Article
Oncology
Jaqueline Loaeza-Loaeza, Berenice Illades-Aguiar, Oscar del Moral-Hernandez, Yaneth Castro-Coronel, Marco A. Leyva-Vazquez, Roberto Dircio-Maldonado, Julio Ortiz-Ortiz, Daniel Hernandez-Sotelo
Summary: This study analyzed the methylation of 8 genes involved in maintaining cell normality and found that high CIMP is significantly associated with the risk of HSIL and CC.
CLINICAL EPIGENETICS
(2022)
Article
Gastroenterology & Hepatology
Rossella Tricarico, Jozef Madzo, Gabrielle Scher, Maya Cohen, Jaroslav Jelinek, Shinji Maegawa, Rajeswari Nagarathinam, Carly Scher, Wen-Chi Chang, Emmanuelle Nicolas, Michael Slifker, Yan Zhou, Karthik Devarajan, Kathy Q. Cai, Tim Kwok, Pamela Nakajima, Jinfei Xu, Pietro Mancuso, Valentina Doneddu, Luigi Bagella, Riley Williams, Siddharth Balachandran, Nicholas Maskalenko, Kerry Campbell, Xueying Ma, Israel Canadas, Julen Viana-Errasti, Victor Moreno, Laura Valle, Sergei Grivennikov, Iuliia Peshkova, Natalia Kurilenko, Aleksandra Mazitova, Ekaterina Koltsova, Hayan Lee, Martin Walsh, Reuben Duttweiler, Johnathan R. Whetstine, Timothy J. Yen, Jean-Pierre Issa, Alfonso Bellacosa
Summary: Aberrant DNA methylation is common in colorectal cancer (CRC), but the underlying mechanisms and pathological consequences are not well understood. In this study, disruption of the Tet1 and/or Tdg genes in mice resulted in increased size and invasive features of colonic adenomas. Furthermore, Tet1 and Tdg mutations led to global DNA hypomethylation and CpG island hypermethylation in colonic adenomas. The mutations also upregulated inflammatory, immune, and interferon response genes.
Article
Biochemical Research Methods
Josephine Yates, Valentina Boeva
Summary: This study utilized a pan-cancer approach to define and explore CpG island methylator phenotype (CIMP) in 26 cancer types. The results confirmed the existence of CIMP in 19 cancers, showed its association with survival differences in eight cancer types, and identified potential drivers of CIMP. The study also found that CIMP was strongly correlated with tumor microenvironment characteristics.
BRIEFINGS IN BIOINFORMATICS
(2022)
Review
Oncology
Xiaofei Zhang, Wenjun Zhang, Pingan Cao
Summary: As the population ages in China, the incidence of colorectal cancer is on the rise, with CpG island methylator phenotype (CIMP) playing an important role in its development. Recent studies have shown a close relationship between CIMP and specific clinicopathological phenotypes and multiple molecular phenotypes in colorectal cancer. This paper introduces the latest progress on CIMP colorectal cancer in terms of chemotherapeutic drugs, targeted agents, and small molecular methylation inhibitors, aiming to provide potential clinical treatment strategies for personalized and precise treatment of colorectal cancer patients.
FRONTIERS IN ONCOLOGY
(2021)
Review
Biotechnology & Applied Microbiology
Nasrullah, Abrar Hussain, Sagheer Ahmed, Mahmood Rasool, Abdul Jabbar Shah
Summary: DNA methylation is a process of adding methyl groups to the DNA molecule, which can alter the function of DNA. The importance and role of DNA methylation vary across different organisms, with mammals showing a strong relationship between DNA methylation and diseases such as cancer and placental development.
Article
Biochemical Research Methods
Jianxiong Tang, Jianxiao Zou, Mei Fan, Qi Tian, Jiyang Zhang, Shicai Fan
Summary: CaMelia, a CatBoost gradient boosting method, predicts missing methylation states based on locally paired intercellular methylation similarity. It significantly improves imputation performance on real single-cell methylation datasets, helping to discover intercellular differentially methylated loci masked by sparsity in raw data. The results demonstrate that CaMelia preserves cell-cell relationships, enhances cell type identification, and improves subpopulation detection.
