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Saba E, Farhat M, Daoud A, Khashan A, Forkush E, Menahem NH, Makkawi H, Pandi K, Angabo S, Kawasaki H, Plaschkes I, Parnas O, Zamir G, Atlan K, Elkin M, Katz L, Nussbaum G. Oral bacteria accelerate pancreatic cancer development in mice. Gut 2024; 73:770-786. [PMID: 38233197 DOI: 10.1136/gutjnl-2023-330941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 12/28/2023] [Indexed: 01/19/2024]
Abstract
OBJECTIVE Epidemiological studies highlight an association between pancreatic ductal adenocarcinoma (PDAC) and oral carriage of the anaerobic bacterium Porphyromonas gingivalis, a species highly linked to periodontal disease. We analysed the potential for P. gingivalis to promote pancreatic cancer development in an animal model and probed underlying mechanisms. DESIGN We tracked P. gingivalis bacterial translocation from the oral cavity to the pancreas following administration to mice. To dissect the role of P. gingivalis in PDAC development, we administered bacteria to a genetically engineered mouse PDAC model consisting of inducible acinar cell expression of mutant Kras (Kras +/LSL-G12D; Ptf1a-CreER, iKC mice). These mice were used to study the cooperative effects of Kras mutation and P. gingivalis on the progression of pancreatic intraepithelial neoplasia (PanIN) to PDAC. The direct effects of P. gingivalis on acinar cells and PDAC cell lines were studied in vitro. RESULTS P. gingivalis migrated from the oral cavity to the pancreas in mice and can be detected in human PanIN lesions. Repetitive P. gingivalis administration to wild-type mice induced pancreatic acinar-to-ductal metaplasia (ADM), and altered the composition of the intrapancreatic microbiome. In iKC mice, P. gingivalis accelerated PanIN to PDAC progression. In vitro, P. gingivalis infection induced acinar cell ADM markers SOX9 and CK19, and intracellular bacteria protected PDAC cells from reactive oxygen species-mediated cell death resulting from nutrient stress. CONCLUSION Taken together, our findings demonstrate a causal role for P. gingivalis in pancreatic cancer development in mice.
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Affiliation(s)
- Elias Saba
- Institute of Biomedical and Oral Research, Hebrew University-Hadassah, Jerusalem, Israel
| | - Maria Farhat
- Institute of Biomedical and Oral Research, Hebrew University-Hadassah, Jerusalem, Israel
| | - Alaa Daoud
- Institute of Biomedical and Oral Research, Hebrew University-Hadassah, Jerusalem, Israel
| | - Arin Khashan
- Institute of Biomedical and Oral Research, Hebrew University-Hadassah, Jerusalem, Israel
| | - Esther Forkush
- Gastroenterology, Hadassah Medical Center, Jerusalem, Israel
| | - Noam Hallel Menahem
- Institute of Biomedical and Oral Research, Hebrew University-Hadassah, Jerusalem, Israel
| | - Hasnaa Makkawi
- Institute of Biomedical and Oral Research, Hebrew University-Hadassah, Jerusalem, Israel
| | - Karthikeyan Pandi
- Institute of Biomedical and Oral Research, Hebrew University-Hadassah, Jerusalem, Israel
| | - Sarah Angabo
- Institute of Biomedical and Oral Research, Hebrew University-Hadassah, Jerusalem, Israel
| | - Hiromichi Kawasaki
- Institute of Biomedical and Oral Research, Hebrew University-Hadassah, Jerusalem, Israel
- Central Research Institute, Wakunaga Pharmaceutical Co Ltd, Koda-cho, Akitakata-shi, Hiroshima, Japan
| | - Inbar Plaschkes
- Info-CORE, Bioinformatics Unit of the I-CORE, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Oren Parnas
- Immunology and Cancer Research, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Gideon Zamir
- Experimental Surgery, Hebrew University Hadassah Medical School, Jerusalem, Israel
| | | | - Michael Elkin
- Oncology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Lior Katz
- Department of Gastroenterology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Gabriel Nussbaum
- Institute of Biomedical and Oral Research, Hebrew University-Hadassah, Jerusalem, Israel
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2
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Gilad N, Mohanam MP, Darlyuk-Saadon I, Heng CKM, Plaschkes I, Benyamini H, Berezhnoy NV, Engelberg D. Asynchronous Pattern of MAPKs' Activity during Aging of Different Tissues and of Distinct Types of Skeletal Muscle. Int J Mol Sci 2024; 25:1713. [PMID: 38338990 PMCID: PMC10855984 DOI: 10.3390/ijms25031713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/17/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
The MAPK p38α was proposed to be a prominent promoter of skeletal muscle aging. The skeletal muscle tissue is composed of various muscle types, and it is not known if p38α is associated with aging in all of them. It is also not known if p38α is associated with aging of other tissues. JNK and ERK were also proposed to be associated with aging of several tissues. Nevertheless, the pattern of p38α, JNK, and ERK activity during aging was not documented. Here, we documented the levels of phosphorylated/active p38α, Erk1/2, and JNKs in several organs as well as the soleus, tibialis anterior, quadriceps, gastrocnemius, and EDL muscles of 1-, 3-, 6-, 13-, 18-, and 24-month-old mice. We report that in most tissues and skeletal muscles, the MAPKs' activity does not change in the course of aging. In most tissues and muscles, p38α is in fact active at younger ages. The quadriceps and the lungs are exceptions, where p38α is significantly active only in mice 13 months old or older. Curiously, levels of active JNK and ERKs are also elevated in aged lungs and quadriceps. RNA-seq analysis of the quadriceps during aging revealed downregulation of proteins related to the extra-cellular matrix (ECM) and ERK signaling. A panel of mRNAs encoding cell cycle inhibitors and senescence-associated proteins, considered to be aging markers, was not found to be elevated. It seems that the pattern of MAPKs' activation in aging, as well as expression of known 'aging' components, are tissue- and muscle type-specific, supporting a notion that the process of aging is tissue- and even cell-specific.
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Affiliation(s)
- Nechama Gilad
- Department of Biological Chemistry, The Institute of Life Science, The Hebrew University of Jerusalem, Jerusalem 91904, Israel;
- Singapore-HUJ Alliance for Research and Enterprise, Mechanisms of Liver Inflammatory Diseases Program, National University of Singapore, Singapore 138602, Singapore
| | - Manju Payini Mohanam
- Singapore-HUJ Alliance for Research and Enterprise, Mechanisms of Liver Inflammatory Diseases Program, National University of Singapore, Singapore 138602, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore
| | - Ilona Darlyuk-Saadon
- Singapore-HUJ Alliance for Research and Enterprise, Mechanisms of Liver Inflammatory Diseases Program, National University of Singapore, Singapore 138602, Singapore
| | - C. K. Matthew Heng
- Singapore-HUJ Alliance for Research and Enterprise, Mechanisms of Liver Inflammatory Diseases Program, National University of Singapore, Singapore 138602, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore
| | - Inbar Plaschkes
- Info-CORE, Bioinformatics Unit of the I-CORE, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Hadar Benyamini
- Info-CORE, Bioinformatics Unit of the I-CORE, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Nikolay V. Berezhnoy
- Singapore-HUJ Alliance for Research and Enterprise, Mechanisms of Liver Inflammatory Diseases Program, National University of Singapore, Singapore 138602, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore
| | - David Engelberg
- Department of Biological Chemistry, The Institute of Life Science, The Hebrew University of Jerusalem, Jerusalem 91904, Israel;
- Singapore-HUJ Alliance for Research and Enterprise, Mechanisms of Liver Inflammatory Diseases Program, National University of Singapore, Singapore 138602, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore
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3
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Elsana H, Bruck‐Haimson R, Zhu H, Siddiqui AA, Zaretsky A, Cohen I, Boocholez H, Roitenberg N, Moll L, Plaschkes I, Naor D, Cohen E. A short peptide protects from age-onset proteotoxicity. Aging Cell 2023; 22:e14013. [PMID: 37897137 PMCID: PMC10726816 DOI: 10.1111/acel.14013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 09/08/2023] [Accepted: 09/27/2023] [Indexed: 10/29/2023] Open
Abstract
Aberrant protein aggregation jeopardizes cellular functionality and underlies the development of a myriad of late-onset maladies including Alzheimer's disease (AD) and Huntington's disease (HD). Accordingly, molecules that mitigate the toxicity of hazardous protein aggregates are of great interest as potential future therapeutics. Here we asked whether a small peptide, composed of five amino acids (5MER peptide) that was derived from the human pro-inflammatory CD44 protein, could protect model nematodes from the toxicity of aggregative proteins that underlie the development of neurodegenerative disorders in humans. We found that the 5MER peptide mitigates the toxicity that stems from both; the AD-causing Aβ peptide and a stretch of poly-glutamine that is accountable for the development of several disorders including HD, while minimally affecting lifespan. This protection was dependent on the activity of aging-regulating transcription factors and associated with enhanced Aβ and polyQ35-YFP aggregation. A transcriptomic analysis unveiled that the peptide modifies signaling pathways, thereby modulating the expression of various genes, including these, which are known as protein homeostasis (proteostasis) regulators such as txt-13 and modifiers of proteasome activity. The knockdown of txt-13 protects worms from proteotoxicity to the same extent as the 5MER peptide, suggesting that the peptide activates the transcellular chaperone signaling to promote proteostasis. Together, our results propose that the 5MER peptide should be considered as a component of future therapeutic cocktails for the treatment of neurodegenerative maladies.
