Epigenetics-Based Molecular Diagnosis Lecture Notes PDF

Epigenetics -based Molecular Diagnosis Hussein Sabit, PhD Lec. 4.. Epigenetically Identical twins are not !identical  Epigenetics Waddington Conrad The studying of DNA change...

Epigenetics -based Molecular Diagnosis Hussein Sabit, PhD Lec. 4.. Epigenetically Identical twins are not !identical  Epigenetics Waddington Conrad The studying of DNA changes, not It is s non- involving changes sequence- Epi = above in sequence, that dependent regulate gene inheritance. expression.  Disease-related methylation changes are Why an attractive source of biomarkers that can epigenetics have a significant impact on precision medicine. -based Therefore, methylation patterns could be diagnosis? used as in-vitro diagnosis (IVD). Epigenetic biomarkers in precision medicine The covalent addition of methyl group (-CH3) to the 5-carbon position of the cytosine is one of the first epigenetic modifications shown to modulate gene expression regulation. In general terms, methylation of cytosines in the gene promoter interferes with gene transcription and can lead to transcriptional gene deactivation. Epigenetics- based IVD Any epigenetic modification of DNA, RNA, or protein that induces gene expression change which in turn results in a specific phenotype is a biomarker of that phenotype. However, only DNA methylation seems to be sufficiently stable epigenetic modification to be utilized as a biomarker in IVD. This modification is stable in somatic cells and is populated to daughter cells with high fidelity. That’s why disease-related methylation changes is a source of IVD biomarkers.  IVD use of the methylation-based biomarkers The IVD tests in Disease risk clinical disease management can be assessment Diagnosis subdivided into four areas representing the natural stages Treatment of the disease personalization development: Post-treatment monitoring  As a general paradigm, early detection of the disease significantly increases the Diagnos chance of cure. tic Studies indicated that methylation changes occur early biomark in disease development. ers It is also well established that the DNA from pathologically changed cells is secreted and can be detected in body fluids such as sputum, plasma, urine, or stool.  Colorectal A liquid biopsy is a less invasive diagnostic method that detects cancer cells or DNA fragments from tumors in the cancer blood or other bodily fluids, such as saliva or urine. This method allows for real-time monitoring of tumor evolution and treatment response without the need for surgical biopsies. FDA-approved Cologuard is a liquid biopsy-based test targeting methylation changes intended for CRC screening. Cologuard works by detecting DNA Cologuard is a multi-target stool DNA test, mutations in the stool, which may indicate the presence of cancerous or intended for CRC screening in adults of 45 precancerous cells. Cologuard vs. or older, who are at typical average risk for colonoscopy. CRC. The test is recommended to be performed These genes can undergo abnormal every 3 years and targets methylation methylation in cancerous tissues, which changes at BMP3 and NDRG4 promoters can be detected in stool samples. This and seven-point mutations in type of non-invasive screening.  Hepatocellular Epi proColon 2.0 is a blood-based test carcinoma designed for detecting colorectal cancer. It specifically looks for methylated DNA biomarkers associated with cancerous tumors, such as the Septin9 gene, in a Epi proColon 2.0 test used to patient's blood sample. This is a non-invasive detect HCC. screening method. The test was able to detect HCC with a sensitivity of 90.6% and a specificity of 87.2% which is significantly higher than the accuracy of alpha-fetoprotein (AFP), a widely used serum diagnostic marker for liver cancer.  Lung cancer Epi proLung is used to diagnose lung cancer in patients at increased risk of the disease. The test detects the methylation landscape in the genes SHOX2 and PTGER4 in the cfDNA extracted from plasma. microRNAs  Background MicroRNAs (miRNAs) are 21–25 nucleotide, single-stranded, non- coding RNA molecules that play an important role in regulating gene expression. Following the discovery of the first miRNA, lin-4, in Caenorhabditis elegans in the year 1993, several miRNAs have been discovered. Currently, >35 000 miRNA sequences have been identified in The Nobel Prize in Physiology or Medicine for 2024 was awarded to Victor Ambros and Gary Ruvkun >270 organisms. for their groundbreaking discovery of microRNAs How miRNA is secreted  An ideal marker should be safe and easy to measure, cost-efficient, modifiable with treatment, and miRNA consistent across gender and ethnic groups. To date, none of the available biomarkers satisfy all of these criteria. miRNA overcomes these limitations. miRNAs are stable and can be easily isolated and miRNAs in Diagnosis Cardiovascul ar diseases (CVD) CVD is routinely diagnosed with cardiac troponin (cTn), CK-MB, and N-terminal prohormone (NT-proBNP). These biomarkers provided false positive results and are also time-dependent. miRNAs have been proven to have an important role in CVD. Plasma levels of miR-1 and miR- 133a/b are elevated in some heart diseases, while miR-122 and miR-375 are lowered.  HIV/AIDS AIDS is a spectrum of conditions caused by infection with HIV. For the diagnosis of HIV/AIDS, several types of tests are there. Plasma miR-29b was highly expressed in HIV-1 patients, while lower levels of plasma miR-29 indicated high viremia. Plasma levels of miR-150 and miR- 146b-5p also varied between different groups of HIV and healthy individuals.  Melanoma Today, a proper melanoma biomarker does not exist. miR-134-5p and miR-320a-3p have been identified as downregulated plasma miRNAs discriminating melanoma patients from healthy subjects. Furthermore, their expression was lower in patients in stage 0 than in healthy individuals and was even reduced in stage I/II patients.  Ovarian cancer The first serum biomarker for ovarian cancer (OC) was discovered in 1965; however, it lacked sensitivity and specificity. miR-106a-5p, let-7d-5p, and miR-93-5p have been identified as significantly increased and miR-122-5p, hsa-miR-185-5p, and miR-99b- 5p as significantly decreased in the exosomes of patients with OC compared with Pancreatic cancer Pancreatic cancer (PaC) is a killer cancer because of its poor prognosis, its high metastatic rate, and the absence of early symptoms. In addition, it is difficult to discriminate chronic pancreatitis (CP) patients from PaC ones. Serum proteins allow monitoring of patient response to therapy and predict recurrence after surgery, but it has low sensitivity and specificity. miR-20a, miR-21, miR-24, miR-25, miR-99a, miR-185, and miR-191 were used to diagnose PaC with high sensitivity. Chronic lymphocytic leukemia Chronic lymphocytic leukemia (CLL) is the most common leukemia, and they are caused by an accumulation of CD5+ B lymphocytes. Nowadays, available tests are unable to predict overall survival and response to treatments. miR-155 plasma level was lower in patients who achieved complete remission than in those who experienced other responses. miR-155, together with miR-150 and the miR-29 family were differentially expressed in the exosomes of CLL patients compared to healthy donors. Rheumatoid arthritis As a chronic inflammatory disease, rheumatoid arthritis (RA) usually leads to cartilage and bone damage, even disability. Earlier detection and diagnosis are crucial to improving therapeutic efficacy. Some miRNAs were used to early diagnose RA; miR-142-5p, miR-1184, miR-1246, and miR- 99b-5p.  Non-Hodgkin lymphoma Non-Hodgkin lymphoma (NHL) consists of a heterogeneous group of lymphoid malignancies due to altered proliferation of B, T, and natural killer lymphocytes. Increased miR-155, miR-210, and miR-21 levels were observed in the serum of patients compared to controls and higher expression of miR-21 was associated with relapse-free survival. What is available in the market thank you!