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Reis LR, Costa-Rocha IA, Abdala-Torres T, Campi-Azevedo AC, Peruhype-Magalhães V, Araújo MSS, Spezialli E, do Valle Antonelli LR, da Silva-Pereira RA, Almeida GG, Fernandes EG, Fantinato FFST, Domingues CMAS, Lemos MCF, Chieppe A, Lemos JAC, Coelho-Dos-Reis JG, de Lima SMB, de Souza Azevedo A, Schwarcz WD, Camacho LAB, de Lourdes de Sousa Maia M, de Noronha TG, Duault C, Rosenberg-Hasson Y, Teixeira-Carvalho A, Maecker HT, Martins-Filho OA. Comprehensive landscape of neutralizing antibody and cell-mediated response elicited by the 1/5 fractional dose of 17DD-YF primary vaccination in adults. Sci Rep 2024; 14:7709. [PMID: 38565882 PMCID: PMC10987530 DOI: 10.1038/s41598-024-57645-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 03/20/2024] [Indexed: 04/04/2024] Open
Abstract
The present study aimed at evaluating the YF-specific neutralizing antibody profile besides a multiparametric analysis of phenotypic/functional features of cell-mediated response elicited by the 1/5 fractional dose of 17DD-YF vaccine, administered as a single subcutaneous injection. The immunological parameters of each volunteer was monitored at two time points, referred as: before (Day 0) [Non-Vaccinated, NV(D0)] and after vaccination (Day 30-45) [Primary Vaccinees, PV(D30-45)]. Data demonstrated high levels of neutralizing antibodies for PV(D30-45) leading to a seropositivity rate of 93%. A broad increase of systemic soluble mediators with a mixed profile was also observed for PV(D30-45), with IFN-γ and TNF-α presenting the highest baseline fold changes. Integrative network mapping of soluble mediators showed increased correlation numbers in PV(D30-45) as compared to NV(D0) (532vs398). Moreover, PV(D30-45) exhibited increased levels of Terminal Effector (CD45RA+CCR7-) CD4+ and CD8+ T-cells and Non-Classical memory B-cells (IgD+CD27+). Dimensionality reduction of Mass Cytometry data further support these findings. A polyfunctional cytokine profile (TNF-α/IFN-γ/IL-10/IL-17/IL-2) of T and B-cells was observed upon in vitro antigen recall. Mapping and kinetics timeline of soluble mediator signatures for PV(D30-45) further confirmed the polyfunctional profile upon long-term in vitro culture, mediated by increased levels of IFN-γ and TNF-α along with decreased production of IL-10. These findings suggest novel insights of correlates of protection elicited by the 1/5 fractional dose of 17DD-YF vaccine.
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Affiliation(s)
- Laise Rodrigues Reis
- Instituto René Rachou, Fundação Oswaldo Cruz - FIOCRUZ-Minas, Belo Horizonte, MG, Brazil
| | | | - Thais Abdala-Torres
- Instituto René Rachou, Fundação Oswaldo Cruz - FIOCRUZ-Minas, Belo Horizonte, MG, Brazil
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | | | | | | | - Elaine Spezialli
- Instituto René Rachou, Fundação Oswaldo Cruz - FIOCRUZ-Minas, Belo Horizonte, MG, Brazil
| | | | | | | | | | | | | | | | - Alexandre Chieppe
- Superintendência de Vigilância em Saúde, Secretaria Municipal de Saúde do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | | | - Jordana Grazziela Coelho-Dos-Reis
- Laboratório de Virologia Básica e Aplicada, Instituto de Ciências Biológicas da Universidade Federal de Minas Gerais - UFMG, Belo Horizonte, MG, Brazil
| | - Sheila Maria Barbosa de Lima
- Departamento de Desenvolvimento Experimental e Pré-Clínico, Instituto de Tecnologia em Imunobiológicos Bio-Manguinhos - FIOCRUZ, Rio de Janeiro, RJ, Brazil
| | - Adriana de Souza Azevedo
- Laboratório de Análise Imunomolecular, Instituto de Tecnologia em Imunobiológicos Bio-Manguinhos - FIOCRUZ, Rio de Janeiro, RJ, Brazil
| | - Waleska Dias Schwarcz
- Laboratório de Análise Imunomolecular, Instituto de Tecnologia em Imunobiológicos Bio-Manguinhos - FIOCRUZ, Rio de Janeiro, RJ, Brazil
| | | | | | - Tatiana Guimarães de Noronha
- Assessoria Clínica, Instituto de Tecnologia em Imunobiológicos Bio-Manguinhos - FIOCRUZ, Rio de Janeiro, RJ, Brazil
| | - Caroline Duault
- Human Immune Monitoring Center, Stanford University, Stanford, CA, USA
| | | | | | - Holden Terry Maecker
- Human Immune Monitoring Center, Stanford University, Stanford, CA, USA.
- Department of Microbiology and Immunology, Stanford University, Stanford, USA.
| | - Olindo Assis Martins-Filho
- Instituto René Rachou, Fundação Oswaldo Cruz - FIOCRUZ-Minas, Belo Horizonte, MG, Brazil.
- Grupo Integrado de Pesquisas em Biomarcadores, Instituto René Rachou, Fundação Oswaldo Cruz - FIOCRUZ-Minas, Belo Horizonte, MG, Brazil.
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Coda DM, Gräff J. From cellular to fear memory: An epigenetic toolbox to remember. Curr Opin Neurobiol 2024; 84:102829. [PMID: 38128422 DOI: 10.1016/j.conb.2023.102829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/28/2023] [Accepted: 11/28/2023] [Indexed: 12/23/2023]
Abstract
Throughout development, the neuronal epigenome is highly sensitive to external stimuli, yet capable of safeguarding cellular memory for a lifetime. In the adult brain, memories of fearful experiences are rapidly instantiated, yet can last for decades, but the mechanisms underlying such longevity remain unknown. Here, we showcase how fear memory formation and storage - traditionally thought to exclusively affect synapse-based events - elicit profound and enduring changes to the chromatin, proposing epigenetic regulation as a plausible molecular template for mnemonic processes. By comparing these to mechanisms occurring in development and differentiation, we notice that an epigenetic machinery similar to that preserving cellular memories might be employed by brain cells so as to form, store, and retrieve behavioral memories.
