NPJ Precision Oncology最新文献

Deciphering the cellular and molecular landscape of cervical cancer progression through single-cell and spatial transcriptomics. 通过单细胞和空间转录组学解读宫颈癌进展的细胞和分子景观。

IF 6.8 1区医学

NPJ Precision Oncology Pub Date : 2025-05-28 DOI: 10.1038/s41698-025-00948-z

Peng Xia, Juanhong Zhou, Rong Shen, Degui Wang

{"title":"Deciphering the cellular and molecular landscape of cervical cancer progression through single-cell and spatial transcriptomics.","authors":"Peng Xia, Juanhong Zhou, Rong Shen, Degui Wang","doi":"10.1038/s41698-025-00948-z","DOIUrl":"https://doi.org/10.1038/s41698-025-00948-z","url":null,"abstract":"Cervical cancer represents a significant global health challenge, with complex cellular and molecular mechanisms driving its progression from HPV infection to invasive malignancy. This study employed an integrated approach combining single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (stRNA-seq) to comprehensively characterize the tumor microenvironment (TME) across different stages of cervical cancer development. Through analysis of samples from normal cervix, HPV-infected normal cervix, high-grade squamous intraepithelial lesions (HSIL), and invasive cervical cancer, we identified distinct cellular populations and their dynamic changes during disease progression. Our findings revealed significant heterogeneity in immune cell populations, particularly highlighting the role of SPP1+ macrophages that were substantially enriched in cervical cancer compared to precancerous and normal tissues. Cell-cell communication networks and spatial mapping demonstrated that SPP1+ macrophages interact extensively with immune cells through the SPP1-CD44 signaling axis. This interaction contributes to an immunosuppressive microenvironment through modulation of T cell function and promotion of tumor cell survival. Furthermore, high expression of SPP1 correlated with advanced tumor stages and poor overall survival in cervical cancer patients, highlighting its potential as a prognostic biomarker. Our comprehensive characterization of the cellular landscape and intercellular communication networks in cervical cancer progression provides valuable insights for the development of targeted therapeutic strategies aimed at modulating the TME, particularly through disruption of the SPP1-CD44 axis. These findings establish a foundation for more effective personalized approaches to improve clinical outcomes in cervical cancer patients.","PeriodicalId":19433,"journal":{"name":"NPJ Precision Oncology","volume":"9 1","pages":"158"},"PeriodicalIF":6.8,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144174268","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Author Correction: Trans-ancestry transcriptome-wide association and functional studies to uncover novel susceptibility genes and therapeutic targets for colorectal cancer. 作者更正：跨祖先转录组全关联和功能研究揭示结直肠癌的新易感基因和治疗靶点。

IF 6.8 1区医学

NPJ Precision Oncology Pub Date : 2025-05-27 DOI: 10.1038/s41698-025-00951-4

Lijuan Wang, Lidan Hu, Jing Sun, Jianhui Zhao, Siyun Zhou, Lexin Liu, Wei Yu, Yeting Hu, Dan Zhou, Xiangrui Meng, Zhongshang Yuan, Honghe Zhang, Susan Farrington, Maria Timofeeva, Kefeng Ding, Julian Little, Malcolm Dunlop, Evropi Theodoratou, Xue Li

引用次数: 0

Circulating tumor DNA in ALK-positive anaplastic large cell lymphoma: a proof-of-concept study. alk阳性间变性大细胞淋巴瘤循环肿瘤DNA：一项概念验证研究。

IF 6.8 1区医学

NPJ Precision Oncology Pub Date : 2025-05-27 DOI: 10.1038/s41698-025-00944-3

Damien Vasseur, Samuel Abbou, Ludovic Lacroix, Laurence Lamant, Noémie Pata-Merci, David Sibon, Francesco Facchinetti, Marc Deloger, Floriane Braye, Véronique Minard-Colin, Laurence Brugières, Etienne Rouleau, Luc Friboulet, Charlotte Rigaud

