Clinicoprognostical features of endometrial cancer patients with somatic mtDNA mutations

Somatic mitochondrial DNA (mtDNA) mutations have been found in a subset of endometrial cancers (EC) from different populations. We have investigated the relationship between mtDNA changes and clinical and pathological variables of women affected by EC. mtDNA mutations were detected both in early (3/32; 9%) and in advanced (1/8; 12%) stages of uterine tumors. However, patients carrying the mtDNA mutations or the normal mtDNA sequence had indistinguishable clinicopathological data, including age, clinical stage, histological grade and type or depth of myometrial invasion. It is noteworthy that mtDNA mutations were not detected in hyperplastic endometrial tissues or in ECs coexisting with hyperplasia, nor in a single case of endometrial stromal sarcoma. LOH at the tumor suppressor genes RB1 and TP53 as well as p16INK4A alterations (LOH, gene deletion) were found in tumors carrying mtDNA mutations. These results suggest that somatic mtDNA mutations are detected in a subset of ECs, although they are unrelated to clinicopathological variables of cancer.     

Multi‐regional sequencing reveals intratumor heterogeneity and positive selection of somatic mtDNA mutations in hepatocellular carcinoma and colorectal cancer

Recent studies have revealed significant intratumor heterogeneity (ITH) of nuclear genome mutations and highlighted its function in tumor progression and treatment resistance. However, the ITH of somatic mitochondrial DNA (mtDNA) mutations detected in cancers remains unknown. In this study, we performed multiregional mtDNA sequencing of tumor and paratumor tissue samples from 12 hepatocellular carcinoma (HCC) and 13 colorectal cancer (CRC) patients. A substantial level of mtDNA mutations was found in paired non‐HCC inflammatory tissues, suggesting that these tissues might not be mtDNA‐genetically “normal.” Moreover, our data indicated that the ITH of somatic mtDNA mutations was a common feature in HCC and CRC patients. In addition, we found that shared mutations which were observed in at least 2 samples in each patient exhibited a significantly higher heteroplasmic level than mutations that were private to a specific tumor region from both HCC (p = 0.039) and CRC patients (p = 0.001). The heteroplasmic level of shared mutations was positively correlated with intratumoral recurrence of mtDNA mutations. We also found that shared mutations in tumor tissues with a higher degree of pathogenicity risk exhibited a higher heteroplasmic level and intratumoral recurrence in both HCC and CRC patients. These findings suggest that some mtDNA mutations may undergo positive selection during the clonal expansion. Taken together, our analyses identified various levels of ITH of somatic mtDNA mutations in HCC and CRC patients and provided evidence supporting the positive selection working on some somatic mtDNA mutations in tumor tissues.     

Downregulation of alpha-fetoprotein expression by LHX4: a critical role in hepatocarcinogenesis

LHX4 is a member of the LIM-homeobox family and plays a critical role in pituitary development and differentiation. Several lines of evidences have reported their aberrant expression in cancers. However, the exact roles of LHX4 in carcinogenesis remain unclear. In this study, LHX4 expression was analyzed in tumor and paired non-tumor tissues obtained from patients with hepatocellular carcinoma (HCC) using western blotting and immunohistochemistry. LHX4 was found to be downregulated in tumor tissues and negatively correlated with differentiation grade and alpha-fetoprotein (AFP) levels in 66 HCC patients. To clarify the biological functions of LHX4, transient or stable transfectants overexpressing LHX4 were generated in human hepatoma cells (Huh7 and HepG2). LHX4 overexpression in Huh7 and HepG2 cells induced a more differentiated phenotype by reducing AFP expression. Using in silico analysis, the evolutionary conserved region within the AFP promoter containing LHX4-binding site was identified, implying that AFP is a putative target for LHX4. Moreover, ectopic LHX4 overexpression attenuated Huh7 and HepG2 proliferation. Importantly, the growth-inhibitory effect of LHX4 was reversed by replenishing AFP to the LHX4-overexpressing cells, providing a functional relevance between LHX4 and AFP. Finally, we analyzed expressions of LHX4 and AFP during normal liver development. Hepatic LHX4 expression increased in adult liver in a manner that parallel AFP repression. In conclusion, these data indicate that LHX4 may act as a potential tumor suppressor in hepatocarcinogenesis, suggesting that targeting LHX4 to downregulate AFP might have therapeutic implications.     

