Establishing an RNA fusions panel in soft tissue sarcoma with clinical validation.

The diagnosis and classification of soft tissue sarcomas (STS) remain challenging because of the rarity and overlapping morphologic manifestations of diverse STS subtypes. Characteristic gene fusions are commonly detected in STS and represent useful diagnostic markers. This study established and validated a custom-designed RNA sequencing panel that identified 64 gene fusions in STS. The analytical performance validation yielded excellent accuracy, with 100% (95% CI, 94.40%-100%) sensitivity and 93.33% (95% CI, 68.05%-99.83%) specificity. Clinical performances were further confirmed with 145 clinical formalin-fixed and paraffin-embedded (FFPE) samples from STS patients. Fusions were detected in 40% of samples (58/145). The common fusions SS18-SSX family, EWSR1-related fusions, COL1A1-PDGFB, FOXO1-associated fusions, and FUS-associated fusions were identified in corresponding STS subtypes. The RNA panel detected specific fusions in several cases where no conclusive diagnosis can be made based on the morphology and immunohistochemistry results. Data collected in this study demonstrate that the RNA fusions panel can better classify STS subtypes and serve as a good supplement for histopathology, exhibiting a great potential for the STS precise diagnosis.

Germline Duplication of SNORA18L5 Increases Risk for HBV-related Hepatocellular Carcinoma by Altering Localization of Ribosomal Proteins and Decreasing Levels of p53.

BACKGROUND & AIMS: Single nucleotide polymorphisms could affect risk for hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC). We performed a germline copy number variation (CNV)-based genome-wide association study (GWAS) in populations of Chinese ancestry to search for germline CNVs that increase risk of HCC. METHODS: We conducted a CNV-based GWAS of 1583 HCC cases (persons with chronic HBV infection and HCC) and 1540 controls (persons with chronic HBV infection without HCC) in Chinese populations. Identified candidates were expressed in L-02, HepG2, or TP53-/- or wild-type HCT116 cells, and knocked down with short hairpin RNAs in HepG2, Bel-7402, and SMMC-7721 cells; proliferation, colony formation, and apoptosis were measured. Formation of xenograft tumors from cell lines was monitored in nude mice. Subcellular localization of ribosome proteins and levels or activity of p53 were investigated by co-immunoprecipitation, immunofluorescence, and immunoblot analyses. Levels of small nucleolar RNA H/ACA box 18-like 5 (SNORA18L5) were quantified by quantitative reverse transcription polymerase chain reaction. RESULTS: We identified a low-frequency duplication at chromosome 15q13.3 strongly associated with risk of HBV-related HCC (overall P = 3.17 × 10-8; odds ratio, 12.02). Copy numbers of the 15q13.3 duplication correlated with the expression of SNORA18L5 in liver tissues. Overexpression of SNORA18L5 increased HCC cell proliferation and growth of xenograft tumors in mice; knockdown reduced HCC proliferation and tumor growth. SNORA18L5 overexpression in HepG2 and SMMC-7721 cells inhibited p53-dependent cell cycle arrest and apoptosis. Overexpression of SNORA18L5 led to hyperactive ribosome biogenesis, increasing levels of mature 18S and 28S ribosomal RNAs and causing the ribosomal proteins RPL5 and RPL11 to stay in the nucleolus, which kept them from binding to MDM2. This resulted in increased MDM2-mediated ubiquitination and degradation of p53. Levels of SNORA18L5 were increased in HCC tissues compared with nontumor liver tissues and associated with shorter survival times of patients. CONCLUSIONS: In a CNV-based GWAS, we associated duplication at 15q13.3 with increased risk of HBV-related HCC. We found SNORA18L5 at this location to promote HCC cell proliferation and tumor growth in mice. SNORA18L5 increases ribosome biogenesis, facilitates ribosomal RNA maturation, and alters localization of RPL5 and RPL11, allowing for increased MDM2-mediated proteolysis of p53 and cell cycle arrest.

