{"title":"Cytokine signaling and resistance to CDK4/6 inhibitors in HR<sup>+</sup>HER2<sup>-</sup> breast cancer.","authors":"Lukas Bolini, Joyce G Habib, Lorenzo Galluzzi","doi":"10.1038/s41698-025-01108-z","DOIUrl":"https://doi.org/10.1038/s41698-025-01108-z","url":null,"abstract":"","PeriodicalId":19433,"journal":{"name":"NPJ Precision Oncology","volume":"9 1","pages":"325"},"PeriodicalIF":6.8,"publicationDate":"2025-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145308397","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}
Petra Bullova, Peng Cui, Maria Arceo, Jiacheng Zhu, Wenyu Li, Monika Plescher, Valentin Poltorachenko, Katerina Stripling, Christian Santangeli, Lidiya Mykhaylechko, Maria Eleni Kastriti, Catharina Larsson, C Christofer Juhlin, Michael Mints, Susanne Schlisio
{"title":"Postnatal sustentacular cells as chromaffin progenitors and tumor cells of origin in VHL-related paragangliomas.","authors":"Petra Bullova, Peng Cui, Maria Arceo, Jiacheng Zhu, Wenyu Li, Monika Plescher, Valentin Poltorachenko, Katerina Stripling, Christian Santangeli, Lidiya Mykhaylechko, Maria Eleni Kastriti, Catharina Larsson, C Christofer Juhlin, Michael Mints, Susanne Schlisio","doi":"10.1038/s41698-025-01145-8","DOIUrl":"https://doi.org/10.1038/s41698-025-01145-8","url":null,"abstract":"<p><p>The cellular source of chromaffin cell regeneration after birth and its relationship to paraganglioma tumorigenesis remains incompletely defined. Here, we identify a postnatal population of SOX2/SOX10-expressing sustentacular glia-like cells in the organ of Zuckerkandl (OZ) and adrenal gland that give rise to chromaffin cells in vivo. These cells differ transcriptionally from embryonic chromaffin progenitors known as Schwann cell precursors and exhibit a unique progenitor signature. Genetic lineage tracing confirms their postnatal contribution to chromaffin cells, and SOX2<sup>+</sup>PHOX2B<sup>+</sup> transitional cells were observed in both human and mouse OZ and adrenal tissues. Single-nuclei RNA-seq and inferCNA analysis of pheochromocytoma and paraganglioma (PPGL) revealed that while most sustentacular cells exhibit a stromal profile, a subset in VHL-mutated PPGLs harbor the hallmark 3p chromosomal loss shared with chief tumor cells, suggesting a clonal origin. In an additional PPGL, widespread SOX2 expression in PHOX2B<sup>+</sup> tumor cells supports this hypothesis. Finally, DLK1-NOTCH signaling was predicted as a central regulator of chromaffin-sustentacular communication, suggesting DLK1 fine-tunes chromaffin regeneration via NOTCH inhibition and may represent a therapeutic target in PPGL.</p>","PeriodicalId":19433,"journal":{"name":"NPJ Precision Oncology","volume":"9 1","pages":"324"},"PeriodicalIF":6.8,"publicationDate":"2025-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145302408","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}
{"title":"RadGLO: an interactive platform for radiomic feature analysis and prognostic modeling in glioma.","authors":"Kavita Kundal, K Divya Rani, Vinodini D, Neeraj Kumar, Rahul Kumar","doi":"10.1038/s41698-025-01124-z","DOIUrl":"10.1038/s41698-025-01124-z","url":null,"abstract":"<p><p>Radiomic features, quantitative descriptors of tumor shape, texture, and intensity derived from MRI serve as powerful non-invasive biomarkers for glioma characterization and prognosis. We present Radiology of Glioma (RadGLO), an interactive platform that leverages these features across multi-institutional datasets (TCGA, UCSF, UPENN) to support grade-wise analysis, gene correlation, and survival prediction. RadGLO integrates two in-house developed modules, RaSPr for risk stratification and TumorVQ for region-specific tumor volume quantification, which also supports user-uploaded MRI data. By enabling personalized prognosis and aiding treatment planning, RadGLO offers a valuable resource that is openly accessible at https://project.iith.ac.in/cgntlab/radglo/ .</p>","PeriodicalId":19433,"journal":{"name":"NPJ Precision Oncology","volume":"9 1","pages":"323"},"PeriodicalIF":6.8,"publicationDate":"2025-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12521371/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145293105","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}
