High throughput sequencing reveals high specificity of TNFAIP3 mutations in ocular adnexal marginal zone B-cell lymphomas

The majority of ocular adnexal (OA) lymphomas (OAL) are extranodal marginal zone lymphomas (MZL). First high throughput sequencing (HTS) studies on OA-MZL showed inconsistent results and the distribution of mutations in reactive lymphoid lesions of this anatomic region has not yet been sufficiently addressed. We characterized OAL and lymphoid lesions of the OA by targeted HTS. The study included 34 OA-MZL, 11 chronic conjunctivitis, five mature small cell B-cell lymphomas spreading to the OA, five diseases with increase of IgG4+ plasma cells, three Burkitt lymphomas (BL), three diffuse large B-cell lymphomas (DLBCL), three mantle cell lymphomas, three idiopathic orbital inflammations/orbital pseudo tumors (PT), and three OA lymphoid hyperplasia. All cases were negative for Chlamydia. The mutational number was highest in BL and lowest in PT. The most commonly (and exclusively) mutated gene in OA-MZL was TNFAIP3 (10 of 34 cases). Altogether, 20 out of 34 patients harbored mutually exclusive mutations of either TNFAIP3, BCL10, MYD88, ATM, BRAF, or NFKBIE, or nonexclusive mutations of IRF8, TNFRSF14, KLHL6, and TBL1XR1, all encoding for NK-κB pathway compounds or regulators. Thirteen patients (38%) had, to a great part, mutually exclusive mutations of chromatin modifier-encoding genes: KMT2D, CREBBP, BCL7A, DNMT3A, EP300, or HIST1H1E. Only four patients harbored co-occurring mutations of genes encoding for NK-κB compounds and chromatin modifiers. Finally, PTEN, KMT2D, PRDM1, and HIST1H2BK mutations were observable in reactive lymphoid lesions too, while such instances were devoid of NF-κB compound mutations and/or mutations of acetyltransferase-encoding genes. In conclusion, 80% of OA-MZL display mutations of either NK-κB compounds or chromatin modifiers. Lymphoid lesions of the OA bearing NF-κB compound mutations and/or mutations of acetyltransferase-encoding genes highly likely represent lymphomas.     

基于转录组测序的牛蒡木质素类物质生物合成途径及关键酶基因分析

目的获得牛蒡Arctiumlappa根功能基因数据库,分析其木质素类化合物生物合成途径及关键酶基因。方法以牛蒡根为研究对象,利用华大基因BGISEQ-500测序平台进行转录组测序,通过从头组装获得Unigene,利用各种已有的核酸和蛋白质数据库对Unigene进行注释和分类,利用KEGG代谢途径分析木质素生物合成途径及其关键酶基因,利用三维同源建模分析苯丙氨酸解氨酶(AlPAL)的结构特点。结果通过转录组测序共获得54 215个Unigene,其中42 003个Unigene被任一数据库注释,1 668个Unigene被注释到54个转录因子家族中;KEGG途径分析鉴定了423个Unigene参与了木质素的生物合成。AlPAL空间结构模型显示其为同型四聚体,每个单体由3个结构域组成,包括4-甲基-咪唑-5-酮(MIO)结构域、核心结构域和屏蔽结构域,其中MIO结构域包含保守的三肽ASG,构成AlPAL酶的催化活性中心。结论对牛蒡根转录组进行分析,为牛蒡功能基因鉴定、次生代谢途径解析及其调控机制研究奠定了实验基础。     

布鲁氏菌A19疫苗株全基因组测序及比较基因组学分析

目的 探索布鲁氏杆菌A19疫苗株全基因组的结构、分子生物学的功能,并对其生物信息学进行研究。方法 采用Illumina Hiseq 4000和PacBio对A19进行全基因组测序,并与GenBank 上的8株菌进行比较基因组学解析。A19基因组3 286 167 bp, 预测3 371个基因,GC含量57.25%。通过注释COG库,对应基因有2 560个,将其归入22类COG中;根据比对KEGG库,得到2 544个基因,共参与33类代谢通路。结果 综合两个数据库结果发现,大多数A19预测基因中的基因功能主要与膜运输、氨基酸转运及碳水化合物代谢有关。结论 通过分析发现, A19和猪羊牛种布鲁氏菌之间存在一定差异,并找出牛种毒力基因。本实验通过测序A19全基因组,为布鲁菌疫苗的研究提供思路。     

Aberrant expression of Wnt/β-catenin signaling pathway genes in aggressive malignant gastric gastrointestinal stromal tumors

