A defined serum-free culture system for human long-term haematopoietic stem cells.

Long-term repopulating haematopoietic stem cells (LT-HSCs) have the ability to reconstitute the entire haematopoietic system following transplantation permanently. Despite great achievements in HSC transplantation, the limited transplantable HSC number, especially LT-HSCs, remains critical for successful transplantation and broader applications. In this study, we established a defined serum-free culture system for in vitro expansion of LT-HSCs. This culture system (E1) expanded LT-HSCs from umbilical cord blood, human mobilization peripheral blood and bone marrow. These E1-expanded HSCs reconstituted the haematopoietic and immune systems in primary and secondary transplanted mice in a short time. Better haematopoietic reconstitution was observed in secondary xenografted mice. Moreover, we obtained the comprehensive expression profile and cellular components of LT-HSCs from umbilical cord blood. Our study provides a valuable tool for LT-HSC research and may improve clinical applications of HSCs.

Genome-Wide Association Identifies Risk Pathways for SAPHO Syndrome.

SAPHO syndrome is a rare chronic inflammatory disease which is characterized by the comprehensive manifestations of bone, joint, and skin. However, little is known about the pathogenesis of SAPHO syndrome. A genome-wide association study (GWAS) of 49 patients and 121 control subjects have primarily focused on identification of common genetic variants associated with SAPHO, the data were analyzed by classical multiple logistic regression. Later, GWAS findings were further validated using whole exome sequencing (WES) in 16 patients and 15 controls to identify potentially functional pathways involved in SAPHO pathogenesis. In general, 40588 SNPs in genomic regions were associated with P < 0.05 after filter process, only 9 SNPs meet the expected cut-off P-value, however, none of them had association with SAPHO syndrome based on published literatures. And then, 15 pathways were found involved in SAPHO pathogenesis, of them, 6 pathways including osteoclast differentiation, bacterial invasion of epithelial cells, et al., had strong association with skin, osteoarticular manifestations of SAPHO or inflammatory reaction based published research. This study identified aberrant osteoclast differentiation and other pathways were involved in SAPHO syndrome. This finding may give insight into the understanding of pathogenic genes of SAPHO and provide the basis for SAPHO research and treatment.

Profiling of the pattern of the human TRB/IGH-CDR3 repertoire in primary biliary cholangitis patients.

INTRODUCTION: Primary biliary cholangitis (PBC) is characterized by lymphocyte cell-induced immune destruction of cholangiole. However, the immunological characteristics of peripheral blood cells in PBC patients remain unknown. This study was designed to reveal the differences in the immunological characteristics between PBC patients and healthy adults. METHODS: We performed high-throughput sequencing to determine the TRB-CDR3 and IGH-CDR3 repertoires of T and B cells in 19 healthy controls and 29 PBC patients. Different immunological characteristics, such as distinctive complementarity determining region 3 (TRB-CDR3) lengths, usage bias of V and J segments, and random nucleotide addition were identified in PBC and healthy control (HC) groups. RESULTS: The diversity of TRB-CDR3 was significantly lower in the PBC group compared with the HC group. CDR3 and the N addition length distribution were significantly changed compared with the HC group. It appeared that the PBC group had more short N additions and the HC group had more long N additions in the TRB-CDR3 repertoire. The results also revealed a set of PBC-associated clonotypes compared with the HC group. CONCLUSION: This study suggested that PBC is a complex autoimmune disease process with evidence of different TRB-CDR3 rearrangements compared with healthy adults that share IGH-CDR3 peptides with some autoimmune diseases. This new insight may contribute to a better understanding of the immune functions of PBC patients and benefit efficient applications of PBC diagnosis and treatments.

Profiling the pattern of human TRB/IGH-CDR3 repertoire in liver transplantation patients via high-throughput sequencing analysis.

