Article
Genetics & Heredity
Liang Chen, Yunhua Lin, Wei Wei, Yue Wang, Fangyue Li, Wang Du, Zhonghua Yang, Yiming Hu, Xiaomei Ying, Qikai Tang, Jiaheng Xie, Hongzhu Yu
Summary: This study developed a glycolysis-related signature that can predict the prognosis and risk subtypes of pancreatic cancer patients, providing personalized management in the clinical setting.
FRONTIERS IN GENETICS
(2022)
Article
Medicine, General & Internal
Qian Lu, Yu Zhang, Xiaojian Chen, Weihong Gu, Xinrong Ji, Zhong Chen
Summary: This study reveals a strong correlation between TME and prognosis in PDAC patients, with higher immune scores associated with better overall survival. Additionally, 90 genes were identified to influence stromal and immune scores, among which CA9, SPOCK2, and CD1D were identified as the most significant prognostic genes.
Article
Oncology
Juha P. Vayrynen, Koichiro Haruki, Sara A. Vayrynen, Mai Chan Lau, Andressa Dias Costa, Jennifer Borowsky, Melissa Zhao, Tomotaka Ugai, Junko Kishikawa, Naohiko Akimoto, Rong Zhong, Shanshan Shi, Tzuu-Wang Chang, Kenji Fujiyoshi, Kota Arima, Tyler S. Twombly, Annacarolina Da Silva, Mingyang Song, Kana Wu, Xuehong Zhang, Andrew T. Chan, Reiko Nishihara, Charles S. Fuchs, Jeffrey A. Meyerhardt, Marios Giannakis, Shuji Ogino, Jonathan A. Nowak
Summary: Myeloid cell populations in the colorectal cancer microenvironment exhibit spatially distinct distributions and subset-specific prognostic significance. Mature CD14(+)HLA-DR+ and immature CD14(+)HLA-DR- monocytic phenotypes show opposite associations. These findings underscore the prognostic utility of multimarker evaluation of myeloid cell infiltrates and reveal a previously unrecognized degree of spatial organization for myeloid cells in the immune microenvironment.
JOURNAL FOR IMMUNOTHERAPY OF CANCER
(2021)
Article
Immunology
Yan Ma, Xiaomeng He, Yang Di, Shanshan Liu, Qilin Zhan, Zhihui Bai, Tianyi Qiu, Christopher Corpe, Jin Wang
Summary: The study constructed a novel immune-related prognostic risk model for pancreatic cancer (PaCa) using long noncoding RNAs (lncRNAs) and evaluated the prognostic prediction of these lncRNAs. The results identified four IRlncRNA signatures that may serve as predictors of survival and potential biomarkers for the immune response in PaCa.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Genetics & Heredity
Zhi Liu, Jun Zhang, Deyun Shen, Xuechun Hu, Zongpan Ke, I. Nyoman Ehrich Lister, Bungaran Sihombing
Summary: This study found that cytoskeleton-associated protein 2-like protein is upregulated in clear cell renal cell carcinoma tissues and may promote disease progression through multiple signaling pathways. It can serve as a prognostic marker and a potential treatment target in clear cell renal cell carcinoma.
FRONTIERS IN GENETICS
(2023)
Article
Cell Biology
Gangping Tu, Wenzhe Gao, Ying Li, Yating Dian, Bingyang Xue, Li Niu, Xiao Yu, Hongwei Zhu
Summary: S100A16, highly expressed in pancreatic cancer tissues, might be associated with poor prognosis. By analyzing gene expression differences, clinical characteristics, and establishing a risk score system, the study successfully predicted the survival time of patients with PDAC.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Kai Sun, Xue-de Zhang, Xiao-yang Liu, Pei Lu
Summary: YAP1 is differently expressed in various cancers, particularly elevated in pancreatic cancer. Its expression is correlated with patient outcomes and tumor immune cell infiltration, making it a valuable prognostic biomarker.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Oncology
Wei Yu, Yongkang Diao, Yi Zhang, Ying Shi, Xiangkang Lv, Chengwu Zhang, Kangjun Zhang, Weifeng Yao, Dongsheng Huang, Jungang Zhang
Summary: The study found that high expression of FOXN3 in pancreatic cancer is associated with poor prognosis, and FOXN3 is involved in the occurrence and progression of pancreatic cancer, which may be useful as a prognostic tool in pancreatic cancer immunotherapy.
