Article
Biochemistry & Molecular Biology
Aleix Noguera-Castells, Carlos A. Garcia-Prieto, Damiana Alvarez-Errico, Manel Esteller
Summary: DNA methylation, a well-studied epigenetic mark, plays a critical role in gene regulation and is altered in cancer and other diseases. The newly developed 900K EPIC v2 microarray provides significant improvements in coverage and includes additional probes for DNA cis-regulatory regions. Validation studies demonstrate the reproducibility and versatility of this updated tool for studying the DNA methylome.
Article
Oncology
Andreas Agathangelidis, Elisavet Vlachonikola, Frederic Davi, Anton W. Langerak, Anastasia Chatzidimitriou
Summary: Precision medicine aims to overcome the complexity of cancer through integrating information from different 'subsystems'. Immunogenetics, facilitated by high-throughput approaches, enables a comprehensive understanding of the immune repertoire and improves clinical decision making. This article highlights the clinical utility of immunogenetic analysis in lymphoid malignancies, including diagnosis, disease monitoring, and its potential for immunotherapy.
SEMINARS IN CANCER BIOLOGY
(2022)
Review
Chemistry, Analytical
Gabrielle Kosoy, Benjamin L. Miller
Summary: Arrayed imaging reflectometry (AIR) is a thin-film interference sensor technique that can be used for detecting various biomolecules and pathogens, and it has high sensitivity and multiplex capability.
Article
Oncology
Jaqueline Loaeza-Loaeza, Berenice Illades-Aguiar, Oscar del Moral-Hernandez, Yaneth Castro-Coronel, Marco A. Leyva-Vazquez, Roberto Dircio-Maldonado, Julio Ortiz-Ortiz, Daniel Hernandez-Sotelo
Summary: This study analyzed the methylation of 8 genes involved in maintaining cell normality and found that high CIMP is significantly associated with the risk of HSIL and CC.
CLINICAL EPIGENETICS
(2022)
Article
Oncology
Min-Qiu Lu, Yu-Qin He, Yin Wu, Hui-Xing Zhou, Yuan Jian, Wen Gao, Li Bao, Wen-Ming Chen
Summary: This study aimed to explore the potential effects of long non-coding RNAs (lncRNAs) in multiple myeloma (MM) patients using two detection methods: high-throughput sequencing and microarray. The study found that certain lncRNAs were aberrantly expressed in MM and identified the top 5 common pathways associated with MM. Furthermore, three microRNAs (miRNAs) were found to constitute competing endogenous RNA (ceRNA) networks in MM. The combination analysis significantly increased our understanding of lncRNAs in MM and identified more overlapping differentially expressed lncRNAs as potential therapeutic targets.
FRONTIERS IN ONCOLOGY
(2023)
Review
Microbiology
Tara E. Ness, Andrew DiNardo, Maha R. Farhat
Summary: High throughput sequencing (HTS) can detect the presence of Mycobacterium tuberculosis DNA in clinical samples and provide information on drug susceptibility. Multiple studies have laid the groundwork for exploring the clinical application of HTS in tuberculosis diagnosis. This article presents the workflow challenges, strengths, and limitations of different sequencing platforms, as well as the tools used for analysis, to provide a framework for further innovations in the field.
Article
Immunology
Son H. McLaren, Nischay Mishra, Nobuko Hijiya, James Ng, Cheng Guo, Susan Whittier, Erica Mariani, Laura Glaser, Irene Frantzis, Marc T. Vindas, Cheng-Shiun Leu, Peter S. Dayan
Summary: In this pilot study, we found that a novel high-throughput sequencing platform, called BacCapSeq, had moderate agreement with blood culture in diagnosing bacteremia among children with cancer presenting with fever. There were discordant organisms, some of which were clinically irrelevant.
PEDIATRIC INFECTIOUS DISEASE JOURNAL
(2023)
Review
Medicine, General & Internal
Xuejun He, Ningzhi Zhang, Wenye Cao, Yiqiao Xing, Ning Yang
Summary: Advancements in high-throughput sequencing (HTS) technology have provided new insights into the etiology, signaling pathways, and biomarkers of ocular diseases, aiding in improving their diagnosis and research.
