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Hu M, Luo R, Yang K, Yu Y, Pan Q, Yuan M, Chen R, Wang H, Qin Q, Ma T, Wang H. Genomic landscape defines peritoneal metastatic pattern and related target of peritoneal metastasis in colorectal cancer. Int J Cancer 2024; 155:1327-1339. [PMID: 38738976 DOI: 10.1002/ijc.35005] [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: 09/17/2023] [Revised: 03/31/2024] [Accepted: 04/17/2024] [Indexed: 05/14/2024]
Abstract
The primary objective of this study is to develop a prediction model for peritoneal metastasis (PM) in colorectal cancer by integrating the genomic features of primary colorectal cancer, along with clinicopathological features. Concurrently, we aim to identify potential target implicated in the peritoneal dissemination of colorectal cancer through bioinformatics exploration and experimental validation. By analyzing the genomic landscape of primary colorectal cancer and clinicopathological features from 363 metastatic colorectal cancer patients, we identified 22 differently distributed variables, which were used for subsequent LASSO regression to construct a PM prediction model. The integrated model established by LASSO regression, which incorporated two clinicopathological variables and seven genomic variables, precisely discriminated PM cases (AUC 0.899; 95% CI 0.860-0.937) with good calibration (Hosmer-Lemeshow test p = .147). Model validation yielded AUCs of 0.898 (95% CI 0.896-0.899) and 0.704 (95% CI 0.622-0.787) internally and externally, respectively. Additionally, the peritoneal metastasis-related genomic signature (PGS), which was composed of the seven genes in the integrated model, has prognostic stratification capability for colorectal cancer. The divergent genomic landscape drives the driver genes of PM. Bioinformatic analysis concerning these driver genes indicated SERINC1 may be associated with PM. Subsequent experiments indicate that knocking down of SERINC1 functionally suppresses peritoneal dissemination, emphasizing its importance in CRCPM. In summary, the genomic landscape of primary cancer in colorectal cancer defines peritoneal metastatic pattern and reveals the potential target of SERINC1 for PM in colorectal cancer.
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Affiliation(s)
- Minhui Hu
- Department of Gastrointestinal Endoscopy, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Rui Luo
- Department of General Surgery, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Keli Yang
- Department of General Surgery, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yang Yu
- Department of General Surgery, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Qiwen Pan
- Department of Radiation Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Mingming Yuan
- Geneplus-Beijing, Medical Park Road, Zhongguancun Life Science Park, Beijing, China
| | - Rongrong Chen
- Geneplus-Beijing, Medical Park Road, Zhongguancun Life Science Park, Beijing, China
| | - Hui Wang
- Department of General Surgery, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Qiyuan Qin
- Department of General Surgery, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Tenghui Ma
- Department of General Surgery, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Huaiming Wang
- Department of General Surgery, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
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Hong L, Patel S, Drusbosky LM, Xiong Y, Chen R, Geng R, Heeke S, Nilsson M, Wu J, Heymach JV, Wang Y, Zhang J, Le X. Molecular landscape of ERBB2 alterations in 3000 advanced NSCLC patients. NPJ Precis Oncol 2024; 8:217. [PMID: 39354054 PMCID: PMC11445497 DOI: 10.1038/s41698-024-00720-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 09/22/2024] [Indexed: 10/03/2024] Open
Abstract
ERBB2 (HER2) represents a newly recognized actionable oncogenic driver in non-small cell lung cancer (NSCLC), with approved targeted therapy available. Understanding the landscape of ERBB2 alterations and co-occurring mutations is essential for guiding treatment decisions. We conducted an analysis involving 3000 NSCLC patients with all types of ERBB2 alterations, drawn from two extensive retrospective cohorts: 1281 from Geneplus (Chinese) and 1719 from Guardant360 (the United States, US). The incidence of all types of ERBB2 alterations was found to be 5.6% in the Chinese group and 5.2% in the US group. In both cohorts, among oncogenic alterations of ERBB2, exon 20 insertion Y772_A775dupYVMA was the most frequent alteration (58% vs 41.6% in the Chinese vs the US), followed by G776delinsVC/LC/VV/IC (10.7% vs 9.7%), and S310X (10.5% vs 15.4%). EGFR ex20 insertions were identified in the A767-V774 region, whereas ERBB2 ex20 insertions were observed in the Y772-P780 region. Notably, EGFR ex20 insertions exhibited greater insertion diversity. Clinical characteristics of EGFR and ERBB2 ex20 NSCLC were similar, characterized by low tumor mutation burden (TMB), a predominant never-smoker population, and a majority of lung adenocarcinoma cases.
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Affiliation(s)
- Lingzhi Hong
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sonia Patel
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | | | | | - Ruixuan Geng
- Department of International Medical Services, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Simon Heeke
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Monique Nilsson
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jia Wu
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John V Heymach
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yingyi Wang
- Department of Medical Oncology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Jianjun Zhang
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Xiuning Le
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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Fujimaru T, Mori T, Sekine A, Chiga M, Mandai S, Kikuchi H, Mori Y, Hara Y, Fujiki T, Ando F, Susa K, Iimori S, Naito S, Hanazawa R, Hirakawa A, Mochizuki T, Suwabe T, Ubara Y, Uchida S, Sohara E. Importance of IFT140 in Patients with Polycystic Kidney Disease Without a Family History. Kidney Int Rep 2024; 9:2685-2694. [PMID: 39291187 PMCID: PMC11403091 DOI: 10.1016/j.ekir.2024.06.021] [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: 12/25/2023] [Revised: 06/03/2024] [Accepted: 06/10/2024] [Indexed: 09/19/2024] Open
Abstract
Introduction Recently, the monoallelic loss-of-function IFT140 variant was identified as a causative gene for autosomal dominant polycystic kidney disease (ADPKD). In patients with polycystic kidneys who have a positive family history, >90% have pathogenic variants in PKD1 or PKD2, whereas only 1% have IFT140. However, approximately 40% of patients with polycystic kidneys without a family history do not have any pathogenic variants in PKD1 and PKD2. Methods We conducted a comprehensive genetic analysis of 157 adult patients with polycystic kidneys whose parents did not have evident polycystic kidneys. We sequenced up to 92 genes associated with inherited cystic kidney disease, including IFT140. Results Of the 157 patients, 7 (4.5%) presented with monoallelic loss-of-function variants in the IFT140 gene, 51 (32.5%) with pathogenic variants in the PKD1 or PKD2 gene, and 7 (4.5%) with pathogenic variants in other genes related to inherited kidney cystic disease. The proportion of monoallelic loss-of-function IFT140 variants in this cohort was higher than that in previously reported cohorts with polycystic kidneys who had a positive family history. None of the patients with monoallelic loss-of-function IFT140 variants had polycystic liver disease (PLD). Furthermore, patients with IFT140 pathogenic variants had a significantly smaller kidney volume and a remarkably higher estimated glomerular filtration rate (eGFR) than those with PKD1 pathogenic variants (P = 0.01 and 0.03, respectively). Conclusion Because the phenotype of polycystic kidneys caused by the IFT140 gene is mild, parental kidney disease may be overlooked. Therefore, patients without a positive family history are more likely to carry pathogenic variants in IFT140.
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Affiliation(s)
- Takuya Fujimaru
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
- Department of Nephrology, St Luke's International Hospital, Tokyo, Japan
| | - Takayasu Mori
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Akinari Sekine
- Nephrology Center, Toranomon Hospital, Tokyo, Japan
- Okinaka Memorial Institute for Medical Research, Toranomon Hospital, Tokyo, Japan
| | - Motoko Chiga
- Clinical Laboratory, Tokyo Medical and Dental University Hospital, Tokyo Japan
| | - Shintaro Mandai
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hiroaki Kikuchi
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yutaro Mori
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yu Hara
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Tamami Fujiki
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Fumiaki Ando
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Koichiro Susa
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Soichiro Iimori
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Shotaro Naito
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Ryoichi Hanazawa
- Department of Clinical Biostatistics, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Akihiro Hirakawa
- Department of Clinical Biostatistics, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | | | - Tatsuya Suwabe
- Nephrology Center, Toranomon Hospital, Tokyo, Japan
- Okinaka Memorial Institute for Medical Research, Toranomon Hospital, Tokyo, Japan
| | - Yoshifumi Ubara
- Nephrology Center, Toranomon Hospital, Tokyo, Japan
- Okinaka Memorial Institute for Medical Research, Toranomon Hospital, Tokyo, Japan
| | - Shinichi Uchida
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Eisei Sohara
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
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Fu R, Xiong Y, Cai M, Li F, Chen R, Wu Y, Zhong W. Evaluation of molecular residual disease in operable non-small cell lung cancer with gene fusions, MET exon skipping or de novo MET amplification. Front Med 2024; 18:735-743. [PMID: 38805102 DOI: 10.1007/s11684-024-1060-z] [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: 09/27/2023] [Accepted: 01/17/2024] [Indexed: 05/29/2024]
Abstract
Gene fusions and MET alterations are rare and difficult to detect in plasma samples. The clinical detection efficacy of molecular residual disease (MRD) based on circulating tumor DNA (ctDNA) in patients with non-small cell lung cancer (NSCLC) with these mutations remains unknown. This prospective, non-intervention study recruited 49 patients with operable NSCLC with actionable gene fusions (ALK, ROS1, RET, and FGFR1), MET exon 14 skipping or de novo MET amplification. We analyzed 43 tumor tissues and 111 serial perioperative plasma samples using 1021- and 338-gene panels, respectively. Detectable MRD correlated with a significantly higher recurrence rate (P < 0.001), yielding positive predictive values of 100% and 90.9%, and negative predictive values of 82.4% and 86.4% at landmark and longitudinal time points, respectively. Patients with detectable MRD showed reduced disease-free survival (DFS) compared to those with undetectable MRD (P < 0.001). Patients who harbored tissue-derived fusion/MET alterations in their MRD had reduced DFS compared to those who did not (P = 0.05). To our knowledge, this is the first comprehensive study on ctDNA-MRD clinical detection efficacy in operable NSCLC patients with gene fusions and MET alterations. Patients with detectable tissue-derived fusion/MET alterations in postoperative MRD had worse clinical outcomes.
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Affiliation(s)
- Rui Fu
- School of Medicine, South China University of Technology, Guangzhou, 510006, China
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, China
| | | | - Miao Cai
- Geneplus-Beijing, Beijing, 102206, China
| | - Fang Li
- Geneplus-Beijing, Beijing, 102206, China
| | | | - Yilong Wu
- School of Medicine, South China University of Technology, Guangzhou, 510006, China
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, China
| | - Wenzhao Zhong
- School of Medicine, South China University of Technology, Guangzhou, 510006, China.
- Guangdong Lung Cancer Institute, Guangdong Provincial Key Laboratory of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, China.
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Tsujikawa T, Ohno K, Morita KI, Saburi S, Mitsuda J, Yoshimura K, Kimura A, Morimoto H, Ogi H, Shibata S, Akashi T, Kurata M, Imoto I, Shimizu Y, Kano S, Watanabe A, Yamazaki T, Asada Y, Hayashi R, Saito Y, Ozawa H, Tsukahara K, Oridate N, Sano D, Horii A, Ueki Y, Maruo T, Mukoyama N, Hanai N, Fukusumi T, Iwai H, Fujisawa T, Fujii T, Nibu KI, Iwae S, Ueda T, Chikuie N, Yasumatsu R, Matsuo M, Umeno H, Ono T, Masuda M, Toh S, Itoh K, Hirano S, Asakage T. Clinical, genomic and immune microenvironmental determinants of nivolumab response in head and neck squamous cell carcinoma. Front Immunol 2024; 15:1390873. [PMID: 39136017 PMCID: PMC11317249 DOI: 10.3389/fimmu.2024.1390873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 07/05/2024] [Indexed: 08/15/2024] Open
Abstract
Background In view of improving biomarkers predicting the efficacy of immunotherapy for head and neck squamous cell carcinoma (R/M HNSCC), this multicenter retrospective study aimed to identify clinical, tumor microenvironmental, and genomic factors that are related to therapeutic response to the anti- Programmed cell death protein 1 (PD-1) antibody, nivolumab, in patients with R/M HNSCC. Methods The study compared 53 responders and 47 non-responders, analyzing formalin-fixed paraffin-embedded samples using 14-marker multiplex immunohistochemistry and targeted gene sequencing. Results Of 100 patients included, responders had significantly lower smoking and alcohol index, higher incidence of immune related adverse events, and higher PD-1 ligand (PD-L1) expression in immune cells as well as PD-L1 combined positive score (CPS) than non-responders. The frequency of natural killer cells was associated with nivolumab response in patients with prior cetuximab use, but not in cetuximab-naïve status. Age-stratified analysis showed nivolumab response was linked to high CPS and lymphoid-inflamed profiles in patients aged ≥ 65. In contrast, lower NLR in peripheral blood counts was associated with response in patients aged < 65. Notably, TP53 mutation-positive group had lower CPS and T cell densities, suggesting an immune-excluded microenvironment. Patients with altered tumor suppressor gene pathways, including TP53, CDKN2A, and SMAD4 mutations, had lower CPS, higher smoking index, and were associated with poor responses. Conclusion Nivolumab treatment efficacy in HNSCC is influenced by a combination of clinical factors, age, prior treatment, immune environmental characteristics, and gene mutation profiles.
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Affiliation(s)
- Takahiro Tsujikawa
- Department of Otolaryngology-Head and Neck Surgery, Kyoto Prefectural University of Medicine, Kyoto, Japan
- Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR, United States
| | - Kazuchika Ohno
- Department of Head and Neck Surgery, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kei-ichi Morita
- Department of Maxillofacial Surgery, Tokyo Medical and Dental University, Tokyo, Japan
| | - Sumiyo Saburi
- Department of Otolaryngology-Head and Neck Surgery, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Junichi Mitsuda
- Department of Otolaryngology-Head and Neck Surgery, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Kanako Yoshimura
- Department of Otolaryngology-Head and Neck Surgery, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Alisa Kimura
- Department of Otolaryngology-Head and Neck Surgery, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Hiroki Morimoto
- Department of Otolaryngology-Head and Neck Surgery, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Hiroshi Ogi
- Department of Pathology and Applied Neurobiology, Kyoto Prefectural University of Medicine, Kyoto, Japan
- SCREEN Holdings, Kyoto, Japan
| | | | - Takumi Akashi
- Department of Diagnostic Pathology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Morito Kurata
- Department of Comprehensive Pathology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Issei Imoto
- Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Yasushi Shimizu
- Department of Medical Oncology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Satoshi Kano
- Department of Otolaryngology-Head and Neck Surgery, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Akihito Watanabe
- Department of Otolaryngology- Head and Neck Surgery, Keiyukai Sapporo Hospital, Sapporo, Japan
| | - Tomoko Yamazaki
- Department Head and Neck Oncology Division, Saitama Medical University International Medical Center, Hidaka, Japan
| | - Yukinori Asada
- Department of Head and Neck Surgery, Miyagi Cancer Center, Natori, Japan
| | - Ryuichi Hayashi
- Department of Head and Neck Surgery, National Cancer Center Hospital East, Kashiwa, Japan
| | - Yuki Saito
- Department of Otolaryngology-Head and Neck Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Ozawa
- Department of Otorhinolaryngology, Head and Neck Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Kiyoaki Tsukahara
- Department of Otorhinolaryngology, Head and Neck Surgery, Tokyo Medical University, Tokyo, Japan
| | - Nobuhiko Oridate
- Department of Otorhinolaryngology, Head and Neck Surgery, Yokohama City University, School of Medicine, Yokohama, Japan
| | - Daisuke Sano
- Department of Otorhinolaryngology, Head and Neck Surgery, Yokohama City University, School of Medicine, Yokohama, Japan
| | - Arata Horii
- Department of Otolaryngology Head and Neck Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Yushi Ueki
- Department of Otolaryngology Head and Neck Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Takashi Maruo
- Department of Otorhinolaryngology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Nobuaki Mukoyama
- Department of Otorhinolaryngology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Nobuhiro Hanai
- Department of Head and Neck Surgery, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Takahito Fukusumi
- Department of Otorhinolaryngology-Head and Neck Surgery, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Hiroshi Iwai
- Department of Otolaryngology, Head and Neck Surgery, Kansai Medical University Hospital, Osaka, Japan
| | - Takuo Fujisawa
- Department of Otolaryngology, Head and Neck Surgery, Kansai Medical University Hospital, Osaka, Japan
| | - Takashi Fujii
- Department of Head and Neck Surgery, Osaka International Cancer Institute, Osaka, Japan
| | - Ken-ichi Nibu
- Department of Otolaryngology–Head and Neck Surgery, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Shigemichi Iwae
- Department of Head and Neck Surgery, Hyogo Cancer Center, Akashi, Japan
| | - Tsutomu Ueda
- Department of Otolaryngology and Head and Neck Surgery, Hiroshima University Hospital, Hiroshima, Japan
| | - Nobuyuki Chikuie
- Department of Otolaryngology and Head and Neck Surgery, Hiroshima University Hospital, Hiroshima, Japan
| | - Ryuji Yasumatsu
- Department of Otorhinolaryngology-Head and Neck Surgery, Faculty of Medicine, Kindai University, Osaka, Japan
| | - Mioko Matsuo
- Department of Otorhinolaryngology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hirohito Umeno
- Department of Otolaryngology-Head and Neck Surgery, Kurume University School of Medicine, Kurume, Japan
| | - Takeharu Ono
- Department of Otolaryngology-Head and Neck Surgery, Kurume University School of Medicine, Kurume, Japan
| | - Muneyuki Masuda
- Department of Head and Neck Surgery, National Hospital Organization Kyushu Cancer Center, Fukuoka, Japan
| | - Satoshi Toh
- Department of Head and Neck Surgery, National Hospital Organization Kyushu Cancer Center, Fukuoka, Japan
| | - Kyoko Itoh
- Department of Pathology and Applied Neurobiology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Shigeru Hirano
- Department of Otolaryngology-Head and Neck Surgery, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Takahiro Asakage
- Department of Head and Neck Surgery, Tokyo Medical and Dental University, Tokyo, Japan
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Kim JY, Park K, Park WY, Ahn JS, Im YH, Lee JE, Kim SW, Nam SJ, Yu J, Park YH. Prognostic value of structural variants in early breast cancer patients. NPJ Breast Cancer 2024; 10:64. [PMID: 39068172 PMCID: PMC11283467 DOI: 10.1038/s41523-024-00669-9] [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: 01/03/2024] [Accepted: 07/08/2024] [Indexed: 07/30/2024] Open
Abstract
Genomic analysis of structural variants(SVs) in breast cancer (BC) patients has been conducted, but the relationship between genomic alterations and BC prognosis remains unclear. We performed RNA sequencing of 297 early BC fresh-frozen tissues. We identified SVs using three tools (STAR.Arriba, STAR.fusion, and STAR.SEQR) with the COSMIC and Mitelman databases as guide references. We found a median of five to eight fusions per sample. In BC intrinsic subtypes, normal subtype had the fewest fusions (median: 1, interquartile range [IQR]: 0, 3) followed by luminal A (median: 5.5, IQR: 2.75, 10.25), luminal B (median: 9, IQR: 6, 16.5), HER2-enriched (median: 9, IQR: 6, 16.5) and basal (median 10, IQR: 6, 15.5) subtypes (p < 0.05). Intrachromosomal fusion was more frequent observed rather than interchromosomal fusion. In location, chromosome 17 had the most fusions followed by chromosome 1 and 11. When samples were divided into high and low fusion groups based on a cut-off value of 11 fusions, five-year event-free survival (5Y-EFS) was 68.1% in the high fusion group (n = 72) and 80.1% in the low fusion group (n = 125) (p = 0.024) while 75.6% among all patients (95% confidence interval: 0.699, 0.819). Among BC subtype, TNBCs with more fusions had shorter EFS compared to those with fewer fusions (5Y-EFS rate: 65.1% vs. 85.7%; p = 0.013) but no EFS differences were observed in other BC subtypes. ESTIMATE ImmuneScore was also associated with the number of fusions in TNBC (p < 0.005) and TNBCs with high ImmuneScore had better 5Y-EFS compared to those with low ImmuneScore (p = 0.041). In conclusion, diverse fusions were observed by BC subtype, and the number of fusions was associated with BC survival outcome and immune status in TNBC.
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Affiliation(s)
- Ji-Yeon Kim
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Kyunghee Park
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea
| | - Woong-Yang Park
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea
| | - Jin Seok Ahn
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Young-Hyuck Im
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jeong Eon Lee
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Seok Won Kim
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Seok Jin Nam
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jonghan Yu
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Yeon Hee Park
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University School of Medicine, Seoul, Korea.
