Article
Oncology
Masanori Oshi, Shipra Gandhi, Rongrong Wu, Mariko Asaoka, Li Yan, Akimitsu Yamada, Shinya Yamamoto, Kazutaka Narui, Takashi Chishima, Takashi Ishikawa, Itaru Endo, Kazuaki Takabe
Summary: We established a novel BRCAness score using BRCA-mutation-related gene expressions and found that it associates with DNA repair and predicts response to PARP inhibitors regardless of BRCA mutation.
BIOMARKER RESEARCH
(2022)
Article
Oncology
Eileen E. Parkes, Kienan I. Savage, Tong Lioe, Clinton Boyd, Sophia Halliday, Steven M. Walker, Keith Lowry, Laura Knight, Niamh E. Buckley, Andrena Grogan, Gemma E. Logan, Alison Clayton, Jane Hurwitz, Stephen J. Kirk, Jiamei Xu, Fatima Abdullahi Sidi, Matthew P. Humphries, Victoria Bingham, Jaqueline A. James, Colin R. James, D. Paul Harkin, Richard D. Kennedy, Stuart A. McIntosh
Summary: This study evaluates the predictive value of the DNA-damage immune-response (DDIR) signature for neoadjuvant chemotherapy response in early breast cancer. The results suggest that DDIR positivity is associated with immune infiltration and upregulated immune-checkpoint gene expression, and may identify a subgroup sensitive to anthracycline chemotherapy. The transcriptomic data indicate that induction with anthracycline-containing regimens in immune restricted, cold tumors may be effective for immune priming.
BRITISH JOURNAL OF CANCER
(2022)
Article
Pharmacology & Pharmacy
Hongyi Wu, Xiaoye Li, Juying Qian, Xin Zhao, Yao Yao, Qianzhou Lv, Junbo Ge
Summary: The study aimed to improve the prediction of ischemic events in Chinese patients treated with clopidogrel by developing the GeneFA risk score, which was found to have moderate predictive ability for high HRPR patients. The GeneFA score exhibited a better prediction for HRPR patients compared to the ABCD-GENE score and showed consistent prognostic value in HRPR incidence and ischemic recurrence.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Genetics & Heredity
Srinivas Rajagopalan, Amartya Singh, Hossein Khiabanian
Summary: The study utilized an unsupervised biclustering approach to analyze a large number of normal and tumor brain samples, identifying co-regulated gene expression profiles linked to specific subsets of gliomas and presenting a cilium-associated signature as predictor of poor survival in tumors. The introduction of a risk score based on expression of 12 cilium-associated genes proved to be informative of survival independently of other prognostic biomarkers, highlighting the potential therapeutic vulnerabilities for aggressive gliomas.
FRONTIERS IN GENETICS
(2021)
Article
Oncology
Ines Guix, Qi Liu, Miquel Angel Pujana, Patrick Ha, Josep Piulats, Isabel Linares, Ferran Guedea, Jian-Hua Mao, Ann Lazar, Jocelyn Chapman, Sue S. Yom, Alan Ashworth, Mary Helen Barcellos-Hoff
Summary: This study confirms the anticorrelation between TGF beta signaling and alt-EJ gene expression signatures, as well as their predictive value for response to genotoxic therapy. The findings validate the role of TGF beta as a key mediator of DNA repair and demonstrate the feasibility of using gene expression to assess TGF beta signaling and DNA repair.
CLINICAL CANCER RESEARCH
(2022)
Article
Medicine, General & Internal
Aleix Prat, Valentina Guarneri, Tomas Pascual, Fara Braso-Maristany, Esther Sanfeliu, Laia Pare, Francesco Schettini, Debora Martinez, Pedro Jares, Gaia Griguolo, Maria Vittoria Dieci, Javier Cortes, Antonio Llombart-Cussac, Benedetta Conte, Mercedes Marin-Aguilera, Nuria Chic, Joan Anton Puig-Butille, Antonio Martinez, Patricia Galvan, Yi-Hsuan Tsai, Blanca Gonzalez-Farre, Aurea Mira, Ana Vivancos, Patricia Villagrasa, Joel S. Parker, Pierfranco Conte, Charles M. Perou
Summary: A new HER2DX risk score and pCR score have been developed to accurately predict survival and treatment response in early-stage HER2-positive breast cancer.
