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Computed tomography-based radiomics and body composition model for predicting hepatic decompensation. 基于计算机断层扫描的放射组学和身体成分模型用于预测肝功能失代偿。
Oncotarget Pub Date : 2024-11-22 DOI: 10.18632/oncotarget.28673
Yashbir Singh, John E Eaton, Sudhakar K Venkatesh, Bradley J Erickson
{"title":"Computed tomography-based radiomics and body composition model for predicting hepatic decompensation.","authors":"Yashbir Singh, John E Eaton, Sudhakar K Venkatesh, Bradley J Erickson","doi":"10.18632/oncotarget.28673","DOIUrl":"10.18632/oncotarget.28673","url":null,"abstract":"<p><p>Primary sclerosing cholangitis (PSC) is a chronic liver disease characterized by inflammation and scarring of the bile ducts, which can lead to cirrhosis and hepatic decompensation. The study aimed to explore the potential value of computational radiomics, a field that extracts quantitative features from medical images, in predicting whether or not PSC patients had hepatic decompensation. We used an in-house developed deep learning model called the body composition model, which quantifies body composition from computed tomography (CT) into four compartments: subcutaneous adipose tissue (SAT), skeletal muscle (SKM), visceral adipose tissue (VAT), and intermuscular adipose tissue (IMAT). We extracted radiomics features from all four body composition compartments and used them to build a predictive model in the training cohort. The predictive model demonstrated good performance in validation cohorts for predicting hepatic decompensation, with an accuracy score of 0.97, a precision score of 1.0, and an area under the curve (AUC) score of 0.97. Computational radiomics using CT images shows promise in predicting hepatic decompensation in primary sclerosing cholangitis patients. Our model achieved high accuracy, but predicting future events remains challenging. Further research is needed to validate clinical utility and limitations.</p>","PeriodicalId":19499,"journal":{"name":"Oncotarget","volume":"15 ","pages":"809-813"},"PeriodicalIF":0.0,"publicationDate":"2024-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11584029/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142687646","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","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 radiology: The promise of topological data analysis and simplicial complexes. 减少放射学中的偏差：拓扑数据分析和简单复合物的前景。
Oncotarget Pub Date : 2024-11-12 DOI: 10.18632/oncotarget.28668
Yashbir Singh, Colleen Farrelly, Quincy A Hathaway, Gunnar Carlsson
{"title":"Mitigating bias in radiology: The promise of topological data analysis and simplicial complexes.","authors":"Yashbir Singh, Colleen Farrelly, Quincy A Hathaway, Gunnar Carlsson","doi":"10.18632/oncotarget.28668","DOIUrl":"10.18632/oncotarget.28668","url":null,"abstract":"<p><p>Topological Data Analysis (TDA) and simplicial complexes offer a novel approach to address biases in AI-assisted radiology. By capturing complex structures, n-way interactions, and geometric relationships in medical images, TDA enhances feature extraction, improves representation robustness, and increases interpretability. This mathematical framework has the potential to significantly improve the accuracy and fairness of radiological assessments, paving the way for more equitable patient care.</p>","PeriodicalId":19499,"journal":{"name":"Oncotarget","volume":"15 ","pages":"782-783"},"PeriodicalIF":0.0,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11559658/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142625258","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Visualizing radiological data bias through persistence images. 通过持久图像可视化放射数据偏差。
Oncotarget Pub Date : 2024-11-12 DOI: 10.18632/oncotarget.28670
Yashbir Singh, Colleen Farrelly, Quincy A Hathaway, Gunnar Carlsson
