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Maly M, Vanwalleghem L, Van Den Eeckhaut A, De Wilde V. Cancer of unknown primary and BRAF V600E meeting the BEACON combination: A case report. Mol Clin Oncol 2024; 21:88. [PMID: 39391046 PMCID: PMC11462391 DOI: 10.3892/mco.2024.2786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 08/29/2024] [Indexed: 10/12/2024] Open
Abstract
The diagnostic work-up of cancer of unknown primary (CUP) is a challenging task; in addition, only a little data on BRAF targeting in CUP are currently available. Traditionally, the identification of favourable and unfavourable CUP subsets directs the choice of treatment. The present article reports the case of a 50-year-old male patient presenting with a BRAF-mutated CUP, a rare and generally unfavourable subset. Based on imaging, immunohistochemistry and a high value of carbohydrate antigen 19-9, an upper gastrointestinal profile was initially presumed. After disease progression on treatment with a first-line platinum-based doublet chemotherapy, a significant response was documented after treatment with the BEACON combination. The present case report highlighted the paradigm shift in diagnosis and treatment of CUP from a histology-based approach to molecular profiling with the introduction of precision medicine.
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Affiliation(s)
- Marlies Maly
- Department of Gastroenterology and Hepatology, Ghent University Hospital, 9000 Ghent, Belgium
- Department of Gastroenterology and Hepatology, AZ Sint-Jan, 8000 Bruges, Belgium
| | | | | | - Vincent De Wilde
- Department of Gastroenterology and Hepatology, AZ Sint-Jan, 8000 Bruges, Belgium
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2
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Cavazzoni A, Salamon I, Fumarola C, Gallerani G, Laprovitera N, Gelsomino F, Riefolo M, Rihawi K, Porcellini E, Rossi T, Mazzeschi M, Naddeo M, Serravalle S, Broseghini E, Agostinis F, Deas O, Roncarati R, Durante G, Pace I, Lauriola M, Garajova I, Calin GA, Bonafè M, D'Errico A, Petronini PG, Cairo S, Ardizzoni A, Sales G, Ferracin M. Synergic activity of FGFR2 and MEK inhibitors in the treatment of FGFR2-amplified cancers of unknown primary. Mol Ther 2024; 32:3650-3668. [PMID: 39033323 DOI: 10.1016/j.ymthe.2024.07.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 04/30/2024] [Accepted: 07/17/2024] [Indexed: 07/23/2024] Open
Abstract
Patients with cancer of unknown primary (CUP) carry the double burden of an aggressive disease and reduced access to therapies. Experimental models are pivotal for CUP biology investigation and drug testing. We derived two CUP cell lines (CUP#55 and #96) and corresponding patient-derived xenografts (PDXs), from ascites tumor cells. CUP cell lines and PDXs underwent histological, immune-phenotypical, molecular, and genomic characterization confirming the features of the original tumor. The tissue-of-origin prediction was obtained from the tumor microRNA expression profile and confirmed by single-cell transcriptomics. Genomic testing and fluorescence in situ hybridization analysis identified FGFR2 gene amplification in both models, in the form of homogeneously staining region (HSR) in CUP#55 and double minutes in CUP#96. FGFR2 was recognized as the main oncogenic driver and therapeutic target. FGFR2-targeting drug BGJ398 (infigratinib) in combination with the MEK inhibitor trametinib proved to be synergic and exceptionally active, both in vitro and in vivo. The effects of the combined treatment by single-cell gene expression analysis revealed a remarkable plasticity of tumor cells and the greater sensitivity of cells with epithelial phenotype. This study brings personalized therapy closer to CUP patients and provides the rationale for FGFR2 and MEK targeting in metastatic tumors with FGFR2 pathway activation.
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MESH Headings
- Animals
- Female
- Humans
- Mice
- Cell Line, Tumor
- Drug Synergism
- Gene Amplification
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic/drug effects
- Neoplasms, Unknown Primary/drug therapy
- Neoplasms, Unknown Primary/genetics
- Neoplasms, Unknown Primary/pathology
- Phenylurea Compounds/pharmacology
- Protein Kinase Inhibitors/pharmacology
- Protein Kinase Inhibitors/therapeutic use
- Pyridones/pharmacology
- Pyrimidines/pharmacology
- Pyrimidines/therapeutic use
- Pyrimidinones/pharmacology
- Receptor, Fibroblast Growth Factor, Type 2/genetics
- Receptor, Fibroblast Growth Factor, Type 2/antagonists & inhibitors
- Receptor, Fibroblast Growth Factor, Type 2/metabolism
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Andrea Cavazzoni
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | - Irene Salamon
- IRCCS, Azienda Ospedaliero-Universitaria di Bologna, 40126 Bologna, Italy
| | - Claudia Fumarola
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy
| | - Giulia Gallerani
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Noemi Laprovitera
- IRCCS, Azienda Ospedaliero-Universitaria di Bologna, 40126 Bologna, Italy
| | | | - Mattia Riefolo
- IRCCS, Azienda Ospedaliero-Universitaria di Bologna, 40126 Bologna, Italy; Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Karim Rihawi
- IRCCS, Azienda Ospedaliero-Universitaria di Bologna, 40126 Bologna, Italy
| | - Elisa Porcellini
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Tania Rossi
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola 47014, Italy
| | - Martina Mazzeschi
- IRCCS, Azienda Ospedaliero-Universitaria di Bologna, 40126 Bologna, Italy
| | - Maria Naddeo
- IRCCS, Azienda Ospedaliero-Universitaria di Bologna, 40126 Bologna, Italy
| | | | | | | | | | - Roberta Roncarati
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy; Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza" (IGM)- Consiglio Nazionale delle Ricerche (CNR), 40136 Bologna, Italy
| | - Giorgio Durante
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Ilaria Pace
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Mattia Lauriola
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Ingrid Garajova
- Medical Oncology Unit, University Hospital of Parma, 43126 Parma, Italy
| | - George A Calin
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Massimiliano Bonafè
- IRCCS, Azienda Ospedaliero-Universitaria di Bologna, 40126 Bologna, Italy; Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Antonia D'Errico
- IRCCS, Azienda Ospedaliero-Universitaria di Bologna, 40126 Bologna, Italy; Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | | | | | - Andrea Ardizzoni
- IRCCS, Azienda Ospedaliero-Universitaria di Bologna, 40126 Bologna, Italy; Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Gabriele Sales
- Department of Biology, University of Padova, 35031 Padua, Italy
| | - Manuela Ferracin
- IRCCS, Azienda Ospedaliero-Universitaria di Bologna, 40126 Bologna, Italy; Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy.
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3
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Gehrmann J, Soenarto DJ, Hidayat K, Beyer M, Quakulinski L, Alkarkoukly S, Berressem S, Gundert A, Butler M, Grönke A, Lennartz S, Persigehl T, Zander T, Beyan O. Seeing the primary tumor because of all the trees: Cancer type prediction on low-dimensional data. Front Med (Lausanne) 2024; 11:1396459. [PMID: 39257886 PMCID: PMC11385615 DOI: 10.3389/fmed.2024.1396459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 08/06/2024] [Indexed: 09/12/2024] Open
Abstract
The Cancer of Unknown Primary (CUP) syndrome is characterized by identifiable metastases while the primary tumor remains hidden. In recent years, various data-driven approaches have been suggested to predict the location of the primary tumor (LOP) in CUP patients promising improved diagnosis and outcome. These LOP prediction approaches use high-dimensional input data like images or genetic data. However, leveraging such data is challenging, resource-intensive and therefore a potential translational barrier. Instead of using high-dimensional data, we analyzed the LOP prediction performance of low-dimensional data from routine medical care. With our findings, we show that such low-dimensional routine clinical information suffices as input data for tree-based LOP prediction models. The best model reached a mean Accuracy of 94% and a mean Matthews correlation coefficient (MCC) score of 0.92 in 10-fold nested cross-validation (NCV) when distinguishing four types of cancer. When considering eight types of cancer, this model achieved a mean Accuracy of 85% and a mean MCC score of 0.81. This is comparable to the performance achieved by approaches using high-dimensional input data. Additionally, the distribution pattern of metastases appears to be important information in predicting the LOP.
