Review
Biochemistry & Molecular Biology
Fuwen Yuan, William Hankey, Eric J. Wagner, Wei Li, Qianben Wang
Summary: Alternative polyadenylation (APA) is a molecular process that generates diversity at the 3' end of RNA polymerase II transcripts from over 60% of human genes, mainly occurring within the untranslated region (3'UTR), leading to significant impact on the regulatory potential of mRNA.
Article
Biotechnology & Applied Microbiology
Zhenying Peng, Shuang Yu, Jingjing Meng, Kai-Hua Jia, Jialei Zhang, Xinguo Li, Wenwei Gao, Shubo Wan
Summary: The study found widespread alternative polyadenylation in peanut genes, crucial for peanut seed maturation. The AhACCA1 gene has four 3' UTRs, each showing tissue-specific expression patterns. Experimental evidence indicates that UTR2 has a stronger impact on gene expression regulation compared to the other UTRs.
Article
Biochemistry & Molecular Biology
Weiwei Jin, Qizhao Zhu, Yanbo Yang, Wenqian Yang, Dongyang Wang, Jiajun Yang, Xiaohui Niu, Debing Yu, Jing Gong
Summary: APA is a crucial post-transcriptional regulatory mechanism that impacts various biological processes in different species. A study systematically characterized APA profiles in 18 species using RNA sequencing data and developed a user-friendly database for further research and exploration.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Medicine, Research & Experimental
Yu-Long Lan, Jianmin Zhang
Summary: RNA modification is a crucial form of regulation in cancer biology, with untranslated region-alternative polyadenylation (UTR-APA) potentially playing a key role in the pathogenesis of glioma. Less targeted strategies, such as inhibitors of UTR-APA regulators, may have superior therapeutic effects in glioma treatment.
BIOMEDICINE & PHARMACOTHERAPY
(2021)
Article
Biochemical Research Methods
Wenbin Ye, Tao Liu, Hongjuan Fu, Congting Ye, Guoli Ji, Xiaohui Wu
Summary: movAPA is an R package for modeling and visualizing alternative polyadenylation dynamics across different biological samples, providing functions for preprocessing, annotation, and statistical analysis of poly(A) sites, as well as identification of poly(A) signals, profiling of APA dynamics, and visualization. It offers seven metrics for measuring tissue-specificity or usages of APA sites across samples, and uses three methods for identifying 3' UTR shortening/lengthening events. It also allows exploration of APA site switching involving non-3' UTR polyadenylation.
Article
Cell Biology
Larry C. Cheng, Dinghai Zheng, Qiang Zhang, Aysegul Guvenek, Hong Cheng, Bin Tian
Summary: Transcripts encoding membrane and secreted proteins can associate with the ER through translation-dependent or translation-independent mechanisms. Certain functional groups of genes, such as those involved in cell signaling, tend to have higher TiERA potentials, indicating the importance of ER association for their mRNA metabolism. Changes in transcript features, such as alternative polyadenylation isoforms and 3' UTR lengthening during cell differentiation, can affect the TiERA potential of transcripts. Competing with translation-dependent ER association, TiERA suggests a limited space on the ER for mRNA association.
Article
Radiology, Nuclear Medicine & Medical Imaging
Sung Eun Song, Ok Hee Woo, Yongwon Cho, Kyu Ran Cho, Kyong Hwa Park, Ju Won Kim
Summary: This study investigated the use of machine learning approaches with breast magnetic resonance imaging (MRI)-derived multiparametric and radiomic features to predict axillary lymph node metastasis (ALNM) in stage I-II triple-negative breast cancer (TNBC) patients. The results showed that radiomic features had good diagnostic performance in predicting ALNM.
ACADEMIC RADIOLOGY
(2023)
Article
Oncology
Walter Carbajal-Ochoa, Daniela C. Bravo-Solarte, Ana M. Bernal, Jesus D. Anampa
Summary: Current guidelines recommendations regarding chemotherapy in small, node-negative triple-negative breast cancer differ due to lack of high-quality data. Our study suggests that adjuvant chemotherapy is beneficial for patients with node-negative, T1c TNBC, but does not improve breast cancer specific survival in patients with node-negative, T1b TNBC.
