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Narayani KR, Narayani RI. Influence of Colorectal Cancer Risk Factors on Predictive Value of a Positive Multitarget Stool DNA Test. J Clin Gastroenterol 2024; 58:471-474. [PMID: 37389965 DOI: 10.1097/mcg.0000000000001884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 05/31/2023] [Indexed: 07/02/2023]
Abstract
GOALS We analyzed if the predictive value of multitarget stool-based DNA (mt-sDNA) varied when patients had pre-existing known colorectal cancer (CRC) risk factors. BACKGROUND mt-sDNA test is approved for CRC screening in average-risk patients. Whether patients with a personal history of adenomatous colon polyps or a family history of CRC (CRC risk factors) benefit from mt-sDNA testing is unknown. STUDY We reviewed charts for all positive mt-sDNA referrals between 2017 and 2021. Diagnostic colonoscopy adherence rates were calculated. In those who had colonoscopy, we compared detection rates for any colorectal neoplasia (CRN), multiple (3 or more) adenomas, sessile serrated polyps (SSP), advanced CRN, and CRC between patients with and without known CRC risk factors. RESULTS Of 1297 referrals for positive mt-sDNA, 1176 (91%) completed a diagnostic colonoscopy. The absence of neoplasia was noted in 27% of colonoscopy exams. When neoplasia was identified, findings were as follows: any CRN (73%), multiple adenomas (34%), SSP (23%), advanced CRN (33%), and CRC (2.5%). One or more CRC risk factors were present in 229 (19%) of cases. In the CRC risk factor subgroup, patients having a prior history of adenomatous polyps or a family history of CRC were no more likely to have any CRN, multiple adenomas, SSP, advanced CRN, or CRC compared to average-risk patients when mt-sDNA was positive. CONCLUSIONS In this real-world analysis of positive mt-sDNA referrals, adherence to subsequent diagnostic colonoscopy recommendations was high. The presence of pre-existing CRC risk factors did not affect the positive predictive value of mt-sDNA.
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Zhang D, Zhang Y, Xiao Y, Wang Y, Shen Y, Wang Z, Qiao H. Giant vesicles form in physiological saline and encapsulate pDNA by the modified electroformation method. Colloids Surf B Biointerfaces 2024; 237:113840. [PMID: 38508085 DOI: 10.1016/j.colsurfb.2024.113840] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 02/26/2024] [Accepted: 03/09/2024] [Indexed: 03/22/2024]
Abstract
Giant vesicles (GVs) are used to study the structures and functions of cells and cell membranes. Electroformation is the most commonly used method for GV preparation. However, the electroformation of GVs is hindered in highly concentrated ionic solutions, limiting their application as cell models for research under physiological conditions. In this study, giant multilayer vesicles were successfully generated in physiological saline using a modified electroformation device by adding an insulating layer between the two electrode plates. The influence of the electric frequency and strength on the electroformation of GVs in physiological saline was explored, and a possible mechanism for this improvement was assessed. It has been shown that an insulating layer between the two electrodes can improve the electroformation of GVs in physiological saline by increasing the electrical impedance, which is weakened by the saline solution, thereby restoring the reduced effective electric field strength. Furthermore, macromolecular plasmid DNA (pDNA) was successfully encapsulated in the electroformed GVs of the modified device. This modified electroformation method may be useful for generating eukaryotic cell models under physiological conditions.
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Affiliation(s)
- Dingshan Zhang
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Medical University, Chongqing 400016, China; Chongqing Key Laboratory of Biomedical Engineering, Chongqing Medical University, Chongqing 400016, China
| | - Yangruizi Zhang
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Medical University, Chongqing 400016, China; Chongqing Key Laboratory of Biomedical Engineering, Chongqing Medical University, Chongqing 400016, China
| | - Yao Xiao
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Medical University, Chongqing 400016, China; Chongqing Key Laboratory of Biomedical Engineering, Chongqing Medical University, Chongqing 400016, China
| | - Yiting Wang
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Medical University, Chongqing 400016, China; Chongqing Key Laboratory of Biomedical Engineering, Chongqing Medical University, Chongqing 400016, China
| | - Yong Shen
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Medical University, Chongqing 400016, China; National Engineering Research Center for Ultrasound Medicine, Chongqing 400016, China
| | - Zhibiao Wang
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Medical University, Chongqing 400016, China; Chongqing Key Laboratory of Biomedical Engineering, Chongqing Medical University, Chongqing 400016, China
| | - Hai Qiao
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Medical University, Chongqing 400016, China; Chongqing Key Laboratory of Biomedical Engineering, Chongqing Medical University, Chongqing 400016, China.
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Pont D. Predicting downstream transport distance of fish eDNA in lotic environments. Mol Ecol Resour 2024; 24:e13934. [PMID: 38318749 DOI: 10.1111/1755-0998.13934] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 01/21/2024] [Accepted: 01/26/2024] [Indexed: 02/07/2024]
Abstract
Environmental DNA (eDNA) is an effective tool for describing fish biodiversity in lotic environments, but the downstream transport of eDNA released by organisms makes it difficult to interpret species detection at the local scale. In addition to biophysical degradation and exchanges at the water-sediment interface, hydrological conditions control the transport distance. A new eDNA transport model described in this paper considers downstream retention and degradation processes in combination with hydraulic conditions and assumes that the sedimentation rate of very fine particles is a correct estimate of the eDNA deposition rate. Based on meta-analyses of available studies, the particle size distribution of fish eDNA (PSD), the relationship between the sedimentation rate and the size of very fine particles in suspension, and the influence of temperature on the degradation rate of fish eDNA were successively modelled. After combining the results in a mechanistic-based model, the eDNA uptake distances (distance required to retain 63.21% of the eDNA particles in the riverbed) observed in a compilation of previous experimental studies were correctly simulated. eDNA degradation is negligible at low flow and temperature but has a comparable influence to background transfer when hydraulic conditions allow a long uptake distance. The wide prediction intervals associated with the simulations reflect the complexity of the processes acting on eDNA after shedding. This model can be useful for estimating eDNA detection distance downstream from a source point and discussing the possibility of false positive detection in eDNA samples, as shown in an example.
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Affiliation(s)
- Didier Pont
- Institute of Hydrobiology and Aquatic Ecosystem Management (IHG), University of Natural Resources and Life Sciences, Vienna, Austria
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Pinnell LJ, Wolfe CA, Castle J, Crosby WB, Doster E, Morley PS. Effectiveness of stabilization methods for the immediate and short-term preservation of bovine fecal and upper respiratory tract genomic DNA. PLoS One 2024; 19:e0300285. [PMID: 38564604 PMCID: PMC10987004 DOI: 10.1371/journal.pone.0300285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 11/22/2023] [Accepted: 02/24/2024] [Indexed: 04/04/2024] Open
Abstract
Previous research on stabilization methods for microbiome investigations has largely focused on human fecal samples. There are a few studies using feces from other species, but no published studies investigating preservation of samples collected from cattle. Given that microbial taxa are differentially impacted during storage it is warranted to study impacts of preservation methods on microbial communities found in samples outside of human fecal samples. Here we tested methods of preserving bovine fecal respiratory specimens for up to 2 weeks at four temperatures (room temperature, 4°C, -20°C, and -80°C) by comparing microbial diversity and community composition to samples extracted immediately after collection. Importantly, fecal specimens preserved and analyzed were technical replicates, providing a look at the effects of preservation method in the absence of biological variation. We found that preservation with the OMNIgene®•GUT kit resulted in community structure most like that of fresh samples extracted immediately, even when stored at room temperature (~20°C). Samples that were flash-frozen without added preservation solution were the next most representative of original communities, while samples preserved with ethanol were the least representative. These results contradict previous reports that ethanol is effective in preserving fecal communities and suggest for studies investigating cattle either flash-freezing of samples without preservative or preservation with OMNIgene®•GUT will yield more representative microbial communities.
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Affiliation(s)
- Lee J. Pinnell
- Veterinary Education, Research and Outreach Program, Texas A&M University, Canyon, TX, United States of America
| | - Cory A. Wolfe
- Veterinary Education, Research and Outreach Program, Texas A&M University, Canyon, TX, United States of America
| | - Jake Castle
- Veterinary Education, Research and Outreach Program, Texas A&M University, Canyon, TX, United States of America
| | - William B. Crosby
- Department of Pathobiology and Population Medicine, College of Veterinary Medicine, Mississippi State University, Starkville, Mississippi State, United States of America
| | - Enrique Doster
- Veterinary Education, Research and Outreach Program, Texas A&M University, Canyon, TX, United States of America
| | - Paul S. Morley
- Veterinary Education, Research and Outreach Program, Texas A&M University, Canyon, TX, United States of America
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Ani V, Sreevidya KV, Unnikrishnan K, Sindhu Mol A, Chacko PM, Shafeeca A. Technical Note: A simple FTA® based method for the direct STR amplification of human foetal tissues. Forensic Sci Int 2024; 357:111971. [PMID: 38447344 DOI: 10.1016/j.forsciint.2024.111971] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/05/2024] [Accepted: 02/22/2024] [Indexed: 03/08/2024]
Abstract
Short tandem repeats (STRs) or microsatellites are short, tandemly repeated DNA sequences that involve a repetitive unit of 1-6 bp. DNA isolation and purification from a large number and often compromised samples gives problems to forensic labs for STR typing. Many of the conventional methods used in the isolation and purification of DNA from forensic samples are time consuming, expensive, hazardous for health and are often associated with greater risks of cross contamination. FTA® technology is a method designed to simplify the collection, shipment, archiving and purification of nucleic acid from a wide variety of biological samples. We report a new method for the direct STR amplification which can amplify STR loci from human foetal tissues spotted on FTA cards, bye-passing the need of DNA purification. The STR loci amplified by this method was compared with conventional method of STR profiling and was found absolutely matching. Therefore, this new method is demonstrated to be very useful for fast, less expensive and non- hazardous forensic DNA analysis.
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Affiliation(s)
- V Ani
- DNA Division, State Forensic Science Laboratory, Thiruvananthapuram, Kerala, India.
| | - K V Sreevidya
- DNA Division, State Forensic Science Laboratory, Thiruvananthapuram, Kerala, India
| | - K Unnikrishnan
- DNA Division, State Forensic Science Laboratory, Thiruvananthapuram, Kerala, India
| | - A Sindhu Mol
- DNA Division, State Forensic Science Laboratory, Thiruvananthapuram, Kerala, India
| | - Priya Mary Chacko
- DNA Division, State Forensic Science Laboratory, Thiruvananthapuram, Kerala, India
| | - A Shafeeca
- DNA Division, State Forensic Science Laboratory, Thiruvananthapuram, Kerala, India
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Tan HP, Kimoto M, Hirao I. Advancing Genetic Alphabet Expansion: Synthesis of 7-(2-Thienyl)-Imidazo[4,5-b]pyridine (Ds) and 4-(4-Pentyne-1,2-diol)-1-Propynyl-2-Nitropyrrole (Diol-Px) for Use in Replicable Unnatural Base Pairs for PCR Applications. Curr Protoc 2024; 4:e1009. [PMID: 38572677 DOI: 10.1002/cpz1.1009] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
Expanding the genetic alphabet enhances DNA recombinant technologies by introducing unnatural base pairs (UBPs) beyond the standard A-T and G-C pairs, leading to biomaterials with novel and increased functionalities. Recent developments include UBPs that effectively function as a third base pair in replication, transcription, and/or translation processes. One such UBP, Ds-Px, demonstrates extremely high specificity in replication. Chemically synthesized DNA fragments containing Ds bases are amplified by PCR with the 5'-triphosphates of Ds and Px deoxyribonucleosides (dDsTP and dPxTP). The Ds-Px pair system has applications in enhanced DNA data storage, generation of high-affinity DNA aptamers, and incorporation of functional elements into RNA through transcription. This protocol describes the synthesis of the amidite derivative of Ds (dDs amidite), the triphosphate dDsTP, and the diol-modified dPxTP (Diol-dPxTP) for PCR amplifications involving the Ds-Px pair. © 2024 Wiley Periodicals LLC. Basic Protocol 1: Synthesis of Ds deoxyribonucleoside (dDs) Basic Protocol 2: Synthesis of dDs amidite Basic Protocol 3: Synthesis of dDs triphosphate (dDsTP) Basic Protocol 4: Synthesis of Pn deoxyribonucleoside (4-iodo-dPn) Basic Protocol 5: Synthesis of acetyl-protected diol-modified Px deoxyribonucleoside (Diol-dPx) Basic Protocol 6: Synthesis of Diol-dPx triphosphate (Diol-dPxTP) Basic Protocol 7: Purification of triphosphates Support Protocol 1: Synthesis of Hoffer's chlorosugar Support Protocol 2: Preparation of 0.5 M pyrophosphate in DMF Support Protocol 3: Preparation of 2 M TEAB buffer.
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Zhou Y, Wang Y, Song M, Jiang L, Sun C, Wang S, Yao H, Wang Z, Wang X, Liu C, Luo H, Song F. A high-throughput droplet digital PCR system aiming eight DNA methylation targets for age prediction. J Pharm Biomed Anal 2024; 240:115943. [PMID: 38181558 DOI: 10.1016/j.jpba.2023.115943] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 12/19/2023] [Accepted: 12/23/2023] [Indexed: 01/07/2024]
Abstract
The droplet digital Polymerase Chain Reaction (ddPCR) has garnered recognition for its distinctive attribute of absolute quantification. And it has found practical utility in age prediction through DNA methylation profiles. However, a prevalent limitation in current ddPCR methodologies is the restricted capacity to detect only two targets concurrently in most instruments, leading to high costs, sample wastage, and labor-intensive procedures. To address the limitations, a novel high-throughput ddPCR system allowing for the simultaneous detection of eight targets was developed. Through the implementation of a new 8-plex ddPCR assay, coupled with comprehensive linear regression analyses involving primers and probes ratios, diverse inputs of single CpG sites with distinct primers and probes, and varying plex assay configurations, stable DNA methylation values for four CpGs and stable measurement precisions for distinct multiplex systems were consistently observed. These findings pave the way for advancing the field of chemistry science by enabling more efficient and cost-effective methods. Furthermore, the comparative validation of ddPCR and SNaPshot demonstrated a remarkable concordance in results, and the system also displayed well in the field of various aspects, including species specificity, DNA input, and aged samples. In this study, the recommended input of bisulfite-converted DNA was determined to be 10-50 ng due to the double-positive droplets. Notably, the Pearson correlation coefficient squared values of four CpGs were 0.4878 (ASPA), 0.4832 (IGSF1), 0.6881 (COL1A1), and 0.6475 (MEIS1-AS3). And the testing set exhibited a mean absolute error of 4.5923 years, indicating the robustness and accuracy of the age-predictive model.
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Affiliation(s)
- Yuxiang Zhou
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Yanyun Wang
- Laboratory of Molecular Translational Medicine, West China Second University Hospital, Sichuan University, China
| | - Mengyuan Song
- Department of Laboratory Medicine, West China Hospital, Sichuan University, China; Med+ Molecular Diagnostics Institute of West China Hospital/West China School of Medicine, China
| | - Lanrui Jiang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Chaoran Sun
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Shuangshuang Wang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Hewen Yao
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Zefei Wang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Xindi Wang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Chunhui Liu
- Scientific Support Center, Sniper Medical Technologies Co., Ltd., Suzhou 215000, China
| | - Haibo Luo
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China.
| | - Feng Song
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China.
