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Kuil LE, Chauhan RK, de Graaf BM, Cheng WW, Kakiailatu NJM, Lasabuda R, Verhaeghe C, Windster JD, Schriemer D, Azmani Z, Brooks AS, Edie S, Reeves RH, Eggen BJL, Shepherd IT, Burns AJ, Hofstra RMW, Melotte V, Brosens E, Alves MM. ATP5PO levels regulate enteric nervous system development in zebrafish, linking Hirschsprung disease to Down Syndrome. Biochim Biophys Acta Mol Basis Dis 2024; 1870:166991. [PMID: 38128843 DOI: 10.1016/j.bbadis.2023.166991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 12/09/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023]
Abstract
Hirschsprung disease (HSCR) is a complex genetic disorder characterized by the absence of enteric nervous system (ENS) in the distal region of the intestine. Down Syndrome (DS) patients have a >50-fold higher risk of developing HSCR than the general population, suggesting that overexpression of human chromosome 21 (Hsa21) genes contribute to HSCR etiology. However, identification of responsible genes remains challenging. Here, we describe a genetic screening of potential candidate genes located on Hsa21, using the zebrafish. Candidate genes were located in the DS-HSCR susceptibility region, expressed in the human intestine, were known potential biomarkers for DS prenatal diagnosis, and were present in the zebrafish genome. With this approach, four genes were selected: RCAN1, ITSN1, ATP5PO and SUMO3. However, only overexpression of ATP5PO, coding for a component of the mitochondrial ATPase, led to significant reduction of ENS cells. Paradoxically, in vitro studies showed that overexpression of ATP5PO led to a reduction of ATP5PO protein levels. Impaired neuronal differentiation and reduced mitochondrial ATP production, were also detected in vitro, after overexpression of ATP5PO in a neuroblastoma cell line. Finally, epistasis was observed between ATP5PO and ret, the most important HSCR gene. Taken together, our results identify ATP5PO as the gene responsible for the increased risk of HSCR in DS patients in particular if RET variants are also present, and show that a balanced expression of ATP5PO is required for normal ENS development.
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Affiliation(s)
- L E Kuil
- Department of Clinical Genetics, Erasmus University Medical Center Rotterdam - Sophia Children's Hospital, Rotterdam, the Netherlands
| | - R K Chauhan
- Department of Clinical Genetics, Erasmus University Medical Center Rotterdam - Sophia Children's Hospital, Rotterdam, the Netherlands
| | - B M de Graaf
- Department of Clinical Genetics, Erasmus University Medical Center Rotterdam - Sophia Children's Hospital, Rotterdam, the Netherlands
| | - W W Cheng
- Department of Clinical Genetics, Erasmus University Medical Center Rotterdam - Sophia Children's Hospital, Rotterdam, the Netherlands
| | - N J M Kakiailatu
- Department of Clinical Genetics, Erasmus University Medical Center Rotterdam - Sophia Children's Hospital, Rotterdam, the Netherlands
| | - R Lasabuda
- Department of Clinical Genetics, Erasmus University Medical Center Rotterdam - Sophia Children's Hospital, Rotterdam, the Netherlands
| | - C Verhaeghe
- Department of Clinical Genetics, Erasmus University Medical Center Rotterdam - Sophia Children's Hospital, Rotterdam, the Netherlands
| | - J D Windster
- Department of Clinical Genetics, Erasmus University Medical Center Rotterdam - Sophia Children's Hospital, Rotterdam, the Netherlands; Department of Pediatric Surgery, Erasmus University Medical Center Rotterdam, Sophia's Children's Hospital, Rotterdam, the Netherlands
| | - D Schriemer
- Department of Biomedical Sciences of Cells and Systems, Section Molecular Neurobiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Z Azmani
- Department of Clinical Genetics, Erasmus University Medical Center Rotterdam - Sophia Children's Hospital, Rotterdam, the Netherlands
| | - A S Brooks
- Department of Clinical Genetics, Erasmus University Medical Center Rotterdam - Sophia Children's Hospital, Rotterdam, the Netherlands
| | - S Edie
- Johns Hopkins University School of Medicine, Department of Physiology and McKusick-Nathans Department of Genetic Medicine, Baltimore, MD, United States of America
| | - R H Reeves
- Johns Hopkins University School of Medicine, Department of Physiology and McKusick-Nathans Department of Genetic Medicine, Baltimore, MD, United States of America
| | - B J L Eggen
- Department of Biomedical Sciences of Cells and Systems, Section Molecular Neurobiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - I T Shepherd
- Department of Biology, Emory University, Atlanta, GA, United States of America
| | - A J Burns