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Zhang X, Feng R, Xu Y, Yang L, Xie F, Yang H, Wang S, Peng Y, Liu M, Wang C, Wang S. Baseline circulating tumor DNA predicts long-term survival outcomes for patients with early breast cancer. Gland Surg 2024; 13:684-696. [PMID: 38845832 PMCID: PMC11150192 DOI: 10.21037/gs-24-115] [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: 04/11/2024] [Accepted: 05/14/2024] [Indexed: 06/09/2024]
Abstract
Background Circulating tumor DNA (ctDNA) is a potential biomarker not only capable of monitoring the treatment response during neoadjuvant therapy (NAT) or rescue therapy, but also identifying minimal residual disease (MRD) and detecting early relapses after primary treatment. However, it remains uncertain whether the detection of ctDNA at diagnosis, before any treatment, can predict the prognosis for patients with early breast cancer. The objective of our study was to evaluate the predictive value of baseline ctDNA for prognosis in patients with early breast cancer. Methods A total of 90 patients with early breast cancer and 24 healthy women were recruited between August 2016 and October 2016. Peripheral blood samples were collected from patients at diagnosis, before any treatment. Blood samples were processed and subjected to targeted deep sequencing with a next-generation sequencing (NGS) panel of 1,021 cancer-related genes. The recurrence-free survival (RFS) and invasive disease-free survival (iDFS) were reported. Results The 90 patients with breast cancer included 6 patients with ductal carcinoma in situ (DCIS) and 84 patients with invasive breast cancer. Within the cohort of patients with invasive breast cancer, ctDNA were detected in 57 patients, with a ctDNA detection rate of 67.9%. Meanwhile, no ctDNA was detected in DCIS patients. Among 84 patients with invasive breast cancer, patients with high-level ctDNA had a significantly lower RFS compared to patients with low-level ctDNA (log-rank P=0.0036). Conclusions Our study suggested that ctDNA at diagnosis, before any treatment, could potentially serve as a biomarker to predict the prognosis for patients with early breast cancer. However, further follow-up and more studies with large sample sizes are required to confirm these findings.
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Affiliation(s)
- Xiangui Zhang
- Breast Center, Peking University People’s Hospital, Beijing, China
| | - Rui Feng
- Breast Surgery, Tianjin Central Hospital of Obstetrics and Gynecology, Nankai University Affiliated Maternity Hospital, Tianjin, China
| | - Yaqian Xu
- Breast Center, Peking University People’s Hospital, Beijing, China
| | - Liu Yang
- Breast Center, Peking University People’s Hospital, Beijing, China
| | - Fei Xie
- Breast Center, Peking University People’s Hospital, Beijing, China
| | - Houpu Yang
- Breast Center, Peking University People’s Hospital, Beijing, China
| | - Siyuan Wang
- Breast Center, Peking University People’s Hospital, Beijing, China
| | - Yuan Peng
- Breast Center, Peking University People’s Hospital, Beijing, China
| | - Miao Liu
- Breast Center, Peking University People’s Hospital, Beijing, China
| | - Chaobin Wang
- Breast Center, Peking University People’s Hospital, Beijing, China
| | - Shu Wang
- Breast Center, Peking University People’s Hospital, Beijing, China
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8
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Zhou J, Yu H, Zeng H, Shen Q, Wang X, Xia Q. Intrahepatic cholangiocarcinoma with FGFR alterations: A series of Chinese cases with an emphasis on their clinicopathologic and genetic features. Dig Liver Dis 2024:S1590-8658(24)00727-8. [PMID: 38734568 DOI: 10.1016/j.dld.2024.04.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 03/24/2024] [Accepted: 04/22/2024] [Indexed: 05/13/2024]
Abstract
Intrahepatic Cholangiocarcinoma (iCCA) with FGFR alterations is relatively rare, and its identification is important in the era of targeted therapy. We collected a large series of FGFR-altered cases in the Chinese population and characterized their clinicopathological and genetic features. Among the 18 FGFR-altered cases out of 260 iCCAs, 10 were males and 8 were females, ranging in age from 35 to 74 years (mean, 57.3 years; median, 58 years). Pathologically, they include 9 cases of large duct (LD, 50 %) and small duct (SD, 50 %) types each. All of them (100 %, 18/18) showed microsatellite stable (MSS) and low tumor mutation burden (TMB). Genetically, FGFR alterations involved FGFR1 (20 %), FGFR2 (70 %), and FGFR3 (10 %), with FGFR2 rearrangement accounting for the most (11/18). The most frequently altered genes/biological processes were development/proliferation-related pathways (44 %), chromatin organization (20 %), and tumor suppressors (32 %). Our study further revealed the clinicopathological and genetic features of FGFR-altered iCCA and demonstrated that its occurrence may show regional or ethnic variability and is less common in the Chinese population. A significant number of LD-type iCCA cases also have FGFR alterations rather than the SD type.
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Affiliation(s)
- Jun Zhou
- Department of Pathology, Zigong Fourth People's Hospital, Sichuan Province, Zigong, 643099, China.
| | - Haoran Yu
- Department of Pathology, Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, Henan, 450000, China
| | - Hong Zeng
- Department of Pathology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510120, China
| | - Qin Shen
- Nanjing Hospital of Traditional Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing, 210022, Jiangsu, China
| | - Xuewen Wang
- Department of Hepatobiliary Surgery, Zigong Fourth People's Hospital, Sichuan Province, Zigong, 643099, China
| | - Qinxin Xia
- Department of Pathology, Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, Henan, 450000, China.
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9
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Lauss M, Phung B, Borch TH, Harbst K, Kaminska K, Ebbesson A, Hedenfalk I, Yuan J, Nielsen K, Ingvar C, Carneiro A, Isaksson K, Pietras K, Svane IM, Donia M, Jönsson G. Molecular patterns of resistance to immune checkpoint blockade in melanoma. Nat Commun 2024; 15:3075. [PMID: 38594286 PMCID: PMC11004175 DOI: 10.1038/s41467-024-47425-y] [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: 07/27/2023] [Accepted: 04/02/2024] [Indexed: 04/11/2024] Open
Abstract
Immune checkpoint blockade (ICB) has improved outcome for patients with metastatic melanoma but not all benefit from treatment. Several immune- and tumor intrinsic features are associated with clinical response at baseline. However, we need to further understand the molecular changes occurring during development of ICB resistance. Here, we collect biopsies from a cohort of 44 patients with melanoma after progression on anti-CTLA4 or anti-PD1 monotherapy. Genetic alterations of antigen presentation and interferon gamma signaling pathways are observed in approximately 25% of ICB resistant cases. Anti-CTLA4 resistant lesions have a sustained immune response, including immune-regulatory features, as suggested by multiplex spatial and T cell receptor (TCR) clonality analyses. One anti-PD1 resistant lesion harbors a distinct immune cell niche, however, anti-PD1 resistant tumors are generally immune poor with non-expanded TCR clones. Such immune poor microenvironments are associated with melanoma cells having a de-differentiated phenotype lacking expression of MHC-I molecules. In addition, anti-PD1 resistant tumors have reduced fractions of PD1+ CD8+ T cells as compared to ICB naïve metastases. Collectively, these data show the complexity of ICB resistance and highlight differences between anti-CTLA4 and anti-PD1 resistance that may underlie differential clinical outcomes of therapy sequence and combination.
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Affiliation(s)
- Martin Lauss
- Division of Oncology, Department of Clinical Sciences, Faculty of Medicine, Lund University, 22185, Lund, Sweden
- Lund University Cancer Center, LUCC, Lund, Sweden
| | - Bengt Phung
- Division of Oncology, Department of Clinical Sciences, Faculty of Medicine, Lund University, 22185, Lund, Sweden
- Lund University Cancer Center, LUCC, Lund, Sweden
| | - Troels Holz Borch
- National Center for Cancer Immune Therapy, Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
| | - Katja Harbst
- Division of Oncology, Department of Clinical Sciences, Faculty of Medicine, Lund University, 22185, Lund, Sweden
- Lund University Cancer Center, LUCC, Lund, Sweden
| | - Kamila Kaminska
- Division of Oncology, Department of Clinical Sciences, Faculty of Medicine, Lund University, 22185, Lund, Sweden
- Lund University Cancer Center, LUCC, Lund, Sweden
| | - Anna Ebbesson
- Division of Oncology, Department of Clinical Sciences, Faculty of Medicine, Lund University, 22185, Lund, Sweden
- Lund University Cancer Center, LUCC, Lund, Sweden
| | - Ingrid Hedenfalk
- Division of Oncology, Department of Clinical Sciences, Faculty of Medicine, Lund University, 22185, Lund, Sweden
- Lund University Cancer Center, LUCC, Lund, Sweden
| | - Joan Yuan
- Division of Molecular Hematology, Department of Laboratory Medicine, Faculty of Medicine, Lund University, 22185, Lund, Sweden
| | - Kari Nielsen
- Lund University Cancer Center, LUCC, Lund, Sweden
- Division of Dermatology, Skåne University Hospital and Department of Clinical Sciences, Faculty of Medicine, Lund University, 22185, Lund, Sweden
| | - Christian Ingvar
- Division of Surgery, Department of Clinical Sciences, Faculty of Medicine, Lund University, 22185, Lund, Sweden
| | - Ana Carneiro
- Division of Oncology, Department of Clinical Sciences, Faculty of Medicine, Lund University, 22185, Lund, Sweden
- Department of Hematology, Oncology and Radiation Physics, Skåne University Hospital Comprehensive Cancer Center, 22185, Lund, Sweden
| | - Karolin Isaksson
- Lund University Cancer Center, LUCC, Lund, Sweden
- Division of Surgery, Department of Clinical Sciences, Faculty of Medicine, Lund University, 22185, Lund, Sweden
- Department of Surgery, Kristianstad Hospital, 29133, Kristianstad, Sweden
| | - Kristian Pietras
- Lund University Cancer Center, LUCC, Lund, Sweden
- Division of Translational Cancer Research, Department of Laboratory Medicine, Faculty of Medicine, Lund University, 22185, Lund, Sweden
| | - Inge Marie Svane
- National Center for Cancer Immune Therapy, Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
| | - Marco Donia
- National Center for Cancer Immune Therapy, Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
| | - Göran Jönsson
- Division of Oncology, Department of Clinical Sciences, Faculty of Medicine, Lund University, 22185, Lund, Sweden.
- Lund University Cancer Center, LUCC, Lund, Sweden.
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10
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Mori T, Fujimaru T, Liu C, Patterson K, Yamamoto K, Suzuki T, Chiga M, Sekine A, Ubara Y, Miller DE, Zalusky MPG, Mandai S, Ando F, Mori Y, Kikuchi H, Susa K, Chong JX, Bamshad MJ, Tan YQ, Zhang F, Uchida S, Sohara E. CFAP47 is a novel causative gene implicated in X-linked polycystic kidney disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.04.05.24304760. [PMID: 38633811 PMCID: PMC11023651 DOI: 10.1101/2024.04.05.24304760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is a well-described condition in which ~80% of cases have a genetic explanation, while the genetic basis of sporadic cystic kidney disease in adults remains unclear in ~30% of cases. This study aimed to identify novel genes associated with polycystic kidney disease (PKD) in patients with sporadic cystic kidney disease in which a clear genetic change was not identified in established genes. A next-generation sequencing panel analyzed known genes related to renal cysts in 118 sporadic cases, followed by whole-genome sequencing on 47 unrelated individuals without identified candidate variants. Three male patients were found to have rare missense variants in the X-linked gene Cilia And Flagella Associated Protein 47 (CFAP47). CFAP47 was expressed in primary cilia of human renal tubules, and knockout mice exhibited vacuolation of tubular cells and tubular dilation, providing evidence that CFAP47 is a causative gene involved in cyst formation. This discovery of CFAP47 as a newly identified gene associated with PKD, displaying X-linked inheritance, emphasizes the need for further cases to understand the role of CFAP47 in PKD.
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Affiliation(s)
- Takayasu Mori
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takuya Fujimaru
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Chunyu Liu
- Soong Ching Ling Institute of Maternal and Child Health, International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Genetic Engineering, Institute of Medical Genetics and Genomics, Fudan University, Shanghai, China
| | - Karynne Patterson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Kohei Yamamoto
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takefumi Suzuki
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Motoko Chiga
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Akinari Sekine
- Department of Nephrology and Rheumatology, Toranomon Hospital, Japan
- Okinaka Memorial Institute for Medical Research, Toranomon Hospital, Tokyo, Japan
| | - Yoshifumi Ubara
- Department of Nephrology and Rheumatology, Toranomon Hospital, Japan
- Okinaka Memorial Institute for Medical Research, Toranomon Hospital, Tokyo, Japan
| | - Danny E Miller
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, 1959 NE Pacific Street, Box 357371, Seattle, WA, 98195, USA
- Brotman-Baty Institute for Precision Medicine, 1959 NE Pacific Street, Box 357657, Seattle, WA, 98195, USA
| | - Miranda PG Zalusky
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, 1959 NE Pacific Street, Box 357371, Seattle, WA, 98195, USA
| | - Shintaro Mandai
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Fumiaki Ando
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yutaro Mori
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hiroaki Kikuchi
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Koichiro Susa
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | | | - Jessica X. Chong
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, 1959 NE Pacific Street, Box 357371, Seattle, WA, 98195, USA
- Brotman-Baty Institute for Precision Medicine, 1959 NE Pacific Street, Box 357657, Seattle, WA, 98195, USA
| | - Michael J. Bamshad
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, 1959 NE Pacific Street, Box 357371, Seattle, WA, 98195, USA
- Brotman-Baty Institute for Precision Medicine, 1959 NE Pacific Street, Box 357657, Seattle, WA, 98195, USA
| | - Yue-Qiu Tan
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
| | - Feng Zhang
- Soong Ching Ling Institute of Maternal and Child Health, International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Genetic Engineering, Institute of Medical Genetics and Genomics, Fudan University, Shanghai, China
| | - Shinichi Uchida
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Eisei Sohara
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
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11
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Illini O, Saalfeld FC, Christopoulos P, Duruisseaux M, Vikström A, Peled N, Demedts I, Dudnik E, Eisert A, Hashemi SMS, Janzic U, Kian W, Mohorcic K, Mohammed S, Silvoniemi M, Rothschild SI, Schulz C, Wesseler C, Addeo A, Armster K, Itchins M, Ivanović M, Kauffmann-Guerrero D, Koivunen J, Kuon J, Pavlakis N, Piet B, Sebastian M, Velthaus-Rusik JL, Wannesson L, Wiesweg M, Wurm R, Albers-Leischner C, Aust DE, Janning M, Fabikan H, Herold S, Klimova A, Loges S, Sharapova Y, Schütz M, Weinlinger C, Valipour A, Overbeck TR, Griesinger F, Jakopovic M, Hochmair MJ, Wermke M. Mobocertinib in Patients with EGFR Exon 20 Insertion-Positive Non-Small Cell Lung Cancer (MOON): An International Real-World Safety and Efficacy Analysis. Int J Mol Sci 2024; 25:3992. [PMID: 38612799 PMCID: PMC11012872 DOI: 10.3390/ijms25073992] [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: 02/26/2024] [Revised: 03/28/2024] [Accepted: 03/29/2024] [Indexed: 04/14/2024] Open
Abstract
EGFR exon 20 (EGFR Ex20) insertion mutations in non-small cell lung cancer (NSCLC) are insensitive to traditional EGFR tyrosine kinase inhibitors (TKIs). Mobocertinib is the only approved TKI specifically designed to target EGFR Ex20. We performed an international, real-world safety and efficacy analysis on patients with EGFR Ex20-positive NSCLC enrolled in a mobocertinib early access program. We explored the mechanisms of resistance by analyzing postprogression biopsies, as well as cross-resistance to amivantamab. Data from 86 patients with a median age of 67 years and a median of two prior lines of treatment were analyzed. Treatment-related adverse events (TRAEs) occurred in 95% of patients. Grade ≥3 TRAEs were reported in 38% of patients and included diarrhea (22%) and rash (8%). In 17% of patients, therapy was permanently discontinued, and two patients died due to TRAEs. Women were seven times more likely to discontinue treatment than men. In the overall cohort, the objective response rate to mobocertinib was 34% (95% CI, 24-45). The response rate in treatment-naïve patients was 27% (95% CI, 8-58). The median progression-free and overall survival was 5 months (95% CI, 3.5-6.5) and 12 months (95% CI, 6.8-17.2), respectively. The intracranial response rate was limited (13%), and one-third of disease progression cases involved the brain. Mobocertinib also showed antitumor activity following EGFR Ex20-specific therapy and vice versa. Potential mechanisms of resistance to mobocertinib included amplifications in MET, PIK3CA, and NRAS. Mobocertinib demonstrated meaningful efficacy in a real-world setting but was associated with considerable gastrointestinal and cutaneous toxicity.
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Affiliation(s)
- Oliver Illini
- Department of Respiratory and Critical Care Medicine, Klinik Floridsdorf, Vienna Healthcare Group, Bruenner Straße 68, A-1210 Vienna, Austria (M.J.H.)
- Karl Landsteiner Institute of Lung Research and Pulmonary Oncology, A-1210 Vienna, Austria
| | - Felix Carl Saalfeld
- Clinic for Internal Medicine I, University Hospital Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; (F.C.S.); (M.W.)
- National Center for Tumor Diseases, 01307 Dresden, Germany
- National Network Genomic Medicine Lung Cancer (nNGM), 50937 Cologne, Germany
| | - Petros Christopoulos
- National Network Genomic Medicine Lung Cancer (nNGM), 50937 Cologne, Germany
- Thoraxklinik and Translational Lung Research Center (TLRC), member of the German Center for Lung Research (DZL), Heidelberg University Hospital, 69126 Heidelberg, Germany
| | - Michaël Duruisseaux
- Respiratory Department and Early Phase, Louis Pradel Hospital, Hospices Civils de Lyon Cancer Institute, 69002 Lyon, France
- Oncopharmacology Laboratory, Cancer Research Center of Lyon, Unité Mixte de Recherche (UMR), Institut National de la Santé et de la Recherche Médicale (INSERM), 1052 Centre National de la Recherche Scientifique (CNRS), 5286 Lyon, France
- Université Claude Bernard, Université de Lyon, 69622 Villeurbanne cedex, France
| | - Anders Vikström
- Department of Pulmonary Medicine, University Hospital Linköping, 58185 Linköping, Sweden
| | - Nir Peled
- The Hemsely Cancer Center, Shaare Zedek Medical Center, Jerusalem 9103102, Israel
| | - Ingel Demedts
- Department of Pulmonary Diseases, AZ Delta, Deltalaan 1, 8800 Roeselare, Belgium;
| | - Elizabeth Dudnik
- Head, Thoracic Oncology Service, Assuta Medical Centers, Tel-Aviv 6329302, Israel
- Faculty of Health Sciences, Ben-Gurion Unversity of the Negev, Be’er Sheva 84105, Israel
| | - Anna Eisert
- National Network Genomic Medicine Lung Cancer (nNGM), 50937 Cologne, Germany
- Lung Cancer Group Cologne, Department I for Internal Medicine and Center for Integrated Oncology Aachen Bonn Cologne Dusseldorf, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50937 Cologne, Germany
| | - Sayed M. S. Hashemi
- Department of Pulmonary Medicine, Amsterdam UMC, VU University Medical Center, Cancer Center Amsterdam, 1081 Amsterdam, The Netherlands
| | - Urska Janzic
- Medical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; (U.J.)
