1
|
Walker A, Wang X, Kim YM, Lu X, Taylor A, Demarzo D, Li S, Pang H. Molecular cytogenetic characterization of partial trisomy of the long arm of chromosome 11 in a patient with multiple congenital anomalies. Mol Cytogenet 2022; 15:17. [PMID: 35440058 PMCID: PMC9019979 DOI: 10.1186/s13039-022-00595-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 03/11/2022] [Indexed: 11/11/2022] Open
Abstract
Background Partial trisomy of the long arm of chromosome 11 is a rare cytogenetic abnormality. It has been characterized by variable sized duplications that lead to a range of phenotypes including growth retardation, developmental delay/intellectual disability, and distinctive craniofacial abnormalities. Congenital heart defects, skeletal abnormalities, urogenital anomalies, and hypotonia are found in some affected individuals. Methods We describe a 16-year-old patient presented with most of the hallmark phenotypes of trisomy 11q syndrome as well as exhibiting symptoms of hearing loss, seizures, and abnormal endocrinological and ophthalmological findings. Routine chromosome analysis and subsequent chromosomal microarray analysis (CMA) were performed to detect genetic abnormalities in this patient. Results We identified an abnormal male karyotype with a derivative chromosome 4 due to an unbalanced translocation between chromosomes 4 and chromosome 11. The CMA results revealed a 56 Mb duplication of chromosome 11q14.1-qter and a 874 Kb terminal deletion of the short arm of chromosome 4. Conclusion A genomic imbalance resulting in partial trisomy 11q was found in a patient with multiple congenital anomalies. We compared the phenotypes of all known “pure” trisomy 11q cases in the literature and find that trisomy 11q23-qter is both recurrent and the most common cytogenetic abnormality found in the reported cases. It is associated with the core features of trisomy 11q syndrome. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13039-022-00595-0.
Collapse
Affiliation(s)
- Austin Walker
- College of Medicine, University of Oklahoma Health Sciences Center, 941 Stanton L. Young Boulevard, Room 241, Oklahoma City, OK, 73104, USA
| | - Xianfu Wang
- Genetics Laboratory, Oklahoma Children's Hospital, OU Health, 1122 NE 13th Street, Suite 1400, Oklahoma City, OK, 73104, USA
| | - Young Mi Kim
- College of Medicine, University of Oklahoma Health Sciences Center, 941 Stanton L. Young Boulevard, Room 241, Oklahoma City, OK, 73104, USA.,Genetics Laboratory, Oklahoma Children's Hospital, OU Health, 1122 NE 13th Street, Suite 1400, Oklahoma City, OK, 73104, USA
| | - Xianglan Lu
- Genetics Laboratory, Oklahoma Children's Hospital, OU Health, 1122 NE 13th Street, Suite 1400, Oklahoma City, OK, 73104, USA
| | - Ashley Taylor
- Pediatric Specialties Clinic, Oklahoma Children's Hospital, OU Health, 1200 N. Children's Ave., Suite 5D, Oklahoma City, OK, 73104, USA
| | - Danielle Demarzo
- College of Medicine, University of Oklahoma Health Sciences Center, 941 Stanton L. Young Boulevard, Room 241, Oklahoma City, OK, 73104, USA.,Pediatric Specialties Clinic, Oklahoma Children's Hospital, OU Health, 1200 N. Children's Ave., Suite 5D, Oklahoma City, OK, 73104, USA
| | - Shibo Li
- College of Medicine, University of Oklahoma Health Sciences Center, 941 Stanton L. Young Boulevard, Room 241, Oklahoma City, OK, 73104, USA
| | - Hui Pang
- College of Medicine, University of Oklahoma Health Sciences Center, 941 Stanton L. Young Boulevard, Room 241, Oklahoma City, OK, 73104, USA. .,Genetics Laboratory, Oklahoma Children's Hospital, OU Health, 1122 NE 13th Street, Suite 1400, Oklahoma City, OK, 73104, USA.
