1
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Shakked A, Petrover Z, Aharonov A, Ghiringhelli M, Umansky KB, Kain D, Elkahal J, Divinsky Y, Nguyen PD, Miyara S, Friedlander G, Savidor A, Zhang L, Perez DE, Sarig R, Lendengolts D, Bueno-Levy H, Kastan N, Levin Y, Bakkers J, Gepstein L, Tzahor E. Redifferentiated cardiomyocytes retain residual dedifferentiation signatures and are protected against ischemic injury. Nat Cardiovasc Res 2023; 2:383-398. [PMID: 37974970 PMCID: PMC10653068 DOI: 10.1038/s44161-023-00250-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 02/09/2023] [Indexed: 11/19/2023]
Abstract
Cardiomyocyte proliferation and dedifferentiation have fueled the field of regenerative cardiology in recent years, whereas the reverse process of redifferentiation remains largely unexplored. Redifferentiation is characterized by the restoration of function lost during dedifferentiation. Previously, we showed that ERBB2-mediated heart regeneration has these two distinct phases: transient dedifferentiation and redifferentiation. Here we survey the temporal transcriptomic and proteomic landscape of dedifferentiation-redifferentiation in adult mouse hearts and reveal that well-characterized dedifferentiation features largely return to normal, although elements of residual dedifferentiation remain, even after the contractile function is restored. These hearts appear rejuvenated and show robust resistance to ischemic injury, even 5 months after redifferentiation initiation. Cardiomyocyte redifferentiation is driven by negative feedback signaling and requires LATS1/2 Hippo pathway activity. Our data reveal the importance of cardiomyocyte redifferentiation in functional restoration during regeneration but also protection against future insult, in what could lead to a potential prophylactic treatment against ischemic heart disease for at-risk patients.
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Affiliation(s)
- Avraham Shakked
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Zachary Petrover
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Alla Aharonov
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Matteo Ghiringhelli
- Sohnis Research Laboratory for Cardiac Electrophysiology and Regenerative Medicine Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa, Israel
| | - Kfir-Baruch Umansky
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - David Kain
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Jacob Elkahal
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yalin Divinsky
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Phong Dang Nguyen
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Shoval Miyara
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Gilgi Friedlander
- Mantoux Bioinformatics Institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Alon Savidor
- De Botton Protein Profiling Institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Lingling Zhang
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Dahlia E. Perez
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Rachel Sarig
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Daria Lendengolts
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Hanna Bueno-Levy
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Nathaniel Kastan
- Howard Hughes Medical Institute and Laboratory of Sensory Neuroscience, The Rockefeller University, New York, NY, USA
| | - Yishai Levin
- De Botton Protein Profiling Institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Jeroen Bakkers
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Lior Gepstein
- Sohnis Research Laboratory for Cardiac Electrophysiology and Regenerative Medicine Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa, Israel
| | - Eldad Tzahor
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
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2
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Aylon Y, Furth N, Mallel G, Friedlander G, Nataraj NB, Dong M, Hassin O, Zoabi R, Cohen B, Drendel V, Salame TM, Mukherjee S, Harpaz N, Johnson R, Aulitzky WE, Yarden Y, Shema E, Oren M. Breast cancer plasticity is restricted by a LATS1-NCOR1 repressive axis. Nat Commun 2022; 13:7199. [PMID: 36443319 PMCID: PMC9705295 DOI: 10.1038/s41467-022-34863-9] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 11/10/2022] [Indexed: 11/29/2022] Open
Abstract
Breast cancer, the most frequent cancer in women, is generally classified into several distinct histological and molecular subtypes. However, single-cell technologies have revealed remarkable cellular and functional heterogeneity across subtypes and even within individual breast tumors. Much of this heterogeneity is attributable to dynamic alterations in the epigenetic landscape of the cancer cells, which promote phenotypic plasticity. Such plasticity, including transition from luminal to basal-like cell identity, can promote disease aggressiveness. We now report that the tumor suppressor LATS1, whose expression is often downregulated in human breast cancer, helps maintain luminal breast cancer cell identity by reducing the chromatin accessibility of genes that are characteristic of a "basal-like" state, preventing their spurious activation. This is achieved via interaction of LATS1 with the NCOR1 nuclear corepressor and recruitment of HDAC1, driving histone H3K27 deacetylation near NCOR1-repressed "basal-like" genes. Consequently, decreased expression of LATS1 elevates the expression of such genes and facilitates slippage towards a more basal-like phenotypic identity. We propose that by enforcing rigorous silencing of repressed genes, the LATS1-NCOR1 axis maintains luminal cell identity and restricts breast cancer progression.
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Affiliation(s)
- Yael Aylon
- grid.13992.300000 0004 0604 7563Department of Molecular Cell Biology, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Noa Furth
- grid.13992.300000 0004 0604 7563Department of Immunology and Regenerative Biology, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Giuseppe Mallel
- grid.13992.300000 0004 0604 7563Department of Molecular Cell Biology, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Gilgi Friedlander
- grid.13992.300000 0004 0604 7563Department of Life Sciences Core Facilities, The Nancy & Stephen Grand Israel National Center for Personalized Medicine (G-INCPM), The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Nishanth Belugali Nataraj
- grid.13992.300000 0004 0604 7563Department of Immunology and Regenerative Biology, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Meng Dong
- grid.502798.10000 0004 0561 903XDr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology and University of Tuebingen, Stuttgart, Germany
| | - Ori Hassin
- grid.13992.300000 0004 0604 7563Department of Molecular Cell Biology, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Rawan Zoabi
- grid.13992.300000 0004 0604 7563Department of Molecular Cell Biology, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Benjamin Cohen
- grid.13992.300000 0004 0604 7563Department of Immunology, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Vanessa Drendel
- grid.416008.b0000 0004 0603 4965Department of Pathology, Robert Bosch Hospital, Stuttgart, Germany
| | - Tomer Meir Salame
- grid.13992.300000 0004 0604 7563Flow Cytometry Unit, Department of Life Sciences Core Facilities, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Saptaparna Mukherjee
- grid.13992.300000 0004 0604 7563Department of Molecular Cell Biology, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Nofar Harpaz
- grid.13992.300000 0004 0604 7563Department of Immunology and Regenerative Biology, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Randy Johnson
- grid.240145.60000 0001 2291 4776Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Walter E. Aulitzky
- grid.416008.b0000 0004 0603 4965Department of Hematology, Oncology and Palliative Medicine, Robert Bosch Hospital, Stuttgart, Germany
| | - Yosef Yarden
- grid.13992.300000 0004 0604 7563Department of Immunology and Regenerative Biology, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Efrat Shema
- grid.13992.300000 0004 0604 7563Department of Immunology and Regenerative Biology, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Moshe Oren
- grid.13992.300000 0004 0604 7563Department of Molecular Cell Biology, The Weizmann Institute of Science, 76100 Rehovot, Israel
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3
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David K, Friedlander G, Pellegrino B, Radomir L, Lewinsky H, Leng L, Bucala R, Becker-Herman S, Shachar I. CD74 as a regulator of transcription in normal B cells. Cell Rep 2022; 41:111572. [DOI: 10.1016/j.celrep.2022.111572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/07/2022] [Accepted: 10/04/2022] [Indexed: 11/07/2022] Open
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4
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David M, Olender T, Mizrahi O, Weingarten-Gabbay S, Friedlander G, Meril S, Goldberg N, Savidor A, Levin Y, Salomon V, Stern-Ginossar N, Bialik S, Kimchi A. DAP5 drives translation of specific mRNA targets with upstream ORFs in human embryonic stem cells. RNA 2022; 28:1325-1336. [PMID: 35961752 PMCID: PMC9479741 DOI: 10.1261/rna.079194.122] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
Death associated protein 5 (DAP5/eIF4G2/NAT1) is a member of the eIF4G translation initiation factors that has been shown to mediate noncanonical and/or cap-independent translation. It is essential for embryonic development and for differentiation of embryonic stem cells (ESCs), specifically its ability to drive translation of specific target mRNAs. In order to expand the repertoire of DAP5 target mRNAs, we compared ribosome profiles in control and DAP5 knockdown (KD) human ESCs (hESCs) to identify mRNAs with decreased ribosomal occupancy upon DAP5 silencing. A cohort of 68 genes showed decreased translation efficiency in DAP5 KD cells. Mass spectrometry confirmed decreased protein abundance of a significant portion of these targets. Among these was KMT2D, a histone methylase previously shown to be essential for ESC differentiation and embryonic development. We found that nearly half of the cohort of DAP5 target mRNAs displaying reduced translation efficiency of their main coding sequences upon DAP5 KD contained upstream open reading frames (uORFs) that are actively translated independently of DAP5. This is consistent with previously suggested mechanisms by which DAP5 mediates leaky scanning through uORFs and/or reinitiation at the main coding sequence. Crosslinking protein-RNA immunoprecipitation experiments indicated that a significant subset of DAP5 mRNA targets bound DAP5, indicating that direct binding between DAP5 protein and its target mRNAs is a frequent but not absolute requirement for DAP5-dependent translation of the main coding sequence. Thus, we have extended DAP5's function in translation of specific mRNAs in hESCs by a mechanism allowing translation of the main coding sequence following upstream translation of short ORFs.
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Affiliation(s)
- Maya David
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tsviya Olender
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Orel Mizrahi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | | | - Gilgi Friedlander
- The Mantoux Bioinformatics Institute, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sara Meril
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Nadav Goldberg
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Alon Savidor
- The de Botton Institute for Protein Profiling of the Nancy and Stephen Grand Israel National Center for Personalized Medicine (G-INCPM), Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yishai Levin
- The de Botton Institute for Protein Profiling of the Nancy and Stephen Grand Israel National Center for Personalized Medicine (G-INCPM), Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Vered Salomon
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Noam Stern-Ginossar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Shani Bialik
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Adi Kimchi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
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5
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Kosenko A, Salame TM, Friedlander G, Barash I. Macrophage-Secreted CSF1 Transmits a Calorie Restriction-Induced Self-Renewal Signal to Mammary Epithelial Stem Cells. Cells 2022; 11:cells11182923. [PMID: 36139499 PMCID: PMC9496835 DOI: 10.3390/cells11182923] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 09/04/2022] [Accepted: 09/12/2022] [Indexed: 11/16/2022] Open
Abstract
Calorie restriction enhances stem cell self-renewal in various tissues, including the mammary gland. We hypothesized that similar to their intestinal counterparts, mammary epithelial stem cells are insulated from sensing changes in energy supply, depending instead on niche signaling. The latter was investigated by subjecting cultures of mammary epithelial stem cells for 8 days to in vivo paracrine calorie-restriction signals collected from a 4-day-conditioned medium of individual mammary cell populations. Conditioned medium from calorie-restricted non-epithelial cells induced latent cell propagation and mammosphere formation—established markers of stem cell self-renewal. Combined RNA-Seq, immunohistochemistry and immunofluorescence analyses of the non-epithelial population identified macrophages and secreted CSF1 as the energy sensor and paracrine signal, respectively. Calorie restriction-induced pStat6 expression in macrophages suggested that skewing to the M2 phenotype contributes to the sensing mechanism. Enhancing CSF1 signaling with recombinant protein and interrupting the interaction with its highly expressed receptor in the epithelial stem cells by neutralizing antibodies were both affected stem cell self-renewal. In conclusion, combined in vivo, in vitro and in silico studies identified macrophages and secreted CSF1 as the energy sensor and paracrine transmitter, respectively, of the calorie restriction-induced effect on mammary stem cell self-renewal.
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Affiliation(s)
- Anna Kosenko
- The Volcani Center, Agricultural Research Organization, Institute of Animal Science, Bet Dagan 50250, Israel
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Jerusalem 9190501, Israel
| | - Tomer Meir Salame
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot 7632706, Israel
| | - Gilgi Friedlander
- The Mantoux Bioinformatics Institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 7632706, Israel
| | - Itamar Barash
- The Volcani Center, Agricultural Research Organization, Institute of Animal Science, Bet Dagan 50250, Israel
- Correspondence:
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6
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Aylon Y, Furth N, Mallel G, Nataraj N, Friedlander G, Hassan O, Zoabi R, Cohen B, Salame T, Mukherjee S, Johnson R, Shema E, Oren M. Abstract 832: Breast cancer plasticity is restricted by a LATS1-NCOR1 repressive function. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-832] [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] [Indexed: 11/16/2022]
Abstract
Abstract
Purpose of study: Understanding the epigenetic mechanism underlying luminal-to-basal plasticity of breast cancer subtypes
Experimental procedures: Epigenetic focused CyTOF, ATAC-seq, RNA-seq, FACS-sorting, Proximity Ligation Assay, orthotopic syngeneic injections of tumor cells to mouse mammary gland, and others.
