Article
Oncology
Qiangda Chen, Hanlin Yin, Siyao Liu, Sami Shoucair, Ni Ding, Yuan Ji, Jicheng Zhang, Dansong Wang, Tiantao Kuang, Xuefeng Xu, Jun Yu, Wenchuan Wu, Ning Pu, Wenhui Lou
Summary: Tumor-associated N2 neutrophils were found to significantly increase, while a low N1/N2 ratio was associated with poorly differentiated tumors, easier lymph node metastases, and higher TNM stage. A high N1/N2 ratio was identified as a significant prognostic indicator for overall survival and recurrence-free survival.
JOURNAL FOR IMMUNOTHERAPY OF CANCER
(2022)
Article
Oncology
Xuan Zou, Xuan Lin, He Cheng, Yusheng Chen, Ruijie Wang, Mingjian Ma, Yu Liu, Zhengjie Dai, Yesboli Tasiheng, Yu Yan, Qinqin Hou, Fei Ding, Huan Chen, Xianjun Yu, Xu Wang, Chen Liu
Summary: This study systematically revealed the cellular properties and prognostic values of intratumoral TLSs in pancreatic ductal adenocarcinoma (PDAC) and described the potential impact of neoadjuvant treatment (NAT) on TLS development and function.
JOURNAL FOR IMMUNOTHERAPY OF CANCER
(2023)
Article
Oncology
Yueqiong Lao, Yuqian Wang, Jie Yang, Tianyuan Liu, Yuling Ma, Yingying Luo, Yanxia Sun, Kai Li, Xuan Zhao, Xiangjie Niu, Yiyi Xi, Ce Zhong
Summary: This study investigates the genomic alterations and neoantigen characteristics of adenocarcinoma at the gastroesophageal junction (ACGEJ), identifying mutation signatures, driver genes, and CD8+ T-cell infiltration-related genes. A risk model is developed to predict patient survival. The findings provide potential immunotherapeutic targets and prognostic biomarkers for ACGEJ treatment.
FRONTIERS IN ONCOLOGY
(2022)
Article
Oncology
Adriana Carino, Luigina Graziosi, Silvia Marchiano, Michele Biagioli, Elisabetta Marino, Valentina Sepe, Angela Zampella, Eleonora Distrutti, Annibale Donini, Stefano Fiorucci
Summary: The study found significant differences in gene expression between the intestinal and diffuse types of gastric cancer, with AQP9, CARD14, and CXCR2 impacting on patients' prognosis. Among them, CXCR2 in the diffuse type is the only factor independently affecting overall survival of patients with gastric cancer.
FRONTIERS IN ONCOLOGY
(2021)
Article
Oncology
Liang Zeng, Hui Xu, Shu-Hua Li, Shuo-Yu Xu, Kai Chen, Liang-Jun Qin, Lei Miao, Fang Wang, Ling Deng, Feng-Hua Wang, Le Li, Sha Fu, Na Liu, Ran Wang, Ying-Qing Li, Hai-Yun Wang
Summary: This study developed an immune checkpoint-based signature (ICS) to assess the survival risk of neuroblastoma (NB) patients and guide patient selection for immunotherapy. The expression levels of 9 immune checkpoints were determined in tumor tissues, and 7 abnormally expressed immune checkpoints were identified. The ICS model based on 4 immune checkpoints showed significant prognostic value in predicting overall survival and event-free survival.
JOURNAL FOR IMMUNOTHERAPY OF CANCER
(2023)
Article
Multidisciplinary Sciences
Alexander Damanakis, Isabell Wahler, Hans Fuchs, Heike Loeser, Wolfgang Schroeder, Thomas Zander, Seung-Hun Chon, Christiane Bruns, Alexander Quaas, Florian Gebauer
Summary: This study demonstrates for the first time the prognostic significance of ITGB1 expression in a large population of patients with esophageal adenocarcinoma (EAC). High expression of ITGB1 is associated with tumor aggressiveness and poor survival.
