1
|
Khabou B, Kallabi F, Abdelaziz RB, Maaloul I, Aloulou H, Chehida AB, Kammoun T, Barbu V, Boudawara TS, Fakhfakh F, Khemakhem B, Sahnoun OS. Molecular and computational characterization of ABCB11 and ABCG5 variants in Tunisian patients with neonatal/infantile low-GGT intrahepatic cholestasis: Genetic diagnosis and genotype-phenotype correlation assessment. Ann Hum Genet 2024; 88:194-211. [PMID: 38108658 DOI: 10.1111/ahg.12542] [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: 07/14/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 12/19/2023]
Abstract
Many inherited conditions cause hepatocellular cholestasis in infancy, including progressive familial intrahepatic cholestasis (PFIC), a heterogeneous group of diseases with highly overlapping symptoms. In our study, six unrelated Tunisian infants with PFIC suspicion were the subject of a panel-target sequencing followed by an exhaustive bioinformatic and modeling investigations. Results revealed five disease-causative variants including known ones: (the p.Asp482Gly and p.Tyr354 * in the ABCB11 gene and the p.Arg446 * in the ABCC2 gene), a novel p.Ala98Cys variant in the ATP-binding cassette subfamily G member 5 (ABCG5) gene and a first homozygous description of the p.Gln312His in the ABCB11 gene. The p.Gln312His disrupts the interaction pattern of the bile salt export pump as well as the flexibility of the second intracellular loop domain harboring this residue. As for the p.Ala98Cys, it modulates both the interactions within the first nucleotide-binding domain of the bile transporter and its accessibility. Two additional potentially modifier variants in cholestasis-associated genes were retained based on their pathogenicity (p.Gly758Val in the ABCC2 gene) and functionality (p.Asp19His in the ABCG8 gene). Molecular findings allowed a PFIC2 diagnosis in five patients and an unexpected diagnosis of sisterolemia in one case. The absence of genotype/phenotype correlation suggests the implication of environmental and epigenetic factors as well as modifier variants involved directly or indirectly in the bile composition, which could explain the cholestasis phenotypic variability.
Collapse
Affiliation(s)
- Boudour Khabou
- Molecular and Functional Genetics Laboratory, Faculty of Sciences, University of Sfax, Sfax, Tunisia
| | - Fakhri Kallabi
- Molecular and Human Genetics Laboratory, Faculty of Medicine, University of Sfax, Sfax, Tunisia
| | - Rim Ben Abdelaziz
- Department of Pediatrics, Hospital La Rabta, Tunis, Tunisia
- Faculty of Medicine of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Ines Maaloul
- Department of Pediatrics, University Hospital Hedi Chaker, Sfax, Tunisia
| | - Hajer Aloulou
- Department of Pediatrics, University Hospital Hedi Chaker, Sfax, Tunisia
| | | | - Thouraya Kammoun
- Department of Pediatrics, University Hospital Hedi Chaker, Sfax, Tunisia
| | - Veronique Barbu
- LCBGM, Medical Biology and Pathology Department, APHP, HUEP, St Antoine Hospital, Sorbonne University, Paris, France
| | | | - Faiza Fakhfakh
- Molecular and Functional Genetics Laboratory, Faculty of Sciences, University of Sfax, Sfax, Tunisia
| | - Bassem Khemakhem
- Plant Biotechnology Laboratory, Faculty of Sciences, Sfax University, Sfax, Tunisia
| | - Olfa Siala Sahnoun
- Molecular and Functional Genetics Laboratory, Faculty of Sciences, University of Sfax, Sfax, Tunisia
| |
Collapse
|
2
|
Salik D, Marangoni M, Dangoisse C, Richert B, Smits G. Efficiency of clinical exome sequencing in the diagnosis of pediatric genodermatoses: A prospective cohort study. J Am Acad Dermatol 2024; 90:1020-1023. [PMID: 38191074 DOI: 10.1016/j.jaad.2023.12.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/10/2023] [Accepted: 12/19/2023] [Indexed: 01/10/2024]
Affiliation(s)
- Deborah Salik
- Department of Dermatology, CHU Saint-Pierre, CHU Brugmann and Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles, Brussels, Belgium; Department of Genetics, Hôpital Erasme, ULB Center of Human Genetics, Université Libre de Bruxelles (ULB), Brussels, Belgium.
| | - Martina Marangoni
- Department of Genetics, Hôpital Erasme, ULB Center of Human Genetics, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Chantal Dangoisse
- Department of Dermatology, CHU Saint-Pierre, CHU Brugmann and Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles, Brussels, Belgium
| | - Bertrand Richert
- Department of Dermatology, CHU Saint-Pierre, CHU Brugmann and Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles, Brussels, Belgium
| | - Guillaume Smits
- Department of Genetics, Hôpital Erasme, ULB Center of Human Genetics, Université Libre de Bruxelles (ULB), Brussels, Belgium; Department of Genetics, Hôpital Universitaire des Enfants Reine Fabiola, ULB Center of Human Genetics, Université Libre de Bruxelles (ULB), Brussels, Belgium; Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles, Brussels, Belgium
| |
Collapse
|
3
|
Cacheiro-Llaguno C, Mösges R, Calzada D, González-de la Fuente S, Quintero E, Carnés J. Polysensitisation is associated with more severe symptoms: The reality of patients with allergy. Clin Exp Allergy 2024. [PMID: 38676405 DOI: 10.1111/cea.14486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 04/03/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024]
Abstract
BACKGROUND Studying the sensitisation profiles of patients with allergies allows for a deeper understanding of the disease which may facilitate the selection of the best-personalised allergen immunotherapy. This observational, cross-sectional, multicentre study aimed to demonstrate the heterogeneity of the German population with allergies by analysing specific immunoglobulin E (sIgE) patterns towards aeroallergens and exploring the relationship between sensitisation and clinical symptoms. METHODS In total, 500 patients with allergies from different regions of Germany were recruited based on their case histories, clinical allergic symptoms and skin prick test data for aeroallergens. Serum samples were analysed using ImmunoCAP assays to determine sIgE levels for 33 allergenic sources and 43 molecular allergens. RESULTS Most patients (81%) were polysensitised. Betula verrucosa pollen was the most common cause of sensitisation (59%), followed by Phleum pratense (58%) and Dermatophagoides pteronyssinus (44%). The highest prevalence rates of molecular allergens were observed for Bet v 1 (84%) from birch pollen, Phl p 1 from grass pollen (82%), Der p 2 (69%) from mites and Fel d 1 (69%) from cat. Polysensitisation was significantly associated with the presence of asthma and the severity of rhinitis symptoms. CONCLUSIONS Our findings show a high rate of polysensitisation and emphasise the importance of molecular diagnosis for more precise and comprehensive insights into sensitisation patterns and their association with clinical symptoms. These data may help improve personalised diagnosis and immunotherapy adapted to the needs of individual patients in the region.
Collapse
Affiliation(s)
| | - Ralph Mösges
- IMSB, Faculty of Medicine, University of Cologne, Cologne, Germany
- ClinCompetence Cologne GmbH, Cologne, Germany
| | - David Calzada
- R&D Allergy and Immunology Unit, LETI Pharma, Madrid, Spain
| | | | - Eliana Quintero
- IMSB, Faculty of Medicine, University of Cologne, Cologne, Germany
- Praxis Dr. Kasche und Kollegen, Hamburg, Germany
| | | |
Collapse
|
4
|
Jiang M, Wu P, Zhang Y, Wang M, Zhang M, Ye Z, Zhang X, Zhang C. Artificial Intelligence-Driven Platform: Unveiling Critical Hepatic Molecular Alterations in Hepatocellular Carcinoma Development. Adv Healthc Mater 2024:e2400291. [PMID: 38657582 DOI: 10.1002/adhm.202400291] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 04/19/2024] [Indexed: 04/26/2024]
Abstract
Since most Hepatocellular Carcinoma (HCC) typically arises as a consequence of long-term liver damage, the hepatic molecular characteristics are closely related to the occurrence of HCC. Gaining comprehensive information about the location, morphology, and hepatic molecular alterations related to HCC is essential for accurate diagnosis. However, there is a dearth of technological advancements capable of concurrently providing precise HCC diagnosis and discerning the accompanying hepatic molecular alterations. In this study, an integrated information system is developed for the pathological-level diagnosis of HCC and the revelation of critical molecular alterations in the liver. This system utilizes computed tomography/Surface-enhanced Raman scattering combined with an artificial intelligence strategy to establish connections between the occurrence of HCC and alterations in hepatic biomolecules. Employing artificial intelligence techniques, the SERS spectra from both healthy and HCC groups are successfully classified into two distinct categories with a remarkable accuracy rate of 91.38%. Based on molecular profiling, it is identified that the nucleotide-to-lipid signal ratio holds significant potential as a reliable indicator for the occurrence of HCC, thereby serving as a promising tool for prevention and therapeutic surveillance.
Collapse
Affiliation(s)
- Miao Jiang
- School of Medical Imaging, Tianjin Medical University, Tianjin, 300203, China
| | - Pengyun Wu
- Department of Nuclear Medicine, Tianjin Medical University General Hospital, 154 Anshan Ave, Heping, 300052, China
| | - Yuwei Zhang
- Department of Radiology, National Clinical Research Centre of Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin Key Laboratory of Digestive Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, China
| | - Mengling Wang
- Department of Radiology, National Clinical Research Centre of Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin Key Laboratory of Digestive Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, China
| | - Mingjie Zhang
- Department of Radiology, National Clinical Research Centre of Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin Key Laboratory of Digestive Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, China
| | - Zhaoxiang Ye
- Department of Radiology, National Clinical Research Centre of Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin Key Laboratory of Digestive Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, China
| | - Xuejun Zhang
- School of Medical Imaging, Tianjin Medical University, Tianjin, 300203, China
| | - Cai Zhang
- Department of Radiology, National Clinical Research Centre of Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin Key Laboratory of Digestive Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, China
| |
Collapse
|
5
|
Singh P, Banegar MT, Lobo RA, Mukherjee S. COMMON LABORATORY ORGANIC SOLVENTS ARE BETTER MEDIUM FOR MOLECULAR DETECTION OF RNA VIRUSES USING PCR. Indian J Med Microbiol 2024:100596. [PMID: 38657792 DOI: 10.1016/j.ijmmb.2024.100596] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/28/2023] [Accepted: 04/17/2024] [Indexed: 04/26/2024]
Abstract
PURPOSE The unavailability of recommended viral transport medium during epidemics of respiratory viral infections is a substantial healthcare concern. It may prompt the use of alternatives, which may give rise to results with questionable validity. The present study was carried out to assess and validate the utility of commonly available solvents in the hospital/healthcare set-ups which may be used as ready and economical alternatives to commercial VTMs. METHODS To evaluate the readily available solvents as an alternative to VTM, cell culture supernatant of pH1N1 2009 isolate with HA titres of 1:4 and extracted viral RNA of SARS-CoV-2 were spiked in a 1:10 ratio in ethanol, acetone, methanol and were compared to commercially available VTM for detection of influenza virus by real time RT-PCR (qRT-PCR). The tubes were kept at room temperature 24 hrs, 48 hrs and 72 hrs. Ct values of the various solvents at different time points were compared and statistical analysis was performed using Python. RESULTS The Ct values of the Influenza and SARS-CoV2 viral genes in each solvent were maintained for 3 days at room temperatures, suggesting viral samples were stably preserved in the solvent for 3 days. CONCLUSION Methanol was found to be the most promising solvent for increasing the stability of viral RNA thereby enhancing the molecular diagnosis of the concerned pathogen.
Collapse
Affiliation(s)
- Pinky Singh
- Department of Clinical Pathology, Haffkine Institute, Mumbai.
| | | | | | | |
Collapse
|
6
|
Fontoura PS, Macedo EG, Calil PR, Corder RM, Rodrigues PT, Tonini J, Esquivel FD, Ladeia WA, Fernandes ARJ, Johansen IC, Silva MF, Fernandes AOS, Ladeia-Andrade S, Castro MC, Ferreira MU. Changing Clinical Epidemiology of Plasmodium vivax Malaria as Transmission Decreases: Population-Based Prospective Panel Survey in the Brazilian Amazon. J Infect Dis 2024; 229:947-958. [PMID: 38324758 PMCID: PMC11011196 DOI: 10.1093/infdis/jiad456] [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: 06/03/2023] [Accepted: 10/16/2023] [Indexed: 02/09/2024] Open
Abstract
BACKGROUND Malarial infections are often missed by microscopy, and most parasite carriers are asymptomatic in low-endemicity settings. Whether parasite detectability and its ability to elicit symptoms change as transmission declines remains unclear. METHODS We performed a prospective panel survey with repeated measurements on the same participants over 12 months to investigate whether Plasmodium vivax detectability by microscopy and risk of symptoms upon infection varied during a community-wide larviciding intervention in the Amazon basin of Brazil that markedly reduced vector density. We screened 1096 to 1400 residents in the intervention site for malaria by microscopy and quantitative TaqMan assays at baseline and twice during intervention. RESULTS We found that more P vivax infections than expected from their parasite densities measured by TaqMan assays were missed by microscopy as transmission decreased. At lower transmission, study participants appeared to tolerate higher P vivax loads without developing symptoms. We hypothesize that changes in the ratio between circulating parasites and those that accumulate in the bone marrow and spleen, by avoiding peripheral blood microscopy detection, account for decreased parasite detectability and lower risk of symptoms under low transmission. CONCLUSIONS P vivax infections are more likely to be subpatent and remain asymptomatic as malaria transmission decreases.