- Medical Oncology Unit, University Clinic Golnik, 4204 Golnik, Slovenia
| | - Waleed Kian
- The Hemsely Cancer Center, Shaare Zedek Medical Center, Jerusalem 9103102, Israel
- Institute of Oncology, Assuta Ashdod University Hospital, Ashdod 7747629, Israel
| | - Katja Mohorcic
- Medical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia; (U.J.)
| | - Saara Mohammed
- Kent Oncology Centre, Maidstone and Tunbridge Wells NHS Trust, Kent TN24QJ, UK
| | - Maria Silvoniemi
- Department of Pulmonary Diseases, Turku University Hospital, University of Turku, 20014 Turku, Finland
| | - Sacha I. Rothschild
- Center for Oncology & Hematology and Comprehensive Cancer Center, Cantonal Hospital Baden, 5404 Baden, Switzerland
| | - Christian Schulz
- National Network Genomic Medicine Lung Cancer (nNGM), 50937 Cologne, Germany
- Department of Internal Medicine II, University Hospital, 93053 Regensburg, Germany
| | - Claas Wesseler
- National Network Genomic Medicine Lung Cancer (nNGM), 50937 Cologne, Germany
- Department of Pneumology, Asklepios Tumorzentrum Hamburg, Klinikum Harburg, 21075 Hamburg, Germany
| | - Alfredo Addeo
- Oncology Department, University Hospital Geneva, 1205 Geneva, Switzerland
| | - Karin Armster
- Department of Pneumology, Universitätsklinikum Krems, 3500 Krems an der Donau, Austria
| | - Malinda Itchins
- Department of Medical Oncology, Royal North Shore Hospital, St Leonards, NSW 2065, Australia
- Northern Clinical School, University of Sydney, St Leonards, NSW 2065, Australia
| | - Marija Ivanović
- Department of Oncology, University Medical Centre Maribor, 2000 Maribor, Slovenia
| | - Diego Kauffmann-Guerrero
- National Network Genomic Medicine Lung Cancer (nNGM), 50937 Cologne, Germany
- Division of Respiratory Medicine and Thoracic Oncology, Department of Medicine V, Thoracic Oncology Center Munich, University Hospital, University of Munich (LMU), 81377 Munich, Germany
| | - Jussi Koivunen
- Department of Oncology and Radiotherapy, Oulu University Hospital, 90014 Oulu, Finland
- Cancer and Translational Medicine Research Unit, University of Oulu, 90014 Oulu, Finland
- Medical Research Center Oulu, 90014 Oulu, Finland
| | - Jonas Kuon
- Department Thoracic Oncology, SLK Fachklinik Löwenstein, 74245 Löwenstein, Germany
| | - Nick Pavlakis
- Department of Medical Oncology, Royal North Shore Hospital, St Leonards, NSW 2065, Australia
- Northern Clinical School, University of Sydney, St Leonards, NSW 2065, Australia
| | - Berber Piet
- Department of Respiratory Medicine, Radboudumc, 6225 GA Nijmegen, The Netherlands
| | - Martin Sebastian
- National Network Genomic Medicine Lung Cancer (nNGM), 50937 Cologne, Germany
- Department of Medicine, Hematology/Oncology, University Hospital, University of Frankfurt, 60596 Frankfurt am Main, Germany
| | - Janna-Lisa Velthaus-Rusik
- National Network Genomic Medicine Lung Cancer (nNGM), 50937 Cologne, Germany
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald Comprehensive Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Luciano Wannesson
- Istituto Oncologico della Svizzera Italiana, 6500 Bellinzona, Switzerland
| | - Marcel Wiesweg
- National Network Genomic Medicine Lung Cancer (nNGM), 50937 Cologne, Germany
- West German Cancer Center, Department of Medical Oncology, University Duisburg-Essen, 45147 Essen, Germany
| | - Robert Wurm
- Division of Pulmonology, Department of Internal Medicine, LKH-Universitätsklinikum, Medical University of Graz, 8036 Graz, Austria
| | - Corinna Albers-Leischner
- National Network Genomic Medicine Lung Cancer (nNGM), 50937 Cologne, Germany
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald Comprehensive Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Daniela E. Aust
- National Network Genomic Medicine Lung Cancer (nNGM), 50937 Cologne, Germany
- Department for Pathology, University Hospital Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany
| | - Melanie Janning
- National Network Genomic Medicine Lung Cancer (nNGM), 50937 Cologne, Germany
- DKFZ-Hector Cancer Institute at the University Medical Center Mannheim, 68167 Mannheim, Germany
- Department of Personalized Oncology, University Hospital Mannheim, Heidelberg University, 68167 Mannheim, Germany
- Division of Personalized Medical Oncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- German Center for Lung Research (DZL), 69120 Heidelberg, Germany
| | - Hannah Fabikan
- Karl Landsteiner Institute of Lung Research and Pulmonary Oncology, A-1210 Vienna, Austria
| | - Sylvia Herold
- National Network Genomic Medicine Lung Cancer (nNGM), 50937 Cologne, Germany
- Department for Pathology, University Hospital Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany
| | - Anna Klimova
- Core Unit for Data Management and Analytics, National Center for Tumor Diseases, 01307 Dresden, Germany
| | - Sonja Loges
- National Network Genomic Medicine Lung Cancer (nNGM), 50937 Cologne, Germany
- DKFZ-Hector Cancer Institute at the University Medical Center Mannheim, 68167 Mannheim, Germany
- Department of Personalized Oncology, University Hospital Mannheim, Heidelberg University, 68167 Mannheim, Germany
- Division of Personalized Medical Oncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- German Center for Lung Research (DZL), 69120 Heidelberg, Germany
| | - Yana Sharapova
- National Network Genomic Medicine Lung Cancer (nNGM), 50937 Cologne, Germany
- DKFZ-Hector Cancer Institute at the University Medical Center Mannheim, 68167 Mannheim, Germany
- Department of Personalized Oncology, University Hospital Mannheim, Heidelberg University, 68167 Mannheim, Germany
- Division of Personalized Medical Oncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- German Center for Lung Research (DZL), 69120 Heidelberg, Germany
| | - Maret Schütz
- National Network Genomic Medicine Lung Cancer (nNGM), 50937 Cologne, Germany
- Department for Pathology, University Hospital Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany
| | - Christoph Weinlinger
- Karl Landsteiner Institute of Lung Research and Pulmonary Oncology, A-1210 Vienna, Austria
| | - Arschang Valipour
- Department of Respiratory and Critical Care Medicine, Klinik Floridsdorf, Vienna Healthcare Group, Bruenner Straße 68, A-1210 Vienna, Austria (M.J.H.)
- Karl Landsteiner Institute of Lung Research and Pulmonary Oncology, A-1210 Vienna, Austria
| | - Tobias Raphael Overbeck
- National Network Genomic Medicine Lung Cancer (nNGM), 50937 Cologne, Germany
- Department of Hematology and Medical Oncology, University Medical Center Göttingen, Göttingen University, 37075 Göttingen, Germany
| | - Frank Griesinger
- National Network Genomic Medicine Lung Cancer (nNGM), 50937 Cologne, Germany
- Department of Hematology and Oncology, Pius University Hospital, University Medicine Oldenburg, 26121 Oldenburg, Germany
| | - Marko Jakopovic
- Department for Respiratory Diseases Jordanovac, University Hospital Center Zagreb, 10000 Zagreb, Croatia
- School of Medicine, University of Zagreb, 10000 Zagreb, Croatia
| | - Maximilian J. Hochmair
- Department of Respiratory and Critical Care Medicine, Klinik Floridsdorf, Vienna Healthcare Group, Bruenner Straße 68, A-1210 Vienna, Austria (M.J.H.)
- Karl Landsteiner Institute of Lung Research and Pulmonary Oncology, A-1210 Vienna, Austria
| | - Martin Wermke
- Clinic for Internal Medicine I, University Hospital Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany; (F.C.S.); (M.W.)
- National Center for Tumor Diseases, 01307 Dresden, Germany
- National Network Genomic Medicine Lung Cancer (nNGM), 50937 Cologne, Germany
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Kasai S, Tamai M, Sugihara E, Oishi N, Hinata K, Akahane K, Goi K, Hata Y, Kondo T, Mitsui T, Tanaka M, Inukai T. In utero tumor development and identification of CTNNB1 mutation in a newborn case of ossifying renal tumor of infancy. Pediatr Blood Cancer 2024; 71:e30868. [PMID: 38217079 DOI: 10.1002/pbc.30868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/19/2023] [Accepted: 01/02/2024] [Indexed: 01/14/2024]
Affiliation(s)
- Shin Kasai
- Department of Pediatrics, Faculty of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Minori Tamai
- Department of Pediatrics, Faculty of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Eiji Sugihara
- Division of Gene Regulation, Cancer Center and Open Facility Center, Research Promotion Headquarters, Fujita Health University School of Medicine, Toyoake, Japan
| | - Naoki Oishi
- Department of Pathology, Faculty of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Kyoko Hinata
- Department of Pediatrics, Faculty of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Koshi Akahane
- Department of Pediatrics, Faculty of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Kumiko Goi
- Department of Pediatrics, Faculty of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Yuko Hata
- Division of Gene Regulation, Cancer Center and Open Facility Center, Research Promotion Headquarters, Fujita Health University School of Medicine, Toyoake, Japan
| | - Tetsuo Kondo
- Department of Pathology, Faculty of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Takahiko Mitsui
- Department of Urology, Faculty of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Mio Tanaka
- Department of Pathology, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Takeshi Inukai
- Department of Pediatrics, Faculty of Medicine, University of Yamanashi, Yamanashi, Japan
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13
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Fujimaru T, Mori T, Chiga M, Mandai S, Kikuchi H, Ando F, Mori Y, Susa K, Nakano Y, Shoji T, Fukudome Y, Inaba N, Kitamura K, Nakanishi T, Uchida K, Kimura T, Tamura T, Ozawa K, Uchida S, Sohara E. Genetic Diagnosis of Adult Hemodialysis Patients With Unknown Etiology. Kidney Int Rep 2024; 9:994-1004. [PMID: 38765603 PMCID: PMC11101786 DOI: 10.1016/j.ekir.2024.01.027] [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: 11/20/2023] [Revised: 12/20/2023] [Accepted: 01/15/2024] [Indexed: 05/22/2024] Open
Abstract
Introduction Kidney disease of unknown etiology accounts for 1 in 10 adult end-stage renal disease (ESRD) cases worldwide. The aim of this study is to clarify the genetic background of patients with chronic kidney disease (CKD) of unknown etiology who initiated renal replacement therapy (RRT) in adulthood. Methods This is a multicenter cross-sectional cohort study. Of the 1164 patients who attended 4 dialysis clinics in Japan, we first selected patients who started RRT between the ages of 20 and 49 years. After excluding patients with apparent causes of CKD (e.g., diabetic nephropathy, polycystic kidney disease (PKD) with family history, patients who underwent renal biopsy), 90 patients with CKD of unknown cause were included. The 298 genes associated with CKD were analyzed using capture-based targeted next-generation sequencing. Results Of the 90 patients, 10 (11.1%) had pathogenic variants in CKD-causing genes and 17 (18.9%) had variant of unknown significance (VUS). Three patients had PKD1 pathogenic variants, and 1 patient had PKD1 and COL4A4 pathogenic variants. In addition, 2 patients were diagnosed with atypical hemolytic uremic syndrome (aHUS) due to C3 or CFHR5. One patient each was diagnosed with Alport syndrome due to COL4A4 and COL4A3 variants, nephronophthisis due to NPHP1 variants, Fabry disease due to GLA variants, and autosomal-dominant tubulointerstitial kidney disease due to UMOD variants. Genetic diagnoses were not concordant with clinical diagnoses, except for patients with PKD1 variant. Conclusion This largest study on genetic analysis in hemodialysis-dependent adults revealed the presence of undiagnosed inherited kidney diseases.
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Affiliation(s)
- Takuya Fujimaru
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takayasu Mori
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Motoko Chiga
- Clinical Laboratory, Tokyo Medical and Dental University (TMDU) Hospital, Tokyo Japan
| | - Shintaro Mandai
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hiroaki Kikuchi
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Fumiaki Ando
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yutaro Mori
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Koichiro Susa
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yuta Nakano
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | | | | | - Naoto Inaba
- Kitakurihama Takuchi Clinic, Yokosuka, Japan
| | | | | | | | | | | | | | - Shinichi Uchida
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Eisei Sohara
- Department of Nephrology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
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14
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Jing X, Qin X, Liu H, Liu H, Wang H, Qin J, Zhang Y, Cao S, Fan X. DNA damage response alterations in clear cell renal cell carcinoma: clinical, molecular, and prognostic implications. Eur J Med Res 2024; 29:107. [PMID: 38326910 PMCID: PMC10848511 DOI: 10.1186/s40001-024-01678-x] [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: 08/11/2023] [Accepted: 09/08/2023] [Indexed: 02/09/2024] Open
Abstract
BACKGROUND DNA damage repair (DDR) pathways modulate cancer risk, progression, and therapeutic responses. Nonetheless, the characteristics and significance of DDR alterations in clear cell renal cell carcinoma (ccRCC) remain undefined. This study aimed to explore the predictive role, molecular mechanism, and tumor immune profile of DDR genes in ccRCC. METHODS We prospectively sequenced 757 tumors and matched blood DNA samples from Chinese patients with ccRCC using next-generation sequencing (NGS) and analyzed data from 537 patients from The Cancer Genome Atlas (TCGA). A comprehensive analysis was performed. RESULTS Fifty-two percent of Chinese patients with ccRCC harbored DDR gene mutations and 57% of TCGA patients. The immunotherapy treatment prognosis of patients with DDR gene mutations was superior to that of patients without DDR gene mutations (p = 0.047). DDR gene mutations were associated with more gene mutations and a higher tumor mutation load (TMB, p < 0.001). Moreover, patients with DDR gene mutations have a distinct mutational signature compared with those with wild-type DDR. Furthermore, the DDR-mut group had elevated neoantigen load (including single-nucleotide variants (SNV) and indel neoantigen load, p = 0.037 and p = 0.002, respectively), TCR Shannon (p = 0.025), and neutrophils (p = 0.010). DDR gene mutations exhibited a distinct immune profile with significantly higher expression levels of TNFSF9, CD70, ICAM1, and indoleamine-2,3-dioxygenase (IDO) and lower expression levels of VTCN1 and IL12A. CONCLUSIONS Our data suggest that the detection of somatic mutations in DDR genes can predict the efficacy of immunotherapy in patients with ccRCC. Furthermore, we revealed the unique molecular and immune mechanisms underlying ccRCC with DDR gene mutations.
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Affiliation(s)
- Xiao Jing
- Department of Urology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Xiangcheng Qin
- Department of Urology, Ningbo Urology and Nephrology Hospital, Ningbo, China
| | - Hao Liu
- Department of Urology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Huanhuan Liu
- Acornmed Biotechnology Co., Ltd., Beijing, China
| | - Huina Wang
- Acornmed Biotechnology Co., Ltd., Beijing, China
| | - Jiayue Qin
- Acornmed Biotechnology Co., Ltd., Beijing, China
| | - Yanui Zhang
- Acornmed Biotechnology Co., Ltd., Beijing, China
| | - Shanbo Cao
- Acornmed Biotechnology Co., Ltd., Beijing, China
| | - Xiaodong Fan
- Department of Urology, Ningbo Urology and Nephrology Hospital, Ningbo, China.
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15
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Chen J, Tang Y, Liu H, Sun G, Liu H, Zhao J, Wang Z, Zhang Y, Lou F, Cao S, Qin J, Wang H, Liao B, Zeng H. The mutational pattern of homologous recombination repair genes in urothelial carcinoma and its correlation with immunotherapeutic response. Cancer Med 2023; 12:22370-22380. [PMID: 37986697 PMCID: PMC10757100 DOI: 10.1002/cam4.6725] [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: 08/22/2023] [Revised: 11/03/2023] [Accepted: 11/07/2023] [Indexed: 11/22/2023] Open
Abstract
BACKGROUND The mutational pattern of homologous recombination repair (HRR)-associated gene alterations in Chinese urothelial carcinoma (UC) necessitates comprehensive sequencing efforts, and the clinical implications of HRR gene mutations in UC remain to be elucidated. MATERIALS AND METHODS We delineated the mutational landscape of 343 Chinese UC patients from West China Hospital and 822 patients from The Cancer Genome Atlas (TCGA) using next-generation sequencing (NGS). Data from 182 metastatic UC patients from MSK-IMPACT cohort were used to assess the association between HRR mutations and immunotherapy efficacy. Comprehensive transcriptomic analysis was performed to explore the impact of HRR mutations on tumor immune microenvironment. RESULTS Among Chinese UC patients, 34% harbored HRR gene mutations, with BRCA2, ATM, BRCA1, CDK12, and RAD51C being the most prevalently mutated genes. Mutational signatures contributing to UC differed between patients with and without HRR mutations. Signature 22 for exposure to aristolochic acid was only observed in Chinese UC patients. The presence of HRR mutations was correlated with higher tumor mutational burden, neoantigen burden, and PD-L1 expression. Importantly, patients with HRR mutations exhibited significantly improved prognosis following immunotherapy compared to those without HRR mutations. CONCLUSIONS Our findings provide valuable insights into the genomic landscape of Chinese UC patients and underscore the molecular rationale for utilizing immunotherapy in UC patients with HRR mutations.
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Affiliation(s)
- Junru Chen
- Department of Urology, Institute of Urology, West China HospitalSichuan UniversityChengduSichuanChina
| | - Yanfeng Tang
- Department of Urology, Institute of Urology, West China HospitalSichuan UniversityChengduSichuanChina
| | | | - Guangxi Sun
- Department of Urology, Institute of Urology, West China HospitalSichuan UniversityChengduSichuanChina
| | - Haoyang Liu
- Department of Urology, Institute of Urology, West China HospitalSichuan UniversityChengduSichuanChina
| | - Junjie Zhao
- Department of Urology, Institute of Urology, West China HospitalSichuan UniversityChengduSichuanChina
| | - Zilin Wang
- Department of Urology, Institute of Urology, West China HospitalSichuan UniversityChengduSichuanChina
| | | | - Feng Lou
- Acornmed Biotechnology Co., Ltd.BeijingChina
| | - Shanbo Cao
- Acornmed Biotechnology Co., Ltd.BeijingChina
| | - Jiayue Qin
- Acornmed Biotechnology Co., Ltd.TianjinChina
| | - Huina Wang
- Acornmed Biotechnology Co., Ltd.BeijingChina
| | - Banghua Liao
- Department of Urology, Institute of Urology, West China HospitalSichuan UniversityChengduSichuanChina
| | - Hao Zeng
- Department of Urology, Institute of Urology, West China HospitalSichuan UniversityChengduSichuanChina
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16
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Chi Y, Su M, Zhou D, Zheng F, Zhang B, Qiang L, Ren G, Song L, Bu B, Fang S, Yu B, Zhou J, Yu J, Li H. Dynamic analysis of circulating tumor DNA to predict the prognosis and monitor the treatment response of patients with metastatic triple-negative breast cancer: A prospective study. eLife 2023; 12:e90198. [PMID: 37929934 PMCID: PMC10627511 DOI: 10.7554/elife.90198] [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: 06/19/2023] [Accepted: 10/22/2023] [Indexed: 11/07/2023] Open
Abstract
Background Limited data are available on applying circulating tumor DNA (ctDNA) in metastatic triple-negative breast cancer (mTNBC) patients. Here, we investigated the value of ctDNA for predicting the prognosis and monitoring the treatment response in mTNBC patients. Methods We prospectively enrolled 70 Chinese patients with mTNBC who had progressed after ≤2 lines of chemotherapy and collected blood samples to extract ctDNA for 457-gene targeted panel sequencing. Results Patients with ctDNA+, defined by 12 prognosis-relevant mutated genes, had a shorter progression-free survival (PFS) than ctDNA- patients (5.16 months vs. 9.05 months, p=0.001), and ctDNA +was independently associated with a shorter PFS (HR, 95% CI: 2.67, 1.2-5.96; p=0.016) by multivariable analyses. Patients with a higher mutant-allele tumor heterogeneity (MATH) score (≥6.316) or a higher ctDNA fraction (ctDNA%≥0.05) had a significantly shorter PFS than patients with a lower MATH score (5.67 months vs.11.27 months, p=0.007) and patients with a lower ctDNA% (5.45 months vs. 12.17 months, p<0.001), respectively. Positive correlations with treatment response were observed for MATH score (R=0.24, p=0.014) and ctDNA% (R=0.3, p=0.002), but not the CEA, CA125, or CA153. Moreover, patients who remained ctDNA +during dynamic monitoring tended to have a shorter PFS than those who did not (3.90 months vs. 6.10 months, p=0.135). Conclusions ctDNA profiling provides insight into the mutational landscape of mTNBC and may reliably predict the prognosis and treatment response of mTNBC patients. Funding This work was supported by the National Natural Science Foundation of China (Grant No. 81902713), Natural Science Foundation of Shandong Province (Grant No. ZR2019LZL018), Breast Disease Research Fund of Shandong Provincial Medical Association (Grant No. YXH2020ZX066), the Start-up Fund of Shandong Cancer Hospital (Grant No. 2020-PYB10), Beijing Science and Technology Innovation Fund (Grant No. KC2021-ZZ-0010-1).