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Affiliation(s)
- Davide Martino Coda
- Laboratory of Neuroepigenetics, Brain Mind Institute, School of Life Sciences, Ecole Polytechnique Federale Lausanne (EPFL), 1015, Lausanne, Switzerland.
| | - Johannes Gräff
- Laboratory of Neuroepigenetics, Brain Mind Institute, School of Life Sciences, Ecole Polytechnique Federale Lausanne (EPFL), 1015, Lausanne, Switzerland.
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Cohen D. Family Constellation therapy: A nascent approach for working with non-local consciousness in a therapeutic container. Prog Biophys Mol Biol 2024; 186:33-38. [PMID: 38052327 DOI: 10.1016/j.pbiomolbio.2023.11.008] [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] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 10/25/2023] [Accepted: 11/24/2023] [Indexed: 12/07/2023]
Abstract
Family Constellations are an emerging therapeutic approach for working with local and non-local consciousness. First developed by German psychoanalyst Bert Hellinger, and now practiced by thousands of licensed and un-licensed facilitators globally, Family Constellations are a transpersonal and systemically oriented therapeutic process. Their aim is to address a focus client's emotional, behavioral, relational, or somatic issues by uncovering and resolving transgenerational entanglements within their family system. The author expands on the proposal of symbiogenesis as a mediator of local and non-local consciousness to query whether applying the Observer Effect to inherited trauma may influence epigenetic marks. An expanded perspective on consciousness, life, death, and quantum fields may provide a more comprehensive framework to address therapeutic interventions for common emotional and behavioral disorders. Innovative features of Family Constellations are its phenomenological orientation, reference to family system entanglements, and potential for symptom relief through cellular mediation of ancestral memory. Family Constellations utilize techniques called representative perception and tuning-in to identify and release ancestral traumas. These are akin to remote viewing and mediumship. While the scientific basis for Family Constellations is speculative, the text references research on the quantum theory of consciousness, mediumship and remote viewing as potential supporting evidence. Four case studies are presented.
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Affiliation(s)
- Dan Cohen
- Seeing with Your Heart, http:seeingwithyourheart.com 14 Rhode Island Avenue, Providence, RI, 02906, USA.
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Chaudhary A, Madhavan R, Babji S, Raju R, Syed C, Kumar A, Saravanan P, Sharon Nikitha O, Leander Xavier JV, David Chelladurai JS, Deborah AA, George A, Kang G, Rose W. Characterization of immune responses to two and three doses of the adenoviral vectored vaccine ChAdOx1 nCov-19 and the whole virion inactivated vaccine BBV152 in a mix-and-match study in India. Vaccine 2023:S0264-410X(23)00744-2. [PMID: 37357073 PMCID: PMC10289125 DOI: 10.1016/j.vaccine.2023.06.059] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/14/2023] [Accepted: 06/15/2023] [Indexed: 06/27/2023]
Abstract
Infections with SARS-CoV-2 variants and declining immunity after primary vaccination, encouraged the use of booster doses. Some countries changed their immunization programmes to boost with vaccines different from the ones in their original schedule, based on results from immunogenicity and effectiveness studies. This study reports immunological analysis of samples collected in a phase 4 randomized trial, where participants who had previously received two primary doses of ChAdOx1 nCov-19 (ChAd) or inactivated BBV152 vaccine were randomized to receive either ChAd or BBV152 booster and further categorized as: Group 1 (two primary doses of ChAd - ChAd booster), Group 2 (two primary doses of ChAd - BBV152 booster), Group 3 (two primary doses of BBV152 - ChAd booster), and Group 4 (two primary doses of BBV152 - BBV152 booster). SARS-CoV-2 specific cellular and humoral responses at day 0 (pre-boost samples 12-36 weeks after the second primary dose), and at day 28 post booster, were measured in a subset of participants (ChAd recipients, n = 37 and BBV152 recipients, n = 36). Additionally, on day180 post-booster humoral responses were assessed for the entire cohort (N = 378). Primary vaccination with 2 doses of BBV152 generated higher memory-B cells (median% 0.41 vs 0.35) and cytokine producing CD8-Tcells (median% 0.09 vs 0.04) while lower anti-spike IgG levels (medianAU/ml: 12,433 vs 27,074) as compared to ChAd. Irrespective of the primary vaccine received, ChAd boosted individuals generated higher memory-B cell frequencies and anti-spike IgG levels as compared to BBV152 booster. The percentage ACE-2 inhibition against Omicron and its sub-variants was higher in Group 3 (median > 60 %) as compared to other groups (median < 25 %). At day180 post booster the hierarchy of the antibody amounts was Group 1 ∼ Group 2 ∼ Group 3 > Group 4. Sustained humoral and robust cellular immune response to SARS-CoV-2 can be obtained with ChAd booster irrespective of the primary vaccination regimen. The trial is registered with ISRTCN (CTRI/2021/08/035648).
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Affiliation(s)
- Anita Chaudhary
- The Wellcome Trust Research Laboratory, Christian Medical College, Vellore, India
| | - Ramya Madhavan
- The Wellcome Trust Research Laboratory, Christian Medical College, Vellore, India
| | - Sudhir Babji
- The Wellcome Trust Research Laboratory, Christian Medical College, Vellore, India
| | - Reshma Raju
- Department of Paediatrics, Christian Medical College, Vellore, India
| | - Chanduni Syed
- The Wellcome Trust Research Laboratory, Christian Medical College, Vellore, India
| | - Ajith Kumar
- The Wellcome Trust Research Laboratory, Christian Medical College, Vellore, India
| | - Poornima Saravanan
- The Wellcome Trust Research Laboratory, Christian Medical College, Vellore, India
| | | | | | | | | | - Anna George
- The Wellcome Trust Research Laboratory, Christian Medical College, Vellore, India
| | - Gagandeep Kang
- The Wellcome Trust Research Laboratory, Christian Medical College, Vellore, India
| | - Winsley Rose
- Department of Paediatrics, Christian Medical College, Vellore, India.