| |
Collapse
|
2
|
Ruiz MF, Gennaro MV, Bastone LC, Godoy AR, Torruella M, Perez GR. Molecular biomarkers and integrated pathological diagnosis in the reclassification of gliomas. Mol Clin Oncol 2021; 15:150. [PMID: 34141429 DOI: 10.3892/mco.2021.2312] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 01/21/2021] [Indexed: 12/21/2022] Open
Abstract
The present study aimed to evaluate the impact caused by the 2016 World Health Organization (WHO) diagnostic classification of gliomas in 139 patients studied in Argentina. Formalin-fixed paraffin-embedded tissues were used for histological and immunohistochemical analysis [glial fibrillary acidic protein, KI67, synaptophysin and isocitrate dehydrogenase (IDH)1-R132H]. DNA from formalin-fixed paraffin-embedded tissues was used for molecular analysis: 1p/19q co-deletion and mutation status of the IDH gene. These experiments were performed by direct Sanger sequencing and multiplex ligation-dependent probe amplification. According to the new classification, diagnoses included oligodendroglioma IDH-mutant and 1p/19q co-deletion (4.20%), anaplastic oligodendroglioma IDH-mutant and 1p/19q co-deletion (2.52%), diffuse astrocytoma IDH-mutant (6.72%), diffuse astrocytoma IDH-wild type (1.68%), anaplastic astrocytoma IDH-mutant (5.04%), anaplastic astrocytoma IDH-wild type (8.40%), glioblastoma IDH-mutant (5.88%) and glioblastoma IDH-wild type (65.56%). Regarding tumor histology, 60% of oligodendrogliomas, 35% of astrocytoma and 100% of unclassified gliomas were re-classified, while glioblastomas maintained their initial classification. Additionally, the present study evaluated the prognostic value of the histological grade for the 2007 and 2016 WHO classifications of gliomas. The histological subgroup associated with longer overall survival (OS) was grade II glioma (OS-2007WHO, 35.6 months; and OS-2016WHO, 47.7 months). Glioblastoma was the subgroup associated with a poor outcome (OS-2007WHO, 10.4 months; and OS-2016WHO, 11.1 months). The present study evaluated the OS of tumor grade subgroups with respect to their IDH status. For all subgroups, IDH-mutant tumors were associated with an improved prognosis compared with IDH-wild type tumors. The results suggested that the incorporation of molecular biomarkers in the new WHO classification improves tumor characterization and prognostic value of the subgroups.
Collapse
Affiliation(s)
- María Fernanda Ruiz
- Center for Pathological Diagnosis SRL (Gamma Group), Rosario, Santa Fe 2000, Argentina.,Faculty of Medical Sciences, National University of Rosario, National University of Rosario, Rosario, Santa Fe 2000, Argentina
| | - María Verónica Gennaro
- Center for Pathological Diagnosis SRL (Gamma Group), Rosario, Santa Fe 2000, Argentina.,Department of Pathological Anatomy, Emergency Hospital 'Dr Clemente Alvarez' (HECA), National University of Rosario, Rosario, Santa Fe 2000, Argentina
| | - Laura C Bastone
- Department of Molecular Diagnostics, Gammalab/Private Hospital of Rosario (Gamma Group), Rosario, Santa Fe 2000, Argentina
| | - Alicia R Godoy
- Center for Pathological Diagnosis SRL (Gamma Group), Rosario, Santa Fe 2000, Argentina
| | - Mónica Torruella
- Department of Molecular Diagnostics, Gammalab/Private Hospital of Rosario (Gamma Group), Rosario, Santa Fe 2000, Argentina
| | - Germán R Perez
- Department of Molecular Diagnostics, Gammalab/Private Hospital of Rosario (Gamma Group), Rosario, Santa Fe 2000, Argentina.,Department of Microbiology, Faculty of Biochemical and Pharmaceutical Sciences, National University of Rosario, Rosario, Santa Fe 2000, Argentina
| |
Collapse
|
3
|
