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Arafat MY, Narula K, Kumar M, Chakraborty N, Chakraborty S. Proteo-metabolomic Dissection of Extracellular Matrix Reveals Alterations in Cell Wall Integrity and Calcium Signaling Governs Wall-Associated Susceptibility during Stem Rot Disease in Jute. J Proteome Res 2024. [PMID: 38572503 DOI: 10.1021/acs.jproteome.3c00781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
The plant surveillance system confers specificity to disease and immune states by activating distinct molecular pathways linked to cellular functionality. The extracellular matrix (ECM), a preformed passive barrier, is dynamically remodeled at sites of interaction with pathogenic microbes. Stem rot, caused by Macrophomina phaseolina, adversely affects fiber production in jute. However, how wall related susceptibility affects the ECM proteome and metabolome remains undetermined in bast fiber crops. Here, stem rot responsive quantitative temporal ECM proteome and metabolome were developed in jute upon M. phaseolina infection. Morpho-histological examination revealed that leaf shredding was accompanied by reactive oxygen species production in patho-stressed jute. Electron microscopy showed disease progression and ECM architecture remodeling due to necrosis in the later phase of fungal attack. Using isobaric tags for relative and absolute quantitative proteomics and liquid chromatography-tandem mass spectrometry, we identified 415 disease-responsive proteins involved in wall integrity, acidification, proteostasis, hydration, and redox homeostasis. The disease-related correlation network identified functional hubs centered on α-galactosidase, pectinesterase, and thaumatin. Gas chromatography-mass spectrometry analysis pointed toward enrichment of disease-responsive metabolites associated with the glutathione pathway, TCA cycle, and cutin, suberin, and wax metabolism. Data demonstrated that wall-degrading enzymes, structural carbohydrates, and calcium signaling govern rot responsive wall-susceptibility. Proteomics data were deposited in Pride (PXD046937; PXD046939).
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Affiliation(s)
- Md Yasir Arafat
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Kanika Narula
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Mohit Kumar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Niranjan Chakraborty
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Subhra Chakraborty
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
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Age and Sex-Dependent ADNP Regulation of Muscle Gene Expression Is Correlated with Motor Behavior: Possible Feedback Mechanism with PACAP. Int J Mol Sci 2020; 21:ijms21186715. [PMID: 32937737 PMCID: PMC7555576 DOI: 10.3390/ijms21186715] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/08/2020] [Accepted: 09/11/2020] [Indexed: 12/21/2022] Open
Abstract
The activity-dependent neuroprotective protein (ADNP), a double-edged sword, sex-dependently regulates multiple genes and was previously associated with the control of early muscle development and aging. Here we aimed to decipher the involvement of ADNP in versatile muscle gene expression patterns in correlation with motor function throughout life. Using quantitative RT-PCR we showed that Adnp+/− heterozygous deficiency in mice resulted in aberrant gastrocnemius (GC) muscle, tongue and bladder gene expression, which was corrected by the Adnp snippet, drug candidate, NAP (CP201). A significant sexual dichotomy was discovered, coupled to muscle and age-specific gene regulation. As such, Adnp was shown to regulate myosin light chain (Myl) in the gastrocnemius (GC) muscle, the language acquisition gene forkhead box protein P2 (Foxp2) in the tongue and the pituitary-adenylate cyclase activating polypeptide (PACAP) receptor PAC1 mRNA (Adcyap1r1) in the bladder, with PACAP linked to bladder function. A tight age regulation was observed, coupled to an extensive correlation to muscle function (gait analysis), placing ADNP as a muscle-regulating gene/protein.
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Otoukesh B, Abbasi M, Gorgani HOL, Farahini H, Moghtadaei M, Boddouhi B, Kaghazian P, Hosseinzadeh S, Alaee A. MicroRNAs signatures, bioinformatics analysis of miRNAs, miRNA mimics and antagonists, and miRNA therapeutics in osteosarcoma. Cancer Cell Int 2020; 20:254. [PMID: 32565738 PMCID: PMC7302353 DOI: 10.1186/s12935-020-01342-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 06/12/2020] [Indexed: 02/07/2023] Open
Abstract
MicroRNAs (miRNAs) involved in key signaling pathways and aggressive phenotypes of osteosarcoma (OS) was discussed, including PI3K/AKT/MTOR, MTOR AND RAF-1 signaling, tumor suppressor P53- linked miRNAs, NOTCH- related miRNAs, miRNA -15/16 cluster, apoptosis related miRNAs, invasion-metastasis-related miRNAs, and 14Q32-associated miRNAs cluster. Herrin, we discussed insights into the targeted therapies including miRNAs (i.e., tumor-suppressive miRNAs and oncomiRNAs). Using bioinformatics tools, the interaction network of all OS-associated miRNAs and their targets was also depicted.
