Article
Gastroenterology & Hepatology
Si-Yu He, Ying-Chun Li, Yong Wang, Hai-Lin Peng, Cheng-Lin Zhou, Chuan-Meng Zhang, Sheng-Lan Chen, Jian-Feng Yin, Mei Lin
Summary: This study used NGS to sequence stool DNA from CRC patients, screened specific genes or gene combinations suitable for diagnosis and prognostic prediction of CRC, and comprehensively evaluated their significance in diagnosing CRC and predicting patients' prognosis. The results of the study showed that TP53 and KRAS genes can be used for CRC screening, diagnosis, and prognostic prediction, and combined testing can improve the detection rate of CRC. Furthermore, new mutation sites were found that require further research to determine their clinical significance.
WORLD JOURNAL OF GASTROENTEROLOGY
(2022)
Article
Oncology
Chun-Ting Hu, Jing-Long Wang, Ting Hou, Zhao-Wen Yan, Li-Dong Zu, Guo-Hui Fu, Wei-Wei Shen
Summary: This study demonstrates discrepancies in the genomic profiles between primary tumors and metastases, especially between liver and lung metastases. The coincidence rate of primary tumors and metastases is 51.8%, with lung metastases showing a significantly higher rate than liver metastases. Furthermore, the number of specific mutations differs between primary tumors, liver metastases, and lung metastases, indicating a possible polyclonal seeding mechanism for liver metastases.
TECHNOLOGY IN CANCER RESEARCH & TREATMENT
(2023)
Article
Oncology
Hongsen Li, Liu Gong, Huanqing Cheng, Huina Wang, Xiaochen Zhang, Chuangzhou Rao, Zhangfa Song, Da Wang, Haizhou Lou, Feng Lou, Shanbo Cao, Hongming Pan, Yong Fang
Summary: This study investigated the molecular characterization of colorectal cancer with situs inversus totalis (SCRC), a rare condition. The results showed significant differences in mutated genes and mutational profiles between SCRC and non-SCRC patients. These findings contribute to personalized therapy and improved clinical management of SCRC patients.
FRONTIERS IN ONCOLOGY
(2022)
Article
Oncology
Tonje Bjornetro, Paula A. A. Bousquet, Kathrine Roe Redalen, Anne-Marie Siebke Troseid, Torben Luders, Espen Stang, Adriana M. M. Sanabria, Christin Johansen, Anniken Jorlo Fuglestad, Christian Kersten, Sebastian Meltzer, Anne Hansen Ree
Summary: Recent studies have found that the entire mitochondrial genome can be secreted in extracellular vesicles (EVs), but the biological characteristics of this cell-free mitochondrial DNA (mtDNA) are not well understood. In this study, the mtDNA derived from plasma EVs of colorectal cancer patients was compared to that of whole blood, peripheral blood mononuclear cells, and tumor tissue. The results showed that EV mtDNA had more variants and low-level heteroplasmy compared to whole blood mtDNA. The EV mtDNA variants were mainly located in the coding regions and had a higher proportion of missense mutations compared to whole blood and tumor tissue.
Article
Oncology
Ta-Chung Chao, Yi-Fang Tsai, Chun-Yu Liu, Pei-Ju Lien, Yen-Shu Lin, Chin-Jung Feng, Yen-Jen Chen, Jiun-I. Lai, Chih-Yi Hsu, Jiun Jen Lynn, Chi-Cheng Huang, Ling-Ming Tseng
Summary: This study examined the frequency of PIK3CA mutations in Taiwanese breast cancer patients. It found that PIK3CA mutations were common in these patients, and early detection of this mutation may impact treatment decisions and improve outcomes.
FRONTIERS IN ONCOLOGY
(2023)
Article
Respiratory System
Ya-Sian Chang, Siang-Jyun Tu, Yu-Chia Chen, Ting-Yuan Liu, Ya-Ting Lee, Ju-Chen Yen, Hsin-Yuan Fang, Jan-Gowth Chang
Summary: This study identified 19 known driver mutations and new variants in Taiwanese patients with non-small cell lung cancer. EGFR mutations were found at a higher frequency compared to Caucasians, while KRAS and TP53 mutations were less common. All ClinVar pathogenic variants were trunk mutations present in the tumor regions.
