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Sun N, Chu J, He Q, Wang Y, Han Q, Yi N, Zhang R, Shen Y. BHAFT: Bayesian heredity-constrained accelerated failure time models for detecting gene-environment interactions in survival analysis. Stat Med 2024. [PMID: 38963094 DOI: 10.1002/sim.10145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 05/06/2024] [Accepted: 06/06/2024] [Indexed: 07/05/2024]
Abstract
In addition to considering the main effects, understanding gene-environment (G × E) interactions is imperative for determining the etiology of diseases and the factors that affect their prognosis. In the existing statistical framework for censored survival outcomes, there are several challenges in detecting G × E interactions, such as handling high-dimensional omics data, diverse environmental factors, and algorithmic complications in survival analysis. The effect heredity principle has widely been used in studies involving interaction identification because it incorporates the dependence of the main and interaction effects. However, Bayesian survival models that incorporate the assumption of this principle have not been developed. Therefore, we propose Bayesian heredity-constrained accelerated failure time (BHAFT) models for identifying main and interaction (M-I) effects with novel spike-and-slab or regularized horseshoe priors to incorporate the assumption of effect heredity principle. The R package rstan was used to fit the proposed models. Extensive simulations demonstrated that BHAFT models had outperformed other existing models in terms of signal identification, coefficient estimation, and prognosis prediction. Biologically plausible G × E interactions associated with the prognosis of lung adenocarcinoma were identified using our proposed model. Notably, BHAFT models incorporating the effect heredity principle could identify both main and interaction effects, which are highly useful in exploring G × E interactions in high-dimensional survival analysis. The code and data used in our paper are available at https://github.com/SunNa-bayesian/BHAFT.
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Affiliation(s)
- Na Sun
- Department of Epidemiology and Biostatistics, School of Public Health, Medical College of Soochow University, Suzhou, China
| | - Jiadong Chu
- Department of Epidemiology and Biostatistics, School of Public Health, Medical College of Soochow University, Suzhou, China
| | - Qida He
- Department of Epidemiology and Biostatistics, School of Public Health, Medical College of Soochow University, Suzhou, China
| | - Yu Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Medical College of Soochow University, Suzhou, China
| | - Qiang Han
- Department of Epidemiology and Biostatistics, School of Public Health, Medical College of Soochow University, Suzhou, China
| | - Nengjun Yi
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Ruyang Zhang
- Department of Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yueping Shen
- Department of Epidemiology and Biostatistics, School of Public Health, Medical College of Soochow University, Suzhou, China
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2
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Grossi S, Berno E, Chiofalo P, Chiaravalli AM, Cinquetti R, Bruno A, Palano MT, Gallazzi M, La Rosa S, Sessa F, Acquati F, Campomenosi P. Proline Dehydrogenase (PRODH) Is Expressed in Lung Adenocarcinoma and Modulates Cell Survival and 3D Growth by Inducing Cellular Senescence. Int J Mol Sci 2024; 25:714. [PMID: 38255788 PMCID: PMC10815008 DOI: 10.3390/ijms25020714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 12/30/2023] [Accepted: 01/02/2024] [Indexed: 01/24/2024] Open
Abstract
The identification of markers for early diagnosis, prognosis, and improvement of therapeutic options represents an unmet clinical need to increase survival in Non-Small Cell Lung Cancer (NSCLC), a neoplasm still characterized by very high incidence and mortality. Here, we investigated whether proline dehydrogenase (PRODH), a mitochondrial flavoenzyme catalyzing the key step in proline degradation, played a role in NSCLC tumorigenesis. PRODH expression was investigated by immunohistochemistry; digital PCR, quantitative PCR, immunoblotting, measurement of reactive oxygen species (ROS), and functional cellular assays were carried out. PRODH expression was found in the majority of lung adenocarcinomas (ADCs). Patients with PRODH-positive tumors had better cancer-free specific and overall survival compared to those with negative tumors. Ectopic modulation of PRODH expression in NCI-H1299 and the other tested lung ADC cell lines decreased cell survival. Moreover, cell proliferation curves showed delayed growth in NCI-H1299, Calu-6 and A549 cell lines when PRODH-expressing clones were compared to control clones. The 3D growth in soft agar was also impaired in the presence of PRODH. PRODH increased reactive oxygen species production and induced cellular senescence in the NCI-H1299 cell line. This study supports a role of PRODH in decreasing survival and growth of lung ADC cells by inducing cellular senescence.