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Affiliation(s)
- Babak Otoukesh
- Orthopedic Surgery Fellowship in Département Hospitalo-Universitaire MAMUTH « Maladies musculo-squelettiques et innovations thérapeutiques » , Université Pierre et Marie-Curie, Sorbonne Université, Paris, France.,Department of Orthopedic Surgery, Bone and Joint Reconstruction Research Center, Iran University of Medical Science, Postal code : 1445613131 Tehran, Iran
| | - Mehdi Abbasi
- Brain Mapping Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Habib-O-Lah Gorgani
- Department of Orthopedic Surgery, Bone and Joint Reconstruction Research Center, Iran University of Medical Science, Postal code : 1445613131 Tehran, Iran
| | - Hossein Farahini
- Department of Orthopedic Surgery, Bone and Joint Reconstruction Research Center, Iran University of Medical Science, Postal code : 1445613131 Tehran, Iran
| | - Mehdi Moghtadaei
- Department of Orthopedic Surgery, Bone and Joint Reconstruction Research Center, Iran University of Medical Science, Postal code : 1445613131 Tehran, Iran
| | - Bahram Boddouhi
- Department of Orthopedic Surgery, Bone and Joint Reconstruction Research Center, Iran University of Medical Science, Postal code : 1445613131 Tehran, Iran
| | - Peyman Kaghazian
- Department of Orthopedic and Traumatology, Universitätsklinikum Bonn, Bonn, Germany
| | - Shayan Hosseinzadeh
- Department of Orthopedic Surgery, Boston Children's Hospital, Harvard Medical School, Boston, MA USA
| | - Atefe Alaee
- Department of Information Sciences, Tehran University of Medical Sciences, Tehran, Iran
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Maximov VV, Akkawi R, Khawaled S, Salah Z, Jaber L, Barhoum A, Or O, Galasso M, Kurek KC, Yavin E, Aqeilan RI. MiR-16-1-3p and miR-16-2-3p possess strong tumor suppressive and antimetastatic properties in osteosarcoma. Int J Cancer 2019; 145:3052-3063. [PMID: 31018244 DOI: 10.1002/ijc.32368] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 03/18/2019] [Accepted: 04/10/2019] [Indexed: 01/07/2023]
Abstract
Osteosarcoma (OS) is an aggressive malignancy affecting mostly children and adolescents. MicroRNAs (miRNAs) play important roles in OS development and progression. Here we found that miR-16-1-3p and miR-16-2-3p "passenger" strands, as well as the "lead" miR-16-5p strand, are frequently downregulated and possess strong tumor suppressive functions in human OS. Furthermore, we report different although strongly overlapping functions for miR-16-1-3p and miR-16-2-3p in OS cells. Ectopic expression of these miRNAs affected primary tumor growth, metastasis seeding and chemoresistance and invasiveness of human OS cells. Loss-of-function experiments verified tumor suppressive functions of these miRNAs at endogenous levels of expression. Using RNA immunoprecipitation (RIP) assays, we identify direct targets of miR-16-1-3p and miR-16-2-3p in OS cells. Moreover, validation experiments identified FGFR2 as a direct target for miR-16-1-3p and miR-16-2-3p. Overall, our findings underscore the importance of passenger strand miRNAs, at least some, in osteosarcomagenesis.
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Affiliation(s)
- Vadim V Maximov
- The Lautenberg Center for General and Tumor Immunology, Department of Immunology and Cancer Research-IMRIC, The Hebrew University-Hadassah Medical School at Ein-Kerem, Jerusalem, Israel
| | - Rania Akkawi
- The Lautenberg Center for General and Tumor Immunology, Department of Immunology and Cancer Research-IMRIC, The Hebrew University-Hadassah Medical School at Ein-Kerem, Jerusalem, Israel
| | - Saleh Khawaled
- The Lautenberg Center for General and Tumor Immunology, Department of Immunology and Cancer Research-IMRIC, The Hebrew University-Hadassah Medical School at Ein-Kerem, Jerusalem, Israel
| | - Zaidoun Salah
- Al Quds-Bard College, Al-Quds University, Al-Bireh, East Jerusalem, Palestine
| | - Lina Jaber
- The Lautenberg Center for General and Tumor Immunology, Department of Immunology and Cancer Research-IMRIC, The Hebrew University-Hadassah Medical School at Ein-Kerem, Jerusalem, Israel
| | - Ahlam Barhoum
- The Lautenberg Center for General and Tumor Immunology, Department of Immunology and Cancer Research-IMRIC, The Hebrew University-Hadassah Medical School at Ein-Kerem, Jerusalem, Israel
| | - Omer Or
- Department of Orthopedics Surgery, Hebrew University Hadassah Medical Center, Jerusalem, Israel
| | - Marco Galasso
- Biosystems Analysis, LTTA, Department of Morphology, Surgery and Experimental Medicine, Università degli Studi, Ferrara, Italy
| | - Kyle C Kurek
- Department of Pathology and Medical Genetics Cumming School of Medicine, University of Calgary, Alberta Children's Hospital & Research Institute, Calgary, AB, Canada
| | - Eylon Yavin
- The Institute for Drug Research, The School of Pharmacy, The Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Rami I Aqeilan
- The Lautenberg Center for General and Tumor Immunology, Department of Immunology and Cancer Research-IMRIC, The Hebrew University-Hadassah Medical School at Ein-Kerem, Jerusalem, Israel.,Department of Cancer Biology & Genetics, The Ohio State University Wexner Medical Center, Columbus, OH
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Lin YN, Lan XF, Liu ZR, Yan YR, Zhou JP, Li N, Sun XW, Li QY. Activation of ATM-c-IAP1 Pathway Mediates the Protective Effects of Estradiol in Human Vascular Endothelial Cells Exposed to Intermittent Hypoxia. Nat Sci Sleep 2019; 11:357-366. [PMID: 31819689 PMCID: PMC6886551 DOI: 10.2147/nss.s231456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 11/05/2019] [Indexed: 11/23/2022] Open
Abstract
