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Liu R, Cao Z, Wu M, Li X, Fan P, Liu Z. Golgi-apparatus genes related signature for predicting the progression-free interval of patients with papillary thyroid carcinoma. BMC Med Genomics 2023; 16:60. [PMID: 36973751 PMCID: PMC10041766 DOI: 10.1186/s12920-023-01485-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 03/11/2023] [Indexed: 03/29/2023] Open
Abstract
BACKGROUND We aimed to build a novel model with golgi apparatus related genes (GaGs) signature and relevant clinical parameters for predicting progression-free interval (PFI) after surgery for papillary thyroid carcinoma (PTC). METHODS We performed a bioinformatic analysis of integrated PTC datasets with the GaGs to identify differentially expressed GaGs (DE-GaGs). Then we generated PFI-related DE-GaGs and established a novel GaGs based signature. After that, we validated the signature on multiple external datasets and PTC cell lines. Further, we conducted uni- and multivariate analyses to identify independent prognostic characters. Finally, we established a signature and clinical parameters-based nomogram for predicting the PFI of PTC. RESULTS We identified 260 DE-GaGs related to PFI in PTC. The functional enrichment analysis showed that the DE-MTGs were associated with an essential oncogenic glycoprotein biosynthetic process. Consequently, we established and optimized a novel 11 gene signature that could distinguish patients with poorer prognoses and predicted PFI accurately. The novel signature had a C-index of 0.78, and the relevant nomogram had a C-index of 0.79. Also, it was closely related to the pivotal clinical characters of and anaplastic potential in datasets and PTC cell lines. And the signature was confirmed a significant independent prognostic factor in PTC. Finally, we built a nomogram by including the signature and relevant clinical factors. Validation analysis showed that the nomogram's efficacy was satisfying in predicting PTC's PFI. CONCLUSION The GaGs signature and nomogram were closely associated with PTC prognosis and may help clinicians improve the individualized prediction of PFI, especially for high-risk patients after surgery.
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Affiliation(s)
- Rui Liu
- Department of Breast and Thyroid Surgery, Hunan Provincial People's Hospital/The First Affiliated Hospital of Hunan Normal University, Changsha, 410005, China
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Zhen Cao
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Mengwei Wu
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Xiaobin Li
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Peizhi Fan
- Department of Breast and Thyroid Surgery, Hunan Provincial People's Hospital/The First Affiliated Hospital of Hunan Normal University, Changsha, 410005, China.
| | - Ziwen Liu
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
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Chiho M, Ono Y, Hayashi A, Takahashi K, Taniue K, Kakisaka R, Mori M, Ishii T, Sato H, Okada T, Kawabata H, Goto T, Tamamura N, Omori Y, Takahashi K, Katanuma A, Karasaki H, Liss AS, Mizukami Y. Multiplex digital PCR assay to detect multiple KRAS and GNAS mutations associated with pancreatic carcinogenesis from minimal specimen amounts. J Mol Diagn 2023; 25:367-377. [PMID: 36965665 DOI: 10.1016/j.jmoldx.2023.02.007] [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: 03/08/2022] [Revised: 02/14/2023] [Accepted: 02/24/2023] [Indexed: 03/27/2023] Open
Abstract
Digital PCR (dPCR) allows for highly sensitive quantification of low-frequency mutations and facilitates early detection of cancer. However, low throughput targeting of single hotspots in dPCR hinders variant specification when multiple probes are used. Here we developed a dPCR method to simultaneously identify major variants related to pancreatic carcinogenesis. Using a 2-D plot of droplet fluorescence under the optimized concentration of two fluorescent probe pools, we determined the absolute quantification of different KRAS and GNAS variants. Successful detection of the multiple driver mutations was verified in 24 surgically resected tumor samples from 19 patients and 22 FNA samples from patients with pancreatic ductal adenocarcinoma. Precise quantification of the variant allele frequency was optimized using template DNA at a concentration as low as 1-10 ng. Furthermore, amplicons targeting multiple hotspots were successfully enriched with fewer false positives using high-fidelity polymerase, allowing for the detection of various KRAS and GNAS mutations with high probability in small cell/tissue specimens. Using this target enrichment, mutations at a rate of 90% in small residual tissues, such as the FNA needle flush and microscopic lesions in resected specimens, have successfully been identified. The proposed method allows for low-cost and accurate detection of driver mutations to diagnose cancers, even with minimal tissue collection.
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Affiliation(s)
- Maeda Chiho
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, 065-0033, Japan
| | - Yusuke Ono
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, 065-0033, Japan; Department of Medicine, Asahikawa Medical University, Asahikawa, 078-8510, Japan.