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Affiliation(s)
- Sarah Grossi
- Dipartimento di Biotecnologie e Scienze della Vita, DBSV, Università degli Studi dell’Insubria, Via J.H. Dunant 3, 21100 Varese, Italy; (S.G.); (E.B.); (P.C.); (R.C.); (A.B.); (F.A.)
| | - Elena Berno
- Dipartimento di Biotecnologie e Scienze della Vita, DBSV, Università degli Studi dell’Insubria, Via J.H. Dunant 3, 21100 Varese, Italy; (S.G.); (E.B.); (P.C.); (R.C.); (A.B.); (F.A.)
| | - Priscilla Chiofalo
- Dipartimento di Biotecnologie e Scienze della Vita, DBSV, Università degli Studi dell’Insubria, Via J.H. Dunant 3, 21100 Varese, Italy; (S.G.); (E.B.); (P.C.); (R.C.); (A.B.); (F.A.)
| | - Anna Maria Chiaravalli
- Unità di Anatomia Patologica, Ospedale di Circolo e Fondazione Macchi, Via O. Rossi 9, 21100 Varese, Italy; (A.M.C.); (S.L.R.); (F.S.)
- Centro di Ricerca per lo Studio dei Tumori Eredo-Famigliari, Università degli Studi dell’Insubria, 21100 Varese, Italy
| | - Raffaella Cinquetti
- Dipartimento di Biotecnologie e Scienze della Vita, DBSV, Università degli Studi dell’Insubria, Via J.H. Dunant 3, 21100 Varese, Italy; (S.G.); (E.B.); (P.C.); (R.C.); (A.B.); (F.A.)
| | - Antonino Bruno
- Dipartimento di Biotecnologie e Scienze della Vita, DBSV, Università degli Studi dell’Insubria, Via J.H. Dunant 3, 21100 Varese, Italy; (S.G.); (E.B.); (P.C.); (R.C.); (A.B.); (F.A.)
- Laboratorio di Immunità Innata, Unità di Patologia Molecolare, Biochimica, e Immunologia, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) MultiMedica, Via Fantoli 16/15, 20138 Milan, Italy; (M.T.P.); (M.G.)
- Centro di Ricerca per l’Invecchiamento di Successo (CRIS), Università degli Studi dell’Insubria, 21100 Varese, Italy
| | - Maria Teresa Palano
- Laboratorio di Immunità Innata, Unità di Patologia Molecolare, Biochimica, e Immunologia, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) MultiMedica, Via Fantoli 16/15, 20138 Milan, Italy; (M.T.P.); (M.G.)
| | - Matteo Gallazzi
- Laboratorio di Immunità Innata, Unità di Patologia Molecolare, Biochimica, e Immunologia, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) MultiMedica, Via Fantoli 16/15, 20138 Milan, Italy; (M.T.P.); (M.G.)
| | - Stefano La Rosa
- Unità di Anatomia Patologica, Ospedale di Circolo e Fondazione Macchi, Via O. Rossi 9, 21100 Varese, Italy; (A.M.C.); (S.L.R.); (F.S.)
- Centro di Ricerca per lo Studio dei Tumori Eredo-Famigliari, Università degli Studi dell’Insubria, 21100 Varese, Italy
- Dipartimento di Medicina e Innovazione Tecnologica, DIMIT, Università degli Studi dell’Insubria, Via Guicciardini 9, 21100 Varese, Italy
| | - Fausto Sessa
- Unità di Anatomia Patologica, Ospedale di Circolo e Fondazione Macchi, Via O. Rossi 9, 21100 Varese, Italy; (A.M.C.); (S.L.R.); (F.S.)
- Dipartimento di Medicina e Innovazione Tecnologica, DIMIT, Università degli Studi dell’Insubria, Via Guicciardini 9, 21100 Varese, Italy
| | - Francesco Acquati
- Dipartimento di Biotecnologie e Scienze della Vita, DBSV, Università degli Studi dell’Insubria, Via J.H. Dunant 3, 21100 Varese, Italy; (S.G.); (E.B.); (P.C.); (R.C.); (A.B.); (F.A.)
- Centro di Ricerca per l’Invecchiamento di Successo (CRIS), Università degli Studi dell’Insubria, 21100 Varese, Italy
| | - Paola Campomenosi
- Dipartimento di Biotecnologie e Scienze della Vita, DBSV, Università degli Studi dell’Insubria, Via J.H. Dunant 3, 21100 Varese, Italy; (S.G.); (E.B.); (P.C.); (R.C.); (A.B.); (F.A.)
