Correction
Multidisciplinary Sciences
Frederic Jehl, Kevin Muret, Maria Bernard, Morgane Boutin, Laetitia Lagoutte, Colette Desert, Patrice Dehais, Diane Esquerre, Herve Acloque, Elisabetta Giuffra, Sarah Djebali, Sylvain Foissac, Thomas Derrien, Frederique Pitel, Tatiana Zerjal, Christophe Klopp, Sandrine Lagarrigue
Summary: An updated version of the paper has been published and can be accessed through a link at the top of the paper.
SCIENTIFIC REPORTS
(2021)
Article
Oncology
Emanuel Goncalves, Rebecca C. Poulos, Zhaoxiang Cai, Syd Barthorpe, Srikanth S. Manda, Natasha Lucas, Alexandra Beck, Daniel Bucio-Noble, Michael Dausmann, Caitlin Hall, Michael Hecker, Jennifer Koh, Howard Lightfoot, Sadia Mahboob, Iman Mali, James Morris, Laura Richardson, Akila J. Seneviratne, Rebecca Shepherd, Erin Sykes, Frances Thomas, Sara Valentini, Steven G. Williams, Yangxiu Wu, Dylan Xavier, Karen L. MacKenzie, Peter G. Hains, Brett Tully, Phillip J. Robinson, Qing Zhong, Mathew J. Garnett, Roger R. Reddel
Summary: The study analyzes the proteomes of multiple cancer cell lines through mass spectrometry and reveals thousands of cancer protein biomarkers that are not significant at the transcript level, demonstrating that the proteome has predictive power for drug response similar to the transcriptome.
Article
Immunology
Rui Gong, Hong Luo, Gangyu Long, Jiqian Xu, Chaolin Huang, Xin Zhou, You Shang, Dingyu Zhang
Summary: In this study, we investigated sensitive non-invasive biomarkers associated with lung pathological changes in ARDS/ALI through integrative proteomic analysis. We identified common DEPs in serum and lung samples from direct ARDS mice and validated their clinical value in COVID-19-related ARDS cases. Six proteins with good clinical diagnostic and prognostic value were identified, providing potential targets for early detection and treatment of direct ARDS.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Oncology
Yoann Pradat, Julien Viot, Andrey A. Yurchenko, Konstantin Gunbin, Luigi Cerbone, Marc Deloger, Guillaume Grisay, Loic Verlingue, Veronique Scott, Ismael Padioleau, Leonardo Panunzi, Stefan Michiels, Antoine Hollebecque, Gerome Jules-Clement, Laura Mezquita, Antoine Laine, Yohann Loriot, Benjamin Besse, Luc Friboulet, Fabrice Andre, Paul-Henry Cournede, Daniel Gautheret, Sergey I. Nikolaev
Summary: Metastatic relapse after treatment is the main cause of cancer mortality, with unknown resistance mechanisms for most treatments. To address this issue, a pan-cancer cohort (META-PRISM) of 1,031 refractory metastatic tumors was analyzed. META-PRISM tumors, especially prostate, bladder, and pancreatic types, exhibited the most transformed genomes compared to untreated tumors. Standard-of-care resistance biomarkers were identified in only 9.6% of META-PRISM tumors, indicating a lack of clinical validation for resistance mechanisms. However, investigational and hypothetical resistance mechanisms were enriched in treated patients, supporting their potential role in treatment resistance. Furthermore, molecular markers improved 6-month survival prediction, particularly for advanced breast cancer patients. The META-PRISM cohort proves valuable for studying resistance mechanisms and conducting predictive analysis in cancer.
Article
Oncology
Argun Akcakanat, Xiaofeng Zheng, Christian X. Cruz Pico, Tae-Beom Kim, Ken Chen, Anil Korkut, Aysegul Sahin, Vijaykumar Holla, Emily Tarco, Gopal Singh, Senthil Damodaran, Gordon B. Mills, Ana Maria Gonzalez-Angulo, Funda Meric-Bernstam
Summary: Molecular profiling in metastatic breast cancer patients revealed common and less frequent but potentially actionable alterations, demonstrating intertumoral heterogeneity and potential evolution of actionable targets with tumor progression. Further optimization of testing and integrated analysis for treatment selection is needed.
