An analysis of genetic factors related to risk of inflammatory bowel disease and colon cancer

Background and aimsPatients with inflammatory bowel disease (IBD) have a higher risk of developing colorectal cancer than the general population. Genome-wide association studies have identified and replicated several loci associated with risk of IBD; however, it is currently unknown whether these loci are also associated with colon cancer risk.MethodsWe selected 15 validated SNPs associated with risk of either Crohn's disease, ulcerative colitis, or both in previous GWAS and tested whether these loci were also associated with colon cancer risk in a two-stage study design.ResultsWe found that rs744166 in STAT3 was associated with colon cancer risk in two studies; however, the direction of the observation was reversed in TP53 mutant tumors possibly due to a nullification of the effect by mutant p53. The SNP, which lies within intron 1 of the STAT3 gene, was associated with lower expression of STAT3 mRNA in TP53 wild-type, but not mutant, tumors.ConclusionsThese data suggest that the STAT3 locus is associated with both IBD and cancer. Further understanding the function of this variant in relation to TP53 could possibly explain the role of this gene in autoimmunity and cancer. Furthermore, an analysis of this locus, specifically in a population with IBD, could help to resolve the relationship between this SNP and cancer.     

The Cassandra retrotransposon landscape in sugar beet (Beta vulgaris) and related Amaranthaceae: recombination and re-shuffling lead to a high structural variability

Background and AimsPlant genomes contain many retrotransposons and their derivatives, which are subject to rapid sequence turnover. As non-autonomous retrotransposons do not encode any proteins, they experience reduced selective constraints leading to their diversification into multiple families, usually limited to a few closely related species. In contrast, the non-coding Cassandra terminal repeat retrotransposons in miniature (TRIMs) are widespread in many plants. Their hallmark is a conserved 5S rDNA-derived promoter in their long terminal repeats (LTRs). As sugar beet (Beta vulgaris) has a well-described LTR retrotransposon landscape, we aim to characterize TRIMs in beet and related genomes.MethodsWe identified Cassandra retrotransposons in the sugar beet reference genome and characterized their structural relationships. Genomic organization, chromosomal localization, and distribution of Cassandra-TRIMs across the Amaranthaceae were verified by Southern and fluorescent in situ hybridization.Key resultsAll 638 Cassandra sequences in the sugar beet genome contain conserved LTRs and thus constitute a single family. Nevertheless, variable internal regions required a subdivision into two Cassandra subfamilies within B. vulgaris. The related Chenopodium quinoa harbours a third subfamily. These subfamilies vary in their distribution within Amaranthaceae genomes, their insertion times and the degree of silencing by small RNAs. Cassandra retrotransposons gave rise to many structural variants, such as solo LTRs or tandemly arranged Cassandra retrotransposons. These Cassandra derivatives point to an interplay of template switch and recombination processes – mechanisms that likely caused Cassandra’s subfamily formation and diversification.ConclusionsWe traced the evolution of Cassandra in the Amaranthaceae and detected a considerable variability within the short internal regions, whereas the LTRs are strongly conserved in sequence and length. Presumably these hallmarks make Cassandra a prime target for unequal recombination, resulting in the observed structural diversity, an example of the impact of LTR-mediated evolutionary mechanisms on the host genome.     

非小细胞肺癌患者肠道微生物特征分析

【目的】分析非小细胞肺癌患者与肺部良性病变患者肠道微生物的构成差异,探究特异肠道菌群对非小细胞肺癌发生发展的影响。【方法】收集63例患者粪便样本,非小细胞肺癌患者39例,其中肺腺癌(ADC) 32例,肺鳞癌(SCC) 7例,肺部良性病变患者24例,进行16S rDNA测序。【结果】毛螺菌属(Lachnospira)、瘤胃球菌属(Ruminococcus)、粪杆菌属(Faecalibacterium)、罗氏菌属(Roseburia)和纺锤链杆属(Fusicatenibacter)在肺腺癌患者中显著富集,在肺鳞癌和肺部良性病变中无明显差异。嗜血杆菌属(Haemophilus)、普雷沃菌属(Prevotella)、链球菌属(Streptococcus)和柠檬酸杆菌属(Citrobacter)在肺部良性病变患者肠道中显著富集。【结论】非小细胞肺癌患者与肺部良性病变患者肠道中均存在特异的微生物菌群。     

A pan-cancer landscape of centromere proteins in tumorigenesis and anticancer drug sensitivity