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Affiliation(s)
- Hassan Elsana
- The Lautenberg Center of Immunology and Cancer ResearchThe Institute for Medical Research Israel – Canada (IMRIC), The Hebrew University School of MedicineJerusalemIsrael
| | - Reut Bruck‐Haimson
- Department of Biochemistry and Molecular BiologyThe Institute for Medical Research Israel – Canada (IMRIC), The Hebrew University School of MedicineJerusalemIsrael
| | - Huadong Zhu
- Department of Biochemistry and Molecular BiologyThe Institute for Medical Research Israel – Canada (IMRIC), The Hebrew University School of MedicineJerusalemIsrael
| | - Atif Ahmed Siddiqui
- Department of Biochemistry and Molecular BiologyThe Institute for Medical Research Israel – Canada (IMRIC), The Hebrew University School of MedicineJerusalemIsrael
| | - Adam Zaretsky
- Department of Biochemistry and Molecular BiologyThe Institute for Medical Research Israel – Canada (IMRIC), The Hebrew University School of MedicineJerusalemIsrael
| | - Irit Cohen
- Department of Biochemistry and Molecular BiologyThe Institute for Medical Research Israel – Canada (IMRIC), The Hebrew University School of MedicineJerusalemIsrael
| | - Hana Boocholez
- Department of Biochemistry and Molecular BiologyThe Institute for Medical Research Israel – Canada (IMRIC), The Hebrew University School of MedicineJerusalemIsrael
| | - Noa Roitenberg
- Department of Biochemistry and Molecular BiologyThe Institute for Medical Research Israel – Canada (IMRIC), The Hebrew University School of MedicineJerusalemIsrael
| | - Lorna Moll
- Department of Biochemistry and Molecular BiologyThe Institute for Medical Research Israel – Canada (IMRIC), The Hebrew University School of MedicineJerusalemIsrael
| | - Inbar Plaschkes
- Info‐COREBioinformatics Unit of the I‐CORE, The Hebrew UniversityJerusalemIsrael
| | - David Naor
- The Lautenberg Center of Immunology and Cancer ResearchThe Institute for Medical Research Israel – Canada (IMRIC), The Hebrew University School of MedicineJerusalemIsrael
| | - Ehud Cohen
- Department of Biochemistry and Molecular BiologyThe Institute for Medical Research Israel – Canada (IMRIC), The Hebrew University School of MedicineJerusalemIsrael
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4
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Xia L, Komissarova A, Jacover A, Shovman Y, Arcila-Barrera S, Tornovsky-Babeay S, Jaya Prakashan MM, Nasereddin A, Plaschkes I, Nevo Y, Shiff I, Yosefov-Levi O, Izhiman T, Medvedev E, Eilon E, Wilensky A, Yona S, Parnas O. Systematic identification of gene combinations to target in innate immune cells to enhance T cell activation. Nat Commun 2023; 14:6295. [PMID: 37813864 PMCID: PMC10562403 DOI: 10.1038/s41467-023-41792-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 09/19/2023] [Indexed: 10/11/2023] Open
Abstract
Genetic engineering of immune cells has opened new avenues for improving their functionality but it remains a challenge to pinpoint which genes or combination of genes are the most beneficial to target. Here, we conduct High Multiplicity of Perturbations and Cellular Indexing of Transcriptomes and Epitopes (HMPCITE-seq) to find combinations of genes whose joint targeting improves antigen-presenting cell activity and enhances their ability to activate T cells. Specifically, we perform two genome-wide CRISPR screens in bone marrow dendritic cells and identify negative regulators of CD86, that participate in the co-stimulation programs, including Chd4, Stat5b, Egr2, Med12, and positive regulators of PD-L1, that participate in the co-inhibitory programs, including Sptlc2, Nckap1l, and Pi4kb. To identify the genetic interactions between top-ranked genes and find superior combinations to target, we perform high-order Perturb-Seq experiments and we show that targeting both Cebpb and Med12 results in a better phenotype compared to the single perturbations or other combinations of perturbations.
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Affiliation(s)
- Lei Xia
- The Lautenberg Center for Immunology and Cancer Research, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 91120, Israel
| | - Anastasia Komissarova
- The Lautenberg Center for Immunology and Cancer Research, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 91120, Israel
| | - Arielle Jacover
- The Lautenberg Center for Immunology and Cancer Research, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 91120, Israel
| | - Yehuda Shovman
- The Lautenberg Center for Immunology and Cancer Research, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 91120, Israel.
| | - Sebastian Arcila-Barrera
- The Lautenberg Center for Immunology and Cancer Research, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 91120, Israel
| | - Sharona Tornovsky-Babeay
- The Lautenberg Center for Immunology and Cancer Research, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 91120, Israel
| | - Milsee Mol Jaya Prakashan
- The Lautenberg Center for Immunology and Cancer Research, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 91120, Israel
| | - Abdelmajeed Nasereddin
- Core Research Facility, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 91120, Israel
| | - Inbar Plaschkes
- I-CORE Bioinformatics Unit of the Hebrew University and Hadassah Medical Center, Jerusalem, 91120, Israel
| | - Yuval Nevo
- I-CORE Bioinformatics Unit of the Hebrew University and Hadassah Medical Center, Jerusalem, 91120, Israel
| | - Idit Shiff
- Core Research Facility, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 91120, Israel
| | - Oshri Yosefov-Levi
- The Lautenberg Center for Immunology and Cancer Research, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 91120, Israel
| | - Tamara Izhiman
- The Lautenberg Center for Immunology and Cancer Research, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 91120, Israel
| | - Eleonora Medvedev
- Core Research Facility, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 91120, Israel
| | - Elad Eilon
- The Lautenberg Center for Immunology and Cancer Research, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 91120, Israel
| | - Asaf Wilensky
- Department of Periodontology, Hadassah Medical Center, Faculty of Dental Medicine, Hebrew University of Jerusalem, Jerusalem, 91120, Israel
| | - Simon Yona
- The Institute of Biomedical and Oral Research, Hebrew University, Jerusalem, 91120, Israel
| | - Oren Parnas
- The Lautenberg Center for Immunology and Cancer Research, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 91120, Israel.
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5
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Sharma A, Mistriel-Zerbib S, Najar RA, Engal E, Bentata M, Taqatqa N, Dahan S, Cohen K, Jaffe-Herman S, Geminder O, Baker M, Nevo Y, Plaschkes I, Kay G, Drier Y, Berger M, Salton M. Isoforms of the TAL1 transcription factor have different roles in hematopoiesis and cell growth. PLoS Biol 2023; 21:e3002175. [PMID: 37379322 DOI: 10.1371/journal.pbio.3002175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 05/30/2023] [Indexed: 06/30/2023] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) protein 1 (TAL1) is a central transcription factor in hematopoiesis. The timing and level of TAL1 expression orchestrate the differentiation to specialized blood cells and its overexpression is a common cause of T-ALL. Here, we studied the 2 protein isoforms of TAL1, short and long, which are generated by the use of alternative promoters as well as by alternative splicing. We analyzed the expression of each isoform by deleting an enhancer or insulator, or by opening chromatin at the enhancer location. Our results show that each enhancer promotes expression from a specific TAL1 promoter. Expression from a specific promoter gives rise to a unique 5' UTR with differential regulation of translation. Moreover, our study suggests that the enhancers regulate TAL1 exon 3 alternative splicing by inducing changes in the chromatin at the splice site, which we demonstrate is mediated by KMT2B. Furthermore, our results indicate that TAL1-short binds more strongly to TAL1 E-protein partners and functions as a stronger transcription factor than TAL1-long. Specifically TAL1-short has a unique transcription signature promoting apoptosis. Finally, when we expressed both isoforms in mice bone marrow, we found that while overexpression of both isoforms prevents lymphoid differentiation, expression of TAL-short alone leads to hematopoietic stem cell exhaustion. Furthermore, we found that TAL1-short promoted erythropoiesis and reduced cell survival in the CML cell line K562. While TAL1 and its partners are considered promising therapeutic targets in the treatment of T-ALL, our results show that TAL1-short could act as a tumor suppressor and suggest that altering TAL1 isoform's ratio could be a preferred therapeutic approach.
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Affiliation(s)
- Aveksha Sharma
- Faculty of Medicine, Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shani Mistriel-Zerbib
- Faculty of Medicine, The Lautenberg Center for Immunology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Rauf Ahmad Najar
- Faculty of Medicine, Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Eden Engal
- Faculty of Medicine, Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Mercedes Bentata
- Faculty of Medicine, Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Nadeen Taqatqa
- Faculty of Medicine, Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Sara Dahan
- Faculty of Medicine, Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Klil Cohen
- Faculty of Medicine, Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shiri Jaffe-Herman
- Faculty of Medicine, Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ophir Geminder
- Faculty of Medicine, Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Mai Baker
- Faculty of Medicine, Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yuval Nevo
- Info-CORE, Bioinformatics Unit of the I-CORE Computation Center, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Inbar Plaschkes
- Info-CORE, Bioinformatics Unit of the I-CORE Computation Center, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Gillian Kay
- Faculty of Medicine, Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yotam Drier
- Faculty of Medicine, The Lautenberg Center for Immunology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Michael Berger
- Faculty of Medicine, The Lautenberg Center for Immunology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Maayan Salton
- Faculty of Medicine, Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
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6
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Soni A, Klebanov-Akopyan O, Erben E, Plaschkes I, Benyamini H, Mitesser V, Harel A, Yamin K, Onn I, Shlomai J. UMSBP2 is chromatin remodeler that functions in regulation of gene expression and suppression of antigenic variation in trypanosomes. Nucleic Acids Res 2023; 51:5678-5698. [PMID: 37207337 PMCID: PMC10287944 DOI: 10.1093/nar/gkad402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 05/03/2023] [Indexed: 05/21/2023] Open
Abstract
Universal Minicircle Sequence binding proteins (UMSBPs) are CCHC-type zinc-finger proteins that bind the single-stranded G-rich UMS sequence, conserved at the replication origins of minicircles in the kinetoplast DNA, the mitochondrial genome of kinetoplastids. Trypanosoma brucei UMSBP2 has been recently shown to colocalize with telomeres and to play an essential role in chromosome end protection. Here we report that TbUMSBP2 decondenses in vitro DNA molecules, which were condensed by core histones H2B, H4 or linker histone H1. DNA decondensation is mediated via protein-protein interactions between TbUMSBP2 and these histones, independently of its previously described DNA binding activity. Silencing of the TbUMSBP2 gene resulted in a significant decrease in the disassembly of nucleosomes in T. brucei chromatin, a phenotype that could be reverted, by supplementing the knockdown cells with TbUMSBP2. Transcriptome analysis revealed that silencing of TbUMSBP2 affects the expression of multiple genes in T. brucei, with a most significant effect on the upregulation of the subtelomeric variant surface glycoproteins (VSG) genes, which mediate the antigenic variation in African trypanosomes. These observations suggest that UMSBP2 is a chromatin remodeling protein that functions in the regulation of gene expression and plays a role in the control of antigenic variation in T. brucei.
