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Wang F, Zhao D, Xu WY, Liu Y, Sun H, Lu S, Ji Y, Jiang J, Chen Y, He Q, Gong C, Liu R, Su Z, Dong Y, Yan Z, Liu L. Blood leukocytes as a non-invasive diagnostic tool for thyroid nodules: a prospective cohort study. BMC Med 2024; 22:147. [PMID: 38561764 PMCID: PMC10986011 DOI: 10.1186/s12916-024-03368-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 03/22/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Thyroid nodule (TN) patients in China are subject to overdiagnosis and overtreatment. The implementation of existing technologies such as thyroid ultrasonography has indeed contributed to the improved diagnostic accuracy of TNs. However, a significant issue persists, where many patients undergo unnecessary biopsies, and patients with malignant thyroid nodules (MTNs) are advised to undergo surgery therapy. METHODS This study included a total of 293 patients diagnosed with TNs. Differential methylation haplotype blocks (MHBs) in blood leukocytes between MTNs and benign thyroid nodules (BTNs) were detected using reduced representation bisulfite sequencing (RRBS). Subsequently, an artificial intelligence blood leukocyte DNA methylation (BLDM) model was designed to optimize the management and treatment of patients with TNs for more effective outcomes. RESULTS The DNA methylation profiles of peripheral blood leukocytes exhibited distinctions between MTNs and BTNs. The BLDM model we developed for diagnosing TNs achieved an area under the curve (AUC) of 0.858 in the validation cohort and 0.863 in the independent test cohort. Its specificity reached 90.91% and 88.68% in the validation and independent test cohorts, respectively, outperforming the specificity of ultrasonography (43.64% in the validation cohort and 47.17% in the independent test cohort), albeit with a slightly lower sensitivity (83.33% in the validation cohort and 82.86% in the independent test cohort) compared to ultrasonography (97.62% in the validation cohort and 100.00% in the independent test cohort). The BLDM model could correctly identify 89.83% patients whose nodules were suspected malignant by ultrasonography but finally histological benign. In micronodules, the model displayed higher specificity (93.33% in the validation cohort and 92.00% in the independent test cohort) and accuracy (88.24% in the validation cohort and 87.50% in the independent test cohort) for diagnosing TNs. This performance surpassed the specificity and accuracy observed with ultrasonography. A TN diagnostic and treatment framework that prioritizes patients is provided, with fine-needle aspiration (FNA) biopsy performed only on patients with indications of MTNs in both BLDM and ultrasonography results, thus avoiding unnecessary biopsies. CONCLUSIONS This is the first study to demonstrate the potential of non-invasive blood leukocytes in diagnosing TNs, thereby making TN diagnosis and treatment more efficient in China.
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Affiliation(s)
- Feihang Wang
- Department of Interventional Radiology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- National Clinical Research Center for Interventional Medicine, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- Shanghai Institute of Medical Imaging, Shanghai, 200032, China
| | - Danyang Zhao
- Department of Interventional Radiology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- National Clinical Research Center for Interventional Medicine, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- Shanghai Institute of Medical Imaging, Shanghai, 200032, China
| | - Wang-Yang Xu
- Singlera Genomics (Shanghai) Ltd., Shanghai, 201203, China
| | - Yiying Liu
- Singlera Genomics (Shanghai) Ltd., Shanghai, 201203, China
| | - Huiyi Sun
- Department of Interventional Radiology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- National Clinical Research Center for Interventional Medicine, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- Shanghai Institute of Medical Imaging, Shanghai, 200032, China
| | - Shanshan Lu
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Yuan Ji
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Jingjing Jiang
- Department of Endocrinology and Metabolism, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Yi Chen
- Department of Interventional Radiology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- National Clinical Research Center for Interventional Medicine, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- Shanghai Institute of Medical Imaging, Shanghai, 200032, China
| | - Qiye He
- Singlera Genomics (Shanghai) Ltd., Shanghai, 201203, China
| | | | - Rui Liu
- Singlera Genomics (Shanghai) Ltd., Shanghai, 201203, China
| | - Zhixi Su
- Singlera Genomics (Shanghai) Ltd., Shanghai, 201203, China.
| | - Yi Dong
- Department of Ultrasound, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China.
| | - Zhiping Yan
- Department of Interventional Radiology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
- National Clinical Research Center for Interventional Medicine, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
- Shanghai Institute of Medical Imaging, Shanghai, 200032, China.
| | - Lingxiao Liu
- Department of Interventional Radiology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
- National Clinical Research Center for Interventional Medicine, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
- Shanghai Institute of Medical Imaging, Shanghai, 200032, China.
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Zhang Z, Liu G, Zhou Z, Su Z, Gu X. Global level of methylation in the sea lamprey (jawless vertebrate) genome is intermediate between invertebrate and jawed vertebrate genomes. J Exp Zool B Mol Dev Evol 2024. [PMID: 38497317 DOI: 10.1002/jez.b.23250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 02/21/2024] [Accepted: 02/26/2024] [Indexed: 03/19/2024]
Abstract
In eukaryotes, cytosine methylation is a primary heritable epigenetic modification of the genome that regulates many cellular processes. In invertebrate, methylated cytosine generally located on specific genomic elements (e.g., gene bodies and silenced repetitive elements) to show a "mosaic" pattern. While in jawed vertebrate (teleost and tetrapod), highly methylated cytosine located genome-wide but only absence at regulatory regions (e.g., promoter and enhancer). Many studies imply that the evolution of DNA methylation reprogramming may have helped the transition from invertebrates to jawed vertebrates, but the detail remains largely elusive. In this study, we used the whole-genome bisulfite-sequencing technology to investigate the genome-wide methylation in three tissues (heart, muscle, and sperm) from the sea lamprey, an extant agnathan (jawless) vertebrate. Strikingly, we found that the methylation level of the sea lamprey is very similar to that in sea urchin (a deuterostome) and sea squirt (a chordate) invertebrates. In sum, the global pattern in sea lamprey is intermediate methylation level (around 30%), that is higher than methylation level in the genomes of pre-bilaterians and protostomes (1%-10%), but lower than methylation level appeared in jawed vertebrates (around 70%, teleost and tetrapod). We anticipate that, in addition to genetic dynamics such as genome duplications, epigenetic dynamics such as global methylation reprograming was also orchestrated toward the emergence and evolution of vertebrates.
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Affiliation(s)
- Zhao Zhang
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Gangbiao Liu
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Zhan Zhou
- Innovation Institute for Artificial Intelligence in Medicine and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Zhixi Su
- Singlera Genomics Ltd., Shanghai, China
| | - Xun Gu
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa, USA
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Chen H, Liu Y, Wang F, Sun J, Gong C, Zhu M, Xu M, He Q, Liu R, Su Z, Zhong D, Liu L. MeIS: DNA methylation-based immune response signatures for thyroid nodule diagnostics. J Clin Endocrinol Metab 2024:dgae141. [PMID: 38450587 DOI: 10.1210/clinem/dgae141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 03/08/2024]
Abstract
CONTEXT Accurately distinguishing between benign thyroid nodules (BTNs) and papillary thyroid cancers (PTCs) with current conventional methods poses a significant challenge. OBJECTIVE We identify DNA methylation markers of immune response-related genes for distinguishing BTNs and PTCs. METHODS In this study, we analyzed a public reduced representative bisulfite sequencing (RRBS) dataset and revealed distinct methylation patterns associated with immune signals in PTCs and BTNs. Based on these findings, we developed a diagnostic classifier named as the Methylation-based Immune Response Signature (MeIS), which was composed of fifteen DNA methylation markers associated with immune response-related genes. We validated the MeIS's performance in two independent cohorts: ZS's retrospective cohort (50 PTC and 18 BTN surgery-leftover samples) and ZS's preoperative cohort (31 PTC and 30 BTN fine-needle aspiration (FNA) samples). RESULTS The MeIS classifier demonstrated significant clinical promise, achieving AUCs of 0.96, 0.98, 0.89 and 0.90 in the training set, validation set, ZS's retrospective cohort, and ZS's preoperative cohort, respectively. For the cytologically indeterminate thyroid nodules, in the ZS's retrospective cohort, MeIS exhibited a sensitivity of 91% and a specificity of 82%; in the ZS's preoperative cohort, MeIS achieved a sensitivity of 84% and a specificity of 74%. Additionally, combining MeIS and BRAFV600E detection improved the detecting performance of cytologically indeterminate thyroid nodules, yielding sensitivities of 98% and 87%, and specificities of 82% and 74% in the ZS's retrospective cohort and ZS's preoperative cohort, respectively. CONCLUSIONS The fifteen markers we identified can be employed to improve the diagnostic of cytologically indeterminate thyroid nodules.
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Affiliation(s)
- Huang Chen
- Department of Pathology, China-Japan Friendship Hospital, Beijing, China
| | - Yiying Liu
- Singlera Genomics (Shanghai) Ltd., Shanghai, 201203, China
| | - Feihang Wang
- Department of Interventional Radiology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- National Clinical Research Center for Interventional Medicine, Zhongshan Hospital, Fudan University, Shanghai, 200030, China
- Shanghai Institute of Medical Imaging, Fudan University, Shanghai, 200032, China
| | - Jin Sun
- Singlera Genomics (Shanghai) Ltd., Shanghai, 201203, China
| | | | - Min Zhu
- Singlera Genomics (Shanghai) Ltd., Shanghai, 201203, China
| | - Minjie Xu
- Singlera Genomics (Shanghai) Ltd., Shanghai, 201203, China
| | - Qiye He
- Singlera Genomics (Shanghai) Ltd., Shanghai, 201203, China
| | - Rui Liu
- Singlera Genomics (Shanghai) Ltd., Shanghai, 201203, China
| | - Zhixi Su
- Singlera Genomics (Shanghai) Ltd., Shanghai, 201203, China
| | - Dingrong Zhong
- Department of Pathology, China-Japan Friendship Hospital, Beijing, China
| | - Lingxiao Liu
- Department of Interventional Radiology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- National Clinical Research Center for Interventional Medicine, Zhongshan Hospital, Fudan University, Shanghai, 200030, China
- Shanghai Institute of Medical Imaging, Fudan University, Shanghai, 200032, China
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Zou Y, Yang J, Zhou J, Liu G, Shen L, Zhou Z, Su Z, Gu X. Anciently duplicated genes continuously recruited to heart expression in vertebrate evolution are associated with heart chamber increase. J Exp Zool B Mol Dev Evol 2024. [PMID: 38361319 DOI: 10.1002/jez.b.23248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 01/22/2024] [Accepted: 01/29/2024] [Indexed: 02/17/2024]
Abstract
Although gene/genome duplications in the early stage of vertebrates have been thought to provide major resources of raw genetic materials for evolutionary innovations, it is unclear whether they continuously contribute to the evolution of morphological complexity during the course of vertebrate evolution, such as the evolution from two heart chambers (fishes) to four heart chambers (mammals and birds). We addressed this issue by our heart RNA-Seq experiments combined with published data, using 13 vertebrates and one invertebrate (sea squirt, as an outgroup). Our evolutionary transcriptome analysis showed that number of ancient paralogous genes expressed in heart tends to increase with the increase of heart chamber number along the vertebrate phylogeny, in spite that most of them were duplicated at the time near to the origin of vertebrates or even more ancient. Moreover, those paralogs expressed in heart exert considerably different functions from heart-expressed singletons: the former are functionally enriched in cardiac muscle and muscle contraction-related categories, whereas the latter play more basic functions of energy generation like aerobic respiration. These findings together support the notion that recruiting anciently paralogous genes that are expressed in heart is associated with the increase of chamber number in vertebrate evolution.
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Affiliation(s)
- Yangyun Zou
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Jingwen Yang
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
- Brown Center for Immunotherapy, School of Medicine, Indiana University, Indianapolis, Indiana, USA
| | - Jingqi Zhou
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
- School of Public Health, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Gangbiao Liu
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Libing Shen
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
- Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Zhan Zhou
- Innovation Institute for Artificial Intelligence in Medicine and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Zhixi Su
- Singlera Genomics Ltd., Shanghai, China
| | - Xun Gu
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa, USA
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Zhang K, Fu R, Liu R, Su Z. Circulating cell-free DNA-based multi-cancer early detection. Trends Cancer 2024; 10:161-174. [PMID: 37709615 DOI: 10.1016/j.trecan.2023.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/03/2023] [Accepted: 08/21/2023] [Indexed: 09/16/2023]
Abstract
Patients benefit considerably from early detection of cancer. Existing single-cancer tests have various limitations, which could be effectively addressed by circulating cell-free DNA (cfDNA)-based multi-cancer early detection (MCED). With sensitive detection and accurate localization of multiple cancer types at a very low and fixed false-positive rate (FPR), MCED has great potential to revolutionize early cancer detection. Herein, we review state-of-the-art approaches for cfDNA-based MCED and their limitations and discuss both technical and clinical challenges in the development and application of MCED tests. Given the constant improvements in technology and understanding of cancer biology, we propose that a cfDNA-based targeted sequencing assay that integrates multimodal features should be optimized for MCED.
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Affiliation(s)
- Kai Zhang
- Department of Cancer Prevention, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 17 South Panjiayuan Lane, Chaoyang District, Beijing 100021, China
| | - Ruiqing Fu
- Singlera Genomics Ltd, Shanghai 201203, China
| | - Rui Liu
- Singlera Genomics Ltd, Shanghai 201203, China
| | - Zhixi Su
- Singlera Genomics Ltd, Shanghai 201203, China.