IntroductionRecent reports on gene expression profiling (GEP) show several genes associated with malignant progression of GIST. However, genes associated with malignant transformation have not been clarified. Here, we aimed to reveal distinct genes in aggressive malignant GIST, using comprehensive gene expression analysis.Materials and methodsWe investigated GEP obtained by microarrays for 43 gastric GISTs, which mostly harbored KIT and PDGFRA mutations and integrated clinicopathological risk information. RT-PCR and immunohistochemistry were performed for FZD7, a receptor of Wnt ligands.ResultsGEP divided 43 gastric GISTs into two clusters. A cluster included seven of eight high-risk GISTs (88%) in modified NIH classification and was defined as high-risk cluster; the other cluster was defined as low-risk cluster. The number of probes with over 3-fold changes between the two clusters was 1,177, in which probes corresponding to 16 oncogenes were included. Genes involved in the Wnt signaling pathway were the most abundant among the 16 oncogenes. Focusing on 73 Wnt signaling pathway genes of the 21,578 probes, 12 upregulated and 5 downregulated genes were found in the high-risk cluster. Major cascade genes promoting the Wnt/β-catenin signaling pathway, including WNT11, FZD family, and DVL2, were upregulated in the high-risk cluster. SNAI1, SNAI2, and BIRC5, which are activated by this pathway and increase cell proliferation, were also upregulated. These gene expression alterations were consistent in the positive direction of this pathway. GISTs in high-risk cluster strongly expressed FZD7.ConclusionWnt/β-catenin signaling pathway may play an important role in malignant transformation of indolent GIST.     

Deciphering the molecular landscape of microcephaly in 87 Indian families by exome sequencing

Microcephaly is a frequent feature of neurodevelopmental disorders (NDDs). Our study presents the heterogeneous spectrum of genetic disorders in patients with microcephaly either in isolated form or in association with other neurological and extra-neural abnormalities. We present data of 91 patients from 87 unrelated families referred to our clinic during 2016–2020 and provide a comprehensive clinical and genetic landscape in the studied cohort. Molecular diagnosis using exome sequencing was made in 45 families giving a yield of 51.7%. In 9 additional families probable causative variants were detected. We identified disease causing variations in 49 genes that are involved in different functional pathways Among these, 36 had an autosomal recessive pattern, 8 had an autosomal dominant pattern (all inherited de novo), and 5 had an X-linked pattern. In 41 probands where sequence variations in autosomal recessive genes were identified 31 were homozygotes (including 16 from non-consanguineous families). The study added 28 novel pathogenic/likely pathogenic variations. The study also calls attention to phenotypic variability and expansion in spectrum as well as uncovers genes where microcephaly is not reported previously or is a rare finding. We here report phenotypes associated with the genes for ultra-rare NDDs with microcephaly namely ATRIP, MINPP1, PNPLA8, AIMP2, ANKLE2, NCAPD2 and TRIT1.     

Motivations and barriers to pursue cancer genomic testing: A systematic review

ObjectivesSingle-gene testing is associated with psycho-social challenges for cancer patients. Genomic testing may amplify these. The aim of this study was to understand patients’ motivations and barriers to pursue cancer genomic testing, to enable healthcare providers to support their patients throughout the testing process and interpretation of test results.MethodsFive databases were searched for original peer reviewed research articles published between January 2001 and September 2018 addressing motivation for genomic cancer testing. QualSyst was used to assess quality.Results182 studies were identified and 17 were included for review. Studies were heterogenous. Both somatic and germline testing were included, and 14 studies used hypothetical scenarios. 3249 participants were analyzed, aged 18 to 94. Most were female and white. The most common diagnoses were breast, ovarian, lung and colorectal cancer. Interest in testing was high. Motivations included ability to predict cancer risk, inform disease management, benefit families, and understand cancer. Barriers included concerns about cost, privacy/confidentiality, clinical utility, and psychological harm.ConclusionsDespite concerns, consumers are interested in cancer genomic testing if it can provide actionable results for themselves and their families.Practice ImplicationsProviders must manage understanding and expectations of testing and translate genetic information into health-promoting behaviours.     