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Affiliation(s)
- Awakash Soni
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel- Canada and the Kuvin Center for the Study of Infectious and Tropical Diseases, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Olga Klebanov-Akopyan
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel- Canada and the Kuvin Center for the Study of Infectious and Tropical Diseases, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Esteban Erben
- Heidelberg University Center for Molecular Biology at Heidelberg University, DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Inbar Plaschkes
- The Info-Core Bioinformatics Unit, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Hadar Benyamini
- The Info-Core Bioinformatics Unit, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Vera Mitesser
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel- Canada and the Kuvin Center for the Study of Infectious and Tropical Diseases, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Amnon Harel
- Azrieli Faculty of Medicine, Bar-Ilan University, 8 Henrietta Szold Street, Safed1311502, Israel
| | - Katereena Yamin
- Azrieli Faculty of Medicine, Bar-Ilan University, 8 Henrietta Szold Street, Safed1311502, Israel
| | - Itay Onn
- Azrieli Faculty of Medicine, Bar-Ilan University, 8 Henrietta Szold Street, Safed1311502, Israel
| | - Joseph Shlomai
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel- Canada and the Kuvin Center for the Study of Infectious and Tropical Diseases, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
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7
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Hefetz I, Israeli O, Bilinsky G, Plaschkes I, Hazkani-Covo E, Hayouka Z, Lampert A, Helman Y. A reversible mutation in a genomic hotspot saves bacterial swarms from extinction. iScience 2023; 26:106043. [PMID: 36824284 PMCID: PMC9941203 DOI: 10.1016/j.isci.2023.106043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 10/10/2022] [Accepted: 01/20/2023] [Indexed: 01/26/2023] Open
Abstract
Microbial adaptation to changing environmental conditions is frequently mediated by hypermutable sequences. Here we demonstrate that such a hypermutable hotspot within a gene encoding a flagellar unit of Paenibacillus glucanolyticus generated spontaneous non-swarming mutants with increased stress resistance. These mutants, which survived conditions that eliminated wild-type cultures, could be carried by their swarming siblings when the colony spread, consequently increasing their numbers at the spreading edge. Of interest, the hypermutable nature of the aforementioned sequence enabled the non-swarming mutants to serve as "seeds" for a new generation of wild-type cells through reversion of the mutation. Using a mathematical model, we examined the survival dynamics of P. glucanolyticus colonies under fluctuating environments. Our experimental and theoretical results suggest that the non-swarming, stress-resistant mutants can save the colony from extinction. Notably, we identified this hypermutable sequence in flagellar genes of additional Paenibacillus species, suggesting that this phenomenon could be wide-spread and ecologically important.
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Affiliation(s)
- Idan Hefetz
- Department of Biotechnology, Institute for Biological Research, Ness-Ziona, Israel,Department of Plant Pathology and Microbiology, IES, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Ofir Israeli
- Department of Biochemistry and Molecular Biology, Institute for Biological Research, Ness-Ziona, Israel
| | - Gal Bilinsky
- Department of Biochemistry and Molecular Biology, Institute for Biological Research, Ness-Ziona, Israel
| | - Inbar Plaschkes
- Info-CORE, Bioinformatics Unit of the I-CORE at the Hebrew University of Jerusalem, Jerusalem, Israel
| | - Einat Hazkani-Covo
- Department of Natural and Life Sciences, The Open University of Israel, Ra’anana, Israel
| | - Zvi Hayouka
- Department of Biochemistry, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Adam Lampert
- Institute of Environmental Sciences (IES), Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel,Corresponding author
| | - Yael Helman
- Department of Plant Pathology and Microbiology, IES, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel,Corresponding author
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8
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Dahan T, Nassar S, Yajuk O, Steinberg E, Benny O, Abudi N, Plaschkes I, Benyamini H, Gozal D, Abramovitch R, Gileles-Hillel A. Chronic Intermittent Hypoxia during Sleep Causes Browning of Interscapular Adipose Tissue Accompanied by Local Insulin Resistance in Mice. Int J Mol Sci 2022; 23:ijms232415462. [PMID: 36555109 PMCID: PMC9779339 DOI: 10.3390/ijms232415462] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 12/01/2022] [Accepted: 12/03/2022] [Indexed: 12/12/2022] Open
Abstract
Obstructive sleep apnea (OSA) is a highly prevalent condition, characterized by intermittent hypoxia (IH), sleep disruption, and altered autonomic nervous system function. OSA has been independently associated with dyslipidemia, insulin resistance, and metabolic syndrome. Brown adipose tissue (BAT) has been suggested as a modulator of systemic glucose tolerance through adaptive thermogenesis. Reductions in BAT mass have been associated with obesity and metabolic syndrome. No studies have systematically characterized the effects of chronic IH on BAT. Thus, we aimed to delineate IH effects on BAT and concomitant metabolic changes. C57BL/6J 8-week-old male mice were randomly assigned to IH during sleep (alternating 90 s cycles of 6.5% FIO2 followed by 21% FIO2) or normoxia (room air, RA) for 10 weeks. Mice were subjected to glucose tolerance testing and 18F-FDG PET-MRI towards the end of the exposures followed by BAT tissues analyses for morphological and global transcriptomic changes. Animals exposed to IH were glucose intolerant despite lower total body weight and adiposity. BAT tissues in IH-exposed mice demonstrated characteristic changes associated with "browning"-smaller lipids, increased vascularity, and a trend towards higher protein levels of UCP1. Conversely, mitochondrial DNA content and protein levels of respiratory chain complex III were reduced. Pro-inflammatory macrophages were more abundant in IH-exposed BAT. Transcriptomic analysis revealed increases in fatty acid oxidation and oxidative stress pathways in IH-exposed BAT, along with a reduction in pathways related to myogenesis, hypoxia, and IL-4 anti-inflammatory response. Functionally, IH-exposed BAT demonstrated reduced absorption of glucose on PET scans and reduced phosphorylation of AKT in response to insulin. Current studies provide initial evidence for the presence of a maladaptive response of interscapular BAT in response to chronic IH mimicking OSA, resulting in a paradoxical divergence, namely, BAT browning but tissue-specific and systemic insulin resistance. We postulate that oxidative stress, mitochondrial dysfunction, and inflammation may underlie these dichotomous outcomes in BAT.
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Affiliation(s)
- Tehila Dahan
- The Wohl Institute for Translational Medicine, Hadassah Medical Center, Jerusalem 91120, Israel
| | - Shahd Nassar
- The Wohl Institute for Translational Medicine, Hadassah Medical Center, Jerusalem 91120, Israel
- Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Olga Yajuk
- Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Eliana Steinberg
- The Institute for Drug Research, The School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Ofra Benny
- The Institute for Drug Research, The School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Nathalie Abudi
- The Wohl Institute for Translational Medicine, Hadassah Medical Center, Jerusalem 91120, Israel
| | - Inbar Plaschkes
- Info-CORE, Bioinformatics Unit of the I-CORE, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Hadar Benyamini
- Info-CORE, Bioinformatics Unit of the I-CORE, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - David Gozal
- Division of Pediatric Pulmonology, Allergy and Immunology, Comprehensive Sleep Medicine Center, Department of Child Health and Child Health Research Institute, MU Children’s Hospital, University of Missouri School of Medicine, Columbia, MO 65201, USA
| | - Rinat Abramovitch
- The Wohl Institute for Translational Medicine, Hadassah Medical Center, Jerusalem 91120, Israel
- Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Alex Gileles-Hillel
- The Wohl Institute for Translational Medicine, Hadassah Medical Center, Jerusalem 91120, Israel
- Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
- Pediatric Pulmonology and Sleep Unit, Department of Pediatrics, Hadassah Medical Center, Jerusalem 91120, Israel
- Correspondence:
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9
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Zlotnik D, Rabinski T, Halfon A, Anzi S, Plaschkes I, Benyamini H, Nevo Y, Gershoni OY, Rosental B, Hershkovitz E, Ben-Zvi A, Vatine GD. P450 oxidoreductase regulates barrier maturation by mediating retinoic acid metabolism in a model of the human BBB. Stem Cell Reports 2022; 17:2050-2063. [PMID: 35961311 PMCID: PMC9481905 DOI: 10.1016/j.stemcr.2022.07.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 07/14/2022] [Accepted: 07/14/2022] [Indexed: 11/26/2022] Open
Abstract
The blood-brain barrier (BBB) selectively regulates the entry of molecules into the central nervous system (CNS). A crosstalk between brain microvascular endothelial cells (BMECs) and resident CNS cells promotes the acquisition of functional tight junctions (TJs). Retinoic acid (RA), a key signaling molecule during embryonic development, is used to enhance in vitro BBB models’ functional barrier properties. However, its physiological relevance and affected pathways are not fully understood. P450 oxidoreductase (POR) regulates the enzymatic activity of microsomal cytochromes. POR-deficient (PORD) patients display impaired steroid homeostasis and cognitive disabilities. Here, we used both patient-specific POR-deficient and CRISPR-Cas9-mediated POR-depleted induced pluripotent stem cell (iPSC)-derived BMECs (iBMECs) to study the role of POR in the acquisition of functional barrier properties. We demonstrate that POR regulates cellular RA homeostasis and that POR deficiency leads to the accumulation of RA within iBMECs, resulting in the impaired acquisition of TJs and, consequently, to dysfunctional development of barrier properties. Retinoic acid (RA) promotes functional barrier properties POR-deficient iPS-brain endothelial-like cells display impaired barrier development POR mediates CYP26-dependent cellular RA catabolism RA accumulation induces a pro-inflammatory response
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Affiliation(s)
- Dor Zlotnik
- The Department of Physiology and Cell Biology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel; Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel; The Regenerative Medicine and Stem Cell (RMSC) Research Center, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel; The Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Tatiana Rabinski
- The Regenerative Medicine and Stem Cell (RMSC) Research Center, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Aviv Halfon
- Department of Developmental Biology and Cancer Research, the Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Shira Anzi
- Department of Developmental Biology and Cancer Research, the Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Inbar Plaschkes
- Bioinformatics Unit of the I-CORE Computation Center, the Hebrew University, Jerusalem 91120, Israel
| | - Hadar Benyamini
- Bioinformatics Unit of the I-CORE Computation Center, the Hebrew University, Jerusalem 91120, Israel
| | - Yuval Nevo
- Bioinformatics Unit of the I-CORE Computation Center, the Hebrew University, Jerusalem 91120, Israel
| | - Orly Yahalom Gershoni
- The Regenerative Medicine and Stem Cell (RMSC) Research Center, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel; The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Benyamin Rosental
- The Regenerative Medicine and Stem Cell (RMSC) Research Center, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel; The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Eli Hershkovitz
- Israel Pediatric Endocrinology and Diabetes Unit, Soroka University Medical Center, Beer Sheva, Israel
| | - Ayal Ben-Zvi
- Department of Developmental Biology and Cancer Research, the Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Gad D Vatine
- The Department of Physiology and Cell Biology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel; The Regenerative Medicine and Stem Cell (RMSC) Research Center, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel; The Zlotowski Center for Neuroscience, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel.
