Article
Medicine, General & Internal
Boel Brynedal, Niyaz Yoosuf, Tinna Bjorg Ulfarsdottir, Daniel Ziemek, Mateusz Maciejewski, Lasse Folkersen, Helga Westerlind, Malin Mueller, Peter Sahlstrom, Scott A. Jelinsky, Aase Hensvold, Leonid Padyukov, Nancy Vivar Pomiano, Anca Catrina, Lars Klareskog, Louise Berg
Summary: This is a multi-omics study on the treatment of rheumatoid arthritis patients with methotrexate. The study found significant differences in molecular and cellular processes in peripheral blood between successful and unsuccessful treatment.
FRONTIERS IN MEDICINE
(2023)
Article
Medicine, General & Internal
Louis Kreitmann, Maxime Bodinier, Aurore Fleurie, Katia Imhoff, Marie-Angelique Cazalis, Estelle Peronnet, Elisabeth Cerrato, Claire Tardiveau, Filippo Conti, Jean-Francois Llitjos, Julien Textoris, Guillaume Monneret, Sophie Blein, Karen Brengel-Pesce
Summary: The immune profiling panel (IPP) gene set shows good performance in predicting 30-day mortality in sepsis patients, especially when gene expression is assayed at later time points during the course of sepsis. Prospective studies are needed to confirm these findings.
FRONTIERS IN MEDICINE
(2022)
Article
Immunology
Vandana Kulkarni, Artur T. L. Queiroz, Shashi Sangle, Anju Kagal, Sonali Salvi, Amita Gupta, Jerrold Ellner, Dileep Kadam, Valeria C. Rolla, Bruno B. Andrade, Padmini Salgame, Vidya Mave
Summary: This study identified an optimal gene signature for diagnosing tuberculosis in patients with advanced HIV using whole-blood RNA sequencing and machine learning algorithms. The signature showed high classification accuracy in cohorts from India and Uganda, indicating potential clinical utility.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Microbiology
Taylor Reiter, Rachel Montpetit, Shelby Byer, Isadora Frias, Esmeralda Leon, Robert Viano, Michael Mcloughlin, Thomas Halligan, Desmon Hernandez, Rosa Figueroa-Balderas, Dario Cantu, Kerri Steenwerth, Ron Runnebaum, Ben Montpetit
Summary: Ribosomal DNA and RNA sequencing data from grape musts and primary fermentations inoculated with Saccharomyces cerevisiae RC212 show that fungal organisms detected in musts are not necessarily active during fermentation and do not significantly impact gene expression of the inoculated yeast strain. However, genetic signatures reflective of vineyard site and region were identified within the sequencing data, providing insights into environmental factors that may influence fermentation outcomes and wine characteristics. These findings contribute to understanding the complexity of vineyard-specific wine fermentation and offer starting points for further research on factors contributing to regional wine distinctiveness.
Article
Microbiology
Jack Albright, Eran Mick, Estella Sanchez-Guerrero, Jack Kamm, Anthea Mitchell, Angela M. Detweiler, Norma Neff, Alexandra Tsitsiklis, Paula Hayakawa Serpa, Kalani Ratnasiri, Diane Havlir, Amy Kistler, Joseph L. DeRisi, Angela Oliveira Pisco, Charles R. Langelier
Summary: In this study, a 2-gene host-based COVID-19 diagnostic classifier was developed and validated using upper respiratory tract gene expression. The classifier demonstrated utility in reducing false-negative results caused by SARS-CoV-2 variants and false-positive viral PCR results due to laboratory cross-contamination.
Article
Oncology
Zhuofan Mou, Jack Spencer, Bridget Knight, Joseph John, Paul McCullagh, John S. McGrath, Lorna W. Harries
Summary: The study identified potential gene markers, including 5 genes, for predicting the survival progression of prostate cancer patients and established an effective nomogram for predicting survival progression.
