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He B, Sun H, Bao M, Li H, He J, Tian G, Wang B. A cross-cohort computational framework to trace tumor tissue-of-origin based on RNA sequencing. Sci Rep 2023; 13:15356. [PMID: 37717102 PMCID: PMC10505149 DOI: 10.1038/s41598-023-42465-8] [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: 06/08/2023] [Accepted: 09/11/2023] [Indexed: 09/18/2023] Open
Abstract
Carcinoma of unknown primary (CUP) is a type of metastatic cancer with tissue-of-origin (TOO) unidentifiable by traditional methods. CUP patients typically have poor prognosis but therapy targeting the original cancer tissue can significantly improve patients' prognosis. Thus, it's critical to develop accurate computational methods to infer cancer TOO. While qPCR or microarray-based methods are effective in inferring TOO for most cancer types, the overall prediction accuracy is yet to be improved. In this study, we propose a cross-cohort computational framework to trace TOO of 32 cancer types based on RNA sequencing (RNA-seq). Specifically, we employed logistic regression models to select 80 genes for each cancer type to create a combined 1356-gene set, based on transcriptomic data from 9911 tissue samples covering the 32 cancer types with known TOO from the Cancer Genome Atlas (TCGA). The selected genes are enriched in both tissue-specific and tissue-general functions. The cross-validation accuracy of our framework reaches 97.50% across all cancer types. Furthermore, we tested the performance of our model on the TCGA metastatic dataset and International Cancer Genome Consortium (ICGC) dataset, achieving an accuracy of 91.09% and 82.67%, respectively, despite the differences in experiment procedures and pipelines. In conclusion, we developed an accurate yet robust computational framework for identifying TOO, which holds promise for clinical applications. Our code is available at http://github.com/wangbo00129/classifybysklearn .
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Affiliation(s)
- Binsheng He
- School of Pharmacy, Changsha Medical University, Changsha, 410219, People's Republic of China
- Academician Workstation, Changsha Medical University, Changsha, 410219, People's Republic of China
| | - Hongmei Sun
- Department of Medical Oncology, The Cancer Hospital of Jia Mu Si, Jiamusi, People's Republic of China
| | - Meihua Bao
- Academician Workstation, Changsha Medical University, Changsha, 410219, People's Republic of China
| | - Haigang Li
- Academician Workstation, Changsha Medical University, Changsha, 410219, People's Republic of China
| | - Jianjun He
- School of Pharmacy, Changsha Medical University, Changsha, 410219, People's Republic of China
- Academician Workstation, Changsha Medical University, Changsha, 410219, People's Republic of China
| | - Geng Tian
- Geneis Beijing Co., Ltd., Beijing, 100102, People's Republic of China
- Qingdao Genesis Institute of Big Data Mining and Precision Medicine, Qingdao, 266000, Shandong, People's Republic of China
| | - Bo Wang
- Geneis Beijing Co., Ltd., Beijing, 100102, People's Republic of China.
- Qingdao Genesis Institute of Big Data Mining and Precision Medicine, Qingdao, 266000, Shandong, People's Republic of China.
