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Arratia LM, Bermudes-Contreras JD, Juarez-Monroy JA, Romero-Macías EA, Luna-Rojas JC, López-Hidalgo M, Vega AV, Zamorano-Carrillo A. Experimental and computational evidence that Calpain-10 binds to the carboxy terminus of Na V1.2 and Na V1.6. Sci Rep 2024; 14:6761. [PMID: 38514708 PMCID: PMC10957924 DOI: 10.1038/s41598-024-57117-8] [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: 11/08/2023] [Accepted: 03/14/2024] [Indexed: 03/23/2024] Open
Abstract
Voltage-gated sodium channels (NaV) are pivotal proteins responsible for initiating and transmitting action potentials. Emerging evidence suggests that proteolytic cleavage of sodium channels by calpains is pivotal in diverse physiological scenarios, including ischemia, brain injury, and neuropathic pain associated with diabetes. Despite this significance, the precise mechanism by which calpains recognize sodium channels, especially given the multiple calpain isoforms expressed in neurons, remains elusive. In this work, we show the interaction of Calpain-10 with NaV's C-terminus through a yeast 2-hybrid assay screening of a mouse brain cDNA library and in vitro by GST-pulldown. Later, we also obtained a structural and dynamic hypothesis of this interaction by modeling, docking, and molecular dynamics simulation. These results indicate that Calpain-10 interacts differentially with the C-terminus of NaV1.2 and NaV1.6. Calpain-10 interacts with NaV1.2 through domains III and T in a stable manner. In contrast, its interaction with NaV1.6 involves domains II and III, which could promote proteolysis through the Cys-catalytic site and C2 motifs.
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Affiliation(s)
- Luis Manuel Arratia
- Carrera de Médico Cirujano, FES Iztacala, UNAM, Av. de los Barrios 1, Los Reyes Iztacala, Tlalnepantla, Edo. Mex, Mexico
- Laboratorio de Biofísica Computacional, Doctorado en Biotecnología, SEPI-ENMH Instituto Politécnico Nacional, Av. Guillermo Massieu Helguera 239, Fracc. La Escalera, Ticomán, Gustavo A. Madero, 07320, Mexico City, Mexico
| | - Juan David Bermudes-Contreras
- Laboratorio de Biofísica Computacional, Doctorado en Biotecnología, SEPI-ENMH Instituto Politécnico Nacional, Av. Guillermo Massieu Helguera 239, Fracc. La Escalera, Ticomán, Gustavo A. Madero, 07320, Mexico City, Mexico
| | - Jorge Armando Juarez-Monroy
- Laboratorio de Biofísica Computacional, Doctorado en Biotecnología, SEPI-ENMH Instituto Politécnico Nacional, Av. Guillermo Massieu Helguera 239, Fracc. La Escalera, Ticomán, Gustavo A. Madero, 07320, Mexico City, Mexico
| | - Erik Alan Romero-Macías
- Carrera de Médico Cirujano, FES Iztacala, UNAM, Av. de los Barrios 1, Los Reyes Iztacala, Tlalnepantla, Edo. Mex, Mexico
- Doctorado en Ciencias Biomédicas, FES Iztacala, UNAM, Av. de los Barrios 1, Los Reyes Iztacala, Tlalnepantla Edo, Mexico City, Mexico
| | - Julio Cesar Luna-Rojas
- Carrera de Médico Cirujano, FES Iztacala, UNAM, Av. de los Barrios 1, Los Reyes Iztacala, Tlalnepantla, Edo. Mex, Mexico
- Maestría en Neurobiología, FES Iztacala, UNAM, Av. de los Barrios 1, Los Reyes Iztacala, Tlalnepantla Edo, Mexico City, Mexico
| | - Marisol López-Hidalgo
- Laboratorio de Biofísica Computacional, Doctorado en Biotecnología, SEPI-ENMH Instituto Politécnico Nacional, Av. Guillermo Massieu Helguera 239, Fracc. La Escalera, Ticomán, Gustavo A. Madero, 07320, Mexico City, Mexico
| | - Ana Victoria Vega
- Carrera de Médico Cirujano, FES Iztacala, UNAM, Av. de los Barrios 1, Los Reyes Iztacala, Tlalnepantla, Edo. Mex, Mexico.
| | - Absalom Zamorano-Carrillo
- Laboratorio de Biofísica Computacional, Doctorado en Biotecnología, SEPI-ENMH Instituto Politécnico Nacional, Av. Guillermo Massieu Helguera 239, Fracc. La Escalera, Ticomán, Gustavo A. Madero, 07320, Mexico City, Mexico.
