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Ram TB, Krishnan S, Jeevanandam J, Danquah MK, Thomas S. Emerging Biohybrids of Aptamer-Based Nano-Biosensing Technologies for Effective Early Cancer Detection. Mol Diagn Ther 2024; 28:425-453. [PMID: 38775897 DOI: 10.1007/s40291-024-00717-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/01/2024] [Indexed: 06/28/2024]
Abstract
Cancer is a leading global cause of mortality, which underscores the imperative of early detection for improved patient outcomes. Biorecognition molecules, especially aptamers, have emerged as highly effective tools for early and accurate cancer cell identification. Aptamers, with superior versatility in synthesis and modification, offer enhanced binding specificity and stability compared with conventional antibodies. Hence, this article reviews diagnostic strategies employing aptamer-based biohybrid nano-biosensing technologies, focusing on their utility in detecting cancer biomarkers and abnormal cells. Recent developments include the synthesis of nano-aptamers using diverse nanomaterials, such as metallic nanoparticles, metal oxide nanoparticles, carbon-derived substances, and biohybrid nanostructures. The integration of these nanomaterials with aptamers significantly enhances sensitivity and specificity, promising innovative and efficient approaches for cancer diagnosis. This convergence of nanotechnology with aptamer research holds the potential to revolutionize cancer treatment through rapid, accurate, and non-invasive diagnostic methods.
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Affiliation(s)
| | | | - Jaison Jeevanandam
- CQM-Centro de Química da Madeira, Universidade da Madeira, Campus da Penteada, 9020-105, Funchal, Madeira, Portugal.
| | - Michael K Danquah
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN, USA
| | - Sabu Thomas
- School of Polymer Science and Technology and School of Chemical Sciences, Mahatma Gandhi University, Kottayam, Kerala, India
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2
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Morales-Velásquez M, Barón-Vera JP, Pulgarín-Osorio MI, Sánchez-Jiménez MM, Ospina-Villa JD. Identification of the ATPase alpha subunit of Trypanosoma cruzi as a potential biomarker for the diagnosis of Chagas disease. Biomarkers 2023; 28:599-607. [PMID: 37667642 DOI: 10.1080/1354750x.2023.2255756] [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: 05/25/2023] [Accepted: 08/30/2023] [Indexed: 09/06/2023]
Abstract
BACKGROUND Chagas disease (CD) is considered by the World Health Organisation (WHO) a neglected disease endemic to the Americas, but it has spread throughout the world due to migrations. The disease is almost 100% curable if detected in time. Still, the lack of rapid diagnostic tests with sufficient sensitivity and specificity leads to a chronic phase with a mortality of about 50,000 people worldwide per year. METHODS Using the total proteins extracted from serum samples of patients confirmed with chronic phase CD; we performed the Bio-SELEX strategy. The best aptamers were selected using next-generation sequencing (NGS) based on their most abundant sequences (reads and rpm). Then, selected aptamers were used to isolate potential biomarkers directly from serum samples of patients with chronic phase CD using pull-down and mass spectrometry experiments. RESULTS CH1 aptamer was the aptamer selected after the NGS results analysis. The pull-down and mass spectrometry experiments identified the presence of the ATPase alpha subunit of T. cruzi circulating in serum samples of patients with chronic phase CD. CONCLUSIONS We report the ATPase alpha subunit of T. cruzi as a potential biomarker for chronic phase CD and CH1 aptamer as a potential tool for diagnosing CD.