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Masuoka S, Hiyama T, Kuno H, Sekiya K, Sakashita S, Kobayashi T. Imaging Approach for Cervical Lymph Node Metastases from Unknown Primary Tumor. Radiographics 2023; 43:e220071. [PMID: 36795593 DOI: 10.1148/rg.220071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Neck swelling due to lymph node (LN) metastasis is one of the initial symptoms of head and neck cancer, and in some cases, the primary tumor is not clinically evident. The purpose of imaging for LN metastasis from an unknown primary site is to identify the primary tumor or detect its absence, which leads to the correct diagnosis and optimal treatment. The authors discuss diagnostic imaging approaches for identifying the primary tumor in cases of unknown primary cervical LN metastases. The distribution and characteristics of LN metastases may help locate the primary site. Unknown primary LN metastasis often occurs at nodal levels II and III, and in recent reports, these were mostly related to human papillomavirus (HPV)-positive squamous cell carcinoma of the oropharynx. Another characteristic imaging finding suggestive of metastasis from HPV-associated oropharyngeal cancer is a cystic change in LN metastases. Other characteristic imaging findings such as calcification may help predict the histologic type and locate the primary site. In cases of LN metastases at nodal levels IV and VB, a primary lesion located outside the head and neck region must also be considered. One clue for detecting the primary lesion at imaging is the disruption of anatomic structures, which can help in identifying small mucosal lesions or submucosal tumors at each subsite. Additionally, fluorine 18 fluorodeoxyglucose PET/CT may help identify a primary tumor. These imaging approaches for identifying primary tumors enable prompt identification of the primary site and assist clinicians in making the correct diagnosis. © RSNA, 2023 Quiz questions for this article are available through the Online Learning Center.
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Affiliation(s)
- Sota Masuoka
- From the Department of Diagnostic Radiology (S.M., T.H., H.K., K.S., T.K.) and Department of Pathology and Clinical Laboratories (S.S.), National Cancer Center Hospital East, 6-5-1 Kashiwanoha, Kashiwa 277-8577, Japan
| | - Takashi Hiyama
- From the Department of Diagnostic Radiology (S.M., T.H., H.K., K.S., T.K.) and Department of Pathology and Clinical Laboratories (S.S.), National Cancer Center Hospital East, 6-5-1 Kashiwanoha, Kashiwa 277-8577, Japan
| | - Hirofumi Kuno
- From the Department of Diagnostic Radiology (S.M., T.H., H.K., K.S., T.K.) and Department of Pathology and Clinical Laboratories (S.S.), National Cancer Center Hospital East, 6-5-1 Kashiwanoha, Kashiwa 277-8577, Japan
| | - Kotaro Sekiya
- From the Department of Diagnostic Radiology (S.M., T.H., H.K., K.S., T.K.) and Department of Pathology and Clinical Laboratories (S.S.), National Cancer Center Hospital East, 6-5-1 Kashiwanoha, Kashiwa 277-8577, Japan
| | - Shingo Sakashita
- From the Department of Diagnostic Radiology (S.M., T.H., H.K., K.S., T.K.) and Department of Pathology and Clinical Laboratories (S.S.), National Cancer Center Hospital East, 6-5-1 Kashiwanoha, Kashiwa 277-8577, Japan
| | - Tatsushi Kobayashi
- From the Department of Diagnostic Radiology (S.M., T.H., H.K., K.S., T.K.) and Department of Pathology and Clinical Laboratories (S.S.), National Cancer Center Hospital East, 6-5-1 Kashiwanoha, Kashiwa 277-8577, Japan
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Mei J, Wang H, Fan H, Ding J, Xu J. Case Report: Successful Immunotherapy Improved the Prognosis of the Unfavorable Subset of Cancer of Unknown Primary. Front Immunol 2022; 13:900119. [PMID: 35812375 PMCID: PMC9256999 DOI: 10.3389/fimmu.2022.900119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 05/23/2022] [Indexed: 12/15/2022] Open
Abstract
Background Cancer of unknown primary (CUP) is heterogeneous and has a wide variety of clinical presentations and a poor prognosis in most patients, with a median overall survival of only 6 months. The development of molecular profiling contributes to precision therapy, and targeted drugs and immune checkpoint inhibitors (ICIs) greatly promote individualized treatment. Case presentation Here, we reported a case of an unfavorable subset of CUP who had a long time of survival after the immunotherapy-prominent comprehensive treatment. A 48-year-old man presented with back pain and a cough. A diagnostic work-up showed bone marrow, multiple bones, and lymph node metastasis. Lymph node pathology implies metastatic poorly differentiated cancer. Next-generation sequencing (NGS) showed no special targets, but the tumor proportion score (TPS) of programmed death-ligand 1 (PD-L1) was 80% and the tumor mutation burden (TMB) was 16.7 per million bases. After two cycles of pembrolizumab 200 mg D1 plus nanoparticle albumin-bound (nab)-paclitaxel 200 mg D1&8 (q3w), PET-CT and bone marrow aspiration cytology showed a complete response (CR). Subsequently, pembrolizumab alone was used for three months. The left inguinal lymph nodes showed new metastasis. After two cycles of the combination treatment of pembrolizumab and (nab)-paclitaxel, a partial response (PR) was achieved. After seven months, retroperitoneal lymph nodes showed new metastasis, and the sequential treatment with radiotherapy and pembrolizumab exhibited encouraging efficacy. To date, the patient has survived nearly 40 months with the combination therapy. Conclusions The ICI-prominent comprehensive treatment provided clinical benefit for the reported case of CUP. Thus, CUP patients with markers of benefiting from immunotherapy should be actively treated with immunotherapy to improve their prognosis.