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Affiliation(s)
- Yajing Chi
- Department of Breast Medical Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical SciencesJinanChina
- School of Medicine, Nankai UniversityTianjinChina
| | - Mu Su
- Department of Bioinformatics, Berry Oncology CorporationBeijingChina
| | - Dongdong Zhou
- Department of Breast Medical Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical SciencesJinanChina
| | - Fangchao Zheng
- Department of Breast Medical Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical SciencesJinanChina
| | - Baoxuan Zhang
- Department of Breast Medical Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical SciencesJinanChina
| | - Ling Qiang
- Department of Breast Medical Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical SciencesJinanChina
| | - Guohua Ren
- Department of Breast Medical Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical SciencesJinanChina
| | - Lihua Song
- Department of Breast Medical Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical SciencesJinanChina
| | - Bing Bu
- Department of Breast Medical Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical SciencesJinanChina
| | - Shu Fang
- Department of Breast Medical Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical SciencesJinanChina
| | - Bo Yu
- Department of Bioinformatics, Berry Oncology CorporationBeijingChina
| | - Jinxing Zhou
- Department of Bioinformatics, Berry Oncology CorporationBeijingChina
| | - Jinming Yu
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical SciencesJinanChina
| | - Huihui Li
- Department of Breast Medical Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical SciencesJinanChina
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Pan Y, Zhang JT, Gao X, Chen ZY, Yan B, Tan PX, Yang XR, Gao W, Gong Y, Tian Z, Liu SYM, Lin H, Sun H, Huang J, Liu SY, Yan HH, Dong S, Xu CR, Chen HJ, Wang Z, Li P, Guan Y, Wang BC, Yang JJ, Tu HY, Yang XN, Zhong WZ, Xia X, Yi X, Zhou Q, Wu YL. Dynamic circulating tumor DNA during chemoradiotherapy predicts clinical outcomes for locally advanced non-small cell lung cancer patients. Cancer Cell 2023; 41:1763-1773.e4. [PMID: 37816331 DOI: 10.1016/j.ccell.2023.09.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/28/2023] [Accepted: 09/06/2023] [Indexed: 10/12/2023]
Abstract
The value of circulating tumor DNA (ctDNA) during chemoradiotherapy (CRT) remains unclear but is critical for detecting molecular residual disease (MRD). In this prospective study, we sequenced 761 blood samples from 139 patients with locally advanced non-small cell lung cancer treated with definitive radiation therapy (RT). ctDNA concentrations showed a significantly declining trend as CRT progressed at on-RT and after-RT time points versus baseline. Thirty-eight (27.3%) patients with early undetectable ctDNA at both on-RT (RT reached 40 Gy) and after-RT time points, indicating early response to CRT, had better survival outcomes for both with or without consolidation immune checkpoint inhibitors. Longitudinal undetectable MRD was found in 20.1% patients. The 2-year cancer-specific progression-free survival of these patients was 88.4%, corresponding to a potentially cured population. Further analysis revealed that pretreatment ctDNA variants serve as an essential MRD informed source. These data provide clinical insights for ctDNA-MRD detection.
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Affiliation(s)
- Yi Pan
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Jia-Tao Zhang
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Xuan Gao
- Geneplus-Beijing Institute, Beijing, China
| | - Zhi-Yong Chen
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Bingfa Yan
- Geneplus-Beijing Institute, Beijing, China
| | - Pei-Xin Tan
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Xiao-Rong Yang
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Wei Gao
- Geneplus-Beijing Institute, Beijing, China
| | - Yuhua Gong
- Geneplus-Beijing Institute, Beijing, China
| | - Zihan Tian
- Geneplus-Beijing Institute, Beijing, China
| | - Si-Yang Maggie Liu
- Department of Hematology, First Affiliated Hospital, Institute of Hematology, School of Medicine; Key Laboratory for Regenerative Medicine of Ministry of Education, Jinan University, Guangzhou, Guangdong, China; Chinese Thoracic Oncology Group (CTONG), Guangzhou, Guangdong, China
| | - Hui Lin
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Hao Sun
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Jie Huang
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Si-Yang Liu
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Hong-Hong Yan
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Song Dong
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Chong-Rui Xu
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Hua-Jun Chen
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Zhen Wang
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Pansong Li
- Geneplus-Beijing Institute, Beijing, China
| | | | - Bin-Chao Wang
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Jin-Ji Yang
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Hai-Yan Tu
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Xue-Ning Yang
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Wen-Zhao Zhong
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | | | - Xin Yi
- Geneplus-Beijing Institute, Beijing, China.
| | - Qing Zhou
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China.
| | - Yi-Long Wu
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China; Chinese Thoracic Oncology Group (CTONG), Guangzhou, Guangdong, China.
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18
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Liu L, Zhang X, Fan X, Zhu X. Genetic analysis of fundic gland‑type gastric adenocarcinoma. Mol Clin Oncol 2023; 19:82. [PMID: 37745263 PMCID: PMC10512195 DOI: 10.3892/mco.2023.2678] [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: 06/20/2023] [Accepted: 08/17/2023] [Indexed: 09/26/2023] Open
Abstract
This study aimed to analyze the molecular characteristics of gastric adenocarcinoma of the fundic-gland type (GAFG) and explore the possible mechanism of tumor development. Samples from 10 Chinese patients with GAFG were collected at the Peking University International Hospital and Liaocheng People's Hospital between January 2015 and March 2022. The nucleic acid sequence of Epstein Barr virus-encoded RNA (EBV-EBER) was detected by in situ hybridization. Genetic mutation information for GNAS, KRAS, NRAS, BRAF, PIK3CA, TP53, APC, CTNNB1, HER2, MLH1, MSH2, MSH6, and PMS2 was obtained by Next-Generation Sequencing, and the relevant literature was reviewed. A total of eight instances of missense mutations were detected, consisting of seven cases with GNAS mutations, two cases with KRAS mutations, and one case with a TP53 mutation. Additionally, two patients had simultaneous missense mutations in GNAS and KRAS. Nonsynonymous mutations in APC, CTNNB1, NRAS, BRAF, PIK3CA, HER2, MLH1, MSH2, MSH6, or PMS2 were not observed in any cases. In addition, all tumors were EBER-negative. GAFG exhibits diversity at the molecular level, and GNAS mutations are more common than KRAS mutations, TP53 mutations, and microsatellite instability. To date, no association between EBV/HER2 and GAFG has been found.
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Affiliation(s)
- Lei Liu
- Department of Pathology, Peking University International Hospital, Beijing 102206, P.R. China
| | - Xuedong Zhang
- Department of Pathology, Liaocheng People's Hospital, Liaocheng, Shandong 252000, P.R. China
| | - Xue Fan
- Department of Gastroenterology, Peking University International Hospital, Beijing 102206, P.R. China
| | - Xiaoyun Zhu
- Department of Pathology, Peking University International Hospital, Beijing 102206, P.R. China
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Ying L, Zhang C, Reuben A, Tian Y, Jin J, Wang C, Bai J, Liu X, Fang J, Feng T, Xu C, Zhu R, Huang M, Lyu Y, Lu T, Pan X, Zhang J, Su D. Immune-active tumor-adjacent tissues are associated with favorable prognosis in stage I lung squamous cell carcinoma. iScience 2023; 26:107732. [PMID: 37694148 PMCID: PMC10483046 DOI: 10.1016/j.isci.2023.107732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 07/07/2023] [Accepted: 08/21/2023] [Indexed: 09/12/2023] Open
Abstract
The immunogenomic features of tumor-adjacent lungs (TALs) in stage I lung squamous cell carcinoma (LUSC) are not clear. Multiomics analyses of tumor tissues and paired TALs from 59 stage I LUSC patients were performed. Compared to tumors, TALs exhibited a better-preserved immune contexture indicated by upregulation of immune pathways, increased immune infiltration, and higher expression of immune effector molecules. Notably, TALs had no mutations in PTEN and KEAP1, a lower incidence of human leukocyte antigen (HLA) loss and higher expression of HLA class I genes, major histocompatibility complex (MHC) I chaperones, and interferon (IFN)-γ-associated genes. Digital spatial profiling validated the generally higher immune infiltration in TALs and revealed a higher level of immune heterogeneity in LUSC tumors. Importantly, patients with higher immune infiltration in TALs had significantly longer survival, while high immune heterogeneity was associated with inferior patient survival. Our work can be considered in the selection of patients for adjuvant therapy, especially immunotherapy.
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Affiliation(s)
- Lisha Ying
- Zhejiang Cancer Institute, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | | | - Alexandre Reuben
- Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yiping Tian
- Department of Pathology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Jiaoyue Jin
- Department of Pathology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Canming Wang
- Department of Pathology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Jing Bai
- Geneplus-Beijing Institute, Beijing, China
| | - Xinyuan Liu
- Department of Pathology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- The Second Clinical Medical College, Zhejiang Chinese Medicine University, Hangzhou, Zhejiang 310053, China
| | - Jianfei Fang
- Department of Pathology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Tingting Feng
- Zhejiang Cancer Institute, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Department of Pathology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Chenyang Xu
- Department of Pathology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Rui Zhu
- Department of Pathology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Minran Huang
- Department of Pathology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Yingqi Lyu
- Department of Pathology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Department of Oncology, The First Clinical Medical College of Wenzhou Medical University, Wenzhou, Zhejiang 325015, China
| | - Tingting Lu
- Department of Pathology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Department of Oncology, The First Clinical Medical College of Wenzhou Medical University, Wenzhou, Zhejiang 325015, China
| | - Xiaodan Pan
- Human Tissue Bank, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Jianjun Zhang
- Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Dan Su
- Department of Pathology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
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Dantas NCB, Funari MFA, Lerário AM, Andrade NLM, Rezende RC, Cellin LP, Alves C, Crisostomo LG, Arnhold IJP, Mendonca B, Scalco RC, Jorge AAL. Identification of a second genetic alteration in patients with SHOX deficiency individuals: a potential explanation for phenotype variability. Eur J Endocrinol 2023; 189:387-395. [PMID: 37695807 DOI: 10.1093/ejendo/lvad128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/31/2023] [Accepted: 08/07/2023] [Indexed: 09/13/2023]
Abstract
OBJECTIVE Our study aimed to assess the impact of genetic modifiers on the significant variation in phenotype that is observed in individuals with SHOX deficiency, which is the most prevalent monogenic cause of short stature. DESIGN AND METHODS We performed a genetic analysis in 98 individuals from 48 families with SHOX deficiency with a target panel designed to capture the entire SHOX genomic region and 114 other genes that modulate growth and/or SHOX action. We prioritized rare potentially deleterious variants. RESULTS We did not identify potential deleterious variants in the promoter or intronic regions of the SHOX genomic locus. In contrast, we found eight heterozygous variants in 11 individuals from nine families in genes with a potential role as genetic modifiers. In addition to a previously described likely pathogenic (LP) variant in CYP26C1 observed in two families, we identified LP variants in PTHLH and ACAN, and variants of uncertain significance in NPR2, RUNX2, and TP53 in more affected individuals from families with SHOX deficiency. Families with a SHOX alteration restricted to the regulatory region had a higher prevalence of a second likely pathogenic variant (27%) than families with an alteration compromising the SHOX coding region (2.9%, P = .04). CONCLUSION In conclusion, variants in genes related to the growth plate have a potential role as genetic modifiers of the phenotype in individuals with SHOX deficiency. In individuals with SHOX alterations restricted to the regulatory region, a second alteration could be critical to determine the penetrance and expression of the phenotype.
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Affiliation(s)
- Naiara C B Dantas
- Unidade de Endocrinologia Genetica, Laboratorio de Endocrinologia Celular e Molecular LIM/25, Disciplina de Endocrinologia, Faculdade de Medicina da Universidade de Sao Paulo, 01246-903 Sao Paulo, SP, Brazil
| | - Mariana F A Funari
- Unidade de Endocrinologia do Desenvolvimento, Laboratorio de Hormonios e Genetica Molecular LIM/42, Disciplina de Endocrinologia, Faculdade de Medicina da Universidade de Sao Paulo, 05403-900 Sao Paulo, SP, Brazil
| | - Antonio M Lerário
- Department of Internal Medicine, Division of Endocrinology, Metabolism and Diabetes, University of Michigan, Ann Arbor, MI 48105, United States
| | - Nathalia L M Andrade
- Unidade de Endocrinologia Genetica, Laboratorio de Endocrinologia Celular e Molecular LIM/25, Disciplina de Endocrinologia, Faculdade de Medicina da Universidade de Sao Paulo, 01246-903 Sao Paulo, SP, Brazil
| | - Raíssa C Rezende
- Unidade de Endocrinologia Genetica, Laboratorio de Endocrinologia Celular e Molecular LIM/25, Disciplina de Endocrinologia, Faculdade de Medicina da Universidade de Sao Paulo, 01246-903 Sao Paulo, SP, Brazil
| | - Laurana P Cellin
- Unidade de Endocrinologia Genetica, Laboratorio de Endocrinologia Celular e Molecular LIM/25, Disciplina de Endocrinologia, Faculdade de Medicina da Universidade de Sao Paulo, 01246-903 Sao Paulo, SP, Brazil
| | - Crésio Alves
- Pediatric Endocrinology Unit, Hospital Universitario Prof. Edgard Santos, Faculdade de Medicina, Universidade Federal da Bahia, 40026-010 Salvador, BA, Brazil
| | - Lindiane G Crisostomo
- Department of Pediatrics, Centro Universitário Sao Camilo, 04263-200 Sao Paulo SP, Brazil
| | - Ivo J P Arnhold
- Unidade de Endocrinologia do Desenvolvimento, Laboratorio de Hormonios e Genetica Molecular LIM/42, Disciplina de Endocrinologia, Faculdade de Medicina da Universidade de Sao Paulo, 05403-900 Sao Paulo, SP, Brazil
| | - Berenice Mendonca
- Unidade de Endocrinologia do Desenvolvimento, Laboratorio de Hormonios e Genetica Molecular LIM/42, Disciplina de Endocrinologia, Faculdade de Medicina da Universidade de Sao Paulo, 05403-900 Sao Paulo, SP, Brazil
| | - Renata C Scalco
- Unidade de Endocrinologia Genetica, Laboratorio de Endocrinologia Celular e Molecular LIM/25, Disciplina de Endocrinologia, Faculdade de Medicina da Universidade de Sao Paulo, 01246-903 Sao Paulo, SP, Brazil
- Disciplina de Endocrinologia, Faculdade de Ciencias Medicas da Santa Casa de Sao Paulo, 01221-020 Sao Paulo SP, Brazil
| | - Alexander A L Jorge
- Unidade de Endocrinologia Genetica, Laboratorio de Endocrinologia Celular e Molecular LIM/25, Disciplina de Endocrinologia, Faculdade de Medicina da Universidade de Sao Paulo, 01246-903 Sao Paulo, SP, Brazil
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Du Y, Zhang S, Zhang G, Hu J, Zhao L, Xiong Y, Shen L, Chen R, Ye K, Xu Y. Mutational profiling of Chinese patients with thyroid cancer. Front Endocrinol (Lausanne) 2023; 14:1156999. [PMID: 37465126 PMCID: PMC10351985 DOI: 10.3389/fendo.2023.1156999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 06/12/2023] [Indexed: 07/20/2023] Open
Abstract
Background The incidence of thyroid cancer in China has rapidly increased in recent decades. As the genetic profiles of thyroid cancer vary dramatically between different geographical regions, a comprehensive genetic landscape of thyroid cancer in the Chinese population is urgently needed. Methods We retrospectively included thyroid cancer patients from three Chinese medical centers between February 2015 and August 2020. To dissect the genomic profiling of these patients, we performed targeted next-generation sequencing on their tumor tissues using a 1,021-gene panel. Results A total of 458 Chinese patients with thyroid cancer were enrolled, including four malignant histological subtypes arising from follicular epithelial thyroid cells. BRAF driver mutations were identified in 76.0% of patients, followed by RET rearrangements (7.6%) and RAS driver mutations (4.1%). Tumors with more somatic mutations correlated with worse clinical characteristics, including older age at diagnosis, less differentiation of tumor, larger tumor size, lymph node metastasis and distal metastasis. Subclonal BRAF mutations occurred in 20% (6/30) of patients and were frequent in poorly differentiated or anaplastic tumors (33.3% [2/6] vs. 4.2% [1/24], P = 0.09) and those with distal metastasis (50.0% [2/4] vs. 8.7% [2/23], P = 0.09). Tumors with TERT promoter mutations had significantly more somatic mutations (average: 6.5 vs. 1.8, P < 0.001). Moreover, TERT promoter mutations were not associated with lymph node metastasis but significantly associated with older age at diagnosis and poorly differentiated or anaplastic tumors, regardless of their clonal architecture. Conclusion Our results shed light on the molecular pathogenesis and clinical characteristics of thyroid cancer in the Chinese population. The number of somatic mutations, TERT promoter mutations, and the clonal architecture of BRAF mutations should be considered in the risk stratification of thyroid cancer.
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Affiliation(s)
- Yaying Du
- Department of Thyroid and Breast Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shu Zhang
- Department of Breast and Thyroid Surgery, Daping Hospital, Army Military Medical University, Chongqing, China
| | - Gang Zhang
- Department of Breast and Thyroid Surgery, Daping Hospital, Army Military Medical University, Chongqing, China
| | - Jiaying Hu
- Ultrasound Diagnostic Department, Daping Hospital, Army Military Medical University, Chongqing, China
| | - Lianhua Zhao
- Department of Pathology, Daping Hospital, Army Military Medical University, Chongqing, China
| | | | - Lu Shen
- Geneplus-Beijing, Beijing, China
| | | | - Ke Ye
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yan Xu
- Department of Breast and Thyroid Surgery, Daping Hospital, Army Military Medical University, Chongqing, China
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22
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Yang K, Yu W, Liu H, Lou F, Cao S, Wang H, He Z. Mutational pattern off homologous recombination repair (HRR)-related genes in upper tract urothelial carcinoma. Cancer Med 2023; 12:15304-15316. [PMID: 37387466 PMCID: PMC10417099 DOI: 10.1002/cam4.6175] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 04/25/2023] [Accepted: 05/19/2023] [Indexed: 07/01/2023] Open
Abstract
BACKGROUND Homologous recombination (HR) repair (HRR) has been indicated to be a biomarker for immunotherapy, chemotherapy, and poly-ADP ribose polymerase inhibitors inhibitors (PARPis). Nonetheless, their molecular correlates in upper tract urothelial carcinoma (UTUC) have not been well studied. This study aimed to explore the molecular mechanism and tumor immune profile of HRR genes and the relevance of their prognostic value in patients with UTUC. MATERIALS AND METHODS One hundred and ninety-seven tumors and matched blood samples from Chinese UTUC were subjected to next-generation sequencing. A total of 186 patients from The Cancer Genome Atlas were included. Comprehensive analysis was performed. RESULTS In Chinese patients with UTUC, 5.01% harbored germline HRR gene mutations, and 1.01% had Lynch syndrome-related genes. A total of 37.6% (74/197) of patients carried somatic or germline HRR gene mutations. There was marked discrepancy in the mutation landscapes, genetic interactions, and driver genes between the HRR-mut cohorts and HRR-wt cohorts. Aristolochic acid signatures and defective DNA mismatch repair signatures only existed in individuals in the HRR-mut cohorts. Inversely, the unknown signature (signature A) and signature SBS55 only existed in patients in the HRR-wt cohorts. HRR gene mutations regulated immune activities by NKT cells, plasmacytoid dendritic cells, hematopoietic stem cell, and M1 macrophages. In patients with local recurrence, patients with HRR gene mutations had poorer DFS rates than patients with wild-type HRR genes. CONCLUSIONS Our results imply that the detection of HRR gene mutations can predict recurrence in patients with UC. In addition, this study provides a path to explore the role of HRR-directed therapies, including PARPis, chemotherapy, and immunotherapy.
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Affiliation(s)
- Kaiwei Yang
- Department of urologyPeking University First HospitalBeijingChina
| | - Wei Yu
- Department of urologyPeking University First HospitalBeijingChina
| | | | - Feng Lou
- AcornMed Biotechnology Co., Ltd.BeijingChina
| | - Shanbo Cao
- AcornMed Biotechnology Co., Ltd.BeijingChina
| | - Huina Wang
- AcornMed Biotechnology Co., Ltd.BeijingChina
| | - Zhisong He
- Department of urologyPeking University First HospitalBeijingChina
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Han Y, Xiong Y, Lu T, Chen R, Liu Y, Tang H, Geng R, Wang Y. Genomic landscape and efficacy of HER2-targeted therapy in patients with HER2-mutant non-small cell lung cancer. Front Oncol 2023; 13:1121708. [PMID: 37077822 PMCID: PMC10106648 DOI: 10.3389/fonc.2023.1121708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/22/2023] [Indexed: 04/05/2023] Open
Abstract
BackgroundHER2-targeted therapy provides survival benefits to HER2-mutant non-small cell lung cancer (NSCLC). A better understanding of the clinical and genomic characterization of treatment-naïve HER2-positive NSCLC, as well as the efficacy of and resistance to HER2-targeted therapy in HER2-altered NSCLC, could promote further improvement of HER2 targeted therapy.MethodsHER2-altered NSCLC patients was retrospectively included and their genomic profiles were performed by next-generation sequencing. The clinical outcomes included overall response rate, disease control rate and progression-free survival.ResultsAmong 176 treatment-naïve patients with HER2 alterations, 64.8% harbored HER2 mutations with/without HER2 amplification, and 35.2% carried HER2 amplification only. Molecular characterization was correlated with tumor stage that late-stage NSCLC with HER2 oncogenic mutations showed a higher prevalence of TP53 mutations and a higher tumor mutation burden. However, this correlation was not found in patients with HER2 amplification only. Twenty-one patients with HER2 alterations treated with pyrotinib or afatinib were retrospectively enrolled. Pyrotinib yielded a longer median progression-free survival than afatinib (5.9 [95% CI, 3.8-13.0] vs. 4.0 months [95% CI, 1.9-6.3], P = 0.06) in these patients. Analysis of the genomic profiles before and after anti-HER2 targeted therapies identified de novo HER2 copy number gain and G518W mutation, as well as mutations involving DNA damage repair signaling, SWI–SNF complex, and epigenetic regulations as potential resistance mechanisms.ConclusionHER2-mutant NSCLC had different molecular features from HER2-amplified NSCLC, and its genomic profile was dependent of tumor stage. Pyrotinib had superior therapeutic effects than afatinib in HER2-altered NSCLC, although larger cohorts are warranted to validate it. HER2-dependent and -independent resistance mechanisms to afatinib and pyrotinib were unveiled.
