Article
Oncology
Kala Visvanathan, Leslie Cope, Mary Jo Fackler, Michael Considine, Lori Sokoll, Lisa A. Carey, Andres Forero-Torres, James N. Ingle, Nancy U. Lin, Rita Nanda, Anna Maria Storniolo, Suzana Tulac, Neesha Venkatesan, Natalie C. Wu, Sudhakar Marla, Scott Campbell, Michael Bates, Christopher B. Umbricht, Antonio C. Wolff, Saraswati Sukumar
Summary: This study evaluated the clinical utility of a novel liquid biopsy-breast cancer methylation (LBx-BCM) prototype assay for early assessment of disease progression in women with metastatic breast cancer (MBC). The results showed that high levels of cumulative methylation (CM) were associated with shorter median progression-free survival (PFS) and overall survival (OS) at week 4. The CM levels at week 4 could be used to predict disease progression as early as 3 months after initiating a new treatment.
CLINICAL CANCER RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Saioa Mendaza, David Guerrero-Setas, Inaki Monreal-Santesteban, Ane Ulazia-Garmendia, Alicia Cordoba Iturriagagoitia, Susana De la Cruz, Esperanza Martin-Sanchez
Summary: A novel DNA methylation signature with potential predictive value for TNBC diagnosis has been discovered. This signature was validated using various samples, confirming its effectiveness in TNBC and BC samples.
Article
Oncology
Rong-Qiang Yuan, Hui Zhao, Yan Wang, Kai Song, Jia Yang, Wei He, Da-Zhuang Miao, Qi Wang, Yun-He Jia
Summary: A minimally invasive blood-based test for the detection of precancerous lesions and early-stage CRC has been developed with high accuracy. The proposed 3-gene methylation signature shows superior performance and has the potential for clinical application.
AMERICAN JOURNAL OF CANCER RESEARCH
(2022)
Article
Oncology
Rong-Qiang Yuan, Hui Zhao, Yan Wang, Kai Song, Jia Yang, Wei He, Da-Zhuang Miao, Qi Wang, Yun-He Jia
Summary: This study developed a minimally invasive blood-based test for detection of precancerous lesions and early-stage colorectal cancer (CRC). By analyzing methylation data, a 3-gene methylation signature model with high accuracy for CRC diagnosis was established. The model demonstrated superior performance in public databases and blood samples, showing potential for clinical application in improving early diagnosis of CRC.
AMERICAN JOURNAL OF CANCER RESEARCH
(2022)
Article
Biochemical Research Methods
Michela Carlotta Massi, Lorenzo Dominoni, Francesca Ieva, Giovanni Fiorito
Summary: This study aims to identify blood DNA methylation (DNAm) profiles associated with Time To Diagnosis (TTD) in cancer biomarker discovery. A deep learning-based approach is developed to assess the relevance of individual CpG Islands in determining TTD and model their combined effect in a survival analysis scenario. This approach effectively deals with the complexities arising from epidemiological studies and demonstrates better performance in identifying biologically relevant pathways.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Thangarajan Rajkumar, Sathyanarayanan Amritha, Veluswami Sridevi, Gopisetty Gopal, Kesavan Sabitha, Sundersingh Shirley, Rajaraman Swaminathan
Summary: Breast cancer is the most common malignancy in women globally. The development of a reliable plasma biomarker panel could provide a non-invasive and cost-effective method for population-based screening of the disease. This study identified several candidate protein markers and epigenetic markers for breast cancer diagnosis and validated their effectiveness in differentiating breast cancer from benign diseases and healthy individuals. A combination of protein markers demonstrated moderate sensitivity and specificity, while the methylation status of SOSTDC1, DACT2, and WIF1 showed high sensitivity and specificity in distinguishing breast cancer.
SCIENTIFIC REPORTS
(2022)
Review
Pathology
Antonios Papanicolau-Sengos, Kenneth Aldape
Summary: Histomorphology and DNA methylation profiling are both important diagnostic methods in cancer pathology. While histomorphology is already well-established, DNA methylation profiling serves as an adjunct tool to improve the accuracy of pathological diagnosis. Besides identifying new entities and consolidating morphologically disparate cancers, DNA methylation profiling holds great promise for non-invasive cancer detection and classification.
ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE
(2022)
Review
Oncology
Simone Karlsson Terp, Malene Pontoppidan Stoico, Karen Dybkaer, Inge Sokilde Pedersen
Summary: Liquid biopsy using circulating tumor DNA (ctDNA) shows promise as a minimally invasive approach for early diagnosis of ovarian cancer. DNA methylation biomarkers detected in ctDNA have the potential to distinguish ovarian cancer patients from those with benign conditions or healthy individuals.