FRONTIERS IN ONCOLOGY
(2022)
Article
Immunology
Qi Wang, Zhangzuo Li, Shujing Zhou, Zhengrui Li, Xufeng Huang, Yiwei He, Yuhan Zhang, Xiaoxian Zhao, Yidan Tang, Min Xu
Summary: Recently, the role of NCAPG2 as an essential participant in the process of chromosome cohesion and stabilization in mitosis has been highlighted, particularly in certain tumors. However, there is a lack of detailed studies exploring its potential functions in pan-cancer. In this study, the potential functions of NCAPG2 in pan-cancer were comprehensively elucidated, and it was found to be overexpressed in almost every tumor and showed significant prognostic and diagnostic efficacy. Additionally, the correlation between NCAPG2 and immune features suggests its potential application in guiding immunotherapy.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Oncology
Zhijian Huang, Jiasheng Yang, Wenjing Qiu, Jing Huang, Zhirong Chen, Yuanyuan Han, Changsheng Ye
Summary: HAUS5 expression is associated with prognosis in breast cancer, with upregulation correlated with poor clinicopathological characteristics, signaling pathways, immune cell infiltration, and tumor cell stemness.
FRONTIERS IN ONCOLOGY
(2022)
Article
Multidisciplinary Sciences
Dhifaf Sarhan, Silke Eisinger, Fei He, Maria Bergsland, Catarina Pelicano, Caroline Driescher, Kajsa Westberg, Itziar Ibarlucea Benitez, Rawan Humoud, Giorgia Palano, Shuijie Li, Valentina Carannante, Jonas Muhr, Bjorn Onfelt, Susanne Schlisio, Jeffrey Ravetch, Rainer Heuchel, Matthias J. Lohr, Mikael C. Karlsson
Summary: Immunotherapy for cancer has revolutionized the treatment of previously lethal cancers, but its efficacy in pancreatic ductal adenocarcinoma (PDAC) has been disappointing. This study shows that the expression of scavenger receptor MARCO is associated with poor prognosis and a tumor phenotype that excludes lymphocytes. Targeting MARCO can remodel the tumor microenvironment and improve the efficiency of immunotherapy in PDAC patients.
Review
Gastroenterology & Hepatology
Samantha B. Kemp, Marina Pasca di Magliano, Howard C. Crawford
Summary: Pancreatic ductal adenocarcinoma (PDA) is a nearly universally lethal malignancy characterized by extensive infiltration of immunosuppressive myeloid cells, inhibiting normal immune functions and promoting carcinogenesis. Current immune checkpoint therapy has not been effective in PDA, highlighting the importance of understanding the mechanisms underlying immune suppression in this type of cancer.
CELLULAR AND MOLECULAR GASTROENTEROLOGY AND HEPATOLOGY
(2021)
Article
Cell Biology
Hsiao-Wen Tsai, Chia-Jung Li, Li-Te Lin, An-Jen Chiang, San-Nung Chen, Zhi-Hong Wen, Kuan-Hao Tsui
Summary: This study aims to investigate the expression of OPA3 protein in ovarian cancer, its association with prognosis and immune infiltration, and its potential value in targeted therapy.