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Affiliation(s)
| | | | | | - Junli Ding
- *Correspondence: Junying Xu, ; Junli Ding,
| | - Junying Xu
- *Correspondence: Junying Xu, ; Junli Ding,
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Huasong H, Shurui S, Shi G, Bin J. Performance of 18F-FDG-PET/CT as a next step in the search of occult primary tumors for patients with head and neck squamous cell carcinoma of unknown primary: a systematic review and meta-analysis. Clin Transl Imaging 2021. [DOI: 10.1007/s40336-021-00429-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Maghami E, Ismaila N, Alvarez A, Chernock R, Duvvuri U, Geiger J, Gross N, Haughey B, Paul D, Rodriguez C, Sher D, Stambuk HE, Waldron J, Witek M, Caudell J. Diagnosis and Management of Squamous Cell Carcinoma of Unknown Primary in the Head and Neck: ASCO Guideline. J Clin Oncol 2020; 38:2570-2596. [PMID: 32324430 DOI: 10.1200/jco.20.00275] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
PURPOSE To provide evidence-based recommendations to practicing physicians and other health care providers on the diagnosis and management of squamous cell carcinoma of unknown primary in the head and neck (SCCUP). METHODS The American Society of Clinical Oncology convened an Expert Panel of medical oncology, surgery, radiation oncology, radiology, pathology, and advocacy experts to conduct a literature search, which included systematic reviews, meta-analyses, randomized controlled trials, and prospective and retrospective comparative observational studies published from 2008 through 2019. Outcomes of interest included survival, local and regional disease control, and quality of life. Expert Panel members used available evidence and informal consensus to develop evidence-based guideline recommendations. RESULTS The literature search identified 100 relevant studies to inform the evidence base for this guideline. Four main clinical questions were addressed, which included subquestions on preoperative evaluations, surgical diagnostic and therapeutic procedures, appropriate pathology techniques, and adjuvant therapy. RECOMMENDATIONS Evidence-based recommendations were developed to address preoperative evaluation for patients with a neck mass, surgical diagnostic and therapeutic procedures, appropriate treatment options in unilateral versus bilateral SCCUP.Additional information is available at www.asco.org/head-neck-cancer-guidelines.
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Affiliation(s)
| | | | | | | | | | | | | | - Bruce Haughey
- Advent Health Medical Group, Otolaryngology, Head and Neck Surgery, Celebration, FL, and University of South Florida, Tampa, FL
| | - Doru Paul
- Weill Cornell Medical College, New York, NY
| | | | - David Sher
- University of Texas Southwestern, Dallas, TX
| | | | - John Waldron
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Matt Witek
- University of Wisconsin School of Medicine and Public Health, Madison, WI
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Lymph Node Disease and Advanced Head and Neck Imaging: A Review of the 2013 Literature. CURRENT RADIOLOGY REPORTS 2014. [DOI: 10.1007/s40134-014-0058-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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