Article
Immunology
Huiting Xiao, Jiashuai Zhang, Kai Wang, Kai Song, Hailong Zheng, Jing Yang, Keru Li, Rongqiang Yuan, Wenyuan Zhao, Yang Hui
Summary: In this study, a novel method called Tumor-infiltrating Immune Cell Proportion Estimator (TICPE) was introduced to estimate the proportion of immune cells in specific types of cancer. The TICPE, based on relative expression orderings of gene pairs, showed superior accuracy in estimating immune cell proportion compared to other methods, and it was found to be insensitive to batch effects. Additionally, TICPE demonstrated the ability to detect prognostic signals in patients with tumors and changes in immune cell fractions during immunotherapy in melanoma.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Immunology
Hanne Locy, Stefaan Verhulst, Wilfried Cools, Wim Waelput, Stefanie Brock, Louise Cras, Ann Schiettecatte, Jan Jonckheere, Leo A. van Grunsven, Marian Vanhoeij, Kris Thielemans, Karine Breckpot
Summary: Scoring of tumor-infiltrating lymphocytes (TILs) in breast cancer specimens is important for prognosis and prediction. Integration of immunohistochemistry and gene expression analysis can refine TIL scoring. Tissue sections stained for CD3 and CD8 show high reproducibility.
FRONTIERS IN IMMUNOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Petra Korac, Mariastefania Antica, Maja Matulic
Summary: miR-7 is an ancient miRNA involved in cell signaling pathways, acting primarily as a tumor suppressor by inhibiting cell proliferation and promoting apoptosis. It also has additional roles in cell regulation and protection, with potential for use in biotherapeutics.
Article
Medicine, General & Internal
Peng Sun, Jiehua He, Xue Chao, Keming Chen, Yuanyuan Xu, Qitao Huang, Jingping Yun, Mei Li, Rongzhen Luo, Jinbo Kuang, Huajia Wang, Haosen Li, Hui Hui, Shuoyu Xu
Summary: This study establishes a computational TIL assessment method using deep learning, providing valuable prognostic information for TNBC patients. A three-tier stratification model combining mTIL and aTIL shows a higher C-index, indicating its potential for improved risk management and decision-making by pathologists.
Review
Oncology
Guoming Hu, Shimin Wang, Songxiang Wang, Qiannan Ding, Liming Huang
Summary: This meta-analysis revealed that the infiltration of LAG-3(+) lymphocytes is associated with improved overall survival in triple-negative breast cancer (TNBC) and HER2-positive breast cancer (BC), suggesting it as a promising prognostic biomarker. However, it is not significantly correlated with disease-free survival. Therefore, the use of anti-LAG-3 antagonists may not be a promising therapeutic strategy for human BC, especially for TNBC.
FRONTIERS IN ONCOLOGY
(2023)
Article
Immunology
DQ. Cai, Diankui Cai, Yiping Zou, Xumeng Chen, Zhixiang Jian, Mude Shi, Ye Lin, Jueming Chen
Summary: CD8+ T cell exhaustion has been found to negatively impact immunotherapy outcomes. The molecular functions and mechanisms of action of this exhaustion in chemoresistance are still unclear. In this study, a chemoresistant TILCD8T signature (cr-TILCD8TSig) was identified using gene expression data, and it was found to independently predict prognosis, chemotherapy response, and immunotherapy outcomes in breast cancer patients.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Medicine, General & Internal
Kathleen Schueler, Daniel Bethmann, Sandy Kaufhold, Carolin Hartung, Kathrin Stueckrath, Tilmann Lantzsch, Christoph Uleer, Volker Hanf, Susanne Peschel, Jutta John, Marleen Poehler, Jorg Buchmann, Karl-Friedrich Buerrig, Edith Weigert, Christoph Thomssen, Eva Johanna Kantelhardt, Martina Vetter
Summary: Tumour-infiltrating lymphocytes (TILs) have prognostic and predictive value for patients with early breast cancer, especially in HER2-positive breast cancer. The distribution of TILs varies among different breast cancer types, and the percentage of TILs is associated with improved prognosis.