Shim JO, Yang HR, Moon JS, Chang JY, Ko JS, Park SS, Seo JK. Multiplex Ligation-dependent Probe Amplification Analysis Subsequent to Direct DNA Full Sequencing for Identifying ATP7B Mutations and Phenotype Correlations in Children with Wilson Disease. J Korean Med Sci 2018; 33:e177. [PMID: 29930488 PMCID: PMC6010744 DOI: 10.3346/jkms.2018.33.e177] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 04/17/2018] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Mutations in ATP7B cause Wilson disease (WD). However, direct DNA full sequencing cannot detect all mutations in patients with WD. Multiplex ligation-dependent probe amplification (MLPA) analysis is reportedly useful in increasing the diagnostic yield in other genetic disorders with large deletions or insertions. The aim of this study was to evaluate whether the detection rate of ATP7B mutations can be increased by using MLPA. METHODS We enrolled 114 children with WD from 104 unrelated families based on biochemical tests and direct DNA full sequencing. The patients with one or zero mutant allele were investigated using MLPA. We analyzed phenotypic correlations. RESULTS Total allele frequency by full sequencing was 87.5%. Full sequencing revealed two mutant alleles in 80 of 104 unrelated children. One mutant allele was detected in 22 children, and no mutations were found in two children. Novel mutations including small deletions with frameshift mutations were identified by DNA sequencing. MLPA revealed no gross deletion or duplication in 24 children with one or zero mutant alleles. The number of detected mutations was not associated with hepatic manifestation, age of onset, Kayser-Fleischer ring, ceruloplasmin, and urinary Cu concentrations. CONCLUSION MLPA showed a limited role to increase the mutation detection rate in children who do not receive a definite genetic diagnosis of WD through DNA full sequencing. This finding suggests that large deletions or duplications might be extremely rare in WD. Further development is needed to improve the genetic diagnosis of WD.
Collapse
Affiliation(s)
- Jung Ok Shim
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Korea
- Department of Pediatrics, Korea University College of Medicine, Seoul, Korea
| | - Hye Ran Yang
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Korea
| | - Jin Soo Moon
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Korea
| | - Ju Young Chang
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Korea
| | - Jae Sung Ko
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Korea
| | - Sung Sup Park
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Jeong Kee Seo
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Korea
| |
Collapse
|
4
|
Yang J, Li W, Zhang Z, Shen J, Zhang N, Yang M, Yang M, Yu Y. PSCArs2294008 T polymorphism increases the risk of bladder cancer in Bai, Dai, and Han ethnicity in China and a potential mechanism. Genes Genomics 2018; 40:531-541. [PMID: 29892961 DOI: 10.1007/s13258-018-0653-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 01/09/2018] [Indexed: 01/31/2023]
Abstract
The aim of this study is to make a comparative evaluation on association of PSCArs2294008 C/T polymorphism with the risk of bladder cancer in Bai, Dai, and Han people in China. A potential mechanism of the T allele risk was also investigated. T allele increased the occurring risk of bladder cancer in Han (OR 1.34; 95% CI 1.17-1.69), Dai, (OR 1.33; 95% CI 1.12-1.70), and Bai (OR 1.14; 95% CI 1.08-1.57) people. T genotype was also observed to associate with invasive bladder cancer in all the three populations (Bai, OR 1.15, 95% CI 1.07-1.87; Dai, OR 1.17, 95% CI 1.05-2.23; Han, OR 1.22, 95% CI 1.10-2.09). PSCA m-RNA levels in T genotype bladder cancer tissues were significantly lower than those in C genotype. An enhancement of PSCA m-RNA level by over-expressing C or T genotype in bladder cancer cells both decreased the cell proliferation and migration, but not affected cell cycle. The increased cell apoptasis due to the over-expression of the two variants was observed. Those change of cell proliferation, migration, and apoptasis was more remarkable in over-expressed C genotype cells than those in over-expressed T genotype. T genotype was genetically high risk to the occurrence of bladder cancer. The decreased PSCA m-RNA levels were involved in the progress of bladder cancer. T allele takes more responsibility for PSCA m-RNA down-regulation to promote cell proliferation and migration and hinder cell apoptasis, thus leading to a higher risk.
