1
|
Qu Y, Zhang X, Qiao R, Di F, Song Y, Wang J, Ji L, Zhang J, Gu W, Fang Y, Han B, Yang R, Dai L, Ouyang S. Blood FOLR3 methylation dysregulations and heterogeneity in non-small lung cancer highlight its strong associations with lung squamous carcinoma. Respir Res 2024; 25:59. [PMID: 38273401 PMCID: PMC10809478 DOI: 10.1186/s12931-024-02691-8] [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: 09/30/2023] [Accepted: 01/14/2024] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND Non-small cell lung cancer (NSCLC) accounts for the vast majority of lung cancers. Early detection is crucial to reduce lung cancer-related mortality. Aberrant DNA methylation occurs early during carcinogenesis and can be detected in blood. It is essential to investigate the dysregulated blood methylation markers for early diagnosis of NSCLC. METHODS NSCLC-associated methylation gene folate receptor gamma (FOLR3) was selected from an Illumina 850K array analysis of peripheral blood samples. Mass spectrometry was used for validation in two independent case-control studies (validation I: n = 2548; validation II: n = 3866). Patients with lung squamous carcinoma (LUSC) or lung adenocarcinoma (LUAD), normal controls (NCs) and benign pulmonary nodule (BPN) cases were included. FOLR3 methylations were compared among different populations. Their associations with NSCLC clinical features were investigated. Receiver operating characteristic analyses, Kruskal-Wallis test, Wilcoxon test, logistics regression analysis and nomogram analysis were performed. RESULTS Two CpG sites (CpG_1 and CpG_2) of FOLR3 was significantly lower methylated in NSCLC patients than NCs in the discovery round. In the two validations, both LUSC and LUAD patients presented significant FOLR3 hypomethylations. LUSC patients were highlighted to have significantly lower methylation levels of CpG_1 and CpG_2 than BPN cases and LUAD patients. Both in the two validations, CpG_1 methylation and CpG_2 methylation could discriminate LUSC from NCs well, with areas under the curve (AUCs) of 0.818 and 0.832 in validation I, and 0.789 and 0.780 in validation II. They could also differentiate LUAD from NCs, but with lower efficiency. CpG_1 and CpG_2 methylations could also discriminate LUSC from BPNs well individually in the two validations. With the combined dataset of two validations, the independent associations of age, gender, and FOLR3 methylation with LUSC and LUAD risk were shown and the age-gender-CpG_1 signature could discriminate LUSC and LUAD from NCs and BPNs, with higher efficiency for LUSC. CONCLUSIONS Blood-based FOLR3 hypomethylation was shown in LUSC and LUAD. FOLR3 methylation heterogeneity between LUSC and LUAD highlighted its stronger associations with LUSC. FOLR3 methylation and the age-gender-CpG_1 signature might be novel diagnostic markers for the early detection of NSCLC, especially for LUSC.
Collapse
Affiliation(s)
- Yunhui Qu
- Department of Clinical Laboratory, the First Affiliated Hospital of Zhengzhou University and the Key Clinical Laboratory of Henan Province, Zhengzhou, 450052, China
| | - Xiuzhi Zhang
- Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou, 4500001, China
| | - Rong Qiao
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, 200030, China
| | - Feifei Di
- Nanjing TANTICA Biotechnology Co. Ltd, Nanjing, 210000, China
| | - Yakang Song
- Nanjing TANTICA Biotechnology Co. Ltd, Nanjing, 210000, China
| | - Jun Wang
- Nanjing TANTICA Biotechnology Co. Ltd, Nanjing, 210000, China
| | - Longtao Ji
- Henan Institute of Medical and Pharmaceutical Sciences & Henan Key Medical Laboratory of Tumor Molecular Biomarkers, Zhengzhou University, Zhengzhou, 450052, China
| | - Jie Zhang
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, 210000, China
| | - Wanjian Gu
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, 210000, China
| | - Yifei Fang
- Department of Respiratory and Sleep Medicine, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Baohui Han
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, 200030, China
| | - Rongxi Yang
- Nanjing TANTICA Biotechnology Co. Ltd, Nanjing, 210000, China.