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Luo R, Su Z, Kang K, Yu M, Zhou X, Wu Y, Yao Z, Xiu W, Zhang X, Yu Y, Zhou L, Na F, Li Y, Xu Y, Liu Y, Zou B, Peng F, Wang J, Zhong R, Gong Y, Huang M, Bai S, Xue J, Yan D, Lu Y. Hybrid Immuno-RT for Bulky Tumors: Standard Fractionation with Partial Tumor SBRT. Int J Radiat Oncol Biol Phys 2023; 117:S166. [PMID: 37784416 DOI: 10.1016/j.ijrobp.2023.06.264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) Bulky tumors remain challenging to be treated. Stereotactic body radiation therapy (SBRT) is effective against radioresistant tumor cells and can induce immunogenic cell death (ICD) that leads to T-cell-mediated antitumor effects. Low-dose radiation (LDRT) can inflame the tumor microenvironment (TME) by recruiting T cells. We designed a novel radiotherapy technique (RT, ERT) whose dose distribution map resembles the "eclipse" by concurrently delivering LDRT to the whole tumor, meanwhile SBRT to only a part of the same tumor. This study examined the safety and efficacy of ERT to bulky lesions with PD-1 inhibitors in mice and patients. MATERIALS/METHODS In mice with CT26 colon or LLC1 lung bulky tumors (400 - 500 cm3), the whole tumor was irradiated by LDRT (2 Gy x 3), meanwhile the tumor center was irradiated by SBRT (10 Gy x 3); αPD-1 was given weekly. The dependence of therapeutic effects on CD8+ T cells was determined using depleting antibodies. Frequencies of CD8+ T cells and M1 macrophages (Mφ) were determined by flow cytometry. Multiplex Immunohistochemistry (mIHC) was applied to analyze the number and the location of CD8+ T cells and their subpopulations, as well as the phospho-eIF2α level (the ICD marker) of tumor cells in TME. Patients with advanced lung or liver bulky tumors who failed standard treatment or with oncologic emergencies were treated. Kaplan-Meier method was applied to estimate patients' progression-free survival (PFS) and overall survival (OS). RESULTS ERT/αPD-1 is superior to SBRT/αPD-1 or LDRT/αPD-1 in controlling bulky tumors in both mouse models in a CD8+ T-cell dependent manner. In the CT26 model, ERT/αPD-1 resulted in complete tumor regression in 3/11 mice and induced more CD8+ T cells and M1 Mφ in TME compared to other groups. mIHC analysis showed that ERT/αPD-1 induced higher bulk, stem-like (TCF1+ TIM3- PD-1+), and more differentiated (TCF1- TIM3+ PD-1+) CD8+ T cells infiltration into the tumor center and periphery compared to other groups. Compared to untreated or LDRT-treated tumor centers, tumor centers irradiated with ERT or SBRT showed elevated phospho-eIF2α accompanied by higher dendritic cell infiltration. In total, 39 advanced cancer patients were treated with ERT/αPD-1 or plus chemotherapy. Radiation-induced pneumonitis occurred in 1 of 26 patients receiving thoracic ERT. There were two cases of grade III toxicity associated with PD-1 inhibitors. No toxicity above grade III was observed. The objective response rate was 38.5%. The median PFS was 5.6 months and median OS was not reached at a median follow-up of 11.7 months. CONCLUSION ERT/αPD-1 showed superior efficacy in controlling bulky tumor in two mouse models. The hybrid immuno-RT (ERT) combing PD-1 inhibitors was safe and effective in patients with bulky tumors. Further clinical trials in combination with bioimaging to identify the optimal SBRT target region for the bulky tumor are warranted.
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Affiliation(s)
- R Luo
- Thoracic Oncology Ward, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China; Department of Radiotherapy, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Z Su
- Thoracic Oncology Ward, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - K Kang
- Thoracic Oncology Ward, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China; Laboratory of Clinical Cell Therapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - M Yu
- Thoracic Oncology Ward, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - X Zhou
- Thoracic Oncology Ward, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China; Department of Radiotherapy, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Y Wu
- Thoracic Oncology Ward, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China; Laboratory of Clinical Cell Therapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Z Yao
- Thoracic Oncology Ward, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China; Laboratory of Clinical Cell Therapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - W Xiu
- Thoracic Oncology Ward, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - X Zhang
- Thoracic Oncology Ward, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China; Department of Radiotherapy, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Y Yu
- Thoracic Oncology Ward, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - L Zhou
- Thoracic Oncology Ward, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China; Department of Radiotherapy, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - F Na
- Thoracic Oncology Ward, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Y Li
- Thoracic Oncology Ward, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Y Xu
- Thoracic Oncology Ward, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China; Department of Radiotherapy, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Y Liu
- Thoracic Oncology Ward, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China; Department of Radiotherapy, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - B Zou
- Thoracic Oncology Ward, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China; Department of Radiotherapy, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - F Peng
- Thoracic Oncology Ward, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - J Wang
- Thoracic Oncology Ward, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China; Department of Radiotherapy, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - R Zhong
- Division of Radiation Physics, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Y Gong
- Thoracic Oncology Ward, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China; Department of Radiotherapy, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - M Huang
- Thoracic Oncology Ward, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - S Bai
- Division of Radiation Physics, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - J Xue
- Thoracic Oncology Ward, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China; Laboratory of Clinical Cell Therapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - D Yan
- Division of Radiation Physics, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Y Lu
- Thoracic Oncology Ward, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China; Department of Radiotherapy, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
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Su Z, Li Y, Wang C, Guo J, Guo L, Gu Y. Directional atherectomy combined with drug-coated balloon angioplasty for superficial femoral arteriosclerosis obliterans. Ann R Coll Surg Engl 2023; 105:627-631. [PMID: 36927132 PMCID: PMC10471432 DOI: 10.1308/rcsann.2022.0164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/26/2022] [Indexed: 03/18/2023] Open
Abstract
INTRODUCTION This study is an analysis of the therapeutic effects of directional atherectomy combined with drug-coated balloon angioplasty (DA+DCB) in treating superficial femoral arteriosclerosis obliterans. METHODS Patients in our hospital with superficial femoral arteriosclerosis obliterans who received DA+DCB during the period June 2016 to February 2019 were identified retrospectively. Preoperative demographics, operative details and postoperative follow-up outcomes were analysed statistically. RESULTS Between June 2016 and February 2019, 48 patients were enrolled in this retrospective study. The average age of the patients was 66.85 ± 11.28 years; 83.3% of the patients were male. During the procedure, flow-limiting dissection occurred frequently (9/48 patients) and there were six bailout stent implantations owing to flow-limiting dissections. The incidence rate of target artery thrombosis was 4.2% (2/48). There was no vessel perforation, embolism or operation-related death. The technical success rate was estimated at 100%. The mean ankle-brachial index of the patients was 0.54 ± 0.28 before the operation and 0.93 ± 0.13 before discharge (p < 0.0001). The mean follow-up time was 19.6 ± 9.0 months. The primary patency rate was 89.4%, 82.4% and 76.5% at 12, 24 and 36 months. The freedom from target lesion revascularisation (TLR) was 97.9%, 93.8% and 84.4% at 12, 24 and 36 months. CONCLUSION The use of DA+DCB showed good clinical benefit for superficial femoral arteriosclerosis obliterans, which had good primary patency and freedom from TLR. Multicentre randomised controlled trials with long-term follow-up are needed.
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Affiliation(s)
- Z Su
- Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Y Li
- Xuanwu Hospital, Capital Medical University, Beijing, China
| | - C Wang
- Xuanwu Hospital, Capital Medical University, Beijing, China
| | - J Guo
- Xuanwu Hospital, Capital Medical University, Beijing, China
| | - L Guo
- Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Y Gu
- Xuanwu Hospital, Capital Medical University, Beijing, China
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Sun J, Su M, Ma J, Xu M, Ma C, Li W, Liu R, He Q, Su Z. Cross-platform comparisons for targeted bisulfite sequencing of MGISEQ-2000 and NovaSeq6000. Clin Epigenetics 2023; 15:130. [PMID: 37582783 PMCID: PMC10426093 DOI: 10.1186/s13148-023-01543-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 07/28/2023] [Indexed: 08/17/2023] Open
Abstract
BACKGROUND An accurate and reproducible next-generation sequencing platform is essential to identify malignancy-related abnormal DNA methylation changes and translate them into clinical applications including cancer detection, prognosis, and surveillance. However, high-quality DNA methylation sequencing has been challenging because poor sequence diversity of the bisulfite-converted libraries severely impairs sequencing quality and yield. In this study, we tested MGISEQ-2000 Sequencer's capability of DNA methylation sequencing with a published non-invasive pancreatic cancer detection assay, using NovaSeq6000 as the benchmark. RESULTS We sequenced a series of synthetic cell-free DNA (cfDNA) samples with different tumor fractions and found MGISEQ-2000 yielded data with similar quality as NovaSeq6000. The methylation levels measured by MGISEQ-2000 demonstrated high consistency with NovaSeq6000. Moreover, MGISEQ-2000 showed a comparable analytic sensitivity with NovaSeq6000, suggesting its potential for clinical detection. As to evaluate the clinical performance of MGISEQ-2000, we sequenced 24 clinical samples and predicted the pathology of the samples with a clinical diagnosis model, PDACatch classifier. The clinical model performance of MGISEQ-2000's data was highly consistent with that of NovaSeq6000's data, with the area under the curve of 1. We also tested the model's robustness with MGISEQ-2000's data when reducing the sequencing depth. The results showed that MGISEQ-2000's data showed matching robustness of the PDACatch classifier with NovaSeq6000's data. CONCLUSIONS Taken together, MGISEQ-2000 demonstrated similar data quality, consistency of the methylation levels, comparable analytic sensitivity, and matching clinical performance, supporting its application in future non-invasive early cancer detection investigations by detecting distinct methylation patterns of cfDNAs.
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Affiliation(s)
- Jin Sun
- Singlera Genomics (Shanghai) Ltd., No. 500, Furonghua Road, Shanghai, 201203, China
| | - Mingyang Su
- Singlera Genomics (Shanghai) Ltd., No. 500, Furonghua Road, Shanghai, 201203, China
| | - Jianhua Ma
- Singlera Genomics (Shanghai) Ltd., No. 500, Furonghua Road, Shanghai, 201203, China
| | - Minjie Xu
- Singlera Genomics (Shanghai) Ltd., No. 500, Furonghua Road, Shanghai, 201203, China
| | - Chengcheng Ma
- Singlera Genomics (Shanghai) Ltd., No. 500, Furonghua Road, Shanghai, 201203, China
| | - Wei Li
- Singlera Genomics (Shanghai) Ltd., No. 500, Furonghua Road, Shanghai, 201203, China
| | - Rui Liu
- Singlera Genomics (Shanghai) Ltd., No. 500, Furonghua Road, Shanghai, 201203, China
| | - Qiye He
- Singlera Genomics (Shanghai) Ltd., No. 500, Furonghua Road, Shanghai, 201203, China.
| | - Zhixi Su
- Singlera Genomics (Shanghai) Ltd., No. 500, Furonghua Road, Shanghai, 201203, China.
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Yu J, Zhang K, Jin S, Su Z, Xu X, Zhang H. [Sinogram interpolation combined with unsupervised image-to-image translation network for CT metal artifact correction]. Nan Fang Yi Ke Da Xue Xue Bao 2023; 43:1214-1223. [PMID: 37488804 PMCID: PMC10366526 DOI: 10.12122/j.issn.1673-4254.2023.07.18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
OBJECTIVE To propose a framework that combines sinogram interpolation with unsupervised image-to-image translation (UNIT) network to correct metal artifacts in CT images. METHODS The initially corrected CT image and the prior image without artifacts, which were considered as different elements in two different domains, were input into the image transformation network to obtain the corrected image. Verification experiments were carried out to assess the effectiveness of the proposed method using the simulation data, and PSNR and SSIM were calculated for quantitative evaluation of the performance of the method. RESULTS The experiment using the simulation data showed that the proposed method achieved better results for improving image quality as compared with other methods, and the corrected images preserved more details and structures. Compared with ADN algorithm, the proposed algorithm improved the PSNR and SSIM by 2.4449 and 0.0023 when the metal was small, by 5.9942 and 8.8388 for images with large metals, and by 8.8388 and 0.0130 when both small and large metals were present, respectively. CONCLUSION The proposed method for metal artifact correction can effectively remove metal artifacts, improve image quality, and preserve more details and structures on CT images.
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Affiliation(s)
- J Yu
- School of Biomedical Engineering, Southern Medical University, Guangzhou 510515, China
| | - K Zhang
- School of Biomedical Engineering, Southern Medical University, Guangzhou 510515, China
| | - S Jin
- School of Biomedical Engineering, Southern Medical University, Guangzhou 510515, China
| | - Z Su
- School of Biomedical Engineering, Southern Medical University, Guangzhou 510515, China
| | - X Xu
- School of Biomedical Engineering, Southern Medical University, Guangzhou 510515, China
| | - H Zhang
- School of Biomedical Engineering, Southern Medical University, Guangzhou 510515, China
- Guangdong Provincial Key Laboratory of Medical Image Processing, Southern Medical University, Guangzhou 510515, China
- Guangdong Provincial Engineering Laboratory for Medical Imaging and Diagnostic Technology, Southern Medical University, Guangzhou 510515, China
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10
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Wang Z, Xie K, Zhu G, Ma C, Cheng C, Li Y, Xiao X, Li C, Tang J, Wang H, Su Z, Liu D, Zhang W, Huang Y, Tang H, Liu R, Li W. Early detection and stratification of lung cancer aided by a cost-effective assay targeting circulating tumor DNA (ctDNA) methylation. Respir Res 2023; 24:163. [PMID: 37330511 DOI: 10.1186/s12931-023-02449-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 05/12/2023] [Indexed: 06/19/2023] Open
Abstract
BACKGROUND Detection of lung cancer at earlier stage can greatly improve patient survival. We aim to develop, validate, and implement a cost-effective ctDNA-methylation-based plasma test to aid lung cancer early detection. METHODS Case-control studies were designed to select the most relevant markers to lung cancer. Patients with lung cancer or benign lung disease and healthy individuals were recruited from different clinical centers. A multi-locus qPCR assay, LunaCAM, was developed for lung cancer alertness by ctDNA methylation. Two LunaCAM models were built for screening (-S) or diagnostic aid (-D) to favor sensitivity or specificity, respectively. The performance of the models was validated for different intended uses in clinics. RESULTS Profiling DNA methylation on 429 plasma samples including 209 lung cancer, 123 benign diseases and 97 healthy participants identified the top markers that detected lung cancer from benign diseases and healthy with an AUC of 0.85 and 0.95, respectively. The most effective methylation markers were verified individually in 40 tissues and 169 plasma samples to develop LunaCAM assay. Two models corresponding to different intended uses were trained with 513 plasma samples, and validated with an independent collection of 172 plasma samples. In validation, LunaCAM-S model achieved an AUC of 0.90 (95% CI: 0.88-0.94) between lung cancer and healthy individuals, whereas LunaCAM-D model stratified lung cancer from benign pulmonary diseases with an AUC of 0.81 (95% CI: 0.78-0.86). When implemented sequentially in the validation set, LunaCAM-S enables to identify 58 patients of lung cancer (90.6% sensitivity), followed by LunaCAM-D to remove 20 patients with no evidence of cancer (83.3% specificity). LunaCAM-D significantly outperformed the blood test of carcinoembryonic antigen (CEA), and the combined model can further improve the predictive power for lung cancer to an overall AUC of 0.86. CONCLUSIONS We developed two different models by ctDNA methylation assay to sensitively detect early-stage lung cancer or specifically classify lung benign diseases. Implemented at different clinical settings, LunaCAM models has a potential to provide a facile and inexpensive avenue for early screening and diagnostic aids for lung cancer.
