1
|
Peng H, Pan M, Zhou Z, Chen C, Xing X, Cheng S, Zhang S, Zheng H, Qian K. The impact of preanalytical variables on the analysis of cell-free DNA from blood and urine samples. Front Cell Dev Biol 2024; 12:1385041. [PMID: 38784382 PMCID: PMC11111958 DOI: 10.3389/fcell.2024.1385041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 04/22/2024] [Indexed: 05/25/2024] Open
Abstract
Cell-free DNA (cfDNA), a burgeoning class of molecular biomarkers, has been extensively studied across a variety of biomedical fields. As a key component of liquid biopsy, cfDNA testing is gaining prominence in disease detection and management due to the convenience of sample collection and the abundant wealth of genetic information it provides. However, the broader clinical application of cfDNA is currently impeded by a lack of standardization in the preanalytical procedures for cfDNA analysis. A number of fundamental challenges, including the selection of appropriate preanalytical procedures, prevention of short cfDNA fragment loss, and the validation of various cfDNA measurement methods, remain unaddressed. These existing hurdles lead to difficulties in comparing results and ensuring repeatability, thereby undermining the reliability of cfDNA analysis in clinical settings. This review discusses the crucial preanalytical factors that influence cfDNA analysis outcomes, including sample collection, transportation, temporary storage, processing, extraction, quality control, and long-term storage. The review provides clarification on achievable consensus and offers an analysis of the current issues with the goal of standardizing preanalytical procedures for cfDNA analysis.
Collapse
Affiliation(s)
- Hongwei Peng
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Ming Pan
- Taihe Skills Training Center, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China
| | - Zongning Zhou
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Congbo Chen
- Department of Urology, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China
| | - Xing Xing
- Department of Urology, The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
| | - Shaoping Cheng
- Department of Urology, The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
| | - Shanshan Zhang
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Hang Zheng
- Department of Urology, Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Kaiyu Qian
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Urology, Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| |
Collapse
|
2
|
He G, Wang W, Zhou Y, Zhao G, Liao J. Ampholytic ion-exchange magnetic beads: a promising tool for selecting short fragments in circulating cell-free DNA analysis. Front Oncol 2024; 14:1397680. [PMID: 38779084 PMCID: PMC11109406 DOI: 10.3389/fonc.2024.1397680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 04/23/2024] [Indexed: 05/25/2024] Open
Abstract
Objective For liquid biopsy of cancer, the extraction of circulating cell-free DNA (cfDNA) from plasma is required. We evaluated the efficacy of use of magnetic submicron particles coated with abundant small zwitterions (MSP-ZEWBs) for extracting short fragments of cfDNA. Methods We developed and optimized an MSP-ZEWB-based cfDNA extraction method using ampholytic ion-exchange materials and compared its results with those using a control kit. We measured the cfDNA concentration by quantitative polymerase-chain-reaction and using the Qubit method and analyzed cfDNA fragmentation patterns using a bioanalyzer. Results The fragment size of cfDNA isolated from glycine hydrochloric acid at a pH of 2.2 exhibited a better alignment with the DNA marker. The highest DNA intensity was observed at the final concentration of 0.8% polyethylene glycol 8000. The intensity of cfDNA decreased significantly when isolated from plasma with DNA marker using MSP-ZEWBs with an adsorption buffer containing guanidine hydrochloride or isothiocyanoguanidine. All fragments were successfully extracted using MSP-ZEWBs from both plasma and phosphate-buffered saline. Notably, the intensity of short cfDNA fragments isolated using MSP-ZEWBs remained consistent for recovery of long DNA fragments. indicating a potential selective of small fragments. Conclusion The extraction of plasma cfDNA with MSP-ZEWBs requires no protein denaturation, shows resistance to cells remaining in plasma, and demonstrates higher overall efficiency and better reproducibility than other extraction methods. Use of MSP-ZEWBs may greatly enhance liquid biopsy of cancers through the analysis of plasma cfDNA in clinical practice.