Camila B Xavier, Mohamed A Gouda, Apostolia M Tsimberidou
{"title":"Prolonged response to dual immune checkpoint blockade in patients with advanced solid tumors: a case series.","authors":"Camila B Xavier, Mohamed A Gouda, Apostolia M Tsimberidou","doi":"10.1038/s41698-025-01115-0","DOIUrl":"10.1038/s41698-025-01115-0","url":null,"abstract":"<p><p>Immunotherapy has substantially changed the landscape of cancer. We present five patients with advanced cancer who had failed standard-of-care therapies, participated in clinical trials with anti-CTLA4/anti-PD1 therapy, and had prolonged progression-free survival (PFS): Pt1: microsatellite stable (MSS) rectal adenocarcinoma (34+ months); Pt2: high grade neuroendocrine carcinoma (68 months); Pt3: MSS colon adenocarcinoma (38+ months); Pt4: deficient mismatch repair (dMMR) prostate adenocarcinoma (68+ months); Pt5: high-grade neuroendocrine carcinoma (69+ months). Grade 3 immune-related adverse events (irAEs; n = 4) were treated successfully, allowing further treatment with the anti-PD1 therapy. Positron-emission tomography (PET)/computed tomography (CT) scans demonstrated complete response in 3 of 4 patients whose CT scans had shown partial response. These cases highlight the exceptional outcomes of selected patients with advanced cancer treated with immunotherapy and exemplify the value of personalized patient monitoring/management of irAEs while assessing response to immunotherapy. Ongoing trials evaluate biomarkers that predict response and toxicity associated with immunotherapy.</p>","PeriodicalId":19433,"journal":{"name":"NPJ Precision Oncology","volume":"9 1","pages":"322"},"PeriodicalIF":6.8,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12511611/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145258681","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}
Yong Shen, Yong Xia, Yinyin Chang, Pingping Xing, Shiyong Li, Wei Wu, Ruidan Zhu, Guolin Zhong, Dandan Zhu, Raphael Brandão, Qingxia Xu, Ling Ji, Mao Mao
{"title":"A large-scale, multi-centre validation study of an AI-empowered blood-based test for multi-cancer early detection.","authors":"Yong Shen, Yong Xia, Yinyin Chang, Pingping Xing, Shiyong Li, Wei Wu, Ruidan Zhu, Guolin Zhong, Dandan Zhu, Raphael Brandão, Qingxia Xu, Ling Ji, Mao Mao","doi":"10.1038/s41698-025-01105-2","DOIUrl":"10.1038/s41698-025-01105-2","url":null,"abstract":"<p><p>Cancer is a critical global health issue, especially in low- and middle-income countries (LMICs). In this study, we integrated four additional cohorts to assess the performance and robustness of an AI-empowered blood-based test (named OncoSeek) for multi-cancer early detection (MCED). It included a case-control cohort of symptomatic cancer patients, a prospective blinded study, and two retrospective cohorts conducted on two distinct platforms. Combining these with previously published one training and two validation cohorts, we evaluated OncoSeek's performance in 15,122 participants (3029 cancer patients and 12,093 non-cancer individuals) from seven centres in three countries, using four platforms and two sample types. OncoSeek showed adequate performance for MCED with an area under the curve (AUC) of 0.829, 58.4% sensitivity, 92.0% specificity, and overall accuracy of 70.6% in tissue of origin (TOO) prediction for the true positives. The test could detect 14 common cancer types, accounting for 72% of global cancer deaths, with sensitivities ranging from 38.9 to 83.3%. Additionally, the symptomatic cohort exhibited a high sensitivity of 73.1% at 90.6% specificity, indicating OncoSeek's potential for cancer early diagnosis. These findings underscore OncoSeek's consistent performances across diverse populations, platforms, and sample types, offering affordable and accessible multi-cancer early detection, especially for LMICs.