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Datta N, Vp S, Parvathy K, A S S, Maliekal TT. ALDH1A1 as a marker for metastasis initiating cells: A mechanistic insight. Exp Cell Res 2024; 442:114213. [PMID: 39173941 DOI: 10.1016/j.yexcr.2024.114213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 08/12/2024] [Accepted: 08/14/2024] [Indexed: 08/24/2024]
Abstract
Since metastasis accounts for the majority of cancer morbidity and mortality, attempts are focused to block metastasis and metastasis initiating cellular programs. It is generally believed that hypoxia, reactive oxygen species (ROS) and the dysregulated redox pathways regulate metastasis. Although induction of epithelial to mesenchymal transition (EMT) can initiate cell motility to different sites other than the primary site, the initiation of a secondary tumor at a distant site depends on self-renewal property of cancer stem cell (CSC) property. That subset of metastatic cells possessing CSC property are referred to as metastasis initiating cells (MICs). Among the different cellular intermediates regulating metastasis in response to hypoxia by inducing EMT and self-renewal property, ALDH1A1 is a critical molecule, which can be used as a marker for MICs in a wide variety of malignancies. The cytosolic ALDHs can irreversibly convert retinal to retinoic acid (RA), which initiates RA signaling, important for self-renewal and EMT. The metastasis permissive tumor microenvironment increases the expression of ALDH1A1, primarily through HIF1α, and leads to metabolic reprograming through OXPHOS regulation. The ALDH1A1 expression and its high activity can reprogram the cancer cells with the transcriptional upregulation of several genes, involved in EMT through RA signaling to manifest hybrid EMT or Hybrid E/M phenotype, which is important for acquiring the characteristics of MICs. Thus, the review on this topic highlights the use of ALDH1A1 as a marker for MICs, and reporters for the marker can be effectively used to trace the population in mouse models, and to screen drugs that target MICs.
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Affiliation(s)
- Nandini Datta
- Cancer Research, Rajiv Gandhi Centre for Biotechnology (BRIC-RGCB), Thiruvananthapuram, Kerala, 695014, India
| | - Snijesh Vp
- Division of Molecular Medicine, St. John's Research Institute, St John's National Academy of Health Sciences, Bangalore, 560034, India
| | - K Parvathy
- Cancer Research, Rajiv Gandhi Centre for Biotechnology (BRIC-RGCB), Thiruvananthapuram, Kerala, 695014, India
| | - Sneha A S
- Cancer Research, Rajiv Gandhi Centre for Biotechnology (BRIC-RGCB), Thiruvananthapuram, Kerala, 695014, India
| | - Tessy Thomas Maliekal
- Cancer Research, Rajiv Gandhi Centre for Biotechnology (BRIC-RGCB), Thiruvananthapuram, Kerala, 695014, India; Regional Centre for Biotechnology, Faridabad, Haryana 121001, India.
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Yang S, Liu D, Song Y, Liang Y, Yu H, Zuo Y. Designing a structure-function alphabet of helix based on reduced amino acid clusters. Arch Biochem Biophys 2024; 754:109942. [PMID: 38387828 DOI: 10.1016/j.abb.2024.109942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 02/16/2024] [Accepted: 02/19/2024] [Indexed: 02/24/2024]
Abstract
Several simple secondary structures could form complex and diverse functional proteins, meaning that secondary structures may contain a lot of hidden information and are arranged according to certain principles, to carry enough information of functional specificity and diversity. However, these inner information and principles have not been understood systematically. In our study, we designed a structure-function alphabet of helix based on reduced amino acid clusters to describe the typical features of helices and delve into the information. Firstly, we selected 480 typical helices from membrane proteins, zymoproteins, transcription factors, and other proteins to define and calculate the interval range, and the helices are classified in terms of hydrophilicity, charge and length: (1) hydrophobic helix (≤43%), amphiphilic helix (43%∼71%), and hydrophilic helix (≥71%). (2) positive helix, negative helix, electrically neutral helix and uncharged helix. (3) short helix (≤8 aa), medium-length helix (9-28 aa), and long helix (≥29 aa). Then, we designed an alphabet containing 36 triplet codes according to the above classification, so that the main features of each helix can be represented by only three letters. This alphabet not only preliminarily defined the helix characteristics, but also greatly reduced the informational dimension of protein structure. Finally, we present an application example to demonstrate the value of the structure-function alphabet in protein functional determination and differentiation.
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Affiliation(s)
- Siqi Yang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010021, China
| | - Dongyang Liu
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; University of Chinese Academy of Sciences, Beijing, China
| | - Yancheng Song
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010021, China
| | - Yuchao Liang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010021, China
| | - Haoyu Yu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010021, China
| | - Yongchun Zuo
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, 010021, China.
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Tang C, Xu J, Zheng M, Qian D, Gao Z, Li X, Zhang W. Potential clinical significance of ALDH3B1 in auxiliary diagnosis of gastric cancer. Biomark Med 2024; 18:15-23. [PMID: 38334412 DOI: 10.2217/bmm-2023-0418] [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] [Indexed: 02/10/2024] Open
Abstract
Objective: This research aimed to explore a diagnostic method based on serum ALDH3B1 and to evaluate the clinical diagnostic efficacy in gastric cancer (GC) by comparing it with the traditional GC diagnostic method, the carcinoembryonic protein (CEA) assay. Methods: Serum samples were collected from 70 healthy volunteers and various patients (GC: 76, benign gastric lesions: 20, postoperative: 37, recurrence: 56). The diagnostic efficacy of serum ALDH3B1, CEA and the co-diagnosis were evaluated by receiver operating characteristic curve. ALDH3B1 protein levels were evaluated by western blot. Results: The co-diagnosis of ALDH3B1 and CEA had the highest diagnostic efficacy (area under the curve = 0.841). Conclusion: Serum ALDH3B1 may be used as an auxiliary diagnostic biomarker for GC, and its co-diagnosis with CEA can improve diagnostic efficacy.