Immune processes in liver transplantation remain poorly understood. Acute allograft rejection in liver transplantation is a kind of T cell-mediated inflammatory disease accompanied by inflammatory cell infiltration. However, the effect of acute allograft rejection on the immunological characteristics of TCRs in peripheral blood mononuclear cell is unknown. In this study, we characterized the pattern of the human T cell receptor beta chain (TRB) and immunoglobulin heavy chain (IGH) complementarity-determining region 3 (CDR3) repertoires via high-throughput sequencing in 11 acute allograft rejection (AG) cases, 23 patients with stable allograft liver function (ST) who had liver transplantation performed and 20 healthy controls (HC). The diversity of TRB-CDR3 was significantly reduced in the AG group compared with the ST group and healthy controls (HC). The CDR3 and N-addition length distribution were not significantly different between the AG and ST groups. However, N-addition length distribution was significantly changed compared to HC. It seemed that AG used more short N-additions and healthy people used more long N-additions in TRB-CDR3 repertoire. Our findings suggested that the TRB-CDR3 region of AG had distinctive V gene use compared with that of HC. The characteristics of ST seemed to be in between those of AG and HC although the difference is not significant. Cluster analysis showed that the TRB repertoire could not effectively distinguish AG from ST. This research might give to a better understanding of the immune process of liver transplantation.

De novo genome assembly of a Han Chinese male and genome-wide detection of structural variants using Oxford Nanopore sequencing.

Advances in third-generation sequencing technologies provide an opportunity to investigate the complex organizational structure of the genome and unravel the genetic mechanisms of disease and physiological traits. Here we report the sequencing and de novo assembly of a healthy male northern Han Chinese genome and detection of structural variants using only nanopore sequencing data. We performed de novo assembly after filtering the raw data. Then, we aligned the assembled contigs to the human reference genome, and visualized chromosomes plot, which illustrated the contiguity of the nanopore assembly. Additionally, genomic structural variants were detected using a structure variation detection tool with long-read sequencing data. Median coverage depth was 30-fold and the read N50 was 27,136 bp. 96.51% of reads had at least one alignment to the human reference genome. The final assembled genome was 2.85 GB in size, with an N50 contig size of 5.4 MB. We identified 20,085 structural variants. Third-generation sequencing technologies have many advantages in de novo whole-genome assembly and detection of structural variants. Our results provide reference data for disease research, and can be used as a novel population-specific dataset of structural variants to support the efficient development of personalized precision medicine.

Copy Number Variation of Multiple Genes in SAPHO Syndrome.

OBJECTIVE: SAPHO (synovitis, acne, pustulosis, hyperostosis, osteitis) syndrome is a type of rare chronic aseptic inflammation of unknown etiology. To date, no research to our knowledge has reported copy number variation (CNV) of genes that could affect predisposition to SAPHO syndrome. We investigated the association between CNV profile and SAPHO syndrome. METHODS: We used array comparative genomic hybridization (CGH) to screen for CNV in a nuclear family including 2 patients and a healthy control. We then validated the copy numbers of candidate genes found in the array CGH assay and other candidate genes by TaqMan real-time PCR in 360 case and control samples. RESULTS: Ten regions from 8 chromosomes were found to have abnormal gene copies in the nuclear family, so the CNV of candidate genes (ADAM5, CSF2RA, IL3RA, and 9 other genes) were tested by TaqMan PCR. Significant copy number loss of CSF2RA (p = 0.000) and NOD2 (p = 0.005), and significant copy number gain of MEGF6 (p = 0.002) and ADAM5 (p = 0.000) were seen in patients with SAPHO compared with controls at the a = 0.05 level. There were no differences in the other 8 candidate genes between patient and control samples (p > 0.05). CONCLUSION: Our study established the first association between CNV in CSF2RA, NOD2, MEGF6, and ADAM5 and SAPHO syndrome. These findings may offer insight into the pathogenesis of SAPHO and provide the basis for improved diagnosis and treatment.