{"title":"Visualizing radiological data bias through persistence images.","authors":"Yashbir Singh, Colleen Farrelly, Quincy A Hathaway, Gunnar Carlsson","doi":"10.18632/oncotarget.28670","DOIUrl":"10.18632/oncotarget.28670","url":null,"abstract":"<p><p>Persistence images, derived from topological data analysis, emerge as a powerful tool for visualizing and mitigating biases in radiological data interpretation and AI model development. This technique transforms complex topological features into stable, interpretable representations, offering unique insights into medical imaging data structure. By providing intuitive visualizations, persistence images enable the identification of subtle structural differences and potential biases in data acquisition, interpretation, and AI model training. Persistence images can also facilitate stratified sampling, matching statistics, and noise filtration, enhancing the accuracy and equity of radiological analysis. Despite challenges in computational complexity and workflow integration, persistence images show promise in developing more accurate, equitable, and trustworthy AI systems in radiology, potentially improving patient outcomes and personalized healthcare delivery.</p>","PeriodicalId":19499,"journal":{"name":"Oncotarget","volume":"15 ","pages":"787-789"},"PeriodicalIF":0.0,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11559657/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142625261","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Persistence landscapes: Charting a path to unbiased radiological interpretation. 持久性景观：为无偏见的放射学解释指明方向。
Oncotarget Pub Date : 2024-11-12 DOI: 10.18632/oncotarget.28671
Yashbir Singh, Colleen Farrelly, Quincy A Hathaway, Gunnar Carlsson
{"title":"Persistence landscapes: Charting a path to unbiased radiological interpretation.","authors":"Yashbir Singh, Colleen Farrelly, Quincy A Hathaway, Gunnar Carlsson","doi":"10.18632/oncotarget.28671","DOIUrl":"10.18632/oncotarget.28671","url":null,"abstract":"<p><p>Persistence landscapes, a sophisticated tool from topological data analysis, offer a promising approach to address biases in radiological interpretation and AI model development. By transforming complex topological features into statistically analyzable functions, they enable robust comparisons between populations and datasets. Persistence landscapes excel in noise filtration, fusion bias mitigation, and enhancing machine learning models. Despite challenges in computation and integration, they show potential to improve the accuracy and equity of radiological analysis, particularly in multi-modal imaging and AI-assisted interpretation.</p>","PeriodicalId":19499,"journal":{"name":"Oncotarget","volume":"15 ","pages":"790-792"},"PeriodicalIF":0.0,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11559655/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142625260","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Persistence barcodes: A novel approach to reducing bias in radiological analysis. 持久性条形码：减少放射分析偏差的新方法。
Oncotarget Pub Date : 2024-11-12 DOI: 10.18632/oncotarget.28667
Yashbir Singh, Colleen Farrelly, Quincy A Hathaway, Gunnar Carlsson
{"title":"Persistence barcodes: A novel approach to reducing bias in radiological analysis.","authors":"Yashbir Singh, Colleen Farrelly, Quincy A Hathaway, Gunnar Carlsson","doi":"10.18632/oncotarget.28667","DOIUrl":"10.18632/oncotarget.28667","url":null,"abstract":"<p><p>Persistence barcodes emerge as a promising tool in radiological analysis, offering a novel approach to reduce bias and uncover hidden patterns in medical imaging. By leveraging topological data analysis, this technique provides a robust, multi-scale perspective on image features, potentially overcoming limitations in traditional methods and Graph Neural Networks. While challenges in interpretation and implementation remain, persistence barcodes show significant potential for improving diagnostic accuracy, standardization, and ultimately, patient outcomes in the evolving field of radiology.</p>","PeriodicalId":19499,"journal":{"name":"Oncotarget","volume":"15 ","pages":"784-786"},"PeriodicalIF":0.0,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11559656/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142625259","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Beyond the hype: Navigating bias in AI-driven cancer detection. 超越炒作：在人工智能驱动的癌症检测中消除偏见。
