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Qi P, Sun Y, Pang Y, Liu J, Cai X, Huang S, Xu Q, Wang Q, Zhou X. Diagnostic Utility of a 90-Gene Expression Assay (Canhelp-Origin) for Patients with Metastatic Cancer with an Unclear or Unknown Diagnosis. Mol Diagn Ther 2024:10.1007/s40291-024-00746-6. [PMID: 39333459 DOI: 10.1007/s40291-024-00746-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2024] [Indexed: 09/29/2024]
Abstract
BACKGROUND Metastatic cancers with unclear or unknown origins pose significant challenges in diagnosis and management, frequently leading to suboptimal outcomes. Studies have demonstrated that a 90-gene expression assay is effective in predicting the primary origin and guiding the site-specific therapy to improve prognosis. This study aimed to evaluate the clinical effectiveness of a 90-gene expression assay in patients with unclear or unknown diagnoses. METHODS The study encompassed patients for whom a 90-gene expression assay was requested as part of standard care. Data on patient demographics, tumor characteristics, and clinical history were collected. The assay's performance was evaluated by comparing its predicted tumor type with the final histopathological diagnosis. RESULTS Among 303 cases analyzed, a 90-gene expression assay successfully identified a molecular-based tumor type for 295 (97.4%) patients. Comparison with histopathological diagnosis revealed an overall agreement of 88.5% (170/192). In patients with a single suspected primary site (n = 140), the assay confirmed the suspected diagnosis in 90.7% of cases. For those with a differential diagnosis (n = 52), the assay narrowed down the possibilities in 82.7% of cases. Moreover, in cases where the histopathology report indicated cancer of unknown primary (n = 103), the assay offered a molecular tumor type prediction with potential clinical significance. CONCLUSIONS This study demonstrates the significant impact of a 90-gene expression assay on diagnosis and potential treatment selection for difficult-to-diagnose patients, highlighting its clinical value as a standardized molecular approach to streamline further diagnostic testing for patients with metastatic cancer of unclear or unknown origin. Further prospective study is required to assess whether employing molecular diagnostic classifiers enhances clinical outcomes in these patients.
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Affiliation(s)
- Peng Qi
- Department of Pathology, Fudan University Shanghai Cancer Center, Fudan University, No. 270 Dongan Road, Shanghai, 200032, People's Republic of China
- Department of Oncology, Shanghai Medical College, Fudan University, No. 270 Dongan Road, Shanghai, 200032, People's Republic of China
| | - Yifeng Sun
- Department of Oncology, Shanghai Medical College, Fudan University, No. 270 Dongan Road, Shanghai, 200032, People's Republic of China
- Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, People's Republic of China
- Canhelp Genomics Research Center, Canhelp Genomics Co., Ltd., No.22 Xinyan Road, Hangzhou, 310000, People's Republic of China
| | - Yue Pang
- Department of Pathology, Fudan University Shanghai Cancer Center, Fudan University, No. 270 Dongan Road, Shanghai, 200032, People's Republic of China
- Department of Oncology, Shanghai Medical College, Fudan University, No. 270 Dongan Road, Shanghai, 200032, People's Republic of China
| | - Jing Liu
- Department of Pathology, Fudan University Shanghai Cancer Center, Fudan University, No. 270 Dongan Road, Shanghai, 200032, People's Republic of China
- Department of Oncology, Shanghai Medical College, Fudan University, No. 270 Dongan Road, Shanghai, 200032, People's Republic of China
| | - Xu Cai
- Department of Pathology, Fudan University Shanghai Cancer Center, Fudan University, No. 270 Dongan Road, Shanghai, 200032, People's Republic of China
- Department of Oncology, Shanghai Medical College, Fudan University, No. 270 Dongan Road, Shanghai, 200032, People's Republic of China
| | - Shenglin Huang
- Department of Oncology, Shanghai Medical College, Fudan University, No. 270 Dongan Road, Shanghai, 200032, People's Republic of China
- Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, People's Republic of China
| | - Qinghua Xu
- Canhelp Genomics Research Center, Canhelp Genomics Co., Ltd., No.22 Xinyan Road, Hangzhou, 310000, People's Republic of China.
| | - Qifeng Wang
- Department of Pathology, Fudan University Shanghai Cancer Center, Fudan University, No. 270 Dongan Road, Shanghai, 200032, People's Republic of China.
- Department of Oncology, Shanghai Medical College, Fudan University, No. 270 Dongan Road, Shanghai, 200032, People's Republic of China.
| | - Xiaoyan Zhou
- Department of Pathology, Fudan University Shanghai Cancer Center, Fudan University, No. 270 Dongan Road, Shanghai, 200032, People's Republic of China.
- Department of Oncology, Shanghai Medical College, Fudan University, No. 270 Dongan Road, Shanghai, 200032, People's Republic of China.