Summary: Breast cancer is the most frequent cancer in women. It is defined by specific types of tumors that are classified into distinct histological and molecular subtypes. However, lately, with the advent of single-cell technologies, the extent of cellular and functional intratumoral heterogeneity within breast cancer subtypes is being appreciated. Much of this heterogeneity, including transitions of luminal-to-basal cell identity, can be attributed to alterations in the activity of chromatin remodelers. The transcriptional corepressor, NCOR1, and the tumor suppressor, LATS1, are downregulated in luminal breast cancer tumors with poor prognosis. Here, we show that LATS1 impedes the emergence of an epigenetically distinct basal-like population in luminal B tumors by augmenting NCOR1 repressive activity and facilitating deacetylation of H3K27ac.
Conclusion: Rigorous repression of ERα-repressed genes facilitated by LATS1-NCOR1 maintains luminal cell identity and restricts progression of luminal breast cancer.
Citation Format: Yael Aylon, Noa Furth, Giuseppe Mallel, Nishanth Nataraj, Gilgi Friedlander, Ori Hassan, Rawan Zoabi, Benjamin Cohen, Tomer Salame, Saptaparna Mukherjee, Randy Johnson, Efrat Shema, Moshe Oren. Breast cancer plasticity is restricted by a LATS1-NCOR1 repressive function [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 832.
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Affiliation(s)
- Yael Aylon
- 1Weizmann Institute of Science, Rechovot, Israel
| | - Noa Furth
- 1Weizmann Institute of Science, Rechovot, Israel
| | | | | | | | - Ori Hassan
- 1Weizmann Institute of Science, Rechovot, Israel
| | - Rawan Zoabi
- 1Weizmann Institute of Science, Rechovot, Israel
| | | | - Tomer Salame
- 1Weizmann Institute of Science, Rechovot, Israel
| | | | | | - Efrat Shema
- 1Weizmann Institute of Science, Rechovot, Israel
| | - Moshe Oren
- 1Weizmann Institute of Science, Rechovot, Israel
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7
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Fishman H, Madiwale S, Geron I, Bari V, Van Loocke W, Kirschenbaum Y, Ganmore I, Kugler E, Rein-Gil A, Friedlander G, Schiby G, Birger Y, Strehl S, Soulier J, Knoechel B, Ferrando A, Noy-Lotan S, Nagler A, Mulloy JC, Van Vlierberghe P, Izraeli S. ETV6-NCOA2 fusion induces T/myeloid mixed-phenotype leukemia through transformation of nonthymic hematopoietic progenitor cells. Blood 2022; 139:399-412. [PMID: 34624096 PMCID: PMC9906988 DOI: 10.1182/blood.2020010405] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [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: 12/13/2020] [Accepted: 09/26/2021] [Indexed: 01/05/2023] Open
Abstract
Mixed-phenotype acute leukemia is a rare subtype of leukemia in which both myeloid and lymphoid markers are co-expressed on the same malignant cells. The pathogenesis is largely unknown, and the treatment is challenging. We previously reported the specific association of the recurrent t(8;12)(q13;p13) chromosomal translocation that creates the ETV6-NCOA2 fusion with T/myeloid leukemias. Here we report that ETV6-NCOA2 initiates T/myeloid leukemia in preclinical models; ectopic expression of ETV6-NCOA2 in mouse bone marrow hematopoietic progenitors induced T/myeloid lymphoma accompanied by spontaneous Notch1-activating mutations. Similarly, cotransduction of human cord blood CD34+ progenitors with ETV6-NCOA2 and a nontransforming NOTCH1 mutant induced T/myeloid leukemia in immunodeficient mice; the immunophenotype and gene expression pattern were similar to those of patient-derived ETV6-NCOA2 leukemias. Mechanistically, we show that ETV6-NCOA2 forms a transcriptional complex with ETV6 and the histone acetyltransferase p300, leading to derepression of ETV6 target genes. The expression of ETV6-NCOA2 in human and mouse nonthymic hematopoietic progenitor cells induces transcriptional dysregulation, which activates a lymphoid program while failing to repress the expression of myeloid genes such as CSF1 and MEF2C. The ETV6-NCOA2 induced arrest at an early immature T-cell developmental stage. The additional acquisition of activating NOTCH1 mutations transforms the early immature ETV6-NCOA2 cells into T/myeloid leukemias. Here, we describe the first preclinical model to depict the initiation of T/myeloid leukemia by a specific somatic genetic aberration.
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Affiliation(s)
- Hila Fishman
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Rina Zaizov Pediatric Hematology Oncology Division, Schneider Children's Medical Center of Israel, Petah Tikvah, Israel
| | - Shreyas Madiwale
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Rina Zaizov Pediatric Hematology Oncology Division, Schneider Children's Medical Center of Israel, Petah Tikvah, Israel
| | - Ifat Geron
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Rina Zaizov Pediatric Hematology Oncology Division, Schneider Children's Medical Center of Israel, Petah Tikvah, Israel
| | - Vase Bari
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital, Cincinnati, OH
| | - Wouter Van Loocke
- Department of Pediatrics and Genetics, Ghent University, Ghent, Belgium
| | - Yael Kirschenbaum
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Cancer Research Center, Chaim Sheba Medical Center at Tel HaShomer, Ramat Gan, Israel
| | - Itamar Ganmore
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Cancer Research Center, Chaim Sheba Medical Center at Tel HaShomer, Ramat Gan, Israel
| | - Eitan Kugler
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Rina Zaizov Pediatric Hematology Oncology Division, Schneider Children's Medical Center of Israel, Petah Tikvah, Israel
| | - Avigail Rein-Gil
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Rina Zaizov Pediatric Hematology Oncology Division, Schneider Children's Medical Center of Israel, Petah Tikvah, Israel
| | - Gilgi Friedlander
- The Mantoux Bioinformatics Institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Ginette Schiby
- Institute for Pathology Laboratory, Hematology Institute, Chaim Sheba Medical Center at Tel HaShomer, Ramat Gan, Israel
| | - Yehudit Birger
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Rina Zaizov Pediatric Hematology Oncology Division, Schneider Children's Medical Center of Israel, Petah Tikvah, Israel
| | - Sabine Strehl
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| | - Jean Soulier
- Genomes and Cell Biology of Disease, Hôpital Saint-Louis, Paris, France
| | - Birgit Knoechel
- Dana-Farber Cancer Institute, Boston Children's Hospital, Boston, MA
| | - Adolfo Ferrando
- Institute for Cancer Genetics, Columbia University, New York, NY
| | - Sharon Noy-Lotan
- Rina Zaizov Pediatric Hematology Oncology Division, Schneider Children's Medical Center of Israel, Petah Tikvah, Israel
| | - Arnon Nagler
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Hematology Division Bone Marrow Transplants and Cord-Blood Bank, Chaim Sheba Medical Center at Tel HaShomer, Ramat Gan, Israel
| | - James C. Mulloy
- Cancer and Blood Diseases Institute, Cincinnati Children's Hospital, Cincinnati, OH
| | | | - Shai Izraeli
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Rina Zaizov Pediatric Hematology Oncology Division, Schneider Children's Medical Center of Israel, Petah Tikvah, Israel
- Department of System Biology, City of Hope, Duarte, CA
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8
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Jacob Berger A, Gigi E, Kupershmidt L, Meir Z, Gavert N, Zwang Y, Prior A, Gilad S, Harush U, Haviv I, Stemmer SM, Blum G, Merquiol E, Mardamshina M, Kaminski Strauss S, Friedlander G, Bar J, Kamer I, Reizel Y, Geiger T, Pilpel Y, Levin Y, Tanay A, Barzel B, Reuveni H, Straussman R. IRS1 phosphorylation underlies the non-stochastic probability of cancer cells to persist during EGFR inhibition therapy. Nat Cancer 2021; 2:1055-1070. [PMID: 35121883 DOI: 10.1038/s43018-021-00261-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 08/23/2021] [Indexed: 02/08/2023]
Abstract
Stochastic transition of cancer cells between drug-sensitive and drug-tolerant persister phenotypes has been proposed to play a key role in non-genetic resistance to therapy. Yet, we show here that cancer cells actually possess a highly stable inherited chance to persist (CTP) during therapy. This CTP is non-stochastic, determined pre-treatment and has a unimodal distribution ranging from 0 to almost 100%. Notably, CTP is drug specific. We found that differential serine/threonine phosphorylation of the insulin receptor substrate 1 (IRS1) protein determines the CTP of lung and of head and neck cancer cells under epidermal growth factor receptor inhibition, both in vitro and in vivo. Indeed, the first-in-class IRS1 inhibitor NT219 was highly synergistic with anti-epidermal growth factor receptor therapy across multiple in vitro and in vivo models. Elucidation of drug-specific mechanisms that determine the degree and stability of cellular CTP may establish a framework for the elimination of cancer persisters, using new rationally designed drug combinations.
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Affiliation(s)
- Adi Jacob Berger
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Elinor Gigi
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Lana Kupershmidt
- TyrNovo Ltd, Rehovot, Israel.,Cancer Personalized Medicine and Diagnostic Genomics Lab, Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, Israel
| | - Zohar Meir
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel.,Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Nancy Gavert
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yaara Zwang
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Amir Prior
- De Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Shlomit Gilad
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Uzi Harush
- Department of Mathematics, Bar-Ilan University, Ramat-Gan, Israel.,Gonda Multidisciplinary Brain Research Center, Bar-Ilan University, Ramat-Gan, Israel
| | - Izhak Haviv
- TyrNovo Ltd, Rehovot, Israel.,Cancer Personalized Medicine and Diagnostic Genomics Lab, Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, Israel.,AID Genomics and Gensort Ltd, Rehovot, Israel
| | - Salomon M Stemmer
- Davidoff Center, Rabin Medical Center, Felsenstien Medical Research Center, Petach Tikva, and Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Galia Blum
- Institute of Drug Research, The School of Pharmacy, Faculty of Medicine, Campus Ein Karem, The Hebrew University, Jerusalem, Israel
| | - Emmanuelle Merquiol
- Institute of Drug Research, The School of Pharmacy, Faculty of Medicine, Campus Ein Karem, The Hebrew University, Jerusalem, Israel
| | - Mariya Mardamshina
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | | | - Gilgi Friedlander
- Ilana and Pascal Mantoux Institute for Bioinformatics, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Jair Bar
- Sheba Medical Center, Ramat Gan, Israel
| | | | - Yitzhak Reizel
- Department of Genetics and Institute for Diabetes Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Tamar Geiger
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yitzhak Pilpel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Yishai Levin
- De Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Amos Tanay
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel.,Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Baruch Barzel
- Department of Mathematics, Bar-Ilan University, Ramat-Gan, Israel.,Gonda Multidisciplinary Brain Research Center, Bar-Ilan University, Ramat-Gan, Israel
| | - Hadas Reuveni
- TyrNovo Ltd, Rehovot, Israel.,Purple Biotech Ltd, Rehovot, Israel
| | - Ravid Straussman
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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9
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Valiulahi P, Vidyawan V, Puspita L, Oh Y, Juwono VB, Sittipo P, Friedlander G, Yahalomi D, Sohn JW, Lee YK, Yoon JK, Shim JW. Generation of caudal-type serotonin neurons and hindbrain-fate organoids from hPSCs. Stem Cell Reports 2021; 16:1938-1952. [PMID: 34242615 PMCID: PMC8365029 DOI: 10.1016/j.stemcr.2021.06.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 06/08/2021] [Accepted: 06/08/2021] [Indexed: 12/12/2022] Open
Abstract
Serotonin (5-HT) neurons, the major components of the raphe nuclei, arise from ventral hindbrain progenitors. Based on anatomical location and axonal projection, 5-HT neurons are coarsely divided into rostral and caudal groups. Here, we propose a novel strategy to generate hindbrain 5-HT neurons from human pluripotent stem cells (hPSCs), which involves the formation of ventral-type neural progenitor cells and stimulation of the hindbrain 5-HT neural development. A caudalizing agent, retinoid acid, was used to direct the cells into the hindbrain cell fate. Approximately 30%–40% of hPSCs successfully developed into 5-HT-expressing neurons using our protocol, with the majority acquiring a caudal rhombomere identity (r5–8). We further modified our monolayer differentiation system to generate 5-HT neuron-enriched hindbrain-like organoids. We also suggest downstream applications of our 5-HT monolayer and organoid cultures to study neuronal response to gut microbiota. Our methodology could become a powerful tool for future studies related to 5-HT neurotransmission. Activation of SHH and RA signaling induces 5-HT neuronal fate from hPSCs The generated 5-HT neurons have caudal hindbrain characteristics Hindbrain-like organoids may form from hPSCs by activation of SHH and RA signaling 5-HT neurons in monolayer and organoid culture can be used as a screening platform
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Affiliation(s)
- Parvin Valiulahi
- Soonchunhyang Institute of Medi-bio Science (SIMS), Soonchunhyang University, 25, Bongjeong-ro, Dongnam-gu, Cheonan-si 31151, Korea; Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan-si 31151, Korea
| | - Vincencius Vidyawan
- Soonchunhyang Institute of Medi-bio Science (SIMS), Soonchunhyang University, 25, Bongjeong-ro, Dongnam-gu, Cheonan-si 31151, Korea; Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan-si 31151, Korea
| | - Lesly Puspita
- Soonchunhyang Institute of Medi-bio Science (SIMS), Soonchunhyang University, 25, Bongjeong-ro, Dongnam-gu, Cheonan-si 31151, Korea; Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan-si 31151, Korea
| | - Youjin Oh
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Virginia Blessy Juwono
- Soonchunhyang Institute of Medi-bio Science (SIMS), Soonchunhyang University, 25, Bongjeong-ro, Dongnam-gu, Cheonan-si 31151, Korea; Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan-si 31151, Korea
| | - Panida Sittipo
- Soonchunhyang Institute of Medi-bio Science (SIMS), Soonchunhyang University, 25, Bongjeong-ro, Dongnam-gu, Cheonan-si 31151, Korea; Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan-si 31151, Korea
| | - Gilgi Friedlander
- The Mantoux Bioinformatics institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Dayana Yahalomi
- The Mantoux Bioinformatics institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Jong-Woo Sohn
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Yun Kyung Lee
- Soonchunhyang Institute of Medi-bio Science (SIMS), Soonchunhyang University, 25, Bongjeong-ro, Dongnam-gu, Cheonan-si 31151, Korea; Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan-si 31151, Korea.
| | - Jeong Kyo Yoon
- Soonchunhyang Institute of Medi-bio Science (SIMS), Soonchunhyang University, 25, Bongjeong-ro, Dongnam-gu, Cheonan-si 31151, Korea; Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan-si 31151, Korea.
| | - Jae-Won Shim
- Soonchunhyang Institute of Medi-bio Science (SIMS), Soonchunhyang University, 25, Bongjeong-ro, Dongnam-gu, Cheonan-si 31151, Korea; Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan-si 31151, Korea.