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Affiliation(s)
- Zhoufeng Wang
- Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Kehui Xie
- Singlera Genomics (Shanghai) Ltd, Shanghai, China
| | - Guonian Zhu
- Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | | | - Cheng Cheng
- Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yangqian Li
- Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xue Xiao
- Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Chengpin Li
- Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jun Tang
- Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Hui Wang
- Singlera Genomics (Shanghai) Ltd, Shanghai, China
| | - Zhixi Su
- Singlera Genomics (Shanghai) Ltd, Shanghai, China
| | - Dan Liu
- Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Wengeng Zhang
- Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yan Huang
- Health Management Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Huairong Tang
- Health Management Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Rui Liu
- Singlera Genomics (Shanghai) Ltd, Shanghai, China.
| | - Weimin Li
- Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
- Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
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Chen Z, Lei Y, Finnell RH, Ding Y, Su Z, Wang Y, Xie H, Chen F. Whole-exome sequencing study of hypospadias. iScience 2023; 26:106663. [PMID: 37168556 PMCID: PMC10165268 DOI: 10.1016/j.isci.2023.106663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/01/2023] [Accepted: 04/07/2023] [Indexed: 05/13/2023] Open
Abstract
Hypospadias results from the impaired urethral development, which is influenced by androgens, but its genetic etiology is still unknown. Through whole exome sequencing analysis, we identified NR5A1, SRD5A2, and AR as mutational hotspots in the etiology of severe hypospadias, as these genes are related to androgen signaling. Additionally, rare damaging variants in cilia-related outer dynein arm heavy chain (ODNAH) genes (DNAH5, DNAH8, DNAH9, DNAH11, and DNAH17) (p = 8.5 × 10-47) were significantly enriched in hypospadias cases. The Dnah8 KO mice exhibited significantly decreased testosterone levels, which had an impact on urethral development and disrupted steroid biosynthesis. Combined with trios data, transcriptomic, and phenotypical and proteomic characterization of a mouse model, our work links ciliary genes with hypospadias. Overall, a panel of ODNAH genes with rare damaging variants was identified in 24% of hypospadias patients, providing significant insights into the underlying pathogenesis of hypospadias as well as genetic counseling.
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Affiliation(s)
- Zhongzhong Chen
- Department of Urology, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200062, China
- Urogenital Development Research Center, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200062, China
| | - Yunping Lei
- Center for Precision Environmental Health, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard H. Finnell
- Center for Precision Environmental Health, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Departments of Molecular and Human Genetics and Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yu Ding
- Department of Urology, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200062, China
| | - Zhixi Su
- School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yaping Wang
- Department of Urology, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200062, China
| | - Hua Xie
- Department of Urology, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200062, China
| | - Fang Chen
- Department of Urology, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200062, China
- Clinical Research Center For Hypospadias Pediatric College, Shanghai Jiao Tong University School of Medicine, Shanghai 200062, China
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12
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Suo C, Zhao R, Jiang Y, Zhang Y, He Q, Su Z, Liu R, Jin L, Chen X. Abstract 4194: The FuSion Project of Pan-Cancer Early Screening in Chinese– An integrative study by Fudan University and Singlera. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-4194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Background: Cancer is the leading cause of premature deaths. Screening in the population can effectively improve the prognosis by diagnosing cancer early. Previous studies have found that cancer biomarkers, for example, ctDNA methylation and protein biomarkers are clearly associated with the occurrence and development of cancer. To evaluate the performance of reported biomarkers for cancer early screening in real world, we launched an integrative study by Fudan University and SInglera for pan-cancer early detectiON (FuSion) project since 2021. Method: The FuSion Project (NCT05159544) is a prospective and multicenter cohort study of pan-cancer screening in Chinese population. We will construct a stepwise model of risk stratification for screening of multiple cancer types, including lung, esophagus, stomach, liver, pancreatic and colorectal cancers. A total of 50,137 individuals recruited in the Taizhou Longitudinal Study (TLS) between 2012 and 2021 are investigated. Eligible participants are aged 20-75 years and without history of cancer. They have completed a questionnaire and provided blood samples for baseline tests, which measure a total of about 50 indicators in the routine blood work, blood biochemistry, and serum cancer biomarkers, such as carbohydrate antigen 19-9 and carcinoembryonic antigen. Informed consent is obtained from all participants. We build risk stratification models based on risk factors collected in the questionnaire and from baseline test results for each cancer type, respectively. Then, 10,000 high-risk- and 5,000 low-risk individuals of cancers are identified by the cancer-specific risk stratification model. They will be screened by the PanSeerX assay using cancer-related DNA methylation markers, and medically followed-up for at least two years. Sensitivity, specificity, positive- and negative-predictive values of the screening models will be determined based on the true cancer incidences. Finally, we will validate the cancer screening strategies using 10,000 average-risk participants recruited from multiple centers by regular checkups and from other large-scale cohort studies.
Citation Format: Chen Suo, Renjia Zhao, Yanfeng Jiang, Yunzhi Zhang, Qiye He, Zhixi Su, Rui Liu, Li Jin, Xingdong Chen. The FuSion Project of Pan-Cancer Early Screening in Chinese– An integrative study by Fudan University and Singlera. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4194.
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Affiliation(s)
- Chen Suo
- 1Fudan University, Shanghai, China
| | | | | | - Yunzhi Zhang
- 2Singlera Genomics (Shanghai) Ltd, Shanghai, China
| | - Qiye He
- 2Singlera Genomics (Shanghai) Ltd, Shanghai, China
| | - Zhixi Su
- 2Singlera Genomics (Shanghai) Ltd, Shanghai, China
| | - Rui Liu
- 2Singlera Genomics (Shanghai) Ltd, Shanghai, China
| | - Li Jin
- 1Fudan University, Shanghai, China
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Luo R, Su Z, Kang K, Yu M, Zhou X, Wu Y, Yao Z, Xiu W, Yu Y, Zhou L, Na F, Li Y, Zhang X, Zou B, Peng F, Wang J, Xue J, Gong Y, Lu Y. 197P Combining stereotactic body radiation and low-dose radiation (EclipseRT) with PD-1 inhibitor in mice models and patients with bulky tumor. J Thorac Oncol 2023. [DOI: 10.1016/s1556-0864(23)00450-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
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14
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Liu C, Si W, Tu C, Tian S, He X, Wang S, Yang X, Yao C, Li C, Kherraf ZE, Ye M, Zhou Z, Ma Y, Gao Y, Li Y, Liu Q, Tang S, Wang J, Saiyin H, Zhao L, Yang L, Meng L, Chen B, Tang D, Zhou Y, Wu H, Lv M, Tan C, Lin G, Kong Q, Shi H, Su Z, Li Z, Yao YG, Jin L, Zheng P, Ray PF, Tan YQ, Cao Y, Zhang F. Deficiency of primate-specific SSX1 induced asthenoteratozoospermia in infertile men and cynomolgus monkey and tree shrew models. Am J Hum Genet 2023; 110:516-530. [PMID: 36796361 PMCID: PMC10027476 DOI: 10.1016/j.ajhg.2023.01.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 01/19/2023] [Indexed: 02/17/2023] Open
Abstract
Primate-specific genes (PSGs) tend to be expressed in the brain and testis. This phenomenon is consistent with brain evolution in primates but is seemingly contradictory to the similarity of spermatogenesis among mammals. Here, using whole-exome sequencing, we identified deleterious variants of X-linked SSX1 in six unrelated men with asthenoteratozoospermia. SSX1 is a PSG expressed predominantly in the testis, and the SSX family evolutionarily expanded independently in rodents and primates. As the mouse model could not be used for studying SSX1, we used a non-human primate model and tree shrews, which are phylogenetically similar to primates, to knock down (KD) Ssx1 expression in the testes. Consistent with the phenotype observed in humans, both Ssx1-KD models exhibited a reduced sperm motility and abnormal sperm morphology. Further, RNA sequencing indicated that Ssx1 deficiency influenced multiple biological processes during spermatogenesis. Collectively, our experimental observations in humans and cynomolgus monkey and tree shrew models highlight the crucial role of SSX1 in spermatogenesis. Notably, three of the five couples who underwent intra-cytoplasmic sperm injection treatment achieved a successful pregnancy. This study provides important guidance for genetic counseling and clinical diagnosis and, significantly, describes the approaches for elucidating the functions of testis-enriched PSGs in spermatogenesis.
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Affiliation(s)
- Chunyu Liu
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering, School of Life Sciences, Institute of Reproduction and Development, Fudan University, Shanghai, China; Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Fudan University, Shanghai, China
| | - Wei Si
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
| | - Chaofeng Tu
- 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
| | - Shixiong Tian
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China; Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai, China
| | - Xiaojin He
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, China; Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Ministry of Education of the People's Republic of China, Hefei, China
| | - Shengnan Wang
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
| | - Xiaoyu Yang
- State Key Laboratory of Reproductive Medicine, Clinical Center for Reproductive Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Chencheng Yao
- Department of Andrology, Center for Men's Health, Urologic Medical Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Key Lab of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Cong Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Zine-Eddine Kherraf
- Université Grenoble Alpes, INSERM U1209, CNRS UMR 5309, Institute for Advanced Biosciences, Team Genetics Epigenetics and Therapies of Infertility, Grenoble, France; CHU Grenoble Alpes, UM GI-DPI, Grenoble, France
| | - Maosen Ye
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, and KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Zixue Zhou
- Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai, China
| | - Yuhua Ma
- National Resource Center for Non-Human Primates, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yang Gao
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, China
| | - Yu Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, and KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Qiwei Liu
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
| | - Shuyan Tang
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering, School of Life Sciences, Institute of Reproduction and Development, Fudan University, Shanghai, China; Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Fudan University, Shanghai, China
| | - Jiaxiong Wang
- Center for Reproduction and Genetics, State Key Laboratory of Reproductive Medicine, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou, China
| | - Hexige Saiyin
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering, School of Life Sciences, Institute of Reproduction and Development, Fudan University, Shanghai, China
| | - Liangyu Zhao
- The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| | - Liqun Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Lanlan Meng
- 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
| | - Bingbing Chen
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
| | - Dongdong Tang
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, China; Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Ministry of Education of the People's Republic of China, Hefei, China
| | - Yiling Zhou
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering, School of Life Sciences, Institute of Reproduction and Development, Fudan University, Shanghai, China; Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Fudan University, Shanghai, China
| | - Huan Wu
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, China; Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Ministry of Education of the People's Republic of China, Hefei, China
| | - Mingrong Lv
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, China; Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Ministry of Education of the People's Republic of China, Hefei, China
| | - Chen 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
| | - Ge Lin
- 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
| | - Qingpeng Kong
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Hong Shi
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
| | - Zhixi Su
- Singlera Genomics (Shanghai) Limited, Shanghai, China
| | - Zheng Li
- Department of Andrology, Center for Men's Health, Urologic Medical Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Key Lab of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, and KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China; National Resource Center for Non-Human Primates, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Li Jin
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering, School of Life Sciences, Institute of Reproduction and Development, Fudan University, Shanghai, China; Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai, China
| | - Ping Zheng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, and KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; National Resource Center for Non-Human Primates, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Pierre F Ray
- Université Grenoble Alpes, INSERM U1209, CNRS UMR 5309, Institute for Advanced Biosciences, Team Genetics Epigenetics and Therapies of Infertility, Grenoble, France; CHU Grenoble Alpes, UM GI-DPI, Grenoble, France
| | - 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
| | - Yunxia Cao
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, China; NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, China; Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Ministry of Education of the People's Republic of China, Hefei, China.
| | - Feng Zhang
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering, School of Life Sciences, Institute of Reproduction and Development, Fudan University, Shanghai, China; Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Fudan University, Shanghai, China; Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai, China.
