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Campagnaro GD, Kaysel Cruz A. Genetic and functional dissection of the glutamate-proline pathway reveals a shortcut for glutamate catabolism in Leishmania. FEBS J 2025; 292:2645-2670. [PMID: 39960766 DOI: 10.1111/febs.70030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 10/22/2024] [Accepted: 02/07/2025] [Indexed: 05/25/2025]
Abstract
Trypanosomatids are early-divergent eukaryotes that have adapted to parasitism. During their life cycles, these parasites switch between a mammalian and an invertebrate host, and the ability to adapt their metabolism to different nutritional sources is instrumental for their success. In the invertebrate host, these protists have access to high amounts of amino acids and efficiently utilise it for energy production. Proline is a particularly efficient energy source for trypanosomes. Glutamate is also efficiently used by Trypanosoma cruzi and can be converted into proline as part of the glutamate-proline pathway prior to its intramitochondrial catabolism. By employing a series of genetic modifications and functional analysis, we show here that Leishmania parasites, the causative agents of leishmaniases, can utilise proline, glutamate and glutamine as energy sources, and although these parasites possess all the genes necessary for the biosynthesis of proline from glutamate, this pathway has, at best, limited function, with at least one of its components (pyrroline-5-carboxylate reductase) assuming divergent functions in different life cycle stages of the parasite. In fact, we show that the catabolism of glutamate is independent of proline biosynthesis and the former is most likely directly imported into the mitochondrion and catabolised to recover the cellular redox metabolism and increase mitochondrial membrane potential. Moreover, our data suggest a relevant role for glutamate dehydrogenase in nutritional stress response in Leishmania. These findings highlight relevant differences in amino acid metabolism between Trypanosoma and Leishmania and suggest a diversification in amino acid metabolic pathways within Trypanosomatidae.
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Affiliation(s)
- Gustavo Daniel Campagnaro
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Brazil
| | - Angela Kaysel Cruz
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Brazil
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2
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Quilles JC, Espada CR, Orsine LA, Defina TA, Almeida L, Holetz F, Cruz AK. A short ncRNA modulates gene expression and affects stress response and parasite differentiation in Leishmania braziliensis. Front Cell Infect Microbiol 2025; 15:1513908. [PMID: 39981380 PMCID: PMC11841412 DOI: 10.3389/fcimb.2025.1513908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2024] [Accepted: 01/15/2025] [Indexed: 02/22/2025] Open
Abstract
The protozoan parasite Leishmania spp. is a causative agent of leishmaniasis, a disease that affects millions of people in more than 80 countries worldwide. Apart from its medical relevance, this organism has a genetic organization that is unique among eukaryotes. Studies of the mechanisms regulating gene expression in Leishmania led us to investigate noncoding RNAs (ncRNAs) as regulatory elements. We previously identified differentially expressed (DE) ncRNAs in Leishmania braziliensis with potential roles in the parasite biology and development. Herein, we present a functional analysis of one such DE ncRNA, the 147-nucleotide-long transcript ncRNA97, which is preferentially expressed in amastigotes, the replicative form within mammalian phagocytes. By RT-qPCR the ncRNA97 was detected in greater quantities in the nucleus under physiological conditions and in the cytoplasm under nutritional stress. Interestingly, the transcript is protected at the 5' end but is not processed by the canonical trypanosomatid trans-splicing mechanism, according to the RNA circularization assay. ncRNA97 knockout (KO) and addback (AB) transfectants were generated and subjected to phenotypic analysis, which revealed that the lack of ncRNA97 impairs the starvation response and differentiation to the infective form. Comparative transcriptomics of ncRNA97KO and parental cells revealed that transcripts encoding amastigote-specific proteins were affected. This pioneering work demonstrates that ncRNAs contribute to the developmental regulatory mechanisms of Leishmania.
