DNA methylation aberrancies as a guide for surveillance and treatment of human cancers

DNA methylation aberrancies are hallmarks of human cancers and are characterized by global DNA hypomethylation of repetitive elements and non-CpG rich regions concomitant with locus-specific DNA hypermethylation. DNA methylation changes may result in altered gene expression profiles, most notably the silencing of tumor suppressors, microRNAs, endogenous retorviruses and tumor antigens due to promoter DNA hypermethylation, as well as oncogene upregulation due to gene-body DNA hypermethylation. Here, we review DNA methylation aberrancies in human cancers, their use in cancer surveillance and the interplay between DNA methylation and histone modifications in gene regulation. We also summarize DNA methylation inhibitors and their therapeutic effects in cancer treatment. In this context, we describe the integration of DNA methylation inhibitors with conventional chemotherapies, DNA repair inhibitors and immune-based therapies, to bring the epigenome closer to its normal state and increase sensitivity to other therapeutic agents to improve patient outcome and survival.     

胰腺癌的生物学临床诊断研究进展

胰腺癌(pancreatic cancer,PC)是一种发病率接近死亡率、死亡率极高的恶性肿瘤.由于胰腺癌早期无明显病症,许多病人确诊时已是癌症末期,错过了最佳的治疗时期,预后极差,因此,迫切需要高效的胰腺癌早期诊断生物标志物.随着高通量测序技术(next-generation sequencing,NGS)、高分辨质...     

Serum vitamin D receptor (VDR) levels as a potential diagnostic marker for colorectal cancer

Colorectal cancer (CRC) is one of the leading causes of mortality and morbidity worldwide, and there has been a significant increase in the incidence of CRC in recent decades. Therefore, there is an urgent need to identify blood biomarkers that can be used for early diagnosis. It is not yet clear whether the level of vitamin D and its receptor, vitamin D receptor (VDR), in the blood are helpful factors in the diagnosis of CRC. Therefore, the study focuses on determining the VDR serum level’s contribution and other chemical parameters to the risk of CRC. A total of 189 Saudi participants (66 CRC patients and 123 control patients) aged 20–80 years old were enrolled in this case-control study. A serum sample was collected from each participant, and the levels of VDR and other bone profile tests were determined using ELISA or chemiluminescent assays. P values < 0.05 were considered statistically significant. The results showed a highly significant reduction in the levels of total vitamin D (P < 0.0001), VDR (P < 0.0001), vitamin D₃ (P < 0.05), and calcium (P < 0.0001) in the serum of CRC patients compared to the controls. However, the alkaline phosphatase level was higher in CRC patients compared to the controls (P < 0.0001). None of the blood markers showed a significant correlation to the progression of CRC (P > 0.05). More investigation is needed to elucidate different physiological processes that can be affected by these blood biomarkers, therefore changing the carcinogenesis of CRC.     

A specific autoantibody against a novel tumour-association antigen derived from human DNA-topoiomerase I is a potential biomarker for early diagnosis and favourable prognosis in patients with colorectal carcinoma

Abstract

Context: We previously reported a novel tumour associated antigen (TTA) with molecular weight around 48?kDa and identified the novel TTA as a fragment derived from human DNA-topoiomerase I (TOP1). We termed the novel TAA as TOPO48 and termed autoantibody against the TAA as anti-TOPO48 autoantibody.

Objective: To explore the clinical significance of anti-TOPO48 autoantibody in patients with colorectal carcinoma (CRC).

Materials and methods: Serum levels of the autoantibody in patients with CRC or benign tumours and healthy volunteers were measured with a specific ELISA.

Results: CRC patients at early stage had higher frequency of positive levels of the autoantibody and CRC patients with positive autoantibody levels had higher overall survival rate than those with negative autoantibody levels.

Conclusion: The autoantibody is a potential biomarker for early diagnosis and favourable prognosis of CRC.     