- Department of Clinical Genetics, Erasmus University Medical Center Rotterdam - Sophia Children's Hospital, Rotterdam, the Netherlands; Birth Defects Research Centre, UCL Institute of Child Health, London, United Kingdom; Gastrointestinal Drug Discovery Unit, Takeda Pharmaceuticals, Cambridge, MA, United States of America
| | - R M W Hofstra
- Department of Clinical Genetics, Erasmus University Medical Center Rotterdam - Sophia Children's Hospital, Rotterdam, the Netherlands
| | - V Melotte
- Department of Clinical Genetics, Erasmus University Medical Center Rotterdam - Sophia Children's Hospital, Rotterdam, the Netherlands; Department of Pathology, GROW-school for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - E Brosens
- Department of Clinical Genetics, Erasmus University Medical Center Rotterdam - Sophia Children's Hospital, Rotterdam, the Netherlands
| | - M M Alves
- Department of Clinical Genetics, Erasmus University Medical Center Rotterdam - Sophia Children's Hospital, Rotterdam, the Netherlands; Department of Pediatric Surgery, Erasmus University Medical Center Rotterdam, Sophia's Children's Hospital, Rotterdam, the Netherlands.
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2
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Hornung BVH, Azmani Z, den Dekker AT, Oole E, Ozgur Z, Brouwer RWW, van den Hout MCGN, van IJcken WFJ. Comparison of Single Cell Transcriptome Sequencing Methods: Of Mice and Men. Genes (Basel) 2023; 14:2226. [PMID: 38137048 PMCID: PMC10743076 DOI: 10.3390/genes14122226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/04/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
Single cell RNAseq has been a big leap in many areas of biology. Rather than investigating gene expression on a whole organism level, this technology enables scientists to get a detailed look at rare single cells or within their cell population of interest. The field is growing, and many new methods appear each year. We compared methods utilized in our core facility: Smart-seq3, PlexWell, FLASH-seq, VASA-seq, SORT-seq, 10X, Evercode, and HIVE. We characterized the equipment requirements for each method. We evaluated the performances of these methods based on detected features, transcriptome diversity, mitochondrial RNA abundance and multiplets, among others and benchmarked them against bulk RNA sequencing. Here, we show that bulk transcriptome detects more unique transcripts than any single cell method. While most methods are comparable in many regards, FLASH-seq and VASA-seq yielded the best metrics, e.g., in number of features. If no equipment for automation is available or many cells are desired, then HIVE or 10X yield good results. In general, more recently developed methods perform better. This also leads to the conclusion that older methods should be phased out, and that the development of single cell RNAseq methods is still progressing considerably.
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Affiliation(s)
- Bastian V. H. Hornung
- Department of Cell Biology, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands; (B.V.H.H.); (M.C.G.N.v.d.H.)
- Genomics Core Facility, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands
| | - Zakia Azmani
- Department of Cell Biology, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands; (B.V.H.H.); (M.C.G.N.v.d.H.)
- Genomics Core Facility, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands
| | - Alexander T. den Dekker
- Department of Cell Biology, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands; (B.V.H.H.); (M.C.G.N.v.d.H.)
- Genomics Core Facility, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands
| | - Edwin Oole
- Department of Cell Biology, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands; (B.V.H.H.); (M.C.G.N.v.d.H.)
- Genomics Core Facility, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands
| | - Zeliha Ozgur
- Department of Cell Biology, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands; (B.V.H.H.); (M.C.G.N.v.d.H.)
- Genomics Core Facility, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands
| | - Rutger W. W. Brouwer
- Department of Cell Biology, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands; (B.V.H.H.); (M.C.G.N.v.d.H.)
- Genomics Core Facility, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands
| | - Mirjam C. G. N. van den Hout
- Department of Cell Biology, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands; (B.V.H.H.); (M.C.G.N.v.d.H.)
- Genomics Core Facility, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands
| | - Wilfred F. J. van IJcken
- Department of Cell Biology, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands; (B.V.H.H.); (M.C.G.N.v.d.H.)
