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Hu J, Wang M, Xiang R. ZAP70: A Key Gene Identified by Differential Expression Analysis for Early Diagnosis of Fetuses with Emanuel Syndrome. Biochem Genet 2024:10.1007/s10528-024-10808-3. [PMID: 38687434 DOI: 10.1007/s10528-024-10808-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 04/08/2024] [Indexed: 05/02/2024]
Abstract
Emanuel syndrome is a rare autosomal disorder characterized by microcephaly, heart defects, cleft palate and developmental delay. However, there is a lack of specific prenatal screening for Emanuel syndrome. To screen for early diagnostic marker genes in fetuses with karyotype+der[22]t(11;22)(q23;q11) of Emanuel syndrome. Transcriptome sequencing and clinical trait data of t(11;22)(q23;q11) translocation samples were screened from the GEO database. The differentially expressed genes (DEGs) were screened by principal component analysis of gene expression by R package, and intersections were taken with balanced and unbalanced DEGs. Then, the correlation with clinical traits was determined by WGCNA analysis, GO and KEGG enrichment analysis, and then univariate Cox analysis and Lasso analysis were performed to obtain the key genes. The core regulatory genes were obtained after protein-protein interaction (PPI) network analysis. A total of 50 DEGs were obtained after differential analysis. WGCNA analysis showed that DEG was associated with the chromosomal imbalance and age module. GO and KEGG enrichment analyses showed candidate genes were associated with exocytic vesicle membrane, synaptic vesicle membranes, glycoprotein complex, dystrophin-associated glycoprotein complex and malaria. COX and Lasso analyses yielded 5 hub genes, including ZBED9, RGS20, SGCB, ETV5, and ZAP70. The results of PPI identified the key regulatory gene associated with chromosomal imbalance as the ZAP70 gene. ZAP70 may be a key gene for early diagnosis of Emanuel syndrome in fetuses with+der[22]t(11;22)(q23;q11) karyotype.
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Affiliation(s)
- Jing Hu
- Department of Obstetrics and Reproductive Medicine Center, The Affiliated Hospital of Yunnan University, Kunming, 650021, Yunnan, China.
| | - Mengyue Wang
- Department of Obstetrics and Reproductive Medicine Center, The Affiliated Hospital of Yunnan University, Kunming, 650021, Yunnan, China
| | - Ruiyao Xiang
- Department of Obstetrics and Reproductive Medicine Center, The Affiliated Hospital of Yunnan University, Kunming, 650021, Yunnan, China
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2
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Soster E, Dyr B, Caldwell S, Sussman A, Magharyous H. Prenatal cfDNA Screening for Emanuel Syndrome and Other Unbalanced Products of Conception in Carriers of the Recurrent Balanced Translocation t(11;22): One Laboratory's Retrospective Experience. Genes (Basel) 2023; 14:1924. [PMID: 37895273 PMCID: PMC10606745 DOI: 10.3390/genes14101924] [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: 08/31/2023] [Revised: 09/25/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023] Open
Abstract
Prenatal cell-free DNA screening (cfDNA) can identify fetal chromosome abnormalities beyond common trisomies. Emanuel syndrome (ES), caused by an unbalanced translocation between chromosomes 11 and 22, has lacked a reliable prenatal screening option for families with a carrier parent. A cohort of cases (n = 46) sent for cfDNA screening with indications and/or results related to ES was queried; diagnostic testing and pregnancy outcomes were requested and analyzed. No discordant results were reported or suspected; there were ten true positives with diagnostic confirmation, six likely concordant positives based on known translocations and consistent cfDNA data, and twenty-six true negatives, by diagnostic testing or birth outcomes. For cases with parental testing, all affected ES cases had maternal translocation carriers. Expanded cfDNA may provide reassurance for t(11;22) carriers with screen negative results, and screen positive results appear to reflect a likely affected fetus, especially with a known maternal translocation. Current society guidelines support the use of expanded cfDNA screening in specific circumstances, such as for translocation carriers, with appropriate counseling. Diagnostic testing is recommended for prenatal diagnosis of ES and other chromosome abnormalities in pregnancy. To our knowledge, this cohort is the largest published group of cases with prenatal screening for carriers of t(11;22).
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Affiliation(s)
- Erica Soster
- Labcorp, La Jolla, San Diego, 92121 CA, USA; (B.D.); (S.C.); (H.M.)
| | - Brittany Dyr
- Labcorp, La Jolla, San Diego, 92121 CA, USA; (B.D.); (S.C.); (H.M.)
| | | | | | - Hany Magharyous
- Labcorp, La Jolla, San Diego, 92121 CA, USA; (B.D.); (S.C.); (H.M.)
