Article
Cell Biology
Yuan Chen, Shiben Ji, Jianxin Ying, Yongchang Sun, Jun Liu, Guohong Yin
Summary: This study identifies a novel biomarker, KRT6A, for early diagnosis of bladder tumors and reveals its role in promoting bladder tumor progression. Additionally, it uncovers the regulatory axis of KRT6A/miR-31-5p in bladder tumor growth.
Article
Oncology
Yi Zhang, Xuebing Di, Guoji Chen, Jiaqi Liu, Bailin Zhang, Lin Feng, Shujun Cheng, Yipeng Wang
Summary: This study aims to develop a TME-associated, immune-related signature to improve prognosis prediction of BRCA. By analyzing the immune gene profiles of 43 BRCA patients, we identified a robust immune-related signature that could stratify patients into high- and low-risk groups based on gene expression levels.
AMERICAN JOURNAL OF CANCER RESEARCH
(2021)
Article
Multidisciplinary Sciences
Zhenchi Li, Jie Zhao, Xing Huang, Jiangping Wang
Summary: Bladder cancer (BC) is an important malignant tumor type, and the role of N7-methyguanosine (m7G)-related lncRNAs in BC remains unclear. In this study, a prognostic model was developed using m7G-related lncRNAs to evaluate BC prognosis and tumor immunity. Patients were classified into high-risk and low-risk groups based on a signature constructed using multivariate Cox and LASSO regression analysis. The signature showed good prognostic value and was associated with tumor immunity. This study highlights the relevance of m7G-related lncRNAs to BC and suggests that the risk signature could serve as a novel prognostic marker for BC patients.
SCIENTIFIC REPORTS
(2023)
Article
Medicine, General & Internal
Tomi Suomi, Inna Starskaia, Ubaid Ullah Kalim, Omid Rasool, Maria K. Jaakkola, Toni Gronroos, Tommi Valikangas, Caroline Brorsson, Gianluca Mazzoni, Sylvaine Bruggraber, Lut Overbergh, David Dunger, Mark Peakman, Piotr Chmura, Seren Brunak, Anke M. Schulte, Chantal Mathieu, Mikael Knip, Riitta Lahesmaa, Laura L. Elo
Summary: This study aimed to identify transcriptional changes associated with disease progression in patients with recent-onset type 1 diabetes. They found that genes and pathways related to innate immunity were downregulated during the first year after diagnosis. Associations between gene expression changes and ZnT8A autoantibody positivity were also observed. Additionally, changes in the expression of 16 genes were found to predict the decline in C-peptide at 24 months, and increased B cell levels and decreased neutrophil levels were associated with rapid progression, consistent with previous reports.
Article
Oncology
Yunxun Liu, Jun Jian, Ye Zhang, Lei Wang, Xiuheng Liu, Zhiyuan Chen
Summary: This study identified cancer-associated fibroblasts (CAFs) related genes in bladder urothelial carcinoma (BLCA) and developed a CAF-based risk signature for predicting patient survival and selecting suitable treatment strategies.
FRONTIERS IN ONCOLOGY
(2023)
Article
Oncology
Huanjun Wang, Yan Mei, Cheng Luo, Qun Huang, Zifeng Wang, Guan-Ming Lu, Lili Qin, Zhun Sun, Chao-Wen Huang, Zhi-Wen Yang, Junxing Chen, Weiguo Yin, Chao-Nan Qian, Jianming Zeng, Lingwu Chen, Qibin Leng, Yan Guo, Guangshuai Jia
Summary: Bladder cancer treatment is challenging due to therapy resistance and high recurrence rates. Profiling intratumor heterogeneity can uncover molecular mechanisms of recurrence. This study used single-cell RNA sequencing and ATAC-seq to analyze tumors from different risk groups and recurrent cases, creating a comprehensive cancer-cell atlas. The research identified a cancer stem-cell subpopulation enriched during recurrence, highlighting the role of EZH2 in maintaining repression of specific genes related to invasion and stemness. Additionally, the study investigated epithelial-mesenchymal transition in clinical samples and identified regulatory networks specific to recurrent bladder cancer.