引用次数: 0

Optimized culturing yields high success rates and preserves molecular heterogeneity, enabling personalized screening for high-grade gliomas. 优化培养产生高成功率和保持分子异质性，使个性化筛选高级别胶质瘤。

IF 6.8 1区医学

NPJ Precision Oncology Pub Date : 2025-05-27 DOI: 10.1038/s41698-025-00946-1

Cassandra Posthoorn-Verheul, Federica Fabro, Ioannis Ntafoulis, Chelsea den Hollander, Iris S C Verploegh, Rutger Balvers, Trisha V Kers, Jessica Hoogeveen, Judith van der Burg, Bert Eussen, Annelies de Klein, Kate J Feller, Miao-Ping Chien, Clemens M F Dirven, Sieger Leenstra, Martine L M Lamfers

{"title":"Optimized culturing yields high success rates and preserves molecular heterogeneity, enabling personalized screening for high-grade gliomas.","authors":"Cassandra Posthoorn-Verheul, Federica Fabro, Ioannis Ntafoulis, Chelsea den Hollander, Iris S C Verploegh, Rutger Balvers, Trisha V Kers, Jessica Hoogeveen, Judith van der Burg, Bert Eussen, Annelies de Klein, Kate J Feller, Miao-Ping Chien, Clemens M F Dirven, Sieger Leenstra, Martine L M Lamfers","doi":"10.1038/s41698-025-00946-1","DOIUrl":"10.1038/s41698-025-00946-1","url":null,"abstract":"To discover new treatment options for high-grade glioma (HGG), robust in vitro models are essential, but reliably establishing patient-derived cell cultures remains challenging. We established glioma stem-like cell (GSC) cultures from 114 consecutive HGG specimens via traditional surgical resection and/or ultrasonic aspiration, using completely dissociated single cell (single cell-derived, SCD) and partially dissociated 3D-derived (3DD) tissue fragments. Higher success rates in culture establishment were obtained from ultrasonic aspirates and 3DD surgical samples. Combining these approaches yielded a 96% success rate. Copy number profiling showed overall genetic similarities between cultures and parental tissue. Single-cell sequencing revealed greater transcriptomic heterogeneity in ultrasonic aspiration-derived cultures. Our protocol enabled the screening of 20 anti-cancer agents within a clinically relevant timeframe for 16 out of 18 HGG samples. This refined protocol serves as a robust tool for establishing HGG cell cultures that retain the molecular characteristics of the tumors and support applications in precision medicine.","PeriodicalId":19433,"journal":{"name":"NPJ Precision Oncology","volume":"9 1","pages":"156"},"PeriodicalIF":6.8,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144160561","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Sotorasib resistance in KRAS G12C-mutant invasive mucinous adenocarcinoma with implications for VEGF-A. KRAS g12c突变型侵袭性粘液腺癌中Sotorasib耐药及其对VEGF-A的影响

IF 6.8 1区医学

NPJ Precision Oncology Pub Date : 2025-05-27 DOI: 10.1038/s41698-025-00953-2

Hiraku Yanada, Ryohei Yoshida, Ryotaro Kida, Kiichi Nitanai, Maya Ikeda, Kazunori Nagasue, Taeka Naraoka, Masashi Ueda, Takashi Watanabe, Ryota Shigaki, Yasuhiro Umekage, Yoshinori Minami, Toshihiro Nagato, Manami Hayashi, Sayaka Yuzawa, Mishie Tanino, Takaaki Sasaki