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10
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Basavaraja R, Drum JN, Sapuleni J, Bibi L, Friedlander G, Kumar S, Sartori R, Meidan R. Downregulated luteolytic pathways in the transcriptome of early pregnancy bovine corpus luteum are mimicked by interferon-tau in vitro. BMC Genomics 2021; 22:452. [PMID: 34134617 PMCID: PMC8207607 DOI: 10.1186/s12864-021-07747-3] [Citation(s) in RCA: 6] [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: 12/16/2020] [Accepted: 05/21/2021] [Indexed: 12/15/2022] Open
Abstract
Background Maintenance of the corpus luteum (CL) beyond the time of luteolysis is essential for establishing pregnancy. Identifying the distinct features of early pregnancy CL remains unresolved, hence we analyzed here the transcriptome of CL on day 18 pregnant (P) and non-pregnant (NP) cows using RNA-Seq. CL of P cows expressed ISGs, verifying exposure to the pregnancy recognition signal, interferon-tau (IFNT), whereas the CL of NP cows had elevated luteal progesterone levels, implying that luteolysis had not yet commenced. Results The DEGs, IPA, and metascape canonical pathways, along with GSEA analysis, differed markedly in the CL of P cows from those of NP cows, at the same day of the cycle. Both metascape and IPA identified similar significantly enriched pathways such as interferon alpha/beta, sonic hedgehog pathway, TNFA, EDN1, TGFB1, and PDGF. However, type-1 interferon and sonic hedgehog pathways were positively enriched whereas most of the enriched pathways were downregulated in the P compared to NP samples. Thirty-four % of these pathways are known to be elevated by PGF2A during luteolysis. Notably, selective DEGs in luteinized granulosa cells were modulated by IFNT in vitro in a similar manner to their regulation in the CL of P cows. Conclusion This study unraveled the unique transcriptomic signature of the IFNT-exposed, early pregnancy CL, highlighting the abundance of downregulated pathways known to be otherwise induced during luteolysis. These and IFNT-regulated in vitro pregnancy-specific DEGs suggest that IFNT contributes to the characteristics and maintenance of early pregnancy CL. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07747-3.
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Affiliation(s)
- Raghavendra Basavaraja
- Department of Animal Sciences, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, 7610001, Rehovot, Israel
| | - Jessica N Drum
- Department of Animal Science, University of São Paulo, Piracicaba, Brazil
| | - Jackson Sapuleni
- Department of Animal Sciences, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, 7610001, Rehovot, Israel
| | - Lonice Bibi
- Department of Animal Sciences, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, 7610001, Rehovot, Israel
| | - Gilgi Friedlander
- The Mantoux Bioinformatics institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Sai Kumar
- Department of Animal Sciences, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, 7610001, Rehovot, Israel
| | - Roberto Sartori
- Department of Animal Science, University of São Paulo, Piracicaba, Brazil
| | - Rina Meidan
- Department of Animal Sciences, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, 7610001, Rehovot, Israel.
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11
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Becker-Herman S, Rozenberg M, Hillel-Karniel C, Gil-Yarom N, Kramer MP, Barak A, Sever L, David K, Radomir L, Lewinsky H, Levi M, Friedlander G, Bucala R, Peled A, Shachar I. CD74 is a regulator of hematopoietic stem cell maintenance. PLoS Biol 2021; 19:e3001121. [PMID: 33661886 PMCID: PMC7963458 DOI: 10.1371/journal.pbio.3001121] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 03/16/2021] [Accepted: 01/29/2021] [Indexed: 11/17/2022] Open
Abstract
Hematopoietic stem and progenitor cells (HSPCs) are a small population of undifferentiated cells that have the capacity for self-renewal and differentiate into all blood cell lineages. These cells are the most useful cells for clinical transplantations and for regenerative medicine. So far, it has not been possible to expand adult hematopoietic stem cells (HSCs) without losing their self-renewal properties. CD74 is a cell surface receptor for the cytokine macrophage migration inhibitory factor (MIF), and its mRNA is known to be expressed in HSCs. Here, we demonstrate that mice lacking CD74 exhibit an accumulation of HSCs in the bone marrow (BM) due to their increased potential to repopulate and compete for BM niches. Our results suggest that CD74 regulates the maintenance of the HSCs and CD18 expression. Its absence leads to induced survival of these cells and accumulation of quiescent and proliferating cells. Furthermore, in in vitro experiments, blocking of CD74 elevated the numbers of HSPCs. Thus, we suggest that blocking CD74 could lead to improved clinical insight into BM transplant protocols, enabling improved engraftment. Hematopoietic stem and progenitor cells (HSPCs) can self-renew and differentiate into all blood cell lineages, making them useful for clinical transplantations and regenerative medicine. This study shows that blocking the MIF receptor CD74 increases the accumulation of HSPCs and could improve the efficacy of bone marrow transplantation protocols.
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Affiliation(s)
| | - Milena Rozenberg
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Naama Gil-Yarom
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Mattias P Kramer
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Avital Barak
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Lital Sever
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Keren David
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Lihi Radomir
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Hadas Lewinsky
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Michal Levi
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Gilgi Friedlander
- Ilana and Pascal Mantoux Institute for Bioinformatics and Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Richard Bucala
- Internal Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Amnon Peled
- Hadassah Hebrew University Hospital, Goldyne Savad Institute of Gene Therapy, Jerusalem, Israel
| | - Idit Shachar
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
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12
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Dadiani M, Friedlander G, Perry G, Balint-Lahat N, Pavlovsky A, Shenoy A, Barshack I, Geiger T, Kaufman B, Gal-Yam EN. Abstract P6-03-01: Mapping a personalized chemo-resistome in breast cancer patients by longitudinal transcriptomics. Cancer Res 2020. [DOI: 10.1158/1538-7445.sabcs19-p6-03-01] [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] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Understanding resistance mechanisms to chemotherapy is key to improving therapeutic outcomes. Despite the considerable importance of tumor drug resistance to cancer morbidity and mortality, our comprehension of the various molecular mechanisms involved in resistance is limited. The actual response of an individual patient remains a ‘black box’. Previous studies profiling pre-and post-treatment samples were based on population statistics and did not result in a personalized view of resistance. To dissect the individualized emergence of resistance in breast cancer patients we applied longitudinal transcriptomics combined with temporal dynamics analysis approach. Methods: Matched triplets of archived tumor biopsies from pre-treatment, post-treatment and adjacent normal epithelium were collected from 33 individual patients that underwent neo-adjuvant chemotherapy treatment. Full transcriptome analysis was performed by mRNA sequencing. Longitudinal pattern analysis algorithm was developed to follow dynamic expression fluctuations in individual patients. Data analysis incorporated long-term clinical and pathological follow-up information. Pathway enrichment was used to map the resistant pathways and create a “chemo-resistome” map in individual patients by following the rewiring of their molecular pathways through the course of therapy. Results: To identify genes associated with resistance we used longitudinal pattern classification. Each pattern represents a different scenario through tumor progression and treatment stages. We identified 253 genes that their pattern is significantly correlated with pathological response score. Enrichment analysis of these genes pinpointed pathways and functions associated with resistance. We found multiple pathways directly related to the mechanism of action of the administered chemotherapies, such as, pathways involved in microtubule polymerization and DNA repair. Other pathways that emerge involve multi-drug resistance pathways, such as, specific subsets of ABC transporters and pathways related to immune-modulation. Interestingly, we noticed that the mechanisms of resistance are patient-specific. We, therefore, calculated a chemo-resistome map for each patient using the most potent resistant pathway categories. The chemo-resistome maps illustrate the co-existence of several resistance categories in the same patient, whereas some categories exhibit patient- or subtype- specific occurrence. Conclusions: Mapping the complexity of the various resistance pathways in individual patients can provide important insights on the mechanisms underlying tumor cell survival. Depicting an individual road map to resistance by analyzing expression rewiring can offer personalized therapeutic strategies in the future.
Citation Format: Maya Dadiani, Gilgi Friedlander, Gili Perry, Nora Balint-Lahat, Anya Pavlovsky, Anjana Shenoy, Iris Barshack, Tamar Geiger, Bella Kaufman, Einav N Gal-Yam. Mapping a personalized chemo-resistome in breast cancer patients by longitudinal transcriptomics [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P6-03-01.
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Affiliation(s)
| | | | - Gili Perry
- 1Sheba Medical Center, Ramat Gan, Israel
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13
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Foult JM, Katsahian S, Nevoret C, Hoffman O, Sabouret P, Attal B, Friedlander G. P1529Coronary and aortic atheroma are not identical diseases: A calcium score comparative study in 1010 patients with a normal SPECT. Eur Heart J 2019. [DOI: 10.1093/eurheartj/ehz748.0291] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Calcium scores of the coronary arteries (CCS) and – more recently – of the the thoracic aorta (TCS), have been established as risk markers for cardiovascular events. Yet, little is known about the relationship between these two calcium scores.
In this study, CCS and TCS were compared in 1010 patients with a normal SPECT. Mean age was 64.5±8.7 yrs with 73.4% of men. CCS and TCS ranged between 0 and 5827 for CCS and from 0 to 58600 for TCS, with means of 281.1 and 1206 respectively. Such a difference was expected since the vascular surface of the thoracic aorta is approximately 5 times larger than that of the coronary arterial tree. Both CCS and TCS increased with the number of risk factors (p=0.000841 and p=0.000579)
No significant relation was found between CCS and TCS for the entire group. However, when adopting a best-fitting curve model, 2 populations could be clearly identified: those with predominant TCS (N=552), and those with a- relatively- predominant CCS – (N=458).
In each of these two groups, CCS and TCS were significantly related (r=0.63 and 0.69 respectively p<2.2e-12). Both groups had a comparable exposition to smoking and diabetes, but Group1 patients had more dyslipemia and high blood pressure than group 2 patients.
Conclusion
Calcified atheroma was frequently observed In patients with a normal SPECT, but no significant relation existed between CCS and TCS; patients with a predominant atheroma of the coronary arteries were not the same than patients with a predominant atheroma of the aorta, with both groups having different expositions to risk factors. This suggests that atheroma of the coronary arteries and of the thoracic aorta are close but not identical diseases.
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Affiliation(s)
- J.-M Foult
- American Hospital of Paris, Neuilly sur Seine, France
| | - S Katsahian
- European Hospital Georges Pompidou, Paris, France
| | - C Nevoret
- European Hospital Georges Pompidou, Paris, France
| | - O Hoffman
- American Hospital of Paris, Neuilly sur Seine, France
| | - P Sabouret
- American Hospital of Paris, Neuilly sur Seine, France
| | - B Attal
- American Hospital of Paris, Neuilly sur Seine, France
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14
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Dadiani M, Friedlander G, Perry G, Lahat-Balint N, Marin I, Pavlovski A, Barshack I, Nili Gal-Yam E, Kaufman B. PO-312 Longitudinal transcriptomics reveals heterogeneous dynamics through the course of disease and therapy in breast cancer. ESMO Open 2018. [DOI: 10.1136/esmoopen-2018-eacr25.342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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15
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Friedlander G, Davies T. The Last Laugh - Reversible myeloneuropathy induced by chronic nitrous oxide use. Acute Med 2018; 17:232-235. [PMID: 30882108] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A previously fit and well 19 year old male presents with a progressive ataxic - sensory neuropathy worsening over 2 - 3 weeks. History and investigations revealed extensive recreational use of nitrous oxide resulting in functional B12 deficiency and consequent subacute combined degeneration of the cord. Abstinence and B12 supplementation resulted in a rapid and full neurological recovery. This case report highlights the importance of considering nitrous oxide abuse in the differential diagnosis of atypical neurological symptoms and signs, and emphasizes the possibility of good clinical outcomes with treatment.