CLINICAL CANCER RESEARCH
(2021)
Article
Immunology
Zhiyong Tan, Xiaorong Chen, Jieming Zuo, Shi Fu, Jiansong Wang, Haifeng Wang
Summary: This study aims to establish bladder cancer (BLCA) risk stratification based on sialylation-related genes and elucidate its role in prognosis, tumor microenvironment, and immunotherapy of BLCA. Core cell types and molecular characteristics of BLCA were identified using RNA-seq data. Risk stratification of BLCA was determined based on prognosis-related sialylation genes, and high-risk patients showed worse survival outcomes and lower immunotherapy response.
JOURNAL OF INFLAMMATION RESEARCH
(2023)
Review
Oncology
Bashdar Mahmud Hussen, Snur Rasool Abdullah, Goran Sedeeq Hama Faraj, Mohammed Fatih Rasul, Abbas Salihi, Soudeh Ghafouri-Fard, Mohammad Taheri, Majid Mokhtari
Summary: Exosomes are membrane vesicles with a diameter of 30-150 nm, secreted by various cancer types and containing circRNAs among other substances. Exo-circRNAs play a crucial role in lung cancer progression, but the specific activities and regulatory mechanisms are still unclear. A better understanding of exo-circRNA regulation and network connections can lead to improved treatment for lung cancer, including potential therapeutic targets.
CANCER CELL INTERNATIONAL
(2022)
Article
Pathology
Jacqueline Fontugne, Evanguelos Xylinas, Clementine Krucker, Victoria Dixon, Clarice S. Groeneveld, Ugo Pinar, Gianluigi Califano, Margot Bucau, Jerome Verine, Francois Desgrandchamps, Jean-Francois Hermieu, Francois Radvanyi, Yves Allory, Alexandra Masson-Lecomte
Summary: Through the study of upper tract urothelial carcinomas (UTUCs), we found that the consensus classification can reliably classify UTUCs and highlight intratumoral molecular heterogeneity, with a higher proportion of luminal papillary subtype compared to muscle-invasive bladder cancer (MIBC).
Article
Multidisciplinary Sciences
Zidan Zhao, Tsz Kin Mak, Yuntao Shi, Kuan Li, Mingyu Huo, Changhua Zhang
Summary: This study identified five CAF subtypes in GC, with CAF_0 subtype associated with poor prognosis. Increased expression of POSTN in both GC tissues and CAFs was linked to poor prognosis in GC patients. The CAFs-score constructed from the CAF_0 subtype showed potential as a biomarker to guide therapeutic decisions, assessing immunotherapy outcomes and personalized treatment in GC patients.
Article
Immunology
Hualin Chen, Wenjie Yang, Yingjie Li, Lin Ma, Zhigang Ji
Summary: Disulfidptosis is a newly discovered form of cell death in bladder cancer. This study identified disulfidptosis-related gene clusters and established a prognostic model based on these genes. The model can predict the prognosis and immunotherapy response of bladder cancer patients. POU5F1 and CTSE were identified as potential therapeutic targets.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Cell Biology
Ziming Jiang, Yiming Zhang, Yu Zhang, Zhankui Jia, Zhengguo Zhang, Jinjian Yang
Summary: The study revealed that exosomes released by bladder cancer cells can promote the immunosuppressive polarization of macrophages, facilitating tumor growth. This process is mediated by down-regulation of PTEN and activation of AKT/STAT3/6 signaling. Inhibiting the generation or secretion of exosomes can suppress the immunosuppressive transformation of macrophages, thereby inhibiting tumor growth.
CELL COMMUNICATION AND SIGNALING
(2021)
Article
Immunology
Yanhong Shou, Ronghui Zhu, Zhenwei Tang, Xiao-Yong Man
Summary: This study identified a glycolysis-related subpopulation of keratinocytes in psoriasis patients and developed a glycolysis signature that can be used to predict treatment effectiveness.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Immunology
Yunzhong Jiang, Xiaowei Qu, Mengzhao Zhang, Lu Zhang, Tao Yang, Minghai Ma, Minxuan Jing, Nan Zhang, Rundong Song, Yuanquan Zhang, Zezhong Yang, Yaodong Zhang, Yuanchun Pu, Jinhai Fan
Summary: This study developed a TAM-related prognostic model in bladder cancer patients based on TCGA data. WGCNA was used to identify key genes related to TAM. GO enrichment and KEGG signaling pathway analysis showed the functional categories of the key genes. A TMA-related prognostic model containing six key genes was established using LASSO and Cox regressions. Single-cell sequencing data suggested that these six genes were expressed specifically in TAM and may be involved in TAM polarization.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Oncology
Hang Zheng, Heshu Liu, Yang Ge, Xin Wang
Summary: The study established a nine-gene prognostic CAF-related signature for CRC, which was validated in multiple cohorts. Patients with higher CAF risk scores showed adverse prognosis and higher CAF infiltrations. The potential strategy of combining chemotherapy with anti-CAF therapy was suggested to improve the efficacy of T-cell based immunotherapies.