{"title":"Sotorasib resistance in KRAS G12C-mutant invasive mucinous adenocarcinoma with implications for VEGF-A.","authors":"Hiraku Yanada, Ryohei Yoshida, Ryotaro Kida, Kiichi Nitanai, Maya Ikeda, Kazunori Nagasue, Taeka Naraoka, Masashi Ueda, Takashi Watanabe, Ryota Shigaki, Yasuhiro Umekage, Yoshinori Minami, Toshihiro Nagato, Manami Hayashi, Sayaka Yuzawa, Mishie Tanino, Takaaki Sasaki","doi":"10.1038/s41698-025-00953-2","DOIUrl":"10.1038/s41698-025-00953-2","url":null,"abstract":"Invasive mucinous adenocarcinoma (IMA) is a rare subtype of lung adenocarcinoma with a poor prognosis. Compared to non-small cell lung cancer, IMA more frequently harbors KRAS mutations in the order p.G12V, p.G12D, and p.G12C. This report describes a patient with a KRAS p.G12C-mutant IMA treated with sotorasib. To date, no studies have investigated the therapeutic efficacy or resistance mechanisms of sotorasib in IMA. The patient was treated with carboplatin and pemetrexed, followed by sotorasib upon disease progression. While the primary lung lesions responded well, metastatic thoracic lymph node lesions continued to increase. A pathological autopsy was performed with the family's consent to investigate potential resistance mechanisms. RNA sequencing and additional analyses revealed increased VEGF-A expression in metastatic lymph node lesions, suggesting a role in sotorasib resistance. These findings provide insights into the potential molecular mechanisms underlying treatment resistance in KRAS p.G12C-mutant IMA.","PeriodicalId":19433,"journal":{"name":"NPJ Precision Oncology","volume":"9 1","pages":"154"},"PeriodicalIF":6.8,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12106728/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144151281","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Mitigating bias in prostate cancer diagnosis using synthetic data for improved AI driven Gleason grading. 使用人工智能驱动的Gleason分级的合成数据减轻前列腺癌诊断的偏倚。

IF 6.8 1区医学

NPJ Precision Oncology Pub Date : 2025-05-23 DOI: 10.1038/s41698-025-00934-5

Derek J Van Booven, Cheng-Bang Chen, Oleksandr N Kryvenko, Sanoj Punnen, Victor Sandoval, Sheetal Malpani, Ahmed Noman, Farhan Ismael, Yujie Wang, Rehana Qureshi, Joshua M Hare, Himanshu Arora

{"title":"Mitigating bias in prostate cancer diagnosis using synthetic data for improved AI driven Gleason grading.","authors":"Derek J Van Booven, Cheng-Bang Chen, Oleksandr N Kryvenko, Sanoj Punnen, Victor Sandoval, Sheetal Malpani, Ahmed Noman, Farhan Ismael, Yujie Wang, Rehana Qureshi, Joshua M Hare, Himanshu Arora","doi":"10.1038/s41698-025-00934-5","DOIUrl":"10.1038/s41698-025-00934-5","url":null,"abstract":"Prostate cancer (PCa) is a leading cause of cancer-related mortality in men, with Gleason grading critical for prognosis and treatment decisions. Machine learning (ML) models offer potential for automated grading but are limited by dataset biases, staining variability, and data scarcity, reducing their generalizability. This study employs generative adversarial networks (GANs) to generate high-quality synthetic histopathological images to address these challenges. A conditional GAN (dcGAN) was developed and validated using expert pathologist review and Spatial Heterogeneous Recurrence Quantification Analysis (SHRQA), achieving 80% diagnostic quality approval. A convolutional neural network (EfficientNet) was trained on original and synthetic images and validated across TCGA, PANDA Challenge, and MAST trial datasets. Integrating synthetic images improved classification accuracy for Gleason 3 (26%, p = 0.0010), Gleason 4 (15%, p = 0.0274), and Gleason 5 (32%, p < 0.0001), with sensitivity and specificity reaching 81% and 92%, respectively. This study demonstrates that synthetic data significantly enhances ML-based Gleason grading accuracy and improves reproducibility, providing a scalable AI-driven solution for precision oncology.","PeriodicalId":19433,"journal":{"name":"NPJ Precision Oncology","volume":"9 1","pages":"151"},"PeriodicalIF":6.8,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12098719/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144128250","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Perfusion-based ex vivo culture of frozen ovarian cancer tissues with preserved tumor microenvironment. 保存肿瘤微环境的冷冻卵巢癌组织体外灌注培养。

