Article
Medicine, General & Internal
Luting Chen, Yuchang Fei, Yurong Zhao, Quan Chen, Peifeng Chen, Lei Pan
Summary: Gastric cancer is a common cancerous tumor and is the third leading cause of cancer mortality worldwide. HDACs play significant roles in tumor initiation and progression, and aberrant expression of HDACs may serve as potential biomarkers for diagnosis or prognosis of gastric cancer. Further studies are needed to validate these findings.
Article
Biochemistry & Molecular Biology
Lingqin Zhu, Qiongfang Yu, Yuanheng Li, Meng Zhang, Zhiwei Peng, Song Wang, Ziyi Quan, Dian Gao
Summary: Gastric cancer (GC) is the third leading cause of cancer-related death worldwide. There is an urgent need to identify biomarkers for early detection, prognosis evaluation, and targeted treatment of GC. Studies have shown that SKAP1 promotes cell proliferation and invasion and is associated with poor prognosis in various cancers, but its role and mechanism in GC are unclear.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Oncology
Wei Zheng, Yubo Zhao, Tengshuang Wang, Xiaoling Zhao, Zhangsen Tan
Summary: This study provides a theoretical basis for elucidating the pathogenesis and evaluating the prognosis of bladder cancer by screening potential biomarkers.
TRANSLATIONAL CANCER RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Jessica Roelands, Peter J. K. Kuppen, Eiman I. Ahmed, Raghvendra Mall, Tariq Masoodi, Parul Singh, Gianni Monaco, Christophe Raynaud, Noel F. C. C. de Miranda, Luigi Ferraro, Tatiana C. Carneiro-Lobo, Najeeb Syed, Arun Rawat, Amany Awad, Julie Decock, William Mifsud, Lance D. Miller, Shimaa Sherif, Mahmoud G. Mohamed, Darawan Rinchai, Marc Van den Eynde, Rosalyn W. Sayaman, Elad Ziv, Francois Bertucci, Mahir Abdulla Petkar, Stephan Lorenz, Lisa Sara Mathew, Kun Wang, Selvasankar Murugesan, Damien Chaussabel, Alexander L. Vahrmeijer, Ena Wang, Anna Ceccarelli, Khalid A. Fakhro, Gabriele Zoppoli, Alberto Ballestrero, Rob A. E. M. Tollenaar, Francesco M. Marincola, Jerome Galon, Souhaila Al Khodor, Michele Ceccarelli, Wouter Hendrickx, Davide Bedognetti
Summary: The lack of multi-omics cancer datasets with extensive follow-up information hinders the identification of accurate biomarkers of clinical outcome. In this cohort study, comprehensive genomic analyses were performed on fresh-frozen samples from 348 patients with primary colon cancer. The study revealed a gene expression signature called Immunologic Constant of Rejection that outperformed conventional prognostic molecular biomarkers. Additionally, a favorable outcome was associated with a microbiome signature driven by Ruminococcus bromii.
Article
Biochemistry & Molecular Biology
Pooja Singh, Salma Jamal, Faraz Ahmed, Najumu Saqib, Seema Mehra, Waseem Ali, Deodutta Roy, Nasreen Z. Ehtesham, Seyed E. Hasnain
Summary: This study aims to develop an updated database including almost all reported substitutions within Mycobacterium tuberculosis drug target genes and use bioinformatics tools to evaluate the impact of these mutations. They have created a comprehensive online resource named MycoTRAP-DB that connects gene mutations with structural, functional, and pathogenic implications. This integrated platform allows for comprehensive analysis and prioritization of SNPs for the development of improved antimycobacterial medications.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Jianfeng Zheng, Jialu Guo, Yahui Wang, Yingling Zheng, Ke Zhang, Jinyi Tong
Summary: This study constructed an FRL-signature for ovarian cancer (OC) patients, identifying FRLs with significant prognostic value and their association with ferroptosis score, immune factors, and microenvironment cells. The study revealed the regulatory mechanisms of FRLs and provided potential therapeutic targets.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biotechnology & Applied Microbiology
Shanglin Wang, Rong Fan, Huayu Gao, Xiaoli Ma, Yufei Wu, Yuanxin Xing, Yunshan Wang, Yanfei Jia
Summary: The overphosphorylation of signal transduction and transcriptional activator 5A (STAT5A) is associated with tumor invasion and poor prognosis in gastric cancer (GC). STAT5A promotes GC cell proliferation by upregulating CD44 expression and directly binds to the CD44 promoter to promote its transcription. The STAT5A/CD44 pathway plays a critical role in GC progression, showing potential clinical applications for improving GC treatment.
Article
Multidisciplinary Sciences
Lauana Pereira de Oliveira, Bruno Viana Navarro, Joao Pedro de Jesus Pereira, Adriana Rios Lopes, Marina C. M. Martins, Diego Mauricio Riano-Pachon, Marcos Silveira Buckeridge
Summary: This study comprehensively analyzed the sequences and expression levels of enzymes involved in trehalose metabolism in sugarcane, and specifically investigated the post-translational modifications and residues involved in catalysis and substrate binding of trehalose-6-phosphate synthase. The findings revealed the presence of multiple genes related to trehalose metabolism in sugarcane, and identified differences in enzyme activity between TPS Class I and TPS Class II.