Association analysis of interleukin-23 receptor SNPs and SAPHO syndrome in Chinese people.

OBJECTIVE: SAPHO syndrome (synovitis, acne, pustulosis, hyperostosis, and osteitis) is an autoimmune disease of unknown etiology that seriously affects patients' daily lives. Family-based investigations support genetic contributions toward disease susceptibility. The present study evaluated whether the previously reported autoimmune disease-associated single nucleotide polymorphisms (SNPs) have any genetic overlap with SAPHO syndrome. METHOD: Genomic DNA was obtained from 71 SAPHO patients and 104 healthy controls. The SNP genotypes of each patient were determined with polymerase chain reaction and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Genotype, allele, and haplotype frequencies were analyzed with SPSS software. RESULTS: Three SNP sites (rs10889677 and rs2201841 of interleukin [IL]-23R, and rs2243248 of IL-4) showed significant correlation with the occurrence of SAPHO syndrome in additive and dominant genetic models, while rs7517847 of IL-23R showed substantial correlation with SAPHO in the dominant genetic model. The G allele of rs2243248 (IL-4) was a high risk factor for SAPHO (P = 2.41e-5, odds ratio [OR] =7.79, 95% CI: 2.59-23.3). The haplotype (A-G-C-G-T), comprising 5 SNPs of the IL-23R gene, had a significantly higher frequency in the SAPHO cohort than in the controls (P = .011, OR = 2.05, 95% CI: 1.12-3.60). CONCLUSION: Variants rs10889677, rs2201841, and rs7517847 of IL-23R, and variant rs2243248 of IL-4, showed strong associations with SAPHO syndrome. Patients carrying the A-G-C-G-T haplotype of IL-23 are significantly more likely to develop SAPHO syndrome.

Deep targeted sequencing reveals the diversity of TRB-CDR3 repertoire in patients with preeclampsia.

Preeclampsia (PE) is one of the major causes of maternal and perinatal mortality worldwide. This study aimed to determine the immunological characteristics of PE patients and normal pregnancy at the T cell receptor beta-chain (TRB) level by using high-throughput sequencing. High-throughput sequencing was performed to analyze the expression of TRB-CDR3 in circulating T cells. T cells were isolated from 36 healthy pregnant women, 24 patients with severe PE, and 18 patients with moderate PE. Rearranged mRNA sequences were assigned to their germline V, D, and J counterparts, and translated into proper amino acids by the IMGT database. In general, PE samples had more TRB-CDR3 reads and types than those of normal pregnant woman in the circulation, but the mean number of TRB-CDR3 reads and unique TRB-CDR3 reads in severe group was lower than that in the moderate group. In PE patients, the V7_9 and V20_1 gene loci were more prevalent than in healthy pregnant women. In addition, 4 kinds of TRB-CDR3 peptides were found to be highly relevant to the pathogenesis of PE. Of them, peptides matched to herpes simplex virus antigen-specific T cells were much lower in PE samples.

Exome sequencing reveals novel IRXI mutation in congenital heart disease.

Genetic variation in specific transcription factors during heart formation may lead to congenital heart disease (CHD) or even miscarriage. The aim of the present study was to identify CHD­associated genes using next generation sequencing (NGS). The whole exome DNA sequence was obtained from a stillborn fetus diagnosed with tricuspid atresia and complete transposition of the great arteries using high­throughput sequencing methods. Subsequently, genetic variants of CHD­associated genes were selected and verified in 215 non­syndromic CHD patients and 249 healthy control subjects using polymerase chain reaction combined with Sanger sequencing. Genetic variants of previously reported CHD­inducing genes, such as cysteine rich with EGF like domains 1 and cbp/p300­interacting transactivator with Glu/Asp rich carboxy­terminal domain 2, were discovered through the NGS analysis. In addition, a novel non­synonymous mutation of the iroquois homeobox 1 (IRX1) gene (p.Gln240Glu) was identified. A total of three non­synonymous mutations (p.Gln240Glu, p.Ser298Asn and p.Ala381Glu) of the IRX1 gene were verified in 215 non­syndromic CHD patients, but not in 249 healthy volunteers. The results demonstrated that NGS is a powerful tool to study the etiology of CHD. In addition, the results suggest that genetic variants of the IRX1 gene may contribute to the pathogenesis of CHD.