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Li F, Zeng M, Ouyang C, Liu J, Ning S, Cui H, Yuan Y, Su Z, Zhou J, Liu W, Wang L, Wang X, Xing C, Qin L, Wang N. WCN23-0614 HUMAN AMNION-DERIVED MESENCHYMAL STEM CELL TREATMENT FOR A MALE UREMIC CALCIPHYLAXIS PATIENT WITH MULTISYSTEM ANGIOPATHY. Kidney Int Rep 2023. [DOI: 10.1016/j.ekir.2023.02.486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2023] Open
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Mo S, Dai W, Wang H, Lan X, Ma C, Su Z, Xiang W, Han L, Luo W, Zhang L, Wang R, Zhang Y, Zhang W, Yang L, Lu R, Guo L, Zheng Y, Huang M, Xu Y, Liang L, Cai S, Cai G. Early detection and prognosis prediction for colorectal cancer by circulating tumour DNA methylation haplotypes: A multicentre cohort study. EClinicalMedicine 2023; 55:101717. [PMID: 36386039 PMCID: PMC9646872 DOI: 10.1016/j.eclinm.2022.101717] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 10/06/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Early detection and prognosis prediction of colorectal cancer (CRC) can significantly reduce CRC-related mortality. Recently, circulating tumour DNA (ctDNA) methylation has shown good application foreground in the early detection and prognosis prediction of multiple tumours. METHODS This multicentre cohort study evaluated ctDNA methylation haplotype patterns based on archived plasma samples (collected between 2010 and 2018) from 1138 individuals at two medical centres: Fudan University Shanghai Cancer Center (Shanghai, China) and Southern Medical University Nanfang Hospital (Guangzhou, Guangdong, China), including 366 healthy individuals, 182 patients with advanced adenoma (AA), and 590 patients with CRC. Samples were processed using the ColonES assay, a targeted bisulfite sequencing method that detects ctDNA methylation haplotype patterns in 191 genomic regions. Among these 1138 samples, 748 were used to develop a classification model, and 390 served as a blinded cohort for independent validation. The study is registered at https://register.clinicaltrials.gov with the unique identifier NCT03737591. RESULTS The model obtained from unblinded samples discriminated patients with CRC or AA from normal controls with high accuracy. In the blinded validation set, the ColonES assay achieved sensitivity values of 79.0% (95% confidence interval (CI), 66%-88%) in AA patients and 86.6% (95% CI, 81%-91%) in CRC patients with a specificity of 88.1% (95% CI, 81%-93%) in healthy individuals. The model area under the curve (AUC) for the blinded validation set was 0.903 for AA samples and 0.937 for CRC samples. Additionally, the prognosis of patients with high preoperative ctDNA methylation levels was worse than that of patients with low ctDNA methylation levels (p = 0.001 for relapse-free survival and p = 0.004 for overall survival). INTERPRETATION We successfully developed and validated an accurate, noninvasive detection method based on ctDNA methylation haplotype patterns that may enable early detection and prognosis prediction for CRC. FUNDING The Grant of National Natural Science Foundation of China (No.81871958), National Natural Science Foundation of China (No. 82203215), Shanghai Science and Technology Committee (No. 19140902100), Scientific Research Fund of Fudan University (No.IDF159052), Shanghai Municipal Health Commission (SHWJRS 2021-99), and Shanghai Sailing Program (22YF1408800).
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Affiliation(s)
- Shaobo Mo
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Weixing Dai
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hui Wang
- Singlera Genomics (Shanghai) Ltd, Shanghai, China
| | - Xiaoliang Lan
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | | | - Zhixi Su
- Singlera Genomics (Shanghai) Ltd, Shanghai, China
| | - Wenqiang Xiang
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Lingyu Han
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wenqin Luo
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Long Zhang
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Cancer Institute, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Renjie Wang
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yaodong Zhang
- Department of Intensive Care Unit, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Wenming Zhang
- Department of Endoscopy, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Lin Yang
- Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Renquan Lu
- Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Lin Guo
- Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Ying Zheng
- Department of Cancer Prevention, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Mingzhu Huang
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Ye Xu
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Corresponding author. Department of Colorectal Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Li Liang
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Southern Medical University, Guangzhou, China
- Corresponding author. Department of Pathology, Nanfang Hospital, Southern Medical University; Guangdong Province Key Laboratory of Molecular Tumor Pathology, Southern Medical University, Guangzhou, China.
| | - Sanjun Cai
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Cancer Institute, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
- Corresponding author. Department of Colorectal Surgery, Fudan University Shanghai Cancer Center; Department of Cancer Institute, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Guoxiang Cai
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Corresponding author. Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
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Liu X, Chen B, Chen J, Su Z, Sun S. The incidence, prevalence, and survival analysis of pancreatic neuroendocrine tumors in the United States. J Endocrinol Invest 2022:10.1007/s40618-022-01985-2. [PMID: 36522587 DOI: 10.1007/s40618-022-01985-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 09/27/2022] [Indexed: 12/23/2022]
Abstract
PURPOSE The incidence of pancreatic neuroendocrine tumors (pNETs) was increasing. The main purpose of this study was to statistically analyze the incidence and prevalence of pNETs and the main risk factors for the prognosis. METHODS Based on the Surveillance, Epidemiology, and End Results (SEER) database, with three registries integrated, this study comprehensively displayed the annual age adjust incidence of pNETs from 1975 to 2018, the estimated 20-year limited-duration prevalence, and conducted the univariate and multivariate survival analysis. RESULTS The incidence of pNETs has increased to about 1.5 per 100,000 population, and the prevalence has reached about 0.008% with the aged, Grade 1 and nonfunctional tumors accounting for the majority. The average median overall survival (OS), 5-year survival rate, and median disease-free survival (DFS) of pNETs patients from 1975 to 2018 were 85 months, 57.55%, and 220 months, respectively. From 2000 to 2018, the median OS was 94 months, and the 5-year survival rate was 59.94%. In multivariate survival analysis, the greatest risk factor was Grade 3&4 with HR = 3.62 (3.10-4.28), followed by distant stage with HR = 2.77 (2.28-3.36), and aged over 80 years old with HR = 2.26 (1.33-3.83). Surgery was a protective prognostic factor with HR = 0.34 (0.29-0.40). CONCLUSION The incidence and prevalence of pNETs were still increasing, but the trend was gradual and aging in recent years. The survival time of pNETs was longer but has not changed much in recent years. The degrees of malignancy, stage, and operation were the most important prognosis factors.
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Affiliation(s)
- X Liu
- Department of General Surgery, Shengjing Hospital of China Medical University, No. 36 Sanhao Street, Heping District, Shenyang, 110004, Liaoning, China
| | - B Chen
- Department of General Surgery, Shengjing Hospital of China Medical University, No. 36 Sanhao Street, Heping District, Shenyang, 110004, Liaoning, China
| | - J Chen
- Department of General Surgery, Shengjing Hospital of China Medical University, No. 36 Sanhao Street, Heping District, Shenyang, 110004, Liaoning, China
| | - Z Su
- Department of General Surgery, Shengjing Hospital of China Medical University, No. 36 Sanhao Street, Heping District, Shenyang, 110004, Liaoning, China
| | - S Sun
- Department of General Surgery, Shengjing Hospital of China Medical University, No. 36 Sanhao Street, Heping District, Shenyang, 110004, Liaoning, China.
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Hao Y, Yang Q, He Q, Hu H, Weng Z, Su Z, Chen S, Peng S, Kuang M, Chen Z, Xu L. Identification of DNA methylation signatures for hepatocellular carcinoma detection and microvascular invasion prediction. Eur J Med Res 2022; 27:276. [PMID: 36464701 PMCID: PMC9720918 DOI: 10.1186/s40001-022-00910-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 11/22/2022] [Indexed: 12/07/2022] Open
Abstract
BACKGROUND AND AIM Preoperative evaluation of microvascular invasion (MVI) in patients with hepatocellular carcinoma (HCC) is important for surgical strategy determination. We aimed to develop and establish a preoperative predictive model for MVI status based on DNA methylation markers. METHODS A total of 35 HCC tissues and the matched peritumoral normal liver tissues as well as 35 corresponding HCC patients' plasma samples and 24 healthy plasma samples were used for genome-wide methylation sequencing and subsequent methylation haplotype block (MHB) analysis. Predictive models were constructed based on selected MHB markers and 3-cross validation was used. RESULTS We grouped 35 HCC patients into 2 categories, including the MVI- group with 17 tissue and plasma samples, and MVI + group with 18 tissue and plasma samples. We identified a tissue DNA methylation signature with an AUC of 98.0% and a circulating free DNA (cfDNA) methylation signature with an AUC of 96.0% for HCC detection. Furthermore, we established a tissue DNA methylation signature for MVI status prediction, and achieved an AUC of 85.9%. Based on the MVI status predicted by the DNA methylation signature, the recurrence-free survival (RFS) and overall survival (OS) were significantly better in the predicted MVI- group than that in the predicted MVI + group. CONCLUSIONS In this study, we identified a cfDNA methylation signature for HCC detection and a tissue DNA methylation signature for MVI status prediction with high accuracy.
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Affiliation(s)
- Yijie Hao
- grid.412615.50000 0004 1803 6239Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, No.58 Zhongshan Er Road, Guangzhou, 510080 Guangdong Province China ,grid.412615.50000 0004 1803 6239Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, No.58 Zhongshan Er Road, Guangzhou, 510080 Guangdong Province China
| | - Qingxia Yang
- grid.412615.50000 0004 1803 6239Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, No.58 Zhongshan Er Road, Guangzhou, 510080 Guangdong Province China ,grid.412615.50000 0004 1803 6239Department of Oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080 Guangdong Province China
| | - Qiye He
- Singlera Genomics (Shanghai) Ltd., Shanghai, 201203 China
| | - Huanjing Hu
- grid.412615.50000 0004 1803 6239Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, No.58 Zhongshan Er Road, Guangzhou, 510080 Guangdong Province China
| | - Zongpeng Weng
- grid.12981.330000 0001 2360 039XDepartment of Biology and Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080 Guangdong Province China
| | - Zhixi Su
- Singlera Genomics (Shanghai) Ltd., Shanghai, 201203 China
| | - Shuling Chen
- grid.412615.50000 0004 1803 6239Department of Medical Ultrasonics, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080 Guangdong Province China
| | - Sui Peng
- grid.412615.50000 0004 1803 6239Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, No.58 Zhongshan Er Road, Guangzhou, 510080 Guangdong Province China ,grid.412615.50000 0004 1803 6239Clinical Trials Unit, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080 Guangdong Province China
| | - Ming Kuang
- grid.412615.50000 0004 1803 6239Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, No.58 Zhongshan Er Road, Guangzhou, 510080 Guangdong Province China ,grid.412615.50000 0004 1803 6239Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, No.58 Zhongshan Er Road, Guangzhou, 510080 Guangdong Province China
| | - Zhihang Chen
- grid.412615.50000 0004 1803 6239Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, No.58 Zhongshan Er Road, Guangzhou, 510080 Guangdong Province China
| | - Lixia Xu
- grid.412615.50000 0004 1803 6239Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, No.58 Zhongshan Er Road, Guangzhou, 510080 Guangdong Province China ,grid.412615.50000 0004 1803 6239Department of Oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080 Guangdong Province China
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Wu H, Guo S, Liu X, Li Y, Su Z, He Q, Liu X, Zhang Z, Yu L, Shi X, Gao S, Wang H, Pan Y, Ma C, Liu R, Dai M, Jin G, Liang Z. Noninvasive detection of pancreatic ductal adenocarcinoma using the methylation signature of circulating tumour DNA. BMC Med 2022; 20:458. [PMID: 36434648 PMCID: PMC9701032 DOI: 10.1186/s12916-022-02647-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 11/01/2022] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Pancreatic ductal adenocarcinoma (PDAC) has the lowest overall survival rate primarily due to the late onset of symptoms and rapid progression. Reliable and accurate tests for early detection are lacking. We aimed to develop a noninvasive test for early PDAC detection by capturing the circulating tumour DNA (ctDNA) methylation signature in blood. METHODS Genome-wide methylation profiles were generated from PDAC and nonmalignant tissues and plasma. Methylation haplotype blocks (MHBs) were examined to discover de novo PDAC markers. They were combined with multiple cancer markers and screened for PDAC classification accuracy. The most accurate markers were used to develop PDACatch, a targeted methylation sequencing assay. PDACatch was applied to additional PDAC and healthy plasma cohorts to train, validate and independently test a PDAC-discriminating classifier. Finally, the classifier was compared and integrated with carbohydrate antigen 19-9 (CA19-9) to evaluate and maximize its accuracy and utility. RESULTS In total, 90 tissues and 546 plasma samples were collected from 232 PDAC patients, 25 chronic pancreatitis (CP) patients and 323 healthy controls. Among 223 PDAC cases with known stage information, 43/119/38/23 cases were of Stage I/II/III/IV. A total of 171 de novo PDAC-specific markers and 595 multicancer markers were screened for PDAC classification accuracy. The top 185 markers were included in PDACatch, from which a 56-marker classifier for PDAC plasma was trained, validated and independently tested. It achieved an area under the curve (AUC) of 0.91 in both the validation (31 PDAC, 26 healthy; sensitivity = 84%, specificity = 89%) and independent tests (74 PDAC, 65 healthy; sensitivity = 82%, specificity = 88%). Importantly, the PDACatch classifier detected CA19-9-negative PDAC plasma at sensitivities of 75 and 100% during the validation and independent tests, respectively. It was more sensitive than CA19-9 in detecting Stage I (sensitivity = 80 and 68%, respectively) and early-stage (Stage I-IIa) PDAC (sensitivity = 76 and 70%, respectively). A combinatorial classifier integrating PDACatch and CA19-9 outperformed (AUC=0.94) either PDACatch (0.91) or CA19-9 (0.89) alone (p < 0.001). CONCLUSIONS The PDACatch assay demonstrated high sensitivity for early PDAC plasma, providing potential utility for noninvasive detection of early PDAC and indicating the effectiveness of methylation haplotype analyses in discovering robust cancer markers.