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, 210000, China.
| | - Liping Dai
- Henan Institute of Medical and Pharmaceutical Sciences & Henan Key Medical Laboratory of Tumor Molecular Biomarkers, Zhengzhou University, Zhengzhou, 450052, China.
| | - Songyun Ouyang
- Department of Respiratory and Sleep Medicine, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
| |
Collapse
|
2
|
Qiao R, Zhu Q, Di F, Liu C, Song Y, Zhang J, Xu T, Wang Y, Dai L, Gu W, Han B, Yang R. Hypomethylation of DYRK4 in peripheral blood is associated with increased lung cancer risk. Mol Carcinog 2023; 62:1745-1754. [PMID: 37530470 DOI: 10.1002/mc.23612] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 06/01/2023] [Accepted: 07/19/2023] [Indexed: 08/03/2023]
Abstract
Lung cancer (LC) is the leading cause of cancer-related deaths worldwide. It is urgent to identify new biomarkers for the early detection of LC. DNA methylation in peripheral blood has been reported to be associated with cancers. We conducted two independent case-control studies and a nested case-control study (168 LC cases and 167 controls in study Ⅰ, 677 LC cases and 833 controls in study Ⅱ, 147 precancers and 21 controls in the nested case-control study). The methylation levels of DYRK4 CpG sites were measured using mass spectrometry and their correlations with LC were analyzed by logistic regression and nonparametric tests. Bonferroni correction was used for the multiple comparisons. LC-related decreased DYRK4 methylation was discovered in Study I and validated in Study II (the odds ratios [ORs] for the lowest vs. highest quartile of all three DYRK4 CpG sites ranged from 1.64 to 2.09, all p < 0.001). Combining the two studies, hypomethylation of DYRK4 was observed in stage I cases (ORs per -10% methylation ranged from 1.16 to 1.38, all p < 5.9E-04), and could be enhanced by male gender (ORs ranged from 1.77 to 4.17 via interquartile analyses, all p < 0.017). Hypomethylation of DYRK4_A_CpG_2 was significantly correlated with tumor size, length, and stage (p = 0.034, 0.002, and 0.002, respectively) in LC cases. Our study disclosed the association between DYRK4 hypomethylation in peripheral blood and LC, suggesting the feasibility of blood-based DNA methylation as new biomarker for LC detection.
Collapse
Affiliation(s)
- Rong Qiao
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Qiang Zhu
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Feifei Di
- Nanjing TANTICA Biotechnology Co. Ltd., Nanjing, China
| | - Chunlan Liu
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yakang Song
- Nanjing TANTICA Biotechnology Co. Ltd., Nanjing, China
| | - Jin Zhang
- Nanjing TANTICA Biotechnology Co. Ltd., Nanjing, China
| | - Tian Xu
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
| | - Yue Wang
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Liping Dai
- Henan Institute of Medical and Pharmaceutical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Wanjian Gu
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
| | - Baohui Han
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Rongxi Yang
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China
- Nanjing TANTICA Biotechnology Co. Ltd., Nanjing, China
| |
Collapse
|
3
|
Qiao R, Di F, Wang J, Wei Y, Xu T, Dai L, Gu W, Han B, Yang R. Identification of FUT7 hypomethylation as the blood biomarker in the prediction of early-stage lung cancer. J Genet Genomics 2023; 50:573-581. [PMID: 36898609 DOI: 10.1016/j.jgg.2023.02.014] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 02/09/2023] [Accepted: 02/17/2023] [Indexed: 03/12/2023]
Abstract
Early detection of lung cancer (LC) is vital for reducing LC-related mortality. However, noninvasive diagnostic tools remain a great challenge. We aim to identify blood-based biomarkers for the early detection of LC. Here, LC-associated hypomethylation in alpha-1,3-fucosyltransferase VII (FUT7) is identified via the Illumina 850K array in a discovery study and validated by mass spectrometry in two independent case-control studies with blood samples from 1720 LC patients (86.8% LC at stage I, blood is collected before surgery and treatment) and 3143 healthy controls. Compared to the controls, blood-based FUT7 hypomethylation is identified in LC patients at stage I, and even in LC patients with malignant nodules ≤ 1 cm and in patients with adenocarcinoma in situ. Gender plays a role in the LC-associated FUT7 hypomethylation in blood, which is more significant in males than in females. We also reveal that FUT7 hypomethylation in LC could be enhanced by the advanced stage of cancer, involvement of lymph nodes, and larger tumor size. Based on a large sample size and semi-quantitative methods, our study reveals a strong association between blood-based FUT7 hypomethylation and LC, suggesting that methylation signatures in blood may be a group of potential biomarkers for detection of early-stage LC.