[Mutation analysis of the PAH gene in children with phenylketonuria from the Qinghai area of China].

OBJECTIVE: To study the mutation characteristics of the phenylalanine hydroxylase (PAH) gene in children with phenylketonuria (PKU) from the Qinghai area of China, in order to provide basic information for genetic counseling and prenatal diagnosis. METHODS: Mutations of the PAH gene were detected in the promoter and exons 1-13 and their flanking intronic sequences of PAH gene by PCR and DNA sequencing in 49 children with PKU and their parents from the Qinghai area of China. RESULTS: A total of 30 different mutations were detected in 80 out of 98 mutant alleles (82%), including 19 missense (63%), 5 nonsense (17%), 3 splice-site (10%) and 3 deletions (10%). Most mutations were detected in exons 3, 6, 7, 11 and intron 4 of PAH gene. The most frequent mutations were p.R243Q (19%), IVS4-1G>A (9%), p.Y356X (7%) and p.EX6-96A>G(5%). Two novel mutations p.N93fsX5 (c.279-282delCATC) and p.G171E (c.512G>A) were found. p.H64fsX9(c.190delC) was documented for the second time in Chinese PAH gene. The mutation spectrum of the gene PAH in the Qinghai population was similar to that in other populations in North China while significantly different from that in the populations from some provinces in southern China, Japan and Europe. CONCLUSIONS: The mutations of PAH gene in the Qinghai area of China demonstrate a unique diversity, complexity and specificity.

Exposure to Hypoxia at High Altitude (5380 m) for 1 Year Induces Reversible Effects on Semen Quality and Serum Reproductive Hormone Levels in Young Male Adults.

This study investigated the effect of hypoxia at high altitude on the semen quality and the serum reproductive hormone levels in male adults. A total of 52 male soldiers were enrolled in this cohort study. They were exposed to hypoxia at high altitude (5380 m) for 12 months when undergoing a service. After exposure, they were followed up for 6 months. The samples of semen and peripheral blood were collected at 1 month before exposure (M0), 6 months of exposure (M6), 12 months of exposure (M12), and 6 months after exposure (M18). The semen quality was assessed with computer-assisted analysis system, and the serum levels of reproductive hormones, including prolactin (PRL), luteinizing hormone (LH), follicle-stimulating hormone (FSH), and testosterone were analyzed by ELISA. Compared with those at M0, total sperm count, sperm density, motility, survival rate, and serum levels of LH, PRL and testosterone were significantly decreased, whereas the liquefaction time was significantly prolonged and serum FSH level was significantly increased at M6 (p<0.05). At M12, total sperm count and sperm density increased, whereas sperm motility, survival rate, and the liquefaction time further decreased. Sperm velocities, progression ratios, and lateral head displacements were also decreased. Serum FSH level decreased while serum LH, PRL, and testosterone levels increased. Compared with those at M6, the changes in these detected parameters of semen and hormone at M12 were significant (p<0.05). At M18, all these detected parameters except testosterone level returned to levels comparable to those before exposure. In conclusion, hypoxia at high altitude causes adverse effects on semen quality and reproductive hormones, and these effects are reversible.

[Analysis of mutations in exon 7 of phenylalanine hydroxylase gene among children with phenylketonuria in Ningxia, China].

OBJECTIVE: To investigate the type and frequency of mutations in exon 7 of phenylalanine hydroxylase (PAH) gene among children with phenylketonuria (PKU) in Ningxia, China and to provide a basis for the genetic diagnosis and prenatal diagnosis of PKU in this region. METHODS: Direct sequencing of PCR product was performed to analyze the sequences of exon 7 and its flanking introns of 146 PAH alleles in 73 children with typical PKU (39 cases of Hui nationality and 34 cases of Han nationality) in Ningxia. RESULTS: Six mutations were detected, including R243Q (14.4%), R241C (6.8%), IVS7+2T→A (2.7%), L255S (0.7%), G247V (0.7%), and G247R (0.7%). The overall frequency of mutations (missense mutation and splice site mutation) in exon 7 was 26.0% (38/146). The detection rate of R241C mutation was significantly higher in children of Hui nationality than in children of Han nationality(10% vs 3%; P<0.05). CONCLUSIONS: In Ningxia, R243Q mutation in exon 7 of PAH gene is most common in children with PKU, followed by R241C. The frequency of R241C mutation in exon 7 of PAH gene varies between children with PKU of Hui and Han nationality.