Different Contributions of CDKAL1, KIF21B, and LRRK2/MUC19 Polymorphisms to SAPHO Syndrome, Rheumatoid Arthritis, Ankylosing Spondylitis, and Seronegative Spondyloarthropathy.

OBJECTIVES: Synovitis, acne, pustulosis, hyperostosis, and osteitis (SAPHO) syndrome, rheumatoid arthritis (RA), ankylosing spondylitis (AS), and seronegative spondyloarthropathy (SPA) are autoimmune diseases of unknown etiology, which share some clinical manifestations in common. Previous family-based investigations support genetic contributions to the susceptibility of these diseases. The current study evaluated whether three previously reported AS-associated single-nucleotide polymorphisms (SNPs), rs6908425 T>C in CDKAL1, rs11584383 T>C near KIF21B, and rs11175593 C>T near LRRK2/MUC19, have any genetic overlap across multiple autoimmune diseases including SAPHO syndrome, RA, AS, and SPA. MATERIALS AND METHODS: Genomic DNA was obtained from 71 SAPHO, 125 RA, 67 AS, and 35 SPA Han Chinese patients, as well as 104 healthy controls. SNPs were genotyped by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Genotype and allele frequencies were analyzed using chi-square test. RESULTS: rs6908425 T>C in CDKAL1 was significantly different between SAPHO cases and healthy controls (odds ratios = 2.056, 95% confidence intervals: 1.211-3.490; p = 0.007), but no SNPs were associated with the risk of developing RA, AS, or SPA (p > 0.05). Analysis of genotype distributions showed similar results. A significant difference was only found in the genotype frequency of rs6908425 in SAPHO cases (p = 0.004); no significant differences were detected among patients with RA, AS, and SPA (p > 0.05). CONCLUSIONS: Our results suggest that rs6908425 in CDKAL1 is associated with the risk of developing SAPHO in Han Chinese populations. People who carry the risk allele T of rs6908425 might be more prone to developing SAPHO syndrome.

High throughput sequencing reveals the diversity of TRB-CDR3 repertoire in patients with psoriasis vulgaris.

Psoriasis is a T cell-mediated chronic inflammatory skin disease with inflammatory cell infiltrates in the dermis and epidermis. Previous studies suggested that there are some expanded T-cell receptor (TCR) clones in psoriatic skin. However, the effect of psoriasis on the immunological characteristics of TCR in circulating blood has not been reported. To address this, we performed high-throughput sequencing to reveal the immunological characteristics of TCR beta chain (TRB) in both psoriasis patients and healthy controls. Our results revealed that the TRB-CDR3 region of psoriasis patients had distinctive immunological characteristics compared with that of healthy controls, including V gene usage, nt of N addition. In addition, three types of TRB-CDR3 peptides were found highly relevant to psoriasis. Our findings show the comprehensive characteristics of psoriasis on the TRB-CDR3 repertoire of circulating blood at sequence-level resolution. These findings may contribute to a better understanding of the pathogenesis of psoriasis and open opportunities to explore potential therapeutic targets.

High-Throughput Sequencing Reveals Immunological Characteristics of the TRB-/IgH-CDR3 Region of Umbilical Cord Blood.