- Genomics Core Facility, Erasmus University Medical Center Rotterdam, Wytemaweg 80, 3015CN Rotterdam, The Netherlands
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3
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Levink IJM, Jansen MPHM, Azmani Z, van IJcken W, van Marion R, Peppelenbosch MP, Cahen DL, Fuhler GM, Bruno MJ. Mutation Analysis of Pancreatic Juice and Plasma for the Detection of Pancreatic Cancer. Int J Mol Sci 2023; 24:13116. [PMID: 37685923 PMCID: PMC10487634 DOI: 10.3390/ijms241713116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/31/2023] [Accepted: 08/02/2023] [Indexed: 09/10/2023] Open
Abstract
Molecular profiling may enable earlier detection of pancreatic cancer (PC) in high-risk individuals undergoing surveillance and allow for personalization of treatment. We hypothesized that the detection rate of DNA mutations is higher in pancreatic juice (PJ) than in plasma due to its closer contact with the pancreatic ductal system, from which pancreatic cancer cells originate, and higher overall cell-free DNA (cfDNA) concentrations. In this study, we included patients with pathology-proven PC or intraductal papillary mucinous neoplasm (IPMN) with high-grade dysplasia (HGD) from two prospective clinical trials (KRASPanc and PACYFIC) for whom both PJ and plasma were available. We performed next-generation sequencing on PJ, plasma, and tissue samples and described the presence (and concordance) of mutations in these biomaterials. This study included 26 patients (25 PC and 1 IPMN with HGD), of which 7 were women (27%), with a median age of 71 years (IQR 12) and a median BMI of 23 kg/m2 (IQR 4). Ten patients with PC (40%) were (borderline) resectable at baseline. Tissue was available from six patients (resection n = 5, biopsy n = 1). A median volume of 2.9 mL plasma (IQR 1.0 mL) and 0.7 mL PJ (IQR 0.1 mL, p < 0.001) was used for DNA isolation. PJ had a higher median cfDNA concentration (2.6 ng/μL (IQR 4.2)) than plasma (0.29 ng/μL (IQR 0.40)). A total of 41 unique somatic mutations were detected: 24 mutations in plasma (2 KRAS, 15 TP53, 2 SMAD4, 3 CDKN2A 1 CTNNB1, and 1 PIK3CA), 19 in PJ (3 KRAS, 15 TP53, and 1 SMAD4), and 8 in tissue (2 KRAS, 2 CDKN2A, and 4 TP53). The mutation detection rate (and the concordance with tissue) did not differ between plasma and PJ. In conclusion, while the concentration of cfDNA was indeed higher in PJ than in plasma, the mutation detection rate was not different. A few cancer-associated genetic variants were detected in both biomaterials. Further research is needed to increase the detection rate and assess the performance and suitability of plasma and PJ for PC (early) detection.
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Affiliation(s)
- Iris J. M. Levink
- Department of Gastroenterology & Hepatology, Erasmus MC, University Medical Center, 3015 GD Rotterdam, The Netherlands; (M.P.P.); (G.M.F.); (M.J.B.)
| | - Maurice P. H. M. Jansen
- Department of Medical Oncology, Erasmus MC, University Medical Center, 3015 GD Rotterdam, The Netherlands
| | - Zakia Azmani
- Center for Biomics, Erasmus MC, University Medical Center, 3015 GD Rotterdam, The Netherlands (W.v.I.)
| | - Wilfred van IJcken
- Center for Biomics, Erasmus MC, University Medical Center, 3015 GD Rotterdam, The Netherlands (W.v.I.)
| | - Ronald van Marion
- Department of Pathology, Erasmus MC, University Medical Center, 3015 GD Rotterdam, The Netherlands;
| | - Maikel P. Peppelenbosch
- Department of Gastroenterology & Hepatology, Erasmus MC, University Medical Center, 3015 GD Rotterdam, The Netherlands; (M.P.P.); (G.M.F.); (M.J.B.)
| | - Djuna L. Cahen
- Department of Gastroenterology & Hepatology, Erasmus MC, University Medical Center, 3015 GD Rotterdam, The Netherlands; (M.P.P.); (G.M.F.); (M.J.B.)
| | - Gwenny M. Fuhler
- Department of Gastroenterology & Hepatology, Erasmus MC, University Medical Center, 3015 GD Rotterdam, The Netherlands; (M.P.P.); (G.M.F.); (M.J.B.)
| | - Marco J. Bruno
- Department of Gastroenterology & Hepatology, Erasmus MC, University Medical Center, 3015 GD Rotterdam, The Netherlands; (M.P.P.); (G.M.F.); (M.J.B.)