- Centro di Ricerca per l’Invecchiamento di Successo (CRIS), Università degli Studi dell’Insubria, 21100 Varese, Italy
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3
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Zhang J, Shi F, Liu X, Wu X, Hu C, Guo J, Yang Q, Xia J, He Y, An G, Qiu L, Feng X, Zhou W. Proline promotes proliferation and drug resistance of multiple myeloma by downregulation of proline dehydrogenase. Br J Haematol 2023; 201:704-717. [PMID: 36755409 DOI: 10.1111/bjh.18684] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 12/28/2022] [Accepted: 01/25/2023] [Indexed: 02/10/2023]
Abstract
Amino acids in the bone marrow microenvironment (BMME) are a critical factor for multiple myeloma (MM) progression. Here, we have determined that proline is elevated in BMME of MM patients and links to poor prognosis in MM. Moreover, exogenous proline regulates MM cell proliferation and drug resistance. Elevated proline in BMME is due to bone collagen degradation and abnormal expression of the key enzyme of proline catabolism, proline dehydrogenase (PRODH). PRODH is downregulated in MM patients, mainly as a result of promoter hypermethylation with high expression of DNMT3b. Thus, overexpression of PRODH suppresses cell proliferation and drug resistance of MM and exhibits therapeutic potential for treatment of MM. Altogether, we identify proline as a key metabolic regulator of MM, unveil PRODH governing MM progression and provide a promising therapeutic strategy for MM treatment.
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Affiliation(s)
- Jingyu Zhang
- Haihe Laboratory of Cell Ecosystem, State Key Laboratory of Experimental Hematology, National Clinical Research Center for Geriatric Disorders, Department of Hematology, Xiangya Hospital, Central South University, Changsha, China.,Key Laboratory for Carcinogenesis and Invasion, Chinese Ministry of Education, Key Laboratory of Carcinogenesis, Chinese Ministry of Health, Cancer Research Institute, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
| | - Fangming Shi
- Haihe Laboratory of Cell Ecosystem, State Key Laboratory of Experimental Hematology, National Clinical Research Center for Geriatric Disorders, Department of Hematology, Xiangya Hospital, Central South University, Changsha, China.,Key Laboratory for Carcinogenesis and Invasion, Chinese Ministry of Education, Key Laboratory of Carcinogenesis, Chinese Ministry of Health, Cancer Research Institute, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
| | - Xing Liu
- Haihe Laboratory of Cell Ecosystem, State Key Laboratory of Experimental Hematology, National Clinical Research Center for Geriatric Disorders, Department of Hematology, Xiangya Hospital, Central South University, Changsha, China.,Key Laboratory for Carcinogenesis and Invasion, Chinese Ministry of Education, Key Laboratory of Carcinogenesis, Chinese Ministry of Health, Cancer Research Institute, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
| | - Xuan Wu
- Haihe Laboratory of Cell Ecosystem, State Key Laboratory of Experimental Hematology, National Clinical Research Center for Geriatric Disorders, Department of Hematology, Xiangya Hospital, Central South University, Changsha, China
| | - Cong Hu
- Haihe Laboratory of Cell Ecosystem, State Key Laboratory of Experimental Hematology, National Clinical Research Center for Geriatric Disorders, Department of Hematology, Xiangya Hospital, Central South University, Changsha, China.,Key Laboratory for Carcinogenesis and Invasion, Chinese Ministry of Education, Key Laboratory of Carcinogenesis, Chinese Ministry of Health, Cancer Research Institute, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
| | - Jiaojiao Guo
- Haihe Laboratory of Cell Ecosystem, State Key Laboratory of Experimental Hematology, National Clinical Research Center for Geriatric Disorders, Department of Hematology, Xiangya Hospital, Central South University, Changsha, China.,Key Laboratory for Carcinogenesis and Invasion, Chinese Ministry of Education, Key Laboratory of Carcinogenesis, Chinese Ministry of Health, Cancer Research Institute, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