</p>","PeriodicalId":19433,"journal":{"name":"NPJ Precision Oncology","volume":"9 1","pages":"321"},"PeriodicalIF":6.8,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12508103/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145252050","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}
Kimani Njoya, Huda Zayed, Li Sun, Donia Alson, Oluwatosin Aina, Sajjad Khan, Ximei Veneklasen, Nikki Lytle, Pradeep Chaluvally-Raghavan, Daochun Sun
{"title":"Natural history of SPP1 signaling in NF1 tumors.","authors":"Kimani Njoya, Huda Zayed, Li Sun, Donia Alson, Oluwatosin Aina, Sajjad Khan, Ximei Veneklasen, Nikki Lytle, Pradeep Chaluvally-Raghavan, Daochun Sun","doi":"10.1038/s41698-025-01078-2","DOIUrl":"10.1038/s41698-025-01078-2","url":null,"abstract":"<p><p>Understanding the heterogeneity of Neurofibromatosis type 1 (NF1)-associated tumors and delineating the natural historical evolution of cell signaling are essential for interpreting tumor initiation, preventing tumor progression from benign plexiform neurofibromas (pNFs) to malignant peripheral nerve sheath tumors (MPNSTs), and engineering effective treatments. The neural crest-derived Schwann cell precursor (SCP)-like tumor population interacts with different cells in the tumor microenvironment (TME), particularly macrophages, continually shaping the intrinsic and extrinsic NF1 tumor heterogeneity. Through integrated analyses of single-cell RNA-seq (scRNA-seq) and spatial transcriptomics, we reveal that SPP1-CD44 signaling is initiated by SCP-like tumor cells in pNF, operating through autocrine mechanisms. However, in MPNST, a distinct subset of macrophages becomes the dominant SPP1 signaling source while the SCP-like cells maintain autocrine signaling. The role of SPP1 in tumorigenesis is validated by the significantly extended survival in the MPNST mouse model with cisNf1<sup>+/-</sup>;Trp53<sup>+/-</sup>;Spp1<sup>-/-</sup> configuration. Notably, our analysis of the pre-tumor stage in the DhhCre;Nf1<sup>-/-</sup> pNF mouse model demonstrates upregulated Spp1 expression compared to control tissue in Nes<sup>+</sup> Schwann lineage cells. Together, these findings elucidate the natural historical dynamics of SPP1-CD44 signaling during tumor initiation and progression from pNF to MPNST, and highlight the SPP1-CD44 signaling axis as a potential therapeutic target to disrupt tumor stemness properties and reprogram the immune TME in malignancies.</p>","PeriodicalId":19433,"journal":{"name":"NPJ Precision Oncology","volume":"9 1","pages":"320"},"PeriodicalIF":6.8,"publicationDate":"2025-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12501028/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145239208","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}
{"title":"Pan cancer research reveals the role of PTGDS in tumor suppression and immune regulation.","authors":"Jiajin Li, Zheng Qu, Dacheng Zhu, Ye Lu, Jiaxin Lu, Zhen Wu, Luxiao Zhang, Pengpeng Zhang, Yiqin Xia, Shengbin Pei","doi":"10.1038/s41698-025-01097-z","DOIUrl":"10.1038/s41698-025-01097-z","url":null,"abstract":"<p><p>Prostaglandin D2 synthase (PTGDS), a newly identified anti-tumor target, shows promise in inhibiting various cancers and plays significant roles in the tumor microenvironment and immune regulation, yet a comprehensive pan-cancer analysis of its expression and prognostic value remains lacking. This study used multi-omics data from public databases