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10
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Paldor M, Levkovitch-Siany O, Eidelshtein D, Adar R, Enk CD, Marmary Y, Elgavish S, Nevo Y, Benyamini H, Plaschkes I, Klein S, Mali A, Rose-John S, Peled A, Galun E, Axelrod JH. Single-cell transcriptomics reveals a senescence-associated IL-6/CCR6 axis driving radiodermatitis. EMBO Mol Med 2022; 14:e15653. [PMID: 35785521 PMCID: PMC9358397 DOI: 10.15252/emmm.202115653] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 05/31/2022] [Accepted: 06/01/2022] [Indexed: 12/22/2022] Open
Abstract
Irradiation‐induced alopecia and dermatitis (IRIAD) are two of the most visually recognized complications of radiotherapy, of which the molecular and cellular basis remains largely unclear. By combining scRNA‐seq analysis of whole skin‐derived irradiated cells with genetic ablation and molecular inhibition studies, we show that senescence‐associated IL‐6 and IL‐1 signaling, together with IL‐17 upregulation and CCR6+‐mediated immune cell migration, are crucial drivers of IRIAD. Bioinformatics analysis colocalized irradiation‐induced IL‐6 signaling with senescence pathway upregulation largely within epidermal hair follicles, basal keratinocytes, and dermal fibroblasts. Loss of cytokine signaling by genetic ablation in IL‐6−/− or IL‐1R−/− mice, or by molecular blockade, strongly ameliorated IRIAD, as did deficiency of CCL20/CCR6‐mediated immune cell migration in CCR6−/− mice. Moreover, IL‐6 deficiency strongly reduced IL‐17, IL‐22, CCL20, and CCR6 upregulation, whereas CCR6 deficiency reciprocally diminished IL‐6, IL‐17, CCL3, and MHC upregulation, suggesting that proximity‐dependent cellular cross talk promotes IRIAD. Therapeutically, topical application of Janus kinase blockers or inhibition of T‐cell activation by cyclosporine effectively reduced IRIAD, suggesting the potential of targeted approaches for the treatment of dermal side effects in radiotherapy patients.
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Affiliation(s)
- Mor Paldor
- The Goldyne-Savad Institute of Gene Therapy, Hadassah Hebrew University Hospital, Jerusalem, Israel
| | - Orr Levkovitch-Siany
- The Goldyne-Savad Institute of Gene Therapy, Hadassah Hebrew University Hospital, Jerusalem, Israel
| | - Dana Eidelshtein
- The Goldyne-Savad Institute of Gene Therapy, Hadassah Hebrew University Hospital, Jerusalem, Israel
| | - Revital Adar
- The Goldyne-Savad Institute of Gene Therapy, Hadassah Hebrew University Hospital, Jerusalem, Israel
| | - Claes D Enk
- Department of Dermatology, Hadassah Hebrew University Hospital, Jerusalem, Israel
| | - Yitzhak Marmary
- The Goldyne-Savad Institute of Gene Therapy, Hadassah Hebrew University Hospital, Jerusalem, Israel
| | - Sharona Elgavish
- Info-CORE, Bioinformatics Unit of the I-CORE, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yuval Nevo
- Info-CORE, Bioinformatics Unit of the I-CORE, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Hadar Benyamini
- Info-CORE, Bioinformatics Unit of the I-CORE, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Inbar Plaschkes
- Info-CORE, Bioinformatics Unit of the I-CORE, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shiri Klein
- The Goldyne-Savad Institute of Gene Therapy, Hadassah Hebrew University Hospital, Jerusalem, Israel
| | - Alex Mali
- Department of Pathology, Hadassah Hebrew University Hospital, Jerusalem, Israel
| | - Stefan Rose-John
- Institut für Biochemie, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Amnon Peled
- The Goldyne-Savad Institute of Gene Therapy, Hadassah Hebrew University Hospital, Jerusalem, Israel
| | - Eithan Galun
- The Goldyne-Savad Institute of Gene Therapy, Hadassah Hebrew University Hospital, Jerusalem, Israel
| | - Jonathan H Axelrod
- The Goldyne-Savad Institute of Gene Therapy, Hadassah Hebrew University Hospital, Jerusalem, Israel
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11
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Mulla W, Hajaj B, Elyagon S, Mor M, Gillis R, Murninkas M, Klapper-Goldstein H, Plaschkes I, Chalifa-Caspi V, Etzion S, Etzion Y. Rapid Atrial Pacing Promotes Atrial Fibrillation Substrate in Unanesthetized Instrumented Rats. Front Physiol 2019; 10:1218. [PMID: 31616316 PMCID: PMC6763969 DOI: 10.3389/fphys.2019.01218] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 09/06/2019] [Indexed: 12/19/2022] Open
Abstract
Aim The self-perpetuating nature of atrial fibrillation (AF) has been a subject of intense research in large mammalian models exposed to rapid atrial pacing (RAP). Recently, rodents are increasingly used to gain insight into the pathophysiology of AF. However, little is known regarding the effects of RAP on the atria of rats and mice. Using an implantable device for electrophysiological studies in rodents, we examined on a daily basis, the effects of continuous RAP on the developed AF substrate of unanesthetized rats and mice. Methods and Results Aggressive burst pacing did not induce AF at baseline in the large majority of rodents, but repeatedly induced AF episodes in rats exposed to RAP for more than 2 days. A microarray study of left atrial tissue from rats exposed to RAP for 2 days vs. control pacing identified 304 differentially expressed genes. Enrichment analysis and comparison with a dataset of atrial tissue from AF patients revealed indications of increased carbohydrate metabolism and changes in pathways that are thought to play critical roles in human AF, including TGF-beta and IL-6 signaling. Among 19 commonly affected genes in comparison with human AF, downregulation of FOXP1 and upregulation of the KCNK2 gene encoding the Kir2.1 potassium channel were conspicuous findings, suggesting NFAT activation. Further results included reduced expression of MIR-26 and MIR-101, which is in line with NFAT activation. Conclusion Our results demonstrate electrophysiological evidence for AF promoting effects of RAP in rats and several molecular similarities between the effects of RAP in large and small mammalian models.
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Affiliation(s)
- Wesam Mulla
- Cardiac Arrhythmia Research Laboratory, Department of Physiology and Cell Biology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.,Regenerative Medicine and Stem Cell Research Center, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Barak Hajaj
- Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Sigal Elyagon
- Cardiac Arrhythmia Research Laboratory, Department of Physiology and Cell Biology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.,Regenerative Medicine and Stem Cell Research Center, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Michal Mor
- Cardiac Arrhythmia Research Laboratory, Department of Physiology and Cell Biology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Roni Gillis
- Cardiac Arrhythmia Research Laboratory, Department of Physiology and Cell Biology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.,Regenerative Medicine and Stem Cell Research Center, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Michael Murninkas
- Cardiac Arrhythmia Research Laboratory, Department of Physiology and Cell Biology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.,Regenerative Medicine and Stem Cell Research Center, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Hadar Klapper-Goldstein
- Cardiac Arrhythmia Research Laboratory, Department of Physiology and Cell Biology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.,Regenerative Medicine and Stem Cell Research Center, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Inbar Plaschkes
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Vered Chalifa-Caspi
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Sharon Etzion
- Regenerative Medicine and Stem Cell Research Center, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Yoram Etzion
- Cardiac Arrhythmia Research Laboratory, Department of Physiology and Cell Biology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.,Regenerative Medicine and Stem Cell Research Center, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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12
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Yang R, Santos Garcia D, Pérez Montaño F, da Silva GM, Zhao M, Jiménez Guerrero I, Rosenberg T, Chen G, Plaschkes I, Morin S, Walcott R, Burdman S. Complete Assembly of the Genome of an Acidovorax citrulli Strain Reveals a Naturally Occurring Plasmid in This Species. Front Microbiol 2019; 10:1400. [PMID: 31281298 PMCID: PMC6595937 DOI: 10.3389/fmicb.2019.01400] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 06/04/2019] [Indexed: 11/13/2022] Open
Abstract
Acidovorax citrulli is the causal agent of bacterial fruit blotch (BFB), a serious threat to cucurbit crop production worldwide. Based on genetic and phenotypic properties, A. citrulli strains are divided into two major groups: group I strains have been generally isolated from melon and other non-watermelon cucurbits, while group II strains are closely associated with watermelon. In a previous study, we reported the genome of the group I model strain, M6. At that time, the M6 genome was sequenced by MiSeq Illumina technology, with reads assembled into 139 contigs. Here, we report the assembly of the M6 genome following sequencing with PacBio technology. This approach not only allowed full assembly of the M6 genome, but it also revealed the occurrence of a ∼53 kb plasmid. The M6 plasmid, named pACM6, was further confirmed by plasmid extraction, Southern-blot analysis of restricted fragments and obtention of M6-derivative cured strains. pACM6 occurs at low copy numbers (average of ∼4.1 ± 1.3 chromosome equivalents) in A. citrulli M6 and contains 63 open reading frames (ORFs), most of which (55.6%) encoding hypothetical proteins. The plasmid contains several genes encoding type IV secretion components, and typical plasmid-borne genes involved in plasmid maintenance, replication and transfer. The plasmid also carries an operon encoding homologs of a Fic-VbhA toxin-antitoxin (TA) module. Transcriptome data from A. citrulli M6 revealed that, under the tested conditions, the genes encoding the components of this TA system are among the highest expressed genes in pACM6. Whether this TA module plays a role in pACM6 maintenance is still to be determined. Leaf infiltration and seed transmission assays revealed that, under tested conditions, the loss of pACM6 did not affect the virulence of A. citrulli M6. We also show that pACM6 or similar plasmids are present in several group I strains, but absent in all tested group II strains of A. citrulli.