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Affiliation(s)
- G Friedlander
- Acute Medical Unit (AMU), University College Hospital, 235 Euston Road, London, NW1 2BU
| | - T Davies
- Acute Medical Unit (AMU), University College Hospital, 235 Euston Road, London, NW1 2BU
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16
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Wekselman I, Zimmerman E, Davidovich C, Belousoff M, Matzov D, Krupkin M, Rozenberg H, Bashan A, Friedlander G, Kjeldgaard J, Ingmer H, Lindahl L, Zengel JM, Yonath A. The Ribosomal Protein uL22 Modulates the Shape of the Protein Exit Tunnel. Structure 2017; 25:1233-1241.e3. [PMID: 28689968 DOI: 10.1016/j.str.2017.06.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 05/08/2017] [Accepted: 06/02/2017] [Indexed: 10/19/2022]
Abstract
Erythromycin is a clinically useful antibiotic that binds to an rRNA pocket in the ribosomal exit tunnel. Commonly, resistance to erythromycin is acquired by alterations of rRNA nucleotides that interact with the drug. Mutations in the β hairpin of ribosomal protein uL22, which is rather distal to the erythromycin binding site, also generate resistance to the antibiotic. We have determined the crystal structure of the large ribosomal subunit from Deinococcus radiodurans with a three amino acid insertion within the β hairpin of uL22 that renders resistance to erythromycin. The structure reveals a shift of the β hairpin of the mutated uL22 toward the interior of the exit tunnel, triggering a cascade of structural alterations of rRNA nucleotides that propagate to the erythromycin binding pocket. Our findings support recent studies showing that the interactions between uL22 and specific sequences within nascent chains trigger conformational rearrangements in the exit tunnel.
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Affiliation(s)
- Itai Wekselman
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ella Zimmerman
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Chen Davidovich
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Matthew Belousoff
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Donna Matzov
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Miri Krupkin
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Haim Rozenberg
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Anat Bashan
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Gilgi Friedlander
- The Ilana and Pascal Mantoux Institute for Bioinformatics, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Jette Kjeldgaard
- Department of Veterinary Disease Biology, University of Copenhagen, 1870 Frederiksbergc, Denmark
| | - Hanne Ingmer
- Department of Veterinary Disease Biology, University of Copenhagen, 1870 Frederiksbergc, Denmark
| | - Lasse Lindahl
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Janice M Zengel
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Ada Yonath
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel.
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17
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Yoffe Y, David M, Kalaora R, Povodovski L, Friedlander G, Feldmesser E, Ainbinder E, Saada A, Bialik S, Kimchi A. Cap-independent translation by DAP5 controls cell fate decisions in human embryonic stem cells. Genes Dev 2017; 30:1991-2004. [PMID: 27664238 PMCID: PMC5066241 DOI: 10.1101/gad.285239.116] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [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: 06/09/2016] [Accepted: 08/18/2016] [Indexed: 12/21/2022]
Abstract
In this study, Yoffe et al. provide insight into a new regulatory mechanism that is critical for stem cell fate decisions toward several cell lineages. They found that DAP5-mediated translation of a specific set of proteins is critical for the transition from pluripotency to differentiation, highlighting the importance of cap-independent translation in stem cell fate decisions. Multiple transcriptional and epigenetic changes drive differentiation of embryonic stem cells (ESCs). This study unveils an additional level of gene expression regulation involving noncanonical, cap-independent translation of a select group of mRNAs. This is driven by death-associated protein 5 (DAP5/eIF4G2/NAT1), a translation initiation factor mediating IRES-dependent translation. We found that the DAP5 knockdown from human ESCs (hESCs) resulted in persistence of pluripotent gene expression, delayed induction of differentiation-associated genes in different cell lineages, and defective embryoid body formation. The latter involved improper cellular organization, lack of cavitation, and enhanced mislocalized apoptosis. RNA sequencing of polysome-associated mRNAs identified candidates with reduced translation efficiency in DAP5-depleted hESCs. These were enriched in mitochondrial proteins involved in oxidative respiration, a pathway essential for differentiation, the significance of which was confirmed by the aberrant mitochondrial morphology and decreased oxidative respiratory activity in DAP5 knockdown cells. Further analysis identified the chromatin modifier HMGN3 as a cap-independent DAP5 translation target whose knockdown resulted in defective differentiation. Thus, DAP5-mediated translation of a specific set of proteins is critical for the transition from pluripotency to differentiation, highlighting the importance of cap-independent translation in stem cell fate decisions.
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Affiliation(s)
- Yael Yoffe
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Maya David
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Rinat Kalaora
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Lital Povodovski
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Gilgi Friedlander
- Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ester Feldmesser
- Bioinformatics Unit, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Elena Ainbinder
- Stem Cell Core Unit, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ann Saada
- Monique and Jacques Roboh Department of Genetic Research, Hadassah-Hebrew University Medical Center, Jerusalem 91120, Israel; Department of Genetics and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem 91120, Israel
| | - Shani Bialik
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Adi Kimchi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
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18
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Zachut M, Kra G, Livshitz L, Portnick Y, Yakoby S, Friedlander G, Levin Y. Proteome dataset of subcutaneous adipose tissue obtained from late pregnant dairy cows during summer heat stress and winter seasons. Data Brief 2017; 12:535-539. [PMID: 28516150 PMCID: PMC5425336 DOI: 10.1016/j.dib.2017.04.042] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 03/17/2017] [Accepted: 04/25/2017] [Indexed: 11/29/2022] Open
Abstract
Adipose tissue has a central role in the regulation of metabolism in dairy cows, and many proteins expressed in this tissue are involved in metabolic responses to stress (Peinado et al., 2012) [1]. Environmental heat stress is one of the main stressors limiting production in dairy cattle (Fuquay, 1981; West, 2003) [2], [3], and there is a complex interaction between heat stress and the transition period from late pregnancy to onset of lactation, which is manifested in heat-stressed late-gestation cows (Tao and Dahl, 2013) [4]. We recently defined the proteome of adipose tissue in peripartum dairy cows, identifying 586 proteins of which 18.9% were differentially abundant in insulin-resistant compared to insulin-sensitive adipose tissue (Zachut, 2015) [5]. That study showed that proteomic techniques constitute a valuable tool for identifying novel biomarkers in adipose tissue that are related to metabolic adaptation to stress in dairy cows. The objective of the present work was to examine the adipose tissue proteome under thermo-neutral or seasonal heat stress conditions in late pregnant dairy cows. We have collected subcutaneous adipose tissue biopsies from 10 late pregnant dairy cows during summer heat stress and from 8 late pregnant dairy cows during winter season, and identified and quantified 1495 proteins in the adipose tissues. This dataset of adipose tissue proteome from dairy cows adds novel information on the variety of proteins that are abundant in this tissue during late pregnancy under thermo-neutral as well as heat stress conditions. Differential abundance of 107 (7.1%) proteins was found between summer and winter adipose. These results are discussed in our recent research article (Zachut et al., 2017) [6].
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Affiliation(s)
- M Zachut
- Department of Ruminant Science, Institute of Animal Sciences, Volcani Center, Rishon Lezion, Israel
| | - G Kra
- Department of Ruminant Science, Institute of Animal Sciences, Volcani Center, Rishon Lezion, Israel
| | - L Livshitz
- Department of Ruminant Science, Institute of Animal Sciences, Volcani Center, Rishon Lezion, Israel
| | - Y Portnick
- Department of Ruminant Science, Institute of Animal Sciences, Volcani Center, Rishon Lezion, Israel
| | - S Yakoby
- Department of Ruminant Science, Institute of Animal Sciences, Volcani Center, Rishon Lezion, Israel
| | - G Friedlander
- The Ilana and Pascal Mantoux Institute for Bioinformatics, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Y Levin
- De Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
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Tal L, Friedlander G, Gilboa NS, Unger T, Gilad S, Eshed Y. Coordination of Meristem Doming and the Floral Transition by Late Termination, a Kelch Repeat Protein. Plant Cell 2017; 29:681-696. [PMID: 28389586 PMCID: PMC5435437 DOI: 10.1105/tpc.17.00030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 03/23/2017] [Accepted: 04/05/2017] [Indexed: 05/02/2023]
Abstract
Enlargement and doming of the shoot apical meristem (SAM) is a hallmark of the transition from vegetative growth to flowering. While this change is widespread, its role in the flowering process is unknown. The late termination (ltm) tomato (Solanum lycopersicum) mutant shows severely delayed flowering and precocious doming of the vegetative SAM LTM encodes a kelch domain-containing protein, with no link to known meristem maintenance or flowering time pathways. LTM interacts with the TOPLESS corepressor and with several transcription factors that can provide specificity for its functions. A subgroup of flowering-associated genes is precociously upregulated in vegetative stages of ltm SAMs, among them, the antiflorigen gene SELF PRUNING (SP). A mutation in SP restored the structure of vegetative SAMs in ltm sp double mutants, and late flowering was partially suppressed, suggesting that LTM functions to suppress SP in the vegetative SAM In agreement, SP-overexpressing wild-type plants exhibited precocious doming of vegetative SAMs combined with late flowering, as found in ltm plants. Strong flowering signals can result in termination of the SAM, usually by its differentiation into a flower. We propose that activation of a floral antagonist that promotes SAM growth in concert with floral transition protects it from such terminating effects.
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Affiliation(s)
- Lior Tal
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Gilgi Friedlander
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Netta Segal Gilboa
- Israel Structural Proteomics Centre, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Tamar Unger
- Israel Structural Proteomics Centre, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Shlomit Gilad
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yuval Eshed
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
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Zachut M, Kra G, Livshitz L, Portnick Y, Yakoby S, Friedlander G, Levin Y. Seasonal heat stress affects adipose tissue proteome toward enrichment of the Nrf2-mediated oxidative stress response in late-pregnant dairy cows. J Proteomics 2017; 158:52-61. [PMID: 28238905 DOI: 10.1016/j.jprot.2017.02.011] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [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: 12/13/2016] [Revised: 02/09/2017] [Accepted: 02/18/2017] [Indexed: 12/19/2022]
Abstract
Environmental heat stress and metabolic stress during transition from late gestation to lactation are main factors limiting production in dairy cattle, and there is a complex interaction between them. Many proteins expressed in adipose tissue are involved in metabolic responses to stress. We aimed to investigate the effects of seasonal heat stress on adipose proteome in late-pregnant cows, and to identify biomarkers of heat stress. Late pregnant cows during summer heat stress (S, n=18), or during the winter season (W, n=12) were used. Subcutaneous adipose tissue biopsies sampled 14days prepartum from S (n=10) and W (n=8) were analyzed by intensity-based, label-free, quantitative shotgun proteomics (nano-LC-MS/MS). Plasma concentrations of malondialdehyde and cortisol were higher in S than in W cows. Proteomic analysis revealed that 107/1495 proteins were differentially abundant in S compared to W (P<0.05 and fold change of at least ±1.5). Top canonical pathways in S vs. W adipose were Nrf2-mediated oxidative stress response, acute-phase response, and FXR/RXR and LXR/RXR activation. Novel biomarkers of heat stress in adipose tissue were found. These findings indicate that seasonal heat stress has a unique effect on adipose tissue in late-pregnant cows. SIGNIFICANCE This work shows that seasonal heat stress increases plasma concentrations of the oxidative stress marker malondialdehyde and cortisol in transition dairy cows. As many proteins expressed in the adipose tissue are involved in metabolic responses to stress, we investigated the effects of heat stress on the proteome of adipose tissue from late-pregnant cows during summer or winter seasons. We demonstrated that heat stress enriches several stress-related pathways, such as the Nrf2-mediated oxidative stress response and the acute-phase response in adipose tissues. Thus, environmental heat stress has a unique effect on adipose tissue in late-pregnant cows, as part of the regulatory adaptations to chronic heat load during the summer season. In addition, this study presents the widest available dataset of adipose tissue proteome in dairy cows, and revealed several novel biomarkers of heat stress in adipose tissue of dairy cows, the use of which awaits further validation.