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Liu X, Zhang X, Jiang S, Mo M, Wang Q, Wang Y, Zhou L, Hu S, Yang H, Hou Y, Chen Y, Lu X, Wang Y, Zhou X, Li W, Chang C, Yang X, Chen K, Cao J, Xu Q, Sun Y, Luo J, Luo Z, Hu X. Site-specific therapy guided by a 90-gene expression assay versus empirical chemotherapy in patients with cancer of unknown primary (Fudan CUP-001): a randomised controlled trial. Lancet Oncol 2024; 25:1092-1102. [PMID: 39068945 DOI: 10.1016/s1470-2045(24)00313-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 05/20/2024] [Accepted: 05/22/2024] [Indexed: 07/30/2024]
Abstract
BACKGROUND Empirical chemotherapy remains the standard of care in patients with unfavourable cancer of unknown primary (CUP). Gene-expression profiling assays have been developed to identify the tissue of origin in patients with CUP; however, their clinical benefit has not yet been demonstrated. We aimed to evaluate the efficacy and safety of site-specific therapy directed by a 90-gene expression assay compared with empirical chemotherapy in patients with CUP. METHODS This randomised controlled trial was conducted at Fudan University Shanghai Cancer Center (Shanghai, China). We enrolled patients aged 18-75 years, with previously untreated CUP (histologically confirmed metastatic adenocarcinoma, squamous cell carcinoma, poorly differentiated carcinoma, or poorly differentiated neoplasms) and an Eastern Cooperative Oncology Group (ECOG) performance status of 0-2, who were not amenable to local radical treatment. Patients were randomly assigned (1:1) by the Pocock and Simon minimisation method to receive either site-specific therapy or empirical chemotherapy (taxane [175 mg/m2 by intravenous infusion on day 1] plus platinum [cisplatin 75 mg/m2 or carboplatin area under the curve 5 by intravenous infusion on day 1], or gemcitabine [1000 mg/m2 by intravenous infusion on days 1 and 8] plus platinum [same as above]). The minimisation factors were ECOG performance status and the extent of the disease. Clinicians and patients were not masked to interventions. The tumour origin in the site-specific therapy group was predicted by the 90-gene expression assay and treatments were administered accordingly. The primary endpoint was progression-free survival in the intention-to-treat population. The trial has been completed and the analysis is final. This study is registered with ClinicalTrials.gov (NCT03278600). FINDINGS Between Sept 18, 2017, and March 18, 2021, 182 patients (105 [58%] male, 77 [42%] female) were randomly assigned to receive site-specific therapy (n=91) or empirical chemotherapy (n=91). The five most commonly predicted tissues of origin in the site-specific therapy group were gastro-oesophagus (14 [15%]), lung (12 [13%]), ovary (11 [12%]), cervix (11 [12%]), and breast (nine [10%]). At the data cutoff date (April 30, 2023), median follow-up was 33·3 months (IQR 30·4-51·0) for the site-specific therapy group and 30·9 months (27·6-35·5) for the empirical chemotherapy group. Median progression-free survival was significantly longer with site-specific therapy than with empirical chemotherapy (9·6 months [95% CI 8·4-11·9] vs 6·6 months [5·5-7·9]; unadjusted hazard ratio 0·68 [95% CI 0·49-0·93]; p=0·017). Among the 167 patients who started planned treatment, 46 (56%) of 82 patients in the site-specific therapy group and 52 (61%) of 85 patients in the empirical chemotherapy group had grade 3 or worse treatment-related adverse events; the most frequent of these in the site-specific therapy and empirical chemotherapy groups were decreased neutrophil count (36 [44%] vs 42 [49%]), decreased white blood cell count (17 [21%] vs 26 [31%]), and anaemia (ten [12%] vs nine [11%]). Treatment-related serious adverse events were reported in five (6%) patients in the site-specific therapy group and two (2%) in the empirical chemotherapy group. No treatment-related deaths were observed. INTERPRETATION This single-centre randomised trial showed that site-specific therapy guided by the 90-gene expression assay could improve progression-free survival compared with empirical chemotherapy among patients with previously untreated CUP. Site-specific prediction by the 90-gene expression assay might provide more disease information and expand the therapeutic armamentarium in these patients. FUNDING Clinical Research Plan of Shanghai Hospital Development Center, Program for Shanghai Outstanding Academic Leader, and Shanghai Anticancer Association SOAR PROJECT. TRANSLATION For the Chinese translation of the abstract see Supplementary Materials section.
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Affiliation(s)
- Xin Liu
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiaowei Zhang
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Shiyu Jiang
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Miao Mo
- Department of Cancer Prevention, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Qifeng Wang
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yanli Wang
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Liangping Zhou
- Department of Radiology, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Silong Hu
- Department of Nuclear Medicine, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Huijuan Yang
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yifeng Hou
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yong Chen
- Department of Musculoskeletal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xueguan Lu
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yu Wang
- Department of Head & Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiaoyan Zhou
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wentao Li
- Department of Interventional Radiology, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Cai Chang
- Department of Ultrasound, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiujiang Yang
- Department of Endoscopy, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ke Chen
- Department of Endoscopy, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jun Cao
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Qinghua Xu
- The Canhelp Genomics Research Center, Canhelp Genomics, Hangzhou, China
| | - Yifeng Sun
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China; The Canhelp Genomics Research Center, Canhelp Genomics, Hangzhou, China; Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Jianfeng Luo
- Department of Biostatistics, School of Public Health, Fudan University, Shanghai, China
| | - Zhiguo Luo
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Xichun Hu
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
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Ma W, Wu H, Chen Y, Xu H, Jiang J, Du B, Wan M, Ma X, Chen X, Lin L, Su X, Bao X, Shen Y, Xu N, Ruan J, Jiang H, Ding Y. New techniques to identify the tissue of origin for cancer of unknown primary in the era of precision medicine: progress and challenges. Brief Bioinform 2024; 25:bbae028. [PMID: 38343328 PMCID: PMC10859692 DOI: 10.1093/bib/bbae028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 12/10/2023] [Accepted: 01/11/2024] [Indexed: 02/15/2024] Open
Abstract
Despite a standardized diagnostic examination, cancer of unknown primary (CUP) is a rare metastatic malignancy with an unidentified tissue of origin (TOO). Patients diagnosed with CUP are typically treated with empiric chemotherapy, although their prognosis is worse than those with metastatic cancer of a known origin. TOO identification of CUP has been employed in precision medicine, and subsequent site-specific therapy is clinically helpful. For example, molecular profiling, including genomic profiling, gene expression profiling, epigenetics and proteins, has facilitated TOO identification. Moreover, machine learning has improved identification accuracy, and non-invasive methods, such as liquid biopsy and image omics, are gaining momentum. However, the heterogeneity in prediction accuracy, sample requirements and technical fundamentals among the various techniques is noteworthy. Accordingly, we systematically reviewed the development and limitations of novel TOO identification methods, compared their pros and cons and assessed their potential clinical usefulness. Our study may help patients shift from empirical to customized care and improve their prognoses.