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Affiliation(s)
- Rongzhi Yang
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Diego Santos Garcia
- Department of Entomology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Francisco Pérez Montaño
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel.,Department of Microbiology, University of Seville, Seville, Spain
| | - Gustavo Mateus da Silva
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Mei Zhao
- Department of Plant Pathology, University of Georgia, Athens, GA, United States
| | - Irene Jiménez Guerrero
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Tally Rosenberg
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Gong Chen
- Department of Plant Pathology, University of Georgia, Athens, GA, United States
| | - Inbar Plaschkes
- Bioinformatics Unit, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Shai Morin
- Department of Entomology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Ron Walcott
- Department of Plant Pathology, University of Georgia, Athens, GA, United States
| | - Saul Burdman
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
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13
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Fishilevich S, Nudel R, Rappaport N, Hadar R, Plaschkes I, Iny Stein T, Rosen N, Kohn A, Twik M, Safran M, Lancet D, Cohen D. GeneHancer: genome-wide integration of enhancers and target genes in GeneCards. Database (Oxford) 2017; 2017:3737828. [PMID: 28605766 PMCID: PMC5467550 DOI: 10.1093/database/bax028] [Citation(s) in RCA: 636] [Impact Index Per Article: 90.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 03/10/2017] [Indexed: 12/14/2022]
Abstract
A major challenge in understanding gene regulation is the unequivocal identification of enhancer elements and uncovering their connections to genes. We present GeneHancer, a novel database of human enhancers and their inferred target genes, in the framework of GeneCards. First, we integrated a total of 434 000 reported enhancers from four different genome-wide databases: the Encyclopedia of DNA Elements (ENCODE), the Ensembl regulatory build, the functional annotation of the mammalian genome (FANTOM) project and the VISTA Enhancer Browser. Employing an integration algorithm that aims to remove redundancy, GeneHancer portrays 285 000 integrated candidate enhancers (covering 12.4% of the genome), 94 000 of which are derived from more than one source, and each assigned an annotation-derived confidence score. GeneHancer subsequently links enhancers to genes, using: tissue co-expression correlation between genes and enhancer RNAs, as well as enhancer-targeted transcription factor genes; expression quantitative trait loci for variants within enhancers; and capture Hi-C, a promoter-specific genome conformation assay. The individual scores based on each of these four methods, along with gene–enhancer genomic distances, form the basis for GeneHancer’s combinatorial likelihood-based scores for enhancer–gene pairing. Finally, we define ‘elite’ enhancer–gene relations reflecting both a high-likelihood enhancer definition and a strong enhancer–gene association. GeneHancer predictions are fully integrated in the widely used GeneCards Suite, whereby candidate enhancers and their annotations are displayed on every relevant GeneCard. This assists in the mapping of non-coding variants to enhancers, and via the linked genes, forms a basis for variant–phenotype interpretation of whole-genome sequences in health and disease. Database URL:http://www.genecards.org/
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Affiliation(s)
- Simon Fishilevich
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ron Nudel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Noa Rappaport
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Rotem Hadar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Inbar Plaschkes
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tsippi Iny Stein
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Naomi Rosen
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Asher Kohn
- LifeMap Sciences Inc, Marshfield, MA 02050, USA
| | - Michal Twik
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Marilyn Safran
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Doron Lancet
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Dana Cohen
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
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14
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Rappaport N, Fishilevich S, Nudel R, Twik M, Belinky F, Plaschkes I, Stein TI, Cohen D, Oz-Levi D, Safran M, Lancet D. Rational confederation of genes and diseases: NGS interpretation via GeneCards, MalaCards and VarElect. Biomed Eng Online 2017; 16:72. [PMID: 28830434 PMCID: PMC5568599 DOI: 10.1186/s12938-017-0359-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Background A key challenge in the realm of human disease research is next generation sequencing (NGS) interpretation, whereby identified filtered variant-harboring genes are associated with a patient’s disease phenotypes. This necessitates bioinformatics tools linked to comprehensive knowledgebases. The GeneCards suite databases, which include GeneCards (human genes), MalaCards (human diseases) and PathCards (human pathways) together with additional tools, are presented with the focus on MalaCards utility for NGS interpretation as well as for large scale bioinformatic analyses. Results VarElect, our NGS interpretation tool, leverages the broad information in the GeneCards suite databases. MalaCards algorithms unify disease-related terms and annotations from 69 sources. Further, MalaCards defines hierarchical relatedness—aliases, disease families, a related diseases network, categories and ontological classifications. GeneCards and MalaCards delineate and share a multi-tiered, scored gene-disease network, with stringency levels, including the definition of elite status—high quality gene-disease pairs, coming from manually curated trustworthy sources, that includes 4500 genes for 8000 diseases. This unique resource is key to NGS interpretation by VarElect. VarElect, a comprehensive search tool that helps infer both direct and indirect links between genes and user-supplied disease/phenotype terms, is robustly strengthened by the information found in MalaCards. The indirect mode benefits from GeneCards’ diverse gene-to-gene relationships, including SuperPaths—integrated biological pathways from 12 information sources. We are currently adding an important information layer in the form of “disease SuperPaths”, generated from the gene-disease matrix by an algorithm similar to that previously employed for biological pathway unification. This allows the discovery of novel gene-disease and disease–disease relationships. The advent of whole genome sequencing necessitates capacities to go beyond protein coding genes. GeneCards is highly useful in this respect, as it also addresses 101,976 non-protein-coding RNA genes. In a more recent development, we are currently adding an inclusive map of regulatory elements and their inferred target genes, generated by integration from 4 resources. Conclusions MalaCards provides a rich big-data scaffold for in silico biomedical discovery within the gene-disease universe. VarElect, which depends significantly on both GeneCards and MalaCards power, is a potent tool for supporting the interpretation of wet-lab experiments, notably NGS analyses of disease. The GeneCards suite has thus transcended its 2-decade role in biomedical research, maturing into a key player in clinical investigation.
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Affiliation(s)
- Noa Rappaport
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.,Institute for Systems Biology, Seattle, WA, USA
| | - Simon Fishilevich
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Ron Nudel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Michal Twik
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Frida Belinky
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.,National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA
| | - Inbar Plaschkes
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Tsippi Iny Stein
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Dana Cohen
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Danit Oz-Levi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Marilyn Safran
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Doron Lancet
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
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15
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Ziv T, Chalifa-Caspi V, Denekamp N, Plaschkes I, Kierszniowska S, Blais I, Admon A, Lubzens E. Dormancy in Embryos: Insight from Hydrated Encysted Embryos of an Aquatic Invertebrate. Mol Cell Proteomics 2017; 16:1746-1769. [PMID: 28729386 DOI: 10.1074/mcp.ra117.000109] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Indexed: 11/06/2022] Open
Abstract
Numerous aquatic invertebrates remain dormant for decades in a hydrated state as encysted embryos. In search for functional pathways associated with this form of dormancy, we used label-free quantitative proteomics to compare the proteomes of hydrated encysted dormant embryos (resting eggs; RE) with nondormant embryos (amictic eggs; AM) of the rotifer Brachionus plicatilisA total of 2631 proteins were identified in rotifer eggs. About 62% proteins showed higher abundance in AM relative to RE (Fold Change>3; p = 0.05). Proteins belonging to numerous putative functional pathways showed dramatic changes during dormancy. Most striking were changes in the mitochondria indicating an impeded metabolism. A comparison between the abundance of proteins and their corresponding transcript levels, revealed higher concordance for RE than for AM. Surprisingly, numerous highly abundant dormancy related proteins show corresponding high mRNA levels in metabolically inactive RE. As these mRNAs and proteins degrade at the time of exit from dormancy they may serve as a source of nucleotides and amino acids during the exit from dormancy. Because proteome analyses point to a similarity in functional pathways of hydrated RE and desiccated life forms, REs were dried. Similar hatching and reproductive rates were found for wet and dried REs, suggesting analogous pathways for long-term survival in wet or dry forms. Analysis by KEGG pathways revealed a few general strategies for dormancy, proposing an explanation for the low transcriptional similarity among dormancies across species, despite the resemblance in physiological phenotypes.
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Affiliation(s)
- Tamar Ziv
- From the ‡Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Vered Chalifa-Caspi
- §National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Nadav Denekamp
- ¶Israel Oceanographic and Limnological Research, Haifa, Israel
| | - Inbar Plaschkes
- §National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | | | - Idit Blais
- **Division of Reproductive Endocrinology and IVF, Department of Obstetrics and Gynecology, Carmel Medical Center, Haifa, Israel
| | - Arie Admon
- From the ‡Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Esther Lubzens
- From the ‡Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel;
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16
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Fishilevich S, Nudel R, Rappaport N, Hadar R, Plaschkes I, Iny Stein T, Rosen N, Kohn A, Twik M, Safran M, Lancet D, Cohen D. GeneHancer: genome-wide integration of enhancers and target genes in GeneCards. Database (Oxford) 2017; 2017:3737828. [PMID: 28605766 DOI: 10.1093/database/bax028/3737828] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 03/10/2017] [Indexed: 05/26/2023]
Abstract
UNLABELLED A major challenge in understanding gene regulation is the unequivocal identification of enhancer elements and uncovering their connections to genes. We present GeneHancer, a novel database of human enhancers and their inferred target genes, in the framework of GeneCards. First, we integrated a total of 434 000 reported enhancers from four different genome-wide databases: the Encyclopedia of DNA Elements (ENCODE), the Ensembl regulatory build, the functional annotation of the mammalian genome (FANTOM) project and the VISTA Enhancer Browser. Employing an integration algorithm that aims to remove redundancy, GeneHancer portrays 285 000 integrated candidate enhancers (covering 12.4% of the genome), 94 000 of which are derived from more than one source, and each assigned an annotation-derived confidence score. GeneHancer subsequently links enhancers to genes, using: tissue co-expression correlation between genes and enhancer RNAs, as well as enhancer-targeted transcription factor genes; expression quantitative trait loci for variants within enhancers; and capture Hi-C, a promoter-specific genome conformation assay. The individual scores based on each of these four methods, along with gene–enhancer genomic distances, form the basis for GeneHancer’s combinatorial likelihood-based scores for enhancer–gene pairing. Finally, we define ‘elite’ enhancer–gene relations reflecting both a high-likelihood enhancer definition and a strong enhancer–gene association. GeneHancer predictions are fully integrated in the widely used GeneCards Suite, whereby candidate enhancers and their annotations are displayed on every relevant GeneCard. This assists in the mapping of non-coding variants to enhancers, and via the linked genes, forms a basis for variant–phenotype interpretation of whole-genome sequences in health and disease. DATABASE URL http://www.genecards.org/.
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Affiliation(s)
- Simon Fishilevich
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ron Nudel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Noa Rappaport
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Rotem Hadar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Inbar Plaschkes
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tsippi Iny Stein
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Naomi Rosen
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Asher Kohn
- LifeMap Sciences Inc, Marshfield, MA 02050, USA
| | - Michal Twik
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Marilyn Safran
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Doron Lancet
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Dana Cohen
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
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17
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Ben-Ari Fuchs S, Lieder I, Stelzer G, Mazor Y, Buzhor E, Kaplan S, Bogoch Y, Plaschkes I, Shitrit A, Rappaport N, Kohn A, Edgar R, Shenhav L, Safran M, Lancet D, Guan-Golan Y, Warshawsky D, Shtrichman R. GeneAnalytics: An Integrative Gene Set Analysis Tool for Next Generation Sequencing, RNAseq and Microarray Data. OMICS 2016; 20:139-51. [PMID: 26983021 PMCID: PMC4799705 DOI: 10.1089/omi.2015.0168] [Citation(s) in RCA: 153] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Postgenomics data are produced in large volumes by life sciences and clinical applications of novel omics diagnostics and therapeutics for precision medicine. To move from “data-to-knowledge-to-innovation,” a crucial missing step in the current era is, however, our limited understanding of biological and clinical contexts associated with data. Prominent among the emerging remedies to this challenge are the gene set enrichment tools. This study reports on GeneAnalytics™ (geneanalytics.genecards.org), a comprehensive and easy-to-apply gene set analysis tool for rapid contextualization of expression patterns and functional signatures embedded in the postgenomics Big Data domains, such as Next Generation Sequencing (NGS), RNAseq, and microarray experiments. GeneAnalytics' differentiating features include in-depth evidence-based scoring algorithms, an intuitive user interface and proprietary unified data. GeneAnalytics employs the LifeMap Science's GeneCards suite, including the GeneCards®—the human gene database; the MalaCards—the human diseases database; and the PathCards—the biological pathways database. Expression-based analysis in GeneAnalytics relies on the LifeMap Discovery®—the embryonic development and stem cells database, which includes manually curated expression data for normal and diseased tissues, enabling advanced matching algorithm for gene–tissue association. This assists in evaluating differentiation protocols and discovering biomarkers for tissues and cells. Results are directly linked to gene, disease, or cell “cards” in the GeneCards suite. Future developments aim to enhance the GeneAnalytics algorithm as well as visualizations, employing varied graphical display items. Such attributes make GeneAnalytics a broadly applicable postgenomics data analyses and interpretation tool for translation of data to knowledge-based innovation in various Big Data fields such as precision medicine, ecogenomics, nutrigenomics, pharmacogenomics, vaccinomics, and others yet to emerge on the postgenomics horizon.