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Affiliation(s)
- M Zachut
- Department of Ruminant Science, Institute of Animal Sciences, Volcani Center, Rishon Lezion, Israel.
| | - G Kra
- Department of Ruminant Science, Institute of Animal Sciences, Volcani Center, Rishon Lezion, Israel
| | - L Livshitz
- Department of Ruminant Science, Institute of Animal Sciences, Volcani Center, Rishon Lezion, Israel
| | - Y Portnick
- Department of Ruminant Science, Institute of Animal Sciences, Volcani Center, Rishon Lezion, Israel
| | - S Yakoby
- Department of Ruminant Science, Institute of Animal Sciences, Volcani Center, Rishon Lezion, Israel
| | - G Friedlander
- The Ilana and Pascal Mantoux Institute for Bioinformatics, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Y Levin
- de Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
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Gaillard F, Flamant M, Lemoine S, Baron S, Timsit MO, Eladari D, Fournier C, Prot-Bertoye C, Bertocchio JP, Vidal-Petiot E, Lamhaut L, Morelon E, Péraldi MN, Vrtovsnik F, Friedlander G, Méjean A, Houillier P, Legendre C, Courbebaisse M. Estimated or Measured GFR in Living Kidney Donors Work-up? Am J Transplant 2016; 16:3024-3032. [PMID: 27273845 DOI: 10.1111/ajt.13908] [Citation(s) in RCA: 27] [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] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 05/25/2016] [Accepted: 05/27/2016] [Indexed: 01/25/2023]
Abstract
The value of estimated glomerular filtration rate (eGFR) in living kidney donors screening is unclear. A recently published web-based application derived from large cohorts, but not living donors, calculates the probability of a measured GFR (mGFR) lower than a determined threshold. Our objectives were to validate the clinical utility of this tool in a cohort of living donors and to test two other strategies based on chronic kidney disease epidemiology collaboration (CKD-EPI) and on MDRD-eGFR. GFR was measured using 51 Cr- ethylene-diamine tetraacetic acid urinary clearance in 311 potential living kidney donors (178 women, mean age 50 ± 11.6 years). The web-based tool was used to predict those with mGFR < 80 mL/min/1.73 m2 . Inputs to the application were sex, age, ethnicity, and plasma creatinine. In our cohort, a web-based probability of mGFR <90 mL/min/1.73 m2 higher than 2% had 100% sensitivity for detection of actual mGFR <80 mL/min/1.73 m2 . The positive predictive value was 0.19. A CKD-EPI-eGFR threshold of 104 mL/min/1.73 m2 and an MDRD-eGFR threshold of 100 mL/min/1.73 m2 had 100% sensitivity to detect donors with actual mGFR <80 mL/min/1.73 m2 . We obtained similar results in an external cohort of 354 living donors. We confirm the usefulness of the web-based application to identify potential donors who should benefit from GFR measurement.
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Affiliation(s)
- F Gaillard
- AP-HP, Hôpital Necker-Enfants Malades, Renal Transplantation Department, Paris Descartes University, Paris, France
| | - M Flamant
- AP-HP, Hôpital Bichat, Department of Renal Physiology, DHU Fire and Paris Diderot University, Sorbonne Paris Cité, Paris, France
| | - S Lemoine
- Hospices civils de Lyon, Hôpital Edouard Herriot, Exploration fonctionnelle rénale Department and INSERM CARMEN 1060, University of Lyon, Lyon, France
| | - S Baron
- AP-HP, Hôpital Européen Georges Pompidou, Physiology Department, Paris Descartes University, Paris, France
| | - M-O Timsit
- AP-HP, Hôpital Européen Georges Pompidou, Urology Department, Paris Descartes University, Paris, France
| | - D Eladari
- AP-HP, Hôpital Européen Georges Pompidou, Physiology Department, Paris Descartes University, and INSERM, Unit 970, Paris, France
| | - C Fournier
- AP-HP, Hôpital Necker-Enfants Malades, Renal Transplantation Department, Paris Descartes University, Paris, France
| | - C Prot-Bertoye
- AP-HP, Hôpital Européen Georges Pompidou, Physiology Department, Paris Descartes University, Paris, France
| | - J-P Bertocchio
- AP-HP, Hôpital Européen Georges Pompidou, Physiology Department, Paris Descartes University, Paris, France
| | - E Vidal-Petiot
- AP-HP, Hôpital Bichat, Department of Renal Physiology, DHU Fire and Paris Diderot University, Sorbonne Paris Cité, Paris, France
| | - L Lamhaut
- AP-HP, Hôpital Necker-Enfants Malades, Anesthesia Department and Intensive Care Unit, Paris Descartes University, Paris, France
| | - E Morelon
- Hospices civils de Lyon, Hôpital Edouard Herriot, Transplantation Department, INSERM U 851, University of Lyon, Centaure Network, Lyon, France
| | - M-N Péraldi
- AP-HP, Hôpital Saint-Louis, Department of Nephrology and Renal Transplantation, Paris Diderot University, Sorbonne Paris Cité, Paris, France
| | - F Vrtovsnik
- AP-HP, Hôpital Bichat, Department of Nephrology, DHU Fire and Paris Diderot University, Sorbonne Paris Cité, Paris, France
| | - G Friedlander
- AP-HP, Hôpital Européen Georges Pompidou, Physiology Department, Paris Descartes University, and INSERM, Unit 1151, Paris, France
| | - A Méjean
- AP-HP, Hôpital Européen Georges Pompidou, Urology Department, Paris Descartes University, Paris, France
| | - P Houillier
- AP-HP, Hôpital Européen Georges Pompidou, Physiology Department, Paris Descartes University, INSERM, Unit umrs1138, and CNRS Unit erl8228, Paris, France
| | - C Legendre
- AP-HP, Hôpital Necker-Enfants Malades, Renal Transplantation Department, Paris Descartes University, Paris, France
| | - M Courbebaisse
- AP-HP, Hôpital Européen Georges Pompidou, Physiology Department, Paris Descartes University, and INSERM, Unit 1151, Paris, France
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Zachut M, Kra G, Friedlander G, Levin Y. 1083 Proteomic analysis reveals increased Nrf2-mediated oxidative stress response in adipose tissue of late pregnant dairy cows during summer heat stress. J Anim Sci 2016. [DOI: 10.2527/jam2016-1083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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23
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Hen-Avivi S, Savin O, Racovita RC, Lee WS, Adamski NM, Malitsky S, Almekias-Siegl E, Levy M, Vautrin S, Bergès H, Friedlander G, Kartvelishvily E, Ben-Zvi G, Alkan N, Uauy C, Kanyuka K, Jetter R, Distelfeld A, Aharoni A. A Metabolic Gene Cluster in the Wheat W1 and the Barley Cer-cqu Loci Determines β-Diketone Biosynthesis and Glaucousness. Plant Cell 2016; 28:1440-60. [PMID: 27225753 PMCID: PMC4944414 DOI: 10.1105/tpc.16.00197] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 05/12/2016] [Accepted: 05/25/2016] [Indexed: 05/19/2023]
Abstract
The glaucous appearance of wheat (Triticum aestivum) and barley (Hordeum vulgare) plants, that is the light bluish-gray look of flag leaf, stem, and spike surfaces, results from deposition of cuticular β-diketone wax on their surfaces; this phenotype is associated with high yield, especially under drought conditions. Despite extensive genetic and biochemical characterization, the molecular genetic basis underlying the biosynthesis of β-diketones remains unclear. Here, we discovered that the wheat W1 locus contains a metabolic gene cluster mediating β-diketone biosynthesis. The cluster comprises genes encoding proteins of several families including type-III polyketide synthases, hydrolases, and cytochrome P450s related to known fatty acid hydroxylases. The cluster region was identified in both genetic and physical maps of glaucous and glossy tetraploid wheat, demonstrating entirely different haplotypes in these accessions. Complementary evidence obtained through gene silencing in planta and heterologous expression in bacteria supports a model for a β-diketone biosynthesis pathway involving members of these three protein families. Mutations in homologous genes were identified in the barley eceriferum mutants defective in β-diketone biosynthesis, demonstrating a gene cluster also in the β-diketone biosynthesis Cer-cqu locus in barley. Hence, our findings open new opportunities to breed major cereal crops for surface features that impact yield and stress response.
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Affiliation(s)
- Shelly Hen-Avivi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Orna Savin
- Faculty of Life Sciences, Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv 69978, Israel
| | - Radu C Racovita
- Department of Chemistry, The University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Wing-Sham Lee
- Plant Biology and Crop Science Department, Rothamsted Research, Harpenden AL5 2JQ, United Kingdom
| | - Nikolai M Adamski
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Sergey Malitsky
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Efrat Almekias-Siegl
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Matan Levy
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Sonia Vautrin
- INRA-Centre National de Ressources Génomiques Végétales, F-31326 Castanet Tolosan, France
| | - Hélène Bergès
- INRA-Centre National de Ressources Génomiques Végétales, F-31326 Castanet Tolosan, France
| | - Gilgi Friedlander
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Elena Kartvelishvily
- Electron Microscopy Unit, Department of Chemical Research Support, Weizmann Institute of Science, Rehovot 76100, Israel
| | | | - Noam Alkan
- Department of Postharvest Science of Fresh Produce, Volcani Center, Agricultural Research Organization, Bet Dagan 50250, Israel
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Kostya Kanyuka
- Plant Biology and Crop Science Department, Rothamsted Research, Harpenden AL5 2JQ, United Kingdom
| | - Reinhard Jetter
- Department of Chemistry, The University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada Department of Botany, The University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Assaf Distelfeld
- Faculty of Life Sciences, Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv 69978, Israel
| | - Asaph Aharoni
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
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24
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Leshkowitz D, Feldmesser E, Friedlander G, Jona G, Ainbinder E, Parmet Y, Horn-Saban S. Using Synthetic Mouse Spike-In Transcripts to Evaluate RNA-Seq Analysis Tools. PLoS One 2016; 11:e0153782. [PMID: 27100792 PMCID: PMC4839710 DOI: 10.1371/journal.pone.0153782] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 04/04/2016] [Indexed: 11/25/2022] Open
Abstract
One of the key applications of next-generation sequencing (NGS) technologies is RNA-Seq for transcriptome genome-wide analysis. Although multiple studies have evaluated and benchmarked RNA-Seq tools dedicated to gene level analysis, few studies have assessed their effectiveness on the transcript-isoform level. Alternative splicing is a naturally occurring phenomenon in eukaryotes, significantly increasing the biodiversity of proteins that can be encoded by the genome. The aim of this study was to assess and compare the ability of the bioinformatics approaches and tools to assemble, quantify and detect differentially expressed transcripts using RNA-Seq data, in a controlled experiment. To this end, in vitro synthesized mouse spike-in control transcripts were added to the total RNA of differentiating mouse embryonic bodies, and their expression patterns were measured. This novel approach was used to assess the accuracy of the tools, as established by comparing the observed results versus the results expected of the mouse controlled spiked-in transcripts. We found that detection of differential expression at the gene level is adequate, yet on the transcript-isoform level, all tools tested lacked accuracy and precision.
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Affiliation(s)
- Dena Leshkowitz
- Biological Services Department, Weizmann Institute of Science, Rehovot, 76100, Israel
- * E-mail:
| | - Ester Feldmesser
- Biological Services Department, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Gilgi Friedlander
- Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Ghil Jona
- Biological Services Department, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Elena Ainbinder
- Biological Services Department, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Yisrael Parmet
- Industrial Engineering and Management Department, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Shirley Horn-Saban
- Biological Services Department, Weizmann Institute of Science, Rehovot, 76100, Israel
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25
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Friedlander G, Moulonguet-Doleris L, Kourilsky O, Nussaume O, Ardaillou R, Sraer JD. Prostaglandin synthesis by glomeruli isolated from normal and chronically rejected human kidneys. Contrib Nephrol 2015; 41:20-2. [PMID: 6396033 DOI: 10.1159/000429258] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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26
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Alkan N, Friedlander G, Ment D, Prusky D, Fluhr R. Simultaneous transcriptome analysis of Colletotrichum gloeosporioides and tomato fruit pathosystem reveals novel fungal pathogenicity and fruit defense strategies. New Phytol 2015; 205:801-15. [PMID: 25377514 DOI: 10.1111/nph.13087] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [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: 07/20/2014] [Accepted: 08/22/2014] [Indexed: 05/20/2023]
Abstract
The fungus Colletotrichum gloeosporioides breaches the fruit cuticle but remains quiescent until fruit ripening signals a switch to necrotrophy, culminating in devastating anthracnose disease. There is a need to understand the distinct fungal arms strategy and the simultaneous fruit response. Transcriptome analysis of fungal-fruit interactions was carried out concurrently in the appressoria, quiescent and necrotrophic stages. Conidia germinating on unripe fruit cuticle showed stage-specific transcription that was accompanied by massive fruit defense responses. The subsequent quiescent stage showed the development of dendritic-like structures and swollen hyphae within the fruit epidermis. The quiescent fungal transcriptome was characterized by activation of chromatin remodeling genes and unsuspected environmental alkalization. Fruit response was portrayed by continued highly integrated massive up-regulation of defense genes. During cuticle infection of green or ripe fruit, fungi recapitulate the same developmental stages but with differing quiescent time spans. The necrotrophic stage showed a dramatic shift in fungal metabolism and up-regulation of pathogenicity factors. Fruit response to necrotrophy showed activation of the salicylic acid pathway, climaxing in cell death. Transcriptome analysis of C. gloeosporioides infection of fruit reveals its distinct stage-specific lifestyle and the concurrent changing fruit response, deepening our perception of the unfolding fungal-fruit arms and defenses race.