| | - Qin Yang
- Department of Hematology, Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jiliang Xia
- Hunan Province Key Laboratory of Tumor Cellular & Molecular Pathology, Cancer Research Institute, Hengyang Medical College, University of South China, Hengyang, Hunan, China
| | - Yanjuan He
- Haihe Laboratory of Cell Ecosystem, State Key Laboratory of Experimental Hematology, National Clinical Research Center for Geriatric Disorders, Department of Hematology, Xiangya Hospital, Central South University, Changsha, China
| | - Gang An
- State Key Laboratory of Experimental Hematology, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Tianjin, China
| | - Lugui Qiu
- State Key Laboratory of Experimental Hematology, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Tianjin, China
| | - Xiangling Feng
- Haihe Laboratory of Cell Ecosystem, State Key Laboratory of Experimental Hematology, National Clinical Research Center for Geriatric Disorders, Department of Hematology, Xiangya Hospital, Central South University, Changsha, China.,Xiangya School of Public Health, Central South University, Changsha, Hunan, China
| | - Wen Zhou
- Haihe Laboratory of Cell Ecosystem, State Key Laboratory of Experimental Hematology, National Clinical Research Center for Geriatric Disorders, Department of Hematology, Xiangya Hospital, Central South University, Changsha, China.,Key Laboratory for Carcinogenesis and Invasion, Chinese Ministry of Education, Key Laboratory of Carcinogenesis, Chinese Ministry of Health, Cancer Research Institute, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
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4
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Chen J, Song Y, Li Y, Wei Y, Shen S, Zhao Y, You D, Su L, Bjaanæs MM, Karlsson A, Planck M, Staaf J, Helland Å, Esteller M, Shen H, Christiani DC, Zhang R, Chen F. A trans-omics assessment of gene-gene interaction in early-stage NSCLC. Mol Oncol 2022; 17:173-187. [PMID: 36408734 PMCID: PMC9812838 DOI: 10.1002/1878-0261.13345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 08/28/2022] [Accepted: 11/17/2022] [Indexed: 11/22/2022] Open
Abstract
Epigenome-wide gene-gene (G × G) interactions associated with non-small-cell lung cancer (NSCLC) survival may provide insights into molecular mechanisms and therapeutic targets. Hence, we proposed a three-step analytic strategy to identify significant and robust G × G interactions that are relevant to NSCLC survival. In the first step, among 49 billion pairs of DNA methylation probes, we identified 175 775 G × G interactions with PBonferroni ≤ 0.05 in the discovery phase of epigenomic analysis; among them, 15 534 were confirmed with P ≤ 0.05 in the validation phase. In the second step, we further performed a functional validation for these G × G interactions at the gene expression level by way of a two-phase (discovery and validation) transcriptomic analysis, and confirmed 25 significant G × G interactions enriched in the 6p21.33 and 6p22.1 regions. In the third step, we identified two G × G interactions using the trans-omics analysis, which had significant (P ≤ 0.05) epigenetic cis-regulation of transcription and robust G × G interactions at both the epigenetic and transcriptional levels. These interactions were cg14391855 × cg23937960 (βinteraction = 0.018, P = 1.87 × 10-12 ), which mapped to RELA × HLA-G (βinteraction = 0.218, P = 8.82 × 10-11 ) and cg08872738 × cg27077312 (βinteraction = -0.010, P = 1.16 × 10-11 ), which mapped to TUBA1B × TOMM40 (βinteraction =-0.250, P = 3.83 × 10-10 ). A trans-omics mediation analysis revealed that 20.3% of epigenetic effects on NSCLC survival were significantly (P = 0.034) mediated through transcriptional expression. These statistically significant trans-omics G × G interactions can also discriminate patients with high risk of mortality. In summary, we identified two G × G interactions at both the epigenetic and transcriptional levels, and our findings may provide potential clues for precision treatment of NSCLC.