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Affiliation(s)
| | | | - Gil Stelzer
- 1 LifeMap Sciences Ltd. , Tel Aviv, Israel .,2 Molecular Genetics, Weizmann Institute of Science , Rehovot, Israel
| | | | - Ella Buzhor
- 3 Institute of Oncology, Sheba Medical Center , Tel Hashomer, Israel
| | | | - Yoel Bogoch
- 4 Surgical Department, Sourasky Medical Centre , Tel Aviv, Israel
| | | | - Alina Shitrit
- 2 Molecular Genetics, Weizmann Institute of Science , Rehovot, Israel
| | - Noa Rappaport
- 2 Molecular Genetics, Weizmann Institute of Science , Rehovot, Israel
| | - Asher Kohn
- 5 LifeMap Sciences, Inc. , Marshfield, Massachusetts, USA
| | - Ron Edgar
- 6 Venividi Solutions LLC , Rockville, Maryland, USA
| | | | - Marilyn Safran
- 2 Molecular Genetics, Weizmann Institute of Science , Rehovot, Israel
| | - Doron Lancet
- 2 Molecular Genetics, Weizmann Institute of Science , Rehovot, Israel
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18
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Rappaport N, Twik M, Plaschkes I, Nudel R, Iny Stein T, Levitt J, Gershoni M, Morrey CP, Safran M, Lancet D. MalaCards: an amalgamated human disease compendium with diverse clinical and genetic annotation and structured search. Nucleic Acids Res 2016; 45:D877-D887. [PMID: 27899610 PMCID: PMC5210521 DOI: 10.1093/nar/gkw1012] [Citation(s) in RCA: 317] [Impact Index Per Article: 39.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 10/14/2016] [Accepted: 10/29/2016] [Indexed: 12/13/2022] Open
Abstract
The MalaCards human disease database (http://www.malacards.org/) is an integrated compendium of annotated diseases mined from 68 data sources. MalaCards has a web card for each of ∼20 000 disease entries, in six global categories. It portrays a broad array of annotation topics in 15 sections, including Summaries, Symptoms, Anatomical Context, Drugs, Genetic Tests, Variations and Publications. The Aliases and Classifications section reflects an algorithm for disease name integration across often-conflicting sources, providing effective annotation consolidation. A central feature is a balanced Genes section, with scores reflecting the strength of disease-gene associations. This is accompanied by other gene-related disease information such as pathways, mouse phenotypes and GO-terms, stemming from MalaCards’ affiliation with the GeneCards Suite of databases. MalaCards’ capacity to inter-link information from complementary sources, along with its elaborate search function, relational database infrastructure and convenient data dumps, allows it to tackle its rich disease annotation landscape, and facilitates systems analyses and genome sequence interpretation. MalaCards adopts a ‘flat’ disease-card approach, but each card is mapped to popular hierarchical ontologies (e.g. International Classification of Diseases, Human Phenotype Ontology and Unified Medical Language System) and also contains information about multi-level relations among diseases, thereby providing an optimal tool for disease representation and scrutiny.
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Affiliation(s)
- Noa Rappaport
- Department of Molecular Genetics, the Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Michal Twik
- Department of Molecular Genetics, the Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Inbar Plaschkes
- Department of Molecular Genetics, the Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Ron Nudel
- Department of Molecular Genetics, the Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Tsippi Iny Stein
- Department of Molecular Genetics, the Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Jacob Levitt
- Department of Molecular Genetics, the Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Moran Gershoni
- Department of Molecular Genetics, the Weizmann Institute of Science, Rehovot, 76100, Israel
| | - C Paul Morrey
- Department of Information Systems and Technology, Utah Valley University, Orem, UT 84058, USA
| | - Marilyn Safran
- Department of Molecular Genetics, the Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Doron Lancet
- Department of Molecular Genetics, the Weizmann Institute of Science, Rehovot, 76100, Israel
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19
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Stelzer G, Plaschkes I, Oz-Levi D, Alkelai A, Olender T, Zimmerman S, Twik M, Belinky F, Fishilevich S, Nudel R, Guan-Golan Y, Warshawsky D, Dahary D, Kohn A, Mazor Y, Kaplan S, Iny Stein T, Baris HN, Rappaport N, Safran M, Lancet D. VarElect: the phenotype-based variation prioritizer of the GeneCards Suite. BMC Genomics 2016; 17 Suppl 2:444. [PMID: 27357693 PMCID: PMC4928145 DOI: 10.1186/s12864-016-2722-2] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Background Next generation sequencing (NGS) provides a key technology for deciphering the genetic underpinnings of human diseases. Typical NGS analyses of a patient depict tens of thousands non-reference coding variants, but only one or very few are expected to be significant for the relevant disorder. In a filtering stage, one employs family segregation, rarity in the population, predicted protein impact and evolutionary conservation as a means for shortening the variation list. However, narrowing down further towards culprit disease genes usually entails laborious seeking of gene-phenotype relationships, consulting numerous separate databases. Thus, a major challenge is to transition from the few hundred shortlisted genes to the most viable disease-causing candidates. Results We describe a novel tool, VarElect (http://ve.genecards.org), a comprehensive phenotype-dependent variant/gene prioritizer, based on the widely-used GeneCards, which helps rapidly identify causal mutations with extensive evidence. The GeneCards suite offers an effective and speedy alternative, whereby >120 gene-centric automatically-mined data sources are jointly available for the task. VarElect cashes on this wealth of information, as well as on GeneCards’ powerful free-text Boolean search and scoring capabilities, proficiently matching variant-containing genes to submitted disease/symptom keywords. The tool also leverages the rich disease and pathway information of MalaCards, the human disease database, and PathCards, the unified pathway (SuperPaths) database, both within the GeneCards Suite. The VarElect algorithm infers direct as well as indirect links between genes and phenotypes, the latter benefitting from GeneCards’ diverse gene-to-gene data links in GenesLikeMe. Finally, our tool offers an extensive gene-phenotype evidence portrayal (“MiniCards”) and hyperlinks to the parent databases. Conclusions We demonstrate that VarElect compares favorably with several often-used NGS phenotyping tools, thus providing a robust facility for ranking genes, pointing out their likelihood to be related to a patient’s disease. VarElect’s capacity to automatically process numerous NGS cases, either in stand-alone format or in VCF-analyzer mode (TGex and VarAnnot), is indispensable for emerging clinical projects that involve thousands of whole exome/genome NGS analyses. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2722-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gil Stelzer
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.,LifeMap Sciences Ltd, Tel Aviv, Israel
| | | | - Danit Oz-Levi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Anna Alkelai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Tsviya Olender
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Shahar Zimmerman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Michal Twik
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Frida Belinky
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Simon Fishilevich
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Ron Nudel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | | | | | - Dvir Dahary
- LifeMap Sciences Ltd, Tel Aviv, Israel.,Toldot Genetics Ltd, Hod Hasharon, Israel
| | - Asher Kohn
- LifeMap Sciences Inc, Marshfield, MA, 02050, USA
| | | | | | - Tsippi Iny Stein
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Hagit N Baris
- The Genetics Institute, Rambam Health Care Campus, Haifa, Israel.,Rappaport School of Medicine, Technion, Haifa, Israel
| | - Noa Rappaport
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Marilyn Safran
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Doron Lancet
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
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20
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Stelzer G, Rosen N, Plaschkes I, Zimmerman S, Twik M, Fishilevich S, Stein TI, Nudel R, Lieder I, Mazor Y, Kaplan S, Dahary D, Warshawsky D, Guan-Golan Y, Kohn A, Rappaport N, Safran M, Lancet D. The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence Analyses. ACTA ACUST UNITED AC 2016; 54:1.30.1-1.30.33. [PMID: 27322403 DOI: 10.1002/cpbi.5] [Citation(s) in RCA: 1990] [Impact Index Per Article: 248.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
GeneCards, the human gene compendium, enables researchers to effectively navigate and inter-relate the wide universe of human genes, diseases, variants, proteins, cells, and biological pathways. Our recently launched Version 4 has a revamped infrastructure facilitating faster data updates, better-targeted data queries, and friendlier user experience. It also provides a stronger foundation for the GeneCards suite of companion databases and analysis tools. Improved data unification includes gene-disease links via MalaCards and merged biological pathways via PathCards, as well as drug information and proteome expression. VarElect, another suite member, is a phenotype prioritizer for next-generation sequencing, leveraging the GeneCards and MalaCards knowledgebase. It automatically infers direct and indirect scored associations between hundreds or even thousands of variant-containing genes and disease phenotype terms. VarElect's capabilities, either independently or within TGex, our comprehensive variant analysis pipeline, help prepare for the challenge of clinical projects that involve thousands of exome/genome NGS analyses. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Gil Stelzer
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.,These authors contributed equally to the paper
| | - Naomi Rosen
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.,These authors contributed equally to the paper
| | - Inbar Plaschkes
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.,LifeMap Sciences Ltd, Tel Aviv, Israel
| | - Shahar Zimmerman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Michal Twik
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Simon Fishilevich
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Tsippi Iny Stein
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Ron Nudel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | | | | | | | - Dvir Dahary
- LifeMap Sciences Ltd, Tel Aviv, Israel.,Toldot Genetics Ltd, Hod Hasharon, Israel
| | | | | | - Asher Kohn
- LifeMap Sciences Inc, Marshfield, Massachusetts
| | - Noa Rappaport
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Marilyn Safran
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Doron Lancet
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.,Corresponding author
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21
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Tynyakov J, Bentov S, Abehsera S, Yehezkel G, Roth Z, Khalaila I, Weil S, Berman A, Plaschkes I, Tom M, Aflalo ED, Sagi A. A crayfish molar tooth protein with putative mineralized exoskeletal chitinous matrix properties. ACTA ACUST UNITED AC 2015; 218:3487-98. [PMID: 26385331 DOI: 10.1242/jeb.123539] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 09/04/2015] [Indexed: 01/08/2023]
Abstract
Some crustaceans possess exoskeletons that are reinforced with calcium carbonate. In the crayfish Cherax quadricarinatus, the molar tooth, which is part of the mandibular exoskeleton, contains an unusual crystalline enamel-like apatite layer. As this layer resembles vertebrate enamel in composition and function, it offers an interesting example of convergent evolution. Unlike other parts of the crayfish exoskeleton, which is periodically shed and regenerated during the molt cycle, molar mineral deposition takes place during the pre-molt stage. The molar mineral composition transforms continuously from fluorapatite through amorphous calcium phosphate to amorphous calcium carbonate and is mounted on chitin. The process of crayfish molar formation is entirely extracellular and presumably controlled by proteins, lipids, polysaccharides, low-molecular weight molecules and calcium salts. We have identified a novel molar protein termed Cq-M15 from C. quadricarinatus and cloned its transcript from the molar-forming epithelium. Its transcript and differential expression were confirmed by a next-generation sequencing library. The predicted acidic pI of Cq-M15 suggests its possible involvement in mineral arrangement. Cq-M15 is expressed in several exoskeletal tissues at pre-molt and its silencing is lethal. Like other arthropod cuticular proteins, Cq-M15 possesses a chitin-binding Rebers-Riddiford domain, with a recombinant version of the protein found to bind chitin. Cq-M15 was also found to interact with calcium ions in a concentration-dependent manner. This latter property might make Cq-M15 useful for bone and dental regenerative efforts. We suggest that, in the molar tooth, this protein might be involved in calcium phosphate and/or carbonate precipitation.
