Article
Oncology
Zainab Al-Taie, Mark Hannink, Jonathan Mitchem, Christos Papageorgiou, Chi-Ren Shyu
Summary: Breast cancer (BC) is a leading cause of death for female cancer patients, with triple-negative breast cancer (TNBC) having the lowest survival rate. This study utilized a novel patient stratification and drug repositioning method to identify subgroups of BC patients with common genetic profiles and responses to drugs. By applying this method to TNBC, five druggable subgroups were identified, with potential drugs selected based on targeted mechanisms specific to each subgroup.
Article
Pharmacology & Pharmacy
Yijun Liu, Fuhu Song, Zhi Li, Liang Chen, Ying Xu, Huiyan Sun, Yi Chang
Summary: Precision medicine in cancer treatment is important to provide specific treatment based on patients' genetic characteristics. However, most current research only focuses on drug effects on cell lines and integrating data for patient treatment requires significant effort. Furthermore, the adverse effects of drugs on patients are often neglected. We developed DBPOM, a web server that considers both efficacy and toxicity of drugs, providing a valuable resource for drug development and mechanism studies.
FRONTIERS IN PHARMACOLOGY
(2023)
Article
Cell Biology
Naveen Kumar, Masoom Raza, Seema Sehrawat
Summary: Triple-negative breast cancer is known for its aggressive metastatic behavior to the brain and bone. Drug repositioning plays a vital role in precision medicine, guiding the development of new therapies and drugs.
MOLECULAR AND CELLULAR BIOCHEMISTRY
(2021)
Review
Pharmacology & Pharmacy
Li Feng, Wuyue Yang, Mengdong Ding, Luke Hou, Claudia Gragnoli, Christopher Griffin, Rongling Wu
Summary: Precision medicine relies on understanding the genetic causes of an individual's drug response. The functional graph (FunGraph) theory presented here combines functional mapping and evolutionary game theory to chart comprehensive pharmacogenetic architecture for each patient. FunGraph visualizes and investigates the movement of epistasis in cells and how it relates to patient-specific genetic architecture in response to organismic physiology. The future implementation of FunGraph for precision medicine is discussed.
DRUG DISCOVERY TODAY
(2023)
Article
Cell Biology
Qing Ye, Rebecca A. Raese, Dajie Luo, Juan Feng, Wenjun Xin, Chunlin Dong, Yong Qian, Nancy Lan Guo
Summary: Breast cancer treatment can be improved through the identification of biomarkers for early detection and personalized therapy. A study identified 86 microRNAs that can distinguish breast cancer tumors from normal breast tissues with 90.4% accuracy. It also discovered potential tumor suppressors and oncomiRs, as well as new drug options for treating breast cancer. This study demonstrates the potential of an artificial intelligence pipeline in discovering biomarkers, therapeutic targets, and repositioning drugs for various types of cancer.
Article
Oncology
Ze-Jia Cui, Min Gao, Yuan Quan, Bo-Min Lv, Xin-Yu Tong, Teng-Fei Dai, Xiong-Hui Zhou, Hong-Yu Zhang
Summary: Breast cancer is a common disease with various subtypes, and the precision drug discovery strategy proposed in this study effectively identifies important disease-related genes in individuals and special groups, supporting its efficiency, high reliability, and practical application value in drug discovery.
Review
Biochemistry & Molecular Biology
Charalabos Antonatos, Paschalia Asmenoudi, Mariza Panoutsopoulou, Yiannis Vasilopoulos
Summary: The emergence of high-throughput approaches in personalized medicine has greatly enhanced our understanding of inheritable variation and facilitated the identification of response biomarkers. The utilization of pharmaco-omics data has allowed for the discovery of key molecular biomarkers that can predict treatment response, optimizing therapy and enabling tailored treatment plans.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Medicine, General & Internal
Yinan Xiao, Meiyu Bi, Hongyan Guo, Mo Li
Summary: This review summarizes the recent advances and perspectives in the use of multi-omics technologies in ovarian cancer research, highlighting their potential applications in identifying novel biomarkers and improving clinical assessments.