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Imperiale TF, Porter K, Zella J, Gagrat ZD, Olson MC, Statz S, Garces J, Lavin PT, Aguilar H, Brinberg D, Berkelhammer C, Kisiel JB, Limburg PJ. Next-Generation Multitarget Stool DNA Test for Colorectal Cancer Screening. N Engl J Med 2024; 390:984-993. [PMID: 38477986 DOI: 10.1056/nejmoa2310336] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
BACKGROUND A next-generation multitarget stool DNA test, including assessments of DNA molecular markers and hemoglobin level, was developed to improve the performance of colorectal cancer screening, primarily with regard to specificity. METHODS In a prospective study, we evaluated a next-generation multitarget stool DNA test in asymptomatic adults 40 years of age or older who were undergoing screening colonoscopy. The primary outcomes were sensitivity of the test for colorectal cancer and specificity for advanced neoplasia (colorectal cancer or advanced precancerous lesions). Advanced precancerous lesions included one or more adenomas or sessile serrated lesions measuring at least 1 cm in the longest dimension, lesions with villous histologic features, and high-grade dysplasia. Secondary objectives included the quantification of sensitivity for advanced precancerous lesions and specificity for nonneoplastic findings or negative colonoscopy and comparison of sensitivities for colorectal cancer and advanced precancerous lesions between the multitarget stool DNA test and a commercially available fecal immunochemical test (FIT). RESULTS Of 20,176 participants, 98 had colorectal cancer, 2144 had advanced precancerous lesions, 6973 had nonadvanced adenomas, and 10,961 had nonneoplastic findings or negative colonoscopy. With the next-generation test, sensitivity for colorectal cancer was 93.9% (95% confidence interval [CI], 87.1 to 97.7), and specificity for advanced neoplasia was 90.6% (95% CI, 90.1 to 91.0). Sensitivity for advanced precancerous lesions was 43.4% (95% CI, 41.3 to 45.6), and specificity for nonneoplastic findings or negative colonoscopy was 92.7% (95% CI, 92.2 to 93.1). With the FIT, sensitivity was 67.3% (95% CI, 57.1 to 76.5) for colorectal cancer and 23.3% (95% CI, 21.5 to 25.2) for advanced precancerous lesions; specificity was 94.8% (95% CI, 94.4 to 95.1) for advanced neoplasia and 95.7% (95% CI, 95.3 to 96.1) for nonneoplastic findings or negative colonoscopy. As compared with FIT, the next-generation test had superior sensitivity for colorectal cancer (P<0.001) and for advanced precancerous lesions (P<0.001) but had lower specificity for advanced neoplasia (P<0.001). No adverse events occurred. CONCLUSIONS The next-generation multitarget stool DNA test showed higher sensitivity for colorectal cancer and advanced precancerous lesions than FIT but also showed lower specificity. (Funded by Exact Sciences; BLUE-C ClinicalTrials.gov number, NCT04144738.).
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Affiliation(s)
- Thomas F Imperiale
- From the Indiana University School of Medicine, Indiana University Melvin and Bren Simon Comprehensive Cancer Center, and Regenstrief Institute, Indianapolis (T.F.I.); Exact Sciences, Madison, WI (K.P., J.Z., Z.D.G., M.C.O., S.S., J.G., P.J.L.); Boston Biostatistics Research Foundation, Framingham, MA (P.T.L.); Louisiana Research Center, Shreveport (H.A.); Great Lakes Gastroenterology Research, Mentor, OH (D.B.); Southwest Gastroenterology, Oak Lawn, IL (C.B.); and the Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN (J.B.K.)
| | - Kyle Porter
- From the Indiana University School of Medicine, Indiana University Melvin and Bren Simon Comprehensive Cancer Center, and Regenstrief Institute, Indianapolis (T.F.I.); Exact Sciences, Madison, WI (K.P., J.Z., Z.D.G., M.C.O., S.S., J.G., P.J.L.); Boston Biostatistics Research Foundation, Framingham, MA (P.T.L.); Louisiana Research Center, Shreveport (H.A.); Great Lakes Gastroenterology Research, Mentor, OH (D.B.); Southwest Gastroenterology, Oak Lawn, IL (C.B.); and the Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN (J.B.K.)
| | - Julia Zella
- From the Indiana University School of Medicine, Indiana University Melvin and Bren Simon Comprehensive Cancer Center, and Regenstrief Institute, Indianapolis (T.F.I.); Exact Sciences, Madison, WI (K.P., J.Z., Z.D.G., M.C.O., S.S., J.G., P.J.L.); Boston Biostatistics Research Foundation, Framingham, MA (P.T.L.); Louisiana Research Center, Shreveport (H.A.); Great Lakes Gastroenterology Research, Mentor, OH (D.B.); Southwest Gastroenterology, Oak Lawn, IL (C.B.); and the Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN (J.B.K.)
| | - Zubin D Gagrat
- From the Indiana University School of Medicine, Indiana University Melvin and Bren Simon Comprehensive Cancer Center, and Regenstrief Institute, Indianapolis (T.F.I.); Exact Sciences, Madison, WI (K.P., J.Z., Z.D.G., M.C.O., S.S., J.G., P.J.L.); Boston Biostatistics Research Foundation, Framingham, MA (P.T.L.); Louisiana Research Center, Shreveport (H.A.); Great Lakes Gastroenterology Research, Mentor, OH (D.B.); Southwest Gastroenterology, Oak Lawn, IL (C.B.); and the Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN (J.B.K.)
| | - Marilyn C Olson
- From the Indiana University School of Medicine, Indiana University Melvin and Bren Simon Comprehensive Cancer Center, and Regenstrief Institute, Indianapolis (T.F.I.); Exact Sciences, Madison, WI (K.P., J.Z., Z.D.G., M.C.O., S.S., J.G., P.J.L.); Boston Biostatistics Research Foundation, Framingham, MA (P.T.L.); Louisiana Research Center, Shreveport (H.A.); Great Lakes Gastroenterology Research, Mentor, OH (D.B.); Southwest Gastroenterology, Oak Lawn, IL (C.B.); and the Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN (J.B.K.)
| | - Sandi Statz
- From the Indiana University School of Medicine, Indiana University Melvin and Bren Simon Comprehensive Cancer Center, and Regenstrief Institute, Indianapolis (T.F.I.); Exact Sciences, Madison, WI (K.P., J.Z., Z.D.G., M.C.O., S.S., J.G., P.J.L.); Boston Biostatistics Research Foundation, Framingham, MA (P.T.L.); Louisiana Research Center, Shreveport (H.A.); Great Lakes Gastroenterology Research, Mentor, OH (D.B.); Southwest Gastroenterology, Oak Lawn, IL (C.B.); and the Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN (J.B.K.)
| | - Jorge Garces
- From the Indiana University School of Medicine, Indiana University Melvin and Bren Simon Comprehensive Cancer Center, and Regenstrief Institute, Indianapolis (T.F.I.); Exact Sciences, Madison, WI (K.P., J.Z., Z.D.G., M.C.O., S.S., J.G., P.J.L.); Boston Biostatistics Research Foundation, Framingham, MA (P.T.L.); Louisiana Research Center, Shreveport (H.A.); Great Lakes Gastroenterology Research, Mentor, OH (D.B.); Southwest Gastroenterology, Oak Lawn, IL (C.B.); and the Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN (J.B.K.)
| | - Philip T Lavin
- From the Indiana University School of Medicine, Indiana University Melvin and Bren Simon Comprehensive Cancer Center, and Regenstrief Institute, Indianapolis (T.F.I.); Exact Sciences, Madison, WI (K.P., J.Z., Z.D.G., M.C.O., S.S., J.G., P.J.L.); Boston Biostatistics Research Foundation, Framingham, MA (P.T.L.); Louisiana Research Center, Shreveport (H.A.); Great Lakes Gastroenterology Research, Mentor, OH (D.B.); Southwest Gastroenterology, Oak Lawn, IL (C.B.); and the Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN (J.B.K.)
| | - Humberto Aguilar
- From the Indiana University School of Medicine, Indiana University Melvin and Bren Simon Comprehensive Cancer Center, and Regenstrief Institute, Indianapolis (T.F.I.); Exact Sciences, Madison, WI (K.P., J.Z., Z.D.G., M.C.O., S.S., J.G., P.J.L.); Boston Biostatistics Research Foundation, Framingham, MA (P.T.L.); Louisiana Research Center, Shreveport (H.A.); Great Lakes Gastroenterology Research, Mentor, OH (D.B.); Southwest Gastroenterology, Oak Lawn, IL (C.B.); and the Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN (J.B.K.)
| | - Don Brinberg
- From the Indiana University School of Medicine, Indiana University Melvin and Bren Simon Comprehensive Cancer Center, and Regenstrief Institute, Indianapolis (T.F.I.); Exact Sciences, Madison, WI (K.P., J.Z., Z.D.G., M.C.O., S.S., J.G., P.J.L.); Boston Biostatistics Research Foundation, Framingham, MA (P.T.L.); Louisiana Research Center, Shreveport (H.A.); Great Lakes Gastroenterology Research, Mentor, OH (D.B.); Southwest Gastroenterology, Oak Lawn, IL (C.B.); and the Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN (J.B.K.)
| | - Charles Berkelhammer
- From the Indiana University School of Medicine, Indiana University Melvin and Bren Simon Comprehensive Cancer Center, and Regenstrief Institute, Indianapolis (T.F.I.); Exact Sciences, Madison, WI (K.P., J.Z., Z.D.G., M.C.O., S.S., J.G., P.J.L.); Boston Biostatistics Research Foundation, Framingham, MA (P.T.L.); Louisiana Research Center, Shreveport (H.A.); Great Lakes Gastroenterology Research, Mentor, OH (D.B.); Southwest Gastroenterology, Oak Lawn, IL (C.B.); and the Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN (J.B.K.)
| | - John B Kisiel
- From the Indiana University School of Medicine, Indiana University Melvin and Bren Simon Comprehensive Cancer Center, and Regenstrief Institute, Indianapolis (T.F.I.); Exact Sciences, Madison, WI (K.P., J.Z., Z.D.G., M.C.O., S.S., J.G., P.J.L.); Boston Biostatistics Research Foundation, Framingham, MA (P.T.L.); Louisiana Research Center, Shreveport (H.A.); Great Lakes Gastroenterology Research, Mentor, OH (D.B.); Southwest Gastroenterology, Oak Lawn, IL (C.B.); and the Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN (J.B.K.)
| | - Paul J Limburg
- From the Indiana University School of Medicine, Indiana University Melvin and Bren Simon Comprehensive Cancer Center, and Regenstrief Institute, Indianapolis (T.F.I.); Exact Sciences, Madison, WI (K.P., J.Z., Z.D.G., M.C.O., S.S., J.G., P.J.L.); Boston Biostatistics Research Foundation, Framingham, MA (P.T.L.); Louisiana Research Center, Shreveport (H.A.); Great Lakes Gastroenterology Research, Mentor, OH (D.B.); Southwest Gastroenterology, Oak Lawn, IL (C.B.); and the Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN (J.B.K.)
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9
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Gagrat ZD, Krockenberger M, Bhattacharya A, Gagrat BZ, Leduc CM, Matter MB, Fourrier KD, Mahoney DW, Edwards V DK, Lidgard GP, Limburg PJ, Johnson SC, Domanico MJ, Kisiel JB. Next-generation Multi-target Stool DNA Panel Accurately Detects Colorectal Cancer and Advanced Precancerous Lesions. Cancer Prev Res (Phila) 2024; 17:119-126. [PMID: 38224564 PMCID: PMC10911803 DOI: 10.1158/1940-6207.capr-23-0285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 08/03/2023] [Revised: 10/10/2023] [Accepted: 01/10/2024] [Indexed: 01/17/2024]
Abstract
The multi-target stool DNA (mt-sDNA) test screens for colorectal cancer by analyzing DNA methylation/mutation and hemoglobin markers to algorithmically derive a qualitative result. A new panel of highly discriminant candidate methylated DNA markers (MDM) was recently developed. Performance of the novel MDM panel, with hemoglobin, was evaluated in a simulated screening population using archived stool samples weighted to early-stage colorectal cancer and prospectively collected advanced precancerous lesions (APL). Marker selection study (MSS) and separate preliminary independent verification studies (VS) were conducted utilizing samples from multi-center, case-control studies. Sample processing included targeted MDM capture, bisulfite conversion, and MDM quantitation. Fecal hemoglobin was quantified using ELISA. Samples were stratified into 75%/25% training-testing sets; model outcomes were cross-validated 1,000 times. All laboratory operators were blinded. The MSS included 232 cases (120 colorectal cancer/112 APLs) and 490 controls. The VS featured 210 cases (112 colorectal cancer/98 APLs) and 567 controls; APLs were 86.7% adenomas and 13.3% sessile serrated lesions (SSL). Average age was 65.5 (cases) and 63.2 (controls) years. Mean sensitivity in the VS from cross-validation was 95.2% for colorectal cancer and 57.2% for APLs, with specificities of 89.8% (no CRC/APLs) and 92.4% (no neoplasia). Subgroup analyses showed colorectal cancer sensitivities of 93.4% (stage I) and 94.2% (stage II). APL sensitivity was 82.9% for high-grade dysplasia, 73.4% for villous lesions, 49.8% for tubular lesions, and 30.2% for SSLs. These data support high sensitivity and specificity for a next-generation mt-sDNA test panel. Further evaluation of assay performance will be characterized in a prospective, multi-center clinical validation study (NCT04144738). PREVENTION RELEVANCE This study highlights performance of the next-generation mt-sDNA test, which exhibits high sensitivity and specificity for detecting colorectal cancer and APLs. This noninvasive option has potential to increase screening participation and clinical outcomes. A multi-center, clinical validation trial is underway. See related commentary by Bresalier, p. 93.
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Affiliation(s)
| | | | | | | | | | | | | | - Douglas W. Mahoney
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
| | | | | | | | | | | | - John B. Kisiel
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
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10
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Bawane H, Kadam K, Mahale V, Kulkarni R. Comprehensive assessment of 12 commercial DNA-binding dyes as alternatives to ethidium bromide for agarose gel electrophoresis. Electrophoresis 2024; 45:442-450. [PMID: 37933673 DOI: 10.1002/elps.202300154] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/19/2023] [Accepted: 10/23/2023] [Indexed: 11/08/2023]
Abstract
Staining and visualization of the nucleic acid bands on agarose gels using ethidium bromide (EB) has been a widely used technique in molecular biology. Although it is an efficient dye for this purpose, EB is known to be mutagenic and genotoxic in humans. This led to the emergence of various alternative dyes, which were claimed to be safer and more efficient than EB. However, these dyes portray varied sensitivity and interference with the electrophoretic mobility of nucleic acids. This work aimed at assessing ten nucleic acid-binding dyes and two prestained dyes for these properties by three staining techniques, such as precasting, preloading, and poststaining. Of these, preloading was not suitable for any of the dye while poststaining worked optimal for most of them. Precasting was suitable for only four dyes viz. DNA Stain G, SYBR™ safe, EZ-Vision® in-gel, and LabSafe™. Poststaining was, in general, a costlier method than precasting. The work gives a comprehensive understanding of the performance of nucleic acid-binding dyes for routine molecular biology experiments.