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Affiliation(s)
- Wenyuan Ma
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hui Wu
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yiran Chen
- Department of Surgical Oncology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Hongxia Xu
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Haining, China
| | - Junjie Jiang
- Department of Gastroenterology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Bang Du
- Real Doctor AI Research Centre, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Mingyu Wan
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaolu Ma
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaoyu Chen
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lili Lin
- Department of Nuclear Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xinhui Su
- Department of Nuclear Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xuanwen Bao
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yifei Shen
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Nong Xu
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jian Ruan
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Haiping Jiang
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yongfeng Ding
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Cao F, Sun H, Yang Z, Bai Y, Hu X, Hou Y, Bian X, Liu Y. Multiple approaches revealed MGc80-3 as a somatic hybrid with HeLa cells rather than a gastric cancer cell line. Int J Cancer 2024; 154:155-168. [PMID: 37543987 DOI: 10.1002/ijc.34677] [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: 02/11/2023] [Revised: 07/11/2023] [Accepted: 07/12/2023] [Indexed: 08/08/2023]
Abstract
The short-tandem-repeats (STR) profiles of MGc80-3 and HeLa partially overlap, raising suspicion of contamination in the MGc80-3 cell line. However, there has not been any relevant study demonstrating whether MGc80-3 was fully replaced by HeLa cells, just mixed with HeLa cells (co-existing), or was a somatic hybrid with HeLa cells. In addition to STR profiling, various approaches, including single nucleotide polymorphisms genotyping, polymerase chain reaction, screening for human papillomaviruses type 18 (HPV-18) fragment, chromosome karyotyping, pathological examination of xenografts, tissue-specific-90-gene expression signature and high-throughput RNA sequencing were used to determine the nature of MGc80-3. Our study found that the abnormal STR profile, partially overlapping with that of HeLa cells (64.62% to 71.64%), could not verify MGc80-3 as a HeLa cell line. However, the STR 13.3 repeat allele in the D13S317 locus that seemed to be unique to HeLa cells was detected in MGc80-3. Almost all the MGc80-3 cells exhibited HPV-18 fragments in the genome as well as certain HeLa marker chromosomes, such as M7 and M12. The molecular assay of the 90-gene expression signature still considered MGc80-3 as a stomach cancer using an algorithmic analysis. The expression pattern of multiple genes in MGc80-3 was quite different from that in HeLa cells, which showed that certain characteristics belonged to gastric cancer cell lines. High throughput RNA sequencing showed the distinct patterns of gene expression in MGc80-3. In conclusion, MGc80-3 cell line is a somatic hybrid with HeLa cells rather than a pure gastric cancer cell line.
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Affiliation(s)
- Fang Cao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pathology, Peking University Cancer Hospital &Institute, Beijing, China
| | - Hao Sun
- Department of Pathology, Cell Resource Center, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Zhenli Yang
- Department of Pathology, Cell Resource Center, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Yanhua Bai
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pathology, Peking University Cancer Hospital &Institute, Beijing, China
| | - Xiao Hu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pathology, Peking University Cancer Hospital &Institute, Beijing, China
| | - Yuhong Hou
- Department of Pathology, Cell Resource Center, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Xiaocui Bian
- Department of Pathology, Cell Resource Center, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Yuqin Liu
- Department of Pathology, Cell Resource Center, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing, China
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Ren M, Cai X, Jia L, Bai Q, Zhu X, Hu X, Wang Q, Luo Z, Zhou X. Comprehensive analysis of cancer of unknown primary and recommendation of a histological and immunohistochemical diagnostic strategy from China. BMC Cancer 2023; 23:1175. [PMID: 38041048 PMCID: PMC10691136 DOI: 10.1186/s12885-023-11563-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 10/24/2023] [Indexed: 12/03/2023] Open
Abstract
BACKGROUND Previous studies on cancer of unknown primary (CUP) mainly focus on treatment and prognosis in western populations and lacked clinical evaluation of different IHC markers, so this study aimed to evaluate characteristics of CUP and recommend a diagnostic strategy from a single center in China. METHODS AND RESULTS Data of 625 patients with CUP were retrospectively collected and reviewed. The patients ranged in age from 20 to 91 years, with a female-to-male ratio of 1.3:1. The predominant histological type was poor or undifferentiated adenocarcinomas (308; 49.3%). The results of Canhelp-Origin molecular testing for the identification of the tissue of origin in 262 of 369 patients (71.0%) were considered predictable (similarity score > 45), with the most common predicted primary tumor site being the breast (57, 21.8%). Unpredictable molecular results correlated with more aggressive clinical parameters and poor survival. Thee positivity rates of several targeted antibodies (GATA3, GCDFP15, TTF1, Napsin A, and PAX8), based on the clinically predicted site, were lower than those reported for the corresponding primary tumors. Nonetheless, TRPS1 and INSM1 were reliable markers of predicted breast carcinoma (75.0%) and neuroendocrine tumors (83.3%), respectively. P16 expression, as well as HPV and EBER testing contributed significantly to the diagnosis of squamous cell carcinomas. Survival analysis revealed that older ages (> 57), ≥ 3 metastatic sites, non-squamous cell carcinomas, bone/liver/lung metastases, unpredictable molecular results, and palliative treatment correlated with poor overall survival. CONCLUSIONS We recommend a CUP diagnostic strategy involving the use of targeted antibody panels as per histological findings that is potentially applicable in clinical practice. The markers TRPS1, INSM1, and P16 expression, as well as HPV and EBER testing are particularly valuable in this aspect. Molecular testing is also predictive of survival rates.