Mutational profiling reveals PIK3CA mutations in gallbladder carcinoma

Background  

The genetics of advanced biliary tract cancers (BTC), which encompass intra- and extra-hepatic cholangiocarcinomas as well as gallbladder carcinomas, are heterogeneous and remain to be fully defined.     

线粒体基因D环区在乳腺癌的高频突变率和高度多态性

目的探讨乳腺癌的线粒体基因D环区的体细胞性突变和多态性变异特征.方法 PCR扩增和测序检查乳腺癌组织和相应的正常组织的线粒体基因D环全序列,并与基因文库和线粒体文库记录的剑桥序列进行对比分析.结果在73例肿瘤中共发现270个种系性变异,28例(38.3%)肿瘤发现体细胞性突变共44例次,其中22.7%位于第一高变区,65.9%位于第二高变区,保留序列区II的303～309位点是突变高发热点.结论乳腺癌的mtDNA 环区是一个具有高频突变率和高度多态性的不稳定区域.     

Uncoupling cancer mutations reveals critical timing of p53 loss in sarcomagenesis

It is well accepted that cancer develops following the sequential accumulation of multiple alterations, but how the temporal order of events affects tumor initiation and/or progression remains largely unknown. Here, we describe a mouse model that allows for temporally distinct cancer mutations. By integrating a Flp-inducible allele of K-ras(G12D) with established methods for Cre-mediated p53 deletion, we were able to separately control the mutation of these commonly associated cancer genes in vitro and in vivo. We show that delaying p53 deletion relative to K-ras(G12D) activation reduced tumor burden in a mouse model of soft-tissue sarcoma, suggesting that p53 strongly inhibits very early steps of transformation in the muscle. Furthermore, using in vivo RNA interference, we implicate the p53 target gene p21 as a critical mediator in this process, highlighting cell-cycle arrest as an extremely potent tumor suppressor mechanism.     

Beyond the exome: the role of non-coding somatic mutations in cancer

The comprehensive identification of mutations contributing to the development of cancer is a priority of large cancer sequencing projects. To date, most studies have scrutinized mutations in coding regions of the genome, but several recent discoveries, including the identification of recurrent somatic mutations in the TERT promoter in multiple cancer types, support the idea that mutations in non-coding regions are also important in tumour development. Furthermore, analysis of whole-genome sequencing data from tumours has elucidated novel mutational patterns and processes etched into cancer genomes. Here, we present an overview of insights gleaned from the analysis of mutations from sequenced cancer genomes. We then review the mechanisms by which non-coding mutations can play a role in cancer. Finally, we discuss recent efforts aimed at identifying non-coding driver mutations, as well as the unique challenges that the analysis of non-coding mutations present in contrast to the identification of driver mutations in coding regions.     

Genetic and epigenetic profiling of CLL disease progression reveals limited somatic evolution and suggests a relationship to memory-cell development

We examined genetic and epigenetic changes that occur during disease progression from indolent to aggressive forms of chronic lymphocytic leukemia (CLL) using serial samples from 27 patients. Analysis of DNA mutations grouped the leukemia cases into three categories: evolving (26%), expanding (26%) and static (47%). Thus, approximately three-quarters of the CLL cases had little to no genetic subclonal evolution. However, we identified significant recurrent DNA methylation changes during progression at 4752 CpGs enriched for regions near Polycomb 2 repressive complex (PRC2) targets. Progression-associated CpGs near the PRC2 targets undergo methylation changes in the same direction during disease progression as during normal development from naive to memory B cells. Our study shows that CLL progression does not typically occur via subclonal evolution, but that certain CpG sites undergo recurrent methylation changes. Our results suggest CLL progression may involve developmental processes shared in common with the generation of normal memory B cells.     

mtDNA mutations in invasive cervix tumors: a retrospective analysis

We tested whether mtDNA mutations are associated with poor outcome in patients with invasive cervix cancer. Tumor samples were banked more than 10 years ago from women with diagnoses of invasive cervix cancer. Automated techniques were used to determine the sequence of the mtDNA-encoded Complex I subunits. Approximately one-third of all tumors had multiple mtDNA sequence alterations. Both univariate and multivariate analysis of the 10 years survival probability showed that the 10 years survival of patients whose tumors had eight or more nucleotide substitutions was significantly worse (P<0.0063 and P<0.012, respectively). The log-rank test also found a significant difference in overall survival (P<0.003). These results suggest that multiple mtDNA mutations are an independent marker of poor prognosis, and that prospective clinical trials that incorporate analysis of mitochondrial genetic alterations in cervix cancer are warranted.     

