1
|
Husseiny MI, Fahmy A, Du W, Gu A, Garcia P, Ferreri K, Kandeel F. Development of Quantitative Methylation-Specific Droplet Digital PCR (ddMSP) for Assessment of Natural Tregs. Front Genet 2020; 11:300. [PMID: 32318096 PMCID: PMC7154152 DOI: 10.3389/fgene.2020.00300] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 03/13/2020] [Indexed: 11/13/2022] Open
Abstract
Regulatory T cells (Tregs) suppress immune responses in vivo in an antigen-specific manner. Of clinical relevance, Tregs can be isolated and expanded in vitro while maintaining immunoregulatory function. Tregs are classified as CD4+CD25highCD127low FOXP3+ cells. Demethylation of the Treg-specific demethylation region (TSDR) of FOXP3 is found in natural Tregs (nTregs). We report a method for the characterization of the differential methylation pattern of the FOXP3 TSDR in patient-derived and expanded nTregs. Human TSDR sequences from nTregs (unmethylated sequence) and pancreatic (methylated sequence) cells were amplified and cloned into plasmids. A droplet digital TaqMan probe-based qPCR (ddPCR) assay using methylation-specific primers and probes was employed to quantify unmethylated and methylated sequences. The methylation-specific droplet digital PCR (ddMSP) assay was specific and selective for unmethylated DNA in mixtures with methylated DNA in the range of 5000 copies/μL to less than 1 copy/μL (R 2 = 0.99) even in the presence of non-selective gDNAs. CD4+CD25highCD127lowFOXP3+ human nTregs, in the presence of Dynabeads or activators, were expanded for 21 days. There was a decrease in the unmethylated ratio of Tregs after expansion with essentially the same ratio at days 10, 14, and 17. However, the activator expanded group showed a significant decrease in unmethylated targets at day 21. The suppression activity of activator-expanded nTregs at day 21 was decreased compared to cells expanded with Dynabeads. These data suggest that the ddMSP can quantitatively monitor nTreg expansion in vitro. These data also indicate that the assay is sensitive and specific at differentiating nTregs from other cells and may be useful for rapid screening of nTregs in clinical protocols.
Collapse
Affiliation(s)
- Mohamed I Husseiny
- Department of Translational Research & Cellular Therapeutics, Diabetes & Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, United States.,Faculty of Pharmacy, Zagazig University, Zagazig, Egypt
| | - Ahmed Fahmy
- East Lancashire Hospitals NHS Trust, Blackburn, United Kingdom
| | - Weiting Du
- Department of Translational Research & Cellular Therapeutics, Diabetes & Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, United States
| | - Angel Gu
- Department of Translational Research & Cellular Therapeutics, Diabetes & Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, United States
| | - Pablo Garcia
- Department of Translational Research & Cellular Therapeutics, Diabetes & Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, United States
| | - Kevin Ferreri
- Department of Translational Research & Cellular Therapeutics, Diabetes & Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, United States
| | - Fouad Kandeel
- Department of Translational Research & Cellular Therapeutics, Diabetes & Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, United States
| |
Collapse
|
2
|
Qian Y, Liu J, Yang Y, Chen M, Jin C, Chen P, Lei Y, Pan H, Dong M. Paternal Low-Level Mosaicism-Caused SATB2-Associated Syndrome. Front Genet 2019; 10:630. [PMID: 31333717 PMCID: PMC6614923 DOI: 10.3389/fgene.2019.00630] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 06/17/2019] [Indexed: 12/27/2022] Open
Abstract
Mutations of SATB2 (OMIM#608148) gene at 2q33.1 have been associated with the autosomal dominant SATB2-associated syndrome (SAS), which is still short of comprehensive diagnosis technologies for small deletions and low-level mosaicism. In this Chinese Han family, single nucleotide polymorphism array identified a 4.9-kb deletion in the SATB2 gene in two consecutive siblings exhibiting obvious developmental delay and dental abnormalities but failed to find so in their parents. Prenatal diagnosis revealed that their third child carried the same deletion in SATB2 and the pregnancy was terminated. To determine the genetic causes behind the inheritance of SATB2 deletion, gap-PCR was performed on peripheral blood-derived genomic DNA of the family and semen-derived DNA from the father. Gap-PCR that revealed the deletions in the two affected siblings were inherited from the father, while the less intense mutant band indicated the mosaicism of this mutation in the father. The deletion was 3,013 bp in size, spanning from chr2: 200,191,313-200,194,324 (hg19), and covering the entire exon 9 and part of intron 8 and 9 sequences. Droplet digital PCR demonstrated mosaicism percentage of 13.2% and 16.7% in peripheral blood-derived genomic DNA and semen-derived DNA of the father, respectively. Hereby, we describe a family of special AT-rich sequence-binding protein 2-associated syndrome caused by paternal low-level mosaicism and provide effective diagnostic technologies for intragenic deletions.