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Affiliation(s)
- Min Ren
- Department of Pathology, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
- Institute of Pathology, Fudan University, Shanghai, 200032, China
| | - Xu Cai
- Department of Pathology, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
- Institute of Pathology, Fudan University, Shanghai, 200032, China
| | - Liqing Jia
- Department of Pathology, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
- Institute of Pathology, Fudan University, Shanghai, 200032, China
| | - Qianming Bai
- Department of Pathology, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
- Institute of Pathology, Fudan University, Shanghai, 200032, China
| | - Xiaoli Zhu
- Department of Pathology, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
- Institute of Pathology, Fudan University, Shanghai, 200032, China
| | - Xichun Hu
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | - Qifeng Wang
- Department of Pathology, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, 200032, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
- Institute of Pathology, Fudan University, Shanghai, 200032, China.
| | - Zhiguo Luo
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.
| | - Xiaoyan Zhou
- Department of Pathology, Fudan University Shanghai Cancer Center, 270 Dong'an Road, Shanghai, 200032, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
- Institute of Pathology, Fudan University, Shanghai, 200032, China.
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Weiss L, Heinrich K, Zhang D, Dorman K, Rühlmann K, Hasselmann K, Klauschen F, Kumbrink J, Jung A, Rudelius M, Mock A, Ormanns S, Kunz WG, Roessler D, Beyer G, Corradini S, Heinzerling L, Haas M, von Bergwelt-Baildon M, Boeck S, Heinemann V, Westphalen CB. Cancer of unknown primary (CUP) through the lens of precision oncology: a single institution perspective. J Cancer Res Clin Oncol 2023:10.1007/s00432-023-04741-y. [PMID: 37062035 PMCID: PMC10374717 DOI: 10.1007/s00432-023-04741-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 04/02/2023] [Indexed: 04/17/2023]
Abstract
PURPOSE For patients with cancer of unknown primary (CUP), treatment options are limited. Precision oncology, the interplay of comprehensive genomic profiling (CGP) and targeted therapies, aims to offer additional treatment options to patients with advanced and hard-to-treat cancers. We aimed to highlight the use of a molecular tumor board (MTB) in the therapeutic management of CUP patients. METHODS In this single-center observational study, CUP patients, presented to the MTB of the Comprehensive Cancer Center Munich LMU, a tertiary care center, were analyzed retrospectively. Descriptive statistics were applied to describe relevant findings. RESULTS Between June 2016 and February 2022, 61 patients with unfavorable CUP were presented to the MTB, detected clinically relevant variants in 74% (45/61) of patients, of which 64% (29/45) led to therapeutic recommendation. In four out of 29 patients (14%), the treatment recommendations were implemented, unfortunately without resulting in clinical benefit. Reasons for not following the therapeutic recommendation were mainly caused by the physicians' choice of another therapy (9/25, 36%), especially in the context of worsening of general condition, lost to follow-up (7/25, 28%) and death (6/25, 24%). CONCLUSION CGP and subsequent presentation to a molecular tumor board led to a high rate of therapeutic recommendations in patients with CUP. Recommendations were only implemented at a low rate; however, late GCP diagnostic and, respectively, MTB referral were found more frequent for the patients with implemented treatment. This contrast underscores the need for early implementation of CGP into the management of CUP patients.
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Affiliation(s)
- L Weiss
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
- Comprehensive Cancer Center Munich, University Hospital, LMU Munich, Munich, Germany
- Bavarian Cancer Research Center (BZKF), Munich, Germany
| | - K Heinrich
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | - D Zhang
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
| | - K Dorman
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
| | - K Rühlmann
- Comprehensive Cancer Center Munich, University Hospital, LMU Munich, Munich, Germany
| | - K Hasselmann
- Comprehensive Cancer Center Munich, University Hospital, LMU Munich, Munich, Germany
| | - F Klauschen
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
- Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - J Kumbrink
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
- Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - A Jung
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
- Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - M Rudelius
- Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - A Mock
- Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Steffen Ormanns
- Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - W G Kunz
- Department of Radiology, University Hospital, LMU Munich, Munich, Germany
| | - D Roessler
- Department of Medicine II, University Hospital, LMU Munich, Munich, Germany
- Bavarian Cancer Research Center (BZKF), Munich, Germany
| | - G Beyer
- Department of Medicine II, University Hospital, LMU Munich, Munich, Germany
- Bavarian Cancer Research Center (BZKF), Munich, Germany
| | - S Corradini
- Department of Radiation Oncology, University Hospital, LMU Munich, Munich, Germany
| | - L Heinzerling
- Department of Dermatology, University Hospital, LMU Munich, Munich, Germany
- Department of Dermatology, University Hospital Erlangen, Erlangen, Germany
| | - M Haas
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | - M von Bergwelt-Baildon
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
| | - S Boeck
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
- Comprehensive Cancer Center Munich, University Hospital, LMU Munich, Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
| | - V Heinemann
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
- Comprehensive Cancer Center Munich, University Hospital, LMU Munich, Munich, Germany
| | - C B Westphalen
- Department of Medicine III, University Hospital, LMU Munich, Munich, Germany.
- Comprehensive Cancer Center Munich, University Hospital, LMU Munich, Munich, Germany.
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany.
- Bavarian Cancer Research Center (BZKF), Munich, Germany.