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Affiliation(s)
- Huanwen Wu
- Department of Pathology, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1, Shuaifuyuan Wangfujing, Dongcheng District, Beijing, 100730, China
| | - Shiwei Guo
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Navy Medical, University (the Second Military Medical University), No.168, Changhai Road, Shanghai, 200433, China
| | - Xiaoding Liu
- Department of Pathology, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1, Shuaifuyuan Wangfujing, Dongcheng District, Beijing, 100730, China
| | - Yatong Li
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1, Shuaifuyuan Wangfujing, Dongcheng District, Beijing, 100730, China
| | - Zhixi Su
- Singlera Genomics (Shanghai) Ltd., No. 500, Furonghua Road, Shanghai, 201203, China
| | - Qiye He
- Singlera Genomics (Shanghai) Ltd., No. 500, Furonghua Road, Shanghai, 201203, China
| | - Xiaoqian Liu
- Department of Pathology, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1, Shuaifuyuan Wangfujing, Dongcheng District, Beijing, 100730, China
| | - Zhiwen Zhang
- Department of Pathology, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1, Shuaifuyuan Wangfujing, Dongcheng District, Beijing, 100730, China
| | - Lianyuan Yu
- Department of Pathology, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1, Shuaifuyuan Wangfujing, Dongcheng District, Beijing, 100730, China
| | - Xiaohan Shi
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Navy Medical, University (the Second Military Medical University), No.168, Changhai Road, Shanghai, 200433, China
| | - Suizhi Gao
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Navy Medical, University (the Second Military Medical University), No.168, Changhai Road, Shanghai, 200433, China
| | - Huan Wang
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Navy Medical, University (the Second Military Medical University), No.168, Changhai Road, Shanghai, 200433, China
| | - Yaqi Pan
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Navy Medical, University (the Second Military Medical University), No.168, Changhai Road, Shanghai, 200433, China
| | - Chengcheng Ma
- Singlera Genomics (Shanghai) Ltd., No. 500, Furonghua Road, Shanghai, 201203, China
| | - Rui Liu
- Singlera Genomics (Shanghai) Ltd., No. 500, Furonghua Road, Shanghai, 201203, China.
| | - Menghua Dai
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1, Shuaifuyuan Wangfujing, Dongcheng District, Beijing, 100730, China.
| | - Gang Jin
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Navy Medical, University (the Second Military Medical University), No.168, Changhai Road, Shanghai, 200433, China.
| | - Zhiyong Liang
- Department of Pathology, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, No.1, Shuaifuyuan Wangfujing, Dongcheng District, Beijing, 100730, China.
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Li D, Zhang JP, Zhang C, Hou BX, Su Z. [Mandibular first premolar with hyper-taurodont and C3 root canal: a case report]. Zhonghua Kou Qiang Yi Xue Za Zhi 2022; 57:1173-1176. [PMID: 36379898 DOI: 10.3760/cma.j.cn112144-20220302-00088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Affiliation(s)
- D Li
- Department of Endodontics, Capital Medical University School of Stomatology, Beijing 100050, China
| | - J P Zhang
- Department of Endodontics, Capital Medical University School of Stomatology, Beijing 100050, China
| | - C Zhang
- Department of Endodontics, Capital Medical University School of Stomatology, Beijing 100050, China
| | - B X Hou
- Center for Microscope Enhanced Dentistry, Capital Medical University School of Stomatology, Beijing 100162, China
| | - Z Su
- Department of Endodontics, Capital Medical University School of Stomatology, Beijing 100050, China
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Su Z, Li Y, Yang S, Guo J, Guo, L, Gu Y. Excimer laser atherectomy combined with drug-coated balloon angioplasty for the treatment of femoropopliteal arteriosclerosis obliterans. Ann R Coll Surg Engl 2022; 104:667-672. [PMID: 35446161 PMCID: PMC9685997 DOI: 10.1308/rcsann.2021.0335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/23/2021] [Indexed: 11/22/2022] Open
Abstract
INTRODUCTION It has been reported that excimer laser atherectomy combined with a drug-coated balloon (ELA+DCB) can achieve better results than simple balloon angioplasty, especially for the treatment of femoropopliteal in-stent restenosis. However, reports on the application of ELA+DCB in China for femoropopliteal arteriosclerosis obliterans are lacking. This study focuses on analysing the effectiveness and safety of ELA+DCB. METHODS This was a single-centre retrospective study that enrolled patients from November 2016 to January 2019 who had femoropopliteal arteriosclerosis obliterans treated by ELA+DCB. Preoperative demographics, operative details and postoperative follow-up outcomes were analysed statistically. RESULTS There were 43 patients with an average patient age of 68.0±8.6 years; 79.1% were male. In 30 cases, the lesions were de novo and the others were in-stent restenosis (ISR). During the procedure, flow-limiting dissection (48.8%) was the main adverse event and there were 17 bailout stent implantations due to dissection. Mean (±sd) ankle-brachial index (ABI) in the patients was 0.42±0.31 before the operation and 0.83±0.13 before discharge. The mean (±sd) follow-up time was 29.35±9.71 months. The primary patency rate was 66.8%, 64.3% and 60.9% at 12, 24 and 36 months. Freedom from target lesion revascularisation (TLR) was 85.7%, 80.7% and 75.3% at 12, 24 and 36 months. Rutherford categories also greatly improved during follow-up. Overall mortality was 6.9% (3/48), and no deaths were related to the intervention. CONCLUSION The use of ELA+DCB had good clinical benefit for femoropopliteal arteriosclerosis obliterans, which had good primary patency and freedom from TLR, although intraoperative complications still required attention. Multicentre randomised controlled trials with long-term follow-up are needed.
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Affiliation(s)
- Z Su
- Xuanwu Hospital, Capital Medical University,Beijing, China
| | - Y Li
- Xuanwu Hospital, Capital Medical University,Beijing, China
| | - S Yang
- Xuanwu Hospital, Capital Medical University,Beijing, China
| | - J Guo
- Xuanwu Hospital, Capital Medical University,Beijing, China
| | - L Guo,
- Xuanwu Hospital, Capital Medical University,Beijing, China
| | - Y Gu
- Xuanwu Hospital, Capital Medical University,Beijing, China
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He Y, Pang Y, Su Z, Zhou Y, Wang Y, Lu Y, Jiang Y, Han X, Song L, Wang L, Li Z, Lv X, Wang Y, Yao J, Liu X, Zhou X, He S, Zhang Y, Song L, Li J, Wang B, Tang L. Symptom burden, psychological distress, and symptom management status in hospitalized patients with advanced cancer: a multicenter study in China. ESMO Open 2022; 7:100595. [PMID: 36252435 PMCID: PMC9808454 DOI: 10.1016/j.esmoop.2022.100595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/31/2022] [Accepted: 09/02/2022] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The management of physical symptoms and psychological distress of cancer patients is an important component of cancer care. The purpose of this study was to evaluate the symptom burden, psychological distress, and management status of hospitalized patients with advanced cancer in China and explore the potential influencing factors of undertreatment and non-treatment of symptoms. PATIENTS AND METHODS A total of 2930 hospitalized patients with advanced cancer (top six types of cancer in China) were recruited from 10 centers all over China. Patient-reported MD Anderson Symptom Inventory, Hospital Anxiety and Depression Scale (HADS), and Patient Health Questionnaire-9 (PHQ-9) scales and symptom management-related information were collected and linked with the patient's clinical data. The proportion of patients reporting moderate-to-severe (MS) symptoms and whether they were currently well managed were examined. Multivariable logistic regression models were applied to explore the factors correlated to undertreatment and non-treatment of symptoms. RESULTS About 27% of patients reported over three MS symptoms, 16% reported over five, and 9% reported over seven. Regarding psychological distress, the prevalence of HADS-anxiety was 29% and that of PHQ-9 depression was 11%. Sixty-one percent of patients have at least one MS symptom without any treatment. Sex [odds ratio (OR) = 2.238, 95% confidence interval (95% CI) 1.502-3.336], Eastern Cooperative Oncology Group (ECOG; OR = 0.404, 95% CI 0.241-0.676), and whether currently undergoing anticancer treatment (OR = 0.667, 95% CI 0.503-0.886) are the main factors correlated with the undertreatment of symptoms. Age (OR = 1.972, 95% CI 1.263-3.336), sex (OR = 0.626, 95% CI 0.414-0.948), ECOG (OR = 0.266, 95% CI 0.175-0.403), whether currently undergoing anticancer treatment (OR = 0.356, 95% CI 0.249-0.509), and comorbidity (OR = 0.713, 95% CI 0.526-0.966) are the main factors correlated with the non-treatment of symptoms. CONCLUSIONS This study shows that hospitalized patients with advanced cancer had a variety of physical and psychological symptoms but lacked adequate management and suggests that a complete symptom screening and management system is needed to deal with this complex problem.
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Affiliation(s)
- Y. He
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Psycho-oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Y. Pang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Psycho-oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Z. Su
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Psycho-oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Y. Zhou
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Psycho-oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Y. Wang
- Department of Breast Cancer Radiotherapy, Chinese Academy of Medical Sciences, Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Y. Lu
- The Fifth Department of Chemotherapy, The Affiliated Cancer Hospital of Guangxi Medical University, Guangxi Zhuang Autonomous Region, Nanning, China
| | - Y. Jiang
- Department of Medical Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - X. Han
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Psycho-oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - L. Song
- Department of Breast Medical Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - L. Wang
- Department of Oncology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Z. Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Psycho-oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - X. Lv
- Department of Oncology, Xiamen Humanity Hospital, Xiamen, China
| | - Y. Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Psycho-oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - J. Yao
- Department of Integrated Chinese and Western Medicine, Shaanxi Provincial Cancer Hospital Affiliated to Medical College of Xi'an Jiaotong University, Xi'an, China
| | - X. Liu
- Department of Clinical Spiritual Care, Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - X. Zhou
- Radiotherapy Center, Hubei Cancer Hospital, Wuhan, China
| | - S. He
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Psycho-oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Y. Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Psycho-oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - L. Song
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Psycho-oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - J. Li
- Department of Psycho-oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - B. Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Psycho-oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - L. Tang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Psycho-oncology, Peking University Cancer Hospital & Institute, Beijing, China,Correspondence to: Dr Lili Tang, Fu-Cheng Road 52, Hai-Dian District, Beijing 100142, China. Tel: +86-1088196648
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Ougland R, Monshaugen I, Su Z, Dutta A, Klungland A. Epitranscriptomic regulation in bladder cancer. EUR UROL SUPPL 2022. [DOI: 10.1016/s2666-1683(22)01955-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Gulley J, Bayliffe A, Donahue R, Tsai Y, Liu K, Katraggada M, Hsu J, Siu L, Wherry E, Chopra R, Schlom J, Su Z. STAR0602, a novel TCR agonist antibody, demonstrates potent antitumor activity in refractory solid tumor models through the expansion of a novel, polyclonal effector memory T cell subset. Eur J Cancer 2022. [DOI: 10.1016/s0959-8049(22)00819-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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25
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Chen S, Su Z, Ma S, Sun Z, Liu X, Huang M. 375P The co-mutations and genetic features of BRAF-mutated gene mutations in a large Chinese MSS colorectal cancer cohort. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.07.513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
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Hofman P, Su Z, Tong X, Bunn V, Jin S, Vincent S. 1087P Predictive value of Krebs von den Lungen-6 (KL-6) and surfactant protein D (SP-D) in patients (pts) with EGFR exon 20 insertion (ex20ins)-positive metastatic non-small cell lung cancer (mNSCLC) receiving mobocertinib therapy. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.07.1213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
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Su Z, McDonnell D, Li Y. Erratum to: Why is COVID-19 more deadly to nursing home residents? QJM 2022; 115:571. [PMID: 34931689 PMCID: PMC9383151 DOI: 10.1093/qjmed/hcab135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Affiliation(s)
- Z Su
- Address correspondence to Dr Z. Su, Ph.D., Center on Smart and Connected Health Technologies, Mays Cancer Center, School of Nursing, UT Health San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, USA.
| | - D McDonnell
- Department of Humanities, Institute of Technology Carlow, Carlow, R93 V960, Ireland
| | - Y Li
- Department of Public Health Sciences, Division of Health Policy and Outcomes Research, University of Rochester Medical Center, 265 Crittenden Blvd., CU 420644, Rochester, New York, 14642, USA
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Guo S, Su M, Ma C, Shi X, Xu M, Gao S, Wang H, Pan Y, He Q, Su Z, Jin G. Aberrant circulating tumour DNA methylations as biomarkers for early detection of pancreatic ductal adenocarcinoma: a retrospective study. Lancet Oncol 2022. [DOI: 10.1016/s1470-2045(22)00413-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Li Y, Xu M, Sun J, He Q, Su Z, Liu R. Abstract 6194: DNA methylation-based immune response signature for thyroid nodule diagnostics. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-6194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Thyroid cancer (TC) account for 90% of endocrine malignant tumor. The association between thyroid inflammation and carcinogenesis has long been recognized. However, the differential immunological mechanisms underlying pathogenesis of papillary thyroid cancers (PTCs) and benign thyroid nodules (BTNs) have not been well characterized. In this study, we aimed to explore the immunological differences between PTCs and BTNs. Further, we attempted to develop a novel classifier based on DNA methylation of immune response genes for thyroid cancer precise diagnosis.
Methods: A publicly available tissue Reduced Representative Bisulfite Sequencing dataset composed of 80 PTCs and 65 BTNs was collected (GSE107738), including a training cohort (39 PTCs, 28 BTNS) and a testing cohort (41 PTCs, 37 BTNs). We identified differentially methylated regions (DMRs) between PTCs and BTNs. Functional enrichment analyses of DMR-associated genes were conducted by hypergeometric test. DNA methylation markers of immune response genes were extracted. A diagnostic classifier based on these markers was developed using a training cohort and was validated in an independent testing cohort. These markers were further confirmed by two independent datasets (GSE53051: 20 PTCs, 32 BTNs; GSE97466: 60 PTCs, 17 BTNs) generated by the Infinium Methylation 450K array. A new classifier based on the corresponding 15 array-based methylation markers was built using these two datasets, and was validated in the 450K array data of 499 thyroid malignant tissue samples in the TCGA database.
