. After dividing the HBV-infected individuals into patients in acute infection, chronic HBV patients, and patients undergoing convalescence, the genotype GT (P = 0.033) and allele G (P = 0.038) of rs8099917 showed statistically higher frequency in the acutely infectious individuals than in the HBV patients undergoing convalescence. HBV viral load was higher in the acutely infectious patients than in the chronic infection group. Strikingly, we found that leukomonocyte (LYM) level was associated with SNPs in the IL28B gene. In addition, the LYM levels were lower in the HBV-infected individuals with genotype CC of rs12979860 and AA of rs12980275 than in the patients with other genotypes of these two SNPs. Conclusion Our results suggested genetic polymorphisms of the IL28B gene were associated with LYM level of HBV-infected individuals.