Collapse
Affiliation(s)
- Pablo S Fontoura
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo
- Secretary of Health Surveillance, Ministry of Health, Brasília, Brazil
| | - Evelyn G Macedo
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo
| | - Priscila R Calil
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo
| | - Rodrigo M Corder
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo
- Divisions of Epidemiology and Biostatistics, Berkeley School of Public Health, University of California
| | - Priscila T Rodrigues
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo
| | - Juliana Tonini
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo
| | - Fabiana D Esquivel
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo
| | - Winni A Ladeia
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo
| | | | - Igor C Johansen
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo
| | - Marcos F Silva
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo
| | - Amanda O S Fernandes
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo
| | | | - Marcia C Castro
- Department of Global Health and Population, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | - Marcelo U Ferreira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo
- Global Health and Tropical Medicine, Institute of Hygiene and Tropical Medicine, Nova University of Lisbon, Portugal
| |
Collapse
|
7
|
Guitard J, Brenier-Pinchart MP, Varlet-Marie E, Dalle F, Rouges C, Argy N, Bonhomme J, Capitaine A, Guégan H, Lavergne RA, Dardé ML, Pelloux H, Robert-Gangneux F, Yera H, Sterkers Y. Multicenter evaluation of the Toxoplasma gondii Real-TM (Sacace) kit performance for the molecular diagnosis of toxoplasmosis. J Clin Microbiol 2024; 62:e0142823. [PMID: 38470023 PMCID: PMC11005372 DOI: 10.1128/jcm.01428-23] [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: 10/30/2023] [Accepted: 02/20/2024] [Indexed: 03/13/2024] Open
Abstract
The molecular detection of Toxoplasma gondii DNA is a key tool for the diagnosis of disseminated and congenital toxoplasmosis. This multicentric study from the Molecular Biology Pole of the French National Reference Center for toxoplasmosis aimed to evaluate Toxoplasma gondii Real-TM PCR kit (Sacace). The study compared the analytical and clinical performances of this PCR assay with the reference PCRs used in proficient laboratories. PCR efficiencies varied from 90% to 112%; linearity zone extended over four log units (R2 > 0.99) and limit of detection varied from 0.01 to ≤1 Tg/mL depending on the center. Determined on 173 cryopreserved DNAs from a large range of clinical specimens, clinical sensitivity was 100% [106/106; 95 confidence interval (CI): 96.5%-100%] and specificity was 100% (67/67; 95 CI: 94.6%-100%). The study revealed two potential limitations of the Sacace PCR assay: the first was the inconsistency of the internal control (IC) when added to the PCR mixture. This point was not found under routine conditions when the IC was added during the extraction step. The second is a lack of practicality, as the mixture is distributed over several vials, requiring numerous pipetting operations. Overall, this study provides useful information for the molecular diagnosis of toxoplasmosis; the analytical and clinical performances of the Sacace PCR kit were satisfactory, the kit having sensitivity and specificity similar to those of expert center methods and being able to detect low parasite loads, at levels where multiplicative analysis gives inconsistently positive results. Finally, the study recommends multiplicative analysis in particular for amniotic fluids, aqueous humor, and other single specimens.
Collapse
Affiliation(s)
- Juliette Guitard
- Sorbonne University, INSERM, Centre de Recherche Saint-Antoine, Assistance Publique-Hôpitaux de Paris, Saint-Antoine Hospital Parasitology-Mycology Laboratory, Paris, France
- Molecular Biology group of the French National Reference Center for Toxoplasmosis, Montpellier, France
| | - Marie-Pierre Brenier-Pinchart
- Molecular Biology group of the French National Reference Center for Toxoplasmosis, Montpellier, France
- Parasitology-Mycology Laboratory, CHU Grenoble Alpes, Grenoble Alpes University, Grenoble, France
| | - Emmanuelle Varlet-Marie
- Molecular Biology group of the French National Reference Center for Toxoplasmosis, Montpellier, France
- Department of Parasitology-Mycology, University of Montpellier, CNRS, IRD, University Hospital Center (CHU) of Montpellier, MiVEGEC, Montpellier, France
| | - Frédéric Dalle
- Molecular Biology group of the French National Reference Center for Toxoplasmosis, Montpellier, France
- Parasitology-Mycology Laboratory, CHU Dijon, Dijon, France
| | - Celia Rouges
- Parasitology-Mycology Laboratory, Cochin Hospital, Paris, France
| | - Nicolas Argy
- Parasitology-Mycology Laboratory, Bichat Hospital, Paris, France
| | - Julie Bonhomme
- Parasitology-Mycology Laboratory, CHU Caen Normandie, Caen, France
| | - Agathe Capitaine
- Parasitology-Mycology Laboratory, CHU Caen Normandie, Caen, France
| | - Hélène Guégan
- Molecular Biology group of the French National Reference Center for Toxoplasmosis, Montpellier, France
- Parasitology-Mycology Laboratory, CHU Rennes, Rennes, France
| | - Rose-Anne Lavergne
- Nantes Université, CHU Nantes, Cibles et Médicaments des Infections et de l’Immunité, IICiMed, UR, Nantes, France
| | | | - Hervé Pelloux
- Molecular Biology group of the French National Reference Center for Toxoplasmosis, Montpellier, France
- Parasitology-Mycology Laboratory, CHU Grenoble Alpes, Grenoble Alpes University, Grenoble, France
| | - Florence Robert-Gangneux
- Molecular Biology group of the French National Reference Center for Toxoplasmosis, Montpellier, France
- Parasitology-Mycology Laboratory, CHU Rennes, Rennes, France
| | - Hélène Yera
- Parasitology-Mycology Laboratory, Cochin Hospital, Paris, France
- Parasitology-Mycology Laboratory, CHU Limoges, Limoges, France
| | - Yvon Sterkers
- Molecular Biology group of the French National Reference Center for Toxoplasmosis, Montpellier, France
- Parasitology-Mycology Laboratory, Cochin Hospital, Paris, France
| |
Collapse
|
8
|
Juchnewitsch AG, Pomm K, Dutta A, Tamp E, Valkna A, Lillepea K, Mahyari E, Tjagur S, Belova G, Kübarsepp V, Castillo-Madeen H, Riera-Escamilla A, Põlluaas L, Nagirnaja L, Poolamets O, Vihljajev V, Sütt M, Versbraegen N, Papadimitriou S, McLachlan RI, Jarvi KA, Schlegel PN, Tennisberg S, Korrovits P, Vigh-Conrad K, O’Bryan MK, Aston KI, Lenaerts T, Conrad DF, Kasak L, Punab M, Laan M. Undiagnosed RASopathies in infertile men. Front Endocrinol (Lausanne) 2024; 15:1312357. [PMID: 38654924 PMCID: PMC11035881 DOI: 10.3389/fendo.2024.1312357] [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] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 03/11/2024] [Indexed: 04/26/2024] Open
Abstract
RASopathies are syndromes caused by congenital defects in the Ras/mitogen-activated protein kinase (MAPK) pathway genes, with a population prevalence of 1 in 1,000. Patients are typically identified in childhood based on diverse characteristic features, including cryptorchidism (CR) in >50% of affected men. As CR predisposes to spermatogenic failure (SPGF; total sperm count per ejaculate 0-39 million), we hypothesized that men seeking infertility management include cases with undiagnosed RASopathies. Likely pathogenic or pathogenic (LP/P) variants in 22 RASopathy-linked genes were screened in 521 idiopathic SPGF patients (including 155 CR cases) and 323 normozoospermic controls using exome sequencing. All 844 men were recruited to the ESTonian ANDrology (ESTAND) cohort and underwent identical andrological phenotyping. RASopathy-specific variant interpretation guidelines were used for pathogenicity assessment. LP/P variants were identified in PTPN11 (two), SOS1 (three), SOS2 (one), LZTR1 (one), SPRED1 (one), NF1 (one), and MAP2K1 (one). The findings affected six of 155 cases with CR and SPGF, three of 366 men with SPGF only, and one (of 323) normozoospermic subfertile man. The subgroup "CR and SPGF" had over 13-fold enrichment of findings compared to controls (3.9% vs. 0.3%; Fisher's exact test, p = 5.5 × 10-3). All ESTAND subjects with LP/P variants in the Ras/MAPK pathway genes presented congenital genitourinary anomalies, skeletal and joint conditions, and other RASopathy-linked health concerns. Rare forms of malignancies (schwannomatosis and pancreatic and testicular cancer) were reported on four occasions. The Genetics of Male Infertility Initiative (GEMINI) cohort (1,416 SPGF cases and 317 fertile men) was used to validate the outcome. LP/P variants in PTPN11 (three), LZTR1 (three), and MRAS (one) were identified in six SPGF cases (including 4/31 GEMINI cases with CR) and one normozoospermic man. Undiagnosed RASopathies were detected in total for 17 ESTAND and GEMINI subjects, 15 SPGF patients (10 with CR), and two fertile men. Affected RASopathy genes showed high expression in spermatogenic and testicular somatic cells. In conclusion, congenital defects in the Ras/MAPK pathway genes represent a new congenital etiology of syndromic male infertility. Undiagnosed RASopathies were especially enriched among patients with a history of cryptorchidism. Given the relationship between RASopathies and other conditions, infertile men found to have this molecular diagnosis should be evaluated for known RASopathy-linked health concerns, including specific rare malignancies.
Collapse
Affiliation(s)
- Anna-Grete Juchnewitsch
- Chair of Human Genetics, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Kristjan Pomm
- Andrology Clinic, Tartu University Hospital, Tartu, Estonia
| | - Avirup Dutta
- Chair of Human Genetics, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Erik Tamp
- Centre of Pathology, East Tallinn Central Hospital, Tallinn, Estonia
| | - Anu Valkna
- Chair of Human Genetics, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Kristiina Lillepea
- Chair of Human Genetics, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Eisa Mahyari
- Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, United States
| | | | - Galina Belova
- Chair of Human Genetics, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Viljo Kübarsepp
- Department of Surgery, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
- Department of Pediatric Surgery, Clinic of Surgery, Tartu University Hospital, Tartu, Estonia
| | - Helen Castillo-Madeen
- Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, United States
| | - Antoni Riera-Escamilla
- Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, United States
| | - Lisanna Põlluaas
- Chair of Human Genetics, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Liina Nagirnaja
- Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, United States
| | - Olev Poolamets
- Andrology Clinic, Tartu University Hospital, Tartu, Estonia
| | | | - Mailis Sütt
- Andrology Clinic, Tartu University Hospital, Tartu, Estonia
| | - Nassim Versbraegen
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, Brussels, Belgium
- Machine Learning Group, Université Libre de Bruxelles, Brussels, Belgium
| | - Sofia Papadimitriou
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, Brussels, Belgium
- Machine Learning Group, Université Libre de Bruxelles, Brussels, Belgium
- Department of Biomolecular Medicine, Faculty of Medicine and Health Science, Ghent University, Ghent, Belgium
| | - Robert I. McLachlan
- Hudson Institute of Medical Research and the Department of Obstetrics and Gynecology, Monash University, Clayton, VIC, Australia
| | - Keith A. Jarvi
- Division of Urology, Department of Surgery, Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada
| | - Peter N. Schlegel
- Department of Urology, Weill Cornell Medical College, New York, NY, United States
| | | | - Paul Korrovits
- Andrology Clinic, Tartu University Hospital, Tartu, Estonia
| | - Katinka Vigh-Conrad
- Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, United States
| | - Moira K. O’Bryan
- School of BioSciences, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Kenneth I. Aston
- Andrology and IVF Laboratory, Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Tom Lenaerts
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, Brussels, Belgium
- Machine Learning Group, Université Libre de Bruxelles, Brussels, Belgium
- Artificial Intelligence Laboratory, Vrije Universiteit Brussel, Brussels, Belgium
| | - Donald F. Conrad
- Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, United States
- Center for Embryonic Cell and Gene Therapy, Oregon Health and Science University, Beaverton, OR, United States
| | - Laura Kasak
- Chair of Human Genetics, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Margus Punab
- Chair of Human Genetics, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
- Andrology Clinic, Tartu University Hospital, Tartu, Estonia
- Department of Surgery, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Maris Laan
- Chair of Human Genetics, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| |
Collapse
|
9
|
Sbruzzi RC, Feira MF, Cadore NA, Giudicelli GC, Kowalski TW, Gregianini TS, Chies JAB, Vianna FSL. An Efficient Extraction Method Allowing the Genetic Evaluation of Host DNA from Samples Collected for Virus Infection Diagnosis in Viral Transport Medium. Biopreserv Biobank 2024; 22:166-173. [PMID: 37579075 DOI: 10.1089/bio.2022.0188] [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: 08/16/2023] Open
Abstract
Introduction: During the COVID-19 pandemic, an extraordinary number of nasopharyngeal secretion samples inoculated in viral transport medium (VTM) were collected and analyzed to detect SARS-CoV-2 infection. In addition to viral detection, those samples can also be a source of host genomic material, providing excellent opportunities for biobanking and research. Objective: To describe a simple, in-house-developed DNA extraction method to obtain high yield and quality genomic DNA from VTM samples for host genetic analysis and assess its relative efficiency by comparing its yield and suitability to downstream applications to two different commercial DNA extraction kits. Methods: In this study, 13 VTM samples were processed by two commercial silica-based kits and compared with an in-House-developed protocol for host DNA extraction. An additional 452 samples were processed by the in-House method. The quantity and quality of the differentially extracted DNA samples were assessed by Qubit and spectrophotometric measurements. The suitability of extracted samples for downstream applications was tested by polymerase chain reaction (PCR) amplification followed by amplicon sequencing and allelic discrimination in real-time PCR. Results: The in-House method provided greater median DNA yield (0.81 μg), being significantly different from the PureLink® method (0.14 μg, p < 0.001), but not from the QIAamp® method (0.47 μg, p = 0.980). Overall satisfactory results in DNA concentrations and purity, in addition to cost, were observed using the in-House method, whose samples were able to produce clear amplification in PCR and sequencing reads, as well as effective allelic discrimination in real-time PCR TaqMan® assay. Conclusion: The described in-House method proved to be suitable and economically viable for genomic DNA extraction from VTM samples for biobanking purposes. These results are extremely valuable for the study of the COVID-19 pandemic and other emergent infectious diseases, allowing host genetic studies to be performed in samples initially collected for diagnosis.
Collapse
Affiliation(s)
- Renan C Sbruzzi
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Mariléa F Feira
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Nathan A Cadore
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Giovanna C Giudicelli
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Instituto Nacional de Ciência e Tecnologia de Genética Médica Populacional, Porto Alegre, Brazil
| | - Thayne W Kowalski
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Instituto Nacional de Ciência e Tecnologia de Genética Médica Populacional, Porto Alegre, Brazil
- Centro Universitário CESUCA, Cachoeirinha, Brazil
- Núcleo de Bioinformática, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | - Tatiana S Gregianini
- Laboratório Central de Saúde Pública, Centro Estadual de Vigilância em Saúde, Secretaria Estadual de Saúde do estado do Rio Grande do Sul (LACEN/CEVS/SES-RS), Porto Alegre, Brazil
| | - José A B Chies
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Fernanda S L Vianna
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Instituto Nacional de Ciência e Tecnologia de Genética Médica Populacional, Porto Alegre, Brazil
- Programa de Pós-Graduação em Ciências Médicas, Faculdade de Medicina, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| |
Collapse
|
10
|
Khongphithakskul P, Tangbubpha N, Khlangtan T, Kadegasem P, Songdej D, Sirachainan N. One-step amplification refractory mutation system-PCR/high-resolution melting curve assay for carrier detection of red blood cell membranopathy caused by common SPTB mutations. Int J Lab Hematol 2024; 46:375-382. [PMID: 37904725 DOI: 10.1111/ijlh.14196] [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: 07/06/2023] [Accepted: 10/14/2023] [Indexed: 11/01/2023]
Abstract
INTRODUCTION Hereditary pyropoikilocytosis (HPP) is the most common cause of non-thalassemic severe inherited hemolytic anemia in Thai population. Up to 90% of affected patients harbor biallelic mutations of SPTB Providence (SPTB c.6055T>C), SPTB Buffalo (SPTB c.6074T>G), and SPTB Chiang Mai (SPTB c.6224A>G). This study aimed to develop a simple assay for mass screening of the three common SPTB mutations and to study their carrier frequencies in a healthy Thai population. METHODS We combined multiplex amplification refractory mutation system-PCR (ARMS-PCR) and high-resolution melting (HRM) curve analysis to create a one-step single-tube assay. The primers were designed to generate products with different melting temperatures in the presence of 6055C, 6074G, and 6224G. Internal control primers were added for quality control. Residual samples from blood donors and healthy adolescents were collected and tested for the three common SPTB mutations using the newly developed assay. RESULTS Optimized multiplex ARMS-PCR/HRM curve assay yielded well-separated melt curves to detect the three SPTB mutations with 4-h turnaround time. The assay was validated in screening of 2261 non-repetitive blood donors and 89 adolescents, in which 10 (0.43%), 2 (0.09%), and 3 (0.13%) individuals were identified as carriers of SPTB Providence, SPTB Buffalo, and SPTB Chiang Mai, respectively. All mutated SPTB and 20 random wild-type samples were confirmed using Sanger sequencing with 100% accuracy. CONCLUSION The novel ARMS-PCR/HRM curve assay is simple, accurate, and time-effective for mass screening of the common SPTB mutations. This can be employed to prevent HPP birth in a Thai population.