BackgroundDuring mitosis and meiosis, centromere proteins (CENPs) play a key role in proper chromosome segregation. Abnormal expression of CENPs leads to chromosome instability, which is the main cause of tumorigenesis.MethodsTo elucidate the functional characteristics of CENPs in pan-cancer, we comprehensively analyzed the expression landscape of CENPs and their relationships with patient survival, genomic alterations, tumor immunity, tumor microenvironment, and anticancer drug sensitivity. The expression patterns and signaling pathways of CENPs were identified through multiple bioinformatics mining and experimental verification. GEPIA2 and PrognoScan were implemented to evaluate the prognostic value of CENPs. The molecular functions of CENPs in pan-cancer were comprehensively assessed using cBioPortal, GSCA, ImmuCellAI, CellMiner, the ROC plotter tool and TIDE.ResultsThe results showed that CENPs were upregulated in most tumors compared with normal tissues. We confirmed this conclusion by immunohistochemistry and real-time quantitative PCR. Survival analysis revealed a significant association between high CENP expression and a poor prognosis. CENP expression is related to genome alterations, copy number variation, single nucleotide variation and methylation. Among CENP family genes, CENPF and CENPE are mutated at high frequencies in various tumors, while CENPM and CENPA are less frequently mutated. Furthermore, CENPs regulate the tumor mutational burden, stemness, and microsatellite instability, and are associated with tumor immunity. Most importantly, we revealed that CENP family gene expression was correlated with chemosensitivity and immunotherapy responses.ConclusionThese findings may clarify the role of CENPs in cancer progression and antitumor drug sensitivity and provide evidence for CENPs as a potential target in pan-cancer.     

Modulation of Mutational Landscape in HER2-Positive Breast Cancer after Neoadjuvant Chemotherapy

IntroductionIn early-stage HER2 positive breast cancer (BC) patients, tumor response to neoadjuvant chemotherapy (NACT) predict survival outcomes. Patients achieving less than pathological complete response (pCR) have a worse prognosis, however, this group is heterogeneous. Nowadays limited data on predictive/prognostic biomarkers in patients with residual cancer disease are available.MethodsUsing next-generation sequencing technology, we evaluated a panel of 21 cancer genes in a group of HER2 positive BC patients with residual disease after NACT. A control group of patients who achieved the pCR was selected too. The BC mutational profile was analyzed on both the tumor diagnostic biopsy and matched residual disease.ResultsOverall, the detection rate of mutations was 79% in the No-pCR group versus 90% in the pCR cohort and 98% in the residual BC. The most mutated genes were TP53 and PIK3CA. No correlations between single gene mutations and survival outcomes were found. In no-pCR cohort, 52% of patients had different mutational profile after NACT, 69% of them had an increased in the number of mutated genes. Mutational profile changes from diagnostic biopsy to residual BC were a negative prognostic factor in term of relapse free survival: recurrence probability in different gene profile sub-group was 42% vs 0% in the same profile one (P = .019).ConclusionsTreatment selective pressure on tumor cells due to NACT changed the gene mutational profile in more than half of BC patient with residual tumor disease. Treatment-induced gene mutations significantly increase the risk of relapse. Profiling primary and residual BC is a major step in order to further personalized adjuvant treatment strategy.     

信号转导与转录因子3和表皮生长因子受体在宫颈不同病变组织中的表达及其临床意义

目的:探讨信号转导与转录因子3(STAT3)与表皮生长因子受体(EGFR)在宫颈不同病变组织中的表达变化及其临床意义。方法:采用Western blot与免疫组化的方法检测100例上皮内瘤样病变(CIN)组织、60例宫颈癌组织及40例正常宫颈组织中STAT3与EGFR的表达;分析STAT3与EGFR的表达与宫颈癌组织病理特征的关系;对宫颈癌组织中STAT3与EGFR的表达的相关性进行分析。结果:宫颈癌组织以及CIN组织中STAT3、EGFR的表达量和阳性率显著高于正常宫颈组织(P0.05),且宫颈癌组织中STAT3、EGFR的表达量和阳性率高于CIN组织,差异有统计学意义(P0.05);STAT3与EGFR在宫颈癌组织中的染色强度较正常宫颈组织以及CIN组织显著增强;STAT3与EGFR的异常表达与宫颈癌患者的组织学分级、临床分期以及是否发生淋巴结转移有关(P0.05),而与年龄以及病理分型无关(P0.05);宫颈癌组织中STAT3和EGFR表达呈正相关(P0.05)。结论:STAT3与EGFR表达与CIN、宫颈癌的进展紧密相关,且与宫颈癌部分病理特征相关,二者有可能作为宫颈癌诊断及预后的参考指标。     

Human omental adipose-derived mesenchymal stem cells enhance autophagy in ovarian carcinoma cells through the STAT3 signalling pathway

BackgroundOur previous study showed that human omental adipose-derived stem cells (ADSCs) promote ovarian cancer growth and metastasis. In this study, the role of autophagy in the ovarian cancer-promoting effects of omental ADSCs was further determined.MethodsThe growth and invasion of ovarian cancer cells were detected by CCK-8 and Transwell assays, respectively. The autophagy of ovarian cancer cells transfected with MRFP-GFP-LC3 adenoviral vectors was evaluated by confocal microscopy and western blot assay. Transfection of STAT3 siRNA was used to inhibit the expression of STAT3.ResultsOur results show that autophagy plays a vital role in ovarian cancer and is promoted by ADSCs. Specifically, we show that proliferation and invasion are correlated with autophagy induction by ADSCs in two ovarian cancer cell lines under hypoxic conditions. Mechanistically, ADSCs activate the STAT3 signalling pathway, thereby promoting autophagy. Knockdown of STAT3 expression using siRNA decreased hypoxia-induced autophagy and decreased the proliferation and metastasis of ovarian cancer cells.ConclusionTaken together, our data indicate that STAT3-mediated autophagy induced by ADSCs promotes ovarian cancer growth and metastasis.     

