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Bao Y, He X, Zhai Y, Shen W, Jing M, Liu Y, Yang H, Chen L. Effects of glyphosate-based herbicide on gut microbes and hepatopancreatic metabolism in Pomacea canaliculata. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 280:116549. [PMID: 38852467 DOI: 10.1016/j.ecoenv.2024.116549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 05/30/2024] [Accepted: 06/02/2024] [Indexed: 06/11/2024]
Abstract
Roundup®, a prominent glyphosate-based herbicide (GBH), holds a significant position in the global market. However, studies of its effects on aquatic invertebrates, including molluscs are limited. Pomacea canaliculata, a large freshwater snail naturally thrives in agricultural environments where GBH is extensively employed. Our investigation involved assessing the impact of two concentrations of GBH (at concentrations of 19.98 mg/L and 59.94 mg/L, corresponding to 6 mg/L and 18 mg/L glyphosate) during a 96 h exposure experiment on the intestinal bacterial composition and metabolites of P. canaliculata. Analysis of the 16 S rRNA gene demonstrated a notable reduction in the alpha diversity of intestinal bacteria due to GBH exposure. Higher GBH concentration caused a significant shift in the relative abundance of dominant bacteria, such as Bacteroides and Paludibacter. We employed widely-targeted metabolomics analysis to analyze alterations in the hepatopancreatic metabolic profile as a consequence of GBH exposure. The shifts in metabolites primarily affected lipid, amino acid, and glucose metabolism, resulting in compromised immune and adaptive capacities in P. canaliculata. These results suggested that exposure to varying GBH concentrations perpetuates adverse effects on intestinal and hepatopancreatic health of P. canaliculata. This study provides an understanding of the negative effects of GBH on P. canaliculata and may sheds light on its potential implications for other molluscs.
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Affiliation(s)
- Yiran Bao
- College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Xinni He
- College of Life Sciences, Nanjing Normal University, Nanjing 210042, China
| | - Yiying Zhai
- College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Wenjia Shen
- College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Muzi Jing
- College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Yuyao Liu
- College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Haiyun Yang
- College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Lian Chen
- College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China.
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2
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Baptista A, Brière G, Baudot A. Random walk with restart on multilayer networks: from node prioritisation to supervised link prediction and beyond. BMC Bioinformatics 2024; 25:70. [PMID: 38355439 PMCID: PMC10865648 DOI: 10.1186/s12859-024-05683-z] [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: 10/18/2023] [Accepted: 01/29/2024] [Indexed: 02/16/2024] Open
Abstract
BACKGROUND Biological networks have proven invaluable ability for representing biological knowledge. Multilayer networks, which gather different types of nodes and edges in multiplex, heterogeneous and bipartite networks, provide a natural way to integrate diverse and multi-scale data sources into a common framework. Recently, we developed MultiXrank, a Random Walk with Restart algorithm able to explore such multilayer networks. MultiXrank outputs scores reflecting the proximity between an initial set of seed node(s) and all the other nodes in the multilayer network. We illustrate here the versatility of bioinformatics tasks that can be performed using MultiXrank. RESULTS We first show that MultiXrank can be used to prioritise genes and drugs of interest by exploring multilayer networks containing interactions between genes, drugs, and diseases. In a second study, we illustrate how MultiXrank scores can also be used in a supervised strategy to train a binary classifier to predict gene-disease associations. The classifier performance are validated using outdated and novel gene-disease association for training and evaluation, respectively. Finally, we show that MultiXrank scores can be used to compute diffusion profiles and use them as disease signatures. We computed the diffusion profiles of more than 100 immune diseases using a multilayer network that includes cell-type specific genomic information. The clustering of the immune disease diffusion profiles reveals shared shared phenotypic characteristics. CONCLUSION Overall, we illustrate here diverse applications of MultiXrank to showcase its versatility. We expect that this can lead to further and broader bioinformatics applications.
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Affiliation(s)
- Anthony Baptista
- School of Mathematical Sciences, Queen Mary University of London, London, UK.
- The Alan Turing Institute, London, UK.
| | | | - Anaïs Baudot
- INSERM, MMG, Turing Center for Living Systems, Aix-Marseille Univ, Marseille, France.
- Barcelona Supercomputing Center, Barcelona, Spain.
