Article
Biochemical Research Methods
Mengsha Tong, Yuxiang Lin, Wenxian Yang, Jinsheng Song, Zheyang Zhang, Jiajing Xie, Jingyi Tian, Shijie Luo, Chenyu Liang, Jialiang Huang, Rongshan Yu
Summary: Colorectal cancer (CRC) is a common gastrointestinal malignancy, but few recurrence risk signatures exist for these patients. In this study, a computational framework called scRank(XMBD) was proposed to prioritize prognostic-associated cell subpopulations based on within-cell relative expression orderings of gene pairs from single-cell transcriptomes. The results of this study facilitate the application of rank-based methods in cancer genomics and precision oncology.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
Ege Ulgen, O. Ugur Sezerman
Summary: The study developed a personalized/batch analysis approach, driveR, which accurately prioritizes cancer driver genes by combining genomics information and prior biological knowledge. Testing showed that driveR performs well and outperforms existing methods. The proposed method is user-friendly and plays a significant role in cancer genomics.
BMC BIOINFORMATICS
(2021)
Article
Cell Biology
Lingling Zu, Jinling He, Ning Zhou, Quanying Tang, Maoli Liang, Song Xu
Summary: This study characterized the transcriptomic landscape of NSCLC cells with organ-specific metastatic potentials and identified miR-660-5p as a key driver associated with NSCLC progression and distant metastasis. A six-gene signature was established to predict NSCLC metastasis, and three genes and two transcription factors from this signature were validated. Aberrant gene signature and miRNA can serve as biomarkers for predicting NSCLC distant metastasis.
CELL DEATH & DISEASE
(2023)
Article
Multidisciplinary Sciences
Anna Diez-Villanueva, Rebeca Sanz-Pamplona, Xavier Sole, David Cordero, Marta Crous-Bou, Elisabet Guino, Adriana Lopez-Doriga, Antoni Berenguer, Susanna Ausso, Laia Pare-Brunet, Mireia Obon-Santacana, Ferran Moratalla-Navarro, Ramon Salazar, Xavier Sanjuan, Cristina Santos, Sebastiano Biondo, Virginia Diez-Obrero, Ainhoa Garcia-Serrano, Maria Henar Alonso, Robert Carreras-Torres, Adria Closa, Victor Moreno
Summary: Colonomics is a multi-omics dataset that includes 250 samples from colon cancer patients and healthy colon mucosa donors. The project aims to explore and integrate these datasets to describe colon cancer at a molecular level and compare normal and tumoral tissues. Additionally, it aims to improve screening for colon cancer by finding biomarkers for diagnosis and prognosis.
Article
Biochemical Research Methods
Isabelle Bichindaritz, Guanghui Liu, Christopher Bartlett
Summary: The study proposes an adaptive multi-task learning method for survival prediction of breast cancer patients using multi-modal learning, achieving more effective results compared to existing approaches. By combining different gene features, reducing dimensions, and introducing auxiliary loss, an ordinal Cox hazards model is built to predict patients' survival risk.
Article
Endocrinology & Metabolism
Na Li, Yalin Li, Peixian Zheng, Xianquan Zhan
Summary: This study established immune-related gene-prognostic models in LUAD and LUSC based on mRNAsi, showing a correlation between tumor stemness index and immune cell infiltration in lung cancer tissues.
FRONTIERS IN ENDOCRINOLOGY
(2021)
Article
Biochemical Research Methods
Dianshuang Zhou, Xin Li, Shipeng Shang, Hui Zhi, Peng Wang, Yue Gao, Shangwei Ning
Summary: This study developed a computational framework to prioritize cancer lncRNA modulators and demonstrated its effectiveness through validation analyses. The method showed high predictive performance and identified several experimentally supported high-risk lncRNA regulators.