Review
Biochemistry & Molecular Biology
Sha Zhu, Qifeng Bai, Lanqing Li, Tingyang Xu
Summary: Drug repositioning plays a significant role in drug development and machine learning methods can accelerate this process. This article focuses on the repurposing potential of type 2 diabetes mellitus drugs for various diseases.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Matthew Cannon, James Stevenson, Kathryn Stahl, Rohit Basu, Adam Coffman, Susanna Kiwala, Joshua F. McMichael, Kori Kuzma, Dorian Morrissey, Kelsy Cotto, Elaine R. Mardis, Obi L. Griffith, Malachi Griffith, Alex H. Wagner
Summary: The Drug-Gene Interaction Database is a publicly accessible resource that aggregates genes, drugs, and drug-gene interaction records to support hypothesis generation and discovery. The latest version includes architectural and functional updates to integrate with clinical and drug discovery pipelines.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Oncology
Xiujing He, Xiaowei Liu, Fengli Zuo, Hubing Shi, Jing Jing
Summary: With biotechnological advancements, omics technologies have emerged to access multi-layer information, enabling comprehensive understanding of tumor behavior. Multi-omics analysis requires efficient algorithms to extract insights from exponentially increasing data. The convergence of multi-omics technologies and artificial intelligence has driven the development of cancer precision medicine. This article presents state-of-the-art omics technologies, outlines a roadmap for multi-omics integration using artificial intelligence, and discusses the advances and challenges in this field.
SEMINARS IN CANCER BIOLOGY
(2023)
Article
Clinical Neurology
Yadi Zhou, Jiansong Fang, Lynn M. Bekris, Young Heon Kim, Andrew A. Pieper, James B. Leverenz, Jeffrey Cummings, Feixiong Cheng
Summary: AlzGPS is a comprehensive systems biology tool that integrates multi-omics data and biological networks to identify therapeutic targets for Alzheimer's disease, provide potential treatment information, and establish links between drugs and disease modules. This tool also includes information from over 1000 clinical trials to accelerate therapeutic development for Alzheimer's disease.
ALZHEIMERS RESEARCH & THERAPY
(2021)
Article
Medicine, Research & Experimental
Occam Kelly Graves, Woonghee Kim, Mehmet Ozcan, Sajda Ashraf, Hasan Turkez, Meng Yuan, Cheng Zhang, Adil Mardinoglu, Xiangyu Li
Summary: This study identified potential therapeutic target genes for lung adenocarcinoma and repurposed existing drugs. The effectiveness of these target genes and drugs was validated through in vitro experiments.
BIOMEDICINE & PHARMACOTHERAPY
(2023)
Article
Cell Biology
Shuyi Ji, Li Feng, Zile Fu, Gaohua Wu, Yingcheng Wu, Youpei Lin, Dayun Lu, Yuanli Song, Peng Cui, Zijian Yang, Chen Sang, Guohe Song, Shangli Cai, Yuanchuang Li, Hanqing Lin, Shu Zhang, Xiaoying Wang, Shuangjian Qiu, Xiaoming Zhang, Guoqiang Hua, Junqiang Li, Jian Zhou, Zhi Dai, Xiangdong Wang, Li Ding, Pei Wang, Daming Gao, Bing Zhang, Henry Rodriguez, Jia Fan, Hans Clevers, Hu Zhou, Yidi Sun, Qiang Gao
Summary: We established a patient-derived liver cancer organoid biobank (LICOB) that comprehensively represents the histological and molecular characteristics of various liver cancer types. Through high-throughput drug screening and integrative analysis, we identified molecular features associated with drug responses and predicted potential drug combinations for personalized patient treatment. The synergistic inhibition effect of mTOR inhibitor temsirolimus and the multitargeted tyrosine kinase inhibitor lenvatinib was validated in organoids and patient-derived xenografts models. We also provide a user-friendly web portal to serve the biomedical research community.