[Analysis for phenylalanine hydroxylase gene mutations in 35 ethnic Hui children from Ningxia with phenylketonuria].

OBJECTIVE: To determine the type and frequency of phenylalanine hydroxylase gene (PAH) mutations in ethnic Hui patients from Ningxia with phenylketonuria (PKU). METHODS: For 35 PKU children patients and 50 healthy individuals, all exons and promoters of the PAH gene were analyzed with PCR and direct sequencing. RESULTS: Twenty mutations, including 8 missense mutations (40%), 5 nonsense mutations (25%), 4 splice site mutations (20%) and 3 deletion mutants (15%) were discovered. The overall detection rate was 68.57% (48/70). Common mutations have included R243Q (12.86%), R241C (11.43%), EX6-96A to G (5.71%), Y356X (5.71%), R413P(4.29%) and Q232X(4.29%), whilst rarer ones have included S16fsX10 (2.86%), R111X (2.86%) and L430P (2.86%). Among these, S16fsX10, L430P, D222G and IVS11+ 1G to A have not been reported previously. Y414X and S303fsX38 have not been reported in Hui ethnic group. No mutation was detected in the 50 normal controls. CONCLUSION: The types and distribution of PAH gene mutations in ethnic Hui from Ningxia have been different from other areas of China. The mutations also showed a rich diversity.

[Mutations of the phenylalanine hydroxylase gene in phenylketonuria patients from Shaanxi].

OBJECTIVE: To investigate the feature of phenylalanine hydroxylase (PAH) gene mutations and provide guidance for genetic and prenatal diagnosis of patients with phenylketonuria from Shaanxi. METHODS: For 55 patients whose blood Phe concentration was over 2.0 mg/dL, potential mutations in 13 exons and flanking sequences of the PAH gene were detected by PCR and DNA sequencing. RESULTS: A total of 98 mutations were detected in 110 PAH alleles, with the detection rate being 89.10%. Nine mutations have been identified in exon 7, which accounted for 33.67% of all. Exon 12 (14.29%) and exon 3 (12.24%) have followed. Thirty eight mutations, locating in exon2-exon12 and the flanking sequence, were detected in the 55 PKU patients. p.R243Q (24.49%) was the commonest mutation, whilstp.A47E, p.I65S and p.A259T were first discovered in China. After querying international databases including PAHdb and HGMD, the p.C334X was verified as the novel PAH gene mutation. CONCLUSION: The mutation spectrum of the PAH gene in Shaanxi has been identified. And a novel mutation has been identified. This may facilitate the diagnosis of PKU in the future.

Characterization of phenylalanine hydroxylase gene mutations in phenylketonuria in Xinjiang of China.

To investigate the spectrum and frequency of phenylalanine hydroxylase (PAH) gene mutations in phenylketonuria (PKU) patients in Xinjiang, China. Polymerase chain reaction (PCR), in combination with single-strand conformation polymorphism (SSCP) and DNA sequencing analyses were performed, to screen potential mutations in the PAH gene in 46 individual PKU patients. Direct DNA sequencing was used to analyze the all of the exons in the PAH gene, including the promoter and flanking intron regions, in another 15 PKU patients. Our results indicated that, 30 different mutation types were identified in all 122 PAH alleles, with the mutation detection rate of 78.7% (96/122). Four novel mutations, i.e., 5'-Flanking -626G>A, 5'-Flanking -480DelACT, S196fsX4, and IVS8+1G>C, were identified for the first time. Similar to other regions in North China, R243Q, EX6-96A>G, IVS4-1A>G, R111X, and Y356X were the most prevalent PAH mutations in PKU patients from Xinjiang. Additionally, common mutations showed different frequencies in Xinjiang, when compared to other areas. Furthermore, sixteen different PAH gene mutation types were identified for the first time in the minorities in Xinjiang. Distinctive mutation spectrum of PAH gene in PKU patients from Xinjiang were characterized, which may promote the construction of PAH gene mutation database and serve as valuable tools for genetic diagnosis and counseling, and prognostic evaluation for PKU cases in the local area.