CLINICAL CANCER RESEARCH
(2021)
Article
Multidisciplinary Sciences
Marian Kalocsay, Matthew J. Berberich, Robert A. Everley, Maulik K. Nariya, Mirra Chung, Benjamin Gaudio, Chiara Victor, Gary A. Bradshaw, Robyn J. Eisert, Marc Hafner, Peter K. Sorger, Caitlin E. Mills, Kartik Subramanian
Summary: Quantitative proteomics was performed on 60 human-derived breast cancer cell line models, resulting in the identification and characterization of subtypes of breast cancer. The datasets were found to conform to known transcriptional subtypes and are freely available for public use. These datasets can be used in combination with other measurements to predict drug response, provide context in signaling pathway models, and identify markers of sensitivity or resistance to therapeutics.
Review
Oncology
Dana C. Borcherding, Kevin He, Neha Amin, Angela C. Hirbe
Summary: This review highlights the role of TYK2 in cancer and metastases, as well as the potential of TYK2 inhibitors as effective cancer therapies. Recent studies have identified TYK2 as an oncogene that is frequently mutated or overexpressed in many types of cancer and metastases. Personalized medicine approaches aid in the more targeted treatment of tumors by detecting specific gene mutations, overexpression, or activity.
Article
Oncology
Richard J. Chen, Ming Y. Lu, Drew F. K. Williamson, Tiffany Y. Chen, Jana Lipkova, Zahra Noor, Muhammad Shaban, Maha Shady, Mane Williams, Bumjin Joo, Faisal Mahmood
Summary: Computational pathology has shown promise in developing prognostic models based on histology images. This study uses multimodal deep learning to integrate pathology images and molecular profile data, and discover prognostic features that correlate with outcomes.
Review
Pharmacology & Pharmacy
Xiaoshuai Li, Qiushi Wang, Rui Wang
Summary: Exosomes are extracellular vesicles that mediate cell-to-cell communication and contain bioactive substances such as DNA, RNA, lipids, and proteins. The DNA in exosomes, mainly consisting of genomic DNA and mitochondrial DNA, plays a crucial role in liquid biopsy of colorectal cancer and immune metabolic regulation. However, research on exosome DNA is still limited.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Jia-Ren Lin, Shu Wang, Shannon Coy, Yu -An Chen, Clarence Yapp, Madison Tyler, Maulik K. Nariya, Cody N. Heiser, Ken S. Lau, Sandro Santagata, Peter K. Sorger
Summary: We used advanced imaging techniques, 3D reconstruction, spatial statistics, and machine learning to identify cell types and states associated with diagnostic and prognostic features in colorectal cancer. We found that at the tumor invasive margin, T cell suppression involves multiple cell types and that seemingly localized features such as tertiary lymphoid structures are interconnected and have graded molecular properties. These findings challenge the notion that discrete changes in tumor state are most important, demonstrating the presence of large-scale morphological and molecular gradients.
Article
Oncology
Hersh Ham-Karim, Ola Negm, Narmeen Ahmad, Mohammad Ilyas
Summary: There are molecular discrepancies between primary colorectal cancer and their respective metastases, including genetic mutations, miRNA expression, and protein biomarker alterations.