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Reis LR, Costa-Rocha IAD, Campi-Azevedo AC, Peruhype-Magalhães V, Coelho-Dos-Reis JG, Costa-Pereira C, Otta DA, Freire LC, Lima SMBD, Azevedo ADS, Schwarcz WD, Ano Bom APD, Silva AMVD, Souza AFD, Castro TDMD, Ferroco CLDV, Filippis AMBD, Nogueira FDB, Homma A, Domingues CM, Sousa ESS, Camacho LAB, Maia MDLDS, Teixeira-Carvalho A, Martins-Filho OA. Exploratory study of humoral and cellular immunity to 17DD Yellow Fever vaccination in children and adults residents of areas without circulation of Yellow Fever Virus. Vaccine 2021; 40:798-810. [PMID: 34969545 DOI: 10.1016/j.vaccine.2021.12.029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 09/16/2021] [Revised: 12/03/2021] [Accepted: 12/12/2021] [Indexed: 11/30/2022]
Abstract
The present investigation comprised two independent observational arms to evaluate the influence of pre-existing flavivirus humoral immunity and the age-impact on 17DD-YF vaccination immunity. Flavivirus (YFV; DENV; ZIKV) serology and YF-specific cellular immunity was evaluated in 288 children/9Mths-4Yrs and 288 adults/18-49Yrs residents of areas without YFV circulation. Data demonstrated that flavivirus seropositivity at baseline was higher in Adults as compared to Children (26%;87%;67% vs 6%;13%;15%, respectively). The heterologous flavivirus seropositivity (DENV; ZIKV) did not impact the YF-specific cellular immune response at baseline. However, higher levels of NCD4, EMCD8, IFN-MCD8, NCD19 and nCMCD19 were observed in subjects with pre-existing YFV seropositivity. Primary vaccination of YFV-seronegative volunteers led to higher levels of YF-neutralizing antibodies in Adults as compared to Younger Children (9Mths-2Yrs). Although similar seropositivity rates observed amongst Children and Adults at D30-45, lower rates were observed in Younger Children (9Mths-2Yrs) at D365 (94%;95%;100% vs 87%;96%;99%, respectively). A progressive decline in antibody levels were reported at D365, being more expressive in Children as compared to Adults. All age-subgroups exhibited at D30-45 increased levels of eEfCD4, EMCD4, IFN-MCD8 and nCMCD19 together with a decrease of eEfCD8 and CMCD8. While an increase of EMCD8 were observed in all subgroups at D30-45, a declined duration at D365 was reported only in Younger Children (9Mths-2Yrs). Biomarker signatures further support that only Younger Children (9Mths-2Yrs) presented a progressive decline of EMCD8 at D365. Together, these findings demonstrated that regardless the similarities observed in YF-neutralizing antibodies, the age impacts the duration of cellular immune response to primary 17DD-YF vaccination.
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Affiliation(s)
- Laise Rodrigues Reis
- Grupo Integrado de Pesquisas em Biomarcadores - Instituto René Rachou, Fundação Oswaldo Cruz - FIOCRUZ-Minas, Belo Horizonte, MG, Brazil.
| | - Ismael Artur da Costa-Rocha
- Grupo Integrado de Pesquisas em Biomarcadores - Instituto René Rachou, Fundação Oswaldo Cruz - FIOCRUZ-Minas, Belo Horizonte, MG, Brazil
| | - Ana Carolina Campi-Azevedo
- Grupo Integrado de Pesquisas em Biomarcadores - Instituto René Rachou, Fundação Oswaldo Cruz - FIOCRUZ-Minas, Belo Horizonte, MG, Brazil
| | - Vanessa Peruhype-Magalhães
- Grupo Integrado de Pesquisas em Biomarcadores - Instituto René Rachou, Fundação Oswaldo Cruz - FIOCRUZ-Minas, Belo Horizonte, MG, Brazil
| | - Jordana Grazziela Coelho-Dos-Reis
- Grupo Integrado de Pesquisas em Biomarcadores - Instituto René Rachou, Fundação Oswaldo Cruz - FIOCRUZ-Minas, Belo Horizonte, MG, Brazil; Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Christiane Costa-Pereira
- Grupo Integrado de Pesquisas em Biomarcadores - Instituto René Rachou, Fundação Oswaldo Cruz - FIOCRUZ-Minas, Belo Horizonte, MG, Brazil
| | - Dayane Andriotti Otta
- Grupo Integrado de Pesquisas em Biomarcadores - Instituto René Rachou, Fundação Oswaldo Cruz - FIOCRUZ-Minas, Belo Horizonte, MG, Brazil
| | - Larissa Chaves Freire
- Grupo Integrado de Pesquisas em Biomarcadores - Instituto René Rachou, Fundação Oswaldo Cruz - FIOCRUZ-Minas, Belo Horizonte, MG, Brazil
| | - Sheila Maria Barbosa de Lima
- Laboratório de Tecnologia Virológica - Instituto de Tecnologia em Imunobiológicos Bio-Manguinhos - FIOCRUZ, Rio de Janeiro, RJ, Brazil
| | - Adriana de Souza Azevedo
- Laboratório de Tecnologia Virológica - Instituto de Tecnologia em Imunobiológicos Bio-Manguinhos - FIOCRUZ, Rio de Janeiro, RJ, Brazil
| | - Waleska Dias Schwarcz
- Laboratório de Tecnologia Virológica - Instituto de Tecnologia em Imunobiológicos Bio-Manguinhos - FIOCRUZ, Rio de Janeiro, RJ, Brazil
| | - Ana Paula Dinis Ano Bom
- Laboratório de Tecnologia Imunológica - Instituto de Tecnologia em Imunobiológicos Bio-Manguinhos - FIOCRUZ, Rio de Janeiro, RJ, Brazil
| | - Andrea Marques Vieira da Silva
- Laboratório de Tecnologia Imunológica - Instituto de Tecnologia em Imunobiológicos Bio-Manguinhos - FIOCRUZ, Rio de Janeiro, RJ, Brazil
| | - Alessandro Fonseca de Souza
- Laboratório de Tecnologia Imunológica - Instituto de Tecnologia em Imunobiológicos Bio-Manguinhos - FIOCRUZ, Rio de Janeiro, RJ, Brazil
| | - Thalita da Matta de Castro
- Assessoria Clínica - Instituto de Tecnologia em Imunobiológicos Bio-Manguinhos - FIOCRUZ, Rio de Janeiro, RJ, Brazil
| | | | | | | | - Akira Homma
- Laboratório de Tecnologia Virológica - Instituto de Tecnologia em Imunobiológicos Bio-Manguinhos - FIOCRUZ, Rio de Janeiro, RJ, Brazil
| | | | | | | | | | - Andréa Teixeira-Carvalho
- Grupo Integrado de Pesquisas em Biomarcadores - Instituto René Rachou, Fundação Oswaldo Cruz - FIOCRUZ-Minas, Belo Horizonte, MG, Brazil
| | - Olindo Assis Martins-Filho
- Grupo Integrado de Pesquisas em Biomarcadores - Instituto René Rachou, Fundação Oswaldo Cruz - FIOCRUZ-Minas, Belo Horizonte, MG, Brazil.