CURRENT BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Maria Jose Jimenez-Santos, Alba Nogueira-Rodriguez, Elena Pineiro-Yanez, Hugo Lopez-Fernandez, Santiago Garcia-Martin, Paula Gomez-Plana, Miguel Reboiro-Jato, Gonzalo Gomez-Lopez, Daniel Glez-Pena, Fatima Al-Shahrour
Summary: PanDrugs2 is an upgraded version of PanDrugs that helps researchers interpret tumor molecular alterations and guide personalized treatment selection. It incorporates multi-omics analysis and considers cancer genetic dependencies, providing therapeutic options for genes that are difficult to target. PanDrugs2 generates an intuitive report to support clinical decision-making. The database has been updated, integrating 23 primary sources that support >74K drug-gene associations obtained from 4642 genes and 14 659 unique compounds. It is freely available for use.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Medicine, General & Internal
Tao Yang, Lizheng Hao, Xinyu Yang, Changyong Luo, Guomi Wang, Caroline Lin Cai, Shuo Qi, Zhong Li
Summary: This study evaluated the association between pretreatment dNLR and prognosis of patients with NSCLC treated with ICIs through systematic review and meta-analysis. The results showed that higher dNLR levels significantly predicted poor overall survival and progression-free survival in NSCLC patients.
Article
Oncology
Joseph M. Chan, Alvaro Quintanal-Villalonga, Vianne Ran Gao, Yubin Xie, Viola Allaj, Ojasvi Chaudhary, Ignas Masilionis, Jacklynn Egger, Andrew Chow, Thomas Walle, Marissa Mattar, Dig V. K. Yarlagadda, James L. Wang, Fathema Uddin, Michael Offin, Metamia Ciampricotti, Besnik Qeriqi, Amber Bahr, Elisa de Stanchina, Umesh K. Bhanot, W. Victoria Lai, Matthew J. Bott, David R. Jones, Arvin Ruiz, Marina K. Baine, Yanyun Li, Natasha Rekhtman, John T. Poirier, Tal Nawy, Triparna Sen, Linas Mazutis, Travis J. Hollmann, Dana Pe'er, Charles M. Rudin
Summary: The study reveals a greater tumor diversity in SCLC compared to lung adenocarcinoma, with a PLCG2-high SCLC phenotype showing stem-like, pro-metastatic features and predicting worse overall survival. Furthermore, SCLC demonstrates greater immune sequestration and less immune infiltration than lung adenocarcinoma.
Article
Rheumatology
Seung Min Jung, Kyung-Su Park, Ki-Jo Kim
Summary: Integrative transcriptomic analysis of lung tissues from patients with systemic sclerosis-associated interstitial lung disease (SSc-ILD) revealed key signatures shared with other fibrosing pulmonary diseases, but also showed distinct differences in certain pathological processes. SSc-ILD exhibited similar molecular and cellular signatures to idiopathic pulmonary fibrosis (IPF) but had stronger signals for myofibroblasts, which were in a senescent and apoptosis-resistant state. The p53 signalling pathway was found to be the most enriched molecular signature in SSc-ILD lung tissues and fibroblasts, and was significantly correlated with clinical parameters such as carbon monoxide diffusing capacity of lung, cellular senescence, and apoptosis. Key regulators such as EEF2, EFF2K, PHKG2, VCAM1, PRKACB, ITGA4, CDK1, CDK2, FN1, and HDAC1 were identified with high diffusion scores in the disease module. This network-based approach provides valuable insights into potential therapeutic targets for treating SSc-ILD.
ANNALS OF THE RHEUMATIC DISEASES
(2022)
Article
Biochemistry & Molecular Biology
Angeliki Chatziantoniou, Apostolos Zaravinos
Summary: In this study, the authors reanalyzed deregulated signatures in lung cancer and identified critical co-deregulated genes. These genes were associated with immune response and cell signaling pathway abnormalities, and exhibited overlapping networks with transcription factors and kinases. Additionally, potential repurposing drugs were highlighted using Connectivity Map. These findings provide an innovative framework for the development of personalized therapeutic strategies.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Oncology
Jialin Li, Xinliang Gao, Suyan Tian, Mingbo Tang, Wei Liu
Summary: This study constructed a model based on exosome-related genes to predict outcomes in lung adenocarcinoma using clinical and transcriptome data, showing that these genes have prognostic value. It also identified immune-related and extracellular matrix-related pathways and differences in immune states between high- and low-risk groups.
Article
Multidisciplinary Sciences
Isabella Wu, Xin Wang
Summary: This article investigates the early diagnosis and treatment of non-small cell lung cancer (NSCLC) and proposes a novel composite selection index (C-Index) to identify effective biomarkers. Through topological data analysis and validation with machine learning models, they discovered a 4-gene biomarker signature that holds promise for the treatment and personalized medicine of NSCLC.