Article
Biochemistry & Molecular Biology
Suman Abhishek, Naveen Kumar Nakarakanti, Waghela Deeksha, Eerappa Rajakumara
Summary: UHRF1 SRA can recognize non-mCpG DNA, with contrasting mechanisms for hemi-mCpG and fully-mCpHpG DNA recognition. While the binding affinity for fully-mCpG is weaker, UHRF1 SRA exhibits higher affinity for fully-mCpHpG.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Oncology
Feline O. Voss, Nikki B. Thuijs, Sylvia Duin, Mujde Ozer, Marc van Beurden, Johannes Berkhof, Renske D. M. Steenbergen, Maaike C. G. Bleeker
Summary: This study aimed to validate the accuracy of previously identified DNA methylation markers for detection of high-grade vulvar intraepithelial neoplasia (VIN). The best-performing individual marker was found to be SST, detecting 80% of high-grade VIN cases, with excellent detection of HPV-independent VIN, known to have the highest cancer risk. Selection of a marker panel including ZNF582, SST, and miR124-2 also yielded high accuracy for detection of high-grade VIN.
INTERNATIONAL JOURNAL OF CANCER
(2023)
Article
Cell Biology
Junnan Liang, Tongtong Liu, Jingyu Liao, Lu Zhang, Mi Zhou, Weiqi Xu, Yi He, Guangzhen Cai, Guannan Jin, Jia Song, Ganxun Li, Huifang Liang, Zeyang Ding, Bixiang Zhang
Summary: The study identified a CIMP-related methylation signature specific for CCA (CMSC) that can classify patients into different risk groups and predict patient outcomes. Additionally, a subset of patients with an unfavorable prognosis correlated with CIMP-H was identified. Gene enrichment analysis suggested a potential mechanism of CIMP as a promoter of carcinogenesis by regulating proliferation.
JOURNAL OF CELLULAR PHYSIOLOGY
(2021)
Article
Multidisciplinary Sciences
Sujun Chen, Jessica Petricca, Wenbin Ye, Jiansheng Guan, Yong Zeng, Nicholas Cheng, Linsey Gong, Shu Yi Shen, Junjie T. Hua, Megan Crumbaker, Michael Fraser, Stanley Liu, Scott Bratman, Theodorus van der Kwast, Trevor Pugh, Anthony M. Joshua, Daniel D. De Carvalho, Kim N. Chi, Philip Awadalla, Guoli Ji, Felix Feng, Alexander W. Wyatt, Housheng Hansen He
Summary: The authors used cell-free DNA methylation analysis to demonstrate changes in hypermethylation in metastatic prostate cancer, and its impact on immune features and clinical outcomes. The results showed that the cell-free DNA methylome can capture variations beyond the tumor, and has a high accuracy in predicting disease types.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Pratik Goswami, Martin Bartas, Matej Lexa, Natalia Bohalova, Adriana Volna, Jiri Cerven, Veronika Cervenova, Petr Pecinka, Vladimir Spunda, Miroslav Fojta, Vaclav Brazda
Summary: By analyzing high-frequency mutations of SARS-CoV-2 and their overlay with IR and CpG island loci, this study found that hot-spot mutations of the virus are significantly enriched within these regions. The hypothesis is that hypermethylation of CpG islands may decrease the transcription of viral ORFs and therefore limit the progression of the disease.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Pharmacology & Pharmacy
Ruizheng Sun, Chao Du, Jiaxin Li, Yanhong Zhou, Wei Xiong, Juanjuan Xiang, Jiheng Liu, Zhigang Xiao, Li Fang, Zheng Li
Summary: The study identified potential risk biomarkers and predictive biomarkers associated with platinum-based chemotherapy through analyzing the methylation patterns of 618 patients, as well as demonstrating the existence of a methylation-transcription axis in the complex biological mechanism of platinum resistance in various cancers. Six differentially methylated positions (DMPs) and four associated genes were proposed as promising epigenetic biomarkers for guiding clinical treatment selection.
FRONTIERS IN PHARMACOLOGY
(2021)
Editorial Material
Genetics & Heredity
Bernhard Horsthemke, Adrian Bird
Summary: The inheritance of acquired traits in mammals is a controversial topic. Recent research suggests that DNA methylation patterns can be transmitted across generations even after removal of foreign DNA. However, there are interpretational issues and alternative explanations to consider.
EPIGENETICS & CHROMATIN
(2023)
Article
Biology
Ayala Tovy, Jaime M. Reyes, Linda Zhang, Yung-Hsin Huang, Carina Rosas, Alexes C. Daquinag, Anna Guzman, Raghav Ramabadran, Chun-Wei Chen, Tianpeng Gu, Sinjini Gupta, Laura Ortinau, Dongsu Park, Aaron R. Cox, Rachel E. Rau, Sean M. Hartig, Mikhail G. Kolonin, Margaret A. Goodell
Summary: DNMT3A plays a crucial role in the differentiation of embryonic and hematopoietic stem cells. Heterozygous mutations in DNMT3A lead to Tatton-Brown-Rahman syndrome, characterized by obesity and excessive height. This study shows that DNMT3A affects feeding behavior and adipocyte progenitor differentiation, contributing to the development of inflammatory obesity.
