DNA Biomarkers Research Articles

OA01.08 Clinical Response to Tepotinib According to Circulating Tumor (ct)DNA Biomarkers in Patients with Advanced/Metastatic NSCLC with High-level MET Amplification (METamp) Detected by Liquid Biopsy (LBx)

OA01.08 Clinical Response to Tepotinib According to Circulating Tumor (ct)DNA Biomarkers in Patients with Advanced/Metastatic NSCLC with High-level MET Amplification (METamp) Detected by Liquid Biopsy (LBx)

Biomarkers of Aggressive Prostate Cancer at Diagnosis.

In the United States, prostate cancer (CaP) remains the second leading cause of cancer deaths in men. CaP is predominantly indolent at diagnosis, with a small fraction (25-30%) representing an aggressive subtype (Gleason score 7-10) that is prone to metastatic progression. This fact, coupled with the criticism surrounding the role of prostate specific antigen in prostate cancer screening, demonstrates the current need for a biomarker(s) that can identify clinically significant CaP and avoid unnecessary biopsy procedures and psychological implications of being diagnosed with low-risk prostate cancer. Although several diagnostic biomarkers are available to clinicians, very few comparative trials have been performed to assess the clinical effectiveness of these biomarkers. It is of note, however, that a majority of these clinical trials have been over-represented by men of Caucasian origin, despite the fact that African American men have a 1.7 times higher incidence and 2.1 times higher rate of mortality from prostate cancer. Biomarkers for CaP diagnosis based on the tissue of origin include urine-based gene expression assays (PCA3, Select MDx, ExoDx Prostate IntelliScore, Mi-Prostate Score, PCA3-PCGEM1 gene panel), blood-based protein biomarkers (4K, PHI), and tissue-based DNA biomarker (Confirm MDx). Another potential direction that has emerged to aid in the CaP diagnosis include multi-parametric magnetic resonance imaging (mpMRI) and bi-parametric magnetic resonance imaging (bpMRI), which in conjunction with clinically validated biomarkers may provide a better approach to predict clinically significant CaP at diagnosis. In this review, we discuss some of the adjunctive biomarker tests along with newer imaging modalities that are currently available to help clinicians decide which patients are at risk of having high-grade CaP on prostate biopsy with the emphasis on clinical utility of the tests across African American (AA) and Caucasian (CA) men.

A highly sensitive electrochemical biosensor via short-stranded DNA activating LAMP(H+) to regulate i-motif folds for signal transduction

Exploring loop-mediated isothermal amplification (LAMP)-based electrochemical assay for short-stranded DNA biomarkers is intriguing. Herein, a HIV-specific DNA segment (tDNA) was introduced to implement a variant LAMP reaction, where the generated by-products H+, vLAMP(H+), acted as signal transducers for developing a sensitive electrochemical biosensor. As proof-of-concept, the tDNA-recognizable complement was programmed in a template hairpin (TH) that was ended with a 3′-terminus phosphate group to avoid non-specific elongation. Upon TH simultaneously hybridizing with tDNA and a precursor hairpin (PH), the PH underwent a loop-mediated extension with Bst polymerase and dNTPs, forming a new stem-loop hairpin in another terminus. Then the elongated product containing a double stem-loop dumbbell-like DNA structure (dDDS) was displaced and released. Using dDDS as an initiator, the vLAMP reaction occurred via consecutively cycled strand displacement for self-primed DNA incorporation. The resulting tDNA-dependent vLAMP(H+) was introduced in the modified electrode surface to guide the pH-sensitive i-motif (iM) folding. Thus, a signaling hairpin labeled with electroactive ferrocene (Fc) was dehybridized and closed, thereby bringing Fc close to the electrode interface for increased current signal readout that was highly sensitive to tDNA down to 0.034 fM. Our electrochemical biosensor would be applicable for detecting various short-stranded DNA or miRNA.