Collapse
Affiliation(s)
- Punnavit Khongphithakskul
- Pediatrics Hematology-Oncology, Department of Pediatrics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Noppawan Tangbubpha
- Pediatrics Hematology-Oncology, Department of Pediatrics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Tanyanee Khlangtan
- Pediatrics Hematology-Oncology, Department of Pediatrics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Praguywan Kadegasem
- Pediatrics Hematology-Oncology, Department of Pediatrics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Duantida Songdej
- Pediatrics Hematology-Oncology, Department of Pediatrics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Nongnuch Sirachainan
- Pediatrics Hematology-Oncology, Department of Pediatrics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| |
Collapse
|
11
|
Nguyen L, Saha A, Kuykendall A, Zhang L. Clinical and Therapeutic Intervention of Hypereosinophilia in the Era of Molecular Diagnosis. Cancers (Basel) 2024; 16:1383. [PMID: 38611061 PMCID: PMC11011008 DOI: 10.3390/cancers16071383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 03/17/2024] [Accepted: 03/17/2024] [Indexed: 04/14/2024] Open
Abstract
Hypereosinophilia (HE) presents with an elevated peripheral eosinophilic count of >1.5 × 109/L and is composed of a broad spectrum of secondary non-hematologic disorders and a minority of primary hematologic processes with heterogenous clinical presentations, ranging from mild symptoms to potentially lethal outcome secondary to end-organ damage. Following the introduction of advanced molecular diagnostics (genomic studies, RNA sequencing, and targeted gene mutation profile, etc.) in the last 1-2 decades, there have been deep insights into the etiology and molecular mechanisms involved in the development of HE. The classification of HE has been updated and refined following to the discovery of clinically novel markers and targets in the 2022 WHO classification and ICOG-EO 2021 Working Conference on Eosinophil Disorder and Syndromes. However, the diagnosis and management of HE is challenging given its heterogeneity and variable clinical outcome. It is critical to have a diagnostic algorithm for accurate subclassification of HE and hypereosinophilic syndrome (HES) (e.g., reactive, familial, idiopathic, myeloid/lymphoid neoplasm, organ restricted, or with unknown significance) and to follow established treatment guidelines for patients based on its clinical findings and risk stratification.
Collapse
Affiliation(s)
- Lynh Nguyen
- Department of Pathology, James A. Haley Veterans’ Hospital, Tampa, FL 33612, USA
| | - Aditi Saha
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA (A.K.)
| | - Andrew Kuykendall
- Department of Malignant Hematology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA (A.K.)
| | - Ling Zhang
- Department of Pathology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
| |
Collapse
|
12
|
Jiang YJ, Xia Y, Hu YX, Han ZJ, Guo AY, Huang T. Identification of P21 (CDKN1A) Activated Kinase 4 as a Susceptibility Gene for Familial Non-Medullary Thyroid Carcinoma. Thyroid 2024. [PMID: 38411500 DOI: 10.1089/thy.2023.0564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Background: Familial non-medullary thyroid carcinoma (FNMTC) is a genetically predisposed disease with unclear genetic mechanisms. This makes research on susceptibility genes important for the diagnosis and treatment options. Methods: This study included a five-member family affected by papillary thyroid carcinoma. The candidate genes were identified through whole-exome sequencing and Sanger sequencing in family members, other FNMTC patients, and sporadic non-medullary thyroid carcinoma patients. The pathogenicity of the mutation was predicted using in silico tools. Cell phenotype experiments in vitro and models of lung distant metastasis in vivo were conducted to confirm the characteristics of the mutation. Transcriptome sequencing and mechanistic validation were employed to compare the disparities between PAK4 wild-type (WT) and PAK4 mutant (MUT) cell lines. Results: This mutation alters the protein structure, potentially increasing instability by affecting hydrophobicity, intra-molecular hydrogen bonding, and phosphorylation sites. It specifically promotes phosphorylated PAK4 nuclear translocation and expression in thyroid tissue and cell lines. Compared with the WT cells line, PAK4 I417T demonstrates enhanced proliferation, invasiveness, accelerated cell division, and inhibition of cell apoptosis in vitro. In addition, it exhibits a significant propensity for metastasis in vivo. It activates tumor necrosis factor signaling through increased phosphorylation of PAK4, JNK, NFκB, and c-Jun, unlike the WT that activates it via the PAK4-NFκ-MMP9 axis. In addition, PAK4 MUT protein interacts with matrix metalloproteinase (MMP)3 and regulates MMP3 promoter activity, which is not observed in the WT. Conclusions: Our study identified PAK4: c.T1250C: p.I417T as a potential susceptibility gene for FNMTC. The study concludes that the mutant form of PAK4 exhibits oncogenic function, suggesting its potential as a novel diagnostic molecular marker for FNMTC.
Collapse
Affiliation(s)
- Yu-Jia Jiang
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College; College of Life Science and Technology; Huazhong University of Science and Technology, Wuhan, China
| | - Yun Xia
- Hubei Bioinformatics and Molecular Imaging Key Laboratory, College of Life Science and Technology; Huazhong University of Science and Technology, Wuhan, China
- Department of Thyroid Surgery, West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yi-Xuan Hu
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College; College of Life Science and Technology; Huazhong University of Science and Technology, Wuhan, China
| | - Zhuo-Jun Han
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College; College of Life Science and Technology; Huazhong University of Science and Technology, Wuhan, China
| | - An-Yuan Guo
- Department of Thyroid Surgery, West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, China
| | - Tao Huang
- Department of Breast and Thyroid Surgery, Union Hospital, Tongji Medical College; College of Life Science and Technology; Huazhong University of Science and Technology, Wuhan, China
| |
Collapse
|
13
|
Li X, Li S, Liu X, Fang M, Lu S. Commentary: Metagenomic next-generation sequencing for Mycobacterium tuberculosis complex detection: a meta-analysis. Front Public Health 2024; 12:1291793. [PMID: 38560444 PMCID: PMC10978714 DOI: 10.3389/fpubh.2024.1291793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 02/26/2024] [Indexed: 04/04/2024] Open
Affiliation(s)
| | | | | | | | - Shuihua Lu
- Department of Pulmonary Disease, Shenzhen Third People's Hospital Affiliated to Southern University of Science and Technology, Shenzhen, China
| |
Collapse
|
14
|
Erratum: Advances in application of CRISPR-Cas13a system. Front Cell Infect Microbiol 2024; 14:1393044. [PMID: 38524180 PMCID: PMC10958657 DOI: 10.3389/fcimb.2024.1393044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 02/28/2024] [Indexed: 03/26/2024] Open
Abstract
[This corrects the article DOI: 10.3389/fcimb.2024.1291557.].
Collapse
|
15
|
Gimonneau G, Hounyèmè RE, Quartey M, Barry I, Ravel S, Boulangé A. Application of biomolecular techniques on tsetse fly puparia for species identification at larvipostion sites. Bull Entomol Res 2024:1-7. [PMID: 38444230 DOI: 10.1017/s0007485324000014] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
Puparia are commonly found in tsetse fly larviposition sites during studies on larval ecology. This chitinous shell is representative of past or ongoing exploitation of these sites by tsetse flies. The morphological characteristics of the puparium are not sufficiently distinctive to allow identification of the species. This study explores the applicability of biomolecular techniques on empty puparia for tsetse fly species identification. Five techniques were compared for DNA extraction from tsetse fly puparia, 1/Chelex® 100 Resin, 2/CTAB, 3/Livak's protocol, 4/DEB + proteinase K and 5/QIAamp® DNA Mini kit, using two homogenisation methods (manual and automated). Using a combination of two primer pairs, Chelex, CTAB, and DEB + K proved the most efficient on fresh puparia with 90, 85, and 70% samples identified, respectively. Shifting from fresh to one- to nine-month-old puparia, the Chelex method gave the best result allowing species identification on puparia up to seven months old. The subsequent testing of the Chelex extraction protocol identified 152 (60%) of 252 field-collected puparia samples at species level. The results show that reliable genetic identification of tsetse flies species can be performed from empty puparia, what can prove of great interest for future ecological studies on larviposition sites. The Chelex technique was the most efficient for DNA extraction, though the age-limit of the samples stood at seven months, beyond which DNA degradation probably compromises the genetic analysis.
Collapse
Affiliation(s)
- Geoffrey Gimonneau
- Unité de Recherche sur les Maladies à Vecteurs et Biodiversité, Centre International de Recherche-Développement sur l'Élevage en zone Subhumide, Bobo-Dioulasso, Burkina Faso
- CIRAD, UMR INTERTRYP, Bobo-Dioulasso 01, Burkina Faso
- INTERTRYP, Université de Montpellier, Cirad, IRD, Montpellier, France
| | - Robert Eustache Hounyèmè
- Unité de Recherche sur les Maladies à Vecteurs et Biodiversité, Centre International de Recherche-Développement sur l'Élevage en zone Subhumide, Bobo-Dioulasso, Burkina Faso
- CIRAD, UMR INTERTRYP, Bobo-Dioulasso 01, Burkina Faso
- INTERTRYP, Université de Montpellier, Cirad, IRD, Montpellier, France
| | - Myra Quartey
- Unité de Recherche sur les Maladies à Vecteurs et Biodiversité, Centre International de Recherche-Développement sur l'Élevage en zone Subhumide, Bobo-Dioulasso, Burkina Faso
| | - Issiaka Barry
- Unité de Recherche sur les Maladies à Vecteurs et Biodiversité, Centre International de Recherche-Développement sur l'Élevage en zone Subhumide, Bobo-Dioulasso, Burkina Faso
| | - Sophie Ravel
- INTERTRYP, Université de Montpellier, Cirad, IRD, Montpellier, France
| | - Alain Boulangé
- Unité de Recherche sur les Maladies à Vecteurs et Biodiversité, Centre International de Recherche-Développement sur l'Élevage en zone Subhumide, Bobo-Dioulasso, Burkina Faso
- CIRAD, UMR INTERTRYP, Bobo-Dioulasso 01, Burkina Faso
- INTERTRYP, Université de Montpellier, Cirad, IRD, Montpellier, France
| |
Collapse
|
16
|
Olivucci G, Iovino E, Innella G, Turchetti D, Pippucci T, Magini P. Long read sequencing on its way to the routine diagnostics of genetic diseases. Front Genet 2024; 15:1374860. [PMID: 38510277 PMCID: PMC10951082 DOI: 10.3389/fgene.2024.1374860] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 02/26/2024] [Indexed: 03/22/2024] Open
Abstract
The clinical application of technological progress in the identification of DNA alterations has always led to improvements of diagnostic yields in genetic medicine. At chromosome side, from cytogenetic techniques evaluating number and gross structural defects to genomic microarrays detecting cryptic copy number variants, and at molecular level, from Sanger method studying the nucleotide sequence of single genes to the high-throughput next-generation sequencing (NGS) technologies, resolution and sensitivity progressively increased expanding considerably the range of detectable DNA anomalies and alongside of Mendelian disorders with known genetic causes. However, particular genomic regions (i.e., repetitive and GC-rich sequences) are inefficiently analyzed by standard genetic tests, still relying on laborious, time-consuming and low-sensitive approaches (i.e., southern-blot for repeat expansion or long-PCR for genes with highly homologous pseudogenes), accounting for at least part of the patients with undiagnosed genetic disorders. Third generation sequencing, generating long reads with improved mappability, is more suitable for the detection of structural alterations and defects in hardly accessible genomic regions. Although recently implemented and not yet clinically available, long read sequencing (LRS) technologies have already shown their potential in genetic medicine research that might greatly impact on diagnostic yield and reporting times, through their translation to clinical settings. The main investigated LRS application concerns the identification of structural variants and repeat expansions, probably because techniques for their detection have not evolved as rapidly as those dedicated to single nucleotide variants (SNV) identification: gold standard analyses are karyotyping and microarrays for balanced and unbalanced chromosome rearrangements, respectively, and southern blot and repeat-primed PCR for the amplification and sizing of expanded alleles, impaired by limited resolution and sensitivity that have not been significantly improved by the advent of NGS. Nevertheless, more recently, with the increased accuracy provided by the latest product releases, LRS has been tested also for SNV detection, especially in genes with highly homologous pseudogenes and for haplotype reconstruction to assess the parental origin of alleles with de novo pathogenic variants. We provide a review of relevant recent scientific papers exploring LRS potential in the diagnosis of genetic diseases and its potential future applications in routine genetic testing.
Collapse
Affiliation(s)
- Giulia Olivucci
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
- Department of Surgical and Oncological Sciences, University of Palermo, Palermo, Italy
| | - Emanuela Iovino
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Giovanni Innella
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
- Medical Genetics Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Daniela Turchetti
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
- Medical Genetics Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Tommaso Pippucci
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Pamela Magini
- Medical Genetics Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| |
Collapse
|
17
|
Laguna JC, García-Pardo M, Alessi J, Barrios C, Singh N, Al-Shamsi HO, Loong H, Ferriol M, Recondo G, Mezquita L. Geographic differences in lung cancer: focus on carcinogens, genetic predisposition, and molecular epidemiology. Ther Adv Med Oncol 2024; 16:17588359241231260. [PMID: 38455708 PMCID: PMC10919138 DOI: 10.1177/17588359241231260] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 01/22/2024] [Indexed: 03/09/2024] Open
Abstract
Lung cancer poses a global health challenge and stands as the leading cause of cancer-related deaths worldwide. However, its incidence, mortality, and characteristics are not uniform across all regions worldwide. Understanding the factors contributing to this diversity is crucial in a prevalent disease where most cases are diagnosed in advanced stages. Hence, prevention and early diagnosis emerge as the most efficient strategies to enhance outcomes. In Western societies, tobacco consumption constitutes the primary risk factor for lung cancer, accounting for up to 90% of cases. In other geographic locations, different significant factors play a fundamental role in disease development, such as individual genetic predisposition, or exposure to other carcinogens such as radon gas, environmental pollution, occupational exposures, or specific infectious diseases. Comprehensive clinical and molecular characterization of lung cancer in recent decades has enabled us to distinguish different subtypes of lung cancer with distinct phenotypes, genotypes, immunogenicity, treatment responses, and survival rates. The ultimate goal is to prevent and individualize lung cancer management in each community and improve patient outcomes.
