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Gambarino S, Galliano I, Clemente A, Calvi C, Montanari P, Pau A, Dini M, Bergallo M. Characteristics of RNA Stabilizer RNApro for Peripheral Blood Collection. Diagnostics (Basel) 2024; 14:971. [PMID: 38786269 PMCID: PMC11120318 DOI: 10.3390/diagnostics14100971] [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: 03/15/2024] [Revised: 04/22/2024] [Accepted: 04/30/2024] [Indexed: 05/25/2024] Open
Abstract
Peripheral blood is the most practical tissue for human immune system gene expression profiling because it is easily accessible, whereas the site of primary infection in certain diseases may not be easily accessible. Due to the ex vivo instability of RNA transcripts, a key challenge in the gene expression analysis of blood samples is the rapid sample handling and stabilization of the mRNA by adding an RNA preservative (PAXgeneTM Blood RNA Tubes, TempusTM Blood RNA tubes, RNAlater Stabilization Reagent, RNAgard® Blood Tubes). BioMole (Turin, Italy) has developed a novel blood stabilizer, called RNApro, in which RNA is stabilized during phlebotomy and sample storage. In this study, RNApro performance intended as RNA yield, integrity, and stability was evaluated. Our results show that blood samples stored at -80 °C and re-extracted after 7 years show no differences in terms of quantity, quality, and amplificability. The samples in the RNAlater stabilization solution can be stored at room temperature for up to one week or at 4 °C for up to one month. Similar results can also be observed for PAXgene tubes, Tempus tubes, and RNAgard tubes. In agreement with these data, the RNApro stabilization solution preserves the RNA from degradation for up to 1 month at 4 °C and 1 week at room temperature. RNApro can be stored indifferently at -80, -20, 4 °C, or room temperature for up to 2 months after, and then could be stored at -80 °C for up to seven years. In summary, our study is the first to analyze the performance of an RNA stabilizer called RNApro. We can conclude that several studies have shown significant differences in gene expression analysis when the sample was preserved in different RNA stabilizers. Therefore, it is desirable to standardize the method of nucleic acid conservation when comparing data from transcriptomic analyses.
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Affiliation(s)
- Stefano Gambarino
- Department of Public Health and Pediatric Sciences, Immunopathology Laboratory, Medical School, University of Turin, Piazza Polonia, 94, 10126 Turin, Italy; (S.G.); (I.G.); (A.C.); (C.C.); (P.M.); (A.P.); (M.D.)
- BioMole srl, Via Quarello 15/A, Turin, 10135, Italy
| | - Ilaria Galliano
- Department of Public Health and Pediatric Sciences, Immunopathology Laboratory, Medical School, University of Turin, Piazza Polonia, 94, 10126 Turin, Italy; (S.G.); (I.G.); (A.C.); (C.C.); (P.M.); (A.P.); (M.D.)
| | - Anna Clemente
- Department of Public Health and Pediatric Sciences, Immunopathology Laboratory, Medical School, University of Turin, Piazza Polonia, 94, 10126 Turin, Italy; (S.G.); (I.G.); (A.C.); (C.C.); (P.M.); (A.P.); (M.D.)
- BioMole srl, Via Quarello 15/A, Turin, 10135, Italy
| | - Cristina Calvi
- Department of Public Health and Pediatric Sciences, Immunopathology Laboratory, Medical School, University of Turin, Piazza Polonia, 94, 10126 Turin, Italy; (S.G.); (I.G.); (A.C.); (C.C.); (P.M.); (A.P.); (M.D.)
| | - Paola Montanari
- Department of Public Health and Pediatric Sciences, Immunopathology Laboratory, Medical School, University of Turin, Piazza Polonia, 94, 10126 Turin, Italy; (S.G.); (I.G.); (A.C.); (C.C.); (P.M.); (A.P.); (M.D.)
| | - Anna Pau
- Department of Public Health and Pediatric Sciences, Immunopathology Laboratory, Medical School, University of Turin, Piazza Polonia, 94, 10126 Turin, Italy; (S.G.); (I.G.); (A.C.); (C.C.); (P.M.); (A.P.); (M.D.)
| | - Maddalena Dini
- Department of Public Health and Pediatric Sciences, Immunopathology Laboratory, Medical School, University of Turin, Piazza Polonia, 94, 10126 Turin, Italy; (S.G.); (I.G.); (A.C.); (C.C.); (P.M.); (A.P.); (M.D.)
- BioMole srl, Via Quarello 15/A, Turin, 10135, Italy
| | - Massimiliano Bergallo
- Department of Public Health and Pediatric Sciences, Immunopathology Laboratory, Medical School, University of Turin, Piazza Polonia, 94, 10126 Turin, Italy; (S.G.); (I.G.); (A.C.); (C.C.); (P.M.); (A.P.); (M.D.)
