Article
Oncology
Yujia Lan, Wei Liu, Wanmei Zhang, Jing Hu, Xiaojing Zhu, Linyun Wan, A. Suru, Yanyan Ping, Yun Xiao
Summary: This study analyzed 506 LUAD tumors and identified mutually exclusive relationships among driver gene mutations in different subtypes, playing crucial roles in cancer progression. Functional analysis revealed enrichment of these mutually exclusive pairs in nuclear division and immune response. Some of the mutually exclusive triples were associated with overall survival and disease-specific survival of LUAD patients.
Article
Cell Biology
Dahua Xu, Liqiang Wang, Sainan Pang, Meng Cao, Wenxiang Wang, Xiaorong Yu, Zhizhou Xu, Jiankai Xu, Hong Wang, Jianping Lu, Kongning Li
Summary: This study constructed dysregulated lncRNA-associated ceRNA networks across eight cancer types, highlighting the significant roles of lncRNAs in these networks. By integrating lncRNA methylation profiles, multiple epigenetically related lncRNAs were identified, revealing their regulatory patterns in cancer. Furthermore, nine pan-cancer epigenetically related lncRNAs were found to predict cancer incidence and outcomes robustly, offering potential therapeutic targets for various cancer types.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biology
Jorge A. Alfaro-Murillo, Jeffrey P. Townsend
Summary: This study introduces a continuous-time Markov chain model that enables the estimation of mutation rates and selection coefficients for cancer genotypes. The model, coupled with a deconvolution approach, allows inference of the most likely routes of variant evolution and estimation of selection strength. The findings reveal both synergistic and antagonistic epistatic effects in oncogenesis, providing important insights for cancer research and personalized therapy development.
MATHEMATICAL BIOSCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Abir Khazaal, Seid Miad Zandavi, Andrei Smolnikov, Shadma Fatima, Fatemeh Vafaee
Summary: Long non-coding RNAs (lncRNAs) have emerged as key regulators in many biological processes, and their dysregulation is associated with numerous diseases, including cancer. Understanding the functional implications of lncRNAs in tumorigenesis can lead to the development of novel biomarkers and therapeutic targets.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Junguk Hur, Ximena Paez-Colasante, Claudia Figueroa-Romero, Ting-wen Lo, Sami J. Barmada, Michelle T. Paulsen, Mats Ljungman, Fadhl M. Alakwaa, Masha G. Savelieff, Stephen A. Goutman, Eva L. Feldman
Summary: This study analyzes the miRNA profiles in patients with amyotrophic lateral sclerosis (ALS) and identifies different miRNA levels in different ALS mutation types. The study also reveals pathways related to ALS and suggests potential targets for future research. These findings contribute to the early diagnosis of ALS.
HUMAN MOLECULAR GENETICS
(2022)
Article
Multidisciplinary Sciences
Chunan Liu, Sudha Ram, Bonnie L. Hurwitz
Summary: This study investigated dysregulated gene co-expression patterns in the skin of type II diabetic patients using network analysis and topological properties. Two gene modules related to type II diabetes were identified and a novel regulatory mechanism (miR-21-PPARA-NCOA6) of dysregulated keratinocyte proliferation, differentiation, and migration in diabetic skin was revealed. Hub genes and key coordinators may serve as therapeutic targets for improving diabetic skincare.
SCIENTIFIC REPORTS
(2022)
Article
Oncology
Li Zhang, Chunmei Wang, Xiaojie Lu, Xiao Xu, Tieliu Shi, Jinlian Chen
Summary: This study utilized transcriptome profiling to explore the role of noncoding RNAs in hepatocellular carcinoma (HCC). The findings identified novel circRNAs, miRNAs, and dysregulated ncRNAs that contribute to HCC tumorigenesis and progression. Additionally, the study provided insights into the molecular mechanisms of how different ncRNAs interact in disease pathogenesis.
FRONTIERS IN ONCOLOGY
(2022)
Article
Cell Biology
Chi Wai Yip, Chung-Chau Hon, Kayoko Yasuzawa, Divya M. Sivaraman, Jordan A. Ramilowski, Youtaro Shibayama, Saumya Agrawal, Anika V. Prabhu, Callum Parr, Jessica Severin, Yan Jun Lan, Josee Dostie, Andreas Petri, Hiromi Nishiyori-Sueki, Michihira Tagami, Masayoshi Itoh, Fernando Lopez-Redondo, Tsukasa Kouno, Jen-Chien Chang, Joachim Luginbuhl, Masaki Kato, Mitsuyoshi Murata, Wing Hin Yip, Xufeng Shu, Imad Abugessaisa, Akira Hasegawa, Harukazu Suzuki, Sakari Kauppinen, Ken Yagi, Yasushi Okazaki, Takeya Kasukawa, Michiel de Hoon, Piero Carninci, Jay W. Shin
Summary: Within the FANTOM6 consortium, we conducted a large-scale knockdown of 200 lncRNAs in human iPSCs and explored their roles in self-renewal and pluripotency. We identified 36 lncRNAs that inhibit cell growth and 36 lncRNAs with molecular phenotypes, potentially affecting pluripotency.