RESPIRATORY RESEARCH
(2021)
Article
Oncology
Chul Seung Lee, Hoon Seok Kim, Jeoffrey Schageman, In Kyu Lee, Myungshin Kim, Yonggoo Kim
Summary: Circulating tumor DNA (ctDNA) is a minimally invasive biomarker that can be analyzed using next-generation sequencing (NGS) to evaluate its clinical and analytical performance in colorectal cancer (CRC) patients. Postoperative ctDNA detection can serve as a valuable marker for identifying the risk of recurrence or persistent tumor lesions in patients with CRC.
Article
Biochemistry & Molecular Biology
Liu Yang, Fei Xie, Chang Liu, Jin Zhao, Taobo Hu, Jinbo Wu, Xiaotao Zhao, Shu Wang
Summary: This study provides insights into the distribution of deleterious germline variants among Chinese breast cancer patients and identifies clinicopathological predictors associated with these variants.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Oncology
Xuan Pei, Libing Xiang, Wei Chen, Wei Jiang, Lina Yin, Xuxia Shen, Xiaoyan Zhou, Huijuan Yang
Summary: Small cell neuroendocrine carcinoma of the cervix (SCNEC) is specifically associated with HPV 18 infection and characterized by a high genetic mutation rate, with mutations in genes related to the p53 pathway potentially affecting prognosis. Some patients harbor mutations in homogeneous recombination repair (HRR) genes, providing therapeutic targets. The study suggests that targeted therapies against certain mutated genes may have potential efficacy in SCNEC patients.
GYNECOLOGIC ONCOLOGY
(2021)
Article
Oncology
Juan A. Santamaria-Barria, Chikako Matsuba, Adam Khader, Anthony J. Scholar, Mary Garland-Kledzik, Trevan D. Fischer, Richard Essner, Matthew P. Salomon, Joshua M. V. Mammen, Melanie Goldfarb
Summary: This study analyzed melanoma samples and identified age-related mutational differences, as well as potential targetable mutations for personalized therapies.
JOURNAL OF SURGICAL ONCOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Paolo Rosa, Elena De Falco, Luca Pacini, Amedeo Piazza, Paolo Ciraci, Luca Ricciardi, Francesco Fiorentino, Sokol Trungu, Massimo Miscusi, Antonino Raco, Antonella Calogero
Summary: This study investigated the feasibility of analyzing the genomic profile of grade IV glioblastoma patients using circulating extracellular vesicles (EVs). The findings revealed lower DNA content in EVs of glioblastoma patients compared to controls, and consistent mutations in the NF1 gene. These results support the clinical utility of EVs as a tool for personalized medicine in glioblastoma.
Letter
Oncology
Steven Olsen, Yoshiaki Nakamura
Summary: A comprehensive genomic profiling (CGP) using plasma-based next-generation sequencing was conducted in a real-world database of metastatic colorectal cancer (mCRC) in the United States. The study revealed potentially actionable genomic profiles for approximately one-third of the patients, and around 60% of all tested patients received treatment consistent with the CGP results in each line of treatment. These findings suggest the potential role of CGP prior to multiple lines of mCRC treatment.
Review
Oncology
Salma Abbes, Simone Baldi, Hayet Sellami, Amedeo Amedei, Leila Keskes
Summary: Colorectal cancer (CRC) is the third most common malignancy and second most deadly cancer worldwide, with a higher incidence in developed countries. It is a heterogeneous genomic disease with various alterations contributing to its development. Previous screening efforts for CRC have been limited by performance issues and low penetrance of standard screening tools, but the advent of next-generation sequencing (NGS) has revolutionized the identification of novel genomic CRC characteristics and understanding of its carcinogenesis. This review focuses on the diagnostic tools used for CRC screening, with an emphasis on recent NGS approaches and their role in identifying clinically actionable targets for personalized medicine.
