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Palazzese L, Turri F, Anzalone DA, Saragusty J, Bonnet J, Colotte M, Tuffet S, Pizzi F, Luciani A, Matsukawa K, Czernik M, Loi P. Reviving vacuum-dried encapsulated ram spermatozoa via ICSI after 2 years of storage. Front Vet Sci 2023; 10:1270266. [PMID: 38098985 PMCID: PMC10720722 DOI: 10.3389/fvets.2023.1270266] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 11/14/2023] [Indexed: 12/17/2023] Open
Abstract
Introduction Freeze-drying techniques give alternative preservation mammalian spermatozoa without liquid nitrogen. However, most of the work has been conducted in the laboratory mouse, while little information has been gathered on large animals that could also benefit from this kind of storage. Methods This work adapted a technique known as vacuum-drying encapsulation (VDE), originally developed for nucleic acid conservation in anhydrous state, to ram spermatozoa, and compared it to canonical lyophilization (FD), testing long-term storage at room temperature (RT) and 4°C. Results and discussion The results demonstrated better structural stability, namely lipid composition and DNA integrity, in VDE spermatozoa than FD ones, with outcomes at RT storage comparable to 4°C. Likewise, in VDE the embryonic development was higher than in FD samples (12.8% vs. 8.7%, p < 0.001, respectively). Our findings indicated that in large mammals, it is important to consider dehydration-related changes in sperm polyunsaturated fatty acids coupled with DNA alterations, given their crucial role in embryonic development.
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Affiliation(s)
- Luca Palazzese
- Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, Warsaw, Poland
| | - Federica Turri
- Institute of Agricultural Biology and Biotechnology (IBBA), National Research Council (CNR), Lodi, Italy
| | | | - Joseph Saragusty
- Department of Veterinary Medicine, University of Teramo, Teramo, Italy
| | - Jacques Bonnet
- Laboratoire de Recherche et Développement, Imagene Company, Pessac, France
- Institut Bergonié, INSERM, Université de Bordeaux, Bordeaux, France
| | - Marthe Colotte
- Plateforme de Production, Imagene, Genopole, Evry, France
| | - Sophie Tuffet
- Plateforme de Production, Imagene, Genopole, Evry, France
| | - Flavia Pizzi
- Institute of Agricultural Biology and Biotechnology (IBBA), National Research Council (CNR), Lodi, Italy
| | - Alessia Luciani
- Department of Veterinary Medicine, University of Teramo, Teramo, Italy
| | | | - Marta Czernik
- Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, Warsaw, Poland
- Department of Veterinary Medicine, University of Teramo, Teramo, Italy
| | - Pasqualino Loi
- Department of Veterinary Medicine, University of Teramo, Teramo, Italy
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Coudy D, Colotte M, Luis A, Tuffet S, Bonnet J. Long term conservation of DNA at ambient temperature. Implications for DNA data storage. PLoS One 2021; 16:e0259868. [PMID: 34763344 PMCID: PMC8585539 DOI: 10.1371/journal.pone.0259868] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 10/27/2021] [Indexed: 11/18/2022] Open
Abstract
DNA conservation is central to many applications. This leads to an ever-increasing number of samples which are more and more difficult and costly to store or transport. A way to alleviate this problem is to develop procedures for storing samples at room temperature while maintaining their stability. A variety of commercial systems have been proposed but they fail to completely protect DNA from deleterious factors, mainly water. On the other side, Imagene company has developed a procedure for long-term conservation of biospecimen at room temperature based on the confinement of the samples under an anhydrous and anoxic atmosphere maintained inside hermetic capsules. The procedure has been validated by us and others for purified RNA, and for DNA in buffy coat or white blood cells lysates, but a precise determination of purified DNA stability is still lacking. We used the Arrhenius law to determine the DNA degradation rate at room temperature. We found that extrapolation to 25°C gave a degradation rate constant equivalent to about 1 cut/century/100 000 nucleotides, a stability several orders of magnitude larger than the current commercialized processes. Such a stability is fundamental for many applications such as the preservation of very large DNA molecules (particularly interesting in the context of genome sequencing) or oligonucleotides for DNA data storage. Capsules are also well suited for this latter application because of their high capacity. One can calculate that the 64 zettabytes of data produced in 2020 could be stored, standalone, for centuries, in about 20 kg of capsules.