Collapse
Affiliation(s)
- Juan Carlos Laguna
- Medical Oncology Department, Hospital Clinic of Barcelona, Barcelona, Spain
- Laboratory of Translational Genomics and Targeted Therapies in Solid Tumors, IDIBAPS, Barcelona, Spain
- Department of Medicine, University of Barcelona, Barcelona, Spain
| | - Miguel García-Pardo
- Department of Medical Oncology, Hospital Universitario Ramón y Cajal, Madrid, Spain
- Department of Medicine, University of Barcelona, Barcelona, Spain
| | - Joao Alessi
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute
| | - Carlos Barrios
- School of Medicine, Porto Alegre, Rio Grande do Sul, Brazil
| | - Navneet Singh
- Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | | | - Herbert Loong
- Department of Clinical Oncology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Miquel Ferriol
- Laboratory of Translational Genomics and Targeted Therapies in Solid Tumors, IDIBAPS, Barcelona, Spain
- Barcelona Neural Networking Center, Universitat Politècnica de Catalunya, Barcelona, Spain
| | | | - Laura Mezquita
- Medical Oncology Department, Hospital Clinic of Barcelona, Calle Villarroel 170, Barcelona 08036, Spain
- Laboratory of Translational Genomics and Targeted Therapies in Solid Tumors, IDIBAPS, Barcelona, Spain
- Department of Medicine, University of Barcelona, Barcelona, Spain
| |
Collapse
|
18
|
Liu A, Liu S, Lv K, Zhu Q, Wen J, Li J, Liang C, Huang X, Gong C, Sun Q, Gu H. Rapid detection of multidrug resistance in tuberculosis using nanopore-based targeted next-generation sequencing: a multicenter, double-blind study. Front Microbiol 2024; 15:1349715. [PMID: 38495513 PMCID: PMC10940340 DOI: 10.3389/fmicb.2024.1349715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 02/13/2024] [Indexed: 03/19/2024] Open
Abstract
Background Resistance to anti-tuberculous drugs is a major challenge in the treatment of tuberculosis (TB). We aimed to evaluate the clinical availability of nanopore-based targeted next-generation sequencing (NanoTNGS) for the diagnosis of drug-resistant tuberculosis (DR-TB). Methods This study enrolled 253 patients with suspected DR-TB from six hospitals. The diagnostic efficacy of NanoTNGS for detecting Mycobacterium tuberculosis and its susceptibility or resistance to first- and second-line anti-tuberculosis drugs was assessed by comparing conventional phenotypic drug susceptibility testing (pDST) and Xpert MTB/RIF assays. NanoTNGS can be performed within 12 hours from DNA extraction to the result delivery. Results NanoTNGS showed a remarkable concordance rate of 99.44% (179/180) with the culture assay for identifying the Mycobacterium tuberculosis complex. The sensitivity of NanoTNGS for detecting drug resistance was 93.53% for rifampicin, 89.72% for isoniazid, 85.45% for ethambutol, 74.00% for streptomycin, and 88.89% for fluoroquinolones. Specificities ranged from 83.33% to 100% for all drugs tested. Sensitivity for rifampicin-resistant tuberculosis using NanoTNGS increased by 9.73% compared to Xpert MTB/RIF. The most common mutations were S531L (codon in E. coli) in the rpoB gene, S315T in the katG gene, and M306V in the embB gene, conferring resistance to rifampicin, isoniazid, and ethambutol, respectively. In addition, mutations in the pncA gene, potentially contributing to pyrazinamide resistance, were detected in 32 patients. Other prevalent variants, including D94G in the gyrA gene and K43R in the rpsL gene, conferred resistance to fluoroquinolones and streptomycin, respectively. Furthermore, the rv0678 R94Q mutation was detected in one sample, indicating potential resistance to bedaquiline. Conclusion NanoTNGS rapidly and accurately identifies resistance or susceptibility to anti-TB drugs, outperforming traditional methods. Clinical implementation of the technique can recognize DR-TB in time and provide guidance for choosing appropriate antituberculosis agents.
Collapse
Affiliation(s)
- Aimei Liu
- Department of Tuberculosis, Guangxi Zhuang Autonomous Region Chest Hospital, Liuzhou, Guangxi, China
| | - Sang Liu
- Department of Tuberculosis, Guangxi Zhuang Autonomous Region Chest Hospital, Liuzhou, Guangxi, China
| | - Kangyan Lv
- Department of Tuberculosis, Guangxi Zhuang Autonomous Region Chest Hospital, Liuzhou, Guangxi, China
| | - Qingdong Zhu
- Department of Tuberculosis, The Fourth People's Hospital of Nanning, Nanning, Guangxi, China
| | - Jun Wen
- Department of Pulmonary Medicine, The Third People's Hospital of Guilin, Guilin, Guangxi, China
| | - Jianpeng Li
- Department of Pulmonary Medicine, The Third People's Hospital of Wuzhou, Wuzhou, Guangxi, China
| | - Chengyuan Liang
- Department of Infectious Diseases, The People's Hospital of Baise, Baise, Guangxi, China
| | - Xuegang Huang
- Department of Infectious Diseases, The First People's Hospital of Fangchenggang, Fangchenggang, Guangxi, China
| | - Chunming Gong
- Department of Tuberculosis, Guangxi Zhuang Autonomous Region Chest Hospital, Liuzhou, Guangxi, China
| | - Qingfeng Sun
- Department of Tuberculosis, Guangxi Zhuang Autonomous Region Chest Hospital, Liuzhou, Guangxi, China
| | - Hongcang Gu
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, China
| |
Collapse
|
19
|
Figueiredo FB, Tomaselli PJ, Hallak J, Mattiello-Sverzut AC, Covaleski APPM, Sobreira CFDR, de Paula Gouvêa S, Marques W. Genetic diversity in hereditary axonal neuropathy: Analyzing 53 Brazilian children. J Peripher Nerv Syst 2024; 29:97-106. [PMID: 38375759 DOI: 10.1111/jns.12617] [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: 01/21/2023] [Revised: 01/24/2024] [Accepted: 01/31/2024] [Indexed: 02/21/2024]
Abstract
BACKGROUND AND AIMS The genetic epidemiology of inherited neuropathies in children remains largely unknown. In this study, we specifically investigated the genetic profile of a Brazilian cohort of pediatric patients with pure or complex axonal neuropathies, a crucial knowledge in the near future for establishing treatment priorities and perspectives for this group of patients. METHODS Fifty-three pediatric patients who were assessed prior to reaching the age of 20, and who had clinical diagnoses of axonal hereditary neuropathy or presented with axonal neuropathy as the primary clinical feature, were included in the study. The recruitment of these cases took place from January 1, 2018, to December 31, 2020. The diagnosis was based on clinical and electrophysiological data. A molecular assessment was made using target-gene panel or whole-exome sequencing. Subsequently, segregation analysis was performed on available family members, and all candidate variants found were confirmed through Sanger. RESULTS A molecular diagnosis was reached in 68% of the patients (n = 36/53), considering only pathogenic and probably pathogenic variants. Variants in MFN2 (n = 15) and GJB1 (n = 3) accounted for half of the genetically confirmed patients (50%; n = 18/36). The other 18 genetically diagnosed patients had variants in several less common genes. INTERPRETATION Apart from MFN2 and GJB1 genes, universally recognized as a frequent cause of axonal neuropathies in most studied population, our Brazilian cohort of children with axonal neuropathies showed an important genetic heterogeneity, probably reflecting the multi ethnicity of the Brazilian population. Diagnostic, counseling, and future interventions should consider this characteristic.
Collapse
Affiliation(s)
- Fernanda Barbosa Figueiredo
- Neuroscience and Behavior Sciences Department, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Pedro José Tomaselli
- Neuroscience and Behavior Sciences Department, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Jaime Hallak
- Neuroscience and Behavior Sciences Department, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
- National Institute of Sciences and Technology-INCT-Translational Medicine-CNPq/FAPESP, Ribeirao Preto, Brazil
| | | | | | | | - Silmara de Paula Gouvêa
- Neuroscience and Behavior Sciences Department, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | - Wilson Marques
- Neuroscience and Behavior Sciences Department, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
- National Institute of Sciences and Technology-INCT-Translational Medicine-CNPq/FAPESP, Ribeirao Preto, Brazil
| |
Collapse
|
20
|
Gudisa R, Harchand R, Rudramurthy SM. Nucleic-Acid-Based Molecular Fungal Diagnostics: A Way to a Better Future. Diagnostics (Basel) 2024; 14:520. [PMID: 38472992 DOI: 10.3390/diagnostics14050520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/20/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
The world has seen a tremendous increase in the number of fungal infections during the past two decades. Recently, the World Health Organisation released the pathogen priority list for fungal infections, signifying the importance of these infections in the fields of research and public health. Microbiology laboratories demand an upgrade in the diagnostic system to keep up with the increased burden of these infections. Diagnosis of fungal infections using conventional techniques has always faced limitations in terms of specificity, sensitivity, and turnaround time. Although these methods are the core pillars of the diagnosis, there is an increased need for molecular approaches. Molecular techniques have revolutionised the field of fungal diagnostics. The diverse array of molecular techniques, including techniques like Polymerase Chain Reaction (PCR), have emerged as a cornerstone in fungal diagnostics. Molecular techniques have transformed fungal diagnostics, providing powerful tools for the rapid and accurate identification of pathogens. As these technologies continue to evolve, their integration into routine clinical practice holds the promise of improving patient outcomes through timely and targeted antifungal interventions. This review will cover the molecular approaches involved in fungal diagnostics, moving from the basic techniques to the advanced-level nucleic-acid-based molecular approaches providing a high throughput and decreased turnaround time for the diagnosis of serious fungal infections.
Collapse
Affiliation(s)
- Rajendra Gudisa
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Ritika Harchand
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Shivaprakash M Rudramurthy
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research, Chandigarh 160012, India
| |
Collapse
|
21
|
Pérez-Vielma NM, Gómez-López M, Martínez-Godínez MDLÁ, Luna-Torres AL, Domínguez López A, Miliar-García Á. Candida Variety in the Oral Cavity of Mexican Subjects with Type 2 Diabetes Mellitus and TLR2 Gene Expression. Clin Pract 2024; 14:417-425. [PMID: 38525710 PMCID: PMC10961687 DOI: 10.3390/clinpract14020031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/19/2024] [Accepted: 02/23/2024] [Indexed: 03/26/2024] Open
Abstract
BACKGROUND The aim was to diagnose Candida in the oral cavity of subjects with type 2 diabetes mellitus (T2DM) using a genotyping technique and compare the results with those from conventional diagnosis by Papanicolaou (Pap) staining. METHODS Palatal mucosa smears were performed on 18 dental care patients diagnosed with T2DM and grade I, II, and III prosthetic stomatitis who met the inclusion criteria; 18 healthy control subjects were also included in the study. Hemoglobin A1c (HbA1c) levels were determined from total blood. Using exfoliative cytology, the Pap staining technique was used to diagnose candidiasis. Exfoliative cytology was also used for molecular diagnosis; DNA was obtained for Candida genotyping, and RNA was used for gene expression studies. RESULTS Clinical patterns indicated that all subjects were positive for Candida; however, Pap analysis revealed only three positive subjects, whereas end-point polymerase chain reaction (PCR) analysis revealed 15 subjects with some type of Candida. The most common Candida species found were Candida guilliermondii (38.8%), Candida krusei (33.3%), Candida tropicalis, and Candida lusitaniae (22.2%). Interestingly, the coexpression of different species of Candida was found in various patients. In all patients, HbA1c levels were increased. Gene expression analysis showed a significant decrease (p ≤ 0.05) in TLR2 expression in positive subjects, whereas TLR4 expression did not differ significantly among patients. CONCLUSIONS The end-point PCR technique showed better sensitivity for the diagnosis of Candida when compared with the diagnosis by Pap staining. T2DM subjects showed an increased presence of C. guilliermondii that was correlated with decreased TLR2 expression.
Collapse
Affiliation(s)
- Nadia Mabel Pérez-Vielma
- Sección de Estudios de Posgrado e Investigación, Centro Interdisciplinario de Ciencias de la Salud Unidad Santo Tomás, Instituto Politécnico Nacional, Mexico City 11340, Mexico; (N.M.P.-V.); (A.L.L.-T.)
| | - Modesto Gómez-López
- Laboratorio de Biología Molecular, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City 11340, Mexico; (M.G.-L.); (M.d.l.Á.M.-G.); (A.D.L.)
| | - María de los Ángeles Martínez-Godínez
- Laboratorio de Biología Molecular, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City 11340, Mexico; (M.G.-L.); (M.d.l.Á.M.-G.); (A.D.L.)
| | - Ana Laura Luna-Torres
- Sección de Estudios de Posgrado e Investigación, Centro Interdisciplinario de Ciencias de la Salud Unidad Santo Tomás, Instituto Politécnico Nacional, Mexico City 11340, Mexico; (N.M.P.-V.); (A.L.L.-T.)
| | - Aarón Domínguez López
- Laboratorio de Biología Molecular, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City 11340, Mexico; (M.G.-L.); (M.d.l.Á.M.-G.); (A.D.L.)
| | - Ángel Miliar-García
- Laboratorio de Biología Molecular, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City 11340, Mexico; (M.G.-L.); (M.d.l.Á.M.-G.); (A.D.L.)
| |
Collapse
|
22
|
Sánchez-Carvajal JM, Vera-Salmoral E, Huerta B, Galán-Relaño Á, Ruedas-Torres I, Larenas-Muñoz F, Luque I, Carrasco L, Gómez-Laguna J. Droplet digital PCR as alternative to microbiological culture for Mycobacterium tuberculosis complex detection in bovine lymph node tissue samples. Front Cell Infect Microbiol 2024; 14:1349999. [PMID: 38469351 PMCID: PMC10925636 DOI: 10.3389/fcimb.2024.1349999] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 02/07/2024] [Indexed: 03/13/2024] Open
Abstract
Introduction Bovine tuberculosis (bTB) caused by Mycobacterium tuberculosis complex (MTC) remains a significant concern for public health. Direct real-time PCR and droplet digital PCR (ddPCR) are proposed as alternative tools to enhance diagnostic precision and efficiency. This study aims to assess the diagnostic performance of a ddPCR assay targeting IS6110 for the detection of MTC DNA in both microbiological culture and fresh lymph node (LN) tissue samples obtained from cattle, in comparison with the established reference standard, the microbiological culture followed by real-time PCR. Methods The fresh LNs (N=100) were collected each from a different cattle carcass at the slaughterhouse. The limit of detection of ddPCR-IS6110 was set to 101 copies per 20 μl reaction. Results DdPCR-IS6110 detected 44 out of 49 reference-standard positive samples and yielded negative results in 47 out of 51 reference-standard negative samples, resulting in adjusted sensitivity (Se) and specificity (Sp) of 90.76% [95% confidence interval (CI): 82.58 - 98.96%)], and 100% (95% CI: 100%) respectively. The estimated adjusted false negative rate (FNR) was 9.23% (95% CI: 1.04 - 17.42%) and the false positive rate (FPR) was 0% (95% CI: 0%). When directly applied from fresh bovine LN tissues, ddPCR-IS6110 identified 47 out of 49 reference-standard positive samples as ddPCR-IS6110-positive and 42 out of 51 reference-standard negative samples as ddPCR-IS6110-negative, resulting in adjusted Se and Sp values of 94.80% [95% (CI): 88.52 - 100%] and 100% (95% CI: 100%), respectively. The adjusted FNR was 5.20% (95% CI: 0 - 11.50%) and the FPR was 0% (95% CI: 0%). Noteworthy, ddPCR-IS6110 disclosed as positive 9 samples negative to reference-standard. Discussion DdPCR-IS6110 proved to be a rapid, highly sensitive, and specific diagnostic tool as an alternative to reference-standard method.