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Affiliation(s)
- José C. Quilles
- Laboratory de Molecular Parasitology, Department of Cell and Molecular Biology, Ribeirão Preto Medical School, FMRP/USP – University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Caroline R. Espada
- Laboratory de Molecular Parasitology, Department of Cell and Molecular Biology, Ribeirão Preto Medical School, FMRP/USP – University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Lissur A. Orsine
- Laboratory de Molecular Parasitology, Department of Cell and Molecular Biology, Ribeirão Preto Medical School, FMRP/USP – University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Tânia A. Defina
- Laboratory de Molecular Parasitology, Department of Cell and Molecular Biology, Ribeirão Preto Medical School, FMRP/USP – University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Letícia Almeida
- Laboratory de Molecular Parasitology, Department of Cell and Molecular Biology, Ribeirão Preto Medical School, FMRP/USP – University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Fabíola Holetz
- Laboratory of Gene Expression Regulation, Carlos Chagas Institute, Oswaldo Cruz Foundation, Curitiba, PR, Brazil
| | - Angela K. Cruz
- Laboratory de Molecular Parasitology, Department of Cell and Molecular Biology, Ribeirão Preto Medical School, FMRP/USP – University of São Paulo, Ribeirão Preto, SP, Brazil
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Ortiz-Hernández R, Millán-Casarrubias EJ, Bolaños J, Munguía-Robledo S, Vázquez-Calzada C, Azuara-Licéaga E, Valdés J, Rodríguez MA. PRMT5 Inhibitor EPZ015666 Decreases the Viability and Encystment of Entamoeba invadens. Molecules 2024; 30:62. [PMID: 39795118 PMCID: PMC11721204 DOI: 10.3390/molecules30010062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2024] [Revised: 12/18/2024] [Accepted: 12/24/2024] [Indexed: 01/13/2025] Open
Abstract
Protein arginine methyltransferase 5 (PRMT5) is an enzyme that produces monomethyl arginine (MMA) and symmetric dimethyl arginine (sDMA), post-translational modifications that regulate several cellular processes, including stage conversion in parasitic protozoans. Entamoeba histolytica, the etiologic agent of human amebiasis, has two stages in its life cycle, the trophozoite, which is the replicative form, and the cyst, corresponding to the infective phase. The study of the molecular mechanisms that regulate differentiation in this parasite has been overdue because of a lack of efficient protocols for in vitro encystment. For this reason, Entamoeba invadens, a parasite of reptiles, has been used as a differentiation model system for the genus. Here, we demonstrated the presence of sDMA in E. invadens, which increases during encystment, and identified the PRMT5 of this microorganism (EiPRMT5). In addition, we performed 3D modeling of this enzyme, as well as its molecular docking with the PRMT5 inhibitor EPZ015666, which predicted the affinity of the drug for the active site of the enzyme. In agreement with these findings, EPZ015666 reduced trophozoite viability and encystment. Therefore, EiPRMT5 is a potential target for inhibiting the spread of amebiasis.
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Affiliation(s)
- Rigoberto Ortiz-Hernández
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City 07360, Mexico; (R.O.-H.); (J.B.); (S.M.-R.); (C.V.-C.)
| | - Elmer Joel Millán-Casarrubias
- Laboratorio de Sistemas de Diagnóstico y Tratamiento de Cáncer, Unidad Profesional Interdisciplinaria en Ingeniería y Tecnologías Avanzadas del Instituto Politécnico Nacional, Mexico City 07340, Mexico;
| | - Jeni Bolaños
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City 07360, Mexico; (R.O.-H.); (J.B.); (S.M.-R.); (C.V.-C.)
| | - Susana Munguía-Robledo
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City 07360, Mexico; (R.O.-H.); (J.B.); (S.M.-R.); (C.V.-C.)
| | - Carlos Vázquez-Calzada
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City 07360, Mexico; (R.O.-H.); (J.B.); (S.M.-R.); (C.V.-C.)
| | - Elisa Azuara-Licéaga
- Programa de Posgraduados en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City 04510, Mexico;
| | - Jesús Valdés
- Departamento de Bioquímica, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City 07360, Mexico;
| | - Mario Alberto Rodríguez
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City 07360, Mexico; (R.O.-H.); (J.B.); (S.M.-R.); (C.V.-C.)
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Adán-Jiménez J, Sánchez-Salvador A, Morato E, Solana JC, Aguado B, Requena JM. A Proteogenomic Approach to Unravel New Proteins Encoded in the Leishmania donovani (HU3) Genome. Genes (Basel) 2024; 15:775. [PMID: 38927711 PMCID: PMC11203134 DOI: 10.3390/genes15060775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 06/10/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024] Open
Abstract
The high-throughput proteomics data generated by increasingly more sensible mass spectrometers greatly contribute to our better understanding of molecular and cellular mechanisms operating in live beings. Nevertheless, proteomics analyses are based on accurate genomic and protein annotations, and some information may be lost if these resources are incomplete. Here, we show that most proteomics data may be recovered by interconnecting genomics and proteomics approaches (i.e., following a proteogenomic strategy), resulting, in turn, in an improvement of gene/protein models. In this study, we generated proteomics data from Leishmania donovani (HU3 strain) promastigotes that allowed us to detect 1908 proteins in this developmental stage on the basis of the currently annotated proteins available in public databases. However, when the proteomics data were searched against all possible open reading frames existing in the L. donovani genome, twenty new protein-coding genes could be annotated. Additionally, 43 previously annotated proteins were extended at their N-terminal ends to accommodate peptides detected in the proteomics data. Also, different post-translational modifications (phosphorylation, acetylation, methylation, among others) were found to occur in a large number of Leishmania proteins. Finally, a detailed comparative analysis of the L. donovani and Leishmania major experimental proteomes served to illustrate how inaccurate conclusions can be raised if proteomes are compared solely on the basis of the listed proteins identified in each proteome. Finally, we have created data entries (based on freely available repositories) to provide and maintain updated gene/protein models. Raw data are available via ProteomeXchange with the identifier PXD051920.