OBJECTIVE: To compare the differences of immunological characteristics between newborn and adults, we performed high-throughput sequencing to reveal the diversity of umbilical cord blood and adult peripheral blood at both T-cell receptor beta chain (TRB) and immunoglobulin heavy chain (IGH) levels. STUDY DESIGN: High-throughput sequencing was performed to analyze the expression of TRB-CDR3 and IGH-CDR3 in circulating T and B cells isolated from 20 healthy adults, 56 pregnant women, and 40 newborns. RESULTS: Our results revealed different immunological characteristics between newborn and adults, such as distinctive complementarity determining region 3 (CDR3) lengths, usage bias of variable and joining segments, random nucleotide addition, a large number of unique CDR3 peptides, and a greater repertoire diversity. Moreover, each newborn had a distinctive TRB-/IGH-CDR3 repertoire that was independent of the maternal immune status. CONCLUSIONS: This study presents comprehensive, unrestricted profiles of the TRB/IGH-CDR3 repertoire of newborns, pregnant women, and healthy adults at a sequence-level resolution. Our data may contribute to a better understanding of the immune system of newborns and benefit the efficient application of umbilical cord blood transplantation in future.

Contribution of TIMP3 polymorphisms to the development of preeclampsia in Han Chinese women.

PURPOSE: The aim of this study was to investigate whether polymorphisms in the tissue inhibitor of metalloproteinase 3 gene (TIMP3) are associated with the risk of preeclampsia (PE) in Han Chinese women. METHODS: Nine single TIMP3 tag-single nucleotide polymorphisms were selected by Haploview and genotyped using the Sequenom method in 181 preeclamptic and 203 healthy pregnant women from eastern China. RESULTS: The allele frequencies of the tag-single nucleotide polymorphisms were not significantly different between groups (P > 0.05). However, the genotype distribution of rs135025 was shown to differ between the multigravidity PE subgroup (>3) and controls under additive (P = 0.018) and recessive models (P = 0.008), while the genotype distribution of rs80272 differed significantly between the severe PE subgroup and controls under additive (P = 0.014) and dominant models (P = 0.041). Moreover, the H2 haplotype (A-C-G-T-A-A-G-C-G) was found to be associated with the risk of PE (P = 0.035). CONCLUSIONS: Genotypes of rs135025 and rs80272 in TIMP3 may therefore influence susceptibility to PE, and pregnant women carrying the H2 haplotype might be more prone to developing PE.

Decreased mRNA and protein expression of TWIST1 in myocardial tissue of fetuses with ventricular septal defects.

Ventricular septal defect (VSD) is the most common type of congenital heart disease (CHD). The single gene mutations or absences that contribute to VSD development are well established; however, the aim of the present study was to measure gene expression variation between VSDs and normal fetal myocardial tissue. TWIST1, an important tumor biomarker, is a basic helix-loop-helix transcription factor that regulates cell proliferation, migration and differentiation in embryonic development and transformed tumor cells. Although growing evidence demonstrates that TWIST1 participates in a variety of human neoplastic diseases, the role of TWIST1 in VSD has remained elusive. Twenty-six VSD fetal myocardial tissue samples and 12 normal samples at matched gestational weeks (22-28 weeks) were included in the present study. Using reverse transcription quantitative polymerase chain reaction (PCR) and real-time PCR, it was demonstrated that TWIST1 mRNA was reduced by almost two-fold in the VSD samples compared with the normal samples. Western blot analysis also revealed that TWIST1 expression was decreased by ~three-fold (P=0.001) in the VSD samples compared with that in the normal samples. Of note, five complete ventricular (also called functionally univentricular or single ventricular) septal ageneses were identified among the specimens. For the five complete ventricular septal agenesis samples, similar results to those for other VSD fetal myocardial tissues were obtained. In conclusion, the results of the present study showed that TWIST1 mRNA and protein levels were reduced in VSDs. The present study was the first, to the best of our knowledge, to report that TWIST1 is not only a tumor biomarker, but may also be involved in the pathogenesis of VSD.

Association between CRP gene polymorphisms and the risk of preeclampsia in Han Chinese women.

