Article
Oncology
Zizhen Zhou, Jinhai Deng, Teng Pan, Zhengjie Zhu, Xiulan Zhou, Chunxin Lv, Huanxin Li, Weixiong Peng, Bihai Lin, Cuidan Cai, Huijuan Wang, Yufeng Cai, Fengxiang Wei, Guanglin Zhou
Summary: This study constructed a risk model based on cuproptosis-related genes in breast cancer patients, demonstrating the usefulness of the model in stratifying subtypes and the importance of cuproptosis-related signature in predicting prognosis.
Article
Multidisciplinary Sciences
Xinyun Li, Lin Yang, Wei Huang, Bo Jia, Yu Lai
Summary: This study reveals the potential role of alternative splicing (AS) events in the prognosis, tumor microenvironment (TME), and immunotherapy of bladder cancer (BLCA), providing new insights into the molecular mechanisms and personalized immunotherapy for BLCA.
Article
Pharmacology & Pharmacy
An Liu, Fei Li, Bao Wang, Le Yang, Hai Xing, Chang Su, Li Gao, Minggao Zhao, Lanxin Luo
Summary: This study comprehensively investigated the landscape of Ca2+ channels, pumps and exchangers in KIRC patients. Significant differences were found in prognosis, immune cell infiltration, and targeted drug sensitivities between high and low CRGs-related risk subtypes. TRPM3 was identified as a key CRG associated with poor prognosis in KIRC patients.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Medicine, General & Internal
Qian Lu, Yu Zhang, Xiaojian Chen, Weihong Gu, Xinrong Ji, Zhong Chen
Summary: This study reveals a strong correlation between TME and prognosis in PDAC patients, with higher immune scores associated with better overall survival. Additionally, 90 genes were identified to influence stromal and immune scores, among which CA9, SPOCK2, and CD1D were identified as the most significant prognostic genes.
Article
Oncology
Xingxin Huang, Fangmeng Fu, Wenhui Guo, Deyong Kang, Xiahui Han, Liqin Zheng, Zhenlin Zhan, Chuan Wang, Qingyuan Zhang, Shu Wang, Shunwu Xu, Jianli Ma, Lida Qiu, Jianxin Chen, Lianhuang Li
Summary: This study explores the prognostic significance of collagen features at breast tumor border using multiphoton imaging and imaging analysis. The results show that the CSTB score as an independent prognostic factor has better predictive performance than the clinical model combining molecular subtype, tumor size, and lymph nodal metastasis. It can greatly improve the accuracy of prognostic prediction and establish a new innovative method for prognosis prediction and clinical decision-making.
Article
Cell Biology
Wei Geng, Zhilei Lv, Jinshuo Fan, Juanjuan Xu, Kaimin Mao, Zhengrong Yin, Wanlu Qing, Yang Jin
Summary: This study identified a signature comprising seven lncRNAs associated with genome instability in LUAD, which independently predicted overall survival and showed correlation with somatic mutation patterns. The established nomogram displayed improved robustness and clinical practicability for predicting patient prognosis, providing a useful indicator for clinical stratification management and treatment decisions for LUAD patients.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Oncology
Haiwei Wang, Xinrui Wang, Liangpu Xu, Ji Zhang, Hua Cao
Summary: This study found that the regulated gene SPATS2L, affected by EGFR amplification and CDKN2A deletion, plays a significant role in the prognosis of patients with GBM or LGG.
FRONTIERS IN ONCOLOGY
(2021)
Article
Ophthalmology
Wenchuan Zhou, Ping Fei, Jing Li
Summary: The study evaluated the prognostic value of AS events as diagnostic and therapeutic markers for uveal melanoma. Through bioinformatics analysis, 1047 candidate AS events were identified, with enrichment in cellular components and molecular functions. The AS prognostic model was confirmed as an independent factor for overall survival, and 17 splicing factors related to the OS of UM patients were identified.
EXPERIMENTAL EYE RESEARCH
(2021)
Review
Genetics & Heredity
Samuel W. Brady, Alexander M. Gout, Jinghui Zhang
Summary: Somatic mutations in cancer genomes are caused by multiple mutational processes, each leaving a characteristic imprint. Decoding these imprints can provide insights into the evolutionary history of tumors. Mutational signatures can also offer therapeutic and prognostic insights, acting as biomarkers for drug response and prognosis. Additionally, therapy-induced mutational signatures have been associated with cancer progression.