PSYCHOSOCIAL AND BEHAVIORAL PREDICTORS OF HEALTH AND AGING

Abstract Crucial to understanding the aging process is to identify modifiable characteristics that can be targeted in hope of optimizing health across adulthood. This symposium brings together a diverse set of talks about the biopsychosocial and behavioral processes that influence aging outcomes. Turiano used a national sample to demonstrate that individuals with higher levels of neuroticism often use food to cope with stressors which ultimately results in a greater central adiposity and elevated glycated hemoglobin. Zavala used an epidemiological sample of long-banked frozen blood samples to successfully extract DNA and methylation biomarkers from 140 adults and found that stress measures are associated with accelerated biological aging. Luo used coordinated analysis to explore how correlations between personality traits and four health outcomes fluctuate over time, and found the associations between personality (level/change) and health increased in strength through middle adulthood and early stage of late adulthood but weakened in very old age. Jackson found that individuals who experienced high and increasing loneliness in older adulthood had worse cognitive function and steeper cognitive decline than expected given their observed post-mortem neuropathology (i.e., worse cognitive resilience). Lastly, Pfund investigated how personality and social support change together and found within and between person associations between personality and social support, and evidence that retirement was associated with an increase in social support. In sum, this symposium presents novel evidence for the associations among personality, stress, social support, and lonliness are associated with physical and cognitive health in old age.

Profile of loiasis infection through clinical and laboratory diagnostics: the importance of biomarkers.

Detection of Loa loa microfilariae in peripheral blood is insensitive given only 30% of individuals are microfilaraemic while 70% are amicrofilaraemic with a variety of clinical signs. Biomarkers may improve the diagnosis of loiasis. A total of 545 individuals exposed to L. loa were analysed using clinical data collected through a questionnaire (requesting information on eye worm, Calabar swelling, pruritis) and detection of microfilariae, immunoglobulin G4 (IgG4), DNA and antigens using microscopy, enzyme-linked immunosorbent assay (ELISA), quantitative polymerase chain reaction (qPCR) and Western blot, respectively. The results revealed that the rates of detection of L. loa microfilariae in the blood, of DNA by qPCR, of IgG4 by ELISA and of antigen by Western blot were 4.7%, 5.5%, 15.60% and 10.09%, respectively. This study showed that clinical signs based on a questionnaire are highly subjective. Therefore it is imperative to use IgG4 and DNA biomarkers as well as antigens detected by Western blot to identify individuals infected with L. loa.

454 Digital quantitative detection of methylated DNA biomarkers: A helpful tool in the early diagnosis of Sézary syndrome

Sézary syndrome (SS) is an aggressive type of cutaneous T-cell lymphoma. Diagnosing SS can be challenging, especially in early stages of disease. Previously, in a genome-wide study, we showed that promoter hypermethylation of PROM1, G0S2, CMTM2, PAM, GNMT and NEXN is frequently observed in late stages of disease, but is neither found in healthy donors nor in benign erythrodermic inflammatory dermatoses (EID) patients. In this study, we evaluated the diagnostic value of these biomarkers in early stages of disease.

A modern view on the clinical value of the study of oral fluid in the practice of a pediatrician

Currently, the attention of the medical community to a non-invasive method of laboratory diagnostics - the study of oral fluid (oral, saliva, saliva test) in various fields of clinical medicine and mainly in adult patients has been updated. Saliva testing has shown good results, especially in the areas of genomics, microbiomics, proteomics, metabolomics, and transcriptomics. The review presents the possibilities of using a non-invasive method for infectious and non-infectious diseases in children. Saliva contains a wide range of protein DNA and RNA biomarkers that help detect many viral infections in children. Oral fluid tests for human immunodeficiency virus, hepatitis B virus have improved access to diagnostics for infants. Both serological and molecular analyzes of the oral fluid are suitable for routine examination and early detection of measles virus RNA, polyomaviruses. Angiotensin-converting enzyme-2 receptor expression was found in the saliva of children with COVID-19, which can be used to diagnose SARS-CoV-2. The saliva test is as effective as the standard test at identifying asymptomatic individuals in contact tracing. The possibilities of saliva diagnostics are positively assessed in transplantology. New biomarkers in saliva have been identified for the diagnosis of many somatic diseases in children. The role of oral fluid as an alternative to blood serum in patients with terminal renal failure, chronic kidney disease (determination of creatinine, urea) in both adults and children is shown. The data obtained may influence the recommendations for the treatment of patients. As a non-invasive method, the study of oral fluid is promising for the diagnosis, prognosis, monitoring of diseases, large-scale typing of children, and the search for new biomarkers.