Article
Oncology
Xinyue Li, Jing Yang
Summary: This study investigated the relationship between tumor deposits and clinicopathological characteristics, tumor-infiltrating lymphocytes, and prognosis in gastric cancer. The results showed a significant association between tumor deposits and various characteristics and prognosis of gastric cancer, with patients having more than 4 tumor deposits having a worse prognosis.
WORLD JOURNAL OF SURGICAL ONCOLOGY
(2022)
Review
Oncology
You Qin, Fei Peng, Lisha Ai, Shidai Mu, Yuting Li, Chensu Yang, Yu Hu
Summary: The meta-analysis shows that a high level of TIL-Bs is associated with longer overall survival, breast cancer-specific survival, and disease-free/relapse-free survival in breast cancer patients. This suggests that TIL-Bs could serve as a promising prognostic marker for breast cancer, and may lead to the development of novel therapeutic strategies by enhancing B cell-mediated antitumor immunity.
CANCER CELL INTERNATIONAL
(2021)
Article
Multidisciplinary Sciences
Chitra Thakur, Yiran Qiu, Qian Zhang, Nicholas J. Carruthers, Miaomiao Yu, Zhuoyue Bi, Yao Fu, Priya Wadgaonkar, Bandar Almutairy, Akimasa Seno, Paul M. Stemmer, Fei Chen
Summary: This report provides evidence of diminished expression of the mineral dust-induced gene (mdig) in human triple negative breast cancer (TNBC). The study demonstrates that mdig promotes the growth of primary tumors but inhibits metastasis of TNBC cells. The findings also suggest a potential role of mdig in regulating genes related to cell motility, invasion, and metastasis.
Article
Medicine, General & Internal
Lijun Wang, Hao Wang, Song Wei, Zhihong Zhang
Summary: This study investigated tumor infiltrating lymphocytes (TILs) and prognosis-associated genes in the tumor microenvironment of female lung adenocarcinoma patients. The results identified key genes and immune cell proportions that are significantly related to overall survival, providing new insights for future clinical studies.
Article
Oncology
Yan Yuan, Wei-Wei Xiao, Wei-Hao Xie, Rong-Zhen Li, Yuan-Hong Gao
Summary: The study revealed that UBE2W was abnormally expressed in breast cancer and significantly correlated with mismatch repair gene mutation levels, DNA methyltransferase, and BRCA1/2 expression. High expression of UBE2W may promote tumor immunosuppression and metastasis, induce endocrine therapy resistance and worsen outcomes for patients with breast cancer. These findings suggest that UBE2W could serve as a potential prognostic biomarker and play a role in tumor-infiltrating immune cells.
Article
Oncology
Surbhi Bansil, Anthony Silva, Alana Taniguchi, Christina Wiedmer, Mayumi Fernandez, Ian Pagano, Koah Vierkoetter, Jeffrey Killeen, Jami Fukui
Summary: Tumor-infiltrating lymphocytes (TILs) have emerged as predictors of breast cancer treatment response and patient outcomes. This study provides preliminary data on the breast cancer tumor microenvironment for Asian and Native Hawaiian/Pacific Islander racial/ethnic groups, which are underrepresented in the literature.
Article
Multidisciplinary Sciences
Jianguo Luo, Shaojun Chen, Jingsen Chen, Yige Zhou, Fei He, Enli Wang
Summary: This study identified differential DNA methylation profile in breast cancer with and without axillary lymph node metastasis (ALNM) using reduced representation bisulfite sequencing (RRBS). The results showed that lymph node positive breast cancer had hypermethylation in promoter regions of genes RASGRF2, AKR1B1, CRMP1, and hypomethylation in promoter region of gene RHOF. These findings provide important insights into the molecular mechanisms underlying ALNM in breast cancer.
Article
Oncology
Wenhua Xu, Wenna Yang, Chunfeng Wu, Xiaocong Ma, Haoyu Li, Jinghui Zheng
Summary: The study reveals that ENO1 expression in multiple tumor tissues is associated with prognosis, tumor stage, and tumor-infiltrating immune cells, suggesting that ENO1 may serve as a potential prognostic biomarker that correlates with cancer progression and immune infiltration.
