How epigenetic biomarkers are being used for medical diagnoses

By Andres Hernandez Maduro

While it is now proving to be effective for diagnosing human cancers, autoimmune diseases, and soon even neurodegeneration, the medical significance of epigenetics has only recently been acknowledged by the scientific community.

By definition, the term ‘epigenetics’ refers to heritable changes in gene expression that occur without sequence alterations. Such mechanisms are widely thought to provide flexibility and regulation to the cell, increasing its ability to adapt to its environment as required. Despite the complexity that comes from this, epigenetic mechanisms can still be boiled down into two kinds: repressive modifications, usually compacting chromatin into heterochromatin to make it inaccessible to transcription factors (TFs); and permissive modifications, which loosen the genome into euchromatin or add alkyl groups that permit TFs to bind to it.¹ Both states are reversible and dynamically regulated in cells.

The adaptability that epigenetics grants cells is now thought to be essential for life to exist, playing a role in embryonic development, genomic imprinting, lineage specification and cell proliferation.² Naturally, defects in epigenetic regulation can be devastating to living organisms. The first human diseases to be associated with epigenetics were colorectal cancer (CRC) and lung cancer, shown by Feinberg & Vogelstein (1983)³ to feature hypomethylated proto-oncogenes. Methyl groups, it should be noted, are the most common epigenetic modifications, occurring primarily in 5’-CpG-3’ repeats and appearing in over 70% of human gene promoters for differential tissue-specific regulation.⁴Thus, abnormally low or high levels of methylation are often the impetus for cancer.

The International Agency for Research on Cancer (IARC) estimates that around 2 million cases of CRC (~10% of all cancers) were diagnosed in 2020,⁵ and we are now aware that CRC is caused far more frequently by abnormal methylation than previously believed. All reported instances of CRC have displayed either hypomethylation in enhancer regions, proto-oncogenes (e.g., MYC and HRAS)⁶ or retrotransposon-like LINEs (e.g., LINE-1)⁷; or hypermethylation in tumour suppressor genes (e.g., CDKN2A, MLH1 and APC).^8,9,10 Alarmingly, some of these changes can quickly instigate mass genomic instability in cells, increasing the rate of DNA mutations and intertwining genetic and epigenetic dysregulation in CRC.

An emerging view is that DNA methylation may be applied as a biomarker for diagnosing cancer. Indeed, some methylation assays have already been commercialised and are included in clinical practices, with a handful that are specific for CRC identification.¹⁰ One such assay is the Epi proColon test, which amplifies and detects hypermethylated SEPT9 in blood samples. SEPT9 codes for septin 9, a protein involved in cytoskeletal rearrangements and vesicular trafficking, and can be found circulating in the blood when it is released from dying tumour cells.¹¹ Consequently, SEPT9 has received much attention from the research community in recent years, with some studies finding that it can identify CRC with a sensitivity of over 90%.¹¹ This, however, can decrease down to only 7.9% in patients with earlier stages of the disease. Since the same trend applies to current epigenetic tests, it is imperative that we continue investigating the role of epigenetics in cancer to improve these tests or find more reliable alternatives.

Cancer is not the only disease triggered by aberrant epigenetic regulation. Albeit less widely understood, neurodegenerative disorders (NDDs) such as Alzheimer’s disease, Huntington’s disease, multiple sclerosis and stroke have all been implicated in epigenetics.¹² In stark contrast, however, there are no corresponding epigenetic biomarkers at the time of writing.^13,14 Current biomarkers for NDDs instead rely on costly and/or invasive procedures, such as neuroimaging or cerebrospinal fluid analysis (CFA).¹⁵ This conundrum was recently addressed by EuroEspes, a pharmaceutical company in Spain.

Analysing global CpG methylation and gene expression in a cohort of 134 patients, Martínez-Iglesias et al. (2022) discovered that levels of cytosine methylation were lower in patients with NDDs.¹⁴ Comparatively, the expression of DNA methylation regulators appeared to decrease with increasing age, suggesting that genome methylation is necessary for age-associated cognition. NRG1, BDNF and SIRT1 – all of which play a role in neuronal survival and growth – were also expressed less in the NDD samples. This could be explained by an upregulated DNA methylation of these genes, meaning that we may be able to use them as epigenetic biomarkers for diagnosis.

Being relatively new, the researchers’ data must be reviewed further before it can be applied for diagnostic settings. Nevertheless, some of their results offer promising implications for detecting early-onset NDDs – particularly with regard to age-related dementia. Studying the patients’ blood samples, Martínez-Iglesias et al. saw that SIRT1expression [VE1] [HA2] had dropped by 80% in patients with an NDD.¹⁴ SIRT1 is already known to be central for cell survival and repair against metabolic disfunction.¹⁶ As such, SIRT1 could very well become integral to medical diagnoses in the future.

Fortunately, while epigenetic biomarkers for NDDs are still in development, a variety of other conditions have seen more progress in the matter. Over the last decade, epigenetic biomarkers have come to the fore in cardiovascular diseases,¹⁷ infectious disorders¹⁸ and autoimmune diseases,¹⁹ amongst other conditions of interest. One recent study from the University of Turku discovered that, in children with type 1 diabetes, differentially methylated signatures could be found in T-cells at very early stages of the disease.²⁰ This could be useful for diabetes prediction and management in the future.