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Affiliation(s)
- Jiajin Chen
- Department of Biostatistics, Center for Global Health, School of Public HealthNanjing Medical UniversityNanjingChina
| | - Yunjie Song
- Department of Biostatistics, Center for Global Health, School of Public HealthNanjing Medical UniversityNanjingChina
| | - Yi Li
- Department of BiostatisticsUniversity of MichiganAnn ArborMIUSA
| | - Yongyue Wei
- Department of Biostatistics, Center for Global Health, School of Public HealthNanjing Medical UniversityNanjingChina,Department of Environmental HealthHarvard T.H. Chan School of Public HealthBostonMAUSA,China International Cooperation Center for Environment and Human HealthNanjing Medical UniversityNanjingChina
| | - Sipeng Shen
- Department of Biostatistics, Center for Global Health, School of Public HealthNanjing Medical UniversityNanjingChina
| | - Yang Zhao
- Department of Biostatistics, Center for Global Health, School of Public HealthNanjing Medical UniversityNanjingChina
| | - Dongfang You
- Department of Biostatistics, Center for Global Health, School of Public HealthNanjing Medical UniversityNanjingChina
| | - Li Su
- Department of Environmental HealthHarvard T.H. Chan School of Public HealthBostonMAUSA,Pulmonary and Critical Care Division, Department of MedicineMassachusetts General Hospital and Harvard Medical SchoolBostonMAUSA
| | - Maria Moksnes Bjaanæs
- Department of Cancer Genetics, Institute for Cancer ResearchOslo University HospitalOsloNorway
| | - Anna Karlsson
- Division of Oncology, Department of Clinical Sciences Lund and CREATE Health Strategic Center for Translational Cancer ResearchLund UniversityLundSweden
| | - Maria Planck
- Division of Oncology, Department of Clinical Sciences Lund and CREATE Health Strategic Center for Translational Cancer ResearchLund UniversityLundSweden
| | - Johan Staaf
- Division of Oncology, Department of Clinical Sciences Lund and CREATE Health Strategic Center for Translational Cancer ResearchLund UniversityLundSweden
| | - Åslaug Helland
- Department of Cancer Genetics, Institute for Cancer ResearchOslo University HospitalOsloNorway,Institute of Clinical MedicineUniversity of OsloOsloNorway
| | - Manel Esteller
- Josep Carreras Leukaemia Research InstituteBarcelonaSpain,Centro de Investigacion Biomedica en Red CancerMadridSpain,Institucio Catalana de Recerca i Estudis AvançatsBarcelonaSpain,Physiological Sciences Department, School of Medicine and Health SciencesUniversity of BarcelonaBarcelonaSpain
| | - Hongbing Shen
- China International Cooperation Center for Environment and Human HealthNanjing Medical UniversityNanjingChina,Department of Epidemiology, School of Public HealthNanjing Medical UniversityNanjingChina,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Cancer Center, Collaborative Innovation Center for Cancer Personalized MedicineNanjing Medical UniversityNanjingChina
| | - David C. Christiani
- Department of Environmental HealthHarvard T.H. Chan School of Public HealthBostonMAUSA,Pulmonary and Critical Care Division, Department of MedicineMassachusetts General Hospital and Harvard Medical SchoolBostonMAUSA
| | - Ruyang Zhang
- Department of Biostatistics, Center for Global Health, School of Public HealthNanjing Medical UniversityNanjingChina,Department of Environmental HealthHarvard T.H. Chan School of Public HealthBostonMAUSA,China International Cooperation Center for Environment and Human HealthNanjing Medical UniversityNanjingChina
| | - Feng Chen
- Department of Biostatistics, Center for Global Health, School of Public HealthNanjing Medical UniversityNanjingChina,China International Cooperation Center for Environment and Human HealthNanjing Medical UniversityNanjingChina,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Cancer Center, Collaborative Innovation Center for Cancer Personalized MedicineNanjing Medical UniversityNanjingChina,State Key Laboratory of Reproductive MedicineNanjing Medical UniversityNanjingChina
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5
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Xu Z, Gu Y, Chen J, Chen X, Song Y, Fan J, Ji X, Li Y, Zhang W, Zhang R. Epigenome-wide gene–age interaction study reveals reversed effects of MORN1 DNA methylation on survival between young and elderly oral squamous cell carcinoma patients. Front Oncol 2022; 12:941731. [PMID: 35965572 PMCID: PMC9366171 DOI: 10.3389/fonc.2022.941731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 06/28/2022] [Indexed: 12/04/2022] Open
Abstract
DNA methylation serves as a reversible and prognostic biomarker for oral squamous cell carcinoma (OSCC) patients. It is unclear whether the effect of DNA methylation on OSCC overall survival varies with age. As a result, we performed a two-phase gene–age interaction study of OSCC prognosis on an epigenome-wide scale using the Cox proportional hazards model. We identified one CpG probe, cg11676291MORN1, whose effect was significantly modified by age (HRdiscovery = 1.018, p = 4.07 × 10−07, FDR-q = 3.67 × 10−02; HRvalidation = 1.058, p = 8.09 × 10−03; HRcombined = 1.019, p = 7.36 × 10−10). Moreover, there was an antagonistic interaction between hypomethylation of cg11676291MORN1 and age (HRinteraction = 0.284; 95% CI, 0.135–0.597; p = 9.04 × 10−04). The prognosis of OSCC patients was well discriminated by the prognostic score incorporating cg11676291MORN1–age interaction (HRhigh vs. low = 3.66, 95% CI: 2.40–5.60, p = 1.93 × 10−09). By adding 24 significant gene–age interactions using a looser criterion, we significantly improved the area under the receiver operating characteristic curve (AUC) of the model at 3- and 5-year prognostic prediction (AUC3-year = 0.80, AUC5-year = 0.79, C-index = 0.75). Our study identified a significant interaction between cg11676291MORN1 and age on OSCC survival, providing a potential therapeutic target for OSCC patients.