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Affiliation(s)
- Jenny Tynyakov
- Department of Life Sciences, Ben-Gurion University, PO Box 653, Beer-Sheva 84105, Israel National Institute for Biotechnology in the Negev, Ben-Gurion University, PO Box 653, Beer-Sheva 84105, Israel
| | - Shmuel Bentov
- Department of Life Sciences, Ben-Gurion University, PO Box 653, Beer-Sheva 84105, Israel National Institute for Biotechnology in the Negev, Ben-Gurion University, PO Box 653, Beer-Sheva 84105, Israel
| | - Shai Abehsera
- Department of Life Sciences, Ben-Gurion University, PO Box 653, Beer-Sheva 84105, Israel
| | - Galit Yehezkel
- Department of Biotechnology Engineering, Ben-Gurion University, PO Box 653, Beer-Sheva 84105, Israel
| | - Ziv Roth
- Department of Life Sciences, Ben-Gurion University, PO Box 653, Beer-Sheva 84105, Israel
| | - Isam Khalaila
- Department of Biotechnology Engineering, Ben-Gurion University, PO Box 653, Beer-Sheva 84105, Israel
| | - Simy Weil
- Department of Life Sciences, Ben-Gurion University, PO Box 653, Beer-Sheva 84105, Israel
| | - Amir Berman
- Department of Biotechnology Engineering, Ben-Gurion University, PO Box 653, Beer-Sheva 84105, Israel
| | - Inbar Plaschkes
- National Institute for Biotechnology in the Negev, Ben-Gurion University, PO Box 653, Beer-Sheva 84105, Israel
| | - Moshe Tom
- Israel Oceanographic and Limnological Research, Haifa 8511911, Israel
| | - Eliahu D Aflalo
- Department of Life Sciences, Ben-Gurion University, PO Box 653, Beer-Sheva 84105, Israel National Institute for Biotechnology in the Negev, Ben-Gurion University, PO Box 653, Beer-Sheva 84105, Israel
| | - Amir Sagi
- Department of Life Sciences, Ben-Gurion University, PO Box 653, Beer-Sheva 84105, Israel National Institute for Biotechnology in the Negev, Ben-Gurion University, PO Box 653, Beer-Sheva 84105, Israel
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22
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Elran R, Raam M, Kraus R, Brekhman V, Sher N, Plaschkes I, Chalifa-Caspi V, Lotan T. Early and late response of Nematostella vectensis transcriptome to heavy metals. Mol Ecol 2014; 23:4722-36. [PMID: 25145541 DOI: 10.1111/mec.12891] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 07/22/2014] [Accepted: 08/13/2014] [Indexed: 12/28/2022]
Abstract
Environmental contamination from heavy metals poses a global concern for the marine environment, as heavy metals are passed up the food chain and persist in the environment long after the pollution source is contained. Cnidarians play an important role in shaping marine ecosystems, but environmental pollution profoundly affects their vitality. Among the cnidarians, the sea anemone Nematostella vectensis is an advantageous model for addressing questions in molecular ecology and toxicology as it tolerates extreme environments and its genome has been published. Here, we employed a transcriptome-wide RNA-Seq approach to analyse N. vectensis molecular defence mechanisms against four heavy metals: Hg, Cu, Cd and Zn. Altogether, more than 4800 transcripts showed significant changes in gene expression. Hg had the greatest impact on up-regulating transcripts, followed by Cu, Zn and Cd. We identified, for the first time in Cnidaria, co-up-regulation of immediate-early transcription factors such as Egr1, AP1 and NF-κB. Time-course analysis of these genes revealed their early expression as rapidly as one hour after exposure to heavy metals, suggesting that they may complement or substitute for the roles of the metal-mediating Mtf1 transcription factor. We further characterized the regulation of a large array of stress-response gene families, including Hsp, ABC, CYP members and phytochelatin synthase, that may regulate synthesis of the metal-binding phytochelatins instead of the metallothioneins that are absent from Cnidaria genome. This study provides mechanistic insight into heavy metal toxicity in N. vectensis and sheds light on ancestral stress adaptations.
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Affiliation(s)
- Ron Elran
- Marine Biology Department, The Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
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Degu A, Hochberg U, Sikron N, Venturini L, Buson G, Ghan R, Plaschkes I, Batushansky A, Chalifa-Caspi V, Mattivi F, Delledonne M, Pezzotti M, Rachmilevitch S, Cramer GR, Fait A. Metabolite and transcript profiling of berry skin during fruit development elucidates differential regulation between Cabernet Sauvignon and Shiraz cultivars at branching points in the polyphenol pathway. BMC Plant Biol 2014; 14:188. [PMID: 25064275 PMCID: PMC4222437 DOI: 10.1186/s12870-014-0188-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 07/11/2014] [Indexed: 05/18/2023]
Abstract
BACKGROUND Grapevine berries undergo complex biochemical changes during fruit maturation, many of which are dependent upon the variety and its environment. In order to elucidate the varietal dependent developmental regulation of primary and specialized metabolism, berry skins of Cabernet Sauvignon and Shiraz were subjected to gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS) based metabolite profiling from pre-veraison to harvest. The generated dataset was augmented with transcript profiling using RNAseq. RESULTS The analysis of the metabolite data revealed similar developmental patterns of change in primary metabolites between the two cultivars. Nevertheless, towards maturity the extent of change in the major organic acid and sugars (i.e. sucrose, trehalose, malate) and precursors of aromatic and phenolic compounds such as quinate and shikimate was greater in Shiraz compared to Cabernet Sauvignon. In contrast, distinct directional projections on the PCA plot of the two cultivars samples towards maturation when using the specialized metabolite profiles were apparent, suggesting a cultivar-dependent regulation of the specialized metabolism. Generally, Shiraz displayed greater upregulation of the entire polyphenol pathway and specifically higher accumulation of piceid and coumaroyl anthocyanin forms than Cabernet Sauvignon from veraison onwards. Transcript profiling revealed coordinated increased transcript abundance for genes encoding enzymes of committing steps in the phenylpropanoid pathway. The anthocyanin metabolite profile showed F3'5'H-mediated delphinidin-type anthocyanin enrichment in both varieties towards maturation, consistent with the transcript data, indicating that the F3'5'H-governed branching step dominates the anthocyanin profile at late berry development. Correlation analysis confirmed the tightly coordinated metabolic changes during development, and suggested a source-sink relation between the central and specialized metabolism, stronger in Shiraz than Cabernet Sauvignon. RNAseq analysis also revealed that the two cultivars exhibited distinct pattern of changes in genes related to abscisic acid (ABA) biosynthesis enzymes. CONCLUSIONS Compared with CS, Shiraz showed higher number of significant correlations between metabolites, which together with the relatively higher expression of flavonoid genes supports the evidence of increased accumulation of coumaroyl anthocyanins in that cultivar. Enhanced stress related metabolism, e.g. trehalose, stilbene and ABA in Shiraz berry-skin are consistent with its relatively higher susceptibility to environmental cues.
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Affiliation(s)
- Asfaw Degu
- The Albert Katz International School, Beer-Sheva, Israel
- The French Associates Institute for Agriculture and Biotechnology of Drylands, the Jacob Blaustein Institute for Desert Research, Ben-Gurion University of the Negev, Sede Boqer 84990, Israel
| | - Uri Hochberg
- The Albert Katz International School, Beer-Sheva, Israel
- The French Associates Institute for Agriculture and Biotechnology of Drylands, the Jacob Blaustein Institute for Desert Research, Ben-Gurion University of the Negev, Sede Boqer 84990, Israel
| | - Noga Sikron
- The French Associates Institute for Agriculture and Biotechnology of Drylands, the Jacob Blaustein Institute for Desert Research, Ben-Gurion University of the Negev, Sede Boqer 84990, Israel
| | - Luca Venturini
- Biotechnology Department, University of Verona, Strada Le Grazie 15, Verona, Italy
| | - Genny Buson
- Biotechnology Department, University of Verona, Strada Le Grazie 15, Verona, Italy
| | - Ryan Ghan
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno 9557, NV, USA
| | - Inbar Plaschkes
- The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Albert Batushansky
- The Albert Katz International School, Beer-Sheva, Israel
- The French Associates Institute for Agriculture and Biotechnology of Drylands, the Jacob Blaustein Institute for Desert Research, Ben-Gurion University of the Negev, Sede Boqer 84990, Israel
| | - Vered Chalifa-Caspi
- The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Fulvio Mattivi
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Italy
| | - Massimo Delledonne
- Biotechnology Department, University of Verona, Strada Le Grazie 15, Verona, Italy
| | - Mario Pezzotti
- Biotechnology Department, University of Verona, Strada Le Grazie 15, Verona, Italy
| | - Shimon Rachmilevitch
- The French Associates Institute for Agriculture and Biotechnology of Drylands, the Jacob Blaustein Institute for Desert Research, Ben-Gurion University of the Negev, Sede Boqer 84990, Israel
| | - Grant R Cramer
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno 9557, NV, USA
| | - Aaron Fait
- The French Associates Institute for Agriculture and Biotechnology of Drylands, the Jacob Blaustein Institute for Desert Research, Ben-Gurion University of the Negev, Sede Boqer 84990, Israel
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Toker L, Bersudsky Y, Plaschkes I, Chalifa-Caspi V, Berry GT, Buccafusca R, Moechars D, Belmaker RH, Agam G. Inositol-related gene knockouts mimic lithium's effect on mitochondrial function. Neuropsychopharmacology 2014; 39:319-28. [PMID: 23924600 PMCID: PMC3870788 DOI: 10.1038/npp.2013.194] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 07/17/2013] [Accepted: 07/18/2013] [Indexed: 01/22/2023]
Abstract
The inositol-depletion hypothesis proposes that lithium attenuates phosphatidylinositol signaling. Knockout (KO) mice of two genes (IMPA1 or Slc5a3), each encoding for a protein related to inositol metabolism, were studied in comparison with lithium-treated mice. Since we previously demonstrated that these KO mice exhibit a lithium-like neurochemical and behavioral phenotype, here we searched for pathways that may mediate lithium's/the KO effects. We performed a DNA-microarray study searching for pathways affected both by chronic lithium treatment and by the KO of each of the genes. The data were analyzed using three different bioinformatics approaches. We found upregulation of mitochondria-related genes in frontal cortex of lithium-treated, IMPA1 and Slc5a3 KO mice. Three out of seven genes differentially expressed in all three models, Cox5a, Ndufs7, and Ndufab, all members of the mitochondrial electron transfer chain, have previously been associated with bipolar disorder and/or lithium treatment. Upregulation of the expression of these genes was verified by real-time PCR. To further support the link between mitochondrial function and lithium's effect on behavior, we determined the capacity of chronic low-dose rotenone, a mitochondrial respiratory chain complex I inhibitor, to alter lithium-induced behavior as measured by the forced-swim and the amphetamine-induced hyperlocomotion paradigms. Rontenone treatment counteracted lithium's effect on behavior, supporting the proposition suggested by the bioinformatics analysis for a mitochondrial function involvement in behavioral effects of lithium mediated by inositol metabolism alterations.The results provide support for the notion that mitochondrial dysfunction is linked to bipolar disorder and can be ameliorated by lithium. The phenotypic similarities between lithium-treated wild-type mice and the two KO models suggest that lithium may affect behavior by altering inositol metabolism.