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Affiliation(s)
- Chenxue Tang
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, China
| | - Jing Xu
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, China
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, China
- Medical School of Nantong University, Nantong University, Nantong, 226001, China
| | - Ming Zheng
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, China
| | - Dongchen Qian
- Department of Anesthesiology, Affiliated Hospital of Nantong University, Nantong, 226001, China
| | - Zhihua Gao
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, China
| | - Xian Li
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, China
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, China
- Medical School of Nantong University, Nantong University, Nantong, 226001, China
| | - Weiwei Zhang
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, China
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, China
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Study of ALDH from Thermus thermophilus-Expression, Purification and Characterisation of the Non-Substrate Specific, Thermophilic Enzyme Displaying Both Dehydrogenase and Esterase Activity. Cells 2021; 10:cells10123535. [PMID: 34944041 PMCID: PMC8699947 DOI: 10.3390/cells10123535] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/10/2021] [Accepted: 12/11/2021] [Indexed: 01/16/2023] Open
Abstract
Aldehyde dehydrogenases (ALDH), found in all kingdoms of life, form a superfamily of enzymes that primarily catalyse the oxidation of aldehydes to form carboxylic acid products, while utilising the cofactor NAD(P)+. Some superfamily members can also act as esterases using p-nitrophenyl esters as substrates. The ALDHTt from Thermus thermophilus was recombinantly expressed in E. coli and purified to obtain high yields (approximately 15–20 mg/L) and purity utilising an efficient heat treatment step coupled with IMAC and gel filtration chromatography. The use of the heat treatment step proved critical, in its absence decreased yield of 40% was observed. Characterisation of the thermophilic ALDHTt led to optimum enzymatic working conditions of 50 °C, and a pH of 8. ALDHTt possesses dual enzymatic activity, with the ability to act as a dehydrogenase and an esterase. ALDHTt possesses broad substrate specificity, displaying activity for a range of aldehydes, most notably hexanal and the synthetic dialdehyde, terephthalaldehyde. Interestingly, para-substituted benzaldehydes could be processed efficiently, but ortho-substitution resulted in no catalytic activity. Similarly, ALDHTt displayed activity for two different esterase substrates, p-nitrophenyl acetate and p-nitrophenyl butyrate, but with activities of 22.9% and 8.9%, respectively, compared to the activity towards hexanal.
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Impaired skin barrier function due to reduced ω- O-acylceramide levels in a mouse model of Sjögren-Larsson syndrome. Mol Cell Biol 2021; 41:e0035221. [PMID: 34370553 DOI: 10.1128/mcb.00352-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sjögren-Larsson syndrome (SLS) is an inherited neurocutaneous disorder whose causative gene encodes the fatty aldehyde dehydrogenase ALDH3A2. To date, the detailed molecular mechanism of the skin pathology of SLS has remained largely unclear. We generated double knockout (DKO) mice for Aldh3a2 and its homolog Aldh3b2 (a pseudogene in humans). These mice showed hyperkeratosis and reduced fatty aldehyde dehydrogenase activity and skin barrier function. The levels of ω-O-acylceramides (acylceramides), which are specialized ceramides essential for skin barrier function, in the epidermis of DKO mice were about 60% of those in wild type mice. In the DKO mice, levels of acylceramide precursors (ω-hydroxy ceramides and triglycerides) were increased, suggesting that the final step of acylceramide production was inhibited. A decrease in acylceramide levels was also observed in human immortalized keratinocytes lacking ALDH3A2. Differentiated keratinocytes prepared from the DKO mice exhibited impaired long-chain base metabolism. Based on these results, we propose that the long-chain-base-derived fatty aldehydes that accumulate in DKO mice and SLS patients attack and inhibit the enzyme involved in the final step of acylceramide. Our findings provide insight into the pathogenesis of the skin symptoms of SLS, i.e., decreased acylceramide production, and its molecular mechanism.
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Song W, He X, Gong P, Yang Y, Huang S, Zeng Y, Wei L, Zhang J. Glycolysis-Related Gene Expression Profiling Screen for Prognostic Risk Signature of Pancreatic Ductal Adenocarcinoma. Front Genet 2021; 12:639246. [PMID: 34249078 PMCID: PMC8261051 DOI: 10.3389/fgene.2021.639246] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 05/25/2021] [Indexed: 12/21/2022] Open
Abstract
Objective: Pancreatic ductal adenocarcinoma (PDAC) is highly lethal. Although progress has been made in the treatment of PDAC, its prognosis remains unsatisfactory. This study aimed to develop novel prognostic genes related to glycolysis in PDAC and to apply these genes to new risk stratification. Methods: In this study, based on the Cancer Genome Atlas (TCGA) PAAD cohort, the expression level of glycolysis-related gene at mRNA level in PAAD and its relationship with prognosis were analyzed. Non-negative matrix decomposition (NMF) clustering was used to cluster PDAC patients according to glycolytic genes. Prognostic glycolytic genes, screened by univariate Cox analysis and LASSO regression analysis were established to calculate risk scores. The differentially expressed genes (DEGs) in the high-risk group and the low-risk group were analyzed, and the signal pathway was further enriched to analyze the correlation between glycolysis genes. In addition, based on RNA-seq data, CIBERSORT was used to evaluate the infiltration degree of immune cells in PDAC samples, and ESTIMATE was used to calculate the immune score of the samples. Results: A total of 319 glycolysis-related genes were retrieved, and all PDAC samples were divided into two clusters by NMF cluster analysis. Survival analysis showed that PDAC patients in cluster 1 had shorter survival time and worse prognosis compared with cluster 2 samples (P < 0.001). A risk prediction model based on 11 glycolysis genes was constructed, according to which patients were divided into two groups, with significantly poorer prognosis in high-risk group than in low-risk group (P < 0.001). Both internal validation and external dataset validation demonstrate good predictive ability of the model (AUC = 0.805, P < 0.001; AUC = 0.763, P < 0.001). Gene aggregation analysis showed that DEGs highly expressed in high-risk group were mainly concentrated in the glycolysis level, immune status, and tumor cell proliferation, etc. In addition, the samples in high-risk group showed immunosuppressed status and infiltrated by relatively more macrophages and less CD8+T cell. Conclusions: These findings suggested that the gene signature based on glycolysis-related genes had potential diagnostic, therapeutic, and prognostic value for PDAC.
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Affiliation(s)
- Wenjing Song
- Department of Breast and Thyroid Surgery, Hubei Key Laboratory of Tumor Biological Behaviors, Hubei Cancer Clinical Study Center, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Xin He
- Department of Breast and Thyroid Surgery, Hubei Key Laboratory of Tumor Biological Behaviors, Hubei Cancer Clinical Study Center, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Pengju Gong
- Department of Breast and Thyroid Surgery, Hubei Key Laboratory of Tumor Biological Behaviors, Hubei Cancer Clinical Study Center, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Yan Yang
- Department of Breast and Thyroid Surgery, Hubei Key Laboratory of Tumor Biological Behaviors, Hubei Cancer Clinical Study Center, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Sirui Huang
- Department of Breast and Thyroid Surgery, Hubei Key Laboratory of Tumor Biological Behaviors, Hubei Cancer Clinical Study Center, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Yifan Zeng
- Department of Breast and Thyroid Surgery, Hubei Key Laboratory of Tumor Biological Behaviors, Hubei Cancer Clinical Study Center, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Lei Wei
- Department of Pathology and Pathophysiology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Jingwei Zhang
- Department of Breast and Thyroid Surgery, Hubei Key Laboratory of Tumor Biological Behaviors, Hubei Cancer Clinical Study Center, Zhongnan Hospital, Wuhan University, Wuhan, China
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Cunha DL, Richardson R, Tracey-White D, Abbouda A, Mitsios A, Horneffer-van der Sluis V, Takis P, Owen N, Skinner J, Welch AA, Moosajee M. REP1 deficiency causes systemic dysfunction of lipid metabolism and oxidative stress in choroideremia. JCI Insight 2021; 6:146934. [PMID: 33755601 PMCID: PMC8262314 DOI: 10.1172/jci.insight.146934] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/17/2021] [Indexed: 12/17/2022] Open
Abstract
Choroideremia (CHM) is an X-linked recessive chorioretinal dystrophy caused by mutations in CHM, encoding for Rab escort protein 1 (REP1). Loss of functional REP1 leads to the accumulation of unprenylated Rab proteins and defective intracellular protein trafficking, the putative cause for photoreceptor, retinal pigment epithelium (RPE), and choroidal degeneration. CHM is ubiquitously expressed, but adequate prenylation is considered to be achieved, outside the retina, through the isoform REP2. Recently, the possibility of systemic features in CHM has been debated; therefore, in this study, whole metabolomic analysis of plasma samples from 25 CHM patients versus age- and sex-matched controls was performed. Results showed plasma alterations in oxidative stress-related metabolites, coupled with alterations in tryptophan metabolism, leading to significantly raised serotonin levels. Lipid metabolism was disrupted with decreased branched fatty acids and acylcarnitines, suggestive of dysfunctional lipid oxidation, as well as imbalances of several sphingolipids and glycerophospholipids. Targeted lipidomics of the chmru848 zebrafish provided further evidence for dysfunction, with the use of fenofibrate over simvastatin circumventing the prenylation pathway to improve the lipid profile and increase survival. This study provides strong evidence for systemic manifestations of CHM and proposes potentially novel pathomechanisms and targets for therapeutic consideration.