Article
Genetics & Heredity
Ting-Ting Yin, Meng-Xing Huang, Fei Wang, Yi-Hua Jiang, Jie Long, Liang Li, Jie Cao
Summary: In this study, the potential roles of lactate-related genes (LRGs) in the diversity and prognosis of the tumor microenvironment (TME) were analyzed. The results of this study will contribute to a better understanding of the characteristics of TME immune cell infiltration and guide the development of more effective immunotherapy strategies.
FRONTIERS IN GENETICS
(2022)
Article
Oncology
Sanjiban Chakrabarty, William F. Quiros-Solano, Maayke M. P. Kuijten, Ben Haspels, Sandeep Mallya, Calvin Shun Yu Lo, Amr Othman, Cinzia Silvestri, Anja van de Stolpe, Nikolas Gaio, Hanny Odijk, Marieke van de Ven, Corrina M. A. de Ridder, Wytske M. van Weerden, Jos Jonkers, Ronald Dekker, Nitika Taneja, Roland Kanaar, Dik C. van Gent
Summary: This study developed a microfluidic platform for evaluating cancer treatment response and predicting drug efficacy in breast and prostate tumors. By culturing tumor slices under controlled growth conditions, the platform allows reliable assessment of chemotherapeutic sensitivity and enables detailed mechanistic studies.
Article
Oncology
Andrew D. James, Theresa K. Leslie, Joshua D. Kaggie, Laura Wiggins, Lewis Patten, John Murphy O'Duinn, Swen Langer, Marie-Christine Labarthe, Frank Riemer, Gabrielle Baxter, Mary A. McLean, Fiona J. Gilbert, Aneurin J. Kennerley, William J. Brackenbury
Summary: In this study, the diagnostic and treatment-monitoring potential of sodium (Na-23) MRI in breast cancer was demonstrated. The researchers found elevated sodium concentration in tumor regions compared to non-tumor regions, and combining Na-23 MRI with other imaging measurements improved the accuracy of tumor classification. This novel MRI method also showed superior sensitivity in assessing treatment response compared to traditional methods.
BRITISH JOURNAL OF CANCER
(2022)
Article
Multidisciplinary Sciences
Nindo B. Punturi, Sinem Seker, Vaishnavi Devarakonda, Aloran Mazumder, Rashi Kalra, Ching Hui Chen, Shunqiang Li, Tina Primeau, Matthew J. Ellis, Shyam M. Kavuri, Svasti Haricharan
Summary: Resistance to endocrine treatment in ER+ breast cancer patients is linked to activation of HER2 due to loss of mismatch repair, and inhibiting HER2 restores sensitivity to treatment. Loss of MutL and upregulation of HER2 are associated with sensitivity to HER inhibitors in ER+/HER2(-) patients.
NATURE COMMUNICATIONS
(2021)
Article
Oncology
Quynh Hoa Tran, Van Thai Than, Phuc Loi Luu, Declan Clarke, Hanh Ngoc Lam, Thanh-Giang Tan Nguyen, Dinh-Truong Nguyen, Phan Q. Duy, Dung Phung, Minh Nam Nguyen
Summary: ASMT expression is reduced in breast cancer, but higher levels are associated with better survival outcomes and improved response to tamoxifen treatment. The ASMT gene signature accurately identifies low-risk cases and provides new strategies for breast cancer treatment.
INTERNATIONAL JOURNAL OF CANCER
(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
Biochemical Research Methods
Wan-Xia Yang, Hong-Wei Gao, Jia-Bo Cui, An-An Zhang, Fang-Fang Wang, Jian-Qin Xie, Ming-Hua Lu, Chong-Ge You
Summary: This study identifies key coagulation-related genes and establishes a risk score model for predicting the prognosis of hepatocellular carcinoma (HCC) patients. The model shows good predictive ability in the TCGA dataset and is validated in an external dataset. Furthermore, a nomogram combining the risk score with age, gender, grade, and stage is constructed to assess survival probability. The study also reveals correlations between the risk score and functional enrichment, pathways, and the tumor immune microenvironment.
