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Meza-Espinoza JP, González-García JR, Nieto-Marín N, Patrón-Baro LI, González-Arreola RM, Arámbula-Meraz E, Benítez-Pascual J, De la Herrán-Arita AK, Norzagaray-Valenzuela CD, Valdez-Flores MA, Carrillo-Cázares TA, Picos-Cárdenas VJ. Chromosomal instability in a patient with ring chromosome 14 syndrome: a case report. Mol Cytogenet 2024; 17:17. [PMID: 39020403 PMCID: PMC11256661 DOI: 10.1186/s13039-024-00686-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2024] [Accepted: 06/26/2024] [Indexed: 07/19/2024] Open
Abstract
BACKGROUND Ring chromosome 14 syndrome is a rare disorder primarily marked by early-onset epilepsy, microcephaly, distinctive craniofacial features, hypotonia, intellectual disability, and delay in both development and language acquisition. CASE PRESENTATION A 21-year-old woman with a history of epileptic seizures since the age of 1.5 years presented with distinctive craniofacial features, including a prominent and narrow forehead, sparse and short eyebrows, palpebral ptosis, horizontal palpebral fissures, a broad nasal bridge, a prominent nasal tip, a flat philtrum, hypertelorism, midfacial hypoplasia, horizontal labial fissures, a thin upper lip, crowded teeth, an ogival palate, retrognathia, and a wide neck. Additional physical abnormalities included kyphosis, lumbar scoliosis, pectus carinatum, cubitus valgus, thenar and hypothenar hypoplasia, bilateral hallux valgus, shortening of the Achilles tendon on the left foot, and hypoplasia of the labia minora. Chromosomal analysis identified a ring 14 chromosome with breakpoints in p11 and q32.33. An aCGH study revealed a ~ 1.7 Mb deletion on chromosome 14qter, encompassing 23 genes. Genomic instability was evidenced by the presence of micronuclei and aneuploidies involving the ring and other chromosomes. CONCLUSION The clinical features of our patient closely resembled those observed in other individuals with ring chromosome 14 syndrome. The most important point was that we were able to verify an instability of the r(14) chromosome, mainly involving anaphasic lags and its exclusion from the nucleus in the form of a micronucleus.
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Affiliation(s)
| | - Juan Ramón González-García
- División de Genética, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social (IMSS), Guadalajara, Jalisco, México
| | - Nayeli Nieto-Marín
- Maestría en Ciencias en Biomedicina Molecular, Facultad de Medicina, Universidad Autónoma de Sinaloa, Culiacán, Sin, México
| | - Liliana Itzel Patrón-Baro
- Maestría en Ciencias en Biomedicina Molecular, Facultad de Medicina, Universidad Autónoma de Sinaloa, Culiacán, Sin, México
| | | | - Eliakym Arámbula-Meraz
- Facultad de Ciencias Químico-Biológicas, Universidad Autónoma de Sinaloa, Culiacán, Sin, México
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Ewunkem AJ, Deve M, Harrison SH, Muganda PM. Diepoxybutane induces the p53-dependent transactivation of the CCL4 gene that mediates apoptosis in exposed human lymphoblasts. J Biochem Mol Toxicol 2023; 37:e23316. [PMID: 36775894 PMCID: PMC10175094 DOI: 10.1002/jbt.23316] [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: 10/15/2022] [Revised: 12/30/2022] [Accepted: 01/31/2023] [Indexed: 02/14/2023]
Abstract
Diepoxybutane (DEB) is the most toxic metabolite of the environmental chemical 1,3-butadiene. We previously demonstrated the occurrence of DEB-induced p53-mediated apoptosis in human lymphoblasts. The p53 protein functions as a master transcriptional regulator in orchestrating the genomic response to a variety of stress signals. Transcriptomic analysis indicated that C-C chemokine ligand 4 (CCL4) gene expression was elevated in a p53-dependent manner in DEB-exposed p53-proficient TK6 cells, but not in DEB-exposed p53-deficient NH32 cells. Thus, the objective of this study was to determine whether the CCL4 gene is a transcriptional target of p53 and deduce its role in DEB-induced apoptosis in human lymphoblasts. Endogenous and exogenous wild-type p53 transactivated the activity of the CCL4 promoter in DEB-exposed lymphoblasts, but mutant p53 activity on this promoter was reduced by ∼80% under the same experimental conditions. Knockdown of the upregulated CCL4 mRNA levels in p53-proficient TK6 cells inhibited DEB-induced apoptosis by ∼45%-50%. Collectively, these observations demonstrate for the first time that the CCL4 gene is upregulated by wild-type p53 at the transcriptional level, and this upregulation mediates apoptosis in DEB-exposed human lymphoblasts.
