Article
Multidisciplinary Sciences
Kodihalli C. Ravindra, Vishal S. Vaidya, Zhenyu Wang, Joel D. Federspiel, Richard Virgen-Slane, Robert A. Everley, Jane I. Grove, Camilla Stephens, Mireia F. Ocana, Mercedes Robles-Diaz, M. Isabel Lucena, Raul J. Andrade, Edmond Atallah, Alexander L. Gerbes, Sabine Weber, Helena Cortez-Pinto, Andrew J. Fowell, Hyder Hussaini, Einar S. Bjornsson, Janisha Patel, Guido Stirnimann, Sumita Verma, Ahmed M. Elsharkawy, William J. H. Griffiths, Craig Hyde, James W. Dear, Guruprasad P. Aithal, Shashi K. Ramaiah
Summary: Diagnosis and distinction of drug-induced liver injury (DILI) from other liver diseases pose significant challenges. This study identifies and validates potential biomarkers for diagnosing DILI and distinguishing it from alternative causes of liver injury. These biomarkers show promising performance characteristics in distinguishing DILI patients from healthy volunteers and patients with non-DILI liver injury.
NATURE COMMUNICATIONS
(2023)
Article
Oncology
Bohyun Kim, Minsun Jung, Kyung Chul Moon, Dohyun Han, Kwangsoo Kim, Hyeyoon Kim, Sunah Yang, Dongjoo Lee, Hyeji Jun, Kyung-Min Lee, Cheng Hyun Lee, Ilias P. Nikas, Sohyeon Yang, Hyebin Lee, Han Suk Ryu
Summary: This study identified TUBB6 as a potential biomarker predicting muscle-invasive urothelial carcinoma of the bladder through high-throughput proteomic analysis and validation using multiple assays and datasets. The results suggest that TUBB6 expression could be used to predict invasion and poor prognosis in patients with bladder urothelial carcinoma and guide treatment decisions.
INTERNATIONAL JOURNAL OF CANCER
(2023)
Review
Biochemistry & Molecular Biology
Natalia A. Shnayder, Victoria B. Sharavii, Marina M. Petrova, Polina Moskaleva, Elena A. Pozhilenkova, Darya S. Kaskaeva, Olga Tutynina, Tatiana E. Popova, Natalia P. Garganeeva, Regina F. Nasyrova
Summary: The research analyzed potential proteomic biomarkers in the serum and urine of chronic headache patients, identified several proteins related to MOH, and discussed their potential roles in identifying patients with MOH development.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Oncology
Luanfeng Li, Wensi Liu, Haichao Tang, Xiangyi Wang, Xinli Liu, Zhaojin Yu, Yanan Gao, Xiaobin Wang, Minjie Wei
Summary: A study established a genetic feature model related to hypoxia in bladder urothelial carcinoma, showing that the high-risk group had better outcomes, each gene affected patient survival, immune-related pathways were enriched, and immune checkpoints were more highly expressed in the high-risk group.
AMERICAN JOURNAL OF CANCER RESEARCH
(2021)
Article
Chemistry, Analytical
Zhiyu Zhang, Xinyu Cheng, Honglv Jiang, Jingyu Gu, Yunfei Yin, Zhijia Shen, Changgang Xu, Zhongjian Pu, Jia-Bin Li, Guoqiang Xu
Summary: The study successfully enriched glycoproteins in 36 urine samples using magnetic ConA nanoparticles, identifying 20 suspicious proteins significantly upregulated in the urine of SCLC patients. Further experiments confirmed that glycosylated cathepsin C and transferrin could serve as potential noninvasive biomarkers for the diagnosis of SCLC patients.
JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS
(2021)
Review
Oncology
Felice Crocetto, Biagio Barone, Matteo Ferro, Gian Maria Busetto, Evelina La Civita, Carlo Buonerba, Giuseppe Di Lorenzo, Daniela Terracciano, Jack A. Schalken
Summary: Bladder cancer is the most common malignancy of the urinary tract. Traditional diagnostic methods are invasive and uncomfortable, while alternative methods have poor sensitivity. Therefore, an improved non-invasive approach is needed for the management of bladder cancer.
CRITICAL REVIEWS IN ONCOLOGY HEMATOLOGY
(2022)
Article
Cell Biology
Whitney Edwards, Todd M. Greco, Gregory E. Miner, Natalie K. Barker, Laura Herring, Sarah Cohen, Frank L. Conlon
Summary: Using quantitative proteomics, researchers discovered that protein dynamics are linked to molecular pathways in embryonic heart development, including the functional role of the mevalonate pathway in regulating the cell cycle of embryonic cardiomyocytes. These proteomic datasets are a valuable resource for studying embryonic heart development and congenital heart disease.