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Qannita RA, Alalami AI, Harb AA, Aleidi SM, Taneera J, Abu-Gharbieh E, El-Huneidi W, Saleh MA, Alzoubi KH, Semreen MH, Hudaib M, Bustanji Y. Targeting Hypoxia-Inducible Factor-1 (HIF-1) in Cancer: Emerging Therapeutic Strategies and Pathway Regulation. Pharmaceuticals (Basel) 2024; 17:195. [PMID: 38399410 PMCID: PMC10892333 DOI: 10.3390/ph17020195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 01/24/2024] [Accepted: 01/29/2024] [Indexed: 02/25/2024] Open
Abstract
Hypoxia-inducible factor-1 (HIF-1) is a key regulator for balancing oxygen in the cells. It is a transcription factor that regulates the expression of target genes involved in oxygen homeostasis in response to hypoxia. Recently, research has demonstrated the multiple roles of HIF-1 in the pathophysiology of various diseases, including cancer. It is a crucial mediator of the hypoxic response and regulator of oxygen metabolism, thus contributing to tumor development and progression. Studies showed that the expression of the HIF-1α subunit is significantly upregulated in cancer cells and promotes tumor survival by multiple mechanisms. In addition, HIF-1 has potential contributing roles in cancer progression, including cell division, survival, proliferation, angiogenesis, and metastasis. Moreover, HIF-1 has a role in regulating cellular metabolic pathways, particularly the anaerobic metabolism of glucose. Given its significant and potential roles in cancer development and progression, it has been an intriguing therapeutic target for cancer research. Several compounds targeting HIF-1-associated processes are now being used to treat different types of cancer. This review outlines emerging therapeutic strategies that target HIF-1 as well as the relevance and regulation of the HIF-1 pathways in cancer. Moreover, it addresses the employment of nanotechnology in developing these promising strategies.
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Affiliation(s)
- Reem A. Qannita
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates; (R.A.Q.); (A.I.A.); (J.T.); (E.A.-G.); (W.E.-H.); (M.A.S.); (K.H.A.); (M.H.S.)
- College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Ayah I. Alalami
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates; (R.A.Q.); (A.I.A.); (J.T.); (E.A.-G.); (W.E.-H.); (M.A.S.); (K.H.A.); (M.H.S.)
- College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Amani A. Harb
- Department of Basic Sciences, Faculty of Arts and Sciences, Al-Ahliyya Amman University, Amman 19111, Jordan;
| | - Shereen M. Aleidi
- School of Pharmacy, The University of Jordan, Amman 11942, Jordan; (S.M.A.); (M.H.)
| | - Jalal Taneera
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates; (R.A.Q.); (A.I.A.); (J.T.); (E.A.-G.); (W.E.-H.); (M.A.S.); (K.H.A.); (M.H.S.)
- College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Eman Abu-Gharbieh
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates; (R.A.Q.); (A.I.A.); (J.T.); (E.A.-G.); (W.E.-H.); (M.A.S.); (K.H.A.); (M.H.S.)
- College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates
- School of Pharmacy, The University of Jordan, Amman 11942, Jordan; (S.M.A.); (M.H.)
| | - Waseem El-Huneidi
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates; (R.A.Q.); (A.I.A.); (J.T.); (E.A.-G.); (W.E.-H.); (M.A.S.); (K.H.A.); (M.H.S.)
- College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Mohamed A. Saleh
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates; (R.A.Q.); (A.I.A.); (J.T.); (E.A.-G.); (W.E.-H.); (M.A.S.); (K.H.A.); (M.H.S.)
- College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Karem H. Alzoubi
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates; (R.A.Q.); (A.I.A.); (J.T.); (E.A.-G.); (W.E.-H.); (M.A.S.); (K.H.A.); (M.H.S.)
- Department of Pharmacy Practice and Pharmacotherapeutics, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Mohammad H. Semreen
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates; (R.A.Q.); (A.I.A.); (J.T.); (E.A.-G.); (W.E.-H.); (M.A.S.); (K.H.A.); (M.H.S.)
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Mohammad Hudaib
- School of Pharmacy, The University of Jordan, Amman 11942, Jordan; (S.M.A.); (M.H.)
| | - Yasser Bustanji
- Research Institute of Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates; (R.A.Q.); (A.I.A.); (J.T.); (E.A.-G.); (W.E.-H.); (M.A.S.); (K.H.A.); (M.H.S.)
- College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates
- School of Pharmacy, The University of Jordan, Amman 11942, Jordan; (S.M.A.); (M.H.)
