scholarly journals TRANSCUP: A Scalable Workflow for Predicting Cancer of Unknown Primary Based on Next-Generation Transcriptome Profiling

2020 ◽  
Vol 4 (1) ◽  
Author(s):  
Li Peng
BMC Cancer ◽  
2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Yosuke Mitani ◽  
Masashi Kanai ◽  
Tadayuki Kou ◽  
Shigeki Kataoka ◽  
Keitaro Doi ◽  
...  

Abstract Background Cancer of unknown primary (CUP) is usually treated with nonselective and empirical chemotherapy; however, its prognosis is generally poor, with a median survival of less than a year. Thus, clinicians eagerly await the development of more effective treatment strategies. In recent years, advances in next-generation sequencing (NGS) have made it possible to analyze comprehensively the genome of individual cancers. NGS has identified many genomic alterations, some of which are potential molecular targets of specific agents. We report a case of CUP that was successfully treated with targeted therapy directed by the genomic data obtained from an NGS-based multiplex assay. Case presentation A 52-year-old Asian woman with right hip joint pain underwent fluorodeoxyglucose-positron emission tomography/computed tomography, which showed multiple metastatic tumors in her right hip joint, thyroid gland, lung, and vertebrae. Brain magnetic resonance imaging showed multiple cerebral metastases. Additional tests, including pathology examination and conventional epidermal growth factor receptor (EGFR) gene mutation analysis (single-strand conformation polymorphism assay), could not identify the primary origin of the tumors, so the patient was diagnosed with CUP. After empirical chemotherapy for CUP, an NGS-based multiplex assay performed using a resected specimen of thyroid tumor detected the EGFR mutation c.2573 T > G p.Leu858Arg (L858R). Her treatment was changed to erlotinib, an EGFR tyrosine-kinase inhibiter, which dramatically shrank the tumors and decreased her serum carcinoembryonic antigen level. She achieved long-term disease control and survived for 2 years and 9 months from the first diagnosis. Conclusion This case might support the strategy that NGS-based multiplex assays could identify actionable molecular targets for individual patients with CUP.


2019 ◽  
Author(s):  
Peng Li

AbstractSummaryCancer of unknown primary site (CUP) accounts for 5% of all cancer diagnoses. These patients may benefit from more precise treatment when primary cancer site was identified. Advances in high-throughput sequencing have enabled cost-effective sequencing the transcriptome for clinical application. Here, we present a free, scalable and extendable software for CUP predication called TRANSCUP, which enables (1) raw data processing, (2) read mapping, (3) quality re-port, (4) gene expression quantification, (5) random forest machine learning model building for cancer type classification. TRANSCUP achieved high accuracy, sensitivity and specificity for tumor type classification based on external RNA-seq datasets. It has potential for broad clinical application for solving the CUP problem.AvailabilityTRANSCUP is open-source and freely available at https://github.com/plsysu/[email protected]


Cancers ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 451
Author(s):  
Noemi Laprovitera ◽  
Mattia Riefolo ◽  
Elisa Ambrosini ◽  
Christiane Klec ◽  
Martin Pichler ◽  
...  

Distant metastases are the main cause of cancer-related deaths in patients with advanced tumors. A standard diagnostic workup usually contains the identification of the tissue-of-origin of metastatic tumors, although under certain circumstances, it remains elusive. This disease setting is defined as cancer of unknown primary (CUP). Accounting for approximately 3–5% of all cancer diagnoses, CUPs are characterized by an aggressive clinical behavior and represent a real therapeutic challenge. The lack of determination of a tissue of origin precludes CUP patients from specific evidence-based therapeutic options or access to clinical trial, which significantly impacts their life expectancy. In the era of precision medicine, it is essential to characterize CUP molecular features, including the expression profile of non-coding RNAs, to improve our understanding of CUP biology and identify novel therapeutic strategies. This review article sheds light on this enigmatic disease by summarizing the current knowledge on CUPs focusing on recent discoveries and emerging diagnostic strategies.


Medicine ◽  
2017 ◽  
Vol 96 (16) ◽  
pp. e6693 ◽  
Author(s):  
Anne-Kirstine Dyrvig ◽  
Knud Bonnet Yderstræde ◽  
Oke Gerke ◽  
Peter Bjødstrup Jensen ◽  
Søren Hess ◽  
...  

Author(s):  
Lars Axelsson ◽  
Erik Holmberg ◽  
Jan Nyman ◽  
Anders Högmo ◽  
Helena Sjödin ◽  
...  

Abstract Introduction Head and neck cancer of unknown primary (HNCUP) is a rare condition whose prognostic factors that are significant for survival vary between studies. No randomized treatment study has been performed thus far, and the optimal treatment is not established. Objective The present study aimed to explore various prognostic factors and compare the two main treatments for HNCUP: neck dissection and (chemo) radiation vs primary (chemo) radiation. Methods A national multicenter study was performed with data from the Swedish Head and Neck Cancer Register (SweHNCR) and from the patients' medical records from 2008 to 2012. Results Two-hundred and sixty HNCUP patients were included. The tumors were HPV-positive in 80%. The overall 5-year survival rate of patients treated with curative intent was 71%. Age (p < 0.001), performance status (p= 0.036), and N stage (p= 0.046) were significant factors for overall survival according to the multivariable analysis. Treatment with neck dissection and (chemo) radiation (122 patients) gave an overall 5-year survival of 73%, and treatment with primary (chemo) radiation (87 patients) gave an overall 5-year survival of 71%, with no significant difference in overall or disease-free survival between the 2 groups. Conclusions Age, performance status, and N stage were significant prognostic factors. Treatment with neck dissection and (chemo) radiation and primary (chemo) radiation gave similar survival outcomes. A randomized treatment study that includes quality of life is needed to establish the optimal treatment.


Author(s):  
Alexander L. R. Grewcock ◽  
Karlijn E. P. E. Hermans ◽  
Matty P. Weijenberg ◽  
Piet A. Brandt ◽  
Caroline Loef ◽  
...  

2021 ◽  
Author(s):  
Ryan W. Huey ◽  
Brandon G. Smaglo ◽  
Jeannelyn S. Estrella ◽  
Aurelio Matamoros ◽  
Michael J. Overman ◽  
...  

Author(s):  
Shumei Kato ◽  
Ahmed Alsafar ◽  
Vighnesh Walavalkar ◽  
John Hainsworth ◽  
Razelle Kurzrock

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