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Affiliation(s)
- M Morales-Velásquez
- Tropical Medicine, Instituto Colombiano de Medicina Tropical - ICMT, Universidad CES, Medellin, Colombia
| | - J P Barón-Vera
- Tropical Medicine, Instituto Colombiano de Medicina Tropical - ICMT, Universidad CES, Medellin, Colombia
| | - M I Pulgarín-Osorio
- Tropical Medicine, Instituto Colombiano de Medicina Tropical - ICMT, Universidad CES, Medellin, Colombia
| | - M M Sánchez-Jiménez
- Tropical Medicine, Instituto Colombiano de Medicina Tropical - ICMT, Universidad CES, Medellin, Colombia
| | - J D Ospina-Villa
- Tropical Medicine, Instituto Colombiano de Medicina Tropical - ICMT, Universidad CES, Medellin, Colombia
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3
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Comparative genomics and interactomics of polyadenylation factors for the prediction of new parasite targets: Entamoeba histolytica as a working model. Biosci Rep 2023; 43:232462. [PMID: 36651565 PMCID: PMC9912109 DOI: 10.1042/bsr20221911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 01/05/2023] [Accepted: 01/13/2023] [Indexed: 01/19/2023] Open
Abstract
Protein-protein interactions (PPI) play a key role in predicting the function of a target protein and drug ability to affect an entire biological system. Prediction of PPI networks greatly contributes to determine a target protein and signal pathways related to its function. Polyadenylation of mRNA 3'-end is essential for gene expression regulation and several polyadenylation factors have been shown as valuable targets for controlling protozoan parasites that affect human health. Here, by using a computational strategy based on sequence-based prediction approaches, phylogenetic analyses, and computational prediction of PPI networks, we compared interactomes of polyadenylation factors in relevant protozoan parasites and the human host, to identify key proteins and define potential targets for pathogen control. Then, we used Entamoeba histolytica as a working model to validate our computational results. RT-qPCR assays confirmed the coordinated modulation of connected proteins in the PPI network and evidenced that silencing of the bottleneck protein EhCFIm25 affects the expression of interacting proteins. In addition, molecular dynamics simulations and docking approaches allowed to characterize the relationships between EhCFIm25 and Ehnopp34, two connected bottleneck proteins. Interestingly, the experimental identification of EhCFIm25 interactome confirmed the close relationships among proteins involved in gene expression regulation and evidenced new links with moonlight proteins in E. histolytica, suggesting a connection between RNA biology and metabolism as described in other organisms. Altogether, our results strengthened the relevance of comparative genomics and interactomics of polyadenylation factors for the prediction of new targets for the control of these human pathogens.
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Brosseau NE, Vallée I, Mayer-Scholl A, Ndao M, Karadjian G. Aptamer-Based Technologies for Parasite Detection. SENSORS (BASEL, SWITZERLAND) 2023; 23:s23020562. [PMID: 36679358 PMCID: PMC9867382 DOI: 10.3390/s23020562] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/26/2022] [Accepted: 12/27/2022] [Indexed: 05/30/2023]
Abstract
Centuries of scientific breakthroughs have brought us closer to understanding and managing the spread of parasitic diseases. Despite ongoing technological advancements in the detection, treatment, and control of parasitic illnesses, their effects on animal and human health remain a major concern worldwide. Aptamers are single-stranded oligonucleotides whose unique three-dimensional structures enable them to interact with high specificity and affinity to a wide range of targets. In recent decades, aptamers have emerged as attractive alternatives to antibodies as therapeutic and diagnostic agents. Due to their superior stability, reusability, and modifiability, aptamers have proven to be effective bioreceptors for the detection of toxins, contaminants, biomarkers, whole cells, pathogens, and others. As such, they have been integrated into a variety of electrochemical, fluorescence, and optical biosensors to effectively detect whole parasites and their proteins. This review offers a summary of the various types of parasite-specific aptamer-based biosensors, their general mechanisms and their performance.