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Affiliation(s)
- Yanjie Han
- Department of Medical Oncology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- 4 + 4 Medical Doctor (MD) Program, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | | | - Tao Lu
- Molecular Pathology Research Center, Department of Pathology, Peking Union Medical College Hospital, and Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | | | - Yuan Liu
- 4 + 4 Medical Doctor (MD) Program, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hui Tang
- 4 + 4 Medical Doctor (MD) Program, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ruixuan Geng
- Department of International Medical Services, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yingyi Wang
- Department of Medical Oncology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- *Correspondence: Yingyi Wang,
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24
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Madariaga A, Garg S, Tchrakian N, Dhani NC, Jimenez W, Welch S, MacKay H, Ethier JL, Gilbert L, Li X, Rodriguez A, Chan L, Bowering V, Clarke B, Zhang T, King I, Downs G, Stockley T, Wang L, Udagani S, Oza AM, Lheureux S. Clinical outcome and biomarker assessments of a multi-centre phase II trial assessing niraparib with or without dostarlimab in recurrent endometrial carcinoma. Nat Commun 2023; 14:1452. [PMID: 36922497 PMCID: PMC10017680 DOI: 10.1038/s41467-023-37084-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 03/02/2023] [Indexed: 03/18/2023] Open
Abstract
This multi-centre, non-randomized, open-label, phase II trial (NCT03016338), assessed niraparib monotherapy (cohort 1, C1), or niraparib and dostarlimab (cohort 2, C2) in patients with recurrent serous or endometrioid endometrial carcinoma. The primary endpoint was clinical benefit rate (CBR), with ≥5/22 overall considered of interest. Secondary outcomes were safety, objective response rate (ORR), duration of response, progression free survival and overall survival. Translational research was an exploratory outcome. Potential biomarkers were evaluated in archival tissue by immunohistochemistry and next generation sequencing panel. In C1, 25 patients were enrolled, and CBR was 20% (95% CI: 9-39) with median clinical benefit duration of 5.3 months. The ORR was 4% (95% CI: 0-20). In C2, 22 patients were enrolled, and the CBR was 31.8% (95% CI: 16-53) with median clinical benefit duration of 6.8 months. The ORR was 14% (95% CI: 3-35). No new safety signals were detected. No significant association was detected between clinical benefit and IHC markers (PTEN, p53, MMR, PD-L1), or molecular profiling (PTEN, TP53, homologous recombination repair genes). In conclusion, niraparib monotherapy did not meet the efficacy threshold. Niraparib in combination with dostarlimab showed modest activity.
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Affiliation(s)
- Ainhoa Madariaga
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- University of Toronto, Toronto, ON, Canada
- Autonomous University of Barcelona, Barcelona, Spain
- Department of Medical Oncology, 12 de Octubre University Hospital, Madrid, Spain
| | - Swati Garg
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Nairi Tchrakian
- University of Toronto, Toronto, ON, Canada
- Department of Pathology and Laboratory Medicine, University Health Network, Toronto, ON, Canada
| | - Neesha C Dhani
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- University of Toronto, Toronto, ON, Canada
| | - Waldo Jimenez
- Division of Gynecologic Oncology, Juravinski Cancer Centre, Hamilton, ON, Canada
| | - Stephen Welch
- Division of Medical Oncology and Hematology, London Health Sciences Center, London Regional Cancer Program, London, ON, Canada
| | - Helen MacKay
- Division of Medical Oncology and Hematology, Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Josee-Lyne Ethier
- Division of Medical Oncology and Hematology, Kingston Health Sciences Cancer Centre, Kingston, ON, Canada
| | - Lucy Gilbert
- Division of Gynecologic Oncology, McGill University Health Centre, Royal Victoria Hospital, Montréal, QC, Canada
| | - Xuan Li
- Department of Biostatistics, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Angela Rodriguez
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Lucy Chan
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Valerie Bowering
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Blaise Clarke
- University of Toronto, Toronto, ON, Canada
- Department of Pathology and Laboratory Medicine, University Health Network, Toronto, ON, Canada
| | - Tong Zhang
- Division of Clinical Laboratory Genetics, Laboratory Medicine Program, University Health Network, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Ian King
- Division of Clinical Laboratory Genetics, Laboratory Medicine Program, University Health Network, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Gregory Downs
- Division of Clinical Laboratory Genetics, Laboratory Medicine Program, University Health Network, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Tracy Stockley
- Division of Clinical Laboratory Genetics, Laboratory Medicine Program, University Health Network, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Lisa Wang
- University of Toronto, Toronto, ON, Canada
- Department of Biostatistics, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Smitha Udagani
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Amit M Oza
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- University of Toronto, Toronto, ON, Canada
| | - Stephanie Lheureux
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
- University of Toronto, Toronto, ON, Canada.
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25
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Pereira BJA, Marcondes Lerario A, Sola PR, Laurentino TDS, Mohan DR, de Almeida AN, Pires de Aguiar PH, da Silva Paiva W, Wakamatsu A, Teixeira MJ, Oba-Shinjo SM, Marie SKN. Impact of a cell cycle and an extracellular matrix remodeling transcriptional signature on tumor progression and correlation with EZH2 expression in meningioma. J Neurosurg 2023; 138:649-662. [PMID: 36029259 DOI: 10.3171/2022.7.jns22953] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 07/06/2022] [Indexed: 11/06/2022]
Abstract
OBJECTIVE The authors searched for genetic and transcriptional signatures associated with tumor progression and recurrence in their cohort of patients with meningiomas, combining the analysis of targeted exome, NF2-LOH, transcriptome, and protein expressions. METHODS The authors included 91 patients who underwent resection of intracranial meningioma at their institution between June 2000 and November 2007. The search of somatic mutations was performed by Next Generation Sequencing through a customized panel and multiplex ligation-dependent probe amplification for NF2 loss of heterozygosity. The transcriptomic profile was analyzed by QuantSeq 3' mRNA-Seq. The differentially expressed genes of interest were validated at the protein level analysis by immunohistochemistry. RESULTS The transcriptomic analysis identified an upregulated set of genes related to metabolism and cell cycle and downregulated genes related to immune response and extracellular matrix remodeling in grade 2 (atypical) meningiomas, with a significant difference in recurrent compared with nonrecurrent cases. EZH2 nuclear positivity associated with grade 2, particularly with recurrent tumors and EZH2 gene expression level, correlated positively with the expression of genes related to cell cycle and negatively to genes related to immune response and regulation of cell motility. CONCLUSIONS The authors identified modules of dysregulated genes in grade 2 meningiomas related to the activation of oxidative metabolism, cell division, cell motility due to extracellular remodeling, and immune evasion that were predictive of survival and exhibited significant correlations with EZH2 expression.
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Affiliation(s)
| | - Antonio Marcondes Lerario
- 2Department of Internal Medicine, Division of Metabolism, Endocrinology and Diabetes, University of Michigan, Ann Arbor, Michigan
| | - Paula Rodrigues Sola
- 1Department of Neurology, Laboratory of Molecular and Cellular Biology, University of São Paulo, São Paulo, Brazil
| | - Talita de Sousa Laurentino
- 1Department of Neurology, Laboratory of Molecular and Cellular Biology, University of São Paulo, São Paulo, Brazil
| | - Dipika R Mohan
- 3Medical Scientist Training Program, and Doctoral Program in Cancer Biology, University of Michigan, Ann Arbor, Michigan
| | | | - Paulo Henrique Pires de Aguiar
- 5Medical Research ABC Medical School, Santo André, Brazil.,6Pontifice Catholic University of São Paulo, Sorocaba, Brazil; and
| | | | - Alda Wakamatsu
- 7Department of Pathology, Hepatic Pathology Laboratory, University of São Paulo, São Paulo, Brazil
| | | | - Sueli Mieko Oba-Shinjo
- 1Department of Neurology, Laboratory of Molecular and Cellular Biology, University of São Paulo, São Paulo, Brazil
| | - Suely Kazue Nagahashi Marie
- 1Department of Neurology, Laboratory of Molecular and Cellular Biology, University of São Paulo, São Paulo, Brazil
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Gan M, Tai Z, Yu Y, Zhang C, Xu J. Next-generation sequencing shows the genomic features of ovarian clear cell cancer and compares the genetic architectures of high-grade serous ovarian cancer and clear cell carcinoma in ovarian and endometrial tissues. PeerJ 2023; 11:e14653. [PMID: 36721777 PMCID: PMC9884475 DOI: 10.7717/peerj.14653] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 12/07/2022] [Indexed: 01/27/2023] Open
Abstract
Ovarian clear cell carcinoma (OCCC) is a special histological type of epithelial ovarian cancer (EOC) that is not derived from epithelial cells of the ovarian or fallopian tube as the most common type of ovarian cancer, high-grade serous ovarian carcinoma (HGSOC), but is closely related to endometriosis and similar to endometrial clear cell carcinoma (ECCC) at morphologic and phenotypic features. However, limited data was shown in OCCC genomic features and compared with that in OCCC, HGSOC and ECCC. Herein, we utilized next-generation sequencing analysis of a panel of 1,021 genes to profile the mutational alterations in 34 OCCC and compared them to those from HGSOC (402 cases) and ECCC (30 cases). In result, the ARID1A and PIK3CA are high-frequency mutations of OCCC. Clonal architectures showed that all the mutations of genes occur in the later stage in the OCCC progress, whereas KRAS mutation is the earlier event compared with mutation of ARID1A or PIK3CA, which usually occurs in a group of ARID1A or PIK3CA mutations. The mutation frequency of main driver genes is similar between OCCC and ECCC, while TP53 is the main mutation in HGSOC and ECCC. Shared mutational signatures between OCCC and ECCC tissues with commonly observed a C>T change indicated a common carcinogens-exposed between these two carcinomas, but HGSOC and ECCC have common and distinct mutational signatures across cohorts respectively. In addition, we identified some novel CNV gains in NF1, ASXL1, TCF7L2, CREBBP and LRP1B and loss in ATM, FANCM, RB1 and FLT in OCCC. Our study offered a new perspective for OCCC tumorigenesis from two organs, the ovary and uterus, at genomic architectures and revealed novel CNV events for helping to provide theoretical support for OCCC treatment.
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Affiliation(s)
- Meifu Gan
- Department of Pathology, Taizhou Hospital affiliated to Wenzhou Medical University, Linhai, Zhejiang Province, China
| | - Zaixian Tai
- Geneplus Shenzhen, Shenzhen, Guangdong province, China
| | - Yijian Yu
- Department of Pathology, Taizhou Hospital affiliated to Wenzhou Medical University, Linhai, Zhejiang Province, China
| | - Chao Zhang
- Geneplus Shenzhen, Shenzhen, Guangdong province, China
| | - Juan Xu
- Department of Pathology, Taizhou Hospital affiliated to Wenzhou Medical University, Linhai, Zhejiang Province, China
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27
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Karali M, Testa F, Di Iorio V, Torella A, Zeuli R, Scarpato M, Romano F, Onore ME, Pizzo M, Melillo P, Brunetti-Pierri R, Passerini I, Pelo E, Cremers FPM, Esposito G, Nigro V, Simonelli F, Banfi S. Genetic epidemiology of inherited retinal diseases in a large patient cohort followed at a single center in Italy. Sci Rep 2022; 12:20815. [PMID: 36460718 PMCID: PMC9718770 DOI: 10.1038/s41598-022-24636-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 11/17/2022] [Indexed: 12/04/2022] Open
Abstract
Inherited retinal diseases (IRDs) are the leading cause of vision loss in the working-age population. We performed a retrospective epidemiological study to determine the genetic basis of IRDs in a large Italian cohort (n = 2790) followed at a single referral center. We provided, mainly by next generation sequencing, potentially conclusive molecular diagnosis for 2036 patients (from 1683 unrelated families). We identified a total of 1319 causative sequence variations in 132 genes, including 353 novel variants, and 866 possibly actionable genotypes for therapeutic approaches. ABCA4 was the most frequently mutated gene (n = 535; 26.3% of solved cases), followed by USH2A (n = 228; 11.2%) and RPGR (n = 102; 5.01%). The other 129 genes had a lower contribution to IRD pathogenesis (e.g. CHM 3.5%, RHO 3.5%; MYO7A 3.4%; CRB1 2.7%; RPE65 2%, RP1 1.8%; GUCY2D 1.7%). Seventy-eight genes were mutated in five patients or less. Mitochondrial DNA variants were responsible for 2.1% of cases. Our analysis confirms the complex genetic etiology of IRDs and reveals the high prevalence of ABCA4 and USH2A mutations. This study also uncovers genetic associations with a spectrum of clinical subgroups and highlights a valuable number of cases potentially eligible for clinical trials and, ultimately, for molecular therapies.
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Affiliation(s)
- Marianthi Karali
- grid.9841.40000 0001 2200 8888Medical Genetics, Department of Precision Medicine, Università degli Studi della Campania ’Luigi Vanvitelli’, Via Luigi De Crecchio 7, 80138 Naples, Italy ,grid.9841.40000 0001 2200 8888Multidisciplinary Department of Medical, Surgical and Dental Sciences, Eye Clinic, Università degli Studi della Campania ’Luigi Vanvitelli’, Via Pansini 5, 80131 Naples, Italy
| | - Francesco Testa
- grid.9841.40000 0001 2200 8888Multidisciplinary Department of Medical, Surgical and Dental Sciences, Eye Clinic, Università degli Studi della Campania ’Luigi Vanvitelli’, Via Pansini 5, 80131 Naples, Italy
| | - Valentina Di Iorio
- grid.9841.40000 0001 2200 8888Multidisciplinary Department of Medical, Surgical and Dental Sciences, Eye Clinic, Università degli Studi della Campania ’Luigi Vanvitelli’, Via Pansini 5, 80131 Naples, Italy
| | - Annalaura Torella
- grid.9841.40000 0001 2200 8888Medical Genetics, Department of Precision Medicine, Università degli Studi della Campania ’Luigi Vanvitelli’, Via Luigi De Crecchio 7, 80138 Naples, Italy ,grid.410439.b0000 0004 1758 1171Telethon Institute of Genetics and Medicine, Via Campi Flegrei 34, 80078 Pozzuoli, Italy
| | - Roberta Zeuli
- grid.9841.40000 0001 2200 8888Medical Genetics, Department of Precision Medicine, Università degli Studi della Campania ’Luigi Vanvitelli’, Via Luigi De Crecchio 7, 80138 Naples, Italy
| | - Margherita Scarpato
- grid.9841.40000 0001 2200 8888Medical Genetics, Department of Precision Medicine, Università degli Studi della Campania ’Luigi Vanvitelli’, Via Luigi De Crecchio 7, 80138 Naples, Italy
| | - Francesca Romano
- grid.9841.40000 0001 2200 8888Medical Genetics, Department of Precision Medicine, Università degli Studi della Campania ’Luigi Vanvitelli’, Via Luigi De Crecchio 7, 80138 Naples, Italy
| | - Maria Elena Onore
- grid.9841.40000 0001 2200 8888Medical Genetics, Department of Precision Medicine, Università degli Studi della Campania ’Luigi Vanvitelli’, Via Luigi De Crecchio 7, 80138 Naples, Italy
| | - Mariateresa Pizzo
- grid.410439.b0000 0004 1758 1171Telethon Institute of Genetics and Medicine, Via Campi Flegrei 34, 80078 Pozzuoli, Italy
| | - Paolo Melillo
- grid.9841.40000 0001 2200 8888Multidisciplinary Department of Medical, Surgical and Dental Sciences, Eye Clinic, Università degli Studi della Campania ’Luigi Vanvitelli’, Via Pansini 5, 80131 Naples, Italy
| | - Raffaella Brunetti-Pierri
- grid.9841.40000 0001 2200 8888Multidisciplinary Department of Medical, Surgical and Dental Sciences, Eye Clinic, Università degli Studi della Campania ’Luigi Vanvitelli’, Via Pansini 5, 80131 Naples, Italy
| | - Ilaria Passerini
- grid.24704.350000 0004 1759 9494Department of Genetic Diagnosis, Careggi Teaching Hospital, Florence, Italy
| | - Elisabetta Pelo
- grid.24704.350000 0004 1759 9494Department of Genetic Diagnosis, Careggi Teaching Hospital, Florence, Italy
| | - Frans P. M. Cremers
- grid.10417.330000 0004 0444 9382Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Gabriella Esposito
- grid.4691.a0000 0001 0790 385XDepartment of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Via Pansini 5, 80131 Naples, Italy ,CEINGE-Advanced Biotechnologies, Via G. Salvatore 486, 80145 Naples, Italy
| | - Vincenzo Nigro
- grid.9841.40000 0001 2200 8888Medical Genetics, Department of Precision Medicine, Università degli Studi della Campania ’Luigi Vanvitelli’, Via Luigi De Crecchio 7, 80138 Naples, Italy ,grid.410439.b0000 0004 1758 1171Telethon Institute of Genetics and Medicine, Via Campi Flegrei 34, 80078 Pozzuoli, Italy
| | - Francesca Simonelli
- grid.9841.40000 0001 2200 8888Multidisciplinary Department of Medical, Surgical and Dental Sciences, Eye Clinic, Università degli Studi della Campania ’Luigi Vanvitelli’, Via Pansini 5, 80131 Naples, Italy
| | - Sandro Banfi
- grid.9841.40000 0001 2200 8888Medical Genetics, Department of Precision Medicine, Università degli Studi della Campania ’Luigi Vanvitelli’, Via Luigi De Crecchio 7, 80138 Naples, Italy ,grid.410439.b0000 0004 1758 1171Telethon Institute of Genetics and Medicine, Via Campi Flegrei 34, 80078 Pozzuoli, Italy
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Chiu Y, Weng H, Lin Y, Lin Y, Yeh Y, Perng C, Ma H, Tsai S, Chou T. Genomic profiling with whole‐exome sequencing revealed distinct mutations and novel pathways in Asian melanoma. J Dermatol 2022; 49:1299-1309. [DOI: 10.1111/1346-8138.16579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 08/04/2022] [Accepted: 08/25/2022] [Indexed: 12/12/2022]
Affiliation(s)
- Yu‐Jen Chiu
- Institute of Clinical Medicine National Yang Ming Chiao Tung University Taipei Taiwan
- Division of Plastic and Reconstructive Surgery, Department of Surgery Taipei Veterans General Hospital Taipei Taiwan
- Department of Surgery, School of Medicine National Yang Ming Chiao Tung University Taipei Taiwan
| | - Hui‐Ying Weng
- Biomedical Industry PhD Program National Yang Ming Chiao Tung University Taipei Taiwan
| | - Yen‐Yu Lin
- Department of Pathology and Laboratory Medicine Taipei Veterans General Hospital Taipei Taiwan
| | - Yung‐Feng Lin
- Institute of Molecular and Genomic Medicine National Health Research Institutes Miaoli Taiwan
| | - Yi‐Chen Yeh
- Department of Pathology and Laboratory Medicine Taipei Veterans General Hospital Taipei Taiwan
| | - Chern‐Kang Perng
- Division of Plastic and Reconstructive Surgery, Department of Surgery Taipei Veterans General Hospital Taipei Taiwan
- Department of Surgery, School of Medicine National Yang Ming Chiao Tung University Taipei Taiwan
| | - Hsu Ma
- Division of Plastic and Reconstructive Surgery, Department of Surgery Taipei Veterans General Hospital Taipei Taiwan
- Department of Surgery, School of Medicine National Yang Ming Chiao Tung University Taipei Taiwan
- Department of Surgery National Defense Medical Center Taipei Taiwan
| | - Shih‐Feng Tsai
- Institute of Molecular and Genomic Medicine National Health Research Institutes Miaoli Taiwan
| | - Teh‐Ying Chou
- Institute of Clinical Medicine National Yang Ming Chiao Tung University Taipei Taiwan
- Department of Pathology and Laboratory Medicine Taipei Veterans General Hospital Taipei Taiwan
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29
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Andrade NLM, Funari MFDA, Malaquias AC, Collett-Solberg PF, Gomes NLRA, Scalco R, Dantas NCB, Rezende RC, Tiburcio AMFP, Souza MAR, Freire BL, Krepischi ACV, Longui CA, Lerario AM, Arnhold IJP, Jorge AAL, Vasques GA. Diagnostic yield of a multigene sequencing approach in children classified as idiopathic short stature. Endocr Connect 2022; 11:e220214. [PMID: 36373817 PMCID: PMC9716379 DOI: 10.1530/ec-22-0214] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 10/12/2022] [Indexed: 11/16/2022]
Abstract
Objective Most children with short stature remain without an etiologic diagnosis after extensive clinical and laboratory evaluation and are classified as idiopathic short stature (ISS). This study aimed to determine the diagnostic yield of a multigene analysis in children classified as ISS. Design and methods We selected 102 children with ISS and performed the genetic analysis as part of the initial investigation. We developed customized targeted panel sequencing, including all genes already implicated in the isolated short-stature phenotype. Rare and deleterious single nucleotide or copy number variants were assessed by bioinformatic tools. Results We identified 20 heterozygous pathogenic (P) or likely pathogenic (LP) genetic variants in 17 of 102 patients (diagnostic yield = 16.7%). Three patients had more than one P/LP genetic alteration. Most of the findings were in genes associated with the growth plate differentiation: IHH (n = 4), SHOX (n = 3), FGFR3 (n = 2), NPR2 (n = 2), ACAN (n = 2), and COL2A1 (n = 1) or involved in the RAS/MAPK pathway: NF1 (n = 2), PTPN11 (n = 1), CBL (n = 1), and BRAF (n = 1). None of these patients had clinical findings to guide a candidate gene approach. The diagnostic yield was higher among children with severe short stature (35% vs 12.2% for height SDS ≤ or > -3; P = 0.034). The genetic diagnosis had an impact on clinical management for four children. Conclusion A multigene sequencing approach can determine the genetic etiology of short stature in up to one in six children with ISS, removing the term idiopathic from their clinical classification.