Article
Genetics & Heredity
L. Sadeghi-Amiri, A. Barzegar, N. Nikbakhsh-Zati, P. Mehraban
Summary: This study analyzed the methylation status of CpG sites within the 5' regulatory region of the CYP1A1 gene and its association with gene expression in gastric cancer. The results indicated that variably methylated CpG sites near the XRE10 regulatory region of CYP1A1 are associated with gene upregulation and likely involved in gastric cancer incidence and metastasis. Methylation analysis of CpG sites around the XRE10 motif in the CYP1A1 promoter may serve as a potential marker for evaluating individual susceptibility to gastric cancer.
Article
Multidisciplinary Sciences
Yunbeom Lee, Ji Ae Lee, Hye Eun Park, Hyojun Han, Yuhnam Kim, Jeong Mo Bae, Jung Ho Kim, Nam-Yun Cho, Hwang-Phill Kim, Tae-You Kim, Gyeong Hoon Kang
Summary: A new computational method and microsatellite marker panels were developed to assess and detect microsatellite instability in CRC, which does not require paired normal tissues. It showed good sensitivity and specificity for different types of samples.
Article
Medical Informatics
Yunsook Kang, Yoo Jung Kim, Seongkeun Park, Gun Ro, Choyeon Hong, Hyungjoon Jang, Sungduk Cho, Won Jae Hong, Dong Un Kang, Jonghoon Chun, Kyoungbun Lee, Gyeong Hoon Kang, Kyoung Chul Moon, Gheeyoung Choe, Kyu Sang Lee, Jeong Hwan Park, Won-Ki Jeong, Se Young Chun, Peom Park, Jinwook Choi
Summary: The study focused on developing a platform for AI researchers to access quality medical data in the form of digital pathology images. Over 3000 pathological slides from five organs were used, with tumor areas annotated by pathologists and AI teams, leading to the development of a web-based data sharing platform with pre-processing algorithms for easy image loading. International data sharing platforms need to consider patient consent due to privacy regulations, but overall, this study shows the platform can meet the demand for quality data among AI developers.
BMC MEDICAL INFORMATICS AND DECISION MAKING
(2021)
Article
Radiology, Nuclear Medicine & Medical Imaging
Hyunjoo Song, Seungjae Lee, Ji Hoon Park, Hae Young Kim, Hooney Daniel Min, Jong-June Jeon, Kyoung Ho Lee
Summary: This study aimed to investigate whether patient triaging with scoring systems can reduce CT use for adolescents and young adults suspected of having appendicitis. The results showed that using clinical scoring systems for selective CT use led to a considerable loss of diagnostic accuracy, with no reduction in CT use when targeting specific sensitivity and specificity values.
Article
Gastroenterology & Hepatology
Hye-Yeong Jin, Seung-Yeon Yoo, Ji-Ae Lee, Xianyu Wen, Younghoon Kim, Hye Eun Park, Yoonjin Kwak, Nam-Yun Cho, Jeong Mo Bae, Jung Ho Kim, Hye Seung Lee, Gyeong Hoon Kang
Summary: Tumor stroma and tumor-infiltrating lymphocytes (TILs) have different effects on the prognosis of colorectal cancer (CRC) patients. The combinatory statuses of tumor-stromal percentage (TSP) and TILs can provide powerful prognostic information for CRCs.
JOURNAL OF GASTROENTEROLOGY AND HEPATOLOGY
(2022)
Article
Pathology
Ji Ae Lee, Mi-Kyoung Seo, Seung-Yeon Yoo, Nam-Yun Cho, Yoonjin Kwak, Kyoungbun Lee, Jung Ho Kim, Gyeong Hoon Kang
Summary: Decreased expression of CDX2, SATB2, and KRT20 in colorectal carcinomas (CRCs) is commonly associated with microsatellite instability-high (MSI-H) and CpG island methylator phenotype-high (CIMP-H), but the specific features associated with the loss of each marker differ in CRCs.
Article
Multidisciplinary Sciences
Xianyu Wen, Hye-Yeong Jin, Meihui Li, Younghoon Kim, Nam-Yun Cho, Yoonjin Kwak, Jeong Mo Bae, Hye Seung Lee, Gyeong Hoon Kang
Summary: Through genome-wide methylation profiling, the methylation markers NCOR2, PARK2, and ZSCAN12 were found to be closely associated with the density of CD3-positive and CD8-positive cells and could serve as biomarkers for predicting the prognosis of patients with gastric carcinoma.