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Affiliation(s)
- Javier Adán-Jiménez
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Departamento de Biología Molecular, Instituto Universitario de Biología Molecular (IUBM), Universidad Autónoma de Madrid, 28049 Madrid, Spain; (J.A.-J.); (A.S.-S.); (E.M.); (J.C.S.)
| | - Alejandro Sánchez-Salvador
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Departamento de Biología Molecular, Instituto Universitario de Biología Molecular (IUBM), Universidad Autónoma de Madrid, 28049 Madrid, Spain; (J.A.-J.); (A.S.-S.); (E.M.); (J.C.S.)
| | - Esperanza Morato
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Departamento de Biología Molecular, Instituto Universitario de Biología Molecular (IUBM), Universidad Autónoma de Madrid, 28049 Madrid, Spain; (J.A.-J.); (A.S.-S.); (E.M.); (J.C.S.)
| | - Jose Carlos Solana
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Departamento de Biología Molecular, Instituto Universitario de Biología Molecular (IUBM), Universidad Autónoma de Madrid, 28049 Madrid, Spain; (J.A.-J.); (A.S.-S.); (E.M.); (J.C.S.)
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Begoña Aguado
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Departamento de Biología Molecular, Instituto Universitario de Biología Molecular (IUBM), Universidad Autónoma de Madrid, 28049 Madrid, Spain; (J.A.-J.); (A.S.-S.); (E.M.); (J.C.S.)
| | - Jose M. Requena
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Departamento de Biología Molecular, Instituto Universitario de Biología Molecular (IUBM), Universidad Autónoma de Madrid, 28049 Madrid, Spain; (J.A.-J.); (A.S.-S.); (E.M.); (J.C.S.)
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas, Instituto de Salud Carlos III, 28029 Madrid, Spain
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Borges FS, Quilles JC, Lorenzon LB, Espada CR, Freitas-Castro F, Defina TPA, Holetz FB, Cruz AK. Leishmania Ribosomal Protein (RP) paralogous genes compensate each other's expression maintaining protein native levels. PLoS One 2024; 19:e0292152. [PMID: 38753846 PMCID: PMC11098316 DOI: 10.1371/journal.pone.0292152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 04/22/2024] [Indexed: 05/18/2024] Open
Abstract
In the protozoan parasite Leishmania, most genes encoding for ribosomal proteins (RPs) are present as two or more copies in the genome. However, their untranslated regions (UTRs) are predominantly divergent and might be associated with a distinct regulation of the expression of paralogous genes. Herein, we investigated the expression profiles of two RPs (S16 and L13a) encoded by duplicated genes in Leishmania major. The genes encoding for the S16 protein possess identical coding sequences (CDSs) and divergent UTRs, whereas the CDSs of L13a diverge by two amino acids and by their UTRs. Using CRISPR/Cas9 genome editing, we generated knockout (Δ) and endogenously tagged transfectants for each paralog of L13a and S16 genes. Combining tagged and Δ cell lines we found evidence of differential expression of both RPS16 and RPL13a isoforms throughout parasite development, with one isoform consistently more abundant than its respective copy. In addition, compensatory expression was observed for each paralog upon deletion of the corresponding isoform, suggesting functional conservation between these proteins. This differential expression pattern relates to post-translational processes, given compensation occurs at the level of the protein, with no alterations detected at transcript level. Ribosomal profiles for RPL13a indicate a standard behavior for these paralogues suggestive of interaction with heavy RNA-protein complexes, as already reported for other RPs in trypanosomatids. We identified paralog-specific bound to their 3'UTRs which may be influential in regulating paralog expression. In support, we identified conserved cis-elements within the 3'UTRs of RPS16 and RPL13a; cis-elements exclusive to the UTR of the more abundant paralog or to the less abundant ones were identified.