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Affiliation(s)
- Julia Gehrmann
- Institute for Biomedical Informatics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Devina Johanna Soenarto
- Institute for Biomedical Informatics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Kevin Hidayat
- Institute for Biomedical Informatics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Maria Beyer
- Institute for Biomedical Informatics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Lars Quakulinski
- Institute for Biomedical Informatics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Samer Alkarkoukly
- Institute for Biomedical Informatics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Medical Data Integration Center (MeDIC), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Scarlett Berressem
- Department of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), Aachen, Germany
| | - Anna Gundert
- Department of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), Aachen, Germany
| | - Michael Butler
- Department of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), Aachen, Germany
| | - Ana Grönke
- Medical Data Integration Center (MeDIC), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Simon Lennartz
- Institute for Diagnostic and Interventional Radiology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Thorsten Persigehl
- Institute for Diagnostic and Interventional Radiology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Thomas Zander
- Department of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf (CIO ABCD), Aachen, Germany
| | - Oya Beyan
- Institute for Biomedical Informatics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Medical Data Integration Center (MeDIC), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Department of Data Science and Artificial Intelligence, Fraunhofer FIT, Sankt Augustin, Germany
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De Wilde J, Van Paemel R, De Koker A, Roelandt S, Van de Velde S, Callewaert N, Van Dorpe J, Creytens D, De Wilde B, De Preter K. A Fast, Affordable, and Minimally Invasive Diagnostic Test for Cancer of Unknown Primary Using DNA Methylation Profiling. J Transl Med 2024; 104:102091. [PMID: 38830578 DOI: 10.1016/j.labinv.2024.102091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 05/16/2024] [Accepted: 05/25/2024] [Indexed: 06/05/2024] Open
Abstract
Currently, we cannot provide a conclusive diagnosis for 3% to 5% of people who are confronted with cancer. These patients have cancer of unknown primary (CUP), ie, a metastasized cancer for which the tissue of origin cannot be determined. Studies have shown that the DNA methylation profile is a unique "fingerprint" that can be used to classify tumors. Here we used cell-free reduced representation bisulfite sequencing (cfRRBS), a technique that allows us to identify the methylation profile starting from minimal amounts of highly fragmented DNA, for CUP diagnosis on formalin-fixed paraffin-embedded (FFPE) tissue and liquid biopsies. We collected 80 primary tumor FFPE samples covering 16 tumor entities together with 15 healthy plasma samples to use as a custom cfRRBS reference data set. Entity-specific methylation regions are defined for each entity to build a classifier based on nonnegative least squares deconvolution. This classification framework was tested on 30 FFPE, 19 plasma, and 40 pleural and peritoneal effusion samples of both known metastatic tumors and clinical CUPs for which pathological investigation finally resulted in a cancer diagnosis. Using this framework, 27 of 30 FFPE (all CUPs) and 16 of 19 plasma samples (10/13 CUPs) obtained an accurate diagnosis, with a minimal DNA input of 400 pg. Diagnosis of the 40 pleural and peritoneal effusion samples is possible in 9 of 27 samples with negative/inconclusive cytology (6/13 CUPs), showing that cell-free DNA (cfDNA) methylation profiling could complement routine cytologic analysis. However, a low "cfDNA - high-molecular weight DNA ratio" has a considerable impact on the prediction accuracy. Moreover, the accuracy improves significantly if the predicted tumor percentage is >7%. This proof-of-concept study shows the feasibility of using DNA methylation profiling on FFPE and liquid biopsy samples such as blood, ascites, and pleural effusions in a fast and affordable way. Our novel RRBS-based technique requires minimal DNA input, can be performed in <1 week, and is highly adaptable to specific diagnostic problems as we only use 5 FFPE references per tumor entity. We believe that cfRRBS methylation profiling could be a valuable addition to the pathologist's toolbox in the diagnosis of CUPs.
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Affiliation(s)
- Jilke De Wilde
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Department of Pathology, Ghent University Hospital, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Ruben Van Paemel
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Andries De Koker
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Center for Medical Biotechnology, VIB-UGent, Ghent, Belgium; Department of Biochemistry and Microbiology, Ghent University, Belgium
| | - Sofie Roelandt
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Center for Medical Biotechnology, VIB-UGent, Ghent, Belgium
| | - Sofie Van de Velde
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Center for Medical Biotechnology, VIB-UGent, Ghent, Belgium
| | - Nico Callewaert
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Center for Medical Biotechnology, VIB-UGent, Ghent, Belgium; Department of Biochemistry and Microbiology, Ghent University, Belgium
| | - Jo Van Dorpe
- Department of Pathology, Ghent University Hospital, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - David Creytens
- Department of Pathology, Ghent University Hospital, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Bram De Wilde
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Katleen De Preter
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Center for Medical Biotechnology, VIB-UGent, Ghent, Belgium.
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5
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Barsouk A, Elghawy O, Stone S, Singh A. Patient with mediastinal carcinoma of unknown primary with RET fusion achieves durable response with RET inhibition. Anticancer Drugs 2024; 35:653-657. [PMID: 38696710 DOI: 10.1097/cad.0000000000001618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2024]
Abstract
Selective RET inhibitors have shown promise in thyroid cancer (TC) and nonsmall cell lung cancer (NSCLC) harboring RET fusions on next-generation sequencing (NGS), although rarity of the rearrangement has led to limited data for certain tumor types, such as carcinoma of unknown primary. We present a 65-year-old female with no history of malignancy, smoking or radiation exposure, who was found to have an anterior mediastinum malignancy of unknown primary, with metastases to supraclavicular lymph nodes. Core biopsy of the mediastinum revealed poorly differentiated carcinoma, while a biopsy of the thyroid revealed atypia of indeterminate significance (Bethesda III). PD-L1 immunohistochemistry was positive (90%), and liquid NGS revealed mutations in TP53 and the TERT promoter (c.-124C>T), as well as a CCDC6-RET fusion. This genetic profile resembled an anaplastic TC vs. NSCLC primary, although thymic primary and poorly differentiated TC remained on the differential. The patient was initiated on selpercatinib, which was held after 3 weeks due to thrombocytopenia and hypertension. At a reduced dosage, patient developed transaminitis, and selpercatinib was switched to pralsetinib. Brain MRI showed a nonenhancing temporal lobe signal abnormality, which on biopsy proved to be glioblastoma (GBM) with TERT promoter c.-124C>T mutation and FGFR3-TACC3 fusion by NGS. Pralsetinib was held during adjuvant chemoradiation for the GBM, and again for 4 weeks due to pneumonitis that resolved with steroids, and pralsetinib was restarted at a reduced dose. The patient has since demonstrated a stable reduction of the mediastinal mass for >15 months with RET inhibition therapy, despite several treatment interruptions.
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Affiliation(s)
- Adam Barsouk
- Department of Medical Oncology, Abramson Cancer Center, Hospital of the University of Pennsylvania
| | - Omar Elghawy
- Department of Medical Oncology, Abramson Cancer Center, Hospital of the University of Pennsylvania
| | - Sara Stone
- Department of Pathology, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Aditi Singh
- Department of Medical Oncology, Abramson Cancer Center, Hospital of the University of Pennsylvania
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Gao F, Liu L, Xu X. Clinical characteristics and prognosis of liver metastases with unknown primary site. Transl Cancer Res 2024; 13:3637-3651. [PMID: 39145069 PMCID: PMC11319942 DOI: 10.21037/tcr-24-136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 05/29/2024] [Indexed: 08/16/2024]
Abstract
Background Liver metastases from cancer of unknown primary (CUPL) constitute a rare disease, particularly among individuals younger than 50 years old. This paper aims to investigate the clinical characteristics of patients with CUPL and analyze prognostic differences across distinct age groups. Methods Data pertaining to patients with CUPL were extracted from the Surveillance, Epidemiology, and End Results (SEER) database. Propensity score matching (PSM) was employed to adjust for clinical variables. Cox regression analysis identified risk factors influencing overall survival (OS), while competing-risk analyses were conducted to determine prognostic factors for cancer-specific survival (CSS). Survival differences were compared using the Kaplan-Meier method and cumulative incidence function (CIF). Results The study encompassed 4,691 patients, with 319 (6.8%) in the age <50 years group and 4,372 (93.2%) in the age ≥50 years group. Individuals with unexplained liver metastases exhibited a 1-year OS rate of 14.7% and a 1-year CSS rate of 23%. Following matching, age, histology, brain metastases, and chemotherapy were identified as independent prognostic factors affecting OS. Additionally, race, grade, histology, brain metastases, and chemotherapy were recognized as independent prognostic factors influencing CSS. Notably, the age <50 years group demonstrated superior OS and CSS compared to the age ≥50 years group before and after PSM. Among patients undergoing chemotherapy, the age <50 years group exhibited enhanced OS and CSS compared to their age ≥50 years counterparts. Furthermore, in individuals subjected to radiotherapy, the age <50 years group demonstrated superior OS, although no significant difference in CSS was observed. Conclusions The survival prognosis of patients with CUPL was found to be poor. However, both OS and CSS were more favorable in the age <50 years group compared to the age ≥50 years group. Additionally, radiotherapy and chemotherapy were associated with an OS benefit for patients in the age <50 years group.