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Affiliation(s)
- Hemangi Bawane
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Lavale, Pune, India
| | - Komal Kadam
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Lavale, Pune, India
| | - Vinit Mahale
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Lavale, Pune, India
| | - Ram Kulkarni
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Lavale, Pune, India
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11
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Tan M, Xue J, Wu Q, Zheng Y, Liu G, Zhang R, Wu M, Song J, Xiao Y, Chen D, Lv M, Liao M, Qu S, Liang W. Improving DNA mixtures analysis using compound markers composed of InDels and SNPs screened from the whole genome with next-generation sequencing. Electrophoresis 2024; 45:463-473. [PMID: 37946554 DOI: 10.1002/elps.202300195] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/23/2023] [Accepted: 10/26/2023] [Indexed: 11/12/2023]
Abstract
Next-generation sequencing (NGS) allows for better identification of insertion and deletion polymorphisms (InDels) and their combination with adjacent single nucleotide polymorphisms (SNPs) to form compound markers. These markers can improve the polymorphism of microhaplotypes (MHs) within the same length range, and thus, boost the efficiency of DNA mixture analysis. In this study, we screened InDels and SNPs across the whole genome and selected highly polymorphic markers composed of InDels and/or SNPs within 300 bp. Further, we successfully developed and evaluated an NGS-based panel comprising 55 loci, of which 24 were composed of both SNPs and InDels. Analysis of 124 unrelated Southern Han Chinese revealed an average effective number of alleles (Ae ) of 7.52 for this panel. The cumulative power of discrimination and cumulative probability of exclusion values of the 55 loci were 1-2.37 × 10-73 and 1-1.19 × 10-28 , respectively. Additionally, this panel exhibited high allele detection rates of over 97% in each of the 21 artificial mixtures involving from two to six contributors at different mixing ratios. We used EuroForMix to calculate the likelihood ratio (LR) and evaluate the evidence strength provided by this panel, and it could assess evidence strength with LR, distinguishing real and noncontributors. In conclusion, our panel holds great potential for detecting and analyzing DNA mixtures in forensic applications, with the capability to enhance routine mixture analysis.
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Affiliation(s)
- Mengyu Tan
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Jiaming Xue
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Qiushuo Wu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Yazi Zheng
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Guihong Liu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Ranran Zhang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Mengna Wu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Jinlong Song
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Yuanyuan Xiao
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Dezhi Chen
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Meili Lv
- Department of Immunology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Miao Liao
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Shengqiu Qu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
| | - Weibo Liang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P. R. China
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12
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Chen Y, Song Y, Wang X, Tang H, Li C. Genetically engineered virus-like particle-armoured and multibranched DNA scaffold-corbelled ultra-sensitive hierarchical hybridization chain reaction for targeting-enhanced imaging in living biosystems under spatiotemporal light powering. Biosens Bioelectron 2024; 247:115943. [PMID: 38141440 DOI: 10.1016/j.bios.2023.115943] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/03/2023] [Accepted: 12/19/2023] [Indexed: 12/25/2023]
Abstract
Although nucleic acids-based fluorescent biosensors, exemplified by the hybridization chain reaction (HCR), have exhibited promise as an imaging tool for detecting disease-related biomolecular makers in living biosystems, they still face certain challenges. These include the need for improved sensitivity, poor bio-targeting capability, the absence of signal enrichment interface and the uncontrollable biosensing initiation. Herein, we present a range of effective solutions. First, a stacking design resembling building blocks is used to construct a special hierarchical HCR (termed H-HCR), for which a hierarchical bridge is employed to graft multiunit HCR products. Furthermore, the H-HCR components are encapsulated into a virus-like particle (VLP) endowed with a naturally peptide-mediated targeting unit through genetic engineering of plasmids, after which the biosensor can specifically identify cancer cytomembranes. By further creating a multibranched DNA scaffold to enrich the H-HCR produced detection signals, the biosensor's analyte recognition module is inserted with a photocleavage-linker, allowing that the biosensing process can be spatiotemporally initiated via a light-powered behavior. Following these innovations, this genetically engineered VLP-armoured and multibranched DNA-scaffold-corbelled H-HCR demonstrates an ultra-sensitive and specific biosensing performance to a cancer-associated microRNA marker (miRNA-155). Beyond the worthy in vitro analysis, our method is also effective in performing imaging assays for such low-abundance analyte in living cells and even bodies, thus providing a roust platform for disease diagnosis.
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Affiliation(s)
- Yaling Chen
- Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Public Health, Wuhan University of Science and Technology, Wuhan, 430065, PR China
| | - Yongyao Song
- Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Public Health, Wuhan University of Science and Technology, Wuhan, 430065, PR China; Institute of Infection, Immunology and Tumor Microenvironment, Medical College, Wuhan University of Science and Technology, Wuhan, 430065, PR China
| | - Xiaomei Wang
- Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Public Health, Wuhan University of Science and Technology, Wuhan, 430065, PR China; Institute of Infection, Immunology and Tumor Microenvironment, Medical College, Wuhan University of Science and Technology, Wuhan, 430065, PR China.
| | - Hongwu Tang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, PR China
| | - Chengyu Li
- Hubei Province Key Laboratory of Occupational Hazard Identification and Control, School of Public Health, Wuhan University of Science and Technology, Wuhan, 430065, PR China.
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13
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Abdelrazig AO, Rijiravanich P, Suwannarat S, Surareungchai W, Somasundrum M. Detection of DNA using gold nanoparticle-coated silica nanoparticles. Anal Biochem 2024; 686:115411. [PMID: 38070665 DOI: 10.1016/j.ab.2023.115411] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/13/2023] [Accepted: 11/24/2023] [Indexed: 12/23/2023]
Abstract
We report a sensitive lateral flow assay (LFA) in which the assay colour change originated from reporter labels constructed from silica spheres (radius = 450 nm) coated with approximately 3.9 × 103 gold nanoparticles (radius = 8.5 nm). These reporter labels were modified with DNA and deposited in the conjugation area of an LFA device assembled on wax-patterned Fusion 5 paper. Test and control zones of the device were pre-loaded with capture probe formed by avidin-coated mesoporous silica nanoparticles attached with biotin-tagged DNA sequences. Proof-of-concept was demonstrated by the detection of a partial sequence of the actin gene of Colletotrichum truncatum. The DNA target could be detected with an LOD of 46 pM, which was 5 times lower than a comparative assay using gold nanoparticles alone. The assay showed good selectivity against the Colletotrichum species C. scovillei and C. gloeosporioides, as well as against DNA from the fungal genera Aspergillus niger and Alternaria alternata. There was negligible change in sensor response over storage for one month at room temperature. The LFA was used to detect PCR products following extraction from mycelium.
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Affiliation(s)
- Amir Osman Abdelrazig
- Sensor Technology Laboratory, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi (KMUTT), Bang Khun Thian, Bangkok, 10150, Thailand
| | - Patsamon Rijiravanich
- BioSciences and Systems Biology Research Team, National Center for Genetic Engineering and Biotechnology, National Sciences and Technology Development Agency at KMUTT, Bang Khun Thian, Bangkok, 10150, Thailand.
| | - Sawita Suwannarat
- Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Werasak Surareungchai
- Analytical Sciences and National Doping Test Institute, Mahidol University, Bangkok, 10400, Thailand; School of Bioresources and Technology, KMUTT, Bang Khun Thian, Bangkok, 10150, Thailand
| | - Mithran Somasundrum
- BioSciences and Systems Biology Research Team, National Center for Genetic Engineering and Biotechnology, National Sciences and Technology Development Agency at KMUTT, Bang Khun Thian, Bangkok, 10150, Thailand.
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14
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McCrane SM, Mulligan CJ. An innovative transfer DNA experimental design and qPCR assay to identify primary, secondary, and tertiary DNA transfer. J Forensic Sci 2024; 69:618-630. [PMID: 38108622 DOI: 10.1111/1556-4029.15444] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 11/09/2023] [Accepted: 11/27/2023] [Indexed: 12/19/2023]
Abstract
"Touch DNA" is a form of trace DNA that is presumed to be deposited when an individual touches something and leaves behind DNA-containing skin cells, sweat, or other fluids. While touch DNA is often the result of direct contact (i.e., primary transfer), it can also be indirectly transferred between surfaces or individuals (e.g., secondary or tertiary transfer). Even experts cannot distinguish between different types of transfer and do not fully understand which variables affect direct versus indirect transfer or how often each type of transfer occurs. In this study, we utilize an innovative protocol that combines a paired male and female transfer DNA experimental design with an Amelogenin qPCR assay to generate data on primary, secondary, and tertiary DNA transfer. We report frequencies of indirect DNA transfer and also investigate the potential effects of participant age, self-identified ethnicity, and skin conditions on DNA transfer. Out of 22 experimental trials, we detected primary transfer (male + female) in 71% of trials, secondary DNA transfer in 50% of trials, and tertiary DNA transfer in 27% of trials. No significant associations were found between primary DNA transfer and age, self-identified ancestry, or skin conditions, however, all individuals with sloughing skin conditions demonstrated primary DNA transfer and we suggest this variable be explored in larger samples. These results contribute to a better understanding of the conditions under which secondary and tertiary DNA transfer occurs and can be used to propose realistic DNA transfer scenarios in court cases.
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Affiliation(s)
- Samantha M McCrane
- Anthropology, University of New Hampshire, Durham, New Hampshire, USA
- Anthropology, University of Florida, Gainesville, Florida, USA
- Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Connie J Mulligan
- Anthropology, University of Florida, Gainesville, Florida, USA
- Genetics Institute, University of Florida, Gainesville, Florida, USA
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15
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Zhou X, Geng H, Shi P, Wang H, Zhang G, Cui Z, Lv S, Bi S. NIR-driven photoelectrochemical-fluorescent dual-mode biosensor based on bipedal DNA walker for ultrasensitive detection of microRNA. Biosens Bioelectron 2024; 247:115916. [PMID: 38104392 DOI: 10.1016/j.bios.2023.115916] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 11/22/2023] [Accepted: 12/04/2023] [Indexed: 12/19/2023]
Abstract
Optical biosensors have become powerful tools for bioanalysis, but most of them are limited by optic damage, autofluorescence, as well as poor penetration ability of ultraviolet (UV) and visible (Vis) light. Herein, a near-infrared light (NIR)-driven photoelectrochemical (PEC)-fluorescence (FL) dual-mode biosensor has been proposed for ultrasensitive detection of microRNA (miRNA) based on bipedal DNA walker with cascade amplification. Fueled by toehold-mediated strand displacement (TMSD), the bipedal DNA walker triggered by target miRNA-21 is formed through catalytic hairpin assembly (CHA), which can efficiently move along DNA tracks on CdS nanoparticles (CdS NPs)-modified fluorine doped tin oxide (FTO) electrode, resulting in the introduction of upconversion nanoparticles (UCNPs) on electrode surface. Under 980 nm laser irradiation, the UCNPs serve as the energy donor to emit UV/Vis light and excite CdS NPs to generate photocurrent for PEC detection, while the upconversion luminescence (UCL) at 803 nm is monitored for FL detection. This PEC-FL dual-mode biosensor has achieved the ultrasensitive and accurate analysis of miRNA-21 in human serum and different gynecological cancer cells. Overall, the proposed dual-mode biosensor can not only couple the inherent features of each single-mode biosensor but also provide mutual authentication of testing results, which opens up a new avenue for early diagnosis of miRNA-related diseases in clinic.
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Affiliation(s)
- Xuemin Zhou
- Department of Obstetrics and Gynecology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, PR China; Department of Ultrasonic Medicine, Binzhou Medical University Hospital, Binzhou, 256603, PR China
| | - Hongyan Geng
- Department of Obstetrics and Gynecology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, PR China; College of Chemistry and Chemical Engineering, Key Laboratory of Shandong Provincial Universities for Functional Molecules and Materials, Qingdao University, Qingdao, 266000, PR China
| | - Pengfei Shi
- College of Chemistry and Chemical Engineering, Key Laboratory of Shandong Provincial Universities for Functional Molecules and Materials, Qingdao University, Qingdao, 266000, PR China; Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, School of Chemistry and Chemical Engineering, Linyi University, Linyi, 276000, PR China
| | - Huijie Wang
- College of Chemistry and Chemical Engineering, Key Laboratory of Shandong Provincial Universities for Functional Molecules and Materials, Qingdao University, Qingdao, 266000, PR China
| | - Guofang Zhang
- Department of Obstetrics and Gynecology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, PR China
| | - Zhumei Cui
- Department of Obstetrics and Gynecology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, PR China.
| | - Shuzhen Lv
- Department of Obstetrics and Gynecology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, PR China; College of Chemistry and Chemical Engineering, Key Laboratory of Shandong Provincial Universities for Functional Molecules and Materials, Qingdao University, Qingdao, 266000, PR China.
| | - Sai Bi
- Department of Obstetrics and Gynecology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266000, PR China; College of Chemistry and Chemical Engineering, Key Laboratory of Shandong Provincial Universities for Functional Molecules and Materials, Qingdao University, Qingdao, 266000, PR China.
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16
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Hong S, Park J, Bok J, Cho E, Rhee J. Assessment of measurement accuracy of amplified DNA using a colorimetric loop-mediated isothermal amplification assay. Biotechniques 2024; 76:114-118. [PMID: 38131320 DOI: 10.2144/btn-2023-0104] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023] Open
Abstract
A colorimetric loop-mediated isothermal amplification assay detects changes in pH during amplification based on color changes at a constant temperature. Currently, various studies have focused on developing and assessing molecular point-of-care testing instruments. In this study, we evaluated amplified DNA concentrations measured using the colorimetric LAMP assay of the 1POT™ Professional device (1drop Inc, Korea). Results of the 1POT analysis of clinical samples were compared with measurements obtained from the Qubit™ 4 and NanoDrop™ 2000 devices (both from Thermo Fisher Scientific, MA, USA). These results showed a correlation of 0.98 (95% CI: 0.96-0.99) and 0.96 (95% CI: 0.92-0.98) between 1POT and the Qubit and NanoDrop. 1POT can measure amplified DNA accurately and is suitable for on-site molecular diagnostics.
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Affiliation(s)
- Seongsoo Hong
- 1drop Inc, 215, Galmachi-ro, Jungwon-gu, Seongnam-si, Gyeonggi-do, Korea
| | - Jeongho Park
- 1drop Inc, 215, Galmachi-ro, Jungwon-gu, Seongnam-si, Gyeonggi-do, Korea
| | - Jaekyung Bok
- 1drop Inc, 215, Galmachi-ro, Jungwon-gu, Seongnam-si, Gyeonggi-do, Korea
| | - Euna Cho
- 1drop Inc, 215, Galmachi-ro, Jungwon-gu, Seongnam-si, Gyeonggi-do, Korea
| | - Joowon Rhee
- 1drop Inc, 215, Galmachi-ro, Jungwon-gu, Seongnam-si, Gyeonggi-do, Korea
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17
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Dierig L, Kunz SN, Wiegand P. Comparison of massively parallel sequencing to capillary electrophoresis for short tandem repeat genotyping of trace DNA. Electrophoresis 2024; 45:451-462. [PMID: 38085164 DOI: 10.1002/elps.202300145] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 09/08/2023] [Accepted: 10/23/2023] [Indexed: 03/20/2024]
Abstract
In forensic genetics, massively parallel sequencing (MPS) offers several advantages over the current golden standard, capillary electrophoresis (CE): additional sequence information, shorter amplicon lengths, and the simultaneous analysis of many markers. These benefits result in a reduced number of reactions necessary while improving the amount of data obtained, thereby conserving valuable sample extracts. This proves particularly advantageous for the analysis of trace DNA. This study assessed the suitability of MPS for short tandem repeat (STR) typing of low template samples compared with results obtained through CE. The MPS genotypes showed higher concordance to reference genotypes, with donor alleles being more frequently assigned to be the major contributor, meeting the requirements for database entry. However, the MPS workflow is more time-consuming and associated with higher costs.