IF 6.8 1区医学

NPJ Precision Oncology Pub Date : 2025-05-23 DOI: 10.1038/s41698-025-00941-6

Monica De Luise, Ivana Kurelac, Sara Coluccelli, Antonio De Leo, Ewelina M Bartoszek, Maria Iorio, Marco Grillini, Camelia Alexandra Coadă, Dario de Biase, Lorena Marchio, Mónica Núñez López, Natalie Rimmer, Anna Myriam Perrone, Pierandrea De Iaco, Anna Maria Porcelli, Viola Heinzelmann, Ivan Martin, Francis Jacob, Manuele Giuseppe Muraro, Giuseppe Gasparre

{"title":"Perfusion-based ex vivo culture of frozen ovarian cancer tissues with preserved tumor microenvironment.","authors":"Monica De Luise, Ivana Kurelac, Sara Coluccelli, Antonio De Leo, Ewelina M Bartoszek, Maria Iorio, Marco Grillini, Camelia Alexandra Coadă, Dario de Biase, Lorena Marchio, Mónica Núñez López, Natalie Rimmer, Anna Myriam Perrone, Pierandrea De Iaco, Anna Maria Porcelli, Viola Heinzelmann, Ivan Martin, Francis Jacob, Manuele Giuseppe Muraro, Giuseppe Gasparre","doi":"10.1038/s41698-025-00941-6","DOIUrl":"10.1038/s41698-025-00941-6","url":null,"abstract":"Ovarian cancer (OC) poses significant treatment challenges due to late-stage diagnosis and a complex tumor microenvironment contributing to therapy resistance. We optimized a U-CUP perfusion-based bioreactor method to culture patient-derived primary and metastatic OC specimens, demonstrating that perfusion better preserves cancer cell viability and proliferation, both when fresh and slow-frozen tissues were used. Perfused cultures maintained key microenvironment components, including cancer-associated fibroblasts, endothelial and immune cells. Genetic analysis confirmed the retention in culture of tumor-specific driver mutations. We hence challenged ad hoc generated cisplatin-sensitive and resistant OC cells with cisplatin during growth in U-CUP, validating our system for the testing of drug response. Finally, treatment of slow-frozen OC tissues with carboplatin/paclitaxel revealed different degrees of response to treatment, as indicated by variations in tumor necrosis and number of residual PAX8+ cells, providing the bases for the prompt evaluation of OC standard chemotherapy efficacy in our ex vivo system.","PeriodicalId":19433,"journal":{"name":"NPJ Precision Oncology","volume":"9 1","pages":"152"},"PeriodicalIF":6.8,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12102267/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144132477","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Evaluating the performance of large language & visual-language models in cervical cytology screening. 评估大语言和视觉语言模型在宫颈细胞学筛查中的表现。

IF 6.8 1区医学

NPJ Precision Oncology Pub Date : 2025-05-23 DOI: 10.1038/s41698-025-00916-7

Qi Hong, Shijie Liu, Liying Wu, Qiqi Lu, Pinglan Yang, Dingyu Chen, Gong Rao, Xinyi Liu, Hua Ye, Peiqi Zhuang, Wenxiu Yang, Shaoqun Zeng, Qianjin Feng, Xiuli Liu, Jing Cai, Shenghua Cheng

