Article
Chemistry, Multidisciplinary
Jia-Bin Wang, Qing-Zhu Qiu, Qiao-Ling Zheng, Ya-Jun Zhao, Yu Xu, Tao Zhang, Shuan-Hu Wang, Quan Wang, Qin-Wen Jin, Yin-Hua Ye, Ping Li, Jian-Wei Xie, Jian-Xian Lin, Jun Lu, Qi-Yue Chen, Long-Long Cao, Ying-Hong Yang, Chao-Hui Zheng, Chang-Ming Huang
Summary: In this study, a gastric cancer immunophenotypic score (IPS) was constructed based on the tumor microenvironment classification, which can predict the effectiveness of immune checkpoint inhibitor therapy. The IPS provides a practical reference for implementing neoadjuvant ICI therapy for patients with gastric cancer.
Article
Biochemistry & Molecular Biology
Hang Zheng, Heshu Liu, Huayu Li, Weidong Dou, Xin Wang
Summary: This study developed a prognostic CAF model based on four genes for GC patients, which not only predicts prognosis but also assesses immunotherapy response. Patients in the high-CAF-risk group have worse prognosis and less likely to respond to immunotherapy. GSEA analysis revealed unique biological characteristics in high-CAF-risk patients.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Oncology
Duo Liu, Jingjing Zhu, Dan Zhou, Emily G. Nikas, Nikos T. Mitanis, Yanfa Sun, Chong Wu, Nicholas Mancuso, Nancy J. Cox, Liang Wang, Stephen J. Freedland, Christopher A. Haiman, Eric R. Gamazon, Jason B. Nikas, Lang Wu
Summary: The study combines transcriptome-wide association study and validation to identify candidate genes potentially involved in prostate cancer development. Analysis revealed 573 genes associated with prostate cancer risk, including 451 novel genes and 122 previously reported genes.
INTERNATIONAL JOURNAL OF CANCER
(2022)
Article
Oncology
Dan Zou, Zhi Li, Fei Lv, Yi Yang, Chunjiao Yang, Jincheng Song, Yang Chen, Zi Jin, Jinpeng Zhou, Yang Jiang, Yanju Ma, Zhitao Jing, Yu Tang, Ye Zhang
Summary: NOS3, a member of the NOS enzyme family, plays a role in NO generation and has been shown to influence apoptosis, angiogenesis, proliferation, and invasiveness. High expression of NOS3 in stomach adenocarcinoma is associated with poor prognosis, and it may affect the occurrence and development of the cancer through various cancer-related pathways. NOS3 could be a potential target for gastric cancer treatment as drug response analysis suggests drugs that suppress NOS3.
FRONTIERS IN ONCOLOGY
(2021)
Article
Genetics & Heredity
Dennis Grishin, Alexander Gusev
Summary: By studying germline cancer variants, we have identified risk-associated loci and understood the mechanisms by which these variants operate. Through chromatin accessibility analysis, we have discovered numerous loci associated with cancer risk and successfully identified new risk loci.
Article
Immunology
Tsz Kin Mak, Xing Li, Huaping Huang, Kaiming Wu, Zhijian Huang, Yulong He, Changhua Zhang
Summary: This study identifies the role of cancer-associated fibroblasts (CAFs) in gastric cancer (GC) by analyzing their association with prognosis, tumor microenvironment, cancer stem cells, immune response, and drug sensitivity using the CAFS-score. The findings provide valuable insights for improving prognosis and response to immunotherapy in GC patients.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Pathology
Zhenpeng Wen, Chunjiao Yang, Dan Zou, Jiaqing Liu, Song Wang, Xuqin Liu, Yi Zhang, Ye Zhang
Summary: PSAP is highly expressed in gastric cancer and is associated with poor prognosis. It serves as an independent prognostic factor in gastric cancer patients. A risk model based on PSAP-associated genes was developed to evaluate the immunotherapy outcomes of gastric adenocarcinoma.
PATHOLOGY RESEARCH AND PRACTICE
(2022)
Article
Biochemistry & Molecular Biology
Antonio Cappuccio, Daniel G. Chawla, Xi Chen, Aliza B. Rubenstein, Wan Sze Cheng, Weiguang Mao, Thomas W. Burke, Ephraim L. Tsalik, Elizabeth Petzold, Ricardo Henao, Micah T. McClain, Christopher W. Woods, Maria Chikina, Olga G. Troyanskaya, Stuart C. Sealfon, Steven H. Kleinstein, Elena Zaslavsky
Summary: By applying a multi-objective optimization framework to analyze blood samples from COVID-19 patients, a COVID-19 signature regulated at both transcriptional and epigenetic levels was identified. The robustness of this signature was validated in multiple independent COVID-19 cohorts. Unlike previously reported signatures, this signature showed no cross-reactivity with other infections or comorbidities, and plasmablasts and memory T cells played important roles in the interpretation of the signature.