BMC BIOINFORMATICS
(2023)
Article
Multidisciplinary Sciences
Yuming Jiang, Zhicheng Zhang, Wei Wang, Weicai Huang, Chuanli Chen, Sujuan Xi, M. Usman Ahmad, Yulan Ren, Shengtian Sang, Jingjing Xie, Jen-Yeu Wang, Wenjun Xiong, Tuanjie Li, Zhen Han, Qingyu Yuan, Yikai Xu, Lei Xing, George A. Poultsides, Guoxin Li, Ruijiang Li
Summary: Significant progress has been made in using deep learning for cancer detection and diagnosis, but predicting treatment response and outcomes remains challenging. This study presents a biology-guided deep learning approach that simultaneously predicts tumor microenvironment status and treatment outcomes from medical images. The model was validated for gastric cancer prognosis and response to adjuvant chemotherapy, and it complements clinically approved biomarkers, providing information for patient selection.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Ibrahim E. Elsemman, Angelica Rodriguez Prado, Pranas Grigaitis, Manuel Garcia Albornoz, Victoria Harman, Stephen W. Holman, Johan van Heerden, Frank J. Bruggeman, Mark M. M. Bisschops, Nikolaus Sonnenschein, Simon Hubbard, Rob Beynon, Pascale Daran-Lapujade, Jens Nielsen, Bas Teusink
Summary: The study developed a metabolic model of yeast cells to predict proteome constraints governing metabolic strategies. Under specific conditions, unicellular organisms rewire their metabolism to adapt to growth and maintenance needs.
NATURE COMMUNICATIONS
(2022)
Article
Oncology
Barry R. Davies, Nin Guan, Armelle Logie, Claire Crafter, Lyndsey Hanson, Vivien Jacobs, Neil James, Philippa Dudley, Kelly Jacques, Brendon Ladd, Celina M. D'Cruz, Michael Zinda, Justin Lindemann, Makoto Kodaira, Kenji Tamura, Emma L. Jenkins
MOLECULAR CANCER THERAPEUTICS
(2015)
Article
Oncology
Kenji Tamura, Jun Hashimoto, Yuko Tanabe, Makoto Kodaira, Kan Yonemori, Takashi Seto, Fumihiko Hirai, Shuji Arita, Gouji Toyokawa, Lan Chen, Hiroshi Yamamoto, Toshio Kawata, Justin Lindemann, Taito Esaki
CANCER CHEMOTHERAPY AND PHARMACOLOGY
(2016)
Article
Oncology
David M. Hyman, Lillian M. Smyth, Mark T. A. Donoghue, Shannon N. Westin, Philippe L. Bedard, Emma J. Dean, Hideaki Bando, Anthony B. El-Khoueiry, Jose A. Perez-Fidalgo, Alain Mita, Jan H. M. Schellens, Matthew T. Chang, Jonathan B. Reichel, Nancy Bouvier, S. Duygu Selcuklu, Tara E. Soumerai, Jean Torrisi, Joseph P. Erinjeri, Helen Ambrose, J. Carl Barrett, Brian Dougherty, Andrew Foxley, Justin P. O. Lindemann, Robert McEwen, Martin Pass, Gaia Schiavon, Michael F. Berger, Sarat Chandarlapaty, David B. Solit, Udai Banerji, Jose Baselga, Barry S. Taylor
JOURNAL OF CLINICAL ONCOLOGY
(2017)
Article
Oncology
Michael Weller, Patrick Roth, Felix Sahm, Isabel Burghardt, Bernhard Schuknecht, Elisabeth J. Rushing, Luca Regli, Justin P. Lindemann, Andreas von Deimling
JNCI-JOURNAL OF THE NATIONAL CANCER INSTITUTE
(2017)
Article
Oncology
Michael Weller, Patrick Roth, Felix Sahm, Isabel Burghardt, Bernhard Schuknecht, Elisabeth J. Rushing, Luca Regli, Justin P. Lindemann, Andreas von Deimling