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Affiliation(s)
- Lisa Dierig
- Institute of Legal Medicine, Ulm University, Ulm, Germany
| | | | - Peter Wiegand
- Institute of Legal Medicine, Ulm University, Ulm, Germany
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18
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Choi N, Schlücker S. Convergence of Surface-Enhanced Raman Scattering with Molecular Diagnostics: A Perspective on Future Directions. ACS Nano 2024; 18:5998-6007. [PMID: 38345242 DOI: 10.1021/acsnano.3c11370] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Molecular diagnostics (MD) is widely employed in multiple scientific disciplines, such as oncology, pathogen detection, forensic investigations, and the pharmaceutical industry. Techniques such as polymerase chain reaction (PCR) revolutionized the rapid and accurate identification of nucleic acids (DNA, RNA). More recently, CRISPR and its CRISPR-associated protein (Cas) have been a ground-breaking discovery that is the latest revolution in molecular biology, including MD. Surface-enhanced Raman scattering (SERS) is a very attractive alternative to fluorescence as the currently most widely used optical readout in MD. In this Perspective, milestones in the development of MD, SERS-PCR, and next-generation approaches to MD, such as Specific High-Sensitivity Enzymatic Reporter UnLOCKing (SHERLOCK) and DNA Endonuclease-Targeted CRISPR Trans Reporter (DETECTR), are briefly summarized. Our perspective on the future convergence of SERS with MD is focused on SERS-based CRISPR/Cas (SERS-CRISPR) since we anticipate many promising applications in this rapidly emerging field. We predict that major future developments will exploit the advantages of real-time monitoring with the superior brightness, photostability, and spectral multiplexing potential of SERS nanotags in an automated workflow for rapid assays under isothermal, amplification-free conditions.
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Affiliation(s)
- Namhyun Choi
- Physical Chemistry I, Department of Chemistry, and Center of Nanointegration Duisburg-Essen (CENIDE) & Center of Medical Biotechnology (ZMB), University of Duisburg-Essen (UDE), 45141 Essen, Germany
| | - Sebastian Schlücker
- Physical Chemistry I, Department of Chemistry, and Center of Nanointegration Duisburg-Essen (CENIDE) & Center of Medical Biotechnology (ZMB), University of Duisburg-Essen (UDE), 45141 Essen, Germany
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19
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Li B, Wang C. Endonuclease IV and T4 ligase enhanced detection of mutations in low abundance. Analyst 2024; 149:1050-1054. [PMID: 38231135 DOI: 10.1039/d3an02083e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
We propose a mutant detection approach based on endonuclease IV and DNA ligase in combination with qPCR. The enzymes functioned cooperatively to facilitate PCR for low abundance DNA detection. We demonstrate that our approach can distinguish mutations as low as 0.01%, indicating the potential application of this strategy in early cancer diagnosis.
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Affiliation(s)
- Bo Li
- Department of Chemistry and Chemical Engineering, Inner Mongolia University, Hohhot, 010020, China.
| | - Chunyan Wang
- Department of Chemistry and Chemical Engineering, Inner Mongolia University, Hohhot, 010020, China.
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Onofri M, Tommolini F, Severini S, Gambelunghe C, Lancia M, Carlini L, Carnevali E. Trace DNA Transfer in Co-Working Spaces: The Importance of Background DNA Analysis. Int J Mol Sci 2024; 25:2207. [PMID: 38396883 PMCID: PMC10888653 DOI: 10.3390/ijms25042207] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/08/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
The presence of background DNA (bgDNA) can hinder the evaluation of DNA evidence at the activity level, especially when the suspect is expected to be retrieved due to their habitual occupation of the investigated environment. Based on real-life casework circumstances, this study investigates the prevalence, composition, origin, and probable transfer routes of bgDNA found on personal items in situations where their owner and person of interest (POI) share the same workspace. Baseline values of bgDNA were evaluated on the participants' personal items. Secondary and higher degree transfer scenarios of non-self DNA deposition were also investigated. The DNA from co-workers and co-inhabiting partners can be recovered from an individual's personal belongings. Non-self DNA present on the hands and deposited on a sterile surface can generate uninformative profiles. The accumulation of foreign DNA on surfaces over time appears to be crucial for the recovery of comparable profiles, resulting in detectable further transfer onto other surfaces. For a thorough evaluation of touch DNA traces at the activity level, it is necessary to collect information not only about DNA transfer probabilities but also about the presence of the POI as part of the 'baseline' bgDNA of the substrates involved.
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Affiliation(s)
- Martina Onofri
- Forensic Sciences Laboratory, Section of Legal Medicine, Department of Medicine and Surgery, Santa Maria Hospital, University of Perugia, 05100 Terni, Italy; (F.T.); (S.S.); (E.C.)
- Section of Legal Medicine, Department of Medicine and Surgery, University of Perugia, 06123 Perugia, Italy; (C.G.); (M.L.); (L.C.)
| | - Federica Tommolini
- Forensic Sciences Laboratory, Section of Legal Medicine, Department of Medicine and Surgery, Santa Maria Hospital, University of Perugia, 05100 Terni, Italy; (F.T.); (S.S.); (E.C.)
| | - Simona Severini
- Forensic Sciences Laboratory, Section of Legal Medicine, Department of Medicine and Surgery, Santa Maria Hospital, University of Perugia, 05100 Terni, Italy; (F.T.); (S.S.); (E.C.)
| | - Cristiana Gambelunghe
- Section of Legal Medicine, Department of Medicine and Surgery, University of Perugia, 06123 Perugia, Italy; (C.G.); (M.L.); (L.C.)
| | - Massimo Lancia
- Section of Legal Medicine, Department of Medicine and Surgery, University of Perugia, 06123 Perugia, Italy; (C.G.); (M.L.); (L.C.)
| | - Luigi Carlini
- Section of Legal Medicine, Department of Medicine and Surgery, University of Perugia, 06123 Perugia, Italy; (C.G.); (M.L.); (L.C.)
| | - Eugenia Carnevali
- Forensic Sciences Laboratory, Section of Legal Medicine, Department of Medicine and Surgery, Santa Maria Hospital, University of Perugia, 05100 Terni, Italy; (F.T.); (S.S.); (E.C.)
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Tanaka Y, Mizuguchi R, Koseki N, Suzuki H, Suzuki T. Quality assessment of enzymatic methyl-seq library constructed using crude cell lysate. Biochem Biophys Res Commun 2024; 696:149488. [PMID: 38219485 DOI: 10.1016/j.bbrc.2024.149488] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Accepted: 01/05/2024] [Indexed: 01/16/2024]
Abstract
Enzymatic methyl-seq (EM-seq), an enzyme-based method, identifies genome-wide DNA methylation, which enables us to obtain reliable methylome data from purified genomic DNA by avoiding bisulfite-induced DNA damage. However, the loss of DNA during purification hinders the methylome analysis of limited samples. The crude DNA extraction method is the quickest and minimal sample loss approach for obtaining useable DNA without requiring additional dissolution and purification. However, it remains unclear whether crude DNA can be used directly for EM-seq library construction. In this study, we aimed to assess the quality of EM-seq libraries prepared directly using crude DNA. The crude DNA-derived libraries provided appropriate fragment sizes and concentrations for sequencing similar to those of the purified DNA-derived libraries. However, the sequencing results of crude samples exhibited lower reference sequence mapping efficiencies than those of the purified samples. Additionally, the lower-input crude DNA-derived sample exhibited a marginally lower cytosine-to-thymine conversion efficiency and hypermethylated pattern around gene regulatory elements than the higher-input crude DNA- or purified DNA-derived samples. In contrast, the methylation profiles of the crude and purified samples exhibited a significant correlation. Our findings indicate that crude DNA can be used as a raw material for EM-seq library construction.
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Affiliation(s)
- Yuki Tanaka
- Laboratory for Cellular Function Conversion Technology, RIKEN Center for Integrative Medical Sciences (IMS), RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan.
| | - Risa Mizuguchi
- Laboratory for Cellular Function Conversion Technology, RIKEN Center for Integrative Medical Sciences (IMS), RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan; Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan.
| | - Norio Koseki
- Laboratory for Cellular Function Conversion Technology, RIKEN Center for Integrative Medical Sciences (IMS), RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan; Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan.
| | - Harukazu Suzuki
- Laboratory for Cellular Function Conversion Technology, RIKEN Center for Integrative Medical Sciences (IMS), RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan.
| | - Takahiro Suzuki
- Laboratory for Cellular Function Conversion Technology, RIKEN Center for Integrative Medical Sciences (IMS), RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan; Department of Obstetrics & Gynecology, Juntendo University Faculty of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan.
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22
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Jiang B, Zhang T, Liu S, Sheng Y, Hu J. Polydopamine-assisted aptamer-carrying tetrahedral DNA microelectrode sensor for ultrasensitive electrochemical detection of exosomes. J Nanobiotechnology 2024; 22:55. [PMID: 38331774 PMCID: PMC10854160 DOI: 10.1186/s12951-024-02318-6] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 01/26/2024] [Indexed: 02/10/2024] Open
Abstract
BACKGROUND Exosomes are nanoscale extracellular vesicles (30-160 nm) with endosome origin secreted by almost all types of cells, which are considered to be messengers of intercellular communication. Cancerous exosomes serve as a rich source of biomarkers for monitoring changes in cancer-related physiological status, because they carry a large number of biological macromolecules derived from parental tumors. The ultrasensitive quantification of trace amounts of cancerous exosomes is highly valuable for non-invasive early cancer diagnosis, yet it remains challenging. Herein, we developed an aptamer-carrying tetrahedral DNA (Apt-TDNA) microelectrode sensor, assisted by a polydopamine (PDA) coating with semiconducting properties, for the ultrasensitive electrochemical detection of cancer-derived exosomes. RESULTS The stable rigid structure and orientation of Apt-TDNA ensured efficient capture of suspended exosomes. Without PDA coating signal amplification strategy, the sensor has a linear working range of 102-107 particles mL-1, with LOD of ~ 69 exosomes and ~ 42 exosomes for EIS and DPV, respectively. With PDA coating, the electrochemical signal of the microelectrode is further amplified, achieving single particle level sensitivity (~ 14 exosomes by EIS and ~ 6 exosomes by DPV). CONCLUSIONS The proposed PDA-assisted Apt-TDNA microelectrode sensor, which integrates efficient exosome capture, sensitive electrochemical signal feedback with PDA coating signal amplification, provides a new avenue for the development of simple and sensitive electrochemical sensing techniques in non-invasive cancer diagnosis and monitoring treatment response.
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Affiliation(s)
- Bowen Jiang
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, China
| | - Tenghua Zhang
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, China
| | - Silan Liu
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, China
| | - Yan Sheng
- Institute of Translational Medicine, Shanghai University, Shanghai, 200444, China.
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, China.
| | - Jiaming Hu
- International Joint Laboratory of Catalytic Chemistry, State Key Laboratory of Advanced Special Steel, Innovation Institute of Carbon Neutrality, College of Sciences, Shanghai University, Shanghai, 200444, China.
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, China.
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Wang Z, Feng N, Zhou Y, Cheng X, Zhou C, Ma A, Wang Q, Li Y, Chen Y. Mesophilic Argonaute-Mediated Polydisperse Droplet Biosensor for Amplification-Free, One-Pot, and Multiplexed Nucleic Acid Detection Using Deep Learning. Anal Chem 2024; 96:2068-2077. [PMID: 38259216 DOI: 10.1021/acs.analchem.3c04426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Detection of nucleic acids from a single multiplexed and amplification-free test is critical for ensuring food safety, clinical diagnostics, and environmental monitoring. In this study, we introduced a mesophilic Argonaute protein from Clostridium butyricum (CbAgo), which exhibits nucleic acid endonuclease activity, to achieve a programmable, amplification-free system (PASS) for rapid nucleic acid quantification at ambient temperatures in one pot. By using CbAgo-mediated binding with specific guide DNA (gDNA) and subsequent targeted cleavage of wild-type target DNAs complementary to gDNA, PASS can detect multiple foodborne pathogen DNA (<102 CFU/mL) simultaneously. The fluorescence signals were then transferred to polydisperse emulsions and analyzed by using deep learning. This simplifies the process and increases the suitability of polydisperse emulsions compared to traditional digital PCR, which requires homogeneous droplets for accurate detection. We believe that PASS has the potential to become a next-generation point-of-care digital nucleic acid detection method.
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Affiliation(s)
- Zhipan Wang
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Niu Feng
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Yanan Zhou
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Xinrui Cheng
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Cuiyun Zhou
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Aimin Ma
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Qinyu Wang
- Department of Computer Science and Technology, Wuhan University of Science and Technology, Wuhan 430000, Hubei China
| | - Yingjun Li
- State Key Laboratory of Agricultural Microbiology and College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Yiping Chen
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
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24
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Larsen L. Why citizen scientists are gathering DNA from hundreds of lakes - on the same day. Nature 2024; 626:934-935. [PMID: 38383651 DOI: 10.1038/d41586-024-00520-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
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25
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Zhuo C, Yu D, Cui J, Song Z, Tang Q, Liao X, Liu Z, Xin N, Lou L, Gao F. Proximity hybridization induced bipedal DNA walker and rolling circle amplification for label-free electrochemical detection of apolipoprotein A4. Bioelectrochemistry 2024; 155:108596. [PMID: 37939432 DOI: 10.1016/j.bioelechem.2023.108596] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 10/30/2023] [Accepted: 10/31/2023] [Indexed: 11/10/2023]
Abstract
Apolipoprotein A4 (Apo-A4) is considered as a prospective molecular biomarker for diagnosis of depression due to its neurosynaptic toxicity. We develop a proximity hybridization-induced DNAzyme-driven bipedal DNA walker strategy for Apo-A4 quantification based on rolling circle amplification (RCA) triggered by poly adenine binding to Ag nanoparticles (AgNPs). With the help of DNAzyme, the free-running bipedal DNA walker can quickly and sequentially shear a molecular beacon that acts as a primer to initiate the RCA process, producing a large number of long DNA strands containing numerous adenines. The long repetitive adenine strands then absorb large amounts of AgNPs on the electrode interface, which is then electrochemically stripped of the AgNPs. The method has a linear detection range of 0.001 ∼ 100 ng mL-1 and a detection limit of 0.46 pg mL-1. The presented detection strategy is label-free, which allows high sensitivity and selectivity for detection of a wide range of protein targets by corresponding DNA-based affinity probes, which have potential applications in bioanalysis.
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Affiliation(s)
- Chenyi Zhuo
- The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi 533000, China
| | - Dehong Yu
- The Affiliated Pizhou Hospital of Xuzhou Medical University, Jiangsu 221399, China
| | - Jiuying Cui
- The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi 533000, China; West Guangxi Key Laboratory for Prevention and Treatment of High-incidence Diseases, Youjiang Medical University for Nationalities, Baise, Guangxi 533000, China
| | - Zichun Song
- The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi 533000, China; West Guangxi Key Laboratory for Prevention and Treatment of High-incidence Diseases, Youjiang Medical University for Nationalities, Baise, Guangxi 533000, China
| | - Qianli Tang
- The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi 533000, China; West Guangxi Key Laboratory for Prevention and Treatment of High-incidence Diseases, Youjiang Medical University for Nationalities, Baise, Guangxi 533000, China
| | - Xianjiu Liao
- West Guangxi Key Laboratory for Prevention and Treatment of High-incidence Diseases, Youjiang Medical University for Nationalities, Baise, Guangxi 533000, China.
| | - Zhao Liu
- School of Pharmacy, Xuzhou Medical University, 221004 Xuzhou, China
| | - Ning Xin
- School of Pharmacy, Xuzhou Medical University, 221004 Xuzhou, China
| | - Lu Lou
- Department of Urology, The Affiliated Xuzhou Municipal Hospital of Xuzhou Medical University, Xuzhou First People's Hospital, Xuzhou, China.
| | - Fenglei Gao
- School of Pharmacy, Xuzhou Medical University, 221004 Xuzhou, China.