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Affiliation(s)
- Delphine Coudy
- Laboratoire de Recherche et développement, Imagene Company, Pessac, France
| | - Marthe Colotte
- Imagene, plateforme de production, Genopole, Evry, France
| | - Aurélie Luis
- Laboratoire de Recherche et développement, Imagene Company, Pessac, France
| | - Sophie Tuffet
- Laboratoire de Recherche et développement, Imagene Company, Pessac, France
- Imagene, plateforme de production, Genopole, Evry, France
| | - Jacques Bonnet
- Laboratoire de Recherche et développement, Imagene Company, Pessac, France
- Université de Bordeaux, Institut Bergonié, INSERM, Bordeaux, France
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Fabre AL, Luis A, Colotte M, Tuffet S, Bonnet J. High DNA stability in white blood cells and buffy coat lysates stored at ambient temperature under anoxic and anhydrous atmosphere. PLoS One 2017; 12:e0188547. [PMID: 29190767 PMCID: PMC5708797 DOI: 10.1371/journal.pone.0188547] [Citation(s) in RCA: 9] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 10/30/2017] [Indexed: 01/28/2023] Open
Abstract
Conventional storage of blood-derived fractions relies on cold. However, lately, ambient temperature preservation has been evaluated by several independent institutions that see economic and logistic advantages in getting rid of the cold chain. Here we validated a novel procedure for ambient temperature preservation of DNA in white blood cell and buffy coat lysates based on the confinement of the desiccated biospecimens under anoxic and anhydrous atmosphere in original hermetic minicapsules. For this validation we stored encapsulated samples either at ambient temperature or at several elevated temperatures to accelerate aging. We found that DNA extracted from stored samples was of good quality with a yield of extraction as expected. Degradation rates were estimated from the average fragment size of denatured DNA run on agarose gels and from qPCR reactions. At ambient temperature, these rates were too low to be measured but the degradation rate dependence on temperature followed Arrhenius’ law, making it possible to extrapolate degradation rates at 25°C. According to these values, the DNA stored in the encapsulated blood products would remain larger than 20 kb after one century at ambient temperature. At last, qPCR experiments demonstrated the compatibility of extracted DNA with routine DNA downstream analyses. Altogether, these results showed that this novel storage method provides an adequate environment for ambient temperature long term storage of high molecular weight DNA in dehydrated lysates of white blood cells and buffy coats.
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Affiliation(s)
- Anne-Lise Fabre
- Imagene, R&D department, Université de Bordeaux, ENSTBB, 146 Rue Léo Saignat, Bordeaux, France
- Imagene, production platform, Rue Henri Desbruères, Genopole campus 1, Bât 6, Evry, France
- * E-mail:
| | - Aurélie Luis
- Imagene, R&D department, Université de Bordeaux, ENSTBB, 146 Rue Léo Saignat, Bordeaux, France
| | - Marthe Colotte
- Imagene, production platform, Rue Henri Desbruères, Genopole campus 1, Bât 6, Evry, France
| | - Sophie Tuffet
- Imagene, R&D department, Université de Bordeaux, ENSTBB, 146 Rue Léo Saignat, Bordeaux, France
| | - Jacques Bonnet
- Imagene, R&D department, Université de Bordeaux, ENSTBB, 146 Rue Léo Saignat, Bordeaux, France
- Institut Bergonié- Université de Bordeaux, INSERM U1218, 229 Cours de l'Argonne, Bordeaux, France
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Li Q, Wang X, Liu X, Liao Q, Sun J, He X, Yang T, Yin J, Jia J, Li X, Colotte M, Bonnet J. Long-Term Room Temperature Storage of Dry Ribonucleic Acid for Use in RNA-Seq Analysis. Biopreserv Biobank 2017; 15:502-511. [PMID: 29022740 DOI: 10.1089/bio.2017.0024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
RNA is an essential biological material for research in genomics and translational medicine. As such, its storage for biobanking is an important field of study. Traditionally, long-term storage in the cold (generally freezers or liquid nitrogen) is used to maintain high-quality (in terms of quantity and integrity) RNA. Room temperature (RT) preservation provides an alternative to the cold, which is plagued by serious problems (mainly cost and safety), for RNA long-term storage. In this study, we evaluated the performance of several RT storage procedures, including the RNAshell® from Imagene, where the RNA is dried and kept protected from the atmosphere, and the vacuum drying of RNA with additives such as the Imagene stabilization solution and a home-made trehalose solution. This evaluation was performed through accelerated (equivalent to 10 years for RNAshell) aging and real-time studies (4 years). To check RNA quality and integrity, we used RNA integrity number values and RNA-seq. Our study shows that isolation from atmosphere offers a superior protective effect for RNA storage compared with vacuum drying alone, and demonstrates that RNAshell permits satisfactory RNA quality for long-term RT storage. Thus, the RNA quality could meet the demand of downstream applications such as RNA-seq.