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Piwowarczyk P, Massalska D, Obodzińska I, Gawlik Zawiślak S, Bijok J, Kucińska-Chahwan A, Roszkowski T. Prenatal diagnosis of Emanuel syndrome - case series and review of the literature. J OBSTET GYNAECOL 2022; 42:2615-2620. [PMID: 36048922 DOI: 10.1080/01443615.2022.2114331] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We present three new cases and review of the literature on the prenatal diagnosis of Emanuel syndrome (ES). Twenty-one foetuses have been analysed. In all three cases diagnosed in our department, posterior fossa abnormalities were seen and in one hypoplastic right ventricle was diagnosed at the first trimester scan. Defects of the posterior fossa (62% of foetuses; 13/21) and left diaphragmatic hernia (29% of foetuses; 6/21) are the most frequently reported prenatal findings in ES syndrome. No pattern of specific prenatal ultrasound markers of ES exists. Abnormalities of the posterior fossa are frequent and may be diagnosed as early as in the first trimester of pregnancy. Specific diagnosis can be made only after invasive genetic testing.IMPACT STATEMENTWhat is already known on this subject? Emanuel syndrome (ES) is a rare genetic disorder. No pattern of specific prenatal ultrasound markers exists. The great majority of cases is diagnosed postnatally and only a few cases of prenatal diagnosis have been published to date.What do the results of this study add? The most frequent structural abnormalities in prenatally detected ES involved central nervous system (80.9%), namely posterior fossa defects (57.1%) and mild ventriculomegaly (23.8%). Other frequent abnormalities include left diaphragmatic hernia (28.6%), renal defects (23.8%) and foetal growth restriction (FGR) (23.8%).What are the implications of these findings for clinical practice and/or further research? Abnormalities of the posterior fossa are the most frequent defects in ES and may be diagnosed as early as in the first trimester of pregnancy. Specific diagnosis can be made only after invasive genetic testing.
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Affiliation(s)
- Patrycja Piwowarczyk
- Department of Gynecologic Oncology and Obstetrics, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - Diana Massalska
- Department of Gynecologic Oncology and Obstetrics, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - Izabela Obodzińska
- Department of Genetics, Institute of Psychiatry and Neurology, Warsaw, Poland
| | | | - Julia Bijok
- Department of Gynecologic Oncology and Obstetrics, Centre of Postgraduate Medical Education, Warsaw, Poland
| | - Anna Kucińska-Chahwan
- Department of Human Genetics, Institute of Mother and Child, Warsaw, Poland.,Department of Obstetrics and Gynecology, Institute of Mother and Child, Warsaw, Poland
| | - Tomasz Roszkowski
- Department of Obstetrics and Gynecology, Institute of Mother and Child, Warsaw, Poland
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Dharmadhikari AV, Pereira EM, Andrews CC., Macera M, Harkavy N, Wapner R, Jobanputra V, Levy B, Ganapathi M, Liao J. Case Report: Prenatal Identification of a De Novo Mosaic Neocentric Marker Resulting in 13q31.1→qter Tetrasomy in a Mildly Affected Girl. Front Genet 2022; 13:906077. [PMID: 35928455 PMCID: PMC9343796 DOI: 10.3389/fgene.2022.906077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/14/2022] [Indexed: 11/13/2022] Open
Abstract
Partial tetrasomy of distal 13q has a reported association with a variable phenotype including microphthalmia, ear abnormalities, hypotelorism, facial dysmorphisms, urogenital defects, pigmentation and skin defects, and severe learning difficulties. A wide range of mosaicism has been reported, which may, to some extent, account for the variable spectrum of observed phenotypes. We report here a pregnancy conceived using intrauterine insemination in a 32-year-old female with a history of infertility. Non-invasive prenatal screening (NIPS) was performed in the first trimester which reported an increased risk for trisomy 13. Follow-up cytogenetic workup using chorionic villus sampling (CVS) and amniotic fluid samples showed a mosaic karyotype with a small supernumerary marker chromosome (sSMC). Chromosomal microarray analysis (CMA) identified a mosaic 31.34 Mb terminal gain on chr13q31.1q34 showing the likely origin of the sSMC to distal chromosome 13q. Follow-up metaphase FISH testing suggested an inverted duplication rearrangement involving 13q31q34 in the marker chromosome and the presence of a neocentromere. At 21 months of age, the proband has a history of gross motor delay, hypotonia, left microphthalmia, strabismus, congenital anomaly of the right optic nerve, hemangiomas, and a tethered spinal cord. Postnatal chromosome analyses in buccal, peripheral blood, and spinal cord ligament tissues were consistent with the previous amniocentesis and CVS findings, and the degree of mosaicism varied from 25 to 80%. It is often challenging to pinpoint the chromosomal identity of sSMCs using banding cytogenetics. A combination of low-pass genome sequencing of cell-free DNA, chromosomal microarray, and FISH enabled the identification of the precise chromosomal rearrangement in this patient. This study adds to the growing list of clinically identified neocentric marker chromosomes and is the first described instance of partial tetrasomy 13q31q34 identified in a mosaic state prenatally. Since NIPS is now being routinely performed along with invasive testing for advanced maternal age, an increased prenatal detection rate for mosaic sSMCs in otherwise normal pregnancies is expected. Future studies investigating how neocentromeres mediate gene expression changes could help identify potential epigenetic targets as treatment options to rescue or reverse the phenotypes seen in patients with congenital neocentromeres.