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Affiliation(s)
- Ziang Xu
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Department of Oral Special Consultation, Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, China
| | - Yan Gu
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Department of Orthodontics, Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, China
| | - Jiajin Chen
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xinlei Chen
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Department of Oral Special Consultation, Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, China
| | - Yunjie Song
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Juanjuan Fan
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xinyu Ji
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yanyan Li
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Department of Oral Special Consultation, Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, China
| | - Wei Zhang
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Department of Oral Special Consultation, Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, China
- *Correspondence: Ruyang Zhang, ; Wei Zhang,
| | - Ruyang Zhang
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- China International Cooperation Center for Environment and Human Health, Nanjing Medical University, Nanjing, China
- *Correspondence: Ruyang Zhang, ; Wei Zhang,
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6
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Zhu J, Guan J, Ji X, Song Y, Xu X, Wang Q, Zhang Q, Guo R, Wang R, Zhang R. A two-phase comprehensive NSCLC prognostic study identifies lncRNAs with significant main effect and interaction. Mol Genet Genomics 2022; 297:591-600. [PMID: 35218396 PMCID: PMC8960609 DOI: 10.1007/s00438-022-01869-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 02/02/2022] [Indexed: 12/25/2022]
Abstract
Long noncoding RNA (lncRNA) are involved in regulating physiological behaviors for various malignant tumors, including non-small-cell lung cancer (NSCLC). However, few studies comprehensively evaluated both lncRNA-lncRNA interaction effects and main effects of lncRNA on overall survival of NSCLC. Hence, we performed a two-phase designed study of lncRNA expression in tumor tissues using 604 NSCLC patients from The Cancer Genome Atlas as the discovery phase and 839 patients from Gene Expression Omnibus as the validation phase. In the discovery phase, we adopted a two-step strategy, Screening before Testing, for dimension reduction and signal detection. These candidate lncRNAs first screened out by the weighted random forest (Ranger), were then tested through the Cox proportional hazards model adjusted for covariates. Significant lncRNAs with either type of effects aforementioned were carried forward into the validation phase to confirm their significances again. As a result, in the discovery phase, 19 lncRNAs were identified by Ranger, among which five lncRNAs and one pair of lncRNA-lncRNA interaction exhibited significant effects (FDR-q ≤ 0.05) main and interaction effects on NSCLC survival, respectively, through Cox model. After the independent validation, we finally observed that one lncRNA (ENSG00000227403.1) with main effect was robustly associated with NSCLC prognosis (HRdiscovery = 0.90, P = 1.20 × 10-3; HRvalidation = 0.94, P = 4.11 × 10-3) and one pair of lncRNAs (ENSG00000267121.4 and ENSG00000272369.1) had significant interaction effect on NSCLC survival (HRdiscovery = 1.12, P = 3.07 × 10-4; HRvalidation = 1.11, P = 0.0397). Our comprehensive NSCLC prognostic study of lncRNA provided population-level evidence for further functional study.
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Affiliation(s)
- Jing Zhu
- Department of Oncology, The Affiliated Jiangning Hospital of Nanjing Medical University, 169 Hushan Road, No. 2 Building, 212 East Ward, Nanjing, 211100, Jiangsu, China
| | - Jinxing Guan
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, SPH Building, Room 406, Nanjing, 211166, Jiangsu, China
| | - Xinyu Ji
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, SPH Building, Room 406, Nanjing, 211166, Jiangsu, China
| | - Yunjie Song
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, SPH Building, Room 406, Nanjing, 211166, Jiangsu, China
| | - Xiaoshuang Xu
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, SPH Building, Room 406, Nanjing, 211166, Jiangsu, China
| | - Qianqian Wang
- Department of Medical Oncology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, No. 3 Building, Floor 10, Nanjing, 210003, Jiangsu, China
| | - Quanan Zhang
- Department of Oncology, The Affiliated Jiangning Hospital of Nanjing Medical University, 169 Hushan Road, No. 2 Building, 212 East Ward, Nanjing, 211100, Jiangsu, China.