Epigenetic biomarkers currently take advantage of differing degrees of DNA methylation at 5’-CpG-3′ repeats and histone acetylation in the genome.² Although tests for these are still in development, they hold much potential for inexpensive, non-invasive early-onset disease diagnoses. There are many branches of epigenetics that have yet to be tested for their predictive capability. Non-CpG methylation is now understood to be a cell-specific mechanism that, unlike CpG methylation, is not maintained after DNA replication. It also accumulates on transcriptionally silent genes in neurons and plays a critical role in vertebrate cognition,²¹ implying that it may be involved in NDDs and could be explored as a potential diagnostic biomarker.

Besides DNA, researchers have discovered that RNA can also be directly regulated by epigenetics in cells. The most abundant modification of the epitranscriptome is N⁶-methyladenosine (m⁶A), for instance, which affects mRNA fate and ribosomal RNA function across all domains of life.²² Involved in cancer, the immune system and brain function, m⁶A markers are yet another target that must be investigated for epigenetic diagnosis. The same applies to non-protein epigenetic regulators, with research on non-coding RNA-mediated epigenetics quickly becoming one of the most prominent fields in cancer biology.¹⁰

Altogether, it is safe to say that we are rapidly adjusting the way we understand and treat human diseases. Cancer diagnosis is more viable than ever; early detection of other diseases is soon to follow – and with the help of epigenetics, the trend is only guaranteed to continue.

References:

1. Allis CD & Jenuwein T. The molecular hallmarks of epigenetic control. Nat Rev Genet 2016;17:487–500.
2. Gopalakrishnan S, Van Emburgh BO & Robertson KD. DNA methylation in development and human disease. Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis 2008;647:30–38.
3. Feinberg AP & Vogelstein B. Hypomethylation distinguishes genes of some human cancers from their normal counterparts. Nature 1983;301:89–92.
4. Saxonov S, Berg P & Brutlag DL. A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proc Natl Acad Sci U S A 2006;103:1412–1417.
5. Sung H, et al. Global Cancer Statistics 2020: GLOBOCAN Estimates of Incidence and Mortality Worldwide for 36 Cancers in 185 Countries. CA: A Cancer Journal for Clinicians 2021;71:209–249.
6. Luo J, Li YN, Wang F, Zhang WM & Geng X. S-Adenosylmethionine Inhibits the Growth of Cancer Cells by Reversing the Hypomethylation Status of c-myc and H-ras in Human Gastric Cancer and Colon Cancer. International Journal of Biological Sciences 2010;6:784–795.
7. Hur K, et al. Hypomethylation of long interspersed nuclear element-1 (LINE-1) leads to activation of proto-oncogenes in human colorectal cancer metastasis. Gut 2014;63:635–646.
8. Bihl MP, Foerster A, Lugli A & Zlobec I. Characterization of CDKN2A(p16) methylation and impact in colorectal cancer: systematic analysis using pyrosequencing. Journal of Translational Medicine 2012;10:173.
9. Liang TJ, et al. APC hypermethylation for early diagnosis of colorectal cancer: a meta-analysis and literature review. Oncotarget 2017;8:46468–46479.
10. Jung G, Hernández-Illán E, Moreira L, Balaguer F & Goel A. Epigenetics of colorectal cancer: biomarker and therapeutic potential. Nat Rev Gastroenterol Hepatol 2020;17:111–130.
11. He N, et al. The Pathological Features of Colorectal Cancer Determine the Detection Performance on Blood ctDNA. Technol Cancer Res Treat 2018;17.
12. Hwang JY, Aromolaran KA & Zukin RS. The emerging field of epigenetics in neurodegeneration and neuroprotection. Nat Rev Neurosci 2017;18:347–361.
13. Ciceri F, Rotllant D & Maes T. Understanding Epigenetic Alterations in Alzheimer’s and Parkinson’s Disease: Towards Targeted Biomarkers and Therapies. Curr. Pharm. Des. 2017;23:839–857.
14. Martínez-Iglesias O, Naidoo V, Cacabelos N & Cacabelos R. Epigenetic Biomarkers as Diagnostic Tools for Neurodegenerative Disorders. International Journal of Molecular Sciences 2022;23:13.
15. El Kadmiri N, Said N, Slassi I, El Moutawakil B & Nadifi S. Biomarkers for Alzheimer Disease: Classical and Novel Candidates’ Review. Neuroscience 2018;370:181–190.
16. Jiao F & Gong Z. The Beneficial Roles of SIRT1 in Neuroinflammation-Related Diseases. Oxidative Medicine and Cellular Longevity 2020;e6782872.
17. Shi Y, et al. Epigenetic regulation in cardiovascular disease: mechanisms and advances in clinical trials. Sig Transduct Target Ther 2022;7:1–28.
18. Kulkarni S, et al. Editorial: Epigenetics of infectious diseases. Front. Immunol. 2022;13:1054151.
19. Mazzone R, et al. The emerging role of epigenetics in human autoimmune disorders. Clinical Epigenetics 2019;11:34.
20. Starskaia I, et al. Early DNA methylation changes in children developing beta cell autoimmunity at a young age. Diabetologia 2022;65:844–860.
21. de Mendoza A, Poppe D, Buckberry S, et al. The emergence of the brain non-CpG methylation system in vertebrates. Nat Ecol Evol 2021;5:369–378.
22. Boulias K, Greer EL. Biological roles of adenine methylation in RNA. Nat Rev Genet 2022.

---

 [VE1]Do you mean the gene or the protein here?  [VE1]

The protein (in terms of its expression by the gene). [HA2]