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7
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Sheng J, Pan H, Han W. Immunochemotherapy achieved a complete response for metastatic adenocarcinoma of unknown primary based on gene expression profiling: a case report and review of the literature. Front Immunol 2023; 14:1181444. [PMID: 37153561 PMCID: PMC10154565 DOI: 10.3389/fimmu.2023.1181444] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 04/04/2023] [Indexed: 05/09/2023] Open
Abstract
Background Cancer of unknown primary (CUP) is a malignant and aggressive tumor whose primary origin is still unknown despite thorough evaluation. CUP can be life-threatening with a median overall survival of less than 1 year based on empirical chemotherapy. Gene detection technology advances the driver gene detection of malignant tumors and the appropriate precise therapy. Immunotherapy has ushered in a new era in cancer therapy, changing the way advanced tumors, including CUP, are treated. Combined with comprehensive clinical and pathological investigations, molecular analysis of the original tissue and detection of potential driver mutations may provide therapeutic recommendations for CUP. Case presentation A 52-year-old female was admitted to hospital for dull abdominal pain, with peripancreatic lesions below the caudate lobe of the liver and posterior peritoneal lymph nodes enlargement. Conventional biopsy under endoscopic ultrasonography and laparoscopic biopsy both revealed poorly differentiated adenocarcinoma based on immunohistochemical series. To help identify tumor origin and molecular characteristics, 90-gene expression assay, tumor gene expression profiling with Next-generation sequencing (NGS) method and Immunohistochemical expression of PD-L1 were employed. Although no gastroesophageal lesions discovered by gastroenteroscopy, the 90-gene expression assay yielded a similarity score and prompted the most likely primary site was gastric/esophagus cancer. NGS revealed high TMB (19.3mutations/Mb) but no druggable driver genes identified. The Dako PD-L1 22C3 assay IHC assay for PD-L1 expression revealed a tumor proportion score (TPS) of 35%. Given the presence of negative predictive biomarkers for immunotherapy, including adenomatous polyposis coli (APC) c.646C>T mutation at exon 7 and Janus kinase 1(JAK1), the patient received immunochemotherapy instead of immunotherapy alone. She was successfully treated with nivolumab plus carboplatin and albumin-bound nanoparticle paclitaxel for six cycles and nivolumab maintenance, which achieved a complete response (CR) maintained for 2 years without severe adverse events. Conclusions This case highlights the value of multidisciplinary diagnosis and individual precision treatment in CUP. Further investigation is needed as an individualized treatment approach combining immunotherapy and chemotherapy based on tumor molecular characteristics and immunotherapy predictors is expected to improve the outcome of CUP therapy.
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Affiliation(s)
- Jin Sheng
- Department of Medical Oncology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Biotherapy of Zhejiang Province, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Hongming Pan
- Department of Medical Oncology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Biotherapy of Zhejiang Province, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Weidong Han
- Department of Medical Oncology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Biotherapy of Zhejiang Province, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- *Correspondence: Weidong Han,
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8
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Lu J, Li J, Ren J, Ding S, Zeng Z, Huang T, Cai YD. Functional and embedding feature analysis for pan-cancer classification. Front Oncol 2022; 12:979336. [PMID: 36248961 PMCID: PMC9559388 DOI: 10.3389/fonc.2022.979336] [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: 06/27/2022] [Accepted: 09/14/2022] [Indexed: 11/13/2022] Open
Abstract
With the increasing number of people suffering from cancer, this illness has become a major health problem worldwide. Exploring the biological functions and signaling pathways of carcinogenesis is essential for cancer detection and research. In this study, a mutation dataset for eleven cancer types was first obtained from a web-based resource called cBioPortal for Cancer Genomics, followed by extracting 21,049 features from three aspects: relationship to GO and KEGG (enrichment features), mutated genes learned by word2vec (text features), and protein-protein interaction network analyzed by node2vec (network features). Irrelevant features were then excluded using the Boruta feature filtering method, and the retained relevant features were ranked by four feature selection methods (least absolute shrinkage and selection operator, minimum redundancy maximum relevance, Monte Carlo feature selection and light gradient boosting machine) to generate four feature-ranked lists. Incremental feature selection was used to determine the optimal number of features based on these feature lists to build the optimal classifiers and derive interpretable classification rules. The results of four feature-ranking methods were integrated to identify key functional pathways, such as olfactory transduction (hsa04740) and colorectal cancer (hsa05210), and the roles of these functional pathways in cancers were discussed in reference to literature. Overall, this machine learning-based study revealed the altered biological functions of cancers and provided a reference for the mechanisms of different cancers.
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Affiliation(s)
- Jian Lu
- Department of Mathematics, School of Sciences, Shanghai University, Shanghai, China
- CAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Science, Shanghai, China
| | - JiaRui Li
- Advanced Research Computing, University of British Columbia, Vancouver, BC, Canada
| | - Jingxin Ren
- School of Life Sciences, Shanghai University, Shanghai, China
| | - Shijian Ding
- School of Life Sciences, Shanghai University, Shanghai, China
| | - Zhenbing Zeng
- Department of Mathematics, School of Sciences, Shanghai University, Shanghai, China
| | - Tao Huang
- CAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Science, Shanghai, China
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, China
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9
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Qi P, Sun Y, Liu X, Wu S, Wo Y, Xu Q, Wang Q, Hu X, Zhou X. Clinicopathological, molecular and prognostic characteristics of cancer of unknown primary in China: An analysis of 1420 cases. Cancer Med 2022; 12:1177-1188. [PMID: 35822433 PMCID: PMC9883567 DOI: 10.1002/cam4.4973] [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: 01/24/2022] [Revised: 05/23/2022] [Accepted: 06/10/2022] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Cancer of unknown primary (CUP) is defined the presence of metastatic disease without an identified primary site. An unidentifiable primary site of cancer creates significant challenges for treatment selection. We aimed to describe the clinicopathological, molecular, and prognostic characteristics of Chinese CUP patients. METHODS Patients with oncologist-confirmed CUP were identified at Fudan University Shanghai Cancer Center from 2019 to 2020. Information on patient characteristics, tumor presentation, treatment, and outcome were retrospectively collected from the inpatient database and pathological consultation database for descriptive analysis. A multivariable logistic regression model was established to identify factors associated with patient prognosis. RESULTS A total of 1420 CUP patients were enrolled in this study. The baseline characteristics of the entire cohort included the following: median age (59 years old), female sex (45.8%), adenocarcinoma (47.7%), and poorly differentiated or undifferentiated tumors (92.1%). For the inpatient cohort, the most common sites where cancer spread included the lymph nodes (41.8%), bone (22.0%), liver (20.1%), and peritoneum/retroperitoneum (16.0%). A total of 77.4% and 58.2% of patients were treated with local therapy and systemic therapy, respectively. Four prognostic factors, including liver metastasis, peritoneal/retroperitoneal metastasis, number of metastatic sites (N ≥ 2), and systemic treatment, were independently associated with overall survival. Additionally, 24.8% (79/318) of patients received molecular testing, including PD-L1, human papillomavirus, genetic variation, and 90-gene expression tests for diagnosis or therapy selection. CONCLUSION Cancer of unknown primary remains a difficult cancer to diagnose and manage. Our findings improve our understanding of Chinese CUP patient characteristics, leading to improved care and outcomes for CUP patients.