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Liu H, Wei W, Song J, Hu J, Wang Z, Lin P. Upconversion-Powered Photoelectrochemical Bioanalysis for DNA Sensing. Sensors (Basel) 2024; 24:773. [PMID: 38339489 PMCID: PMC10856881 DOI: 10.3390/s24030773] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/18/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024]
Abstract
In this work, we report a new concept of upconversion-powered photoelectrochemical (PEC) bioanalysis. The proof-of-concept involves a PEC bionanosystem comprising a NaYF4:Yb,Tm@NaYF4 upconversion nanoparticles (UCNPs) reporter, which is confined by DNA hybridization on a CdS quantum dots (QDs)/indium tin oxide (ITO) photoelectrode. The CdS QD-modified ITO electrode was powered by upconversion absorption together with energy transfer effect through UCNPs for a stable photocurrent generation. By measuring the photocurrent change, the target DNA could be detected in a specific and sensitive way with a wide linear range from 10 pM to 1 μM and a low detection limit of 0.1 pM. This work exploited the use of UCNPs as signal reporters and realized upconversion-powered PEC bioanalysis. Given the diversity of UCNPs, we believe it will offer a new perspective for the development of advanced upconversion-powered PEC bioanalysis.
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Affiliation(s)
- Hong Liu
- Shenzhen Key Laboratory of Special Functional Materials & Guangdong Research Center for Interfacial Engineering of Functional Materials, College of Materials Science and Engineering, Shenzhen University, Shenzhen 518060, China; (H.L.); (J.S.); (J.H.)
| | - Weiwei Wei
- Shenzhen Key Laboratory of Special Functional Materials & Guangdong Research Center for Interfacial Engineering of Functional Materials, College of Materials Science and Engineering, Shenzhen University, Shenzhen 518060, China; (H.L.); (J.S.); (J.H.)
| | - Jiajun Song
- Shenzhen Key Laboratory of Special Functional Materials & Guangdong Research Center for Interfacial Engineering of Functional Materials, College of Materials Science and Engineering, Shenzhen University, Shenzhen 518060, China; (H.L.); (J.S.); (J.H.)
| | - Jin Hu
- Shenzhen Key Laboratory of Special Functional Materials & Guangdong Research Center for Interfacial Engineering of Functional Materials, College of Materials Science and Engineering, Shenzhen University, Shenzhen 518060, China; (H.L.); (J.S.); (J.H.)
| | - Zhezhe Wang
- Fujian Provincial Key Laboratory of Quantum Manipulation and New Energy Materials, College of Physics and Energy, Fujian Normal University, Fuzhou 350117, China;
| | - Peng Lin
- Shenzhen Key Laboratory of Special Functional Materials & Guangdong Research Center for Interfacial Engineering of Functional Materials, College of Materials Science and Engineering, Shenzhen University, Shenzhen 518060, China; (H.L.); (J.S.); (J.H.)
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27
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Fan W, Zhao L, Yu L, Zhou Y. Chip-based digital PCR as a direct quantification method for residual DNA in mRNA drugs. J Pharm Biomed Anal 2024; 238:115837. [PMID: 37952451 DOI: 10.1016/j.jpba.2023.115837] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 11/14/2023]
Abstract
Residual exogenous DNA, as common contaminants in biological products, must be monitored and removed to ensure safety. Digital PCR (dPCR) technology is widely applied in DNA quantitative analysis due to high specificity, sensitivity, absolute quantification, etc. Data support is relatively lacking in deciphering the dPCR technology application in residual DNA of mRNA drugs. The current study helped establish the dPCR methods corresponding to two different mRNA vaccines to detect the residual DNA template. The established dPCR methods have a wide linear range, good precision, accuracy, and specificity without being interfered with by encapsulating and demulsifying reagents. The method is simple, rapid, and sensitive which demonstrates that dPCR can directly quantitate other types of risky DNA in mRNA drugs accurately as well.
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Affiliation(s)
- Wenchao Fan
- Key Laboratory of the Ministry of Health for Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug Control, No. 2, Tiantan Xili, Dongcheng District, Beijing 100050, China
| | - Lan Zhao
- Key Laboratory of the Ministry of Health for Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug Control, No. 2, Tiantan Xili, Dongcheng District, Beijing 100050, China
| | - Lei Yu
- Key Laboratory of the Ministry of Health for Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug Control, No. 2, Tiantan Xili, Dongcheng District, Beijing 100050, China
| | - Yong Zhou
- Key Laboratory of the Ministry of Health for Research on Quality and Standardization of Biotech Products, National Institutes for Food and Drug Control, No. 2, Tiantan Xili, Dongcheng District, Beijing 100050, China.
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28
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Li W, Ren Q, Feng J, Lee SY, Liu Y. DNA barcoding for the identification and authentication of medicinal deer (Cervus sp.) products in China. PLoS One 2024; 19:e0297164. [PMID: 38241246 PMCID: PMC10798443 DOI: 10.1371/journal.pone.0297164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 12/30/2023] [Indexed: 01/21/2024] Open
Abstract
Deer products from sika deer (Cervus nippon) and red deer (C. elaphus) are considered genuine and used for Traditional Chinese Medicine (TCM) materials in China. Deer has a very high economic and ornamental value, resulting in the formation of a characteristic deer industry in the prescription preparation of traditional Chinese medicine, health food, cosmetics, and other areas of development and utilization. Due to the high demand for deer products, the products are expensive and have limited production, but the legal use of deer is limited to only two species of sika deer and red deer; other wild deer are prohibited from hunting, so there are numerous cases of mixing and adulteration of counterfeit products and so on. There have been many reports that other animal (pig, cow, sheep, etc.) tissues or organs are often used for adulteration and confusion, resulting in poor efficacy of deer traditional medicine and trade fraud in deer products. To authenticate the deer products in a rapid and effective manner, the analysis used 22 deer products (antler, meat, bone, fetus, penis, tail, skin, and wool) that were in the form of blind samples. Total DNA extraction using a modified protocol successfully yielded DNA from the blind samples that was useful for PCR. Three candidate DNA barcoding loci, cox1, Cyt b, and rrn12, were evaluated for their discrimination strength through BLAST and phylogenetic clustering analyses. For the BLAST analysis, the 22 blind samples obtained 100% match identity across the three gene loci tested. It was revealed that 12 blind samples were correctly labeled for their species of origin, while three blind samples that were thought to originate from red deer were identified as C. nippon, and seven blind samples that were thought to originate from sika deer were identified as C. elaphus, Dama dama, and Rangifer tarandus. DNA barcoding analysis showed that all three gene loci were able to distinguish the two Cervus species and to identify the presence of adulterant species. The DNA barcoding technique was able to provide a useful and sensitive approach in identifying the species of origin in deer products.
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Affiliation(s)
- Wenlan Li
- School of Pharmacy, Harbin University of Commerce, Harbin, China
| | - Qiqi Ren
- School of Pharmacy, Harbin University of Commerce, Harbin, China
- Hainan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Haikou, China
| | - Jian Feng
- Hainan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Haikou, China
| | - Shiou Yih Lee
- Faculty of Health and Life Sciences, INTI International University, Nilai, Malaysia
| | - Yangyang Liu
- Hainan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Haikou, China
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29
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Yang R, Hu J, Zhang L, Liu X, Huang Y, Zhang L, Fan Q. Recent advances in optical biosensing and imaging of telomerase activity and relevant signal amplification strategies. Analyst 2024; 149:290-303. [PMID: 38099470 DOI: 10.1039/d3an01900d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Telomerase as a new valuable biomarker for early diagnosis and prognosis evaluation of cancer has attracted much interest in the field of biosensors, cell imaging, and drug screening. In this review, we mainly focus on different optical techniques and various signal amplification strategies for telomerase activity determination. Fluorometric, colorimetry, chemiluminescence, surface-enhanced Raman scattering (SERS), and dual-mode techniques for telomerase sensing and imaging are summarized. Signal amplification strategies include two categories: one is nucleic acid-based amplification, such as rolling circle amplification (RCA), the hybridization chain reaction (HCR), and catalytic hairpin assembly (CHA); the other is nanomaterial-assisted amplification, including metal nanoclusters, quantum dots, transition metal compounds, graphene oxide, and DNA nanomaterials. Challenges and prospects are also discussed to provide new insights for future development of multifunctional strategies and techniques for in situ and in vivo analysis of biomarkers for accurate cancer diagnosis.
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Affiliation(s)
- Ruining Yang
- The State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Junbo Hu
- The State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Longsheng Zhang
- The State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Xingfen Liu
- The State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Yanqin Huang
- The State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Lei Zhang
- The State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Quli Fan
- The State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
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Feng Q, Wang C, Miao X, Wu M. A novel paper-based electrochemiluminescence biosensor for non-destructive detection of pathogenic bacteria in real samples. Talanta 2024; 267:125224. [PMID: 37751632 DOI: 10.1016/j.talanta.2023.125224] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/13/2023] [Accepted: 09/18/2023] [Indexed: 09/28/2023]
Abstract
The demand for sensitive, portable, and non-destructive analysis of pathogenic bacteria is of significance in point-of-care diagnosis. Herein, we constructed a smart electrochemiluminescence (ECL) biosensor by integrating a flexible paper-based sensing device and a disposable three-electrode detecting system. Staphylococcus aureus (S. aureus)-responsive cellulose paper was prepared by employing aptamer as recognition element and a probe DNA (probe DNA-GOD) tagged with glucose oxidase (GOD) as a signal amplification unit. The formation of aptamer-S. aureus complex mediated the quantitative release of probe DNA-GOD. The remaining probe DNA-GOD on the paper-based aptasensor was then activated by glucose, which resulted in a significant decrease in ECL signal. To further improve the ECL performance of biosensor, a large number of Ru(bpy)32+ molecules were embedded into porous zinc-based metal-organic frameworks (MOFs) to form Ru(bpy)32+ functionalized MOF nanoflowers (Ru-MOF-5 NFs). Such biosensor enabled accurate, non-destructive, and real-time monitoring of S. aureus-contaminated food samples, opening a new avenue for sensitive recognition of pathogenic bacteria.
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Affiliation(s)
- Qiumei Feng
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou, 221116, China
| | - Chengcheng Wang
- School of Chemistry and Materials Science, Jiangsu Normal University, Xuzhou, 221116, China
| | - Xiangmin Miao
- School of Life Science, Jiangsu Normal University, Xuzhou, 221116, PR China.
| | - Meisheng Wu
- Department of Chemistry, College of Sciences, Nanjing Agricultural University, 1 Weigang, Nanjing, 210095, China.
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Ding M, Xiao X, Yang Y, Yao Z, Dong Z, Gao Q, Tian B. AND-Logic Cascade Rolling Circle Amplification for Optomagnetic Detection of Dual Target SARS-CoV-2 Sequences. Anal Chem 2024; 96:455-462. [PMID: 38123506 DOI: 10.1021/acs.analchem.3c04533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
DNA logic operations are accurate and specific molecular strategies that are appreciated in target multiplexing and intelligent diagnostics. However, most of the reported DNA logic operation-based assays lack amplifiers prior to logic operation, resulting in detection limits at the subpicomolar to nanomolar level. Herein, a homogeneous and isothermal AND-logic cascade amplification strategy is demonstrated for optomagnetic biosensing of two different DNA inputs corresponding to a variant of concern sequence (containing spike L452R) and a highly conserved sequence from SARS-CoV-2. With an "amplifiers-before-operator" configuration, two input sequences are recognized by different padlock probes for amplification reactions, which generate amplicons used, respectively, as primers and templates for secondary amplification, achieving the AND-logic operation. Cascade amplification products can hybridize with detection probes grafted onto magnetic nanoparticles (MNPs), leading to hydrodynamic size increases and/or aggregation of MNPs. Real-time optomagnetic MNP analysis offers a detection limit of 8.6 fM with a dynamic detection range spanning more than 3 orders of magnitude. The accuracy, stability, and specificity of the system are validated by testing samples containing serum, salmon sperm, a single-nucleotide variant, and biases of the inputs. Clinical samples are tested with both quantitative reverse transcription-PCR and our approach, showing highly consistent measurement results.
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Affiliation(s)
- Mingming Ding
- Department of Biomedical Engineering, School of Basic Medical Sciences, Central South University, Changsha 410013, China
| | - Xiaozhou Xiao
- Department of Biomedical Engineering, School of Basic Medical Sciences, Central South University, Changsha 410013, China
| | - Yulin Yang
- Department of Biomedical Engineering, School of Basic Medical Sciences, Central South University, Changsha 410013, China
| | - Ziyang Yao
- Department of Biomedical Engineering, School of Basic Medical Sciences, Central South University, Changsha 410013, China
| | - Zhuxin Dong
- Department of Biomedical Engineering, School of Basic Medical Sciences, Central South University, Changsha 410013, China
- Furong Laboratory, Changsha 410008, China
| | - Qian Gao
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Bo Tian
- Department of Biomedical Engineering, School of Basic Medical Sciences, Central South University, Changsha 410013, China
- Furong Laboratory, Changsha 410008, China
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Tang Q, Li Z, Li J, Chen H, Yan H, Deng J, Liu L. PCR-Free, Label-Free, and Centrifugation-Free Diagnosis of Multiplex Antibiotic Resistance Genes by Combining mDNA-Au@Fe 3O 4 from Heating Dry and DNA Concatamers with G-Triplex. Anal Chem 2024; 96:292-300. [PMID: 38141016 DOI: 10.1021/acs.analchem.3c04060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
Accurate identification of antibiotic resistance genes (ARGs) is crucial for improving treatment and controlling the spread of antibiotic-resistant bacteria (ARB). Herein, a novel PCR-free, centrifugation-free, and label-free magnetic fluorescent biosensor (MFB) was developed by combining polyA-medium DNA-polyT (mDNA, which contained a partial sequence of a target DNA), gold nanoparticle (AuNP)-anchored magnetic nanoparticle (Au@Fe3O4), complementary strand DNA (CS) of the target DNA, DNA concatamer with G-triplex (G3), and thioflavin T (ThT). Thereinto, Au@Fe3O4 nanoparticles were first capped by mDNA strands within 20 min using a simple hot drying method, and then CS was added and hybridized with mDNA on Au@Fe3O4. Second, a DNA concatamer was used to bind with CS on Au@Fe3O4. When an ARG was present in the sample, the CS would recognize it and release the DNA concatamer into solution by a toehold-mediated strand displacement reaction. Finally, under magnetic separation, the free DNA concatamers with G3 were taken out easily and bound with ThT, resulting in strong fluorescence signals. The fluorescence intensity of ThT was positively correlated with the concentration of the ARG. The whole analysis was accomplished within 1.5 h using 96-well plates. Remarkably, our MFB was universal; eight ARGs were detected by replacing the corresponding mDNA and CS in this study. To verify the practicability of our method, 12 clinically isolated strains were analyzed. The results of the MFB method were in good agreement with those of the quantitative real-time PCR method with an area under the curve of 0.92 (95% confidence interval: 0.8479 to 0.9932), sensitivity of 92.00%, and specificity of 91.55%. Above all, the MFB assay established here is simple, low-cost, and universal and has great potential for applications in the identification of ARGs.