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Affiliation(s)
- Fuli Gao
- Department of Gastroenterology, Changshu Hospital Affiliated to Soochow University, First People's Hospital of Changshu City, Changshu, China
| | - Luojie Liu
- Department of Gastroenterology, Changshu Hospital Affiliated to Soochow University, First People's Hospital of Changshu City, Changshu, China
| | - Xiaodan Xu
- Department of Gastroenterology, Changshu Hospital Affiliated to Soochow University, First People's Hospital of Changshu City, Changshu, China
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Raghu A, Raghu A, Wise JF. Deep Learning-Based Identification of Tissue of Origin for Carcinomas of Unknown Primary Using MicroRNA Expression: Algorithm Development and Validation. JMIR BIOINFORMATICS AND BIOTECHNOLOGY 2024; 5:e56538. [PMID: 39046787 PMCID: PMC11306940 DOI: 10.2196/56538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 04/02/2024] [Accepted: 04/25/2024] [Indexed: 07/25/2024]
Abstract
BACKGROUND Carcinoma of unknown primary (CUP) is a subset of metastatic cancers in which the primary tissue source of the cancer cells remains unidentified. CUP is the eighth most common malignancy worldwide, accounting for up to 5% of all malignancies. Representing an exceptionally aggressive metastatic cancer, the median survival is approximately 3 to 6 months. The tissue in which cancer arises plays a key role in our understanding of sensitivities to various forms of cell death. Thus, the lack of knowledge on the tissue of origin (TOO) makes it difficult to devise tailored and effective treatments for patients with CUP. Developing quick and clinically implementable methods to identify the TOO of the primary site is crucial in treating patients with CUP. Noncoding RNAs may hold potential for origin identification and provide a robust route to clinical implementation due to their resistance against chemical degradation. OBJECTIVE This study aims to investigate the potential of microRNAs, a subset of noncoding RNAs, as highly accurate biomarkers for detecting the TOO through data-driven, machine learning approaches for metastatic cancers. METHODS We used microRNA expression data from The Cancer Genome Atlas data set and assessed various machine learning approaches, from simple classifiers to deep learning approaches. As a test of our classifiers, we evaluated the accuracy on a separate set of 194 primary tumor samples from the Sequence Read Archive. We used permutation feature importance to determine the potential microRNA biomarkers and assessed them with principal component analysis and t-distributed stochastic neighbor embedding visualizations. RESULTS Our results show that it is possible to design robust classifiers to detect the TOO for metastatic samples on The Cancer Genome Atlas data set, with an accuracy of up to 97% (351/362), which may be used in situations of CUP. Our findings show that deep learning techniques enhance prediction accuracy. We progressed from an initial accuracy prediction of 62.5% (226/362) with decision trees to 93.2% (337/362) with logistic regression, finally achieving 97% (351/362) accuracy using deep learning on metastatic samples. On the Sequence Read Archive validation set, a lower accuracy of 41.2% (77/188) was achieved by the decision tree, while deep learning achieved a higher accuracy of 80.4% (151/188). Notably, our feature importance analysis showed the top 3 most important features for predicting TOO to be microRNA-10b, microRNA-205, and microRNA-196b, which aligns with previous work. CONCLUSIONS Our findings highlight the potential of using machine learning techniques to devise accurate tests for detecting TOO for CUP. Since microRNAs are carried throughout the body via extracellular vesicles secreted from cells, they may serve as key biomarkers for liquid biopsy due to their presence in blood plasma. Our work serves as a foundation toward developing blood-based cancer detection tests based on the presence of microRNA.
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Affiliation(s)
- Ananya Raghu
- Quarry Lane School, San Ramon, CA, United States
| | - Anisha Raghu
- Quarry Lane School, San Ramon, CA, United States
| | - Jillian F Wise
- Department of Biology and Biomedical Sciences, Salve Regina University, Newport, RI, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Pre-College Programs, Tufts University, Medford, MA, United States
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8
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Tanaka K, Miyoshi H, Kawamoto K, Shimasaki Y, Nakashima K, Imamoto T, Yamada K, Takeuchi M, Moritsubo M, Furuta T, Kohno K, Tamura S, Sonoki T, Ohshima K. Clinicopathological analysis of CD47 and signal regulatory protein alpha expression in myeloid sarcoma patients: CD47 expression is a favourable prognostic factor. Pathology 2024; 56:81-91. [PMID: 38110323 DOI: 10.1016/j.pathol.2023.10.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 09/04/2023] [Accepted: 10/02/2023] [Indexed: 12/20/2023]
Abstract
Myeloid sarcoma is a rare extramedullary haematopoietic malignancy. Interaction between CD47 and signal regulatory protein α (SIRPα) inhibits phagocytosis. CD47-positive tumours confer poor prognoses in various malignant tumours, including acute myeloid leukaemia. This study aimed to investigate the clinicopathological effects of CD47 and SIRPα expression in myeloid sarcoma. Immunohistochemistry (IHC) of CD47 and SIRPα was performed in 84 biopsy samples obtained from patients with myeloid sarcoma, some of which were CD47-positive. Patients were categorised into the following two groups based on IHC of SIRPα: those with SIRPα-positive neoplastic cells (nSIRPα) and, SIRPα expression on non-neoplastic stromal cells in tumour microenvironment (miSIRPα). In addition, patients with CD47 positivity had higher lymphocytic infiltration into the tumour microenvironment. Overall, these patients had significantly higher overall survival, however, no significant difference was observed in progression-free survival. No significant prognostic differences were observed between the nSIRPα and miSIRPα groups. This is the first study to demonstrate an association between CD47 expression and improved prognosis in myeloid sarcoma. Nonetheless, it will be necessary to conduct additional research on gene expression and genomic abnormalities to elucidate the corresponding pathogenesis of myeloid sarcoma.
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Affiliation(s)
- Ken Tanaka
- Department of Pathology, Kurume University School of Medicine, Kurume, Japan; Department of Haematology/Oncology, Wakayama Medical University, Wakayama, Japan
| | - Hiroaki Miyoshi
- Department of Pathology, Kurume University School of Medicine, Kurume, Japan.
| | - Keisuke Kawamoto
- Department of Pathology, Kurume University School of Medicine, Kurume, Japan
| | - Yasumasa Shimasaki
- Department of Pathology, Kurume University School of Medicine, Kurume, Japan
| | - Kazutaka Nakashima
- Department of Pathology, Kurume University School of Medicine, Kurume, Japan
| | - Teppei Imamoto
- Department of Pathology, Kurume University School of Medicine, Kurume, Japan
| | - Kyohei Yamada
- Department of Pathology, Kurume University School of Medicine, Kurume, Japan
| | - Mai Takeuchi
- Department of Pathology, Kurume University School of Medicine, Kurume, Japan
| | - Mayuko Moritsubo
- Department of Pathology, Kurume University School of Medicine, Kurume, Japan
| | - Takuya Furuta
- Department of Pathology, Kurume University School of Medicine, Kurume, Japan
| | - Kei Kohno
- Department of Pathology, Kurume University School of Medicine, Kurume, Japan
| | - Shinobu Tamura
- Department of Haematology/Oncology, Wakayama Medical University, Wakayama, Japan
| | - Takashi Sonoki
- Department of Haematology/Oncology, Wakayama Medical University, Wakayama, Japan
| | - Koichi Ohshima
- Department of Pathology, Kurume University School of Medicine, Kurume, Japan
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9
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Wang Y, Huang Q, Zhong G, Lv J, Guo Q, Ma Y, Wang X, Zeng J. Sequential PET/CT and pathological biomarker crosstalk predict response to PD-1 blockers alone or combined with sunitinib in propensity score-matched cohorts of cancer of unknown primary treatment. Front Oncol 2023; 13:1191611. [PMID: 38205137 PMCID: PMC10777842 DOI: 10.3389/fonc.2023.1191611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 10/26/2023] [Indexed: 01/12/2024] Open
Abstract
Introduction The efficacy of immune checkpoint inhibitors (ICIs), including toripalimab and pembrolizumab, has not been confirmed in the treatment of cancer of unknown primary (CUP), which has a very poor prognosis. Combined with anti-angiogenic therapies, ICIs are hypothesized to be effective in prolonging overall survival. The study aims to give evidence on the treatment effects of sunitinib combined with ICIs, find pathological biomarkers associated with changes in volumetric 18F FDG PET/CT parameters, and investigate inner associations among these markers associated with response on PET/CT. Methods The study recruited patients receiving combined treatment (ICIs + sunitinib), compared the effects of combined treatment with those of separate treatment and age-matched negative controls, and analyzed propensity score-matched (PSM) pairs. Markers associated with survival were identified, and their inner associations were tested using structural equation modeling. Results A total of 292 patients were enrolled in the final analysis, with 53 patients receiving combined treatment. Survival analysis demonstrated significantly prolonged survival in either combined or separate treatment, with the combined arm showing better response when PSM-paired using pre-treatment whole-body PET/CT parameters. The angiogenic markers KDR and VEGF mediate the PD-1 blockade impact on volumetric value changes in positive and negative manners. Conclusion The anti-angiogenic agent sunitinib may potentiate PD-1 blockade by diminishing angiogenesis or its downstream effects. The combined separate treatment increased the survival of CUP patients, and the responses could be evaluated using volumetric PET/CT parameters.