Collapse
Affiliation(s)
- Rong Qiao
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai 200030, China
| | - Feifei Di
- Nanjing TANTICA Biotechnology Co. Ltd, Nanjing, Jiangsu 210061, China
| | - Jun Wang
- Nanjing TANTICA Biotechnology Co. Ltd, Nanjing, Jiangsu 210061, China
| | - Yujie Wei
- Nanjing TANTICA Biotechnology Co. Ltd, Nanjing, Jiangsu 210061, China
| | - Tian Xu
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu 210029, China
| | - Liping Dai
- Henan Institute of Medical and Pharmaceutical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Wanjian Gu
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu 210029, China
| | - Baohui Han
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai 200030, China.
| | - Rongxi Yang
- Nanjing TANTICA Biotechnology Co. Ltd, Nanjing, Jiangsu 210061, China; Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China; Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China; Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China.
| |
Collapse
|
4
|
Sidoli C, Zambon A, Tassistro E, Rossi E, Mossello E, Inzitari M, Cherubini A, Marengoni A, Morandi A, Bellelli G, Tarasconi A, Sella M, Paternò G, Faggian G, Lucarelli C, De Grazia N, Alberto C, Porcella L, Nardiello I, Chimenti E, Zeni M, Romairone E, Minaglia C, Ceccotti C, Guerra G, Mantovani G, Monacelli F, Minaglia C, Candiani T, Santolini F, Minaglia C, Rosso M, Bono V, Sibilla S, Dal Santo P, Ceci M, Barone P, Schirinzi T, Formenti A, Nastasi G, Isaia G, Gonella D, Battuello A, Casson S, Calvani D, Boni F, Ciaccio A, Rosa R, Sanna G, Manfredini S, Cortese L, Rizzo M, Prestano R, Greco A, Lauriola M, Gelosa G, Piras V, Arena M, Cosenza D, Bellomo A, LaMontagna M, Gabbani L, Lambertucci L, Perego S, Parati G, Basile G, Gallina V, Pilone G, Giudice C, Pietrogrande L, Mosca M, Corazzin I, Rossi P, Nunziata V, D’Amico F, Grippa A, Giardini S, Barucci R, Cossu A, Fiorin L, Arena M, Distefano M, Lunardelli M, Brunori M, Ruffini I, Abraham E, Varutti A, Fabbro E, Catalano A, Martino G, Leotta D, Marchet A, Dell’Aquila G, Scrimieri A, Davoli M, Casella M, Cartei A, Polidori G, Basile G, Brischetto D, Motta S, Saponara R, Perrone P, Russo G, Del D, Car C, Pirina T, Franzoni S, Cotroneo A, Ghiggia F, Volpi G, Menichetti C, Bo M, Panico A, Calogero P, Corvalli G, Mauri M, Lupia E, Manfredini R, Fabbian F, March A, Pedrotti M, Veronesi M, Strocchi E, Borghi C, Bianchetti A, Crucitti A, DiFrancesco V, Fontana G, Geriatria A, Bonanni L, Barbone F, Serrati C, Ballardini G, Simoncelli M, Ceschia G, Scarpa C, Brugiolo R, Fusco S, Ciarambino T, Biagini C, Tonon E, Porta M, Venuti D, DelSette M, Poeta M, Barbagallo G, Trovato G, Delitala A, Arosio P, Reggiani F, Zuliani G, Ortolani B, Mussio E, Girardi A, Coin A, Ruotolo G, Castagna A, Masina M, Cimino R, Pinciaroli A, Tripodi G, Cassadonte F, Vatrano M, Scaglione L, Fogliacco P, Muzzuilini C, Romano F, Padovani A, Rozzini L, Cagnin A, Fragiacomo F, Desideri G, Liberatore E, Bruni A, Orsitto G, Franco M, Bonfrate L, Bonetto M, Pizio N, Magnani G, Cecchetti G, Longo A, Bubba V, Marinan L, Cotelli M, Turla M, Brunori M, Sessa M, Abruzzi L, Castoldi G, LoVetere D, Musacchio C, Novello M, Cavarape A, Bini A, Leonardi A, Seneci F, Grimaldi W, Seneci F, Fimognari F, Bambar V, Saitta A, Corica F, Braga M, Servi, Ettorre E, Camellini Bellelli CG, Annoni G, Marengoni A, Bruni A, Crescenzo A, Noro G, Turco R, Ponzetto M, Giuseppe L, Mazzei B, Maiuri G, Costaggiu D, Damato R, Fabbro E, Formilan M, Patrizia G, Santuar L, Gallucci M, Minaglia C, Paragona M, Bini P, Modica D, Abati C, Clerici M, Barbera I, NigroImperiale F, Manni A, Votino C, Castiglioni C, Di M, Degl’Innocenti M, Moscatelli G, Guerini S, Casini C, Dini D, DeNotariis S, Bonometti F, Paolillo C, Riccardi A, Tiozzo A, SamySalamaFahmy A, Riccardi A, Paolillo C, DiBari M, Vanni S, Scarpa A, Zara D, Ranieri P, Alessandro M, Calogero P, Corvalli G, Di F, Pezzoni D, Platto C, D’Ambrosio V, Ivaldi C, Milia P, DeSalvo F, Solaro C, Strazzacappa