JOURNAL OF CLINICAL MEDICINE
(2022)
Review
Chemistry, Analytical
Lina Shi, Sutong Liu, Xue Li, Xiwei Huang, Hongzhi Luo, Qianwen Bai, Zhu Li, Lijun Wang, Xiaoxin Du, Cheng Jiang, Shan Liu, Chenzhong Li
Summary: High-throughput screening platforms are crucial for processing large amounts of experimental data rapidly and efficiently. The development of miniaturized high-throughput screening platforms is essential in the fields of biotechnology, medicine, and pharmacology. Droplet microarrays, as novel screening platforms, can effectively overcome the disadvantages of traditional microtiter plates, such as high reagent and cell consumption, low throughput, and cross-contamination. This article provides a brief overview of the preparation and compound addition methods of droplet microarrays, as well as their applications in biomedicine, drug development, and individualized medicine.
Article
Biotechnology & Applied Microbiology
Aziz M. Al'Khafaji, Jonathan T. Smith, Kiran V. Garimella, Mehrtash Babadi, Victoria Popic, Moshe Sade-Feldman, Michael Gatzen, Siranush Sarkizova, Marc A. Schwartz, Emily M. Blaum, Allyson Day, Maura Costello, Tera Bowers, Stacey Gabriel, Eric Banks, Anthony A. Philippakis, Genevieve M. Boland, Paul C. Blainey, Nir Hacohen
Summary: Full-length RNA-sequencing methods using long-read technologies are limited in throughput. We introduce MAS-ISO-seq, a technique that programmably concatenates cDNAs for long-read sequencing, increasing throughput by >15-fold to nearly 40 million cDNA reads per run. Applied to single-cell RNA sequencing of tumor-infiltrating T cells, MAS-ISO-seq showed a 12- to 32-fold increase in the discovery of differentially spliced genes.
NATURE BIOTECHNOLOGY
(2023)
Article
Chemistry, Multidisciplinary
George I. Lambrou, Kleanthis Vichos, Dimitrios Koutsouris, Apostolos Zaravinos
Summary: Urinary bladder cancer (UBC) is the second most common urogenital solid tumor, with several new candidate prognostic markers identified. This study aimed to detect global gene co-expression profiles among a high number of UBC tumors, resulting in the identification of novel candidate markers and potential drugs for the disease.
APPLIED SCIENCES-BASEL
(2021)
Article
Chemistry, Multidisciplinary
Junfang Xie, Daobo Han, Shuai Xu, Haitong Zhang, Yonghe Li, Mingshan Zhang, Zhichao Deng, Jianguo Tian, Qing Ye
Summary: A high-throughput and high-content drug screening method was established by preparing a superhydrophobic microwell array plate (SMAP) and combining it with protein-retention expansion microscopy (proExM). The SMAP was prepared using photolithography, and cells were cultured and treated with different drugs using a microcolumn-microwell sandwiching technology. ProExM was then applied for super-resolution imaging. The successful combination of high throughput and high content was demonstrated by collecting a 7 x 7 image array of microtubules within 3 hours with 68 nm resolution, and revealing more details of microtubule and mitochondria morphological changes after drug treatment.
Article
Chemistry, Analytical
Haixu Yang, Jiahui Yu, Luhong Jin, Yunpeng Zhao, Qi Gao, Changrong Shi, Lei Ye, Dong Li, Hai Yu, Yingke Xu
Summary: Droplet digital PCR (ddPCR) is a technique for quantifying nucleic acid molecules, and accurate recognition of positive droplets in ddPCR images is crucial for accurate analysis. In this study, we developed a deep learning-based ddPCR droplet detection framework that can achieve high-precision localization and classification of droplets under different illumination conditions, improving the accuracy and robustness of analysis.
Article
Biology
James K. Bonfield, John Marshall, Petr Danecek, Heng Li, Valeriu Ohan, Andrew Whitwham, Thomas Keane, Robert M. Davies
Summary: This paper introduces a software library for programmatic access to sequencing alignment and variant formats, derived from SAMtools and BCFtools applications, with many improvements and new features added. Performance has significantly improved since the original Samtools release, with wide adoption and integration into different languages.
Article
Health Care Sciences & Services
Lingyu Huang, Tongxiang Zou, Wenken Liang, Chune Mo, Jianfen Wei, Yecheng Deng, Minglin Ou
Summary: Rotundine inhibits the development and progression of colorectal cancer by regulating the expression of prognosis-related genes, providing new directions for the treatment of colorectal cancer.