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Sakuma I, Gaspar RC, Luukkonen PK, Kahn M, Zhang D, Zhang X, Murray S, Golla JP, Vatner DF, Samuel VT, Petersen KF, Shulman GI. Lysophosphatidic acid triggers inflammation in the liver and white adipose tissue in rat models of 1-acyl-sn-glycerol-3-phosphate acyltransferase 2 deficiency and overnutrition. Proc Natl Acad Sci U S A 2023; 120:e2312666120. [PMID: 38127985 PMCID: PMC10756285 DOI: 10.1073/pnas.2312666120] [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: 07/27/2023] [Accepted: 11/10/2023] [Indexed: 12/23/2023] Open
Abstract
AGPAT2 (1-acyl-sn-glycerol-3-phosphate-acyltransferase-2) converts lysophosphatidic acid (LPA) into phosphatidic acid (PA), and mutations of the AGPAT2 gene cause the most common form of congenital generalized lipodystrophy which leads to steatohepatitis. The underlying mechanism by which AGPAT2 deficiency leads to lipodystrophy and steatohepatitis has not been elucidated. We addressed this question using an antisense oligonucleotide (ASO) to knockdown expression of Agpat2 in the liver and white adipose tissue (WAT) of adult male Sprague-Dawley rats. Agpat2 ASO treatment induced lipodystrophy and inflammation in WAT and the liver, which was associated with increased LPA content in both tissues, whereas PA content was unchanged. We found that a controlled-release mitochondrial protonophore (CRMP) prevented LPA accumulation and inflammation in WAT whereas an ASO against glycerol-3-phosphate acyltransferase, mitochondrial (Gpam) prevented LPA content and inflammation in the liver in Agpat2 ASO-treated rats. In addition, we show that overnutrition, due to high sucrose feeding, resulted in increased hepatic LPA content and increased activated macrophage content which were both abrogated with Gpam ASO treatment. Taken together, these data identify LPA as a key mediator of liver and WAT inflammation and lipodystrophy due to AGPAT2 deficiency as well as liver inflammation due to overnutrition and identify LPA as a potential therapeutic target to ameliorate these conditions.
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Affiliation(s)
- Ikki Sakuma
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT06520
- Department of Molecular Diagnosis, Graduate School of Medicine Chiba University, Chiba260-8670, Japan
| | - Rafael C. Gaspar
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT06520
| | - Panu K. Luukkonen
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT06520
| | - Mario Kahn
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT06520
| | - Dongyan Zhang
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT06520
| | - Xuchen Zhang
- Department of Pathology, Yale School of Medicine, New Haven, CT06520
| | | | - Jaya Prakash Golla
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT06520
| | - Daniel F. Vatner
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT06520
| | - Varman T. Samuel
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT06520
| | - Kitt Falk Petersen
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT06520
| | - Gerald I. Shulman
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT06520
- Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, CT06520
- Howard Hughes Medical Institute, Chevy Chase, MD20815
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5
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Guo Z, Bergeron KF, Lingrand M, Mounier C. Unveiling the MUFA-Cancer Connection: Insights from Endogenous and Exogenous Perspectives. Int J Mol Sci 2023; 24:9921. [PMID: 37373069 DOI: 10.3390/ijms24129921] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/01/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
Monounsaturated fatty acids (MUFAs) have been the subject of extensive research in the field of cancer due to their potential role in its prevention and treatment. MUFAs can be consumed through the diet or endogenously biosynthesized. Stearoyl-CoA desaturases (SCDs) are key enzymes involved in the endogenous synthesis of MUFAs, and their expression and activity have been found to be increased in various types of cancer. In addition, diets rich in MUFAs have been associated with cancer risk in epidemiological studies for certain types of carcinomas. This review provides an overview of the state-of-the-art literature on the associations between MUFA metabolism and cancer development and progression from human, animal, and cellular studies. We discuss the impact of MUFAs on cancer development, including their effects on cancer cell growth, migration, survival, and cell signaling pathways, to provide new insights on the role of MUFAs in cancer biology.