M, Bo M, Panico A, Cazzadori M, Bonetto M, Grasso M, Troisi E, Magnani G, Cecchetti G, Guerini V, Bernardini B, Corsini C, Boffelli S, Filippi A, Delpin K, Faraci B, Bertoletti E, Vannucci M, Crippa P, Malighetti A, Caltagirone C, DiSant S, Bettini D, Maltese F, Formilan M, Abruzzese G, Minaglia C, Cosimo D, Azzini M, Cazzadori M, Colombo M, Procino G, Fascendini S, Barocco F, Del P, D’Amico F, Grippa A, Mazzone A, Cottino M, Vezzadini G, Avanzi S, Brambilla C, Orini S, Sgrilli F, Mello A, Lombardi Muti LE, Dijk B, Fenu S, Pes C, Gareri P, Castagna A, Passamonte M, Rigo R, Locusta L, Caser L, Rosso G, Cesarini S, Cozzi R, Santini C, Carbone P, Cazzaniga I, Lovati R, Cantoni A, Ranzani P, Barra D, Pompilio G, Dimori S, Cernesi S, Riccò C, Piazzolla F, Capittini E, Rota C, Gottardi F, Merla L, Barelli A, Millul A, De G, Morrone G, Bigolari M, Minaglia C, Macchi M, Zambon F, D’Amico F, D’Amico F, Pizzorni C, DiCasaleto G, Menculini G, Marcacci M, Catanese G, Sprini D, DiCasalet T, Bocci M, Borga S, Caironi P, Cat C, Cingolani E, Avalli L, Greco G, Citerio G, Gandini L, Cornara G, Lerda R, Brazzi L, Simeone F, Caciorgna M, Alampi D, Francesconi S, Beck E, Antonini B, Vettoretto K, Meggiolaro M, Garofalo E, Bruni A, Notaro S, Varutti R, Bassi F, Mistraletti G, Marino A, Rona R, Rondelli E, Riva I, Cortegiani A, Pistidda L, D’Andrea R, Querci L, Gnesin P, Todeschini M, Lugano M, Castelli G, Ortolani M, Cotoia A, Maggiore S, DiTizio L, Graziani R, Testa I, Ferretti E, Castioni C, Lombardi F, Caserta R, Pasqua M, Simoncini S, Baccarini F, Rispoli M, Grossi F, Cancelliere L, Carnelli M, Puccini F, Biancofiore G, Siniscalchi A, Laici C, Mossello E, Torrini M, Pasetti G, Palmese S, Oggioni R, Mangani V, Pini S, Martelli M, Rigo E, Zuccalà F, Cherri A, Spina R, Calamai I, Petrucci N, Caicedo A, Ferri F, Gritti P, Brienza N, Fonnesu R, Dessena M, Fullin G, Saggioro D. Prevalence and features of delirium in older patients admitted to rehabilitation facilities: a multicenter study. Aging Clin Exp Res 2022; 34:1827-1835. [PMID: 35396698 DOI: 10.1007/s40520-022-02099-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 02/16/2022] [Indexed: 11/01/2022]
Abstract
BACKGROUND Delirium is thought to be common across various settings of care; however, still little research has been conducted in rehabilitation. AIM We investigated the prevalence of delirium, its features and motor subtypes in older patients admitted to rehabilitation facilities during the three editions of the "Delirium Day project". METHODS We conducted a cross-sectional study in which 1237 older patients (age ≥ 65 years old) admitted to 50 Italian rehabilitation wards during the three editions of the "Delirium Day project" (2015 to 2017) were included. Delirium was evaluated through the 4AT and its motor subtype with the Delirium Motor Subtype Scale. RESULTS Delirium was detected in 226 patients (18%), and the most recurrent motor subtype was mixed (37%), followed by hypoactive (26%), hyperactive (21%) and non-motor one (16%). In a multivariate Poisson regression model with robust variance, factors associated with delirium were: disability in basic (PR 1.48, 95%CI: 1.17-1.9, p value 0.001) and instrumental activities of daily living (PR 1.58, 95%CI: 1.08-2.32, p value 0.018), dementia (PR 2.10, 95%CI: 1.62-2.73, p value < 0.0001), typical antipsychotics (PR 1.47, 95%CI: 1.10-1.95, p value 0.008), antidepressants other than selective serotonin reuptake inhibitors (PR 1.3, 95%CI: 1.02-1.66, p value 0.035), and physical restraints (PR 2.37, 95%CI: 1.68-3.36, p value < 0.0001). CONCLUSION This multicenter study reports that 2 out 10 patients admitted to rehabilitations had delirium on the index day. Mixed delirium was the most prevalent subtype. Delirium was associated with unmodifiable (dementia, disability) and modifiable (physical restraints, medications) factors. Identification of these factors should prompt specific interventions aimed to prevent or mitigate delirium.