Oncotarget Pub Date : 2024-11-07 DOI: 10.18632/oncotarget.28665
Yashbir Singh, Heenaben Patel, Diana V Vera-Garcia, Quincy A Hathaway, Deepa Sarkar, Emilio Quaia
{"title":"Beyond the hype: Navigating bias in AI-driven cancer detection.","authors":"Yashbir Singh, Heenaben Patel, Diana V Vera-Garcia, Quincy A Hathaway, Deepa Sarkar, Emilio Quaia","doi":"10.18632/oncotarget.28665","DOIUrl":"10.18632/oncotarget.28665","url":null,"abstract":"","PeriodicalId":19499,"journal":{"name":"Oncotarget","volume":"15 ","pages":"764-766"},"PeriodicalIF":0.0,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11546210/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142605449","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Retraction: MicroRNA-20a-5p promotes colorectal cancer invasion and metastasis by downregulating Smad4. 撤回：MicroRNA-20a-5p 通过下调 Smad4 促进结直肠癌的侵袭和转移
Oncotarget Pub Date : 2024-11-07 DOI: 10.18632/oncotarget.28669
Dantong Cheng, Senlin Zhao, Huamei Tang, Dongyuan Zhang, Hongcheng Sun, Fudong Yu, Weiliang Jiang, Ben Yue, Jingtao Wang, Meng Zhang, Yang Yu, Xisheng Liu, Xiaofeng Sun, Zongguang Zhou, Xuebin Qin, Xin Zhang, Dongwang Yan, Yugang Wen, Zhihai Peng
{"title":"Retraction: MicroRNA-20a-5p promotes colorectal cancer invasion and metastasis by downregulating Smad4.","authors":"Dantong Cheng, Senlin Zhao, Huamei Tang, Dongyuan Zhang, Hongcheng Sun, Fudong Yu, Weiliang Jiang, Ben Yue, Jingtao Wang, Meng Zhang, Yang Yu, Xisheng Liu, Xiaofeng Sun, Zongguang Zhou, Xuebin Qin, Xin Zhang, Dongwang Yan, Yugang Wen, Zhihai Peng","doi":"10.18632/oncotarget.28669","DOIUrl":"10.18632/oncotarget.28669","url":null,"abstract":"","PeriodicalId":19499,"journal":{"name":"Oncotarget","volume":"15 ","pages":"767"},"PeriodicalIF":0.0,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11546209/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142605455","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Understanding the interplay between extracellular matrix topology and tumor-immune interactions: Challenges and opportunities. 了解细胞外基质拓扑结构与肿瘤免疫相互作用之间的相互作用：挑战与机遇。
Oncotarget Pub Date : 2024-11-07 DOI: 10.18632/oncotarget.28666
Yijia Fan, Alvis Chiu, Feng Zhao, Jason T George
{"title":"Understanding the interplay between extracellular matrix topology and tumor-immune interactions: Challenges and opportunities.","authors":"Yijia Fan, Alvis Chiu, Feng Zhao, Jason T George","doi":"10.18632/oncotarget.28666","DOIUrl":"10.18632/oncotarget.28666","url":null,"abstract":"<p><p>Modern cancer management comprises a variety of treatment strategies. Immunotherapy, while successful at treating many cancer subtypes, is often hindered by tumor immune evasion and T cell exhaustion as a result of an immunosuppressive tumor microenvironment (TME). In solid malignancies, the extracellular matrix (ECM) embedded within the TME plays a central role in T cell recognition and cancer growth by providing structural support and regulating cell behavior. Relative to healthy tissues, tumor associated ECM signatures include increased fiber density and alignment. These and other differentiating features contributed to variation in clinically observed tumor-specific ECM configurations, collectively referred to as Tumor-Associated Collagen Signatures (TACS) 1-3. TACS is associated with disease progression and immune evasion. This review explores our current understanding of how ECM geometry influences the behaviors of both immune cells and tumor cells, which in turn impacts treatment efficacy and cancer evolutionary progression. We discuss the effects of ECM remodeling on cancer cells and T cell behavior and review recent <i>in silico</i> models of cancer-immune interactions.</p>","PeriodicalId":19499,"journal":{"name":"Oncotarget","volume":"15 ","pages":"768-781"},"PeriodicalIF":0.0,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11546212/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142605461","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Initiation of tumor dormancy by the lymphovascular embolus. 淋巴管栓塞引发肿瘤休眠