| | - Akihiro Hayashi
- Department of Medicine, Asahikawa Medical University, Asahikawa, 078-8510, Japan
| | - Kenji Takahashi
- Department of Medicine, Asahikawa Medical University, Asahikawa, 078-8510, Japan
| | - Kenzui Taniue
- Department of Medicine, Asahikawa Medical University, Asahikawa, 078-8510, Japan; Isotope Science Center, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Rika Kakisaka
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, 065-0033, Japan
| | - Miyuki Mori
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, 065-0033, Japan
| | - Takahiro Ishii
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, 065-0033, Japan
| | - Hiroki Sato
- Department of Medicine, Asahikawa Medical University, Asahikawa, 078-8510, Japan; Division of Gastrointestinal and Oncologic Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114
| | - Tetsuhiro Okada
- Department of Medicine, Asahikawa Medical University, Asahikawa, 078-8510, Japan
| | - Hidemasa Kawabata
- Department of Medicine, Asahikawa Medical University, Asahikawa, 078-8510, Japan
| | - Takuma Goto
- Department of Medicine, Asahikawa Medical University, Asahikawa, 078-8510, Japan
| | - Nobue Tamamura
- Department of Medicine, Asahikawa Medical University, Asahikawa, 078-8510, Japan
| | - Yuko Omori
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, 065-0033, Japan; Department of Investigative Pathology, Tohoku University Graduate School of Medicine, Sendai, 980-8575, Japan
| | - Kuniyuki Takahashi
- Center for Gastroenterology, Teine Keijinkai Hospital, Sapporo, 006-0811, Japan
| | - Akio Katanuma
- Center for Gastroenterology, Teine Keijinkai Hospital, Sapporo, 006-0811, Japan
| | - Hidenori Karasaki
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, 065-0033, Japan
| | - Andrew Scott Liss
- Division of Gastrointestinal and Oncologic Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114
| | - Yusuke Mizukami
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, 065-0033, Japan; Department of Medicine, Asahikawa Medical University, Asahikawa, 078-8510, Japan
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Liu R, Cao Z, Pan M, Wu M, Li X, Yuan H, Liu Z. A novel prognostic model for papillary thyroid cancer based on epithelial-mesenchymal transition-related genes. Cancer Med 2022; 11:4703-4720. [PMID: 35608185 PMCID: PMC9741981 DOI: 10.1002/cam4.4836] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/08/2022] [Accepted: 05/04/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The frequent incidence of postsurgical recurrence issues in papillary thyroid cancer (PTC) patients is a primary concern considering the low cancer-related mortality. Previous studies have demonstrated that epithelial-mesenchymal transition (EMT) activation is closely related to PTC progression and invasion. In this study, we aimed to develop a novel EMT signature and ancillary nomogram to improve personalized prediction of progression-free interval (PFI). METHODS First, we carried out a differential analysis of PTC samples and pairwise normal thyroid samples to explore the differentially expressed genes (DEGs). The intersection of the DEGs with EMT-related genes (ERGs) were identified as differentially expressed EMT-related genes (DE-ERGs). We determined PFI-related DE-ERGs by Cox regression analysis and then established a novel gene classifier by LASSO regression analysis. We validated the signature in external datasets and in multiple cell lines. Further, we used uni- and multivariate analyses to identify independent prognostic characters. RESULTS We identified 244 prognosis-related DE-ERGs. The 244 DE-ERGs were associated with several pivotal oncogenic processes. We also constructed a novel 10-gene signature and relevant prognostic model for recurrence prediction of PTC. The 10-gene signature had a C-index of 0.723 and the relevant nomogram had a C-index of 0.776. The efficacy of the signature and nomogram was satisfying and closely correlated with relevant clinical parameters. Furthermore, the signature also had a unique potential in differentiating anaplastic thyroid cancer (ATC) samples. CONCLUSIONS The novel EMT signature and nomogram are useful and convenient for personalized management for thyroid cancer.
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Affiliation(s)
- Rui Liu
- Department of General Surgery, Peking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingPeople's Republic of China
| | - Zhen Cao
- Department of General Surgery, Peking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingPeople's Republic of China
| | - Meng Pan
- State Key Laboratory of Medical Molecular Biology & Department of ImmunologyInstitute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical CollegeBeijingPeople's Republic of China
| | - Mengwei Wu
- Department of General Surgery, Peking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingPeople's Republic of China
| | - Xiaobin Li
- Department of General Surgery, Peking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingPeople's Republic of China
| | - Hongwei Yuan
- Department of General Surgery, Peking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingPeople's Republic of China
| | - Ziwen Liu
- Department of General Surgery, Peking Union Medical College HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingPeople's Republic of China
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Fang JM, Li J, Shi J. An update on the diagnosis of gastroenteropancreatic neuroendocrine neoplasms. World J Gastroenterol 2022; 28:1009-1023. [PMID: 35431496 PMCID: PMC8968521 DOI: 10.3748/wjg.v28.i10.1009] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 11/26/2021] [Accepted: 02/10/2022] [Indexed: 02/06/2023] Open
Abstract
Gastroenteropancreatic neuroendocrine neoplasms (GEP-NENs) arise from neuroendocrine cells found throughout the gastrointestinal tract and islet cells of the pancreas. The incidence and prevalence of GEP-NENs have been increasing each year due to higher awareness, improved diagnostic modalities, and increased incidental detection on cross-sectional imaging and endoscopy for cancer screening and other conditions and symptoms. GEP-NENs are a heterogeneous group of tumors and have a wide range in clinical presentation, histopathologic features, and molecular biology. Clinical presentation most commonly depends on whether the GEP-NEN secretes an active hormone. The World Health Organization recently updated the classification of GEP-NENs to introduce a distinction between high-grade neuroendocrine tumors and neuroendocrine carcinomas, which can be identified using histology and molecular studies and are more aggressive with a worse prognosis compared to high-grade neuroendocrine tumors. As our understanding of the biology of GEP-NENs has grown, new and improved diagnostic modalities can be developed and optimized. Here, we discuss clinical features and updates in diagnosis, including histopathological analysis, biomarkers, molecular techniques, and radiology of GEP-NENs. We review established diagnostic tests and discuss promising novel diagnostic tests that are currently in development or require further investigation and validation prior to broad utilization in patient care.
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Affiliation(s)
- Jiayun M Fang
- Department of Pathology & Clinical Labs, University of Michigan, Ann Arbor, MI 48109, United States
| | - Jay Li
- Medical Scientist Training Program, University of Michigan, Ann Arbor, MI 48109, United States
| | - Jiaqi Shi
- Department of Pathology & Clinical Labs, University of Michigan, Ann Arbor, MI 48109, United States
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