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Affiliation(s)
- Dulce Lima Cunha
- Department of Development, Ageing and Disease, UCL Institute of Ophthalmology, London, United Kingdom
| | - Rose Richardson
- Department of Development, Ageing and Disease, UCL Institute of Ophthalmology, London, United Kingdom
| | - Dhani Tracey-White
- Department of Development, Ageing and Disease, UCL Institute of Ophthalmology, London, United Kingdom
| | - Alessandro Abbouda
- Department of Development, Ageing and Disease, UCL Institute of Ophthalmology, London, United Kingdom
- Department of Genetics, Moorfields Eye Hospital NHS Foundation Trust, London, United Kingdom
| | - Andreas Mitsios
- Department of Development, Ageing and Disease, UCL Institute of Ophthalmology, London, United Kingdom
- Department of Genetics, Moorfields Eye Hospital NHS Foundation Trust, London, United Kingdom
| | | | - Panteleimon Takis
- MRC-NIHR National Phenome Centre, Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Nicholas Owen
- Department of Development, Ageing and Disease, UCL Institute of Ophthalmology, London, United Kingdom
| | - Jane Skinner
- Department of Public Health & Primary Care, Norwich Medical School, Norfolk, United Kingdom
| | - Ailsa A. Welch
- Department of Public Health & Primary Care, Norwich Medical School, Norfolk, United Kingdom
| | - Mariya Moosajee
- Department of Development, Ageing and Disease, UCL Institute of Ophthalmology, London, United Kingdom
- Department of Genetics, Moorfields Eye Hospital NHS Foundation Trust, London, United Kingdom
- Department of Ophthalmology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
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Wang M, Xu G, Tang Y, Su S, Wang Y, Zhu Z. Investigation of the Molecular Mechanisms of Antioxidant Damage and Immune Response Downregulation in Liver of Coilia nasus Under Starvation Stress. Front Endocrinol (Lausanne) 2021; 12:622315. [PMID: 33732214 PMCID: PMC7959721 DOI: 10.3389/fendo.2021.622315] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 01/08/2021] [Indexed: 01/11/2023] Open
Abstract
Commercial fishing of estuarine tapertail anchovy (Coilia nasus), an important anadromous fish species in the Yangtze River of China, has been prohibited due to the serious damage overfishing has caused to the wild population. Research regarding the energy metabolism is important for migratory fish to ensure the continuation of their existence. In this study, we performed, for the first time, a comparative transcriptome analysis of the liver of C. nasus subjected to long-term starvation stress. The results indicated that the damaging effects involved downregulation of the antioxidant capacity and immune response. The positive response to starvation involved upregulation of the anti-allergy and anticancer capacity, which supports the function of starvation in cancer inhibition, as has also been determined for human beings. This study revealed regulatory pathways, differentially expressed genes (DEGs), and mechanisms leading to damage of the liver in C. nasus affected by starvation. This research contributes information for the further study of the energy metabolism mechanism of C. nasus and provides a theoretical reference for starvation metabolism research of other fish species and even human beings.
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Affiliation(s)
- Meiyao Wang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
- Aquatic Animal Genome Center of Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Gangchun Xu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
- *Correspondence: Gangchun Xu, ; Yongkai Tang,
| | - Yongkai Tang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
- Aquatic Animal Genome Center of Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
- *Correspondence: Gangchun Xu, ; Yongkai Tang,
| | - Shengyan Su
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
- Aquatic Animal Genome Center of Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Yinping Wang
- Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Changjiang River, Ministry of Agriculture and Rural Affairs, Wuxi, China
| | - Zhixiang Zhu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
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Sun H, Zhang M, Li L, Huang Z. ALDH3B1 Is an Independent Prognostic Biomarker of Lung Adenocarcinoma. Technol Cancer Res Treat 2020; 19:1533033820946018. [PMID: 32744175 PMCID: PMC7412899 DOI: 10.1177/1533033820946018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background: Lung cancer is the leading cause of cancer-related death, and adenocarcinoma is the most common type of lung cancer. Although emerging evidence implicates the role of several aldehyde dehydrogenases in cancer progression, the expression and clinical significance of aldehyde dehydrogenase 3B1 in lung adenocarcinoma has never been studied. Materials: In our study, the expression of aldehyde dehydrogenase 3B1 in 250 cases of lung adenocarcinoma was detected with immunohistochemistry, and the patients were further divided into subgroups with different aldehyde dehydrogenase 3B1 expression. Using real-time polymerase chain reaction, we investigated the aldehyde dehydrogenase 3B1 messenger RNA in 20 lung adenocarcinoma and paired normal lung tissues. With the χ2 test, we evaluated the clinical significance of aldehyde dehydrogenase 3B1 by analyzing its correlation with the clinicopathological factors. Propensity score matching was performed to balance the baseline of cohort. With univariate and multivariate analyses, we screened the prognostic factors of lung adenocarcinoma and identified the independent prognostic factors before and after the propensity score matching. Results: Aldehyde dehydrogenase 3B1 expression was significantly associated with the sex and age of patients, tumor size, and histological grade. High expression of aldehyde dehydrogenase 3B1 predicted the poor prognosis (P = .003). Moreover, male patients (P = .020), large tumor size (P = .009), advanced T stage (P = .001), positive lymphatic invasion (P < .001), and advanced tumor–node–metastasis stage (P < .001) were all the prognostic factors for unfavorable outcome. Aldehyde dehydrogenase 3B1 was an independent prognostic biomarker of lung adenocarcinoma, indicating the poor prognosis. In addition, after balancing the baseline characteristics by propensity score matching, we also demonstrated that aldehyde dehydrogenase 3B1 was an independent prognostic biomarker of lung adenocarcinoma (P = .007). Conclusions: Aldehyde dehydrogenase 3B1 was an independent prognostic biomarker of lung adenocarcinoma, indicating the unfavorable prognosis. Postoperative detection of aldehyde dehydrogenase 3B1 would help stratify the high-risk patients with lung adenocarcinoma and guide individual treatment.