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Dong Y, Guo C, Zhou W, Li W, Zhang L. Using a new HSPC senescence model in vitro to explore the mechanism of cellular memory in aging HSPCs. Stem Cell Res Ther 2021; 12:444. [PMID: 34365970 PMCID: PMC8351417 DOI: 10.1186/s13287-021-02455-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 02/16/2021] [Accepted: 06/10/2021] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Age-associated changes attenuate human blood system functionality through the aging of hematopoietic stem and progenitor cells (HSPCs), manifested in human populations an increase in myeloproliferative disease and even leukemia; therefore, study on HSPC senescence bears great significance to treat hematopoietic-associated disease. Furthermore, the mechanism of HSPC aging is lacking, especially the cellular memory mechanism. Here, we not only reported a new HSPC senescence model in vitro, but also propose and verify the cellular memory mechanism of HSPC aging of the Polycomb/Trithorax system. METHODS HSPCs (Lin-c-kit+ cells) were isolated and purified by magnetic cell sorting (MACS). The proportions and cell cycle distribution of cells were determined by flow cytometry; senescence-related β-galactosidase assay, transmission electron microscope (TEM), and colony-forming unit (CFU)-mix assay were detected for identification of the old HSPC model. Proteomic tests and RNA-seq were applied to analyze differential pathways and genes in the model cells. qPCR, Western blot (WB), and chromatin immunoprecipitation PCR (CHIP-PCR) were used to detect the gene expression of cell memory-related proteins. Knockdown of cell memory-related key genes was performed with shRNA interference. RESULTS In the model old HSPCs, β-gal activity, cell cycle, colony-forming ability, aging-related cell morphology, and metabolic pathway were significantly changed compared to the young HSPCs. Furthermore, we found the model HSPCs have more obvious aging manifestations than those of natural mice, and IL3 is the major factor contributing to HSPC aging in the model. We also observed dramatic changes in the expression level of PRC/TrxG complexes. After further exploring the downstream molecules of PRC/TrxG complexes, we found that Uhrf1 and TopII played critical roles in HSPC aging based on the HSPC senescence model. CONCLUSIONS These findings proposed a new HSPC senescence model in vitro which we forecasted could be used to preliminary screen the drugs of the HSPC aging-related hemopathy and suggested cellular memory mechanism of HSPC aging.
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Affiliation(s)
- Yongpin Dong
- grid.412540.60000 0001 2372 7462Institute of Basic Medicine, Shanghai University of Traditional Chinese Medicine, 1200 CaiLun Ave., Pudong, Shanghai, 201203 China ,grid.73113.370000 0004 0369 1660Department of Emergency and Critical Care Medicine, Shanghai Changzheng Hospital, The Second Military Medical University, Shanghai, China
| | - Chunni Guo
- grid.16821.3c0000 0004 0368 8293Department of Neurology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wuxiong Zhou
- grid.412540.60000 0001 2372 7462Institute of Basic Medicine, Shanghai University of Traditional Chinese Medicine, 1200 CaiLun Ave., Pudong, Shanghai, 201203 China
| | - Wenfang Li
- Department of Emergency and Critical Care Medicine, Shanghai Changzheng Hospital, The Second Military Medical University, Shanghai, China.
| | - Lina Zhang
- Institute of Basic Medicine, Shanghai University of Traditional Chinese Medicine, 1200 CaiLun Ave., Pudong, Shanghai, 201203, China.
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Abstract
Long viewed as paradigm-shifting, but rare, prions have recently been discovered in all domains of life. Protein sequences that can drive this form of self-assembly are strikingly common in eukaryotic proteomes, where they are enriched in proteins involved in information flow and signal transduction. Although prions were thought to be a consequence of random errors in protein folding, recent studies suggest that prion formation can be a controlled process initiated by defined cellular signals. Many are present in normal biological contexts, yet are invisible to most technologies used to interrogate the proteome. Here, we review mechanisms by which protein self-assembly can create a stable record of past stimuli, altering adaptive responses, and how prion behavior is controlled by signaling processes. We touch on the diverse implications that this has for normal biological function and regulation, ranging from drug resistance in fungi to the innate immune response in humans. Finally, we discuss the potential for prion domains in transcription factors and RNA-binding proteins to orchestrate heritable gene expression changes in response to transient signals, such as during development.