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Affiliation(s)
- Noam Alkan
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel; Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, the Volcani Center, Bet Dagan, 50250, Israel
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27
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Levin S, Pevsner-Fischer M, Kagan S, Lifshitz H, Weinstock A, Gataulin D, Friedlander G, Zipori D. Divergent levels of LBP and TGFβ1 in murine MSCs lead to heterogenic response to TLR and proinflammatory cytokine activation. Stem Cell Rev Rep 2014; 10:376-88. [PMID: 24664302 DOI: 10.1007/s12015-014-9498-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The outstanding heterogeneity of stem cell populations is a major obstacle on the way to their clinical application. It is therefore paramount to identify the molecular mechanisms that underlay this heterogeneity. Individually derived bone marrow mesenchymal stromal cells (MSCs) preparations, studied here, diverged markedly in various properties, despite of being all tripotent in their differentiation potential. Microarray analysis showed that MSC diversity is evident also in highly variable gene expression patterns. Differentially expressed genes were significantly enriched in toll-like receptors (TLRs) and differentiation pathways. Marked differences were observed in LPS binding protein (LBP) and transforming growth factor (TGF)β1 expression. These differences correlated with MSC functionality. Therefore, the possible contribution of these molecules to MSC diversity was examined. In the TLR signaling pathway, LBP levels predicted the ability of specific MSCs to secrete interleukin (IL)-6 in response to LPS. A relatively higher expression of TGFβ1 endowed MSCs with a capacity to respond to IL-1β by reduced osteogenic differentiation. This study thus demonstrates major diversity within MSC isolates, which appears early on following derivation and persists following long-term culture. MSC heterogeneity results from highly variable transcriptome. Differential expression of LBP and TGFβ1, along with other genes, in different MSC preparations, produces the variable responses to external stimuli.
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Affiliation(s)
- Sarit Levin
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel, 76100
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28
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Zigmond E, Bernshtein B, Friedlander G, Walker CR, Yona S, Kim KW, Brenner O, Krauthgamer R, Varol C, Müller W, Jung S. Macrophage-restricted interleukin-10 receptor deficiency, but not IL-10 deficiency, causes severe spontaneous colitis. Immunity 2014; 40:720-33. [PMID: 24792913 DOI: 10.1016/j.immuni.2014.03.012] [Citation(s) in RCA: 397] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 03/18/2014] [Indexed: 02/07/2023]
Abstract
Interleukin-10 (IL-10) is a pleiotropic anti-inflammatory cytokine produced and sensed by most hematopoietic cells. Genome-wide association studies and experimental animal models point at a central role of the IL-10 axis in inflammatory bowel diseases. Here we investigated the importance of intestinal macrophage production of IL-10 and their IL-10 exposure, as well as the existence of an IL-10-based autocrine regulatory loop in the gut. Specifically, we generated mice harboring IL-10 or IL-10 receptor (IL-10Rα) mutations in intestinal lamina propria-resident chemokine receptor CX3CR1-expressing macrophages. We found macrophage-derived IL-10 dispensable for gut homeostasis and maintenance of colonic T regulatory cells. In contrast, loss of IL-10 receptor expression impaired the critical conditioning of these monocyte-derived macrophages and resulted in spontaneous development of severe colitis. Collectively, our results highlight IL-10 as a critical homeostatic macrophage-conditioning agent in the colon and define intestinal CX3CR1(hi) macrophages as a decisive factor that determines gut health or inflammation.
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Affiliation(s)
- Ehud Zigmond
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel; The Research Center for Digestive Tract and Liver Diseases, Tel Aviv-Sourasky Medical Center and Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 64239, Israel
| | - Biana Bernshtein
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Gilgi Friedlander
- Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Catherine R Walker
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Simon Yona
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ki-Wook Kim
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ori Brenner
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Rita Krauthgamer
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Chen Varol
- The Research Center for Digestive Tract and Liver Diseases, Tel Aviv-Sourasky Medical Center and Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 64239, Israel
| | - Werner Müller
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Steffen Jung
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel.
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Lotem J, Levanon D, Negreanu V, Leshkowitz D, Friedlander G, Groner Y. Runx3-mediated transcriptional program in cytotoxic lymphocytes. PLoS One 2013; 8:e80467. [PMID: 24236182 PMCID: PMC3827420 DOI: 10.1371/journal.pone.0080467] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2013] [Accepted: 10/02/2013] [Indexed: 12/03/2022] Open
Abstract
The transcription factor Runx3 is highly expressed in CD8+ T and NK cytotoxic lymphocytes and is required for their effective activation and proliferation but molecular insights into the transcription program regulated by Runx3 in these cells are still missing. Using Runx3-ChIP-seq and transcriptome analysis of wild type vs. Runx3-/- primary cells we have now identified Runx3-regulated genes in the two cell types at both resting and IL-2-activated states. Runx3-bound genomic regions in both cell types were distantly located relative to gene transcription start sites and were enriched for RUNX and ETS motifs. Bound genomic regions significantly overlapped T-bet and p300-bound enhancer regions in Runx3-expressing Th1 helper cells. Compared to resting cells, IL-2-activated CD8+ T and NK cells contain three times more Runx3-regulated genes that are common to both cell types. Functional annotation of shared CD8+ T and NK Runx3-regulated genes revealed enrichment for immune-associated terms including lymphocyte activation, proliferation, cytotoxicity, migration and cytokine production, highlighting the role of Runx3 in CD8+ T and NK activated cells.
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MESH Headings
- Animals
- Core Binding Factor Alpha 3 Subunit/genetics
- Enhancer Elements, Genetic
- Gene Expression Profiling
- Gene Expression Regulation/drug effects
- Histones/metabolism
- Interleukin-2/metabolism
- Interleukin-2/pharmacology
- Killer Cells, Natural/drug effects
- Killer Cells, Natural/immunology
- Killer Cells, Natural/metabolism
- Lymphocyte Activation/genetics
- Lymphocyte Activation/immunology
- Mice
- Mice, Knockout
- Nucleotide Motifs
- Position-Specific Scoring Matrices
- Protein Binding
- Resting Phase, Cell Cycle/genetics
- T-Lymphocytes, Cytotoxic/drug effects
- T-Lymphocytes, Cytotoxic/immunology
- T-Lymphocytes, Cytotoxic/metabolism
- Transcription Factor AP-1/metabolism
- Transcription Initiation Site
- Transcription, Genetic
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Affiliation(s)
- Joseph Lotem
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Ditsa Levanon
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Varda Negreanu
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Dena Leshkowitz
- Israel National Center for Personalized Medicine Bioinformatics Unit, Weizmann Institute of Science, Rehovot, Israel
| | - Gilgi Friedlander
- Israel National Center for Personalized Medicine Bioinformatics Unit, Weizmann Institute of Science, Rehovot, Israel
| | - Yoram Groner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
- * E-mail:
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Alkan N, Meng X, Friedlander G, Reuveni E, Sukno S, Sherman A, Thon M, Fluhr R, Prusky D. Global aspects of pacC regulation of pathogenicity genes in Colletotrichum gloeosporioides as revealed by transcriptome analysis. Mol Plant Microbe Interact 2013; 26:1345-58. [PMID: 23902260 DOI: 10.1094/mpmi-03-13-0080-r] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Colletotrichum gloeosporioides alkalinizes its surroundings during colonization of host tissue. The transcription factor pacC is a regulator of pH-controlled genes and is essential for successful colonization. We present here the sequence assembly of the Colletotrichum fruit pathogen and use it to explore the global regulation of pathogenicity by ambient pH. The assembled genome size was 54 Mb, encoding 18,456 genes. Transcriptomes of the wild type and ΔpacC mutant were established by RNA-seq and explored for their global pH-dependent gene regulation. The analysis showed that pacC upregulates 478 genes and downregulates 483 genes, comprising 5% of the fungal genome, including transporters, antioxidants, and cell-wall-degrading enzymes. Interestingly, gene families with similar functionality are both up- and downregulated by pacC. Global analysis of secreted genes showed significant pacC activation of degradative enzymes at alkaline pH and during fruit infection. Select genes from alkalizing-type pathogen C. gloeosporioides and from acidifying-type pathogen Sclerotinia sclerotiorum were verified by quantitative reverse-transcription polymerase chain reaction analysis at different pH values. Knock out of several pacC-activated genes confirmed their involvement in pathogenic colonization of alkalinized surroundings. The results suggest a global regulation by pacC of key pathogenicity genes during pH change in alkalinizing and acidifying pathogens.
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31
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Madar S, Harel E, Goldstein I, Stein Y, Kogan-Sakin I, Kamer I, Solomon H, Dekel E, Tal P, Goldfinger N, Friedlander G, Rotter V. Mutant p53 attenuates the anti-tumorigenic activity of fibroblasts-secreted interferon beta. PLoS One 2013; 8:e61353. [PMID: 23630584 PMCID: PMC3632588 DOI: 10.1371/journal.pone.0061353] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Accepted: 03/08/2013] [Indexed: 12/12/2022] Open
Abstract
Mutations in the p53 tumor suppressor protein are highly frequent in tumors and often endow cells with tumorigenic capacities. We sought to examine a possible role for mutant p53 in the cross-talk between cancer cells and their surrounding stroma, which is a crucial factor affecting tumor outcome. Here we present a novel model which enables individual monitoring of the response of cancer cells and stromal cells (fibroblasts) to co-culturing. We found that fibroblasts elicit the interferon beta (IFNβ) pathway when in contact with cancer cells, thereby inhibiting their migration. Mutant p53 in the tumor was able to alleviate this response via SOCS1 mediated inhibition of STAT1 phosphorylation. IFNβ on the other hand, reduced mutant p53 RNA levels by restricting its RNA stabilizer, WIG1. These data underscore mutant p53 oncogenic properties in the context of the tumor microenvironment and suggest that mutant p53 positive cancer patients might benefit from IFNβ treatment.
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Affiliation(s)
- Shalom Madar
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Einav Harel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Ido Goldstein
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yan Stein
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Ira Kogan-Sakin
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Iris Kamer
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Hilla Solomon
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Elya Dekel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Perry Tal
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Naomi Goldfinger
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Gilgi Friedlander
- Faculty of Biochemistry, Biological Services Unit, Weizmann Institute of Science, Rehovot, Israel
| | - Varda Rotter
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
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Zigmond E, Varol C, Farache J, Elmaliah E, Satpathy AT, Friedlander G, Mack M, Shpigel N, Boneca IG, Murphy KM, Shakhar G, Halpern Z, Jung S. Ly6C hi monocytes in the inflamed colon give rise to proinflammatory effector cells and migratory antigen-presenting cells. Immunity 2012; 37:1076-90. [PMID: 23219392 DOI: 10.1016/j.immuni.2012.08.026] [Citation(s) in RCA: 539] [Impact Index Per Article: 44.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 08/29/2012] [Indexed: 12/15/2022]
Abstract
Ly6C(hi) monocytes seed the healthy intestinal lamina propria to give rise to resident CX(3)CR1(+) macrophages that contribute to the maintenance of gut homeostasis. Here we report on two alternative monocyte fates in the inflamed colon. We showed that CCR2 expression is essential to the recruitment of Ly6C(hi) monocytes to the inflamed gut to become the dominant mononuclear cell type in the lamina propria during settings of acute colitis. In the inflammatory microenvironment, monocytes upregulated TLR2 and NOD2, rendering them responsive to bacterial products to become proinflammatory effector cells. Ablation of Ly6C(hi) monocytes ameliorated acute gut inflammation. With time, monocytes differentiated into migratory antigen-presenting cells capable of priming naive T cells, thus acquiring hallmarks reminiscent of dendritic cells. Collectively, our results highlight cellular dynamics in the inflamed colon and the plasticity of Ly6C(hi) monocytes, marking them as potential targets for inflammatory bowel disease (IBD) therapy.
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Affiliation(s)
- Ehud Zigmond
- Department of Immunology, The Weizmann Institute of Science, Rehovot, Israel
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Benaboud S, Urien S, Thervet E, Prié D, Legendre C, Souberbielle JC, Hirt D, Friedlander G, Treluyer JM, Courbebaisse M. Détermination du traitement optimal par cholécalciférol chez le patient transplanté rénal : approche de population. Nephrol Ther 2012. [DOI: 10.1016/j.nephro.2012.07.344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Yifhar T, Pekker I, Peled D, Friedlander G, Pistunov A, Sabban M, Wachsman G, Alvarez JP, Amsellem Z, Eshed Y. Failure of the tomato trans-acting short interfering RNA program to regulate AUXIN RESPONSE FACTOR3 and ARF4 underlies the wiry leaf syndrome. Plant Cell 2012; 24:3575-89. [PMID: 23001036 PMCID: PMC3480288 DOI: 10.1105/tpc.112.100222] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Revised: 07/17/2012] [Accepted: 08/29/2012] [Indexed: 05/21/2023]
Abstract
Interfering with small RNA production is a common strategy of plant viruses. A unique class of small RNAs that require microRNA and short interfering (siRNA) biogenesis for their production is termed trans-acting short interfering RNAs (ta-siRNAs). Tomato (Solanum lycopersicum) wiry mutants represent a class of phenotype that mimics viral infection symptoms, including shoestring leaves that lack leaf blade expansion. Here, we show that four WIRY genes are involved in siRNA biogenesis, and in their corresponding mutants, levels of ta-siRNAs that regulate AUXIN RESPONSE FACTOR3 (ARF3) and ARF4 are reduced, while levels of their target ARFs are elevated. Reducing activity of both ARF3 and ARF4 can rescue the wiry leaf lamina, and increased activity of either can phenocopy wiry leaves. Thus, a failure to negatively regulate these ARFs underlies tomato shoestring leaves. Overexpression of these ARFs in Arabidopsis thaliana, tobacco (Nicotiana tabacum), and potato (Solanum tuberosum) failed to produce wiry leaves, suggesting that the dramatic response in tomato is exceptional. As negative regulation of orthologs of these ARFs by ta-siRNA is common to land plants, we propose that ta-siRNA levels serve as universal sensors for interference with small RNA biogenesis, and changes in their levels direct species-specific responses.