Collapse
Affiliation(s)
- Yeqing Qian
- Women's Hospital, School of Medicine Zhejiang University, Hangzhou, China.,Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou, China
| | - Jiao Liu
- Prenatal Diagnosis Center, Lishui Maternity and Child Health Care Hospital, Lishui, China
| | - Yanmei Yang
- Women's Hospital, School of Medicine Zhejiang University, Hangzhou, China.,Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou, China
| | - Min Chen
- Women's Hospital, School of Medicine Zhejiang University, Hangzhou, China.,Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou, China
| | - Chunlei Jin
- Prenatal Diagnosis Center, Lishui Maternity and Child Health Care Hospital, Lishui, China
| | - Penglong Chen
- Prenatal Diagnosis Center, Lishui Maternity and Child Health Care Hospital, Lishui, China
| | - Yongliang Lei
- Prenatal Diagnosis Center, Lishui Maternity and Child Health Care Hospital, Lishui, China
| | - Hangyi Pan
- Women's Hospital, School of Medicine Zhejiang University, Hangzhou, China.,Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou, China
| | - Minyue Dong
- Women's Hospital, School of Medicine Zhejiang University, Hangzhou, China.,Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou, China
| |
Collapse
|
3
|
Bertini V, Gana S, Orsini A, Bonuccelli A, Peroni D, Angelo V. Advantages of Array Comparative Genomic Hybridization Using Buccal Swab DNA for Detecting Pallister-Killian Syndrome. Ann Lab Med 2019; 39:232-234. [PMID: 30430791 PMCID: PMC6240520 DOI: 10.3343/alm.2019.39.2.232] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 07/11/2018] [Accepted: 10/22/2018] [Indexed: 12/01/2022] Open
Affiliation(s)
- Veronica Bertini
- Department of Medicine of Laboratory, Section of Cytogenetics, Azienda Ospedaliero Universitaria Pisana, Pisa, Italy.
| | - Simone Gana
- Internal Medicine 1, Section of Medical Genetics, Azienda Ospedaliero Universitaria Pisana, Pisa, Italy
| | - Alessandro Orsini
- Department of Clinical and Experimental Medicine, Section of Pediatrics, University of Pisa, Italy
| | - Alice Bonuccelli
- Department of Clinical and Experimental Medicine, Section of Pediatrics, University of Pisa, Italy
| | - Diego Peroni
- Department of Clinical and Experimental Medicine, Section of Pediatrics, University of Pisa, Italy
| | - Valetto Angelo
- Department of Medicine of Laboratory, Section of Cytogenetics, Azienda Ospedaliero Universitaria Pisana, Pisa, Italy
| |
Collapse
|
4
|
Salzano E, Raible SE, Kaur M, Wilkens A, Sperti G, Tilton RK, Bettini LR, Rocca A, Cocchi G, Selicorni A, Conlin LK, McEldrew D, Gupta R, Thakur S, Izumi K, Krantz ID. Prenatal profile of Pallister-Killian syndrome: Retrospective analysis of 114 pregnancies, literature review and approach to prenatal diagnosis. Am J Med Genet A 2018; 176:2575-2586. [PMID: 30289601 DOI: 10.1002/ajmg.a.40499] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 06/23/2018] [Accepted: 07/14/2018] [Indexed: 01/10/2023]
Abstract
Pallister-Killian syndrome (PKS) is a tissue limited mosaic disorder, characterized by variable degrees of neurodevelopmental delay and intellectual disability, typical craniofacial findings, skin pigmentation anomalies and multiple congenital malformations. The wide phenotypic spectrum of PKS in conjunction with the mosaic distribution of the i(12p) makes PKS an underdiagnosed disorder. Recognition of prenatal findings that should raise a suspicion of PKS is complicated by the fragmentation of data currently available in the literature and challenges in diagnosing a mosaic diagnosis on prenatal testing. Ultrasound anomalies, especially congenital diaphragmatic hernia, congenital heart defects, and rhizomelic limb shortening, have been related to PKS, but they are singularly not specific and are not present in all affected fetuses. We have combined prenatal data from 86 previously published reports and from our cohort of 114 PKS probands (retrospectively reviewed). Summarizing this data we have defined a prenatal growth profile and identified markers of perinatal outcome which collectively provide guidelines for early recognition of the distinctive prenatal profile and consideration of a diagnosis of PKS as well as for management and genetic counseling.