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Affiliation(s)
- Shady Saad
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Daniel F Jarosz
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA; Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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8
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Reichert P, Caudron F. Mnemons and the memorization of past signaling events. Curr Opin Cell Biol 2021; 69:127-135. [PMID: 33618243 DOI: 10.1016/j.ceb.2021.01.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 10/10/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 11/28/2022]
Abstract
Current advances are raising our awareness of the diverse roles that protein condensation plays in the biology of cells. Particularly, findings in organisms as diverse as yeast and Drosophila suggest that cells may utilize protein condensation to establish long-lasting changes in cellular activities and thereby encode a memory of past signaling events. Proteins that oligomerize to confer such cellular memory have been termed 'mnemons'. In the forming of super-assemblies, mnemons change their function and modulate the influence that the affected protein originally had on cellular processes. Because mnemon assemblies are self-templating, they allow cells to retain the memory of past decisions over larger timescales. Here, we review the mechanisms behind the formation of cellular memory with an emphasis on mnemon-mediated memorization of past signaling events.
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Affiliation(s)
- Polina Reichert
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Fabrice Caudron
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK.
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9
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Berenguer J, Celià-Terrassa T. Cell memory of epithelial-mesenchymal plasticity in cancer. Curr Opin Cell Biol 2021; 69:103-110. [PMID: 33578288 DOI: 10.1016/j.ceb.2021.01.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 10/15/2020] [Revised: 12/29/2020] [Accepted: 01/04/2021] [Indexed: 11/26/2022]
Abstract
Fundamental biological processes of cell identity and cell fate determination are controlled by complex regulatory networks. These processes require molecular mechanisms that confer cellular phenotypic memory and state persistence. In this minireview, we will summarize mechanisms of cell memory based on regulatory hysteretic feedback loops and explore epigenetic mechanisms widely represented in nature, with special focus on epithelial-to-mesenchymal plasticity. We will also discuss the functional consequences of cell memory and epithelial-to-mesenchymal plasticity dynamics during development and cancer metastasis.
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Affiliation(s)
- Jordi Berenguer
- Cancer Research Program, IMIM (Hospital del Mar Medical Research Institute), 08003 Barcelona, Spain
| | - Toni Celià-Terrassa
- Cancer Research Program, IMIM (Hospital del Mar Medical Research Institute), 08003 Barcelona, Spain.
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10
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Jiang Y, Hao N. Memorizing environmental signals through feedback and feedforward loops. Curr Opin Cell Biol 2021; 69:96-102. [PMID: 33549848 DOI: 10.1016/j.ceb.2020.11.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 09/30/2020] [Revised: 11/25/2020] [Accepted: 11/26/2020] [Indexed: 12/12/2022]
Abstract
Cells in diverse organisms can store the information of previous environmental conditions for long periods of time. This form of cellular memory adjusts the cell's responses to future challenges, providing fitness advantages in fluctuating environments. Many biological functions, including cellular memory, are mediated by specific recurring patterns of interactions among proteins and genes, known as 'network motifs.' In this review, we focus on three well-characterized network motifs - negative feedback loops, positive feedback loops, and feedforward loops, which underlie different types of cellular memories. We describe the latest studies identifying these motifs in various molecular processes and discuss how the topologies and dynamics of these motifs can enable memory encoding and storage.
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Affiliation(s)
- Yanfei Jiang
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Nan Hao
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
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Abstract
Epigenetics researchers in developmental, cell, and molecular biology greatly diverge in their understanding and definitions of epigenetics. In contrast, social epigeneticists, e.g., sociologists, scholars of STS, and behavioural scientists, share a focus and definition of epigenetics that is environmentally caused and trans-generationally inherited. This article demonstrates that this emphasis on the environment and on so-called Lamarckian inheritance, in addition to other factors, reflects an interdisciplinary power struggle with genetics, in which epigenetics appears to grant the social sciences a higher epistemic status. Social scientists' understanding of epigenetics, thus, appears in part to be socially constructed, i.e., the result of extra-scientific factors, such as social processes and the self-interest of the discipline. This article argues that social epigeneticists make far-reaching claims by selecting elements from research labelled epigenetics in biology while ignoring widely confirmed scientific facts in genetics and cell biology, such as the dependence of epigenetic marks on DNA sequence-specific events, or the lack of evidence for the lasting influence of the environment on epigenetic marks or the epigenome. Moreover, they treat as a given crucial questions that are far from resolved, such as what role, if any, DNA methylation plays in the complex biochemical system of regulating gene activity. The article also points out incorrect perceptions and media hypes among biological epigeneticists and calls attention to an apparent bias among scientific journals that prefer papers that promote transgenerational epigenetic inheritance over articles that critique it. The article concludes that while research labelled epigenetics contributes significantly to our knowledge about chromatin and the genome, it does not, as is often claimed, rehabilitate Lamarck or overthrow the fundamental biological principles of gene regulation, which are based on specific regulatory sequences of the genome.
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Affiliation(s)
- Ute Deichmann
- Jacques Loeb Centre for the History and Philosophy of the Life Sciences, Ben-Gurion University of the Negev, P.O. Box 653, Beer Sheva, 8410500, Israel.
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Hayashi S, Tamura K, Yokoyama H. Chromatin dynamics underlying the precise regeneration of a vertebrate limb - Epigenetic regulation and cellular memory. Semin Cell Dev Biol 2020; 97:16-25. [PMID: 30991117 DOI: 10.1016/j.semcdb.2019.04.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 04/01/2019] [Accepted: 04/09/2019] [Indexed: 12/13/2022]
Abstract
Wound healing, tissue regeneration, and organ regrowth are all regeneration phenomena observed in vertebrates after an injury. However, the ability to regenerate differs greatly among species. Mammals can undergo wound healing and tissue regeneration, but cannot regenerate an organ; for example, they cannot regrow an amputated limb. In contrast, amphibians and fish have much higher capabilities for organ-level regeneration. In addition to medical studies and those in conventional mammalian models such as mice, studies in amphibians and fish have revealed essential factors for and mechanisms of regeneration, including the regrowth of a limb, tail, or fin. However, the molecular nature of the cellular memory needed to precisely generate a new appendage from an amputation site is not fully understood. Recent reports have indicated that organ regeneration is closely related to epigenetic regulation. For example, the methylation status of genomic DNA is related to the expression of regeneration-related genes, and histone-modification enzymes are required to control the chromatin dynamics for regeneration. A proposed mechanism of cellular memory involving an inheritable system of epigenetic modification led us to hypothesize that epigenetic regulation forms the basis for cellular memory in organ regeneration. Here we summarize the current understanding of the role of epigenetic regulation in organ regeneration and discuss the relationship between organ regeneration and epigenetic memory.