CANCER CELL INTERNATIONAL
(2023)
Article
Biochemistry & Molecular Biology
Izabela Neska-Dlugosz, Karolina Buchholz, Justyna Durslewicz, Maciej Gagat, Dariusz Grzanka, Krzysztof Tojek, Anna Klimaszewska-Wisniewska
Summary: The study indicates that the expression levels of KIF11 and KIF14 in CRC are associated with clinical outcomes of patients and can effectively differentiate overall survival in CRC patients independently of other risk factors. Additionally, the expression of these two proteins in pathways related to the cell cycle, DNA replication, and repair are closely linked to CRC development.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Oncology
Maria Gonzalez-Gonzalez, Maria Laura Gutierrez, Jose Maria Sayagues, Luis Munoz-Bellvis, Alberto Orfao
Summary: Sporadic colorectal cancer (sCRC) is the third leading cause of cancer death in the Western world, with approximately a quarter of patients presenting metastatic dissemination at the time of diagnosis. Patients with sCRC generally have a worse prognosis compared to those with primary colorectal tumors, and there are still many genetic alterations involved in the metastatic process that need to be further identified and studied.
SEMINARS IN CANCER BIOLOGY
(2021)
Article
Biochemical Research Methods
Licai Huang, James P. Long, Ehsan Irajizad, James D. Doecke, Kim-Anh Do, Min Jin Ha
Summary: This study introduces a mediation analysis framework for multilevel molecular tumor profiling, which can handle various types of outcome variables and is suitable for high-throughput molecular profiling data. By analyzing kidney renal clear cell carcinoma proteogenomic data, genes that are mediated by proteins and the underlying mechanisms for various survival outcomes are identified, capturing disease-specific clinical characteristics in both short and long-term.
Article
Biochemistry & Molecular Biology
Natalia Soloveva, Svetlana Novikova, Tatiana Farafonova, Olga Tikhonova, Victor Zgoda
Summary: Using targeted mass spectrometry, the levels of EV-associated proteins were measured in colorectal cancer cell lines and blood plasma samples from CRC patients and healthy volunteers. Downregulation of TLN1, ITGB3, and TUBA4A with simultaneous upregulation of HSPG2 protein were observed in cancer samples compared to healthy controls. The proteomic cargo of CRC-associated EVs represents a promising source of potential prognostic markers.
Article
Computer Science, Artificial Intelligence
S. Pradeepa, K. R. Manjula, S. Vimal, Mohammad S. Khan, Naveen Chilamkurti, Ashish Kr Luhach
Summary: The study proposes a method to detect the risk of stroke by finding relevant symptoms and preventive measures from social media content, providing a viable approach for stroke risk detection.
NEURAL PROCESSING LETTERS
(2023)
Retraction
Computer Science, Hardware & Architecture
V. Subramaniyaswamy, Gunasekaran Manogaran, R. Logesh, V. Vijayakumar, Naveen Chilamkurti, D. Malathi, N. Senthilselvan
JOURNAL OF SUPERCOMPUTING
(2023)
Article
Biochemistry & Molecular Biology
Zilu Wang, Huimin Hu, Luuk Heitink, Kelly Rogers, Yue You, Tao Tan, Connie Li Wai Suen, Alex Garnham, Hao Chen, Elizabeth Lieschke, Sarah T. T. Diepstraten, Catherine Chang, Diane Moujalled, Kate Sutherland, Guillaume Lessene, Oliver M. M. Sieber, Jane Visvader, Gemma L. L. Kelly, Andreas Strasser
Summary: APR-246 can kill malignant cells irrespective of their TP53/TRP53 status. It induces various programmed cell death pathways, such as apoptosis, necroptosis, and ferroptosis. Therefore, the clinical testing of APR-246 should be expanded to cancers expressing wild-type TP53 or TP53-deficient.
CELL DEATH AND DIFFERENTIATION
(2023)
Article
Pathology
Romy Walker, Peter Georgeson, Khalid Mahmood, Jihoon E. Joo, Enes Makalic, Mark Clendenning, Julia Como, Susan Preston, Sharelle Joseland, Bernard J. Pope, Ryan A. Hutchinson, Kais Kasem, Michael D. Walsh, Finlay A. Macrae, Aung K. Win, John L. Hopper, Dmitri Mouradov, Peter Gibbs, Oliver M. Sieber, Dylan E. O'Sullivan, Darren R. Brenner, Steven Gallinger, Mark A. Jenkins, Christophe Rosty, Ingrid M. Winship, Daniel D. Buchanan
Summary: Identifying dMMR is crucial for precision medicine. Tumor features obtained from whole-exome and panel sequencing were evaluated for their accuracy in detecting dMMR. Multiple approaches, including individual features, statistical models, and additive feature combination, were assessed for dMMR prediction.
