# Current status of development of methylation biomarkers for in vitro diagnostic IVD applications

**Authors:** Olga Taryma-Leśniak, Katarzyna Ewa Sokolowska, Tomasz Kazimierz Wojdacz

PMC · DOI: 10.1186/s13148-020-00886-6 · Clinical Epigenetics · 2020-07-06

## TL;DR

This review discusses the current state of methylation biomarker tests for clinical use and highlights the challenges in translating research into approved diagnostic tools.

## Contribution

The paper provides an overview of methylation-based IVD tests in development or approval, analyzing their technologies and clinical validation studies.

## Key findings

- Methylation changes are promising biomarkers for precision medicine but face challenges in clinical translation.
- Current methylation-based IVD tests require robust clinical studies to meet regulatory standards for approval.
- Examples of advanced methylation tests are analyzed to guide future clinical investigations.

## Abstract

A significant volume of research clearly shows that disease-related methylation changes can be used as biomarkers at all stages of clinical disease management, including risk assessment and predisposition screening through early diagnostics to personalization of patient care and monitoring of the relapse and chronic disease. Thus disease-related methylation changes are an attractive source of the biomarkers that can have significant impact on precision medicine. However, the translation of the research findings in methylation biomarkers field to clinical practice is at the very least not satisfactory. That is mainly because the evidence generated in research studies indicating the utility of the disease-related methylation change to predict clinical outcome is in majority of the cases not sufficient to postulate the diagnostic use of the biomarker. The research studies need to be followed by well-designed and systematic investigations of clinical utility of the biomarker that produce data of sufficient quality to meet regulatory approval for the test to be used to make clinically valid decision. In this review, we describe methylation-based IVD tests currently approved for IVD use or at the advanced stages of the development for the diagnostic use. For each of those tests, we analyze the technologies that the test utilizes for methylation detection as well as describe the types of the clinical studies that were performed to show clinical validity of the test and warrant regulatory approval. The examples reviewed here should help with planning of clinical investigations and delivery of the clinical evidence required for the regulatory approval of potential methylation biomarker based IVD tests.