DEVELOPMENTAL CELL
(2023)
Article
Biochemistry & Molecular Biology
Feng Zhang, Shuijiao Guo, Wenhui Zhong, Kaijun Huang, Yubin Liu
Summary: The study demonstrated that metallothionein isoforms have aberrant expression and varying prognostic value in hepatocellular carcinoma. The repression of MT1H in HCC was found to be detrimental to patient outcomes.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Medicine, General & Internal
Xue Li, Nai-Ren Zheng, Lin-Heng Wang, Zhong-Wu Li, Zong-Chao Liu, Hua Fan, Yi Wang, Jin Dai, Xiao-Tian Ni, Xin Wei, Ming-Wei Liu, Kai Li, Zhe-Xuan Li, Tong Zhou, Yang Zhang, Jing-Ying Zhang, Gaohaer Kadeerhan, Sha Huang, Wen-Hui Wu, Wei-Dong Liu, Xiu-Zhen Wu, Lan-Fu Zhang, Jian-Ming Xu, Markus Gerhard, Wei-Cheng You, Kai-Feng Pan, Wen-Qing Li, Jun Qin
Summary: By analyzing the proteomic landscape, we identified protein signatures associated with the progression of gastric lesions and the risk of early gastric cancer. These findings have important implications for identifying high-risk populations and early detection of gastric cancer.
Article
Oncology
Vittorio Fasulo, Marco Paciotti, Massimo Lazzeri, Roberto Contieri, Paolo Casale, Alberto Saita, Giovanni Lughezzani, Pietro Diana, Nicola Frego, Pier Paolo Avolio, Piergiuseppe Colombo, Grazia Maria Elefante, Giorgio Guazzoni, Nicolo Maria Buffi, Michael Bates, Rodolfo Hurle
Summary: The study found that longitudinally repeating the Xpert BC Monitor assay can significantly reduce the number of unnecessary cystoscopies and urine cytology during follow-up.
FRONTIERS IN ONCOLOGY
(2022)
Article
Genetics & Heredity
Qiongli Su, Qiuhong Tan, Xin Liu, Ling Wu
Summary: Bladder cancer and bladder urothelial cancer are common cancers of the urinary system. This study developed an Ensemble model to predict circRNA-Disease Associations (CDA) and screen potential biomarkers for these cancers. The model combines disease and circRNA similarity measures and evaluates circRNA-disease pairs using random walk with restart and Laplacian regularized least squares. The results show that circHIPK3 may serve as a potential biomarker for bladder cancer, while circSMARCA5 may be a possible biomarker for bladder urothelial cancer.
FRONTIERS IN GENETICS
(2022)
Article
Multidisciplinary Sciences
Tingting Shi, Jun Bai, Diyuan Yang, Li Huang, Hui-Feng Fan, Dong-Wei Zhang, Tongzheng Liu, Gen Lu
Summary: The study identified differentially expressed proteins in mild and severe ADV CAP patients compared to healthy controls, such as LAP3 being the most significantly up-regulated protein in severe ADV CAP. These proteins may serve as potential diagnostic biomarkers for assessing the severity of ADV CAP.
Article
Biochemistry & Molecular Biology
Angelique Stalmach, Ines Boehm, Marco Fernandes, Alison Rutter, Richard J. E. Skipworth, Holger Husi
Summary: The importance of investigating the muscle proteome related to muscle atrophy diseases is highlighted in this study. By conducting a meta-analysis using gene ontology analysis of multiple human proteomic studies, common biological processes of muscle wasting conditions can be identified. Integrating proteomics data from tissue samples and biofluids is recommended for a comprehensive overview of the human skeletal muscle proteome.
Article
Orthopedics
Zhenyuan Wei, Shang Guo, Hongwei Wang, Yang Zhao, Jiren Yan, Chi Zhang, Biao Zhong
Summary: In this study, a new animal model was established to investigate the progression of traumatic heterotopic ossification (tHO) using a proteomics approach. The study identified distinct pathways and potential biomarkers that may help predict the severity of tHO. The findings have translational potential for early prediction and treatment of tHO.
JOURNAL OF ORTHOPAEDIC TRANSLATION
(2022)
Article
Medicine, General & Internal
Karla B. Pena, Francesc Riu, Anna Hernandez, Carmen Guilarte, Joan Badia, David Parada
Summary: Urothelial bladder cancer is a heterogeneous disease with high recurrence and progression rates. This study evaluated the usefulness of a urine DNA methylation test in the follow-up of urothelial bladder cancer patients with atypical urine cytology. The study found a positive correlation between the DNA methylation test and the diagnosis of urothelial cell atypia.