- BioMole srl, Via Quarello 15/A, Turin, 10135, Italy
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Owen BM, Phie J, Huynh J, Needham S, Fraser C. Evaluation of quantitative biomarkers of aging in human PBMCs. FRONTIERS IN AGING 2023; 4:1260502. [PMID: 37780865 PMCID: PMC10540680 DOI: 10.3389/fragi.2023.1260502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/01/2023] [Indexed: 10/03/2023]
Abstract
Functional decline with age contributes significantly to the burden of disease in developed countries. There is growing interest in the development of therapeutic interventions which slow or even reverse aging. Time and cost constraints prohibit the testing of a large number of interventions for health and lifespan extension in model organisms. Cell-based models of aging could enable high throughput testing of potential interventions. Despite extensive reports in the literature of cell properties that correlate with donor age, few are robustly observed across different laboratories. This casts doubt on the extent that aging signatures are captured in cultured cells. We tested molecular changes previously reported to correlate with donor age in peripheral blood mononuclear cells (PBMCs) and evaluated their suitability for inclusion in a panel of functional aging measures. The tested measures spanned several pathways implicated in aging including epigenetic changes, apoptosis, proteostasis, and intracellular communication. Surprisingly, only two markers correlated with donor age. DNA methylation age accurately predicted donor age confirming this is a robust aging biomarker. Additionally, the apoptotic marker CD95 correlated with donor age but only within subsets of PBMCs. To demonstrate cellular rejuvenation in response to a treatment will require integration of multiple read-outs of cell function. However, building a panel of measures to detect aging in cells is challenging and further research is needed to identify robust predictors of age in humans.
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Koval A, Larasati YA, Savitsky M, Solis GP, Good JM, Quinodoz M, Rivolta C, Superti-Furga A, Katanaev VL. In-depth molecular profiling of an intronic GNAO1 mutant as the basis for personalized high-throughput drug screening. MED 2023; 4:311-325.e7. [PMID: 37001522 DOI: 10.1016/j.medj.2023.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 03/01/2023] [Accepted: 03/07/2023] [Indexed: 04/03/2023]
Abstract
BACKGROUND The GNAO1 gene, encoding the major neuronal G protein Gαo, is mutated in a subset of pediatric encephalopathies. Most such mutations consist of missense variants. METHODS In this study, we present a precision medicine workflow combining next-generation sequencing (NGS) diagnostics, molecular etiology analysis, and personalized drug discovery. FINDINGS We describe a patient carrying a de novo intronic mutation (NM_020988.3:c.724-8G>A), leading to epilepsy-negative encephalopathy with motor dysfunction from the second decade. Our data show that this mutation creates a novel splice acceptor site that in turn causes an in-frame insertion of two amino acid residues, Pro-Gln, within the regulatory switch III region of Gαo. This insertion misconfigures the switch III loop and creates novel interactions with the catalytic switch II region, resulting in increased GTP uptake, defective GTP hydrolysis, and aberrant interactions with effector proteins. In contrast, intracellular localization, Gβγ interactions, and G protein-coupled receptor (GPCR) coupling of the Gαo[insPQ] mutant protein remain unchanged. CONCLUSIONS This in-depth analysis characterizes the heterozygous c.724-8G>A mutation as partially dominant negative, providing clues to the molecular etiology of this specific pathology. Further, this analysis allows us to establish and validate a high-throughput screening platform aiming at identifying molecules that could correct the aberrant biochemical functions of the mutant Gαo. FUNDING This work was supported by the Joint Seed Money Funding scheme between the University of Geneva and the Hebrew University of Jerusalem.
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Affiliation(s)
- Alexey Koval
- Translational Research Center in Oncohaematology, Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
| | - Yonika A Larasati
- Translational Research Center in Oncohaematology, Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
| | - Mikhail Savitsky
- Translational Research Center in Oncohaematology, Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
| | - Gonzalo P Solis
- Translational Research Center in Oncohaematology, Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
| | - Jean-Marc Good
- Division of Genetic Medicine, Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), 4031 Basel, Switzerland; Department of Ophthalmology, University of Basel, 4031 Basel, Switzerland; Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), 4031 Basel, Switzerland; Department of Ophthalmology, University of Basel, 4031 Basel, Switzerland; Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Andrea Superti-Furga
- Division of Genetic Medicine, Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Vladimir L Katanaev
- Translational Research Center in Oncohaematology, Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland; Institute of Life Sciences and Biomedicine, Far Eastern Federal University, 690090 Vladivostok, Russia.
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Ferrante JA, Smith CH, Thompson LM, Hunter ME. Genome-wide SNP analysis of three moose subspecies at the southern range limit in the contiguous United States. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01402-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AbstractGenome-wide evaluations of genetic diversity and population structure are important for informing management and conservation of trailing-edge populations. North American moose (Alces alces) are declining along portions of the southern edge of their range due to disease, species interactions, and marginal habitat, all of which may be exacerbated by climate change. We employed a genotyping by sequencing (GBS) approach in an effort to collect baseline information on the genetic variation of moose inhabiting the species’ southern range periphery in the contiguous United States. We identified 1920 single nucleotide polymorphisms (SNPs) from 155 moose representing three subspecies from five states: A. a. americana (New Hampshire), A. a. andersoni (Minnesota), and A. a. shirasi (Idaho, Montana, and Wyoming). Molecular analyses supported three geographically isolated clusters, congruent with currently recognized subspecies. Additionally, while moderately low genetic diversity was observed, there was little evidence of inbreeding. Results also indicated > 20% shared ancestry proportions between A. a. shirasi samples from northern Montana and A. a. andersoni samples from Minnesota, indicating a putative hybrid zone warranting further investigation. GBS has proven to be a simple and effective method for genome-wide SNP discovery in moose and provides robust data for informing herd management and conservation priorities. With increasing disease, predation, and climate related pressure on range edge moose populations in the United States, the use of SNP data to identify gene flow between subspecies may prove a powerful tool for moose management and recovery, particularly if hybrid moose are more able to adapt.
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