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
Cell Biology
Han Zhao, Yun Chen, Peijun Shen, Lan Gong
Summary: This study analyzed the immune cell infiltration landscape of uveal melanoma using CIBERSORT and ESTIMATE algorithms, finding that patients with high ICI scores had poorer prognosis and increased expression levels of immune checkpoint-related genes. The study demonstrated that ICI scores are an independent prognostic biomarker and have value in predicting immunotherapeutic outcomes.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Oncology
Hannah L. Williams, Andressa Dias Costa, Jinming Zhang, Srivatsan Raghavan, Peter S. Winter, Kevin S. Kapner, Scott P. Ginebaugh, Sara A. Vayrynen, Juha P. Vayrynen, Chen Yuan, Andrew W. Navia, Junning Wang, Annan Yang, Timothy L. Bosse, Radha L. Kalekar, Kristen E. Lowder, Mai Chan Lau, Dalia Elganainy, Vicente Morales-Oyarvide, Douglas A. Rubinson, Harshabad Singh, Kimberly Perez, James M. Cleary, Thomas E. Clancy, Jiping Wang, Joseph D. Mancias, Lauren K. Brais, Emma R. Hill, Margaret M. Kozak, David C. Linehan, Richard F. Dunne, Daniel T. Chang, Albert C. Koong, Aram F. Hezel, William C. Hahn, Alex K. Shalek, Andrew J. Aguirre, Jonathan A. Nowak, Brian M. Wolpin
Summary: A multiplex immunofluorescence (mIF) pipeline was developed to investigate the protein expression and intratumoral heterogeneity of pancreatic ductal adenocarcinoma (PDAC). The results showed that PDAC tumors exhibit extensive intratumoral heterogeneity, which is associated with patient outcomes and can be reduced in patient-derived organoid cultures. Co-expressor cells expressing both classical and basal markers were found in the majority of tumors, suggesting an intermediate state between subtype poles. This clinically applicable pipeline has implications for prognosis and treatment selection in PDAC patients.
Article
Oncology
Mehrdad Rakaee, Elio Adib, Biagio Ricciuti, Lynette M. Sholl, Weiwei Shi, Joao Alessi, Alessio Cortellini, Claudia A. M. Fulgenzi, Patrizia Viola, David J. Pinato, Sayed Hashemi, Idris Bahce, Ilias Houda, Ezgi B. Ulas, Teodora Radonic, Juha P. Vayrynen, Elin Richardsen, Simin Jamaly, Sigve Andersen, Tom Donnem, Mark M. Awad, David J. Kwiatkowski
Summary: This study developed a machine-learning-based approach to evaluate the association between tumor-infiltrating lymphocytes (TILs) and immune checkpoint inhibitor (ICI) therapy in lung cancer patients. The results showed that high levels of TILs were associated with ICI treatment response and could be used for patient selection and precision therapy guidance.
Article
Oncology
Meeri Kastinen, Paeivi Sirnio, Hanna Elomaa, Maarit Ahtiainen, Sara A. Vayrynen, Karl-Heinz Herzig, Sanna Merilainen, Raila Aro, Reetta Haivala, Tero Rautio, Juha Saarnio, Erkki-Ville Wirta, Olli Helminen, Toni T. Seppala, Teijo Kuopio, Jan Bohm, Anne Tuomisto, Jukka-Pekka Mecklin, Markus J. Makinen, Juha P. Vayrynen
Summary: This study analyzed data from 1413 patients with colorectal cancer and found associations between tumor necrosis percentage and tumor characteristics, immune cell infiltrates, serum cytokine concentrations, as well as prognosis. The results showed that high tumor necrosis percentage is associated with shorter colorectal cancer-specific survival, independent of other factors. Tumor necrosis is therefore considered an important prognostic factor in colorectal cancer.
BRITISH JOURNAL OF CANCER
(2023)
Article
Oncology
Hanna Elomaa, Maarit Ahtiainen, Sara A. Vaeyrynen, Shuji Ogino, Jonathan A. Nowak, Mai Chan Lau, Olli Helminen, Erkki-Ville Wirta, Toni T. Seppaelae, Jan Boehm, Jukka-Pekka Mecklin, Teijo Kuopio, Juha P. Vaeyrynen
Summary: The expression patterns and prognostic significance of PD-L1 and PD-1 in the colorectal cancer microenvironment are inadequately characterised. This study found that PD-L1(+) macrophages and PD-1(+) T cells were associated with better clinical outcomes in colorectal cancer patients. These findings enhance the understanding of immune checkpoints in the tumor microenvironment and could contribute to the development of improved immunotherapies.