Collapse
Affiliation(s)
- José María Sánchez-Carvajal
- Department of Anatomy and Comparative Pathology and Toxicology, Pathology and Immunology Group (UCO-PIG), Unidad de Investigación Competitiva (UIC) Zoonosis y Enfermedades Emergentes ENZOEM, University of Córdoba, Córdoba, Spain
| | - Eduardo Vera-Salmoral
- Department of Anatomy and Comparative Pathology and Toxicology, Pathology and Immunology Group (UCO-PIG), Unidad de Investigación Competitiva (UIC) Zoonosis y Enfermedades Emergentes ENZOEM, University of Córdoba, Córdoba, Spain
- Department of Animal Health, Unidad de Investigación Competitiva (UIC) Zoonosis y Enfermedades Emergentes (ENZOEM), University of Córdoba, University of Córdoba, Córdoba, Spain
| | - Belén Huerta
- Department of Animal Health, Unidad de Investigación Competitiva (UIC) Zoonosis y Enfermedades Emergentes (ENZOEM), University of Córdoba, University of Córdoba, Córdoba, Spain
| | - Ángela Galán-Relaño
- Department of Animal Health, Unidad de Investigación Competitiva (UIC) Zoonosis y Enfermedades Emergentes (ENZOEM), University of Córdoba, University of Córdoba, Córdoba, Spain
| | - Inés Ruedas-Torres
- Department of Anatomy and Comparative Pathology and Toxicology, Pathology and Immunology Group (UCO-PIG), Unidad de Investigación Competitiva (UIC) Zoonosis y Enfermedades Emergentes ENZOEM, University of Córdoba, Córdoba, Spain
- UK Health Security Agency (UKHSA), Salisbury, United Kingdom
| | - Fernanda Larenas-Muñoz
- Department of Anatomy and Comparative Pathology and Toxicology, Pathology and Immunology Group (UCO-PIG), Unidad de Investigación Competitiva (UIC) Zoonosis y Enfermedades Emergentes ENZOEM, University of Córdoba, Córdoba, Spain
| | - Inmaculada Luque
- Department of Animal Health, Unidad de Investigación Competitiva (UIC) Zoonosis y Enfermedades Emergentes (ENZOEM), University of Córdoba, University of Córdoba, Córdoba, Spain
| | - Librado Carrasco
- Department of Anatomy and Comparative Pathology and Toxicology, Pathology and Immunology Group (UCO-PIG), Unidad de Investigación Competitiva (UIC) Zoonosis y Enfermedades Emergentes ENZOEM, University of Córdoba, Córdoba, Spain
| | - Jaime Gómez-Laguna
- Department of Anatomy and Comparative Pathology and Toxicology, Pathology and Immunology Group (UCO-PIG), Unidad de Investigación Competitiva (UIC) Zoonosis y Enfermedades Emergentes ENZOEM, University of Córdoba, Córdoba, Spain
| |
Collapse
|
23
|
Lin DI, Huang RSP, Ladas I, Keller RB, Patel NR, Lakis S, Decker B, Janovitz T, Mata DA, Ross JS, Vergilio JA, Elvin JA, Herbst RS, Mack PC, Killian JK. Precision needle-punch tumor enrichment from paraffin blocks improves the detection of clinically actionable genomic alterations and biomarkers. Front Oncol 2024; 14:1328512. [PMID: 38444675 PMCID: PMC10912171 DOI: 10.3389/fonc.2024.1328512] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/11/2024] [Indexed: 03/07/2024] Open
Abstract
Background While many molecular assays can detect mutations at low tumor purity and variant allele frequencies, complex biomarkers such as tumor mutational burden (TMB), microsatellite instability (MSI), and genomic loss of heterozygosity (gLOH) require higher tumor purity for accurate measurement. Scalable, quality-controlled, tissue-conserving methods to increase tumor nuclei percentage (TN%) from tumor specimens are needed for complex biomarkers and hence necessary to maximize patient matching to approved therapies or clinical trial enrollment. We evaluated the clinical utility and performance of precision needle-punch enrichment (NPE) compared with traditional razor blade macroenrichment of tumor specimens on molecular testing success. Methods Pathologist-directed NPE was performed manually on formalin-fixed, paraffin embedded (FFPE) blocks. Quality control of target capture region and quantity of residual tumor in each tissue block was determined via a post-enrichment histologic slide recut. Resultant tumor purity and biomarker status were determined by the computational analysis pipeline component of the FDA-approved next-generation sequencing (NGS) assay, FoundationOne®CDx. Following NPE implementation for real-world clinical samples, assay performance and biomarker (MSI, TMB, gLOH) detection were analyzed. Results In real-world clinical samples, enrichment rate via NPE was increased to ~50% over a 2.5-year period, exceeding the prior use of razor blade macro-enrichment (<30% of cases) prior to NPE implementation due to proven efficacy in generating high quality molecular results from marginal samples and the ease of use for both pathologist and histotechnologists. NPE was associated with lower test failures, higher computational tumor purity, and higher rates of successful TMB, MSI and gLOH determination when stratified by pre-enriched (incipient) tumor nuclei percentage. In addition, challenging cases in which tumor content was initially insufficient for testing were salvaged for analysis of biomarker status, gene amplification/deletion, and confident mutant or wild-type gene status determination. Conclusions Pathologist-directed precision enrichment from tissue blocks (aka NPE) increases tumor purity, and consequently, yields a greater number of successful tests and complex biomarker determinations. Moreover, this process is rapid, safe, inexpensive, scalable, and conserves patient surgical pathology material. NPE may constitute best practice with respect to enriching tumor cells from low-purity specimens for biomarker detection in molecular laboratories.
Collapse
Affiliation(s)
- Douglas I Lin
- Department of Pathology and Diagnostic Medicine, Foundation Medicine, Inc., Cambridge, MA, United States
| | - Richard S P Huang
- Department of Pathology and Diagnostic Medicine, Foundation Medicine, Inc., Cambridge, MA, United States
| | - Ioannis Ladas
- Department of Pathology and Diagnostic Medicine, Foundation Medicine, Inc., Cambridge, MA, United States
| | - Rachel B Keller
- Department of Pathology and Diagnostic Medicine, Foundation Medicine, Inc., Cambridge, MA, United States
| | - Nimesh R Patel
- Department of Pathology and Diagnostic Medicine, Foundation Medicine, Inc., Cambridge, MA, United States
| | - Sotirios Lakis
- Foundation Medicine GmbH, Pathology Department, Penzberg, Germany
| | - Brennan Decker
- Department of Pathology and Diagnostic Medicine, Foundation Medicine, Inc., Cambridge, MA, United States
| | - Tyler Janovitz
- Department of Pathology and Diagnostic Medicine, Foundation Medicine, Inc., Cambridge, MA, United States
| | - Douglas A Mata
- Department of Pathology and Diagnostic Medicine, Foundation Medicine, Inc., Cambridge, MA, United States
| | - Jeffrey S Ross
- Department of Pathology and Diagnostic Medicine, Foundation Medicine, Inc., Cambridge, MA, United States
| | - Jo-Anne Vergilio
- Department of Pathology and Diagnostic Medicine, Foundation Medicine, Inc., Cambridge, MA, United States
| | - Julia A Elvin
- Department of Pathology and Diagnostic Medicine, Foundation Medicine, Inc., Cambridge, MA, United States
| | - Roy S Herbst
- Department of Medical Oncology, Yale School of Medicine, Yale Cancer Center, New Haven, CT, United States
| | - Philip C Mack
- Division of Hematology and Oncology, Department of Medicine, Tisch Cancer Institute at Mount Sinai, New York, NY, United States
| | - Jonathan K Killian
- Department of Pathology and Diagnostic Medicine, Foundation Medicine, Inc., Cambridge, MA, United States
| |
Collapse
|
24
|
Ding T, Diao Y, Zeng X, Zhou L, Wu G, Liu J, Hao X. Influential factors on urine EV DNA methylation detection and its diagnostic potential in prostate cancer. Front Genet 2024; 15:1338468. [PMID: 38440192 PMCID: PMC10909848 DOI: 10.3389/fgene.2024.1338468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 02/06/2024] [Indexed: 03/06/2024] Open
Abstract
The value of Extracellular vesicles (EVs) diagnostic markers is widely recognized. However, current research on EV DNA remains limited. This study investigates the biological properties, preprocessing factors, and diagnostic potential of EV DNA. We found that DNA positive vesicles account for 23.3% ± 6.7% of the urine total EV, with a large amount of DNA attached to the outside. EV DNA fragments are large, there is no significant effect on uEV DNA when store urine less than 6 h at 4°C. In addition, the influence of different EV extraction methods on methylation detection is also minor. More importantly, RASSF1A methylation in urine total EV DNA can distinguish between PCa and BPH, with an AUC of 0.874. Our results suggest the potential of urine EV DNA as a novel marker for PCa diagnosis. This provides a new idea for the study of urinary tumor markers.
Collapse
Affiliation(s)
- Ting Ding
- Fourth Military Medical University (Air Force Medical University), Xi’an, China
- School of Medicine, Northwest University, Xi’an, China
| | - Yanjun Diao
- Fourth Military Medical University (Air Force Medical University), Xi’an, China
| | - Xianfei Zeng
- School of Medicine, Northwest University, Xi’an, China
- Shanxi Lifegen Co., Ltd., Xi’an, China
| | - Lei Zhou
- Fourth Military Medical University (Air Force Medical University), Xi’an, China
| | - Guojun Wu
- School of Medicine, Northwest University, Xi’an, China
- Department of Urology, Xi’an People’s Hospital(Xi’an Fourth Hospital), Xi’an, China
| | - Jiayun Liu
- Fourth Military Medical University (Air Force Medical University), Xi’an, China
| | - Xiaoke Hao
- Fourth Military Medical University (Air Force Medical University), Xi’an, China
- School of Medicine, Northwest University, Xi’an, China
| |
Collapse
|
25
|
Zhang Y, Li S, Li R, Qiu X, Fan T, Wang B, Zhang B, Zhang L. Advances in application of CRISPR-Cas13a system. Front Cell Infect Microbiol 2024; 14:1291557. [PMID: 38524179 PMCID: PMC10958658 DOI: 10.3389/fcimb.2024.1291557] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 01/26/2024] [Indexed: 03/26/2024] Open
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) and CRISPR-associated (Cas) proteins serve as an adaptive immune system that safeguards prokaryotes and some of the viruses that infect prokaryotes from foreign nucleic acids (such as viruses and plasmids). The genomes of the majority of archaea and about half of all bacteria contain various CRISPR-Cas systems. CRISPR-Cas systems depend on CRISPR RNAs (crRNAs). They act as a navigation system to specifically cut and destroy foreign nucleic acids by recognizing invading foreign nucleic acids and binding Cas proteins. In this review, we provide a brief overview of the evolution and classification of the CRISPR-Cas system, focusing on the functions and applications of the CRISPR-Cas13a system. We describe the CRISPR-Cas13a system and discuss its RNA-directed ribonuclease function. Meanwhile, we briefly introduce the mechanism of action of the CRISPR-Cas13a system and summarize the applications of the CRISPR-Cas13a system in pathogen detection, eukaryotes, agriculture, biosensors, and human gene therapy. We are right understanding of CRISPR-Cas13a has been broadened, and the CRISPR-Cas13a system will be useful for developing new RNA targeting tools. Therefore, understanding the basic details of the structure, function, and biological characterization of CRISPR-Cas13a effector proteins is critical for optimizing RNA targeting tools.
Collapse
Affiliation(s)
- Yue Zhang
- The Department of Immunology, School of Basic Medicine, Qingdao University, Qingdao, Shandong, China
| | - Shengjun Li
- The Department of Clinical Laboratory, Qingdao Women and Children’s Hospital, Qingdao, Shandong, China
| | - Rongrong Li
- The Department of Medical Imaging, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Xu Qiu
- The Department of Immunology, School of Basic Medicine, Qingdao University, Qingdao, Shandong, China
| | - Tianyu Fan
- The Department of Hematology, Taian City Central Hospital, Taian, Shandong, China
| | - Bin Wang
- The Department of Immunology, School of Basic Medicine, Qingdao University, Qingdao, Shandong, China
| | - Bei Zhang
- The Department of Immunology, School of Basic Medicine, Qingdao University, Qingdao, Shandong, China
| | - Li Zhang
- The Department of Immunology, School of Basic Medicine, Qingdao University, Qingdao, Shandong, China
| |
Collapse
|
26
|
Pandey M, Kumar T, Koshiol J. Editorial: Advances in molecular classification and targeting of solid tumors. Front Oncol 2024; 14:1373599. [PMID: 38414742 PMCID: PMC10896838 DOI: 10.3389/fonc.2024.1373599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 01/26/2024] [Indexed: 02/29/2024] Open
Affiliation(s)
- Manoj Pandey
- Department of Surgical Oncology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Tarun Kumar
- Department of Surgical Oncology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Jill Koshiol
- Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, MD, United States
| |
Collapse
|
27
|
Nieto-García A, Abel-Fernández E, Nieto-Cid M, Pineda de la Losa F. 360° approach to the patient with mite allergy: from scientific evidence to clinical practice. Front Allergy 2024; 5:1298816. [PMID: 38379594 PMCID: PMC10876833 DOI: 10.3389/falgy.2024.1298816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 01/23/2024] [Indexed: 02/22/2024] Open
Abstract
In the recent years, several important advances have been made in the diagnosis of allergy using molecular techniques. The aetiological diagnosis of allergy using molecular components of allergens allows a more precise definition of the patient's IgE repertoire. Precision medicine is a structural model aimed at personalising healthcare and places the patient at the centre of the specialist's decision-making process. To this end, an accurate characterisation of the external exposome at a molecular level and their putative role as clinically relevant allergens is essential to elucidate the phenotypic diversity of atopic disease, with a view to personalising diagnosis and therapy. It has been proposed a decision algorithm, the Top-Down approach, where the clinical history is set first and is followed by the use of skin tests or specific IgE techniques, which facilitates the clinicians to make decisions. The therapeutic intervention driven by the standard diagnostic approach, but supported by these innovative tools, can lead to a better phenotyping of highly complex patients, and a more appropriate prescription of AIT. To this end, the allergen extracts used for diagnosis require to be of proven quality and contain the most relevant allergens. Likewise, allergen vaccines must gather efficacy, safety, duration, and patient compliance, hence the demand for new vaccines to overcome these drawbacks.