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13
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Vermeersch L, Perez-Samper G, Cerulus B, Jariani A, Gallone B, Voordeckers K, Steensels J, Verstrepen KJ. On the duration of the microbial lag phase. Curr Genet 2019; 65:721-727. [PMID: 30666394 PMCID: PMC6510831 DOI: 10.1007/s00294-019-00938-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [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: 12/19/2018] [Revised: 01/11/2019] [Accepted: 01/11/2019] [Indexed: 12/19/2022]
Abstract
When faced with environmental changes, microbes enter a lag phase during which cell growth is arrested, allowing cells to adapt to the new situation. The discovery of the lag phase started the field of gene regulation and led to the unraveling of underlying mechanisms. However, the factors determining the exact duration and dynamics of the lag phase remain largely elusive. Naively, one would expect that cells adapt as quickly as possible, so they can resume growth and compete with other organisms. However, recent studies show that the lag phase can last from several hours up to several days. Moreover, some cells within the same population take much longer than others, despite being genetically identical. In addition, the lag phase duration is also influenced by the past, with recent exposure to a given environment leading to a quicker adaptation when that environment returns. Genome-wide screens in Saccharomyces cerevisiae on carbon source shifts now suggest that the length of the lag phase, the heterogeneity in lag times of individual cells, and the history-dependent behavior are not determined by the time it takes to induce a few specific genes related to uptake and metabolism of a new carbon source. Instead, a major shift in general metabolism, and in particular a switch between fermentation and respiration, is the major bottleneck that determines lag duration. This suggests that there may be a fitness trade-off between complete adaptation of a cell’s metabolism to a given environment, and a short lag phase when the environment changes.
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Affiliation(s)
- Lieselotte Vermeersch
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Gaston Geenslaan 1, 3001, Leuven, Belgium.,CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Gaston Geenslaan 1, 3001, Leuven, Belgium
| | - Gemma Perez-Samper
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Gaston Geenslaan 1, 3001, Leuven, Belgium.,CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Gaston Geenslaan 1, 3001, Leuven, Belgium
| | - Bram Cerulus
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Gaston Geenslaan 1, 3001, Leuven, Belgium.,CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Gaston Geenslaan 1, 3001, Leuven, Belgium
| | - Abbas Jariani
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Gaston Geenslaan 1, 3001, Leuven, Belgium.,CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Gaston Geenslaan 1, 3001, Leuven, Belgium
| | - Brigida Gallone
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Gaston Geenslaan 1, 3001, Leuven, Belgium.,CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Gaston Geenslaan 1, 3001, Leuven, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium.,VIB Center for Plant Systems Biology, Technologiepark 927, 9052, Ghent, Belgium
| | - Karin Voordeckers
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Gaston Geenslaan 1, 3001, Leuven, Belgium.,CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Gaston Geenslaan 1, 3001, Leuven, Belgium
| | - Jan Steensels
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Gaston Geenslaan 1, 3001, Leuven, Belgium.,CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Gaston Geenslaan 1, 3001, Leuven, Belgium
| | - Kevin J Verstrepen
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Gaston Geenslaan 1, 3001, Leuven, Belgium. .,CMPG Laboratory of Genetics and Genomics, Department M2S, KU Leuven, Gaston Geenslaan 1, 3001, Leuven, Belgium.
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14
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Cheikhi A, Wallace C, St Croix C, Cohen C, Tang WY, Wipf P, Benos PV, Ambrosio F, Barchowsky A. Mitochondria are a substrate of cellular memory. Free Radic Biol Med 2019; 130:528-541. [PMID: 30472365 DOI: 10.1016/j.freeradbiomed.2018.11.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 11/19/2018] [Accepted: 11/21/2018] [Indexed: 12/26/2022]
Abstract
Cellular memory underlies cellular identity, and thus constitutes a unifying mechanism of genetic disposition, environmental influences, and cellular adaptation. Here, we demonstrate that enduring physicochemical changes of mitochondrial networks invoked by transient stress, a phenomenon we term 'mitoengrams', underlie the transgenerational persistence of epigenetically scripted cellular behavior. Using C2C12 myogenic stem-like cells, we show that stress memory elicited by transient, low-level arsenite exposure is stored within a self-renewing subpopulation of progeny cells in a mitochondrial-dependent fashion. Importantly, we demonstrate that erasure of mitoengrams by administration of mitochondria-targeted electron scavenger was sufficient to reset key epigenetic marks of cellular memory and redirect the identity of the mitoengram-harboring progeny cells to a non-stress-like state. Together, our findings indicate that mnemonic information emanating from mitochondria support the balance between the persistence and transience of cellular memory.
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Affiliation(s)
- Amin Cheikhi
- Division of Geriatric Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA; Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA 15261, USA.
| | - Callen Wallace
- Center for Biological Imaging, University of Pittsburgh, Pittsburgh, PA 15261, USA.
| | - Claudette St Croix
- Center for Biological Imaging, University of Pittsburgh, Pittsburgh, PA 15261, USA; Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA.
| | - Charles Cohen
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Wan-Yee Tang
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA.
| | - Peter Wipf
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| | - Panagiotis V Benos
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA.
| | - Fabrisia Ambrosio
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA 15261, USA; Department of Physical Medicine and Rehabilitation, University of Pittsburgh, Pittsburgh, PA, USA; McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA; Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA 15261, USA.
| | - Aaron Barchowsky
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA 15261, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA.