Simultaneous measurement of soluble carcinoembryonic antigen and the tissue inhibitor of metalloproteinase TIMP1 serum levels for use as markers of pre-invasive to invasive colorectal cancer

Matrix metalloproteinases (MMP) are members of a multigene family of zinc-dependent enzymes involved in the degradation of extracellular matrix components. Cancer research suggest that MMP and tissue inhibitors of metalloproteinases (TIMP) may be involved in disease progression; these enzymes could therefore be used as markers in cancer prevention programmes and for clinical monitoring. To establish whether MMP and TIMP can be used effectively as markers we determined serum levels of MMP1 and TIMP1, and studied the relationships between these enzymes and the stage of disease. The potential diagnostic and prognostic value of serum level measurements of MMP1 and TIMP1 was evaluated by comparing them with serum levels of soluble carcinoembryonic antigens (sCEA) and p53 antibodies. Our overall results indicate that simultaneous measurements of serum sCEA and TIMP1 in patients with colorectal cancer could be used as prognostic and diagnostic markers for disease progression from the pre-invasive nodal phase to the invasive phase (stages I, II to III, IV). In addition, serum levels of TIMP1 could be used as a selective marker for metastatic disease (stage III to IV). In fact, the 95% confidence interval of the serum levels of sCEA at stage III (18.4 ≤ sCEA ≤ 68.6 ng/ml) and TIMP1 at stage IV (1620 ≤ TIMP1 ≤ 3906 ng/ml) identified statistically significant ranges of values (sCEA P = 0.02, TIMP1 P = 0.02), which may be useful in the monitoring of patients at these disease phases. More specifically, our data suggest that, when the serum level of sCEA is below 18.4 ng/ml and the level of TIMP1 below 1620 ng/ml, there is a 95% probability that the disease is in the pre-invasive nodal phase; when the serum level of sCEA falls between 18.4 ng/ml and 68.6 ng/ml and the level of TIMP1 is below 1620 ng/ml, there is a 95% probability that the disease is in the phase when lymph node infiltration occurs; when the level of sCEA is above 68.6 ng/ml and the level of TIMP1 is at least 1620 ng/ml, there is a 95% probability that the disease is in the metastatic phase. Received: 30 March 2000 / Accepted: 18 May 2000     

LINE-1 and inflammatory gene methylation levels are early biomarkers of metabolic changes: association with adiposity

We analyzed whether global and inflammatory genes methylation can be early predictors of metabolic changes and their associations with the diet, in a cross-sectional study (n?=?40). Higher global methylation was associated to adiposity, insulin resistance, and lower quality of the diet. Methylation of IL-6, SERPINE1 and CRP genes was related to adiposity traits and macronutrients intake. SERPINE1 hypermethylation was also related to some metabolic alterations. CRP methylation was a better predictor of insulin resistance than CRP plasma concentrations. Global and inflammatory gene promoter hypermethylation can be good early biomarkers of adiposity and metabolic changes and are associated to the quality of the diet.     

Serum and salivary levels of albumin as diagnostic tools for oral pre-malignancy and oral malignancy

The role of oxygen free radicals in the initiation, promotion and progression of carcinogenesis and the protective role of antioxidants has been a subject of much speculation. There are few studies that report evaluation of serum albumin and only one study in which salivary albumin was found and only one study that reports of salivary albumin in oral Leukoplakia and Oral Squamous Cell Carcinoma (OSCC). We evaluated serum and salivary albumin levels in normal individuals, patients with oral pre-malignancy and patients with oral malignancy, and we compared serum and salivary albumin levels in patients with oral pre-malignancy and oral malignancy. Our study comprised 45 subjects separated into three groups of 15: normal healthy, oral pre-malignancy and oral malignancy patients. Venous blood was drawn and unstimulated saliva was collected early in the morning. Albumin levels were estimated using the bromocresol green method. Serum albumin levels decreased in oral pre-malignancy and oral malignancy cases compared to healthy individuals. Salivary albumin levels increased in oral pre-malignancy and oral malignancy cases compared to healthy individuals. Our results suggest that albumin may play a role in early diagnosis and prognosis of oral pre-malignant and oral malignant tissues.     