Personalized cancer care.

The completion of the Human Genome Project in 2003 has led to the development of molecular profiling platforms that have changed the trajectory of cancer care. These technologies continue to advance, and with the development of next-generation sequencing, targeted gene panels are now commercially available to analyze DNA, RNA, and protein biomarkers and can detect germline (inherited) and somatic (acquired) mutations through genomic profiling of tumor tissue and/or blood. These targeted panels are useful in practice and can affect clinical decision making. The results of molecular profiling can lead to an increasing number of FDA approved treatment options and/or clinical trial opportunities with novel drugs linked to these alterations, most notably in more advanced disease. This ability to individualize treatment options has led to precision medicine, providing a more personalized approach to cancer care.

Increased risk of low infant birth weight in pregnant women with low PAPP-A values measured in the first trimester

Objectives: Testing pregnant women as early as in the first trimester has multiple advantages. Firstly, the first trimester screening combining ultrasound and serum marker testing (PAPP-A and free β-hCG) offers the highest currently possible — except for expensive tests using cell-free DNA biomarkers from the mother’s blood (ccf DNA) — detectability of aneuploid fetuses. Secondly, nuchal translucency (NT) measurement helps determine the risk of numerous abnormalities other than aneuoploidies. Lastly, nearly complete ultrasound assessment of fetal anatomy can be performed as early as in the first trimester of pregnancy. Material and methods: This study is based on prospective analysis. Study subjects were 236 pregnant women. One hundred thirty-one patients with a single pregnancy were qualified into the study group and had a combined ultrasound and biochemical screening for Down’s syndrome performed between 11 + 0 and 13 + 6 weeks of gestation, with the measured PAPP-A value at ≤ 0.50 MoM (multiples of the median). The control group comprised 105 pregnant women with PAPP-A value at a similar stage of pregnancy at > 0.5 MoM. Results: The average observed value of the PAPP-A in the study group was 0.35 MoM while in the control group 1.29 MoM. Moreover, combined observation of infant birth weights in both groups compared to the PAPP-A MoM values has shown a significant relationship between those characteristics (r = 0.15, p = 0.0184). Conclusions: The results showed that pregnant women with low PAPP-A MoM value measured during the first trimester have a higher risk of giving birth to a low-birth-weight infant (which is the value below 2500 g), than the pregnant women whose PAPP-A MoM value in the first trimester did not meet this criterion.

Epigenome-wide association study of biomarkers of liver function identifies albumin-associated DNA methylation sites among male veterans with HIV.

Background: Liver disease (LD) is an important cause of morbidity and mortality for people with HIV (PWH). The molecular factors linked with LD in PWH are varied and incompletely characterized. We performed an epigenome-wide association study (EWAS) to identify associations between DNA methylation (DNAm) and biomarkers of liver function-aspartate transaminase, alanine transaminase, albumin, total bilirubin, platelet count, FIB-4 score, and APRI score-in male United States veterans with HIV. Methods: Blood samples and clinical data were obtained from 960 HIV-infected male PWH from the Veterans Aging Cohort Study. DNAm was assessed using the Illumina 450K or the EPIC 850K array in two mutually exclusive subsets. We performed a meta-analysis for each DNAm site measured by either platform. We also examined the associations between four measures of DNAm age acceleration (AA) and liver biomarkers. Results: Nine DNAm sites were positively associated with serum albumin in the meta-analysis of the EPIC and 450K EWAS after correcting for multiple testing. Four DNAm sites (cg16936953, cg18942579, cg01409343, and cg12054453), annotated within the TMEM49 and four of the remaining five sites (cg18181703, cg03546163, cg20995564, and cg23966214) annotated to SOCS3, FKBP5, ZEB2, and SAMD14 genes, respectively. The DNAm site, cg12992827, was not annotated to any known coding sequence. No significant associations were detected for the other six liver biomarkers. Higher PhenoAA was significantly associated with lower level of serum albumin (β = -0.007, p-value = 8.6 × 10-4, CI: -0.011116, -0.002884). Conclusion: We identified epigenetic associations of both individual DNAm sites and DNAm AA with liver function through serum albumin in men with HIV. Further replication analyses in independent cohorts are warranted to confirm the epigenetic mechanisms underlying liver function and LD in PWH.