PURPOSE Chronic intermittent hypoxia (CIH) contributes to the increased risk of cardiovascular diseases in obstructive sleep apnea (OSA). We previously reported the anti-apoptotic effects of estradiol (E2) on IH-exposed human umbilical vein endothelial cells (HUVECs). Herein, we employed a proteomic analysis to elucidate the mechanisms of the protective effects of E2 under IH exposure. METHODS HUVECs were divided into three groups: control, IH, and IH+E2 group. Isobaric tags for relative and absolute quantification (iTRAQ) were performed to compare protein profiles among the groups. Some of the identified proteins were validated by Western blotting. RESULTS A total of 185 proteins were differentially expressed in the IH+E2 group compared to the IH group. Bioinformatics analysis indicated that the effects of E2 may be linked to the regulation of cellular stress response. Among the differentially expressed proteins, we identified that serine-protein kinase ataxia telangiectasia mutated (ATM) and its downstream target, cellular inhibitor of apoptosis protein 1 (c-IAP1), were up-regulated by E2. We also observed that E2 decreased the level of cleaved caspase-3 and inhibited cell apoptosis in IH-exposed HUVECs. The inhibition of ATM abolished the anti-apoptotic effect of E2. CONCLUSION The ATM-c-IAP1 pathway is involved in the cardioprotective effects of E2 in HUVECs exposed to IH.
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Affiliation(s)
- Ying Ni Lin
- Department of Respiratory and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, People's Republic of China.,Institute of Respiratory Disease, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, People's Republic of China
| | - Xiao Fei Lan
- Department of Respiratory and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, People's Republic of China.,Department of Respiratory Medicine, Shanghai Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200335, People's Republic of China
| | - Zhuo Ran Liu
- Department of Thyroid and Vascular Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, People's Republic of China
| | - Ya Ru Yan
- Department of Respiratory and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, People's Republic of China.,Institute of Respiratory Disease, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, People's Republic of China
| | - Jian Ping Zhou
- Department of Respiratory and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, People's Republic of China.,Institute of Respiratory Disease, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, People's Republic of China
| | - Ning Li
- Department of Respiratory and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, People's Republic of China.,Institute of Respiratory Disease, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, People's Republic of China
| | - Xian Wen Sun
- Department of Respiratory and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, People's Republic of China.,Institute of Respiratory Disease, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, People's Republic of China
| | - Qing Yun Li
- Department of Respiratory and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, People's Republic of China.,Institute of Respiratory Disease, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, People's Republic of China
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Zhan X, Zhou T, Li N, Li H. The differentially mitochondrial proteomic dataset in human ovarian cancer relative to control tissues. Data Brief 2018; 20:459-462. [PMID: 30186894 PMCID: PMC6123609 DOI: 10.1016/j.dib.2018.08.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 07/21/2018] [Accepted: 08/09/2018] [Indexed: 11/29/2022] Open
Abstract
This data article presents a differentially mitochondrial proteomic dataset in human ovarian cancer tissues relative to control tissues. The mitochondrial samples were prepared from human ovarian cancer and control ovary tissues, and were digested with trypsin. The tryptic peptides from ovarian cancer and control mitochondrial samples were labeled by isobaric tags for relative and absolute quantification (iTRAQ) reagents, followed by strong-cation exchange (SCX) chromatography, liquid chromatography (LC)-tandem mass spectrometry (MS/MS), and bioinformatic analysis. This data article is related to a published article (Li et al., 2018) [1].
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Affiliation(s)
- Xianquan Zhan
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008, PR China
- Hunan Engineering Laboratory for Structural Biology and Drug Design, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008, PR China
- State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008, PR China
- The Laboratory of Medical Genetics, Central South University, 88 Xiangya Road, Changsha, Hunan 410008, PR China
- Corresponding author at: Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008, PR China.
| | - Tian Zhou
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008, PR China
- Hunan Engineering Laboratory for Structural Biology and Drug Design, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008, PR China
- State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008, PR China
| | - Na Li
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008, PR China
- Hunan Engineering Laboratory for Structural Biology and Drug Design, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008, PR China
- State Local Joint Engineering Laboratory for Anticancer Drugs, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008, PR China
| | - Huanni Li
- Department of Obstetrics and Gynecology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China
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