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Affiliation(s)
- Youlong Wang
- Hainan Hospital of PLA General Hospital, Department of General Surgery, Haitang District, Sanya, China
| | - Qi Huang
- Department of Clinical Laboratory, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Guanqing Zhong
- Department of Clinical Laboratory, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jun Lv
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Qinzhi Guo
- Pancreas Center of Guangdong Provincial People’s Hospital, Guangzhou, China
| | - Yifei Ma
- Department of Spine Surgery, The Second Affiliated Hospital, Shantou University Medical College, Shantou, China
| | - Xinjia Wang
- Department of Spine Surgery, The Second Affiliated Hospital, Shantou University Medical College, Shantou, China
| | - Jiling Zeng
- Department of Nuclear Medicine, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Center, Guangzhou, China
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10
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Atarbashi-Moghadam S, Jafarian M, Dowdani S. Metastatic Adenocarcinoma of Mandible with Unknown Primary Origin (CUP Syndrome): a Rare Case Report. JOURNAL OF DENTISTRY (SHIRAZ, IRAN) 2023; 24:444-448. [PMID: 38149229 PMCID: PMC10749435 DOI: 10.30476/dentjods.2023.97749.2034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/08/2023] [Accepted: 07/02/2023] [Indexed: 12/28/2023]
Abstract
Metastatic lesions of the jaws are a diagnostic challenge because of their scarcity and uncharacteristic clinical-radiographic features. Carcinoma of unknown primary origin (CUP) is characterized by the existence of metastatic disease with no recognized primary neoplasm after a comprehensive work-up. CUP shows a poor prognosis with limited treatment choices. This paper presents a 64-year-old male with a chief complaint of paresthesia of the chin and lower lip. Panoramic radiography showed an ill-defined radiolucency in the left mandibular molar area and the residue of the first molar root. Microscopic examination demonstrated features of mucin-producing adenocarcinoma and was not similar to common neoplasms of the jaw. The whole-body scan revealed multiple osseous uptakes. CDX2 was diffusely positive. However, in the end, the origin of the primary tumor was not determined. Considering the aforementioned data, the diagnosis of metastatic adenocarcinoma with unknown primary origin was made. CUP of the oral cavity is an extremely rare event. The possibility of metastasis should be raised in a patient who complains of paresthesia. Awareness of the clinical and histopathologic features of these malignancies is crucial for clinicians and pathologists to have a proper diagnosis.
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Affiliation(s)
- Saede Atarbashi-Moghadam
- Dept. of Oral and Maxillofacial Pathology, School of Dentistry, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Jafarian
- Dept. of Oral and Maxillofacial Surgery, Taleghani Medical Center, School of Dentistry, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shaghayegh Dowdani
- Graduated Student, School of Dentistry, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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11
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Borch WR, Monaco SE. Current Approach to Undifferentiated Neoplasms, With Focus on New Developments and Novel Immunohistochemical Stains. Arch Pathol Lab Med 2023; 147:1364-1373. [PMID: 36943241 DOI: 10.5858/arpa.2022-0459-ra] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/12/2022] [Indexed: 03/23/2023]
Abstract
CONTEXT.— Workup of the poorly differentiated or undifferentiated tumor remains a significant and challenging entity in the practice of anatomic pathology. Particularly in the setting of small biopsies and limited material, these cases demand a balanced approach that considers the patient's clinical and radiologic presentation, a basic assessment of tumor morphology, a reasonably broad immunohistochemical panel, and diligent preservation of tissue for prognostic and therapeutic studies. OBJECTIVE.— To illustrate some of the new and emerging immunohistochemical markers in the evaluation of tumors with undifferentiated or poorly differentiated morphology, with a focus on the workup in limited tissue samples to raise awareness of the issues involved with the pathologic workup in these challenging tumors. DATA SOURCES.— A literature review of new ancillary studies that can be applied to cytologic specimens was performed. CONCLUSIONS.— Knowledge of the patient's history and communication with the patient's clinical team is essential in formulating a differential diagnosis that can appropriately limit the differential diagnosis based on morphology, especially in small specimens. This information, in conjunction with classifying the tumor morphology (eg, epithelioid, spindled, neuroendocrine, basaloid/biphasic, mixed) gives a logical approach to choosing an initial immunohistochemical panel. Fortunately, immunohistochemistry is evolving quickly in the wake of groundbreaking molecular studies to develop new and better markers to further classify these difficult tumors beyond where we traditionally have been able to go.
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Affiliation(s)
- William R Borch
- From the Department of Laboratory Medicine, Geisinger Medical Center, Danville, Pennsylvania
| | - Sara E Monaco
- From the Department of Laboratory Medicine, Geisinger Medical Center, Danville, Pennsylvania
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12
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Kobayashi K, Shibata N, Ohmoto K, Omori M, Umekawa Y. Autopsy-Confirmed Undifferentiated Carcinoma of the Liver With Rapid Bone Metastasis. Cureus 2023; 15:e49848. [PMID: 38169930 PMCID: PMC10758540 DOI: 10.7759/cureus.49848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/02/2023] [Indexed: 01/05/2024] Open
Abstract
A male in his late 70s, with progressive hip pain, was diagnosed with a metastatic iliac bone tumor, initially misinterpreted as septic arthritis. Despite extensive imaging, the primary tumor site was undetected until autopsy, which confirmed undifferentiated carcinoma of the liver with secondary lung involvement. The patient's poor performance status and rapid health decline precluded aggressive treatment, leading to his demise. This case underscores the difficulties in diagnosing such carcinomas and suggests that early identification and innovative therapies like nivolumab could potentially extend life in similar cases.
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Affiliation(s)
- Keigo Kobayashi
- Department of Internal Medicine, Kurashiki Medical Center, Kurashiki, JPN
| | - Norikuni Shibata
- Division of Hepatology, Kurashiki Medical Center, Kurashiki, JPN
| | - Kenji Ohmoto
- Division of Hepatology, Kurashiki Medical Center, Kurashiki, JPN
| | - Masako Omori
- Division of Pathology, Kurashiki Medical Center, Kurashiki, JPN
| | - Yasuhiro Umekawa
- Department of Internal Medicine, Kurashiki Medical Center, Kurashiki, JPN
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13
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Choi YJ, Park S, Son SM, Seo HW, Hwang J, Jung SJ, Shin YD. Postoperative peritoneal inflammatory granuloma mimicking peritoneal metastasis in a patient with breast cancer: a case report. Am J Transl Res 2023; 15:6247-6254. [PMID: 37969180 PMCID: PMC10641338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 09/22/2023] [Indexed: 11/17/2023]
Abstract
Peritoneal metastasis from breast cancer is a relatively rare life-threatening condition. The gold standard for diagnosing peritoneal metastasis is a direct peritoneal biopsy. In this report, we describe an interesting case of peritoneal inflammation mimicking peritoneal metastasis in a patient with breast cancer, as confirmed by laparoscopic peritoneal biopsy. A 45-year-old woman with a history of right breast cancer presented with a peritoneal wall mass seen on an abdominal computed tomography (CT) in routine follow-up. She underwent right skin-sparing mastectomy with sentinel lymph node biopsy with direct to implant reconstruction 6 years prior and underwent right salpingo-oophorectomy 2 years before. Positron emission tomography-computed tomography (PET-CT) and abdominopelvic CT showed multiple enhancing nodules in small bowel mesentery and right peritoneal wall with a small amount of ascites, which led to a strong suspicion of peritoneal metastasis. After a multidisciplinary conference, the possibility of peritoneal seeding became doubtful. Laparoscopic biopsy was performed, and peritoneal wall mass biopsy was subsequently performed. Pathologic results showed no evidence of peritoneal metastasis of breast cancer. The peritoneal biopsy specimen revealed postoperative fibrosis and inflammation with some meal content. Although rare in breast cancer, peritoneal metastasis can produce a devastating outcome if left undiagnosed. Despite the imaging findings strongly suggesting metastasis, biopsy confirmation for the suspected lesion was necessary. This not only verifies true metastasis but also determines the treatment options available for the patient and thus unnecessary treatment can be avoided.