Collapse
Affiliation(s)
- Gan He
- Gastrointestinal Surgery, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Weixuan Wang
- Institute of Life Sciences, Chongqing Medical University, Chongqing, China
| | - Yongxia Zhou
- Department of Radiology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
- Center Laboratory, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Guowei Zhao
- Gastrointestinal Surgery, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Juan Liao
- Center Laboratory, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Geriatric Disease Clinical Research Center, Chongqing, China
| |
Collapse
|
3
|
Afzal M, Naeem MA, Ahmed S, Amin N, Rahim A, Munawar M, Ishaq M, Rathore A, Maria K. Noninvasive prenatal testing of beta-thalassemia for common Pakistani mutations: a comparative study using cell-free fetal DNA from maternal plasma and chorionic villus sampling. Hematology 2022; 27:353-359. [PMID: 35287566 DOI: 10.1080/16078454.2022.2045052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND The discovery of circulating cell-free fetal DNA (cff-DNA) in maternal plasma has inspired the noninvasive prenatal testing (NIPT) approaches for various genetic fetal screening including rhesus D typing, sex determination, aneuploidies, and single-gene disorders. OBJECTIVE Noninvasive determination of paternally inherited beta-thalassemia mutations in maternal total cell-free DNA (cf-DNA) by using allele-specific amplification refractory mutation system (ARMS) real-time PCR (RT-PCR) in concordance with the conventional invasive method. METHODS An observational study was conducted at the Armed Forces Institute of Blood Transfusion in collaboration with the genetics resource center from March 2021 to August 2021. A total number of 26 couples were selected having a history of previously affected children with beta-thalassemia. A routine chorionic villus sampling (CVS) invasive procedure was carried out, and the mutation analysis was done using conventional PCR. To assess NIPT, a total cf-DNA was also extracted from maternal plasma and analyzed using allele-specific ARMS RT-PCR. RESULTS Based on conventional PCR testing, 13 of 26 couples were found having beta-thalassemia carriers with homozygous mutation, and 13 couples were carriers with heterozygous mutations. Further to assess NIPT, the cf-DNA of 13 pregnant females among the couples with different mutational patterns was analyzed by allele-specific ARMS RT-PCR to detect paternally inherited mutations. In comparison with conventional PCR, 11 cases (84.6%) were matched successfully, while two cases (15.4%) had no concordance with conventional invasive prenatal testing (IPT). CONCLUSION NIPT using maternal cf-DNA by allele-specific ARMS RT-PCR can be feasible to screen paternal inherited mutant alleles to rule out pregnant women from invasive procedures where the test would be negative for paternal inheritance. However, a low amount of fetal DNA in maternal plasma is a limiting factor and required further improvement to enrich fetal cf-DNA for complete concordance with conventional IPT.
Collapse
Affiliation(s)
- Muhammad Afzal
- Biochemistry, Riphah International University Islamabad, Rawalpindi, Pakistan
| | | | - Suhaib Ahmed
- Biochemistry, Riphah International University Islamabad, Rawalpindi, Pakistan
| | - Nayyar Amin
- Hematology, Armed Forces Institute of Transfusion, Rawalpindi, Pakistan
| | - Amena Rahim
- Biochemistry, Riphah International University Islamabad, Rawalpindi, Pakistan
| | - Manazza Munawar
- Biochemistry, Riphah International University Islamabad, Rawalpindi, Pakistan
| | - Mansoor Ishaq
- Hematology, Armed Forces Institute of Transfusion, Rawalpindi, Pakistan
| | - Ali Rathore
- Hematology, Armed Forces Institute of Transfusion, Rawalpindi, Pakistan
| | - K Maria
- Hematology, Armed Forces Institute of Transfusion, Rawalpindi, Pakistan
| |
Collapse
|
4
|
Mahmoudian F, Akbariqomi M, Heidari R, Ghahremani MH, Roshan N, Adabi M, Absalan M, Karimi F, Bahrami S, Fathi S, Tavoosidana G. Designing a fluorescence padlock probe-based biosensor and colorimetric assay for the detection of G12D KRAS mutation. Biomark Med 2021; 15:1741-1754. [PMID: 34784779 DOI: 10.2217/bmm-2021-0333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: Cell-free DNA in the plasma is known to be a potential biomarker for noninvasive diagnosis of oncogenic mutations. The authors aimed to design an optimized padlock probe-based hyperbranched rolling circle amplification biosensor to detect the KRAS G12D mutation using fluorescence and colorimetric methods. Methods: Single-factor experiments, Plackett-Burman design and response surface methodology were applied to optimize the padlock probe-based hyperbranched rolling circle amplification reaction. Results: The maximum fluorescence intensity was achieved at a padlock probe concentration of 1.5 pM and target concentration of 9 pM at 38°C ligation temperature. The proposed biosensor has a low detection limit of 60 fM of target DNA and a linear response in the concentration range of 60 fM to 0.2 pM. Conclusion: The results indicated the power of these assays to detect KRAS point mutations in liquid state reactions.