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Affiliation(s)
- Noah Emerson Brosseau
- UMR BIPAR, Anses, Laboratoire de Santé Animale, INRAE, Ecole Nationale Vétérinaire d’Alfort, 94700 Maisons-Alfort, France
- Infectious Diseases and Immunity in Global Health (IDIGH) Program, Research Institute of McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Isabelle Vallée
- UMR BIPAR, Anses, Laboratoire de Santé Animale, INRAE, Ecole Nationale Vétérinaire d’Alfort, 94700 Maisons-Alfort, France
| | - Anne Mayer-Scholl
- Department of Biological Safety, German Federal Institute for Risk Assessment, 10589 Berlin, Germany
| | - Momar Ndao
- Infectious Diseases and Immunity in Global Health (IDIGH) Program, Research Institute of McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Grégory Karadjian
- UMR BIPAR, Anses, Laboratoire de Santé Animale, INRAE, Ecole Nationale Vétérinaire d’Alfort, 94700 Maisons-Alfort, France
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5
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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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Wan Q, Liu X, Zu Y. Oligonucleotide aptamers for pathogen detection and infectious disease control. Theranostics 2021; 11:9133-9161. [PMID: 34522231 PMCID: PMC8419047 DOI: 10.7150/thno.61804] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 08/04/2021] [Indexed: 12/21/2022] Open
Abstract
During an epidemic or pandemic, the primary task is to rapidly develop precise diagnostic approaches and effective therapeutics. Oligonucleotide aptamer-based pathogen detection assays and control therapeutics are promising, as aptamers that specifically recognize and block pathogens can be quickly developed and produced through simple chemical synthesis. This work reviews common aptamer-based diagnostic techniques for communicable diseases and summarizes currently available aptamers that target various pathogens, including the SARS-CoV-2 virus. Moreover, this review discusses how oligonucleotide aptamers might be leveraged to control pathogen propagation and improve host immune system responses. This review offers a comprehensive data source to the further develop aptamer-based diagnostics and therapeutics specific for infectious diseases.
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Affiliation(s)
| | | | - Youli Zu
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA
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7
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Vishwakarma A, Lal R, Ramya M. Aptamer-based approaches for the detection of waterborne pathogens. Int Microbiol 2021; 24:125-140. [PMID: 33404933 DOI: 10.1007/s10123-020-00154-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 10/13/2020] [Accepted: 12/14/2020] [Indexed: 02/06/2023]
Abstract
Waterborne ailments pose a serious threat to public health and are a huge economic burden. Lack of hygiene in drinking and recreational water is the chief source of microbial pathogens in developing countries. Poor water quality and sanitation account for more than 3.4 million deaths a year worldwide. This has urged authorities and researchers to explore different avenues of pathogen detection. There is a growing demand for rapid and reliable sensor technologies, in particular those that can detect in situ and perform in harsh conditions. Some of the major waterborne pathogens include Vibrio cholerae, Leptospira interrogans, Campylobacter jejuni, Shigella spp., enterotoxigenic Escherichia coli, Clostridium difficile, Cryptosporidium parvum, Entamoeba histolytica, and Hepatitis A virus. While conventional methods of pathogen detection like serodiagnosis and microbiological methods have been superseded by nucleic acid amplification methods, there is still potential for improvement. This review provides an insight into aptamers and their utility in the form of aptasensors. It discusses how aptamer-based approaches have emerged as a novel strategy and its advantages over more resource-intensive and complex biochemical approaches.
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Affiliation(s)
- Archana Vishwakarma
- Molecular Genetics Laboratory, Department of Genetic Engineering, College of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur 603203, Kanchipuram, Chennai, TN, India
| | - Roshni Lal
- Molecular Genetics Laboratory, Department of Genetic Engineering, College of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur 603203, Kanchipuram, Chennai, TN, India
| | - Mohandass Ramya
- Molecular Genetics Laboratory, Department of Genetic Engineering, College of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur 603203, Kanchipuram, Chennai, TN, India.
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8
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Taneja V, Goel M, Shankar U, Kumar A, Khilnani GC, Prasad HK, Prasad GBKS, Gupta UD, Sharma TK. An Aptamer Linked Immobilized Sorbent Assay (ALISA) to Detect Circulatory IFN-α, an Inflammatory Protein among Tuberculosis Patients. ACS COMBINATORIAL SCIENCE 2020; 22:656-666. [PMID: 33063508 DOI: 10.1021/acscombsci.0c00108] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Dysregulation of IFN-α is the basis for pathogenesis of autoimmune as well as infectious diseases. Identifying inflammatory signatures in peripheral blood of patients is an approach for monitoring active infection. Hence, estimation of type I IFNs as an inflammatory biomarker to scrutinize disease status after treatment is useful. Accordingly, an Aptamer Linked Immobilized Sorbent Assay (ALISA) for the detection of IFN-α in serum samples was developed. Sixteen aptamers were screened for their ability to bind IFN-α. Aptamer IFNα-3 exhibited specificity for IFN-α with no cross-reactivity with interferons β and γ and human serum albumin. The disassociation constant (Kd) was determined to be 3.96 ± 0.36 nM, and the limit of detection was ∼2 ng. The characterized IFNα-3 aptamer was used in ALISA to screen tuberculosis (TB) patients' sera. An elevated IFN-α level in sera derived from untreated TB patients (median = 0.31), compared to nontuberculous household contacts (median = 0.13) and healthy volunteers (median = 0.12), and further a decline in IFN-α level among treated patients (median = 0.13) were seen. The ALISA assay facilitates direct estimation of inflammatory protein(s) in circulation unlike mRNA estimation by real time PCR. Designing of aptamers similar to the IFNα-3 aptamer provides a novel approach to assess other inflammatory protein(s) in patients before, during, and after completion of treatment and would denote clinical improvement in successfully treated patients.