{"title":"Evaluating the performance of large language & visual-language models in cervical cytology screening.","authors":"Qi Hong, Shijie Liu, Liying Wu, Qiqi Lu, Pinglan Yang, Dingyu Chen, Gong Rao, Xinyi Liu, Hua Ye, Peiqi Zhuang, Wenxiu Yang, Shaoqun Zeng, Qianjin Feng, Xiuli Liu, Jing Cai, Shenghua Cheng","doi":"10.1038/s41698-025-00916-7","DOIUrl":"10.1038/s41698-025-00916-7","url":null,"abstract":"Large language models (LLMs) and large visual-language models (LVLMs) have exhibited near-human levels of knowledge, image comprehension, and reasoning abilities, and their performance has undergone evaluation in some healthcare domains. However, a systematic evaluation of their capabilities in cervical cytology screening has yet to be conducted. Here, we constructed CCBench, a benchmark dataset dedicated to the evaluation of LLMs and LVLMs in cervical cytology screening, and developed a GPT-based semi-automatic evaluation pipeline to assess the performance of six LLMs (GPT-4, Bard, Claude-2.0, LLaMa-2, Qwen-Max, and ERNIE-Bot-4.0) and five LVLMs (GPT-4V, Gemini, LLaVA, Qwen-VL, and ViLT) on this dataset. CCBench comprises 773 question-answer (QA) pairs and 420 visual-question-answer (VQA) triplets, making it the first dataset in cervical cytology to include both QA and VQA data. We found that LLMs and LVLMs demonstrate promising accuracy and specialization in cervical cytology screening. GPT-4 achieved the best performance on the QA dataset, with an accuracy of 70.5% for close-ended questions and average expert evaluation score of 6.9/10 for open-ended questions. On the VQA dataset, Gemini achieved the highest accuracy for close-ended questions at 67.8%, while GPT-4V attained the highest expert evaluation score of 6.1/10 for open-ended questions. Besides, LLMs and LVLMs revealed varying abilities in answering questions across different topics and difficulty levels. However, their performance remains inferior to the expertise exhibited by cytopathology professionals, and the risk of generating misinformation could lead to potential harm. Therefore, substantial improvements are required before these models can be reliably deployed in clinical practice.","PeriodicalId":19433,"journal":{"name":"NPJ Precision Oncology","volume":"9 1","pages":"153"},"PeriodicalIF":6.8,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12102327/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144132146","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

HDAC6 facilitates LUAD progression by inducing EMT and enhancing macrophage polarization towards the M2 phenotype. HDAC6通过诱导EMT和增强巨噬细胞向M2表型的极化来促进LUAD的进展。

IF 6.8 1区医学

NPJ Precision Oncology Pub Date : 2025-05-22 DOI: 10.1038/s41698-025-00949-y

Yantao Jiang, Ju Zhang, Junjie Yu, Wei Luo, Qingwu Du, Wenting Liu, Qi Xu, Xueyang Li, Huiyan Liu, Dingzhi Huang, Tingting Qin

引用次数: 0

Tumor diagnosis recharacterization enabled by comprehensive genomic profiling to guide precision medicine strategy. 肿瘤诊断再表征，使全面基因组分析指导精准医疗策略。

IF 6.8 1区医学

NPJ Precision Oncology Pub Date : 2025-05-21 DOI: 10.1038/s41698-025-00942-5

Ann Carr, Jennifer B Jackson, Chris Coldren, Pranil Chandra, Faezeh Koohestani, Michelle Shiller, Robert Auber

{"title":"Tumor diagnosis recharacterization enabled by comprehensive genomic profiling to guide precision medicine strategy.","authors":"Ann Carr, Jennifer B Jackson, Chris Coldren, Pranil Chandra, Faezeh Koohestani, Michelle Shiller, Robert Auber","doi":"10.1038/s41698-025-00942-5","DOIUrl":"10.1038/s41698-025-00942-5","url":null,"abstract":"Comprehensive genomic profiling (CGP) via next-generation sequencing is standard clinical practice for advanced and metastatic cancers in the U.S. and can help identify clinically actionable alterations in patients who may benefit from targeted therapies. CGP can also complement clinicopathological findings and in certain cases, may lead to diagnostic recharacterization resulting in more precise therapeutic strategies. Here, we highlight examples where molecular findings resulted in tumor re-evaluation and subsequent recharacterization. Twenty-eight cases where CGP results were inconsistent with initial pathological diagnosis and clinical presentation were selected for secondary clinicopathological review to explore alternative diagnostic explanations more consistent with the genomic results. Genomic profiling identified clinically actionable and prognostic variants leading to more accurate therapeutic recommendations based on the updated diagnoses highlighting the value of CGP beyond biomarker detection for therapy selection and supporting its complementary use in diagnostic confirmation to unveil opportunities for precision medicine strategies.","PeriodicalId":19433,"journal":{"name":"NPJ Precision Oncology","volume":"9 1","pages":"149"},"PeriodicalIF":6.8,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12095656/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144120441","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0