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Mordenti M, Capicchioni V, Corsini S, Locatelli M, Abelli E, Banchelli F, Boarini M, Sangiorgi L. Preanalytical DNA assessment for downstream applications: How to optimize the management of human biospecimens to support molecular diagnosis-An experimental study. J Clin Lab Anal 2022; 36:e24531. [PMID: 35666551 PMCID: PMC9279999 DOI: 10.1002/jcla.24531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 11/09/2022] Open
Abstract
Background The development of next‐generation sequencing approaches has accelerated the diagnostic process, although at present, there is a lack of a clear consensus on efficient management of human samples for downstream applications. This study aims to investigate timeframe (in terms of short preservation), temperature, and additional preservation procedures (i.e., freeze and thaw cycles) for human biospecimens to implement the reliability and reproducibility of molecular investigations. Methods Overall, 45 whole peripheral bloods, 22 peripheral blood mononuclear cells samples, 15 saliva, and 15 buccal swab biospecimens (through the extracted DNA) were investigated, assessing yield, integrity, amplifiability, and sizing accuracy via the most common molecular techniques. Results Based on the overall evaluation criteria, the results indicate that DNA extracted from all samples, shortly preserved, have suitable quality and reliable reproducibility to be used in diagnostic activities and biomedical research, even if DNA from peripheral blood mononuclear cells is more affected by the experimental conditions. Conclusion Our findings confirm the reliability of peripheral blood samples in almost all the experimental conditions. Saliva and buccal swabs are efficient almost as well, while peripheral blood mononuclear cells, albeit remain a primary source of DNA for molecular screenings, represent a less efficient source.
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Affiliation(s)
- Marina Mordenti
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Valentina Capicchioni
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy.,Ministry of Education, San Marino, Repubic of San Marino
| | - Serena Corsini
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Manuela Locatelli
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Elisabetta Abelli
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Federico Banchelli
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Manila Boarini
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Luca Sangiorgi
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
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Song J, Zhou J. Effects of preservation duration at 4 °C on the quality of RNA in rabbit blood specimens. PeerJ 2020; 8:e8940. [PMID: 32309050 PMCID: PMC7153556 DOI: 10.7717/peerj.8940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 03/18/2020] [Indexed: 11/30/2022] Open
Abstract
A prolonged preservation duration of blood specimens at 4 °C may occur due to the distance from collection points to storage facilities in many biobanks, especially for multicenter studies. This could lead to RNA degradation, affecting downstream analyses. However, effects of preservation durations at 4 °C on RNA quality in blood specimens need to be studied. We collected rabbit blood using EDTA tubes and stored them at 4 °C for different preservation durations. Then, we examined the quality of RNA from whole blood and leukocytes isolated from rabbit blood. Our results show that the purity of whole blood RNA and leukocyte RNA does not indicate significant change after rabbit blood is stored at 4 °C for different preservation durations (from 1 h to 7 days). The integrity of leukocyte RNA indicates the same result as above, but the integrity of whole blood RNA is significantly decreased after rabbit blood is stored at 4 °C for over 3 days. Moreover, expression of SMAD7, MKI67, FOS, TGFβ1 and HIF1α of whole blood RNA and leukocyte RNA remains basically stable, but PCNA expression of whole blood RNA or leukocyte RNA is significantly decreased after rabbit blood is stored at 4 °C for over 24 h or 7 days. Therefore, these results suggest that high-quality RNA is obtained from the fresher blood specimens and if blood specimens are stored for over 3 days at 4 °C, the quality of leukocyte RNA is more stable and of better quality than that of whole blood RNA.
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Affiliation(s)
- Jiaojiao Song
- Children's Hospital of Shanghai, Shanghai, China.,Children's Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, China
| | - Junmei Zhou
- Children's Hospital of Shanghai, Shanghai, China.,Children's Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, China
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Wang C, Wang Z, You Y, Xu W, Lv Z, Liu Z, Chen W, Shi Y. Response of Arthrobacter QD 15-4 to dimethyl phthalate by regulating energy metabolism and ABC transporters. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 174:146-152. [PMID: 30825737 DOI: 10.1016/j.ecoenv.2019.02.078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 02/22/2019] [Accepted: 02/25/2019] [Indexed: 06/09/2023]
Abstract
Ubiquitous dimethyl phthalate (DMP) has severely threatened environmental safety and the health of organisms. Therefore, it is necessary to degrade DMP, removing it from the environment. Microbiological degradation is an efficient and safe method for degrading DMP. In this study, the response of Arthrobacter QD 15-4 to DMP was investigated. The results showed that the growth of Arthrobacter QD 15-4 was not impacted by DMP and Arthrobacter QD 15-4 could degrade DMP. RNA-Seq and RT-qPCR results showed that DMP treatment caused some changes in the expression of key genes in Arthrobacter QD 15-4. The transcriptional expressions of pstSCAB and phoU were downregulated by DMP. The transcriptional expressions of potACD, gluBC, oppAB, pdhAB, aceAF, gltA were upregulated by DMP. The genes are mainly involved in regulating energy metabolism and ATP-binding cassette (ABC) transporters. The increasing of pyruvic acid and citrate in Arthrobacter QD 15-4 further supported the energy metabolism was improved by DMP. It was clearly shown that Arthrobacter QD 15-4 made response to dimethyl phthalate by regulating energy metabolism and ABC transporters.