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Affiliation(s)
- Vibha Taneja
- National JALMA Institute of Leprosy and Other Mycobacterial Diseases, Tajganj, Agra, 282001, India
- Department of Biochemistry, Jiwaji University, Gwalior, Madhya Pradesh 474011, India
- Aptamer Technology and Diagnostics Laboratory, Multidisciplinary Clinical and Translational Research Group, Translational Health Science and Technology Institute, Incubator, NCR Biotech Science Cluster, Third Milestone, Faridabad, Gurgaon Expressway, Faridabad, 121001, India
- Department of Biotechnology, All India Institute of Medical Sciences (AIIMS), New Delhi 110029, India
| | - Manish Goel
- Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences (AIIMS), New Delhi 110029, India
| | - Uma Shankar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, 453552, India
| | - Amit Kumar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, 453552, India
| | - Gopi C. Khilnani
- Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences (AIIMS), New Delhi 110029, India
| | - Hanumanthappa K. Prasad
- Department of Biotechnology, All India Institute of Medical Sciences (AIIMS), New Delhi 110029, India
| | | | - Umesh D. Gupta
- National JALMA Institute of Leprosy and Other Mycobacterial Diseases, Tajganj, Agra, 282001, India
| | - Tarun K. Sharma
- Aptamer Technology and Diagnostics Laboratory, Multidisciplinary Clinical and Translational Research Group, Translational Health Science and Technology Institute, Incubator, NCR Biotech Science Cluster, Third Milestone, Faridabad, Gurgaon Expressway, Faridabad, 121001, India
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Wong LW, Ong KS, Khoo JR, Goh CBS, Hor JW, Lee SM. Human intestinal parasitic infection: a narrative review on global prevalence and epidemiological insights on preventive, therapeutic and diagnostic strategies for future perspectives. Expert Rev Gastroenterol Hepatol 2020; 14:1093-1105. [PMID: 32755242 DOI: 10.1080/17474124.2020.1806711] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
INTRODUCTION Intestinal parasitic infection (IPI) is a global health concern among socioeconomically deprived communities in many developing countries. Many preventative strategies have been deployed to control IPI, however, there is a lack in standards on the techniques used to diagnose and monitor the prevalence of IPI. AREAS COVERED The present article will review the diseases associated with IPI and discuss the current IPI control strategies such as the water, sanitation, and hygiene (WASH) interventions, community-led total sanitation (CLTS) approach, and regular anthelminthic treatments. For the first time, this review will also evaluate all currently practised diagnostic techniques for the detection of intestinal parasites and provide insights on future IPI control strategies. EXPERT OPINION Advanced and improved diagnostic methods such as qPCR coupled with a high-resolution melting curve, aptamers, biosensors, and detection of extracellular vesicles can be used for detection of IPI. Vaccination against intestinal parasites can be made available to increase antibodies to interfere with the blood-feeding process by the parasites, which subsequently reduces the reproductive rates of the parasites. These methods collectively can serve as future management strategies for intestinal parasitic infections.