to assess PTGDS's expression, mutation, and modification in multiple cancers, integrated single-cell and spatial transcriptomic data to explore its relationship with immune cells, and conducted in vitro and in vivo experiments in breast cancer (BRCA). Results showed that PTGDS is significantly dysregulated in most cancers, with its expression associated with different outcomes depending on cancer type. It correlates with epigenetic and biological functions, and low expression in BRCA indicates poor prognosis. Overexpression of PTGDS can inhibit breast cancer cell proliferation and invasion, increase CD8+ T - cell activity, and enhance anti-tumor immunity. Combining it with anti-PD-L1 improves BRCA treatment. PTGDS is a potential prognostic biomarker and a novel immunotherapy target for BRCA.</p>","PeriodicalId":19433,"journal":{"name":"NPJ Precision Oncology","volume":"9 1","pages":"319"},"PeriodicalIF":6.8,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12484698/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145200443","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}
Ivan Juric, Emily E Fink, Hong Qiu, Pierre-Emmanuel Desprez, Arvind Ravi, Mark Holton, Vladimir Makarov, Nima Almassi, Booki Min, Gad Getz, Timothy A Chan, Tyler Alban, Angela H Ting, Byron H Lee
{"title":"Single-cell RNA-sequencing of BCG naïve and recurrent non-muscle invasive bladder cancer reveals a CD6/ALCAM-mediated immune-suppressive pathway.","authors":"Ivan Juric, Emily E Fink, Hong Qiu, Pierre-Emmanuel Desprez, Arvind Ravi, Mark Holton, Vladimir Makarov, Nima Almassi, Booki Min, Gad Getz, Timothy A Chan, Tyler Alban, Angela H Ting, Byron H Lee","doi":"10.1038/s41698-025-01093-3","DOIUrl":"10.1038/s41698-025-01093-3","url":null,"abstract":"<p><p>Bacillus Calmette-Guérin (BCG) is the mainstay of treatment for intermediate- and high-risk non-muscle invasive bladder cancer (NMIBC), yet recurrence rates remain high. To improve the efficacy of BCG, a better understanding of the immune landscape underlying BCG resistance is critical. Here, we performed single-cell RNA-sequencing (scRNA-seq) and whole-exome sequencing on tumors from NMIBC patients before and after BCG treatment. Our analysis revealed a marked increase in CD6/ALCAM interactions between T cells and urothelial cells in BCG recurrent tumors. CD6-high T cells were enriched in recurrent tumors and exhibited downregulation of activation-related genes, indicative of functional impairment. These observations were supported by analysis of an independent BCG-treated NMIBC cohort, in which CD6/ALCAM signaling was correlated with shorter recurrence-free survival (p = 0.00059). Our findings reveal a previously unrecognized association between CD6/ALCAM signaling and BCG resistance in NMIBC patients and highlight this pathway as a potential therapeutic target to enhance response to BCG.</p>","PeriodicalId":19433,"journal":{"name":"NPJ Precision Oncology","volume":"9 1","pages":"318"},"PeriodicalIF":6.8,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12475466/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145177098","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}
Wenxuan Hu, Jian Yang, Zhike Chen, Yongsen Li, Gaomeng Luo, Kang Hu, Zihao Lu, Xin Lv, Yonghao Cao, Haoyang Yuan, Cong Cao, Jun Zhao, Chun Xu