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Affiliation(s)
- Francisca S. Borges
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, FMRP/USP–University of São Paulo, São Paulo, Brazil
| | - José C. Quilles
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, FMRP/USP–University of São Paulo, São Paulo, Brazil
| | - Lucas B. Lorenzon
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, FMRP/USP–University of São Paulo, São Paulo, Brazil
| | - Caroline R. Espada
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, FMRP/USP–University of São Paulo, São Paulo, Brazil
| | - Felipe Freitas-Castro
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, FMRP/USP–University of São Paulo, São Paulo, Brazil
| | - Tânia P. A. Defina
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, FMRP/USP–University of São Paulo, São Paulo, Brazil
| | - Fabíola B. Holetz
- Laboratory of Gene Expression Regulation, Carlos Chagas Institute, Oswaldo Cruz Foundation, Curitiba, Paraná, Brazil
| | - Angela K. Cruz
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, FMRP/USP–University of São Paulo, São Paulo, Brazil
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Campagnaro GD, Lorenzon LB, Rodrigues MA, Defina TPA, Pinzan CF, Ferreira TR, Cruz AK. Overexpression of Leishmania major protein arginine methyltransferase 6 reduces parasite infectivity in vivo. Acta Trop 2023; 244:106959. [PMID: 37257676 DOI: 10.1016/j.actatropica.2023.106959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/26/2023] [Accepted: 05/28/2023] [Indexed: 06/02/2023]
Abstract
Arginine methylation is catalysed by Protein Arginine Methyltransferases (PRMTs) and can affect how a target protein functions and how it interacts with other macromolecules, which in turn impacts on cell metabolism and gene expression control. Leishmania parasites express five different PRMTs, and although the presence of each individual PRMT is not essential per se, the imbalanced activity of these PRMTs can impact the virulence of Leishmania parasites in vitro and in vivo. Here we created a Leishmania major cell line overexpressing PRMT6 and show that similar to what was observed for the T. brucei homologous enzyme, L. major PRMT6 probably has a narrow substrate range. However, its overexpression notably impairs the infection in mice, with a mild reduction in the number of viable parasites in the lymph nodes. Our results indicate that arginine methylation by LmjPRMT6 plays a significant role in the adaptation of the parasite to the environment found in the mammalian host.
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Affiliation(s)
- Gustavo Daniel Campagnaro
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Lucas Bigolin Lorenzon
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Mateus Augusto Rodrigues
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Tânia Paula Aquino Defina
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Camila Figueiredo Pinzan
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Tiago Rodrigues Ferreira
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Angela Kaysel Cruz
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil.
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Aldrich CC, Calderón F, Conway SJ, He C, Hooker JM, Huryn DM, Lindsley CW, Liotta DC, Müller CE. Virtual Special Issue: Epigenetics 2022. ACS Chem Biol 2022; 17:2673-2678. [PMID: 36268572 DOI: 10.1021/acschembio.2c00661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Aldrich CC, Calderón F, Conway SJ, He C, Hooker JM, Huryn DM, Lindsley CW, Liotta DC, Müller CE. Virtual Special Issue: Epigenetics 2022. ACS Pharmacol Transl Sci 2022; 5:829-834. [PMID: 36268124 PMCID: PMC9578134 DOI: 10.1021/acsptsci.2c00169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Indexed: 11/28/2022]
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Aldrich CC, Calderón F, Conway SJ, He C, Hooker JM, Huryn DM, Lindsley CW, Liotta DC, Müller CE. Virtual Special Issue: Epigenetics 2022. ACS Infect Dis 2022; 8:1975-1980. [PMID: 36073808 DOI: 10.1021/acsinfecdis.2c00434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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Aldrich CC, Calderón F, Conway SJ, He C, Hooker JM, Huryn DM, Lindsley CW, Liotta DC, Müller CE. Virtual Special Issue: Epigenetics 2022. ACS Med Chem Lett 2022; 13:1524-1529. [PMID: 36262399 PMCID: PMC9575161 DOI: 10.1021/acsmedchemlett.2c00393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Indexed: 11/30/2022] Open
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Aldrich CC, Calderón F, Conway SJ, He C, Hooker JM, Huryn DM, Lindsley CW, Liotta DC, Müller CE. Virtual Special Issue: Epigenetics 2022. J Med Chem 2022; 65:11894-11899. [PMID: 36073827 DOI: 10.1021/acs.jmedchem.2c01386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Aldrich CC, Calderón F, Conway SJ, He C, Hooker JM, Huryn DM, Lindsley CW, Liotta DC, Müller CE. Virtual Special Issue: Epigenetics 2022. ACS Chem Neurosci 2022. [PMID: 36067366 DOI: 10.1021/acschemneuro.2c00501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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