Article
Biochemistry & Molecular Biology
Yali Wang, Kun Zheng, Xiuqiong Chen, Rui Chen, Yanmei Zou
Summary: The study identified pivotal genes associated with gastric cancer and explored their prognostic significance. COL1A1, THBS2, and SPP1 were found to potentially predict immunotherapy response in GC patients.
BIOSCIENCE REPORTS
(2021)
Article
Oncology
Anna Faldt Beding, Peter Larsson, Khalil Helou, Zakaria Einbeigi, Toshima Z. Parris
Summary: Our study suggests that BIRC5 overexpression is associated with the initiation and progression of several cancer types, and therefore holds promise as a prognostic biomarker.
Article
Immunology
Harry Robertson, Jennifer Li, Hani Jieun Kim, Jake W. Rhodes, Andrew N. Harman, Ellis Patrick, Natasha M. Rogers
Summary: The research team successfully identified an independent set of differentially expressed genes characterizing human tolerogenic DC (tolDC) by analyzing transcriptomic data. By validating this transcriptomic signature and exploring gene differences according to the method of tolDC generation, the study potentially offers insights into transcriptional regulators of tolerance and standardized identification of tolDC in clinical trials.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Multidisciplinary Sciences
Yunhao Wu, Jin Shang, Qiang Ruan, Xiaodong Tan
Summary: This study based on disulfidoptosis-related genes (DRGs) holds promise in classifying pancreatic cancer patients and predicting their prognosis, mutational landscape, immune microenvironment, and drug therapy, providing new opportunities for understanding the role of DRGs in pancreatic cancer and offering more effective treatment strategies.
SCIENTIFIC REPORTS
(2023)
Article
Allergy
Lena Moebus, Elke Rodriguez, Inken Harder, Nicole Boraczynski, Silke Szymczak, Matthias Huebenthal, Dora Stoelzl, Sascha Gerdes, Andreas Kleinheinz, Susanne Abraham, Annice Heratizadeh, Christiane Handrick, Eva Haufe, Thomas Werfel, Jochen Schmitt, Stephan Weidinger
Summary: This study explored the blood transcriptomic features of moderate to severe atopic dermatitis (AD). The results showed that AD patients exhibited pronounced inflammatory expression signatures and could be stratified into eosinophilic and noneosinophilic endotypes. Additionally, treatment strategies for the eosinophil-high endotype may require more attention to the restoration of natural killer cell function.
JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY
(2022)
Article
Oncology
Anthony Goncalves, Pascal Finetti, Daniel Birnbaum, Francois Bertucci
Summary: CINSARC, a multigene expression signature, has been shown to have prognostic impact in breast cancer, particularly in the Luminal B subtype. It can provide additional prognostic information beyond traditional clinicopathological features, allowing for better patient stratification and guiding adjuvant treatment. High-risk Luminal B CINSARC tumors are predicted to be less sensitive to endocrine therapy and CDK4/6 inhibitors, but more vulnerable to homologous recombination targeting and immunotherapy.
Article
Oncology
Simeng Zhang, Mengzhu Lv, Yu Cheng, Shuo Wang, Ce Li, Xiujuan Qu
Summary: In this study, three immune-related subtypes of AGC were identified, with the Immunity_H subtype showing higher immune cell infiltration and activities with a favorable prognosis. Through gene co-expression network analysis and Molecular Complex Detection algorithm, a gene module significantly correlated with the Immunity_H subtype was identified, with ADAMDEC1 identified as a key gene associated with favorable prognosis in multiple datasets. These findings may contribute to the development of novel immune therapeutic targets for advanced gastric cancer.