BACKGROUND: As an inflammatory marker, C-reactive protein (CRP) has elevated expression in preeclampsia (PE), which is implicated in the pathogenesis of PE, but there has been a lack of information on the possible association between genetic variants of CRP and PE. In this study, we aimed to assess the genetic association between CRP polymorphisms and the risk of PE in Han Chinese Women. METHODS: Five single-nucleotide polymorphisms of CRP, rs2794521 (T>C), rs3091244 (C>T>A), rs3093068 (C>G), rs876538 (C>T), and rs1205 (C>T) were genotyped using the Sequenom method in 181 PE patients and 203 controls. RESULTS: The T allele frequency for rs2794521 was significantly higher in PE patients than in controls (odds ratios [OR]=4.091; 95% confidence interval [CI]: 1.533-10.917; p=0.002). The TT genotype of rs2794521 conferred a risk for PE (TT vs. TC+CC: OR=4.062; 95% CI: 1.499-11.008; p=0.003) and severe PE (TT vs. TC+CC: OR=9.577; 95% CI: 1.267-72.397; p=0.006). The other four polymorphic loci were not different between the groups. The CRP H2 haplotype (T-C-C-G-C) was associated with PE (OR=2.129; 95% CI: 1.47-3.085; p<0.001), whereas the H1 haplotype (C-C-C-G-C) offered protection (OR=0.23; 95% CI: 0.066-0.8; p=0.01). CONCLUSIONS: The CRP variant rs2794521 shows a strong association with PE in Han Chinese women. Pregnant women with the TT genotype of rs2794521 have higher odds of having PE, which further supports a possible role for CRP in PE.

Associations between UGT1A1*6 or UGT1A1*6/*28 polymorphisms and irinotecan-induced neutropenia in Asian cancer patients.

PURPOSE: Neutropenia is a life-threatening side effect of irinotecan, and uridine diphosphate glucuronosyltransferases (UGTs) gene polymorphisms are considered to be one of the predictive markers of irinotecan-related toxicities. Many studies have demonstrated that patients bearing UGT1A1*28 have a higher risk of severe neutropenia on toxicity of irinotecan. However, UGT1A1 (TA7/TA7) was very rare in Asian populations. Some researches reported that UGT1A1*28 and/or UGT1A1*6 could predict irinotecan-induced toxicities in Asian populations, but controversial conclusions still remained. This study aims to investigate the association between UGT1A1 gene polymorphisms *6, *6/*28 and irinotecan-related neutropenia in Asian cancer patients receiving irinotecan regimen chemotherapy. EXPERIMENTAL DESIGN: Meta-analyses were done to assess the relationship between UGT1A1*6 or UGT1A1*6/*28 and irinotecan-induced neutropenia. RESULTS: The risk of neutropenia was significantly higher among patients with a UGT1A1*6 genotype than among those carrying the UGT1A1*1 allele(s) [odds ratio (OR) 3.276; 95 % confidence interval (CI) 1.887-5.688; P = 0.000 (*6/*6 vs. *1/*6 or *1/*1)], [OR 1.542; 95 % CI 1.180-2.041; P = 0.001 (*6/*6 or *1/*6 vs. *1/*1)]. Also, the risk was significantly higher among patients with a UGT1A1*6/*28 than among those carrying the UGT1A1*1 allele(s) [OR 3.275; 95 % CI 2.152-4.983; P = 0.000 (*6/*6 or *28/*28 or *6/*28 vs. *1/*6 or *1/*28 or *1/*1)]. CONCLUSIONS: In conclusion, the UGT1A1*6 and UGT1A1*6/*28 genotypes were associated with an increased risk of irinotecan-induced neutropenia in Asian cancer patients.

Effects of the NQO1 609C>T polymorphism on leukemia susceptibility: evidence from a meta-analysis.