Collapse
Affiliation(s)
- Antonio Nieto-García
- Pediatric Allergy and Pneumology Unit, La Fe Hospital, Valencia, Spain
- La Fe Health Research Institute, Valencia, Spain
| | | | - María Nieto-Cid
- Allergy Service, University Hospital of La Plana, Vila-real, Spain
| | | |
Collapse
|
28
|
Jacob-Nascimento LC, Portilho MM, Anjos RO, Moreira PSS, Stauber C, Weaver SC, Kitron U, Reis MG, Ribeiro GS. Detection of Chikungunya Virus RNA in Oral Fluid and Urine: An Alternative Approach to Diagnosis? Viruses 2024; 16:235. [PMID: 38400011 PMCID: PMC10891727 DOI: 10.3390/v16020235] [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: 12/28/2023] [Revised: 01/19/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
To evaluate whether oral fluids (OF) and urine can serve as alternative, non-invasive samples to diagnose chikungunya virus (CHIKV) infection via RT-qPCR, we employed the same RNA extraction and RT-qPCR protocols on paired serum, OF and urine samples collected from 51 patients with chikungunya during the acute phase of the illness. Chikungunya patients were confirmed through RT-qPCR in acute-phase sera (N = 19), IgM seroconversion between acute- and convalescent-phase sera (N = 12), or IgM detection in acute-phase sera (N = 20). The controls included paired serum, OF and urine samples from patients with non-arbovirus acute febrile illness (N = 28) and RT-PCR-confirmed dengue (N = 16). Nine (47%) of the patients with positive RT-qPCR for CHIKV in sera and two (17%) of those with CHIKV infection confirmed solely via IgM seroconversion had OF positive for CHIKV in RT-qPCR. One (5%) patient with CHIKV infection confirmed via serum RT-qPCR was positive in the RT-qPCR performed on urine. None of the negative control group samples were positive. Although OF may serve as an alternative sample for diagnosing acute chikungunya in specific settings, a negative result cannot rule out an infection. Further research is needed to investigate whether OF and urine collected later in the disease course when serum becomes RT-qPCR-negative may be helpful in CHIKV diagnosis and surveillance, as well as to determine whether urine and OF pose any risk of CHIKV transmission.
Collapse
Affiliation(s)
- Leile Camila Jacob-Nascimento
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil; (L.C.J.-N.); (M.M.P.); (R.O.A.); (P.S.S.M.); (M.G.R.)
- Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador 40026-010, Brazil
| | - Moyra M. Portilho
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil; (L.C.J.-N.); (M.M.P.); (R.O.A.); (P.S.S.M.); (M.G.R.)
| | - Rosângela O. Anjos
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil; (L.C.J.-N.); (M.M.P.); (R.O.A.); (P.S.S.M.); (M.G.R.)
| | - Patrícia S. S. Moreira
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil; (L.C.J.-N.); (M.M.P.); (R.O.A.); (P.S.S.M.); (M.G.R.)
| | - Christine Stauber
- School of Public Health, Georgia State University, Atlanta, GA 30303, USA;
| | - Scott C. Weaver
- Department of Microbiology & Immunology and World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX 77555, USA;
| | - Uriel Kitron
- Department of Environmental Sciences, Emory University, Atlanta, GA 30322, USA;
| | - Mitermayer G. Reis
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil; (L.C.J.-N.); (M.M.P.); (R.O.A.); (P.S.S.M.); (M.G.R.)
- Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador 40026-010, Brazil
- Yale School of Public Health, Yale University, New Haven, CT 06520-8034, USA
| | - Guilherme S. Ribeiro
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil; (L.C.J.-N.); (M.M.P.); (R.O.A.); (P.S.S.M.); (M.G.R.)
- Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador 40026-010, Brazil
| |
Collapse
|
29
|
Jiang J, Cai X, Qu H, Yao Q, He T, Yang M, Zhou H, Zhang X. Case report: Identification of facioscapulohumeral muscular dystrophy 1 in two siblings with normal phenotypic parents using optical genome mapping. Front Neurol 2024; 15:1258831. [PMID: 38361638 PMCID: PMC10867183 DOI: 10.3389/fneur.2024.1258831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 01/05/2024] [Indexed: 02/17/2024] Open
Abstract
Objective Facioscapulohumeral muscular dystrophy type 1 (FSHD1) is one of the most common forms of autosomal-dominant muscular dystrophies characterized by variable disease penetrance due to shortened D4Z4 repeat units on 4q35. The molecular diagnosis of FSHD1 is usually made by Southern blotting, which is complex, time-consuming, and lacks clinical practicality. Therefore, in this study, optical genome mapping (OGM) is employed for the genetic diagnosis of FSHD1. Furthermore, epigenetic heterogeneity is determined from methylation analysis. Methods Genomic DNA samples from four members of the same family were subjected to whole-exome sequencing. OGM was used to identify structural variations in D4Z4, while sodium bisulfite sequencing helped identify the methylation levels of CpG sites in a region located distally to the D4Z4 array. A multidisciplinary team collected the clinical data, and comprehensive family analyses aided in the assessment of phenotypes and genotypes. Results Whole-exome sequencing did not reveal variants related to clinical phenotypes in the patients. OGM showed that the proband was a compound heterozygote for the 4qA allele with four and eight D4Z4 repeat units, whereas the affected younger brother had only one 4qA allele with four D4Z4 repeat units. Both the proband and her younger brother were found to display asymmetric weakness predominantly involving the facial, shoulder girdle, and upper arm muscles, whereas the younger brother had more severe clinical symptoms. The proband's father, who was found to be normal after a neurological examination, also carried the 4qA allele with eight D4Z4 repeat units. The unaffected mother exhibited 49 D4Z4 repeat units of the 4qA allele and a minor mosaic pattern with four D4Z4 repeat units of the 4qA allele. Consequently, the presence of the 4qA allele in the four D4Z4 repeat units strongly pointed to the occurrence of maternal germline mosaicism. The CpG6 methylation levels were lower in symptomatic patients compared to those in the asymptomatic parents. The older sister had lower clinical scores and ACSS and higher CpG6 methylation levels than that of her younger brother. Conclusions In this study, two siblings with FSHD1 with phenotypically normal parents were identified by OGM. Our findings suggest that the 4qA allele of four D4Z4 repeats was inherited through maternal germline mosaicism. The clinical phenotype heterogeneity is influenced by the CpG6 methylation levels. The results of this study greatly aid in the molecular diagnosis of FSHD1 and in also understanding the clinical phenotypic variability underlying the disease.
Collapse
Affiliation(s)
- Jieni Jiang
- Department of Medical Genetics and Prenatal Diagnosis Center, West China Second University Hospital, Sichuan University, Chengdu, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Xiaotang Cai
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
- Department of Rehabilitation, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Haibo Qu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
- Department of Radiology, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Qiang Yao
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Tiantian He
- Department of Medical Genetics and Prenatal Diagnosis Center, West China Second University Hospital, Sichuan University, Chengdu, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Mei Yang
- Department of Medical Genetics and Prenatal Diagnosis Center, West China Second University Hospital, Sichuan University, Chengdu, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Hui Zhou
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
- Department of Rehabilitation, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Xuemei Zhang
- Department of Medical Genetics and Prenatal Diagnosis Center, West China Second University Hospital, Sichuan University, Chengdu, China
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| |
Collapse
|
30
|
Carrillo YD, Rueda-Gaitán P, Gualdrón O, Estrada-Serrato C, Castro-Cuesta TA, Londoño O, Rodríguez-Salazar L, Isaza-Ruget M, Arcos-Burgos M, López Rivera JJ. Diagnostic yield of chromosomal microarray in the largest Latino clinical cohort. Am J Med Genet A 2024; 194:218-225. [PMID: 37795898 DOI: 10.1002/ajmg.a.63427] [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: 01/06/2023] [Revised: 08/30/2023] [Accepted: 09/19/2023] [Indexed: 10/06/2023]
Abstract
Copy number variants (CNVs) remain a major etiological cause of neurodevelopmental delay and congenital malformations. Chromosomal microarray analysis (CMA) represents the gold standard for CNVs molecular characterization. We applied CMA throughout the patient's clinical diagnostic workup, as the patient's medical provider requested. We collected CMA results of 3380 patients enrolled for 5 years (2016-2021). We found 830 CNVs in 719 patients with potential clinical significance, that is, (i) pathogenic, (ii) likely pathogenic, and (iii) variants of uncertain significance (VUS), from which 10.6% (predominantly involving chromosomes 15 and 22) were most likely the final cause underpinning the patients' clinical phenotype. For those associated with neurodevelopmental phenotypes, the rate of pathogenic or likely pathogenic findings among the patients with CNVs was 60.75%. When considering epileptic phenotypes, it was 59%. Interestingly, our protocol identified two gains harbored in 17q21.31 and 9q34.3, internationally classified initially as VUS. However, because of their high frequency, we propose that these two VUS be reclassified as likely benign in this widely heterogeneous phenotypic population. These results support the diagnostic yield efficiency of CMA in characterizing CNVs to define the final molecular cause of genetic diseases in this cohort of Colombian patients, the most significant sample of patients from a Latino population, and define new benign polymorphic CNVs.
Collapse
Affiliation(s)
- Yina D Carrillo
- Laboratorio Clínico Especializado, Clinica Universitaria Colombia, Clínica Colsanitas, Bogotá, Colombia
| | - Paula Rueda-Gaitán
- Laboratorio Clínico Especializado, Clinica Universitaria Colombia, Clínica Colsanitas, Bogotá, Colombia
| | - Orlando Gualdrón
- Laboratorio Clínico Especializado, Clinica Universitaria Colombia, Clínica Colsanitas, Bogotá, Colombia
- Grupo de investigación INPAC, Grupo Keralty, Bogotá, Colombia
| | - Carlos Estrada-Serrato
- Grupo de Genética Médica, Clínica Universitaria Colombia y Clínica Pediátrica Colsanitas, Clínica Colsanitas, Bogotá, Colombia
| | - Taryn A Castro-Cuesta
- Grupo de Genética Médica, Clínica Universitaria Colombia y Clínica Pediátrica Colsanitas, Clínica Colsanitas, Bogotá, Colombia
| | - Olga Londoño
- Grupo de Genética Médica, Clínica Universitaria Colombia y Clínica Pediátrica Colsanitas, Clínica Colsanitas, Bogotá, Colombia
| | - Luna Rodríguez-Salazar
- Laboratorio Clínico Especializado, Clinica Universitaria Colombia, Clínica Colsanitas, Bogotá, Colombia
| | - Mario Isaza-Ruget
- Grupo de investigación INPAC, Grupo Keralty, Bogotá, Colombia
- Fundación Universitaria Sanitas, Grupo de investigación INPAC, Bogotá, Colombia
- Laboratorio Clínico y de Patología, Clínica Colsanitas, Grupo Keralty, Bogotá, Colombia
| | - Mauricio Arcos-Burgos
- Instituto de Investigaciones Médicas, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
| | - Juan Javier López Rivera
- Laboratorio Clínico Especializado, Clinica Universitaria Colombia, Clínica Colsanitas, Bogotá, Colombia
- Grupo de investigación INPAC, Grupo Keralty, Bogotá, Colombia
- Grupo de Genética Médica, Clínica Universitaria Colombia y Clínica Pediátrica Colsanitas, Clínica Colsanitas, Bogotá, Colombia
- Clínica Pediátrica, Clínica Colsanitas, Bogotá, Colombia
| |
Collapse
|
31
|
Guo XM, Xing JY, Li A, Qiu L, Zhang QL, Huang J. Establishment of a real-time PCR for the detection of decapod iridescent virus 1 (DIV1). J Fish Dis 2024:e13926. [PMID: 38300509 DOI: 10.1111/jfd.13926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/08/2024] [Accepted: 01/14/2024] [Indexed: 02/02/2024]
Affiliation(s)
- Xiao-Meng Guo
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Jing-Yi Xing
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- College of Aquaculture, Tianjin Agricultural University, Tianjin, China
| | - Anqi Li
- College of Aquaculture, Tianjin Agricultural University, Tianjin, China
| | - Liang Qiu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Qing-Li Zhang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
- College of Aquaculture, Tianjin Agricultural University, Tianjin, China
| | - Jie Huang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Key Laboratory of Maricultural Organism Disease Control, Ministry of Agriculture and Rural Affairs, Qingdao Key Laboratory of Mariculture Epidemiology and Biosecurity, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
- Network of Aquaculture Centres in Asia-Pacific, Bangkok, Thailand
| |
Collapse
|
32
|
Anguinze RS, Touré A, Cissé F, Grayo S, Troupin C, Tordo N, Kouamou E, Roques P. Viral etiology of measles-like rash in Guinean children during the COVID epidemic in 2022. J Med Virol 2024; 96:e29437. [PMID: 38305059 DOI: 10.1002/jmv.29437] [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: 09/06/2023] [Revised: 01/16/2024] [Accepted: 01/19/2024] [Indexed: 02/03/2024]
Abstract
Covid-19 in West Africa masked outbreaks of vaccine-preventable diseases such as the measles epidemic in children in Guinea in 2021-2022 characterized by a lack of confirmation of suspected clinical cases. During weeks 13-22 of 2022, saliva samples were collected from 213 children (3-60 months old) with measles-like symptoms within the St Gabriel dispensary in Conakry. Samples were processed in Virus Transport Medium (VTM) and tested on the same day by triplex reverse transcriptase -real-time polymerase chain reaction for Measles, Rubella and RNaseP. Samples were also tested for HHV6 and Parvovirus B19, viruses causing clinical signs similar to measles. We confirmed 146 (68.5%) measles cases, 27 (12.7%) rubella, 5 (2.3%) double-positive measles-rubella, 35 (16.4%) HHV-6 and 8 (3.75%) Parvovirus B19. To test the assay's robustness, 27 samples were kept at 26-30°C. Measles and rubella were still detected after 7 days at 26-30°C, and after 21 days measles and rubella were still detectable in all samples but one. Sequencing indicated the circulation of the B3 measles genotype, as expected in West Africa. This study highlights the robustness of the measles/rubella diagnostic test on saliva samples stored in VTM. The high level of rubella detection questioned the single valence measles vaccination strategy.