乳腺癌早期筛查和诊断生物标志物研究进展

2020年全球乳腺癌(breast cancer,BC)新发病例达226万例,占全部肿瘤新发病例的11.7%,是全世界发病率最高的癌症。早期发现、早期诊断和早期治疗是降低乳腺癌死亡率及改善预后的关键。尽管乳房X光筛查被广泛用作乳腺癌筛查的工具,但其假阳性、辐射性和过度诊断仍是亟待解决的问题。因此,亟需开发易于获取且稳定可靠的生物标志物,用于乳腺癌无创筛查和诊断。近年来多项研究显示来自乳腺癌患者血液中的循环肿瘤细胞DNA(circulating tumor cell DNA,ctDNA)、癌胚抗原(carcinoembryonic antigen,CEA)、糖类抗原15-3(carbohydrate antigen 15-3,CA15-3)、细胞外囊泡(extracellular vesicles,EV)、循环miRNA和BRCA基因突变等生物标志物,以及来自人体尿液、呼出气体(volatile organic compounds,VOCs)和乳头吸出液(nipple aspirate fluid,NAF)中的磷脂、miRNA、苯乙酮和十六烷等多种生物标志物与乳腺癌早期筛查和诊断密切相关。本文综述了上述生物标志物在乳腺癌早期筛查和诊断中的应用。     

Abnormally expressed long noncoding RNA B3GALT5-AS1 may serve as a biomarker for the diagnostic and prognostic of gastric cancer

Early diagnosis of gastric cancer (GC) is an effective method to improve prognosis. Increasing number of long noncoding RNAs (lncRNAs) have been reported as biomarkers for several cancers. We aim to detect the level of lncRNA B3GALT5-AS1 and its association with clinical parameters and to further explore its application value in GC. We measured serum B3GALT5-AS1 expression in 107 patients with GC, 40 polyp patients, and 87 normal controls to explore the significance of serum B3GALT5-AS1 in GC using the quantitative real-time polymerase chain reaction method. The result demonstrated that B3GALT5-AS1 level was markedly richer in GC patients than that in normal people (P < .001). B3GALT5-AS1 may be served as a diagnostic marker for distinguishing GC patients from healthy people, and the proportion under the receiver operating characteristics curve is 0.816 (95% confidence interval, 0.758-0.874; P = .03). Further exploration validated that high serum B3GALT5-AS1 level was related to TNM stage (P = .024), and lymph node metastasis (P = .023). Our study suggested that serum B3GALT5-AS1 may be employed as an ideal biomarker for early screening of GC.     

Quantitative analysis of mRNA expression levels and DNA methylation profiles of three neighboring genes: FUS1, NPRL2/G21 and RASSF1A in non-small cell lung cancer patients

Background

Tumor suppressor gene (TSG) inactivation plays a crucial role in carcinogenesis. FUS1, NPRL2/G21 and RASSF1A are TSGs from LUCA region at 3p21.3, a critical chromosomal region in lung cancer development. The aim of the study was to analyze and compare the expression levels of these 3 TSGs in NSCLC, as well as in macroscopically unchanged lung tissue surrounding the primary lesion, and to look for the possible epigenetic mechanism of TSG inactivation via gene promoter methylation.

Methods

Expression levels of 3 TSGs and 2 DNA methyltransferases, DNMT1 and DNMT3B, were assessed using real-time PCR method (qPCR) in 59 primary non-small cell lung tumors and the matched macroscopically unchanged lung tissue samples. Promoter methylation status of TSGs was analyzed using methylation-specific PCRs (MSP method) and Methylation Index (MI) value was calculated for each gene.

Results

The expression of all three TSGs were significantly different between NSCLC subtypes: RASSF1A and FUS1 expression levels were significantly lower in squamous cell carcinoma (SCC), and NPRL2/G21 in adenocarcinoma (AC). RASSF1A showed significantly lower expression in tumors vs macroscopically unchanged lung tissues. Methylation frequency was 38–76 %, depending on the gene. The highest MI value was found for RASSF1A (52 %) and the lowest for NPRL2/G21 (5 %). The simultaneous decreased expression and methylation of at least one RASSF1A allele was observed in 71 % tumor samples. Inverse correlation between gene expression and promoter methylation was found for FUS1 (rs = −0.41) in SCC subtype. Expression levels of DNMTs were significantly increased in 75–92 % NSCLCs and were significantly higher in tumors than in normal lung tissue. However, no correlation between mRNA expression levels of DNMTs and DNA methylation status of the studied TSGs was found.