JOURNAL OF MOLECULAR DIAGNOSTICS
(2023)
Article
Oncology
Gio Fidelito, David P. De Souza, Birunthi Niranjan, William De Nardo, Shivakumar Keerthikumar, Kristin Brown, Renea A. Taylor, Matthew J. Watt
Summary: Cancer cells undergo metabolic reprogramming to meet increased bioenergetic demands. Glucose, glutamine, and fatty acid oxidation were upregulated in malignant PDXs compared with benign PDXs. Fatty acid uptake and oxidation are targetable metabolic dependencies in human prostate cancer.
MOLECULAR CANCER RESEARCH
(2023)
Article
Oncology
Laura J. Jenkins, Ian Y. Luk, W. Douglas Fairlie, Erinna F. Lee, Michelle Palmieri, Kael L. Schoffer, Tao Tan, Irvin Ng, Natalia Vukelic, Sharon Tran, Janson W. T. Tse, Rebecca Nightingale, Zakia Alam, Fiona Chionh, George Iatropoulos, Matthias Ernst, Shoukat Afshar-Sterle, Jayesh Desai, Peter Gibbs, Oliver M. Sieber, Amardeep S. Dhillon, Niall C. Tebbutt, John M. Mariadason
Summary: The EGFR/RAS/MEK/ERK signaling pathway is hyperactivated in most colorectal cancers. Inhibitors of this pathway primarily induce cytostatic effects, but also induce expression of proapoptotic factors, suggesting they may prime colorectal cancer cells for apoptosis. Histone deacetylase inhibitors (HDACis) have the potential to synergize with ERK/MAPK inhibitors to trigger colorectal cancer cell apoptosis.
MOLECULAR CANCER THERAPEUTICS
(2023)
Correction
Biochemistry & Molecular Biology
Zilu Wang, Huimin Hu, Luuk Heitink, Kelly Rogers, Yue You, Tao Tan, Connie Li Wai Suen, Alex Garnham, Hao Chen, Elizabeth Lieschke, Sarah T. Diepstraten, Catherine Chang, Tianwei Chen, Diane Moujalled, Kate Sutherland, Guillaume Lessene, Oliver M. Sieber, Jane Visvader, Gemma L. Kelly, Andreas Strasser
CELL DEATH AND DIFFERENTIATION
(2023)
Article
Biochemical Research Methods
Michelle Palmieri, Bruno Catimel, Dmitri Mouradov, Anuratha Sakthianandeswaren, Eugene Kapp, Ching-Seng Ang, Nicholas A. Williamson, Cameron J. Nowell, Michael Christie, Jayesh Desai, Peter Gibbs, Antony W. Burgess, Oliver M. Sieber
Summary: The nuclear translocation of PI3K alpha regulates the subcellular levels of PtdIns(3,4,5)P3 in colorectal cancer cell lines, and 867 potential nuclear PtdIns(3,4,5)P3 effector proteins have been identified. These effector proteins are mainly involved in RNA metabolism and may play a role in modulating pre-mRNA splicing. These findings suggest that nuclear PI3K alpha signaling through PtdIns(3,4,5)P3 effector proteins is important for CRC development.