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Affiliation(s)
- Avinash V. Dharmadhikari
- Department of Pathology & Cell Biology, Columbia University Vagelos College of Physicians and Surgeons and New York-Presbyterian Morgan Stanley Children’s Hospital, New York, NY, United States
| | - Elaine M. Pereira
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons and New York-Presbyterian Morgan Stanley Children’s Hospital, New York, NY, United States
| | - Carli C . Andrews
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, United States
| | - Michael Macera
- Clinical Cytogenetics Laboratory, New York Presbyterian Morgan Stanley Children’s Hospital, New York, NY, United States
| | - Nina Harkavy
- Department of Obstetrics and Gynecology, Columbia University Vagelos College of Physicians and Surgeons and New York-Presbyterian Morgan Stanley Children’s Hospital, New York, NY, United States
| | - Ronald Wapner
- Department of Obstetrics and Gynecology, Columbia University Vagelos College of Physicians and Surgeons and New York-Presbyterian Morgan Stanley Children’s Hospital, New York, NY, United States
| | - Vaidehi Jobanputra
- Department of Pathology & Cell Biology, Columbia University Vagelos College of Physicians and Surgeons and New York-Presbyterian Morgan Stanley Children’s Hospital, New York, NY, United States
| | - Brynn Levy
- Department of Pathology & Cell Biology, Columbia University Vagelos College of Physicians and Surgeons and New York-Presbyterian Morgan Stanley Children’s Hospital, New York, NY, United States
- Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, United States
| | - Mythily Ganapathi
- Department of Pathology & Cell Biology, Columbia University Vagelos College of Physicians and Surgeons and New York-Presbyterian Morgan Stanley Children’s Hospital, New York, NY, United States
| | - Jun Liao
- Department of Pathology & Cell Biology, Columbia University Vagelos College of Physicians and Surgeons and New York-Presbyterian Morgan Stanley Children’s Hospital, New York, NY, United States
- *Correspondence: Jun Liao,
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Zeng Y, Gao J, Yuan H, Zhou L, Cheng D, Che M, Qian Y, Fan J, Zhang L, Qian F, Gao Y, Luo T, Chen W, Wang T, Jin Y, Zhao J, Shi X, Li H, Pan H, Xiong C, Ni Y, Qiu S, Zhang T. Application of FF-QuantSC for the Precise Estimation of Fetal Fraction in Non-invasive Prenatal Testing in Two SRY-Translocation Cases. Front Genet 2020; 11:570333. [PMID: 33193669 PMCID: PMC7592396 DOI: 10.3389/fgene.2020.570333] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 09/21/2020] [Indexed: 11/13/2022] Open
Abstract
Background: Non-invasive prenatal testing (NIPT) is a commonly employed clinical method to screen for fetal aneuploidy, while the Y chromosome-based NIPT method is regarded as the gold standard for the estimation of fetal fraction (FF) of male fetuses. However, when the fetus has a derivative Y chromosome thereby containing a partial Y chromosome, the Y chromosome-based NIPT method cannot accurately calculate FF. Therefore, alternative methods to precisely calculate FF are required. Methods: Two prenatal cases could not be detected effectively using the Y chromosome-based NIPT method because of low FF. According to the Y chromosome-based method, the FF of the fetuses were 1.730 ± 0.050% (average gestation week: 18+1) and 2.307 ± 0.191% (average gestation week: 20+0) for cases 1 and 2, respectively. Using various genetic diagnostic techniques, including the BoBs™ assay, karyotype analysis, improved nucleolus-organizing region (NOR)-banding analysis, Affymetrix CytoScan 750K Array, and fluorescence in situ hybridization (FISH) analysis, we determined the genetic defects of two fetuses with translocations of the SRY locus. Further, we reassessed the FF using FF-QuantSC and X chromosome-based methods. The distribution diagram of reads for chromosome Y was also analyzed. Results: The FF of the fetuses determined by FF-QuantSC were 10.330% (gestation week: 18+4) in case 1 and 9.470% (gestation week: 21+4) in case 2, while the FF of the fetuses determined using the X chromosome-based method were 8.889% (gestation week: 18+4) in case 1 and 2.296% (gestation week: 21+4) in case 2. Both the distribution diagrams of reads for chromosome Y of the two cases showed the deletion in the long arm of the Y chromosome. Conclusion: For repeatedly low FF samples detected using the Y chromosome-based NIPT method for a long gestational week, we believe that FF-QuantSC and distribution diagrams of reads could be used as a supplement to NIPT, especially for rare cases of sex reversal caused by SRY translocation.