WORLD JOURNAL OF GASTROINTESTINAL ONCOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Thais Maloberti, Antonio De Leo, Sara Coluccelli, Viviana Sanza, Elisa Gruppioni, Annalisa Altimari, Stefano Zagnoni, Francesca Giunchi, Francesco Vasuri, Michelangelo Fiorentino, Veronica Mollica, Simona Ferrari, Sara Miccoli, Michela Visani, Daniela Turchetti, Francesco Massari, Giovanni Tallini, Dario de Biase
Summary: Despite advances in therapy, metastatic CRPC remains lethal. This study aimed to verify the effectiveness of a panel in analyzing mCRPC and mutations in BRCA1/BRCA2 and HRR genes. 50 mCRPC cases were analyzed using a multi-gene next-generation sequencing panel, and mutations were found in 46.0% of cases, with BRCA2 being the most commonly mutated gene. The panel and clinical algorithm are now used for managing mCRPC patients.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Oncology
Youngjun Park, Dominik Heider, Anne-Christin Hauschild
Summary: In recent years, advancements in next-generation sequencing and artificial intelligence have led to the development of various algorithms and applications. Integrating systems biology and machine learning has been crucial in addressing challenges posed by big data. Machine learning algorithms and network-based models play a key role in analyzing NGS data effectively.
Article
Oncology
Mayank Jauhri, Akanksha Bhatnagar, Satish Gupta, Manasa Bp, Sachin Minhas, Yogender Shokeen, Shyam Aggarwal
Article
Multidisciplinary Sciences
Mariah Beaver, Akanksha Bhatnagar, Priyalakshmi Panikker, Haolin Zhang, Renee Snook, Visha Parmar, Gayathri Vijayakumar, Niteesha Betini, Sunya Akhter, Felice Elefant
SCIENTIFIC REPORTS
(2020)
Article
Neurosciences
Haolin Zhang, Bhanu Chandra Karisetty, Akanksha Bhatnagar, Ellen M. Armour, Mariah Beaver, Tiffany V. Roach, Sina Mortazavi, Shreya Mandloi, Felice Elefant
MOLECULAR AND CELLULAR NEUROSCIENCE
(2020)
Article
Biochemistry & Molecular Biology
Mariah Beaver, Bhanu Chandra Karisetty, Haolin Zhang, Akanksha Bhatnagar, Ellen Armour, Visha Parmar, Reshma Brown, Merry Xiang, Felice Elefant
Summary: The study in Drosophila brains revealed that disruptions in gene control in Alzheimer's Disease are predominantly seen in neuronal genes, with Tip60 HAT and HDAC2 playing a key role in this process. Additionally, transcription factor binding sites near Tip60/HDAC2 co-peaks in neuronal genes may be involved in coenzyme recruitment.
Article
Neurosciences
Akanksha Bhatnagar, Keegan Krick, Bhanu Chandra Karisetty, Ellen M. Armour, Elizabeth A. Heller, Felice Elefant
Summary: The severity of Alzheimer's disease (AD) progression involves complex interactions between genetics, age, and environmental factors regulated by neuroepigenetic mechanisms. This study reveals a new RNA binding function for Tip60 in addition to its known histone acetyltransferase (HAT) function. The study shows that Tip60 interacts with pre-mRNAs from chromatin neural gene targets and this RNA binding function is disrupted in AD models and patient hippocampus. Furthermore, Tip60's RNA targeting modulates splicing decisions, and splicing defects associated with AD pathology may be caused by disruption of Tip60's splicing function.
JOURNAL OF NEUROSCIENCE
(2023)
Article
Behavioral Sciences
Akanksha Bhatnagar, Visha Parmar, Nicholas Barbieri, Frank Bearoff, Felice Elefant, Sandhya Kortagere
Summary: Glutamate excitotoxicity is the direct cause of motor dysfunction and cognitive deficits in Huntington's disease. We have designed three novel EAAT2 activators, which have been proven to significantly improve motor and cognitive impairments in patients with Huntington's disease by promoting glutamate transport and protecting neurons. These results suggest that these novel EAAT2 activators could be promising therapeutic drugs for Huntington's disease.
FRONTIERS IN BEHAVIORAL NEUROSCIENCE
(2023)
Review
Neurosciences
Bhanu Chandra Karisetty, Akanksha Bhatnagar, Ellen M. Armour, Mariah Beaver, Haolin Zhang, Felice Elefant
FRONTIERS IN MOLECULAR NEUROSCIENCE
(2020)