Collapse
|
5
|
Qiao R, Zhong R, Liu C, Di F, Zhang Z, Wang L, Xu T, Wang Y, Dai L, Gu W, Han B, Yang R. Novel blood-based hypomethylation of SH3BP5 is associated with very early-stage lung adenocarcinoma. Genes Genomics 2021; 44:445-453. [PMID: 34783986 DOI: 10.1007/s13258-021-01190-0] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 11/08/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND Early detection is essential to improve the survival of lung cancer (LC). The quantitative measurement of specific DNA methylation changes in the peripheral blood could provide an efficient strategy for the detection of early cancer. OBJECTIVE We applied a candidate approach and assess the association between blood-based SH3BP5 methylation and the risk of lung adenocarcinoma (LUAD) in a case-control cohort. METHODS The methylation level of four CpG sites in the promoter of SH3BP5 gene was quantitatively determined by mass spectrometry in 171 very early-stage LUAD patients (93.6% LUAD at stage I) and 190 age and gender-matched controls. The logistic regression and non-parametric tests were used for the statistical analyses. RESULTS We observed a significant association between decreased methylation of SH3BP5_CpG_4 in the peripheral blood and increased risk of LUAD (odds ratio (OR) per-10% methylation = 1.51, P = 0.006, FDR = 0.024), and even for the LUAD at stage I (OR per-10% methylation = 1.53, P = 0.006, FDR = 0.024). Moreover, the lower quartile of SH3BP5_CpG_4 methylation was correlated with increased risk for LUAD with a P trend of 0.011. Further investigation disclosed that the hypomethylation of SH3BP5_CpG_4 was mostly associated with LUAD in younger subjects (OR per-10% methylation = 2.02, P = 0.010, age < 55 years old) and probably could be enhanced by advance stage. CONCLUSION Our study revealed an association between blood-based SH3BP5 hypomethylation and very early-stage LUAD, which provides a novel support for the blood-based methylation signatures as a potential marker for the evaluation of cancer risk.
Collapse
Affiliation(s)
- Rong Qiao
- Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, 200030, China
| | - Runbo Zhong
- Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, 200030, China
| | - Chunlan Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 210000, China
| | - Feifei Di
- Nanjing TANTICA Biotechnology Co. Ltd, Nanjing, 210000, China
| | - Zheng Zhang
- Nanjing TANTICA Biotechnology Co. Ltd, Nanjing, 210000, China
| | - Ling Wang
- Nanjing TANTICA Biotechnology Co. Ltd, Nanjing, 210000, China
| | - Tian Xu
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, 210000, China
| | - Yue Wang
- Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, 200030, China
| | - Liping Dai
- Henan Institute of Medical and Pharmaceutical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, 450052, China
| | - Wanjian Gu
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, 210000, China
| | - Baohui Han
- Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, 200030, China.
| | - Rongxi Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 210000, China. .,Nanjing TANTICA Biotechnology Co. Ltd, Nanjing, 210000, China.
| |
Collapse
|
6
|
Qiao R, Di F, Wang J, Wei Y, Zhang Y, Xu T, Wang Y, Gu W, Han B, Yang R. The Association Between RAPSN Methylation in Peripheral Blood and Early Stage Lung Cancer Detected in Case-Control Cohort. Cancer Manag Res 2020; 12:11063-11075. [PMID: 33173339 PMCID: PMC7646459 DOI: 10.2147/cmar.s275321] [Citation(s) in RCA: 8] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 10/03/2020] [Indexed: 12/24/2022] Open
Abstract
Background Early detection is essential to improve the survival and life quality of lung cancer (LC) patients. Changes of peripheral blood DNA methylation could be associated with malignancy but were mostly studied in Caucasians. Methods Here, in a Chinese population, we performed mass spectrometry assays to investigate the association between very early stage LC and methylation levels of RAPSN in the peripheral blood by a case–control cohort using of 221 LC patients (93.2% LC at stage I) and 285 unrelated cancer free control individuals. Results The odds ratios (ORs) of all CpG sites were evaluated for their risk to LC using inter-quartile analyses by logistic regression. In general, we observed an association between very early LC and decreased methylation of RAPSN_CpG_1.15 and RAPSN_CpG_3.4 (referring to Q4, OR range from 1.64 to 1.81, p<0.05). Stratified by gender, while hypomethylation of RAPSN_CpG_1.15, RAPSN_CpG_3.4 and RAPSN_CpG_7.14 were associated with LC in males (referring to Q4, ORs range from 1.94 to 2.31, p<0.05), RAPSN_CpG_2 and RAPSN_CpG_5 showed significantly lower methylation in female LC patients comparing to controls (referring to Q4, ORs range from 2.49 to 3.60, p<0.05). The risk of RAPSN hypomethylation to LC was enhanced by aging, and typically for people older than 55 years (referring to Q4, ORs range from 2.17 to 3.61 in six out of all 10 analyzed CpG groups, p<0.05). Conclusion Our study reveals an association between RAPSN hypomethylation in peripheral blood and LC and suggests the occurrence of altered blood-based methylation at the early stage of cancer.
