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Sun Z, Wang J, Fan Z, Yang Y, Meng X, Ma Z, Niu J, Guo R, Tran LJ, Zhang J, Jiang T, Liu Y, Yang Q, Ma B. Investigating the prognostic role of lncRNAs associated with disulfidptosis-related genes in clear cell renal cell carcinoma. J Gene Med 2024; 26:e3608. [PMID: 37897262 DOI: 10.1002/jgm.3608] [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: 06/20/2023] [Revised: 09/05/2023] [Accepted: 09/20/2023] [Indexed: 10/30/2023] Open
Abstract
INTRODUCTION Renal cell carcinoma (RCC) is a grave malignancy that poses a significant global health burden with over 400,000 new cases annually. Disulfidptosis, a newly discovered programmed cell death process, is linked to the actin cytoskeleton, which plays a vital role in maintaining cell shape and survival. The role of disulfidptosis is poorly depicted in the clear cell histologic variant of RCC (ccRCC). METHODS Three sets of ccRCC cohorts, ICGC_RECA-EU (n = 91), GSE76207 (n = 32) and TCGA-KIRC (n = 607), were included in our study, the batch effect of which was removed using the "combat" function. Correlation was calculated using the "rcorr" function of the "Hmisc" package for Pearson analysis, which was visualized using the "pheatmap" package. Principal component analysis was performed by the "vegan" package, visualized using the "scatterplot3d" package. Long non-coding RNAs (lncRNAs) associated with disulfidptosis were screened out using least absolute shrinkage and selection operator (LASSO) and COX analysis. Tumor mutation, immune landscaping and immunotherapy prediction were performed for further characterization of two risk groups. RESULTS A total of 1822 disulfidptosis-related lncRNAs was selected, among which 308 lncRNAs were found to be significantly associated with the clinical outcome of ccRCC patients. We retained 11 disulfidptosis-related lncRNAs, namely, AP000439.3, RP11-417E7.1, RP11-119D9.1, LINC01510, SNHG3, AC156455.1, RP11-291B21.2, EMX2OS, AC093850.2, HAGLR and RP11-389C8.2, through LASSO and COX analysis for prognosis model construction, which displayed satisfactory accuracy (area under the curve, AUC, values all above 0.6 in multiple cohorts) in stratification of ccRCC prognosis. A nomogram model was constructed by integrating clinical factors with risk score, which further enhanced the prediction efficacy (AUC values all above 0.7 in multiple cohorts). We found that patients of male gender, higher clinical stages and advanced pathological T stage were inclined to have higher risk score values. Dactinomycin_1911, Vinblastine_1004, Daporinad_1248 and Vinorelbine_2048 were identified as promising candidate drugs for treating ccRCC patients of higher risk score value. Moreover, patients of higher risk value were prone to be resistant to immunotherapy. CONCLUSION We developed a prognosis predicting model based on 11 selected disulfidptosis-related lncRNAs, the efficacy of which was verified in different cohorts. Furthermore, we delineated an intricate portrait of tumor mutation, immune topography and pharmacosensitivity evaluations within disparate risk stratifications.
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Affiliation(s)
- Zhou Sun
- Department of Urology, Xiaogan Hospital Affiliated to Wuhan University of Science and Technology, Xiaogan, China
- Department of Urology, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Jie Wang
- Department of Urology, China-Japan Union Hospital of Jilin University, Changchun, China
- Department of Urology, The Second People's Hospital of Meishan City, Meishan, China
| | - Zheqi Fan
- Department of Urology, Xiaogan Hospital Affiliated to Wuhan University of Science and Technology, Xiaogan, China
| | - Yongjin Yang
- Department of Urology, The Second Hospital of Lanzhou University, Lanzhou, China
- Second Clinical School, Lanzhou University, Lanzhou, China
| | - Xiangdi Meng
- Department of Urology, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Zhaosen Ma
- Department of Urology, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Jiqiang Niu
- Department of Urology, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Rui Guo
- Department of Urology, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Lisa Jia Tran
- Department of General, Visceral, and Transplant Surgery, Ludwig Maximilian University of Munich, Munich, Germany
| | - Jing Zhang
- Division of Basic Biomedical Sciences, The University of South Dakota Sanford School of Medicine, Vermillion, South Dakota, USA
| | - Tianxiao Jiang
- Department of General, Visceral, and Transplant Surgery, Ludwig Maximilian University of Munich, Munich, Germany
| | - Yunfei Liu
- Department of General, Visceral, and Transplant Surgery, Ludwig Maximilian University of Munich, Munich, Germany
| | - Qiwei Yang
- Depanrtment of Urology, The Third Affiliated Hospital of Naval Military Medical University (Eastern Hepatobiliary Surgery Hospital), Shanghai, China
| | - Baoluo Ma
- Department of Urology, China-Japan Union Hospital of Jilin University, Changchun, China
- Department of Urology, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, China
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Jiao J, Yao L, Fu JX, Lu Y, Gai QY, Feng X, He XJ, Cao RZ, Fu YJ. Cocultivation of pigeon pea hairy root cultures and Aspergillus for the enhanced production of cajaninstilbene acid. Appl Microbiol Biotechnol 2023; 107:1931-1946. [PMID: 36800029 DOI: 10.1007/s00253-023-12437-z] [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: 11/21/2022] [Revised: 01/23/2023] [Accepted: 02/04/2023] [Indexed: 02/18/2023]
Abstract
