Tumor discovery最新文献

{"title":"Structural variants integration and visualization: A comprehensive R package for integration of somatic structural variations from multiple callers and visualization","authors":"Lei Yu, Le Zhang, Lili Wang, Zhenyu Jia","doi":"10.36922/td.0894","DOIUrl":"https://doi.org/10.36922/td.0894","url":null,"abstract":"Whole genome sequencing (WGS) emerges as a powerful tool for detecting structural variations (SVs) in genomes. However, different SV callers can produce variable results due to the distinct rationale and sensitivity of pipelines, highlighting the need for effective tools to compare and merge results from multiple callers. Here, we developed an R package, structural variants integration and visualization, to facilitate the integration, classification, and visualization of SV results from multiple callers, allowing for accurate identification of the most reliable SVs. Our package relies on a complex translocation projection and clustering method, enabling the projection of each translation to a point in a Cartesian coordinate system and visualization of SVs at both whole-genome and individual chromosome levels. Thus, our approach provides a valuable framework for analyzing SVs from WGS data, improving the accuracy and efficiency of SV detection, and enhancing the potential of WGS for clinical and research applications.","PeriodicalId":94260,"journal":{"name":"Tumor discovery","volume":"10 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74518455","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Stereotactic radiotherapy with simultaneous integrated protection planning technique for synovial sarcoma with stomach abutment: A case report of a complete response","authors":"M. Bonù, Eneida Mataj, Jacopo Balduzzi, M. Cefaratti, G. Pedersoli, Gianluca Cossali, L. Triggiani, D. Tomasini, M. Buglione, S. Magrini","doi":"10.36922/td.356","DOIUrl":"https://doi.org/10.36922/td.356","url":null,"abstract":"Here, we report the clinical case of a 44-year-old lady, affected by synovial sarcoma (SS) of the mediastinum which was treated in 2014, and relapsed in the upper abdomen in 2020. SS is a relatively radioresistant disease, radiotherapy (RT) is routinely reserved for the neoadjuvant/adjuvant or palliative context. In our scenario, stereotactic RT consisting in 45Gy in 6 fractions was proposed to manage the upper abdominal relapse. Exploiting simultaneous integrated protection, a deliberated reduction in the dose prescription in area of planning target volume overlapped with stomach was achieved, obtaining reasonable dosimetric goals. Acute toxicity in the patient was acceptable, and she did not experience late toxicity and was still free from disease, as noted in last follow-up, 15 months after treatment.","PeriodicalId":94260,"journal":{"name":"Tumor discovery","volume":"46 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76512830","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Practice and Consideration of Master Protocol in Clinical Trials","authors":"Jiali Song, Zhiwei Rong, Xinwen Zhong, Yuhong Lu, Jike Huang, Yipe Yu, Zhilin Liu, Xuyuan Quan, Nana Chen, Kang Li, Fengyu Sun, Yan Hou","doi":"10.36922/td.342","DOIUrl":"https://doi.org/10.36922/td.342","url":null,"abstract":"There is great interest in accelerating late-stage therapy development by efficiently performing a trial design with multiple therapies or multiple subpopulations simultaneously under a single protocol. The master protocols are termed to describe the design of such trials, with a variety of terms such as umbrella, basket, or platform describing specific designs, which are, in contrast to the traditional trial designs, full of complexity. What should we consider in designing a trial ensuring the safety of human subjects and demonstrating the efficacy of new therapy? This paper overviews the master protocol framework, comprehensively unifies the definitions and illustrates essential design elements of representative example trials conducted in drugs and medical devices. Besides, to understand the master protocols deeply, it is also a need to summarize the commonly-used types of master protocols in various disease and treatment fields, along with the reasons for these phenomena by analyzing the characteristics of the diseases, the mechanism of therapeutic products, and the principles of various types of master protocols. Finally, we also propose practical considerations, including the design, ethical, statistics, and funding considerations that arise from implementing complex master protocols to help practitioners better design and identify potential valuable therapies.","PeriodicalId":94260,"journal":{"name":"Tumor discovery","volume":"24 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78176608","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A novel gene prognostic signature lymphocyte cytosolic protein 2 regulates melanoma progression by activating tumor-infiltrating CD8+ T-cells through the interferon regulatory factor 5 signaling pathway","authors":"Hongyin Sun, Kui Deng, Xin Zhou, Dongsheng Cao, Yong Cheng, Xiang Chen, Mingzhu Yin","doi":"10.36922/td.318","DOIUrl":"https://doi.org/10.36922/td.318","url":null,"abstract":"Cutaneous malignant melanoma is the most lethal skin cancer. The advent of immunotherapy has revolutionized the status of clinical therapies of melanoma, which brought new hope to these patients. However, only a small proportion of patients are responders. Therefore, the identification of novel prognostic and immune-related biomarkers is crucial to guide the development of melanoma clinical treatments. Herein, RNA-seq data of the cutaneous melanoma from public database were used for identifying prognostic gene signatures, and we found