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Affiliation(s)
- Li Wen Wong
- School of Science, Monash University Malaysia , Bandar Sunway, Malaysia
| | - Kuan Shion Ong
- School of Science, Monash University Malaysia , Bandar Sunway, Malaysia.,Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia , Bandar Sunway, Malaysia
| | - Jun Rong Khoo
- School of Science, Monash University Malaysia , Bandar Sunway, Malaysia
| | - Calvin Bok Sun Goh
- School of Science, Monash University Malaysia , Bandar Sunway, Malaysia.,Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia , Bandar Sunway, Malaysia
| | - Jia Wei Hor
- Department of Medicine, Faculty of Medicine, University of Malaya , Kuala Lumpur, Malaysia
| | - Sui Mae Lee
- School of Science, Monash University Malaysia , Bandar Sunway, Malaysia.,Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia , Bandar Sunway, Malaysia
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Ospina-Villa JD, Cisneros-Sarabia A, Sánchez-Jiménez MM, Marchat LA. Current Advances in the Development of Diagnostic Tests based on Aptamers in Parasitology: A Systematic Review. Pharmaceutics 2020; 12:pharmaceutics12111046. [PMID: 33142793 PMCID: PMC7693570 DOI: 10.3390/pharmaceutics12111046] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/25/2020] [Accepted: 10/27/2020] [Indexed: 02/07/2023] Open
Abstract
Aptamers are single-stranded DNA or RNA sequences of 20–80 nucleotides that interact with different targets such as: proteins, ions, viruses, or toxins, through non-covalent interactions and their unique three-dimensional conformation. They are obtained in vitro by the systematic evolution of ligands by exponential enrichment (SELEX). Because of their ability of target recognition with high specificity and affinity, aptamers are usually compared to antibodies. However, they present many advantages that make them promising molecules for the development of new methods for the diagnosis and treatment of human diseases. In medical parasitology, aptamers also represent an attractive alternative for the implementation of new parasite detection methods, easy to apply in endemic regions. The aim of this study was to describe the current advances in the development of diagnostic tests based on aptamers in parasitology. For this, articles were selected following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, with specific inclusion and exclusion criteria. The 26 resulting articles deal with the use of aptamers for the detection of six important protozoa that affect human health. This systematic review clearly demonstrates the specificity, sensitivity and selectivity of aptamers and aptasensors, that certainly will soon become standard methods in medical parasitology.
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Affiliation(s)
- Juan David Ospina-Villa
- Instituto Colombiano de Medicina Tropical, Universidad CES, Sabaneta CP 055450, Antioquia, Colombia; (J.D.O.-V.); (M.M.S.-J.)
| | - Alondra Cisneros-Sarabia
- ENMH, Instituto Politécnico Nacional, Guillermo Massieu Helguera 239, Fracc. La Escalera, Ticomán, Del. Gustavo A. Madero, Mexico City CP 07320, Mexico;
| | - Miryan Margot Sánchez-Jiménez
- Instituto Colombiano de Medicina Tropical, Universidad CES, Sabaneta CP 055450, Antioquia, Colombia; (J.D.O.-V.); (M.M.S.-J.)
| | - Laurence A. Marchat
- ENMH, Instituto Politécnico Nacional, Guillermo Massieu Helguera 239, Fracc. La Escalera, Ticomán, Del. Gustavo A. Madero, Mexico City CP 07320, Mexico;
- Correspondence: ; Tel.: +52-55-5729-6300 (ext. 55543)
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Aptamers as a novel diagnostic and therapeutic tool and their potential use in parasitology. ACTA ACUST UNITED AC 2020; 40:148-165. [PMID: 32463617 PMCID: PMC7449109 DOI: 10.7705/biomedica.4765] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Indexed: 02/07/2023]
Abstract
Los aptámeros son secuencias de ADN o ARN de cadena sencilla que adoptan la forma de estructuras tridimensionales únicas, lo cual les permite reconocer un blanco específico con gran afinidad. Sus usos potenciales abarcan, entre otros, el diagnóstico de enfermedades, el desarrollo de nuevos agentes terapéuticos, la detección de riesgos alimentarios, la producción de biosensores, la detección de toxinas, el transporte de fármacos en el organismo y la señalización de nanopartículas. El pegaptanib es el único aptámero aprobado para uso comercial por la Food and Drug Administration (FDA). Otros aptámeros para el tratamiento de enfermedades están en la fase clínica de desarrollo. En parasitología, se destacan los estudios que se vienen realizando en Leishmania spp., con la obtención de aptámeros que reconocen la proteína de unión a poliA (LiPABP) y que pueden tener potencial utilidad en la investigación, el diagnóstico y el tratamiento de la leishmaniasis. En cuanto a la malaria, se han obtenido aptámeros que permiten identificar eritrocitos infectados e inhiben la formación de rosetas, y otros que prometen ser alternativas para el diagnóstico al detectar de forma específica la proteína lactato deshidrogenasa (PfLDH). Para Cryptosporidium parvuum se han seleccionado aptámeros que detectan ooquistes a partir de alimentos o aguas contaminadas. Para Entamoeba histolytica se han aislado dos aptámeros llamados C4 y C5, que inhiben la proliferación in vitro de los trofozoítos y tienen potencial terapéutico. Los aptámeros contra Trypanosoma cruzi inhiben la invasión de células LLC-MK2 (de riñón de mono) en un 50 a 70 % y aquellos contra T. brucei transportan moléculas tóxicas al lisosoma parasitario como una novedosa estrategia terapéutica. Los datos recopilados en esta revisión destacan los aptámeros como una alternativa para la investigación, el diagnóstico y el tratamiento contra parásitos de interés nacional.