| | - Renhua Guo
- Department of Medical Oncology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, No. 3 Building, Floor 10, Nanjing, 210003, Jiangsu, China.
| | - Rui Wang
- Department of Medical Oncology, Jinling Hospital, School of Medicine, Nanjing University, 34 Yanggongjing Street, Building 1, Floor 6, Nanjing, 210002, Jiangsu, China.
| | - Ruyang Zhang
- Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, SPH Building, Room 406, Nanjing, 211166, Jiangsu, China. .,Department of Medical Oncology, Jinling Hospital, School of Medicine, Nanjing University, 34 Yanggongjing Street, Building 1, Floor 6, Nanjing, 210002, Jiangsu, China.
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Ji X, Lin L, Fan J, Li Y, Wei Y, Shen S, Su L, Shafer A, Bjaanæs MM, Karlsson A, Planck M, Staaf J, Helland Å, Esteller M, Zhang R, Chen F, Christiani DC. Epigenome-wide three-way interaction study identifies a complex pattern between TRIM27, KIAA0226, and smoking associated with overall survival of early-stage NSCLC. Mol Oncol 2022; 16:717-731. [PMID: 34932879 PMCID: PMC8807353 DOI: 10.1002/1878-0261.13167] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 11/23/2021] [Accepted: 12/20/2021] [Indexed: 01/12/2023] Open
Abstract
The interaction between DNA methylation of tripartite motif containing 27 (cg05293407TRIM27 ) and smoking has previously been identified to reveal histologically heterogeneous effects of TRIM27 DNA methylation on early-stage non-small-cell lung cancer (NSCLC) survival. However, to understand the complex mechanisms underlying NSCLC progression, we searched three-way interactions. A two-phase study was adopted to identify three-way interactions in the form of pack-year of smoking (number of cigarettes smoked per day × number of years smoked) × cg05293407TRIM27 × epigenome-wide DNA methylation CpG probe. Two CpG probes were identified with FDR-q ≤ 0.05 in the discovery phase and P ≤ 0.05 in the validation phase: cg00060500KIAA0226 and cg17479956EXT2 . Compared to a prediction model with only clinical information, the model added 42 significant three-way interactions using a looser criterion (discovery: FDR-q ≤ 0.10, validation: P ≤ 0.05) had substantially improved the area under the receiver operating characteristic curve (AUC) of the prognostic prediction model for both 3-year and 5-year survival. Our research identified the complex interaction effects among multiple environment and epigenetic factors, and provided therapeutic target for NSCLC patients.
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Affiliation(s)
- Xinyu Ji
- Department of BiostatisticsCenter for Global HealthSchool of Public HealthNanjing Medical UniversityNanjingChina
| | - Lijuan Lin
- Department of BiostatisticsCenter for Global HealthSchool of Public HealthNanjing Medical UniversityNanjingChina
| | - Juanjuan Fan
- Department of BiostatisticsCenter for Global HealthSchool of Public HealthNanjing Medical UniversityNanjingChina
| | - Yi Li
- Department of BiostatisticsUniversity of MichiganAnn ArborMIUSA
| | - Yongyue Wei
- Department of BiostatisticsCenter for Global HealthSchool of Public HealthNanjing Medical UniversityNanjingChina,Department of Environmental HealthHarvard T.H. Chan School of Public HealthBostonMAUSA,China International Cooperation Center for Environment and Human HealthNanjing Medical UniversityNanjingChina
| | - Sipeng Shen
- Department of BiostatisticsCenter for Global HealthSchool of Public HealthNanjing Medical UniversityNanjingChina
| | - Li Su
- Department of Environmental HealthHarvard T.H. Chan School of Public HealthBostonMAUSA
| | - Andrea Shafer
- Pulmonary and Critical Care DivisionDepartment of MedicineMassachusetts General Hospital and Harvard Medical SchoolBostonMAUSA
| | - Maria Moksnes Bjaanæs
- Department of Cancer GeneticsInstitute for Cancer ResearchOslo University HospitalOsloNorway
| | - Anna Karlsson
- Division of OncologyDepartment of Clinical Sciences Lund and CREATE Health Strategic Center for Translational Cancer ResearchLund UniversityLundSweden
| | - Maria Planck
- Division of OncologyDepartment of Clinical Sciences Lund and CREATE Health Strategic Center for Translational Cancer ResearchLund UniversityLundSweden
| | - Johan Staaf
- Division of OncologyDepartment of Clinical Sciences Lund and CREATE Health Strategic Center for Translational Cancer ResearchLund UniversityLundSweden
| | - Åslaug Helland
- Department of Cancer GeneticsInstitute for Cancer ResearchOslo University HospitalOsloNorway,Institute of Clinical MedicineUniversity of OsloOsloNorway