Results: We identified 220 DMRs between PTCs and BTNs. DMR-associated genes were significantly enriched in immune response biological processes. The classifier comprised of 15 DNA methylation markers from immune response genes achieved 100% sensitivity, 76% specificity, 82% positive predictive value (PPV), 100% negative predictive value (NPV) and 88% accuracy in the testing cohort. This classifier also demonstrated high accuracy for cytologically indeterminate thyroid nodules (25 PTCs, 29 BTNs). Leave-one-out cross validation using the corresponding array methylation markers in two independent datasets achieved prediction accuracy of 92% and 95%, respectively. An array-based classifier trained on all samples of the methylation array data achieved a sensitivity of 89% in classifying 499 thyroid malignant tissue samples in the TCGA database.
Conclusion: Our study demonstrated that DNA methylation signature of immune response gene could be used to differentiate PTCs from BTNs with high accuracy, which may be caused by the different immunological microenvironments in response to PTCs and BTNs.
Citation Format: Yiying Li, Minjie Xu, Jin Sun, Qiye He, Zhixi Su, Rui Liu. DNA methylation-based immune response signature for thyroid nodule diagnostics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6194.
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Affiliation(s)
| | | | - Jin Sun
- 1Singlera Genomics, Shanghai, China
| | - Qiye He
- 1Singlera Genomics, Shanghai, China
| | - Zhixi Su
- 1Singlera Genomics, Shanghai, China
| | - Rui Liu
- 1Singlera Genomics, Shanghai, China
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Wang Z, Xu M, Chen H, Xie K, Su M, He Q, Su Z, Liu R, Li W. Abstract 6202: Plasma cell-free DNA fragmentation patterns combined with tumor mutation detection in diagnosis of lung cancer. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-6202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Lung cancer is one of the deadliest types of cancer in China. Its 5-year survival rates at early stages are significantly higher than advanced stages. LDCT has been adopted for lung cancer screening in high-risk individuals; however, debate regarding its accuracy is still ongoing. Mutation detection on cell free DNA (cfDNA) has traditionally been used to monitor DNA molecular changes derived from lung cancer cells in blood, while recently fragmentation pattern profiling of cfDNA has been shown as a promising alternative for early cancer detection. We aimed to combine mutation detection and fragmentation pattern analysis on cfDNA to develop a non-invasive assay to screen early lung cancer.
Methods: Candidate DNA mutations were curated from literature and public databases, including COSMIC and TCGA. DNA fragmentation markers were collected from literature and whole genome sequencing (WGS) datasets. A panel of 407 primers covering selected mutation and fragmentation markers was developed to distinguish lung adenocarcinoma (ADC) plasma and normal plasma. We enrolled a total of 122 plasma samples (64 normal, 58 ADC) for this study. 49 normal samples and 44 ADC samples were used to construct a mutation-based classification model and a fragmentation-based classification model separately. The tuning parameters and features were determined by inner 4-fold cross validation. For the mutation-based model, baseline was set using normal samples in training set. Maximum allele frequency was calculated for each sample in test data (15 normal, 14 ADC), which was filtered by the background baseline. For the fragmentation-based model, we used the DELFI fragment score to construct fragmentation profiles, which was the ratio between short fragments (100-150bp) and long fragments (151-220bp). After optimization, the two models were integrated by Logistic Regression to create a combined model, which was validated by 4-fold nested cross validation.
Results: ADC and normal plasma were sequenced by the aforementioned panel at an average depth of 2,000X to ensure the reliability of model construction and classification results. In classifying normal and ADC plasma, the mutation model alone is only modestly accurate as it produced an AUC of 0.69. But the fragmentation model demonstrated significantly higher accuracy, achieving AUC of 0.85. Furthermore, the combined model performed better than either model along, achieving an elevated AUC of 0.87.
Conclusions: We demonstrate that DNA mutation and fragmentation pattern of cfDNA can classify lung cancer and normal plasmas separately, but fragmentation pattern are more accurate than mutation in this task. Combining the two models further improved prediction accuracy, suggesting they complement each other. Although this is a pilot study of limited cases, it demonstrated the potential of combining markers for accurate lung ADC detection in plasma.
Citation Format: Zhoufeng Wang, Minjie Xu, Hua Chen, Kehui Xie, Minyang Su, Qiye He, Zhixi Su, Rui Liu, Weimin Li. Plasma cell-free DNA fragmentation patterns combined with tumor mutation detection in diagnosis of lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6202.
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Affiliation(s)
| | | | - Hua Chen
- 2Singlera Genomics, Shanghai, China
| | | | | | - Qiye He
- 2Singlera Genomics, Shanghai, China
| | - Zhixi Su
- 2Singlera Genomics, Shanghai, China
| | - Rui Liu
- 2Singlera Genomics, Shanghai, China
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Xu XQ, Zhang JW, Chen RM, Luo JS, Chen SK, Zheng RX, Wu D, Zhu M, Wang CL, Liang Y, Yao H, Wei HY, Su Z, Maimaiti M, Du HW, Luo FH, Li P, Si ST, Wu W, Huang K, Dong GP, Yu YX, Fu JF. [Relationship between body mass index and sexual development in Chinese children]. Zhonghua Er Ke Za Zhi 2022; 60:311-316. [PMID: 35385936 DOI: 10.3760/cma.j.cn112140-20210906-00754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Objective: To investigate the relationship between body mass index (BMI) and sexual development in Chinese children. Methods: A nationwide multicenter and population-based large cross-sectional study was conducted in 13 provinces, autonomous regions and municipalities of China from January 2017 to December 2018. Data on sex, age, height, weight were collected, BMI was calculated and sexual characteristics were analyzed. The subjects were divided into four groups based on age, including ages 3-<6 years, 6-<10 years, 10-<15 years and 15-<18 years. Multiple Logistic regression models were used for evaluating the associations of BMI with sexual development in children. Dichotomous Logistic regression was used to compare the differences in the distribution of early and non-early puberty among normal weight, overweight and obese groups. Curves were drawn to analyze the relationship between the percentage of early puberty and BMI distribution in girls and boys at different Tanner stages. Results: A total of 208 179 healthy children (96 471 girls and 111 708 boys) were enrolled in this study. The OR values of B2, B3 and B4+ in overweight girls were 1.72 (95%CI: 1.56-1.89), 3.19 (95%CI: 2.86-3.57), 7.14 (95%CI: 6.33-8.05) and in obese girls were 2.05 (95%CI: 1.88-2.24), 4.98 (95%CI: 4.49-5.53), 11.21 (95%CI: 9.98-12.59), respectively; while the OR values of G2, G3, G4+ in overweight boys were 1.27 (95%CI: 1.17-1.38), 1.52 (95%CI: 1.36-1.70), 1.88 (95%CI: 1.66-2.14) and in obese boys were 1.27 (95%CI: 1.17-1.37), 1.59 (95%CI: 1.43-1.78), and 1.93 (95%CI: 1.70-2.18) (compared with normal weight Tanner 1 group,all P<0.01). Analysis in different age groups found that OR values of obese girls at B2 stage and boys at G2 stage were 2.02 (95%CI: 1.06-3.86) and 2.32 (95%CI:1.05-5.12) in preschool children aged 3-<6 years, respectively (both P<0.05). And in the age group of 6-10 years, overweight girls had a 5.45-fold risk and obese girls had a 12.54-fold risk of B3 stage compared to girls with normal BMI. Compared with normal weight children, the risk of early puberty was 2.67 times higher in overweight girls, 3.63 times higher in obese girls, and 1.22 times higher in overweight boys, 1.35 times higher in obese boys (all P<0.01). Among the children at each Tanner stages, the percentage of early puberty increased with the increase of BMI, from 5.7% (80/1 397), 16.1% (48/299), 13.8% (27/195) to 25.7% (198/769), 65.1% (209/321), 65.4% (157/240) in girls aged 8-<9, 10-<11 and 11-<12 years, and 6.6% (34/513), 18.7% (51/273), 21.6% (57/264) to 13.3% (96/722), 46.4% (140/302), 47.5% (105/221) in boys aged 9-<10, 12-<13 and 13-<14 years, respectively. Conclusions: BMI is positively correlated with sexual development in both Chinese boys and girls, and the correlation is stronger in girls. Obesity is a risk factor for precocious puberty in preschool children aged 3-<6 years, and 6-<10 years of age is a high risk period for early development in obese girls.
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Affiliation(s)
- X Q Xu
- Department of Endocrinology, the Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, China
| | - J W Zhang
- Department of Pediatrics, Shaoxing Maternity and Child Health Care Hospital, Shaoxing 312000, China
| | - R M Chen
- Department of Endocrinology, Fuzhou Children's Hospital of Fujian Province, Fuzhou 350000, China
| | - J S Luo
- Department of Endocrinology and Genetic Diseases, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530003, China
| | - S K Chen
- Department of Endocrinology and Genetic Diseases, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530003, China
| | - R X Zheng
- Department of Pediatrics, Tianjin Medical University General Hospital, Tianjin 350002, China
| | - D Wu
- Department of Endocrinology Genetics and Metabolism, Beijing Children's Hospital, Capital Medical University, Beijing 100045, China
| | - M Zhu
- Department of Endocrinology, Children's Hospital of Chongqing Medical University, Chongqing 400014, China
| | - C L Wang
- Department of Pediatrics, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310053, China
| | - Y Liang
- Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - H Yao
- Department of Genetic Metabolism and Endocrinology, Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430016, China
| | - H Y Wei
- Department of Endocrinology and Metabolism, Genetics, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou 450000, China
| | - Z Su
- Department of Endocrinology, Shenzhen Children's Hospital, Shenzhen 518028, China
| | - Mireguli Maimaiti
- Department of Pediatrics, the First Affiliated Hospital of Xinjiang Medical University, Urumchi 830054, China
| | - H W Du
- Department of Pediatrics, the First Bethune Hospital of Jilin University, Changchun 130021, China
| | - F H Luo
- Department of Endocrinology, Children's Hospital of Fudan University, Shanghai 201102, China
| | - P Li
- Department of Endocrinology, Children's Hospital of Shanghai, Shanghai 200062, China
| | - S T Si
- School of Public Health, Zhejiang University, Hangzhou 310014, China
| | - W Wu
- Department of Endocrinology, the Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, China
| | - K Huang
- Department of Endocrinology, the Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, China
| | - G P Dong
- Department of Endocrinology, the Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, China
| | - Y X Yu
- School of Public Health, Zhejiang University, Hangzhou 310014, China
| | - J F Fu
- Department of Endocrinology, the Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, China
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Cai G, Cai M, Feng Z, Liu R, Liang L, Zhou P, Zhu B, Mo S, Wang H, Lan X, Cai S, Xu Y, Wang R, Dai W, Han L, Xiang W, Wang B, Guo W, Zhang L, Zhou C, Luo B, Li Y, Nie Y, Ma C, Su Z. A Multilocus Blood-Based Assay Targeting Circulating Tumor DNA Methylation Enables Early Detection and Early Relapse Prediction of Colorectal Cancer. Gastroenterology 2021; 161:2053-2056.e2. [PMID: 34487783 DOI: 10.1053/j.gastro.2021.08.054] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 08/13/2021] [Accepted: 08/30/2021] [Indexed: 02/08/2023]
Affiliation(s)
- Guoxiang Cai
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Mingyan Cai
- Endoscopy Center and Endoscopy Research Institute, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Zhiqiang Feng
- Department of Gastroenterology, Guangzhou First People's Hospital, South China University of Technology, Guangzhou, Guangdong, China
| | - Rui Liu
- Singlera Genomics (Shanghai) Ltd, Shanghai, China.
| | - Li Liang
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China.
| | - Pinghong Zhou
- Endoscopy Center and Endoscopy Research Institute, Zhongshan Hospital, Fudan University, Shanghai, China.
| | | | - Boqun Zhu
- Endoscopy Center and Endoscopy Research Institute, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Shaobo Mo
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hui Wang
- Singlera Genomics (Shanghai) Ltd, Shanghai, China
| | - Xiaoliang Lan
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Sanjun Cai
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ye Xu
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Renjie Wang
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Weixin Dai
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Lingyu Han
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wenqiang Xiang
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Beili Wang
- Department of Laboratory medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Wei Guo
- Department of Laboratory medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Lijing Zhang
- Department of Gastroenterology, Dalian University affiliated Xinhua Hospital, Dalian, China
| | - Changjiang Zhou
- Department of Gastroenterology, Dalian University affiliated Xinhua Hospital, Dalian, China
| | - Binyang Luo
- Department of Gastroenterology, West China Hospital, Sichuan University, China
| | - Yingfei Li
- Department of Gastroenterology, Guangzhou First People's Hospital, South China University of Technology, Guangzhou, Guangdong, China
| | - Yuqiang Nie
- Department of Gastroenterology, Guangzhou First People's Hospital, South China University of Technology, Guangzhou, Guangdong, China
| | | | - Zhixi Su
- Singlera Genomics (Shanghai) Ltd, Shanghai, China
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Wang Z, Li Z, Zhou K, Wang C, Jiang L, Zhang L, Yang Y, Luo W, Qiao W, Wang G, Ni Y, Dai S, Guo T, Ji G, Xu M, Liu Y, Su Z, Che G, Li W. Deciphering cell lineage specification of human lung adenocarcinoma with single-cell RNA sequencing. Nat Commun 2021; 12:6500. [PMID: 34764257 PMCID: PMC8586023 DOI: 10.1038/s41467-021-26770-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 10/22/2021] [Indexed: 02/08/2023] Open
Abstract
Lung adenocarcinomas (LUAD) arise from precancerous lesions such as atypical adenomatous hyperplasia, which progress into adenocarcinoma in situ and minimally invasive adenocarcinoma, then finally into invasive adenocarcinoma. The cellular heterogeneity and molecular events underlying this stepwise progression remain unclear. In this study, we perform single-cell RNA sequencing of 268,471 cells collected from 25 patients in four histologic stages of LUAD and compare them to normal cell types. We detect a group of cells closely resembling alveolar type 2 cells (AT2) that emerged during atypical adenomatous hyperplasia and whose transcriptional profile began to diverge from that of AT2 cells as LUAD progressed, taking on feature characteristic of stem-like cells. We identify genes related to energy metabolism and ribosome synthesis that are upregulated in early stages of LUAD and may promote progression. MDK and TIMP1 could be potential biomarkers for understanding LUAD pathogenesis. Our work shed light on the underlying transcriptional signatures of distinct histologic stages of LUAD progression and our findings may facilitate early diagnosis.