Collapse
Affiliation(s)
- Rong Qiao
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai 200030, People's Republic of China
| | - Feifei Di
- Department of Research and Academic, Nanjing TANTICA Biotechnology Co. Ltd, Nanjing 210000, People's Republic of China
| | - Jun Wang
- Department of Research and Academic, Nanjing TANTICA Biotechnology Co. Ltd, Nanjing 210000, People's Republic of China
| | - Yujie Wei
- Department of Research and Academic, Nanjing TANTICA Biotechnology Co. Ltd, Nanjing 210000, People's Republic of China
| | - Yanman Zhang
- Department of Research and Academic, Nanjing TANTICA Biotechnology Co. Ltd, Nanjing 210000, People's Republic of China
| | - Tian Xu
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210000, People's Republic of China
| | - Yue Wang
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai 200030, People's Republic of China
| | - Wanjian Gu
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210000, People's Republic of China
| | - Baohui Han
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai 200030, People's Republic of China
| | - Rongxi Yang
- Department of Research and Academic, Nanjing TANTICA Biotechnology Co. Ltd, Nanjing 210000, People's Republic of China.,Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 210000, People's Republic of China
| |
Collapse
|
7
|
Di F, Wang T, Ding Y, Chen X, Wang H, Li J, Liu L. Genetic Mapping Combined with a Transcriptome Analysis to Screen for Candidate Genes Responsive to Abscisic Acid Treatment in Brassica napus Embryos During Seed Germination. DNA Cell Biol 2020; 39:533-547. [PMID: 32031882 DOI: 10.1089/dna.2019.5169] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Brassica napus embryos contain precursor tissues for the leaves, stem, and root, as well as the cotyledons, and these precursor tissues play key roles in seed germination, seedling survival, and subsequent seedling growth. Abscisic acid (ABA) plays a prominent role in the inhibition of seed germination. The underlying molecular mechanisms of the embryo responses to ABA stress followed by inhibited seed germination have not been reported in B. napus to date. In this study, we conducted quantitative trait locus (QTL) analysis of B. napus seed in response to ABA stress using 170 recombinant inbred lines. Furthermore, we performed transcriptome sequencing (RNA-seq) analyses by using B. napus ZS11 embryos under sterile deionized water (control) and 10 mg/L (10A), 20 mg/L (20A), and 30 mg/L (30A) ABA treatment conditions. In total, 10 QTLs were screened for explaining 2.70-6.73% of the phenotypic variation under ABA stress. In addition, 1495, 3332, and 3868 differentially expressed genes (DEGs) were identified in the "control vs 10A," "control vs 20A," and "control vs 30A" comparisons, respectively. Gene Ontology (GO) enrichment analysis indicated that DEG functions are mainly related to response to stimuli, response to oxygen-containing compounds, response to lipids, and the transport and seed dormancy processes. These DEGs mainly participated in the response to plant hormone signal transduction, starch and sucrose metabolism, cutin, suberine, and wax biosynthesis, and phenylpropanoid biosynthesis processes pathways. Our results provide a foundation for further explorations of the molecular regulatory mechanisms of B. napus embryos in response to abiotic stress during the seed germination stage.