JOURNAL OF PERSONALIZED MEDICINE
(2023)
Article
Oncology
I-Ying Kuo, Danping Liu, Wu-Wei Lai, Yi-Ching Wang, Y. Peng Loh
Summary: This study evaluates the efficacy of CPE/CPE-Delta N mRNA as a biomarker for predicting recurrence in lung adenocarcinoma patients. The results show that CPE/CPE-Delta N copy number is associated with recurrence and death, and it performs better in predicting recurrence in stage I and II patients.
Article
Medicine, Research & Experimental
Pei-Shan Yang, Min-Hua Yu, Ya-Chin Hou, Chih-Peng Chang, Shao-Chieh Lin, I-Ying Kuo, Pei-Chia Su, Hung-Chi Cheng, Wu-Chou Su, Yan-Shen Shan, Yi-Ching Wang
Summary: This study provides the first evidence that Rab37 mediates CHI3L1 secretion in immune cells and highlights the dual properties of CHI3L1 nAbs that can target both cancer cells and the tumor microenvironment.
Article
Oncology
Hsueh-Chien Chiang, Meng-Ying Lin, Forn-Chia Lin, Nai-Jung Chiang, Yi-Ching Wang, Wu-Wei Lai, Wei-Lun Chang, Bor-Shyang Sheu
Summary: This study aimed to compare the sensitivity of serum prealbumin, transferrin, and albumin in detecting malnutrition and predicting survival in esophageal cancer patients. The results showed that prealbumin and transferrin outperformed albumin in identifying malnutrition and poor prognosis.
NUTRITION AND CANCER-AN INTERNATIONAL JOURNAL
(2022)
Article
Oncology
Yung-Ching Chen, Ming-Jer Young, Hui-Ping Chang, Chia-Yu Liu, Chia-Chi Lee, Yau-Lin Tseng, Yi-Ching Wang, Wen-Chang Chang, Jan-Jong Hung
Summary: This study reveals that estrogen negatively regulates DNMT1 and p53 expression in female lung cancer, which not only affects tumor cells but also modulates the tumor microenvironment, leading to a poor prognosis.
Review
Medicine, Research & Experimental
Chih-Hsiung Hsieh, Yi-Ching Wang
Summary: The protein gelsolin plays a significant role in controlling cytoskeletal remodeling, cell morphology, differentiation, movement, and apoptosis. Its expression has been found to be decreased in various pathological conditions and it has emerged as a potential diagnostic biomarker for early disease detection. Gelsolin can function as either an oncoprotein or a tumor suppressor depending on the type of carcinoma. This review discusses the roles of gelsolin in inflammation and wound healing, cancers, and tumor microenvironment, as well as future prospects for related studies and clinical application.
KAOHSIUNG JOURNAL OF MEDICAL SCIENCES
(2022)
Article
Oncology
Yi-Zih Kuo, Ya-Rong Kang, Wei-Lun Chang, Lydia Chin-Ling Sim, Tzu-Chin Hsieh, Chu-Han Chang, Yi-Ching Wang, Ching-Jung Tsai, Li-Chun Huang, Sen-Tien Tsai, Li-Wha Wu
Summary: YAP1 acts as a tumor suppressor in esophageal cancer, while TAZ plays a pro-tumor role. YAP1 negatively regulates the expression of TAZ through transcriptional and translational control.
Article
Cell Biology
Shan-Ying Wu, Hung-Tsung Wu, Yi-Ching Wang, Chih-Jen Chang, Yan-Shen Shan, Shang-Rung Wu, Yen-Chi Chiu, Chia-Lang Hsu, Hsueh-Fen Juan, Kai-Ying Lan, Chi-Wen Chu, Ying-Ray Lee, Sheng-Hui Lan, Hsiao-Sheng Liu
Summary: This study reveals that secretory autophagy promotes RAB37-mediated insulin secretion to maintain the homeostasis of insulin and glucose.
Correction
Oncology
Yi-Zih Kuo, Ya-Rong Kang, Wei-Lun Chang, Lydia Chin Ling Sim, Tzu-Chin Hsieh, Chu-Han Chang, Yi-Ching Wang, Ching-Jung Tsai, Li-Chun Huang, Sen-Tien Tsai, Li-Wha Wu
Article
Biochemistry & Molecular Biology
Wei-Lun Chang, Chih-Hsiung Hsieh, I-Ying Kuo, Chien-Hsun Lin, Yu-Lin Huang, Yi-Ching Wang
Summary: A novel therapeutic agent, Nutlin-3, has been proposed to enhance the treatment efficacy of chemoradiation-resistant ESCC by regulating the expression of transcription factor proteins p53 and RB and downregulating the level of DNA methyltransferase. It has the potential for clinical application.