## Full-text entities

- **Genes:** NINJ2 (ninjurin 2) [NCBI Gene 4815], AFP (alpha fetoprotein) [NCBI Gene 174] {aka AFPD, FETA, HPAFP}, BCAT1 (branched chain amino acid transaminase 1) [NCBI Gene 586] {aka BCATC, BCT1, ECA39, MECA39, PNAS121, PP18}, SEPTIN9 (septin 9) [NCBI Gene 10801] {aka AF17q25, MSF, MSF1, PNUTL4, SEPT9, SINT1}, TWIST1 (twist family bHLH transcription factor 1) [NCBI Gene 7291] {aka ACS3, BPES2, BPES3, CRS, CRS1, CSO}, KRAS (KRAS proto-oncogene, GTPase) [NCBI Gene 3845] {aka 'C-K-RAS, C-K-RAS, CFC2, K-RAS2A, K-RAS2B, K-RAS4A}, CEACAM3 (CEA cell adhesion molecule 3) [NCBI Gene 1084] {aka CD66D, CEA, CGM1, CGM1a, W264, W282}, GSTP1 (glutathione S-transferase pi 1) [NCBI Gene 2950] {aka DFN7, FAEES3, GST3, GSTP, GSTP1-1, HEL-S-22}, PTGER4 (prostaglandin E receptor 4) [NCBI Gene 5734] {aka EP4, EP4R}, RXFP3 (relaxin family peptide receptor 3) [NCBI Gene 51289] {aka GPCR135, RLN3R1, RXFPR3, SALPR}, TAFA4 (TAFA chemokine like family member 4) [NCBI Gene 151647] {aka FAM19A4, TAFA-4}, ONECUT2 (one cut homeobox 2) [NCBI Gene 9480] {aka OC-2, OC2}, TRIM68 (tripartite motif containing 68) [NCBI Gene 55128] {aka GC109, RNF137, SS-56, SS56}, HRAS (HRas proto-oncogene, GTPase) [NCBI Gene 3265] {aka C-BAS/HAS, C-H-RAS, C-HA-RAS1, CTLO, H-RASIDX, HAMSV}, ITGA4 (integrin subunit alpha 4) [NCBI Gene 3676] {aka CD49D, IA4}, ASTN1 (astrotactin 1) [NCBI Gene 460] {aka ASTN}, FGFR3 (fibroblast growth factor receptor 3) [NCBI Gene 2261] {aka ACH, CD333, CEK2, HSFGFR3EX, JTK4}, MGMT (O-6-methylguanine-DNA methyltransferase) [NCBI Gene 4255], IRAK3 (interleukin 1 receptor associated kinase 3) [NCBI Gene 11213] {aka ASRT5, IRAKM}, AHRR (aryl hydrocarbon receptor repressor) [NCBI Gene 57491] {aka AHH, AHHR, bHLHe77}, HOXA1 (homeobox A1) [NCBI Gene 3198] {aka BSAS, HOX1, HOX1F}, ZNF582 (zinc finger protein 582) [NCBI Gene 147948], IKZF1 (IKAROS family zinc finger 1) [NCBI Gene 10320] {aka CVID13, Hs.54452, IK1, IKAROS, LYF1, LyF-1}, EMX1 (empty spiracles homeobox 1) [NCBI Gene 2016], SDC2 (syndecan 2) [NCBI Gene 6383] {aka CD362, HSPG, HSPG1, SYND2}, RASSF1 (Ras association domain family member 1) [NCBI Gene 11186] {aka 123F2, NORE2A, RASSF1A, RDA32, REH3P21}, OTX1 (orthodenticle homeobox 1) [NCBI Gene 5013], TIPE2 (TNF alpha induced protein 8 like 2) [NCBI Gene 79626] {aka TNFAIP8L2}, CD4 (CD4 molecule) [NCBI Gene 920] {aka CD4mut, IMD79, Leu-3, OKT4D, T4}, TSPYL5 (TSPY like 5) [NCBI Gene 85453], SOX17 (SRY-box transcription factor 17) [NCBI Gene 64321] {aka PPH7, VUR3}, ERBB2 (erb-b2 receptor tyrosine kinase 2) [NCBI Gene 2064] {aka CD340, HER-2, HER-2/neu, HER2, MLN 19, MLN-19}, MIR124-2 (microRNA 124-2) [NCBI Gene 406908] {aka MIRN124-2, MIRN124A2, mir-124-2}, SOX1 (SRY-box transcription factor 1) [NCBI Gene 6656], MYO1G (myosin IG) [NCBI Gene 64005] {aka HA2, HLA-HA2, MHAG}, BMP3 (bone morphogenetic protein 3) [NCBI Gene 651] {aka BMP-3A}, APC (APC regulator of Wnt signaling pathway) [NCBI Gene 324] {aka BTPS2, DESMD, DP2, DP2.5, DP3, GS}, DLX1 (distal-less homeobox 1) [NCBI Gene 1745], NDRG4 (NDRG family member 4) [NCBI Gene 65009] {aka BDM1, SMAP-8, SMAP8}, ESR1 (estrogen receptor 1) [NCBI Gene 2099] {aka ER, ESR, ESRA, ESTRR, Era, NR3A1}, EREG (epiregulin) [NCBI Gene 2069] {aka EPR, ER, Ep}, SHOX2 (SHOX homeobox 2) [NCBI Gene 6474] {aka OG12, OG12X, SHOT}, GSTM1 (glutathione S-transferase mu 1) [NCBI Gene 2944] {aka GST1, GSTM1-1, GSTM1a-1a, GSTM1b-1b, GTH4, GTM1}, PITX2 (paired like homeodomain 2) [NCBI Gene 5308] {aka ARP1, ASGD4, Brx1, IDG2, IGDS, IGDS2}, DAB2IP (DAB2 interacting protein) [NCBI Gene 153090] {aka AF9Q34, AIP-1, AIP1, DIP1/2}, ZNF671 (zinc finger protein 671) [NCBI Gene 79891], CRIM1 (cysteine rich transmembrane BMP regulator 1) [NCBI Gene 51232] {aka CRIM-1, S52}, PAX1 (paired box 1) [NCBI Gene 5075] {aka HUP48, OFC2, OTFCS2}, TERT (telomerase reverse transcriptase) [NCBI Gene 7015] {aka CMM9, DKCA2, DKCB4, EST2, PFBMFT1, TCS1}
- **Diseases:** Prostate cancer (MESH:D011471), pneumonia (MESH:D011014), adenomatous polyps (MESH:D018256), ARMS (MESH:D012030), lymph node (MESH:D000072717), CIN (MESH:D002578), kidney cancer (MESH:D007680), Lung cancer (MESH:D008175), cirrhosis (MESH:D005355), WGBS (MESH:C531766), hematuria (MESH:D006417), sepsis (MESH:D018805), asthma (MESH:D001249), CIS (MESH:D002278), Liver Diseases (MESH:D008107), LDT (MESH:D007757), Cancers (MESH:D009369), meningioma (MESH:D008579), chronic obstructive pulmonary disease (MESH:D029424), liver cirrhosis (MESH:D008103), lymph node metastasis (MESH:D008207), diabetes (MESH:D003920), death (MESH:D003643), toxicity (MESH:D064420), cardiovascular diseases (MESH:D002318), HCC (MESH:D006528), Breast cancer (MESH:D001943), breast, prostate, colon, and pancreas (MESH:D011472), stage I carcinomas (MESH:D062706), arteriosclerosis (MESH:D001161), Cervical cancer (MESH:D002583), cardiovascular and lung diseases (MESH:D008171), chronic diseases (MESH:D002908), brain tumor (MESH:D001932), neoplasm of the urinary system (MESH:D014571), non-Hodgkin lymphoma (MESH:D008228), CRC (MESH:D015179), bronchitis (MESH:D001991), premalignant lesion (MESH:D009059), smoking (MESH:D015208), hyperplastic polyps (MESH:D011127), invasive cancer (MESH:D009362), infection (MESH:D007239), adenomas (MESH:D000236), UC (MESH:D014523), BC (MESH:D001749), arthritis (MESH:D001168), MIBC (MESH:D000093284), Triple-negative breast cancer (MESH:D064726), OS (MESH:D011475), GBM (MESH:D005909), autoimmune diseases (MESH:D001327)
- **Chemicals:** Lead (MESH:D007854), Formalin (MESH:D005557), TCE (MESH:D014241), Epi proColon  2.0 CE (-), PM (MESH:D011399), anthracycline (MESH:D018943), metal (MESH:D008670), temozolomide (MESH:D000077204), cytosine (MESH:D003596), paraffin (MESH:D010232), bevacizumab (MESH:D000068258), arsenic (MESH:D001151),  (MESH:D011933),  (MESH:D015415)
- **Species:** Homo sapiens (human, species) [taxon 9606], Human papillomavirus (species) [taxon 10566]

## Full text

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## Figures

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## References

91 references — full list in the complete paper: https://tomesphere.com/paper/PMC7336678/full.md

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Source: https://tomesphere.com/paper/PMC7336678