[Lineage polymorphism of TCR Vα CDR3 in peripheral blood of uveitis patients].

OBJECTIVE: To study the lineage polymorphism of TCR Vα complementarity determining region 3 (CDR3) in the peripheral blood of uveitis patients. METHODS: Thirty-four subfamilies of TCR Vα CDR3 in the peripheral blood mononuclear cells (PBMC) of uveitis patients were amplified by RT-PCR, and then TCR Vα CDR3 lineage polymorphism was analyzed by immunoscope spectratyping. RESULTS: Most spectral type of the 34 subfamilies in 5 normal controls showed Gauss distribution. TCR Vα CDR3 scanning spectrum of 4 uveitis patients showed abnormal distribution peak, including monoclonal, oligoclonal/oligoclonal trend, skewing peak and irregular abnormal peak. The frequencies of abnormal peak type varied in the 34 TCR Vα subfamilies. A higher frequency of abnormal peak type was found in Vα13 and Vα17 subfamilies, while no abnormal peak type was found in Vα1.1, Vα10, Vα20 and Vα28 subfamilies. Abnormal peak was shown in Vα7 subfamily in the HLA-B27-negative patient (U2) , but no abnormal peak was shown in Vα7 subfamily in the 3 HLA-B27-positive patients (U1, U3, U4); Conversely, abnormal peak type of TCR Vα13 was found in all the 3 HLA-B27-positive patients, but normal in HLA-B27-negative patients. CONCLUSION: TCR Vα CDR3 lineage has significant characteristic polymorphism in the peripheral blood of uveitis patients. Monoclonal/oligoclonal expansion of T cells may be autoreactive T cells in nature and they may be involved in pathogenesis of uveitis.

[Sperm DNA damage in young men working on the plateau].

OBJECTIVE: To investigate whether long working in the high-altitude area can damage sperm DNA in men. METHODS: We enlisted 51 service men stationed on the plateau in an observation group and another 53 living in the low-altitude area in a control group. We detected and compared the damages to sperm DNA in the semen samples from the two groups using single cell gel electrophoresis and the sperm chromatin dispersion test. RESULTS: The percentages of total, G1, G2 and G3 comet cells and abnormal sperm of the observation group were (5.56 +/- 3.98)%, (3.72 +/- 1.85)%, (1.57 +/- 1.07)%, (0.27 +/- 0.34)% and (16.59 +/- 12.07)%, respectively, before stationed on the plateau, but significantly increased at 6 months of plateau life ([11.15 +/- 8.59]%, [5.97 +/- 3.26]%, [3.83 +/- 2.13%, [1.35 +/- 1.53]% and [22.03 +/- 15.33]%, P<0.05). The percentages of G2 comet cells and abnormal sperm were decreased to (3.32 +/- 1.83)% and (20.54 +/- 15.52)% at 12 months, but still significantly higher than the baseline (P<0.05). CONCLUSION: Long working on the plateau may damage sperm DNA, but its influence on male fertility deserves further investigation. Therefore, it is important to reinforce reproductive health protection for males working on the plateau.

[Characteristics of the PAH gene mutation in Chinese patients with phenylketonuria in Xinjiang].