糖尿病肛漏创面应用美洲大蠊提取液的lncRNA高通量测序及维恩图分析＊

目的 基于高通量测序及维恩图预测美洲大蠊提取液促进糖尿病肛漏创面愈合的顺、反式lncRNA及Pathway。方法 选取湖南中医药大学第二附属医院收治的糖尿病肛漏患者术后创面12例，利用高通量测序技术检测6例术后创面组（A组）和6例术后创面应用美洲大蠊提取液创面组（B组）中lncRNAs和mRNAs表达，进行GO分析和KEGG通路分析，构建lncRNA-mRNA的共表达网络图，并通过Cis-及Trans-预测与创面愈合相关lncRNA。结果 实验组差异表达的lncRNAs2242个（上调649个，下调1593个），mRNAs有13186个（上调5162个，下调8024个）。GO分析发现差异表达的lncRNA-cis主要富集在表皮细胞分化、上皮细胞分化、细胞代谢过程的调节等；差异表达的lncRNA-trans主要富集在细胞代谢过程、蛋白质结合、细胞内部分等。通过KEGG通路分析，筛选出与本研究相关的3条通路：IBD、MAPK signaling pathway、AMPK signaling pathway；lncRNA靶标基因预测中最终筛选出3个lncRNA（ENST00000443364、ENST00000576797、ENST00000620167），进行PCR验证，lncRNAENST00000443364、ENST00000576797与芯片结果一致。结论 美洲大蠊提取液可能通过lncRNAENST00000443364、ENST00000576797顺式及反式调控靶标基因，影响表皮细胞分化、上皮细胞分化、细胞代谢过程的调节等功能以及影响IBD、MAPK signaling pathway、AMPK signaling pathway促进糖尿病肛漏创面愈合。     

Absence of FGFR3–TACC3 rearrangement in hematological malignancies with numerical chromosomal alteration

FGFR–TACC, found in different tumor types, is characterized by the fusion of a member of fibroblast grown factor receptor (FGFR) tyrosine kinase (TK) family to a member of the transforming acidic coiled-coil (TACC) proteins. Because chromosome numerical alterations, hallmarks of FGFR–TACC fusions are present in many hematological disorders and there are no data on the prevalence, we studied a series of patients with acute myeloid leukemia and myelodysplastic syndrome who presented numerical alterations using cytogenetic traditional analysis. None of the analyzed samples showed FGFR3–TACC3 gene fusion, so screening for this mutation at diagnosis is not recommended.     

基于16S rDNA测序的肠道菌群探讨解郁祛痰化浊方对高脂饮食大鼠肠-肝轴的影响

目的 研究解郁祛痰化浊方（JQHP）对高脂饮食大鼠肠道菌群的影响，探讨中药调控肠道微生物群进而恢复肠-肝轴的平衡。方法 将70只雄性SPF级别Wistar大鼠随机分为正常组（10只）与模型组（60只），正常组饲喂正常饲料，模型组饲喂高脂饲料。12周后将模型组随机分为6组，每组10只，即模型组，血脂康组，立普妥组，JQHP低、中、高剂量组。JQHP低、中、高剂量组分别灌胃JQHP颗粒剂0.4，0.8，1.6 g·kg^-1，立普妥组予立普妥2 mg·kg^-1，血脂康组予血脂康0.1 g·kg^-1，正常组和模型组大鼠灌胃同等量蒸馏水，连续灌胃8周后收集粪便，进行16S rRNA基因测序，行腹主动脉取血检测血脂，取肝脏组织及回肠组织苏木素-伊红（HE）染色后进行病理形态学观察。结果 与正常组比较，模型组大鼠血脂四项总胆固醇（TC），甘油三酯（TG），低密度脂蛋白胆固醇（LDL-C）均见明显升高，高密度脂蛋白胆固醇（HDL-C）降低（P<0.01）；与模型组比较，血脂康组、立普妥组TC，TG显著性下降（P<0.01），血脂康组HDL-C升高（P<0.05）。JQHP中剂量组较模型组对肝脏脂肪样变有一定的缓解作用，可以减轻炎性细胞的浸润情况。JQHP可使回肠结构淋巴组织增生情况好转，且中剂量组疗效最显著。Shannon曲线结果表明，与正常组比较，JQHP中剂量组显著提高（P<0.01）；与模型组比较，JQHP中、高剂量组明显升高（P<0.05，P<0.01）；与JQHP中剂量组比较，其他用药组降低（P<0.05，P<0.01）。主成分多样性分析（PCA）示中药中剂量组多样性和丰度高于其他用药组。线性判别分析（LDA）中，与正常组比较，模型组拟杆菌纲，瘤胃球菌科，拟杆菌S24-7，瘤胃球菌UCG-005下调（P<0.01），脱硫弧菌目、丹毒丝菌目、毛螺菌科上调（P<0.05，P<0.01）。与模型组比较，JQHP中剂量组的拟杆菌纲，瘤胃球菌科，拟杆菌S24-7，瘤胃球菌UCG-005上调（P<0.05，P<0.01），丹毒丝菌目下调（P<0.01）。与JQHP中剂量组比较，其他用药组拟杆菌纲，瘤胃球菌科，拟杆菌S24-7，瘤胃球菌UCG-005中降低（P<0.05，P<0.01），在丹毒丝菌目、毛螺菌科中升高（P<0.05，P<0.01）。结论 JQHP调整肠道物种丰度和多样性，改善肝脏组织和回肠黏膜状态，调节血脂水平，恢复正常肠道生态环境，可能与调节与炎症相关的肠道菌群而恢复肠-肝轴平衡有关，以中剂量组效果最佳。