Oncotarget Pub Date : 2024-10-11 DOI: 10.18632/oncotarget.28658
Yin Ye, Justin Wang, Michael G Izban, Billy R Ballard, Sanford H Barsky
{"title":"Initiation of tumor dormancy by the lymphovascular embolus.","authors":"Yin Ye, Justin Wang, Michael G Izban, Billy R Ballard, Sanford H Barsky","doi":"10.18632/oncotarget.28658","DOIUrl":"10.18632/oncotarget.28658","url":null,"abstract":"<p><p>Cancer dormancy followed by recurrence remains an enigma in cancer biology. Since both local and systemic recurrences are thought to emanate from dormant micrometastasis which take origin from lymphovascular tumor emboli we wondered whether the process of dormancy might initiate within lymphovascular emboli. This study combines experimental studies with a patient-derived xenograft (PDX) of inflammatory breast cancer (Mary-X) that spontaneously forms spheroids <i>in vitro</i> and budding lymphovascular tumor emboli <i>in vivo</i> with observational studies utilizing tissue microarrays (TMAs) of human breast cancers. In the experimental studies, Mary-X during both lymphovascular emboli formation <i>in vivo</i> and spheroidgenesis <i>in vitro</i> exhibited decreased proliferation, a G<sub>0</sub>/G<sub>1</sub> cell cycle arrest and decreased mTOR signaling. This induction of dormancy required calpain-mediated E-cadherin proteolysis and was mediated by decreased P13K signaling, resulting in decreased mTOR activity. In observational human breast cancer studies, increased E-cadherin immunoreactivity due to increased E-cad/NTF-1 but both decreased Ki-67 and mTOR activity was observed selectively and differentially within the lymphovascular tumor emboli. Both our experimental as well as observational studies indicate that <i>in vivo</i> lymphovascular tumor emboli and their <i>in vitro</i> spheroid equivalent initiate dormancy through these pathways.</p>","PeriodicalId":19499,"journal":{"name":"Oncotarget","volume":"15 ","pages":"726-740"},"PeriodicalIF":0.0,"publicationDate":"2024-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11468568/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142400906","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Complete response to encorafenib plus binimetinib in a BRAF V600E-mutant metastasic malignant glomus tumor. BRAF V600E突变转移性恶性胶质瘤患者对安戈非尼加比尼替尼治疗的完全应答。
Oncotarget Pub Date : 2024-10-11 DOI: 10.18632/oncotarget.28654
Marta Arregui, Antonio Calles, María Del Mar Galera, Ana Gutiérrez, Carlos López-Jiménez, Carolina Agra, Adriana Fernández, Natalia Gutiérrez, María de Toro, Rosa Álvarez
{"title":"Complete response to encorafenib plus binimetinib in a <i>BRAF V600E</i>-mutant metastasic malignant glomus tumor.","authors":"Marta Arregui, Antonio Calles, María Del Mar Galera, Ana Gutiérrez, Carlos López-Jiménez, Carolina Agra, Adriana Fernández, Natalia Gutiérrez, María de Toro, Rosa Álvarez","doi":"10.18632/oncotarget.28654","DOIUrl":"10.18632/oncotarget.28654","url":null,"abstract":"<p><p>Glomus tumors (GT) are very rare mesenchymal neoplasms arising from glomus bodies, arteriovenous structures located in the dermis and involved in thermoregulation. Although most are benign, they may occasionally present malignant histological features associated with aggressive clinical behavior, metastatic spread, and poor response to conventional chemotherapy. The BRAF V600E mutation has been identified in a subset of malignant GT, highlighting a promising therapeutic target. Here, we report the impressive clinical and morpho-metabolic response of a metastatic BRAF V600E-mutated glomangiosarcoma after treatment with encorafenib and binimetinib.</p>","PeriodicalId":19499,"journal":{"name":"Oncotarget","volume":"15 ","pages":"717-724"},"PeriodicalIF":0.0,"publicationDate":"2024-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11468407/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142400895","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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