that lymphocyte cytosolic protein 2 (LCP2) was highly expressed in melanoma patient, which was associated with better prognosis for melanoma. Kyoto Encyclopedia of Genes and Genomes and gene ontology analyses demonstrated that the differentially expressed genes are significantly involved in lysosome, B-cell receptor signaling pathways, Fc epsilon RI signaling pathway, and T-cell receptor signaling pathway, indicating that these signaling pathways play important roles in melanoma. LCP2 expression was positively correlated with CD8+ T-cell and the overall survival of melanoma patients, and this positive correlation was directly confirmed by fluorescence-activated cell sorting experiment. The in vivo experiment showed that LCP2 knockdown significantly promoted the melanoma progression and decreased interferon regulatory factor 5 (IRF5) expression. In conclusion, we identified that LCP2 is a possible prognostic gene signature for progression-free survival of melanoma patients and regulates melanoma progression by activating tumor-infiltrating CD8+ T-cells through the IRF5 signaling pathway, indicating that LCP2 could serve as a prognostic biomarker and therapeutic target in immunotherapy.","PeriodicalId":94260,"journal":{"name":"Tumor discovery","volume":"35 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80323740","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Malignant versus normal breast tissue: Optical differentiation exploiting hyperspectral imaging system","authors":"M. Aref, Ibrahim H. Aboughaleb, Abdallah Abdelkader Hussein, Ayman Mohammed Farag, Sara Abd El-Ghaffar, Yasser H. El-Sharkawy","doi":"10.36922/td.258","DOIUrl":"https://doi.org/10.36922/td.258","url":null,"abstract":"Breast malignancy is a critical problem that severely affects women’s health globally with a high-frequency rate, necessitating fast, effective, and early diagnostic methods. The present study aims to measure the breast tissue’s optical properties by capturing the spectral signatures from malignant and normal breast tissue for therapeutic and diagnostic applications. The optical imaging system incorporates a hyperspectral (HS) camera to capture the spectral signatures for both the malignant and normal breast tissues within 400 ~ 1000 nm. The system was subdivided into two exploratory (reflection/transmission) to measure the tissue’s diffuse reflectance (Rd) and light transmission (Tr), respectively. The study involved 30 breast tissue (normal/tumor) samples from 30 females in the age range of 46 ~ 72 years, who were optically inspected in the visible and near-infrared (VIS-NIR) spectra. Then, the inverse adding doubling (IAD) method for breast tissue characterization and descriptive analysis (T-test) was exploited to verify the significant difference between the various types of breast tissues and select the optimum wavelength. Finally, comparing the study outcome with the histopathological examination to evaluate the system’s effectiveness by calculation (sensitivity, specificity, and accuracy). The average outcome values demonstrated that the optimal spectral bands distinguishing between the normal and the tumor tissues regarding the reflectance approach were 600 ~ 680 nm and 750 ~ 960 nm at the VIS and NIR spectrum, respectively. Then, for the transmission technique, the optimal spectral bands were 560 ~ 590 nm and 760 ~ 810 nm at the VIS and NIR spectra, respectively. Later, the T-test and the IAD verified that the highest Rd values for discrimination were 600 ~ 640 nm and 800 ~ 840 nm at the VIS and NIR spectra, respectively. On the other side, the highest Tr values were 600 ~ 640 nm and 760 ~ 800 nm at the VIS and NIR spectra, respectively. The investigation’s average reading accuracy, sensitivity, and specificity were 85%, 81.88%, and 88.8%, respectively. The experimental trials revealed that the system could identify the optimal wavelength for therapeutic and diagnostic applications through the light interaction behavior of the breast tissue’s optical properties.","PeriodicalId":94260,"journal":{"name":"Tumor discovery","volume":"59 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90505785","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An overview of the risk, underlying factors, and mechanism of cancer progression in polycystic ovary syndrome","authors":"Rubiat Afrin Ayon, Md. Azmain Faike, Sumiya Zaman Ononna, Aminul Hassan, Shoumik Kundu, Farhana Akhter, Mohammad Mahfuz Ali Khan Shawan, Md. Mozammel Hossain, Md. Ibrahim Khalil, Md. Ashraful Hasan","doi":"10.36922/td.328","DOIUrl":"https://doi.org/10.36922/td.328","url":null,"abstract":"Polycystic ovary syndrome (PCOS) is the most common endocrine and metabolic disorder among women of reproductive age. PCOS is characterized by ovulatory dysfunction, clinical or biochemical features of hyperandrogenism, and polycystic ovaries. The risk of cancer among PCOS patients has been a topic of discussion for decades due to the overlapping metabolic and endocrine abnormalities. This review article focuses on the association of PCOS with various types of reproductive (such as endometrial cancer, ovarian cancer, and breast cancer) and non-reproductive cancers, considering different aspects, such as the risk of cancer progression in PCOS patients, the underlying factors, and the mechanism through which PCOS might progress to cancer. The information provided in this article would help create awareness among PCOS patients about the need to take risk-reducing measures. This article might also aid in the effort of identifying novel therapeutic targets to counteract the progression of cancer in PCOS.","PeriodicalId":94260,"journal":{"name":"Tumor discovery","volume":"34 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88028380","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An