OBJECTIVE: To study the characteristics of the PAH gene mutation in patients with phenylketonuria (PKU) in Xinjiang area. METHODS: The mutations in exons 3, 5, 6, 7, 11 and 12 and the flanking intronic sequence of the PAH gene were detected by PCR/SSCP analysis and direct DNA sequencing in 46 PKU patients. RESULTS: Twenty different mutations were found in 68/92 alleles (73.9%). The prevalent mutations of R243Q, EX6 96A>G, R111X, Y356X and V399V were similar to that of Northern China populations. The mutations F161S, L255S, P281L, and R413P were significantly different from that in other Chinese populations. It was the second time that E280G and A434D mutations were reported in the world, that L255S, P281L, R261Q, and I65T mutations were found in China. Thirteen different mutations were first found in Chinese Uygur, which showed a distinct ethnic characteristics. CONCLUSION: The study showed not only a distinct and conservative, but also a crossed and syncretic genetic characteristics in Xinjiang Uygur population. The results suggest that Xinjiang could be an ideal genetic resource repertoire for studying diversity of gene mutations, heterogeneity of PAH gene, human origins and migration.

[Semen analysis of sterile patients among occupational computermen].

OBJECTIVE: To explore temn possible correlation between the computer occupational semen quality. METHODS: We included in this study 224 sterile males (118 computermen and 106 non-computermen) treated in our clinic of male sterility and 125 normal fertile men as controls, and analyzed such parameters as semen liquefaction time and sperm density, vitality and motility according to the WHO standard. RESULTS: Compared with the normal controls, there was a significant decrease in the semen volume and sperm density, vitality and motility (P < 0.05-0.01) and a marked increase in liquefaction time in the infertile computermen and non-computermen (P < 0.01). The semen volume and sperm vitality and motility were significantly lower in the infertile computermen than in the infertile non-eomputermen (P < 0.05). The three parameters were also significantly decreased in the 0-5, 6-10 and > 10 h/d computer use groups. Similarly, significantly lower sperm density, vitality and motility were observed in the > 10 hid group than in the 0-5 and 6-10 h/d groups (P < 0.05-0.01), but with no statistical difference between the latter two (P > 0.05). CONCLUSION: Computer occupation is associated with abnormal semen quality, and long-term computer use ( > 10 h/d) may be one of the factors of male infertility.

[The mutant spectrum of phenylalanine hydroxylase gene in Northern Chinese].

OBJECTIVE: To understand the mutant spectrum of phenylalanine hydroxylase (PAH) gene in Northern Chinese. METHODS: All the exons and flaking introns of PAH gene were detected by PCR-single strand conformation polymorphism (PCR/SSCP) and sequencing in 230 patients with phenylketonuria (PKU). RESULTS: (1) A total of 75 different mutations were detected in 435 out of 460 mutant alleles (94.6%). Among them 3 mutations (S251-R252>SfsX89, Y387D and A389G) have not been reported previously. The mutations, R243Q, EX6-96A>G, R111X, R413P and Y356X, were the prevalent mutations with relative frequencies of 21.7%, 10.2%, 8.3%, 6.5%, and 6.1% respectively, followed by V399V(4.1%), IVS4-1G>A (3.5%), IVS7+2T>A (2.2%) and R241C(2.2%). Most mutations were detected in exons 3, 5, 6, 7, 11 and 12 and flaking introns of PAH gene. (2) Ten polymorphism sites were detected in the study. Four sites, IVS3-22C>T, IVS10+97G>A, Q232Q and V245V, had high relative frequencies of 56.7%, 75.9%, 89.0% and 81.9% respectively. It would suggest that the race diversity exists in PAH cDNA sequence. CONCLUSION: The mutation spectrum of PAH gene in Northern Chinese is similar to other Asian populations but significantly different from European populations.

[Comparison of sperm parameters between male adults at different altitudes].