FRONTIERS IN ONCOLOGY
(2022)
Article
Immunology
Yang Peng, Haochen Yu, Yudi Jin, Fanli Qu, Haoyu Ren, Zhenrong Tang, Yingzi Zhang, Chi Qu, Beige Zong, Shengchun Liu
Summary: The study established a gene signature to predict patient prognosis and treatment responses based on the relationship between immune cells and breast cancer progression. A higher immune infiltration-related risk score indicated a worse prognosis and less sensitivity to immunotherapy. A new nomogram combining gene signature and clinicopathological features was created to improve risk stratification and risk assessment for individual patients.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Immunology
Min Lin, Tian Du, Xiaofeng Tang, Ying Liao, Lan Cao, Yafang Zhang, Wei Zheng, Jianhua Zhou
Summary: This study aimed to construct an estrogen response-related gene signature for predicting response to immunotherapy in melanoma. The results showed that this gene signature can predict the response to immunotherapy in melanoma and is correlated with tumor-infiltrating lymphocytes.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Biology
Cuicui Liu, Zhijun Xiao, Shenghong Wu, Zhen Yang, Guowen Ji, Jingjing Duan, Ting Zhou, Jinming Cao, Xiufeng Liu, Feng Xu
Summary: The development of the HCC4 gene signature using machine learning algorithms shows significant potential in predicting survival outcomes, recurrence, tumor volume doubling time, treatment responses, and non-invasive detection of HCC. Patients with high HCC4 scores exhibit distinct genomic, transcriptomic, and proteomic features, as well as increased sensitivity to certain drugs. HCC4 outperforms previously published gene signatures in predicting overall survival.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Medicine, General & Internal
Shan Wu, Jing Xu, Guang Li, Xi Jin
Summary: This study aimed to identify gene signatures associated with radiosensitivity in gliomas for clinically stratifying patients who will benefit from adjuvant radiotherapy. The study integrated multiple predictive markers and established a new 12-gene radiosensitivity predictive index (PI12), which showed promising performance in terms of predictive ability and discriminative capacity. Furthermore, a nomogram combining clinical features and PI12 improved the histological grading system for gliomas.
MEDICINA-LITHUANIA
(2022)
Article
Oncology
Nan Zhao, Yanhui Zhang, Runfen Cheng, Danfang Zhang, Fan Li, Yuhong Guo, Zhiqiang Qiu, Xueyi Dong, Xinchao Ban, Baocun Sun, Xiulan Zhao
Summary: This study investigated the heterogeneity of tissue-wide gene expression in hepatocellular carcinoma (HCC) using spatial transcriptomics (ST) technology. It identified gene expression profiles associated with satellite nodules and constructed a gene signature model for HCC prognosis. These findings provide insights into the heterogeneity of HCC and potential therapeutic targets.
CANCER CELL INTERNATIONAL
(2022)
Article
Plant Sciences
Weiwei Xiao, Peng Liu, Kai Wang, Zhaoguang Yang, Lin Wang
Summary: The cultivation of paddy rice in flooded fields can lead to higher arsenic accumulation compared to other terrestrial crops. This study investigated the ionomics and transcriptomic variations in rice plants under arsenite stress, revealing that the upregulation of transporter genes was crucial for nutrient translocation to cope with arsenic toxicity. Further research is needed to fully understand the molecular mechanisms involved in the ionomics of rice plants.
ENVIRONMENTAL AND EXPERIMENTAL BOTANY
(2021)
Article
Cell Biology
Jinlai Zhao, Yigang Wang, Jianchao Gao, Yang Wang, Xuan Zhong, Xiaotang Wu, Hua Li
Summary: This study established a risk predication model based on 9 genes to effectively predict the prognosis of colon carcinoma patients. The high-risk group showed lower survival rates according to Kaplan-Meier curve, and significant differences in biological pathways were observed between high and low-risk groups through GSEA analysis. The model could efficiently predict prognosis in patients of different ages and stages, laying a foundation for further research on the molecular mechanisms of colon carcinoma development.
Article
Immunology
Shiao Tong, Minqi Xia, Yang Xu, Qian Sun, Liguo Ye, Jiayang Cai, Zhang Ye, Daofeng Tian
Summary: This study explores the hub genes of gliomas and their prognostic and diagnostic usefulness. Through analysis of multiple databases, the study identifies 170 DEGs related to gliomas and reveals their involvement in gliogenesis and extracellular matrix. Additionally, the study constructs a prognostic signature and validates its accuracy, and identifies hub genes with potential drug targeting capabilities. The study also finds that RPL39, one of the hub genes, is closely related to the prognosis of glioma patients. Knockdown of RPL39 inhibits the proliferation, migration, polarization, and infiltration of glioma cells. Overall, this study provides potential therapeutic strategies for glioma patients.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Medicine, General & Internal
Maria Tio-Coma, Szymon M. Kielbasa, Susan J. F. van den Eeden, Hailiang Mei, Johan Chandra Roy, Jacco Wallinga, Marufa Khatun, Sontosh Soren, Abu Sufian Chowdhury, Khorshed Alam, Anouk van Hooij, Jan Hendrik Richardus, Annemieke Geluk
Summary: The study identified a prospective transcriptional risk signature in blood that can predict the development of leprosy 4 to 61 months before clinical diagnosis. Using a machine learning approach, a leprosy signature was identified and validation showed potential value in confirming leprosy risk.