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Affiliation(s)
- Peng Qi
- Department of PathologyFudan University Shanghai Cancer CenterShanghaiChina,Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiChina,Institute of PathologyFudan UniversityShanghaiChina,The Cancer of Unknown Primary Group of Pathology CommitteeChinese Research Hospital AssociationShanghaiChina
| | - Yifeng Sun
- The Canhelp Genomics Research CenterCanhelp Genomics Co., Ltd.HangzhouChina
| | - Xin Liu
- Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiChina,Department of Head & Neck Tumors and Neuroendocrine TumorsFudan University Shanghai Cancer CenterShanghaiChina
| | - Sheng Wu
- The Canhelp Genomics Research CenterCanhelp Genomics Co., Ltd.HangzhouChina
| | - Yixin Wo
- The Canhelp Genomics Research CenterCanhelp Genomics Co., Ltd.HangzhouChina
| | - Qinghua Xu
- The Cancer of Unknown Primary Group of Pathology CommitteeChinese Research Hospital AssociationShanghaiChina,The Canhelp Genomics Research CenterCanhelp Genomics Co., Ltd.HangzhouChina,The Institute of Machine Learning and Systems Biology, College of Electronics and Information EngineeringTongji UniversityShanghaiChina,Xuzhou Engineering Research Center of Medical Genetics and Transformation, Department of GeneticsXuzhou Medical UniversityXuzhouChina
| | - Qifeng Wang
- Department of PathologyFudan University Shanghai Cancer CenterShanghaiChina,Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiChina,Institute of PathologyFudan UniversityShanghaiChina,The Cancer of Unknown Primary Group of Pathology CommitteeChinese Research Hospital AssociationShanghaiChina
| | - Xichun Hu
- Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiChina,Department of Medical OncologyFudan University Shanghai Cancer CenterShanghaiChina
| | - Xiaoyan Zhou
- Department of PathologyFudan University Shanghai Cancer CenterShanghaiChina,Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiChina,Institute of PathologyFudan UniversityShanghaiChina,The Cancer of Unknown Primary Group of Pathology CommitteeChinese Research Hospital AssociationShanghaiChina
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10
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Yu B, Wang Q, Liu X, Hu S, Zhou L, Xu Q, Sun Y, Hu X, Luo Z, Zhang X. Case Report: Molecular Profiling Assists in the Diagnosis and Treatment of Cancer of Unknown Primary. Front Oncol 2022; 12:723140. [PMID: 35433426 PMCID: PMC9005951 DOI: 10.3389/fonc.2022.723140] [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: 06/29/2021] [Accepted: 02/24/2022] [Indexed: 11/17/2022] Open
Abstract
Background For cancer of unknown primary (CUP), non-selective empiric chemotherapy is usually used. However, patients suffering from CUP are generally assumed to have a dismal prognosis with median overall survival of less than 1 year. Therefore, clinicians eagerly await the establishment of effective strategies for diagnosis and treatment. In recent years, the remarkable advances in next-generation sequencing (NGS) technology have enabled the wide usage of DNA/RNA sequencing to comprehensively analyze the molecular information of individual tumors and identify potential targets for patients’ diagnosis and treatment. Here, we describe a patient of CUP who was successfully diagnosed and treated with targeted therapy directed by comprehensive molecular profiling. Case Presentation A 61-year-old Asian woman with a painless, slow-growing mass lesion in the mesosternum underwent fluorodeoxyglucose-positron emission tomography/computed tomography and was found to have malignant metastatic tumors in the mesosternum. Conventional pathological examination of metastatic lesions could not conclude the primary origin of the tumors. The patient was diagnosed with CUP at first. Then, comprehensive molecular profiling was employed to identify the tumor origin and genetic alterations. A gene expression-based tissue origin assay was performed using a tissue biopsy sample. The test result suggested that the lesion tumors might be breast cancer metastasis. Furthermore, liquid biopsy-based circulating tumor DNA profiling detected an ERBB2 copy number amplification. Subsequent surgery and additional postoperative pathology analysis confirmed that the primary tumor site was indeed located in the right outer upper quadrant of the breast. After local surgical resection, the patient received 8 cycles of Docetaxel + Carboplatin + Trastuzumab + Pertuzumab (TCbHP) chemotherapy with subsequent human epidermal growth factor receptor 2 (HER2)-targeted maintenance therapy. Currently, the patient is on regular follow-up and has achieved disease control for up to 6 months. Conclusion Our findings suggest that molecular identification of the tumor origin and the detection of actionable molecular alterations may offer promise for improved diagnostic accuracy and important therapeutic implications for patients with the CUP syndrome.