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Affiliation(s)
- Zhiqiang Guo
- Biological Sciences Department, Université du Québec à Montréal (UQAM), Montréal, QC H3P 3P8, Canada
| | - Karl-Frédérik Bergeron
- Biological Sciences Department, Université du Québec à Montréal (UQAM), Montréal, QC H3P 3P8, Canada
| | - Marine Lingrand
- Department of Biochemistry, McGill University, Montréal, QC H3A 1A3, Canada
| | - Catherine Mounier
- Biological Sciences Department, Université du Québec à Montréal (UQAM), Montréal, QC H3P 3P8, Canada
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Chen J, Wang Y, Meng W, Zhao R, Lin W, Xiao H, Liao Y. Stearoyl-CoA Desaturases1 Accelerates Non-Small Cell Lung Cancer Metastasis by Promoting Aromatase Expression to Improve Estrogen Synthesis. Int J Mol Sci 2023; 24:ijms24076826. [PMID: 37047797 PMCID: PMC10095487 DOI: 10.3390/ijms24076826] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/27/2023] [Accepted: 04/02/2023] [Indexed: 04/14/2023] Open
Abstract
Metastases contribute to the low survival rate of non-small cell lung cancer (NSCLC) patients. Targeting lipid metabolism for anticancer therapies is attractive. Accumulative evidence shows that stearoyl-CoA desaturases1 (SCD1), a key enzyme in lipid metabolism, enables tumor metastasis and the underlying mechanism remains unknown. In this study, immunohistochemical staining of 96 clinical specimens showed that the expression of SCD1 was increased in tumor tissues (p < 0.001). SCD1 knockdown reduced the migration and invasion of HCC827 and PC9 cells in transwell and wound healing assays. Aromatase (CYP19A1) knockdown eliminated cell migration and invasion caused by SCD1 overexpression. Western blotting assays demonstrated that CYP19A1, along with β-catenin protein levels, was reduced in SCD1 knocked-down cells, and estrogen concentration was reduced (p < 0.05) in cell culture medium measured by enzyme-linked immunosorbent assay. SCD1 overexpression preserving β-catenin protein stability was evaluated by coimmunoprecipitation and Western blotting. The SCD1 inhibitor A939572, and a potential SCD1 inhibitor, grape seed extract (GSE), significantly inhibited cell migration and invasion by blocking SCD1 and its downstream β-catenin, CYP19A1 expression, and estrogen concentration. In vivo tumor formation assay and a tail vein metastasis model indicated that knockdown of SCD1 blocked tumor growth and metastasis. In conclusion, SCD1 could accelerate metastasis by maintaining the protein stability of β-catenin and then promoting CYP19A1 transcription to improve estrogen synthesis. SCD1 is expected to be a promised therapeutic target, and its novel inhibitor, GSE, has great therapeutic potential in NSCLC.
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Affiliation(s)
- Jiaping Chen
- Department of Thoracic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Yangwei Wang
- Department of Thoracic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Wangyang Meng
- Department of Thoracic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Rong Zhao
- Department of Thoracic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Wei Lin
- Department of Thoracic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Han Xiao
- Department of Thoracic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Yongde Liao
- Department of Thoracic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
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7
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Yachida N, Hoshino F, Murakami C, Ebina M, Miura Y, Sakane F. Saturated fatty acid- and/or monounsaturated fatty acid-containing phosphatidic acids selectively interact with heat shock protein 27. J Biol Chem 2023; 299:103019. [PMID: 36791913 PMCID: PMC10023972 DOI: 10.1016/j.jbc.2023.103019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 01/30/2023] [Accepted: 02/06/2023] [Indexed: 02/17/2023] Open
Abstract
Diacylglycerol kinase (DGK) α, which is a key enzyme in the progression of cancer and, in contrast, in T-cell activity attenuation, preferentially produces saturated fatty acid (SFA)- and/or monounsaturated fatty acid (MUFA)-containing phosphatidic acids (PAs), such as 16:0/16:0-, 16:0/18:0-, and 16:1/16:1-PA, in melanoma cells. In the present study, we searched for the target proteins of 16:0/16:0-PA in melanoma cells and identified heat shock protein (HSP) 27, which acts as a molecular chaperone and contributes to cancer progression. HSP27 more strongly interacted with PA than other phospholipids, including phosphatidylcholine, phosphatidylserine, phosphatidylglycerol, cardiolipin, phosphatidylinositol, phosphatidylinositol 4-monophosphate, and phosphatidylinositol 4,5-bisphosphate. Moreover, HSP27 is more preferentially bound to SFA- and/or MUFA-containing PAs, including 16:0/16:0- and 16:0/18:1-PAs, than PUFA-containing PAs, including 18:0/20:4- and 18:0/22:6-PA. Furthermore, HSP27 and constitutively active DGKα expressed in COS-7 cells colocalized in a DGK activity-dependent manner. Notably, 16:0/16:0-PA, but not phosphatidylcholine or 16:0/16:0-phosphatidylserine, induced oligomer dissociation of HSP27, which enhances its chaperone activity. Intriguingly, HSP27 protein was barely detectable in Jurkat T cells, while the protein band was intensely detected in AKI melanoma cells. Taken together, these results strongly suggest that SFA- and/or MUFA-containing PAs produced by DGKα selectively target HSP27 and regulate its cancer-progressive function in melanoma cells but not in T cells.