Article
Biochemistry & Molecular Biology
Tiantongfei Jiang, Weiwei Zhou, Zhenghong Chang, Haozhe Zou, Jing Bai, Qisen Sun, Tao Pan, Juan Xu, Yongsheng Li, Xia Li
Summary: The study comprehensively explores the crucial role of immune system gene regulation in the development of various types of cancer, identifying potential immunology regulons and clinically relevant genes. Analyzing regulon atlas across cancers helps researchers gain insights into the relationships between immune cell infiltrations, checkpoint expression, and cancer prognosis. Developing a user-friendly resource like ImmReg will facilitate the future development of RNA-based cancer immunotherapies.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Bo Gao, Yue Zhao, Yonghang Gao, Guojun Li, Ling-Yun Wu
Summary: High-throughput biological data has provided an opportunity to illuminate the mechanisms of tumor emergence and evolution, with the tool ComCovEx being developed to explore common cancer driver gene modules between two cancers and reveal their associations. The research results offer new insights into the pathological basis of different cancer types and provide new clues for the diagnosis and treatment of associated cancers.
Article
Immunology
Song Li, Pengxiang Chen, Bo Cheng, Yuchen Liu, Xue Zhang, Qian Xu, Miao Huang, Xin Dai, Kai Huang, Lin Zhang, Yufeng Cheng, Lian Liu
Summary: This study evaluated the impact of Pyroptosis potential in cancer patients and found that high potential is associated with tumor characteristics and response rates to immunotherapy. Pyroptosis scoring showed predictive value in immunotherapy outcomes. Additionally, systemic treatments can enhance Pyroptosis in drug-resistant tumors.
CLINICAL IMMUNOLOGY
(2022)
Article
Cell Biology
Fan Zhang, Qilin Zhang, Jiajun Zhu, Boyuan Yao, Chi Ma, Nidan Qiao, Shiman He, Zhao Ye, Yunzhi Wang, Rui Han, Jinwen Feng, Yongfei Wang, Zhaoyu Qin, Zengyi Ma, Kai Li, Yichao Zhang, Sha Tian, Zhengyuan Chen, Subei Tan, Yue Wu, Peng Ran, Ye Wang, Chen Ding, Yao Zhao
Summary: Pituitary neuroendocrine tumor (PitNET) is a common intracranial tumor, and further studies are needed to explore the causative molecular mechanisms and potential therapeutic targets. Through integrative genomics analysis on 200 PitNET patients, potential therapeutic targets were identified, providing possibilities for improving current treatment strategies.
Article
Cell Biology
Roudabeh Vakil Monfared, Wedad Alhassen, Tri Minh Truong, Michael Angelo Maglalang Gonzales, Vincent Vachirakorntong, Siwei Chen, Pierre Baldi, Olivier Civelli, Amal Alachkar
Summary: The study found that gene expression of G-protein-coupled receptors (GPCRs) is altered in psychiatric disorders, especially in autism spectrum disorder (ASD), schizophrenia (SCZ), bipolar disorder (BP), and major depressive disorder (MDD). Age-associated GPCRs are more likely to be dysregulated in ASD. The results highlight the central role of GPCR signaling pathways in the etiology and pathophysiology of psychiatric disorders.
Review
Geosciences, Multidisciplinary
Remus Pravalie
Summary: This review paper explores global land degradation through an interdisciplinary and holistic approach, identifying 17 different pathways of land degradation. Among them, five major pathways are considered crucial, eroding ecosystem functions and services. The study emphasizes the urgent need for multidimensional research on land degradation and advocates for prioritizing it in governmental and international policies.