BRITISH JOURNAL OF CANCER
(2023)
Letter
Hematology
Tero Vuolio, Outi Kuittinen, Juha P. Vayrynen, Hanna-Riikka Teppo, Roosa E. I. Prusil, Maria Ramet, Hanne Kuitunen, Timo Paloneva, Milla E. L. Kuusisto
BRITISH JOURNAL OF HAEMATOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Davide Placido, Bo Yuan, Jessica X. Hjaltelin, Chunlei Zheng, Amalie D. Haue, Piotr J. Chmura, Chen Yuan, Jihye Kim, Renato Umeton, Gregory Antell, Alexander Chowdhury, Alexandra Franz, Lauren Brais, Elizabeth Andrews, Debora S. Marks, Aviv Regev, Siamack Ayandeh, Mary T. Brophy, Nhan V. Do, Peter Kraft, Brian M. Wolpin, Michael H. Rosenthal, Nathanael R. Fillmore, Soren Brunak, Chris Sander
Summary: This study used artificial intelligence methods to analyze clinical data from Denmark and the United States and developed a model to predict the occurrence of pancreatic cancer within 36 months. The model showed promising performance in retrospective validation and can potentially aid in early detection.
Article
Multidisciplinary Sciences
Liisa Petainen, Juha P. Vayrynen, Pekka Ruusuvuori, Ilkka Polonen, Sami Ayramo, Teijo Kuopio
Summary: This study proposes an automated method for estimating tumor-stroma ratio (TSR) from histopathological images of colorectal cancer using convolutional neural networks. The models achieved high accuracy in classifying stroma, tumor, and other tissues, with the best model reaching 99.3% accuracy for tumor classification. The predicted TSR values showed moderate correlation with pathologist estimations (0.57).
Article
Pathology
Topias Karjula, Anne Niskakangas, Olli Mustonen, Iiris Puro, Hanna Elomaa, Maarit Ahtiainen, Teijo Kuopio, Jukka-Pekka Mecklin, Toni T. Seppala, Erkki-Ville Wirta, Eero Sihvo, Fredrik Yannopoulos, Olli Helminen, Juha P. Vayrynen
Summary: In this study, the prognostic effect of tertiary lymphoid structures (TLSs) on colorectal cancer (CRC) pulmonary metastases and primary tumors was analyzed. The density and diameter of TLSs showed no prognostic value in pulmonary metastases, but higher density and diameter were associated with lower mortality in primary tumors.
Article
Multidisciplinary Sciences
Yin Zhang, Qiao-Li Wang, Chen Yuan, Alice A. Lee, Ana Babic, Kimmie Ng, Kimberly Perez, Jonathan A. Nowak, Jesper Lagergren, Meir J. Stampfer, Edward L. Giovannucci, Chris Sander, Michael H. Rosenthal, Peter Kraft, Brian M. Wolpin
Summary: Recent medication changes, such as initiating antidiabetic or anticoagulant medications, as well as discontinuing antihypertensive medications, are associated with an increased risk of pancreatic cancer diagnosis within the next two years. The risk of pancreatic cancer increases as the number of relevant medication changes increases. These findings suggest that recent medication changes should be considered as potential factors in multi-factor risk models for pancreatic cancer.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Pei-Chen Tsai, Tsung-Hua Lee, Kun-Chi Kuo, Fang-Yi Su, Tsung-Lu Michael Lee, Eliana Marostica, Tomotaka Ugai, Melissa Zhao, Mai Chan Lau, Juha P. Vayrynen, Marios Giannakis, Yasutoshi Takashima, Seyed Mousavi Kahaki, Kana Wu, Mingyang Song, Jeffrey A. Meyerhardt, Andrew T. Chan, Jung-Hsien Chiang, Jonathan Nowak, Shuji Ogino, Kun-Hsing Yu