FRONTIERS IN ONCOLOGY
(2021)
Article
Oncology
Qin Huo, Jianhui Yuan, Ting Zhu, Zhenwei Li, Ni Xie
Summary: The study identified a significant correlation between ABCG2 expression and clinical-pathological parameters in breast cancer patients, as well as its involvement in multiple oncogenic pathways. Using magnetic nanoparticles to deliver siRNA targeting ABCG2 effectively improved the therapeutic effect of DOX on tumors.
RECENT PATENTS ON ANTI-CANCER DRUG DISCOVERY
(2021)
Article
Oncology
Qin Huo, Xi He, Zhenwei Li, Fan Yang, Shengnan He, Ling Shao, Ye Hu, Siqi Chen, Ni Xie
Summary: The study found that SCUBE3 is significantly upregulated in breast cancer tissue, and high expression is associated with poorer prognosis in ER-, PR-, and HER2+ breast cancer patients. Multivariate Cox regression analysis indicated that high SCUBE3 expression is linked to poor prognosis in breast cancer.
CANCER CELL INTERNATIONAL
(2021)
Article
Genetics & Heredity
Qin Huo, Siqi Chen, Zhenwei Li, Juan Wang, Jiaying Li, Ni Xie
Summary: The study found that TACC3 is highly expressed in breast cancer tissues and positively correlated with clinical features, potentially serving as a diagnostic indicator. Inhibition of TACC3 promotes cell proliferation and viability of breast cancer cells, while also impacting cell migration. Overall, TACC3 may serve as a prognostic and therapeutic indicator of breast cancer.
FRONTIERS IN GENETICS
(2021)
Article
Biochemical Research Methods
Ran Wang, Xubin Zheng, Jun Wang, Shibiao Wan, Fangda Song, Man Hon Wong, Kwong Sak Leung, Lixin Cheng
Summary: This study introduces a new method called scPAGE, which utilizes single-cell pair-wise gene expression to transfer knowledge across platforms, with applications in acute myeloid leukemia research. The results show that scGPS performs better in bulk RNA-seq classification than traditional gene expression strategies, demonstrating potential in revealing the molecular mechanisms of AML and emphasizing the benefits of gene signature transfer.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Juan Wang, Fan Yang, Jialang Zhuang, Qin Huo, Jiaying Li, Ni Xie
Summary: This study reveals the role of TRIM58 in the development of chemotherapy resistance in breast cancer and provides potential therapeutic targets through the interaction with DDX3 and the P53/P21 pathway.
INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY
(2022)
Article
Oncology
Tingting Deng, Yang Liu, Jialang Zhuang, Yizhe Tang, Qin Huo
Summary: The high expression of ASPM is associated with poor prognosis and increased levels of immune cell infiltration in kidney renal clear cell carcinoma (KIRC) and liver hepatocellular carcinoma (LIHC).
FRONTIERS IN ONCOLOGY
(2022)
Article
Biochemical Research Methods
Qiong Wu, Xubin Zheng, Kwong-Sak Leung, Man-Hon Wong, Stephen Kwok-Wing Tsui, Lixin Cheng
Summary: This study introduces a novel strategy using DNA methylation and RNA expression data to discriminate hepatocellular carcinoma (HCC). Immune genes with negative correlations between expression and promoter methylation are identified as candidates for HCC detection. A methylation GPS (mGPS) and an expression GPS (eGPS) are separately constructed and then assembled into a meGPS, which successfully detects and predicts HCC with reliable performance validated by independent datasets. This study provides potential molecular targets for the detection and therapy of HCC.
Article
Genetics & Heredity
Lvwen Ning, Qin Huo, Ni Xie
Summary: This study analyzed the expression pattern and prognostic values of TRIMs in breast cancer, and identified several TRIMs that may contribute to tumor progression and TRIM45 as a potential new prognostic biomarker for breast cancer.