BREAST CANCER RESEARCH AND TREATMENT
(2023)
Article
Biochemical Research Methods
Xiaohui Wu, Tao Liu, Congting Ye, Wenbin Ye, Guoli Ji
Summary: APA plays a crucial role in transcriptome diversity and gene expression regulation. The newly developed tool scAPAtrap can accurately identify poly(A) sites at the whole genome level in individual cells, even for sites with low read coverage, without relying on priori genome annotation. Compared to existing methods, scAPAtrap shows higher accuracy and sensitivity in identifying poly(A) sites, making it a valuable tool for exploring APA dynamics and heterogeneous APA isoform expression at the single-cell level.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Plant Sciences
Taotao Wang, Wenbin Ye, Jiaxiang Zhang, Han Li, Weike Zeng, Sheng Zhu, Guoli Ji, Xiaohui Wu, Liuyin Ma
Summary: High-salt stress induces global alternative polyadenylation (APA) dynamics in Spartina alterniflora, leading to 3'UTR lengthening of transcripts and increased protein synthesis. These alternative 3'UTRs are mainly enriched in salt stress-related ion transporters, such as SaHKT1. Regulatory AU-rich elements in alternative 3'UTRs enhance the protein level of SaHKT1, and the biogenesis of 3'UTR lengthening in SaHKT1 is controlled by SaCPSF30. Over-expression of SaHKT1 with an alternative 3'UTR in rice protoplasts promotes the mRNA accumulation of salt-tolerance genes.
Article
Oncology
Wenting Peng, Caijin Lin, Shanshan Jing, Guanhua Su, Xi Jin, Genhong Di, Zhiming Shao
Summary: This study established clinical prognostic model, seven-gene signature, and combined model for predicting distant metastasis risk in lymph node-negative TNBC patients. The seven-gene signature showed significant differentiation of distant metastasis risk in both training and validation sets. The composite clinical and gene signature demonstrated improved prognostic accuracy compared to the clinical signature.
FRONTIERS IN ONCOLOGY
(2021)
Article
Genetics & Heredity
Zhongxiao Li, Yisheng Li, Bin Zhang, Yu Li, Yongkang Long, Juexiao Zhou, Xudong Zou, Min Zhang, Yuhui Hu, Wei Chen, Xin Gao
Summary: In this study, we propose a deep learning architecture, DeeReCT-APA, to quantitatively predict the usage of all alternative polyadenylation sites (PASs) of a given gene. Compared to existing methods, DeeReCT-APA outperforms in multiple tasks and can be used to predict the effect of genetic variations on APA patterns.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2022)
Article
Medicine, General & Internal
Marina Popovic Krneta, Dragana Sobic Saranovic, Ljiljana Mijatovic Teodorovic, Nemanja Krajcinovic, Natasa Avramovic, Zivko Bojovic, Zoran Bukumiric, Ivan Markovic, Sasa Rajsic, Biljana Bazic Djorovic, Vera Artiko, Mihajlo Karlicic, Miljana Tanic
Summary: This study evaluated and compared four machine learning-based classifiers to predict the presence of cervical lymph node metastasis in clinically node-negative T1 and T2 papillary thyroid carcinoma patients. The k-Nearest Neighbor classifier was found to be the best fit, with an area under the receiver operating characteristic curve of 0.72. A web application based on the sensitivity-optimized kNN classifier was also created to predict the potential of cervical lymph node metastasis. These findings suggest that machine learning can improve the prediction of lymph node metastasis in papillary thyroid carcinoma, aiding in individual treatment planning.
JOURNAL OF CLINICAL MEDICINE
(2023)
Article
Oncology
Aleksander Slusarczyk, Piotr Zapala, Tomasz Piecha, Pawel Rajwa, Marco Moschini, Piotr Radziszewski
Summary: The benefit of lymph node dissection (LND) in lymph node-negative UTUC remains controversial. This study aimed to assess the association between LND and survival in LN-negative UTUC. The findings suggest that LND, especially when at least four lymph nodes were removed, is associated with improved cancer-specific survival and overall survival in UTUC patients.
Article
Genetics & Heredity
Shaofeng Lin, Yanping Chen, Jianchao Wang, Yibin Cai, Xiaohui Chen, Yuanmei Chen, Yi Shi, Gang Chen, Kunshou Zhu
Summary: In this study, whole-exome sequencing was performed on tissue samples from six esophageal cancer patients with lymph node metastasis. Significant differences in somatic mutations between metastatic lymph nodes and primary lesions were identified, and pathway enrichment analysis and subclonality analysis revealed commonalities and heterogeneity among the patients, highlighting the potential of identifying tumor-specific mutations for effective intervention and improving prognosis.
FRONTIERS IN GENETICS
(2022)