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Affiliation(s)
- Naoto Yachida
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba, Japan
| | - Fumi Hoshino
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba, Japan
| | - Chiaki Murakami
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba, Japan; Institute for Advanced Academic Research, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba, Japan
| | - Masayuki Ebina
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba, Japan
| | - Yuri Miura
- Research Team for Mechanism of Aging, Tokyo Metropolitan Institute of Gerontology, Itabashi, Tokyo, Japan
| | - Fumio Sakane
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba, Japan.
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Wen P, Wang R, Xing Y, Ouyang W, Yuan Y, Zhang S, Liu Y, Peng Z. The prognostic value of the GPAT/AGPAT gene family in hepatocellular carcinoma and its role in the tumor immune microenvironment. Front Immunol 2023; 14:1026669. [PMID: 36845084 PMCID: PMC9950581 DOI: 10.3389/fimmu.2023.1026669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 01/27/2023] [Indexed: 02/12/2023] Open
Abstract
Background Liver cancer is the sixth most commonly diagnosed cancer and the third leading cause of cancer-related death worldwide. Hepatocellular carcinoma accounts for an estimated 90% of all liver cancers. Many enzymes of the GPAT/AGPAT family are required for the synthesis of triacylglycerol. Expression of AGPAT isoenzymes has been reported to be associated with an increased risk of tumorigenesis or development of aggressive phenotypes in a variety of cancers. However, whether members of the GPAT/AGPAT gene family also influence the pathophysiology of HCC is unknown. Methods Hepatocellular carcinoma datasets were obtained from the TCGA and ICGC databases. Predictive models related to the GPAT/AGPAT gene family were constructed based on LASSO-Cox regression using the ICGC-LIRI dataset as an external validation cohort. Seven immune cell infiltration algorithms were used to analyze immune cell infiltration patterns in different risk groups. IHC, CCK-8, Transwell assay, and Western blotting were used for in vitro validation. Results Compared with low-risk patients, high-risk patients had shorter survival and higher risk scores. Multivariate Cox regression analysis showed that risk score was a significant independent predictor of overall survival (OS) after adjustment for confounding clinical factors (p < 0.001). The established nomogram combined risk score and TNM staging to accurately predict survival at 1, 3, and 5 years in patients with HCC with AUC values of 0.807, 0.806, and 0.795, respectively. This risk score improved the reliability of the nomogram and guided clinical decision-making. In addition, we comprehensively analyzed immune cell infiltration (using seven algorithms), response to immune checkpoint blockade, clinical relevance, survival, mutations, mRNA expression-based stemness index, signaling pathways, and interacting proteins related to the three core genes of the prognostic model (AGPAT5, LCLAT1, and LPCAT1). We also performed preliminary validation of the differential expression, oncological phenotype, and potential downstream pathways of the three core genes by IHC, CCK-8, Transwell assay, and Western blotting. Conclusion These results improve our understanding of the function of GPAT/AGPAT gene family members and provide a reference for prognostic biomarker research and individualized treatment of HCC.
