Mutations analysis of STK11 ene in Chinese families with Peutz-Jeghers syndrome

Peutz-Jeghers syndrome (PJS) is an autosomal dominantly inherited disease characterized by multiple gastrointestinal hamartomatous polyps and melanin spots on lips and buccal mucosa, with an increased risk for various cancers. ThePJS gene, a potential tumour suppressor gene, encoding a serine/ threonie kinase (STK11), was mapped to chromosome 19p13.3. To investigate the mutations of STK11 gene in Chinese with PJS, we analyzed its coding sequence in fifteen patientsand twenty unaffected members of six families, including three multigenerational families with PJS and three sporadic families with PJS, by PCR, PCR-DHPLC and DNA sequencing techniques. Ten point mutations were found in the six families, including five missense mutations, one acceptor-splice site mutation, a nonsense mutation and three silent mutations. Our data showed that five missense mutations occurrd at codon 123 (CAG to CAT) in exon 2, codon 161 (ATT to AGT) in exon 4,codon 194 (GAC to GAG) in exon 4, codon 245 (CTC to TTC) in exon 5 and codon 354 (TTC to TTG) in exon 8. One kind of nonsense mutation was detected at codon 37(CAG to TAG) in exon 1. Furthermore, we found an intronic mutation at a splice-acceptor site: a one base substitution from AG to AA in intron 4. These mutations were not detected in 20 normal DNA samples. In three sporadic families, only in one patient, we detected a missense mutation in exon 5. In addition, we found three silent mutations, which may cause polymorphisms of STK11 gene in introns 1(+36), 3(-51) and 5(+27). These results indicated that the point mutation in STK11 might be involved in PJS pathogenesis. Mutation frequency is higher in the families suffering PJS in three or more generations than that of the sporadic cases.     

Mutations in UBQLN2 cause dominant X-linked juvenile and adult-onset ALS and ALS/dementia

Amyotrophic lateral sclerosis (ALS) is a paralytic and usually fatal disorder caused by motor-neuron degeneration in the brain and spinal cord. Most cases of ALS are sporadic but about 5-10% are familial. Mutations in superoxide dismutase 1 (SOD1), TAR DNA-binding protein (TARDBP, also known as TDP43) and fused in sarcoma (FUS, also known as translocated in liposarcoma (TLS)) account for approximately 30% of classic familial ALS. Mutations in several other genes have also been reported as rare causes of ALS or ALS-like syndromes. The causes of the remaining cases of familial ALS and of the vast majority of sporadic ALS are unknown. Despite extensive studies of previously identified ALS-causing genes, the pathogenic mechanism underlying motor-neuron degeneration in ALS remains largely obscure. Dementia, usually of the frontotemporal lobar type, may occur in some ALS cases. It is unclear whether ALS and dementia share common aetiology and pathogenesis in ALS/dementia. Here we show that mutations in UBQLN2, which encodes the ubiquitin-like protein ubiquilin?2, cause dominantly inherited, chromosome-X-linked ALS and ALS/dementia. We describe novel ubiquilin?2 pathology in the spinal cords of ALS cases and in the brains of ALS/dementia cases with or without UBQLN2 mutations. Ubiquilin?2 is a member of the ubiquilin family, which regulates the degradation of ubiquitinated proteins. Functional analysis showed that mutations in UBQLN2 lead to an impairment of protein degradation. Therefore, our findings link abnormalities in ubiquilin?2 to defects in the protein degradation pathway, abnormal protein aggregation and neurodegeneration, indicating a common pathogenic mechanism that can be exploited for therapeutic intervention.     

基于网络药理学研究雷公藤抗肝癌的分子机制及初步验证

基于中药系统药理学数据库与分析平台（TCMSP）筛选雷公藤抗肝癌的有效成分,采用GeneCards、OMIM、Drugbank、GEO等疾病数据库筛选差异性表达基因,找到相互映射的核心物质及靶点,构建药效成分-靶点（C-T）网络、蛋白互作网络（PPI）,进行gene ontology （GO）和Kyoto encyclopedia of genes and genomes （KEGG）富集分析,获知其生物学机制,并利用分子对接技术和生物学实验进行验证。结果表明,雷公藤的主要药效成分为雷公藤甲素和雷公藤红素,PTGS2、CXCL8、TGFB1、STAT3等核心靶点主要富集于癌症及多条炎症因子的相关通路中,雷公藤甲素与PTGS2以及雷公藤红素与PTGS2、CXCL8、STAT3有着很强的结合活性,雷公藤甲素和雷公藤红素可以抑制PTGS2和STAT3蛋白的表达。以上结果表明,雷公藤可能作用于这些靶点,通过调控细胞的增殖和凋亡,发挥抗炎、调节免疫的作用,从而抑制肝癌的恶化。     

Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma

Glioblastoma multiforme (GBM) is a lethal brain tumour in adults and children. However, DNA copy number and gene expression signatures indicate differences between adult and paediatric cases. To explore the genetic events underlying this distinction, we sequenced the exomes of 48 paediatric GBM samples. Somatic mutations in the H3.3-ATRX-DAXX chromatin remodelling pathway were identified in 44% of tumours (21/48). Recurrent mutations in H3F3A, which encodes the replication-independent histone 3 variant H3.3, were observed in 31% of tumours, and led to amino acid substitutions at two critical positions within the histone tail (K27M, G34R/G34V) involved in key regulatory post-translational modifications. Mutations in ATRX (α-thalassaemia/mental retardation syndrome X-linked) and DAXX (death-domain associated protein), encoding two subunits of a chromatin remodelling complex required for H3.3 incorporation at pericentric heterochromatin and telomeres, were identified in 31% of samples overall, and in 100% of tumours harbouring a G34R or G34V H3.3 mutation. Somatic TP53 mutations were identified in 54% of all cases, and in 86% of samples with H3F3A and/or ATRX mutations. Screening of a large cohort of gliomas of various grades and histologies (n = 784) showed H3F3A mutations to be specific to GBM and highly prevalent in children and young adults. Furthermore, the presence of H3F3A/ATRX-DAXX/TP53 mutations was strongly associated with alternative lengthening of telomeres and specific gene expression profiles. This is, to our knowledge, the first report to highlight recurrent mutations in a regulatory histone in humans, and our data suggest that defects of the chromatin architecture underlie paediatric and young adult GBM pathogenesis.     

Effects of STAT3 antisense RNA on IL-6-induced differentiation and growth arrest of Ml leukemia cells

To investigate the biological roles of STAT3 in the regulation of growth and differentiation of leukemia cells, we modified a murine myeloid leukemia cell line Ml with STAT3 antisense RNA. The effects of STAT3 antisense RNA on the growth arrest and terminal differentiation of Ml cells induced by interleukin 6 (IL-6) were determined. It was found that STAT3 antisense RNA blocked the activation of STAT3, and reduced the growth arrest and terminal differentiation of IL-6-induced Ml leukemia cells. These results indicate that STAT3 activation is a necessary process for IL-6-induced growth arrest of Ml cells and for the differentiation of Ml cells into macrophage.     

口腔扁平苔藓中Caspase-3和PTEN 蛋白的免疫组织化学观察

目的：探讨Caspase-3和FIEN蛋白在口腔扁平苔藓病变发生发展中的作用及两者间的关系。方法：采用S—P免疫组化方法对28例口腔扁平苔藓及5例正常口腔黏膜中Caspase-3和PTEN蛋白表达进行检测。结果：口腔扁平苔藓病损中Caspase-3的阳性率上皮层和固有层均为100％，与正常口腔黏膜相比，表达有显著统计学意义（P〈0．01）。口腔扁平苔藓病损中PTEN蛋白阳性率为100％，与正常口腔黏膜相比，无统计学差异（P〉0．05）。口腔扁平苔藓中Caspase-3与PTEN蛋白表达呈正相关，（P〈0．05）。结论：Caspase-3和PTEN蛋白均参与口腔扁平苔藓病变的发生及发展过程，且两者之间具有相关性。     

Frequent pathway mutations of splicing machinery in myelodysplasia

Myelodysplastic syndromes and related disorders (myelodysplasia) are a heterogeneous group of myeloid neoplasms showing deregulated blood cell production with evidence of myeloid dysplasia and a predisposition to acute myeloid leukaemia, whose pathogenesis is only incompletely understood. Here we report whole-exome sequencing of 29 myelodysplasia specimens, which unexpectedly revealed novel pathway mutations involving multiple components of the RNA splicing machinery, including U2AF35, ZRSR2, SRSF2 and SF3B1. In a large series analysis, these splicing pathway mutations were frequent (～45 to ～85%) in, and highly specific to, myeloid neoplasms showing features of myelodysplasia. Conspicuously, most of the mutations, which occurred in a mutually exclusive manner, affected genes involved in the 3'-splice site recognition during pre-mRNA processing, inducing abnormal RNA splicing and compromised haematopoiesis. Our results provide the first evidence indicating that genetic alterations of the major splicing components could be involved in human pathogenesis, also implicating a novel therapeutic possibility for myelodysplasia.     