Comorbidity trajectories in working age cancer survivors: A national study of Swedish men

BackgroundA large proportion of cancer survivors are of working age, and maintaining health is of interest both for their working and private life. However, patterns and determinants of comorbidity over time among adult cancer survivors are incompletely described. We aimed to identify distinct comorbidity trajectories and their potential determinants.MethodsIn a cohort study of Swedish men born between 1952 and 1956, men diagnosed with cancer between 2000 and 2003 (n = 878) were matched with cancer-free men (n = 4340) and followed over five years after their first year of survival. Comorbid diseases were identified using hospital diagnoses and included in the analysis using group-based trajectory modelling. The association of socioeconomic and developmental characteristics were assessed using multinomial logit models.ResultsFour distinct comorbidity trajectories were identified. As many as 84% of cancer survivors remained at very low levels of comorbidity, and the distribution of trajectories was similar among the cancer survivors and the cancer-free men. Increases in comorbidity were seen among those who had comorbid disease at baseline and among those with poor summary disease scores in adolescence. Socioeconomic characteristics and physical, cognitive and psychological function were associated with types of trajectory in unadjusted models but did not retain independent relationships with them after simultaneous adjustment.ConclusionsAmong working-age male cancer survivors, the majority remained free or had very low levels of comorbidity. Those with poorer health in adolescence and pre-existing comorbid diseases at cancer diagnosis may, however, benefit from follow-up to prevent further increases in comorbidity.     

Age and sun exposure-related widespread genomic blocks of hypomethylation in nonmalignant skin

BackgroundAging and sun exposure are the leading causes of skin cancer. It has been shown that epigenetic changes, such as DNA methylation, are well established mechanisms for cancer, and also have emerging roles in aging and common disease. Here, we directly ask whether DNA methylation is altered following skin aging and/or chronic sun exposure in humans.ResultsWe compare epidermis and dermis of both sun-protected and sun-exposed skin derived from younger subjects (under 35 years old) and older subjects (over 60 years old), using the Infinium HumanMethylation450 array and whole genome bisulfite sequencing. We observe large blocks of the genome that are hypomethylated in older, sun-exposed epidermal samples, with the degree of hypomethylation associated with clinical measures of photo-aging. We replicate these findings using whole genome bisulfite sequencing, comparing epidermis from an additional set of younger and older subjects. These blocks largely overlap known hypomethylated blocks in colon cancer and we observe that these same regions are similarly hypomethylated in squamous cell carcinoma samples.ConclusionsThese data implicate large scale epigenomic change in mediating the effects of environmental damage with photo-aging.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-015-0644-y) contains supplementary material, which is available to authorized users.     

Modulation of cardiac AKT and STAT3 signalling in preclinical cancer models and their impact on the heart

BackgroundAdvanced cancer induces fundamental cardiac changes and promotes body wasting and heart failure. We evaluated the impact of cancer on major cardiac signalling pathways, and resulting consequences for the heart.Methods and resultsMetastatic melanoma disease was induced in male C57BL/6 N mice by intraperitoneal injection of the melanoma cell line B16F10 and lead to cardiac atrophy and heart failure. Analyses of key cardiac signalling pathways in left ventricular tissue revealed increased activation of STAT3 and reduced activation of AKT, p38 and ERK1/2. Markers of the ubiquitin proteasomal system (UPS: Atrogin-1) and of mitophagy/autophagy (LC3b, BNIP3) were upregulated. Tumour-bearing C57BL/6 N mice with a cardiomyocyte-specific overexpression of a constitutively active AKT transgene (AKTtg) displayed less cardiac atrophy and dysfunction and normalized Atrogin-1, LC3b and BNIP3 expression while the cardiomyocyte-specific knockout of STAT3 (CKO) had no major effect on these parameters compared to WT.ConclusionCancer alters major cardiac signalling pathways and subsequently the UPS, mitophagy and autophagy. The present study suggests that cancer-induced reduction of cardiomyocyte AKT contributes to these alterations as they were attenuated in tumour-bearing AKTtg mice. In turn, increased cardiomyocyte STAT3 activation appears less relevant, as tumour-induced impairment on the heart was largely similar in CKO and WT mice. Since oncologic therapies frequently target AKT and/or STAT3, their impact on the heart might be different in tumour-bearing mice compared to healthy mice, a feature suggesting to test tumour therapies also in tumour disease models and not only under healthy conditions. This article is part of a Special Issue entitled: Cardiomyocyte biology: new pathways of differentiation and regeneration edited by Marijke Brink, Marcus C. Schaub, and Christian Zuppinger.