Conclusions

The results indicate the potential role of the studied TSGs in the differentiation of NSCLC histopathological subtypes. The significant differences in RASSF1A expression levels between NSCLC and macroscopically unchanged lung tissue highlight its possible diagnostic role in lung cancer in situ recognition. High percentage of lung tumor samples with simultaneous RASSF1A decreased expression and gene promoter methylation indicates its epigenetic silencing. However, DNMT overexpression doesn’t seem to be a critical determinate of its promoter hypermethylation.     

Biochemical markers as a useful tool for the early identification of Fusarium oxysporum f.sp. cubense,race 1 resistance banana clones

Abstract

Panama disease of banana (Musa spp) caused by the fungus Fusarium oxysporum f. sp. Cubense (FOC), is a serious constraint both to the commercial production of banana and cultivation for subsistence agriculture. Chemical control is not economically effective and is also hazardous to the environment and human health. Breeding for disease resistance is an alternative strategy, which leads to the development of resistance clones. Field evaluation is the most reliable method of screening for disease resistance, but it is demanding in terms of cost, manpower and space requirements. Another approach of screening hybrids at the sucker's stage (planting material) through biochemical markers has been found to be effective in early identification of resistant hybrids. The resistance mechanisms involving the role of phenol, PAL, oxidative enzymes like peroxidase (PO), polyphenol oxidase (PPO), superoxide dismutase (SOD), catalase and PR-proteins like chitinase, β-1-3 glucanase were studied and they showed relatively higher activity in resistant hybrids than susceptible hybrids. Isozyme analysis of peroxidase (PO) and polyphenol oxidase (PPO) was also carried out in cultivars and hybrids, which revealed the induction of specific isoforms in the resistant hybrids upon challenge inoculation. This could be a useful tool for early identification of F. oxysporum f. sp. cubense resistance banana clones.     

Relative impact of earlier diagnosis and improved treatment on survival for colorectal cancer: A US database study among elderly patients

PurposesTo estimate what proportion of improvement in relative survival was attributable to smaller stage/size due to early detection and what proportion was attributable to cancer chemotherapy in patients with colorectal cancer (CRC).MethodsWe studied 69,718 patients with CRC aged ≥66 years in 1992–2009 from Surveillance, Epidemiology, and End Results registries. Study periods were categorized into three periods according to the major changes or advances in screening and chemotherapy regimens: (1) Period-1 (1992–1995), during which there was no evidence-based recommendation for routine CRC screening and 5-fluorouracil was the mainstay for chemotherapy; (2) Period-2 (1996–2000), during which evidences and guidelines supported the use of fecal occult blood test (FOBT) and sigmoidoscopy for routine CRC screening; and (3) Period-3 (2001–2009), during which Medicare Program added the full coverage for colonoscopy screening to average-risk individuals, and several newly developed chemotherapy regimens were approved. Outcome variables included the likelihood of being diagnosed at an early stage or with a small tumor size, and improvement in relative survival.ResultsCompared to period-1, likelihood of being diagnosed with early stage CRC increased by 20% in period-2 (odds ratio = 1.2, 95%CI: 1.1–1.2) and 30% in period-3 (1.3, 1.2–1.4); and likelihood of being diagnosed with small-size CRC increased by 60% in period-2 and 110% in period-3. Similarly, 5-year overall relative survival increased from 51% in period-1 to 56% in period-2 and 60% in period-3. Increase in survival attributable to migration in stage/size was 9% in period-2 and 20% in period-3, while the remaining survival improvement during period-2 and period-3 were largely attributable to more effective chemotherapy regimens (≥71.6%) and other treatment factors (≤25%).ConclusionsImprovements in CRC screening resulted in a migration of CRC toward earlier tumor stage and smaller size, which contributed to ≤20% of survival increase. Survival improvement over the past 2 decades was largely explained by more effective chemotherapy regimens (≥71.6%).     