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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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13
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Afrasiabi S, Pourhajibagher M, Raoofian R, Tabarzad M, Bahador A. Therapeutic applications of nucleic acid aptamers in microbial infections. J Biomed Sci 2020; 27:6. [PMID: 31900238 PMCID: PMC6941257 DOI: 10.1186/s12929-019-0611-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 12/19/2019] [Indexed: 02/07/2023] Open
Abstract
Today, the treatment of bacterial infections is a major challenge, due to growing rate of multidrug-resistant bacteria, complication of treatment and increased healthcare costs. Moreover, new treatments for bacterial infections are limited. Oligonucleotide aptamers are single stranded DNAs or RNAs with target-selective high-affinity feature, which considered as nucleic acid-based affinity ligands, replacing monoclonal antibodies. The aptamer-based systems have been found to be talented tools in the treatment of microbial infections, regarding their promising anti-biofilm and antimicrobial activities; they can reduce or inhibit the effects of bacterial toxins, and inhibit pathogen invasion to immune cell, as well as they can be used in drug delivery systems. The focus of this review is on the therapeutic applications of aptamers in infections. In this regard, an introduction of infections and related challenges were presented, first. Then, aptamer definition and selection, with a brief history of aptamers development against various pathogens and toxins were reviewed. Diverse strategies of aptamer application in drug delivery, as well as, the effect of aptamers on the immune system, as the main natural agents of human defense against pathogens, were also discussed. Finally, the future trends in clinical applications of this technology were discussed.
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Affiliation(s)
- Shima Afrasiabi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Pourhajibagher
- Dental Research Center, Dentistry Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Raoofian
- Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran
| | - Maryam Tabarzad
- Protein Technology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Abbas Bahador
- Oral Microbiology Laboratory, Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
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14
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Nagaraja S, Ankri S. Target identification and intervention strategies against amebiasis. Drug Resist Updat 2019; 44:1-14. [PMID: 31112766 DOI: 10.1016/j.drup.2019.04.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Revised: 04/27/2019] [Accepted: 04/30/2019] [Indexed: 12/22/2022]
Abstract
Entamoeba histolytica is the etiological agent of amebiasis, which is an endemic parasitic disease in developing countries and is the cause of approximately 70,000 deaths annually. E. histolytica trophozoites usually reside in the colon as a non-pathogenic commensal in most infected individuals (90% of infected individuals are asymptomatic). For unknown reasons, these trophozoites can become virulent and invasive, cause amebic dysentery, and migrate to the liver where they cause hepatocellular damage. Amebiasis is usually treated either by amebicides which are classified as (a) luminal and are active against the luminal forms of the parasite, (b) tissue and are effective against those parasites that have invaded tissues, and (c) mixed and are effective against the luminal forms of the parasite and those forms which invaded the host's tissues. Of the amebicides, the luminal amebicide, metronidazole (MTZ), is the most widely used drug to treat amebiasis. Although well tolerated, concerns about its adverse effects and the possible emergence of MTZ-resistant strains of E. histolytica have led to the development of new therapeutic strategies against amebiasis. These strategies include improving the potency of existing amebicides, discovering new uses for approved drugs (repurposing of existing drugs), drug rediscovery, vaccination, drug targeting of essential E. histolytica components, and the use of probiotics and bioactive natural products. This review examines each of these strategies in the light of the current knowledge on the gut microbiota of patients with amebiasis.