FRONTIERS IN GENETICS
(2022)
Article
Biology
Haili Li, Xubin Zheng, Jing Gao, Kwong-Sak Leung, Man-Hon Wong, Shu Yang, Yakun Liu, Ming Dong, Huimin Bai, Xiufeng Ye, Lixin Cheng
Summary: The regulation of non-coding RNA is associated with the diagnosis and targeted therapy of complex diseases. By constructing a ceRNA network and using a novel motif, SOC index was found to be negatively correlated with the CD8+/CD4+ ratio in tumor infiltration, reflecting the migration and growth of tumor cells in ovarian cancer progression.
COMPUTERS IN BIOLOGY AND MEDICINE
(2022)
Article
Pharmacology & Pharmacy
Cong Xu, Wanyang Li, Tangzhiming Li, Jie Yuan, Xinli Pang, Tao Liu, Benhui Liang, Lixin Cheng, Xin Sun, Shaohong Dong
Summary: This study constructed a molecular signature of ACS based on iron metabolism-related genes and identified novel iron metabolism gene markers for early stage of ACS. By using Elastic Net algorithm, five genes with optimal performance were screened, and the prediction model can be used for early diagnosis of ACS.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Biochemical Research Methods
Ran Wang, Xubin Zheng, Fangda Song, Man Hon Wong, Kwong Sak Leung, Lixin Cheng
Summary: Human gut microbiota dysbiosis is associated with various diseases, and it is crucial to uncover the associations between gut microbiota and disease states along with other factors. Existing methods may lead to false associations, so we propose a new method to investigate gut microbiota using groups of related taxa instead of individual taxa. The results show that this method can better explain the relationships between gut microbiota and clinical factors, and it demonstrates effectiveness in identifying microbial modules.
Review
Biochemical Research Methods
Jun Wang, Marc Horlacher, Lixin Cheng, Ole Winther
Summary: RNA localization is important for spatial translation regulation, and this review discusses its molecular mechanisms, experimental techniques, and machine learning-based prediction tools. The three main molecular mechanisms controlling RNA localization to distinct cellular compartments, including directed transport, mRNA degradation protection, and diffusion/local entrapment, are reviewed. Advances in experimental methods provide ample data resources for the design of powerful machine learning models in RNA localization prediction. The review also covers publicly available predictive tools, serving as a guide for users and encouraging the development of more effective prediction models. Lastly, an overview of multimodal learning is presented as a potential new avenue for RNA localization prediction.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Engineering, Environmental
Liuzhi Hao, Shuwen Huang, Tongling Huang, Dan Yi, Chenmin Wang, Lixin Cheng, Min Guan, Jun Wu, Di Chen, Haobo Pan, William W. Lu, Xiaoli Zhao
Summary: This study provides a feasible and effective strategy for modifying engineered exosomes to enhance bone regeneration.
CHEMICAL ENGINEERING JOURNAL
(2023)
Article
Biochemical Research Methods
Lixin Cheng, Haonan Wu, Xubin Zheng, Ning Zhang, Pengfei Zhao, Ran Wang, Qiong Wu, Tao Liu, Xiaojun Yang, Qingshan Geng
Summary: This study developed an ensemble gene pair signature based on the IDH and 1p/19q status, which can serve as an independent predictor for risk stratification and survival prediction in glioma. The results showed that this ensemble signature had higher predictive accuracy compared to other prognostic signatures.
Article
Biochemical Research Methods
Qizhi Li, Xubin Zheng, Jize Xie, Ran Wang, Mengyao Li, Man-Hon Wong, Kwong-Sak Leung, Shuai Li, Qingshan Geng, Lixin Cheng
Summary: A diagnostic model based on host gene expression was used to diagnose acute infections. However, its clinical usage was limited due to small sample sizes. In this study, a large-scale dataset was constructed and analyzed using a sophisticated strategy to build gene pair signatures for bacterial, viral, and noninfected patients. These signatures were further combined into an antibiotic decision model with strong performance in distinguishing bacterial and viral infections.
