• Molecules and Cells
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• 제45권5호
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• pp.343-352
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• 2022

The advent of the assay for transposase-accessible chromatin using sequencing (ATAC-seq) has shown great potential as a leading method for analyzing the genome-wide profiling of chromatin accessibility. A comprehensive reference to the ATAC-seq dataset for disease progression is important for understanding the regulatory specificity caused by genetic or epigenetic changes. In this study, we present a genome-wide chromatin accessibility profile of 44 liver samples spanning the full histological spectrum of nonalcoholic fatty liver disease (NAFLD). We analyzed the ATAC-seq signal enrichment, fragment size distribution, and correlation coefficients according to the histological severity of NAFLD (healthy control vs steatosis vs fibrotic nonalcoholic steatohepatitis), demonstrating the high quality of the dataset. Consequently, 112,303 merged regions (genomic regions containing one or multiple overlapping peak regions) were identified. Additionally, we found differentially accessible regions (DARs) and performed transcription factor binding motif enrichment analysis and de novo motif analysis to determine new biomarker candidates. These data revealed the gene-regulatory interactions and noncoding factors that can affect NAFLD progression. In summary, our study provides a valuable resource for the human epigenome by applying an advanced approach to facilitate diagnosis and treatment by understanding the non-coding genome of NAFLD.

• Journal of Digestive Cancer Research
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• 제10권2호
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• pp.99-106
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• 2022

Clinical research ultimately aimed to promptly diagnose and prevent diseases through precise biomarker development. Finding the optimal cut-off point of a regularly measured biomarker can help its interpretation and ultimately help in disease investigation and diagnosis, more specifically in determining the presence of diseases. Therefore, this study aimed to use the characteristics of outcome variables in clinical research to explain how to determine the optimal cutoff point. The outcome variables can be divided into dichotomous, ordinal, and survival types. The optimal cut-off point can be determined by finding points that maximize the Youden index, extended Youden index, and log-rank statistics. This study will enable clinical researchers to accurately determine the optimal cut-off points for regularly measured biomarkers, thereby enabling prompt disease diagnosis for effective treatment.

• 대한의용생체공학회:의공학회지
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• 제38권5호
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• pp.271-276
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• 2017

Cancer biomarkers are using in the diagnosis, staging, prognosis and prediction of disease progression. But, there are not sufficiently profiled and validated in early detection and risk classification of prostate cancer. In this study, we have devoted to finding a panel of serum biomarkers that are able to detect the diagnosis of prostate cancer. The serum samples were consisted of 111 prostate cancer and 343 control samples and examined. Eleven biomarkers were constructed in this study, and then nine biomarkers were relevant to candidate biomarkers by using t test. Finally, four biomarkers, PSA, ApoA2, CYFRA21.1 and TTR, were selected as the prostate cancer biomarker panel, logistic regression was used to identify algorithms for diagnostic biomarker combinations(AUC = 0.9697). A panel of combination biomarkers is less invasive and could supplement clinical diagnostic accuracy.

• 한국임상수의학회지
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• 제32권1호
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• pp.62-68
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• 2015

There is no reliable indicator available for the diagnosis of horse laminitis, although the disease is common and costly. This study was performed to develop a specific diagnostic biomarker for laminitis. We have identified 33 differentially expressed proteins in plasma of a horse suffering laminitis that is experimentally induced by an overdose of oligofructose, in comparison with normal horse plasma. Among the proteins, myosin-9 mRNA was found in RNA sequencing analysis to be expressed specifically in laminitis tissues compared to other horse tissues. It is thus suggested that expression of plasma myosin-9 may be used for the diagnosis of equine laminitis.

• Tuberculosis and Respiratory Diseases
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• 제80권3호
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• pp.313-315
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• 2017

• KSBB Journal
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• 제26권4호
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• pp.352-356
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• 2011

The detection of biomarkers is an important issue for disease diagnosis. However, many systems are not suitable to detect the biomarker itself directly. For direct detection of biomarker proteins in human serum, a new affinity-capture method using aptamers combined with the mass spectrometry was suggested. Since signals from protein samples cannot be amplified, modified chromatin immunoprecipitation (ChIP) and subsequent cross-linking with formaldehyde between aptamers and target proteins were used not to lose the captured target proteins, which allowed us to perform a harsh washing step to remove the non-specifically bound proteins. As a model system, a thrombin aptamer was used as a bait and thrombin as a target protein. Using our modified ChIP and affinity-capture method, non-specific binding proteins on the beads decreased significantly, suggesting that our new method is efficient and can be applied to developing diagnosis systems for various biomarkers.