approach for classification of lung nodules","authors":"Naveen Hm, N. C, M. Vn","doi":"10.36922/td.317","DOIUrl":"https://doi.org/10.36922/td.317","url":null,"abstract":"The main objective of the proposed work is to develop an automated computer-aided detection (CAD) system to classify lung nodules using various classifiers from computed tomography (CT) images. One of the most important steps in lung nodule detection is the classification of nodule and non-nodule patterns in CT. The early detection of the condition helps lower the mortality rate. The developed CAD systems consist of segmentation, feature extraction, and classification. In this work, a filter method is used to segment the infected region. Later, we extracted features through and fed into classifiers such as Decision Stump (DS), Random Forest (RF), and Back Propagation Neural Network (BPNN). The experimentation was conducted on LIDC-IDRI dataset, and the results with BPNN outperformed those with DS and RF classifiers.","PeriodicalId":94260,"journal":{"name":"Tumor discovery","volume":"10 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87469261","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Choroid plexus tumors: A spectrum from benign to malignant.","authors":"Ali A Mohamed, Thomas Caussat, Sophie Kelly, Phillip M Johansen, Brandon Lucke-Wold","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Choroid plexus tumors (CPT) are believed to originate from outgrowths of the choroid plexus. Despite their broad spectrum of symptoms, invasive nature, and prognosis, most CPTs typically exhibit similar presentations due to their relationship with the cerebral ventricles, as well as the mechanical obstruction and mass effect associated with their growth. In addition, these tumors mainly affect the pediatric population, further complicating the differentiation between benign and malignant subtypes. The World Health Organization classifies CPTs into three grades, namely, grades I, II, or III, based on their mitotic activity, which determine the benign or malignant nature of the tumors. CPTs classified by the World Health Organization (WHO) include choroid plexus papillomas (CPP), atypical CPPs (aCPP), and malignant choroid plexus carcinomas (CPC). Choroid plexus adenomas represent an additional category of benign CPTs not officially classified by the WHO. Despite the variations in histology, immunohistochemistry, imaging, treatment, and prognosis, CPTs cannot be reliably distinguished based solely on clinical presentation. Therefore, in this review, we aim to provide a comprehensive overview of each tumor subtype, along with the current management approach and emerging treatments.</p>","PeriodicalId":94260,"journal":{"name":"Tumor discovery","volume":"2 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41161597","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A case report of aggressive sebaceous carcinoma of the scalp","authors":"S. Jagtap, Swati S. Jagtap, S. Mishra, Kaushiki Varshney, Shuchita Gaur","doi":"10.36922/td.v1i2.203","DOIUrl":"https://doi.org/10.36922/td.v1i2.203","url":null,"abstract":"Malignant pilosebaceous neoplasm of the scalp is a very rare tumor. A 60-year-old man presented with a rapidly enlarging, ulcerated, and firm nodular mass over the scalp for a duration of 3 months. A few months back, the patient noticed a subcutaneous nodule at the same site, and it was reported as sebaceous adenoma on histopathology. The swelling recurred at the same site and was surgically excised and sent for histopathology. A histological diagnosis of sebaceous carcinoma of the scalp was made. On follow-up, there was no recurrence or distant metastasis. Due to the rarity and aggressive behavior of the malignant pilosebaceous neoplasm of the scalp, we present this case along with clinical and histopathological findings.","PeriodicalId":94260,"journal":{"name":"Tumor discovery","volume":"20 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87642838","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Facts and challenges of immunotherapy in triple-negative breast cancer","authors":"Xuehai Wang, Feng-Li Wang, Weiyi Xia, Siyuan Deng, Hongxiang Zhang, Xinyuan Zhao","doi":"10.36922/td.v1i2.196","DOIUrl":"https://doi.org/10.36922/td.v1i2.196","url":null,"abstract":"Triple-negative breast cancer (TNBC) is an aggressive but common cancer subtype in clinical practice. Immune activation has been observed in a subgroup of TNBC, suggesting that immunotherapy may be a potential therapeutic option. With the widespread use of monotherapy, specific immune checkpoint inhibitors (ICIs) such as avelumab, pembrolizumab, and atezolizumab have made significant contributions to improving outcomes in both early and advanced TNBC. In addition, the expressions of immune regulators such as cytotoxic T-lymphocyte-associated protein 4, programmed cell death 1 (PD-1), and programmed cell death-ligand 1 (PD-L1), which are influenced by tumor-infiltrating lymphocytes (TILs), are also critical factors in determining the effect of immunotherapy in TNBC. This review focuses on the updates on the biological underpinnings of TNBC and the associated treatment advances. We present the current landscape of well-known immune regulators and widely used ICIs for TNBC and highlight the future directions that are significant for further improving the efficacy and effect of targeted therapeutic strategies to immunotherapy in TNBC and more reliable prognostic predictions for tailored therapy in the future.","PeriodicalId":94260,"journal":{"name":"Tumor discovery","volume":"132 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85757787","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}