TRENDS IN GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Pavel Ershov, Evgeniy Yablokov, Yuri Mezentsev, Alexis Ivanov
Summary: The aim of this study was to investigate the associations of uncharacterized chromosome-specific open-reading frame genes (CxORFx) expression and ORF proteins' subinteractomes with cancer-related cellular processes and molecular pathways. Through systems biology and bioinformatic analysis, 219 differentially expressed CxORFx genes in cancers were identified, and the prognostic significance of transcriptomic signatures as well as the subinteractome composition were analyzed. The results revealed cancer-associated ORF proteins and their protein-protein interactions, expanding the understanding of the functions of poorly annotated CxORFx in the context of cancer.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Nicole E. James, Morgan Woodman, Jennifer R. Ribeiro
Summary: EOC patients have low response rates to immunotherapies, but evidence suggests ovarian tumors are immunogenic and immune-related genomic profiles can serve as prognostic markers. Specific research areas that need to be addressed include developing immune-based prognostic signatures and driving advancements in this field.
Review
Biotechnology & Applied Microbiology
Rongqiang Liu, Weihao Kong, Shiyang Zheng, Chenyu Yu, Yajie Yu, Yuling Xu, Linsen Ye, Yi Shao
Summary: Elevated expression of miR-24 in tumors is significantly associated with poor overall survival and may serve as a promising prognostic marker across different cancers. Further validation through additional investigations is warranted.
Article
Cell Biology
Xiaolong Tang, Xiangqing Ren, Tian Huang, Yandong Miao, Wuhua Ha, Zheng Li, Lixia Yang, Denghai Mi
Summary: This study investigates the prognostic and immunological significance of cuproptosis in hepatocellular carcinoma (HCC) patients. The researchers identified two cuproptosis-related subtypes of HCC patients, with one subtype showing a worse prognosis and higher immune activity. They developed a prognostic risk signature based on cuproptosis-related genes, which can independently predict the prognosis of HCC patients and is associated with clinical features. Furthermore, high-risk patients were found to have a higher response rate to immune checkpoint inhibitors.
MEDIATORS OF INFLAMMATION
(2023)
Article
Biochemistry & Molecular Biology
Lias Saed, Agnieszka Jelen, Marek Mirowski, Aleksandra Salagacka-Kubiak
Summary: HMGA1 is a protein involved in DNA transcription, replication, recombination, and repair. Its overexpression is associated with malignancy, metastasis, and poor survival in several types of cancer. However, the prognostic significance of HMGA1 in lung cancer is not clear. This study found that HMGA1 is highly expressed in lung tumors and is associated with certain clinicopathological features. High expression of HMGA1 is linked to shorter survival time in lung adenocarcinoma patients but not in lung squamous cell carcinoma patients. HMGA1 interacts with proteins involved in cellular senescence, cell cycle control, transcription regulation, chromatin assembly and remodeling, and cholesterol and isoprene biosynthesis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Oncology
Feng Xian, Xuegang Yang, Guohui Xu
Summary: This meta-analysis found a significant correlation between high expression of CDC20 and poor prognosis in human malignancy tumors. CDC20 may serve as a valuable prognostic predictive biomarker and a potential therapeutic target.
FRONTIERS IN ONCOLOGY
(2022)
Article
Cell Biology
Ryosuke Shirasaki, Geoffrey M. Matthews, Sara Gandolfi, Ricardo de Matos Simoes, Dennis L. Buckley, Joseline Raja Vora, Quinlan L. Sievers, Johanna B. Bruggenthies, Olga Dashevsky, Haley Poarch, Huihui Tang, Megan A. Bariteau, Michal Sheffer, Yiguo Hu, Sondra L. Downey-Kopyscinski, Paul J. Hengeveld, Brian J. Glassner, Eugen Dhimolea, Christopher J. Ott, Tinghu Zhang, Nicholas P. Kwiatkowski, Jacob P. Laubach, Robert L. Schlossman, Paul G. Richardson, Aedin C. Culhane, Richard W. J. Groen, Eric S. Fischer, Francisca Vazquez, Aviad Tsherniak, William C. Hahn, Joan Levy, Daniel Auclair, Jonathan D. Licht, Jonathan J. Keats, Lawrence H. Boise, Benjamin L. Ebert, James E. Bradner, Nathanael S. Gray, Constantine S. Mitsiades
Summary: The resistance mechanisms to degraders targeting different oncoproteins are mainly due to prevention, rather than adaptation, of the breakdown of target oncoproteins, which is possibly caused by the loss of function of the cognate E3 ligase or its interactors/regulators.
