Methodological and Biological Factors Influencing Global DNA Methylation Results Measured by LINE-1 Pyrosequencing Assay in Colorectal Tissue and Liquid Biopsy Samples

Long interspersed nuclear element 1 (LINE-1) bisulfite pyrosequencing is a widely used technique for genome-wide methylation analyses. We aimed to investigate the effects of experimental and biological factors on its results to improve the comparability. LINE-1 bisulfite pyrosequencing was performed on colorectal tissue (n = 222), buffy coat (n = 39), and plasma samples (n = 9) of healthy individuals and patients with colorectal tumors. Significantly altered methylation was observed between investigated LINE-1 CpG positions of non-tumorous tissues (p ≤ 0.01). Formalin-fixed, paraffin-embedded biopsies (73.0 ± 5.3%) resulted in lower methylation than fresh frozen samples (76.1 ± 2.8%) (p ≤ 0.01). DNA specimens after long-term storage showed higher methylation levels (+3.2%, p ≤ 0.01). In blood collection tubes with preservatives, cfDNA and buffy coat methylation significantly changed compared to K3EDTA tubes (p ≤ 0.05). Lower methylation was detected in older (>40 years, 76.8 ± 1.7%) vs. younger (78.1 ± 1.0%) female patients (p ≤ 0.05), and also in adenomatous tissues with MTHFR 677CT, or 1298AC mutations vs. wild-type (p ≤ 0.05) comparisons. Based on our findings, it is highly recommended to consider the application of standard DNA samples in the case of a possible clinical screening approach, as well as in experimental research studies.

A Detailed Overview About the Single-Cell Analyses of Solid Tumors Focusing on Colorectal Cancer

In recent years, the evolution of the molecular biological technical background led to the widespread application of single-cell sequencing, a versatile tool particularly useful in the investigation of tumor heterogeneity. Even 10 years ago the comprehensive characterization of colorectal cancers by The Cancer Genome Atlas was based on measurements of bulk samples. Nowadays, with single-cell approaches, tumor heterogeneity, the tumor microenvironment, and the interplay between tumor cells and their surroundings can be described in unprecedented detail. In this review article we aimed to emphasize the importance of single-cell analyses by presenting tumor heterogeneity and the limitations of conventional investigational approaches, followed by an overview of the whole single-cell analytic workflow from sample isolation to amplification, sequencing and bioinformatic analysis and a review of recent literature regarding the single-cell analysis of colorectal cancers.

Global DNA hypomethylation of colorectal tumours detected in tissue and liquid biopsies may be related to decreased methyl-donor content

Background

Hypomethylation of long interspersed nuclear element 1 (LINE-1) is characteristic of various cancer types, including colorectal cancer (CRC). Malfunction of several factors or alteration of methyl-donor molecules’ (folic acid and S-adenosylmethionine) availability can contribute to DNA methylation changes. Detection of epigenetic alterations in liquid biopsies can assist in the early recognition of CRC. Following the investigations of a Hungarian colon tissue sample set, our goal was to examine the LINE-1 methylation of blood samples along the colorectal adenoma-carcinoma sequence and in inflammatory bowel disease. Moreover, we aimed to explore the possible underlying mechanisms of global DNA hypomethylation formation on a multi-level aspect.

Methods

LINE-1 methylation of colon tissue (n = 183) and plasma (n = 48) samples of healthy controls and patients with colorectal tumours were examined with bisulfite pyrosequencing. To investigate mRNA expression, microarray analysis results were reanalysed in silico (n = 60). Immunohistochemistry staining was used to validate DNA methyltransferases (DNMTs) and folate receptor beta (FOLR2) expression along with the determination of methyl-donor molecules’ in situ level (n = 40).