EARTH-SCIENCE REVIEWS
(2021)
Article
Biochemistry & Molecular Biology
Areej Mesleh, Hanan Ehtewish, Alberto de la Fuente, Hawra Al-shamari, Iman Ghazal, Fatema Al-Faraj, Fouad Al-Shaban, Houari B. Abdesselem, Mohamed Emara, Nehad M. Alajez, Abdelilah Arredouani, Julie Decock, Omar Albagha, Lawrence W. Stanton, Sara A. Abdulla, Omar M. A. El-Agnaf
Summary: Autism spectrum disorder (ASD) is a group of neurodevelopmental disorders characterized by impairments in social and communication skills, along with repetitive and restrictive behaviors or interests. Currently, there are no approved biomarkers for ASD diagnosis, and the diagnosis heavily relies on physician's assessment and awareness of symptoms. This study identified potential blood proteomic biomarkers for ASD using proximity extension assay (PEA) and machine learning analysis. Dysregulation of SNARE vesicular transport and ErbB pathways were found in ASD cases, and proteins from these pathways were correlated with ASD severity.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Genetics & Heredity
Hangnoh Lee, Dong-Yeon Cho, Damian Wojtowicz, Susan T. Harbison, Steven Russell, Brian Oliver, Teresa M. Przytycka
G3-GENES GENOMES GENETICS
(2018)
Article
Genetics & Heredity
Jing Guo, Hao Chen, Peng Yang, Yew Ti Lee, Min Wu, Teresa M. Przytycka, Chee Keong Kwoh, Jie Zheng
BMC MEDICAL GENOMICS
(2018)
Article
Biochemistry & Molecular Biology
Yijie Wang, Jan Hoinka, Yong Liang, Tomasz Adamus, Piotr Swiderski, Teresa M. Przytycka
NUCLEIC ACIDS RESEARCH
(2018)
Letter
Medicine, Research & Experimental
Jan Hoinka, Rolf Backofen, Teresa M. Przytycka
MOLECULAR THERAPY-NUCLEIC ACIDS
(2018)
Article
Medicine, General & Internal
Holger Froehlich, Rudi Balling, Niko Beerenwinkel, Oliver Kohlbacher, Santosh Kumar, Thomas Lengauer, Marloes H. Maathuis, Yves Moreau, Susan A. Murphy, Teresa M. Przytycka, Michael Rebhan, Hannes Rost, Andreas Schuppert, Matthias Schwab, Rainer Spang, Daniel Stekhoven, Jimeng Sun, Andreas Weber, Daniel Ziemek, Blaz Zupan
Article
Multidisciplinary Sciences
Yijie Wang, Dong-Yeon Cho, Hangnoh Lee, Justin Fear, Brian Oliver, Teresa M. Przytycka
NATURE COMMUNICATIONS
(2018)
Article
Multidisciplinary Sciences
Shambhavi Shubham, Jan Hoinka, Soma Banerjee, Emma Swanson, Jacob A. Dillard, Nicholas J. Lennemann, Teresa M. Przytycka, Wendy Maury, Marit Nilsen-Hamilton
SCIENTIFIC REPORTS
(2018)
Article
Biochemistry & Molecular Biology
Soumitra Pal, Jan Hoinka, Teresa M. Przytycka
NUCLEIC ACIDS RESEARCH
(2019)
Correction
Multidisciplinary Sciences
Yijie Wang, Dong-Yeon Cho, Hangnoh Lee, Justin Fear, Brian Oliver, Teresa M. Przytycka
NATURE COMMUNICATIONS
(2019)
Article
Biochemical Research Methods
Soumitra Pal, Teresa M. Przytycka
Article
Genetics & Heredity
Yoo-Ah Kim, Damian Wojtowicz, Rebecca Sarto Basso, Itay Sason, Welles Robinson, Dorit S. Hochbaum, Mark D. M. Leiserson, Roded Sharan, Fabio Vandin, Teresa M. Przytycka
Article
Biochemistry & Molecular Biology
Yoo-Ah Kim, Ermin Hodzic, Bayarbaatar Amgalan, Ariella Saslafsky, Damian Wojtowicz, Teresa M. Przytycka
Summary: This paper explores the use of mutational signatures to study environment-induced changes in gene expression in control lung tissues from lung adenocarcinoma samples. The analysis shows the combined impact of smoking and tumor-related micro-environments on gene expression and cell-type composition in non-neoplastic lung tissue. The study provides evidence for the utility of mutational signatures as sensors of environmental exposures and demonstrates the valuable information that can be obtained from cancer databases for non-cancer lung tissue research.
Article
Genetics & Heredity
Bayarbaatar Amgalan, Damian Wojtowicz, Yoo-Ah Kim, Teresa M. Przytycka
Summary: In recent years, the study of mutagenic processes has been enhanced through the analysis of mutational signatures. However, the links between mutagens and observed mutation patterns, as well as their interactions with molecular pathways, are not fully understood. To address this, we developed a network-based method called GeneSigNet, which reveals the relationships between genes and mutational signatures. By applying GeneSigNet to cancer datasets, we identified important connections between mutational signatures and cellular processes, providing insights into cancer-related mechanisms.
Article
Biochemical Research Methods
Soumitra Pal, Brian Oliver, Teresa M. Przytycka
Summary: This study developed a computationally efficient method called EvoGeneX based on the OU process for modeling gene expression evolution and tested its performance through extensive simulations. A formal measure of evolutionary expression divergence was also introduced for comparative analysis. The results showed that genes with adaptive expression evolution tend to be body-part specific, while genes with constrained evolution are shared across body-parts.
JOURNAL OF COMPUTATIONAL BIOLOGY
(2023)
Article
Biochemical Research Methods
Xiaoqing Huang, Damian Wojtowicz, Teresa M. Przytycka