CANCER CELL INTERNATIONAL
(2021)
Article
Oncology
Maud Fagny, John Platig, Marieke Lydia Kuijjer, Xihong Lin, John Quackenbush
BRITISH JOURNAL OF CANCER
(2020)
Article
Oncology
Matthew Schwede, Levi Waldron, Samuel C. Mok, Wei Wei, Azfar Basunia, Melissa A. Merritt, Constantine S. Mitsiades, Giovanni Parmigiani, David P. Harrington, John Quackenbush, Michael J. Birrer, Aedin C. Culhane
CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION
(2020)
Article
Cell Biology
Camila M. Lopes-Ramos, Cho-Yi Chen, Marieke L. Kuijjer, Joseph N. Paulson, Abhijeet R. Sonawane, Maud Fagny, John Platig, Kimberly Glass, John Quackenbush, Dawn L. DeMeo
Article
Multidisciplinary Sciences
Elodie Hatchi, Liana Goehring, Serena Landini, Konstantina Skourti-Stathaki, Derrick K. DeConti, Fieda O. Abderazzaq, Priyankana Banerjee, Timothy M. Demers, Yaoyu E. Wang, John Quackenbush, David M. Livingston
Summary: Strong connections are found between R-loops, genome instability, and human disease. R-loops play a role in maintaining homeostasis by regulating certain physiological processes, such as the synthesis of antisense transcripts through transcription termination pause sites. A species of single-stranded, DNA-damage-associated small RNA (sdRNA) generated by a BRCA1-RNAi complex promotes DNA repair at transcriptional termination pause sites forming R-loops.
Article
Mathematical & Computational Biology
Albert T. Young, Xavier Carette, Michaela Helmel, Hanno Steen, Robert N. Husson, John Quackenbush, John Platig
Summary: The inhibition of Mtb serine/threonine protein kinases PknA and PknB leads to changes in the TF regulatory network, affecting regulatory programs involved in cell wall integrity, stress response, and energy production. This highlights the importance of incorporating signal-driven TF modifications in regulatory network approaches.
NPJ SYSTEMS BIOLOGY AND APPLICATIONS
(2021)
Article
Oncology
Camila M. Lopes-Ramos, Tatiana Belova, Tess H. Brunner, Marouen Ben Guebila, Daniel Osorio, John Quackenbush, Marieke L. Kuijjer
Summary: Analysis identified seven pathways associated with survival in glioblastoma patients, with dysregulation of PD1 signaling correlating with poor prognosis. This suggests a new approach to predict patient survival and highlights potential therapeutic interventions based on gene regulatory network analysis.
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
Cell Biology
Rebekka Burkholz, John Quackenbush, Daniel Bojar
Summary: Glycans pose substantial challenges for computational biology due to their nonlinear and diverse nature. Sweet-Net, a graph convolutional neural network, outperforms other computational methods in predicting glycan properties and can learn representations that are predictive of organismal phenotypic and environmental properties. Additionally, glycan-focused machine learning can be used to predict viral glycan binding and discover viral receptors.
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
Mathematical & Computational Biology
Abhijeet Rajendra Sonawane, Dawn L. DeMeo, John Quackenbush, Kimberly Glass
Summary: The study focuses on the application of epigenetic data in gene regulatory networks, developing the SPIDER method for network reconstruction, which shows high accuracy and cell-line-specific interactions, and has the potential to identify novel hypotheses for better characterizing cell-type and phenotype-specific regulatory mechanisms.
NPJ SYSTEMS BIOLOGY AND APPLICATIONS
(2021)
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
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
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)
Article
Urology & Nephrology
Kinsuk Chauhan, Girish N. Nadkarni, Fergus Fleming, James McCullough, Cijiang J. He, John Quackenbush, Barbara Murphy, Michael J. Donovan, Steven G. Coca, Joseph Bonventre
Article
Computer Science, Information Systems
Jipeng Qiang, Wei Ding, Marieke Kuijjer, John Quackenbush, Ping Chen