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Affiliation(s)
- Shruti Nagaraja
- Department of Molecular Microbiology, Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Serge Ankri
- Department of Molecular Microbiology, Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel.
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15
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Zhang Y, Lai BS, Juhas M. Recent Advances in Aptamer Discovery and Applications. Molecules 2019; 24:molecules24050941. [PMID: 30866536 PMCID: PMC6429292 DOI: 10.3390/molecules24050941] [Citation(s) in RCA: 335] [Impact Index Per Article: 67.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 03/03/2019] [Accepted: 03/04/2019] [Indexed: 12/22/2022] Open
Abstract
Aptamers are short, single-stranded DNA, RNA, or synthetic XNA molecules that can be developed with high affinity and specificity to interact with any desired targets. They have been widely used in facilitating discoveries in basic research, ensuring food safety and monitoring the environment. Furthermore, aptamers play promising roles as clinical diagnostics and therapeutic agents. This review provides update on the recent advances in this rapidly progressing field of research with particular emphasis on generation of aptamers and their applications in biosensing, biotechnology and medicine. The limitations and future directions of aptamers in target specific delivery and real-time detection are also discussed.
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Affiliation(s)
- Yang Zhang
- College of Science, Harbin Institute of Technology, Shenzhen 518055, China.
| | - Bo Shiun Lai
- School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA.
| | - Mario Juhas
- Institute of Medical Microbiology, University of Zurich, Gloriastrasse 28/30, CH-8006 Zurich, Switzerland.
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16
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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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17
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Ospina-Villa JD, García-Contreras J, Rosas-Trigueros JL, Ramírez-Moreno E, López-Camarillo C, Zamora-López B, Marchat LA, Zamorano-Carrillo A. Importance of amino acids Leu135 and Tyr236 for the interaction between EhCFIm25 and RNA: a molecular dynamics simulation study. J Mol Model 2018; 24:202. [PMID: 30003410 DOI: 10.1007/s00894-018-3729-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 06/19/2018] [Indexed: 11/28/2022]
Abstract
The CFIm25 subunit of the heterotetrameric cleavage factor Im (CFIm) is a critical factor in the formation of the poly(A) tail at mRNA 3' end, regulating the recruitment of polyadenylation factors, poly(A) site selection, and cleavage/polyadenylation reactions. We previously reported the homologous protein (EhCFIm25) in Entamoeba histolytica, the protozoan causing human amoebiasis, and showed the relevance of conserved Leu135 and Tyr236 residues for RNA binding. We also identified the GUUG sequence as the recognition site of EhCFIm25. To understand the interactions network that allows the EhCFIm25 to maintain its three-dimensional structure and function, here we performed molecular dynamics simulations of wild-type (WT) and mutant proteins, alone or interacting with the GUUG molecule. Our results indicated that in the presence of the GUUG sequence, WT converged more quickly to lower RMSD values in comparison with mutant proteins. However, RMSF values showed that movements of amino acids of WT and EhCFIm25*L135 T were almost identical, interacting or not with the GUUG molecule. Interestingly, EhCFIm25*L135 T, which is the only mutant with a slight RNA binding activity experimentally, presents the same stabilization of bend structures and alpha helices as WT, notably in the C-terminus. Moreover, WT and EhCFIm25*L135 T presented almost the same number of contacts that mainly involve lysine residues interacting with the G4 nucleotide. Overall, our data proposed a clear description of the structural and mechanistic data that govern the RNA binding capacity of EhCFIm25.