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Affiliation(s)
- Peizhen Wen
- Organ Transplantation Clinical Medical Center of Xiamen University, Department of Organ Transplantation, Xiang’an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
- Organ Transplantation Institute of Xiamen University, Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Rui Wang
- Organ Transplantation Clinical Medical Center of Xiamen University, Department of Organ Transplantation, Xiang’an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
- Organ Transplantation Institute of Xiamen University, Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Yiqun Xing
- Organ Transplantation Clinical Medical Center of Xiamen University, Department of Organ Transplantation, Xiang’an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
- Organ Transplantation Institute of Xiamen University, Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Wanxin Ouyang
- Organ Transplantation Clinical Medical Center of Xiamen University, Department of Organ Transplantation, Xiang’an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
- Organ Transplantation Institute of Xiamen University, Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Yixin Yuan
- Organ Transplantation Clinical Medical Center of Xiamen University, Department of Organ Transplantation, Xiang’an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
- Organ Transplantation Institute of Xiamen University, Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Shuaishuai Zhang
- Organ Transplantation Clinical Medical Center of Xiamen University, Department of Organ Transplantation, Xiang’an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
- Organ Transplantation Institute of Xiamen University, Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Yuan Liu
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Zhihai Peng
- Organ Transplantation Clinical Medical Center of Xiamen University, Department of Organ Transplantation, Xiang’an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
- Organ Transplantation Institute of Xiamen University, Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, School of Medicine, Xiamen University, Xiamen, Fujian, China
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9
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Xu L, Huang Z, Zeng Z, Li J, Xie H, Xie C. An integrative analysis of DNA methylation and gene expression to predict lung adenocarcinoma prognosis. Front Genet 2022; 13:970507. [PMID: 36105089 PMCID: PMC9465336 DOI: 10.3389/fgene.2022.970507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/03/2022] [Indexed: 12/09/2022] Open
Abstract
Background: Abnormal DNA methylation of gene promoters is an important feature in lung adenocarcinoma (LUAD). However, the prognostic value of DNA methylation remains to be further explored. Objectives. We sought to explore DNA methylation characteristics and develop a quantifiable criterion related to DNA methylation to improve survival prediction for LUAD patients. Methods: Illumina Human Methylation450K array data, level 3 RNA-seq data and corresponding clinical information were obtained from TCGA. Cox regression analysis and the Akaike information criterion were used to construct the best-prognosis methylation signature. Receiver operating characteristic curve analysis was used to validate the prognostic ability of the DNA methylation-related feature score. qPCR was used to measure the transcription levels of the identified genes upon methylation. Results: We identified a set of DNA methylation features composed of 11 genes (MYEOV, KCNU1, SLC27A6, NEUROD4, HMGB4, TACR3, GABRA5, TRPM8, NLRP13, EDN3 and SLC34A1). The feature score, calculated based on DNA methylation features, was independent of tumor recurrence and TNM stage in predicting overall survival. Of note, the combination of this feature score and TNM stage provided a better overall survival prediction than either of them individually. The transcription levels of all the hypermethylated genes were significantly increased after demethylation, and the expression levels of 3 hypomethylated proteins were significantly higher in tumor tissues than in normal tissues, as indicated by immunohistochemistry data from the Human Protein Atlas. Our results suggested that these identified genes with prognostic features were regulated by DNA methylation of their promoters. Conclusion: Our studies demonstrated the potential application of DNA methylation markers in the prognosis of LUAD.
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Affiliation(s)
- Liexi Xu
- Department of Radiation and Medical Oncology, Wuhan University of Zhongnan Hospital, Wuhan, China
| | - Zhengrong Huang
- Department of Radiation and Medical Oncology, Wuhan University of Zhongnan Hospital, Wuhan, China
- Tumor Precision Diagnosis and Treatment Technology and Translational Medicine, Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zihang Zeng
- Department of Radiation and Medical Oncology, Wuhan University of Zhongnan Hospital, Wuhan, China
| | - Jiali Li
- Department of Radiation and Medical Oncology, Wuhan University of Zhongnan Hospital, Wuhan, China
| | - Hongxin Xie
- Department of Radiation and Medical Oncology, Wuhan University of Zhongnan Hospital, Wuhan, China
| | - Conghua Xie
- Department of Radiation and Medical Oncology, Wuhan University of Zhongnan Hospital, Wuhan, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, China
- *Correspondence: Conghua Xie,
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Allen CNS, Arjona SP, Santerre M, Sawaya BE. Hallmarks of Metabolic Reprogramming and Their Role in Viral Pathogenesis. Viruses 2022; 14:602. [PMID: 35337009 PMCID: PMC8955778 DOI: 10.3390/v14030602] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/09/2022] [Accepted: 03/10/2022] [Indexed: 02/07/2023] Open
Abstract
Metabolic reprogramming is a hallmark of cancer and has proven to be critical in viral infections. Metabolic reprogramming provides the cell with energy and biomass for large-scale biosynthesis. Based on studies of the cellular changes that contribute to metabolic reprogramming, seven main hallmarks can be identified: (1) increased glycolysis and lactic acid, (2) increased glutaminolysis, (3) increased pentose phosphate pathway, (4) mitochondrial changes, (5) increased lipid metabolism, (6) changes in amino acid metabolism, and (7) changes in other biosynthetic and bioenergetic pathways. Viruses depend on metabolic reprogramming to increase biomass to fuel viral genome replication and production of new virions. Viruses take advantage of the non-metabolic effects of metabolic reprogramming, creating an anti-apoptotic environment and evading the immune system. Other non-metabolic effects can negatively affect cellular function. Understanding the role metabolic reprogramming plays in viral pathogenesis may provide better therapeutic targets for antivirals.