Article
Biochemistry & Molecular Biology
Marouen Ben Guebila, Camila M. Lopes-Ramos, Deborah Weighill, Abhijeet Rajendra Sonawane, Rebekka Burkholz, Behrouz Shamsaei, John Platig, Kimberly Glass, Marieke L. Kuijjer, John Quackenbush
Summary: Gene regulation networks play a crucial role in tissue identity, disease development, and therapeutic response. The GRAND database provides computationally-inferred gene regulatory network models and targeting scores for predicting drug effects on network structures and matching potential therapeutic drugs to disease states.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Deborah Weighill, Marouen Ben Guebila, Kimberly Glass, John Quackenbush, John Platig
Summary: Understanding how individual genotypes influence gene regulation can improve our understanding of human health and development. EGRET is a method that infers genotype-specific gene regulatory networks to reveal the genetic associations driving complex phenotypes.
Article
Oncology
Wail Ba-Alawi, Sisira Kadambat Nair, Bo Li, Anthony Mammoliti, Petr Smirnov, Arvind Singh Mer, Linda Z. Penn, Benjamin Haibe-Kains
Summary: Identifying predictive biomarkers for drug response in cancer cells is a major challenge in precision oncology. This study presents a new machine learning pipeline that utilizes logic modeling and bimodally expressed genes to build interpretable models for drug response. The approach has shown high validation rates in large-scale pharmacogenomic datasets and holds potential for clinical translation.
Editorial Material
Oncology
Trevor J. Pugh, Benjamin Haibe-Kains
Summary: Li and colleagues introduce REFLECT, a computational approach for precision oncology that utilizes diverse publicly available genomic, transcriptomic, and proteomic data to nominate effective drug combinations. The preliminary validation of REFLECT in preclinical and clinical trial settings demonstrates its potential for clinical implementation, although challenges remain.
Article
Oncology
Yufei Wang, Alicia Buck, Marion Grimaud, Aedin C. Culhane, Sreekumar Kodangattil, Cecile Razimbaud, Dennis M. Bonal, Quang-De Nguyen, Zhu Zhu, Kevin Wei, Madison L. O'Donnell, Ying Huang, Sabina Signoretti, Toni K. Choueiri, Gordon J. Freeman, Quan Zhu, Wayne A. Marasco
Summary: Improving CAR-T cell therapy for solid tumors requires a better understanding of CAR design and cellular composition. A study found that CAR-T cells with a CD4/CD8 ratio of BB zeta exhibited superior efficacy in clearing clear-cell renal cell carcinoma (ccRCC) in a mouse model, demonstrating long-term tumor-free outcome.
MOLECULAR THERAPY-ONCOLYTICS
(2022)
Article
Multidisciplinary Sciences
Lukas Moeller, Eric J. Aird, Markus S. Schroeder, Lena Kobel, Lucas Kissling, Lilly van de Venn, Jacob E. Corn
Summary: This study presents a HDR improvement strategy called Recursive Editing, which selectively retargets undesired indel outcomes to create more opportunities for HDR. The authors introduce a software tool called REtarget for the design of Recursive Editing experiments. By using REtarget-designed guide RNAs, Recursive Editing can simultaneously enhance HDR efficiency and reduce undesired indels. This approach proves to be easy to use and has little experimental burden.
NATURE COMMUNICATIONS
(2022)
Article
Oncology
Jin-Young Yoon, Nastaran Daneshgar, Yi Chu, Biyi Chen, Marco Hefti, Ajit Vikram, Kaikobad Irani, Long-Sheng Song, Charles Brenner, E. Dale Abel, Barry London, Dao-Fu Dai
Summary: This study reveals the mechanistic explanations for cardiac bradyarrhythmia, diastolic dysfunction, and neuronal apoptosis observed in models of Leigh syndrome (LS).