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4
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Deger T, Boers RG, de Weerd V, Angus L, van der Put MMJ, Boers JB, Azmani Z, van IJcken WFJ, Grünhagen DJ, van Dessel LF, Lolkema MPJK, Verhoef C, Sleijfer S, Martens JWM, Gribnau J, Wilting SM. High-throughput and affordable genome-wide methylation profiling of circulating cell-free DNA by methylated DNA sequencing (MeD-seq) of LpnPI digested fragments. Clin Epigenetics 2021; 13:196. [PMID: 34670587 PMCID: PMC8529776 DOI: 10.1186/s13148-021-01177-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 09/10/2021] [Indexed: 01/06/2023] Open
Abstract
Background DNA methylation detection in liquid biopsies provides a highly promising and much needed means for real-time monitoring of disease load in advanced cancer patient care. Compared to the often-used somatic mutations, tissue- and cancer-type specific epigenetic marks affect a larger part of the cancer genome and generally have a high penetrance throughout the tumour. Here, we describe the successful application of the recently described MeD-seq assay for genome-wide DNA methylation profiling on cell-free DNA (cfDNA). The compatibility of the MeD-seq assay with different types of blood collection tubes, cfDNA input amounts, cfDNA isolation methods, and vacuum concentration of samples was evaluated using plasma from both metastatic cancer patients and healthy blood donors (HBDs). To investigate the potential value of cfDNA methylation profiling for tumour load monitoring, we profiled paired samples from 8 patients with resectable colorectal liver metastases (CRLM) before and after surgery. Results The MeD-seq assay worked on plasma-derived cfDNA from both EDTA and CellSave blood collection tubes when at least 10 ng of cfDNA was used. From the 3 evaluated cfDNA isolation methods, both the manual QIAamp Circulating Nucleic Acid Kit (Qiagen) and the semi-automated Maxwell® RSC ccfDNA Plasma Kit (Promega) were compatible with MeD-seq analysis, whereas the QiaSymphony DSP Circulating DNA Kit (Qiagen) yielded significantly fewer reads when compared to the QIAamp kit (p < 0.001). Vacuum concentration of samples before MeD-seq analysis was possible with samples in AVE buffer (QIAamp) or water, but yielded inconsistent results for samples in EDTA-containing Maxwell buffer. Principal component analysis showed that pre-surgical samples from CRLM patients were very distinct from HBDs, whereas post-surgical samples were more similar. Several described methylation markers for colorectal cancer monitoring in liquid biopsies showed differential methylation between pre-surgical CRLM samples and HBDs in our data, supporting the validity of our approach. Results for MSC, ITGA4, GRIA4, and EYA4 were validated by quantitative methylation specific PCR. Conclusions The MeD-seq assay provides a promising new method for cfDNA methylation profiling. Potential future applications of the assay include marker discovery specifically for liquid biopsy analysis as well as direct use as a disease load monitoring tool in advanced cancer patients. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01177-4.
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Affiliation(s)
- Teoman Deger
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus Medical Center, Rotterdam, Netherlands
| | - Ruben G Boers
- Department of Developmental Biology, Erasmus Medical Center, Rotterdam, Netherlands
| | - Vanja de Weerd
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus Medical Center, Rotterdam, Netherlands
| | - Lindsay Angus
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus Medical Center, Rotterdam, Netherlands
| | - Marjolijn M J van der Put
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus Medical Center, Rotterdam, Netherlands
| | - Joachim B Boers
- Department of Developmental Biology, Erasmus Medical Center, Rotterdam, Netherlands
| | - Z Azmani
- Center for Biomics, Erasmus Medical Center, Rotterdam, Netherlands
| | | | - Dirk J Grünhagen
- Department of Oncologic Surgery, Erasmus MC Cancer Institute, Erasmus Medical Center, Rotterdam, Netherlands
| | - Lisanne F van Dessel
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus Medical Center, Rotterdam, Netherlands
| | - Martijn P J K Lolkema
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus Medical Center, Rotterdam, Netherlands
| | - Cornelis Verhoef
- Department of Oncologic Surgery, Erasmus MC Cancer Institute, Erasmus Medical Center, Rotterdam, Netherlands
| | - Stefan Sleijfer
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus Medical Center, Rotterdam, Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus Medical Center, Rotterdam, Netherlands
| | - Joost Gribnau
- Department of Developmental Biology, Erasmus Medical Center, Rotterdam, Netherlands
| | - Saskia M Wilting
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus Medical Center, Rotterdam, Netherlands.