Collapse
Affiliation(s)
- Feifei Di
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Academy of Agricultural Sciences, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Southwest University, Chongqing, China
| | - Tengyue Wang
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Academy of Agricultural Sciences, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Southwest University, Chongqing, China
| | - Yiran Ding
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Academy of Agricultural Sciences, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Southwest University, Chongqing, China
| | - Xueping Chen
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Academy of Agricultural Sciences, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Southwest University, Chongqing, China
| | - Hao Wang
- Hybrid Rapeseed Research Center of Shaanxi Province, Shanxi Rapeseed Branch of National Center for Oil Crops Genetic Improvement, Yangling, China
| | - Jiana Li
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Academy of Agricultural Sciences, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Southwest University, Chongqing, China
| | - Liezhao Liu
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Academy of Agricultural Sciences, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Southwest University, Chongqing, China
| |
Collapse
|
8
|
Ding Y, Jian H, Wang T, Di F, Wang J, Li J, Liu L. Screening of candidate gene responses to cadmium stress by RNA sequencing in oilseed rape (Brassica napus L.). Environ Sci Pollut Res Int 2018; 25:32433-32446. [PMID: 30232771 DOI: 10.1007/s11356-018-3227-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 09/13/2018] [Indexed: 06/08/2023]
Abstract
Cadmium (Cd) stress is one of the most serious threats to agriculture in the world. Oilseed rape (Brassica napus L.) is an important oil crop; however, Cd can easily accumulate in rapeseed and thus harm human health through the food chain. In the first experiment, our purpose was to measure the Cd accumulation in mature B. napus plants and its influences on fatty acid composition. The results showed that most Cd was accumulated in the root, and the seed fatty acid content was considerably different at different Cd toxicity levels. In the second experiment, 7-day-old B. napus seedlings stressed by Cd (1 mM) for 0 h (CK-0h), 24 h (T-24h), or 72 h (T-72h) were submitted to physiological and biological analyses, RNA-Seq and qRT-PCR. In total, 5469 and 6769 differentially expressed genes (DEGs) were identified in the comparisons of "CK-0h vs T-24h" and "CK-0h vs T-72h", respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses showed that the photosynthetic and glutathione (GSH) pathways were significantly enriched in response to Cd stress. Key factors in the response to Cd stress included BnPCS1, BnGSTU12, BnGSTU5, and BnHMAs. The transcription factors BnWRKY11 (BnaA03g51590D), BnWRKY28 (BnaA03g43640D), BnWRKY33 (BnaA03g17820D), and BnWRKY75 (BnaA03g04160D) were upregulated after Cd exposure. The present study revealed that upregulation of the genes encoding GST and PCS under Cd stress promoted the formation of low-molecular weight complexes (PC-Cd), and upregulation of heavy metal ATPase genes induced PC-Cd transfer to vacuoles. These findings may provide the basis for the molecular mechanism of the response of B. napus to Cd.
Collapse
MESH Headings
- Adaptation, Physiological/genetics
- Adenosine Triphosphatases/genetics
- Aminoacyltransferases/genetics
- Aminoacyltransferases/metabolism
- Biological Transport
- Brassica napus/drug effects
- Brassica napus/genetics
- Brassica napus/metabolism
- Cadmium/metabolism
- Cadmium/pharmacology
- Crops, Agricultural/drug effects
- Crops, Agricultural/genetics
- Crops, Agricultural/metabolism
- Fatty Acids/metabolism
- Gene Expression Regulation, Plant
- Genes, Plant
- Glutathione/genetics
- Glutathione/metabolism
- Humans
- Metals, Heavy/metabolism
- Metals, Heavy/pharmacology
- Photosynthesis
- Plant Development
- Plant Proteins/genetics
- Plant Proteins/metabolism
- Plant Roots/metabolism
- RNA, Plant/analysis
- Seedlings/metabolism
- Seeds/metabolism
- Sequence Analysis, RNA
- Stress, Physiological
- Transcription Factors/genetics
- Transcription Factors/metabolism
- Up-Regulation
Collapse
Affiliation(s)
- Yiran Ding
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Academy of Agricultural Sciences, Southwest University, Chongqing, 400716, China
| | - Hongju Jian
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Academy of Agricultural Sciences, Southwest University, Chongqing, 400716, China
| | - Tengyue Wang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Academy of Agricultural Sciences, Southwest University, Chongqing, 400716, China
| | - Feifei Di
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Academy of Agricultural Sciences, Southwest University, Chongqing, 400716, China
| | - Jia Wang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Academy of Agricultural Sciences, Southwest University, Chongqing, 400716, China
| | - Jiana Li
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Academy of Agricultural Sciences, Southwest University, Chongqing, 400716, China
| | - Liezhao Liu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Academy of Agricultural Sciences, Southwest University, Chongqing, 400716, China.