Frequent mtDNA mutations and its role in gastric carcinogenesis

In order to disclose the relationship between mutations of mitochondrial DNA (mtDNA) and gastric carcinogenesis, we screened the entire mtDNA sequence in 30 cases of human gastric cancer and matched normal tissues by using denaturing high-performance liquid chromatography (DHPLC) and DNA sequencing. Our data showed that high frequency (66.7%, 20/30) of mitochondrial genome mutation occurred in gastric cancer. Among these variants, 17 cases (56.7%, 17/30) were identified to be somatic mutation. High level mutant frequency was found in ND4, ND5 coding genes and D-loop control region, which was 36.7%, 26.7% and 30% respectively. Comparing with complexes Ⅲ, Ⅳ and Ⅴof the electron transport chain, we found that variants appeared to be more frequent in the subunit genes of complexⅠ. Most of mutations were base substitutions (85.4%, 41/48). Our results suggested that mutations of subunit genes encoding complexⅠ, especially ND3, ND4 and ND5 genes, might contribute to human gastric carcinogenesis.     

Mutations analysis of STK_(11) gene in Chinese families with Peutz-Jeghers syndrome

Peutz-Jeghers syndrome (PJS) is an autosomal dominant disease that is characterized by multiple gastrointestinal hamartomatous polyps and melanin spots on lips and buccal mucosa at young age[1,2]. Previous studies have demonstrated that PJS predisposes carriers to cancers of gastrointestinal tract, uterus, ovary, testis, breast and other extragastrointestinal organs[3—5]. The STK11 gene, encoding a serine/threonine kinase at chro-mosome 19p13.3, was identified in 1998 as the main causativ…     

Proteomic and molecular investigations revealed that Acidithiobacillus caldus adopts multiple strategies for adaptation to NaCl stress

Acidithiobacillus caldus plays an important role in commercial bioleaching.To understand how NaCl stress adaptation occurs in A.caldus,we grew A.caldus strain SM-1 in media containing high NaCl concentrations.SM-1 grew at concentrations of up to 1.0-mol L~(-1)NaCl,but growth was severely inhibited at higher concentrations.Proteomic analysis showed that SM-1 used multiple strategies to respond to NaCl stress.In addition to several heatshock proteins,enzymes involved in proline biosynthesis increased under NaCl stress.In addition,two DNA-binding proteins and a third protein of unknown function(Atc_(1291)),which was subsequently identified as a putative single-stranded DNA-binding protein,were up-regulated in the presence of NaCl stress.These DNA-binding proteins might play a role in response to osmotic stress.Atc_(1291)was cloned and expressed in Escherichia coli.Surprisingly,we found that E.coli BL21/pET28a-atc_(1291)grew to higher cell densities than E.coli BL21/pET28a,regardless of NaCI stress.Homologs to Atc_(1291)were identified in several groups of Proleohacleria.The role of Atc_(1291)in enhancing cell growth needs further investigation.     