Could cell-free DNA and host biomarkers assist in antimicrobial stewardship with organ transplant recipients?

Antimicrobial stewardship in solid organ transplant (SOT) recipients is important to prevent antimicrobial-associated complications, but traditional stewardship principles are challenging to implement for SOT patients. Newer methodologies to optimize stewardship efforts are needed. PubMed was searched using the keywords "cell free DNA," "metagenomic sequencing," "host biomarker," "antimicrobial stewardship," and "SOT." Metagenomic sequencing of cell free DNA has the potential to be a stewardship tool for SOT recipients. Various studies have shown its use for antimicrobial de-escalation and duration shortening. Host gene expression profiles can differentiate between infectious and noninfectious syndromes and may assist in stewardship efforts. However, information in immunocompromised hosts is conflicting. Microbial cell free DNA sequencing and host gene expression profiling show promise as stewardship tools in SOT recipients. Future studies on antimicrobial stewardship in SOT recipients should focus on their clinical use and feasibility.

Electron transfer characteristics of amino acid adsorption on epitaxial graphene FETs on SiC substrates

Clarifying the adsorption characteristics of biomolecules on graphene surfaces is critical for the development of field-effect transistor (FET)-based biosensors for detecting pH, DNA, proteins, and other biomarkers. Although there are many reports on biomolecule detection using graphene FETs, the detection mechanism has not yet been clarified. In this study, the adsorption behavior and electron transfer characteristics of 20 proteinogenic amino acids on graphene field-effect transistors are investigated. Large single-crystal graphene films were epitaxially grown on SiC substrates by a resist-free metal stencil mask lithography process then patterned by air plasma etching to form FET devices. Amino acids with different charge conditions (positive or negative charge) were introduced onto the epitaxial graphene surface in solution. The charge neutral points of the drain current vs gate voltage curves shifted in the negative gate voltage direction after the introduction of all amino acids, regardless of the type of amino acid and its charge condition. These amino acid adsorption characteristics agree well with previously reported protein adsorption characteristics on epitaxial graphene surfaces, indicating that the adsorption of proteins in the liquid phase occurs by electron doping to the graphene surface. These results indicate that non-specific protein binding always leads to electron doping of epitaxial graphene FETs.

68P Urinary biomarkers for prognosis of histologically confirmed small renal tumors

Adequate clinical management of small renal tumors (SRTs, <4 cm) is important despite their slow growth and low metastatic potential. Surgical resection or nephrectomy remains the main treatment strategy. However, up to 30% of SRTs suspicious for malignancy by preoperative imaging reveal to be benign on final pathological examination after surgery. Moreover, most incidental tumors are detected in the elderly with comorbidities unsuitable for surgical treatment. Up to date, tumor growth rate is the only parameter determining aggressiveness of unresectable SRTs The study aimed at selection of methylated DNA biomarkers for non-invasive urine-based active surveillance of patients, diagnosed with SRTs.

S419 Discovery of Methylated DNA Biomarkers for the Potential Non-Endoscopic Detection of Barrett's Esophagus (BE)