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5
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van der Sijde F, Azmani Z, Besselink MG, Bonsing BA, de Groot JWB, Groot Koerkamp B, Haberkorn BCM, Homs MYV, van IJcken WFJ, Janssen QP, Lolkema MP, Luelmo SAC, Mekenkamp LJM, Mustafa DAM, van Schaik RHN, Wilmink JW, Vietsch EE, van Eijck CHJ. Circulating TP53 mutations are associated with early tumor progression and poor survival in pancreatic cancer patients treated with FOLFIRINOX. Ther Adv Med Oncol 2021; 13:17588359211033704. [PMID: 34422118 PMCID: PMC8377319 DOI: 10.1177/17588359211033704] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 06/30/2021] [Indexed: 01/05/2023] Open
Abstract
Background: Biomarkers predicting treatment response may be used to stratify pancreatic ductal adenocarcinoma (PDAC) patients for therapy. The aim of this study was to identify circulating tumor DNA (ctDNA) mutations that associate with tumor progression during FOLFIRINOX chemotherapy, and overall survival (OS). Methods: Circulating cell-free DNA was analyzed with a 57 gene next-generation sequencing panel using plasma samples of 48 PDAC patients of all disease stages. Patients received FOLFIRINOX as initial treatment. Chemotherapy response was determined on CT scans as disease control (n = 30) or progressive disease (n = 18) within eight cycles of FOLFIRINOX, based on RECIST 1.1 criteria. Results: Detection of a TP53 ctDNA mutation before start of FOLFIRINOX [odds ratio (OR) 10.51, 95% confidence interval (CI) 1.40–79.14] and the presence of a homozygous TP53 Pro72Arg germline variant (OR 6.98, 95% CI 1.31–37.30) were predictors of early tumor progression during FOLFIRINOX in multivariable analysis. Five patients presented with the combination of a TP53 ctDNA mutation before start of FOLFIRINOX and the homozygous Pro72Arg variant. All five patients showed progression during FOLFIRINOX. The combination of the TP53 mutation and TP53 germline variant was associated with shorter survival (median OS 4.4 months, 95% CI 2.6–6.2 months) compared with patients without any TP53 alterations (median OS 13.0 months, 95% CI 8.6–17.4 months). Conclusion: The combination of a TP53 ctDNA mutation before start of FOLFIRINOX and a homozygous TP53 Pro72Arg variant is a promising biomarker, associated with early tumor progression during FOLFIRINOX and poor OS. The results of this exploratory study need to be validated in an independent cohort.
