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Nakayama M, Yamamoto S, Hirabayashi H. Novel Cell Quantification Method Using a Single Surrogate Calibration Curve Across Various Biological Samples. AAPS J 2023; 25:26. [PMID: 36806998 DOI: 10.1208/s12248-023-00791-9] [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: 11/29/2022] [Accepted: 02/02/2023] [Indexed: 02/19/2023] Open
Abstract
Quantitative polymerase chain reaction (qPCR) is generally used to quantify transplanted cell therapy products in biological samples. As the matrix effects on PCR amplification and variability in DNA recovery from biological samples are well-known limitations that hinder the assay's performance, a calibration curve is conventionally established for each matrix. Droplet digital PCR (ddPCR) is based on the endpoint assay and advantageous in avoiding matrix effects. Moreover, the use of an external control gene may correct assay fluctuations to minimize the effects caused by inconsistent DNA recovery. In this study, we aimed to establish a novel and robust ddPCR method capable of quantifying human cells across various mouse biological samples using a single surrogate calibration curve in combination with an external control gene and DNA recovery normalization. Acceptable accuracy and precision were observed for quality control samples from different tissues, indicating the excellent quantitative and versatile potential of the developed method. Furthermore, the established method enabled the evaluation of human CD8+ T cell biodistribution in immunodeficient mice. Our findings provide new insights into the use of ddPCR-based quantification methods in biodistribution studies of cell therapy products.
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Affiliation(s)
- Miyu Nakayama
- Drug Metabolism and Pharmacokinetics Research Laboratories, Preclinical and Translational Sciences, Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-Chome, Fujisawa, Kanagawa, Japan.
| | - Syunsuke Yamamoto
- Drug Metabolism and Pharmacokinetics Research Laboratories, Preclinical and Translational Sciences, Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-Chome, Fujisawa, Kanagawa, Japan
| | - Hideki Hirabayashi
- Drug Metabolism and Pharmacokinetics Research Laboratories, Preclinical and Translational Sciences, Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-Chome, Fujisawa, Kanagawa, Japan
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Fontana C, Marasca F, Provitera L, Mancinelli S, Pesenti N, Sinha S, Passera S, Abrignani S, Mosca F, Lodato S, Bodega B, Fumagalli M. Early maternal care restores LINE-1 methylation and enhances neurodevelopment in preterm infants. BMC Med 2021; 19:42. [PMID: 33541338 PMCID: PMC7863536 DOI: 10.1186/s12916-020-01896-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 12/22/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Preterm birth affects almost 9-11% of newborns and is one of the leading causes of childhood neurodevelopmental disabilities; the underlying molecular networks are poorly defined. In neurons, retrotransposons LINE-1 (L1) are an active source of genomic mosaicism that is deregulated in several neurological disorders; early life experience has been shown to regulate L1 activity in mice. METHODS Very preterm infants were randomized to receive standard care or early intervention. L1 methylation was measured at birth and at hospital discharge. At 12 and 36 months, infants' neurodevelopment was evaluated with the Griffiths Scales. L1 methylation and CNVs were measured in mouse brain areas at embryonic and postnatal stages. RESULTS Here we report that L1 promoter is hypomethylated in preterm infants at birth and that an early intervention program, based on enhanced maternal care and positive multisensory stimulation, restores L1 methylation levels comparable to healthy newborns and ameliorates neurodevelopment in childhood. We further show that L1 activity is fine-tuned in the perinatal mouse brain, suggesting a sensitive and vulnerable window for the L1 epigenetic setting. CONCLUSIONS Our results open the field on the inspection of L1 activity as a novel molecular and predictive approach to infants' prematurity-related neurodevelopmental outcomes. TRIAL REGISTRATION ClinicalTrial.gov ( NCT02983513 ). Registered on 6 December 2016, retrospectively registered.
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Affiliation(s)
- Camilla Fontana
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Federica Marasca
- Istituto Nazionale di Genetica Molecolare "Enrica e Romeo Invernizzi" (INGM), Milan, Italy
| | - Livia Provitera
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, NICU, Milan, Italy
| | - Sara Mancinelli
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy.,IRCCS Humanitas Clinical and Research Center, Rozzano, Milan, Italy
| | - Nicola Pesenti
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, NICU, Milan, Italy.,Department of Statistics and Quantitative Methods, Division of Biostatistics, Epidemiology and Public Health, University of Milano-Bicocca, Milan, Italy
| | - Shruti Sinha
- Istituto Nazionale di Genetica Molecolare "Enrica e Romeo Invernizzi" (INGM), Milan, Italy
| | - Sofia Passera
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, NICU, Milan, Italy
| | - Sergio Abrignani
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy.,Istituto Nazionale di Genetica Molecolare "Enrica e Romeo Invernizzi" (INGM), Milan, Italy
| | - Fabio Mosca
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy.,Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, NICU, Milan, Italy
| | - Simona Lodato
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy.,IRCCS Humanitas Clinical and Research Center, Rozzano, Milan, Italy
| | - Beatrice Bodega
- Istituto Nazionale di Genetica Molecolare "Enrica e Romeo Invernizzi" (INGM), Milan, Italy.
| | - Monica Fumagalli
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy. .,Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, NICU, Milan, Italy.
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Kuroki R, Murata Y, Fuke S, Nakachi Y, Nakashima J, Kujoth GC, Prolla TA, Bundo M, Kato T, Iwamoto K. Establishment of Quantitative PCR Assays for Active Long Interspersed Nuclear Element-1 Subfamilies in Mice and Applications to the Analysis of Aging-Associated Retrotransposition. Front Genet 2020; 11:519206. [PMID: 33193604 PMCID: PMC7525186 DOI: 10.3389/fgene.2020.519206] [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: 12/11/2019] [Accepted: 08/20/2020] [Indexed: 01/01/2023] Open
Abstract
The retrotransposon long interspersed nuclear element-1 (LINE-1) can autonomously increase its copy number within a host genome through the retrotransposition process. LINE-1 is active in the germline and in neural progenitor cells, and its somatic retrotransposition activity has a broad impact on neural development and susceptibility to neuropsychiatric disorders. The method to quantify the genomic copy number of LINE-1 would be important in unraveling the role of retrotransposition, especially in the brain. However, because of the species-specific evolution of LINE-1 sequences, methods for quantifying the copy number should be independently developed. Here, we developed a quantitative PCR (qPCR) assay to measure the copy number of active LINE-1 subfamilies in mice. Using the assay, we investigated aging-associated alterations of LINE-1 copy number in several brain regions in wild-type mice and Polg+/D257A mice as a model for accelerated aging. We found that aged Polg+/D257A mice showed higher levels of the type GfII LINE-1 in the basal ganglia than the wild-type mice did, highlighting the importance of assays that focus on an individual active LINE-1 subfamily.
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Affiliation(s)
- Ryota Kuroki
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Yui Murata
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Satoshi Fuke
- Lab for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Wako, Japan
| | - Yutaka Nakachi
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Jun Nakashima
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Gregory C Kujoth
- Department of Genetics and Medical Genetics, University of Wisconsin, Madison, WI, United States
| | - Tomas A Prolla
- Department of Genetics and Medical Genetics, University of Wisconsin, Madison, WI, United States
| | - Miki Bundo
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan.,PRESTO, Japan Science and Technology Agency, Saitama, Japan
| | - Tadafumi Kato
- Lab for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Wako, Japan
| | - Kazuya Iwamoto
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
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