{"title":"SLC25A39 overexpression exacerbates lung adenocarcinoma progression and is negatively regulated by AFG3L2.","authors":"Wenxuan Hu, Jian Yang, Zhike Chen, Yongsen Li, Gaomeng Luo, Kang Hu, Zihao Lu, Xin Lv, Yonghao Cao, Haoyang Yuan, Cong Cao, Jun Zhao, Chun Xu","doi":"10.1038/s41698-025-01081-7","DOIUrl":"10.1038/s41698-025-01081-7","url":null,"abstract":"<p><p>Lung adenocarcinoma (LUAD), the most common lung cancer subtype, has a poor prognosis and limited treatments, underscoring the need for new biomarkers and targets, particularly in mitochondrial metabolism. Our study identifies SLC25A39, a mitochondrial glutathione transporter, as a key oncogenic factor in LUAD. Bioinformatics and tissue analyses revealed significantly elevated SLC25A39 protein levels despite stable mRNA expression, correlating with poorer patient survival. Functionally, SLC25A39 overexpression promoted LUAD cell proliferation and migration, while its knockdown or deletion suppressed these malignant traits in vitro and in vivo. Mechanistically, SLC25A39 loss impaired mitochondrial oxidative phosphorylation, increased reactive oxygen species (ROS), and triggered apoptosis. Notably, we found that reduced expression of the m-AAA protease AFG3L2 in LUAD post-translationally stabilizes SLC25A39, leading to its accumulation. These findings demonstrate that AFG3L2 downregulation drives SLC25A39's oncogenic activity, positioning SLC25A39 as a promising therapeutic target for LUAD.</p>","PeriodicalId":19433,"journal":{"name":"NPJ Precision Oncology","volume":"9 1","pages":"317"},"PeriodicalIF":6.8,"publicationDate":"2025-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12460834/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145138355","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}
{"title":"Multi-modal characterization of metabolic and immune gene clusters in adrenocortical carcinoma treatment.","authors":"Wenjun Hao, Luhan Yao, Yanlong Wang, Jiayu Wan, Yuyan Zhu, Zhihong Dai, Xu Sun, Bo Fan, Yuchao Wang, Hao Xiang, Xiang Gao, Peng Liang, Haolin Zhao, Liang Wang, Ying Wang, Hongyu Wang, Deyong Yang, Zhiyu Liu","doi":"10.1038/s41698-025-01092-4","DOIUrl":"10.1038/s41698-025-01092-4","url":null,"abstract":"<p><p>Adrenocortical carcinoma (ACC) is an uncommon and aggressive endocrine malignancy, characterized by limited therapeutic options and considerable variability in patient outcomes. The challenge is to combine the complex information of ACC with artificial intelligence (AI) and clinical and pathology data to achieve precision medicine and improve patient prognosis. We developed the Steroid-related Immune Score (SIS) using multi-modal analysis of genomics, digital pathology, and artificial intelligence and validated it in external datasets. In addition, we conducted single-cell RNA sequencing (scRNA-seq) of small samples and in vitro functional experiments. SIS delivered a stable performance with an AUC of 0.8 ± 0.01 in the ResNet50 and Vision Transformer-B16 models. We validated the best model in external ACC cohorts. Using Class Activation Maps (CAMs) technology revealed that SIS was associated with lymphocyte infiltration, establishing it as a new feature in addition to the Weiss scoring system. Patients in the high SIS group responded well to immunotherapy, while the low SIS group showed adaptability to hormone inhibition therapy. Single-cell RNA sequencing data revealed the relationship between the tumor microenvironment and drug resistance in ACC. In vitro functional assays demonstrated that elevated DHCR7 gene expression correlated with unfavorable prognosis and treatment sensitivity, identifying it as a prospective therapeutic target. Furthermore, there are similarities between the metabolic characteristics of ACC and schizophrenia, such as calcium and iron ion levels. Our multi-modal analysis comprehensively characterizes the immune microenvironment of ACC, emphasizing the synergistic regulation of metabolic and immune gene clusters that influence ACC patients' responses to immune and hormone therapies.</p>","PeriodicalId":19433,"journal":{"name":"NPJ Precision Oncology","volume":"9 1","pages":"314"},"PeriodicalIF":6.8,"publicationDate":"2025-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12446433/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145086125","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}