Results

Significantly decreased LINE-1 methylation level was observed in line with cancer progression both in tissue (adenoma: 72.7 ± 4.8%, and CRC: 69.7 ± 7.6% vs. normal: 77.5 ± 1.7%, p ≤ 0.01) and liquid biopsies (adenoma: 80.0 ± 1.7%, and CRC: 79.8 ± 1.3% vs. normal: 82.0 ± 2.0%, p ≤ 0.01). However, no significant changes were recognized in inflammatory bowel disease cases. According to in silico analysis of microarray data, altered mRNA levels of several DNA methylation-related enzymes were detected in tumours vs. healthy biopsies, namely one-carbon metabolism-related genes—which met our analysing criteria—showed upregulation, while FOLR2 was downregulated. Using immunohistochemistry, DNMTs, and FOLR2 expression were confirmed. Moreover, significantly diminished folic acid and S-adenosylmethionine levels were observed in parallel with decreasing 5-methylcytosine staining in tumours compared to normal adjacent to tumour tissues (p ≤ 0.05).

Conclusion

Our results suggest that LINE-1 hypomethylation may have a distinguishing value in precancerous stages compared to healthy samples in liquid biopsies. Furthermore, the reduction of global DNA methylation level could be linked to reduced methyl-donor availability with the contribution of decreased FOLR2 expression.

Abstract 164: Alteration of DNA methylation, DNA repair and epithelial-mesenchymal transition in colorectal cancer cell lines by S-adenosylmethionine treatment

Global DNA hypomethylation can be observed along with the aging of normal cells, and it is also related to tumor initiation and progression. S-adenosylmethionine (SAM) is a universal methyl donor molecule, used as a dietary supplement. SAM is involved in DNA methylation processes, thereby it may have a favorable effect on gene expression of cancer-associated genes through epigenetic modifications, but may also influence DNA folding during repair processes.

Our aim was to analyze the effect of SAM treatment on global and promoter-specific DNA methylation level, gene expression, DNA integrity, cell cycle and the proliferation of two different colorectal cancer cell lines (HT-29, SW480).

HT-29 and SW480 cells were treated with SAM in different concentrations (0, 0.5, 1 mmol/l) for 48 hours. Global DNA methylation status was analyzed by bisulfite pyrosequencing of long interspersed nuclear element-1 (LINE-1) retrotransposons. Promoter-specific DNA methylation alterations were determined by Reduced Representation Bisulfite Sequencing (RRBS) method. Gene expression changes were detected using Human Transcriptome Array 2.0 (HTA 2.0). DNA integrity analysis was performed with γH2AX ELISA, immunostaining and Comet Assay. Flow cytometry measurement and Sulforhodamine B (SRB) assay were assessed for cell cycle and proliferation determination.

Global and promoter-specific DNA methylation alterations, as well as decreased expression (p< 0.05) of genes, that are involved in epithelial-mesenchymal transition were observed after SAM treatment. Increased phosphorylation of H2AX (74.9, 166.5, 200.6 pM) and decreased micronucleus number (1.47, 0.76, 0.45% of cells) were referred to the activation of reparative processes, that was supported by the changes of comet tail lengths. Proportion of cells was decreased in the G0/G1 (48.4, 28.5, 20.4%) phase; however, it was increased in both S (45.7, 61.7, 67.0%) and G2/M (6.0, 10.7, 12.5%) phases. Significant (p< 0.05) decrease of cell proliferation (99.5, 78.0, 70.6%) was also detected with SRB assay.

SAM is able to alter the DNA methylation pattern of tumor cells and can induce DNA repair. Activation of these processes can lead to cell cycle arrest, decreased proliferation, and inhibition of epithelial-mesenchymal transition. Tumor cells could be targeted by SAM through different pathways; therefore, it may enhance the effect of chemotherapeutic agents.

Citation Format: Sára Zsigrai, Alexandra Kalmár, Krisztina Andrea Szigeti, Zsófia Brigitta Nagy, Barbara K. Barták, Gábor Valcz, Orsolya Galamb, Titanilla Dankó, Zsolt Tulassay, Péter Igaz, Béla Molnár. Alteration of DNA methylation, DNA repair and epithelial-mesenchymal transition in colorectal cancer cell lines by S-adenosylmethionine treatment [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 164.

