1
|
E J, Liu SY, Ma DN, Zhang GQ, Cao SL, Li B, Lu XH, Luo HY, Bao L, Lan XM, Fu RG, Zheng YL. Nanopore-based full-length transcriptome sequencing for understanding the underlying molecular mechanisms of rapid and slow progression of diabetes nephropathy. BMC Med Genomics 2024; 17:246. [PMID: 39379958 PMCID: PMC11463056 DOI: 10.1186/s12920-024-02006-2] [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: 11/17/2023] [Accepted: 09/05/2024] [Indexed: 10/10/2024] Open
Abstract
BACKGROUND Diabetic nephropathy (DN) has been a major factor in the outbreak of end-stage renal disease for decades. As the underlying mechanisms of DN development remains unclear, there is no ideal methods for the diagnosis and therapy. OBJECTIVE We aimed to explore the key genes and pathways that affect the rate progression of DN. METHODS Nanopore-based full-length transcriptome sequencing was performed with serum samples from DN patients with slow progression (DNSP, n = 5) and rapid progression (DNRP, n = 6). RESULTS Here, transcriptome proclaimed 22,682 novel transcripts and obtained 45,808 simple sequence repeats, 1,815 transcription factors, 5,993 complete open reading frames, and 1,050 novel lncRNA from the novel transcripts. Moreover, a total of 341 differentially expressed transcripts (DETs) and 456 differentially expressed genes (DEGs) between the DNSP and DNRP groups were identified. Functional analyses showed that DETs mainly involved in ferroptosis-related pathways such as oxidative phosphorylation, iron ion binding, and mitophagy. Moreover, Functional analyses revealed that DEGs mainly involved in oxidative phosphorylation, lipid metabolism, ferroptosis, autophagy/mitophagy, apoptosis/necroptosis pathway. CONCLUSION Collectively, our study provided a full-length transcriptome data source for the future DN research, and facilitate a deeper understanding of the molecular mechanisms underlying the differences in fast and slow progression of DN.
Collapse
Affiliation(s)
- Jing E
- Department of Nephrology, People's Hospital of Ningxia Hui Autonomous Region, People's Hospital of Ningxia Hui Autonomous Region, No.157, West 5th Road, Yinchuan, 750002, China
- Department of clinical medicine, Xi'an Jiaotong University, Xi'an, China
| | - Shun-Yao Liu
- Department of Nephrology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Institute of Nephrology, Jinan, China
| | - Dan-Na Ma
- Department of Nephrology, People's Hospital of Ningxia Hui Autonomous Region, People's Hospital of Ningxia Hui Autonomous Region, No.157, West 5th Road, Yinchuan, 750002, China
- Department of clinical medicine, Xi'an Jiaotong University, Xi'an, China
| | - Guo-Qing Zhang
- Department of Nephrology, People's Hospital of Ningxia Hui Autonomous Region, People's Hospital of Ningxia Hui Autonomous Region, No.157, West 5th Road, Yinchuan, 750002, China
- The Third Clinical Medical College of Ningxia Medical University, Yinchuan, China
| | - Shi-Lu Cao
- Department of Nephrology, Chengdu first people's hospital, Chengdu, Sichuan, 610000, China
| | - Bo Li
- Department of Nephrology, People's Hospital of Ningxia Hui Autonomous Region, People's Hospital of Ningxia Hui Autonomous Region, No.157, West 5th Road, Yinchuan, 750002, China
- Department of clinical medicine, Xi'an Jiaotong University, Xi'an, China
| | - Xiao-Hua Lu
- Department of Nephrology, People's Hospital of Ningxia Hui Autonomous Region, People's Hospital of Ningxia Hui Autonomous Region, No.157, West 5th Road, Yinchuan, 750002, China
| | - Hong-Yan Luo
- Department of Nephrology, People's Hospital of Ningxia Hui Autonomous Region, People's Hospital of Ningxia Hui Autonomous Region, No.157, West 5th Road, Yinchuan, 750002, China
| | - Li Bao
- Department of Nephrology, People's Hospital of Ningxia Hui Autonomous Region, People's Hospital of Ningxia Hui Autonomous Region, No.157, West 5th Road, Yinchuan, 750002, China
| | - Xiao-Mei Lan
- Department of clinical medicine, Xi'an Jiaotong University, Xi'an, China
- Department of Geriatrics, People's Hospital of Ningxia Hui Autonomous Region, Yinchuan, China
| | - Rong-Guo Fu
- Department of Nephrology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.
| | - Ya-Li Zheng
- Department of Nephrology, People's Hospital of Ningxia Hui Autonomous Region, People's Hospital of Ningxia Hui Autonomous Region, No.157, West 5th Road, Yinchuan, 750002, China.