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Affiliation(s)
- Hongmei Sun
- Department of Gastrointestinal Surgery, YIDU Central Hospital, Weifang, China.,Hongmei Sun and Mingying Zhang contributed equally to the paper
| | - Mingying Zhang
- Department of Child Healthcare, YIDU Central Hospital, Weifang, China.,Hongmei Sun and Mingying Zhang contributed equally to the paper
| | - Li Li
- Department of Respiratory Medicine, YIDU Central Hospital, Weifang, China
| | - Zongwen Huang
- Department of Respiratory Medicine, 970th Hospital of Chinese PLA, Weihai, China
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Holmes RS. Polyploidy among salmonid aldehyde dehydrogenase genes and proteins. Chem Biol Interact 2019; 303:22-26. [PMID: 30776359 DOI: 10.1016/j.cbi.2019.01.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 01/17/2019] [Accepted: 01/25/2019] [Indexed: 01/22/2023]
Abstract
Bioinformatic analyses of salmon (Salmo salar) ALDH amino acid sequences supported the presence of at least 30 ALDH genes, which is more than for any other higher vertebrate and is greater than the 19 human ALDH genes currently reported. These included 8 polyploid ALDH genes and proteins: ALDH1A2 (chromosomes 11 and 26); ALDH1L2 (chromosomes 7 and 17); ALDH2, encoding mitochondrial ALDH2 (chromosomes 2 and 5); ALDH3A2 (chromosomes 4, 9 and 20), for which evidence for 5 genes was obtained; ALDH3B1 (chromosomes 3, 6 and 24); ALDH4A1 (chromosomes 12 and 22); ALDH6A1 (chromosomes 1, 6 and 15); and ALDH18A1 (chromosomes 19 and 28). In contrast, 7 salmon ALDH gene families (ALDH1A1, ALDH1A3, ALDH5, ALDH7, ALDH8, ALDH9 and ALDH16) possessed only one gene family member. Phylogenetic studies of salmon and rainbow trout ALDH3A2 genes and proteins suggested that salmonid gene tetraploidy has occurred in at least 2 distinct stages of ALDH3A2 gene evolution.
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Affiliation(s)
- Roger S Holmes
- Griffith Institute for Drug Discovery and School of Environment and Science, Griffith University, Nathan, 4111, QLD, Australia.
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Yeast Mpo1 Is a Novel Dioxygenase That Catalyzes the α-Oxidation of a 2-Hydroxy Fatty Acid in an Fe 2+-Dependent Manner. Mol Cell Biol 2019; 39:MCB.00428-18. [PMID: 30530523 DOI: 10.1128/mcb.00428-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 12/02/2018] [Indexed: 01/05/2023] Open
Abstract
Phytosphingosine (PHS) is the major long-chain base component of sphingolipids in Saccharomyces cerevisiae The PHS metabolic pathway includes a fatty acid (FA) α-oxidation reaction. Recently, we identified the novel protein Mpo1, which is involved in PHS metabolism. However, the details of the FA α-oxidation reaction and the role of Mpo1 in PHS metabolism remained unclear. In the present study, we revealed that Mpo1 is involved in the α-oxidation of 2-hydroxy (2-OH) palmitic acid (C16:0-COOH) in the PHS metabolic pathway. Our in vitro assay revealed that not only the Mpo1-containing membrane fraction but also the soluble fraction was required for the α-oxidation of 2-OH C16:0-COOH. The addition of Fe2+ eliminated the need for the soluble fraction. Purified Mpo1 converted 2-OH C16:0-COOH to C15:0-COOH in the presence of Fe2+, indicating that Mpo1 is the enzyme body responsible for catalyzing the FA α-oxidation reaction. This reaction was also found to require an oxygen molecule. Our findings indicate that Mpo1 catalyzes the FA α-oxidation reaction as 2-OH fatty acid dioxygenase, mediated by iron(IV) peroxide. Although numerous Mpo1 homologs exist in bacteria, fungi, protozoa, and plants, their functions had not yet been clarified. However, our findings suggest that these family members function as dioxygenases.
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Identification of cancer-type specific expression patterns for active aldehyde dehydrogenase (ALDH) isoforms in ALDEFLUOR assay. Cell Biol Toxicol 2018; 35:161-177. [PMID: 30220009 PMCID: PMC6424948 DOI: 10.1007/s10565-018-9444-y] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Accepted: 08/16/2018] [Indexed: 12/26/2022]
Abstract
Aldehyde dehydrogenases (ALDHs) defend intracellular homeostasis by catalyzing the conversion of toxic aldehydes into non-toxic carboxylic acids, which is of particular importance to the self-renewal of stem cells and cancer stem cells. The widely used ALDEFLUOR assay was initially designed to indicate the activity of ALDH1A1 in leukemia and has been demonstrated to detect the enzyme activity of several other ALDH isoforms in various cancer types in recent years. However, it is still elusive which isoforms, among the 19 ALDH isoforms in human genome, are the potential contributors in catalyzing ALDEFLUOR assay in different cancers. In the current study, we performed a screening via overexpressing each ALDH isoform to assess their ability of catalyzing ALDEFLUOR assay. Our results demonstrate that nine isoforms are active in ALDEFLUOR assay, whose overexpression significantly increases ALDH-positive (ALDH+) population. Further analysis of the expression of these active isoforms in various cancers reveals cancer-type specific expression patterns, suggesting that different cancer types may exhibit ALDEFLUOR activity through expression of specific active ALDH isoforms. This study strongly indicates that a detailed elucidation of the functions for each active ALDH isoform in CSCs is necessary and important for a profound understanding of the underlying mechanisms of ALDH-associated stemness.