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Affiliation(s)
- Qing Tang
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Zhijie Li
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jincheng Li
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Hanren Chen
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Hong Yan
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jieqi Deng
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Lihong Liu
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
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Papaioannou VE, Behringer RR. Sex Genotyping Mice by Polymerase Chain Reaction. Cold Spring Harb Protoc 2024; 2024:pdb.prot108062. [PMID: 37932078 DOI: 10.1101/pdb.prot108062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
A simple method to determine the genetic sex of a mouse is to amplify DNA from a male-specific gene by polymerase chain reaction (PCR). This protocol is used to detect the Y-chromosome-specific gene Sry in tissue lysates of tail tip or ear punch samples.
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Affiliation(s)
- Virginia E Papaioannou
- Department of Genetics and Development, Columbia University Medical Center, New York, New York 10032, USA
| | - Richard R Behringer
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
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Berrino E, Bellomo SE, Chesta A, Detillo P, Bragoni A, Gagliardi A, Naccarati A, Cereda M, Witel G, Sapino A, Bussolati B, Bussolati G, Marchiò C. Alternative Tissue Fixation Protocols Dramatically Reduce the Impact of DNA Artifacts, Unraveling the Interpretation of Clinical Comprehensive Genomic Profiling. J Transl Med 2024; 104:100280. [PMID: 38345263 DOI: 10.1016/j.labinv.2023.100280] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 10/03/2023] [Accepted: 10/25/2023] [Indexed: 02/15/2024] Open
Abstract
Formalin-fixed paraffin-embedded (FFPE) samples represent the cornerstone of tissue-based analysis in precision medicine. Targeted next-generation sequencing panels are routinely used to analyze a limited number of genes to guide treatment decision-making for advanced-stage patients. The number and complexity of genetic alterations to be investigated are rapidly growing; in several instances, a comprehensive genomic profiling analysis is needed. The poor quality of genetic material extracted from FFPE samples may impact the feasibility/reliability of sequencing data. We sampled 9 colorectal cancers to allow 4 parallel fixations: (1) neutral buffered formalin (NBF), (2) acid-deprived formalin fixation (ADF), (3) precooled ADF (coldADF), and (4) glyoxal acid free (GAF). DNA extraction, fragmentation analysis, and sequencing by 2 large next-generation sequencing panels (OCAv3 and TSO500) followed. We comprehensively analyzed library and sequencing quality controls and the quality of sequencing results. Libraries from coldADF samples showed significantly longer reads than the others with both panels. ADF-derived and coldADF-derived libraries showed the lowest level of noise and the highest levels of uniformity with the OCAv3 panel, followed by GAF and NBF samples. The data uniformity was confirmed by the TSO500 results, which also highlighted the best performance in terms of the total region sequenced for the ADF and coldADF samples. NBF samples had a significantly smaller region sequenced and displayed a significantly lower number of evaluable microsatellite loci and a significant increase in single-nucleotide variations compared with other protocols. Mutational signature 1 (aging and FFPE artifact related) showed the highest (37%) and lowest (17%) values in the NBF and coldADF samples, respectively. Most of the identified genetic alterations were shared by all samples in each lesion. Five genes showed a different mutational status across samples and/or panels: 4 discordant results involved NBF samples. In conclusion, acid-deprived fixatives (GAF and ADF) guarantee the highest DNA preservation/sequencing performance, thus allowing more complex molecular profiling of tissue samples.
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Affiliation(s)
- Enrico Berrino
- Department of Medical Sciences, University of Turin, Turin, Italy; Candiolo Cancer Institute, FPO-IRCCS, Candiolo, TO, Italy.
| | | | - Anita Chesta
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, TO, Italy
| | | | - Alberto Bragoni
- Department of Medical Sciences, University of Turin, Turin, Italy; Candiolo Cancer Institute, FPO-IRCCS, Candiolo, TO, Italy
| | - Amedeo Gagliardi
- Department of Medical Sciences, University of Turin, Turin, Italy; IIGM-Italian Institute for Genomic Medicine, c/o IRCCS, Candiolo, TO, Italy
| | - Alessio Naccarati
- Department of Medical Sciences, University of Turin, Turin, Italy; IIGM-Italian Institute for Genomic Medicine, c/o IRCCS, Candiolo, TO, Italy
| | - Matteo Cereda
- IIGM-Italian Institute for Genomic Medicine, c/o IRCCS, Candiolo, TO, Italy
| | - Gianluca Witel
- Department of Medical Sciences, University of Turin, Turin, Italy; Candiolo Cancer Institute, FPO-IRCCS, Candiolo, TO, Italy
| | - Anna Sapino
- Department of Medical Sciences, University of Turin, Turin, Italy; Candiolo Cancer Institute, FPO-IRCCS, Candiolo, TO, Italy
| | - Benedetta Bussolati
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Gianni Bussolati
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Caterina Marchiò
- Department of Medical Sciences, University of Turin, Turin, Italy; Candiolo Cancer Institute, FPO-IRCCS, Candiolo, TO, Italy.
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Boering P, Seeley J, Buule J, Kamacooko O, King R. A Comparison of Self-reported Condomless Sex and Yc-DNA Biomarker Data from Young Women Engaged in High Risk Sexual Activity in Kampala, Uganda. AIDS Behav 2024; 28:320-331. [PMID: 37751111 PMCID: PMC10803388 DOI: 10.1007/s10461-023-04177-y] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/11/2023] [Indexed: 09/27/2023]
Abstract
Reporting of condom-use can limit researchers' understanding of high-risk sexual behaviours. We compared self-reported condom-use with the Yc-DNA biomarker data and investigated potential factors influencing participation in, and reporting of, sexual behaviours. Self-reported data were collected using Audio Computer Assisted Self Interviews (ACASI) and samples for Yc-DNA biomarker were collected using self-administered and health worker-collected vaginal swabs from 644 women (aged 15-24 years) who were not living with HIV. Yc-DNA results and interview data were compared using McNemar-Bowker Analysis and Cohen's Kappa. Test statistics for Yc-DNA biomarker were calculated. Log Binomial models for Yc-DNA and self-reported results were conducted to assess for association. We found strong evidence (p < 0.001) for a difference between Yc-DNA and self-reported results. 13.7% of participants reported consistent condom-use with all partners, regardless of HIV status. Self-reported condom-use was discordant in 50.0% (n = 206) of cases, when compared to Yc-DNA results. Positive Yc-DNA results were found to be associated with older age (RR 1.36; 95%CI 1.04, 1.76 p = 0.023). Self-reported condom-use with partners with unknown HIV status was associated with higher education (RR 0.76; 95%CI 0.58,0.99 p = 0.043). Sensitivity analysis did not determine difference between methods for controlling for missing data. We found significant under-reporting of condomless sex in the self-reported data when compared to Yc-DNA results.
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Affiliation(s)
- Pippa Boering
- London School of Hygiene and Tropical Medicine, London, UK
| | - Janet Seeley
- London School of Hygiene and Tropical Medicine, London, UK.
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda.
| | - Joshua Buule
- Uganda Virus Research Institute, Entebbe, Uganda
| | | | - Rachel King
- University of California, San Francisco, CA, USA
- INSERM, 60 Rue de Navacelles, 34090, Montpellier, France
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36
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Ginart S, Garrigos Calivares L, Caputo M, Corach D, Sala A. Improving the efficiency of Y-chromosome detection and the quality of STR typing in forensic casework with an in-house made qPCR and HRM system based on SYTO™ 9 chemistry. Forensic Sci Int 2024; 354:111893. [PMID: 38064775 DOI: 10.1016/j.forsciint.2023.111893] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 11/13/2023] [Accepted: 11/21/2023] [Indexed: 01/12/2024]
Abstract
DNA quantification prior to STR amplification is a crucial step in forensic casework. Obtaining good-quality genetic STR profiles depends mainly on the amount and integrity of the DNA input in the PCR. In addition, the detection of male trace DNA provides key information for forensic investigation. AIM To evaluate the correlation between the quantification results obtained with the previously developed Amel-Y system, and its ability to detect Y-chromosome DNA by HRM, with the resulting STR profiles, and to ultimately show that Amel-Y can be routinely used in forensic casework to improve STR and Y-STR results. MATERIAL & METHODS Biological samples derived from forensic casework (85 reference and 391 evidence samples) were quantified by the Amel-Y system (a duplex qPCR/HRM based on SYTO™ 9 chemistry) using Rotor-Gene 6000. STRs were amplified and analyzed with GeneAmp™ PCR System 9700 or Veriti™ Thermal Cyclers and ABI 3500 Genetic Analyzer, respectively. RESULTS After DNA normalization, a total of 386 STR profiles were obtained (305 full and 81 partial). Sex typing by HRM was 100% successful in reference samples. Male DNA was detected by HRM in 210 evidence samples. 80/201 were mixed with an excess of female DNA. In addition, Amel-Y was able to detect Y-chromosome DNA in mixed samples that did not amplify the Y-variant of Amelogenin marker with commercial STR kits. The reproducibility and precision of the Amel-Y system were demonstrated (CVCt% ≤ 9.55) within the dynamic range analyzed (0.016-50 ng/µL; 41 independent runs). Amel-Y also proved to be compatible with other real-time PCR platforms. CONCLUSION We demonstrated that Amel-Y is a robust quantification system that can be routinely used in forensic casework to obtain reliable autosomal STR profiles and can be suitable as a predictor for Y-STR typing success when male DNA is detected. HRM can be used as a rapid screening tool for male DNA detection in mixed samples. Alternative designs like Amel-Y offer independence from commercial quantification kits in forensic labs.
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Affiliation(s)
- S Ginart
- Centro de referencia en Identificación Genética Humana de la Universidad de Buenos Aires, Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956 CP 1113, Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Tecnológicas-CONICET, Godoy Cruz 2290 CP 1425, Ciudad Autónoma de Buenos Aires, Argentina.
| | - L Garrigos Calivares
- Centro de referencia en Identificación Genética Humana de la Universidad de Buenos Aires, Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956 CP 1113, Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Tecnológicas-CONICET, Godoy Cruz 2290 CP 1425, Ciudad Autónoma de Buenos Aires, Argentina
| | - M Caputo
- Centro de referencia en Identificación Genética Humana de la Universidad de Buenos Aires, Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956 CP 1113, Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Tecnológicas-CONICET, Godoy Cruz 2290 CP 1425, Ciudad Autónoma de Buenos Aires, Argentina
| | - D Corach
- Centro de referencia en Identificación Genética Humana de la Universidad de Buenos Aires, Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956 CP 1113, Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Tecnológicas-CONICET, Godoy Cruz 2290 CP 1425, Ciudad Autónoma de Buenos Aires, Argentina
| | - A Sala
- Centro de referencia en Identificación Genética Humana de la Universidad de Buenos Aires, Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956 CP 1113, Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Tecnológicas-CONICET, Godoy Cruz 2290 CP 1425, Ciudad Autónoma de Buenos Aires, Argentina
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Dørum G, Hänggi NV, Burri D, Marti Y, Banemann R, Kulstein G, Courts C, Gosch A, Hadrys T, Haas C, Neubauer J. Selecting mRNA markers in blood for age estimation of the donor of a biological stain. Forensic Sci Int Genet 2024; 68:102976. [PMID: 38000161 DOI: 10.1016/j.fsigen.2023.102976] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/13/2023] [Accepted: 11/04/2023] [Indexed: 11/26/2023]
Abstract
RNA has gained a substantial amount of attention within the forensic field over the last decade. There is evidence that RNAs are differentially expressed with biological age. Since RNA can be co-extracted with DNA from the same piece of evidence, RNA-based analysis appears as a promising molecular alternative for predicting the biological age and hence inferring the chronological age of a person. Using RNA-Seq data we searched for markers in blood potentially associated with age. We used our own RNA-Seq data from dried blood stains as well as publicly available RNA-Seq data from whole blood, and compared two different approaches to select candidate markers. The first approach focused on individual gene analysis with DESeq2 to select the genes most correlated with age, while the second approach employed lasso regression to select a set of genes for optimal prediction of age. We present two lists with 270 candidate markers, one for each approach.
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Affiliation(s)
- Guro Dørum
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | | | - Dario Burri
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | - Yael Marti
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
| | | | | | - Cornelius Courts
- University Hospital of Cologne, Institute of Legal Medicine, Cologne, Germany
| | - Annica Gosch
- University Hospital of Cologne, Institute of Legal Medicine, Cologne, Germany
| | - Thorsten Hadrys
- Bavarian State Criminal Police Office (BLKA), Munich, Germany
| | - Cordula Haas
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland.
| | - Jacqueline Neubauer
- Zurich Institute of Forensic Medicine, University of Zurich, Zurich, Switzerland
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Frégeau CJ, Laurin N. Processing biological samples from simulated radiological terrorist events using Rapid DNA instruments. Forensic Sci Int 2024; 354:111887. [PMID: 38007870 DOI: 10.1016/j.forsciint.2023.111887] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 10/26/2023] [Accepted: 11/15/2023] [Indexed: 11/28/2023]
Abstract
Two commercially available portable Rapid DNA instruments were evaluated for their ability to process 1 µL and 10 µL saliva samples deposited on metal and plastic surfaces and contaminated with surrogates of cesium (Cs)-137, strontium (Sr)-90 and cobalt (Co)-60; radioactive materials potentially released during a nuclear weapon accident or a radiological dispersal device detonation. A comparable success rate was noted for both Rapid DNA instruments when considering the number of complete and balanced DNA profiles, the number of profiles with a minimum of 10 autosomal STR loci (out of 23 [FlexPlex™ 27] or 21 [GlobalFiler™ Express]), and the possibility to search a national DNA database in Canada and the United States. Cobalt had an adverse impact on the quality of the megaplex short tandem repeat (STR) DNA profiles derived on each instrument for two of the three contamination levels tested in this study, i.e., 0.05 M and 0.1 M as reflected by a reduced number of detected alleles and decreased profile peak heights. Strontium exhibited some adverse effect on the Rapid DNA results when used at the highest contamination level (0.1 M) whereas cesium had none. No new artifacts were observed in the Rapid DNA profiles of samples spiked with the non-radiogenic surrogates. Importantly, in the context of a radiological/nuclear (RN) event, the ANDE™ 6C offers the possibility to dispose of all radioactive materials associated with contaminated samples quickly using a chip on which all steps of the Rapid DNA process are performed whereas the RapidHIT™ ID accumulates radioactive materials for many days before disposal. An individual handling 25 samples in a week (5 per day) on the RapidHIT™ ID at a 30.5 cm distance with a 5 min exposure to the radioactive source estimated at every run would exceed the 0.042 µSv/5 min limit with gamma dose rates for Cs at 0.13 mSv and for Co at 3.8 mSv. Beta dose rates calculated for the surrogate isotopes at the three concentrations tested were also above the recommended radiation exposure limit of 1 mSv/yr (0.042 µSv/5 min). Various potential mechanisms of action behind the interference noted for Sr and Co at high concentrations are presented. These elements may play a role in the steps prior to PCR (at the DNA molecule by binding to bases or to phosphate groups), during PCR (at the DNA polymerase as cofactors for catalytic sites), or even during amplified DNA fragment detection (as fluorescence quenchers).