SCIENCE TRANSLATIONAL MEDICINE
(2023)
Article
Chemistry, Medicinal
Yi Hua, Xiaowen Dai, Yuan Xu, Guomeng Xing, Haichun Liu, Tao Lu, Yadong Chen, Yanmin Zhang
Summary: Compared with traditional drug discovery, drug repurposing offers a cost-effective and efficient approach. Some drugs may show better effects in different diseases than their original indications. Drug repurposing has proven to be valuable, especially in addressing public health emergencies such as the COVID-19 pandemic.
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
(2022)
Article
Endocrinology & Metabolism
B. Aydin, H. Beklen, K. Y. Arga, F. Bayrakli, B. Turanli
Summary: This study proposes a novel approach for the treatment of non-functioning pituitary neuroendocrine tumors by integrating epigenome and transcriptome data. The construction of a disease-specific network and the identification of hub proteins provide potential targets for drug repositioning. In silico confirmations further validate the potential of the repositioned drugs as therapeutics for the management of NF-PitNETs.
JOURNAL OF ENDOCRINOLOGICAL INVESTIGATION
(2023)
Article
Biochemistry & Molecular Biology
Indu Sinha, Rachel L. Fogle, Gizem Gulfidan, Anne E. Stanley, Vonn Walter, Christopher S. Hollenbeak, Kazim Y. Arga, Raghu Sinha
Summary: Breast cancer is a leading cause of death in women in the US, and current diagnostic methods have high false positivity rates. This study aimed to identify protein markers in saliva and serum for early breast cancer detection. Through rigorous analysis using iTRAQ technique, a total of 591 and 371 differentially expressed proteins were identified in saliva and serum samples, respectively. These proteins were mainly related to exocytosis, secretion, immune response, and signaling pathways. A network biology approach was used to evaluate potential biomarkers for breast cancer diagnosis and prognosis. The findings suggest that saliva and serum samples from the same women can provide a feasible platform for studying responsive proteomic profiles in benign and malignant breast disease.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biology
Elif Kubat Oktem, Ummuhan Demir, Metin Yazar, Kazim Yalcin Arga
Summary: This study examined differentially expressed genes in spinal cord samples from regenerative organisms and nonregenerative organisms. Based on these gene signatures, three small compounds were identified as potential candidates for the treatment of cancer, and they showed anticancer effects in prostate cancer cell cultures. These findings contribute to the evaluation of mechanisms and gene signatures related to cancer and the development of new cancer therapies.
COMPUTATIONAL BIOLOGY AND CHEMISTRY
(2023)
Article
Biotechnology & Applied Microbiology
Muhammed Fatih Kircali, Beste Turanli
Summary: To uncover novel molecular signatures of idiopathic pulmonary fibrosis (IPF), this study established a regulatory network involving messenger RNA (mRNA), micro RNAs (miRNAs), and circular RNAs (circRNA). Through analysis of multiple datasets, differentially expressed genes (DEGs) and miRNAs (DEmiRNA) were identified, and interactions between proteins, mRNA-miRNA, and miRNA-circRNA were constructed. The findings deepen our understanding of IPF mechanisms and offer potential leads for diagnostics and therapeutics research and development.
OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Hulya Gundesli, Medi Kori, Kazim Yalcin Arga
Summary: This study identifies dysregulation of several PLEC isoforms in different cancer types and stages, and highlights PLEC 1d and PLEC 1f as potential biomarkers for early cancer detection. Further functional studies are needed to uncover the role of plectin isoforms in cancer development and guide the development of novel cancer therapeutics.
OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY
(2023)
Letter
Biotechnology & Applied Microbiology
Ceyda Kula, Kazim Yalcin Arga
OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Elif Kubat Oktem, Busra Aydin, Gizem Gulfidan, Kazim Yalcin Arga
Summary: Cancer and arachidonic acid (AA) are closely linked, with AA metabolites regulating several critical functions associated with carcinogenesis. This study analyzed transcriptome data from 12 different cancer types and identified 77 differentially expressed AAP gene signatures and 37 associated metabolites. These findings provide potential therapeutic and diagnostic targets for precision/personalized medicine in oncology.
OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Beste Turanli
Summary: This study aimed to uncover gene expression signatures associated with inflammation and their potential as biomarkers and drug candidates in tumorigenesis. By analyzing gene expression profiles of various cancers, a set of inflammation-associated genes (TIS) consisting of 45 proteins was identified. Several potential drug candidates for drug repurposing and biomarkers related to inflammation were also discovered.
OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Onur Erdogan, Seyma Colakoglu Ozkaya, Can Erzik, Kaya Bilguvar, Kazim Yalcin Arga, Fatih Bayrakli
Summary: Precision/personalized medicine in oncology, particularly in glioblastoma, holds great promise for improving treatment options and outcomes for patients through molecular profiling and personalized reporting.
OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Firat Kurt, Mustafa Agaoglu, Kazim Yalcin Arga
Summary: This study utilized a machine learning approach to precision oncology research in breast cancer and identified a candidate mRNA panel that can diagnose and stratify breast cancer. The ensemble model showed high accuracy and sensitivity in stratifying patients and differentiating breast cancer subtypes from healthy individuals.
OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Nurdan Kelesoglu, Medi Kori, Beste Turanli, Kazim Yalcin Arga, Betul Karademir Yilmaz, Ozlem Ates Duru
Summary: This study utilized a systems medicine and multiomics approach to integrate AML transcriptome data and reporter biomolecules at multiple levels. New multiomics molecular signatures related to AML were identified, and PTPRG was found to have prognostic potential.
OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY
(2022)
Letter
Biotechnology & Applied Microbiology
Betul Karademir Yilmaz, Kazim Yalcin Arga
OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Medi Kori, Defne Cig, Kazim Yalcin Arga, Ceyda Kasavi
Summary: Cardiovascular disease is the leading cause of death in developed countries, with abdominal aortic aneurysm and aortic occlusive disease being particularly important due to high mortality rates in the elderly. A systematic analysis of genome-wide expression data revealed molecular mechanisms such as alterations in lipid metabolism and amino acid metabolism, as well as involvement of immunity, inflammation, and oxidative phosphorylation pathways in AAA and AOD. This study provides insights into potential prognostic biomarkers and therapeutic targets for these diseases.
OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Hulya Yilmaz Aydogan, Nurdan Gul, Deniz Kanca Demirci, Ummu Mutlu, Gizem Gulfidan, Kazim Yalcin Arga, Aclan Ozder, Ahmet Adil Camli, Yildiz Tutuncu, Oguz Ozturk, Canan Cacina, Feyza Darendeliler, Sukran Poyrazoglu, Ilhan Satman
Summary: This study investigated mutations in 13 MODY genes using next-generation DNA sequencing and identified several novel and known causative variants. Patients with double- and triple-heterozygosity mutations exhibited more severe clinical features, and the effects of BLK mutations appeared to be exacerbated in the presence of obesity. These findings provide valuable insights for clinical diagnosis and research on diabetes with genetic underpinnings in different populations.
OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY
(2022)
Review
Biotechnology & Applied Microbiology
Busra Aydin, Esra Yildirim, Onur Erdogan, Kazim Yalcin Arga, Betul Karademir Yilmaz, Suheyla Uyar Bozkurt, Fatih Bayrakli, Beste Turanli
Summary: Innovation roadmaps are crucial for encouraging creativity, anticipating challenges, and providing potential strategies for the treatment of PitNETs.
OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY
(2022)