Possibility of selection against mtDNA mutations in tumors

Several studies of tumors have revealed substantial numbers of clonally expanded somatic mutations in mitochondrial DNA (mtDNA), not observed in adjacent intact tissues. These findings were interpreted as indicating the involvement of mtDNA mutations in tumorigenesis. Such comparisons, however, ignore an important confounding factor: the monoclonal origin of tumors as opposed to the highly polyclonal nature of normal tissues. Analysis of recently published data on the incidence of somatic mutations in nontumor monoclonal cells suggests that, contrary to the prevailing view, the process of tumorigenesis may be accompanied by active selection against detrimental mtDNA mutations.     

乳腺癌患者血浆线粒体D环高变区基因突变研究

目的:研究检测血浆线粒体DNA基因突变对于乳腺癌诊断的参考价值。方法:选取乳腺癌患者35例,健康 对照者10人,提取血浆DNA,设计两对引物,采用聚合酶链反应(PCR)扩增血浆线粒体DNA的D环HVR1和HVR2,然后用 变性高效液相色谱法(DHPLC)对产物进行突变筛选。结果:乳腺癌患者的血浆DNA扩增率(46/140)和筛选的突变率(5/46) 与对照组比较,差异具有显著性(P<0.05)。结论:检测血浆线粒体DNA基因突变可能对于乳腺癌的诊断具有重要意义。     

Comprehensive characterization of CRC with germline mutations reveals a distinct somatic mutational landscape and elevated cancer risk in the Chinese population

Objective: Hereditary colorectal cancer(CRC) accounts for approximately 5%–10% of all CRC cases. The full profile of CRC-related germline mutations and the corresponding somatic mutational profile have not been fully determined in the Chinese population.Methods: We performed the first population study investigating the germline mutation status in more than 1,000(n = 1,923) Chinese patients with CRC and examined their relationship with the somatic mutational landscape. Germline alterations were e...     

MicroRNA profiling of Chinese primary glioblastoma reveals a temozolomide-chemoresistant subtype

Accumulating evidence demonstrates that defining molecular subtypes based on objective genetic alterations may permit a more rational, patient-specific approach to molecular targeted therapy across various cancers. The objective of this study was to subtype primary glioblastoma (pGBM) based on MicroRNA (miRNA) profiling in Chinese population. Here, miRNA expression profiles from 82 pGBM samples were analyzed and 78 independent pGBM samples were used for qRT-PCR validation. We found that two distinct subgroups with different prognosis and chemosensitivities to temozolomide (TMZ) in Chinese pGBM samples. One subtype is TMZ chemoresistant (termed the TCR subtype) and confers a poor prognosis. The other subtype is TMZ-chemosensitive (termed the TCS subtype) and confers a relatively better prognosis compared with the TCR subtype. A classifier consisting of seven miRNAs was then identified (miR-1280, miR-1238, miR-938 and miR-423-5p (overexpressed in the TCR subtype); and let-7i, miR-151-3p and miR-93 (downregulated in the TCR subtype)), which could be used to assign pGBM samples to the corresponding subtype. The classifier was validated using both internal and external samples. Meanwhile, the genetic alterations of the TCR and TCS subtypes were also analyzed. The TCR subtype was characterized by no IDH1 mutation, and EGFR and Ki-67 overexpression. The TCS subtype displayed the opposite situation. Taken together, the results indicate a distinct subgroup with poor prognosis and TMZ-chemoresistance.     

mtDNA mutations in tumors of the central nervous system reflect the neutral evolution of mtDNA in populations

Mitochondrial DNA (mtDNA) instability has been observed in different types of cancer, including colorectal, breast, and gastric cancer. The relationship between the occurrence of such alteration and the nuclear microsatellite instability (nMI) status of the neoplastic cells remains controversial. In an attempt to clarify this issue, we sequenced the first and second mtDNA hypervariable regions, and typed the mitochondrial (CA)(n) dinucleotide polymorphism in 69 patients with primary tumors of the central nervous system (CNS), previously screened for nMI. Tumor samples showed 27 D-loop sequence changes (39.1%) compared to the corresponding blood samples. Microsatellite homoplasmic allele mutations were detected in four cases (5.8%). We did not find significant associations of the mtDNA instability status with clinicopathological parameters including sex, age, tumor size, and duration of clinical course. Neither did we find any association between mtDNA and nuclear instabilities, indicating that, at least in CNS tumors, they respond to different DNA repair mechanisms. We have also compiled the mtDNA instabilities previously reported by other authors for several types of tumors, comparing them to mtDNA polymorphisms in human populations. Most of the tumor-associated changes are common human polymorphisms and mutational hotspots. To explain the molecular behavior of mtDNA instability in tumors, we propose a model also common to other biological situations.     