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Affiliation(s)
| | - Mariana Ferreira de Assis Funari
- Unidade de Endocrinologia do Desenvolvimento, Laboratorio de Hormonios e Genetica Molecular (LIM42), Hospital das Clinicas da Faculdade de Medicina, Universidade de Sao Paulo (USP), Sao Paulo, Brasil
| | | | - Paulo Ferrez Collett-Solberg
- Disciplina de Endocrinologia, Departamento de Medicina Interna, Faculdade de Ciências Medicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Nathalia L R A Gomes
- Serviço de Endocrinologia, Unidade de Crescimento, Santa Casa de Belo Horizonte, Belo Horizonte, Minas Gerais, Brasil
| | - Renata Scalco
- Unidade de Endocrinologia do Desenvolvimento, Laboratorio de Hormonios e Genetica Molecular (LIM42), Hospital das Clinicas da Faculdade de Medicina, Universidade de Sao Paulo (USP), Sao Paulo, Brasil
- Departamento de Medicina, Faculdade de Ciencias Medicas da Santa Casa de Sao Paulo, Sao Paulo, Brasil
| | - Naiara Castelo Branco Dantas
- Unidade de Endocrinologia Genetica (LIM 25), Hospital das Clínicas da Faculdade de Medicina, Universidade de São Paulo (USP), Sao Paulo, Brasil
| | - Raissa C Rezende
- Unidade de Endocrinologia Genetica (LIM 25), Hospital das Clínicas da Faculdade de Medicina, Universidade de São Paulo (USP), Sao Paulo, Brasil
| | - Angelica M F P Tiburcio
- Serviço de Endocrinologia, Unidade de Crescimento, Santa Casa de Belo Horizonte, Belo Horizonte, Minas Gerais, Brasil
| | - Micheline A R Souza
- Serviço de Endocrinologia do Instituto de Puericultura e Pediatria Martagao Gesteira/Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Bruna L Freire
- Unidade de Endocrinologia Genetica (LIM 25), Hospital das Clínicas da Faculdade de Medicina, Universidade de São Paulo (USP), Sao Paulo, Brasil
- Unidade de Endocrinologia do Desenvolvimento, Laboratorio de Hormonios e Genetica Molecular (LIM42), Hospital das Clinicas da Faculdade de Medicina, Universidade de Sao Paulo (USP), Sao Paulo, Brasil
| | - Ana C V Krepischi
- Centro de Pesquisa em Genoma Humano e Células-Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de Sao Paulo, São Paulo, Brasil
| | - Carlos Alberto Longui
- Departamento de Pediatria, Faculdade de Ciencias Medicas da Santa Casa de Sao Paulo, Sao Paulo, Brasil
| | - Antonio Marcondes Lerario
- Division of Metabolism, Endocrinology and Diabetes, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Ivo J P Arnhold
- Unidade de Endocrinologia do Desenvolvimento, Laboratorio de Hormonios e Genetica Molecular (LIM42), Hospital das Clinicas da Faculdade de Medicina, Universidade de Sao Paulo (USP), Sao Paulo, Brasil
| | - Alexander A L Jorge
- Unidade de Endocrinologia Genetica (LIM 25), Hospital das Clínicas da Faculdade de Medicina, Universidade de São Paulo (USP), Sao Paulo, Brasil
- Unidade de Endocrinologia do Desenvolvimento, Laboratorio de Hormonios e Genetica Molecular (LIM42), Hospital das Clinicas da Faculdade de Medicina, Universidade de Sao Paulo (USP), Sao Paulo, Brasil
| | - Gabriela Andrade Vasques
- Unidade de Endocrinologia Genetica (LIM 25), Hospital das Clínicas da Faculdade de Medicina, Universidade de São Paulo (USP), Sao Paulo, Brasil
- Unidade de Endocrinologia do Desenvolvimento, Laboratorio de Hormonios e Genetica Molecular (LIM42), Hospital das Clinicas da Faculdade de Medicina, Universidade de Sao Paulo (USP), Sao Paulo, Brasil
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Zhang X, Yu Z, Xu Y, Chao Y, Hu Q, Li C, Ye M, Zhu X, Cui L, Bai J, Gong Y, Guan Y, Zhou M, Huang J, Zhang H, Ren T, Shen Q, Wang K, Hou Y, Xia X, Pu X, Carbone DP, Zhang X. Utility of cell-free DNA from bronchial washing fluid in diagnosis and genomic determination for radiology-suspected pulmonary nodules. Br J Cancer 2022; 127:2154-2165. [PMID: 36253524 PMCID: PMC9727069 DOI: 10.1038/s41416-022-01969-2] [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: 07/12/2021] [Revised: 07/05/2022] [Accepted: 08/23/2022] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Bronchial washing fluid (BWF) is a less-invasive specimen. Due to the limited sensitivity of BWF cellular component diagnosis, the aim of this study was to explore the potential role of BWF supernatant as a source of liquid biopsy of lung cancer. METHODS This prospective study enrolled 76 suspected and 5 progressed lung cancer patients. Transbronchial biopsy tissues, BWF supernatant (BWF_Sup) and BWF precipitant (BWF_Pre) were tested by a targeted panel of 1021 genes. RESULTS BWF_Sup cell-free DNA (cfDNA) was superior to tissue biopsy and BWF_Pre in determining mutational allele frequency, tumour mutational burden, and chromosomal instability. Moreover, BWF_Sup and BWF_Pre achieved comparable efficacy to tissue samples in differentiating malignant and benign patients, but only BWF_Sup persisted differentiated performance after excluding 55 malignancies pathologically diagnosed by bronchoscopic biopsy. Among 67 malignant patients, 82.1% and 71.6% of tumour-derived mutations (TDMs) were detected in BWF_Sup and BWF_Pre, respectively, and the detectability of TDMs in BWF_Sup was independent of the cytological examination of BWF. BWF_Sup outperformed BWF_Pre in providing more subclonal information and thus might yield advantage in tracking drug-resistant markers. CONCLUSIONS BWF_Sup cfDNA is a reliable medium for lung cancer diagnosis and genomic profiles and may provide important information for subsequent therapeutic regimens.
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Affiliation(s)
- Xinyu Zhang
- Zhongshan Hospital, Fudan University, No. 180 Fenglin Road, Xuhui District, 200032, Shanghai, China
| | - Zhuo Yu
- Beijing Tsinghua Changgung Hospital, 168 Litang Road, Changping District, 102218, Beijing, China
| | - Yaping Xu
- Geneplus-Beijing Institute, 9th Floor, No. 6 Building, Peking University Medical Industrial Park, Zhongguancun Life Science Park, 102206, Beijing, China
| | - Yencheng Chao
- Zhongshan Hospital, Fudan University, No. 180 Fenglin Road, Xuhui District, 200032, Shanghai, China
| | - Qin Hu
- Zhongshan Hospital, Fudan University, No. 180 Fenglin Road, Xuhui District, 200032, Shanghai, China
| | - Chun Li
- Zhongshan Hospital, Fudan University, No. 180 Fenglin Road, Xuhui District, 200032, Shanghai, China
| | - Maosong Ye
- Zhongshan Hospital, Fudan University, No. 180 Fenglin Road, Xuhui District, 200032, Shanghai, China
| | - Xiuli Zhu
- Geneplus-Beijing Institute, 9th Floor, No. 6 Building, Peking University Medical Industrial Park, Zhongguancun Life Science Park, 102206, Beijing, China
| | - Liang Cui
- Geneplus-Beijing Institute, 9th Floor, No. 6 Building, Peking University Medical Industrial Park, Zhongguancun Life Science Park, 102206, Beijing, China
| | - Jing Bai
- Geneplus-Beijing Institute, 9th Floor, No. 6 Building, Peking University Medical Industrial Park, Zhongguancun Life Science Park, 102206, Beijing, China
| | - Yuhua Gong
- Geneplus-Beijing Institute, 9th Floor, No. 6 Building, Peking University Medical Industrial Park, Zhongguancun Life Science Park, 102206, Beijing, China
| | - Yanfang Guan
- Geneplus-Beijing Institute, 9th Floor, No. 6 Building, Peking University Medical Industrial Park, Zhongguancun Life Science Park, 102206, Beijing, China
| | - Min Zhou
- Ruijin Hospital, Shanghai Jiao Tong University, No. 197 Ruijin Second Road, Huangpu District, 200025, Shanghai, China
| | - Jian'an Huang
- First People's Hospital, Suzhou University, No. 899 Pinghai Road, Gusu District, 215008, Suzhou, China
| | - Hua Zhang
- Zhengzhou Central Hospital, Zhengzhou University, No. 195 Tongbai Road, Zhongyuan District, 450000, Zhengzhou, China
| | - Tao Ren
- Shanghai Sixth People's Hospital, No 600 Yishan Road, Xuhui District, 200233, Shanghai, China
| | - Qian Shen
- First Affiliated Hospital of Zhejiang University, No. 79 Qingchun Road, Shangcheng District, 310002, Hangzhou, China
| | - Kai Wang
- Fourth Affiliated Hospital of Zhejiang University, No 88 Jiefang Road, Shangcheng District, 310002, Hangzhou, China
| | - Yingyong Hou
- Zhongshan Hospital, Fudan University, No. 180 Fenglin Road, Xuhui District, 200032, Shanghai, China
| | - Xuefeng Xia
- Geneplus-Beijing Institute, 9th Floor, No. 6 Building, Peking University Medical Industrial Park, Zhongguancun Life Science Park, 102206, Beijing, China
| | - Xingxiang Pu
- Department of Thoracic Medical Oncology, Hunan Cancer Hospital/the affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283 Tongzipo Road, Yuelu District, 410013, Changsha, Hunan, China.
| | - David P Carbone
- Comprehensive Cancer Center, The Ohio State University, 460W 12th Ave., Columbus, OH, 43210, USA.
| | - Xin Zhang
- Zhongshan Hospital, Fudan University, No. 180 Fenglin Road, Xuhui District, 200032, Shanghai, China.
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Kumar AA, Loeys B, Van De Beek G, Peeters N, Wuyts W, Van Laer L, Vandeweyer G, Alaerts M. varAmpliCNV: analyzing variance of amplicons to detect CNVs in targeted NGS data. Bioinformatics 2022; 39:6849518. [PMID: 36440912 PMCID: PMC9805572 DOI: 10.1093/bioinformatics/btac756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 09/30/2022] [Accepted: 11/25/2022] [Indexed: 11/30/2022] Open
Abstract
MOTIVATION Computational identification of copy number variants (CNVs) in sequencing data is a challenging task. Existing CNV-detection methods account for various sources of variation and perform different normalization strategies. However, their applicability and predictions are restricted to specific enrichment protocols. Here, we introduce a novel tool named varAmpliCNV, specifically designed for CNV-detection in amplicon-based targeted resequencing data (Haloplex™ enrichment protocol) in the absence of matched controls. VarAmpliCNV utilizes principal component analysis (PCA) and/or metric dimensional scaling (MDS) to control variances of amplicon associated read counts enabling effective detection of CNV signals. RESULTS Performance of VarAmpliCNV was compared against three existing methods (ConVaDING, ONCOCNV and DECoN) on data of 167 samples run with an aortic aneurysm gene panel (n = 30), including 9 positive control samples. Additionally, we validated the performance on a large deafness gene panel (n = 145) run on 138 samples, containing 4 positive controls. VarAmpliCNV achieved higher sensitivity (100%) and specificity (99.78%) in comparison to competing methods. In addition, unsupervised clustering of CNV segments and visualization plots of amplicons spanning these regions are included as a downstream strategy to filter out false positives. AVAILABILITY AND IMPLEMENTATION The tool is freely available through galaxy toolshed and at: https://hub.docker.com/r/cmgantwerpen/varamplicnv. Supplementary Data File S1: https://tinyurl.com/2yzswyhh; Supplementary Data File S2: https://tinyurl.com/ycyf2fb4. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ajay Anand Kumar
- Center of Medical Genetics, University of Antwerp/Antwerp University Hospital, Antwerp (Edegem) 2650, Belgium,Biomedical Informatics, Antwerp University Hospital, Antwerp (Wilrijk) 2610, Belgium,Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom,European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom
| | - Bart Loeys
- Center of Medical Genetics, University of Antwerp/Antwerp University Hospital, Antwerp (Edegem) 2650, Belgium
| | - Gerarda Van De Beek
- Center of Medical Genetics, University of Antwerp/Antwerp University Hospital, Antwerp (Edegem) 2650, Belgium
| | - Nils Peeters
- Center of Medical Genetics, University of Antwerp/Antwerp University Hospital, Antwerp (Edegem) 2650, Belgium
| | - Wim Wuyts
- Center of Medical Genetics, University of Antwerp/Antwerp University Hospital, Antwerp (Edegem) 2650, Belgium
| | - Lut Van Laer
- Center of Medical Genetics, University of Antwerp/Antwerp University Hospital, Antwerp (Edegem) 2650, Belgium
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Li Y, Yang X, Zhu W, Xu Y, Ma J, He C, Wang F. SWI/SNF complex gene variations are associated with a higher tumor mutational burden and a better response to immune checkpoint inhibitor treatment: a pan-cancer analysis of next-generation sequencing data corresponding to 4591 cases. Cancer Cell Int 2022; 22:347. [DOI: 10.1186/s12935-022-02757-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 10/20/2022] [Indexed: 11/15/2022] Open
Abstract
Abstract
Background
Genes related to the SWItch/sucrose nonfermentable (SWI/SNF) chromatin remodeling complex are frequently mutated across cancers. SWI/SNF-mutant tumors are vulnerable to synthetic lethal inhibitors. However, the landscape of SWI/SNF mutations and their associations with tumor mutational burden (TMB), microsatellite instability (MSI) status, and response to immune checkpoint inhibitors (ICIs) have not been elucidated in large real-world Chinese patient cohorts.
Methods
The mutational rates and variation types of six SWI/SNF complex genes (ARID1A, ARID1B, ARID2, SMARCA4, SMARCB1, and PBRM1) were analyzed retrospectively by integrating next-generation sequencing data of 4591 cases covering 18 cancer types. Thereafter, characteristics of SWI/SNF mutations were depicted and the TMB and MSI status and therapeutic effects of ICIs in the SWI/SNF-mutant and SWI/SNF-non-mutant groups were compared.
Results
SWI/SNF mutations were observed in 21.8% of tumors. Endometrial (54.1%), gallbladder and biliary tract (43.4%), and gastric (33.9%) cancers exhibited remarkably higher SWI/SNF mutational rates than other malignancies. Further, ARID1A was the most frequently mutated SWI/SNF gene, and ARID1A D1850fs was identified as relatively crucial. The TMB value, TMB-high (TMB-H), and MSI-high (MSI-H) proportions corresponding to SWI/SNF-mutant cancers were significantly higher than those corresponding to SWI/SNF-non-mutant cancers (25.8 vs. 5.6 mutations/Mb, 44.3% vs. 10.3%, and 16.0% vs. 0.9%, respectively; all p < 0.0001). Furthermore, these indices were even higher for tumors with co-mutations of SWI/SNF genes and MLL2/3. Regarding immunotherapeutic effects, patients with SWI/SNF variations showed significantly longer progression-free survival (PFS) rates than their SWI/SNF-non-mutant counterparts (hazard ratio [HR], 0.56 [95% confidence interval {CI} 0.44–0.72]; p < 0.0001), and PBRM1 mutations were associated with relatively better ICI treatment outcomes than the other SWI/SNF gene mutations (HR, 0.21 [95% CI 0.12–0.37]; p = 0.0007). Additionally, patients in the SWI/SNF-mutant + TMB-H (HR, 0.48 [95% CI 0.37–0.54]; p < 0.0001) cohorts had longer PFS rates than those in the SWI/SNF-non-mutant + TMB-low cohort.
Conclusions
SWI/SNF complex genes are frequently mutated and are closely associated with TMB-H status, MSI-H status, and superior ICI treatment response in several cancers, such as colorectal cancer, gastric cancer, and non-small cell lung cancer. These findings emphasize the necessity and importance of molecular-level detection and interpretation of SWI/SNF complex mutations.
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Zaremba A, Jansen P, Murali R, Mayakonda A, Riedel A, Philip M, Rose C, Schaller J, Müller H, Kutzner H, Möller I, Stadtler N, Kretz J, Sucker A, Bankfalvi A, Livingstone E, Zimmer L, Horn S, Paschen A, Plass C, Schadendorf D, Hadaschik E, Lutsik P, Griewank K. Genetic and methylation profiles distinguish benign, malignant and spitzoid melanocytic tumors. Int J Cancer 2022; 151:1542-1554. [PMID: 35737508 PMCID: PMC9474633 DOI: 10.1002/ijc.34187] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 04/26/2022] [Accepted: 05/04/2022] [Indexed: 11/07/2022]
Abstract
Accurate classification of melanocytic tumors is important for prognostic evaluation, treatment and follow-up protocols of patients. The majority of melanocytic proliferations can be classified solely based on clinical and pathological criteria, however in select cases a definitive diagnostic assessment remains challenging and additional diagnostic biomarkers would be advantageous. We analyzed melanomas, nevi, Spitz nevi and atypical spitzoid tumors using parallel sequencing (exons of 611 genes and 507 gene translocation analysis) and methylation arrays (850k Illumina EPIC). By combining detailed genetic and epigenetic analysis with reference-based and reference-free DNA methylome deconvolution we compared Spitz nevi to nevi and melanoma and assessed the potential for these methods in classifying challenging spitzoid tumors. Results were correlated with clinical and histologic features. Spitz nevi were found to cluster independently of nevi and melanoma and demonstrated a different mutation profile. Multiple copy number alterations and TERT promoter mutations were identified only in melanomas. Genome-wide methylation in Spitz nevi was comparable to benign nevi while the Leukocytes UnMethylation for Purity (LUMP) algorithm in Spitz nevi was comparable to melanoma. Histologically difficult to classify Spitz tumor cases were assessed which, based on methylation arrays, clustered between Spitz nevi and melanoma and in terms of genetic profile or copy number variations demonstrated worrisome features suggesting a malignant neoplasm. Comprehensive sequencing and methylation analysis verify Spitz nevi as an independent melanocytic entity distinct from both nevi and melanoma. Combined genetic and methylation assays can offer additional insights in diagnosing difficult to classify Spitzoid tumors.