Collapse
Affiliation(s)
- Fatemeh Mahmoudian
- Department of Molecular Medicine, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mostafa Akbariqomi
- Department of Molecular Medicine, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Heidari
- Department of Molecular Medicine, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad H Ghahremani
- Department of Toxicology and Pharmacology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Nader Roshan
- Department of Internal Medicine, Division of Gastroenterology, Imam Khomeini Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahdi Adabi
- Department of Medical Nanotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Moloud Absalan
- Department of Molecular Medicine, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Karimi
- Department of Medical Nanotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Samira Bahrami
- Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Samaneh Fathi
- Department of Medical Nanotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Gholamreza Tavoosidana
- Department of Molecular Medicine, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| |
Collapse
|
5
|
Krasic J, Abramovic I, Vrtaric A, Nikolac Gabaj N, Kralik-Oguic S, Katusic Bojanac A, Jezek D, Sincic N. Impact of Preanalytical and Analytical Methods on Cell-Free DNA Diagnostics. Front Cell Dev Biol 2021; 9:686149. [PMID: 34552921 PMCID: PMC8451956 DOI: 10.3389/fcell.2021.686149] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 08/13/2021] [Indexed: 01/18/2023] Open
Abstract
While tissue biopsy has for the longest time been the gold-standard in biomedicine, precision/personalized medicine is making the shift toward liquid biopsies. Cell-free DNA (cfDNA) based genetic and epigenetic biomarkers reflect the molecular status of its tissue-of-origin allowing for early and non-invasive diagnostics of different pathologies. However, selection of preanalytical procedures (including cfDNA isolation) as well as analytical methods are known to impact the downstream results. Calls for greater standardization are made continuously, yet comprehensive assessments of the impact on diagnostic parameters are lacking. This study aims to evaluate the preanalytic and analytic factors that influence cfDNA diagnostic parameters in blood and semen. Text mining analysis has been performed to assess cfDNA research trends, and identify studies on isolation methods, preanalytical and analytical impact. Seminal and blood plasma were tested as liquid biopsy sources. Traditional methods of cfDNA isolation, commercial kits (CKs), and an in-house developed protocol were tested, as well as the impact of dithiothreitol (DTT) on cfDNA isolation performance. Fluorimetry, qPCR, digital droplet PCR (ddPCR), and bioanalyzer were compared as cfDNA quantification methods. Fragment analysis was performed by qPCR and bioanalyzer while the downstream application (cfDNA methylation) was analyzed by pyrosequencing. In contrast to blood, semen as a liquid biopsy source has only recently begun to be reported as a liquid biopsy source, with almost half of all publications on it being review articles. Experimental data revealed that cfDNA isolation protocols give a wide range of cfDNA yields, both from blood and seminal plasma. The addition of DTT to CKs has improved yields in seminal plasma and had a neutral/negative impact in blood plasma. Capillary electrophoresis and fluorometry reported much higher yields than PCR methods. While cfDNA yield and integrity were highly impacted, cfDNA methylation was not affected by isolation methodology or DTT. In conclusion, NucleoSnap was recognized as the kit with the best overall performance. DTT improved CK yields in seminal plasma. The in-house developed protocol has shown near-kit isolation performance. ddPCR LINE-1 assay for absolute detection of minute amounts of cfDNA was established and allowed for quantification of samples inhibited in qPCR. cfDNA methylation was recognized as a stable biomarker unimpacted by cfDNA isolation method. Finally, semen was found to be an abundant source of cfDNA offering potential research opportunities and benefits for cfDNA based biomarkers development related to male reproductive health.