| | - Manel Esteller
- Josep Carreras Leukaemia Research InstituteBarcelonaSpain,Centro de Investigacion Biomedica en Red CancerMadridSpain,Institucio Catalana de Recerca i Estudis AvançatsBarcelonaSpain,Physiological Sciences DepartmentSchool of Medicine and Health SciencesUniversity of BarcelonaBarcelonaSpain
| | - Ruyang Zhang
- Department of BiostatisticsCenter for Global HealthSchool of Public HealthNanjing Medical UniversityNanjingChina,Department of Environmental HealthHarvard T.H. Chan School of Public HealthBostonMAUSA,China International Cooperation Center for Environment and Human HealthNanjing Medical UniversityNanjingChina
| | - Feng Chen
- Department of BiostatisticsCenter for Global HealthSchool of Public HealthNanjing Medical UniversityNanjingChina,China International Cooperation Center for Environment and Human HealthNanjing Medical UniversityNanjingChina,State Key Laboratory of Reproductive MedicineNanjing Medical UniversityNanjingChina,Jiangsu Key Lab of Cancer Biomarkers, Prevention and TreatmentCancer CenterCollaborative Innovation Center for Cancer Personalized MedicineNanjing Medical UniversityNanjingChina
| | - David C. Christiani
- Department of Environmental HealthHarvard T.H. Chan School of Public HealthBostonMAUSA,Pulmonary and Critical Care DivisionDepartment of MedicineMassachusetts General Hospital and Harvard Medical SchoolBostonMAUSA
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Liu Y, Mao C, Liu S, Xiao D, Shi Y, Tao Y. Proline dehydrogenase in cancer: apoptosis, autophagy, nutrient dependency and cancer therapy. Amino Acids 2021; 53:1891-1902. [PMID: 34283310 DOI: 10.1007/s00726-021-03032-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 06/27/2021] [Indexed: 01/03/2023]
Abstract
L-proline catabolism is emerging as a key pathway that is critical to cellular metabolism, growth, survival, and death. Proline dehydrogenase (PRODH) enzyme, which catalyzes the first step of proline catabolism, has diverse functional roles in regulating many pathophysiological processes, including apoptosis, autophagy, cell senescence, and cancer metastasis. Notably, accumulated evidence demonstrated that PRODH plays complex role in many types of cancers. In this review, we briefly introduce the function of PRODH, then its expression in different types of cancer. We next discuss the regulation of PRODH in cancer, the downstream pathways of PRODH and the therapies that are under investigation. Finally, we propose novel insights for future perspectives on the modulation of PRODH.
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Affiliation(s)
- Yating Liu
- Postdoctoral Research Station of Clinical Medicine & Department of Hematology and Critical Care Medicine, Central South University, the 3rd Xiangya Hospital, Changsha, 410000, People's Republic of China.,Department of Pathology, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Xiangya Hospital, Central South University, Hunan, 410078, China.,NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, Changsha, 410078, Hunan, China
| | - Chao Mao
- Department of Pathology, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Xiangya Hospital, Central South University, Hunan, 410078, China.,NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, Changsha, 410078, Hunan, China
| | - Shuang Liu
- Department of Oncology, Institute of Medical Sciences, Center for Geriatric Disorders, National Clinical Research, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Desheng Xiao
- Department of Pathology, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Xiangya Hospital, Central South University, Hunan, 410078, China. .,NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, Changsha, 410078, Hunan, China.
| | - Ying Shi
- Department of Pathology, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Xiangya Hospital, Central South University, Hunan, 410078, China. .,NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, Changsha, 410078, Hunan, China.
| | - Yongguang Tao
- Department of Pathology, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Xiangya Hospital, Central South University, Hunan, 410078, China. .,NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, Changsha, 410078, Hunan, China. .,Hunan Key Laboratory of Early Diagnosis and Precision Therapy in Lung Cancer, Second Xiangya Hospital, Central South University, Changsha, 410011, China.
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