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15
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Abstract
Transient exposures to environmental stresses induce altered physiological states in exposed cells that persist after the stresses have been removed. These states, referred to as cellular memory, can even be passed on to daughter cells and may thus be thought of as embodying a form of epigenetic inheritance. We find that meiotically produced spores in the budding yeast S. cerevisiae possess a state of heightened stress resistance that, following their germination, persists for numerous mitotic generations. As yeast meiotic development is essentially a starvation response that a/alpha diploid cells engage, we sought to model this phenomenon by subjecting haploid cells to starvation conditions. We find also that haploid cells exposed to glucose withdrawal acquire a state of elevated stress resistance that persists after the reintroduction of these cells to glucose-replete media. Following release from lengthy durations of glucose starvation, we confirm that this physiological state of enhanced stress resistance is propagated in descendants of the exposed cells through two mitotic divisions before fading from the population. In both haploid starved cells and diploid produced meiotic spores we show that their cellular memories are not attributable to trehalose, a widely regarded stress protectant that accumulates in these cell types. Moreover, the transiently heritable stress resistant state induced by glucose starvation in haploid cells is independent of the Msn2/4 transcription factors, which are known to program cellular memory induced by exposure of cells to NaCl. Our findings identify new developmentally and nutritionally induced states of cellular memory that exhibit striking degrees of persistence and mitotic heritability.
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Affiliation(s)
- Heldder Gutierrez
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Bakhtiyar Taghizada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Marc D Meneghini
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
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16
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Papatsenko D, Waghray A, Lemischka IR. Feedback control of pluripotency in embryonic stem cells: Signaling, transcription and epigenetics. Stem Cell Res 2018; 29:180-188. [DOI: 10.1016/j.scr.2018.02.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 02/06/2018] [Accepted: 02/16/2018] [Indexed: 12/19/2022] Open
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17
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Abbas G, Mahmood W, Khan F. Can memory exist outside of brain and be transferred? Historical review, issues & ways forward. Med Hypotheses 2017; 109:106-110. [PMID: 29150267 DOI: 10.1016/j.mehy.2017.10.003] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Revised: 09/22/2017] [Accepted: 10/05/2017] [Indexed: 10/18/2022]
Abstract
Learning and memory are among the executive functions attributed to intelligent forms of life. Unfortunately, there is a lack of clear understanding regarding the underlying mechanisms governing these functions. Most of the modern day scientists attribute these functions solely to brain. However, in the latter half of last century, a number of reports suggested existence of extra-cranial memory and potential of its transfer between animals. Some have linked this phenomenon to RNA while others believed that peptides were responsible. The terms like "educated RNA" and "scotophobin" were coined. This atypical work involving flatworms, yeast RNA and scotophobin was received with deep skepticism and ultimately disregarded. However, the recent reproduction of some of this earlier work by scientists at Tufts University has reignited the debate on the mechanisms of learning and memory. Keeping this in view, we believe it is high time to summarize this historical work and discuss the possibilities to delineate these atypical claims. The objective is to incite the present day researchers to explore this opportunity under the perspective of newer advancements in science.
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Affiliation(s)
- Ghulam Abbas
- H.E.J. Research Institute of Chemistry, International Center for Chemical & Biological Sciences, University of Karachi, Karachi 75270, Pakistan.
| | - Wajahat Mahmood
- Department of Pharmacy, COMSATS Institute of Information Technology, Abbottabad 22060, K.P.K., Pakistan
| | - Faisal Khan
- Dr. Panjwani Center for Molecular Medicine & Drug Research, International Center for Chemical & Biological Sciences, University of Karachi, Karachi 75270, Pakistan
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18
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Kiese K, Jablonski J, Hackenbracht J, Wrosch JK, Groemer TW, Kornhuber J, Blümcke I, Kobow K. Epigenetic control of epilepsy target genes contributes to a cellular memory of epileptogenesis in cultured rat hippocampal neurons. Acta Neuropathol Commun 2017; 5:79. [PMID: 29089052 PMCID: PMC5664434 DOI: 10.1186/s40478-017-0485-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 10/25/2017] [Indexed: 02/01/2023] Open
Abstract
Hypersynchronous neuronal excitation manifests clinically as seizure (ictogenesis), and may recur spontaneously and repetitively after a variable latency period (epileptogenesis). Despite tremendous research efforts to describe molecular pathways and signatures of epileptogenesis, molecular pathomechanisms leading to chronic epilepsy remain to be clarified. We hypothesized that epigenetic modifications may form the basis for a cellular memory of epileptogenesis, and used a primary neuronal cell culture model of the rat hippocampus to study the translation of massive neuronal excitation into persisting changes of epigenetic signatures and pro-epileptogenic target gene expression. Increased spontaneous activation of cultured neurons was detected 3 and 7 days after stimulation with 10 μM glutamate when compared to sham-treated time-matched controls using calcium-imaging in vitro. Chromatin-immunoprecipitation experiments revealed short-term (3 h, 7 h, and 24 h) and long-term (3 d and 2 weeks) changes in histone modifications, which were directly linked to decreased expression of two selected epilepsy target genes, e.g. excitatory glutamate receptor genes Gria2 and Grin2a. Increased promoter methylation observed 4 weeks after glutamate stimulation at respective genes suggested long-term repression of Gria2 and Grin2a genes. Inhibition of glutamatergic activation or blocking the propagation of action potentials in cultured neurons rescued altered gene expression and regulatory epigenetic modifications. Our data support the concept of a cellular memory of epileptogenesis and persisting epigenetic modifications of epilepsy target genes, which are able to turn normal into pro-epileptic neurons and circuits.