Collapse
Affiliation(s)
- Jure Krasic
- Department of Medical Biology, School of Medicine, University of Zagreb, Zagreb, Croatia
- Scientific Group for Research on Epigenetic Biomarkers, School of Medicine, University of Zagreb, Zagreb, Croatia
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Irena Abramovic
- Department of Medical Biology, School of Medicine, University of Zagreb, Zagreb, Croatia
- Scientific Group for Research on Epigenetic Biomarkers, School of Medicine, University of Zagreb, Zagreb, Croatia
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Alen Vrtaric
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Zagreb, Croatia
- Department of Clinical Chemistry, Sestre Milosrdnice University Hospital Center, Zagreb, Croatia
| | - Nora Nikolac Gabaj
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Zagreb, Croatia
- Department of Clinical Chemistry, Sestre Milosrdnice University Hospital Center, Zagreb, Croatia
- Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia
| | - Sasa Kralik-Oguic
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Zagreb, Croatia
- Clinical Institute of Laboratory Diagnostics, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Ana Katusic Bojanac
- Department of Medical Biology, School of Medicine, University of Zagreb, Zagreb, Croatia
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Davor Jezek
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Zagreb, Croatia
- Department of Histology and Embryology, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Nino Sincic
- Department of Medical Biology, School of Medicine, University of Zagreb, Zagreb, Croatia
- Scientific Group for Research on Epigenetic Biomarkers, School of Medicine, University of Zagreb, Zagreb, Croatia
- Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Zagreb, Croatia
| |
Collapse
|
6
|
Rigi G, Rostami A, Ghomi H, Ahmadian G, Mirbagheri VS, Jeiranikhameneh M, Vahed M, Rahimi S. Optimization of expression, purification and secretion of functional recombinant human growth hormone in Escherichia coli using modified staphylococcal protein a signal peptide. BMC Biotechnol 2021; 21:51. [PMID: 34399745 PMCID: PMC8369807 DOI: 10.1186/s12896-021-00701-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 06/10/2021] [Indexed: 11/10/2022] Open
Abstract
Background Human Growth Hormone (hGH) is a glycoprotein released from the pituitary gland. Due to the wide range of effects in humans, any disruption in hGH secretion could have serious consequences. This highlights the clinical importance of hGH production in the treatment of different diseases associated with a deficiency of this hormone. The production of recombinant mature hormone in suitable hosts and secretion of this therapeutic protein into the extracellular space can be considered as one of the best cost-effective approaches not only to obtain the active form of the protein but also endotoxin-free preparation. Since the natural growth hormone signal peptide is of eukaryotic origin and is not detectable by any of the Escherichia coli secretory systems, including Sec and Tat, and is therefore unable to secrete hGH in the prokaryotic systems, designing a new and efficient signal peptide is essential to direct hGh to the extracellular space. Results In this study, using a combination of the bioinformatics design and molecular genetics, the protein A signal peptide from Staphylococcus aureus was modified, redesigned and then fused to the mature hGH coding region. The recombinant hGH was then expressed in E. coli and successfully secreted to the medium through the Sec pathway. Secretion of the hGH into the medium was verified using SDS-PAGE and western blot analysis. Recombinant hGH was then expressed in E. coli and successfully secreted into cell culture medium via the Sec pathway. The secretion of hGH into the extracellular medium was confirmed by SDS-PAGE and Western blot analysis. Furthermore, the addition of glycine was shown to improve hGH secretion onto the culture medium. Equations for determining the optimal conditions were also determined. Functional hGH analysis using an ELISA-based method confirmed that the ratio of the active form of secreted hGH to the inactive form in the periplasm is higher than this ratio in the cytoplasm. Conclusions Since the native signal protein peptide of S. aureus protein A was not able to deliver hGH to the extracellular space, it was modified using bioinformatics tools and fused to the n-terminal region of hGh to show that the redesigned signal peptide was functional. Supplementary Information The online version contains supplementary material available at 10.1186/s12896-021-00701-x.
Collapse
Affiliation(s)
- Garshasb Rigi
- Department of Genetics, Faculty of Basic Science, Shahrekord University, P. O. Box 115, Shahrekord, 881 863 4141, Iran.,Department of Industrial Biotechnology, Research Institute of Biotechnology, Shahrekord University, Shahrekord, Iran
| | - Amin Rostami
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Habib Ghomi
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Gholamreza Ahmadian
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.