OBJECTIVE: To investigate the influence of long-term anoxic exposure on the sperm function of male adults at different altitudes. METHODS: A total of 28 male adults that had stayed at the altitude of 5 340 m for 1-3 years were included as a high-altitude group (HAG), 34 at the mean altitude of 3 800 m for 2-5 years as a middle-altitude group (MAG) and 31 permanently at the altitude of 1 300 m as controls. Semen specimens were collected and the real-time semen analysis was performed by using computer-assisted semen analysis (CASA) system. RESULTS: The sperm density, VCL, VSL, VAP and LIN in the HAG were (51.12 +/- 14.61) x 10(6)/ ml, (48.17 +/- 13. 52) microm/s, (32.64 +/- 6.70) microm/s, (41.21 +/- 9.32) microm/s and 52.24 +/- 8.14, respectively, significantly lower than those of the control (P < 0.01 or P < 0.05). Compared with the control group, there was a progressive decrease in sperm concentration, sperm motility rate, VSL, VCL, LIN, VAP and ALH in the MAG. CONCLUSION: The higher the altitude, the more obvious was the negative effect of anoxic exposure on the sperm function of male adults.

[Pro-apoptotic efficiencies of three reconstructed human caspase-8 on cervical cancer cell line HeLa].

BACKGROUND & OBJECTIVE: Apoptosis is a kind of evolutional high conservative cell death. Transferring high active pro-apoptotic molecules into cancer cells to induce apoptosis is a potential strategy for cancer gene therapy. Based on our previous generation of reconstructed human caspase-8, which can continuously induce apoptosis of cervical cancer cell line HeLa, by reversing its large and small subunits, this study was designed to investigate the pro-apoptotic efficiencies of 3 reconstructed human caspase-8 (Casp8CD, Rev8, and Rev8L) on HeLa cells, and to explore the feasibility of reconstructed human caspase-8 as potential apoptosis-inducing candidates. METHODS: The eukaryotic expression vectors pIRES2-EGFP carrying Casp8CD, Rev8, and Rev8L genes were transfected into HeLa cells, and breast cancer MCF-7 cells. Expressions and pro-apoptotic effects of Casp8CD, Rev8, and Rev8L genes were observed under fluorescent microscope, and their pro-apoptotic efficiencies were assessed by MTT assay and cells counting. The flexibilities of linking-peptides between subunits of Rev8 and Rev8L were analyzed by bioinformatics. RESULTS: Expressions of the 3 reconstructed caspase-8 genes were observed under fluorescent microscope, and the HeLa and MCF-7 cells expressing Rev8 or Rev8L genes displayed typical apoptotic volume decrease (AVD). MTT assay showed that compared with control cells, A(570) values of Rev8- and Rev8L-transfected cells began to decrease 20 h after transfection. Cell counting results indicated that cell death ratio of Casp8CD-, Rev8-, and Rev8L-transfected cells were 16.9%, 52.3%, and 47.7%, respectively, 24 h after transfection; and 12.9%, 51.6%,and 61.2%,respectively,48 h after transfection. Bioinformatics analysis showed that the linking-peptides between subunits of Rev8 and Rev8L were flexible. CONCLUSION: Rev8 and Rev8L molecules have similar pro-apoptotic effects and efficiencies, but over-expressed Casp8CD had no significant pro-apoptotic effects.

[The chromosomal location of AD7C-NTP gene and the prediction of transmembrane domains of its deduced protein].

AIM: To characterize the chromosomal location of AD7C-NTP gene and predict the transmembrane domains and sub-cellular location of its deduced protein. METHODS: The AD7C-NTP mRNA sequence was alignmented with human genomic DNA sequence by Blat server. The transmembrane domains and sub-cellular location of AD7C-NTP protein were predicted by using PHDhtm, TMHMM2.0, HMMTOP2.0, SMART and PSORT servers, etc. RESULTS: The AD7C-NTP gene located in minus strand of 1p36.11, without intron. The AD7C-NTP protein was predicted to have 3 potential transmembrane domains and locate on peroxisome's membrane. CONCLUSION: Bioinformatics analysis of the AD7C-NTP gene and its deduced protein provides valuable clues for further gene cloning and study of function.