Validation of differential GDAP1 DNA methylation in alcohol dependence and its potential function as a biomarker for disease severity and therapy outcome

Alcohol dependence is a severe disorder contributing substantially to the global burden of disease. Despite the detrimental consequences of chronic alcohol abuse and dependence, effective prevention strategies as well as treatment options are largely missing to date. Accumulating evidence suggests that gene-environment interactions, including epigenetic mechanisms, play a role in the etiology of alcohol dependence. A recent epigenome-wide study reported widespread alterations of DNA methylation patterns in alcohol dependent patients compared to control individuals. In the present study, we validate and replicate one of the top findings from this previous investigation in an independent cohort: the hypomethylation of GDAP1 in patients. To our knowledge, this is the first independent replication of an epigenome-wide finding in alcohol dependence. Furthermore, the AUDIT as well as the GSI score were negatively associated with GDAP1 methylation and we found a trend toward a negative association between GDAP1 methylation and the years of alcohol dependency, pointing toward a potential role of GDAP1 hypomethylation as biomarker for disease severity. In addition, we show that the hypomethylation of GDAP1 in patients reverses during a short-term alcohol treatment program, suggesting that GDAP1 DNA methylation could also serve as a potential biomarker for treatment outcome. Our data add to the growing body of knowledge on epigenetic effects in alcohol dependence and support GDAP1 as a novel candidate gene implicated in this disorder. As the role of GDAP1 in alcohol dependence is unknown, this novel candidate gene should be followed up in future studies.     

Histone deacetylases 1 and 2 regulate DNA replication and DNA repair: potential targets for genome stability-mechanism-based therapeutics for a subset of cancers

Histone deacetylases 1 and 2 (HDAC1,2) belong to the class I HDAC family, which are targeted by the FDA-approved small molecule HDAC inhibitors currently used in cancer therapy. HDAC1,2 are recruited to DNA break sites during DNA repair and to chromatin around forks during DNA replication. Cancer cells use DNA repair and DNA replication as survival mechanisms and to evade chemotherapy-induced cytotoxicity. Hence, it is vital to understand how HDAC1,2 function during the genome maintenance processes (DNA replication and DNA repair) in order to gain insights into the mode-of-action of HDAC inhibitors in cancer therapeutics. The first-in-class HDAC1,2-selective inhibitors and Hdac1,2 conditional knockout systems greatly facilitated dissecting the precise mechanisms by which HDAC1,2 control genome stability in normal and cancer cells. In this perspective, I summarize the findings on the mechanistic functions of class I HDACs, specifically, HDAC1,2 in genome maintenance, unanswered questions for future investigations and views on how this knowledge could be harnessed for better-targeted cancer therapeutics for a subset of cancers.     

Proteomic-based identification of the APC-binding protein EB1 as a candidate of novel tissue biomarker and therapeutic target for colorectal cancer

Novel candidates of biomarker and therapeutic target in colorectal cancer (CRC) were investigated using a proteomic approach. The proteome of normal colorectal epithelial tissues was compared with that of the tumor ones in 59 CRC patients using two-dimensional difference gel electrophoresis. Of 3458 protein spots, 110 exhibited statistically significant (p<0.01) differences in intensity (more than 2.5-folds) between the normal and tumor tissue groups. Of 67 unique gene products that were identified for 105 of the 110 protein spots, we focused on the higher expression of the adenoma polyposis coli-binding protein EB1 (EB1). EB1 was originally discovered as a binding protein of APC, which is a tumor suppressor gene product, and the expression of EB1 has been associated with poor prognosis in several malignancies but not in CRC. Immunohistochemical analysis of the 132 CRC cases revealed that EB1 was overexpressed in tumor cells in correlation with poor prognosis. Suppression of EB1 by RNAi inhibited CRC cell proliferation and invasion. In this study, the overexpression of EB1 in CRC tissues correlating with prognosis, and its functional contribution to the malignant phenotypes of CRC cells are described. The present findings indicate that EB1 is a potential biomarker and therapeutic target in CRC.     