Collapse
Affiliation(s)
| | | | | | | | - Cécile Troupin
- Medical Virology and Rabies group, Institut Pasteur du Laos, Vientiane, Laos
| | - Noël Tordo
- Institut Pasteur de Guinée, Conakry, Guinea
| | | | - Pierre Roques
- Institut Pasteur de Guinée, Conakry, Guinea
- CEA, Institut François Jacob, Fontenay-aux-Roses, France
- Université Paris-Saclay, INSERM, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial diseases (IMVA-HB/IDMIT), Le Kremlin Bicêtre, France
| |
Collapse
|
33
|
Aftab A, Raina OK, Maxton A, Masih SA. Advances in diagnostic approaches to Fasciola infection in animals and humans: An overviews. J Helminthol 2024; 98:e12. [PMID: 38269544 DOI: 10.1017/s0022149x23000950] [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: 01/26/2024]
Abstract
Fasciolosis, caused by Fasciola hepatica and F. gigantica, is an impediment to the livestock industry’s expansion and has a massively negative socio-economic impact due to its widespread prevalence in livestock. It is a waterborne zoonosis affecting human populations in the countries where rural economies are associated with livestock rearing. Conventional diagnosis of Fasciola infection is done by detecting parasite eggs in the faeces of infected animals or by immunological methods. Accurate and quick immunodiagnosis of Fasciola infection in animals and humans is based on the detection of antibodies and specific antigens expressed in the prepatent stage of the parasite. Both molecular and serodiagnostic tests developed thus far have enhanced the reliability of Fasciola diagnosis in both man and animals but are not widely available in resource-poor nations. A pen-side diagnostic test based on a lateral flow assay or a DNA test like loop-mediated isothermal amplification (LAMP) would be simple, fast, and cost-effective, enabling clinicians to treat animals in a targeted manner and avoid the development of drug resistance to the limited flukicides. This review focuses on the recent advances made in the diagnosis of this parasite infection in animals and humans.
Collapse
Affiliation(s)
- A Aftab
- Molecular and Cellular Engineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj-211007, Uttar Pradesh, India
- Division of Parasitology, Indian Veterinary Research Institute, Izatnagar-243122, Bareilly, Uttar Pradesh, India
| | - O K Raina
- Division of Parasitology, Indian Veterinary Research Institute, Izatnagar-243122, Bareilly, Uttar Pradesh, India
| | - A Maxton
- Genetics and Plant Breeding, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj-211007, Uttar Pradesh, India
| | - S A Masih
- Molecular and Cellular Engineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj-211007, Uttar Pradesh, India
| |
Collapse
|
34
|
Burban A, Słupik D, Reda A, Szczerba E, Grabowski M, Kołodzińska A. Novel Diagnostic Methods for Infective Endocarditis. Int J Mol Sci 2024; 25:1245. [PMID: 38279244 PMCID: PMC10816594 DOI: 10.3390/ijms25021245] [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: 01/14/2024] [Accepted: 01/15/2024] [Indexed: 01/28/2024] Open
Abstract
Infective endocarditis (IE) remains a dangerous disease and continues to have a high mortality rate. Unfortunately, despite continuous improvements in diagnostic methods, in many cases, blood cultures remain negative, and the pathogen causing endocarditis is unknown. This makes targeted therapy and the selection of appropriate antibiotics impossible. Therefore, we present what methods can be used to identify the pathogen in infective endocarditis. These are mainly molecular methods, including PCR and MGS, as well as imaging methods using radiotracers, which offer more possibilities for diagnosing IE. However, they are still not widely used in the diagnosis of IE. The article summarizes in which cases we should choose them and what we are most hopeful about in further research into the diagnosis of IE. In addition, registered clinical trials that are currently underway for the diagnosis of IE are also presented.
Collapse
Affiliation(s)
- Anna Burban
- 1st Chair and Department of Cardiology, Medical University of Warsaw, 02-097 Warsaw, Poland
- Doctoral School, Medical University of Warsaw, 02-091 Warsaw, Poland
| | - Dorota Słupik
- 1st Chair and Department of Cardiology, Medical University of Warsaw, 02-097 Warsaw, Poland
| | - Aleksandra Reda
- 1st Chair and Department of Cardiology, Medical University of Warsaw, 02-097 Warsaw, Poland
| | - Ewa Szczerba
- 1st Chair and Department of Cardiology, Medical University of Warsaw, 02-097 Warsaw, Poland
| | - Marcin Grabowski
- 1st Chair and Department of Cardiology, Medical University of Warsaw, 02-097 Warsaw, Poland
| | - Agnieszka Kołodzińska
- 1st Chair and Department of Cardiology, Medical University of Warsaw, 02-097 Warsaw, Poland
| |
Collapse
|
35
|
Lee B, Hwang S, Bae H, Choi KH, Suh YL. Diagnostic utility of genetic alterations in distinguishing IDH-wildtype glioblastoma from lower-grade gliomas: Insight from next-generation sequencing analysis of 479 cases. Brain Pathol 2024:e13234. [PMID: 38217295 DOI: 10.1111/bpa.13234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 12/20/2023] [Indexed: 01/15/2024] Open
Abstract
The accurate diagnosis and classification of gliomas are essential for appropriate treatment planning and prognosis prediction. This study aimed to investigate the molecular diagnostics of IDH-wildtype diffuse astrocytic gliomas and identify potential genetic variants that could differentiate glioblastoma (GBM) from lower-grade gliomas when DNA methylation analysis is not feasible. In total, 479 H3-and IDH-wildtype diffuse astrocytic gliomas were included in this study. All the cases were diagnosed according to the 2021 World Health Organization (WHO) classification of central nervous system (CNS) tumors. Panel sequencing data were collected, and clinicopathological information was retrieved from medical records. Genetic alterations and histological findings were analyzed to determine their diagnostic utility and prognostic implications. Out of 479 cases, 439 (91.6%) were diagnosed with GBM, including 28 cases that were molecularly diagnosed as GBM. However, 40 (8.4%) cases could not be classified according to the 2021 WHO classification and were diagnosed as lower-grade diffuse astrocytic glioma, IDH-wildtype, not elsewhere classified (LGNEC). In addition to the three genetic alterations included in the diagnostic criteria of GBM, PTEN and EGFR mutations were found to be enriched in GBM. Patients harboring mTOR pathway mutations demonstrated a more favorable prognosis and often exhibited morphology resembling subependymal giant cell astrocytoma, along with a high tumor mutational burden. Among patients with mTOR pathway mutations, those lacking molecular diagnostic features of GBM exhibited outstanding survival outcomes, even in the presence of grade 4 histology. Integration of molecular features enhanced the diagnostic accuracy of IDH-wildtype gliomas. Some molecular alterations enriched in GBM offer valuable insights for molecular diagnosis and glioma classification. Furthermore, high-grade diffuse astrocytic gliomas featuring mTOR pathway mutations in the absence of molecular diagnostic features of GBM could represent more favorable tumor types distinct from GBM.
Collapse
Affiliation(s)
- Boram Lee
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Soohyun Hwang
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Hyunsik Bae
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- Pathology center, Seegene Medical Foundation, Seoul 04805, Republic of Korea
| | - Kyue-Hee Choi
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Yeon-Lim Suh
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| |
Collapse
|
36
|
Song L, Rauf F, Hou CW, Qiu J, Murugan V, Chung Y, Lai H, Adam D, Magee DM, Trivino Soto G, Peterson M, Anderson KS, Rice SG, Readhead B, Park JG, LaBaer J. Quantitative assessment of multiple pathogen exposure and immune dynamics at scale. Microbiol Spectr 2024; 12:e0239923. [PMID: 38063388 PMCID: PMC10783028 DOI: 10.1128/spectrum.02399-23] [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: 06/07/2023] [Accepted: 11/13/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE Serology reveals exposure to pathogens, as well as the state of autoimmune and other clinical conditions. It is used to evaluate individuals and their histories and as a public health tool to track epidemics. Employing a variety of formats, studies nearly always perform serology by testing response to only one or a few antigens. However, clinical outcomes of new infections also depend on which previous infections may have occurred. We developed a high-throughput serology method that evaluates responses to hundreds of antigens simultaneously. It can be used to evaluate thousands of samples at a time and provide a quantitative readout. This tool will enable doctors to monitor which pathogens an individual has been exposed to and how that changes in the future. Moreover, public health officials could track populations and look for infectious trends among large populations. Testing many potential antigens at a time may also aid in vaccine development.
Collapse
Affiliation(s)
- Lusheng Song
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Femina Rauf
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Ching-Wen Hou
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Ji Qiu
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Vel Murugan
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Yunro Chung
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
- College of Health Solutions, Arizona State University, Tempe, Arizona, USA
| | - Huafang Lai
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Deborah Adam
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - D. Mitchell Magee
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Guillermo Trivino Soto
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Milene Peterson
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Karen S. Anderson
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Stephen G. Rice
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Benjamin Readhead
- Arizona State University-Banner Neurodegenerative Disease Research Center, Tempe, Arizona, USA
| | - Jin G. Park
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Joshua LaBaer
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA
| |
Collapse
|
37
|
Miller K, Choudry J, Mahmoud ES, Lodh N. Accurate Diagnosis of Schistosoma mansoni and S. haematobium from Filtered Urine Samples Collected in Tanzania, Africa. Pathogens 2024; 13:59. [PMID: 38251366 PMCID: PMC10820911 DOI: 10.3390/pathogens13010059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/04/2024] [Accepted: 01/06/2024] [Indexed: 01/23/2024] Open
Abstract
Schistosomiasis is a bloodborne, and waterborne parasitic disease caused by the human Schistosoma species, namely Schistosoma mansoni and S. haematobium. The parasite requires an intermediate snail host, where they grow and develop, along with a human host (definitive). Schistosoma egg detection in feces (S. mansoni) and urine (S. haematobium) are the WHO-recommended confirmatory diagnostic tests. The goal of our research was to determine the efficacy of detecting single or dual Schistosome species from filtered human urine samples collected in Tanzania by amplifying species-specific cell-free repeat DNA fragments via polymerase chain reaction (PCR) and gel electrophoresis. In total, 104 filtered human urine samples were evaluated and collected from individuals residing in the village of Kayenze, Tanzania. All samples were detected with 100% accuracy and no cross-amplification was present. For a single infection of S. mansoni, 22 (21%) of the samples were positive, while 15 (14%) of the samples were negative via PCR. Moreover, for a single infection of S. haematobium, 7 (7%) of the samples were positive, while 15 (14%) of the samples were negative. Dual infections were found in a higher percentage, with 60 (58%) of the samples being positive. Thus, we have justified that PCR is more sensitive and specific by amplifying species-specific cell-free repeat DNA fragments from the same urine sample than WHO-recommended methods of processing stool and urine.
Collapse
Affiliation(s)
| | | | | | - Nilanjan Lodh
- Department of Medical Laboratory Science, Marquette University, Milwaukee, WI 53217, USA; (K.M.); (J.C.); (E.S.M.)
| |
Collapse
|
38
|
Ray SK, Mukherjee S. Innovation and Patenting Activities During COVID-19 and Advancement of Biochemical and Molecular Diagnosis in the Post- COVID-19 Era. Recent Pat Biotechnol 2024; 18:210-226. [PMID: 37779409 DOI: 10.2174/0118722083262217230921042127] [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: 05/29/2023] [Revised: 07/13/2023] [Accepted: 07/30/2023] [Indexed: 10/03/2023]
Abstract
The COVID-19 pandemic is to escalate globally and acquire new mutations quickly, so accurate diagnostic technologies play a vital role in controlling and understanding the epidemiology of the disease. A plethora of technologies acquires diagnosis of individuals and informs clinical management of COVID. Some important biochemical parameters for COVID diagnosis are the elevation of liver enzymes, creatinine, and nonspecific inflammatory markers such as C-reactive protein (CRP) and Interleukin 6 (IL-6). The main progression predictors are lymphopenia, elevated D-dimer, and hyperferritinemia, although it is also necessary to consider LDH, CPK, and troponin in the marker panel of diagnosis. Owing to the greater sensitivity and accuracy, molecular technologies such as conventional polymerase chain reaction (PCR), reverse transcription (RT)-PCR, nested PCR, loop-mediated isothermal amplification (LAMP), and xMAP technology have been extensively used for COVID diagnosis for some time now. To make so many diagnostics accessible to general people, many techniques may be exploited, including point of care (POC), also called bedside testing, which is developing as a portable promising tool in pathogen identification. Some other lateral flow assay (LFA)-centered techniques like SHERLOCK, CRISPR-Cas12a (AIOD-CRISPR), and FNCAS9 editor limited uniform detection assay (FELUDA), etc. have shown auspicious results in the rapid detection of pathogens. More recently, low-cost sequencing and advancements in big data management have resulted in a slow but steady rise of next-generation sequencing (NGS)-based approaches for diagnosis that have potential relevance for clinical purposes and may pave the way toward a better future. Due to the COVID-19 pandemic, various institutions provided free, specialized websites and tools to promote research and access to critically needed advanced solutions by alleviating research and analysis of data within a substantial body of scientific and patent literature regarding biochemical and molecular diagnosis published since January 2020. This circumstance is unquestionably unique and difficult for anyone using patent information to find pertinent disclosures at a specific date in a trustworthy manner.
Collapse
Affiliation(s)
- Suman Kumar Ray
- Independent Researcher, Bhopal, Madhya Pradesh-462020, India
| | - Sukhes Mukherjee
- Department of Biochemistry, All India Institute of Medical Sciences, Bhopal, Madhya Pradesh-462020, India
| |
Collapse
|
39
|
Saejung W, Khumtong K, Rapichai W, Ratanabunyong S, Rattanasrisomporn A, Choowongkomon K, Rungsuriyawiboon O, Rattanasrisomporn J. Detection of feline immunodeficiency virus by neutral red-based loop-mediated isothermal amplification assay. Vet World 2024; 17:72-81. [PMID: 38406374 PMCID: PMC10884571 DOI: 10.14202/vetworld.2024.72-81] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 12/13/2023] [Indexed: 02/27/2024] Open
Abstract
Background and Aim Feline immunodeficiency virus (FIV) is a retroviral pathogen globally responsible for immunodeficiency disease in cats. However, the current diagnosis based on antibody detection has limitations and can also produce false-positive results. This study aimed to develop a one-pot loop-mediated isothermal amplification (LAMP) process integrated with neutral red (NR-LAMP) assay for detection of FIV proviral DNA. Materials and Methods We developed a one-pot, gag gene-based NR-LAMP for convenient, rapid, specific, and sensitive colorimetric inspection of FIV proviral DNA. Results The developed NR-LAMP was capable of amplifying at an optimum temperature of 65°C for 40 min. No cross-amplification was detected between FIV and other feline viruses tested, indicating the high specificity (98.44%) of the novel FIV-LAMP primer. Our NR-LAMP assay has a detection limit of 4.2 × 101 copies/μL. A total of 80 clinical samples with a background of FIV infection were collected and tested using the proposed method. The NR-LAMP assay showed a high sensitivity of 100% compared to conventional polymerase chain reaction assay. Conclusion These results support the suitability of NR-LAMP as a potential future alternative clinical molecular approach for further use in the diagnosis of FIV-infected cats.