CLINICAL EPIGENETICS
(2023)
Article
Oncology
Maosen Dou, Dan Li, Mengchan Zhu, Wei Guo, Changhong Miao, Min Li, Ying Xue, Ruiping He, Nan Jiang, Di Ge, Qin Hu, Yue Shao, Yingyong Hou, Xuefei Wang, Xingxu Huang, Tianshu Liu, Qi Wang, Yuehong Wang, Jiayuan Sun, Weibing Wang, Yuanlin Song, Jie Hu, Qihong Huang
Summary: Non-diagnostic findings are commonly found in transbronchial lung biopsy (TBLB) and endobronchial ultrasound-guided transbronchial lung biopsy (EBUS-TBLB). To improve lung cancer detection, a study used an 850 K methylation chip to identify methylation sites that can differentiate malignant from benign lung nodules. The findings showed that a combination of HOXA7, SHOX2, and SCT methylation analysis was most effective in diagnosing lung cancer using bronchial washing and brushing samples.
INTERNATIONAL JOURNAL OF CANCER
(2023)
Article
Medicine, General & Internal
Luyao Zhao, Muran Li, Shiwu Zhang, Yandi Liu
Summary: This study evaluated the potential performance of plasma SEPT9 methylation as a noninvasive biomarker for the diagnosis of gastric cancer. The results suggest that mSEPT9 may serve as a useful and noninvasive biomarker for the diagnosis of gastric cancer.
JOURNAL OF CLINICAL MEDICINE
(2022)
Review
Chemistry, Medicinal
Shoghag Panjarian, Jean-Pierre J. Issa
Summary: Triple-negative breast cancers (TNBCs) are highly heterogeneous and molecularly diverse, with a distinct DNA methylation profile characterized by hypomethylation and lower gains of methylations compared to other subtypes. The balance between DNA methylases (DNMTs) and DNA demethylases (TETs) plays a crucial role in regulating DNA methylation in TNBCs.
Article
Medicine, Research & Experimental
Yihan Wang, Yan Zhang, Yan Huang, Chuangeng Chen, Xingda Zhang, Ying Xing, Yue Gu, Mengyan Zhang, Li Cai, Shouping Xu, Baoqing Sun
Summary: In breast cancer, high intratumor DNA methylation heterogeneity may lead to drug resistance, metastasis, and poor prognosis. The analysis of differential epialleles between tumor core and periphery regions reveals a correlation between intratumor methylation heterogeneity and hypoxic microenvironment, which could provide guidance for developing effective treatment schemes for breast cancer patients.
Review
Biochemistry & Molecular Biology
Lingyuan Ma, Chenyu Li, Hanlin Yin, Jiashu Huang, Shenghao Yu, Jin Zhao, Yongxu Tang, Min Yu, Jie Lin, Lei Ding, Qinghua Cui
Summary: Breast cancer is the most common cancer worldwide, and its treatment methods include radiotherapy, chemotherapy, targeted therapy, and surgery. The molecular subtype of breast cancer determines the specific treatment measures, making the exploration of molecular mechanisms and therapeutic targets essential. Abnormal methylation of tumor suppressor genes by DNMTs is associated with poor prognosis in breast cancer. MiRNAs, as non-coding RNAs, play crucial roles in breast cancer and their aberrant methylation can lead to drug resistance. Therefore, regulating miRNA methylation could be a potential therapeutic target in breast cancer.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemical Research Methods
Isabelle Bichindaritz, Guanghui Liu, Christopher Bartlett
Summary: The study proposes an adaptive multi-task learning method for survival prediction of breast cancer patients using multi-modal learning, achieving more effective results compared to existing approaches. By combining different gene features, reducing dimensions, and introducing auxiliary loss, an ordinal Cox hazards model is built to predict patients' survival risk.