SCIENTIFIC REPORTS
(2022)
Article
Immunology
Xiaogang Zhou, Yu Liu, Jing Xiang, Yuntao Wang, Qiqian Wang, Jianling Xia, Yunfei Chen, Yifeng Bai
Summary: In the treatment of COAD patients with immune checkpoint inhibitors, IL-1 signaling mutation status is associated with a better prognosis and longer overall survival. The IL-1-MT group exhibits higher levels of immune cell infiltration and immunogenicity, with significantly upregulated expression of immune-related genes and checkpoint molecules.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Cell Biology
Qiang Chen, Jiakang Ma, Xiaoyi Wang, Xiangqing Zhu
Summary: This study reveals the transcriptome characteristics in LUADs with different immune phenotypes and identifies key genes and non-coding RNAs associated with LUAD immune phenotypes. Gene coexpression networks and prognostic signature models are established. The findings provide novel insights into the immunological mechanism in LUAD biology and predicting the prognosis of LUAD patients.
Article
Oncology
Cong Shang, Qingyan Chen, Fuqiang Zu, Weidong Ren
Summary: Through integrated analysis, we identified the crucial role of miR-127 in the prognosis and progression of breast cancer. Low expression of miR-127 is associated with migration, invasion, and tumorigenesis in breast cancer. Furthermore, miR-127 is involved in multiple cancer pathways in breast cancer.
Article
Biochemistry & Molecular Biology
Kailun Xu, Shu Zheng, Baosheng Li, Yingkuan Shao, Xiaoyang Yin
Summary: The molecular atlas of tumor microenvironments in adenocarcinoma and mucinous adenocarcinoma were studied, revealing different biological behaviors and clinical features. Adenocarcinoma was immune-active but exposed to a hypoxic microenvironment, while mucinous adenocarcinoma cells could protect against DNA damage but had an unfavorable microenvironment for leukocyte transendothelial migration. Potential molecular and cellular targets were identified for future research, highlighting the importance of cell interactions in distinguishing between the two types of cancer.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Article
Oncology
Jiayu Ma, Xiaochuan Chen, Mingqiang Lin, Zhiping Wang, Yahua Wu, Jiancheng Li
Summary: This study demonstrated the overexpression of CENPK in lung adenocarcinoma (LAC) and its association with clinical progression. CENPK may serve as a novel diagnostic and prognostic biomarker in LAC patients. The activation of CENPK-related signaling pathways in LAC patients was also observed.
CANCER CELL INTERNATIONAL
(2021)
Article
Cell Biology
Anran Zhang, Jinpo Yang, Chao Ma, Feng Li, Huan Luo
Summary: This study established a novel 15-gene signature related to ferroptosis, which accurately predicts the prognosis of LUAD and is associated with specific immune cells. The findings demonstrate the independent prognostic value of this gene signature in patients with LUAD.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Xianfeng Li, Yan Wang, Qingjie Min, Weimin Zhang, Huajing Teng, Chao Li, Kun Zhang, Leisheng Shi, Bin Wang, Qimin Zhan
Summary: In this study, a comprehensive comparison of the transcriptomes of esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma (EAC) was conducted, revealing shared and distinct transcriptomic signatures between these two cancer subtypes and uncovering possible common and unique mechanisms involved in tumorigenesis.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Oncology
Andromachi Kotsafti, Matteo Fassan, Francesco Cavallin, Valentina Angerilli, Luca Saadeh, Matteo Cagol, Rita Alfieri, Pierluigi Pilati, Carlo Castoro, Ignazio Castagliuolo, Melania Scarpa, Marco Scarpa
Summary: This study found that immune marker expression, oncogene status, and intra- and peritumoral immune infiltrating cells are associated with lymph node metastasis in patients with esophageal adenocarcinoma. These results suggest that immune surveillance failure is the key driver of lymph node metastasis.