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Affiliation(s)
- Yan Zeng
- Shaoxing Maternity and Child Health Care Hospital, Shaoxing, China.,Obstetrics and Gynecology Hospital of Shaoxing University, Shaoxing, China
| | - Jiong Gao
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, China
| | - Hua Yuan
- Shaoxing Maternity and Child Health Care Hospital, Shaoxing, China.,Obstetrics and Gynecology Hospital of Shaoxing University, Shaoxing, China
| | - Lijun Zhou
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, China
| | - Dehua Cheng
- Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China
| | - Ming Che
- Shaoxing Maternity and Child Health Care Hospital, Shaoxing, China.,Obstetrics and Gynecology Hospital of Shaoxing University, Shaoxing, China
| | - Yandi Qian
- Shaoxing Maternity and Child Health Care Hospital, Shaoxing, China.,Obstetrics and Gynecology Hospital of Shaoxing University, Shaoxing, China
| | - Jiaming Fan
- Shaoxing Maternity and Child Health Care Hospital, Shaoxing, China.,Obstetrics and Gynecology Hospital of Shaoxing University, Shaoxing, China
| | - Lifang Zhang
- Shaoxing Maternity and Child Health Care Hospital, Shaoxing, China.,Obstetrics and Gynecology Hospital of Shaoxing University, Shaoxing, China
| | - Feiyan Qian
- Shaoxing Maternity and Child Health Care Hospital, Shaoxing, China.,Obstetrics and Gynecology Hospital of Shaoxing University, Shaoxing, China
| | - Yuling Gao
- Shaoxing Maternity and Child Health Care Hospital, Shaoxing, China.,Obstetrics and Gynecology Hospital of Shaoxing University, Shaoxing, China
| | - Tingting Luo
- Shaoxing Maternity and Child Health Care Hospital, Shaoxing, China.,Obstetrics and Gynecology Hospital of Shaoxing University, Shaoxing, China
| | - Weiping Chen
- Shaoxing Maternity and Child Health Care Hospital, Shaoxing, China.,Obstetrics and Gynecology Hospital of Shaoxing University, Shaoxing, China
| | - Ting Wang
- Shaoxing Maternity and Child Health Care Hospital, Shaoxing, China.,Obstetrics and Gynecology Hospital of Shaoxing University, Shaoxing, China
| | - Yaoxiang Jin
- Shaoxing Maternity and Child Health Care Hospital, Shaoxing, China.,Obstetrics and Gynecology Hospital of Shaoxing University, Shaoxing, China
| | - Jian Zhao
- Shaoxing Maternity and Child Health Care Hospital, Shaoxing, China.,Obstetrics and Gynecology Hospital of Shaoxing University, Shaoxing, China
| | - Xiaoliang Shi
- Shaoxing Maternity and Child Health Care Hospital, Shaoxing, China.,Obstetrics and Gynecology Hospital of Shaoxing University, Shaoxing, China
| | - Hongmei Li
- Shaoxing Maternity and Child Health Care Hospital, Shaoxing, China.,Obstetrics and Gynecology Hospital of Shaoxing University, Shaoxing, China
| | - Haitao Pan
- Shaoxing Maternity and Child Health Care Hospital, Shaoxing, China.,Obstetrics and Gynecology Hospital of Shaoxing University, Shaoxing, China
| | - Cheng Xiong
- Shaoxing Maternity and Child Health Care Hospital, Shaoxing, China.,Obstetrics and Gynecology Hospital of Shaoxing University, Shaoxing, China
| | - Yunqin Ni
- Shaoxing Maternity and Child Health Care Hospital, Shaoxing, China.,Obstetrics and Gynecology Hospital of Shaoxing University, Shaoxing, China
| | - Shuchao Qiu
- Shaoxing Maternity and Child Health Care Hospital, Shaoxing, China.,Obstetrics and Gynecology Hospital of Shaoxing University, Shaoxing, China
| | - Tao Zhang
- Shaoxing Maternity and Child Health Care Hospital, Shaoxing, China.,Obstetrics and Gynecology Hospital of Shaoxing University, Shaoxing, China
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