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Affiliation(s)
- Tamar Yifhar
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Irena Pekker
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Dror Peled
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Gilgi Friedlander
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Anna Pistunov
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Moti Sabban
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Guy Wachsman
- Department of Biology, Technion, Israel Institute of Technology, Haifa 32000, Israel
| | - John Paul Alvarez
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ziva Amsellem
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yuval Eshed
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
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36
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Bonani M, Brockmann J, Cohen CD, Fehr T, Nocito A, Schiesser M, Serra AL, Blum M, Struker M, Frey DF, Wuthrich RP, Kim YW, Park SJ, Kim TH, Kim YH, Kang SW, Webb L, Casula A, Tomson C, Ben-Shlomo Y, Webb L, Casula A, Ben-Shlomo Y, Tomson C, Mansour H, Akl A, Wafa E, El Shahawy M, Palma R, Swaminathan S, Irish AB, Kolonko A, Chudek J, Wiecek A, Vanrenterghem Y, Kuypers D, Katrien DV, Evenepoel P, Claes K, Bammens B, Meijers B, Naesens M, Kolonko A, Chudek J, Wiecek A, Lo S, Chan CK, Yong D, Wong PN, Kwan TH, Cheng YL, Fung KS, Choy BY, Chau KF, Leung CB, Ebben J, Liu J, Chen SC, Collins A, Ho YW, Abelli M, Ferrario DI Torvajana A, Ticozzelli E, Maiga B, Ferrario DI Torvajana A, Patane A, Albrizio P, Gregorini M, Libetta C, Rampino T, Albrizio P, Geraci P, Dal Canton A, Rotter MT, Jacobi J, Pressmar K, Amann K, Eckardt KU, Weidemann A, Muller K, Stein M, Diezemann C, Sefrin A, Babel N, Reinke P, Schachtner T, Costa C, Touscoz GA, Sidoti F, Sinesi F, Mantovani S, Simeone S, Balloco C, Piasentin Alessio E, Messina M, Segoloni G, Cavallo R, Sharma R.K, Kaul DA, Gupta RK, Gupta A, Prasad N, Bhadhuria D, Suresh KJ, Benaboud S, Prie D, Thervet E, Urien S, Legendre C, Souberbielle JC, Hirt D, Friedlander G, Treluyer JM, Courbebaisse M, Arias M, Arias M, Campistol J, Pascual J, Grinyo JM, Hernandez D, Morales JM, Pallardo LM, Seron D, Senecal L, Boucher A, Dandavino R, Boucher A, Colette S, Vallee M, Lafrance JP, Tung-Min Y, Min-Ju W, Cheng-Hsu C, Chi-Hung C, Kuo-Hsiung S, Mei-Chin W, Direkze S, Khorsavi M, Khorsavi M, Stuart S, Goode A, Jones G, Chudek J, Kolonko A, Wiecek A, Massimetti C, Napoletano I, Imperato G, Muratore MT, Fazio S, Pessina G, Brescia F, Feriozzi S, Tanaka K, Sakai K, Futaki A, Hyoudo Y, Muramatsu M, Kawamura T, Shishido S, Hara S, Kushiyama A, Aikawa A, Jankowski K, Gozdowska J, Lewandowska D, Kwiatkowski A, Durlik M, Pruszczyk P, Obi Y, Ichimaru N, Kato T, Okumi M, Kaimori J, Yazawa K, Nonomura N, Isaka Y, Takahara S, Aimele M, Christophe R, Geraldine D, Eric R, Alexandre H, Masson I, Nicolas M, Ivan T, Acil J, Lise T, Aoumeur HA, Laurence D, Pierre D, Etienne C, Lionel R, Nassim K, Emmanuel M, Eric A, Christophe M, Webb L, Casula A, Tomson C, Ben-Shlomo Y, Alexandre K, Pierre B, Jean-Philippe H, Dominique P, Christophe L, Alexei G, Michel D, Shah P, Kute VB, Vanikar A, Gumber M, Modi P, Trivedi H, GoIebiewska J, Debska-Slizien A, Rutkowski B, Domanski L, Dutkiewicz G, Kloda K, Pawlik A, Ciechanowicz A, Binczak-Kuleta A, Rozanski J, Myslak M, Safranow K, Ciechanowski K, Aline CS, Basset T, Delavenne X, Alamartine E, Mariat C, Kloda K, Domanski L, Pawlik A, Bobrek-Lesiakowska K, Wisniewska M, Romanowski M, Safranow K, Kurzawski M, Rozanski J, Myslak M, Ciechanowski K, De Borst M, Baia L, Navis G, Bakker S, Ranghino A, Tognarelli G, Basso E, Messina M, Manzione AM, Daidola G, Segoloni GP, Kimura T, Yagisawa T, Ishikawa N, Sakuma Y, Hujiwara T, Nukui A, Yashi M, Kim JH, Kim SS, Han DJ, Park SK, Randhawa G, Gumber M, Kute VB, Shah P, Patel H, Vanikar A, Modi P, Trivedi H, Taheri S, Goker-Alpan O, Ibrahim J, Nedd K, Shankar S, Lein H, Barshop B, Boyd E, Holida M, Hillman R, Ibrahim J, Mardach R, Wienreb N, Rever B, Forte R, Desai A, Wijatyk A, Chang P, Martin R. Transplantation - clinical I. Nephrol Dial Transplant 2012. [DOI: 10.1093/ndt/gfs230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Abstract
Many protein-protein interactions are mediated by domain-motif interaction, where a domain in one protein binds a short linear motif in its interacting partner. Such interactions are often involved in key cellular processes, necessitating their tight regulation. A common strategy of the cell to control protein function and interaction is by post-translational modifications of specific residues, especially phosphorylation. Indeed, there are motifs, such as SH2-binding motifs, in which motif phosphorylation is required for the domain-motif interaction. On the contrary, there are other examples where motif phosphorylation prevents the domain-motif interaction. Here we present a large-scale integrative analysis of experimental human data of domain-motif interactions and phosphorylation events, demonstrating an intriguing coupling between the two. We report such coupling for SH3, PDZ, SH2 and WW domains, where residue phosphorylation within or next to the motif is implied to be associated with switching on or off domain binding. For domains that require motif phosphorylation for binding, such as SH2 domains, we found coupled phosphorylation events other than the ones required for domain binding. Furthermore, we show that phosphorylation might function as a double switch, concurrently enabling interaction of the motif with one domain and disabling interaction with another domain. Evolutionary analysis shows that co-evolution of the motif and the proximal residues capable of phosphorylation predominates over other evolutionary scenarios, in which the motif appeared before the potentially phosphorylated residue, or vice versa. Our findings provide strengthening evidence for coupled interaction-regulation units, defined by a domain-binding motif and a phosphorylated residue. Domain-motif interactions are instrumental for many central cellular processes, and are therefore tightly regulated. Phosphorylation events are known modulators of protein-protein interactions in general, including domain-motif interactions. Here, we addressed the association of phosphorylation and domain-motif interaction taking a motif-centred view. We integrated human domain-motif interaction and phosphorylation data for four representative domains (SH2, WW, SH3 and PDZ), and showed that the adjacency between phosphorylation and domain-motif interactions is extensive, suggesting interesting functional links between them that extend the classical and widely studied phospho-regulation of SH2 or WW domain-motif interactions. Furthermore, we show that such interaction-regulation units may function as double switches, concurrently enabling interaction of the motif with one domain and disabling interaction with another domain. These latter interaction-regulation units are more conserved in evolution than the individual units comprising them. Assuming that the four analyzed domain-motif interaction types are reliable representatives of such interactions, our results support the existence of units comprising motifs and associated phosphorylation sites, in which the regulation of domain-motif interaction is inherent.
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Affiliation(s)
- Eyal Akiva
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Gilgi Friedlander
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Zohar Itzhaki
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Hanah Margalit
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
- * E-mail:
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Bonnet F, Cathrin L, Lepicard E, Constant F, Hawili N, Friedlander G. P007 Déficit hydrique après le petit déjeuner chez des enfants français de 9 à 11 ans. NUTR CLIN METAB 2011. [DOI: 10.1016/s0985-0562(11)70075-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Courbebaisse M, Ribeil JA, Chatellier G, Prié D, Khira N, Pouchot J, Friedlander G, Arlet JB. Carence en vitamine D et fragilité osseuse chez les patients drépanocytaires adultes. Nephrol Ther 2011. [DOI: 10.1016/j.nephro.2011.07.307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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40
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Courbebaisse M, Ribeil JA, Chatellier G, Khira N, Friedlander G, Pouchot J, Prié D, Arlet JB. Prévalence de l’hyperuricémie chez les patients drépanocytaires adultes et facteurs de risque associés. Nephrol Ther 2011. [DOI: 10.1016/j.nephro.2011.07.225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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41
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Courbebaisse M, Ribeil JA, Chatellier G, Friedlander G, Khira N, Pouchot J, Prié D, Arlet JB. L’équation CKD-EPI sans l’ajustement par le facteur « race » est la meilleure formule d’estimation du débit de filtration glomérulaire chez les patients drépanocytaires adultes. Nephrol Ther 2011. [DOI: 10.1016/j.nephro.2011.07.222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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42
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Gump B, McMullan D, Cauthon D, Moore MS, Whitt JA, Tedeschi J, Mundo JD, Letham T, Friedlander G, Kim PJ, Pingel J, Langberg H, Carroll CC. The effect of acetaminophen on post‐exercise IL‐6 levels in human Achilles peritendinous tissue. FASEB J 2011. [DOI: 10.1096/fasebj.25.1_supplement.1107.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Brian Gump
- PhysiologyMidwestern UniversityGlendaleAZ
| | - D McMullan
- PhysiologyMidwestern UniversityGlendaleAZ
| | - D Cauthon
- PhysiologyMidwestern UniversityGlendaleAZ
| | - M S Moore
- PhysiologyMidwestern UniversityGlendaleAZ
| | - J A Whitt
- PhysiologyMidwestern UniversityGlendaleAZ
| | - J Tedeschi
- PhysiologyMidwestern UniversityGlendaleAZ
| | | | - T Letham
- PhysiologyMidwestern UniversityGlendaleAZ
| | | | | | - J Pingel
- Bispebjerg HospitalInstitute of Sports MedicineCopenhagenDenmark
| | - H Langberg
- Bispebjerg HospitalInstitute of Sports MedicineCopenhagenDenmark
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Shimoni Y, Friedlander G, Hetzroni G, Niv G, Altuvia S, Biham O, Margalit H. Regulation of gene expression by small non-coding RNAs: a quantitative view. Mol Syst Biol 2007; 3:138. [PMID: 17893699 PMCID: PMC2013925 DOI: 10.1038/msb4100181] [Citation(s) in RCA: 235] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2007] [Accepted: 08/23/2007] [Indexed: 01/02/2023] Open
Abstract
The importance of post-transcriptional regulation by small non-coding RNAs has recently been recognized in both pro- and eukaryotes. Small RNAs (sRNAs) regulate gene expression post-transcriptionally by base pairing with the mRNA. Here we use dynamical simulations to characterize this regulation mode in comparison to transcriptional regulation mediated by protein–DNA interaction and to post-translational regulation achieved by protein–protein interaction. We show quantitatively that regulation by sRNA is advantageous when fast responses to external signals are needed, consistent with experimental data about its involvement in stress responses. Our analysis indicates that the half-life of the sRNA–mRNA complex and the ratio of their production rates determine the steady-state level of the target protein, suggesting that regulation by sRNA may provide fine-tuning of gene expression. We also describe the network of regulation by sRNA in Escherichia coli, and integrate it with the transcription regulation network, uncovering mixed regulatory circuits, such as mixed feed-forward loops. The integration of sRNAs in feed-forward loops provides tight repression, guaranteed by the combination of transcriptional and post-transcriptional regulations.