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Affiliation(s)
- Young Jin Choi
- Department of Surgery, Chungbuk National University Hospital, Chungbuk National University College of Medicine1 Chungdae-ro, Seowon-gu, Cheongju 28644, South Korea
| | - Sungmin Park
- Department of Surgery, Chungbuk National University Hospital, Chungbuk National University College of Medicine1 Chungdae-ro, Seowon-gu, Cheongju 28644, South Korea
| | - Seung-Myoung Son
- Department of Pathology, Chungbuk National University Hospital, Chungbuk National University College of Medicine1 Chungdae-ro, Seowon-gu, Cheongju 28644, South Korea
| | - Hae-Won Seo
- Department of Anesthesiology and Pain Medicine, Chungbuk National University Hospital, Chungbuk National University College of Medicine1 Chungdae-ro, Seowon-gu, Cheongju 28644, South Korea
| | - Jihye Hwang
- Department of Anesthesiology and Pain Medicine, Chungbuk National University Hospital, Chungbuk National University College of Medicine1 Chungdae-ro, Seowon-gu, Cheongju 28644, South Korea
| | - Se Joon Jung
- Department of Anesthesiology and Pain Medicine, Chungbuk National University Hospital, Chungbuk National University College of Medicine1 Chungdae-ro, Seowon-gu, Cheongju 28644, South Korea
| | - Young Duck Shin
- Department of Anesthesiology and Pain Medicine, Chungbuk National University Hospital, Chungbuk National University College of Medicine1 Chungdae-ro, Seowon-gu, Cheongju 28644, South Korea
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14
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Zhang S, He S, Zhu X, Wang Y, Xie Q, Song X, Xu C, Wang W, Xing L, Xia C, Wang Q, Li W, Zhang X, Yu J, Ma S, Shi J, Gu H. DNA methylation profiling to determine the primary sites of metastatic cancers using formalin-fixed paraffin-embedded tissues. Nat Commun 2023; 14:5686. [PMID: 37709764 PMCID: PMC10502058 DOI: 10.1038/s41467-023-41015-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 08/18/2023] [Indexed: 09/16/2023] Open
Abstract
Identifying the primary site of metastatic cancer is critical to guiding the subsequent treatment. Approximately 3-9% of metastatic patients are diagnosed with cancer of unknown primary sites (CUP) even after a comprehensive diagnostic workup. However, a widely accepted molecular test is still not available. Here, we report a method that applies formalin-fixed, paraffin-embedded tissues to construct reduced representation bisulfite sequencing libraries (FFPE-RRBS). We then generate and systematically evaluate 28 molecular classifiers, built on four DNA methylation scoring methods and seven machine learning approaches, using the RRBS library dataset of 498 fresh-frozen tumor tissues from primary cancer patients. Among these classifiers, the beta value-based linear support vector (BELIVE) performs the best, achieving overall accuracies of 81-93% for identifying the primary sites in 215 metastatic patients using top-k predictions (k = 1, 2, 3). Coincidentally, BELIVE also successfully predicts the tissue of origin in 81-93% of CUP patients (n = 68).
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Affiliation(s)
- Shirong Zhang
- Translational Medicine Research Center, Hangzhou First People's Hospital, 310006, Hangzhou, Zhejiang Province, China
- Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Hangzhou First People's Hospital, 310006, Hangzhou, Zhejiang Province, China
| | - Shutao He
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 200031, Shanghai, China
- Institute of Biotechnology and Health, Beijing Academy of Science and Technology, 100089, Beijing, China
| | - Xin Zhu
- Key Laboratory of Head & Neck Cancer Translational Research of Zhejiang Province, Zhejiang Cancer Hospital, 310022, Hangzhou, Zhejiang Province, China
| | - Yunfei Wang
- Zhejiang ShengTing Biotech Co. Ltd, 310018, Hangzhou, Zhejiang Province, China
| | - Qionghuan Xie
- Zhejiang ShengTing Biotech Co. Ltd, 310018, Hangzhou, Zhejiang Province, China
| | - Xianrang Song
- Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, 250117, Jinan, Shandong Province, China
| | - Chunwei Xu
- Department of Respiratory Medicine, Jinling Hospital, Nanjing University School of Medicine, 210002, Nanjing, Jiangshu Province, China
| | - Wenxian Wang
- Key Laboratory of Head & Neck Cancer Translational Research of Zhejiang Province, Zhejiang Cancer Hospital, 310022, Hangzhou, Zhejiang Province, China
| | - Ligang Xing
- Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, 250117, Jinan, Shandong Province, China
| | - Chengqing Xia
- Zhejiang ShengTing Biotech Co. Ltd, 310018, Hangzhou, Zhejiang Province, China
| | - Qian Wang
- Department of Respiratory Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, 210029, Nanjing, Jiangshu Province, China
| | - Wenfeng Li
- Department of Medical Oncology, The First Affiliated Hospital of Wenzhou Medical University, 325000, Wenzhou, Zhejiang Province, China
| | - Xiaochen Zhang
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, 310006, Hangzhou, Zhejiang Province, China
| | - Jinming Yu
- Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, 250117, Jinan, Shandong Province, China
| | - Shenglin Ma
- Translational Medicine Research Center, Hangzhou First People's Hospital, 310006, Hangzhou, Zhejiang Province, China.
- Department of Oncology, Hangzhou Cancer Hospital, 310006, Hangzhou, Zhejiang Province, China.
| | - Jiantao Shi
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 200031, Shanghai, China.
| | - Hongcang Gu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, 230031, Hefei, Anhui Province, China.
- Hefei Cancer Hospital, Chinese Academy of Sciences, 230031, Hefei, Anhui Province, China.
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15
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Pisacane A, Cascardi E, Berrino E, Polidori A, Sarotto I, Casorzo L, Panero M, Boccaccio C, Verginelli F, Benvenuti S, Dellino M, Comoglio P, Montemurro F, Geuna E, Marchiò C, Sapino A. Real-world histopathological approach to malignancy of undefined primary origin (MUO) to diagnose cancers of unknown primary (CUPs). Virchows Arch 2023; 482:463-475. [PMID: 36346458 PMCID: PMC9640798 DOI: 10.1007/s00428-022-03435-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 10/10/2022] [Accepted: 10/15/2022] [Indexed: 11/10/2022]
Abstract
The aim of this study is to envisage a streamlined pathological workup to rule out CUPs in patients presenting with MUOs. Sixty-four MUOs were classified using standard histopathology. Clinical data, immunocytochemical markers, and results of molecular analysis were recorded. MUOs were histologically subdivided in clear-cut carcinomas (40 adenocarcinomas, 11 squamous, and 3 neuroendocrine carcinomas) and unclear-carcinoma features (5 undifferentiated and 5 sarcomatoid tumors). Cytohistology of 7/40 adenocarcinomas suggested an early metastatic cancer per se. In 33/40 adenocarcinomas, CK7/CK20 expression pattern, gender, and metastasis sites influenced tissue-specific marker selection. In 23/40 adenocarcinomas, a "putative-immunophenotype" of tissue of origin addressed clinical-diagnostic examinations, identifying 9 early metastatic cancers. Cell lineage markers were used to confirm squamous and neuroendocrine differentiation. Pan-cytokeratins were used to confirm the epithelial nature of poorly differentiated tumors, followed by tissue and cell lineage markers, which identified one melanoma. In total, 47/64 MUOs (73.4%) were confirmed CUP. Molecular analysis, feasible in 37/47 CUPs (78.7%), had no diagnostic impact. Twenty CUP patients, mainly with squamous carcinomas and adenocarcinomas with putative-gynecologic-immunophenotypes, presented with only lymph node metastases and had longer median time to progression and overall survival (< 0.001), compared with patients with other metastatic patterns. We propose a simplified histology-driven workup which could efficiently rule out CUPs and identify early metastatic cancer.
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Affiliation(s)
- Alberto Pisacane
- Candiolo Cancer Institute, FPO-IRCCS, 10060, Candiolo, Turin, Italy
| | - Eliano Cascardi
- Candiolo Cancer Institute, FPO-IRCCS, 10060, Candiolo, Turin, Italy.