JOURNAL OF CLINICAL MEDICINE
(2022)
Article
Oncology
Minsoo Son, Hongbeom Kim, Dohyun Han, Yoseop Kim, Iksoo Huh, Youngmin Han, Seung-Mo Hong, Wooil Kwon, Haeryoung Kim, Jin-Young Jang, Youngsoo Kim
Summary: The study identified four risk subgroups associated with patient outcomes and developed a classification model with 24 protein features that can predict the risk subgroups of PDAC patients with relative accuracy.
CLINICAL CANCER RESEARCH
(2021)
Article
Oncology
Yoseop Kim, Injoon Yeo, Iksoo Huh, Jaenyeon Kim, Dohyun Han, Jin-Young Jang, Youngsoo Kim
Summary: The study developed a multi-marker panel containing 14 proteins for improved pancreatic ductal adenocarcinoma detection. The panel achieved high AUC values in both the training and validation sets. Compared to CA 19-9 alone, the multi-marker panel showed significant improvements in diagnostic performance.
CLINICAL CANCER RESEARCH
(2021)
Article
Biochemical Research Methods
Jee-Soo Lee, Dohyun Han, So Yeon Kim, Ki Ho Hong, Myoung-jin Jang, Man Jin Kim, Young-gon Kim, Jae Hyeon Park, Sung Im Cho, Wan Beom Park, Kyung Bok Lee, Ho Seob Shin, Hyeon Sae Oh, Taek Soo Kim, Sung Sup Park, Moon-Woo Seong
Summary: This study identified potential early prognostic protein markers and 40 potential biomarkers that reflect the clinical progression of COVID-19. These findings provide insights into host response to SARS-CoV-2 infection and may support better prediction and monitoring of progression to severe COVID-19.
Article
Psychiatry
Hyeyoung Kim, Sang Jin Rhee, Hyunju Lee, Dohyun Han, Tae Young Lee, Minah Kim, Eun Young Kim, Jun Soo Kwon, Hyunsuk Shin, Hyeyoon Kim, Yong Min Ahn, Kyooseob Ha
Summary: High-throughput proteomic technologies were used to identify dysregulated proteins in the plasma of patients with major depressive disorder (MDD) and bipolar disorder (BD). Several proteins were found to be altered in both disorders, with higher fold changes observed in MDD patients. These findings may aid in identifying candidate biomarkers for mood disorders.
PSYCHIATRY RESEARCH
(2021)
Article
Microbiology
Hyo Shin Yoon, Chung Hwan Cho, Myeong Sik Yun, Sung Jae Jang, Hyun Ju You, Jun-hyeong Kim, Dohyun Han, Kwang Hyun Cha, Sung Hyun Moon, Kiuk Lee, Yeon-Ji Kim, Sung-Joon Lee, Tae-Wook Nam, GwangPyo Ko
Summary: The study demonstrates that Akkermansia muciniphila increases thermogenesis and GLP-1 secretion in mice by inducing uncoupling protein 1. A protein secreted by A. muciniphila, P9, interacts with ICAM-2 and can target metabolic diseases. This interaction could be a potential therapeutic target for such diseases.
NATURE MICROBIOLOGY
(2021)
Article
Biochemical Research Methods
Hyeyoon Kim, Jongmin Woo, Kisoon Dan, Kyung-Min Lee, Min-Sun Jin, In Ae Park, Han Suk Ryu, Dohyun Han
Summary: CD44 is a key regulator in the claudin-low subtype of breast cancer, with its suppression leading to significant functional alterations related to oncogenic cellular processes, including proliferation, metabolism, adhesion, and gene expression regulation.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Oncology
Han Na Jang, Sun Joon Moon, Kyeong Cheon Jung, Sang Wan Kim, Hyeyoon Kim, Dohyun Han, Jung Hee Kim
Summary: Adrenal cortical carcinoma (ACC) is a rare disease with uncertain prognosis. Through mass-spectrometry-based proteomics and machine learning algorithm, potential prognostic protein biomarkers of ACC were identified in this study, which could guide the treatment plan for patients.