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Kanetake T, Sassa T, Nojiri K, Sawai M, Hattori S, Miyakawa T, Kitamura T, Kihara A. Neural symptoms in a gene knockout mouse model of Sjögren-Larsson syndrome are associated with a decrease in 2-hydroxygalactosylceramide. FASEB J 2018; 33:928-941. [PMID: 30085884 DOI: 10.1096/fj.201800291r] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Insulation by myelin lipids is essential to fast action potential conductivity: changes in their quality or amount can cause several neurologic disorders. Sjögren-Larsson syndrome (SLS) is one such disorder, which is caused by mutations in the fatty aldehyde dehydrogenase ALDH3A2. To date, the molecular mechanism underlying SLS pathology has remained unknown. In this study, we found that Aldh3a2 is expressed in oligodendrocytes and neurons in the mouse brain, and neurons of Aldh3a2 knockout (KO) mice exhibited impaired metabolism of the long-chain base, a component of sphingolipids. Aldh3a2 KO mice showed several abnormalities corresponding to SLS symptoms in behavioral tests, including increased paw slips on a balance beam and light-induced anxiety. In their brain tissue, 2-hydroxygalactosylceramide, an important lipid for myelin function and maintenance, was reduced by the inactivation of fatty acid 2-hydroxylase. Our findings provide important new insights into the molecular mechanisms responsible for neural pathogenesis caused by lipid metabolism abnormalities.-Kanetake, T., Sassa, T., Nojiri, K., Sawai, M., Hattori, S., Miyakawa, T., Kitamura, T., Kihara, A. Neural symptoms in a gene knockout mouse model of Sjögren-Larsson syndrome are associated with a decrease in 2-hydroxygalactosylceramide.
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Affiliation(s)
- Tsukasa Kanetake
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan; and
| | - Takayuki Sassa
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan; and
| | - Koki Nojiri
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan; and
| | - Megumi Sawai
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan; and
| | - Satoko Hattori
- Division of Systems Medical Science, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Japan
| | - Tsuyoshi Miyakawa
- Division of Systems Medical Science, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Japan
| | - Takuya Kitamura
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan; and
| | - Akio Kihara
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan; and
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14
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Zhang N, Zoltner M, Leung KF, Scullion P, Hutchinson S, del Pino RC, Vincent IM, Zhang YK, Freund YR, Alley MRK, Jacobs RT, Read KD, Barrett MP, Horn D, Field MC. Host-parasite co-metabolic activation of antitrypanosomal aminomethyl-benzoxaboroles. PLoS Pathog 2018; 14:e1006850. [PMID: 29425238 PMCID: PMC5823473 DOI: 10.1371/journal.ppat.1006850] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 02/22/2018] [Accepted: 01/03/2018] [Indexed: 12/22/2022] Open
Abstract
Recent development of benzoxaborole-based chemistry gave rise to a collection of compounds with great potential in targeting diverse infectious diseases, including human African Trypanosomiasis (HAT), a devastating neglected tropical disease. However, further medicinal development is largely restricted by a lack of insight into mechanism of action (MoA) in pathogenic kinetoplastids. We adopted a multidisciplinary approach, combining a high-throughput forward genetic screen with functional group focused chemical biological, structural biology and biochemical analyses, to tackle the complex MoAs of benzoxaboroles in Trypanosoma brucei. We describe an oxidative enzymatic pathway composed of host semicarbazide-sensitive amine oxidase and a trypanosomal aldehyde dehydrogenase TbALDH3. Two sequential reactions through this pathway serve as the key underlying mechanism for activating a series of 4-aminomethylphenoxy-benzoxaboroles as potent trypanocides; the methylamine parental compounds as pro-drugs are transformed first into intermediate aldehyde metabolites, and further into the carboxylate metabolites as effective forms. Moreover, comparative biochemical and crystallographic analyses elucidated the catalytic specificity of TbALDH3 towards the benzaldehyde benzoxaborole metabolites as xenogeneic substrates. Overall, this work proposes a novel drug activation mechanism dependent on both host and parasite metabolism of primary amine containing molecules, which contributes a new perspective to our understanding of the benzoxaborole MoA, and could be further exploited to improve the therapeutic index of antimicrobial compounds. Human African Trypanomiasis (HAT) is among a list of Neglected Tropical Diseases (NTDs) that impose devastating burdens on both public health and economy of some of the most unprivileged societies across the world. To secure the long-term global control of the disease, it is critical to understand the mechanisms underlying the interactions of drugs and drug candidates with the causative agents as well as resistance potentially arising from use of the compounds. We demonstrated here a metabolic enzymatic cascade dependent on a host-pathogen interaction that determines potency against T. brucei of a series of benzoxaborole compounds. More importantly, this pathway represents a metabolic interaction network between host and pathogen, illuminating an important perspective on understanding mechanism of action.
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Affiliation(s)
- Ning Zhang
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Martin Zoltner
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Ka-Fai Leung
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Paul Scullion
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Sebastian Hutchinson
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Ricardo C. del Pino
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Isabel M. Vincent
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Yong-Kang Zhang
- Anacor Pharmaceuticals, Inc., Palo Alto, California, United States of America
| | - Yvonne R. Freund
- Anacor Pharmaceuticals, Inc., Palo Alto, California, United States of America
| | - Michael R. K. Alley
- Anacor Pharmaceuticals, Inc., Palo Alto, California, United States of America
| | - Robert T. Jacobs
- Anacor Pharmaceuticals, Inc., Palo Alto, California, United States of America
| | - Kevin D. Read
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Michael P. Barrett
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - David Horn
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Mark C. Field
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United Kingdom
- * E-mail:
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15
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Phytosphingosine degradation pathway includes fatty acid α-oxidation reactions in the endoplasmic reticulum. Proc Natl Acad Sci U S A 2017; 114:E2616-E2623. [PMID: 28289220 DOI: 10.1073/pnas.1700138114] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Although normal fatty acids (FAs) are degraded via β-oxidation, unusual FAs such as 2-hydroxy (2-OH) FAs and 3-methyl-branched FAs are degraded via α-oxidation. Phytosphingosine (PHS) is one of the long-chain bases (the sphingolipid components) and exists in specific tissues, including the epidermis and small intestine in mammals. In the degradation pathway, PHS is converted to 2-OH palmitic acid and then to pentadecanoic acid (C15:0-COOH) via FA α-oxidation. However, the detailed reactions and genes involved in the α-oxidation reactions of the PHS degradation pathway have yet to be determined. In the present study, we reveal the entire PHS degradation pathway: PHS is converted to C15:0-COOH via six reactions [phosphorylation, cleavage, oxidation, CoA addition, cleavage (C1 removal), and oxidation], in which the last three reactions correspond to the α-oxidation. The aldehyde dehydrogenase ALDH3A2 catalyzes both the first and second oxidation reactions (fatty aldehydes to FAs). In Aldh3a2-deficient cells, the unmetabolized fatty aldehydes are reduced to fatty alcohols and are incorporated into ether-linked glycerolipids. We also identify HACL2 (2-hydroxyacyl-CoA lyase 2) [previous name, ILVBL; ilvB (bacterial acetolactate synthase)-like] as the major 2-OH acyl-CoA lyase involved in the cleavage (C1 removal) reaction in the FA α-oxidation of the PHS degradation pathway. HACL2 is localized in the endoplasmic reticulum. Thus, in addition to the already-known FA α-oxidation in the peroxisomes, we have revealed the existence of FA α-oxidation in the endoplasmic reticulum in mammals.