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Liu W, Pang Y, Yu X, Lu D, Yang Y, Meng F, Xu C, Yuan L, Nan Y. Pan-cancer analysis of NUDT21 and its effect on the proliferation of human head and neck squamous cell carcinoma. Aging (Albany NY) 2024; 16:3363-3385. [PMID: 38349866 PMCID: PMC10929839 DOI: 10.18632/aging.205539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 01/08/2024] [Indexed: 02/15/2024]
Abstract
BACKGROUND Based on bioinformatics research of NUDT21 in pan-cancer, we aimed to clarify the mechanism of NUDT21 in HHNC by experiment. METHODS The correlation between differential expression of NUDT21 in pan-cancer and survival prognosis, genomic instability, tumor stemness, DNA repair, RNA methylation and with immune microenvironment were analyzed by the application of different pan-cancer analysis web databases. In addition, immunohistochemistry staining and genetic detection of NUDT21 in HHNCC tumor tissues by immunohistochemistry and qRT-PCR. Then, through in vitro cell experiments, NUDT21 was knocked down by lentivirus to detect the proliferation, cycle, apoptosis of FaDu and CNE-2Z cells, and finally by PathScan intracellular signaling array reagent to detect the apoptotic protein content. RESULTS Based on the pan-cancer analysis, we found that elevated expression of NUDT21 in most cancers was significantly correlated with TMB, MSI, neoantigens and chromosomal ploidy, and in epigenetics, elevated NUDT21 expression was strongly associated with genomic stability, mismatch repair genes, tumor stemness, and RNA methylation. Based on immunosuppressive score, we found that NUDT21 plays an essential role in the immunosuppressive environment by suppressing immune checkpointing effect in most cancers. In addition, using HHNSCC as a study target, PCR and pathological detection of NUDT21 in tumor tissues was significantly increased than that in paracancerous normal tissues. In vitro cellular assays, silencing NUDT21 inhibited proliferation and promoted apoptosis in FaDu and CNE-2Z cells, and blocked the cell cycle in the G2/M phase. Therefore, the experiments confirmed that NUDT21 promotes the proliferation of FaDu by suppressing the expression of apoptotic.
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Affiliation(s)
- Wenjing Liu
- Key Laboratory of Ningxia Minority Medicine Modernization Ministry of Education, Ningxia Medical University, Yinchuan 750004, Ningxia Hui Autonomous Region, China
| | - Yingna Pang
- Department of Otolaryngology Head and Neck Surgery, The Second Hospital of Jilin University, Changchun 130000, China
| | - Xiaolu Yu
- Department of Otolaryngology Head and Neck Surgery, The Second Hospital of Jilin University, Changchun 130000, China
| | - Doudou Lu
- Clinical Medical College, Ningxia Medical University, Yinchuan 750004, Ningxia Hui Autonomous Region, China
| | - Yating Yang
- Traditional Chinese Medicine College, Ningxia Medical University, Yinchuan 750004, Ningxia Hui Autonomous Region, China
| | - Fandi Meng
- Traditional Chinese Medicine College, Ningxia Medical University, Yinchuan 750004, Ningxia Hui Autonomous Region, China
| | - Chengbi Xu
- Department of Otolaryngology Head and Neck Surgery, The Second Hospital of Jilin University, Changchun 130000, China
| | - Ling Yuan
- College of Pharmacy, Ningxia Medical University, Yinchuan 750004, Ningxia Hui Autonomous Region, China
| | - Yi Nan
- Key Laboratory of Ningxia Minority Medicine Modernization Ministry of Education, Ningxia Medical University, Yinchuan 750004, Ningxia Hui Autonomous Region, China
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Salgado-Martínez AI, Avila-Bonilla RG, Ramírez-Moreno E, Castañón-Sánchez CA, López-Camarillo C, Marchat LA. Unraveling the relevance of the polyadenylation factor EhCFIm25 in Entamoeba histolytica through proteomic analysis. FEBS Open Bio 2021; 11:2819-2835. [PMID: 34486252 PMCID: PMC8487052 DOI: 10.1002/2211-5463.13287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 08/06/2021] [Accepted: 09/02/2021] [Indexed: 11/16/2022] Open
Abstract
We recently reported that silencing of the polyadenylation factor EhCFIm25 in Entamoeba histolytica, the protozoan which causes human amoebiasis, affects trophozoite proliferation, death, and virulence, suggesting that EhCFIm25 may have potential as a new biochemical target. Here, we performed a shotgun proteomic analysis to identify modulated proteins that could explain this phenotype. Data are available via ProteomeXchange with identifier PXD027784. Our results revealed changes in the abundance of 75 proteins. Interestingly, STRING analysis, functional GO‐term annotations, KEGG analyses, and literature review showed that modulated proteins are mainly related to glycolysis and carbon metabolism, cytoskeleton dynamics, and parasite virulence, as well as gene expression and protein modifications. Further studies are needed to confirm the hypotheses emerging from this proteomic analysis, to thereby acquire a comprehensive view of the molecular mechanisms involved.