- Department of Medical Sciences, University of Turin, 10100, Turin, Italy.
| | - Enrico Berrino
- Candiolo Cancer Institute, FPO-IRCCS, 10060, Candiolo, Turin, Italy
- Department of Medical Sciences, University of Turin, 10100, Turin, Italy
| | - Alessio Polidori
- Candiolo Cancer Institute, FPO-IRCCS, 10060, Candiolo, Turin, Italy
| | - Ivana Sarotto
- Candiolo Cancer Institute, FPO-IRCCS, 10060, Candiolo, Turin, Italy
| | - Laura Casorzo
- Candiolo Cancer Institute, FPO-IRCCS, 10060, Candiolo, Turin, Italy
| | - Mara Panero
- Candiolo Cancer Institute, FPO-IRCCS, 10060, Candiolo, Turin, Italy
| | - Carla Boccaccio
- Candiolo Cancer Institute, FPO-IRCCS, 10060, Candiolo, Turin, Italy
- Department of Oncology, University of Turin Medical School, 10060, Candiolo, Turin, Italy
| | | | - Silvia Benvenuti
- Candiolo Cancer Institute, FPO-IRCCS, 10060, Candiolo, Turin, Italy
| | - Miriam Dellino
- Department of Biomedical Sciences and Human Oncology, University of Bari "Aldo Moro", Bari, Italy
| | - Paolo Comoglio
- IFOM, FIRC Institute of Molecular Oncology, 20019, Milan, Italy
| | | | - Elena Geuna
- Candiolo Cancer Institute, FPO-IRCCS, 10060, Candiolo, Turin, Italy
| | - Caterina Marchiò
- Candiolo Cancer Institute, FPO-IRCCS, 10060, Candiolo, Turin, Italy
- Department of Medical Sciences, University of Turin, 10100, Turin, Italy
| | - Anna Sapino
- Candiolo Cancer Institute, FPO-IRCCS, 10060, Candiolo, Turin, Italy
- Department of Medical Sciences, University of Turin, 10100, Turin, Italy
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16
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Yu L, Lin J, Li H, Sun L, Wang S, Chen Y, Chen H, Lin L. Case Report: Clinical benefit from multi-target tyrosine kinase inhibitor and PARP inhibitor in a patient with cancer of unknown primary with BRCA1 large genomic rearrangement. Front Pharmacol 2023; 14:997760. [PMID: 36755949 PMCID: PMC9899799 DOI: 10.3389/fphar.2023.997760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 01/09/2023] [Indexed: 01/24/2023] Open
Abstract
Background: Cancer of unknown primary (CUP), which accounts for 3%-5% of new cancer cases every year, involves the presence of a type of histologically confirmed metastatic tumors whose primary site cannot be confirmed by conventional diagnostic methods. This difficulty in identifying the primary site means that CUP patients fail to receive precisely targeted therapy. Most patients are treated with empiric chemotherapy, with a median survival of 6 months and even poorer prognosis within an unfavorable subset of CUP. Case report: An 80-year-old woman presented with masses in the abdomen. Following comprehensive imagological and immunohistochemical examinations, she was diagnosed with CUP. She emphatically declined chemotherapy; thus, anlotinib has been administered with patient consent since 02/07/2019, and stable disease (SD) was observed for 2 years. During subsequent treatment, a large genomic rearrangement in BRCA1 was identified in the patient via NGS, and SD was observed for a further 6 months following olaparib treatment. The type of LGR identified in this patient was discovered to be BRCA1 exon 17-18 inversion (inv), which has never been previously reported. Conclusion: For CUP patients, a chemo-free regimen seems to be acceptable as a first-line treatment, and NGS-guided targeted treatment could improve patient outcomes.
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Affiliation(s)
- Ling Yu
- Department of Oncology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jietao Lin
- Department of Oncology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Hanhan Li
- Department of Oncology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Lingling Sun
- Department of Oncology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Shubo Wang
- The Medical Department, 3D Medicines Inc., Shanghai, China
| | - Yaoxu Chen
- The Medical Department, 3D Medicines Inc., Shanghai, China
| | - Hanrui Chen
- Department of Oncology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China,*Correspondence: Hanrui Chen, ; Lizhu Lin,
| | - Lizhu Lin
- Department of Oncology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China,*Correspondence: Hanrui Chen, ; Lizhu Lin,
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17
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Telekes A, Horváth A. The Role of Cell-Free DNA in Cancer Treatment Decision Making. Cancers (Basel) 2022; 14:6115. [PMID: 36551600 PMCID: PMC9776613 DOI: 10.3390/cancers14246115] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022] Open
Abstract
The aim of this review is to evaluate the present status of the use of cell-free DNA and its fraction of circulating tumor DNA (ctDNA) because this year July 2022, an ESMO guideline was published regarding the application of ctDNA in patient care. This review is for clinical oncologists to explain the concept, the terms used, the pros and cons of ctDNA; thus, the technical aspects of the different platforms are not reviewed in detail, but we try to help in navigating the current knowledge in liquid biopsy. Since the validated and adequately sensitive ctDNA assays have utility in identifying actionable mutations to direct targeted therapy, ctDNA may be used for this soon in routine clinical practice and in other different areas as well. The cfDNA fragments can be obtained by liquid biopsy and can be used for diagnosis, prognosis, and selecting among treatment options in cancer patients. A great proportion of cfDNA comes from normal cells of the body or from food uptake. Only a small part (<1%) of it is related to tumors, originating from primary tumors, metastatic sites, or circulating tumor cells (CTCs). Soon the data obtained from ctDNA may routinely be used for finding minimal residual disease, detecting relapse, and determining the sites of metastases. It might also be used for deciding appropriate therapy, and/or emerging resistance to the therapy and the data analysis of ctDNA may be combined with imaging or other markers. However, to achieve this goal, further clinical validations are inevitable. As a result, clinicians should be aware of the limitations of the assays. Of course, several open questions are still under research and because of it cfDNA and ctDNA testing are not part of routine care yet.
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Affiliation(s)
- András Telekes
- Omnimed-Etosz, Ltd., 81 Széher Rd., 1021 Budapest, Hungary
- Semmelweis University, 26. Üllői Rd., 1085 Budapest, Hungary
| | - Anna Horváth
- Department of Internal Medicine and Haematology, Semmelweis University, 46. Szentkirályi Rd., 1088 Budapest, Hungary
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18
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Blecua P, Davalos V, de Villasante I, Merkel A, Musulen E, Coll-SanMartin L, Esteller M. Refinement of computational identification of somatic copy number alterations using DNA methylation microarrays illustrated in cancers of unknown primary. Brief Bioinform 2022; 23:6582004. [PMID: 35524475 PMCID: PMC9487591 DOI: 10.1093/bib/bbac161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 03/30/2022] [Accepted: 04/10/2022] [Indexed: 11/14/2022] Open
Abstract
High-throughput genomic technologies are increasingly used in personalized cancer medicine. However, computational tools to maximize the use of scarce tissues combining distinct molecular layers are needed. Here we present a refined strategy, based on the R-package 'conumee', to better predict somatic copy number alterations (SCNA) from deoxyribonucleic acid (DNA) methylation arrays. Our approach, termed hereafter as 'conumee-KCN', improves SCNA prediction by incorporating tumor purity and dynamic thresholding. We trained our algorithm using paired DNA methylation and SNP Array 6.0 data from The Cancer Genome Atlas samples and confirmed its performance in cancer cell lines. Most importantly, the application of our approach in cancers of unknown primary identified amplified potentially actionable targets that were experimentally validated by Fluorescence in situ hybridization and immunostaining, reaching 100% specificity and 93.3% sensitivity.
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Affiliation(s)
- Pedro Blecua
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
| | - Veronica Davalos
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
| | - Izar de Villasante
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
| | - Angelika Merkel
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
| | - Eva Musulen
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain.,Department of Pathology, Hospital Universitari General de Catalunya-Grupo Quirónsalud, Sant Cugat del Vallès, Barcelona, Catalonia, Spain
| | - Laia Coll-SanMartin
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain.,Centro de Investigación Biomédica en Red de Cancer (CIBERONC), Madrid, Spain.,Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain.,Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Catalonia, Spain
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19
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Yulian ED, Hwei LRY, Tambun R, Siswoyo AD, Ham MF, Suroyo I. Comprehensive evaluation on cancer of unknown primary site and how we managed it: A case report. Int J Surg Case Rep 2022; 93:106954. [PMID: 35339815 PMCID: PMC8961183 DOI: 10.1016/j.ijscr.2022.106954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/13/2022] [Accepted: 03/13/2022] [Indexed: 11/30/2022] Open
Abstract
Introduction and importance Cancer of unknown primary site (CUP) is metastatic cancer without primary tumor found from comprehensive medical history, physical examination, and regular laboratory examination. Eighty percent of CUP include unfavorable groups with 3 to 6 months of median survival despite chemotherapy treatment. Case presentation A 52-year-old male was presented with a chief complaint of a recurrent lump in the neck and axilla. After comprehensive examinations over three years, the primary site of the metastatic tumor could not be found. Therefore, this patient was diagnosed with cancer of an unknown primary site. Clinical discussion In patient with CUP, more precise therapy can only begin when the exact form of cancer is identified. However, the delay in diagnosis would worsen the patient's condition, as treatment measures cannot be implemented. Conclusion Trimodal modalities including surgery, chemotherapy, and radiotherapy are suitable for CUP with squamous cell carcinoma proven in immunohistochemistry evaluation. Precise therapy for patients with CUP can only begin when the exact form of cancer is identified. Although PET/CT is suitable to assess the complete body state for CUP, other radiological and histopathology modalities are needed to confirm the diagnosis. Trimodal modalities including surgery, chemotherapy, and radiotherapy are required for CUP with squamous cell carcinoma.