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Affiliation(s)
- Zhoufeng Wang
- grid.412901.f0000 0004 1770 1022Department of Respiratory and Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan China ,grid.412901.f0000 0004 1770 1022Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, Sichuan China ,grid.412901.f0000 0004 1770 1022Research Units of West China, Chinese Academy of Medical Sciences, West China Hospital, Chengdu, Sichuan China
| | - Zhe Li
- Singlera Genomics Ltd, Shanghai, China
| | - Kun Zhou
- grid.13402.340000 0004 1759 700XDepartment of Thoracic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China ,grid.412901.f0000 0004 1770 1022Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Chengdi Wang
- grid.412901.f0000 0004 1770 1022Department of Respiratory and Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Lili Jiang
- grid.412901.f0000 0004 1770 1022Department of Pathology, West China Hospital of Sichuan University, Chengdu, China
| | - Li Zhang
- grid.412901.f0000 0004 1770 1022Department of Respiratory and Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Ying Yang
- grid.412901.f0000 0004 1770 1022Department of Respiratory and Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Wenxin Luo
- grid.412901.f0000 0004 1770 1022Department of Respiratory and Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Wenliang Qiao
- grid.412901.f0000 0004 1770 1022Lung Cancer Center, West China Hospital Sichuan University, Chengdu, Sichuan China
| | - Gang Wang
- grid.412901.f0000 0004 1770 1022Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Yinyun Ni
- grid.412901.f0000 0004 1770 1022Department of Respiratory and Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Shuiping Dai
- grid.412901.f0000 0004 1770 1022Center of Gerontology and Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Tingting Guo
- grid.412901.f0000 0004 1770 1022Department of Respiratory and Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Guiyi Ji
- grid.412901.f0000 0004 1770 1022Health Management Center, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Minjie Xu
- Singlera Genomics Ltd, Shanghai, China
| | | | - Zhixi Su
- Singlera Genomics Ltd, Shanghai, China
| | - Guowei Che
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
| | - Weimin Li
- Department of Respiratory and Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China. .,Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China. .,Research Units of West China, Chinese Academy of Medical Sciences, West China Hospital, Chengdu, Sichuan, China.
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Abstract
COVID-19 is deadly to older adults, with research showing that being older and having underlying chronic diseases are significant risk factors for COVID-19 related deaths. However, though similarities exist between both nursing home residents and older community-dwelling people, nursing home residents are substantially more vulnerable to COVID-19. A closer review of both demographic groups provides clarity concerning the difference within the context of COVID-19. Therefore, to address the research gap, drawing insights from Maslow's hierarchy of needs model, this article aims to examine similarities and differences in COVID-19 risk factors experienced by nursing home residents and community-dwelling older people.
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Affiliation(s)
- Z Su
- From the Center on Smart and Connected Health Technologies, Mays Cancer Center, School of Nursing, UT Health San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, USA
- Address correspondence to Dr Z. Su, Ph.D., Incoming Postdoctoral Fellow, Center on Smart and Connected Health Technologies, Mays Cancer Center, School of Nursing, UT Health San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, USA.
| | - D McDonnell
- Department of Humanities, Institute of Technology, Kilkenny Road, Carlow, Ireland
| | - Y Li
- Department of Public Health Sciences, Division of Health Policy and Outcomes Research, University of Rochester Medical Center, 265 Crittenden Blvd., CU 420644, Rochester, New York, 14642, USA
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Hsi W, Ricci J, Su Z, Mund K, Dawson R, Indelicato D. The Root-Cause Analysis on Failed Patient-Specific Measurements of Pencil-Beam-Scanning Protons. Int J Radiat Oncol Biol Phys 2021. [DOI: 10.1016/j.ijrobp.2021.07.1420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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36
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Cao L, Jiang K, Shao Z, Wang Y, Liu S, Lu X, Wu Y, Chen C, Su Z, Wang L, Liu W, Shi D, Cao Z. Synthesis and Anti-Cholinesterase Activity of Novel Glycosyl Benzofuranylthiazole Derivatives. Russ J Org Chem 2021. [DOI: 10.1134/s1070428021090190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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37
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Ma S, Chen S, Zhou C, An H, Su Z, Cui Y, Lin Y. P-296 Establishment of adoptive cell therapy with tumor-infiltrating lymphocytes for liver and oesophageal cancer. Ann Oncol 2021. [DOI: 10.1016/j.annonc.2021.05.350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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38
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Zhu W, Su Z, Xu W, Sun HX, Gao JF, Tu DF, Ren CH, Zhang ZJ, Cao HG. Garlic skin induces shifts in the rumen microbiome and metabolome of fattening lambs. Animal 2021; 15:100216. [PMID: 34051409 DOI: 10.1016/j.animal.2021.100216] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 12/16/2022] Open
Abstract
Garlic (Allium sativum L.) and its constituents have been shown to modify rumen fermentation and improve growth performance. Garlic skin, a by-product of garlic processing, contains similar bioactive components as garlic bulb. This study aimed to investigate the effects of garlic skin supplementation on growth performance, ruminal microbes, and metabolites in ruminants. Twelve Hu lambs were randomly assigned to receive a basal diet (CON) or a basal diet supplemented with 80 g/kg DM of garlic skin (GAS). The experiment lasted for 10 weeks, with the first 2 weeks serving as the adaptation period. The results revealed that the average daily gain and volatile fatty acid concentration were higher (P < 0.05) in lambs fed GAS than those in the CON group. Garlic skin supplementation did not significantly (P > 0.10) affect the α-diversity indices, including the Chao1 index, the abundance-based coverage estimator value, and the Shannon and Simpson indices. At the genus level, garlic skin supplementation altered the ruminal bacterial composition by increasing (P < 0.05) the relative abundances of Prevotella, Bulleidia, Howardella, and Methanosphaera and decreasing (P < 0.05) the abundance of Fretibacterium. Concentrations of 139 metabolites significantly differed (P < 0.05) between the GAS and the CON groups. Among them, substrates for rumen microbial protein synthesis were enriched in the GAS group. The pathways of pyrimidine metabolism, purine metabolism, and vitamin B6 metabolism were influenced (P < 0.05) by garlic skin supplementation. Integrated correlation analysis also provided a link between the significantly altered rumen microbiota and metabolites. Thus, supplementation of garlic skin improved the growth performance of lambs by modifying rumen fermentation through shifts in the rumen microbiome and metabolome.
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Affiliation(s)
- W Zhu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China; Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-breeding, Anhui Agricultural University, Hefei 230036, PR China
| | - Z Su
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China; Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-breeding, Anhui Agricultural University, Hefei 230036, PR China
| | - W Xu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China; Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-breeding, Anhui Agricultural University, Hefei 230036, PR China
| | - H X Sun
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China; Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-breeding, Anhui Agricultural University, Hefei 230036, PR China
| | - J F Gao
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China; Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-breeding, Anhui Agricultural University, Hefei 230036, PR China
| | - D F Tu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China; Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-breeding, Anhui Agricultural University, Hefei 230036, PR China
| | - C H Ren
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China; Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-breeding, Anhui Agricultural University, Hefei 230036, PR China
| | - Z J Zhang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China; Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-breeding, Anhui Agricultural University, Hefei 230036, PR China
| | - H G Cao
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China; Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-breeding, Anhui Agricultural University, Hefei 230036, PR China.
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Zheng RF, Su Z, Wang L, Zhao X, Li ZG. [MIRAGE syndrome caused by variation of sterile alpha motif domain-containing protein 9 gene]. Zhonghua Er Ke Za Zhi 2021; 59:417-419. [PMID: 33902229 DOI: 10.3760/cma.j.cn112140-20201014-00939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- R F Zheng
- Department of Endocrinology, Shenzhen Children's Hospital, Shenzhen 518023, China
| | - Z Su
- Department of Endocrinology, Shenzhen Children's Hospital, Shenzhen 518023, China
| | - L Wang
- Department of Endocrinology, Shenzhen Children's Hospital, Shenzhen 518023, China
| | - X Zhao
- Department of Endocrinology, Shenzhen Children's Hospital, Shenzhen 518023, China
| | - Z G Li
- Department of Endocrinology, Shenzhen Children's Hospital, Shenzhen 518023, China
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40
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Chen M, Wei R, Wei G, Xu M, Su Z, Zhao C, Ni T. Systematic evaluation of the effect of polyadenylation signal variants on the expression of disease-associated genes. Genome Res 2021; 31:890-899. [PMID: 33875481 PMCID: PMC8092010 DOI: 10.1101/gr.270256.120] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 03/02/2021] [Indexed: 01/18/2023]
Abstract
Single nucleotide variants (SNVs) within polyadenylation signals (PASs), a specific six-nucleotide sequence required for mRNA maturation, can impair RNA-level gene expression and cause human diseases. However, there is a lack of genome-wide investigation and systematic confirmation tools for identifying PAS variants. Here, we present a computational strategy to integrate the most reliable resources for discovering distinct genomic features of PAS variants and also develop a credible and convenient experimental tool to validate the effect of PAS variants on expression of disease-associated genes. This approach will greatly accelerate the deciphering of PAS variation-related human diseases.
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Affiliation(s)
- Meng Chen
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences and Eye & ENT Hospital, Fudan University, Shanghai, 200438, China.,Eye Institute, Eye & ENT Hospital, Shanghai Medical College, Fudan University, Shanghai, 200031, China.,NHC Key Laboratory of Myopia (Fudan University), Key Laboratory of Myopia, Chinese Academy of Medical Sciences, and Shanghai Key Laboratory of Visual Impairment and Restoration (Fudan University), Shanghai, 200031, China
| | - Ran Wei
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai, 200438, China.,Department of Pathology, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Gang Wei
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai, 200438, China.,MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Mingqing Xu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center of Genetics and Development, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Zhixi Su
- Singlera Genomics (Shanghai) Limited, Shanghai, 201318, China
| | - Chen Zhao
- Eye Institute, Eye & ENT Hospital, Shanghai Medical College, Fudan University, Shanghai, 200031, China.,NHC Key Laboratory of Myopia (Fudan University), Key Laboratory of Myopia, Chinese Academy of Medical Sciences, and Shanghai Key Laboratory of Visual Impairment and Restoration (Fudan University), Shanghai, 200031, China
| | - Ting Ni
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai, 200438, China.,Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan University, Shanghai, 200438, China
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41
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Zhang H, Zhang Z, Liu X, Duan H, Xiang T, He Q, Su Z, Wu H, Liang Z. DNA Methylation Haplotype Block Markers Efficiently Discriminate Follicular Thyroid Carcinoma from Follicular Adenoma. J Clin Endocrinol Metab 2021; 106:1011-1021. [PMID: 33394038 PMCID: PMC7993581 DOI: 10.1210/clinem/dgaa950] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Indexed: 12/19/2022]
Abstract
CONTEXT Follicular thyroid carcinoma (FTC) is the second most common type of thyroid carcinoma and must be pathologically distinguished from benign follicular adenoma (FA). Additionally, the clinical assessment of thyroid tumors with uncertain malignant potential (TT-UMP) demands effective indicators. OBJECTIVE We aimed to identify discriminating DNA methylation markers between FA and FTC. METHODS DNA methylation patterns were investigated in 33 FTC and 33 FA samples using reduced representation bisulfite sequencing and methylation haplotype block-based analysis. A prediction model was constructed and validated in an independent cohort of 13 FTC and 13 FA samples. Moreover, 36 TT-UMP samples were assessed using this model. RESULTS A total of 70 DNA methylation markers, approximately half of which were located within promoters, were identified to be significantly different between the FTC and FA samples. All the Gene Ontology terms enriched among the marker-associated genes were related to "DNA binding," implying that the inactivation of DNA binding played a role in FTC development. A random forest model with an area under the curve of 0.994 was constructed using those markers for discriminating FTC from FA in the validation cohort. When the TT-UMP samples were scored using this model, those with fewer driver mutations also exhibited lower scores. CONCLUSION An FTC-predicting model was constructed using DNA methylation markers, which distinguished between FA and FTC tissues with a high degree of accuracy. This model can also be used to help determine the potential of malignancy in TT-UMP.
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Affiliation(s)
- Hui Zhang
- Department of Pathology, Molecular Pathology Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Science, Beijing, China
| | | | - Xiaoding Liu
- Department of Pathology, Molecular Pathology Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Science, Beijing, China
| | - Huanli Duan
- Department of Pathology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | | | - Qiye He
- Singlera Genomics Inc. Shanghai, China
| | - Zhixi Su
- Singlera Genomics Inc. Shanghai, China
| | - Huanwen Wu
- Department of Pathology, Molecular Pathology Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Science, Beijing, China
- Correspondence: Zhiyong Liang, PhD, Chinese Academy of Medical Sciences and Peking Union Medical College Hospital, Beijing, China. ; or Huanwen Wu, Chinese Academy of Medical Sciences and Peking Union Medical College Hospital, Beijing, China.
| | - Zhiyong Liang
- Department of Pathology, Molecular Pathology Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Science, Beijing, China
- Correspondence: Zhiyong Liang, PhD, Chinese Academy of Medical Sciences and Peking Union Medical College Hospital, Beijing, China. ; or Huanwen Wu, Chinese Academy of Medical Sciences and Peking Union Medical College Hospital, Beijing, China.