| | - Vasiqe Sadat Mirbagheri
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.,Fisheries products processing group, Faculty of Fisheries and Environmental Sciences, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran
| | - Meisam Jeiranikhameneh
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Majid Vahed
- Pharmaceutical Sciences Research Center, Shahid Beheshti University of Medical Sciences, Niayesh Highway, Valiasr Ave, Tehran, Iran.,Department of Toxico/Pharmacology, School of Pharmacy, Shahid Beheshti, University of Medical Sciences, Niayesh Highway, Valiasr Ave, Tehran, Iran
| | - Sahel Rahimi
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| |
Collapse
|
7
|
The first report on molecular cloning, functional expression, purification, and statistical optimization of Escherichia coli-derived recombinant Ficin from Iranian fig tree (Ficus carica cv.Sabz). Int J Biol Macromol 2020; 165:2126-2135. [PMID: 33069821 DOI: 10.1016/j.ijbiomac.2020.10.050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/27/2020] [Accepted: 10/07/2020] [Indexed: 01/20/2023]
Abstract
The enzyme ficin, abundantly found in the leaves of the common Fig (Ficus carica. L), is a cysteine protease of the plant endopeptidase family. In terms of activity, this enzyme mimics the activity of the papain enzyme. However, the enzyme is more acidic than papain and binds with higher efficiency to its substrate. Ficin is widely used in the food and pharmaceutical industry along with the medical diagnosis. To date, there are no available data on cloning and recombinant production of various isoforms of ficin. In the present study, after the cloning process and optimized expression of ficin in E. coli BL21, by means of the central composite design (CCD) and approach-based response surface methodology (RSM), the recombinant protein was purified using the Ni-sepharose column and gel filtration. The activity of ficin was determined by its ability to hydrolyze the bovine casein enzyme as a substrate. These results showed the presence of different isoforms of ficin in this cultivar that they are distinct in terms of DNA coding sequences. The optimum conditions for maximum production of the recombinant ficin enzyme in E. coli were as follows; a cell density of 1.25, post-induction time 7 h, 10% (w/v) lactose concentration, and shaking at 115 rpm at 24 °C. The concentration of purified product was reported to be 0.27 mg/ml. The optimization procedures increased the amounts of ficin production by approximately 3 folds (0.67 mg/ml) compared with the expiration level (in the absence of optimization). Also, our findings showed that the recombinant ficin was able to hydrolyze casein, denoting the functionality of the enzyme when used in-vitro. The pitfall of cutting-off the young branches of the common fig tree to purify the enzyme from the young shoots was successfully solved in this study.
Collapse
|
8
|
Wienzek-Lischka S, Bachmann S, Froehner V, Bein G. Potential of Next-Generation Sequencing in Noninvasive Fetal Molecular Blood Group Genotyping. Transfus Med Hemother 2020; 47:14-22. [PMID: 32110190 DOI: 10.1159/000505161] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 11/28/2019] [Indexed: 12/23/2022] Open
Abstract
Hemolytic disease of the fetus and newborn and fetal and neonatal alloimmune thrombocytopenia are caused by maternal antibodies against fetal alloantigens on red blood cells or platelets that are inherited from the father. After transplacental transport to the fetal circulation, antibodies of the IgG class may cause severe fetal anemia or bleeding complications. The indication for noninvasive fetal blood group genotyping is given if a clinically relevant antibody is detected in a pregnant woman and if the father is heterozygous (or unknown) for the implicated blood group allele. This mini-review will focus on the advantages and current limitations of next-generation sequencing (NGS) for noninvasive diagnosis of fetal blood groups which is, in contrast to fetal aneuploidy screening, proposed only by some research groups. Targeted massively parallel sequencing of short DNA fragments from maternal cell-free plasma samples enables counting of fetal alleles for many single nucleotide polymorphisms in parallel. This information can be utilized for estimation of the fetal fraction of cell-free DNA (cfDNA) as well as detection of the paternal blood group allele in question. Adherence to a cut-off of ≥4% fetal fraction for reporting conclusive results is recommended to avoid false-negative results due to low fetal fraction. For screening purposes of fetal RHD in RhD-negative pregnant women, real-time PCR methods are very well established. However, for diagnostic purposes, the targeted amplicon-based NGS approach has the inherent capability to estimate the fetal fraction of cfDNA. In the future, improving the accuracy of NGS by consensus sequencing of single cfDNA molecules may enable reliable fetal blood group genotyping already in the first trimester of pregnancy.
Collapse
Affiliation(s)
- Sandra Wienzek-Lischka
- Institute for Clinical Immunology and Transfusion Medicine, Justus-Liebig University, Giessen, Germany
| | - Sandy Bachmann
- Institute for Clinical Immunology and Transfusion Medicine, Justus-Liebig University, Giessen, Germany
| | - Vanessa Froehner
- Institute for Clinical Immunology and Transfusion Medicine, Justus-Liebig University, Giessen, Germany
| | - Gregor Bein
- Institute for Clinical Immunology and Transfusion Medicine, Justus-Liebig University, Giessen, Germany
| |
Collapse
|