SCIENTIFIC REPORTS
(2022)
Article
Gastroenterology & Hepatology
Sang Sik Cho, Ji Won Park, Gyeong Hoon Kang, Jung Ho Kim, Jeong Mo Bae, Sae-Won Han, Tae-You Kim, Min Jung Kim, Seung-Bum Ryoo, Seung-Yong Jeong, Kyu Joo Park
Summary: This study aimed to determine whether the location of lymphatic invasion, vascular invasion, and perineural invasion could affect the survival of patients with stage II colon cancer. The results showed that extramural invasion was associated with a worse prognosis, while intramural invasion was not. Therefore, pathologic reports about the location of invasion may be helpful for predicting prognosis and determining the need for adjuvant chemotherapy in stage II colon cancers.
DISEASES OF THE COLON & RECTUM
(2023)
Article
Genetics & Heredity
Jeong Mo Bae, Ji Young Ahn, Heonyi Lee, Hoon Jang, Hyojun Han, Jaehwan Jeong, Nam-Yun Cho, Kwangsoo Kim, Gyeong Hoon Kang
Summary: DNA methylation profiling is a promising method for predicting the tissue of origin in cancer patients. By extracting genomic DNA from formalin-fixed tissues, a targeted bisulfite sequencing panel based on hybrid capture has been developed and found to be useful in clinical practice.
Review
Pathology
Younghoon Kim, Nam Yun Cho, Gyeong Hoon Kang
Summary: The association between F. nucleatum and prognosis or clinicopathological features in colorectal cancer varies among studies and may be influenced by the type of biospecimen.
JOURNAL OF PATHOLOGY AND TRANSLATIONAL MEDICINE
(2022)
Article
Oncology
Jeong-ki Kim, Ye-Young Rhee, Jeong Mo Bae, Jung Ho Kim, Seong-Joon Koh, Hyun Jung Lee, Jong Pil Im, Min Jung Kim, Seung-Bum Ryoo, Seung-Yong Jeong, Kyu Joo Park, Ji Won Park, Gyeong Hoon Kang
Summary: The optimal tumor budding cut-off number for estimating LN metastasis in submucosal CRC was determined and a composite scoring system (CSS) was developed.
Article
Pathology
Minsun Jung, Ji Ae Lee, Seung-Yeon Yoo, Jeong Mo Bae, Gyeong Hoon Kang, Jung Ho Kim
Summary: This study investigates the spatial heterogeneity of tumor-infiltrating lymphocytes (TILs) in colorectal carcinomas (CRCs) and identifies its prognostic and immunologic significance. It demonstrates that TILs density and spatial distribution have a significant impact on prognosis in CRCs. TIL-low CRCs can be divided into two subgroups with distinct prognosis and immunologic characteristics based on the spatial heterogeneity of TILs. These findings suggest that the intratumoral spatial heterogeneity of TILs can be a key element for clinically relevant immunologic subtyping of tumors.
Article
Multidisciplinary Sciences
Mingyu Lee, Yi-Sook Kim, Suha Lim, Seung-Hyun Shin, Iljin Kim, Jiyoung Kim, Min Choi, Jung Ho Kim, Seong-Joon Koh, Jong-Wan Park, Hyun-Woo Shin
Summary: NF-kappa B activation contributes to the development of colitis-associated colorectal cancer. The authors found that the NF-kappa B subunit p65 stabilizes ITF2, which suppresses NF-kappa B downstream genes and inhibits cancer progression. Increased expression of ITF2 and p65 was observed under inflammatory conditions, and they showed a positive correlation. p65 overexpression stabilizes ITF2 protein levels by interfering with the binding of Parkin to ITF2. Intestinal epithelial-specific deletion of ITF2 led to increased tumorigenesis of colitis-associated cancer. Lost ITF2 expression in carcinoma tissues and increased p65 expression in dysplastic and carcinoma regions were observed in colitis-associated cancer patients. These findings suggest that ITF2 plays a critical role in repressing colitis-associated cancer progression and could be a potential target for inflammatory diseases, including colitis-associated cancer.
NATURE COMMUNICATIONS
(2023)
Article
Oncology
Younghoon Kim, Gyeong Hoon Kang, Haeryoung Kim
Summary: A systematic review and meta-analysis showed that the presence of heterologous component is associated with worse overall survival in gynecologic carcinosarcoma, but not with recurrence-free survival and disease-free survival.
JOURNAL OF GYNECOLOGIC ONCOLOGY
(2023)
