Necroptosis is a new type of programmed cell death and involves the occurrence and development of various cancers. Moreover, the aberrantly expressed lncRNA can also affect tumorigenesis, migration, and invasion. However, there are few types of research on the necroptosis-related lncRNA (NRL), especially in kidney renal clear cell carcinoma (KIRC). In this study, we analyzed the sequencing data obtained from the TGCA-KIRC dataset, then applied the LASSO and COX analysis to identify 6 NRLs (AC124854.1, AL117336.1, DLGAP1-AS2, EPB41L4A-DT, HOXA-AS2, and LINC02100) to construct a risk model. Patients suffering from KIRC were divided into high- and low-risk groups according to the risk score, and the patients in the low-risk group had a longer OS. This signature can be used as an indicator to predict the prognosis of KIRC independent of other clinicopathological features. In addition, the gene set enrichment analysis showed that some tumor and immune-associated pathways were more enriched in a high-risk group. We also found significant differences between the high and low-risk groups in the infiltrating immune cells, immune functions, and expression of immune checkpoint molecules. Finally, we use the "pRRophetic" package to complete the drug sensitivity prediction, and the risk score could reflect patients' response to 8 small molecule compounds. In general, NRLs divided KIRC into two subtypes with different risk scores. Furthermore, this signature based on the 6 NRLs could provide a promising method to predict the prognosis and immune response of KIRC patients. To some extent, our findings helped give a reference for further research between NRLs and KIRC and find more effective therapeutic drugs for KIRC.

BACKGROUND Somatic mutations of mitochondrial DNA (mtDNA) have been extensively identified mainly by traditional Sanger sequencing technology in various cancer types. However, low detection sensitivity of traditional methods greatly limits the comprehensive profiling of mtDNA somatic mutations in cancers, especially in hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC). Moreover, the functional roles of mtDNA mutation in HBV-related hepatocarcinogenesis have not been systematically revealed. PATIENTS AND METHODS Next-generation sequencing (NGS) platform was applied to profile the somatic mtDNA mutations of HCC and paired paratumor (non-HCC) tissues from a large cohort of 156 HBV-HCC patients. RESULTS Our data revealed the common existence of mtDNA mutation in both inflammatory and cancer tissues with significantly different mutation pattern. The mutation density (mutation number/region length) of D-loop region was much higher than that of other regions in both HCC and non-HCC tissues. Unexpectedly, the average mutation number in D-loop region of HCC tissues was significantly less than that of non-HCC tissues. In contrast, the heteroplasmy level of D-loop region mutations was significantly increased in HCC tissues, implying that the D-loop mutations might be positively selected in HCC tissues. Furthermore, our results indicated that the patients with D-loop mutations had a significantly lower mtDNA copy number and were more likely to relapse. In vitro experiments demonstrated that proliferation, invasion and metastasis ability of HCC cells with D-loop region mutations were significantly higher than those without D-loop region mutations. CONCLUSION These results emphasize the critical contributing role of somatic mtDNA D-loop mutations in HBV-related hepatocarcinogenesis.

Heteroplasmic mutations in mitochondrial DNA (mtDNA) play critical roles in mitochondria disease, aging, and cancer. Recently, next-generation sequencing (NGS) has been widely used to detect mtDNA mutations for diagnosis and monitoring of the above-mentioned diseases. However, little attention is paid on inherent cross-contamination generated during mtDNA capture and sequencing of mixed samples, which may seriously reduce the detection accuracy of mtDNA heteroplasmic mutations. In this study, a novel sequencing strategy based on a unique double-barcode design was established. The results showed that when single barcode-based analysis strategy was used, cross-contamination level of 20 DNA samples ranged from 0.27% to 11.90% on HiSeq 2500 and from 0.93% to 17.70% on HiSeq X ten, whereas double barcode-based strategy could effectively eliminate cross-contamination. Moreover, the data indicated that cross-contamination was mainly derived from capture process and was significantly affected by different NGS platforms. In addition, contamination level was negatively related to sequencing depth. Moreover, cross-contamination significantly increased the false-positive calling of mtDNA heteroplasmic mutations and remarkably affected the heteroplasmy level of mtDNA mutations. In contrast, cross-contamination had no notable effect on classification of mtDNA haplogroup. Taken together, our novel double barcode-based sequencing strategy is effective in eliminating cross-contamination, enhancing the detection accuracy of mtDNA NGS, and improving its application in diagnosis or monitoring of diseases associated with mtDNA mutations.

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.