Article
Multidisciplinary Sciences
Huy Q. Dinh, Feng Pan, Geng Wang, Qing-Feng Huang, Claire E. Olingy, Zhi-Yong Wu, Shao-Hong Wang, Xin Xu, Xiu-E Xu, Jian-Zhong He, Qian Yang, Sandra Orsulic, Marcela Haro, Li-Yan Li, Guo-Wei Huang, Joshua J. Breunig, H. Phillip Koeffler, Catherine C. Hedrick, Li-Yan Xu, De-Chen Lin, En-Min Li
Summary: This study utilized single-cell RNA sequencing to characterize the heterogeneous microenvironment of ESCC, identifying a tumor-specific subset of CST1(+) myofibroblasts with prognostic values and immunosuppressive features. The analysis of stromal cell types in the ESCC microenvironment provides a rich resource for further understanding of ESCC biology.
NATURE COMMUNICATIONS
(2021)
Article
Gastroenterology & Hepatology
Jaffer A. Ajani, Yan Xu, Longfei Huo, Ruiping Wang, Yuan Li, Ying Wang, Melissa Pool Pizzi, Ailing Scott, Kazuto Harada, Lang Ma, Xiaodan Yao, Jiankang Jin, Wei Zhao, Xiaochuan Dong, Brian D. Badgwell, Namita Shanbhag, Ghia Tatlonghari, Jeannelyn Santiano Estrella, Sinchita Roy-Chowdhuri, Makoto Kobayashi, Jody V. Vykoukal, Samir M. Hanash, George Adrian Calin, Guang Peng, Ju-Seog Lee, Randy L. Johnson, Zhenning Wang, Linghua Wang, Shumei Song
Summary: YAP1 is highly upregulated in peritoneal carcinomatosis tumor cells, contributing to cancer stem cell properties and metastasis. Inhibition of YAP1 can significantly slow tumor growth and eliminate peritoneal carcinomatosis in preclinical models. Pharmacological inhibition of YAP1 can reduce cancer stem cell-like properties and suppress tumor growth, especially in combination with cytotoxic drugs in vivo models.
Article
Oncology
Takahito M. Miyake, Sunila Pradeep, Emine Bayraktar, Elaine Stur, Katelyn F. Handley, Sherry Y. Wu, Cristian Rodriguez-Aguayo, Ju-Seog Lee, Gabriel Lopez-Berestein, Robert L. Coleman, Anil K. Sood
MOLECULAR CANCER THERAPEUTICS
(2020)
Article
Cell Biology
Eui Hyun Kim, Bo Hwa Sohn, Young-Gyu Eun, Dong Jin Lee, Sun Young Yim, Seok-Gu Kang, Ju-Seog Lee
Article
Gastroenterology & Hepatology
Changyu Zhu, Yu-Jui Ho, Marcela A. Salomao, Dianne H. Dapito, Alberto Bartolome, Robert F. Schwabe, Ju-Seog Lee, Scott W. Lowe, Utpal B. Pajvani
Summary: The study revealed that Notch activity characterizes a distinct molecular subtype of HCC in humans, associated with unique histology and prognosis. Sustained Notch signaling in chronic liver diseases can drive tumor formation without acquiring specific genomic driver mutations.
JOURNAL OF HEPATOLOGY
(2021)
Article
Cell Biology
Sun Young Yim, Sang Hee Kang, Ji-Hyun Shin, Yun Seong Jeong, Bo Hwa Sohn, Soon Ho Um, Ju-Seog Lee
Article
Oncology
Changhee Park, Kyeonghun Jeong, Joon-Hyeong Park, Sohee Jung, Jeong Mo Bae, Kwangsoo Kim, Chan-Young Ock, Miso Kim, Bhumsuk Keam, Tae Min Kim, Yoon Kyung Jeon, Se-Hoon Lee, Ju-Seog Lee, Dong-Wan Kim, Gyeong Hoon Kang, Doo Hyun Chung, Dae Seog Heo
Summary: The study demonstrated a negative correlation between overall methylation aberrancy and tumor immunogenicity, indicating the importance of methylation aberrancy for tumors to evade immune surveillance. This highlights the need for further development of methylation biomarkers in cancer research.