Article
Multidisciplinary Sciences
Ah Jung Heo, Su Bin Kim, Chang Hoon Ji, Dohyun Han, Su Jin Lee, Su Hyun Lee, Min Ju Lee, Ji Su Lee, Aaron Ciechanover, Bo Yeon Kim, Yong Tae Kwon
Summary: Cellular homeostasis requires sensing and adaptation to intracellular oxygen and reactive oxygen species. The Arg/N-degron pathway targets proteins for degradation through oxidation, arginylation, and ubiquitylation. Proteins may be partially stabilized under acute hypoxia, but can be chemically oxidized by ROS to generate a lysosomal N-degron under prolonged hypoxia.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
Hyo Kyeong Cha, Seongmin Cheon, Hyeyoon Kim, Kyung-Min Lee, Han Suk Ryu, Dohyun Han
Summary: This study used proteomics and bioinformatics to explore the mechanisms of chemoresistance in breast cancer cells. The results revealed that different anticancer drugs were associated with different mechanisms of resistance, such as Notch signaling, immune response, and protein re-localization processes. Furthermore, potential prognostic proteins with significant effects on overall survival were identified.
Article
Biochemistry & Molecular Biology
Hyebin Lee, Han Suk Ryu, Hee Chul Park, Jeong Il Yu, Gyu Sang Yoo, Changhoon Choi, Heerim Nam, Jason Joon Bock Lee, In-Gu Do, Dohyun Han, Sang Yun Ha
Summary: This study utilized mass spectrometry to analyze the proteomic profile of rectal cancer patients and validated the predictive capacity of protein biomarkers through immunohistochemical staining. The results revealed significantly differentially expressed proteins between different response groups, with biological processes related to cytoskeletal organization and immune response enriched in the complete responder group, and biosynthesis and transcription associated processes enriched in the non-complete responder group. Using machine learning algorithms, dual oxidase 2 (DUOX2) was identified as a potential biomarker for predicting treatment response. Overall, the study highlights the impact of pre-treatment tumor microenvironment on treatment response and suggests DUOX2 as an early predictor for non-complete response after chemoradiation therapy.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemical Research Methods
Jin Woo Jung, Yu-jung Hwang, Myung-Whan Suh, Dohyun Han, Seung Ha Oh
Summary: In this study, proteome changes in human perilymph after steroid treatment were investigated. The results showed that upregulated proteins after steroid treatment are related to apoptosis signaling, reactive oxygen species, and immune responses. Protein-protein interaction analysis revealed the potential signaling circuitry involved in cellular response to steroid treatment.
Article
Pathology
Jun Yong Kim, Dohyun Han, Hyeyoon Kim, Minsun Jung, Han Suk Ryu
Summary: By using proteomic analysis, we found that cystitis glandularis (CG) is more similar to normal urothelium (NU) than to urothelial carcinoma (UC). We also confirmed the presence of a small subset of common differentially expressed proteins (DEPs) in UC and CG, indicating potential cancerous risks in CG.
JOURNAL OF PATHOLOGY AND TRANSLATIONAL MEDICINE
(2023)
Article
Medicine, General & Internal
Jung-Ki Yoon, Sungjoon Park, Kyoung-Hee Lee, Dabin Jeong, Jisu Woo, Jieun Park, Seung-Muk Yi, Dohyun Han, Chul-Gyu Yoo, Sun Kim, Chang-Hoon Lee
Summary: A machine learning algorithm identified ferroptosis as the most distinctive feature of cultured COPD epithelial cells compared to non-COPD cells upon exposure to smoke extract. The study revealed that COPD epithelial cells are particularly vulnerable to the effects of smoke, with ferroptosis being enriched in basal, goblet, and club cells.
JOURNAL OF KOREAN MEDICAL SCIENCE
(2023)
Article
Allergy
Yi Sook Kim, Dohyun Han, Ji Hun Mo, Yong Min Kim, Dae Woo Kim, Hyo Guen Choi, Jong Wan Park, Hyun Woo Shin
Summary: This study examined the effects of antibiotics on the nasal microbiome and secreted proteome in chronic rhinosinusitis patients, finding that antibiotics may have stronger effects on patients with nasal polyps.
ALLERGY ASTHMA & IMMUNOLOGY RESEARCH
(2021)
Article
Chemistry, Multidisciplinary
Ji Hyeon Kim, Jeeyoung Lee, Won Hoon Choi, Seoyoung Park, Seo Hyeong Park, Jung Hoon Lee, Sang Min Lim, Ji Young Mun, Hyun-Soo Cho, Dohyun Han, Young Ho Suh, Min Jae Lee
Summary: Research has shown that tau protein undergoes multiple post-translational modifications and conformational changes under pathological conditions, leading to the formation of insoluble filaments. The interaction between tau PTMs during the aggregation process plays a crucial role in driving fibrillization, indicating that targeting tau ubiquitylation may be an effective strategy to alleviate tauopathies.