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16
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Medeiros de Oliveira Silva R, Bonvino Stafuzza N, de Oliveira Fragomeni B, Miguel Ferreira de Camargo G, Matos Ceacero T, Noely dos Santos Gonçalves Cyrillo J, Baldi F, Augusti Boligon A, Zerlotti Mercadante ME, Lino Lourenco D, Misztal I, Galvão de Albuquerque L. Genome-Wide Association Study for Carcass Traits in an Experimental Nelore Cattle Population. PLoS One 2017; 12:e0169860. [PMID: 28118362 PMCID: PMC5261778 DOI: 10.1371/journal.pone.0169860] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Accepted: 12/22/2016] [Indexed: 12/22/2022] Open
Abstract
The purpose of this study was to identify genomic regions associated with carcass traits in an experimental Nelore cattle population. The studied data set contained 2,306 ultrasound records for longissimus muscle area (LMA), 1,832 for backfat thickness (BF), and 1,830 for rump fat thickness (RF). A high-density SNP panel (BovineHD BeadChip assay 700k, Illumina Inc., San Diego, CA) was used for genotyping. After genomic data quality control, 437,197 SNPs from 761 animals were available, of which 721 had phenotypes for LMA, 669 for BF, and 718 for RF. The SNP solutions were estimated using a single-step genomic BLUP approach (ssGWAS), which calculated the variance for windows of 50 consecutive SNPs and the regions that accounted for more than 0.5% of the additive genetic variance were used to search for candidate genes. The results indicated that 12, 18, and 15 different windows were associated to LMA, BF, and RF, respectively. Confirming the polygenic nature of the studied traits, 43, 65, and 53 genes were found in those associated windows, respectively for LMA, BF, and RF. Among the candidate genes, some of them, which already had their functions associated with the expression of energy metabolism, were found associated with fat deposition in this study. In addition, ALKBH3 and HSD17B12 genes, which are related in fibroblast death and metabolism of steroids, were found associated with LMA. The results presented here should help to better understand the genetic and physiologic mechanism regulating the muscle tissue deposition and subcutaneous fat cover expression of Zebu animals. The identification of candidate genes should contribute for Zebu breeding programs in order to consider carcass traits as selection criteria in their genetic evaluation.
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Affiliation(s)
- Rafael Medeiros de Oliveira Silva
- School of Agricultural and Veterinarian Sciences, FCAV/ UNESP–Sao Paulo State University, Department of Animal Science, Jaboticabal-SP, Brazil
| | - Nedenia Bonvino Stafuzza
- School of Agricultural and Veterinarian Sciences, FCAV/ UNESP–Sao Paulo State University, Department of Animal Science, Jaboticabal-SP, Brazil
| | | | - Gregório Miguel Ferreira de Camargo
- School of Agricultural and Veterinarian Sciences, FCAV/ UNESP–Sao Paulo State University, Department of Animal Science, Jaboticabal-SP, Brazil
| | - Thaís Matos Ceacero
- APTA Center of Beef Cattle, Animal Science Institute, Sertaozinho, SP, Brazil
| | | | - Fernando Baldi
- School of Agricultural and Veterinarian Sciences, FCAV/ UNESP–Sao Paulo State University, Department of Animal Science, Jaboticabal-SP, Brazil
| | | | | | - Daniela Lino Lourenco
- University of Georgia, Department of Animal and Dairy Science, Athens, GA, United States of America
| | - Ignacy Misztal
- University of Georgia, Department of Animal and Dairy Science, Athens, GA, United States of America
| | - Lucia Galvão de Albuquerque
- School of Agricultural and Veterinarian Sciences, FCAV/ UNESP–Sao Paulo State University, Department of Animal Science, Jaboticabal-SP, Brazil
- * E-mail:
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17
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Payet LA, Leroux M, Willison JC, Kihara A, Pelosi L, Pierrel F. Mechanistic Details of Early Steps in Coenzyme Q Biosynthesis Pathway in Yeast. Cell Chem Biol 2016; 23:1241-1250. [PMID: 27693056 DOI: 10.1016/j.chembiol.2016.08.008] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 07/20/2016] [Accepted: 08/01/2016] [Indexed: 11/17/2022]
Abstract
Coenzyme Q (Q) is a redox lipid that is central for the energetic metabolism of eukaryotes. The biosynthesis of Q from the aromatic precursor 4-hydroxybenzoic acid (4-HB) is understood fairly well. However, biosynthetic details of how 4-HB is produced from tyrosine remain elusive. Here, we provide key insights into this long-standing biosynthetic problem by uncovering molecular details of the first and last reactions of the pathway in the yeast Saccharomyces cerevisiae, namely the deamination of tyrosine to 4-hydroxyphenylpyruvate by Aro8 and Aro9, and the oxidation of 4-hydroxybenzaldehyde to 4-HB by Hfd1. Inactivation of the HFD1 gene in yeast resulted in Q deficiency, which was rescued by the human enzyme ALDH3A1. This suggests that a similar pathway operates in animals, including humans, and led us to propose that patients with genetically unassigned Q deficiency should be screened for mutations in aldehyde dehydrogenase genes, especially ALDH3A1.
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Affiliation(s)
- Laurie-Anne Payet
- Université Grenoble Alpes, Laboratoire Technologies de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications, Grenoble (TIMC-IMAG), 38000 Grenoble, France; Centre National de Recherche Scientifique (CNRS), TIMC-IMAG, 38000 Grenoble, France
| | - Mélanie Leroux
- CEA-Grenoble, DRF-BIG-CBM, UMR5249, 38000 Grenoble, France
| | | | - Akio Kihara
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12-jo, Nishi 6-chome, Kita-ku, Sapporo 060-0812, Japan
| | - Ludovic Pelosi
- Université Grenoble Alpes, Laboratoire Technologies de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications, Grenoble (TIMC-IMAG), 38000 Grenoble, France; Centre National de Recherche Scientifique (CNRS), TIMC-IMAG, 38000 Grenoble, France
| | - Fabien Pierrel
- Université Grenoble Alpes, Laboratoire Technologies de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications, Grenoble (TIMC-IMAG), 38000 Grenoble, France; Centre National de Recherche Scientifique (CNRS), TIMC-IMAG, 38000 Grenoble, France.
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18
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Mitochondrial protein functions elucidated by multi-omic mass spectrometry profiling. Nat Biotechnol 2016; 34:1191-1197. [PMID: 27669165 PMCID: PMC5101133 DOI: 10.1038/nbt.3683] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 08/26/2016] [Indexed: 02/08/2023]
Abstract
Mitochondrial dysfunction is associated with many human diseases, including cancer and neurodegeneration, that are often linked to proteins and pathways that are not well-characterized. To begin defining the functions of such poorly characterized proteins, we used mass spectrometry to map the proteomes, lipidomes, and metabolomes of 174 yeast strains, each lacking a single gene related to mitochondrial biology. 144 of these genes have human homologs, 60 of which are associated with disease and 39 of which are uncharacterized. We present a multi-omic data analysis and visualization tool that we use to find covariance networks that can predict molecular functions, correlations between profiles of related gene deletions, gene-specific perturbations that reflect protein functions, and a global respiration deficiency response. Using this multi-omic approach, we link seven proteins including Hfd1p and its human homolog ALDH3A1 to mitochondrial coenzyme Q (CoQ) biosynthesis, an essential pathway disrupted in many human diseases. This Resource should provide molecular insights into mitochondrial protein functions.