Review
Biochemistry & Molecular Biology
Fabio Coppede, Utsa Bhaduri, Andrea Stoccoro, Vanessa Nicoli, Eleonora Di Venere, Giuseppe Merla
Summary: The central objective of combining discovery science with biomedical applications is to benefit patients and reduce the global disease burden. The conversion of DNA methylation (DNAm) from a biological process to a diagnostic tool is a prime example of this transformation, which took nearly a century. In recent years, DNAm studies have been standardized in clinical applications more than ever before, offering great potential for diagnosing various diseases associated with epigenetic alterations. DNAm detection plays a role in noninvasive prenatal testing and indicates prenatal risk factors in very preterm infants. In the field of cancer, liquid biopsy-based DNAm profiling provides valuable epigenetic biomarkers for early-stage diagnosis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Menha Swellam, Rasha F. K. Zahran, Hossam Abo El-Sadat Taha, Nashwa El-Khazragy, Camelia Abdel-Malak
ARCHIVES OF PHYSIOLOGY AND BIOCHEMISTRY
(2019)
Article
Biochemistry & Molecular Biology
Menha Swellam, Magda Sayed Mahmoud, Maha Hashim, Naglaa M. Hassan, Mohamed Emam Sobeih, Amira M. Nageeb
JOURNAL OF CELLULAR BIOCHEMISTRY
(2019)
Article
Biochemistry & Molecular Biology
Nashwa El-Khazragy, Mohamed Ahmed Noshi, Camelia Abdel-Malak, Rasha F. Zahran, Menha Swellam
JOURNAL OF CELLULAR BIOCHEMISTRY
(2019)
Article
Biochemistry & Molecular Biology
Nashwa El-Khazragy, Mona M. Khalifa, Ahmed M. Salem, Menha Swellam, Marwa Hegazy
JOURNAL OF CELLULAR BIOCHEMISTRY
(2019)
Article
Biochemistry & Molecular Biology
Menha Swellam, Amal Ramadan, Enas A. El-Hussieny, Noha M. Bakr, Naglaa M. Hassan, Mohamed Emam Sobeih, Lobna R. EzzElArab
JOURNAL OF CELLULAR BIOCHEMISTRY
(2019)
Article
Biochemistry & Molecular Biology
Menha Swellarn, Rasha F. K. Zahran, Samar Ayman Ghonem, Camelia Abdel-Malak
Summary: miR 27a shows potential as a diagnostic marker for breast cancer, with its expression being more effective than tumor markers, especially in early detection of high-risk breast cancer patients.
ARCHIVES OF PHYSIOLOGY AND BIOCHEMISTRY
(2021)
Article
Oncology
Menha Swellam, Lobna Ezz El Arab, Amr S. Al-Posttany, Samy B. Said
JOURNAL OF NEURO-ONCOLOGY
(2019)
Article
Biochemistry & Molecular Biology
Amal Ramadan, Maha Hashim, Naglaa M. Hassan, Menha Swellam
Summary: This study investigated the role of miR-335 in breast cancer and evaluated the feasibility and clinical utility of MMP2 and MMP9 as biomarkers for early detection of breast cancer. The results showed down-regulated expression of miR-335 and up-regulated expression of MMP2 and MMP9 in breast cancer, suggesting their potential as diagnostic markers for the early detection of breast cancer.
ARCHIVES OF PHYSIOLOGY AND BIOCHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Amira M. Nageeb, Magdy M. Mohamed, Lobna R. Ezz El Arab, Mohamed K. Khalifa, Menha Swellam
Summary: In this study, NGS was used to detect BRCA1 and BRCA2 germ line mutations in GBM patients. The results showed previously reported mutations in BRCA1 and new mutations in BRCA2, suggesting their potential diagnostic and prognostic roles in GBM.
ARCHIVES OF PHYSIOLOGY AND BIOCHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Elham Ali Ahmed, Sohir A. Abd El-Basit, Mona A. Mohamed, Menha Swellam
Summary: Expression levels of miR-29a and miR-335 have significant potential as biomarkers in breast cancer diagnosis.
ARCHIVES OF PHYSIOLOGY AND BIOCHEMISTRY
(2022)
Article
Neurosciences
Ahmed Kamal, Menha Swellam, Nevin M. Shalaby, Marwa K. Darwish, Eslam M. El-Nahrery
Summary: Cognitive impairment is a common feature of multiple sclerosis (MS), and the dysregulation of synaptic plasticity is a direct cause. Long non-coding RNAs (lncRNAs) may play a role in synaptic plasticity, but their role in MS-related cognitive impairment is not fully understood. This study examined the expression of two specific lncRNAs, BACE1-AS and BC200, in MS patients with and without cognitive impairment. Both lncRNAs were overexpressed in both patient groups, with higher levels in the cognitively impaired group. There was a strong positive correlation between the expression levels of these lncRNAs. The findings suggest that these lncRNAs may have a significant impact on the pathogenesis of MS and cognitive function.
Article
Biotechnology & Applied Microbiology
Amal Ramadan, Maha Hashim, Amr Abouzid, Menha Swellam
Summary: The study evaluated the clinical impact of PTEN methylation as a prognostic marker in breast cancer, showing PTEN methylation to be a good discriminator of cancer patients with high sensitivity and specificity. The study found that PTEN methylation levels were significantly higher in breast cancer patients compared to benign and control groups, and were associated with poor progression-free and overall survival.
JOURNAL OF GENETIC ENGINEERING AND BIOTECHNOLOGY
(2021)