CLINICAL AND TRANSLATIONAL MEDICINE
(2022)
Article
Neurosciences
Lindsay J. Agostinelli, Scott C. Seaman, Clifford B. Saper, Dustin P. Fykstra, Marco M. Hefti, Timothy R. Koscik, Brian J. Dlouhy, Alexander G. Bassuk
Summary: Researchers report a study that combines high-resolution MRI and detailed histology to study the impact of neurologic disease on specific cell groups in the human brainstem and cerebellum. These findings are crucial for understanding and diagnosing brainstem lesions.
JOURNAL OF NEUROSCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Katherine H. Shutta, Deborah Weighill, Rebekka Burkholz, Marouen Ben Guebila, Dawn L. DeMeo, Helena U. Zacharias, John Quackenbush, Michael Altenbuchinger
Summary: In this study, we propose a network approach based on Gaussian Graphical Models (GGMs) called DRAGON, which allows for the joint analysis of multi-omic data. DRAGON adapts to the differences between omics layers, improving model inference and edge recovery, and can identify key molecular mechanisms.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Immunology
Romina Marone, Emmanuelle Landmann, Anna Devaux, Rosalba Lepore, Denis Seyres, Jessica Zuin, Thomas Burgold, Corinne Engdahl, Giuseppina Capoferri, Alessandro Dell'Aglio, Clement Larrue, Federico Simonetta, Julia Rositzka, Manuel Rhiel, Geoffroy Andrieux, Danielle N. Gallagher, Markus S. Schroder, Amelie Wiederkehr, Alessandro Sinopoli, Valentin Do Sacramento, Anna Haydn, Laura Garcia-Prat, Christopher Divsalar, Anna Camus, Liwen Xu, Lorenza Bordoli, Torsten Schwede, Matthew Porteus, Jerome Tamburini, Jacob E. Corn, Toni Cathomen, Tatjana I. Cornu, Stefanie Urlinger, Lukas T. Jeker
Summary: Targeted immunotherapy against CD123 shows promise for hematologic diseases, but the shared expression on healthy hematopoietic stem cells poses risks. Epitope-engineered HSPCs can be shielded from immunotherapy while remaining functional. Transplantation of genome-edited HSPCs enables tumor-selective immunotherapy and reconstruction of a fully functional hematopoietic system.
JOURNAL OF EXPERIMENTAL MEDICINE
(2023)
Article
Computer Science, Artificial Intelligence
Emily So, Fengqing Yu, Bo Wang, Benjamin Haibe-kains
Summary: This Reusability Report revisits a recently developed machine learning method called 'transfer of cell line response prediction' (TCRP) for precision oncology, confirming its reproducibility and reusability in drug-response prediction in new case studies. The study supports the superiority of TCRP over established statistical and machine learning approaches in preclinical and clinical settings.
NATURE MACHINE INTELLIGENCE
(2023)
Article
Biochemical Research Methods
Sheila M. Gaynor, Maud Fagny, Xihong Lin, John Platig, John Quackenbush
Summary: This study constructed twenty-nine tissue-specific eQTL networks using GTEx data and evaluated different network specifications. The researchers found that using a thresholded Benjamini-Hochberg q value weighted by the Z-statistic balanced metric reproducibility and computational efficiency. The eQTL networks were complementary to gene regulatory networks in understanding regulation, and highly connected nodes were enriched for tissue-relevant traits.
CELL REPORTS METHODS
(2022)
Article
Clinical Neurology
Samuel S. Shin, Amy C. Gottschalk, Vanessa M. Mazandi, Todd J. Kilbaugh, Marco M. Hefti
Summary: This study investigates the gene expression changes between the injured and uninjured sides of pig cerebral cortex after traumatic brain injury (TBI) using a large animal model. The results show that genes related to immune system activation, regulation of immune response, and leukocyte activation are differentially expressed after TBI.
NEUROTRAUMA REPORTS
(2022)
Article
Genetics & Heredity
Marouen Ben Guebila, Daniel C. Morgan, Kimberly Glass, Marieke L. Kuijjer, Dawn L. DeMeo, John Quackenbush
Summary: Gene regulatory network inference allows for modeling genome-scale regulatory processes. Researchers have developed a collection of tools to model various regulatory processes and improve their performance through GPU-accelerated calculations.
NAR GENOMICS AND BIOINFORMATICS
(2022)