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Affiliation(s)
- Akamu J. Ewunkem
- Department of Energy and Environmental Systems, North Carolina Agricultural and Technical State University, Greensboro, NC, 27411 USA
| | - Maya Deve
- Department of Biology, North Carolina Agricultural and Technical State University, Greensboro, NC, 27411 USA
| | - Scott H. Harrison
- Department of Biology, North Carolina Agricultural and Technical State University, Greensboro, NC, 27411 USA
| | - Perpetua M. Muganda
- Department of Biology, North Carolina Agricultural and Technical State University, Greensboro, NC, 27411 USA
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Chen X, Wang CC, Yin J, You ZH. Novel Human miRNA-Disease Association Inference Based on Random Forest. MOLECULAR THERAPY. NUCLEIC ACIDS 2018; 13:568-579. [PMID: 30439645 PMCID: PMC6234518 DOI: 10.1016/j.omtn.2018.10.005] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 07/30/2018] [Accepted: 10/05/2018] [Indexed: 01/23/2023]
Abstract
Since the first microRNA (miRNA) was discovered, a lot of studies have confirmed the associations between miRNAs and human complex diseases. Besides, obtaining and taking advantage of association information between miRNAs and diseases play an increasingly important role in improving the treatment level for complex diseases. However, due to the high cost of traditional experimental methods, many researchers have proposed different computational methods to predict potential associations between miRNAs and diseases. In this work, we developed a computational model of Random Forest for miRNA-disease association (RFMDA) prediction based on machine learning. The training sample set for RFMDA was constructed according to the human microRNA disease database (HMDD) version (v.)2.0, and the feature vectors to represent miRNA-disease samples were defined by integrating miRNA functional similarity, disease semantic similarity, and Gaussian interaction profile kernel similarity. The Random Forest algorithm was first employed to infer miRNA-disease associations. In addition, a filter-based method was implemented to select robust features from the miRNA-disease feature set, which could efficiently distinguish related miRNA-disease pairs from unrelated miRNA-disease pairs. RFMDA achieved areas under the curve (AUCs) of 0.8891, 0.8323, and 0.8818 ± 0.0014 under global leave-one-out cross-validation, local leave-one-out cross-validation, and 5-fold cross-validation, respectively, which were higher than many previous computational models. To further evaluate the accuracy of RFMDA, we carried out three types of case studies for four human complex diseases. As a result, 43 (esophageal neoplasms), 46 (lymphoma), 47 (lung neoplasms), and 48 (breast neoplasms) of the top 50 predicted disease-related miRNAs were verified by experiments in different kinds of case studies. The results of cross-validation and case studies indicated that RFMDA is a reliable model for predicting miRNA-disease associations.
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Affiliation(s)
- Xing Chen
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou 221116, China.
| | - Chun-Chun Wang
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou 221116, China
| | - Jun Yin
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou 221116, China
| | - Zhu-Hong You
- Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Science, Ürümqi 830011, China.
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Eluka-Okoludoh E, Ewunkem AJ, Thorpe S, Blanchard A, Muganda P. Diepoxybutane-induced apoptosis is mediated through the ERK1/2 pathway. Hum Exp Toxicol 2018; 37:1080-1091. [PMID: 29405768 DOI: 10.1177/0960327118755255] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Diepoxybutane (DEB) is the most potent active metabolite of butadiene, a regulated air pollutant. We previously reported the occurrence of DEB-induced, p53-dependent, mitochondrial-mediated apoptosis in human lymphoblasts. The present study investigated the role of the extracellular signal-regulated protein kinases 1 and 2 (ERK1/2) pathway in DEB-induced apoptotic signaling in exposed human lymphoblasts. Activated ERK1/2 and mitogen-activated protein (MAP) kinase/ERK1/2 kinase (MEK) levels were significantly upregulated in DEB-exposed human lymphoblasts. The MEK inhibitor PD98059 and ERK1/2 siRNA significantly inhibited apoptosis, ERK1/2 activation, as well as p53 and phospho-p53 (serine-15) levels in human lymphoblasts undergoing DEB-induced apoptosis. Collectively, these results demonstrate that DEB induces apoptotic signaling through the MEK-ERK1/2-p53 pathway in human lymphoblasts. This is the first report implicating the activation of the ERK1/2 pathway and its subsequent role in mediating DEB-induced apoptotic signaling in human lymphoblasts. These findings contribute towards the understanding of DEB toxicity, as well as the signaling pathways mediating DEB-induced apoptosis in human lymphoblasts.
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Affiliation(s)
- E Eluka-Okoludoh
- 1 Department of Biology, North Carolina A&T State University, Greensboro, NC, USA.,2 Department of Energy and Environmental Systems, North Carolina A&T State University, Greensboro, North Carolina, USA
| | - A J Ewunkem
- 2 Department of Energy and Environmental Systems, North Carolina A&T State University, Greensboro, North Carolina, USA
| | - S Thorpe
- 1 Department of Biology, North Carolina A&T State University, Greensboro, NC, USA
| | - A Blanchard
- 1 Department of Biology, North Carolina A&T State University, Greensboro, NC, USA
| | - P Muganda
- 1 Department of Biology, North Carolina A&T State University, Greensboro, NC, USA
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