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Affiliation(s)
- Qiyuan Li
- 1 China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
| | - Xian Wang
- 1 China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
| | - Xiaopan Liu
- 1 China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
| | - Qiuyan Liao
- 1 China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
| | - Jianbo Sun
- 1 China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
| | - Xuheng He
- 1 China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
| | - Ting Yang
- 1 China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
| | - Jiefang Yin
- 1 China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
| | - Jia Jia
- 1 China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
| | - Xue Li
- 1 China National GeneBank-Shenzhen , BGI-Shenzhen, Shenzhen, China
| | - Marthe Colotte
- 2 Imagene, Production Platform , Rue Henri Desbruères, Evry, France
| | - Jacques Bonnet
- 3 Institut Bergonié, Université de Bordeaux , Bordeaux, France .,4 Imagene, R&D Department, Université de Bordeaux , ENSTBB, Bordeaux, France
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Colotte M, Coudy D, Tuffet S, Bonnet J. Adverse effect of air exposure on the stability of DNA stored at room temperature. Biopreserv Biobank 2014; 9:47-50. [PMID: 24850205 DOI: 10.1089/bio.2010.0028] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Marthe Colotte
- 1 Société Imagene, Plateforme de Production, Evry, France
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Bonnet J, Colotte M, Coudy D, Couallier V, Portier J, Morin B, Tuffet S. Chain and conformation stability of solid-state DNA: implications for room temperature storage. Nucleic Acids Res 2009; 38:1531-46. [PMID: 19969539 PMCID: PMC2836546 DOI: 10.1093/nar/gkp1060] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
There is currently wide interest in room temperature storage of dehydrated DNA. However, there is insufficient knowledge about its chemical and structural stability. Here, we show that solid-state DNA degradation is greatly affected by atmospheric water and oxygen at room temperature. In these conditions DNA can even be lost by aggregation. These are major concerns since laboratory plastic ware is not airtight. Chain-breaking rates measured between 70 degrees C and 140 degrees C seemed to follow Arrhenius' law. Extrapolation to 25 degrees C gave a degradation rate of about 1-40 cuts/10(5) nucleotides/century. However, these figures are to be taken as very tentative since they depend on the validity of the extrapolation and the positive or negative effect of contaminants, buffers or additives. Regarding the secondary structure, denaturation experiments showed that DNA secondary structure could be preserved or fully restored upon rehydration, except possibly for small fragments. Indeed, below about 500 bp, DNA fragments underwent a very slow evolution (almost suppressed in the presence of trehalose) which could end in an irreversible denaturation. Thus, this work validates using room temperature for storage of DNA if completely protected from water and oxygen.
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Affiliation(s)
- Jacques Bonnet
- Université de Bordeaux-plateforme Génomique Fonctionnelle, Institut Bergonié-INSERM U916 VINCO, Bordeaux, France.
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Colotte M, Couallier V, Tuffet S, Bonnet J. Simultaneous assessment of average fragment size and amount in minute samples of degraded DNA. Anal Biochem 2009; 388:345-7. [DOI: 10.1016/j.ab.2009.02.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Macgrogan G, Hostein I, Chibon F, Geneste G, Petersen M, Velasco V, De Mascarel I, Soubeyran I, Bui M, Coindre J, Parrens M, De Mascarel A, Belaud-Rotureau M, Idrissi Y, Turmot M, Merlio J, Bonnet J, Colotte M, Tuffet S. Accélération de la fixation par le micro-ondes : l’expérience bordelaise. Ann Pathol 2007. [DOI: 10.1016/s0242-6498(07)92881-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Bellott R, Le Morvan V, Charasson V, Laurand A, Colotte M, Zanger UM, Klein K, Smith D, Bonnet J, Robert J. Functional study of the 830C>G polymorphism of the human carboxylesterase 2 gene. Cancer Chemother Pharmacol 2007; 61:481-8. [PMID: 17483951 DOI: 10.1007/s00280-007-0493-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2007] [Accepted: 04/02/2007] [Indexed: 01/02/2023]
Abstract
PURPOSE Carboxylesterase 2 (CES2) is involved in the activation of the anticancer drug irinotecan to its active metabolite SN-38. We previously identified a single nucleotide polymorphism (SNP), with an allele frequency around 10%, as possibly involved in enzyme expression (Clin Pharmacol Ther 76:528-535, 2004), which could explain the large individual variation in SN-38 disposition. METHODS The 830C>G SNP, located in the 5' untranslated region of the gene, was analysed in various DNA samples extracted from: (1) the National Cancer Institute NCI-60 panel of human tumour cell lines; (2) a collection of 104 samples of normal tissue from colorectal cancer patients; (3) blood samples from a population of 95 normal subjects; (4) a collection of 285 human livers. CES2 genotypes were tentatively related to irinotecan cytotoxicity and CES2 expression in the NCI-60 panel; to response to treatment and event-free survival in colorectal cancer patients; and to CES2 expression and catalytic activity in subsets of the human liver collection. RESULTS No significant relationship was found in the NCI-60 panel between CES2 830C>G genotype and irinotecan cytotoxicity or CES2 expression. No significant relationship was found between CES2 830C>G genotype and the toxicity and therapeutic efficacy (tumour response, event-free survival) of irinotecan in colorectal cancer patients. There was no significant relationship between CES2 830C>G genotype and CES2 expression and catalytic activity determined in a subset of genotype-selected liver samples. CONCLUSION The 830C>G SNP of CES2 is unlikely to have significant functional consequences on CES2 expression, activity or function.
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Affiliation(s)
- Ricardo Bellott
- Laboratoire de Pharmacologie des Agents Anticancéreux, Institut Bergonié, Université Victor Segalen Bordeaux 2, France
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