Abstract 155: Global DNA hypomethylation can be caused by decreased methyl-donor content in tissue and liquid biopsy samples in colorectal cancer progression

Backgrounds: Global DNA hypomethylation is characteristic in various cancer types including colorectal cancer. Alterations of DNA methylation related enzymes expression and decreased level of methyl-donor molecules (folic acid (FA), S-adenosylmethionine (SAM)) can lead to aberrant DNA methylation pattern and elevated homocysteine level. Aims: Our aim was to examine global DNA methylation changes during aging and colorectal normal-adenoma-carcinoma sequence and in inflammatory bowel disease in tissue and liquid biopsy samples for diagnostic purposes. Moreover, we aimed to explore the reasons of global hypomethylation on gene expression level and methyl-donor molecule content.

Methods: Bisulfite treatment was performed on DNA isolated from 30 normal (N), 10 adenoma (Ad), 10 colorectal carcinoma (CRC), 10 colitis ulcerosa (UC) tissue samples and on 11 N, 10 Ad, 15 CRC, 12 UC plasma specimens. 30 N samples contained different age groups derived from under 20 to 70 years old healthy controls for examination of aging process. LINE-1 PCR product was generated and pyrosequenced. Whole genome expression level of 60 biopsy samples was evaluated by HTA 2.0 RNA microarraychip (Affymetrix). In situ tissue appearance of 5-methylcytosine, FA, SAM, homocysteine, and expression of DNA methyltransferases (DNMTs) were analyzed by immunohistochemistry staining (IHC).

Results: According to LINE-1 bisulfite sequencing results, DNA methylation was 72.6±1% in samples of healthy controls under 50 years old and 71.6±1.8% in specimens of patients over 50 years old. Significant DNA hypomethylation was found in CRC (62.9±8.7%; p<0.001, early stages: 67.4±7.8%, late stages: 58.3±0.1%), Ad (66.7±5.1%; p<0.001) tissue samples in comparison with N samples (72±1.4%). Significant decrease of DNA methylation was observed in CRC (78.8±1.7%; p<0.02), and Ad (80.1±1.7%; p<0.02) plasma samples compared to N specimens (82.2±1.8%). Global DNA hypomethylation was not detected in UC samples. Significantly elevated RNA expression of enzymes connected to nucleotide synthesis was observed in Ad and CRC samples compared to N (p<0.05), while no changes were detected in the RNA levels of DNA methylation-related proteins. The intensity of 5-mC labeling of CRC and Ad samples was lower than in N tissue samples. Decreased FA, SAM, and increased homocysteine levels were noticed in CRC compared to N specimens; however no expression changes of DNMT enzymes were observed.

Conclusion: Significant decrease in DNA methylation level was found in tissue and liquid biopsy samples of colorectal normal-adenoma-carcinoma sequence, but not in UC specimens. Our results suggest that determination of global DNA hypomethylation could have prognostic and diagnostic value as well, and reduction of DNA methylation level could be linked to decreased FA and SAM availability and not to methylation related ezymes activity.

Citation Format: Krisztina A. Szigeti, Orsolya Galamb, Alexandra Kalmár, Gábor Valcz, Sára Zsigrai, Barbara K. Barták, Zsófia B. Nagy, Zsolt Tulassay, Péter Igaz, Béla Molnár. Global DNA hypomethylation can be caused by decreased methyl-donor content in tissue and liquid biopsy samples in colorectal cancer progression [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 155.

S-Adenosylmethionine Treatment of Colorectal Cancer Cell Lines Alters DNA Methylation, DNA Repair and Tumor Progression-Related Gene Expression

Global DNA hypomethylation is a characteristic feature of colorectal carcinoma (CRC). The tumor inhibitory effect of S-adenosylmethionine (SAM) methyl donor has been described in certain cancers including CRC. However, the molecular impact of SAM treatment on CRC cell lines with distinct genetic features has not been evaluated comprehensively. HT-29 and SW480 cells were treated with 0.5 and 1 mmol/L SAM for 48 h followed by cell proliferation measurements, whole-genome transcriptome and methylome analyses, DNA stability assessments and exome sequencing. SAM reduced cell number and increased senescence by causing S phase arrest, besides, multiple EMT-related genes (e.g., TGFB1) were downregulated in both cell lines. Alteration in the global DNA methylation level was not observed, but certain methylation changes in gene promoters were detected. SAM-induced γ-H2AX elevation could be associated with activated DNA repair pathway showing upregulated gene expression (e.g., HUS1). Remarkable genomic stability elevation, namely, decreased micronucleus number and comet tail length was observed only in SW480 after treatment. SAM has the potential to induce senescence, DNA repair, genome stability and to reduce CRC progression. However, the different therapeutic responses of HT-29 and SW480 to SAM emphasize the importance of the molecular characterization of CRC cases prior to methyl donor supplementation.