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Affiliation(s)
- Anne Zaremba
- Department of Dermatology, University Hospital Essen, University of Duisburg-Essen, Germany, and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Philipp Jansen
- Department of Dermatology, University Hospital Essen, University of Duisburg-Essen, Germany, and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Rajmohan Murali
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Anand Mayakonda
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Helmholtz International Graduate School for Cancer Research, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Anna Riedel
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Helmholtz International Graduate School for Cancer Research, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Manuel Philip
- Department of Dermatology, University Hospital Essen, University of Duisburg-Essen, Germany, and German Cancer Consortium (DKTK), Heidelberg, Germany
| | | | | | | | - Heinz Kutzner
- Dermatopathologie Friedrichshafen, Medical faculty of the University Leipzig, Leipzig, Germany
| | - Inga Möller
- Department of Dermatology, University Hospital Essen, University of Duisburg-Essen, Germany, and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Nadine Stadtler
- Department of Dermatology, University Hospital Essen, University of Duisburg-Essen, Germany, and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Julia Kretz
- Department of Dermatology, University Hospital Essen, University of Duisburg-Essen, Germany, and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Antje Sucker
- Department of Dermatology, University Hospital Essen, University of Duisburg-Essen, Germany, and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Agnes Bankfalvi
- Department of Pathology, University Hospital Essen, University of Duisburg-Essen, Germany, and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Elisabeth Livingstone
- Department of Dermatology, University Hospital Essen, University of Duisburg-Essen, Germany, and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Lisa Zimmer
- Department of Dermatology, University Hospital Essen, University of Duisburg-Essen, Germany, and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Susanne Horn
- Department of Dermatology, University Hospital Essen, University of Duisburg-Essen, Germany, and German Cancer Consortium (DKTK), Heidelberg, Germany
- Rudolf-Schönheimer-Institute of Biochemistry, Medical faculty of the University Leipzig, Leipzig, Germany
| | - Annette Paschen
- Department of Dermatology, University Hospital Essen, University of Duisburg-Essen, Germany, and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dirk Schadendorf
- Department of Dermatology, University Hospital Essen, University of Duisburg-Essen, Germany, and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Eva Hadaschik
- Department of Dermatology, University Hospital Essen, University of Duisburg-Essen, Germany, and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Pavlo Lutsik
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Klaus Griewank
- Department of Dermatology, University Hospital Essen, University of Duisburg-Essen, Germany, and German Cancer Consortium (DKTK), Heidelberg, Germany
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Rosa-Rosa JM, Cuenca I, Medina A, Vázquez I, Sánchez-delaCruz A, Buenache N, Sánchez R, Jiménez C, Rosiñol L, Gutiérrez NC, Ruiz-Heredia Y, Barrio S, Oriol A, Martin-Ramos ML, Blanchard MJ, Ayala R, Ríos-Tamayo R, Sureda A, Hernández MT, de la Rubia J, Alkorta-Aranburu G, Agirre X, Bladé J, Mateos MV, Lahuerta JJ, San-Miguel JF, Calasanz MJ, Garcia-Sanz R, Martínez-Lopez J. NGS-Based Molecular Karyotyping of Multiple Myeloma: Results from the GEM12 Clinical Trial. Cancers (Basel) 2022; 14:cancers14205169. [PMID: 36291952 PMCID: PMC9601262 DOI: 10.3390/cancers14205169] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/07/2022] [Accepted: 10/12/2022] [Indexed: 12/01/2022] Open
Abstract
Simple Summary Multiple Myeloma (MM) is considered an incurable chronic disease, which prognosis depends on the presence of different genomic alterations. To accomplish a complete molecular diagnosis in a single essay, we have designed and validated a capture-based NGS approach to reliably identify pathogenic mutations (SNVs and indels), genomic alterations (CNVs and chromosomic translocations), and IGH rearrangements. We have observed a good correlation of the results obtained using our capture panel with data obtained by both FISH and WES techniques. In this study, the molecular classification performed using our approach was significantly associated with the stratification and outcome of MM patients. Additionally, this panel has been proven to detect specific IGH rearrangements that could be used as biomarkers in patient follow-ups through minimal residual disease (MRD) assays. In conclusion, we think that MM patients could benefit from the use of this capture-based NGS approach with a more accurate, single-essay molecular diagnosis. Abstract Next-generation sequencing (NGS) has greatly improved our ability to detect the genomic aberrations occurring in multiple myeloma (MM); however, its transfer to routine clinical labs and its validation in clinical trials remains to be established. We designed a capture-based NGS targeted panel to identify, in a single assay, known genetic alterations for the prognostic stratification of MM. The NGS panel was designed for the simultaneous study of single nucleotide and copy number variations, insertions and deletions, chromosomal translocations and V(D)J rearrangements. The panel was validated using a cohort of 149 MM patients enrolled in the GEM2012MENOS65 clinical trial. The results showed great global accuracy, with positive and negative predictive values close to 90% when compared with available data from fluorescence in situ hybridization and whole-exome sequencing. While the treatments used in the clinical trial showed high efficacy, patients defined as high-risk by the panel had shorter progression-free survival (p = 0.0015). As expected, the mutational status of TP53 was significant in predicting patient outcomes (p = 0.021). The NGS panel also efficiently detected clonal IGH rearrangements in 81% of patients. In conclusion, molecular karyotyping using a targeted NGS panel can identify relevant prognostic chromosomal abnormalities and translocations for the clinical management of MM patients.
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Affiliation(s)
- Juan Manuel Rosa-Rosa
- Hematology Department, Hospital 12 de Octubre, 28041 Madrid, Spain
- H12O–CNIO Hematological Malignancies Clinical Research Unit, Spanish National Cancer Research (CNIO), 29029 Madrid, Spain
- Correspondence: (J.M.R.-R.); (J.M.-L.)
| | - Isabel Cuenca
- Hematology Department, Hospital 12 de Octubre, 28041 Madrid, Spain
- H12O–CNIO Hematological Malignancies Clinical Research Unit, Spanish National Cancer Research (CNIO), 29029 Madrid, Spain
| | - Alejandro Medina
- Unidad de Biología Molecular-HLA, Laboratorio de Hematología, Hospital Universitario de Salamanca, 37007 Salamanca, Spain
| | - Iria Vázquez
- Center for Applied Medical Research (CIMA) LAB Diagnostics, Universidad de Navarra, 31008 Pamplona, Spain
| | - Andrea Sánchez-delaCruz
- H12O–CNIO Hematological Malignancies Clinical Research Unit, Spanish National Cancer Research (CNIO), 29029 Madrid, Spain
| | - Natalia Buenache
- Hematology Department, Hospital 12 de Octubre, 28041 Madrid, Spain
- H12O–CNIO Hematological Malignancies Clinical Research Unit, Spanish National Cancer Research (CNIO), 29029 Madrid, Spain
| | - Ricardo Sánchez
- Hematology Department, Hospital 12 de Octubre, 28041 Madrid, Spain
- H12O–CNIO Hematological Malignancies Clinical Research Unit, Spanish National Cancer Research (CNIO), 29029 Madrid, Spain
| | - Cristina Jiménez
- Unidad de Biología Molecular-HLA, Laboratorio de Hematología, Hospital Universitario de Salamanca, 37007 Salamanca, Spain
- Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), 37007 Salamanca, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Laura Rosiñol
- Hospital Clinic de Barcelona, 08036 Barcelona, Spain
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain
| | - Norma C. Gutiérrez
- Unidad de Biología Molecular-HLA, Laboratorio de Hematología, Hospital Universitario de Salamanca, 37007 Salamanca, Spain
- Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), 37007 Salamanca, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Yanira Ruiz-Heredia
- Hematology Department, Hospital 12 de Octubre, 28041 Madrid, Spain
- H12O–CNIO Hematological Malignancies Clinical Research Unit, Spanish National Cancer Research (CNIO), 29029 Madrid, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Santiago Barrio
- Hematology Department, Hospital 12 de Octubre, 28041 Madrid, Spain
- H12O–CNIO Hematological Malignancies Clinical Research Unit, Spanish National Cancer Research (CNIO), 29029 Madrid, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Albert Oriol
- Clinical Research Support Unit, Institut Català d’Oncologia, 08036 Barcelona, Spain
| | | | | | - Rosa Ayala
- Hematology Department, Hospital 12 de Octubre, 28041 Madrid, Spain
| | | | - Anna Sureda
- Institut Catalá d’Oncologia-l’Hospitalet, Institut de Investigació Biomèdica de Bellvitge (IDIBELL), Universitat de Barcelona, 08908 Barcelona, Spain
| | | | | | - Gorka Alkorta-Aranburu
- Center for Applied Medical Research (CIMA) LAB Diagnostics, Universidad de Navarra, 31008 Pamplona, Spain
| | - Xabier Agirre
- Center for Applied Medical Research (CIMA) LAB Diagnostics, Universidad de Navarra, 31008 Pamplona, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029 Madrid, Spain
- Instituto de Investigaciones Sanitarias de Navarra (IdiSNA), Universidad de Navarra, 31008 Pamplona, Spain
| | - Joan Bladé
- Hospital Clinic de Barcelona, 08036 Barcelona, Spain
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036 Barcelona, Spain
| | - María-Victoria Mateos
- Unidad de Biología Molecular-HLA, Laboratorio de Hematología, Hospital Universitario de Salamanca, 37007 Salamanca, Spain
- Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), 37007 Salamanca, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Juan-José Lahuerta
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Jesús F. San-Miguel
- Center for Applied Medical Research (CIMA) LAB Diagnostics, Universidad de Navarra, 31008 Pamplona, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029 Madrid, Spain
- Instituto de Investigaciones Sanitarias de Navarra (IdiSNA), Universidad de Navarra, 31008 Pamplona, Spain
| | - María-José Calasanz
- Center for Applied Medical Research (CIMA) LAB Diagnostics, Universidad de Navarra, 31008 Pamplona, Spain
| | - Ramón Garcia-Sanz
- Unidad de Biología Molecular-HLA, Laboratorio de Hematología, Hospital Universitario de Salamanca, 37007 Salamanca, Spain
- Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), 37007 Salamanca, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029 Madrid, Spain
| | - Joaquín Martínez-Lopez
- Hematology Department, Hospital 12 de Octubre, 28041 Madrid, Spain
- H12O–CNIO Hematological Malignancies Clinical Research Unit, Spanish National Cancer Research (CNIO), 29029 Madrid, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), 28029 Madrid, Spain
- Correspondence: (J.M.R.-R.); (J.M.-L.)
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Wang X, Xu Y, Zhang Y, Wang S, Zhang X, Yi X, Zhang S, Wang J. HRD-MILN: Accurately estimate tumor homologous recombination deficiency status from targeted panel sequencing data. Front Genet 2022; 13:990244. [PMID: 36246633 PMCID: PMC9554509 DOI: 10.3389/fgene.2022.990244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 09/09/2022] [Indexed: 11/15/2022] Open
Abstract
Homologous recombination deficiency (HRD) is a critical feature guiding drug and treatment selection, mainly for ovarian and breast cancers. As it cannot be directly observed, HRD status is estimated on a small set of genomic instability features from sequencing data. The existing methods often perform poorly when handling targeted panel sequencing data; however, the targeted panel is the most popular sequencing strategy in clinical practices. Thus, we proposed HRD-MILN to overcome the computational challenges from targeted panel sequencing. HRD-MILN incorporated a multi-instance learning framework to discover as many loss of heterozygosity (LOH) associated with HRD status to cluster as possible. Then the HRD score is obtained based on the association between the LOHs and the cluster in the sample to be estimated, and finally, the HRD status is estimated based on the score. In comparison experiments on targeted panel sequencing data, the Precision of HRD-MILN could achieve 87%, significantly improved from 63% reported by the existing methods, where the highest margin of improvement reached 14%. It also presented advantages on whole exome sequencing data. Based on our best knowledge, HRD-MILN is the first practical tool for estimating HRD status from targeted panel sequencing data and could benefit clinical applications.
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Affiliation(s)
- Xuwen Wang
- School of Computer Science and Technology, Xi’an Jiaotong University, Xi’an, China
- Shaanxi Engineering Research Center of Medical and Health Big Data, Xi’an Jiaotong University, Xi’an, China
| | - Ying Xu
- School of Computer Science and Technology, Xi’an Jiaotong University, Xi’an, China
- Shaanxi Engineering Research Center of Medical and Health Big Data, Xi’an Jiaotong University, Xi’an, China
| | - Yinbin Zhang
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Shenjie Wang
- School of Computer Science and Technology, Xi’an Jiaotong University, Xi’an, China
- Shaanxi Engineering Research Center of Medical and Health Big Data, Xi’an Jiaotong University, Xi’an, China
| | - Xuanping Zhang
- School of Computer Science and Technology, Xi’an Jiaotong University, Xi’an, China
- Shaanxi Engineering Research Center of Medical and Health Big Data, Xi’an Jiaotong University, Xi’an, China
| | - Xin Yi
- Geneplus-Beijing Institute, Beijing, China
| | - Shuqun Zhang
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- *Correspondence: Jiayin Wang, ; Shuqun Zhang,
| | - Jiayin Wang
- School of Computer Science and Technology, Xi’an Jiaotong University, Xi’an, China
- Shaanxi Engineering Research Center of Medical and Health Big Data, Xi’an Jiaotong University, Xi’an, China
- *Correspondence: Jiayin Wang, ; Shuqun Zhang,
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Liquid biopsy using ascitic fluid and pleural effusion supernatants for genomic profiling in gastrointestinal and lung cancers. BMC Cancer 2022; 22:1020. [PMID: 36167530 PMCID: PMC9513868 DOI: 10.1186/s12885-022-09922-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 07/15/2022] [Indexed: 11/10/2022] Open
Abstract
Background Precision medicine highlights the importance of incorporating molecular genetic testing into standard clinical care. Next-generation sequencing can detect cancer-specific gene mutations, and molecular-targeted drugs can be designed to be effective for one or more specific gene mutations. For patients with special site metastases, it is particularly important to use appropriate samples for genetic profiling. This study aimed to determine whether genomic profiling using ASC and PE is effective in detecting genetic mutations. Methods Tissues, plasma, ascites (ASC) supernatants, and pleural effusion (PE) samples from gastrointestinal cancer patients with peritoneal metastasis and lung cancer patients with pleural metastasis were collected for comprehensive genomic profiling. The samples were subjected to next-generation sequencing using a panel of 59 or 1021 cancer-relevant genes panel. Results A total of 156 tissues, 188 plasma samples, 45 ASC supernatants, and 1 PE samples from 304 gastrointestinal cancer patients and 446 PE supernatants, 122 tissues, 389 plasma samples, and 45 PE sediments from 407 lung cancer patients were analyzed. The MSAF was significantly higher in ASC and PE supernatant than that in plasma ctDNA (50.00% vs. 3.00%, p < 0.0001 and 28.5% vs. 1.30%, p < 0.0001, respectively). The ASC supernatant had a higher actionable mutation rate and more actionable alterations than the plasma ctDNA in 26 paired samples. The PE supernatant had a higher total actionable mutation rate than plasma (80.3% vs. 48.4%, p < 0.05). The PE supernatant had a higher frequency of uncommon variations than the plasma regardless of distant organ metastasis. Conclusion ASC and PE supernatants could be better alternative samples when tumor tissues are not available, especially in patients with only peritoneal or pleural metastases. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09922-5.
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Hain C, Stadler R, Kalinowski J. Unraveling the Structural Variations of Early-Stage Mycosis Fungoides-CD3 Based Purification and Third Generation Sequencing as Novel Tools for the Genomic Landscape in CTCL. Cancers (Basel) 2022; 14:4466. [PMID: 36139626 PMCID: PMC9497107 DOI: 10.3390/cancers14184466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/08/2022] [Accepted: 09/12/2022] [Indexed: 11/16/2022] Open
Abstract
Mycosis fungoides (MF) is the most common cutaneous T-cell lymphoma (CTCL). At present, knowledge of genetic changes in early-stage MF is insufficient. Additionally, low tumor cell fraction renders calling of copy-number variations as the predominant mutations in MF challenging, thereby impeding further investigations. We show that enrichment of T cells from a biopsy of a stage I MF patient greatly increases tumor fraction. This improvement enables accurate calling of recurrent MF copy-number variants such as ARID1A and CDKN2A deletion and STAT5 amplification, undetected in the unprocessed biopsy. Furthermore, we demonstrate that application of long-read nanopore sequencing is especially useful for the structural variant rich CTCL. We detect the structural variants underlying recurrent MF copy-number variants and show phasing of multiple breakpoints into complex structural variant haplotypes. Additionally, we record multiple occurrences of templated insertion structural variants in this sample. Taken together, this study suggests a workflow to make the early stages of MF accessible for genetic analysis, and indicates long-read sequencing as a major tool for genetic analysis for MF.
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Affiliation(s)
- Carsten Hain
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
| | - Rudolf Stadler
- University Clinic for Dermatology, Johannes Wesling Medical Centre, UKRUB, University of Bochum, 32429 Minden, Germany
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
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Wang X, Xu Y, Liu R, Lai X, Liu Y, Wang S, Zhang X, Wang J. PEcnv: accurate and efficient detection of copy number variations of various lengths. Brief Bioinform 2022; 23:6686740. [PMID: 36056740 PMCID: PMC9487654 DOI: 10.1093/bib/bbac375] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 06/19/2022] [Accepted: 08/08/2022] [Indexed: 11/14/2022] Open
Abstract
Copy number variation (CNV) is a class of key biomarkers in many complex traits and diseases. Detecting CNV from sequencing data is a substantial bioinformatics problem and a standard requirement in clinical practice. Although many proposed CNV detection approaches exist, the core statistical model at their foundation is weakened by two critical computational issues: (i) identifying the optimal setting on the sliding window and (ii) correcting for bias and noise. We designed a statistical process model to overcome these limitations by calculating regional read depths via an exponentially weighted moving average strategy. A one-run detection of CNVs of various lengths is then achieved by a dynamic sliding window, whose size is self-adopted according to the weighted averages. We also designed a novel bias/noise reduction model, accompanied by the moving average, which can handle complicated patterns and extend training data. This model, called PEcnv, accurately detects CNVs ranging from kb-scale to chromosome-arm level. The model performance was validated with simulation samples and real samples. Comparative analysis showed that PEcnv outperforms current popular approaches. Notably, PEcnv provided considerable advantages in detecting small CNVs (1 kb–1 Mb) in panel sequencing data. Thus, PEcnv fills the gap left by existing methods focusing on large CNVs. PEcnv may have broad applications in clinical testing where panel sequencing is the dominant strategy. Availability and implementation: Source code is freely available at https://github.com/Sherwin-xjtu/PEcnv
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Affiliation(s)
- Xuwen Wang
- Department of Computer Science and Technology, School of Electronics and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China.,Institute of Data Science and Information Quality, Shaanxi Engineering Research Center of Medical and Health Big Data, Xi'an Jiaotong University, Xi'an 710049, China
| | - Ying Xu
- Department of Computer Science and Technology, School of Electronics and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China.,Institute of Data Science and Information Quality, Shaanxi Engineering Research Center of Medical and Health Big Data, Xi'an Jiaotong University, Xi'an 710049, China
| | - Ruoyu Liu
- Department of Computer Science and Technology, School of Electronics and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China.,Institute of Data Science and Information Quality, Shaanxi Engineering Research Center of Medical and Health Big Data, Xi'an Jiaotong University, Xi'an 710049, China
| | - Xin Lai
- Department of Computer Science and Technology, School of Electronics and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China.,Institute of Data Science and Information Quality, Shaanxi Engineering Research Center of Medical and Health Big Data, Xi'an Jiaotong University, Xi'an 710049, China
| | - Yuqian Liu
- Department of Computer Science and Technology, School of Electronics and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China.,Institute of Data Science and Information Quality, Shaanxi Engineering Research Center of Medical and Health Big Data, Xi'an Jiaotong University, Xi'an 710049, China
| | - Shenjie Wang
- Department of Computer Science and Technology, School of Electronics and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China.,Institute of Data Science and Information Quality, Shaanxi Engineering Research Center of Medical and Health Big Data, Xi'an Jiaotong University, Xi'an 710049, China
| | - Xuanping Zhang
- Department of Computer Science and Technology, School of Electronics and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China.,Institute of Data Science and Information Quality, Shaanxi Engineering Research Center of Medical and Health Big Data, Xi'an Jiaotong University, Xi'an 710049, China
| | - Jiayin Wang
- Department of Computer Science and Technology, School of Electronics and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China.,Institute of Data Science and Information Quality, Shaanxi Engineering Research Center of Medical and Health Big Data, Xi'an Jiaotong University, Xi'an 710049, China
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Genetic and Methylation Analysis of CTNNB1 in Benign and Malignant Melanocytic Lesions. Cancers (Basel) 2022; 14:cancers14174066. [PMID: 36077603 PMCID: PMC9454999 DOI: 10.3390/cancers14174066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/19/2022] [Accepted: 07/26/2022] [Indexed: 11/21/2022] Open
Abstract
Simple Summary Recurrent CTNNB1 exon 3 mutations have been recognized in the distinct group of melanocytic tumors showing deep penetrating nevus-like morphology and in 1–2% of advanced melanoma. We performed a detailed genetic analysis of difficult-to-classify nevi and melanomas with CTNNB1 mutations and found that benign tumors (nevi) show characteristic morphological, genetic and epigenetic traits, which distinguish them from other nevi and melanoma. Malignant CTNNB1-mutant tumors (melanoma) demonstrated a different genetic profile, grouping clearly with other non-CTNNB1 melanomas in methylation assays. To further evaluate the role of CTNNB1 mutations in melanoma, we assessed a large cohort of clinically sequenced melanomas, identifying 38 tumors with CTNNB1 exon 3 mutations, including recurrent S45 (n = 13, 34%), G34 (n = 5, 13%), and S27 (n = 5, 13%) mutations. Locations and histological subtype of CTNNB1-mutated melanoma varied; none were reported as showing deep penetrating nevus-like morphology. The most frequent concurrent activating mutations were BRAF V600 (55%) and NRAS Q61 (34%). Abstract Melanocytic neoplasms have been genetically characterized in detail during the last decade. Recurrent CTNNB1 exon 3 mutations have been recognized in the distinct group of melanocytic tumors showing deep penetrating nevus-like morphology. In addition, they have been identified in 1–2% of advanced melanoma. Performing a detailed genetic analysis of difficult-to-classify nevi and melanomas with CTNNB1 mutations, we found that benign tumors (nevi) show characteristic morphological, genetic and epigenetic traits, which distinguish them from other nevi and melanoma. Malignant CTNNB1-mutant tumors (melanomas) demonstrated a different genetic profile, instead grouping clearly with other non-CTNNB1 melanomas in methylation assays. To further evaluate the role of CTNNB1 mutations in melanoma, we assessed a large cohort of clinically sequenced melanomas, identifying 38 tumors with CTNNB1 exon 3 mutations, including recurrent S45 (n = 13, 34%), G34 (n = 5, 13%), and S27 (n = 5, 13%) mutations. Locations and histological subtype of CTNNB1-mutated melanoma varied; none were reported as showing deep penetrating nevus-like morphology. The most frequent concurrent activating mutations were BRAF V600 (n = 21, 55%) and NRAS Q61 (n = 13, 34%). In our cohort, four of seven (58%) and one of nine (11%) patients treated with targeted therapy (BRAF and MEK Inhibitors) or immune-checkpoint therapy, respectively, showed disease control (partial response or stable disease). In summary, CTNNB1 mutations are associated with a unique melanocytic tumor type in benign tumors (nevi), which can be applied in a diagnostic setting. In advanced disease, no clear characteristics distinguishing CTNNB1-mutant from other melanomas were observed; however, studies of larger, optimally prospective, cohorts are warranted.