BACKGROUND:Tumor necrosis factor-α has been proven an effective anticancer agent in preclinical studies. However, the translation of TNFα from research to clinic has been blocked by significant systemic toxicity and limited efficacy at maximal tolerated dose, which need urgently to be solved.METHODS:The level of cytosolic Ca2+ was assessed by Fura-2 in HCC cells. After changing cytosolic Ca2+ level by using agonists or inhibitors, cell apoptosis was detected by flow cytometry. We also detected the effect of ionomycin or parvalbumin on the anti-tumor activity of TNFα in a mice model. Lastly, we studied the roles of cytosolic Ca2+ in the mitochondrial-dependent intrinsic apoptosis pathway.RESULTS:Here, we demonstrated that TNFα induced extracellular Ca2+ influx into cytoplasm through transient receptor potential channel in HCC cells. Both cytosolic Ca2+ scavenger and Ca2+-binding protein PV effectively desensitized hepatocellular carcinoma cells to TNFα, whereas combination ionomycin or 1,4,5-inositol triphosphate significantly sensitized HCC cells to TNFα, indicating that the increased level of cytosolic Ca2+ was positively correlated with the TNFα-induced cell apoptosis in vitro. In a nude mice xenograft model, our data revealed that TNFα combined with ionomycin remarkably synergized the anti-tumor effect of TNFα. Furthermore, we found that TNFα-mediated extracellular Ca2+ influx accelerated TNFα-induced extrinsic apoptosis through activating calpain/IAP/caspase3 pathway.CONCLUSIONS:Our study provides the evidence supporting a novel mechanism by which TNFα induces extracellular Ca2+ influx to enhance cell apoptosis and suggests that increasing the level of cytosolic Ca2+ might be an alternative strategy to improve the pro-apoptotic activity of TNFα in HCC cells, although suitable chemical or biological reagents need to be further tested.

Background: Previous studies have indicated that mitochondrial genetic variations were associated with the risk of many cancers. However, there are few reports on the association between single nucleotide polymorphisms (SNPs) or haplogroups of mitochondrial DNA (mtDNA) and the risk or prognosis of hepatocellular carcinoma (HCC).Methods: In order to investigate the predictive and prognostic role of mtDNA SNPs and haplogroups in HCC, the mitochondrial genome of 188 HCC patients and 344 healthy controls were sequenced by next generation sequencing technology. Then, logistic regression analysis was used to determine the effect of mtDNA SNP or haplogroup on risk and prognosis of HCC patients.Results: The haplogroup M7 had an odds ratio (OR) of 0.47 (95% CI=0.24-0.91; P=0.026) to develop HCC. The frequency of 152T/C, 199T/C, 4048G/A, 9824T/C, 15784T/C, 16185C/T and 16399A/G was significantly different between HCC patients and the controls. In addition, multivariate analysis with COX hazards model showed that the patients with haplogroup M8 had lower survival rate than the patients with haplogroup D4 (HR=2.62, 95% CI=1.03-6.68; P=0.044). Three SNPs 15784T/C, 16185C/T and 16399A/G were also identified to have a statistically significant association with postoperative survival in HCC.Conclusions: To date, these results provide the first evidence that mtDNA SNPs and haplogroups may be potential risk factors for susceptibility and survival of HCC patients. (C) 2017. Published by Elsevier Masson SAS

Background Previous studies have indicated that tumor mitochondrial DNA (mtDNA) mutations are primarily shaped by relaxed negative selection, which is contradictory to the critical roles of mtDNA mutations in tumorigenesis. Therefore, we hypothesized that site-specific selection may influence tumor mtDNA mutations. Methods To test our hypothesis, we developed the largest collection of tumor mtDNA mutations to date and evaluated how natural selection shaped mtDNA mutation patterns. Results Our data demonstrated that both positive and negative selections acted on specific positions or functional units of tumor mtDNAs, although the landscape of these mutations was consistent with the relaxation of negative selection. In particular, mutation rate (mutation number in a region/region bp length) in complex V and tRNA coding regions, especially in ATP8 within complex V and in loop and variable regions within tRNA, were significantly lower than those in other regions. While the mutation rate of most codons and amino acids were consistent with the expectation under neutrality, several codons and amino acids had significantly different rates. Moreover, the mutations under selection were enriched for changes that are predicted to be deleterious, further supporting the evolutionary constraints on these regions. Conclusion These results indicate the existence of site-specific selection and imply the important role of the mtDNA mutations at some specific sites in tumor development.