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Affiliation(s)
- Chantal J Frégeau
- Royal Canadian Mounted Police, Forensic Science & Identification Services, National Forensic Laboratory Services, Biology Policy & Program Support, 1200 Vanier Parkway, Ottawa, Ontario K1A 0R2, Canada.
| | - Nancy Laurin
- Royal Canadian Mounted Police, Forensic Science & Identification Services, Science & Strategic Policy, 1200 Vanier Parkway, Ottawa, Ontario K1A 0R2, Canada
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Zhang W, Cui L, Wang Y, Xie Z, Wei Y, Zhu S, Nawaz M, Mak WC, Ho HP, Gu D, Zeng S. An Integrated ddPCR Lab-on-a-Disc Device for Rapid Screening of Infectious Diseases. Biosensors (Basel) 2023; 14:2. [PMID: 38275303 PMCID: PMC10813669 DOI: 10.3390/bios14010002] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/14/2023] [Accepted: 12/16/2023] [Indexed: 01/27/2024]
Abstract
Digital droplet PCR (ddPCR) is a powerful amplification technique for absolute quantification of viral nucleic acids. Although commercial ddPCR devices are effective in the lab bench tests, they cannot meet current urgent requirements for on-site and rapid screening for patients. Here, we have developed a portable and fully integrated lab-on-a-disc (LOAD) device for quantitively screening infectious disease agents. Our designed LOAD device has integrated (i) microfluidics chips, (ii) a transparent circulating oil-based heat exchanger, and (iii) an on-disc transmitted-light fluorescent imaging system into one compact and portable box. Thus, droplet generation, PCR thermocycling, and analysis can be achieved in a single LOAD device. This feature is a significant attribute for the current clinical application of disease screening. For this custom-built ddPCR setup, we have first demonstrated the loading and ddPCR amplification ability by using influenza A virus-specific DNA fragments with different concentrations (diluted from the original concentration to 107 times), followed by analyzing the droplets with an external fluorescence microscope as a standard calibration test. The measured DNA concentration is linearly related to the gradient-dilution factor, which validated the precise quantification for the samples. In addition to the calibration tests using DNA fragments, we also employed this ddPCR-LOAD device for clinical samples with different viruses. Infectious samples containing five different viruses, including influenza A virus (IAV), respiratory syncytial virus (RSV), varicella zoster virus (VZV), Zika virus (ZIKV), and adenovirus (ADV), were injected into the device, followed by analyzing the droplets with an external fluorescence microscope with the lowest detected concentration of 20.24 copies/µL. Finally, we demonstrated the proof-of-concept detection of clinical samples of IAV using the on-disc fluorescence imaging system in our fully integrated device, which proves the capability of this device in clinical sample detection. We anticipate that this integrated ddPCR-LOAD device will become a flexible tool for on-site disease detection.
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Grants
- GRF14204621, GRF14207920, GRF14207419, GRF14207121, N_CUHK407/16 Hong Kong Research Grants Council
- No.2021A1515220084, No. 2022B1111020001 the National Key Research and Development Program of China
- ZDSYS20210623092001003, GJHZ20200731095604013, JSGG20220301090003004, No. 201906133000069, No. SGLH20180625171602058, and JCYJ20200109120205924 Shenzhen Science and Technology Foundation
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Affiliation(s)
- Wanyi Zhang
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 999077, China; (W.Z.); (Z.X.); (Y.W.); (S.Z.); (M.N.); (W.-C.M.)
| | - Lili Cui
- School of Public Health, Guangdong Medical University, Dongguan 523808, China;
- Laboratory Medicine, Shenzhen Key Laboratory of Medical Laboratory and Molecular Diagnostics, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen 518035, China;
| | - Yuye Wang
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China;
| | - Zhenming Xie
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 999077, China; (W.Z.); (Z.X.); (Y.W.); (S.Z.); (M.N.); (W.-C.M.)
| | - Yuanyuan Wei
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 999077, China; (W.Z.); (Z.X.); (Y.W.); (S.Z.); (M.N.); (W.-C.M.)
| | - Shaodi Zhu
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 999077, China; (W.Z.); (Z.X.); (Y.W.); (S.Z.); (M.N.); (W.-C.M.)
- Light, Nanomaterials & Nanotechnologies (L2n), CNRS-EMR 7004, Université de Technologie de Troyes, 10000 Troyes, France
| | - Mehmood Nawaz
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 999077, China; (W.Z.); (Z.X.); (Y.W.); (S.Z.); (M.N.); (W.-C.M.)
| | - Wing-Cheung Mak
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 999077, China; (W.Z.); (Z.X.); (Y.W.); (S.Z.); (M.N.); (W.-C.M.)
| | - Ho-Pui Ho
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong SAR 999077, China; (W.Z.); (Z.X.); (Y.W.); (S.Z.); (M.N.); (W.-C.M.)
| | - Dayong Gu
- Laboratory Medicine, Shenzhen Key Laboratory of Medical Laboratory and Molecular Diagnostics, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen 518035, China;
| | - Shuwen Zeng
- Light, Nanomaterials & Nanotechnologies (L2n), CNRS-EMR 7004, Université de Technologie de Troyes, 10000 Troyes, France
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40
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Siuta J, Dobosz A, Kawecki J, Dobosz T. DNA Content of Various Fluids and Tissues of the Human Body. Genes (Basel) 2023; 15:17. [PMID: 38275599 PMCID: PMC10815331 DOI: 10.3390/genes15010017] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/16/2023] [Accepted: 12/19/2023] [Indexed: 01/27/2024] Open
Abstract
Due to the scarcity of literature data on the DNA content of different human tissues, this study aimed to isolate DNA from different tissues and fluids of the human body together with the determination of its content in the samples studied. Material was collected and tests were performed between 1990 and 2010, during autopsies performed for prosecutor's offices in the Department of Forensic Medicine. Goiter and thyroid cancer tissues were obtained from the Department of General Surgery, Gastroenterology and Endocrinology of Wroclaw Medical University. Isolated samples were measured spectrophotometrically, yielding an R 260/280 nm between 1.5 and 1.6. In some cases (when a sufficiently pure preparation could not be obtained), isolation was continued using the silica-based commercial QIAquick PCR Purification Kit (Qiagen). If the sampling tissues showed signs of decomposition such as bad odour or colour, the results were calibrated by Real-Time PCR, using the Quantifiler DNA assay (Thermo Fisher Scientific, Applied Biosystems). The results have shown that the maximum amount of genetic material was obtained from hair roots, adrenal glands, gonads and lymph nodes. The lowest DNA content per gram or milliliter of tissue or body fluid was found in adipose tissue, blood, saliva, bile, sweat, tears and the vitreous body of the eye. The presented findings indicate the best sources of high-quality DNA from the human body: gonads, kidneys, muscle (including heart), blood and bones (after decalcification).
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Affiliation(s)
- Jędrzej Siuta
- Department of Forensic Medicine, Wroclaw Medical University, Mikulicza-Redeckiego 4, 50-345 Wroclaw, Poland (T.D.)
| | - Agnieszka Dobosz
- Division of Basic Medical Science, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211, 50-556 Wroclaw, Poland
| | - Jerzy Kawecki
- Department of Forensic Medicine, Wroclaw Medical University, Mikulicza-Redeckiego 4, 50-345 Wroclaw, Poland (T.D.)
| | - Tadeusz Dobosz
- Department of Forensic Medicine, Wroclaw Medical University, Mikulicza-Redeckiego 4, 50-345 Wroclaw, Poland (T.D.)
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Hu XG, Zhao Y, Peng Y, Chen XM, Wang LF, Lin ZT, Zhao J, Hu S. In-situ label-free temperature-compensated DNA hybridization detection with a fiber-optic interferometer and a fiber Bragg grating for microfluidic chip. Biosens Bioelectron 2023; 242:115703. [PMID: 37820556 DOI: 10.1016/j.bios.2023.115703] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 09/04/2023] [Accepted: 09/20/2023] [Indexed: 10/13/2023]
Abstract
We demonstrated a temperature-compensated optofluidic DNA biosensor available for microfluidic chip. The optofluidic sensor was composed of an interferometer and a fiber Bragg grating (FBG) by femtosecond laser direct writing micro/nano processing technology. The sensing arm of the interferometer was suspended on the inner wall of the microchannel and could directly interact with the microfluid. With the immobilization of the single stranded probe DNA (pDNA), this optofluidic biosensor could achieve specific detection of single stranded complementary DNA (scDNA). The experimental results indicated that a linear response within 50 nM and the detection limit of 1.87 nM were achieved. In addition, the optofluidic biosensor could simultaneously monitor temperature to avoid temperature fluctuations interfering with the DNA hybridization detection process. And, the optofluidic detection channel could achieve fast sample replacement within 10 s at a flow rate of 2 μL/min and sample consumption only required nanoliters. This optofluidic DNA biosensor had the advantages of label-free, good specificity, dual parameter detection, low sample consumption, fast response, and easy repeatable preparation, which was of great significance for the field of DNA hybridization research and solving the temperature sensitivity problem of biosensors and had good prospects in biological analysis.
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Affiliation(s)
- Xu-Guang Hu
- College of Information Science and Engineering, Northeastern University, Shenyang, 110819, China
| | - Yong Zhao
- College of Information Science and Engineering, Northeastern University, Shenyang, 110819, China; State Key Laboratory of Synthetical Automation for Process Industries, Shenyang, 110819, China; Hebei Key Laboratory of Micro-Nano Precision Optical Sensing and Measurement Technology, Qinhuangdao, 066004, China.
| | - Yun Peng
- College of Information Science and Engineering, Northeastern University, Shenyang, 110819, China; Hebei Key Laboratory of Micro-Nano Precision Optical Sensing and Measurement Technology, Qinhuangdao, 066004, China
| | - Xiao-Ming Chen
- College of Information Science and Engineering, Northeastern University, Shenyang, 110819, China; Hebei Key Laboratory of Micro-Nano Precision Optical Sensing and Measurement Technology, Qinhuangdao, 066004, China
| | - Lu-Feng Wang
- College of Information Science and Engineering, Northeastern University, Shenyang, 110819, China
| | - Zi-Ting Lin
- College of Information Science and Engineering, Northeastern University, Shenyang, 110819, China
| | - Jian Zhao
- College of Information Science and Engineering, Northeastern University, Shenyang, 110819, China
| | - Sheng Hu
- College of Information Science and Engineering, Northeastern University, Shenyang, 110819, China; Hebei Key Laboratory of Micro-Nano Precision Optical Sensing and Measurement Technology, Qinhuangdao, 066004, China
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Hu Z, Wang H, Chen H, Fan GC, Luo X. Target-triggered cascade signal amplification in nanochannels: An ingenious strategy for ultrasensitive photoelectrochemical DNA bioanalysis. Biosens Bioelectron 2023; 242:115724. [PMID: 37801836 DOI: 10.1016/j.bios.2023.115724] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/23/2023] [Accepted: 09/30/2023] [Indexed: 10/08/2023]
Abstract
Artificial solid-state nanochannels have aroused intense interests in biosensors and bioelectronics because of their special architectures. Herein, we pioneered an ingenious approach of target-triggered cascade signal amplification in porous anodic aluminum oxide (AAO) nanochannels for ultrasensitive photoelectrochemical (PEC) DNA bioanalysis. In the design, AAO nanochannels were modified initially with capture DNA (cDNA) and then incorporated with a photoelectrode, yielding the desired architecture of highly ordered nanoarrays on top of the signal transducer. For target DNA (tDNA) probing, exonuclease III (Exo-III) mediated target recycling (ETR) was first activated to generate plenty of output DNA (oDNA) fragments. After oDNA and the conjugate of Au-labeled probe DNA (Au-pDNA) were anchored within the nanochannels via DNA hybridization, in-situ synthesis of Ag shells on tethered Au nanoparticles was conducted. The resulting large-sized Au@Ag core-shell nanostructure within the nanochannels would cause conspicuous blocking effect to hinder the transportation of electrons accessing the photoelectrode. Since the signal inhibition was directly related to tDNA concentration, an innovative nanochannels PEC DNA assay was exploited and qualified for ultrasensitive detection. The anti-interference ability of this platform was also emphasized by the split AAO membrane for biological incubation without participation of the photoelectrode. This featured nanochannels PEC strategy with cascade amplification launched a novel detecting platform for trace levels of DNA, and it could spark more inspiration for a follow-up exploration of other smart nanochannels PEC bioassays.
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Affiliation(s)
- Ze Hu
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China
| | - Hao Wang
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China
| | - Huimin Chen
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China
| | - Gao-Chao Fan
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China.
| | - Xiliang Luo
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China.
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Yang L, Guo H, Gao Q, Hou T, Zhang J, Liu X, Li F. Integrating Reliable Pt-S Bond-Mediated 3D DNA Nanomachine with Magnetic Separation in a Homogeneous Electrochemical Strategy for Exosomal MicroRNA Detection with Low Background and High Sensitivity. Anal Chem 2023; 95:17834-17842. [PMID: 37988125 DOI: 10.1021/acs.analchem.3c03914] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2023]
Abstract
Precise and sensitive analysis of exosomal microRNA (miRNA) is of great importance for noninvasive early disease diagnosis, but it remains a great challenge to detect exosomal miRNA in human blood samples because of their small size, high sequence homology, and low abundance. Herein, we integrated reliable Pt-S bond-mediated three-dimensional (3D) DNA nanomachine and magnetic separation in a homogeneous electrochemical strategy for the detection of exosomal miRNA with low background and high sensitivity. The 3D DNA nanomachine was easily prepared via a facile and rapid freezing method, and it was capable of resisting the influence of biothiols, thus endowing it with high stability. Notably, the as-developed magnetic 3D DNA nanomachine not only enabled the detection system to have a low background but also coupled with liposome nanocarriers to synergistically amplify the current signal. Consequently, by ingeniously combining the low background and multiple signal-amplification strategies in homogeneous electrochemical biosensing, highly sensitive detection of exosomal miRNA was successfully achieved. More significantly, with good anti-interference ability, the as-proposed method could effectively discriminate plasma samples from cancer patients and healthy subjects, thus showing a high potential for application in the nondestructive early clinical diagnosis of disease.
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Affiliation(s)
- Limin Yang
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, People's Republic of China
| | - Heng Guo
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, People's Republic of China
| | - Qian Gao
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, People's Republic of China
| | - Ting Hou
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, People's Republic of China
| | - Jingang Zhang
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, People's Republic of China
| | - Xiaojuan Liu
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, People's Republic of China
| | - Feng Li
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, People's Republic of China
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Kalendar R, Ivanov KI, Samuilova O, Kairov U, Zamyatnin AA. Isolation of High-Molecular-Weight DNA for Long-Read Sequencing Using a High-Salt Gel Electroelution Trap. Anal Chem 2023; 95:17818-17825. [PMID: 37993972 DOI: 10.1021/acs.analchem.3c03894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Abstract
Long-read sequencing technologies require high-molecular-weight (HMW) DNA of sufficient purity and integrity, which can be difficult to obtain from complex biological samples. We propose a method for purifying HMW DNA that takes advantage of the fact that DNA's electrophoretic mobility decreases in a high-ionic-strength environment. The method begins with the separation of HMW DNA from various impurities by electrophoresis in an agarose gel-filled channel. After sufficient separation, a high-salt gel block is placed ahead of the DNA band of interest, leaving a gap between the separating gel and the high-salt gel that serves as a reservoir for sample collection. The DNA is then electroeluted from the separating gel into the reservoir, where its migration slows due to electrostatic shielding of the DNA's negative charge by excess counterions from the high-salt gel. As a result, the reservoir accumulates HMW DNA of high purity and integrity, which can be easily collected and used for long-read sequencing and other demanding applications without additional desalting. The method is simple and inexpensive, yields sequencing-grade HMW DNA even from difficult plant and soil samples, and has the potential for automation and scalability.