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Zaremba A, Meier F, Schlein C, Jansen P, Lodde G, Song M, Kretz J, Möller I, Stadtler N, Livingstone E, Zimmer L, Hadaschik E, Sucker A, Schadendorf D, Griewank K. Clinical and pathological characteristics of familial melanoma with germline TERT promoter variants. Pigment Cell Melanoma Res 2022; 35:573-586. [PMID: 35912549 DOI: 10.1111/pcmr.13060] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/19/2022] [Accepted: 07/29/2022] [Indexed: 11/30/2022]
Abstract
Around 10% of melanoma occur in patients with a suspected familial predisposition. TERT promoter mutations are the most common somatic hotspot mutations in human cancers. However, only two families with germline mutations have been identified to date. We present detailed histological, clinical and molecular pathologic analyses of affected patients and details of newly identified individuals in one of these previously reported families. TERT (NM_198253.3) Chr.5:1,295,161T>C (c.-57 T>C) promoter variants were detected in all melanoma-affected (n=18) and one non-diseased family member. Median age at diagnosis was 30 years (n=18, range 16-46 years, 2 unknown). While most primary melanoma arose on the upper extremities (n=7, 21%) and were superficial spreading melanoma (SSM, n=8, 24%), many primary melanoma also originated from non UV-exposed mucosal (n=2, 6%) and acral (n=4, 12%) locations. One SSM sample harboured a Chr.5:1,295,228C>T TERT promoter region in addition to the germline Chr.5:1,295,161T>C variant, arguing additional pathway activation can support tumor pathogenesis. Patients treated with BRAF inhibitor and/or immune checkpoint inhibition (ICI) showed responses, although of limited duration. One mucosal melanoma harboured both a KIT copy number gain and an activating c.1727 p.Leu576Pro mutation. Following modest response to ICI, subsequent KIT inhibitor (imatinib) therapy demonstrated an ongoing complete pathological response (currently 7 months).
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Affiliation(s)
- Anne Zaremba
- Department of Dermatology, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45122 Essen, Germany, and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Friedegund Meier
- Skin Cancer Center at the University Cancer Centre and National Center for Tumor Diseases, Department of Dermatology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technical University Dresden, Dresden, Germany
| | - Christian Schlein
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Philipp Jansen
- Department of Dermatology, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45122 Essen, Germany, and German Cancer Consortium (DKTK), Heidelberg, Germany.,Clinic and Polyclinic for Dermatology and Allergology, University Hospital Bonn, Bonn, Germany
| | - Georg Lodde
- Department of Dermatology, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45122 Essen, Germany, and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Mingxia Song
- Department of Dermatology, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45122 Essen, Germany, and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Julia Kretz
- Department of Dermatology, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45122 Essen, Germany, and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Inga Möller
- Department of Dermatology, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45122 Essen, Germany, and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Nadine Stadtler
- Department of Dermatology, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45122 Essen, Germany, and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Elisabeth Livingstone
- Department of Dermatology, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45122 Essen, Germany, and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Lisa Zimmer
- Department of Dermatology, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45122 Essen, Germany, and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Eva Hadaschik
- Department of Dermatology, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45122 Essen, Germany, and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Antje Sucker
- Department of Dermatology, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45122 Essen, Germany, and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Dirk Schadendorf
- Department of Dermatology, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45122 Essen, Germany, and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Klaus Griewank
- Department of Dermatology, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45122 Essen, Germany, and German Cancer Consortium (DKTK), Heidelberg, Germany
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O'Fallon B, Durtschi J, Kellogg A, Lewis T, Close D, Best H. Algorithmic improvements for discovery of germline copy number variants in next-generation sequencing data. BMC Bioinformatics 2022; 23:285. [PMID: 35854218 PMCID: PMC9297596 DOI: 10.1186/s12859-022-04820-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 06/06/2022] [Indexed: 12/03/2022] Open
Abstract
Background Copy number variants (CNVs) play a significant role in human heredity and disease. However, sensitive and specific characterization of germline CNVs from NGS data has remained challenging, particularly for hybridization-capture data in which read counts are the primary source of copy number information. Results We describe two algorithmic adaptations that improve CNV detection accuracy in a Hidden Markov Model (HMM) context. First, we present a method for computing target- and copy number-specific emission distributions. Second, we demonstrate that the Pointwise Maximum a posteriori (PMAP) HMM decoding procedure yields improved sensitivity for small CNV calls compared to the more common Viterbi HMM decoder. We develop a prototype implementation, called Cobalt, and compare it to other CNV detection tools using sets of simulated and previously detected CNVs with sizes spanning a single exon to a full chromosome. Conclusions In both the simulation and previously detected CNV studies Cobalt shows similar sensitivity but significantly fewer false positive detections compared to other callers. Overall sensitivity is 80–90% for deletion CNVs spanning 1–4 targets and 90–100% for larger deletion events, while sensitivity is somewhat lower for small duplication CNVs.
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Affiliation(s)
- Brendan O'Fallon
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, USA.
| | - Jacob Durtschi
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, USA
| | - Ana Kellogg
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, USA
| | - Tracey Lewis
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, USA
| | - Devin Close
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, USA
| | - Hunter Best
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, USA
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Moradi N, Ohadian Moghadam S, Heidarzadeh S. Application of next-generation sequencing in the diagnosis of gastric cancer. Scand J Gastroenterol 2022; 57:842-855. [PMID: 35293278 DOI: 10.1080/00365521.2022.2041717] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Objectives: Gastric cancer (GC) is a disease with high mortality, poor prognosis and numerous risk factors. GC has an asymptomatic nature in early stages of the diseases, making timely diagnosis complicated using common conventional approaches, namely pathological examinations and imaging tests. Recently, molecular profiling of GC using next generation sequencing (NGS) has opened new doors to efficient prognostic, diagnostic, and therapeutic strategies. The current review aims to thoroughly discuss and compare the current NGS techniques and commercial platforms utilized for GC diagnosis and treatment, highlighting the most recent NGS-based GC studies. Furthermore, this review addresses the challenges of clinical implementation of NGS in GC.Materials and methods: This review was conducted according to the eligible studies identified via search of Web of Science, PubMed, Scopus, Embase and the Cochrane Library. In the present study, data on gastric cancer patients and NGS methods used to diagnose the disease were reviewed.Conclusion: Given the ever-rising advancements in NGS technologies, bioinformatics, healthcare guidelines and refined classifications, it is hoped that these technologies can actualize their advantages and optimize GC patients' experience.
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Affiliation(s)
- Narges Moradi
- Department of Life Technologies, University of Turku, Turku, Finland
| | | | - Siamak Heidarzadeh
- Department of Microbiology and Virology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
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Abstract
Distilling biologically meaningful information from cancer genome sequencing data requires comprehensive identification of somatic alterations using rigorous computational methods. As the amount and complexity of sequencing data have increased, so has the number of tools for analysing them. Here, we describe the main steps involved in the bioinformatic analysis of cancer genomes, review key algorithmic developments and highlight popular tools and emerging technologies. These tools include those that identify point mutations, copy number alterations, structural variations and mutational signatures in cancer genomes. We also discuss issues in experimental design, the strengths and limitations of sequencing modalities and methodological challenges for the future.
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Genomic and TCR profiling data reveal the distinct molecular traits in epithelial ovarian cancer histotypes. Oncogene 2022; 41:3093-3103. [PMID: 35468938 DOI: 10.1038/s41388-022-02277-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 01/24/2022] [Accepted: 03/11/2022] [Indexed: 11/08/2022]
Abstract
Epithelial ovarian cancer (EOC) is classified into five major histotypes: high-grade serous (HGSOC), low-grade serous (LGSOC), clear cell (CCOC), endometrioid (ENOC), and mucinous (MOC). However, the landscape of molecular and immunological alterations in these histotypes, especially LGSOC, CCOC, ENOC, and MOC, is largely uncharacterized. We collected 101 treatment-naive EOC patients. The resected tumor tissues and paired preoperative peripheral blood samples were collected and subjected to target sequencing of 1021 cancer-associated genes and T cell repertoire sequencing. Distinct characteristics of mutations were identified among the five histotypes. Furthermore, tumor mutation burden (TMB) was found to be higher in CCOC and ENOC, but lower in LGSOC and HGSOC. Alterations associated with DNA damage repair (DDR) pathways and homologous recombination deficiencies (HRD) were prevalent in five histotypes. CCOC demonstrated increased level of T cell clonality compared with HSGOC. Interestingly, the proportion of the 100 most common T cell clones was associated with TMB and tumor neoantigen burden in CCOC, highlighting more sensitive anti-tumor responses in this histotype, which was also evidenced by the enhanced convergent recombination of T cell clones. These findings shed light on the molecular traits of genomic alteration and T cell repertoire in the five major EOC histotypes and may help optimize clinical management of EOC with different histotypes.
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Gomes NL, Batista RL, Nishi MY, Lerário AM, Silva TE, de Moraes Narcizo A, Benedetti AFF, de Assis Funari MF, Faria Junior JA, Moraes DR, Quintão LML, Montenegro LR, Ferrari MTM, Jorge AA, Arnhold IJP, Costa EMF, Domenice S, Mendonca BB. Contribution of Clinical and Genetic Approaches for Diagnosing 209 Index Cases With 46,XY Differences of Sex Development. J Clin Endocrinol Metab 2022; 107:e1797-e1806. [PMID: 35134971 DOI: 10.1210/clinem/dgac064] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Indexed: 11/19/2022]
Abstract
CONTEXT Massively parallel sequencing (MPS) technologies have emerged as a first-tier approach for diagnosing several pediatric genetic syndromes. However, MPS has not been systematically integrated into the diagnostic workflow along with clinical/biochemical data for diagnosing 46,XY differences of sex development (DSD). OBJECTIVE To analyze the contribution of phenotypic classification either alone or in association with genetic evaluations, mainly MPS, for diagnosing a large cohort of 46,XY DSD patients. DESIGN/PATIENTS 209 nonsyndromic 46,XY DSD index cases from a Brazilian DSD center were included. Patients were initially classified into 3 subgroups according to clinical and biochemical data: gonadal dysgenesis (GD), disorders of androgen secretion/action, and DSD of unknown etiology. Molecular genetic studies were performed by Sanger sequencing and/or MPS. RESULTS Clinical/biochemical classification into either GD or disorders of hormone secretion/action was obtained in 68.4% of the index cases. Among these, a molecular diagnosis was obtained in 36% and 96.5%, respectively. For the remainder 31.6% classified as DSD of clinically unknown etiology, a molecular diagnosis was achieved in 31.8%. Overall, the molecular diagnosis was achieved in 59.3% of the cohort. The combination of clinical/biochemical and molecular approaches diagnosed 78.9% of the patients. Clinical/biochemical classification matched with the genetic diagnosis in all except 1 case. DHX37 and NR5A1 variants were the most frequent genetic causes among patients with GD and DSD of clinical unknown etiology, respectively. CONCLUSIONS The combination of clinical/biochemical with genetic approaches significantly improved the diagnosis of 46,XY DSD. MPS potentially decreases the complexity of the diagnostic workup as a first-line approach for diagnosing 46,XY DSD.
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Affiliation(s)
- Nathalia Lisboa Gomes
- Unidade de Endocrinologia do Desenvolvimento/ LIM42, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Unidade de Adrenal, Serviço de Endocrinologia, Santa Casa de Belo Horizonte, Belo Horizonte, Brazil
| | - Rafael Loch Batista
- Unidade de Endocrinologia do Desenvolvimento/ LIM42, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Mirian Y Nishi
- Unidade de Endocrinologia do Desenvolvimento/ LIM42, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Antônio Marcondes Lerário
- Division of Metabolism, Department of Internal Medicine, Endocrinology and Diabetes, University of Michigan, Ann Arbor, MI, USA
| | - Thatiana E Silva
- Unidade de Endocrinologia do Desenvolvimento/ LIM42, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Amanda de Moraes Narcizo
- Laboratório de Sequenciamento em Larga Escala (SELA), Faculdade de Medicina da Universidade de São Paulo FMUSP, São Paulo, Brazil
| | - Anna Flávia Figueredo Benedetti
- Laboratório de Sequenciamento em Larga Escala (SELA), Faculdade de Medicina da Universidade de São Paulo FMUSP, São Paulo, Brazil
| | - Mariana Ferreira de Assis Funari
- Unidade de Endocrinologia do Desenvolvimento/ LIM42, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - José Antônio Faria Junior
- Unidade de Endocrinologia do Desenvolvimento/ LIM42, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Daniela Rodrigues Moraes
- Unidade de Endocrinologia do Desenvolvimento/ LIM42, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Lia Mesquita Lousada Quintão
- Unidade de Endocrinologia do Desenvolvimento/ LIM42, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Luciana Ribeiro Montenegro
- Unidade de Endocrinologia do Desenvolvimento/ LIM42, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Maria Teresa Martins Ferrari
- Unidade de Endocrinologia do Desenvolvimento/ LIM42, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Alexander A Jorge
- Unidade de Endocrinologia do Desenvolvimento/ LIM42, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Unidade de Endocrinologia Genética, Laboratório de Endocrinologia Celular e Molecular LIM25, Disciplina de Endocrinologia da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Ivo J P Arnhold
- Unidade de Endocrinologia do Desenvolvimento/ LIM42, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Elaine Maria Frade Costa
- Unidade de Endocrinologia do Desenvolvimento/ LIM42, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Sorahia Domenice
- Unidade de Endocrinologia do Desenvolvimento/ LIM42, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Berenice Bilharinho Mendonca
- Unidade de Endocrinologia do Desenvolvimento/ LIM42, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
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Rapti M, Zouaghi Y, Meylan J, Ranza E, Antonarakis SE, Santoni FA. CoverageMaster: comprehensive CNV detection and visualization from NGS short reads for genetic medicine applications. Brief Bioinform 2022; 23:6537346. [PMID: 35224620 PMCID: PMC8921749 DOI: 10.1093/bib/bbac049] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 01/28/2022] [Accepted: 01/31/2022] [Indexed: 12/27/2022] Open
Abstract
CoverageMaster (CoM) is a copy number variation (CNV) calling algorithm based on depth-of-coverage maps designed to detect CNVs of any size in exome [whole exome sequencing (WES)] and genome [whole genome sequencing (WGS)] data. The core of the algorithm is the compression of sequencing coverage data in a multiscale Wavelet space and the analysis through an iterative Hidden Markov Model. CoM processes WES and WGS data at nucleotide scale resolution and accurately detects and visualizes full size range CNVs, including single or partial exon deletions and duplications. The results obtained with this approach support the possibility for coverage-based CNV callers to replace probe-based methods such as array comparative genomic hybridization and multiplex ligation-dependent probe amplification in the near future.
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Affiliation(s)
- Melivoia Rapti
- Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland.,Univesity of Lausanne, Lausanne, Switzerland
| | - Yassine Zouaghi
- Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland.,Univesity of Lausanne, Lausanne, Switzerland
| | - Jenny Meylan
- Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
| | - Emmanuelle Ranza
- Medigenome, Swiss Institute of Genomic Medicine, Geneva, Switzerland
| | - Stylianos E Antonarakis
- Medigenome, Swiss Institute of Genomic Medicine, Geneva, Switzerland.,University of Geneva Medical Faculty, Geneva, Switzerland
| | - Federico A Santoni
- Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland.,Medigenome, Swiss Institute of Genomic Medicine, Geneva, Switzerland.,Univesity of Lausanne, Lausanne, Switzerland
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Lee JK, Kwon WK, Hong SN, Chang DK, Kim HC, Jang JH, Kim JW. Necessity of Multiplex Ligation Probe Amplification in Genetic Tests: Germline variant analysis of the APC gene in familial adenomatous polyposis patients. Cancer Genet 2022; 262-263:95-101. [DOI: 10.1016/j.cancergen.2022.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 01/10/2022] [Accepted: 02/09/2022] [Indexed: 11/02/2022]
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Abstract
Detection of copy number variants from targeted sequencing, including whole-exome sequencing, can be particularly difficult since the break points of the CNV are not always captured. Here we describe DECoN, a software tool which uses changes in read depth to identify CNVs that affect whole exons. It is optimized for clinical use and allows for interactive visualization of CNVs identified.
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Affiliation(s)
- Anna Fowler
- Department of Health Data Science, Institute of Population Health, University of Liverpool, Liverpool, UK.
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Identification of Copy Number Alterations from Next-Generation Sequencing Data. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1361:55-74. [DOI: 10.1007/978-3-030-91836-1_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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50
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Xie H, Yin H, Ye X, Liu Y, Liu N, Zhang Y, Chen X, Chen X. Detection of Small CYP11B1 Deletions and One Founder Chimeric CYP11B2/CYP11B1 Gene in 11β-Hydroxylase Deficiency. Front Endocrinol (Lausanne) 2022; 13:882863. [PMID: 35685215 PMCID: PMC9171383 DOI: 10.3389/fendo.2022.882863] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 03/22/2022] [Indexed: 12/02/2022] Open
Abstract
OBJECTIVE 11β-Hydroxylase deficiency (11β-OHD) caused by mutations in the CYP11B1 gene is the second most common form of congenital adrenal hyperplasia. Both point mutations and genomic rearrangements of CYP11B1 are important causes of 11β-OHD. However, the high degree of sequence identity between CYP11B1 and its homologous gene CYP11B2, presents unique challenges for molecular diagnosis of suspected 11β-OHD. The aim of this study was to detect the point mutation, indel, small deletion of CYP11B1 and chimeric CYP11B2/CYP11B1 gene in a one-tube test, improving the genetic diagnosis of 11β-OHD. METHODS Optimized custom-designed target sequencing strategy was performed in three patients with suspected 11β-OHD, in which both the coverage depth of paired-end reads and the breakpoint information of split reads from sequencing data were analysed in order to detect genomic rearrangements covering CYP11B1. Long-range PCR was peformed to validate the speculated CYP11B1 rearrangements with the breakpoint-specifc primers. RESULTS Using the optimized target sequencing approach, we detected two intragenic/intergenic deletions of CYP11B1 and one chimeric CYP11B2/CYP11B1 gene from three suspected patients with 11β-OHD besides three pathogenic heterozygous point mutation/indels. Furthermore, we mapped the precise breakpoint of this chimeric CYP11B2/CYP11B1 gene located on chr8:143994517 (hg19) and confirmed it as a founder rearrangement event in the Chinese population. CONCLUSIONS Our optimized target sequencing approach improved the genetic diagnosis of 11β-OHD.
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Affiliation(s)
- Hua Xie
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing, China
| | - Hui Yin
- Department of Endocrinology, Affiliated Children’s Hospital of Capital Institute of Pediatrics, Beijing, China
| | - Xue Ye
- Department of Endocrinology, Affiliated Children’s Hospital of Capital Institute of Pediatrics, Beijing, China
| | - Ying Liu
- Department of Endocrinology, Affiliated Children’s Hospital of Capital Institute of Pediatrics, Beijing, China
| | - Na Liu
- Bioinformation Department, Beijing Mygenostics Co., Ltd, Beijing, China
| | - Yu Zhang
- Department of Laboratory Center, Capital Institute of Pediatrics, Beijing, China
| | - Xiaoli Chen
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing, China
- *Correspondence: Xiaobo Chen, ; Xiaoli Chen,
| | - Xiaobo Chen
- Department of Endocrinology, Affiliated Children’s Hospital of Capital Institute of Pediatrics, Beijing, China
- *Correspondence: Xiaobo Chen, ; Xiaoli Chen,
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