Collapse
Affiliation(s)
- E Salzano
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - S E Raible
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - M Kaur
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - A Wilkens
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - G Sperti
- Neonatology Unit, St. Orsola-Malpighi Polyclinic, Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | - R K Tilton
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - L R Bettini
- Dipartimento di Scienze Della Salute, San Paolo Hospital Medical School, Università degli Studi di Milano, Milan, Italy
| | - A Rocca
- Neonatology Unit, St. Orsola-Malpighi Polyclinic, Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | - G Cocchi
- Neonatology Unit, St. Orsola-Malpighi Polyclinic, Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | | | - L K Conlin
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - D McEldrew
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - R Gupta
- Department of Fetal Medicine, Maharaja Agrasen Hospital, Delhi & Sonepat Genetic and Fetal Medicine Centre, Sonepat, Haryana
| | - S Thakur
- Department of Genetic & Fetal Medicine, Fortis Hospital, Delhi-NCR & Apollo Hospital, Delhi, India
| | - K Izumi
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - I D Krantz
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| |
Collapse
|
5
|
Biderman Waberski M, Lindhurst M, Keppler-Noreuil KM, Sapp JC, Baker L, Gripp KW, Adams DM, Biesecker LG. Urine cell-free DNA is a biomarker for nephroblastomatosis or Wilms tumor in PIK3CA-related overgrowth spectrum (PROS). Genet Med 2018; 20:1077-1081. [PMID: 29300373 PMCID: PMC9365240 DOI: 10.1038/gim.2017.228] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 11/06/2017] [Indexed: 12/19/2022] Open
Abstract
Purpose We set out to facilitate the molecular diagnosis of patients with PIK3CA-related overgrowth spectrum (PROS), a heterogeneous somatic disorder characterized by variable presentations of segmental overgrowth, vascular malformations, skin lesions, and nephroblastomatosis, rare precursor lesions to Wilms tumor (WT). Molecular diagnosis of PROS is challenging due to its mosaic nature, often requiring invasive biopsies. Methods Digital droplet polymerase chain reaction was used to analyze tissues including urine, saliva, buccal cells, and blood, from eight patients with PROS. Further analyses were performed on plasma and urine cell-free DNA (cfDNA). Results PIK3CA variants were detected in plasma cfDNA at levels up to 0.5% in 50% of tested samples. In addition, high levels of PIK3CA variants in urine cfDNA correlated with a history of nephroblastomatosis compared to patients without renal involvement (p<0.05). Conclusion Digital droplet PCR is a sensitive molecular tool that enables low-level variant detection of PIK3CA in various tissue types, providing an alternative diagnostic method. Furthermore, urine cfDNA is a candidate biomarker for nephroblastomatosis in PROS, which may be useful to refine screening guidelines for tumor risk in these patients.
Collapse
|
6
|
Butchbach MER. Applicability of digital PCR to the investigation of pediatric-onset genetic disorders. BIOMOLECULAR DETECTION AND QUANTIFICATION 2016; 10:9-14. [PMID: 27990344 PMCID: PMC5154671 DOI: 10.1016/j.bdq.2016.06.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 06/08/2016] [Accepted: 06/21/2016] [Indexed: 12/12/2022]
Abstract
Early-onset rare diseases have a strong impact on child healthcare even though the incidence of each of these diseases is relatively low. In order to better manage the care of these children, it is imperative to quickly diagnose the molecular bases for these disorders as well as to develop technologies with prognostic potential. Digital PCR (dPCR) is well suited for this role by providing an absolute quantification of the target DNA within a sample. This review illustrates how dPCR can be used to identify genes associated with pediatric-onset disorders, to identify copy number status of important disease-causing genes and variants and to quantify modifier genes. It is also a powerful technology to track changes in genomic biomarkers with disease progression. Based on its capability to accurately and reliably detect genomic alterations with high sensitivity and a large dynamic detection range, dPCR has the potential to become the tool of choice for the verification of pediatric disease-associated mutations identified by next generation sequencing, copy number determination and noninvasive prenatal screening.
Collapse
Affiliation(s)
- Matthew E R Butchbach
- Center for Applied Clinical Genomics, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for Children, Wilmington, DE, USA; Center for Pediatric Research, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for Children, Wilmington, DE, USA; Department of Biological Sciences, University of Delaware, Newark, DE, USA; Department of Pediatrics, Thomas Jefferson University, Philadelphia, PA, USA
| |
Collapse
|