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Affiliation(s)
- Charles N. S. Allen
- Molecular Studies of Neurodegenerative Diseases Lab, FELS Cancer Institute for Personalized Medicine Institute, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA; (C.N.S.A.); (S.P.A.); (M.S.)
| | - Sterling P. Arjona
- Molecular Studies of Neurodegenerative Diseases Lab, FELS Cancer Institute for Personalized Medicine Institute, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA; (C.N.S.A.); (S.P.A.); (M.S.)
| | - Maryline Santerre
- Molecular Studies of Neurodegenerative Diseases Lab, FELS Cancer Institute for Personalized Medicine Institute, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA; (C.N.S.A.); (S.P.A.); (M.S.)
| | - Bassel E. Sawaya
- Molecular Studies of Neurodegenerative Diseases Lab, FELS Cancer Institute for Personalized Medicine Institute, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA; (C.N.S.A.); (S.P.A.); (M.S.)
- Departments of Neurology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
- Department of Cancer and Cell Biology, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
- Department of Neural Sciences, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
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11
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Yuan Q, Zhang W, Shang W. Identification and validation of a prognostic risk-scoring model based on sphingolipid metabolism-associated cluster in colon adenocarcinoma. Front Endocrinol (Lausanne) 2022; 13:1045167. [PMID: 36518255 PMCID: PMC9742378 DOI: 10.3389/fendo.2022.1045167] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 10/24/2022] [Indexed: 11/29/2022] Open
Abstract
Colon adenocarcinoma (COAD) is the primary factor responsible for cancer-related mortalities in western countries, and its development and progression are affected by altered sphingolipid metabolism. The current study aimed at investigating the effects of sphingolipid metabolism-related (SLP) genes on multiple human cancers, especially on COAD. We obtained 1287 SLP genes from the GeneCard and MsigDb databases along with the public transcriptome data and the related clinical information. The univariate Cox regression analysis suggested that 26 SLP genes were substantially related to the prognosis of COAD, and a majority of SLP genes served as the risk genes for the tumor, insinuating a potential pathogenic effect of SLP in COAD development. Pan-cancer characterization of SLP genes summarized their expression traits, mutation traits, and methylation levels. Subsequently, we focused on the thorough research of COAD. With the help of unsupervised clustering, 1008 COAD patients were successfully divided into two distinct subtypes (C1 and C2). C1 subtype is characterized by a poor prognosis, activation of SLP pathways, high expression of SLP genes, disordered carcinogenic pathways, and immune microenvironment. Based on the clusters of SLP, we developed and validated a novel prognostic model, consisting of ANO1, C2CD4A, EEF1A2, GRP, HEYL, IGF1, LAMA2, LSAMP, RBP1, and TCEAL2, to quantitatively evaluate the clinical outcomes of COAD. The Kaplain-Meier survival curves and ROC curves highlighted the accuracy of our SLP model in both internal and external cohorts. Compared to normal colon tissues, expression of C2CD4A was detected to be significantly higher in COAD; whereas, expression levels of EEF1A2, IGF1, and TCEAL2 were detected to be significantly lower in COAD. Overall, our research emphasized the pathogenic role of SLP in COAD and found that targeting SLP might help improve the clinical outcomes of COAD. The risk model based on SLP metabolism provided a new horizon for prognosis assessment and customized patient intervention.
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Affiliation(s)
- Qihang Yuan
- Department of General Surgery, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
- Laboratory of Integrative Medicine, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
- *Correspondence: Qihang Yuan,
| | - Weizhi Zhang
- Dalian No.24 High School, Dalian, Liaoning, China
| | - Weijia Shang
- Dalian No.24 High School, Dalian, Liaoning, China
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