目的:建立新的线粒体基因组DNA杂交捕获探针制备方法并用进行初步应用.方法:通过PCR技术扩增特异线粒体DNA片段,并与生物素偶联,最后与标记磁珠的亲和素混合获得捕获探针.并自行制备的线粒体基因组DNA文库捕获探针与肝癌全基因组测序文库进行液相杂交.分离捕获产物后PCR扩增并进行测序分析.结果:成功建立了线粒体基因组杂交捕获探针制备方法并成功分离线粒体基因组DNA;对测序数据的分析显示:90％以上测序数据来自线粒体基因组DNA,且覆盖率达到100％,且均一性良好.检测到的同质性变异位点数量和异质性变异位点数量与全基因组测序数据产生的结果接近(P=0.9152,P=0.8409).结论:新方法制备的线粒体基因组DNA杂交捕获探针可以从全基因组文库中高效捕获线粒体基因组DNA测序文库.

Hypoxia-inducible factor 1α (HIF-1α) plays an important role in tumor growth and metastasis. Genetic variations of HIF1A gene have been shown to influence the developing risk and prognosis in many types of human malignancies. However, their association with clinical outcomes of hepatocellular carcinoma (HCC) patients remains unclear. To investigate the predictive role of single nucleotide polymorphisms (SNPs) in HIF1A gene in HCC patients' outcomes, we genotyped three functional SNPs (rs2057482, rs1957757 and rs2301113) in HIF1A gene and assessed their associations with clinicopathological parameters and prognosis of 492 surgical HCC patients. The patients with variant alleles (CT+TT) of SNP rs2057482 had a significantly lower recurrence risk when compared with patients with the CC genotype. In stratified analysis, the protective effect of rs2057482 CT+TT genotype was more evident in patients with adverse strata, compared with patients with favorable strata. Additionally, strong joint predictive effect between rs2057482 genotypes and AFP level, stage or differentiation were observed. Functional assay also indicated the significant effect of rs2057482 on gene expression. In conclusion, SNP rs2057482 in HIF1A gene is significantly associated with clinical outcomes of Chinese HCC patients after surgery, especially in those with aggressive status, which warrants further validation in other patient populations.

BACKGROUND:Increasing evidence suggests that alterations in mitochondrial DNA (mtDNA) content may be implicated in the tumorigenesis of several malignancies. However, the association between mtDNA content in peripheral blood lymphocytes (PBLs) and glioma risk has not been investigated.METHODS:Real-time PCR was used to examine the mtDNA content in PBLs of 414 glioma patients and 414 matched controls in a hospital-based case-control study. The association between mtDNA content and glioma risk was evaluated using an unconditional multivariate logistic regression model.RESULTS:We found that glioma patients exhibited a significantly higher median mtDNA content than healthy controls (0.99 vs. 0.71, P < 0.001). Unconditional multivariate logistic regression analysis adjusting for age, gender, smoking status, and family cancer history showed that there was an S-shaped association between mtDNA content and glioma risk. Higher mtDNA content was significantly associated with an elevated risk of glioma. Compared with the first quartile, the odds ratio (95% confidence interval) for subjects in the second, third, and fourth quartiles of mtDNA content were 0.90 (0.52-1.53), 3.38 (2.15-5.31), and 5.81 (3.74-9.03), respectively (P for nonlinearity = 0.009). Stratified analysis showed that the association between mtDNA content and glioma risk was not modulated by major host characteristics.CONCLUSIONS:Our findings demonstrate for the first time that a higher mtDNA content in PBLs is associated with an elevated risk of glioma, which warrants further investigation in larger populations.

IntroductionNon-small cell lung cancer (NSCLC) is characterized by poor prognosis and only a few molecular markers may be potentially used to predict the outcome. Metabolic reprogramming is a hallmark of cancer, including the alterations of tricarboxylic acid (TCA) cycle key enzymes. However, the significance of single nucleotide polymorphisms (SNPs) in genes encoding these key enzymes has not been investigated in NSCLC.Patients and methodsIn this study, we genotyped 18 potentially functional SNPs in 7 genes belonging to 3 TCA cycle enzyme families (SDH, FH and IDH) using Sequenom iPLEX genotyping system in a cohort of 500 NSCLC patients. Multivariate Cox proportional hazards model and Kaplan–Meier curve were used for the survival analysis.ResultsOur results showed that SDHC gene: SNP rs12064957, IDH2 gene: SNP rs11540478 and FH gene: SNP rs1414493 were associated with overall survival (OS) and SDHA gene: SNP rs13173911, IDH2 gene: SNP rs4932158 were associated with recurrence-free survival (RFS) of NSCLC patients. Unfavorable genotypes of these SNPs showed a significant cumulative effect on OS and RFS of NSCLC patients (both P<0.001). Furthermore, survival tree analysis indicated that FH: rs1414493 was the primary risk factor contributing to OS of NSCLC patients and the IDH2: rs4932158 was the primary risk factor contributing to RFS of NSCLC patients.ConclusionOur data suggest that SNPs in TCA cycle key enzyme genes may serve as potential biomarkers to predict the outcomes of NSCLC. Further studies with different ethnicities are needed to validate our findings and generalize their clinical utility.