Expression profiling reveals genes associated with transendothelial migration of tumor cells: a functional role for alphavbeta3 integrin

Transendothelial migration is a key step in the extravasation of tumor cells during metastasis formation. Here, we have classified 45 human tumor cell lines derived from various tissues according to their capacity for transendothelial migration in vitro. We could distinguish cell lines showing strong transmigration (TEM+ cell lines) from others that did not transmigrate (TEM- cell lines). By DNA microarray analysis we could cluster TEM+ and TEM- cell lines according to their gene expression pattern and identify genes differentially expressed between the 2 groups. Among these we found the integrin beta3 subunit to be highly expressed in TEM+ cell lines as compared to TEM- cell lines. Cell surface localization of alphavbeta3 integrin receptors was exclusively found in TEM+ cell lines. Transendothelial migration of TEM+ cells but not their adhesion to the endothelial cells, or invasion into collagen gels could be blocked with an antibody against alphavbeta3 integrin and by RNAi mediated knock-down of the integrin beta3 subunit. These data establishes alphavbeta3 integrin as one key component of the transendothelial migration process of tumor cells, and as a potential target for anti-metastatic therapy. Our gene expression analysis of a defined collection of tumor cell lines can be used as a starting point to identify further genes functionally involved in transendothelial migration.     

IL-10 deficiency leads to somatic mutations in a model of IBD

Individuals with inflammatory bowel disease (IBD) are at increased risk of developing gastrointestinal cancer. Here, we have tested the possibility that chronic inflammation could trigger mutations. For this, we have used IL-10-deficient (IL-10-/-) mice, which spontaneously develop intestinal inflammation, in combination with a transgenic gpt gene and red/gam gene (gpt+IL-10-/-), which is a well-characterized mutation reporter locus. The total mutation frequency in the colon of gpt+IL-10-/- mice was about five times higher than that in normal gpt+IL-10+/+ mice. In the particular case of G:C to A:T transitions, the frequency of mutations in gpt+IL-10-/- mice was 4.1 times higher than that in control mice. Interestingly, the frequency of small deletions and insertions was also strikingly increased (approximately 10 times). The majority of the deletion or insertion mutations were observed in the monotonous base runs or adjacent repeats of short tandem sequences. In contrast, the frequency of large deletions, detected by loss of the Spi marker present in the red/gam transgene, was similar among the mouse strains. Finally, as a control, the mutation frequency in non-inflamed tissues, such as the liver, were similar between gpt+IL-10-/- mice and gpt+IL-10+/+ mice. Our data demonstrate that the chronic inflammatory environment in the colon promotes the generation of mutations.     

A cancer registry-based analysis on the non-white populations reveals a critical role of the female sex in early-onset melanoma

Purpose

Most melanoma studies have been performed in the white population who exhibits the highest incidence rate due to their skin sensitivity to UV radiation. Previous publications have shown that young women (approximately under the menopausal age) exhibit higher incidence rates than men of the same age, and the causes are mostly attributed to their sun behavior or indoor tanning. In our recent publications, we suggested that higher risk in younger women was due to pathophysiological factors, such as hormonal impact, and thus this higher risk in young women should be shared across ethnicities regardless of their skin color or UV behavior.

Methods

A total of 13,208 non-white melanoma patients from SEER and 15,226 from WHO CI5-Plus were extracted for analysis. Age-specific incidence rates, female-to-male incidence rate ratios, and p values were calculated.

Results

As observed in the white population, younger women and older men showed higher melanoma incidence rates than their peers of the other gender in all ethnic groups. The highest female-to-male incidence rate ratios were observed in the pubescent and reproductive ages. Previously this gender discrepancy in the white population was attributed to the preference of skin tanning in young females. There is no evidence to show that darker-skinned young females adopt a similar tanning preference. Thus the age-dependent gender difference in the risk of melanoma is shared across ethnic groups and is perhaps independent of UV behavior.

Conclusions

Our results highlight the importance of gender as one of the melanoma risk factors beyond traditional UV radiation, which warrants further investigation and may provide a base for an improved prevention strategy.