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Mo S, Wang H, Han L, Xiang W, Dai W, Zhao P, Pei F, Su Z, Ma C, Li Q, Wang Z, Cai S, Wang H, Liu R, Cai G. Fecal Multidimensional Assay for Non-Invasive Detection of Colorectal Cancer: Fecal Immunochemical Test, Stool DNA Mutation, Methylation, and Intestinal Bacteria Analysis. Front Oncol 2021; 11:643136. [PMID: 33718241 PMCID: PMC7947614 DOI: 10.3389/fonc.2021.643136] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 01/15/2021] [Indexed: 12/15/2022] Open
Abstract
Background Fecal immunochemical test (FIT), DNA mutation, DNA methylation, and microbial dysbiosis all showed promising in colorectal cancer (CRC) non-invasive detection. We assessed CRC detection with an assay combining all these strategies and investigated the effect of clinical features on the performance of this comprehensive test. Methods We performed a multidimensional analysis study using stool samples collected from 108 patients with CRC, 18 patients with colorectal adenoma, and 36 individuals with no evidence of colorectal disease. The multidimensional analysis of stool samples including FIT, stool DNA (sDNA) tests for three methylated genes (Septin9, NDRG4, BMP3) and three mutated genes (KRAS, BRAF, PI3KCA) using next generation sequencing as well as detection of stool bacteria level of Fusobacterium nucleatum and Parvimonas micra using qPCR method. We used a linear support vector classification model to analyze the data. Results The sensitivity of FIT alone was 69.4% for CRC and 11.1% for adenoma. Separately, the sensitivity of the detection of intestinal bacteria, DNA mutation, and DNA methylation for CRC was 58.3, 50.0, and 51.9%, respectively. The combination of FIT and sDNA tests had a sensitivity of 81.5% for CRC (AUC: 0.93, better than FIT alone, P = 0.017) and 27.8% for adenoma with 94.4% specificity. Sensitivity of the multidimensional test to detect CRC with stage II (84.6%) and III (91.9%) CRC was relatively higher (88.2%) than that of patients with stage I (60.0%) and stage IV (75.0%) (P = 0.024). The rate of CRC detection increased with tumor size (P = 0.008) and age (P = 0.04). Interestingly, the rate of CRC detection was higher in smoking persons than non-smokers with marginal significance (P = 0.08). Conclusions The multidimensional assay of stool samples combining FIT and stool DNA tests further improved the diagnostic sensitivity for CRC. This could provide new approach for improvement of CRC screening and further demonstrations are warranted.
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Affiliation(s)
- Shaobo Mo
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hui Wang
- Department of Research and Development, Singlera Genomics (Shanghai) Ltd., Shanghai, China
| | - Lingyu Han
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wenqiang Xiang
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Weixing Dai
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Pengfei Zhao
- Department of Research and Development, Singlera Genomics (Shanghai) Ltd., Shanghai, China
| | - Fengchun Pei
- Department of Research and Development, Singlera Genomics (Shanghai) Ltd., Shanghai, China
| | - Zhixi Su
- Department of Research and Development, Singlera Genomics (Shanghai) Ltd., Shanghai, China
| | - Chengcheng Ma
- Department of Research and Development, Singlera Genomics (Shanghai) Ltd., Shanghai, China
| | - Qi Li
- Department of Medical Oncology and Cancer Institute, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Zhimin Wang
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center, Shanghai Industrial Technology Institute, Shanghai, China
| | - Sanjun Cai
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Department of Cancer Institute, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Hao Wang
- Department of Colorectal Surgery, Chang Hai Hospital, Naval Medical University, Shanghai, China
| | - Rui Liu
- Department of Research and Development, Singlera Genomics (Shanghai) Ltd., Shanghai, China
| | - Guoxiang Cai
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
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Liu X, Guo S, Ma C, Li Y, Liu X, Zhang Z, Yu L, Dai M, Shen S, Wu HM, Su Z, He Q, Liu R, Gang J, Liang Z. Circulating tumor DNA methylation as markers for early detection of pancreatic ductal adenocarcinoma (PDAC). J Clin Oncol 2021. [DOI: 10.1200/jco.2021.39.3_suppl.395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
395 Background: PDAC is a cancer of high mortality and low survival. Its early detection is critical due to symptoms often occur only at advanced stages. However there is no reliable screening tool to identify high-risk patients. ctDNA methylation has recently emerged as a promising new target to differentiate PDAC plasma from normal plasma for its early detection. Methods: Reduced representation bisulfite sequencing libraries were made in 46 PDAC tissues, 30 para-PDAC tissues and 20 PDAC plasmas to screen PDAC-specific markers, which was done by quantifying and comparing methylation levels of genomic regions and individual CpG sites between those groups. Markers were validated in plasma samples from 84 PDAC patients and 64 normal controls to propose a blood classifier. The best-performing markers were developed into a targeted sequencing panel, which was tested on a larger collection of plasma samples from patients of a variety of pancreatic diseases to build and validate a PDAC-predicting model. Results: We profiled genome-wide methylation patterns of tissues samples to identify 171 PDAC-specific markers. We reiterated training and cross-validating PDAC classification models using SVM method, and achieved an average sensitivity of 86% and specificity of 88%. To prove the feasibility of a non-invasive detection in plasma, a targeted methylation assay using those markers was tested on PDAC and normal plasmas, and yielded an average sensitivity of 68.4% and a specificity of 85.8%. We refined the panel by selecting the most discriminatory markers and built the version II of the panel, which was named PANcreatic Cancer Detection Assay, or PANDA, for a more efficient target capture, which was validated in an independent cohort of plasma samples that included 94 PDAC cases, 25 chronic pancreatitis (CP) cases and 80 normal samples from multiple centers. The PANDA achieved an AUC of 0.906 when classifying PDAC from normal, and an AUC of 0.882 when separating PDAC from CPs, both of which are more accurate than CA19-9, the conventional blood marker for PDAC. We further integrated test subjects’ age and their CA19-9 level as features into the PANDA model, which further elevated their AUC to 0.882 and 0.933 when classifying PDAC plasma from either CP plasma or normal plasma, respectively. Conclusions: We have developed PANDA, an NGS based target assay covering PDAC-specific DNA methylation targets by screening and validation on PDAC tissues and plasmas. Combined with age and CA19-9 blood level, PANDA has shown encouraging results to classify PDAC plasma from non-malignant diseases, demonstrating its potential to be optimized into non-invasive diagnostics for blood-based early PDAC screening.
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Affiliation(s)
- Xiaoding Liu
- Department of Pathology, Peking Union Hospital, Beijing, China
| | - Shiwei Guo
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Navy Medical University (the Second Military Medical University), Shanghai, China
| | | | - Yatong Li
- Department of General Surgery, Peking Union Hospital, Beijing, China
| | - Xiaoqian Liu
- Department of Pathology, Peking Union Hospital, Beijing, China
| | - Zhiwen Zhang
- Department of General Surgery, Peking Union Hospital, Beijing, China
| | - Lianyuan Yu
- Department of Pathology, Peking Union Hospital, Beijing, China
| | - Menghua Dai
- Department of Pathology, Peking Union Hospital, Beijing, China
| | - Shuo Shen
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Navy Medical University (the Second Military Medical University), Shanghai, China
| | - Huanwen M. Wu
- Department of Pathology, Peking Union Hospital, Beijing, Dongchen Distric, China
| | - Zhixi Su
- Singlera Genomics Inc., Shanghai, China
| | - Qiye He
- Singlera Genomics Inc., Shanghai, China
| | - Rui Liu
- Singlera Genomics Inc., Shanghai, China
| | - Jin Gang
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Navy Medical University (the Second Military Medical University), Shanghai, China
| | - Zhiyong Liang
- Department of Pathology, Peking Union Hospital, Beijing, China
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Wu Y, Lei D, Su Z, Yang J, Zou J. HaYABBY Gene Is Associated with the Floral Development of Ligulate-Like Tubular Petal Mutant Plants of Sunflower. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795420120145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Su Z, Liu HL, Qi B, Liu Y. Effects of propofol on proliferation and apoptosis of cardia cancer cells via MAPK/ERK signaling pathway. Eur Rev Med Pharmacol Sci 2021; 24:428-433. [PMID: 31957857 DOI: 10.26355/eurrev_202001_19942] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
OBJECTIVE To explore the influences of propofol on the proliferation and apoptosis of cardia cancer cells via mitogen-activated protein kinase/extracellular signal-regulated kinase (MAPK/ERK) signaling pathway. PATIENTS AND METHODS A total of 65 surgical resection specimens of cardia cancer were selected as research objects and divided into control group and with low (12.5 μmol/L), medium (25 μmol/L), and high (50 μmol/L) propofol concentration groups. The apoptosis of cancer cells, ERK1/2 phosphorylation level, expressions of Caspase-3, B-cell lymphoma-2 (Bcl-2), and Bcl-2 associated X protein (Bax) in each group were detected. RESULTS Propofol in different concentrations could all effectively inhibit the proliferation of cardia cancer cells in a dose-dependent manner. Different concentrations of propofol promoted the apoptosis of cardia cancer cells, and the apoptosis rate constantly increased with the rising concentration of propofol (p<0.05). Propofol could repress the expression of Bcl-2 and up-regulate the expression levels of Caspase-3, Bax, and phosphorylated ERK1/2. CONCLUSIONS Propofol can inhibit the proliferation and induce the apoptosis of cardia cancer cells, and the action mechanism may be correlated with the inhibition on the MAPK/ERK signaling pathway.
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Affiliation(s)
- Z Su
- Department of Anesthesiology, Huai'an First People's Hospital, Nanjing Medical University, Huai'an, Jiangsu, China.
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Wang J, Chen X, He F, Song X, Huang S, Yue W, Chen Y, Su Z, Wang C. Global Analysis of Gene Expression Profiles Provides Novel Insights into the Development and Evolution of the Large Crustacean Eriocheir sinensis. Genomics Proteomics Bioinformatics 2020; 18:443-454. [PMID: 33346084 PMCID: PMC8242267 DOI: 10.1016/j.gpb.2019.01.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 01/04/2019] [Accepted: 02/20/2019] [Indexed: 12/13/2022]
Abstract
Chinese mitten crab (Eriocheir sinensis) is an important aquaculture species in Crustacea. Functional analysis, although essential, has been hindered due to the lack of sufficient genomic or transcriptomic resources. In this study, transcriptome sequencing was conducted on 59 samples representing diverse developmental stages (fertilized eggs, zoea, megalopa, three sub-stages of larvae, juvenile crabs, and adult crabs) and different tissues (eyestalk, hepatopancreas, and muscle from juvenile crabs, and eyestalk, hepatopancreas, muscle, heart, stomach, gill, thoracic ganglia, intestine, ovary, and testis from adult crabs) of E. sinensis. A comprehensive reference transcriptome was assembled, including 19,023 protein-coding genes. Hierarchical clustering based on 128 differentially expressed cuticle-related genes revealed two distinct expression patterns during the early larval developmental stages, demonstrating the distinct roles of these genes in “crab-like” cuticle formation during metamorphosis and cuticle calcification after molting. Phylogenetic analysis of 1406 one-to-one orthologous gene families identified from seven arthropod species and Caenorhabditis elegans strongly supported the hypothesis that Malacostraca and Branchiopoda do not form a monophyletic group. Furthermore, Branchiopoda is more phylogenetically closely related to Hexapoda, and the clade of Hexapoda and Branchiopoda and the clade of Malacostraca belong to the Pancrustacea. This study offers a high-quality transcriptome resource for E. sinensis and demonstrates the evolutionary relationships of major arthropod groups. The differentially expressed genes identified in this study facilitate further investigation of the cuticle-related gene expression networks which are likely associated with “crab-like” cuticle formation during metamorphosis and cuticle calcification after molting.
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Affiliation(s)
- Jun Wang
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai 201306, China
| | - Xiaowen Chen
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai 201306, China
| | - Funan He
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xiao Song
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University, Shanghai 200433, China
| | - Shu Huang
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai 201306, China
| | - Wucheng Yue
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai 201306, China
| | - Yipei Chen
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai 201306, China
| | - Zhixi Su
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200438, China.
| | - Chenghui Wang
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai 201306, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China; Shanghai Engineering Research Center of Aquaculture, Shanghai 201306, China.
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Mendenhall N, Bryant C, Hoppe B, Nichols R, Mendenhall W, Morris C, Li Z, Su Z, Liang X, Balaji K, Bandyk M, Costa J, Henderson R. Ten-Year Outcomes From Three Prospective Clinical Trials Of Image-Guided Proton Therapy In Prostate Cancer. Int J Radiat Oncol Biol Phys 2020. [DOI: 10.1016/j.ijrobp.2020.07.553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Jiang Y, Su Z, Wang R, Wen Y, Li C, He J, Liang W. 433P Association between aspirin and cancer risk: A Mendelian randomization analysis. Ann Oncol 2020. [DOI: 10.1016/j.annonc.2020.10.425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Hong S, Su Z, Li J, Yu S, Lin B, Ke Z, Zhang Q, Guo Z, Lv W, Peng S, Cheng L, He Q, Liu R, Xiao H. 307P Development of circulating free DNA methylation markers for thyroid nodule diagnostics. Ann Oncol 2020. [DOI: 10.1016/j.annonc.2020.10.301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Henderson R, Bryant C, Nichols R, Mendenhall W, Hoppe B, Su Z, Morris C, Mendenhall N. Five-year Outcomes for Moderately Accelerated Hypofractionated Proton Therapy for Prostate Cancer. Int J Radiat Oncol Biol Phys 2020. [DOI: 10.1016/j.ijrobp.2020.07.424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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