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Affiliation(s)
- Bo Yu
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Qifeng Wang
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Xin Liu
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Silong Hu
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Department of Nuclear Medicine, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Liangping Zhou
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Department of Radiology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Qinghua Xu
- Canhelp Genomics Research Center, Canhelp Genomics, Hangzhou, China.,Institute of Machine Learning and Systems Biology, College of Electronics and Information Engineering, Tongji University, Shanghai, China
| | - Yifeng Sun
- Canhelp Genomics Research Center, Canhelp Genomics, Hangzhou, China
| | - Xichun Hu
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhiguo Luo
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiaowei Zhang
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
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11
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Sun W, Wu W, Wang Q, Yao Q, Feng Q, Wang Y, Sun Y, Liu Y, Lai Q, Zhang G, Qi P, Sun Y, Qian C, Ren W, Luo Z, Chen J, Wang H, Xu Q, Zhou X, Sun W, Lin D. Clinical validation of a 90-gene expression test for tumor tissue of origin diagnosis: a large-scale multicenter study of 1417 patients. J Transl Med 2022; 20:114. [PMID: 35255924 PMCID: PMC8900384 DOI: 10.1186/s12967-022-03318-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 02/23/2022] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Once malignancy tumors were diagnosed, the determination of tissue origin and tumor type is critical for clinical management. Although the significant advance in imaging techniques and histopathological approaches, the diagnosis remains challenging in patients with metastatic and poorly differentiated or undifferentiated tumors. Gene expression profiling has been demonstrated the ability to classify multiple tumor types. The present study aims to assess the performance of a 90-gene expression test for tumor classification (i.e. the determination of tumor tissue of origin) in real clinical settings. METHODS Formalin-fixed paraffin-embedded samples and associated clinicopathologic information were collected from three cancer centers between January 2016 and January 2021. A total of 1417 specimens that met quality control criteria (RNA quality, tumor cell content ≥ 60% and so on) were analyzed by the 90-gene expression test to identify the tumor tissue of origin. The performance was evaluated by comparing the test results with histopathological diagnosis. RESULTS The 1417 samples represent 21 main tumor types classified by common tissue origins and anatomic sites. Overall, the 90-gene expression test reached an accuracy of 94.4% (1338/1417, 95% CI: 0.93 to 0.96). Among different tumor types, sensitivities were ranged from 74.2% (head&neck tumor) to 100% (adrenal carcinoma, mesothelioma, and prostate cancer). Sensitivities for the most prevalent cancers of lung, breast, colorectum, and gastroesophagus are 95.0%, 98.4%, 93.9%, and 90.6%, respectively. Moreover, specificities for all 21 tumor types are greater than 99%. CONCLUSIONS These findings showed robust performance of the 90-gene expression test for identifying the tumor tissue of origin and support the use of molecular testing as an adjunct to tumor classification, especially to those poorly differentiated or undifferentiated tumors in clinical practice.
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Affiliation(s)
- Wei Sun
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, No.52 Fucheng Road, Wu Ke Song, Haidian District, Beijing, China
| | - Wei Wu
- Department of Pathology, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), No.1 East Road of Banshan, Hangzhou, Zhejiang, China
| | - Qifeng Wang
- Department of Pathology, Fudan University Shanghai Cancer Center, No.270 Dong'An Road, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
- The Cancer of Unknown Primary Group of Pathology Committee, Chinese Research Hospital Association, Shanghai, China
| | - Qian Yao
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, No.52 Fucheng Road, Wu Ke Song, Haidian District, Beijing, China
| | - Qin Feng
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, No.52 Fucheng Road, Wu Ke Song, Haidian District, Beijing, China
| | - Yue Wang
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, No.52 Fucheng Road, Wu Ke Song, Haidian District, Beijing, China
| | - Yu Sun
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, No.52 Fucheng Road, Wu Ke Song, Haidian District, Beijing, China
| | - Yunying Liu
- Department of Pathology, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), No.1 East Road of Banshan, Hangzhou, Zhejiang, China
| | - Qian Lai
- Department of Pathology, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), No.1 East Road of Banshan, Hangzhou, Zhejiang, China
| | - Gu Zhang
- Department of Pathology, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), No.1 East Road of Banshan, Hangzhou, Zhejiang, China
| | - Peng Qi
- Department of Pathology, Fudan University Shanghai Cancer Center, No.270 Dong'An Road, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
- The Cancer of Unknown Primary Group of Pathology Committee, Chinese Research Hospital Association, Shanghai, China
| | - Yifeng Sun
- The Canhelp Genomics Research Center, Canhelp Genomics Co., Ltd., Hangzhou, China
| | - Chenhui Qian
- The Canhelp Genomics Research Center, Canhelp Genomics Co., Ltd., Hangzhou, China
| | - Wanli Ren
- The Canhelp Genomics Research Center, Canhelp Genomics Co., Ltd., Hangzhou, China
| | - Zhengzhi Luo
- The Canhelp Genomics Research Center, Canhelp Genomics Co., Ltd., Hangzhou, China
| | - Jinying Chen
- The Canhelp Genomics Research Center, Canhelp Genomics Co., Ltd., Hangzhou, China
| | - Hongying Wang
- The Canhelp Genomics Research Center, Canhelp Genomics Co., Ltd., Hangzhou, China
| | - Qinghua Xu
- The Cancer of Unknown Primary Group of Pathology Committee, Chinese Research Hospital Association, Shanghai, China
- The Canhelp Genomics Research Center, Canhelp Genomics Co., Ltd., Hangzhou, China
- The Institute of Machine Learning and Systems Biology, College of Electronics and Information Engineering, Tongji University, Shanghai, China
- Xuzhou Engineering Research Center of Medical Genetics and Transformation, Department of Genetics, Xuzhou Medical University, Xuzhou, China
| | - Xiaoyan Zhou
- Department of Pathology, Fudan University Shanghai Cancer Center, No.270 Dong'An Road, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
- Institute of Pathology, Fudan University, Shanghai, China.
- The Cancer of Unknown Primary Group of Pathology Committee, Chinese Research Hospital Association, Shanghai, China.
| | - Wenyong Sun
- Department of Pathology, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), No.1 East Road of Banshan, Hangzhou, Zhejiang, China.
| | - Dongmei Lin
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, No.52 Fucheng Road, Wu Ke Song, Haidian District, Beijing, China.