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Affiliation(s)
- Yishai Shimoni
- Racah Institute of Physics, The Hebrew University, Jerusalem, Israel
| | - Gilgi Friedlander
- Department of Molecular Genetics and Biotechnology, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Guy Hetzroni
- Racah Institute of Physics, The Hebrew University, Jerusalem, Israel
| | - Gali Niv
- Department of Molecular Genetics and Biotechnology, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Shoshy Altuvia
- Department of Molecular Genetics and Biotechnology, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Ofer Biham
- Racah Institute of Physics, The Hebrew University, Jerusalem, Israel
- Racah Institute of Physics, The Hebrew University, Jerusalem 91904, Israel. Tel.: +972 2 658 4363; Fax: +972 2 652 0089;
| | - Hanah Margalit
- Department of Molecular Genetics and Biotechnology, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
- Department of Molecular Genetics and Biotechnology, Faculty of Medicine, The Hebrew University, PO Box 12272, Jerusalem 91120, Israel. Tel.: +972 2 675 8614; Fax: +972 2 675 7308;
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Abstract
Klotho gene mutation leads to a syndrome strangely resembling chronic kidney disease patients undergoing dialysis with multiple accelerated age-related disorders, including hypoactivity, sterility, skin thinning, muscle atrophy, osteoporosis, vascular calcifications, soft-tissue calcifications, defective hearing, thymus atrophy, pulmonary emphysema, ataxia, and abnormalities of the pituitary gland, as well as hypoglycemia, hyperphosphatemia, and paradoxically high-plasma calcitriol levels. Conversely, mice overexpressing klotho show an extended existence and a slow aging process through a mechanism that may involve the induction of a state of insulin and oxidant stress resistance. Two molecules are produced by the klotho gene, a membrane bound form and a circulating form. However, their precise biological roles and molecular functions have been only partly deciphered. Klotho can act as a circulating factor or hormone, which binds to a not yet identified high-affinity receptor and inhibits the intracellular insulin/insulin-like growth factor-1 (IGF-1) signaling cascade; klotho can function as a novel beta-glucuronidase, which deglycosylates steroid beta-glucuronides and the calcium channel transient receptor potential vallinoid-5 (TRPV5); as a cofactor essential for the stimulation of fibroblast growth factor (FGF) receptor by FGF23. The two last functions have propelled klotho to the group of key factors regulating mineral and vitamin D metabolism, and have also stimulated the interest of the nephrology community. The purpose of this review is to provide a nephrology-oriented overview of klotho and its potential implications in normal and altered renal function states.
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Affiliation(s)
- P-Ureña Torres
- Service de Néphrologie et Dialyse, Clinique de l'Orangerie, Aubervilliers, France.
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Levy S, Ihmels J, Carmi M, Weinberger A, Friedlander G, Barkai N. Strategy of transcription regulation in the budding yeast. PLoS One 2007; 2:e250. [PMID: 17327914 PMCID: PMC1803021 DOI: 10.1371/journal.pone.0000250] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2007] [Accepted: 01/30/2007] [Indexed: 12/03/2022] Open
Abstract
Cells must adjust their gene expression in order to compete in a constantly changing environment. Two alternative strategies could in principle ensure optimal coordination of gene expression with physiological requirements. First, characters of the internal physiological state, such as growth rate, metabolite levels, or energy availability, could be feedback to tune gene expression. Second, internal needs could be inferred from the external environment, using evolutionary-tuned signaling pathways. Coordination of ribosomal biogenesis with the requirement for protein synthesis is of particular importance, since cells devote a large fraction of their biosynthetic capacity for ribosomal biogenesis. To define the relative contribution of internal vs. external sensing to the regulation of ribosomal biogenesis gene expression in yeast, we subjected S. cerevisiae cells to conditions which decoupled the actual vs. environmentally-expected growth rate. Gene expression followed the environmental signal according to the expected, but not the actual, growth rate. Simultaneous monitoring of gene expression and growth rate in continuous cultures further confirmed that ribosome biogenesis genes responded rapidly to changes in the environments but were oblivious to longer-term changes in growth rate. Our results suggest that the capacity to anticipate and prepare for environmentally-mediated changes in cell growth presented a major selection force during yeast evolution.
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MESH Headings
- Alcohol Dehydrogenase/biosynthesis
- Alcohol Dehydrogenase/genetics
- Culture Media/pharmacology
- Feedback, Physiological
- Fermentation/genetics
- Gene Expression Profiling
- Gene Expression Regulation, Fungal/drug effects
- Gene Expression Regulation, Fungal/physiology
- Genes, Fungal
- Genes, cdc
- Mycology/methods
- Nucleotides/metabolism
- Oligonucleotide Array Sequence Analysis
- RNA, Fungal/biosynthesis
- RNA, Fungal/genetics
- RNA, Messenger/biosynthesis
- RNA, Messenger/genetics
- RNA, Ribosomal/biosynthesis
- RNA, Ribosomal/genetics
- RNA, Transfer/biosynthesis
- RNA, Transfer/genetics
- Reproduction, Asexual
- Ribosomes/metabolism
- Saccharomyces cerevisiae/cytology
- Saccharomyces cerevisiae/drug effects
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/growth & development
- Saccharomyces cerevisiae Proteins/biosynthesis
- Saccharomyces cerevisiae Proteins/genetics
- Transcription, Genetic/drug effects
- Transcription, Genetic/physiology
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Affiliation(s)
- Sagi Levy
- Department of Molecular Genetics and Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Jan Ihmels
- Department of Molecular Genetics and Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
- Howard Hughes Medical Institute, Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, United States of America
| | - Miri Carmi
- Department of Molecular Genetics and Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Adina Weinberger
- Department of Molecular Genetics and Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Gilgi Friedlander
- Department of Molecular Genetics and Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Naama Barkai
- Department of Molecular Genetics and Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
- * To whom correspondence should be addressed. E-mail:
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46
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Friedlander G, Joseph-Strauss D, Carmi M, Zenvirth D, Simchen G, Barkai N. Modulation of the transcription regulatory program in yeast cells committed to sporulation. Genome Biol 2006; 7:R20. [PMID: 16542486 PMCID: PMC1557749 DOI: 10.1186/gb-2006-7-3-r20] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2005] [Revised: 12/22/2005] [Accepted: 02/09/2006] [Indexed: 11/23/2022] Open
Abstract
Analysis of the gene expression program in yeast cells suggests that commitment to sporulation involves an active modulation of the gene expression program. Background Meiosis in budding yeast is coupled to the process of sporulation, where the four haploid nuclei are packaged into a gamete. This differentiation process is characterized by a point of transition, termed commitment, when it becomes independent of the environment. Not much is known about the mechanisms underlying commitment, but it is often assumed that positive feedback loops stabilize the underlying gene-expression cascade. Results We describe the gene-expression program of committed cells. Sporulating cells were transferred back to growth medium at different stages of the process, and their transcription response was characterized. Most sporulation-induced genes were immediately downregulated upon transfer, even in committed cells that continued to sporulate. Focusing on the metabolic-related transcription response, we observed that pre-committed cells, as well as mature spores, responded to the transfer to growth medium in essentially the same way that vegetative cells responded to glucose. In contrast, committed cells elicited a dramatically different response. Conclusion Our results suggest that cells ensure commitment to sporulation not by stabilizing the process, but by modulating their gene-expression program in an active manner. This unique transcriptional program may optimize sporulation in an environment-specific manner.
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Affiliation(s)
- Gilgi Friedlander
- Departments of Molecular Genetics and Physics of Complex System, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Daphna Joseph-Strauss
- Departments of Molecular Genetics and Physics of Complex System, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Miri Carmi
- Departments of Molecular Genetics and Physics of Complex System, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Drora Zenvirth
- Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Giora Simchen
- Department of Genetics, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Naama Barkai
- Departments of Molecular Genetics and Physics of Complex System, Weizmann Institute of Science, Rehovot 76100, Israel
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Ledoux S, Runembert I, Koumanov K, Michel JB, Trugnan G, Friedlander G. Hypoxia enhances Ecto-5'-Nucleotidase activity and cell surface expression in endothelial cells: role of membrane lipids. Circ Res 2003; 92:848-55. [PMID: 12663485 DOI: 10.1161/01.res.0000069022.95401.fe] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Extracellular adenosine production by the glycosyl-phosphatidyl-inositol-anchored Ecto-5'-Nucleotidase plays an important role in the defense against hypoxia, particularly in the intravascular space. The present study was designed in order to elucidate the mechanisms underlying hypoxia-induced stimulation of Ecto-5'-Nucleotidase in endothelial cells. For this purpose, aortic endothelial cells (SVARECs) were submitted to hypoxic gas mixture. Hypoxia (0% O2 for 18 hours) induced a 2-fold increase of Ecto-5'-Nucleotidase activity (Vmax 19.78+/-0.53 versus 8.82+/-1.12 nmol/mg protein per min), whereas mRNA abundance and total amount of the protein were unmodified. By contrast, hypoxia enhanced cell surface expression of Ecto-5'-Nucleotidase, as evidenced both by biotinylation and immunostaining. This effect was accompanied by a decrease of Ecto-5'-Nucleotidase endocytosis, without modification of Ecto-5'-Nucleotidase association with detergent-resistant membranes. Finally, whereas cholesterol content was unmodified, hypoxia induced a time-dependent increase of saturated fatty acids in SVARECs, which was reversed by reoxygenation, in parallel to Ecto-5'-Nucleotidase stimulation. Incubation of normoxic cells with palmitic acid enhanced Ecto-5'-Nucleotidase activity and cell surface expression. In conclusion, hypoxia enhances cell surface expression of Ecto-5'-Nucleotidase in endothelial cells. This effect could be supported by a decrease of Ecto-5'-Nucleotidase endocytosis through modification of plasma membrane fatty acid composition.
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MESH Headings
- 5'-Nucleotidase/genetics
- 5'-Nucleotidase/metabolism
- Adenosine Monophosphate/pharmacology
- Animals
- Blotting, Western
- Cell Membrane/chemistry
- Cell Membrane/drug effects
- Cell Membrane/enzymology
- Cells, Cultured
- Dose-Response Relationship, Drug
- Endocytosis
- Endothelium, Vascular/cytology
- Endothelium, Vascular/drug effects
- Endothelium, Vascular/enzymology
- Gas Chromatography-Mass Spectrometry
- Gene Expression Regulation, Enzymologic/drug effects
- Hypoxia/physiopathology
- Membrane Lipids/chemistry
- Oxygen/pharmacology
- Palmitic Acid/metabolism
- RNA, Messenger/drug effects
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Rats
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Affiliation(s)
- S Ledoux
- INSERM U426, Faculté de Médecine Xavier Bichat, Université Paris 7, BP416, 16 rue Henri Huchard, 75870 Paris, Cedex 18, France.
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48
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Tzaban S, Friedlander G, Schonberger O, Horonchik L, Yedidia Y, Shaked G, Gabizon R, Taraboulos A. Protease-sensitive scrapie prion protein in aggregates of heterogeneous sizes. Biochemistry 2002; 41:12868-75. [PMID: 12379130 DOI: 10.1021/bi025958g] [Citation(s) in RCA: 178] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The pathological prion protein PrP(Sc) is the only known component of the infectious prion. In cells infected with prions, PrP(Sc) is formed posttranslationally by the refolding of the benign cell surface glycoprotein PrP(C) into an aberrant conformation. The two PrP isoforms possess very different properties, as PrP(Sc) has a protease-resistant core, forms very large amyloidic aggregates in detergents, and is only weakly immunoreactive in its native form. We now show that prion-infected rodent brains and cultured cells contain previously unrecognized protease-sensitive PrP(Sc) varieties. In both ionic (Sarkosyl) and nonionic (n-octyl beta-D-glucopyranoside) detergents, the novel protease-sensitive PrP(Sc) species formed aggregates as small as 600 kDa, as measured by gel filtration. The denaturation dependence of PrP(Sc) immunoreactivity correlated with the size of the aggregate. The small PrP(Sc) aggregates described here are consistent with the previous demonstration of scrapie infectivity in brain fractions with a sedimentation coefficient as small as 40 S [Prusiner et al. (1980) J. Neurochem. 35, 574-582]. Our results demonstrate for the first time that prion-infected tissues contain protease-sensitive PrP(Sc) molecules that form low MW aggregates. Whether these new PrP(Sc) species play a role in the biogenesis or the pathogenesis of prions remains to be established.
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Affiliation(s)
- Salit Tzaban
- Department of Molecular Biology, The Hebrew University-Hadassah Medical School, and Hadassah University Hospital, Jerusalem 91120, Israel
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49
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Abstract
Standard clustering methods can classify genes successfully when applied to relatively small data sets, but have limited use in the analysis of large-scale expression data, mainly owing to their assignment of a gene to a single cluster. Here we propose an alternative method for the global analysis of genome-wide expression data. Our approach assigns genes to context-dependent and potentially overlapping 'transcription modules', thus overcoming the main limitations of traditional clustering methods. We use our method to elucidate regulatory properties of cellular pathways and to characterize cis-regulatory elements. By applying our algorithm systematically to all of the available expression data on Saccharomyces cerevisiae, we identify a comprehensive set of overlapping transcriptional modules. Our results provide functional predictions for numerous genes, identify relations between modules and present a global view on the transcriptional network.
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Affiliation(s)
- Jan Ihmels
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel
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50
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Beuhler RJ, Friedlander G, Friedman L. Fusion reactions in dense hot atom assemblies generated by cluster impact. [Erratum to document cited in CA115(6):58473r]. Acc Chem Res 2002. [DOI: 10.1021/ar00018a005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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