Introduction: Barrett’s esophagus (BE) is a known precursor of esophageal adenocarcinoma (EAC), the type of esophageal cancer that accounts for over 80% of all esophageal cancer cases in the United States. The current gold standard for diagnosis of BE is endoscopic biopsy with histologic examination. Unfortunately, most individuals in the United States do not undergo endoscopy and thus BE is not diagnosed, resulting in progression toward fatal EAC in most undiagnosed BE cases. For this reason, minimally invasive sponge or balloon devices have been studied in conjunction with various types of biomarkers. However, most markers used in current BE diagnostic biomarker panels are outdated, lacking in sufficient specificity and sensitivity, and warrant substantial improvement. Methods: Using a novel approach, we accessed and integrated 6 Infinium HumanMethylation450 BeadChip datasets from various research groups within the Gene Expression Omnibus (GEO) database, from which we selected probes that were highly methylated in Barrett’s (beta ≥ 0.30) and mostly unmethylated in normal esophageal and gastric tissues (beta ≤ 0.05) yielding 30 candidate BE-specific markers. All 30 were identified from research groups who used microdissection and/or careful histopathologic review of each tissue biopsy. We then analyzed 248 BE, 184 normal esophageal, and 101 normal gastric tissue samples from our archives. After designing qMSP primers and probes, and further testing, we assayed 14 candidate markers in 21 matched normal-BE tissue pairs, 8 matched normal-BE-tumor tissue triplets, and 17 matched normal-tumor tissue pairs. Results: All 14 biomarkers tested exhibited significantly higher methylation levels in BE DNAs vs. matched normal DNAs (p < 0.01 by Wilcoxon rank-sum test). 4 of the 14 markers showed significantly higher methylation levels in tumor DNAs vs. matched normal DNAs (P < 0.01). 3 markers were statistically significantly different across matched normal, BE, and tumor tissue triplets (Kruskal-Wallis test, p < 0.05), and these 3 markers were used to develop a diagnostic panel for future testing on minimally invasively obtained cytologic DNAs from sponge-capsule samples. Conclusion: This discriminatory biomarker panel shows potential for BE diagnosis using an inexpensive, minimally invasive sampling technique and thus merits further study in case-control sponge studies. Due to our systematic and rigid method of selecting these markers, these genes are expected to be extremely important for the diagnosis of BE.

69P Novel urinary methylated DNA biomarkers for kidney cancer detection and prognosis

69P Novel urinary methylated DNA biomarkers for kidney cancer detection and prognosis

A computational approach to biological pathogenicity.

The current pandemic (COVID-19) has made evident the need to approach pathogenicity from a deeper and more systematic perspective that might lead to methodologies to quickly predict new strains of microbes that could be pathogenic to humans. Here we propose as a solution a general and principled definition of pathogenicity that can be practically implemented in operational ways in a framework for characterizing and assessing the (degree of) potential pathogenicity of a microbe to a given host (e.g., a human individual) just based on DNA biomarkers, and to the point of predicting its impact on a host a priori to a meaningful degree of accuracy. The definition is based on basic biochemistry, the Gibbs free Energy of duplex formation between oligonucleotides and some deep structural properties of DNA revealed by an approximation with certain properties. We propose two operational tests based on the nearest neighbor (NN) model of the Gibbs Energy and an approximating metric (the h-distance.) Quality assessments demonstrate that these tests predict pathogenicity with an accuracy of over 80%, and sensitivity and specificity over 90%. Other tests obtained by training machine learning models on deep features extracted from DNA sequences yield scores of 90% for accuracy, 100% for sensitivity and 80% for specificity. These results hint towards the possibility of an operational, objective, and general conceptual framework for prior identification of pathogens and their impact without the cost of death or sickness in a host (e.g., humans.) Consequently, a reasonable prediction of possible pathogens might pave the way to eventually transform the way we handle and prepare for future pandemic events and mitigate the adverse impact on human health, while reducing the number of clinical trials to obtain similar results.

Fecal biomarkers: Non-invasive diagnosis of colorectal cancer.

Colorectal cancer (CRC) is the third most common cancer in the world in terms of morbidity and mortality, which brings great health hazards and economic burdens to patients and society. A fecal examination is an effective method for clinical examination and the most commonly used method for the census. It is simple, non-invasive, and suitable for large-scale population screening. With the development of molecular biology, lots of efforts have been made to discover new fecal biomarkers for the early screening of colorectal cancer. In this review, we summarize and discuss the recent advances of fecal biomarkers for CRC screening or diagnosis, including DNA biomarkers, RNA biomarkers, protein biomarkers, gut microbes and volatile organic compounds focusing on their diagnostic evaluation for CRC, which can provide a basis for the further development of new and effective CRC fecal screening and early diagnosis techniques.