Pigeon pea hairy root cultures (PPHRCs) have been proven to be a promising alternative for the production of health-beneficial phenolic compounds, such as the most important health-promoting compound, i.e., cajaninstilbene acid (CSA). In this study, PPHRCs were cocultured with live Aspergillus fungi for further improving phenolic productivity via biological elicitation. Aspergillus oryzae CGMCC 3.951 (AO 3.951) was found to be the optimal fungus that could achieve the maximum increment of CSA (10.73-fold increase) in 42-day-old PPHRCs under the inoculum size of mycelia 0.50% and cocultivation time 36 h. More precisely, the contents of CSA in hairy roots and culture media after fungal elicitation increased by 9.87- and 62.18-fold over control, respectively. Meanwhile, the contents of flavonoid glycosides decreased, while aglycone yields increased upon AO 3.951 elicitation. Moreover, AO 3.951 could trigger the oxidative stress and pathogen defense response thus activating the expression of biosynthesis- and ABC transporter-related genes, which contributed to the intracellular accumulation and extracellular secretion of phenolic compounds (especially CSA) in PPHRCs. And PAL2, 4CL2, STS1, and I3'H were likely to be the potential key enzyme genes regulating the biosynthesis of CSA, and ABCB11X1-1, ABCB11, and ABCG24X2 were closely related to the transmembrane transport of CSA. Overall, the cocultivation approach could make PPHRCs more commercially attractive for the production of high-value phenolic compounds such as CSA and flavonoid aglycones in nutraceutical/medicinal fields. And the elucidation of crucial biosynthesis and transport genes was important for systematic metabolic engineering aimed at increasing CSA productivity. KEY POINTS: • Cocultivation of PPHRCs and live fungi was to enhance CSA production and secretion. • PPHRCs augmented CSA productivity 10.73-fold when cocultured with AO 3.951 mycelia. • Several biosynthesis and transport genes related to CSA production were clarified.
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Affiliation(s)
- Jiao Jiao
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, 150040, People's Republic of China
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin, 150040, People's Republic of China
- Engineering Research Center of Forest Bio-Preparation, Ministry of Education, Northeast Forestry University, Harbin, 150040, People's Republic of China
- Heilongjiang Provincial Key Laboratory of Ecological Utilization of Forestry-Based Active Substances, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Lan Yao
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, 150040, People's Republic of China
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin, 150040, People's Republic of China
- Engineering Research Center of Forest Bio-Preparation, Ministry of Education, Northeast Forestry University, Harbin, 150040, People's Republic of China
- Heilongjiang Provincial Key Laboratory of Ecological Utilization of Forestry-Based Active Substances, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Jin-Xian Fu
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, 150040, People's Republic of China
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin, 150040, People's Republic of China
- Engineering Research Center of Forest Bio-Preparation, Ministry of Education, Northeast Forestry University, Harbin, 150040, People's Republic of China
- Heilongjiang Provincial Key Laboratory of Ecological Utilization of Forestry-Based Active Substances, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Yao Lu
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, 150040, People's Republic of China
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin, 150040, People's Republic of China
- Engineering Research Center of Forest Bio-Preparation, Ministry of Education, Northeast Forestry University, Harbin, 150040, People's Republic of China
- Heilongjiang Provincial Key Laboratory of Ecological Utilization of Forestry-Based Active Substances, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Qing-Yan Gai
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, 150040, People's Republic of China.
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin, 150040, People's Republic of China.
- Engineering Research Center of Forest Bio-Preparation, Ministry of Education, Northeast Forestry University, Harbin, 150040, People's Republic of China.
- Heilongjiang Provincial Key Laboratory of Ecological Utilization of Forestry-Based Active Substances, Northeast Forestry University, Harbin, 150040, People's Republic of China.
| | - Xue Feng
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, 150040, People's Republic of China
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin, 150040, People's Republic of China
- Engineering Research Center of Forest Bio-Preparation, Ministry of Education, Northeast Forestry University, Harbin, 150040, People's Republic of China
- Heilongjiang Provincial Key Laboratory of Ecological Utilization of Forestry-Based Active Substances, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Xiao-Jia He
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, 150040, People's Republic of China
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin, 150040, People's Republic of China
- Engineering Research Center of Forest Bio-Preparation, Ministry of Education, Northeast Forestry University, Harbin, 150040, People's Republic of China
- Heilongjiang Provincial Key Laboratory of Ecological Utilization of Forestry-Based Active Substances, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Run-Ze Cao
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, 150040, People's Republic of China
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin, 150040, People's Republic of China
- Engineering Research Center of Forest Bio-Preparation, Ministry of Education, Northeast Forestry University, Harbin, 150040, People's Republic of China
- Heilongjiang Provincial Key Laboratory of Ecological Utilization of Forestry-Based Active Substances, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Yu-Jie Fu
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, 150040, People's Republic of China
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin, 150040, People's Republic of China
- Engineering Research Center of Forest Bio-Preparation, Ministry of Education, Northeast Forestry University, Harbin, 150040, People's Republic of China
- Heilongjiang Provincial Key Laboratory of Ecological Utilization of Forestry-Based Active Substances, Northeast Forestry University, Harbin, 150040, People's Republic of China
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