Summary: The authors develop a machine learning-based platform, MOMA, to systematically identify and interpret the relationship between patients' histologic patterns, multi-omics, and clinical profiles. MOMA successfully predicts the overall survival, disease-free survival, and copy number alterations of colorectal cancer patients. Additionally, MOMA identifies interpretable pathology patterns predictive of gene expression profiles, microsatellite instability status, and clinically actionable genetic alterations.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Jouni Harkonen, Petri Polonen, Ashik Jawahar Deen, Ilakya Selvarajan, Hanna-Riikka Teppo, Elitsa Y. Dimova, Thomas Kietzmann, Maarit Ahtiainen, Juha P. Vayrynen, Sara A. Vayrynen, Hanna Elomaa, Niko Tynkkynen, Tiia Eklund, Teijo Kuopio, Eva-Maria Talvitie, Pekka Taimen, Markku Kallajoki, Minna U. Kaikkonen, Merja Heinaniemi, Anna-Liisa Levonen
Summary: The NRF2 pathway is frequently activated in various cancer types, but a comprehensive analysis of its effects across different malignancies is currently lacking. We developed a NRF2 activity metric and conducted a pan-cancer analysis of oncogenic NRF2 signaling using it. Our findings revealed an immunoevasive phenotype in squamous malignancies of the lung, head and neck area, cervix, and esophagus, where high NRF2 activity is associated with low interferon-gamma (IFNγ), HLA-I expression, and T cell and macrophage infiltration. These tumors have a molecular phenotype with amplification of SOX2/TP63, TP53 mutation, and CDKN2A loss, and are associated with upregulation of immunomodulatory genes NAMPT, WNT5A, SPP1, SLC7A11, SLC2A1, and PD-L1. Our functional genomics analyses suggest that these genes are candidate NRF2 targets, indicating a direct modulation of the tumor immune milieu. Single-cell mRNA data shows that cancer cells of this subtype exhibit decreased expression of IFNγ responsive ligands and increased expression of immunosuppressive ligands NAMPT, SPP1, and WNT5A involved in intercellular crosstalk. Moreover, the negative relationship between NRF2 and immune cells is explained by stromal populations of lung squamous cell carcinoma, indicating a potential effect across multiple squamous malignancies based on our molecular subtyping and deconvolution data.
Article
Oncology
Melissa Zhao, Mai Chan Lau, Koichiro Haruki, Juha P. Vayrynen, Carino Gurjao, Sara A. Vayrynen, Andressa Dias Costa, Jennifer Borowsky, Kenji Fujiyoshi, Kota Arima, Tsuyoshi Hamada, Jochen K. Lennerz, Charles S. Fuchs, Reiko Nishihara, Andrew T. Chan, Kimmie Ng, Xuehong Zhang, Jeffrey A. Meyerhardt, Mingyang Song, Molin Wang, Marios Giannakis, Jonathan A. Nowak, Kun-Hsing Yu, Tomotaka Ugai, Shuji Ogino
Summary: By using Bayesian additive regression trees (BART), a statistical learning technique, the study aimed to improve the prediction of prognosis for colorectal cancer by comprehensively analyzing patient-specific tumor characteristics. The BART risk model identified seven stable survival predictors and the risk stratifications based on model-predicted survival were statistically significant. BART demonstrated flexibility, interpretability, and comparable or superior performance to other machine-learning models, making it a valuable tool for prognostic stratifications in colorectal cancer patients.
NPJ PRECISION ONCOLOGY
(2023)
Article
Respiratory System
Topias Karjula, Anne Niskakangas, Olli Mustonen, Iiris Puro, Juha P. Vayrynen, Olli Helminen, Fredrik Yannopoulos
Summary: A considerable proportion of intended pulmonary metastasectomies turn out as new incidental primary lung cancers. The study highlights the diagnostic importance of pulmonary metastasectomy and suggests segmentectomy as a primary procedure for patients with a long disease-free interval and a heavy smoking history.
JOURNAL OF THORACIC DISEASE
(2023)