Deep sequencing reveals clonal evolution patterns and mutation events associated with relapse in B-cell lymphomas

Background

Molecular mechanisms associated with frequent relapse of diffuse large B-cell lymphoma (DLBCL) are poorly defined. It is especially unclear how primary tumor clonal heterogeneity contributes to relapse. Here, we explore unique features of B-cell lymphomas - VDJ recombination and somatic hypermutation - to address this question.

Results

We performed high-throughput sequencing of rearranged VDJ junctions in 14 pairs of matched diagnosis-relapse tumors, among which 7 pairs were further characterized by exome sequencing. We identify two distinctive modes of clonal evolution of DLBCL relapse: an early-divergent mode in which clonally related diagnosis and relapse tumors diverged early and developed in parallel; and a late-divergent mode in which relapse tumors developed directly from diagnosis tumors with minor divergence. By examining mutation patterns in the context of phylogenetic information provided by VDJ junctions, we identified mutations in epigenetic modifiers such as KMT2D as potential early driving events in lymphomagenesis and immune escape alterations as relapse-associated events.

Conclusions

Altogether, our study for the first time provides important evidence that DLBCL relapse may result from multiple, distinct tumor evolutionary mechanisms, providing rationale for therapies for each mechanism. Moreover, this study highlights the urgent need to understand the driving roles of epigenetic modifier mutations in lymphomagenesis, and immune surveillance factor genetic lesions in relapse.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0432-0) contains supplementary material, which is available to authorized users.     

The full-length clone of cucumber green mottle mosaic virus and its application as an expression system for Hepatitis B surface antigen

A cucumber green mosaic mottle virus (CGMMV) full-length clone was developed for the expression of Hepatitis B surface antigen (HBsAg). The expression of the surface displayed HBsAg by the chimeric virus was confirmed through a double antibody sandwich ELISA. Assessment of the coat protein composition of the chimeric virus particles by SDS-PAGE analysis showed that 50% of the coat proteins were fused to the HBsAg. Biological activity of the expressed HBsAg was assessed through the stimulation of in vitro antibody production by cultured peripheral blood mononuclear cells (PBMC). PBMC that were cultured in the presence of the chimeric virus showed up to an approximately three-fold increase in the level of anti HBsAg immunoglobulin thus suggesting the possible use of this new chimeric virus as an effective Hepatitis B vaccine.     

P53，Rb和c－myc基因在人脑原发性肿瘤中的转录表达

采用RNA斑点杂交分析,对21例人脑原发性胶质瘤和11例人脑膜瘤中p53,Rb和c-myc基因转录水平的表达进行研究.发现48.4%的肿瘤中p53基因表达减弱,21.9%的肿瘤中Rb基因表达减弱;71.9%的肿瘤中c-myc基因表达增强.在p53基因表达减弱的15例病例中有13例(80%)c-myc基因表达增强.结果表明,p53基因表达减弱和c-myc基因表达增强与人脑原发性肿瘤的发生有关.     

重组大肠杆菌表达铜绿假单胞菌溶血性磷脂酶C

[目的]构建产溶血性磷脂酶C (Hemolytic Phospholipase C,PLCH)的重组大肠杆菌(Escherich coli菌株,并初步优化其发酵条件.[方法]首先利用卵黄硼砂平板分离法筛选到一株产磷脂酶C(Phospholipase C,PLC)活性较高的菌株,命名为铜绿假单胞菌(Pseudomonas aeruginosa)41;进一步以P.aeruginosa 41基因组DNA为模板设计引物,PCR扩增获得溶血性磷脂酶C(PLCH)基因,构建重组大肠杆菌表达质粒并转化大肠杆菌E.coli BL21 (DE3);筛选转化子并检测PLC活性和溶血能力,并初步优化其发酵条件.[结果]成功构建了重组大肠杆菌E.coli BL21(DE3) /pET28a-plcH;在硼砂卵黄平板上对重组菌进行PLC活性测定,显示重组菌有明显的磷脂酶C活性;在哥伦比亚血琼脂平板上对重组菌进行溶血性试验,表明PLCH具有较强的溶血活性;初步优化摇瓶发酵条件为:5％转接量,37℃、200 r/min下培养4h添加IPTG至终浓度为0.9 mmol/L,转为25℃、150 r/min诱导培养14 h;优化后重组菌的酶活可达到722.89±0.47 U/mL.[结论]本文成功构建了一株产溶血性磷脂酶C活性较高的重组大肠杆菌菌株,并通过优化发酵条件使其酶活达到了722.89±0.47 U/mL,本实验在国内首次实现了铜绿假单胞菌来源的溶血性磷脂酶C基因在大肠杆菌的胞内表达,该研究为研究磷脂酶C产业化奠定了一定的基础.     

In vitro and in vivo growth and casein gene expression of mouse mammary tumor epithelial cells in response to hormones

Cells from autochthonous mouse mammary carcinomas which display estrogen-independent growth _vivo were studied for their hormonal responses in primary culture. A culture system employing insulin-supplemented, serum-free medium and basement membrane Matrigel as a substratum was used to cultivate tumor cells. The cells did not exhibit in vitro estrogenor prolactin-dependent growth. Primary tumors still displayed a constitutional expression of α-, β-, and γ-casein mRNAs. These messages were dramatically reduced during the culture period. However, seven to eightfold increases in α- and β-casein mRNAs were inducible in the 5-day cultures by treatment with prolactin and hydrocortisone. If the hormones were present through a 2-week culture period, the levels of α-, β-, and γ-casein mRNAs in the cells were maintained and displayed in a time-dependent increase with a peak at 10–14 days. The accumulation of β-casein mRNA in vitro did not require DNA synthesis. Administration of prolactin directly into the growing tumors in vivo could also enhance β-casein mRNA levels in the tumor cells. Morphological studies of the cells cultured in the presence of prolactin and hydrocortisone did not reveal visible changes compared with those without hormonal treatment. Transplantation of tumor cells cultured in the presence or absence of hormones resulted in the development of tumors in mice at approximately the same time. The current studies suggest that the autochthonous mammary tumor cells, independent of estrogen for cell growth, were still inducible for casein gene expression in vitro and in vivo by appropriate hormones. The induction and maintenance of casein messages by a single hormonal treatment did not appear to correlate with morphology and DNA synthesis of cells in vitro or with tumor-producing capacities in vivo.