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Hohos NM, Lee K, Ji L, Yu M, Kandasamy MM, Phillips BG, Baile CA, He C, Schmitz RJ, Meagher RB. DNA cytosine hydroxymethylation levels are distinct among non-overlapping classes of peripheral blood leukocytes. J Immunol Methods 2016; 436:1-15. [PMID: 27164004 PMCID: PMC5131182 DOI: 10.1016/j.jim.2016.05.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 04/19/2016] [Accepted: 05/02/2016] [Indexed: 12/22/2022]
Abstract
BACKGROUND Peripheral blood leukocytes are the most commonly used surrogates to study epigenome-induced risk and epigenomic response to disease-related stress. We considered the hypothesis that the various classes of peripheral leukocytes differentially regulate the synthesis of 5-methylcytosine (5mCG) and its removal via Ten-Eleven Translocation (TET) dioxygenase catalyzed hydroxymethylation to 5-hydroxymethylcytosine (5hmCG), reflecting their responsiveness to environment. Although it is known that reductions in TET1 and/or TET2 activity lead to the over-proliferation of various leukocyte precursors in bone marrow and in development of chronic myelomonocytic leukemia and myeloproliferative neoplasms, the role of 5mCG hydroxymethylation in peripheral blood is less well studied. RESULTS We developed simplified protocols to rapidly and reiteratively isolate non-overlapping leukocyte populations from a single small sample of fresh or frozen whole blood. Among peripheral leukocyte types we found extreme variation in the levels of transcripts encoding proteins involved in cytosine methylation (DNMT1, 3A, 3B), the turnover of 5mC by demethylation (TET1, 2, 3), and DNA repair (GADD45A, B, G) and in the global and gene-region-specific levels of DNA 5hmCG (CD4+ T cells≫CD14+ monocytes>CD16+ neutrophils>CD19+ B cells>CD56+ NK cells>Siglec8+ eosinophils>CD8+ T cells). CONCLUSIONS Our data taken together suggest a potential hierarchy of responsiveness among classes of leukocytes with CD4+, CD8+ T cells and CD14+ monocytes being the most distinctly poised for a rapid methylome response to physiological stress and disease.
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Affiliation(s)
- Natalie M Hohos
- Department of Foods and Nutrition, University of Georgia, Athens, GA, USA.
| | - Kevin Lee
- Department of Genetics, University of Georgia, Athens, GA, USA.
| | - Lexiang Ji
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA.
| | - Miao Yu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA.
| | | | - Bradley G Phillips
- Clinical and Administrative Pharmacy, University of Georgia, Athens, GA, USA.
| | - Clifton A Baile
- Department of Foods and Nutrition, University of Georgia, Athens, GA, USA
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA.
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Abstract
Restoring chromatin structure with high fidelity after mitosis is critical for cell survival. Transcriptional reactivation of genes is the first step toward establishing identity of the daughter cell. During mitosis, chromatin bookmarking factors associated with specific chromatin regions ensure the restoration of the original gene expression pattern in daughter cells. Recent findings have provided new insights into the mechanisms, regulation, and biological significance of gene bookmarking in eukaryotes. In this review, we discuss how epigenetic factors, such as Poly(ADP-ribose) Polymerase-1, establish epigenetic memory in mitotic chromatin.
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Hayashi S, Kawaguchi A, Uchiyama I, Kawasumi-Kita A, Kobayashi T, Nishide H, Tsutsumi R, Tsuru K, Inoue T, Ogino H, Agata K, Tamura K, Yokoyama H. Epigenetic modification maintains intrinsic limb-cell identity in Xenopus limb bud regeneration. Dev Biol 2015; 406:271-82. [PMID: 26282893 DOI: 10.1016/j.ydbio.2015.08.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 08/11/2015] [Accepted: 08/13/2015] [Indexed: 11/21/2022]
Abstract
Many amphibians can regenerate limbs, even in adulthood. If a limb is amputated, the stump generates a blastema that makes a complete, new limb in a process similar to developmental morphogenesis. The blastema is thought to inherit its limb-patterning properties from cells in the stump, and it retains the information despite changes in morphology, gene expression, and differentiation states required by limb regeneration. We hypothesized that these cellular properties are maintained as epigenetic memory through histone modifications. To test this hypothesis, we analyzed genome-wide histone modifications in Xenopus limb bud regeneration. The trimethylation of histone H3 at lysine 4 (H3K4me3) is closely related to an open chromatin structure that allows transcription factors access to genes, whereas the trimethylation of histone H3 at lysine 27 (H3K27me3) is related to a closed chromatin state that blocks the access of transcription factors. We compared these two modification profiles by high-throughput sequencing of samples prepared from the intact limb bud and the regenerative blastema by chromatin immunoprecipitation. For many developmental genes, histone modifications at the transcription start site were the same in the limb bud and the blastema, were stable during regeneration, and corresponded well to limb properties. These results support our hypothesis that histone modifications function as a heritable cellular memory to maintain limb cell properties, despite dynamic changes in gene expression during limb bud regeneration in Xenopus.
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Kulkarni VV, Kareenhalli V, Viswananthan GA, Riedel M. Characterizing the memory of the GAL regulatory network in Saccharomyces cerevisiae. Syst Synth Biol 2011. [PMID: 23205153 DOI: 10.1007/s11693-011-9086-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Genetic regulatory networks respond dynamically to perturbations in the intracellular and extracellular environments of an organism. The GAL system in the yeast Saccharomyces cerevisiae has evolved to utilize galactose as an alternative carbon and energy source, in the absence of glucose in the environment. We present a dynamic model for GAL system in Saccharomyces cerevisiae, which includes a novel mechanism for Gal3p activation upon induction with galactose. The modification enables the model to simulate the experimental observation that in absence of galactose, oversynthesis of Gal3p can also induce the GAL system. We then characterize the memory of the GAL system as the domain of attraction of the steady states.
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Affiliation(s)
- Vishwesh V Kulkarni
- Department of Electrical Engineering, Indian Institute of Technology, Bombay, Mumbai 400 076 India
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