• BMB Reports
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• 제41권9호
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• pp.626-634
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• 2008

Novel cancer biomarkers are required to achieve early diagnosis and optimized therapy for individual patients. Cancer is a disease of the genome, and tumor tissues are a rich source of cancer biomarkers as they contain the functional translation of the genome, namely the proteome. Investigation of the tumor tissue proteome allows the identification of proteomic signatures corresponding to clinico-pathological parameters, and individual proteins in such signatures will be good biomarker candidates. Tumor tissues are also a rich source for plasma biomarkers, because proteins released from tumor tissues may be more cancer specific than those from non-tumor cells. Two-dimensional difference gel electrophoresis (2D-DIGE) with novel ultra high sensitive fluorescent dyes (CyDye DIGE Fluor satulation dye) enables the efficient protein expression profiling of laser-microdissected tissue samples. The combined use of laser microdissection allows accurate proteomic profiling of specific cells in tumor tissues. To develop clinical applications using the identified biomarkers, collaboration between research scientists, clinicians and diagnostic companies is essential, particularly in the early phases of the biomarker development projects. The proteomics modalities currently available have the potential to lead to the development of clinical applications, and channeling the wealth of produced information towards concrete and specific clinical purposes is urgent.

• Journal of Preventive Medicine and Public Health
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• 제42권6호
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• pp.343-348
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• 2009

The final decision of study design in molecular and genetic epidemiology is usually a compromise between the research study aims and a number of logistical and ethical barriers that may limit the feasibility of the study or the interpretation of results. Although biomarker measurements may improve exposure or disease assessments, it is necessary to address the possibility that biomarker measurement inserts additional sources of misclassification and confounding that may lead to inconsistencies across the research literature. Studies targeting multi-causal diseases and investigating gene-environment interactions must not only meet the needs of a traditional epidemiologic study but also the needs of the biomarker investigation. This paper is intended to highlight the major issues that need to be considered when developing an epidemiologic study utilizing biomarkers. These issues covers from molecular and genetic epidemiology (MGE) study designs including cross-sectional, cohort, case-control, clinical trials, nested case-control, and case-only studies to matching the study design to the MGE research goals. This review summarizes logistical barriers and the most common epidemiological study designs most relevant to MGE and describes the strengths and limitations of each approach in the context of common MGE research aims to meet specific MEG objectives.

• Journal of Microbiology and Biotechnology
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• 제23권8호
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• pp.1167-1175
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• 2013

Paratuberculosis (PTB) or Johne's disease is one of the most serious chronic debilitating diseases of ruminants worldwide that is caused by Mycobacterium avium subsp. paratuberculosis (MAP). MAP is a slow-growing bacterium that has very long latent periods, resulting in difficulties in diagnosing and controlling the disease, especially regarding the diagnosis of fecal shedders of MAP without any clinical signs. Based on this situation, attempts were made to identify biomarkers that show early responses to MAP infection in a macrophage cell line, RAW 264.7. In response to the infection with the bacterium, a lot of genes were turned on and/or off in the cells. Of the altered genes, three different categories were identified based on the time-dependent gene expression patterns. Those genes were considered as possible candidates for biomarkers of MAP infection after confirmation by quantitative RT-PCR analysis. To the best of our knowledge, this is the first attempt at discovering the host transcriptomic biomarkers of PTB, although further investigation will be required to determine whether these biomarker candidates are associated within the natural host.

• Clinical and Experimental Pediatrics
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• 제62권8호
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• pp.287-291
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• 2019

Fecal calprotectin (FC) is a calcium- and zinc-binding protein of the S100 family, mainly expressed by neutrophils and released during inflammation. FC became an increasingly useful tool both for gastroenterologists and for general practitioners for distinguishing inflammatory bowel disease (IBD) from irritable bowel syndrome. Increasing evidences support the use of this biomarker for diagnosis, follow-up and evaluation of response to therapy of several pediatric gastrointestinal diseases, ranging from IBD to nonspecific colitis and necrotizing enterocolitis. This article summarizes the current literature on the use of FC in clinical practice.