Emerging noninvasive methylation biomarkers of cancer prognosis and drug response prediction. (August 2022)

• Record Type: Journal Article
• Authors: Oliver, Javier; Garcia-Aranda, Marilina; Chaves, Patricia; Alba, Emilio; Cobo-Dols, Manuel; Onieva, Juan Luis; Barragan, Isabel
• Is Part Of: Seminars in cancer biology. Volume 83(2022)
• Page Start: 584
• Page End: 595
• Publication Date: 2022-08
• Subjects: DNMT1 DNA Methyltransferase 1 -- DNMT3A DNA Methyltransferase 3 Alpha -- DNMT3B DNA Methyltransferase 3 Beta -- MDR multidrug resistance gene -- FERD3L Fer3 Like BHLH Transcription Factor -- TRIP10 Thyroid Hormone Receptor Interactor 10 -- BRD9 Bromodomain Containing 9 -- ADME absorption, distribution, metabolism and excretion -- CYP3A4 Cytochrome P450 Family 3 Subfamily A Member 4 -- CYP1A2 Cytochrome P450 Family 1 Subfamily A Member 2 -- CYP2C19 Cytochrome P450 Family 2 Subfamily C Member 19 -- UGT1A1 UDP Glucuronosyltransferase Family 1 Member A1 -- ABCB1 ATP Binding Cassette Subfamily B Member 1 -- ABCG2 ATP Binding Cassette Subfamily G Member 2 -- DNMTs DNA methyltransferases -- HDACs histone deacetylases -- CYP1A1 Cytochrome P450 Family 1 Subfamily A Member 1 -- CYP1B1 Cytochrome P450 Family 1 Subfamily B Member 1 -- CYP2D6 Cytochrome P450 Family 2 Subfamily D Member 6 -- CYP2E1 Cytochrome P450 Family 2 Subfamily E Member 1 -- CYP2W1 Cytochrome P450 Family 2 Subfamily W Member 1 -- TET Tet Methylcytosine Dioxygenase -- CYTIP Cytohesin 1 Interacting Protein -- TNF Tumour Necrosis Factor -- TNFSF8 TNF Superfamily Member 8 -- PD-L1 Programmed Cell Death 1 Ligand 1 -- PD-1 Programmed Cell Death 1 -- CTLA-4 Cytotoxic T-Lymphocyte Associated Protein 4 -- LAG3 Lymphocyte Activating 3 -- ctDNA circulating tumor DNA -- CTCs circulating tumor cells -- HER2 epidermal growth factor receptor 2 -- ER estrogen receptor -- PR progesterone receptor -- SEPT9 Septin-9 -- TIMP3 TIMP Metallopeptidase Inhibitor 3 -- XAF1 XIAP Associated Factor 1 -- MINT2 Amyloid Beta Precursor Protein Binding Family A Member 2 -- SOX17 SRY-Box Transcription Factor 17 -- RARb2 Retinoic Acid Receptor Beta 2 -- 5-hmC 5-hydroxymethylcytosine -- 5-mC 5-Methylcytosine -- BCL11A BAF Chromatin Remodeling Complex Subunit BCL11A -- KCNK9 Potassium Two Pore Domain Channel Subfamily K Member 9 -- NTSR1 Neurotensin Receptor 1 -- BC breast cancer -- RASSF1A Ras Association Domain Family Member 1 -- APC Adenomatous Polyposis Coli Protein -- PITX2 Paired Like Homeodomain 2 -- 14-3-3-σ Stratifin -- DFS Disease-free survival -- OS overall survival -- WNT5A Wnt Family Member 5A -- KLK10 Kallikrein Related Peptidase 10 -- CMI cumulative index of methylation -- AKR1B1 Aldo-Keto Reductase Family 1 Member B -- HOXB4 Homeobox B4 -- RASGRF2 Ras Protein Specific Guanine Nucleotide Releasing Factor 2 -- HIST1H3C H3 Clustered Histone 3 -- TM6SF1 Transmembrane 6 Superfamily Member 1 -- BRCA1 Breast Cancer 1 -- MGMT O-6-Methylguanine-DNA Methyltransferase -- GSTP1 Glutathione S-Transferase Pi 1 -- PARP poly ADP ribose polymerase -- TNBC Triple Negative Breast Cancer -- PC Prostate cancer -- PSA Prostate-specific antigen -- RASSF2A Ras Association Domain Family Member 2 -- CDH13 Cadherin 13 -- PCDH17 Protocadherin 17 -- PCDC10 Programmed Cell Death 10 -- PCDH Protocadherins -- IARC Agency for Research on Cancer -- LC lung cancer -- WHO World Health Organization -- NSCLC Non-Small Cell Lung Cancer -- CHFR Checkpoint With Forkhead And Ring Finger Domains -- EGFR Epidermal Growth Factor Receptor -- NGS Next Generation Sequencing -- DCLK1 Doublecortin Like Kinase 1 -- SHOX2 Short Stature Homeobox 2 -- CRC Colorectal cancer -- VEGF vascular endothelial growth factor -- HLTF Helicase Like Transcription Factor -- HPPI intraflagellar transport 57 -- MLH1 MutL Homolog 1 -- TFPI2 Tissue Factor Pathway Inhibitor 2 -- SFRP2 Secreted Frizzled Related Protein 2 -- RUNX3 RUNX Family Transcription Factor 3 -- SST Somatostatin -- (CDKN2A) p16INK4a Cyclin Dependent Kinase Inhibitor 2A -- EYA4 EYA Transcriptional Coactivator And Phosphatase 4 -- GRIA4 Glutamate Ionotropic Receptor AMPA Type Subunit 4 -- ITGA4 Integrin Subunit Alpha 4 -- MAP3K14-AS1 MAP3K14 Antisense RNA 1 -- MSC Musculin -- WIF1 WNT Inhibitory Factor 1 -- dMMR mismatch repair deficiency -- HNSCC Head and Neck Squamous Cell Carcinoma -- PTEN Phosphatase And Tensin Homolog -- OSCC oral squamous cell carcinoma -- CDKN2B Cyclin Dependent Kinase Inhibitor 2B -- LINE-1 long interspersed nucleotide element 1 -- DAP-K Death Associated Protein Kinase -- cfDNA Circulating free DNA -- AIM1 Absent In Melanoma 1 Protein -- HCC Hepatocellular carcinoma; Liquid biopsy -- Methylation -- Cancer treatment -- Prognosis -- Drug response -- Biomarkers; Cancer -- Periodicals; Neoplasms -- Periodicals; Review Literature; Cancer -- Périodiques; Electronic journals; 616.994
• DOI: 10.1016/j.semcancer.2021.03.012
• Languages: English
• ISSNs: 1044-579X