CANCER IMMUNOLOGY IMMUNOTHERAPY
(2021)
Article
Biochemistry & Molecular Biology
Yeon-Su Lee, Xiaoyong Bao, Hwi-Ho Lee, Jiyoung Joan Jang, Enkhjin Saruuldalai, Gaeul Park, Wonkyun Ronny Im, Jong-Lyul Park, Seon-Young Kim, Sooyong Shin, Sung Ho Jeon, Sangmin Kang, Hyun-Sung Lee, Ju-Seog Lee, Ke Zhang, Eun Jung Park, In-Hoo Kim, Yong Sun Lee
Summary: The noncoding RNA nc886 acts as a novel suppressor for the IFN-beta signaling and inflammation by inhibiting the activation of IRF3, NF-kappa B, and AP-1 through inhibiting PKR. This leads to decreased expression of IFN-beta and IFN-stimulated genes. Its role is to restrict the IFN-beta signaling from hyperactivation, which may explain the variability of innate immune responses to pathogens based on biological settings.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Gastroenterology & Hepatology
Ji H. Nahm, Hye S. Lee, Haeryoung Kim, Sun Y. Yim, Ji-hyun Shin, Jeong E. Yoo, Sang H. Ahn, Jin S. Choi, Ju-Seog Lee, Young N. Park
Summary: This study developed a nomogram for predicting late recurrence of hepatocellular carcinoma (HCC) based on clinicopathological and molecular factors. The combination of pSTAT3, pERK1/2 and SYK immunoexpression with high lobular inflammatory activity and cirrhosis was found to predict late HCC recurrence.
LIVER INTERNATIONAL
(2021)
Review
Oncology
Sun Young Yim, Ju-Seog Lee
Summary: Tumor classifications based on alterations in the genome, epigenome, or proteome have shown promise in improving patient outcomes, especially with regards to personalized treatment. Understanding the molecular and genomic subtypes of hepatocellular carcinoma (HCC) is crucial for discovering new targets and biomarkers, and the development of new technical platforms for analyzing patient samples holds great potential for future advancements in treatment.
JOURNAL OF HEPATOCELLULAR CARCINOMA
(2021)
Article
Biochemical Research Methods
Zachary B. Abrams, Dwayne G. Tally, Lynne Abruzzo, Kevin R. Coombes
Summary: Cytogenetics data, stored as karyotypes, are now being analyzed on a large scale thanks to tools like CytoGPS. The development of RCytoGPS further facilitates the analysis and visualization of karyotype data, advancing the field of computational cytogenetic pathology.
Article
Oncology
Soo-Mi Kweon, Gayeoun Kim, Yunseong Jeong, Wendong Huang, Ju-Seog Lee, Keane K. Y. Lai
Summary: Liver cancer, one of the deadliest cancers, may be influenced by the little-known gene midnolin, which has been found to correlate with poor prognosis in patients and may have a significant impact on liver cancer development.
Article
Biochemistry & Molecular Biology
Caitlin E. Coombes, Kevin R. Coombes, Naleef Fareed
Summary: We present a novel model of time-series analysis for learning from electronic health record (EHR) data in the context of infection occurrence in the intensive care unit (ICU). By applying methods from proteomics and Bayesian statistics, we analyzed a large dataset of ICU patients and identified physician actions that were individually associated with increased risk of infection. Our approach also demonstrated the ability to predict the administration of antibiotics with reasonably high accuracy.
CHEMISTRY & BIODIVERSITY
(2022)
Article
Oncology
Joann Jung, Sowon Park, Yeonwoo Jang, Sung-Hwan Lee, Yun Seong Jeong, Sun Young Yim, Ju-Seog Lee
Summary: Hepatocellular carcinoma (HCC) is a common cancer that causes a large number of deaths worldwide. Metabolic reprogramming is a key feature of HCC, allowing cancer cells to meet the high energy demands for fast growth. By comparing genomic data from mice and humans, we identified three distinct metabolic subtypes of HCC and found clinical and molecular characteristics associated with each subtype. Notably, we discovered that the high metabolic subtype is resistant to immunotherapy and uncovered a potential mechanism for this resistance.
Letter
Gastroenterology & Hepatology
Sun Young Yim, Ju-Seog Lee
Meeting Abstract
Oncology
Sung Hwan Lee, Sunyoung S. Lee, Ju-Seog Lee
JOURNAL OF CLINICAL ONCOLOGY
(2020)