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Affiliation(s)
- Erwin Danil Yulian
- Division of Surgical Oncology, Department of Surgery, Dr. Cipto Mangunkusumo General Hospital, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia.
| | - Lie Rebecca Yen Hwei
- Division of Surgical Oncology, Department of Surgery, Dr. Cipto Mangunkusumo General Hospital, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Renaningtyas Tambun
- Department of Anatomical Pathology, Sint Carolus Hospital, Jakarta, Indonesia
| | - Alvita Dewi Siswoyo
- Department of Radiology, Dr. Cipto Mangunkusumo General Hospital, Faculty of Medicine, Universitas Indonesia, Indonesia
| | - Maria Fransisca Ham
- Department of Anatomical Pathology, Dr. Cipto Mangunkusumo General Hospital, Faculty of Medicine, Universitas Indonesia, Indonesia
| | - Indrati Suroyo
- Department of Radiology, Dr. Cipto Mangunkusumo General Hospital, Faculty of Medicine, Universitas Indonesia, Indonesia
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20
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Jia X, Zhao S, Li X, Lv L, Chen X, Pan E, Ou Q, Song C, Sun S, Zhao J, Xu L, Li M. Favorable Response to Olaparib in a Patient with Cancer of Unknown Primary Carrying a Germline BRCA1 R71K Mutation. Onco Targets Ther 2021; 14:5353-5360. [PMID: 34866915 PMCID: PMC8636970 DOI: 10.2147/ott.s334847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 11/16/2021] [Indexed: 11/23/2022] Open
Abstract
The treatment options for cancer of unknown primary (CUP) are challenging due to the lack of knowledge about the primary sites, often resulting in a poor prognosis. The emerging next-generation sequencing (NGS) technique has provided a reliable approach to facilitate tumor primary site prediction and targetable gene alteration identification for CUP patients. In this report, we described a 63-year-old female patient who experienced recurrent CUP. NGS-based genetic profiling results revealed a pathogenic germline BRCA1 R71K mutation. Accordingly, the patient received the poly(adenosine diphosphate [ADP]-ribose) polymerase (PARP) inhibitor olaparib treatment and demonstrated a favorable response to this treatment. Our case suggests that NGS holds great promise for providing improved diagnosis and treatment options to patients with CUP, warranting further clinical investigation.
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Affiliation(s)
- Xiaomeng Jia
- Department of Oncology, The Second Hospital of Dalian Medical University, Dalian, 116023, People's Republic of China
| | - Shanshan Zhao
- Department of Oncology, The Second Hospital of Dalian Medical University, Dalian, 116023, People's Republic of China
| | - Xiang Li
- Department of Radiology, The Second Hospital of Dalian Medical University, Dalian, 116023, People's Republic of China
| | - Li Lv
- Department of Pathology, The Second Hospital of Dalian Medical University, Dalian, 116023, People's Republic of China
| | - Xin Chen
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, 210032, People's Republic of China
| | - Evenki Pan
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, 210032, People's Republic of China
| | - Qiuxiang Ou
- Geneseeq Research Institute, Nanjing Geneseeq Technology Inc., Nanjing, 210032, People's Republic of China
| | - Chen Song
- Department of Oncology, The Second Hospital of Dalian Medical University, Dalian, 116023, People's Republic of China
| | - Siwen Sun
- Department of Oncology, The Second Hospital of Dalian Medical University, Dalian, 116023, People's Republic of China
| | - Jinbo Zhao
- Department of Oncology, The Second Hospital of Dalian Medical University, Dalian, 116023, People's Republic of China
| | - Lingzhi Xu
- Department of Oncology, The Second Hospital of Dalian Medical University, Dalian, 116023, People's Republic of China
| | - Man Li
- Department of Oncology, The Second Hospital of Dalian Medical University, Dalian, 116023, People's Republic of China
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21
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Zhang Y, Xia L, Ma D, Wu J, Xu X, Xu Y. 90-Gene Expression Profiling for Tissue Origin Diagnosis of Cancer of Unknown Primary. Front Oncol 2021; 11:722808. [PMID: 34692498 PMCID: PMC8529103 DOI: 10.3389/fonc.2021.722808] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 09/21/2021] [Indexed: 11/13/2022] Open
Abstract
Cancer of unknown primary (CUP), in which metastatic diseases exist without an identifiable primary location, accounts for about 3-5% of all cancer diagnoses. Successful diagnosis and treatment of such patients are difficult. This study aimed to assess the expression characteristics of 90 genes as a method of identifying the primary site from CUP samples. We validated a 90-gene expression assay and explored its potential diagnostic utility in 44 patients at Jiangsu Cancer Hospital. For each specimen, the expression of 90 tumor-specific genes in malignant tumors was analyzed, and similarity scores were obtained. The types of malignant tumors predicted were compared with the reference diagnosis to calculate the accuracy. In addition, we verified the consistency of the expression profiles of the 90 genes in CUP secondary malignancies and metastatic malignancies in The Cancer Genome Atlas. We also reported a detailed description of the next-generation coding sequences for CUP patients. For each clinical medical specimen collected, the type of malignant tumor predicted and analyzed by the 90-gene expression assay was compared with its reference diagnosis, and the overall accuracy was 95.4%. In addition, the 90-gene expression profile generally accurately classified CUP into the cluster of its primary tumor. Sequencing of the exome transcriptome containing 556 high-frequency gene mutation oncogenes was not significantly related to the 90 genes analysis. Our results demonstrate that the expression characteristics of these 90 genes can be used as a powerful tool to accurately identify the primary sites of CUP. In the future, the inclusion of the 90-gene expression assay in pathological diagnosis will help oncologists use precise treatments, thereby improving the care and outcomes of CUP patients.
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Affiliation(s)
- Yi Zhang
- Department of Pathology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Lei Xia
- Department of Pathology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Dawei Ma
- Department of Pathology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Jing Wu
- Department of Radiation Oncology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Xinyu Xu
- Department of Pathology, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Youtao Xu
- Department of Thoracic Surgery, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
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22
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Yang J, Wang L, Yao Y, Liu J, Yang J. Small cell carcinoma of the brain without apparent extracranial origin in the same intracranial region one year following resection of malignant glioma. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2021; 14:875-880. [PMID: 34527130 PMCID: PMC8414428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 03/22/2021] [Indexed: 06/13/2023]
Abstract
Primary small cell carcinoma (SCC) of the brain is rare, and there have been no reports of small cell carcinoma located at the resection site of a glioma without extracranial tumours. Herein, we report a case of brain SCC in the same intracranial region from which a malignant glioma had been surgically resected a year prior. The patient, a 68-year-old male, had headaches as a symptom, and brain CT and MRI revealed a hyperdense region measuring 5.5×5 centimetres. Blood test results showed no significant changes. H&E staining suggested that these tumour cells had the characteristics of small cell lung carcinoma cells. Immunohistochemical staining for the glioma marker S100 was negative, but immunohistochemical staining for the neuroendocrine marker synaptophysin and for the cell adhesion molecule CD56 was strongly positive; meanwhile, staining for thyroid transcription factor-1 (TTF-1), a relatively specific marker of lung and thyroid carcinoma, was positive, and the Ki67 index was 75%. The pathological examination strongly suggested that the tumour was a small cell lung carcinoma, but CT and MRI scans indicated that there were no extracranial tumours. Hence, the tumour could be a primary small cell brain carcinoma. The patient underwent surgical resection again; the excised tumour was a mass of grey and white tissues with fragmentary morphology, and its dimensions were 3.0 cm×1.5 cm×0.8 cm.