Abstract

Abstract: Cancer is the second leading cause of death worldwide being responsible for 9.6 million deaths in 2018. Epigenetic alterations are key in directing the aberrant expression of tumor-associated genes that drive cellular malignant transformation and cancer progression. Among epigenetic alterations, DNA methylation is the most deeply studied one in relation to environmental exposure. Tissue biopsies have traditionally been the main procedure by which a small sample of body tissue is excised to confirm cancer diagnosis or to indicate the primary site when cancer has spread. In contrast, the analysis of circulating tumor-derived material, or tumor circulome, by means of liquid biopsy of peripheral blood, urine, saliva or sputum is a noninvasive, fast and reproducible alternative to tissue biopsy. Recently, the assessment of epigenetic alterations such as DNA methylation and hydroxymethylation in circulating free DNA has been proved possible. These marks can be associated to prognosis and response to a variety of treatments including chemotherapy, hormonotherapy or immunotherapy. Epigenetic biomarkers may offer some advantages over RNA or genetic biomarkers given their stability in bodily fluids and their high tissue-specificity. While many challenges are still ahead, the unique advantages of these types of biomarkers is urging the scientific community to persevere in their clinical validation and integration into reliable prediction models. This review aims at recapitulating the emerging noninvasive DNA methylated biomarkers of importance for prediction of prognosis and drug response in cancer.