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Affiliation(s)
| | | | - Esther Ramírez-Moreno
- Laboratorio de Biomedicina Molecular II, ENMH, Instituto Politécnico Nacional, Mexico City, Mexico
| | | | - César López-Camarillo
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México (UACM), Mexico
| | - Laurence A Marchat
- Laboratorio de Biomedicina Molecular II, ENMH, Instituto Politécnico Nacional, Mexico City, Mexico
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Ospina-Villa JD, Tovar-Ayona BJ, López-Camarillo C, Soto-Sánchez J, Ramírez-Moreno E, Castañón-Sánchez CA, Marchat LA. mRNA Polyadenylation Machineries in Intestinal Protozoan Parasites. J Eukaryot Microbiol 2020; 67:306-320. [PMID: 31898347 DOI: 10.1111/jeu.12781] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 12/16/2019] [Accepted: 12/22/2019] [Indexed: 12/22/2022]
Abstract
In humans, mRNA polyadenylation involves the participation of about 20 factors in four main complexes that recognize specific RNA sequences. Notably, CFIm25, CPSF73, and PAP have essential roles for poly(A) site selection, mRNA cleavage, and adenosine residues polymerization. Besides the relevance of polyadenylation for gene expression, information is scarce in intestinal protozoan parasites that threaten human health. To better understand polyadenylation in Entamoeba histolytica, Giardia lamblia, and Cryptosporidium parvum, which represent leading causes of diarrhea worldwide, genomes were screened for orthologs of human factors. Results showed that Entamoeba histolytica and C. parvum have 16 and 12 proteins out of the 19 human proteins used as queries, respectively, while G. lamblia seems to have the smallest polyadenylation machinery with only six factors. Remarkably, CPSF30, CPSF73, CstF77, PABP2, and PAP, which were found in all parasites, could represent the core polyadenylation machinery. Multiple genes were detected for several proteins in Entamoeba, while gene redundancy is lower in Giardia and Cryptosporidium. Congruently with their relevance in the polyadenylation process, CPSF73 and PAP are present in all parasites, and CFIm25 is only missing in Giardia. They conserve the functional domains and predicted folding of human proteins, suggesting they may have the same roles in polyadenylation.
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Affiliation(s)
- Juan David Ospina-Villa
- Independent Researcher, Transversal 27A Sur # 42-14, C.P. 055421, Envigado, Antioquia, Colombia
| | - Brisna Joana Tovar-Ayona
- Posgrados en Biomedicina Molecular y en Biotecnología, ENMH, Instituto Politécnico Nacional, Av. Guillermo Massieu Helguera 239, Col. La Escalera, Gustavo A. Madero, C.P. 07320, Ciudad de México, Mexico
| | - César López-Camarillo
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, San Lorenzo 290, Col. del Valle Sur, Benito Juárez, C.P. 03100, Ciudad de México, Mexico
| | - Jacqueline Soto-Sánchez
- Posgrados en Biomedicina Molecular y en Biotecnología, ENMH, Instituto Politécnico Nacional, Av. Guillermo Massieu Helguera 239, Col. La Escalera, Gustavo A. Madero, C.P. 07320, Ciudad de México, Mexico
| | - Esther Ramírez-Moreno
- Posgrados en Biomedicina Molecular y en Biotecnología, ENMH, Instituto Politécnico Nacional, Av. Guillermo Massieu Helguera 239, Col. La Escalera, Gustavo A. Madero, C.P. 07320, Ciudad de México, Mexico
| | - Carlos A Castañón-Sánchez
- Hospital Regional de Alta Especialidad de Oaxaca, Aldama s/n, Col. Centro, C.P. 71256 San Bartolo Coyotepec, Oaxaca, Mexico
| | - Laurence A Marchat
- Posgrados en Biomedicina Molecular y en Biotecnología, ENMH, Instituto Politécnico Nacional, Av. Guillermo Massieu Helguera 239, Col. La Escalera, Gustavo A. Madero, C.P. 07320, Ciudad de México, Mexico
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Advances on Aptamers against Protozoan Parasites. Genes (Basel) 2018; 9:genes9120584. [PMID: 30487456 PMCID: PMC6316487 DOI: 10.3390/genes9120584] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 11/16/2018] [Accepted: 11/26/2018] [Indexed: 02/07/2023] Open
Abstract
Aptamers are single-stranded DNA or RNA sequences with a unique three-dimensional structure that allows them to recognize a particular target with high affinity. Although their specific recognition activity could make them similar to monoclonal antibodies, their ability to bind to a large range of non-immunogenic targets greatly expands their potential as tools for diagnosis, therapeutic agents, detection of food risks, biosensors, detection of toxins, drug carriers, and nanoparticle markers, among others. One aptamer named Pegaptanib is currently used for treating macular degeneration associated with age, and many other aptamers are in different clinical stages of development of evaluation for various human diseases. In the area of parasitology, research on aptamers has been growing rapidly in the past few years. Here we describe the development of aptamers raised against the main protozoan parasites that affect hundreds of millions of people in underdeveloped and developing countries, remaining a major health concern worldwide, i.e. Trypanosoma spp., Plasmodium spp., Leishmania spp., Entamoeba histolytica, and Cryptosporidium parvuum. The latest progress made in this area confirmed that DNA and RNA aptamers represent attractive alternative molecules in the search for new tools to detect and treat these parasitic infections that affect human health worldwide.
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