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Affiliation(s)
- Jiaying Yang
- Department of Neurosurgery, Lanling People’s HospitalLanling 277700, Shandong, P. R. China
| | - Lei Wang
- Department of Otolaryngological, Lanling People’s HospitalLanling 277700, Shandong, P. R. China
| | - Yongjun Yao
- Department of Pathology, Lanling People’s HospitalLanling 277700, Shandong, P. R. China
| | - Jie Liu
- Department of Neurosurgery, Lanling People’s HospitalLanling 277700, Shandong, P. R. China
| | - Jinju Yang
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of SciencesBeijing 100190, P. R. China
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23
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Laprovitera N, Salamon I, Gelsomino F, Porcellini E, Riefolo M, Garonzi M, Tononi P, Valente S, Sabbioni S, Fontana F, Manaresi N, D’Errico A, Pantaleo MA, Ardizzoni A, Ferracin M. Genetic Characterization of Cancer of Unknown Primary Using Liquid Biopsy Approaches. Front Cell Dev Biol 2021; 9:666156. [PMID: 34178989 PMCID: PMC8222689 DOI: 10.3389/fcell.2021.666156] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 05/03/2021] [Indexed: 12/15/2022] Open
Abstract
Cancers of unknown primary (CUPs) comprise a heterogeneous group of rare metastatic tumors whose primary site cannot be identified after extensive clinical-pathological investigations. CUP patients are generally treated with empirical chemotherapy and have dismal prognosis. As recently reported, CUP genome presents potentially druggable alterations for which targeted therapies could be proposed. The paucity of tumor tissue, as well as the difficult DNA testing and the lack of dedicated panels for target gene sequencing are further relevant limitations. Here, we propose that circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) could be used to identify actionable mutations in CUP patients. Blood was longitudinally collected from two CUP patients. CTCs were isolated with CELLSEARCH® and DEPArrayTM NxT and Parsortix systems, immunophenotypically characterized and used for single-cell genomic characterization with Ampli1TM kits. Circulating cell-free DNA (ccfDNA), purified from plasma at different time points, was tested for tumor mutations with a CUP-dedicated, 92-gene custom panel using SureSelect Target Enrichment technology. In parallel, FFPE tumor tissue was analyzed with three different assays: FoundationOne CDx assay, DEPArray LibPrep and OncoSeek Panel, and the SureSelect custom panel. These approaches identified the same mutations, when the gene was covered by the panel, with the exception of an insertion in APC gene. which was detected by OncoSeek and SureSelect panels but not FoundationOne. FGFR2 and CCNE1 gene amplifications were detected in single CTCs, tumor tissue, and ccfDNAs in one patient. A somatic variant in ARID1A gene (p.R1276∗) was detected in the tumor tissue and ccfDNAs. The alterations were validated by Droplet Digital PCR in all ccfDNA samples collected during tumor evolution. CTCs from a second patient presented a pattern of recurrent amplifications in ASPM and SEPT9 genes and loss of FANCC. The 92-gene custom panel identified 16 non-synonymous somatic alterations in ccfDNA, including a deletion (I1485Rfs∗19) and a somatic mutation (p. A1487V) in ARID1A gene and a point mutation in FGFR2 gene (p.G384R). Our results support the feasibility of non-invasive liquid biopsy testing in CUP cases, either using ctDNA or CTCs, to identify CUP genetic alterations with broad NGS panels covering the most frequently mutated genes.
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Affiliation(s)
- Noemi Laprovitera
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
- Department of Life Sciences and Biotechnologies, University of Ferrara, Ferrara, Italy
| | - Irene Salamon
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
- Center for Applied Biomedical Research (CRBA), University of Bologna, Italy
| | - Francesco Gelsomino
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
- Divisione di Oncologia Medica, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Elisa Porcellini
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Mattia Riefolo
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
- Pathology Unit, Sant’Orsola Hospital, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | | | - Paola Tononi
- Menarini Silicon Biosystems S.p.A, Bologna, Italy
| | - Sabrina Valente
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Silvia Sabbioni
- Center for Applied Biomedical Research (CRBA), University of Bologna, Italy
| | | | | | - Antonia D’Errico
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
- Pathology Unit, Sant’Orsola Hospital, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Maria A. Pantaleo
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
- Divisione di Oncologia Medica, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Andrea Ardizzoni
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
- Divisione di Oncologia Medica, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Manuela Ferracin
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
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24
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Laprovitera N, Riefolo M, Porcellini E, Durante G, Garajova I, Vasuri F, Aigelsreiter A, Dandachi N, Benvenuto G, Agostinis F, Sabbioni S, Berindan Neagoe I, Romualdi C, Ardizzoni A, Trerè D, Pichler M, D'Errico A, Ferracin M. MicroRNA expression profiling with a droplet digital PCR assay enables molecular diagnosis and prognosis of cancers of unknown primary. Mol Oncol 2021; 15:2732-2751. [PMID: 34075699 PMCID: PMC8486570 DOI: 10.1002/1878-0261.13026] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 04/30/2021] [Accepted: 05/28/2021] [Indexed: 12/16/2022] Open
Abstract
Metastasis is responsible for the majority of cancer‐related deaths. Particularly, challenging is the management of metastatic cancer of unknown primary site (CUP), whose tissue of origin (TOO) remains undetermined even after extensive investigations and whose therapy is rather unspecific and poorly effective. Molecular approaches to identify the most probable TOO of CUPs can overcome some of these issues. In this study, we applied a predetermined set of 89 microRNAs (miRNAs) to infer the TOO of 53 metastatic cancers of unknown or uncertain origin. The miRNA expression was assessed with droplet digital PCR in 159 samples, including primary tumors from 17 tumor classes (reference set) and metastases of known and unknown origin (test set). We combined two different statistical models for class prediction to obtain the most probable TOOs: the nearest shrunken centroids approach of Prediction Analysis of Microarrays (PAMR) and the least absolute shrinkage and selection operator (LASSO) models. The molecular test was successful for all formalin‐fixed paraffin‐embedded samples and provided a TOO identification within 1 week from the biopsy procedure. The most frequently predicted origins were gastrointestinal, pancreas, breast, lung, and bile duct. The assay was applied also to multiple metastases from the same CUP, collected from different metastatic sites: The predictions showed a strong agreement, intrinsically validating our assay. The final CUPs' TOO prediction was compared with the clinicopathological hypothesis of primary site. Moreover, a panel of 13 miRNAs proved to have prognostic value and be associated with overall survival in CUP patients. Our study demonstrated that miRNA expression profiling in CUP samples could be employed as diagnostic and prognostic test. Our molecular analysis can be performed on request, concomitantly with standard diagnostic workup and in association with genetic profiling, to offer valuable indications about the possible primary site, thereby supporting treatment decisions.
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Affiliation(s)
- Noemi Laprovitera
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Italy.,Department of Life Sciences and Biotechnologies, University of Ferrara, Italy
| | - Mattia Riefolo
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Italy.,Pathology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Italy
| | - Elisa Porcellini
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Italy
| | - Giorgio Durante
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Italy
| | | | - Francesco Vasuri
- Pathology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Italy
| | - Ariane Aigelsreiter
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Austria
| | - Nadia Dandachi
- Division of Oncology, Medical University of Graz, Austria
| | | | | | - Silvia Sabbioni
- Department of Life Sciences and Biotechnologies, University of Ferrara, Italy
| | - Ioana Berindan Neagoe
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | | | - Andrea Ardizzoni
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Italy.,Division of Medical Oncology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Italy
| | - Davide Trerè
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Italy
| | - Martin Pichler
- Division of Oncology, Medical University of Graz, Austria
| | - Antonietta D'Errico
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Italy.,Pathology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Italy
| | - Manuela Ferracin
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Italy
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25
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Koval AP, Blagodatskikh KA, Kushlinskii NE, Shcherbo DS. The Detection of Cancer Epigenetic Traces in Cell-Free DNA. Front Oncol 2021; 11:662094. [PMID: 33996585 PMCID: PMC8118693 DOI: 10.3389/fonc.2021.662094] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 04/12/2021] [Indexed: 12/23/2022] Open
Abstract
Nucleic acid fragments found in blood circulation originate mostly from dying cells and carry signs pointing to specific features of the parental cell types. Deciphering these clues may be transformative for numerous research and clinical applications but strongly depends on the development and implementation of robust analytical methods. Remarkable progress has been achieved in the reliable detection of sequence alterations in cell-free DNA while decoding epigenetic information from methylation and fragmentation patterns requires more sophisticated approaches. This review discusses the currently available strategies for detecting and analyzing the epigenetic marks in the liquid biopsies.
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Affiliation(s)
- Anastasia P Koval
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Konstantin A Blagodatskikh
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Nikolay E Kushlinskii
- Laboratory of Clinical Biochemistry, N.N. Blokhin Cancer Research Medical Center of Oncology, Moscow, Russia
| | - Dmitry S Shcherbo
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
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