MOLECULAR CARCINOGENESIS
(2022)
Editorial Material
Cell Biology
Shan-Ying Wu, Yi-Ching Wang, Roberto Zuchini, Kai-Ying Lan, Hsiao-Sheng Liu, Sheng-Hui Lan
Summary: RAB37 GTPase regulates cargo exocytosis by cycling between GDP-bound and GTP-bound forms. It also simultaneously regulates autophagy activation and TIMP1 secretion in lung cancer cells under starvation conditions. Secretory autophagy participates in TIMP1 secretion in a RAB37- and Sec22b-dependent manner. Autophagy induction facilitates TIMP1 secretion and suppresses the motility and metastasis of lung cancer cells in a RAB37-dependent manner in a lung-to-lung mouse model.
Article
Cell Biology
Shaifali Singh, Nai Yang Yeat, Ya-Ting Wang, Shu-Yu Lin, I-Ying Kuo, Kuen-Phon Wu, Won-Jing Wang, Wen-Ching Wang, Wu-Chou Su, Yi-Ching Wang, Ruey-Hwa Chen
Summary: WDR4/PTPN23 axis plays a central role in the trafficking of EGFR and c-MET in non-small cell lung cancer (NSCLC). WDR4-mediated PTPN23 ubiquitination inhibits lysosome trafficking and degradation, sustaining EGFR and c-MET signaling and promoting NSCLC proliferation, migration, and metastasis. Clinical studies show that low expression of PTPN23 is associated with high expression of WDR4 and poor prognosis in lung cancer. Targeting WDR4-mediated PTPN23 ubiquitination may be a potential therapeutic strategy for EGFR TKI-resistant NSCLC.
CELL DEATH & DISEASE
(2023)
Article
Cell Biology
Shan-Ying Wu, Jia-Wen Chen, Hsi-Yu Liu, Yi-Ching Wang, Yeh-Shiu Chu, Chi-Ying Huang, Kai-Ying Lan, Hsiao-Sheng Liu, Sheng-Hui Lan
Summary: This study is the first to report that autophagy promotes the secretion and metastasis of TIMP1 in a Rab37-dependent manner in lung cancer cells and a lung-to-lung mouse model.
JOURNAL OF BIOMEDICAL SCIENCE
(2022)
Article
Cell Biology
Chih-Hsiung Hsieh, Wen-Hui Kuan, Wei-Lun Chang, I-Ying Kuo, Hsun Liu, Dar-Bin Shieh, Hsuan Liu, Bertrand Tan, Yi-Ching Wang
Summary: This study identifies a novel SOX17(low)/NRF2(high) signature in ESCC patients with poor prognosis, recognizes SOX17 as a transcriptional repressor of NRF2, and provides a promising strategy targeting SOX17/NRF2 axis to overcome resistance.
JOURNAL OF BIOMEDICAL SCIENCE
(2022)
Review
Cell Biology
I. -Ying Kuo, Chih-Hsiung Hsieh, Wan-Ting Kuo, Chih-Peng Chang, Yi-Ching Wang
Summary: Cells in the tumor microenvironment require a class of checkpoints to regulate various secretion and transport processes. Recent studies have shown that Rab proteins mediate communication between diverse cargoes and substrates through vesicular trafficking and secretion pathways in the tumor microenvironment. This review focuses on the role and regulation of vesicular secretion pathways in the tumor microenvironment, and describes the latest research advances and future directions.
JOURNAL OF BIOMEDICAL SCIENCE
(2022)
Article
Cell Biology
Ming-Jer Young, Yung-Ching Chen, Shao-An Wang, Hui-Ping Chang, Wen-Bin Yang, Chia-Chi Lee, Chia-Yu Liu, Yau-Lin Tseng, Yi-Ching Wang, H. Sunny Sun, Wen-Chang Chang, Jan-Jong Hung
Summary: Decreased Sp1 levels in lung cancer are associated with poor prognosis and are related to estrogen. It has been found that E2 can decrease Sp1 levels by increasing the expression of RNF4, and ultimately lead to malignancy in lung cancer.
JOURNAL OF BIOMEDICAL SCIENCE
(2022)