Diagnostic and prognostic potential of tissue and circulating long non-coding RNAs in colorectal tumors

Long non-coding RNAs (lncRNAs) are members of the non-protein coding RNA family longer than 200 nucleotides. They participate in the regulation of gene and protein expression influencing apoptosis, cell proliferation and immune responses, thereby playing a critical role in the development and progression of various cancers, including colorectal cancer (CRC). As CRC is one of the most frequently diagnosed malignancies worldwide with high mortality, its screening and early detection are crucial, so the identification of disease-specific biomarkers is necessary. LncRNAs are promising candidates as they are involved in carcinogenesis, and certain lncRNAs (e.g., CCAT1, CRNDE, CRCAL1-4) show altered expression in adenomas, making them potential early diagnostic markers. In addition to being useful as tissue-specific markers, analysis of circulating lncRNAs (e.g., CCAT1, CCAT2, BLACAT1, CRNDE, NEAT1, UCA1) in peripheral blood offers the possibility to establish minimally invasive, liquid biopsy-based diagnostic tests. This review article aims to describe the origin, structure, and functions of lncRNAs and to discuss their contribution to CRC development. Moreover, our purpose is to summarise lncRNAs showing altered expression levels during tumor formation in both colon tissue and plasma/serum samples and to demonstrate their clinical implications as diagnostic or prognostic biomarkers for CRC.

Comparison of Automated and Manual DNA Isolation Methods for DNA Methylation Analysis of Biopsy, Fresh Frozen, and Formalin-Fixed, Paraffin-Embedded Colorectal Cancer Samples

Automated DNA isolation can decrease hands-on time in routine pathology. Our aim was to apply automated DNA isolation and perform DNA methylation analyses. DNA isolation was performed manually from fresh frozen (CRC = 10, normal = 10) specimens and colonic biopsies (CRC = 10, healthy = 10) with QIAamp DNA Mini Kit and from FFPE blocks (CRC = 10, normal = 10) with QIAamp DNA FFPET Kit. Automated DNA isolation was performed with MagNA Pure DNA and Viral NA SV kit on MagNA Pure 96 system. DNA methylation of MAL, SFRP1, and SFRP2 were analyzed with methylation-specific high-resolution melting analysis. Yield of automatically isolated samples was equal in fresh frozens and significantly lower compared to manually isolated biopsy and FFPE samples. OD260/280 of fresh frozen and biopsy samples were similar after both isolations, automated isolation resulted in lower purity in FFPE samples. Both protocols resulted in similar OD260/230 from fresh frozens, automated isolation method was superior in biopsies and manual protocol in FFPE samples. DNA methylation of biopsies, fresh frozen samples were highly similar after both methods, results of automatically and manually isolated FFPE samples were different. Automated DNA isolation from fresh frozen samples can be suitable for high-throughput laboratories.

Complete genes may pass from food to human blood

Our bloodstream is considered to be an environment well separated from the outside world and the digestive tract. According to the standard paradigm large macromolecules consumed with food cannot pass directly to the circulatory system. During digestion proteins and DNA are thought to be degraded into small constituents, amino acids and nucleic acids, respectively, and then absorbed by a complex active process and distributed to various parts of the body through the circulation system. Here, based on the analysis of over 1000 human samples from four independent studies, we report evidence that meal-derived DNA fragments which are large enough to carry complete genes can avoid degradation and through an unknown mechanism enter the human circulation system. In one of the blood samples the relative concentration of plant DNA is higher than the human DNA. The plant DNA concentration shows a surprisingly precise log-normal distribution in the plasma samples while non-plasma (cord blood) control sample was found to be free of plant DNA.