SCIENTIFIC REPORTS
(2023)
Review
Oncology
Jordi Remon, Benjamin Lacas, Roy Herbst, Martin Reck, Edward B. Garon, Giorgio V. Scagliotti, Rodryg Ramlau, Nasser Hanna, Johan Vansteenkiste, Kiyotaka Yoh, Harry J. M. Groen, John V. Heymach, Sumithra J. Mandrekar, Isamu Okamoto, Joel W. Neal, Rebecca S. Heist, David Planchard, Jean-Pierre Pignon, Benjamin Besse
Summary: This study validates the efficacy of combining angiogenesis inhibitors with second-line treatment in advanced non-small cell lung cancer (NSCLC) patients, showing significant improvements in overall survival and progression-free survival, particularly in younger patients and those who started the first-line therapy more recently.
EUROPEAN JOURNAL OF CANCER
(2022)
Article
Oncology
Sally C. M. Lau, Aline Fusco Fares, Lisa W. Le, Kate M. Mackay, Spencer Soberano, Sze Wah Chan, Elliot Smith, Malcolm Ryan, Ming Sound Tsao, Penelope A. Bradbury, Prodipto Pal, Frances A. Shepherd, Geoffrey Liu, Natasha B. Leighl, Adrian G. Sacher
Summary: Mutation subtypes, such as EGFR exon 20 and HER2, are associated with better response and progression-free survival in non-small-cell lung cancer patients treated with immune checkpoint inhibitors (ICIs), making ICIs an important therapeutic option for these patients.
CLINICAL LUNG CANCER
(2021)
Article
Oncology
B. C. John Cho, Laura Donahoe, Penelope A. Bradbury, Natasha Leighl, Shaf Keshavjee, Andrew Hope, Prodipto Pal, Michael Cabanero, Kasia Czarnecka, Karen McRae, Ming-Sound Tsao, Marc de Perrot
Summary: A novel treatment approach called Surgery for Mesothelioma After Radiotherapy (SMART) was developed for managing malignant pleural mesothelioma, with promising results in clinical feasibility. However, minimizing severe treatment-related events is challenging and may impact survival beyond the post-operative period.
Article
Critical Care Medicine
Jane Turner, Gregory R. Pond, Alain Tremblay, Michael Johnston, Glen Goss, Garth Nicholas, Simon Martel, Rick Bhatia, Geoffrey Liu, Heidi Schmidt, Martin C. Tammemagi, Serge Puksa, Sukhinder Atkar-Khattra, Ming-Sound Tsao, Stephen Lam, John R. Goffin
Summary: The study found that perceived lung cancer risk was positively associated with calculated risk, but not consistently related to worry. Factors such as younger age and family history were associated with higher risk perception, as well as with lung cancer worry and reported intent to quit smoking. Promotion of screening programs may benefit from focusing on factors associated with higher risk perception.
Article
Cardiac & Cardiovascular Systems
Reenika Aggarwal, Andrew Cl Lam, Jingyue Huang, Katrina Hueniken, Daniel Nguyen, Khaleeq Khan, Taariq Shaikh, Frances A. Shepherd, Ming-Sound Tsao, Wei Xu, John Kavanagh, Geoffrey Liu
Summary: This study identified individuals ineligible for lung cancer screening who are most likely to become eligible in the future. Factors such as smoking history, current smoking status, lower education level, and presence of chronic obstructive pulmonary disease (COPD) were significantly associated with becoming eligible for screening. The predictive model based on observed health behaviors reasonably predicted changes in lung cancer risk and can help identify participants who should be closely monitored for potential future eligibility.