| |
Collapse
|
9
|
Di F, Jian H, Wang T, Chen X, Ding Y, Du H, Lu K, Li J, Liu L. Genome-Wide Analysis of the PYL Gene Family and Identification of PYL Genes That Respond to Abiotic Stress in Brassica napus. Genes (Basel) 2018. [PMID: 29534558 PMCID: PMC5867877 DOI: 10.3390/genes9030156] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [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] [Indexed: 11/16/2022] Open
Abstract
Abscisic acid (ABA) is an endogenous phytohormone that plays important roles in the regulation of plant growth, development, and stress responses. The pyrabactin resistance 1-like (PYR/PYL) protein is a core regulatory component of ABA signaling networks in plants. However, no details regarding this family in Brassica napus are available. Here, 46 PYLs were identified in the B. napus genome. Based on phylogenetic analysis, BnPYR1 and BnPYL1-3 belong to subfamily I, BnPYL7-10 belong to subfamily II, and BnPYL4-6 and BnPYL11-13 belong to subfamily III. Analysis of BnPYL conserved motifs showed that every subfamily contained four common motifs. By predicting cis-elements in the promoters, we found that all BnPYL members contained hormone- and stress-related elements and that expression levels of most BnPYLs were relatively higher in seeds at the germination stage than those in other organs or at other developmental stages. Gene Ontology (GO) enrichment showed that BnPYL genes mainly participate in responses to stimuli. To identify crucial PYLs mediating the response to abiotic stress in B. napus, expression changes in 14 BnPYL genes were determined by quantitative real-time RT-PCR after drought, heat, and salinity treatments, and identified BnPYR1-3, BnPYL1-2, and BnPYL7-2 in respond to abiotic stresses. The findings of this study lay a foundation for further investigations of PYL genes in B. napus.
Collapse
Affiliation(s)
- Feifei Di
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Southwest University, Chongqing 400716, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China.
| | - Hongju Jian
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Southwest University, Chongqing 400716, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China.
| | - Tengyue Wang
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Southwest University, Chongqing 400716, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China.
| | - Xueping Chen
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Southwest University, Chongqing 400716, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China.
| | - Yiran Ding
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Southwest University, Chongqing 400716, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China.
| | - Hai Du
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Southwest University, Chongqing 400716, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China.
| | - Kun Lu
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Southwest University, Chongqing 400716, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China.
| | - Jiana Li
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Southwest University, Chongqing 400716, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China.
| | - Liezhao Liu
- College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Southwest University, Chongqing 400716, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China.
| |
Collapse
|
10
|
Chang Z, Di F, Zhou F. [Quantitative determination of cholic acid in Calulus Bovis]. Zhongguo Zhong Yao Za Zhi 1999; 24:684-5, 703. [PMID: 12212089] [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: 02/26/2023]
Abstract
OBJECTIVE To establish a method to determine the Content of cholic acid in Calulus Bovis. METHOD The content was determined by TLCS. RESULT Recovery rate was 96.54%, RSD was 1.68%. CONCLUSION Accurate and reproducible, this method can be used for the quality control of Calulus Bovis.
Collapse
Affiliation(s)
- Z Chang
- Beijing Municipal Institute for Drug Control, Beijing 100035
| | | | | |
Collapse
|
11
|
Wang W, Di F. Treatment of omocervical syndrome in 115 cases primarily with acupuncture at point zhongping. J TRADIT CHIN MED 1995; 15:110-1. [PMID: 7650956] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- W Wang
- 292 Hospital of Chinese PLA, Beijing
| | | |
Collapse
|
12
|
Di F, Kun L, Su CQ. Ligation of the thoracic duct without thoracotomy for the treatment of postoperative chylothorax: a newly designed surgical procedure. J R Coll Surg Edinb 1995; 40:60-1. [PMID: 7738903] [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: 01/26/2023]
Abstract
A newly designed surgical procedure of ligation of the thoracic duct without thoracotomy for the treatment of postoperative chylothorax is presented. A case of chylothorax following resection of carcinoma of the oesophagus was treated successfully with ligation of the thoracic duct without thoracotomy. Its advantages were very prominent consisting of maintenance of the integrity of the thorax, less traumatization, no need of a drainage tube and shorter hospitalization, much easier to expose the thoracic duct than the conventional transthoracic approach. We can find no similar report in any published literature.
Collapse
Affiliation(s)
- F Di
- Department of Thoracic Surgery, Tangdu Hospital, Xi'an, China
| | | | | |
Collapse
|
13
|
Wang W, Yin X, He Y, Wei J, Wang J, Di F. Treatment of periarthritis of the shoulder with acupuncture at the zhongping (foot) extrapoint in 345 cases. J TRADIT CHIN MED 1990; 10:209-12. [PMID: 2277523] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- W Wang
- Beijing Garrison Hospital
| | | | | | | | | | | |
Collapse
|