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19
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Naganuma T, Takagi S, Kanetake T, Kitamura T, Hattori S, Miyakawa T, Sassa T, Kihara A. Disruption of the Sjögren-Larsson Syndrome Gene Aldh3a2 in Mice Increases Keratinocyte Growth and Retards Skin Barrier Recovery. J Biol Chem 2016; 291:11676-88. [PMID: 27053112 DOI: 10.1074/jbc.m116.714030] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Indexed: 11/06/2022] Open
Abstract
The fatty aldehyde dehydrogenase (FALDH) ALDH3A2 is the causative gene of Sjögren Larsson syndrome (SLS). To date, the molecular mechanism underlying the symptoms characterizing SLS has been poorly understood. Using Aldh3a2(-/-) mice, we found here that Aldh3a2 was the major FALDH active in undifferentiated keratinocytes. Long-chain base metabolism was greatly impaired in Aldh3a2(-/-) keratinocytes. Phenotypically, the intercellular spaces were widened in the basal layer of the Aldh3a2(-/-) epidermis due to hyperproliferation of keratinocytes. Furthermore, oxidative stress-induced genes were up-regulated in Aldh3a2(-/-) keratinocytes. Upon keratinocyte differentiation, the activity of another FALDH, Aldh3b2, surpassed that of Aldh3a2 As a result, Aldh3a2(-/-) mice were indistinguishable from wild-type mice in terms of their whole epidermis FALDH activity, and their skin barrier function was uncompromised under normal conditions. However, perturbation of the stratum corneum caused increased transepidermal water loss and delayed barrier recovery in Aldh3a2(-/-) mice. In conclusion, Aldh3a2(-/-) mice replicated some aspects of SLS symptoms, especially at the basal layer of the epidermis. Our results suggest that hyperproliferation of keratinocytes via oxidative stress responses may partly contribute to the ichthyosis symptoms of SLS.
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Affiliation(s)
- Tatsuro Naganuma
- From the Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Shuyu Takagi
- From the Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Tsukasa Kanetake
- From the Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Takuya Kitamura
- From the Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Satoko Hattori
- the Division of Systems Medical Science, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake 470-1192, Japan, and
| | - Tsuyoshi Miyakawa
- the Division of Systems Medical Science, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake 470-1192, Japan, and the Center for Genetic Analysis of Behavior, National Institute for Physiological Sciences, Okazaki 444-8585, Japan
| | - Takayuki Sassa
- From the Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Akio Kihara
- From the Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan,
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20
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Niu H, Hadwiger G, Fujiwara H, Welch JS. Pathways of retinoid synthesis in mouse macrophages and bone marrow cells. J Leukoc Biol 2016; 99:797-810. [PMID: 26768478 DOI: 10.1189/jlb.2hi0415-146rr] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 12/18/2015] [Indexed: 12/31/2022] Open
Abstract
In vivo pathways of natural retinoid metabolism and elimination have not been well characterized in primary myeloid cells, even though retinoids and retinoid receptors have been strongly implicated in regulating myeloid maturation. With the use of a upstream activation sequence-GFP reporter transgene and retrovirally expressed Gal4-retinoic acid receptor α in primary mouse bone marrow cells, we identified 2 distinct enzymatic pathways used by mouse myeloid cells ex vivo to synthesize retinoic acid receptor α ligands from free vitamin A metabolites (retinyl acetate, retinol, and retinal). Bulk Kit(+) bone marrow progenitor cells use diethylaminobenzaldehyde-sensitive enzymes, whereas bone marrow-derived macrophages use diethylaminobenzaldehyde-insensitive enzymes to synthesize natural retinoic acid receptor α-activating retinoids (all-trans retinoic acid). Bone marrow-derived macrophages do not express the diethylaminobenzaldehyde-sensitive enzymes Aldh1a1, Aldh1a2, or Aldh1a3 but instead, express Aldh3b1, which we found is capable of diethylaminobenzaldehyde-insensitive synthesis of all trans-retinoic acid. However, under steady-state and stimulated conditions in vivo, diverse bone marrow cells and peritoneal macrophages showed no evidence of intracellular retinoic acid receptor α-activating retinoids, despite expression of these enzymes and a vitamin A-sufficient diet, suggesting that the enzymatic conversion of retinal is not the rate-limiting step in the synthesis of intracellular retinoic acid receptor α-activating retinoids in myeloid bone marrow cells and that retinoic acid receptor α remains in an unliganded configuration during adult hematopoiesis.
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Affiliation(s)
- Haixia Niu
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA and
| | - Gayla Hadwiger
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA and
| | - Hideji Fujiwara
- Diabetic Cardiovascular Disease Center, Washington University School of Medicine, St. Louis, Missouri, USA
| | - John S Welch
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA and
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21
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Wilderman A, Guo Y, Divakaruni AS, Perkins G, Zhang L, Murphy AN, Taylor SS, Insel PA. Proteomic and Metabolic Analyses of S49 Lymphoma Cells Reveal Novel Regulation of Mitochondria by cAMP and Protein Kinase A. J Biol Chem 2015. [PMID: 26203188 DOI: 10.1074/jbc.m115.658153] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cyclic AMP (cAMP), acting via protein kinase A (PKA), regulates many cellular responses, but the role of mitochondria in such responses is poorly understood. To define such roles, we used quantitative proteomic analysis of mitochondria-enriched fractions and performed functional and morphologic studies of wild-type (WT) and kin(-) (PKA-null) murine S49 lymphoma cells. Basally, 75 proteins significantly differed in abundance between WT and kin(-) S49 cells. WT, but not kin(-), S49 cells incubated with the cAMP analog 8-(4-chlorophenylthio)adenosine cAMP (CPT-cAMP) for 16 h have (a) increased expression of mitochondria-related genes and proteins, including ones in pathways of branched-chain amino acid and fatty acid metabolism and (b) increased maximal capacity of respiration on branched-chain keto acids and fatty acids. CPT-cAMP also regulates the cellular rate of ATP-utilization, as the rates of both ATP-linked respiration and proton efflux are decreased in WT but not kin(-) cells. CPT-cAMP protected WT S49 cells from glucose or glutamine deprivation, In contrast, CPT-cAMP did not protect kin(-) cells or WT cells treated with the PKA inhibitor H89 from glutamine deprivation. Under basal conditions, the mitochondrial structure of WT and kin(-) S49 cells is similar. Treatment with CPT-cAMP produced apoptotic changes (i.e. decreased mitochondrial density and size and loss of cristae) in WT, but not kin(-) cells. Together, these findings show that cAMP acts via PKA to regulate multiple aspects of mitochondrial function and structure. Mitochondrial perturbation thus likely contributes to cAMP/PKA-mediated cellular responses.