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12
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Pu X, Yang S, Xu Y, Chen B, Wang Q, Gong Q, Wu L. Case Report: Tissue Origin Identification for Cancer of Unknown Primary: Gene Expression Profiling Approach. Front Oncol 2021; 11:702887. [PMID: 34858803 PMCID: PMC8632144 DOI: 10.3389/fonc.2021.702887] [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: 04/30/2021] [Accepted: 10/25/2021] [Indexed: 11/13/2022] Open
Abstract
The treatment of cancer of unknown primary (CUP) is a huge challenge for clinicians. Gene expression profiling can help identify the tissue origin of tumors by detecting the expression levels of specific genes in tumor tissues. Herein, we report four CUP cases. All of them have been successfully identified with the corresponding primary tumor sites through gene expression profiling analysis. Then all patients received accurate treatment, providing reference to guide therapeutic decisions to treat CUP tumors in the future.
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Affiliation(s)
- Xingxiang Pu
- Department of Thoracic Medical Oncology, Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Sa Yang
- Department of Pharmacy, Xiangxiang People's Hospital, Xiangxiang, China
| | - Yan Xu
- Department of Thoracic Medical Oncology, Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Bolin Chen
- Department of Thoracic Medical Oncology, Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Qianzhi Wang
- Department of Thoracic Medical Oncology, Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Qian Gong
- Department of Pharmacy, Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Lin Wu
- Department of Thoracic Medical Oncology, Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
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13
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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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14
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Wang Q, Li F, Jiang Q, Sun Y, Liao Q, An H, Li Y, Li Z, Fan L, Guo F, Xu Q, Wo Y, Ren W, Yue J, Meng B, Liu W, Zhou X. Gene Expression Profiling for Differential Diagnosis of Liver Metastases: A Multicenter, Retrospective Cohort Study. Front Oncol 2021; 11:725988. [PMID: 34631555 PMCID: PMC8493028 DOI: 10.3389/fonc.2021.725988] [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: 06/16/2021] [Accepted: 08/18/2021] [Indexed: 02/05/2023] Open
Abstract
Background Liver metastases (LM) are the most common tumors encountered in the liver and continue to be a significant cause of morbidity and mortality. Identification of the primary tumor of any LM is crucial for the implementation of effective and tailored treatment approaches, which still represents a difficult problem in clinical practice. Methods The resection or biopsy specimens and associated clinicopathologic data were archived from seven independent centers between January 2017 and December 2020. The primary tumor sites of liver tumors were verified through evaluation of available medical records, pathological and imaging information. The performance of a 90-gene expression assay for the determination of the site of tumor origin was assessed. Result A total of 130 LM covering 15 tumor types and 16 primary liver tumor specimens that met all quality control criteria were analyzed by the 90-gene expression assay. Among 130 LM cases, tumors were most frequently located in the colorectum, ovary and breast. Overall, the analysis of the 90-gene signature showed 93.1% and 100% agreement rates with the reference diagnosis in LM and primary liver tumor, respectively. For the common primary tumor types, the concordance rate was 100%, 95.7%, 100%, 93.8%, 87.5% for classifying the LM from the ovary, colorectum, breast, neuroendocrine, and pancreas, respectively. Conclusion The overall accuracy of 93.8% demonstrates encouraging performance of the 90-gene expression assay in identifying the primary sites of liver tumors. Future incorporation of the 90-gene expression assay in clinical diagnosis will aid oncologists in applying precise treatments, leading to improved care and outcomes for LM patients.
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Affiliation(s)
- Qifeng Wang
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Institute of Pathology, Fudan University, Shanghai, China.,The Cancer of Unknown Primary Group of Pathology Committee, Chinese Research Hospital Association, Shanghai, China
| | - Fen Li
- Department of Pathology, Chengdu Second People's Hospital, Chengdu, China
| | - Qingming Jiang
- Department of Pathology, Chongqing University Cancer Hospital, Chongqing, China
| | - Yifeng Sun
- The Canhelp Genomics Research Center, Canhelp Genomics Co., Ltd., Hangzhou, China
| | - Qiong Liao
- The Cancer of Unknown Primary Group of Pathology Committee, Chinese Research Hospital Association, Shanghai, China.,Department of Pathology, Sichuan Cancer Hospital, Chengdu, China
| | - Huimin An
- The Cancer of Unknown Primary Group of Pathology Committee, Chinese Research Hospital Association, Shanghai, China.,Department of Pathology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Yunzhu Li
- Department of Pathology, Sichuan Cancer Hospital, Chengdu, China
| | - Zhenyu Li
- Department of Pathology, Chongqing University Cancer Hospital, Chongqing, China
| | - Lifang Fan
- Department of Pathology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fang Guo
- Department of Pathology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qinghua Xu
- The Cancer of Unknown Primary Group of Pathology Committee, Chinese Research Hospital Association, Shanghai, China.,The Canhelp Genomics Research Center, Canhelp Genomics Co., Ltd., Hangzhou, China.,The Institute of Machine Learning and Systems Biology, College of Electronics and Information Engineering, Tongji University, Shanghai, China.,Xuzhou Engineering Research Center of Medical Genetics and Transformation, Department of Genetics, Xuzhou Medical University, Xuzhou, China
| | - Yixin Wo
- The Canhelp Genomics Research Center, Canhelp Genomics Co., Ltd., Hangzhou, China
| | - Wanli Ren
- The Canhelp Genomics Research Center, Canhelp Genomics Co., Ltd., Hangzhou, China
| | - Junqiu Yue
- The Cancer of Unknown Primary Group of Pathology Committee, Chinese Research Hospital Association, Shanghai, China.,Department of Pathology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Bin Meng
- The Cancer of Unknown Primary Group of Pathology Committee, Chinese Research Hospital Association, Shanghai, China.,Department of Pathology, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Weiping Liu
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, China
| | - Xiaoyan Zhou
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Institute of Pathology, Fudan University, Shanghai, China.,The Cancer of Unknown Primary Group of Pathology Committee, Chinese Research Hospital Association, Shanghai, China
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