JNCI-JOURNAL OF THE NATIONAL CANCER INSTITUTE
(2017)
Article
Oncology
Emma Dean, Udai Banerji, Jan H. M. Schellens, Matthew G. Krebs, Begona Jimenez, Emilie van Brummelen, Chris Bailey, Ed Casson, Diana Cripps, Marie Cullberg, Stephen Evans, Andrew Foxley, Justin Lindemann, Paul Rugman, Nigel Taylor, Guy Turner, James Yates, Peter Lawrence
CANCER CHEMOTHERAPY AND PHARMACOLOGY
(2018)
Article
Oncology
Erika P. Hamilton, Manish R. Patel, Anne C. Armstrong, Richard D. Baird, Komal Jhaveri, Matthias Hoch, Teresa Klinowska, Justin P. O. Lindemann, Shethah R. Morgan, Gaia Schiavon, Hazel M. Weir, Seock-Ah Im
CLINICAL CANCER RESEARCH
(2018)
Article
Oncology
Sally Anne Garnett, Miguel Martin, Guy Jerusalem, Lubos Petruzelka, Roberto Torres, Igor N. Bondarenko, Rustem Khasanov, Didier Verhoeven, Jose L. Pedrini, Iva Smirnova, Mikhail R. Lichinitser, Kelly Pendergrass, Justin P. O. Lindemann, Angelo Di Leo
BREAST CANCER RESEARCH AND TREATMENT
(2013)
Review
Oncology
John F. R. Robertson, Justin Lindemann, Sally Garnett, Elizabeth Anderson, Robert I. Nicholson, Irene Kuter, Julia M. W. Gee
CLINICAL BREAST CANCER
(2014)
Article
Oncology
Neill Patani, Anita K. Dunbier, Helen Anderson, Zara Ghazoui, Ricardo Ribas, Elizabeth Anderson, Qiong Gao, Roger A'hern, Alan Mackay, Justin Lindemann, Robert Wellings, Jill Walker, Irene Kuter, Lesley-Ann Martin, Mitch Dowsett
CLINICAL CANCER RESEARCH
(2014)
Article
Critical Care Medicine
Gordon R. Bernard, Bruno Francois, Jean-Paul Mira, Jean-Louis Vincent, R. Phillip Dellinger, James A. Russell, Steven P. LaRosa, Pierre-Francois Laterre, Mitchell M. Levy, Wayne Dankner, Nicola Schmitt, Justin Lindemann, Xavier Wittebole
CRITICAL CARE MEDICINE
(2014)
Article
Multidisciplinary Sciences
Elza C. de Bruin, Jessica L. Whiteley, Claire Corcoran, Pauline M. Kirk, Jayne C. Fox, Javier Armisen, Justin P. O. Lindemann, Gaia Schiavon, Helen J. Ambrose, Alexander Kohlmann
Article
Oncology
Costanza Paoletti, Gaia Schiavon, Emily M. Dolce, Elizabeth P. Darga, T. Hedley Carr, Joseph Geradts, Matthias Hoch, Teresa Klinowska, Justin Lindemann, Gayle Marshall, Shethah Morgan, Parul Patel, Vicky Rowlands, Nitharsan Sathiyayogan, Kimberly Aung, Erika Hamilton, Manish Patel, Anne Armstrong, Komal Jhaveri, Seock-Ah Im, Nadia Iqbal, Fouziah Butt, Caroline Dive, Elizabeth A. Harrington, J. Carl Barrett, Richard Baird, Daniel F. Hayes
CLINICAL CANCER RESEARCH
(2018)
Article
Oncology
Udai Banerji, Emma J. Dean, J. Alejandro Perez-Fidalgo, Gerald Batist, Philippe L. Bedard, Benoit You, Shannon N. Westin, Peter Kabos, Michelle D. Garrett, Mathew Tall, Helen Ambrose, J. Carl Barrett, T. Hedley Carr, S. Y. Amy Cheung, Claire Corcoran, Marie Cullberg, Barry R. Davies, Elza C. de Bruin, Paul Elvin, Andrew Foxley, Peter Lawrence, Justin P. O. Lindemann, Rhiannon Maudsley, Martin Pass, Vicky Rowlands, Paul Rugman, Gaia Schiavon, James Yates, Jan H. M. Schellens
CLINICAL CANCER RESEARCH
(2018)