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Affiliation(s)
- Chunlong Wang
- School of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar, Heilongjiang 161006, China
| | - Zhigang Wang
- School of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar, Heilongjiang 161006, China.
| | - Yimin You
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Weihui Xu
- School of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar, Heilongjiang 161006, China
| | - Zhihang Lv
- School of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar, Heilongjiang 161006, China
| | - Zeping Liu
- School of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar, Heilongjiang 161006, China
| | - Wenjing Chen
- School of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar, Heilongjiang 161006, China
| | - Yiran Shi
- School of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar, Heilongjiang 161006, China
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4
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Wang Z, Wang C, You Y, Xu W, Lv Z, Liu Z, Chen W, Shi Y, Wang J. Response of Pseudomonas fluorescens to dimethyl phthalate. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 167:36-43. [PMID: 30292974 DOI: 10.1016/j.ecoenv.2018.09.078] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 09/14/2018] [Accepted: 09/18/2018] [Indexed: 06/08/2023]
Abstract
Dimethyl phthalate (DMP) is a ubiquitous pollutant that is very harmful to organisms due to its mutagenicity, teratogenicity and carcinogenicity. Pseudomonas fluorescens (P. fluorescens) is one of the most important bacteria in the environment. In this study, the response of P. fluorescens to DMP was investigated. It was found that DMP greatly inhibited the growth and glucose utilization of P. fluorescens when the concentration of DMP was ranged from 20 to 40 mg/l. The surface hydrophobicity and membrane permeability of P. fluorescens were also increased by DMP. DMP could lead to the deformations of cell membrane and the mis-opening of membrane channels. RNA-Seq and RT-qPCR results showed that the expression of some genes in P. fluorescens were altered, including the genes involved in energy metabolism, ATP-binding cassette (ABC) transporting and two-component systems. Additionally, the productions of lactic acid and pyruvic acid were reduced and the activity of hexokinase was inhibited in P. fluorescens by DMP. Clearly, the results suggested that DMP contamination could alter the biological function of P. fluorescens in the environment.
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Affiliation(s)
- Zhigang Wang
- School of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar, Heilongjiang, 161006, China.
| | - Chunlong Wang
- School of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar, Heilongjiang, 161006, China.
| | - Yimin You
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Weihui Xu
- School of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar, Heilongjiang, 161006, China.
| | - Zhihang Lv
- School of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar, Heilongjiang, 161006, China.
| | - Zeping Liu
- School of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar, Heilongjiang, 161006, China.
| | - Wenjing Chen
- School of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar, Heilongjiang, 161006, China.
| | - Yiran Shi
- School of Life Science and Agriculture and Forestry, Qiqihar University, Qiqihar, Heilongjiang, 161006, China.
| | - Junhe Wang
- Qiqihar Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar, Heilongjiang, 161006, China.
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Jia Y, Xu H, Li Y, Wei C, Guo R, Wang F, Wu Y, Liu J, Jia J, Yan J, Qi X, Li Y, Gao X. A Modified Ficoll-Paque Gradient Method for Isolating Mononuclear Cells from the Peripheral and Umbilical Cord Blood of Humans for Biobanks and Clinical Laboratories. Biopreserv Biobank 2017; 16:82-91. [PMID: 29232525 DOI: 10.1089/bio.2017.0082] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Although the Ficoll-Paque method is classically used to isolate peripheral blood mononuclear cells (PBMCs), modifications in this method are required for a more rapid and economic output for biobanks and clinical laboratories, particularly in developing countries. In this study, we addressed this issue by modifying the Ficoll-Paque method for the isolation of PBMCs or mononuclear cells from the peripheral and the umbilical cord blood of healthy and diseased (infected, anemic, and chronic obstructive pulmonary disease) adult individuals. In the modified method, we initiated the cell isolation process from the buffy coat layer, which appears in the interface between the plasma and sediments after centrifugation, instead of using the whole blood as described in the classic method. Although the PBMC yield by the modified method was about 12% less than in the classic method, the number of PBMCs isolated by the modified method was more than one million, which is enough for different research/diagnostic purposes, such as multi-omics detection. Assessment of cell viability and purity by hematology analyzer and trypan blue showed no significant difference between the viability and purity of the PBMCs isolated by these two methods in almost all groups, except samples from the infected and cord blood groups, where lower PBMC purity with higher granulocyte contamination were observed. In addition, at delayed processing time points, all parameters for the two methods were decreased in a time-dependent manner, especially at 8, 12, or 24 hours after the sample collection. In summary, the performance of PBMC isolation by the classic and modified methods mainly relies on the PBMC ratio in original samples. The modified method could be preferred for PBMC isolation because of its time and cost savings, especially for the biobanks and clinical laboratories in developing countries.
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Affiliation(s)
- Yanjuan Jia
- 1 The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital , Lanzhou, China
| | - Hui Xu
- 1 The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital , Lanzhou, China
| | - Yonghong Li
- 1 The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital , Lanzhou, China
| | - Chaojun Wei
- 1 The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital , Lanzhou, China
| | - Rui Guo
- 1 The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital , Lanzhou, China
| | - Fang Wang
- 2 The Clinical Laboratory Centre, Gansu Provincial Hospital , Lanzhou, China
| | - Yu Wu
- 1 The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital , Lanzhou, China
| | - Jing Liu
- 2 The Clinical Laboratory Centre, Gansu Provincial Hospital , Lanzhou, China
| | - Jing Jia
- 1 The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital , Lanzhou, China
| | - Junwen Yan
- 2 The Clinical Laboratory Centre, Gansu Provincial Hospital , Lanzhou, China
| | - Xiaoming Qi
- 1 The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital , Lanzhou, China
| | - Yuanting Li
- 1 The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital , Lanzhou, China
| | - Xiaoling Gao
- 1 The Institute of Clinical Research and Translational Medicine, Gansu Provincial Hospital , Lanzhou, China
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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] [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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