Role of Molecular Biomarkers in Colorectal Cancer

Colorectal cancer (CRC) is amongst the most widespread cancers and is a most common cause of cancer associated mortality universally. Since previous decades, it has been cleared that CRC develops owing to the buildup of a series of genetic and epigenetic changes in the normal colonic epithelium. Regardless of the current development in surgery and therapies, overall survival of end stage CRC patients is extremely low. Different biomarkers are valuable means found in tissue, blood, or stool samples usually, they are efficiently used for CRC monitoring, because they occur in initial stage of disease and provide better identification, diagnosis, prognostication, and prediction of cancer. An accurate biomarker-based treatment and prediction approach will help Patients to get rid of unsuccessful treatments, involving clinical trial-based methods. It will also definitely inhibit under and over dosages of treatment as well as it will decrease pointless harmful side effects. This review focusses upon epidemiology, risk factors, molecular pathways, as well as Different DNA biomarkers and RNA biomarkers related to CRC. In this review, we will highlight the existing knowledge and advances in DNA based biomarkers (RAS, BRAF, cell free DNA, DNA methylation-based biomarkers, and Microsatellite Instability) and RNA-based biomarkers (MicroRNAs, non-coding RNAs, circular RNAs and PiRNAs) for CRC. Herein, we put emphasis for gathering of the latest facts related to biomarkers for obtaining their maximum possible advantages by promoting the clinical practice. New studies show the frequent usage of biomarkers, which will help in optimizing the best possible treatment approaches ultimately.

Molecular actions of exosomes and their theragnostics in colorectal cancer: current findings and limitations.

Extracellular vesicles (EVs) are cell-released, membranous structures essential for intercellular communication. The biochemical compositions and physiological impacts of exosomes, lipid-bound, endosomal origin EVs, have been focused on, especially on the tumor-host interactions in a defined tumor microenvironment (TME). Despite recent progress in targeted therapy and cancer immunotherapy in colorectal cancer (CRC), cancer patients still suffer from distal metastasis and tumor relapse, suggesting unmet needs for biomarkers directing therapeutic interventions and predicting treatment responsiveness. As exosomes are indispensable for intercellular communication and high exosome abundance makes them feasible biomarker molecules, this review discusses exosome heterogeneity and how exosomes orchestrate the interplay among tumor cells, cancer stem cells (CSCs) and host cells, including stromal cells, endothelial cells and immunocytes, in the CRC TME. This review also discusses mechanisms for loading exosomal contents and potential exosomal DNA, RNA and protein biomarkers for early CRC detection. Finally, we summarize the diagnostic and therapeutic exosomes in clinical trials. We envision that detecting and targeting cancer-specific exosomes could provide therapeutic advances in developing personalized cancer medicine.

Electrochemical DNA biosensor coupled to LAMP reaction for early diagnostics of cervical precancerous lesions

Electrochemical (EC) biosensors are potentially useful tools for detection of DNA and RNA cancer biomarkers. Gold screen-printed electrodes (AuSPEs) are especially popular due to their easy manufacturing and surface modifications, making them useful candidates in biosensor fabrication. On the other hand, biosensors based on AuSPEs are still not often applied to clinical samples from cancer patients or compared with routine laboratory methods. Therefore, we tried to address these challenges by developing AuSPE-based biosensor for detection of DNA from two highly oncogenic types of human papillomavirus (HPV), HPV16 and HPV18, that cause cervical cancer in women. We coupled loop-mediated isothermal amplification (LAMP) of HPV DNA from fifteen clinical samples, with the capture of amplified products at the surface of the AuSPE and with final EC detection in a multielectrode format. We show excellent selectivity of designed primers and probes by comparing HPV-positive and HPV-negative cancer cell lines, and most importantly, very good sensitivity and specificity of the proposed biosensor for detection of clinical samples when compared to the PCR used as a gold standard.