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Affiliation(s)
- Lilach Toker
- Department of Clinical Biochemistry and Pharmacology, Ben-Gurion University of the Negev, Beer-Sheva, Israel,Psychiatry Research Unit, Ben-Gurion University of the Negev, Beer-Sheva, Israel,Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Yuly Bersudsky
- Psychiatry Research Unit, Ben-Gurion University of the Negev, Beer-Sheva, Israel,Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel,Mental Health Center, Beer-Sheva, Israel
| | - Inbar Plaschkes
- National Institute for Biotechnology in the Negev (NIBN), Beer-Sheva, Israel
| | - Vered Chalifa-Caspi
- National Institute for Biotechnology in the Negev (NIBN), Beer-Sheva, Israel
| | - Gerard T Berry
- Metabolism Program Division of Genetics, Children's Hospital Boston, Harvard Medical School, Boston, MA, USA
| | - Roberto Buccafusca
- Metabolism Program Division of Genetics, Children's Hospital Boston, Harvard Medical School, Boston, MA, USA
| | - Dieder Moechars
- Johnson & Johnson Pharmaceutical Research and Development, Beerse, Belgium
| | - R H Belmaker
- Psychiatry Research Unit, Ben-Gurion University of the Negev, Beer-Sheva, Israel,Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel,Mental Health Center, Beer-Sheva, Israel
| | - Galila Agam
- Department of Clinical Biochemistry and Pharmacology, Ben-Gurion University of the Negev, Beer-Sheva, Israel,Psychiatry Research Unit, Ben-Gurion University of the Negev, Beer-Sheva, Israel,Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel,Division of Basic Sciences, Department of Clinical Biochemistry and Pharmacology, and Psychiatry Research Unit, Faculty of Health Sciences, Ben-Gurion University of the Negev and Mental Health Center, PO Box 4600, Beer-Sheva 84170, Israel, Tel: +972 8640 1737, E-mail:
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Bakshi S, Chalifa-Caspi V, Plaschkes I, Perevozkin I, Gurevich M, Schwartz R. Gene expression analysis reveals functional pathways of glatiramer acetate activation. Expert Opin Ther Targets 2013; 17:351-62. [PMID: 23469939 DOI: 10.1517/14728222.2013.778829] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
BACKGROUND Glatiramer acetate (GA, Copaxone®), a mixture of polymers comprising four amino acids, is approved for treatment of relapsing-remitting multiple sclerosis and clinically isolated syndrome. GA mediates its activity by induction of GA-specific T cells that shift the T cell balance from a dominant proinflammatory phenotype (Th1/Th17) to an anti-inflammatory phenotype (Th2/Treg). OBJECTIVE To characterize the functional pathways by which GA acts on immune cells, the authors conducted gene expression profiling using glatiramoid-stimulated splenocytes. METHODS Mice were immunized with GA and harvested splenocytes were reactivated ex vivo with GA or a purported generic GA. Gene expression profiles and functional pathways were evaluated in reactivated splenocytes. RESULTS Overall, 1,474 genes were significantly upregulated or downregulated by GA. The main functional pathways induced by GA were: increased proliferation and activation of immune cells including T and B lymphocytes, stimulation of antigen presenting cells and differentiation of effector T lymphocytes. T-helper cell differentiation was the most significant canonical pathway associated with gene transcripts altered by GA. These expression patterns were not observed when splenocytes were activated with generic GA. CONCLUSION GA-induced functional pathways coincide with known mechanisms of GA activity in MS patients and further support the unique therapeutic effect of this drug.
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Affiliation(s)
- Shlomo Bakshi
- Teva Pharmaceutical Industries, P.O. Box 8077, Netanya 42504, Israel
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Grafi G, Chalifa-Caspi V, Nagar T, Plaschkes I, Barak S, Ransbotyn V. Plant response to stress meets dedifferentiation. Planta 2011; 233:433-8. [PMID: 21312042 DOI: 10.1007/s00425-011-1366-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Accepted: 01/20/2011] [Indexed: 05/08/2023]
Abstract
Plant response to various stress conditions often results in expression of common genes, known as stress-responsive/inducible genes. Accumulating data point to a common, yet elusive process underlying the response of plant cells to stress. Evidence derived from transcriptome profiling of shoot apical meristem stem cells, dedifferentiating protoplast cells as well as from senescing cells lends support to a model in which a common response of cells to certain biotic and abiotic stresses converges on cellular dedifferentiation whereby cells first acquire a stem cell-like state before assuming a new fate.
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Affiliation(s)
- Gideon Grafi
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben-Gurion, 84990, Israel.
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Damri M, Granot G, Ben-Meir H, Avivi Y, Plaschkes I, Chalifa-Caspi V, Wolfson M, Fraifeld V, Grafi G. Senescing Cells Share Common Features with Dedifferentiating Cells. Rejuvenation Res 2009; 12:435-43. [DOI: 10.1089/rej.2009.0887] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Meytal Damri
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Beer-Sheva, Israel and Midreshet Ben-Gurion, Israel
- The Shraga Segal Department of Microbiology and Immunology, Faculty of Health Sciences, Center for Multidisciplinary Research on Aging, Ben-Gurion University of the Negev, Beer-Sheva, Israel and Midreshet Ben-Gurion, Israel
| | - Gila Granot
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Beer-Sheva, Israel and Midreshet Ben-Gurion, Israel
| | - Hagit Ben-Meir
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Beer-Sheva, Israel and Midreshet Ben-Gurion, Israel
| | - Yigal Avivi
- Department of Plant Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Inbar Plaschkes
- The National Institute for Biotechnology, Ben-Gurion University of the Negev, Beer-Sheva, Israel and Midreshet Ben-Gurion, Israel
| | - Vered Chalifa-Caspi
- The National Institute for Biotechnology, Ben-Gurion University of the Negev, Beer-Sheva, Israel and Midreshet Ben-Gurion, Israel
| | - Marina Wolfson
- The Shraga Segal Department of Microbiology and Immunology, Faculty of Health Sciences, Center for Multidisciplinary Research on Aging, Ben-Gurion University of the Negev, Beer-Sheva, Israel and Midreshet Ben-Gurion, Israel
| | - Vadim Fraifeld
- The Shraga Segal Department of Microbiology and Immunology, Faculty of Health Sciences, Center for Multidisciplinary Research on Aging, Ben-Gurion University of the Negev, Beer-Sheva, Israel and Midreshet Ben-Gurion, Israel
| | - Gideon Grafi
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Beer-Sheva, Israel and Midreshet Ben-Gurion, Israel
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28
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Rosenfeld R, Bangio H, Gerwig GJ, Rosenberg R, Aloni R, Cohen Y, Amor Y, Plaschkes I, Kamerling JP, Maya RBY. A lectin array-based methodology for the analysis of protein glycosylation. ACTA ACUST UNITED AC 2006; 70:415-26. [PMID: 17112594 DOI: 10.1016/j.jbbm.2006.09.008] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2006] [Revised: 09/17/2006] [Accepted: 09/17/2006] [Indexed: 02/07/2023]
Abstract
Glycosylation is the most versatile and one of the most abundant protein modifications. It has a structural role as well as diverse functional roles in many specific biological functions, including cancer development, viral and bacterial infections, and autoimmunity. The diverse roles of glycosylation in biological processes are rapidly growing areas of research, however, Glycobiology research is limited by the lack of a technology for rapid analysis of glycan composition of glycoproteins. Currently used methods for glycoanalysis are complex, typically requiring high levels of expertise and days to provide answers, and are not readily available to all researcher. We have developed a lectin array-based method, Qproteome GlycoArray kits, for rapid analysis of glycosylation profiles of glycoproteins. Glycoanalysis is performed on intact glycoproteins, requiring only 4-6 h for most analysis types. The method, demonstrated in this manuscript by several examples, is based on binding of an intact glycoprotein to the arrayed lectins, resulting in a characteristic fingerprint that is highly sensitive to changes in the protein's glycan composition. The large number of lectins, each with its specific recognition pattern, ensures high sensitivity to changes in the glycosylation pattern. A set of proprietary algorithms automatically interpret the fingerprint signals to provide a comprehensive glycan profile output.
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Abstract
Topoisomerase I (topo I) is a nuclear enzyme responsible for the topological state of DNA and therefore participates in most DNA transactions, particularly in transcription. Topo I, a ubiquitous enzyme, was identified and characterized in various cell types and tissues; however, the characterization of topo I in the intact central nervous system was not performed. Here we investigated, for the first time, the activity, level, and distribution pattern of topo I in the various selected brain regions in the mouse. In the visual cortex, cerebellum, and striatum the activity of topo I was 3-4-fold higher compared to that found in the hippocampus and hypothalamus. Immunohistochemical and immunofluorescence analyses revealed specific distribution patterns of topo I protein in neurons of each of the areas examined. The highest topo I levels were observed in inhibitory neurons. In addition to the expected nuclear localization of this protein, some neurons exhibited significant cytoplasmic content as well. The activity and level of topo I is age- and gender-dependent. It increases from birth to maturity and decreases, more significantly in males, with senescence. These results point to a possible importance and involvement of topo I activity and regulation in various brain functions.
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Affiliation(s)
- Inbar Plaschkes
- Department of Microbiology & Immunology, the Ben-Gurion University Cancer Research Center, Beer-Sheva 84105, Israel
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