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Affiliation(s)
- Fleur van der Sijde
- Department of Surgery, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Zakia Azmani
- Center for Biomics, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Marc G. Besselink
- Department of Surgery, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, Amsterdam, Noord-Holland, The Netherlands
| | - Bert A. Bonsing
- Department of Surgery, Leiden University Medical Center, Leiden, Zuid-Holland, The Netherlands
| | | | - Bas Groot Koerkamp
- Department of Surgery, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | | | - Marjolein Y. V. Homs
- Department of Medical Oncology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | | | - Quisette P. Janssen
- Department of Surgery, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Martijn P. Lolkema
- Department of Medical Oncology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Saskia A. C. Luelmo
- Department of Medical Oncology, Leiden University Medical Center, Leiden, Zuid-Holland, The Netherlands
| | - Leonie J. M. Mekenkamp
- Department of Medical Oncology, Medisch Spectrum Twente, Enschede, Overijssel, The Netherlands
| | - Dana A. M. Mustafa
- Department of Pathology, Tumor Immuno-Pathology Laboratory, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Ron H. N. van Schaik
- Department of Clinical Chemistry, Erasmus MC, University Medical Center, Rotterdam, Zuid-Holland, The Netherlands
| | - Johanna W. Wilmink
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
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6
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Wessels MW, Cnossen MH, van Dijk TB, Gillemans N, Schmidt KLJ, van Lom K, Vinjamur DS, Coyne S, Kurita R, Nakamura Y, de Man SA, Pfundt R, Azmani Z, Brouwer RWW, Bauer DE, van den Hout MCGN, van IJcken WFJ, Philipsen S. Molecular analysis of the erythroid phenotype of a patient with BCL11A haploinsufficiency. Blood Adv 2021; 5:2339-2349. [PMID: 33938942 PMCID: PMC8114548 DOI: 10.1182/bloodadvances.2020003753] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 03/12/2021] [Indexed: 12/29/2022] Open
Abstract
The BCL11A gene encodes a transcriptional repressor with essential functions in multiple tissues during human development. Haploinsufficiency for BCL11A causes Dias-Logan syndrome (OMIM 617101), an intellectual developmental disorder with hereditary persistence of fetal hemoglobin (HPFH). Due to the severe phenotype, disease-causing variants in BCL11A occur de novo. We describe a patient with a de novo heterozygous variant, c.1453G>T, in the BCL11A gene, resulting in truncation of the BCL11A-XL protein (p.Glu485X). The truncated protein lacks the 3 C-terminal DNA-binding zinc fingers and the nuclear localization signal, rendering it inactive. The patient displayed high fetal hemoglobin (HbF) levels (12.1-18.7% of total hemoglobin), in contrast to the parents who had HbF levels of 0.3%. We used cultures of patient-derived erythroid progenitors to determine changes in gene expression and chromatin accessibility. In addition, we investigated DNA methylation of the promoters of the γ-globin genes HBG1 and HBG2. HUDEP1 and HUDEP2 cells were used as models for fetal and adult human erythropoiesis, respectively. Similar to HUDEP1 cells, the patient's cells displayed Assay for Transposase-Accessible Chromatin (ATAC) peaks at the HBG1/2 promoters and significant expression of HBG1/2 genes. In contrast, HBG1/2 promoter methylation and genome-wide gene expression profiling were consistent with normal adult erythropoiesis. We conclude that HPFH is the major erythroid phenotype of constitutive BCL11A haploinsufficiency. Given the essential functions of BCL11A in other hematopoietic lineages and the neuronal system, erythroid-specific targeting of the BCL11A gene has been proposed for reactivation of γ-globin expression in β-hemoglobinopathy patients. Our data strongly support this approach.
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Affiliation(s)
| | - Marjon H Cnossen
- Department of Pediatric Hematology
- Academic Center for Hemoglobinopathies and Rare Anemias
| | - Thamar B van Dijk
- Academic Center for Hemoglobinopathies and Rare Anemias
- Department of Cell Biology, and
| | - Nynke Gillemans
- Academic Center for Hemoglobinopathies and Rare Anemias
- Department of Cell Biology, and
| | - K L Juliëtte Schmidt
- Academic Center for Hemoglobinopathies and Rare Anemias
- Department of Cell Biology, and
| | - Kirsten van Lom
- Academic Center for Hemoglobinopathies and Rare Anemias
- Department of Hematology, Erasmus MC, Rotterdam, The Netherlands
| | - Divya S Vinjamur
- Division of Hematology/Oncology, Department of Pediatric Oncology, Boston Children's Hospital, Boston, MA
- Dana-Farber Cancer Institute, Boston, MA
- Harvard Stem Cell Institute, Boston, MA
- Broad Institute, Boston, MA
- Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Steven Coyne
- Division of Hematology/Oncology, Department of Pediatric Oncology, Boston Children's Hospital, Boston, MA
- Dana-Farber Cancer Institute, Boston, MA
- Harvard Stem Cell Institute, Boston, MA
- Broad Institute, Boston, MA
- Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Ryo Kurita
- Department of Research and Development, Central Blood Institute, Blood Service Headquarters, Japanese Red Cross Society, Tokyo, Japan
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN, BioResource Center, Tsukuba, Japan
| | - Stella A de Man
- Department of Pediatrics, Amphia Hospital, Breda, The Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands; and
| | - Zakia Azmani
- Department of Cell Biology, and
- Center for Biomics, Erasmus MC, Rotterdam, The Netherlands
| | - Rutger W W Brouwer
- Department of Cell Biology, and
- Center for Biomics, Erasmus MC, Rotterdam, The Netherlands
| | - Daniel E Bauer
- Division of Hematology/Oncology, Department of Pediatric Oncology, Boston Children's Hospital, Boston, MA
- Dana-Farber Cancer Institute, Boston, MA
- Harvard Stem Cell Institute, Boston, MA
- Broad Institute, Boston, MA
- Department of Pediatrics, Harvard Medical School, Boston, MA
| | | | - Wilfred F J van IJcken
- Department of Cell Biology, and
- Center for Biomics, Erasmus MC, Rotterdam, The Netherlands
| | - Sjaak Philipsen
- Academic Center for Hemoglobinopathies and Rare Anemias
- Department of Cell Biology, and
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Litjens NHR, Langerak AW, van der List ACJ, Klepper M, de Bie M, Azmani Z, den Dekker AT, Brouwer RWW, Betjes MGH, Van IJcken WFJ. Validation of a Combined Transcriptome and T Cell Receptor Alpha/Beta (TRA/TRB) Repertoire Assay at the Single Cell Level for Paucicellular Samples. Front Immunol 2020; 11:1999. [PMID: 33013853 PMCID: PMC7500136 DOI: 10.3389/fimmu.2020.01999] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 07/23/2020] [Indexed: 11/13/2022] Open
Abstract
Transcriptomics can be combined with TRA and TRB clonotype analysis at the single cell level. The aim of this study was to validate this approach on the ICELL8 Single-Cell system and to evaluate its usefulness to analyse clinical paucicellular samples. For this purpose, we carefully selected T cell lines with defined TRA/TRB clonotypes as well as clinical samples enriched for CD3+ T cells that possess a complex TCR repertoire. Low cell numbers of the different samples were dispensed in a chip on the ICELL8 Single-Cell System. Two sequencing libraries were generated from each single cell cDNA preparation, one for the TRA/TRB repertoire and one for the 5' ends of transcripts, and subsequently sequenced. Transcriptome analysis revealed that the cell lines on average express 2,268 unique genes/cell and T cells of clinical samples 770 unique genes/cell. The expected combined TRA/TRB clonotype was determined for on average 71% of the cells of the cell lines. In the clinical samples the TRA/TRB repertoire was more complex than those of the cell lines. Furthermore, the TRB clonotype distribution of the clinical samples was positively correlated to frequencies of TCRVβ families in CD3+ T cells obtained by a flow cytometry-based approach (Spearman's Rho correlation coefficient 0.81, P = 6.49 * 10-7). Combined analyses showed that transcriptome-based cell type-specific clusters in clinical samples corresponded to clinical features such as CMV status. In conclusion, we showed that the ICELL8 Single-Cell System enabled combined interrogation of both TRA/TRB repertoire and transcriptome of paucicellular clinical samples. This opens the way to study the response of single T cells within heterogeneous samples for both their transcriptome and TRA/TRB clonotypes in disease or upon treatment.
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Affiliation(s)
- Nicolle H R Litjens
- Department of Internal Medicine Section Nephrology and Transplantation, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Anton W Langerak
- Laboratory Medical Immunology, Department of Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Amy C J van der List
- Department of Internal Medicine Section Nephrology and Transplantation, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Mariska Klepper
- Department of Internal Medicine Section Nephrology and Transplantation, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Maaike de Bie
- Laboratory Medical Immunology, Department of Immunology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Zakia Azmani
- Center for Biomics, Erasmus MC, University Medical Center, Rotterdam, Netherlands.,Department of Cell Biology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Alexander T den Dekker
- Center for Biomics, Erasmus MC, University Medical Center, Rotterdam, Netherlands.,Department of Cell Biology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Rutger W W Brouwer
- Center for Biomics, Erasmus MC, University Medical Center, Rotterdam, Netherlands.,Department of Cell Biology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Michiel G H Betjes
- Department of Internal Medicine Section Nephrology and Transplantation, Erasmus MC, University Medical Center, Rotterdam, Netherlands
| | - Wilfred F J Van IJcken
- Center for Biomics, Erasmus MC, University Medical Center, Rotterdam, Netherlands.,Department of Cell Biology, Erasmus MC, University Medical Center, Rotterdam, Netherlands
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