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Affiliation(s)
- Ruslan Kalendar
- Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki 00014, Finland
- Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana 010000, Kazakhstan
| | - Konstantin I Ivanov
- Department of Microbiology, University of Helsinki, Helsinki 00014, Finland
- Research Center for Translational Medicine, Sirius University of Science and Technology, Sochi 354340, Russian Federation
| | - Olga Samuilova
- Department of Biological Chemistry, Institute of Biodesign and Modeling of Complex Systems, Sechenov First Moscow State Medical University, Moscow 119991, Russian Federation
- HSE University, Faculty of Biology and Biotechnology, Moscow 117418, Russian Federation
| | - Ulykbek Kairov
- Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana 010000, Kazakhstan
| | - Andrey A Zamyatnin
- Research Center for Translational Medicine, Sirius University of Science and Technology, Sochi 354340, Russian Federation
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119234, Russian Federation
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russian Federation
- Institute of Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, Moscow 119991, Russian Federation
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Haarkötter C, Saiz M, Gálvez X, Vinueza-Espinosa DC, Medina-Lozano MI, Lorente JA, Álvarez JC. Performance comparison of four qPCR and three autosomal STR commercial kits from degraded skeletal remains. Forensic Sci Int 2023; 353:111856. [PMID: 37863006 DOI: 10.1016/j.forsciint.2023.111856] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 09/12/2023] [Accepted: 10/09/2023] [Indexed: 10/22/2023]
Abstract
This research evaluates the current DNA quantification (Quantifiler™ Trio, PowerQuant®, Investigator® Quantiplex® Pro and InnoQuant® HY Fast) and autosomal STRs amplification kits (GlobalFiler™, PowerPlex® Fusion 6 C, Investigator® 24Plex QS) using 62 degraded skeletal remains from armed conflicts (petrous bone, femur, tibia, and tooth) with several parameters (autosomal small, large, and male target, degradation index, probability of degradation, number of alleles above analytical threshold, number of alleles above stochastic threshold, RFU, peak height ratio, number of reportable loci). The best qPCR/autosomal STRs amplification tandem was determined by comparing quantification results by a DNA quantity estimation based on sample average RFU. InnoQuant® HY Fast was the most sensitive kit, and no significative differences were observed among amplification kits; however, Investigator® 24 Plex QS was found to be the most sensitive in our samples. That is why InnoQuant™ and Investigator® 24Plex QS were determined to be the best tandem.
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Affiliation(s)
- Christian Haarkötter
- University of Granada, Laboratory of Genetic Identification. Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, Avd. de la Investigación 11- 18016 - PTS, Granada, Spain
| | - María Saiz
- University of Granada, Laboratory of Genetic Identification. Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, Avd. de la Investigación 11- 18016 - PTS, Granada, Spain.
| | - Xiomara Gálvez
- University of Granada, Laboratory of Genetic Identification. Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, Avd. de la Investigación 11- 18016 - PTS, Granada, Spain
| | - Diana C Vinueza-Espinosa
- University of Granada, Laboratory of Genetic Identification. Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, Avd. de la Investigación 11- 18016 - PTS, Granada, Spain
| | - María Isabel Medina-Lozano
- University of Granada, Laboratory of Genetic Identification. Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, Avd. de la Investigación 11- 18016 - PTS, Granada, Spain
| | - José Antonio Lorente
- University of Granada, Laboratory of Genetic Identification. Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, Avd. de la Investigación 11- 18016 - PTS, Granada, Spain
| | - Juan Carlos Álvarez
- University of Granada, Laboratory of Genetic Identification. Department of Legal Medicine, Toxicology and Physical Anthropology, Faculty of Medicine, Avd. de la Investigación 11- 18016 - PTS, Granada, Spain
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Suprun EV, Khmeleva SA, Bibik KV, Ptitsyn KG, Kurbatov LK, Radko SP. Polymerase incorporation of fluorescein or rhodamine modified 2'-deoxyuridine-5'-triphosphates into double-stranded DNA for direct electrochemical detection. J Pharm Biomed Anal 2023; 236:115737. [PMID: 37774487 DOI: 10.1016/j.jpba.2023.115737] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/15/2023] [Accepted: 09/18/2023] [Indexed: 10/01/2023]
Abstract
The 2'-deoxyuridine-5'-triphosphates modified with fluorescein (dUTP-Fl) or rhodamine (dUTP-Rh) were tested as bearers of electroactive labels and as proper substrates for polymerases used in polymerase chain reaction (PCR) and isothermal recombinase polymerase amplification (RPA) with the aim of electrochemical detection of double-stranded DNA (dsDNA) amplification products. For this purpose, electrochemical behavior of free fluorescein and rhodamine as well as the modified nucleotides, dUTP-Fl and dUTP-Rh, was studied by cyclic (CV) and square wave (SWV) voltammetry on carbon screen printed electrodes. Both free fluorescein and dUTP-Fl underwent a two-step oxidation at the peak potentials (Ep) of 0.6-0.7 V and 0.8-0.9 V (phosphate buffer, pH 7.4). The reduction peaks of fluorescein and dUTP-Fl were registered between -0.9 V and -1 V, but they did not depend on concentration. The free rhodamine and dUTP-Rh have demonstrated the well-defined oxidation peaks at 0.8-0.9 V. In addition, the distinct reduction peaks at Ep between -0.8 V and -0.9 V were registered for both rhodamine and dUTP-Rh. The dUTP-Fl and dUTP-Rh were further tested as substrates to incorporate an electroactive label into 210 or 206 base pair long dsDNA amplicons generated either by PCR or RPA. Among two dUTP derivatives tested, dUTP-Fl revealed significantly better compatibility with PCR and RPA, producing the full-size amplicons at 50-90% substitution of dTTP in the reaction mixture. In the PCR, the best compromise between amplicon output and labeling was achieved at the dUTP-Fl : dTTP and dUTP-Rh : dTTP molar ratios of 70% : 30% and 20% : 80% in the PCR mixture, respectively, allowing the direct electrochemical detection of amplicons at micromolar concentrations. Alongside with fluorescence DNA assays, the fluorescein and rhodamine modified dUTP appear as promising electroactive labels to develop direct electrochemical DNA assays for detecting PCR and RPA products.
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Affiliation(s)
- Elena V Suprun
- Chemistry Faculty of M.V. Lomonosov Moscow State University, Lenin Hills, 1/3, Moscow 119991, Russia; Institute of Biomedical Chemistry, Pogodinskaya Street, 10/8, Moscow 119121, Russia.
| | - Svetlana A Khmeleva
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10/8, Moscow 119121, Russia
| | - Konstantin V Bibik
- Chemistry Faculty of M.V. Lomonosov Moscow State University, Lenin Hills, 1/3, Moscow 119991, Russia; Institute of Biomedical Chemistry, Pogodinskaya Street, 10/8, Moscow 119121, Russia
| | - Konstantin G Ptitsyn
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10/8, Moscow 119121, Russia
| | - Leonid K Kurbatov
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10/8, Moscow 119121, Russia
| | - Sergey P Radko
- Institute of Biomedical Chemistry, Pogodinskaya Street, 10/8, Moscow 119121, Russia
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Zupanič Pajnič I, Mlinšek T, Počivavšek T, Leskovar T. Genetic sexing of subadult skeletal remains. Sci Rep 2023; 13:20463. [PMID: 37993531 PMCID: PMC10665466 DOI: 10.1038/s41598-023-47836-9] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 11/19/2023] [Indexed: 11/24/2023] Open
Abstract
When subadult skeletons need to be identified, biological sex diagnosis is one of the first steps in the identification process. Sex assessment of subadults using morphological features is unreliable, and molecular genetic methods were applied in this study. Eighty-three ancient skeletons were used as models for poorly preserved DNA. Three sex-informative markers on the Y and X chromosome were used for sex identification: a qPCR test using the PowerQuant Y target included in PowerQuant System (Promega), the amelogenin test included in ESI 17 Fast STR kit (Promega), and a Y-STR amplification test using the PowerPlex Y-23 kit (Promega). Sex was successfully determined in all but five skeletons. Successful PowerQuant Y-target, Y-amelogenin, and Y-chromosomal STR amplifications proved the presence of male DNA in 35 skeletons, and in 43 subadults female sex was established. No match was found between the genetic profiles of subadult skeletons, and the elimination database and negative control samples produced no profiles, indicating no contamination issue. Our study shows that genetic sex identification is a very successful approach for biological sexing of subadult skeletons whose sex cannot be assessed by anthropological methods. The results of this study are applicable for badly preserved subadult skeletons from routine forensic casework.
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Affiliation(s)
- Irena Zupanič Pajnič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia.
| | - Teo Mlinšek
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia
| | - Tadej Počivavšek
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia
| | - Tamara Leskovar
- Centre for Interdisciplinary Research in Archaeology, Department of Archaeology, Faculty of Arts, University of Ljubljana, Ljubljana, Slovenia
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48
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Jo TS. Validating post-enrichment steps in environmental RNA analysis for improving its availability from water samples. Funct Integr Genomics 2023; 23:338. [PMID: 37975936 DOI: 10.1007/s10142-023-01269-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 11/19/2023]
Abstract
Environmental RNA (eRNA) analysis is expected to inclusively provide the physiological information of a population and community without individual sampling, having the potential for the improved monitoring of biodiversity and ecosystem function. Protocol development for maximizing eRNA availability is crucial to interpret its detection and quantification results with high accuracy and reliability, but the methodological validation and improvement of eRNA collection and processing methods are scarce. In this study, the technical steps after eRNA extraction, including genomic DNA (gDNA) removal and reverse transcription, were focused on and their performances were compared by zebrafish (Danio rerio) aquarium experiments. Additionally, this study also focused on the eRNA quantification variabilities between replicates and compared them between the PCR and sample levels. Results showed that (i) there was a trade-off between gDNA removal approaches and eRNA yields and an excess gDNA removal could lead to the false-negative eRNA detection, (ii) the use of the gene-specific primers for reverse transcription could increase the eRNA yields for multiple mitochondrial and nuclear genes compared with the random hexamer primers, and (iii) the coefficient of variation (CV) values of eRNA quantifications between PCR replicates were substantially lower for those between samples. Including the study, further knowledge for the sensitive and precise detection of macro-organismal eRNA should be needed for increasing the reliability and robustness of eRNA-based biomonitoring.
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Affiliation(s)
- Toshiaki S Jo
- Japan Society for the Promotion of Science, 5-3-1 Kojimachi, Chiyoda-Ku, Tokyo, 102-0083, Japan.
- Ryukoku Center for Biodiversity Science, 1-5, Yokotani, Oe-Cho, Seta, Otsu City, Shiga, 520-2194, Japan.
- Faculty of Advanced Science and Technology, Ryukoku University, 1-5, Yokotani, Oe-Cho, Seta, Otsu City, Shiga, 520-2194, Japan.
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49
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Yang C, He M, Liu C, Liu X, Lun M, Su Q, Han X, Liu H, Wang M, Chen L, Liu C. Development and validation of a custom panel including 114 InDels using massively parallel sequencing for forensic application. Electrophoresis 2023; 44:1704-1713. [PMID: 37622566 DOI: 10.1002/elps.202300044] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 05/13/2023] [Accepted: 08/04/2023] [Indexed: 08/26/2023]
Abstract
Insertion/deletion polymorphisms (InDels) have particular characteristics, such as a relatively low mutation rate, small amplicon size, and no stutter artifacts when genotyped via the capillary electrophoresis platform. It would be an important complementary tool for individual identification and certain kinship analyses. At present, massively parallel sequencing (MPS) has shown excellent application value in forensic studies. Therefore, in this study, we developed a custom MPS InDel panel that contains 114 InDels [77 autosomal InDels (A-InDels), 32 X-chromosomal InDels (X-InDels), and 5 Y-chromosomal InDels) based on previous studies. To assess this panel's performance, several validation experiments were performed, including sensitivity, inhibitor, degraded DNA testing, species specificity, concordance, repeatability, case-type samples, and population studies. The results showed that the lowest DNA input was 0.25 ng. All genotypes were obtained in the presence of 80 ng/µL humic acid, 2000 µmol/L calcium, 3000 µmol/L EDTA and indigo. In degraded DNA testing, 90% of loci could be detected for 16-day-old formalin-fixed hearts. In addition, this panel has good species specificity. The values of combined power of discrimination and the combined power of exclusion for 77 A-InDels were 1-3.9951 × 10-32 and 1-4.2956 × 10-7 , respectively. The combined mean exclusion chance for 32 X-InDels was 0.99999 in trios and 0.99904 in duos. The validation results indicate that this newly developed MPS multiplex system is a robust tool for forensic applications.
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Affiliation(s)
- Chengliang Yang
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Meiyun He
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Changhui Liu
- Guangzhou Forensic Science Institute, Guangzhou, P. R. China
| | - Xueyuan Liu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Miaoqiang Lun
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Qin Su
- Guangzhou Forensic Science Institute, Guangzhou, P. R. China
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, P. R. China
| | - Xiaolong Han
- Guangzhou Forensic Science Institute, Guangzhou, P. R. China
| | - Hong Liu
- Guangzhou Forensic Science Institute, Guangzhou, P. R. China
| | - Mengge Wang
- Guangzhou Forensic Science Institute, Guangzhou, P. R. China
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, P. R. China
| | - Ling Chen
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
| | - Chao Liu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, P. R. China
- National Anti-Drug Laboratory Guangdong Regional Center, Guangzhou, P. R. China
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50
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Casanova-Adán L, Mosquera-Miguel A, González-Bao J, Ambroa-Conde A, Ruiz-Ramírez J, Cabrejas-Olalla A, González-Martín E, Freire-Aradas A, Rodríguez-López A, Phillips C, Lareu MV, de la Puente M. Adapting an established Ampliseq microhaplotype panel to nanopore sequencing through direct PCR. Forensic Sci Int Genet 2023; 67:102937. [PMID: 37812882 DOI: 10.1016/j.fsigen.2023.102937] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/21/2023] [Accepted: 09/27/2023] [Indexed: 10/11/2023]
Abstract
We have adapted an established Ampliseq microhaplotype panel for nanopore sequencing with the Oxford Nanopore Technologies (ONT) system, as a cost-effective and highly scalable solution for forensic genetics applications. For this purpose, we designed a protocol combining direct PCR amplification from unextracted DNA with ONT library construction and sequencing using the MinION device and workflow. The analysis of reference samples at input amounts of 5-10 ng of DNA demonstrates stable coverage patterns, allele balance, and strand bias, reaching profile completeness and concordance rates of ∼95%. Similar levels were achieved when using direct-PCR from blood, buccal and semen swabs. Dilution series results indicate sensitivity is maintained down to 250 pg of input DNA, and informative profiles are produced down to 62.5 pg. Finally, we demonstrated the forensic utility of the nanopore workflow by analyzing two third degree pedigrees that showed low likelihood ratio values after the analysis of an extended panel of 38 STRs, achieving likelihood ratios 2-3 orders of magnitude higher when testing with the MinION-based haplotype data.
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Affiliation(s)
- L Casanova-Adán
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - A Mosquera-Miguel
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - J González-Bao
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - A Ambroa-Conde
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - J Ruiz-Ramírez
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - A Cabrejas-Olalla
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - E González-Martín
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - A Freire-Aradas
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - A Rodríguez-López
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - C Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - M V Lareu
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - M de la Puente
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain.
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