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Affiliation(s)
- Andrea Wilderman
- From the Department of Pharmacology, University of California San Diego, La Jolla, California 92093-0626
| | - Yurong Guo
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093-0654
| | - Ajit S Divakaruni
- From the Department of Pharmacology, University of California San Diego, La Jolla, California 92093-0626
| | - Guy Perkins
- National Center for Microscopy and Imaging Research, University of California San Diego, La Jolla, California 92093-0608, and
| | - Lingzhi Zhang
- From the Department of Pharmacology, University of California San Diego, La Jolla, California 92093-0626
| | - Anne N Murphy
- From the Department of Pharmacology, University of California San Diego, La Jolla, California 92093-0626
| | - Susan S Taylor
- From the Department of Pharmacology, University of California San Diego, La Jolla, California 92093-0626, Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093-0654
| | - Paul A Insel
- From the Department of Pharmacology, University of California San Diego, La Jolla, California 92093-0626, Department of Medicine, University of California San Diego, La Jolla, California 92093
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22
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Mouse aldehyde dehydrogenase ALDH3B2 is localized to lipid droplets via two C-terminal tryptophan residues and lipid modification. Biochem J 2014; 465:79-87. [DOI: 10.1042/bj20140624] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The mouse aldehyde dehydrogenases ALDH3B2 and ALDH3B3 exhibit similar substrate specificity but distinct intracellular localization (ALDH3B2, lipid droplets; ALDH3B3, plasma membrane). The C-terminal prenylation and two tryptophan residues are important for the lipid droplet localization of ALDH3B2.
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23
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Keller MA, Zander U, Fuchs JE, Kreutz C, Watschinger K, Mueller T, Golderer G, Liedl KR, Ralser M, Kräutler B, Werner ER, Marquez JA. A gatekeeper helix determines the substrate specificity of Sjögren-Larsson Syndrome enzyme fatty aldehyde dehydrogenase. Nat Commun 2014; 5:4439. [PMID: 25047030 PMCID: PMC4109017 DOI: 10.1038/ncomms5439] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 06/17/2014] [Indexed: 11/09/2022] Open
Abstract
Mutations in the gene coding for membrane-bound fatty aldehyde dehydrogenase (FALDH) lead to toxic accumulation of lipid species and development of the Sjögren-Larsson Syndrome (SLS), a rare disorder characterized by skin defects and mental retardation. Here, we present the crystallographic structure of human FALDH, the first model of a membrane-associated aldehyde dehydrogenase. The dimeric FALDH displays a previously unrecognized element in its C-terminal region, a 'gatekeeper' helix, which extends over the adjacent subunit, controlling the access to the substrate cavity and helping orientate both substrate cavities towards the membrane surface for efficient substrate transit between membranes and catalytic site. Activity assays demonstrate that the gatekeeper helix is important for directing the substrate specificity of FALDH towards long-chain fatty aldehydes. The gatekeeper feature is conserved across membrane-associated aldehyde dehydrogenases. Finally, we provide insight into the previously elusive molecular basis of SLS-causing mutations.
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Affiliation(s)
- Markus A. Keller
- Division of Biological Chemistry, Biocenter, Innsbruck Medical University, Innrain 80-82, 6020 Innsbruck, Austria
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis court Rd, Cambridge CB2 1GA, UK
| | - Ulrich Zander
- European Molecular Biology Laboratory, Grenoble Outstation, 6 rue Jules Horowitz, 38042 Grenoble, France
| | - Julian E. Fuchs
- Institute of General, Inorganic and Theoretical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Katrin Watschinger
- Division of Biological Chemistry, Biocenter, Innsbruck Medical University, Innrain 80-82, 6020 Innsbruck, Austria
| | - Thomas Mueller
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Georg Golderer
- Division of Biological Chemistry, Biocenter, Innsbruck Medical University, Innrain 80-82, 6020 Innsbruck, Austria
| | - Klaus R. Liedl
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Markus Ralser
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis court Rd, Cambridge CB2 1GA, UK
- MRC National Institute for Medical Research, the Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Bernhard Kräutler
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Ernst R. Werner
- Division of Biological Chemistry, Biocenter, Innsbruck Medical University, Innrain 80-82, 6020 Innsbruck, Austria
- These authors contributed equally to this work
| | - Jose A. Marquez
- European Molecular Biology Laboratory, Grenoble Outstation, 6 rue Jules Horowitz, 38042 Grenoble, France
- Unit of Virus Host-Cell Interactions, University of Grenoble Alpes-EMBL-CNRS, 6 rue Jules Horowitz, 38042 Grenoble, France
- These authors contributed equally to this work
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24
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Rizzo WB. Fatty aldehyde and fatty alcohol metabolism: review and importance for epidermal structure and function. Biochim Biophys Acta Mol Cell Biol Lipids 2013; 1841:377-89. [PMID: 24036493 DOI: 10.1016/j.bbalip.2013.09.001] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 09/02/2013] [Accepted: 09/04/2013] [Indexed: 01/23/2023]
Abstract
Normal fatty aldehyde and alcohol metabolism is essential for epidermal differentiation and function. Long-chain aldehydes are produced by catabolism of several lipids including fatty alcohols, sphingolipids, ether glycerolipids, isoprenoid alcohols and certain aliphatic lipids that undergo α- or ω-oxidation. The fatty aldehyde generated by these pathways is chiefly metabolized to fatty acid by fatty aldehyde dehydrogenase (FALDH, alternately known as ALDH3A2), which also functions to oxidize fatty alcohols as a component of the fatty alcohol:NAD oxidoreductase (FAO) enzyme complex. Genetic deficiency of FALDH/FAO in patients with Sjögren-Larsson syndrome (SLS) results in accumulation of fatty aldehydes, fatty alcohols and related lipids (ether glycerolipids, wax esters) in cultured keratinocytes. These biochemical changes are associated with abnormalities in formation of lamellar bodies in the stratum granulosum and impaired delivery of their precursor membranes to the stratum corneum (SC). The defective extracellular SC membranes are responsible for a leaky epidermal water barrier and ichthyosis. Although lamellar bodies appear to be the pathogenic target for abnormal fatty aldehyde/alcohol metabolism in SLS, the precise biochemical mechanisms are yet to be elucidated. Nevertheless, studies in SLS highlight the critical importance of FALDH and normal fatty aldehyde/alcohol metabolism for epidermal function. This article is part of a Special Issue entitled The Important Role of Lipids in the Epidermis and their Role in the Formation and Maintenance of the Cutaneous Barrier. Guest Editors: Kenneth R. Feingold and Peter Elias.
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Affiliation(s)
- William B Rizzo
- Department of Pediatrics, University of Nebraska Medical Center, Omaha, NE 68198-5456, USA.
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