MOLECULAR & CELLULAR PROTEOMICS
(2023)
Article
Multidisciplinary Sciences
Ashish Sethi, Stephen M. Rawlinson, Abhinav Dubey, Ching-Seng Ang, Yoon Hee Choi, Fei Yan, Kazuma Okada, Ashley M. Rozario, Aaron M. Brice, Naoto Ito, Nicholas A. Williamson, Danny M. Hatters, Toby D. M. Bell, Haribabu Arthanari, Gregory W. Moseley, Paul R. Gooley
Summary: Viruses interact extensively with host proteins to modulate the infected cell's biology, often through multifunctional viral proteins. Traditional models cannot explain specific functions observed in certain viral proteins. In this study, we found that the unique phenotype of rabies virus P3 protein is determined by conformational arrangements rather than the presence of functional modules.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Correction
Multidisciplinary Sciences
Lars Togel, Rebecca Nightingale, Rui Wu, Anderly C. Chueh, Sheren Al-Obaidi, Ian Luk, Mercedes Davalos-Salas, Fiona Chionh, Carmel Murone, Daniel D. Buchanan, Zac Chatterton, Oliver M. Sieber, Diego Arango, Niall C. Tebbutt, David Williams, Amardeep S. Dhillon, John M. Mariadason
SCIENTIFIC REPORTS
(2023)
Article
Gastroenterology & Hepatology
Dmitri Mouradov, Paul Greenfield, Shan Li, Eun-Jung In, Claire Storey, Anuratha Sakthianandeswaren, Peter Georgeson, Daniel D. Buchanan, Robyn L. Ward, Nicholas J. Hawkins, Iain Skinner, Ian T. Jones, Peter Gibbs, Chenkai Ma, Yi Jin Liew, Kim Y. C. Fung, Oliver M. Sieber
Summary: By profiling the tumor and normal mucosa of 423 colorectal cancer patients, it was found that tumors can be classified into three distinct microbiota-based subtypes with different clinicomolecular features and outcomes. These findings provide new insights and a framework for microbiota-based stratification of colorectal cancer.
Article
Biochemical Research Methods
Rahul Sanwlani, Taeyoung Kang, Sriram Gummadi, Christina Nedeva, Ching-Seng Ang, Suresh Mathivanan
Summary: In this study, bovine milk-derived extracellular vesicles (MEVs) were isolated and characterized. It was found that MEVs sensitize triple-negative breast cancer (TNBC) cells to doxorubicin, reducing their metabolic potential and cell viability. Proteomic analysis suggests that combinatorial treatment depletes pro-tumorigenic gene products and metabolic proteins, which are therapeutic targets in TNBC. The study highlights the potential of bovine MEVs to enhance the sensitivity of TNBC cells to doxorubicin and pave the way for novel treatment regimens.
Article
Computer Science, Theory & Methods
Ngoc Duy Pham, Alsharif Abuadbba, Yansong Gao, Khoa Tran Phan, Naveen Chilamkurti
Summary: This paper proposes a split learning (SL) approach for training deep learning models without sharing raw data, thereby preserving data privacy. The SL local layers are binarized to enable faster computation and reduced memory usage. Experimental results demonstrate the effectiveness of the binarized SL models in lightweight IoT/mobile applications with high privacy-preservation requirements.
IEEE TRANSACTIONS ON INFORMATION FORENSICS AND SECURITY
(2023)
Article
Cell Biology
Sushma Anand, Christina Nedeva, Sai V. Chitti, Pamali Fonseka, Taeyoung Kang, Lahiru Gangoda, Nishat I. Tabassum, Suad Abdirahman, Thiruma V. Arumugam, Tracy L. Putoczki, Sharad Kumar, Suresh Mathivanan
Summary: This study provides evidence for the role of ubiquitin ligase NEDD4 in regulating resistance to the commonly used CRC chemotherapeutic drug 5-fluorouracil (5-FU).
CELL DEATH & DISEASE
(2023)
Review
Medicine, Research & Experimental
Ramanuj DasGupta, Aixin Yap, Elena Yong Yaqing, Shumei Chia
Summary: Cancer treatment is evolving towards individualized and precise approaches based on patient-specific tumor features. The aim is to maximize treatment effectiveness while reducing ineffective therapy and side effects.
WIRES MECHANISMS OF DISEASE
(2023)