Formamide as a denaturant for bisulfite conversion of genomic DNA: Bisulfite sequencing of the GSTPi and RARβ2 genes of 43 formalin-fixed paraffin-embedded prostate cancer specimens

Analysis of methylated DNA, which refers to 5-methycytosine (5mC) versus cytosine (C) at specific loci in genomic DNA (gDNA), has received increased attention in epigenomics, particularly in the area of cancer biomarkers. Many different methods for analysis of methylated DNA rely on initial reaction of gDNA with concentrated acidic sodium bisulfite to quantitatively convert C to uracil (U) via sulfonation of denatured, single-stranded gDNA under conditions where 5mC is resistant to analogous sulfonation leading to thymine (T). These methods typically employ polymerase chain reaction (PCR) amplification after bisulfite conversion, thereby leading to readily detectable amounts of amplicons where T and C are measured as surrogates for C and 5mC in the original unconverted gDNA. However, incomplete bisulfite conversion of C in gDNA has been reported to be a common source of error in analysis of methylated DNA. Incomplete conversion can be revealed during the course of bisulfite sequencing, which is the generally accepted “gold standard” for analysis of methylated DNA. Previous bisulfite sequencing investigations of conventional predenaturation of gDNA with NaOH followed by the use of bisulfite containing added urea to maintain denaturation and thus mitigate incomplete conversion of C have been reported to give conflicting results. The current study describes a new approach where conventional predenaturation of gDNA with NaOH is instead achieved with formamide and maintains denaturation during subsequent sample handling and sulfonation. This formamide-based method was applied to 46 formalin-fixed/paraffin-embedded (FFPE) biopsy tissue specimens from well-characterized patients with primary prostate cancer. These specimens were representative of difficult-to-analyze samples due to the chemically compromised nature of the gDNA, which was recovered by modifying the protocol for a commercially available total RNA/DNA extraction kit (RecoverALL). An additional novel aspect of this study was analysis of CpG-rich promoter regions of two prostate cancer-related genes: glutathione S-transferase pi (GSTPi) and retinoic acid receptor beta2 (RARβ2). High-quality bisulfite sequencing results were obtained for both genes in 43 of 46 (93%) specimens. Detection of methylated GSTPi and RARβ2 genes was significantly associated with primary prostate cancer as compared with the benign prostate (Fisher’s exact test, P < 0.001). The sensitivity and specificity of detection of methylated GSTPi and RARβ2 genes were 86% and 100% and 91% and 100%, respectively. Moreover, the presence of either methylated gene was detected in primary prostate cancer with sensitivity and specificity of 100% and 100%, respectively. The results demonstrated a high degree of reliability of formamide-based denaturation and bisulfite conversion that should extend, generally, to FFPE and other types of samples intended for any analytical method predicated on bisulfite conversion. This pilot study also demonstrated the efficacy of determining methylation of these two genes with high sensitivity and specificity in FFPE biopsy tissue specimens. Moreover, the results showed a highly significant association of methylated GSTPi and RARβ2 genes with primary prostate cancer. Finally, this improved procedure for determining these two methylated genes may allow the detection of prostate cancer cells in core biopsy specimens with insufficient numbers of cells and poor morphology.     

Smartphone‐based spectral imaging otoscope: System development and preliminary study for evaluation of its potential as a mobile diagnostic tool

We develop a novel smartphone‐based spectral imaging otoscope for telemedicine and examine its capability for the mobile diagnosis of middle ear diseases. The device was applied to perform spectral imaging and analysis of an ear‐mimicking phantom and a normal and abnormal tympanic membrane for evaluation of its potential for the mobile diagnosis. Spectral classified images were obtained via online spectral analysis in a remote server. The phantom experimental results showed that it allowed us to distinguish four different fluids located behind a semitransparent membrane. Also, in the spectral classified images of normal ears (n = 3) and an ear with chronic otitis media (n = 1), the normal and abnormal regions in each ear could be quantitatively distinguished with high contrast. These preliminary results thus suggested that it might have the potentials for providing quantitative information for the mobile diagnosis of various middle ear diseases.