It has been reported that CD147 and CD98 heavy chain (CD98hc) form a complex on the cell plasma membrane of several cancers; however, whether this complex exists in non-small cell lung cancer (NSCLC) cells and affects the prognosis of patients remains to be elucidated.

Objective: Previous studies proved that somatic mutations of mitochondrial DNA(mtDNA) are strongly associated with tumorigenesis and tumor progression.However,conventional sequencing methods are not able to detect mtDNA mutations with high-throughput and high accuracy.In this study,we established a new approach for detecting mutations in mtDNA based on next-generation sequencing technology.Methods: mtDNA were amplified by PCR using genome DNA samples obtained from tumor tissue,paired normal tissue or peripheral blood.The PCR products went through blunt end ligation,sticky end ligation,or amino-modification before sequencing library preparation.The mtDNA libraries were sequenced utilizing Illumina HiSeq 2000 platform.The sequences were then compared with human mtDNA referencing sequences,and further analysis using bioinformatical methods.Results: After assessing the genomic DNA samples with different qualities,we found that using three pairs of PCR primers is applicable to most mtDNA enrichment reactions.We also found the amino-modified PCR primers could significantly improve the coverage uniformity,and reduce the sequencing costs.Conclusion: A method to optimize mtDNA enching and the coverage uniformity has been built up in this study based on next-generation sequencing technology.Further a sensitive mtDNA mutation detecting system with high specificity and high-throughput was aslo established.This system may provide a new method for research in mtDNA mutation detection and disease association studies.

线粒体是细胞进行氧化磷酸化产生ATP的主要场所,在能量代谢、细胞凋亡、氧化应激等生命活动中扮演重要角色.近年来随着研究的不断深入,线粒体DNA(mtDNA)变异在恶性肿瘤发生及进展中的作用机制逐渐引起人们的广泛关注,成为肿瘤基础研究与临床研究领域的新兴热点.研究表明,肿瘤细胞中mtDNA变异包括点突变、缺失、插入以及拷贝数变异,并且这些变异可参与肿瘤细胞的增殖、生长、侵袭和转移.因此,进一步深入理解mtDNA变异的发生规律及作用机制,将为恶性肿瘤诊断、治疗及预后判断提供有意义的参考.

The KRAB-type zinc-finger protein Apak was recently identified as a negative regulator of p53-mediated apoptosis. However, the mechanism of this selective regulation is not fully understood. Here, we show that Apak recognizes the TCTTN2−30TTGT consensus sequence through its zinc-fingers. This sequence is specifically found in intron 1 of the proapoptotic p53 target gene p53AIP1 and largely overlaps with the p53-binding sequence. Apak competes with p53 for binding to this site to inhibit p53AIP1 expression. Upon DNA damage, Apak dissociates from the DNA, which abolishes its inhibitory effect on p53-mediated apoptosis.

Recent efforts suggest an aetiological role of hepatitis B virus (HBV) infection in intrahepatic cholangiocarcinoma (ICC). The purpose of this study was to clarify the clinicopathologic characteristics and surgical outcomes of patients with HBV-associated ICC. All patients with chronic HBV infection were identified from a database of patients with ICC that underwent surgical resection between 1 January 2005 and 31 December 2006. Their clinicopathologic and survival characteristics were compared with ICC patients without chronic HBV infection. The age of the HBV-associated ICC patients tend to be younger than that of ICC patients without chronic HBV infection. HBV-associated ICC patients tend to have higher abnormal α-fetoprotein levels and lower abnormal serum carbohydrate antigen19-9 (CA19-9), r-glutamyltransferase (r-GT) and alkaline phosphatase levels. The pathologic features of the resected specimens revealed that HBV-associated ICC patients tended to be of the mass-forming type have a lower prevalence of lymphatic involvement and poorer tumour differentiation, and a higher prevalence of capsule formation and liver cirrhosis. Patients with HBV-associated ICC had a significantly better survival than patients without chronic HBV infection. The clinicopathological features of HBV-associated ICC patients showed significant differences from ICC patients without HBV infection. These tumours are characterized by the mass-forming growth pattern and appeared to have a more favourable prognosis.