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
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
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)
Article
Oncology
Narikazu Boku, Taroh Satoh, Min-Hee Ryu, Yee Chao, Ken Kato, Hyun Cheol Chung, Jen-Shi Chen, Kei Muro, Won Ki Kang, Kun-Huei Yeh, Takaki Yoshikawa, Sang Cheul Oh, Li-Yuan Bai, Takao Tamura, Keun-Wook Lee, Yasuo Hamamoto, Jong Gwang Kim, Keisho Chin, Do-Youn Oh, Keiko Minashi, Jae Yong Cho, Masahiro Tsuda, Taihei Nishiyama, Li-Tzong Chen, Yoon-Koo Kang
Summary: The study confirmed the long-term efficacy of nivolumab in patients with advanced gastric cancer, showing a longer overall survival compared to placebo. Nivolumab also demonstrated potential benefits in the treatment beyond disease progression.
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
Oncology
Boyeon Kim, Yoonjung Kim, Saeam Shin, Seung-Tae Lee, Jae Yong Cho, Kyung-A Lee
Summary: CRISPR-CPPC is a useful mutant enrichment tool for the sensitive detection of target mutation. When tested in patients with progressive disease, the diagnostic performance of CRISPR-CPPC assay is exceptionally better than that of any other currently available methods.
CANCER CELL INTERNATIONAL
(2022)
Article
Oncology
Sofie Claerhout, Stefan Lehnert, Sara Vander Borght, Lien Spans, Christophe Dooms, Els Wauters, Johan Vansteenkiste, Birgit Weynand, Karen Deraedt, Claire Bourgain, Isabelle Vanden Bempt
Summary: The study evaluated the performance of tRNA-seq in NSCLC tissue and showed that it can efficiently detect actionable gene fusions, splice variants, SNVs, and indels. This approach is crucial for identifying currently recommended targetable molecular alterations in NSCLC samples.
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
Oncology
Imran Khan, Mohammad Hassan Baig, Sadaf Mahfooz, Mohammad Azhar Imran, Mohd Imran Khan, Jae-June Dong, Jae Yong Cho, Mustafa Aziz Hatiboglu
Summary: Glioblastoma, the most aggressive form of brain tumor, has poor prognosis despite aggressive treatment strategies. The blood-brain barrier (BBB) hinders drug delivery to the tumor site, but nanomedicine strategies hold promise in enhancing drug permeability.
SEMINARS IN CANCER BIOLOGY
(2022)
Article
Gastroenterology & Hepatology
Nofar Rosenberg, Matthias Van Haele, Tali Lanton, Neta Brashi, Zohar Bromberg, Hanan Adler, Hilla Giladi, Amnon Peled, Daniel S. Goldenberg, Jonathan H. Axelrod, Alina Simerzin, Chofit Chai, Mor Paldor, Auerlia Markezana, Dayana Yaish, Zohar Shemulian, Dvora Gross, Shanny Barnoy, Maytal Gefen, Osher Amran, Sofie Claerhout, Mirian Fernandez-Vaquero, Maria Garcia-Beccaria, Danijela Heide, Michal Shoshkes-Carmel, Dirk Schmidt Arras, Sharona Elgavish, Yuval Nevo, Hadar Benyamini, Janina E. E. Tirnitz-Parker, Aranzazu Sanchez, Blanca Herrera, Rifaat Safadi, Klaus H. Kaestner, Stefan Rose-John, Tania Roskams, Mathias Heikenwalder, Eithan Galun
Summary: This study reveals that combined hepatocellular carcinoma-cholangiocarcinoma (cHCC-CCA) originates from hepatic progenitor cells (HPCs), not hepatocellular carcinoma (HCC). IL-6 plays a significant role in the aging process of HPCs, suggesting potential therapeutic targets for cHCC-CCA tumors.
JOURNAL OF HEPATOLOGY
(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.
Article
Biochemistry & Molecular Biology
Roshan Vaid, Akram Mendez, Ketan Thombare, Rebeca Burgos-Panadero, Remy Robinot, Barbara F. Fonseca, Nikhil R. Gandasi, Johan Ringlander, Mohammad Hassan Baig, Jae-June Dong, Jae Yong Cho, Bjorn Reinius, Lisa A. Chakrabarti, Kristina Nystrom, Tanmoy Mondal
Summary: Research reveals that SARS-CoV-2 variants infection leads to the loss of m(6)A in cellular RNAs, accompanied by abnormal localization of METTL3. Furthermore, down-regulation of transcripts with m(6)A modification is observed postinfection. Inhibition of XPO1 restores METTL3 localization, m(6)A modification, and mRNA expression, as well as stress granule formation, resulting in reduced viral infection in vitro.
Letter
Gastroenterology & Hepatology
Sun Young Yim, Ju-Seog Lee