RESPIRATORY MEDICINE
(2021)
Editorial Material
Oncology
Ming-Sound Tsao, Andrew G. Nicholson, Joseph J. Maleszewski, Alexander Marx, William D. Travis
JOURNAL OF THORACIC ONCOLOGY
(2022)
Article
Oncology
Ku-Geng Huo, Hirotsugu Notsuda, Zhenhao Fang, Ningdi Feng Liu, Teklab Gebregiworgis, Quan Li, Nhu-An Pham, Ming Li, Ni Liu, Frances A. Shepherd, Christopher B. Marshall, Mitsuhiko Ikura, Nadeem Moghal, Ming-Sound Tsao
Summary: This study found that clinically approved EGFR TKIs can be used to treat patients with non-small cell lung cancer harboring the BRAF(G469V) mutation. Through experiments with a xenograft model and a cell line, it was confirmed that BRAF G469v is the oncogenic driver in this mutation. Structural modeling and experiments further demonstrated that BRAF(G469V) is a direct target of EGFR TKIs.
JOURNAL OF THORACIC ONCOLOGY
(2022)
Article
Oncology
Dalam Ly, Quan Li, Roya Navab, Cedric Zeltz, Linan Fang, Michael Cabanero, Chang-Qi Zhu, Ming-Sound Tsao, Li Zhang
Summary: Understanding how the immune system regulates the tumor microenvironment is crucial for the development of effective cancer treatments. This study reveals the adverse prognostic role of LAIR2 expression in regulatory T cells and identifies it as a potential target for future immunotherapies.
Article
Biochemistry & Molecular Biology
Cedric Zeltz, Maryam Khalil, Roya Navab, Ming-Sound Tsao
Summary: Collagen type XI restrains collagen remodeling and cell migration mediated by cancer-associated fibroblasts (CAF), thereby limiting the invasion of lung cancer cells.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Oncology
Joshua C. Rosen, Adrian Sacher, Ming-Sound Tsao
Summary: KRAS(G12C) inhibitors have shown promising results in clinical trials with overall response rates ranging between 32% and 46%, and have been granted FDA approvals as second-line or later monotherapies. However, rapid tumor resistance complicates their use as a monotherapy.
THERAPEUTIC ADVANCES IN MEDICAL ONCOLOGY
(2023)
Article
Oncology
Shelley Kuang, Andrea S. Fung, Kirstin A. Perdrizet, Kaitlin Chen, Janice J. N. Li, Lisa W. Le, Michael Cabanero, Ola Abu Al Karsaneh, Ming S. Tsao, Josh Morganstein, Laura Ranich, Adam C. Smith, Cuihong Wei, Carol Cheung, Frances A. Shepherd, Geoffrey Liu, Penelope Bradbury, Prodipto Pal, Joerg Schwock, Adrian G. Sacher, Jennifer H. Law, Tracy L. Stockley, Natasha B. Leighl
Summary: In NSCLC patients, reflex testing using NGS panels can identify actionable genetic variants in the majority of cases with minimal increase in testing cost. Implementation of NGS panels is essential for the treatment of NSCLC patients as treatment paradigms continue to evolve.
Meeting Abstract
Medicine, Research & Experimental
Ellen Yang, Najd Alshamlan, Jessica Weiss, Michael Cabanero, Ming Tsao
LABORATORY INVESTIGATION
(2022)
Meeting Abstract
Oncology
M. Khalil, M. Tsao
JOURNAL OF THORACIC ONCOLOGY
(2021)
Meeting Abstract
Oncology
S. Lau, M. Rabindranath, J. Weiss, J. Li, S. Nirmalakumar, H. Ruff, S. Boerner, L. C. Tong, M. Tsao, P. Pal, M. Cabanero, Y. H. Hsu, A. Fung, A. Sacher, F. A. Shepherd, G. Liu, P. Bradbury, K. Yasufuku, K. Czarnecka-Kujawa, H. M. Ko, N. Leighl, J. Schwock
JOURNAL OF THORACIC ONCOLOGY
(2021)
Meeting Abstract
Oncology
S. Lau, K. Perdrizet, D. Giffoni M. M. Mata, A. Fung, G. Liu, P. Bradbury, F. A. Shepherd, A. Sacher, B. Sheffield, D. Hwang, M. Tsao, S. Cheng, P. Cheema, N. Leighl
JOURNAL OF THORACIC ONCOLOGY
(2021)
Meeting Abstract
Oncology
S. Lau, S. Wong, B. Wang, D. Patel, A. Fares, M. Tsao, P. Bradbury, G. Liu, F. Shepherd, N. Leighl, T. Mcgaha, P. Ohashi, A. Sacher
JOURNAL OF THORACIC ONCOLOGY
(2021)