| |
Collapse
|
2
|
Syed RU, Alshammari MD, Banu H, Khojali WMA, Jafar M, Nagaraju P, Alshammari A. Targeting the autophagy-miRNA axis in prostate cancer: toward novel diagnostic and therapeutic strategies. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024; 397:7421-7437. [PMID: 38761210 DOI: 10.1007/s00210-024-03153-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 05/07/2024] [Indexed: 05/20/2024]
Abstract
Since prostate cancer is one of the leading causes of cancer-related death, a better understanding of the molecular pathways guiding its development is imperative. A key factor in prostate cancer is autophagy, a cellular mechanism that affects both cell survival and death. Autophagy is essential in maintaining cellular homeostasis. Autophagy is a physiological mechanism wherein redundant or malfunctioning cellular constituents are broken down and recycled. It is essential for preserving cellular homeostasis and is implicated in several physiological and pathological conditions, including cancer. Autophagy has been linked to metastasis, tumor development, and treatment resistance in prostate cancer. The deregulation of miRNAs related to autophagy appears to be a crucial element in the etiology of prostate cancer. These miRNAs influence the destiny of cancer cells by finely regulating autophagic mechanisms. Numerous investigations have emphasized the dual function of specific miRNAs in prostate cancer, which alter autophagy-related pathways to function as either tumor suppressors or oncogenes. Notably, miRNAs have been linked to the control of autophagy and the proliferation, apoptosis, and migration of prostate cancer cells. To create customized therapy approaches, it is imperative to comprehend the dynamic interplay between autophagy and miRNAs in prostate cancer. The identification of key miRNAs provides potential diagnostic and prognostic markers. Unraveling the complex network of lncRNAs, like PCA3, also expands the repertoire of molecular targets for therapeutic interventions. This review explores the intricate interplay between autophagy and miRNAs in prostate cancer, focusing on their regulatory roles in cellular processes ranging from survival to programmed cell death.
Collapse
Affiliation(s)
- Rahamat Unissa Syed
- Department of Pharmaceutics, College of Pharmacy, University of Hail, 81442, Hail, Saudi Arabia.
| | - Maali D Alshammari
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, 81442, Hail, Saudi Arabia
| | - Humera Banu
- Department of Clinical Nutrition, College of Applied Medical Sciences, University of Hail, Hail, Kingdom of Saudi Arabia
| | - Weam M A Khojali
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, 81442, Hail, Saudi Arabia
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Omdurman Islamic University, Omdurman, 14415, Sudan
| | - Mohammed Jafar
- Department of Pharmaceutics, College of Clinical Pharmacy, Imam Abdulrahman Bin Faisal University, P. O. Box 1982, Dammam, 34212, Saudi Arabia.
| | - Potnuri Nagaraju
- Department of Pharmaceutics, Mandesh Institute of Pharmaceutical Science and Research Center, Mhaswad, Maharashtra, India
| | - Alia Alshammari
- Department of Pharmaceutics, College of Pharmacy, University of Hail, 81442, Hail, Saudi Arabia
| |
Collapse
|
3
|
Rogov VV, Nezis IP, Tsapras P, Zhang H, Dagdas Y, Noda NN, Nakatogawa H, Wirth M, Mouilleron S, McEwan DG, Behrends C, Deretic V, Elazar Z, Tooze SA, Dikic I, Lamark T, Johansen T. Atg8 family proteins, LIR/AIM motifs and other interaction modes. AUTOPHAGY REPORTS 2023; 2:27694127.2023.2188523. [PMID: 38214012 PMCID: PMC7615515 DOI: 10.1080/27694127.2023.2188523] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
The Atg8 family of ubiquitin-like proteins play pivotal roles in autophagy and other processes involving vesicle fusion and transport where the lysosome/vacuole is the end station. Nuclear roles of Atg8 proteins are also emerging. Here, we review the structural and functional features of Atg8 family proteins and their protein-protein interaction modes in model organisms such as yeast, Arabidopsis, C. elegans and Drosophila to humans. Although varying in number of homologs, from one in yeast to seven in humans, and more than ten in some plants, there is a strong evolutionary conservation of structural features and interaction modes. The most prominent interaction mode is between the LC3 interacting region (LIR), also called Atg8 interacting motif (AIM), binding to the LIR docking site (LDS) in Atg8 homologs. There are variants of these motifs like "half-LIRs" and helical LIRs. We discuss details of the binding modes and how selectivity is achieved as well as the role of multivalent LIR-LDS interactions in selective autophagy. A number of LIR-LDS interactions are known to be regulated by phosphorylation. New methods to predict LIR motifs in proteins have emerged that will aid in discovery and analyses. There are also other interaction surfaces than the LDS becoming known where we presently lack detailed structural information, like the N-terminal arm region and the UIM-docking site (UDS). More interaction modes are likely to be discovered in future studies.
Collapse
Affiliation(s)
- Vladimir V. Rogov
- Institute for Pharmaceutical Chemistry, Department of Biochemistry, Chemistry and Pharmacy, Goethe University, 60438 Frankfurt, am Main, and Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe University, 60438 Frankfurt am Main, Germany
| | - Ioannis P. Nezis
- School of Life Sciences, University of Warwick, CV4 7AL Coventry, UK
| | | | - Hong Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China and College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yasin Dagdas
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Nobuo N. Noda
- Institute for Genetic Medicine, Hokkaido University, Kita 15, Nishi 7, Kita-ku, Sapporo 060-0815, Japan
| | - Hitoshi Nakatogawa
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Martina Wirth
- Molecular Cell Biology of Autophagy, The Francis Crick Institute, London, UK
| | - Stephane Mouilleron
- Structural Biology Science Technology Platform, The Francis Crick Institute, London, UK
| | | | - Christian Behrends
- Munich Cluster of Systems Neurology, Ludwig-Maximilians-Universität München, München, Germany
| | - Vojo Deretic
- Autophagy, Inflammation and Metabolism Center of Biochemical Research Excellence, Albuquerque, NM and Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM
| | - Zvulun Elazar
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Sharon A. Tooze
- Molecular Cell Biology of Autophagy, The Francis Crick Institute, London, UK
| | - Ivan Dikic
- Institute of Biochemistry II, Medical Faculty, Goethe-University, Frankfurt am Main, and Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | - Trond Lamark
- Autophagy Research Group, Department of Medical Biology, University of Tromsø - The Arctic University of Norway, Tromsø, Norway
| | - Terje Johansen
- Autophagy Research Group, Department of Medical Biology, University of Tromsø - The Arctic University of Norway, Tromsø, Norway
| |
Collapse
|