SCIENTIFIC REPORTS
(2022)
Article
Plant Sciences
Mouboni Dutta, Anusree Saha, Mazahar Moin, Pulugurtha Bharadwaja Kirti
Summary: This study analyzed the expression patterns of rice GRAS TF genes under abiotic and biotic stress conditions, identifying genes that were induced immediately after stress onset, especially in the roots of ABA-treated plants. OsGRAS39 was found to be highly expressed under sheath blight infection and abiotic stress treatments, with OsGRAS8, OsSHR1 and OsSLR1 also showing responsiveness. The research suggests that GRAS genes are potential candidate genes for enhancing stress tolerance in rice and other crop plants.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Multidisciplinary Sciences
Yingyan Yu, Zhen Zhang, Xiaorui Dong, Ruixin Yang, Zhongqu Duan, Zhen Xiang, Jun Li, Guichao Li, Fazhe Yan, Hongzhang Xue, Du Jiao, Jinyuan Lu, Huimin Lu, Wenmin Zhang, Yangzhen Wei, Shiyu Fan, Jing Li, Jingya Jia, Jun Zhang, Jun Ji, Pixu Liu, Hui Lu, Hongyu Zhao, Saijuan Chen, Chaochun Wei, Hongzhuan Chen, Zhenggang Zhu
Summary: Pangenomic study can improve the completeness of the human reference genome and advance precision medicine. In gastric cancer research, highly absent genes were identified and new genes associated with gastric cancer were predicted.
NATURE COMMUNICATIONS
(2022)
Article
Biology
Tong Xu, Mathijs Verhagen, Rosalie Joosten, Wenjie Sun, Andrea Sacchetti, Leonel Munoz Sagredo, Veronique Orian-Rousseau, Riccardo Fodde
Summary: Phenotypic plasticity plays a crucial role in allowing carcinoma cells to acquire transient mesenchymal features for invasion and metastasis. Epithelial-to-mesenchymal (EMT) and mesenchymal-to-epithelial (MET) transitions are regulated by a broad range of epigenetic mechanisms, including alternative splicing (AS). In this study, we focus on the role of AS in eliciting phenotypic plasticity in colon cancer and identify specific RNA-binding proteins (RBPs) that alter AS patterns, leading to the generation of splicing isoforms associated with increased invasion and metastasis. Further validation studies show that these RBPs and splicing isoforms promote local invasion and distant metastasis in colon cancer and are associated with poor survival.
Article
Immunology
Chao Li, Tan Yang, Yu Yuan, Rou Wen, Huan Yu
Summary: This study aimed to identify key biomarkers and elucidate immune cell infiltration and related pathways in gastric cancer (GC). The results showed that certain genes were closely associated with GC, and immune cell infiltration was observed in patients with GC. This is of great importance for understanding the development of GC, identifying new immunotherapeutic targets, and disease prevention.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Cell Biology
Alina van Dieken, Hinrich Staecker, Heike Schmitt, Jennifer Harre, Andreas Pich, Willi Rossberg, Thomas Lenarz, Martin Durisin, Athanasia Warnecke
Summary: This study analyzes the perilymph proteome of cochlear implantation patients, identifying multiple proteins and patterns that can characterize patient subgroups. By predicting the protein composition of perilymph, the study helps understand the contribution of cochlear cells and proposes a human atlas of the cochlea. Additionally, druggable targets within the perilymph proteome are identified.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Review
Oncology
Carlo Ganini, Ivano Amelio, Riccardo Bertolo, Pierluigi Bove, Oreste Claudio Buonomo, Eleonora Candi, Chiara Cipriani, Nicola Di Daniele, Hartmut Juhl, Alessandro Mauriello, Carla Marani, John Marshall, Sonia Melino, Paolo Marchetti, Manuela Montanaro, Maria Emanuela Natale, Flavia Novelli, Giampiero Palmieri, Mauro Piacentini, Erino Angelo Rendina, Mario Roselli, Giuseppe Sica, Manfredi Tesauro, Valentina Rovella, Giuseppe Tisone, Yufang Shi, Ying Wang, Gerry Melino
Summary: Advancements in sequencing technologies have enabled more accurate and comprehensive cancer sequencing projects, such as deep sequencing of entire genomes, bypassing the high costs of whole-genome sequencing. Large-scale WGS applications on databases have allowed scientists to analyze molecular features, large structural variations, and noncoding regions of the genome globally for the first time. Thorough deciphering of the vast amount of data is needed, with the emergence of machine-learning approaches expected to lead to the development of personalized approaches for cancer medicine.
MOLECULAR ONCOLOGY
(2021)
Article
Multidisciplinary Sciences
Dovydas Sirvinskas, Omid Omrani, Jing Lu, Mahdi Rasa, Anna Krepelova, Lisa Adam, Sandra Kaeppel, Felix Sommer, Francesco Neri
Summary: We performed single-cell sequencing of aging mouse colonic epithelium and immune cells, and identified significant aging-associated changes in cell composition and signaling pathways. Our study provides new insights into the normal and age-associated states of the colon.