A functional polymorphism in the NQO1 gene, featuring a 609C>T substitution,leading to proline to serine amino-acid and enzyme activity changes, has been implicated in cancer risk. However, individually published investigations showed inconclusive results, especially for leukemia. In this study, we therefore performed a meta- analysis of 21 publications with a total of 3,634 cases and 4,827controls, mainly for leukemia. We summarized the data on the association between the NQO1 609C>T polymorphism and risk of leukemia and performed subgroup analyses by ethnicity and leukemia type. We found that the variant TT homozygous genotype o was associated with a modestly increased risk of leukemia (TT versus CT/CC: OR = 1.23, 95%CI = 1.00 - 1.51, heterogeneity = 0.76; I2 = 0%). Following further stratified analyses, increased risk was only observed in subgroups of Caucasians. This meta-analysis suggests that the NQO1 609T allele is a high-penetrance risk factor for leukemia in Caucasians. The effect on leukemia may be modified by ethnicity and leukemia type, and the small sample sizes of the subgroup analyses suggest that further larger studies are needed.

The effect of CHEK2 variant I157T on cancer susceptibility: evidence from a meta-analysis.

Cell cycle checkpoint kinase 2 (CHEK2) is a checkpoint kinase that plays an important role in the DNA damage signaling network. Numerous epidemiological studies have evaluated the association between the CHEK2 I157T variant and cancer susceptibility. However, the results of these studies on the association remain conflicting. The main purpose of this study was to integrate previous results and explore whether the CHEK2 I157T variant is associated with cancer susceptibility. PubMed, Embase (before 2012-10-1), Google Scholar, and CBMdisc were searched for studies on the relationship of the CHEK2 I157T variant and the incidence of cancer. Eligible articles were included for data extraction. The main outcome was the frequency of CHEK2 I157T polymorphisms between cases and controls. Comparison of the distribution of SNP was mainly performed using Review Manager 5.0. The odds ratio (OR) and its 95% confidence interval (95% CI) were used to assess the strength of association. In total, 26,336 cases and 44,219 controls from 18 case-control studies were used in this meta-analysis, and significant associations of the CHEK2 I157T variant with cancer susceptibility were found (OR, 1.39; 95% CI, 1.19-1.63; p<0.0001), breast cancer (OR=1.58, 95% CI=1.42-1.75, p<0.00001) and colorectal cancer (OR=1.67, 95% CI=1.24-2.26, p=0.0008). We also found an association of the CHEK2 I157T variant with familial cases (OR=1.85, 95% CI=1.51-2.26, p<0.00001). However, the association was not established for other types of cancer (OR=1.09, 95% CI=0.75-1.57, p=0.66). This meta-analysis demonstrates that the CHEK2 I157T variant was an important cancer gene, which increases cancer risk, especially in breast and colorectal cancer in Caucasian, and the bioinformatic analysis showed this change was mainly attributed to the decreased hydrophobicity of CHEK2 157T.

A novel variant of Oct3/4 gene in mouse embryonic stem cells.

OCT4 is a highly conserved gene and plays an important role during early embryonic development and differentiation. Similar to human OCT4, mouse Oct4 gene generates variants. Oct4A is a master regulator of self-renewal in pluripotent stem cells. In this study, we have identified a novel Oct4 spliced variant, designated mouse Oct4B, encoding 3 isoforms, termed Oct4B-247aa, Oct4B-190aa and Oct4B-164aa. Furthermore, we have examined the expression pattern of these isoforms in non-pluripotent cells and their function in somatic cell reprogramming. The results revealed the isoforms 247aa, 164aa localized mainly in nucleus and 190aa expressed dotted in the cytoplasm. In contrast to Oct4A, Oct4B does not function in somatic reprogramming as that of Oct4A. Taken together, our data for first time described the intact coding sequence of mouse Oct4B and its function in somatic cell reprogramming. These findings will be important for further analysis of the epigenetic mechanisms of reprogramming and highlight the necessity of discriminating Oct4 isoforms in future stem cell research.