Oncogenically active MYD88 mutations in human lymphoma

The activated B-cell-like (ABC) subtype of diffuse large B-cell lymphoma (DLBCL) remains the least curable form of this malignancy despite recent advances in therapy. Constitutive nuclear factor (NF)-κB and JAK kinase signalling promotes malignant cell survival in these lymphomas, but the genetic basis for this signalling is incompletely understood. Here we describe the dependence of ABC DLBCLs on MYD88, an adaptor protein that mediates toll and interleukin (IL)-1 receptor signalling, and the discovery of highly recurrent oncogenic mutations affecting MYD88 in ABC DLBCL tumours. RNA interference screening revealed that MYD88 and the associated kinases IRAK1 and IRAK4 are essential for ABC DLBCL survival. High-throughput RNA resequencing uncovered MYD88 mutations in ABC DLBCL lines. Notably, 29% of ABC DLBCL tumours harboured the same amino acid substitution, L265P, in the MYD88 Toll/IL-1 receptor (TIR) domain at an evolutionarily invariant residue in its hydrophobic core. This mutation was rare or absent in other DLBCL subtypes and Burkitt's lymphoma, but was observed in 9% of mucosa-associated lymphoid tissue lymphomas. At a lower frequency, additional mutations were observed in the MYD88 TIR domain, occurring in both the ABC and germinal centre B-cell-like (GCB) DLBCL subtypes. Survival of ABC DLBCL cells bearing the L265P mutation was sustained by the mutant but not the wild-type MYD88 isoform, demonstrating that L265P is a gain-of-function driver mutation. The L265P mutant promoted cell survival by spontaneously assembling a protein complex containing IRAK1 and IRAK4, leading to IRAK4 kinase activity, IRAK1 phosphorylation, NF-κB signalling, JAK kinase activation of STAT3, and secretion of IL-6, IL-10 and interferon-β. Hence, the MYD88 signalling pathway is integral to the pathogenesis of ABC DLBCL, supporting the development of inhibitors of IRAK4 kinase and other components of this pathway for the treatment of tumours bearing oncogenic MYD88 mutations.     

The clonal and mutational evolution spectrum of primary triple-negative breast cancers

Primary triple-negative breast cancers (TNBCs), a tumour type defined by lack of oestrogen receptor, progesterone receptor and ERBB2 gene amplification, represent approximately 16% of all breast cancers. Here we show in 104 TNBC cases that at the time of diagnosis these cancers exhibit a wide and continuous spectrum of genomic evolution, with some having only a handful of coding somatic aberrations in a few pathways, whereas others contain hundreds of coding somatic mutations. High-throughput RNA sequencing (RNA-seq) revealed that only approximately 36% of mutations are expressed. Using deep re-sequencing measurements of allelic abundance for 2,414 somatic mutations, we determine for the first time-to our knowledge-in an epithelial tumour subtype, the relative abundance of clonal frequencies among cases representative of the population. We show that TNBCs vary widely in their clonal frequencies at the time of diagnosis, with the basal subtype of TNBC showing more variation than non-basal TNBC. Although p53 (also known as TP53), PIK3CA and PTEN somatic mutations seem to be clonally dominant compared to other genes, in some tumours their clonal frequencies are incompatible with founder status. Mutations in cytoskeletal, cell shape and motility proteins occurred at lower clonal frequencies, suggesting that they occurred later during tumour progression. Taken together, our results show that understanding the biology and therapeutic responses of patients with TNBC will require the determination of individual tumour clonal genotypes.     

The landscape of cancer genes and mutational processes in breast cancer

All cancers carry somatic mutations in their genomes. A subset, known as driver mutations, confer clonal selective advantage on cancer cells and are causally implicated in oncogenesis, and the remainder are passenger mutations. The driver mutations and mutational processes operative in breast cancer have not yet been comprehensively explored. Here we examine the genomes of 100 tumours for somatic copy number changes and mutations in the coding exons of protein-coding genes. The number of somatic mutations varied markedly between individual tumours. We found strong correlations between mutation number, age at which cancer was diagnosed and cancer histological grade, and observed multiple mutational signatures, including one present in about ten per cent of tumours characterized by numerous mutations of cytosine at TpC dinucleotides. Driver mutations were identified in several new cancer genes including AKT2, ARID1B, CASP8, CDKN1B, MAP3K1, MAP3K13, NCOR1, SMARCD1 and TBX3. Among the 100 tumours, we found driver mutations in at least 40 cancer genes and 73 different combinations of mutated cancer genes. The results highlight the substantial genetic diversity underlying this common disease.     

Initial genome sequencing and analysis of multiple myeloma

Multiple myeloma is an incurable malignancy of plasma cells, and its pathogenesis is poorly understood. Here we report the massively parallel sequencing of 38 tumour genomes and their comparison to matched normal DNAs. Several new and unexpected oncogenic mechanisms were suggested by the pattern of somatic mutation across the data set. These include the mutation of genes involved in protein translation (seen in nearly half of the patients), genes involved in histone methylation, and genes involved in blood coagulation. In addition, a broader than anticipated role of NF-κB signalling was indicated by mutations in 11 members of the NF-κB pathway. Of potential immediate clinical relevance, activating mutations of the kinase BRAF were observed in 4% of patients, suggesting the evaluation of BRAF inhibitors in multiple myeloma clinical trials. These results indicate that cancer genome sequencing of large collections of samples will yield new insights into cancer not anticipated by existing knowledge.