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Affiliation(s)
- Juan David Ospina-Villa
- Programa Institucional de Biomedicina Molecular, Programa de Doctorado en Ciencias en Biotecnología, ENMH, Instituto Politécnico Nacional, Guillermo Massieu Helguera 239, Fracc. La Escalera, Ticomán, Del. Gustavo A. Madero, CP 07320, Ciudad de México, Mexico
| | - Juan García-Contreras
- Programa Institucional de Biomedicina Molecular, Programa de Doctorado en Ciencias en Biotecnología, ENMH, Instituto Politécnico Nacional, Guillermo Massieu Helguera 239, Fracc. La Escalera, Ticomán, Del. Gustavo A. Madero, CP 07320, Ciudad de México, Mexico
| | - Jorge Luis Rosas-Trigueros
- Laboratorio Transdisciplinario de Investigación en Sistemas Evolutivos, ESCOM, Instituto Politécnico Nacional, Av. Juan de Dios Bátiz esq. Miguel Othón de Mendizábal, Col. Lindavista, Del. Gustavo A. Madero, CP 07738, Ciudad de México, Mexico
| | - Esther Ramírez-Moreno
- Programa Institucional de Biomedicina Molecular, Programa de Doctorado en Ciencias en Biotecnología, ENMH, Instituto Politécnico Nacional, Guillermo Massieu Helguera 239, Fracc. La Escalera, Ticomán, Del. Gustavo A. Madero, CP 07320, Ciudad de México, Mexico
| | - César López-Camarillo
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, San Lorenzo 290, Colonia del Valle, CP 03100, Ciudad de México, Mexico
| | - Beatriz Zamora-López
- Departamento de Psiquiatría y Salud Mental, Facultad de Medicina, UNAM, Circuito Interior y Cerro del Agua, CP 04510, Ciudad de México, Mexico
| | - Laurence A Marchat
- Programa Institucional de Biomedicina Molecular, Programa de Doctorado en Ciencias en Biotecnología, ENMH, Instituto Politécnico Nacional, Guillermo Massieu Helguera 239, Fracc. La Escalera, Ticomán, Del. Gustavo A. Madero, CP 07320, Ciudad de México, Mexico
| | - Absalom Zamorano-Carrillo
- Programa Institucional de Biomedicina Molecular, Programa de Doctorado en Ciencias en Biotecnología, ENMH, Instituto Politécnico Nacional, Guillermo Massieu Helguera 239, Fracc. La Escalera, Ticomán, Del. Gustavo A. Madero, CP 07320, Ciudad de México, Mexico.
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Valdés-Flores J, López-Rosas I, López-Camarillo C, Ramírez-Moreno E, Ospina-Villa JD, Marchat LA. Life and Death of mRNA Molecules in Entamoeba histolytica. Front Cell Infect Microbiol 2018; 8:199. [PMID: 29971219 PMCID: PMC6018208 DOI: 10.3389/fcimb.2018.00199] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 05/28/2018] [Indexed: 02/05/2023] Open
Abstract
In eukaryotic cells, the life cycle of mRNA molecules is modulated in response to environmental signals and cell-cell communication in order to support cellular homeostasis. Capping, splicing and polyadenylation in the nucleus lead to the formation of transcripts that are suitable for translation in cytoplasm, until mRNA decay occurs in P-bodies. Although pre-mRNA processing and degradation mechanisms have usually been studied separately, they occur simultaneously and in a coordinated manner through protein-protein interactions, maintaining the integrity of gene expression. In the past few years, the availability of the genome sequence of Entamoeba histolytica, the protozoan parasite responsible for human amoebiasis, coupled to the development of the so-called “omics” technologies provided new opportunities for the study of mRNA processing and turnover in this pathogen. Here, we review the current knowledge about the molecular basis for splicing, 3′ end formation and mRNA degradation in amoeba, which suggest the conservation of events related to mRNA life throughout evolution. We also present the functional characterization of some key proteins and describe some interactions that indicate the relevance of cooperative regulatory events for gene expression in this human parasite.
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Affiliation(s)
- Jesús Valdés-Flores
- Departamento de Bioquímica, CINVESTAV, Ciudad de Mexico, Mexico City, Mexico
| | - Itzel López-Rosas
- CONACyT Research Fellow - Colegio de Postgraduados Campus Campeche, Campeche, Mexico
| | - César López-Camarillo
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México Ciudad de Mexico, Mexico City, Mexico
| | - Esther Ramírez-Moreno
- Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional Ciudad de Mexico, Mexico City, Mexico
| | - Juan D Ospina-Villa
- Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional Ciudad de Mexico, Mexico City, Mexico
| | - Laurence A Marchat
- Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional Ciudad de Mexico, Mexico City, Mexico
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