Collapse
Affiliation(s)
- Junfeng Yang
- Department of Urology, First People's Hospital of Yunnan Province, Kunming, 650032, Yunnan, People's Republic of China
| | - Wei Li
- Department of Urology, First People's Hospital of Yunnan Province, Kunming, 650032, Yunnan, People's Republic of China
| | - Zhuorui Zhang
- Department of Urology, First People's Hospital of Yunnan Province, Kunming, 650032, Yunnan, People's Republic of China
| | - Jie Shen
- Department of Urology, First People's Hospital of Yunnan Province, Kunming, 650032, Yunnan, People's Republic of China
| | - Ningnan Zhang
- Department of Urology, First People's Hospital of Yunnan Province, Kunming, 650032, Yunnan, People's Republic of China
| | - Min Yang
- Department of Urology, First People's Hospital of Yunnan Province, Kunming, 650032, Yunnan, People's Republic of China
| | - Maolin Yang
- Department of Urology, First People's Hospital of Yunnan Province, Kunming, 650032, Yunnan, People's Republic of China
| | - Yanhong Yu
- Department of Urology, First People's Hospital of Yunnan Province, Kunming, 650032, Yunnan, People's Republic of China.
| |
Collapse
|
5
|
Mazza A, Klockmeier K, Wanker E, Sharan R. An integer programming framework for inferring disease complexes from network data. Bioinformatics 2017; 32:i271-i277. [PMID: 27307626 PMCID: PMC4908347 DOI: 10.1093/bioinformatics/btw263] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
MOTIVATION Unraveling the molecular mechanisms that underlie disease calls for methods that go beyond the identification of single causal genes to inferring larger protein assemblies that take part in the disease process. RESULTS Here, we develop an exact, integer-programming-based method for associating protein complexes with disease. Our approach scores proteins based on their proximity in a protein-protein interaction network to a prior set that is known to be relevant for the studied disease. These scores are combined with interaction information to infer densely interacting protein complexes that are potentially disease-associated. We show that our method outperforms previous ones and leads to predictions that are well supported by current experimental data and literature knowledge. AVAILABILITY AND IMPLEMENTATION The datasets we used, the executables and the results are available at www.cs.tau.ac.il/roded/disease_complexes.zip CONTACT roded@post.tau.ac.il.
Collapse
Affiliation(s)
- Arnon Mazza
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | | | - Erich Wanker
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Roded Sharan
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| |
Collapse
|
6
|
Li G, Ma D, Chen Y. Cellular functions of programmed cell death 5. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:572-80. [PMID: 26775586 DOI: 10.1016/j.bbamcr.2015.12.021] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Revised: 12/24/2015] [Accepted: 12/29/2015] [Indexed: 01/01/2023]
Abstract
Programmed cell death 5 (PDCD5) was originally identified as an apoptosis-accelerating protein that is widely expressed and has been well conserved during the process of evolution. PDCD5 has complex biological functions, including programmed cell death and immune regulation. It can accelerate apoptosis in different type of cells in response to different stimuli. During this process, PDCD5 rapidly translocates from the cytoplasm to the nucleus. PDCD5 regulates the activities of TIP60, HDAC3, MDM2 and TP53 transcription factors. These proteins form part of a signaling network that is disrupted in most, if not all, cancer cells. Recent evidence suggests that PDCD5 participates in immune regulation by promoting regulatory T cell function via the PDCD5-TIP60-FOXP3 pathway. The stability and expression of PDCD5 are finely regulated by other molecules, such as NF-κB p65, OTUD5, YAF2 and DNAJB1. PDCD5 is phosphorylated by CK2 at Ser119, which is required for nuclear translocation in response to genotoxic stress. In this review, we describe what is known about PDCD5 and its cellular functions.
Collapse
Affiliation(s)
- Ge Li
- Department of Immunology, Peking University School of Basic Medical Sciences, 38 Xueyuan Road, Beijing 100191, China; Center for Human Disease Genomics, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Dalong Ma
- Department of Immunology, Peking University School of Basic Medical Sciences, 38 Xueyuan Road, Beijing 100191, China; Center for Human Disease Genomics, Peking University, 38 Xueyuan Road, Beijing 100191, China
| | - Yingyu Chen
- Department of Immunology, Peking University School of Basic Medical Sciences, 38 Xueyuan Road, Beijing 100191, China; Center for Human Disease Genomics, Peking University, 38 Xueyuan Road, Beijing 100191, China.
| |
Collapse
|