Collapse
Affiliation(s)
- Wichayet Saejung
- Graduate Program in Animal Health and Biomedical Sciences, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand
- Department of Companion Animal Clinical Sciences, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand
| | - Kotchaporn Khumtong
- Graduate Program in Animal Health and Biomedical Sciences, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand
- Department of Companion Animal Clinical Sciences, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand
| | - Witsanu Rapichai
- Department of Companion Animal Clinical Sciences, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Siriluk Ratanabunyong
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Amonpun Rattanasrisomporn
- Interdisciplinary of Genetic Engineering and Bioinformatics, Graduate School, Kasetsart University, Bangkok, Thailand
| | | | - Oumaporn Rungsuriyawiboon
- Department of Veterinary Technology, Faculty of Veterinary Technology, Kasetsart University, Bangkok, Thailand
| | - Jatuporn Rattanasrisomporn
- Graduate Program in Animal Health and Biomedical Sciences, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand
- Department of Companion Animal Clinical Sciences, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, Thailand
| |
Collapse
|
40
|
Casa MDS, Vettori JDM, De Souza KM, Todeschini PRB, Miletti LC, Vogel CIG, Lima ALF, Fonteque JH. Prevalence and risk factors associated with Babesia bovis infection in Crioula Lageana cattle. J Infect Dev Ctries 2023; 17:1821-1828. [PMID: 38252736 DOI: 10.3855/jidc.18052] [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: 02/08/2023] [Accepted: 06/27/2023] [Indexed: 01/24/2024] Open
Abstract
INTRODUCTION Bovine babesiosis caused by the protozoan Babesia bovis is a worldwide disease and causes great economic damage to livestock. There are no studies on the epidemiology of this disease in native breeds such as Crioula Lageana cattle raised in the South of Brazil. METHODOLOGY DNA samples from 311 animals were amplified by polymerase chain reaction (PCR) for the identification of the gene rap-1 (Rhoptry Associated Protein 1) from B. bovis. An epidemiological questionnaire was used to determine the risk factors associated with infection. RESULTS The prevalence of B. bovis infection was 72% (224/311). Age and tick infestation affected infection. The factors associated with infection were the breeding objective (p = 0.042; CI = 0.746-0.995; OR = 0.861), contact of cattle with other animal species (p = 0.002; CI = 0.517-0.860; OR = 0.484), absence of tick control (p = < 0.001; CI = 0.074-0.480; OR = 0.188) and timing of tick treatment (p = 0.026; CI = 0.673-0.975; OR = 0.810), and these were considered to be factors that can protect against the disease. CONCLUSIONS The Crioula Lageana cattle breed has near enzootic stability with regards to B. bovis infection.
Collapse
Affiliation(s)
- Mariana da Silva Casa
- Postgraduate Program in Animal Science, Santa Catarina State University, Lages, SC, Brazil
| | | | - Ketriane Mota De Souza
- Postgraduate Program in Biochemistry and Molecular Biology, Santa Catarina State University, Lages, SC, Brazil
| | | | - Luiz Claudio Miletti
- Postgraduate Program in Biochemistry and Molecular Biology, Santa Catarina State University, Lages, SC, Brazil
| | - Carla Ivane Ganz Vogel
- Postgraduate Program in Biochemistry and Molecular Biology, Santa Catarina State University, Lages, SC, Brazil
| | - André Luiz Ferreira Lima
- Department of Animal Husbandry and Rural Development, Santa Catarina Federal University, Florianópolis, SC, Brazil
| | | |
Collapse
|
41
|
Charoenwisedsil R, Asawapaithulsert P, Pisutsan P, Chotivanich K, Matsee W. Challenges of Plasmodium vivax and Plasmodium knowlesi co-infection. J Travel Med 2023; 30:taad120. [PMID: 37694850 DOI: 10.1093/jtm/taad120] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/05/2023] [Accepted: 09/06/2023] [Indexed: 09/12/2023]
Abstract
A Burmese man was diagnosed with severe Plasmodium vivax (P. vivax) malaria infection admitted to a hospital in Thailand. Interestingly, following RT-PCR analysis, infections with both P. vivax and Plasmodium knowlesi were identified, potentially contributing to severe manifestation. Co-infection risk, especially in severe P. vivax cases, warrants vigilant consideration.
Collapse
Affiliation(s)
- Rachata Charoenwisedsil
- Thai Travel Clinic, Hospital for Tropical Diseases, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Punyisa Asawapaithulsert
- Thai Travel Clinic, Hospital for Tropical Diseases, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Phimphan Pisutsan
- Thai Travel Clinic, Hospital for Tropical Diseases, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Kesinee Chotivanich
- Thai Travel Clinic, Hospital for Tropical Diseases, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Wasin Matsee
- Thai Travel Clinic, Hospital for Tropical Diseases, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| |
Collapse
|
42
|
Kim J, Álvarez-Rodríguez A, Li Z, Radwanska M, Magez S. Recent Progress in the Detection of Surra, a Neglected Disease Caused by Trypanosoma evansi with a One Health Impact in Large Parts of the Tropic and Sub-Tropic World. Microorganisms 2023; 12:44. [PMID: 38257871 PMCID: PMC10819111 DOI: 10.3390/microorganisms12010044] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/17/2023] [Accepted: 12/21/2023] [Indexed: 01/24/2024] Open
Abstract
Surra is a wasting disease triggered by infection with Trypanosoma evansi, a protozoan blood parasite that causes mortality and morbidity in a broad spectrum of wild and domestic animals and occasionally humans. Trypanosoma evansi has the widest geographical spread among all pathogenic trypanosomes, inflicting significant worldwide economic problems due to its adverse effects on meat and milk production. For diagnosis, most endemic countries continue to rely on traditional parasitological and serological techniques, such as the analysis of blood smears by microscopy and the Card Agglutination Test for T. evansi (CATT/T. evansi). Although these techniques suffer from a limited positive predictive value (PPV), resource constraints in endemic countries often hinder the adoption of more advanced diagnostic tools such as PCR. This paper addresses diverse diagnostic approaches for identifying T. evansi and assesses their viability in field settings. Moreover, it underscores the urgency of transitioning towards molecular diagnostic techniques such as Loop-Mediated Isothermal Amplification (LAMP) and Recombinase Polymerase Amplification (RPA) for dependable high-PPV point-of-care (POC) diagnostics. Finally, this review delves into strategies to enhance and refine next-generation diagnostics for Surra as part of a One Health approach.
Collapse
Affiliation(s)
- Jeongmin Kim
- Laboratory for Biomedical Research, Department of Environmental Technology, Food Technology and Molecular Biotechnology KR01, Ghent University Global Campus, Incheon 21985, Republic of Korea; (J.K.); (A.Á.-R.); (M.R.)
| | - Andrés Álvarez-Rodríguez
- Laboratory for Biomedical Research, Department of Environmental Technology, Food Technology and Molecular Biotechnology KR01, Ghent University Global Campus, Incheon 21985, Republic of Korea; (J.K.); (A.Á.-R.); (M.R.)
- Brussels Center for Immunology (BCIM), Department of Bioengineering Sciences (DBIT), Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium;
- Department of Biochemistry and Microbiology WE10, Ghent University, 9000 Ghent, Belgium
| | - Zeng Li
- Brussels Center for Immunology (BCIM), Department of Bioengineering Sciences (DBIT), Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium;
| | - Magdalena Radwanska
- Laboratory for Biomedical Research, Department of Environmental Technology, Food Technology and Molecular Biotechnology KR01, Ghent University Global Campus, Incheon 21985, Republic of Korea; (J.K.); (A.Á.-R.); (M.R.)
- Department of Biomedical Molecular Biology WE14, Ghent University, 9000 Ghent, Belgium
| | - Stefan Magez
- Laboratory for Biomedical Research, Department of Environmental Technology, Food Technology and Molecular Biotechnology KR01, Ghent University Global Campus, Incheon 21985, Republic of Korea; (J.K.); (A.Á.-R.); (M.R.)
- Brussels Center for Immunology (BCIM), Department of Bioengineering Sciences (DBIT), Vrije Universiteit Brussel (VUB), 1050 Brussels, Belgium;
- Department of Biochemistry and Microbiology WE10, Ghent University, 9000 Ghent, Belgium
| |
Collapse
|
43
|
Huang H, Kai Z, Wang Y, Zhang X, Wang J, Zhang W, Xue Q, Zhang H, Jin H, Meng P, Zhang S, Yang Y, Yang H, Liang W, Zha G, Luo P, Xu Y, Shi W, Ruan Z. Evaluating personalized circulating tumor DNA detection for early-stage lung cancer. Cancer Med 2023. [PMID: 38112031 DOI: 10.1002/cam4.6817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/20/2023] [Accepted: 12/03/2023] [Indexed: 12/20/2023] Open
Abstract
Circulating tumor DNA (ctDNA) has been widely used as a minimally invasive biomarker in clinical routine. However, a number of factors such as panel design, sample quality, patients' disease stages are known to influence ctDNA detection sensitivity. In this study, we systematically evaluated common factors associated with the variability of ctDNA detection in plasma and investigated ctDNA abundance in bronchoalveolar lavage (BAL). Whole exome profiling was conducted on 61 tumor tissue samples to identify tumor-specific variants, which were then used to design personalized assay MarRyDa® for ctDNA detection. DNA extracted from BAL fluid and plasma were genotyped using MarRyDa® platform. Our analysis showed that histological subtypes and disease stages had significant differences in ctDNA detection rate. Furthermore, we found that DNA purified from BAL supernatants contains the highest levels of ctDNA compared with BAL precipitates and plasma; therefore, utilizing BAL supernatants for tumor detection might provide additional benefits. Finally, we demonstrated that tumor cellularity played significant roles in the design of personalized ctDNA panel which eventually impacts ctDNA detection sensitivity. We suggest setting a flexible criteria for sample quality control and utilization of BAL might benefit more patients in clinics.
Collapse
Affiliation(s)
- Haihua Huang
- Department of Thoracic Surgery, Shanghai First People's Hospital, Shanghai, China
| | - Zhentian Kai
- Department of research and Development, Zhejiang Shaoxing Topgen Biomedical Technology Co., Ltd., Shanghai, China
| | - Yuchen Wang
- Department of Thoracic Surgery, Shanghai First People's Hospital, Shanghai, China
| | - Xiaomiao Zhang
- Department of Thoracic Surgery, Shanghai First People's Hospital, Shanghai, China
| | - Jin Wang
- Department of Thoracic Surgery, Shanghai First People's Hospital, Shanghai, China
| | - Wei Zhang
- Department of Thoracic Surgery, Shanghai First People's Hospital, Shanghai, China
| | - Qian Xue
- Department of Thoracic Surgery, Shanghai First People's Hospital, Shanghai, China
| | - Hang Zhang
- Department of Thoracic Surgery, Shanghai First People's Hospital, Shanghai, China
| | - Hansong Jin
- Department of Thoracic Surgery, Shanghai First People's Hospital, Shanghai, China
| | - Peize Meng
- Department of Thoracic Surgery, Shanghai First People's Hospital, Shanghai, China
| | - Shuilong Zhang
- Department of research and Development, Zhejiang Shaoxing Topgen Biomedical Technology Co., Ltd., Shanghai, China
| | - Yueyue Yang
- Department of research and Development, Zhejiang Shaoxing Topgen Biomedical Technology Co., Ltd., Shanghai, China
| | - Honghua Yang
- Department of research and Development, Zhejiang Shaoxing Topgen Biomedical Technology Co., Ltd., Shanghai, China
| | - Wanning Liang
- Department of research and Development, Zhejiang Shaoxing Topgen Biomedical Technology Co., Ltd., Shanghai, China
| | - Guangbing Zha
- Department of research and Development, Zhejiang Shaoxing Topgen Biomedical Technology Co., Ltd., Shanghai, China
| | - Peng Luo
- Department of research and Development, Zhejiang Shaoxing Topgen Biomedical Technology Co., Ltd., Shanghai, China
| | - Yan Xu
- Department of research and Development, Zhejiang Shaoxing Topgen Biomedical Technology Co., Ltd., Shanghai, China
| | - Weiwei Shi
- Department of research and Development, Zhejiang Shaoxing Topgen Biomedical Technology Co., Ltd., Shanghai, China
| | - Zheng Ruan
- Department of Thoracic Surgery, Shanghai First People's Hospital, Shanghai, China
| |
Collapse
|
44
|
Trecourt A, Donzel M, Alsadoun N, Allias F, Devouassoux-Shisheboran M. Relevance of Molecular Pathology for the Diagnosis of Sex Cord-Stromal Tumors of the Ovary: A Narrative Review. Cancers (Basel) 2023; 15:5864. [PMID: 38136408 PMCID: PMC10741682 DOI: 10.3390/cancers15245864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
Ovarian sex cord-stromal tumors (SCSTs) account for 8% of all primary ovarian neo-plasms. Accurate diagnosis is crucial since each subtype has a specific prognostic and treatment. Apart from fibrosarcomas, stromal tumors are benign while sex cord tumors may recur, sometimes with a significant time to relapse. Although the diagnosis based on morphology is straightforward, in some cases the distinction between stromal tumors and sex cord tumors may be tricky. Indeed, the immunophenotype is usually nonspecific between stromal tumors and sex cord tumors. Therefore, molecular pathology plays an important role in the diagnosis of such entities, with pathognomonic or recurrent alterations, such as FOXL2 variants in adult granulosa cell tumors. In addition, these neoplasms may be associated with genetic syndromes, such as Peutz-Jeghers syndrome for sex cord tumors with annular tubules, and DICER1 syndrome for Sertoli-Leydig cell tumors (SLCTs), for which the pathologist may be in the front line of syndromic suspicion. Molecular pathology of SCST is also relevant for patient prognosis and management. For instance, the DICER1 variant is associated with moderately to poorly differentiated SLCTS and a poorer prognosis. The present review summarizes the histomolecular criteria useful for the diagnosis of SCST, using recent molecular data from the literature.
Collapse
Affiliation(s)
- Alexis Trecourt
- Service de Pathologie Multi-Site—Site Sud, Centre Hospitalier Lyon Sud, Hospices Civils de Lyon, 69310 Lyon, France; (A.T.); (M.D.); (N.A.); (F.A.)
- UR 3738, Centre pour l’Innovation en Cancérologie de Lyon (CICLY), Université Claude Bernard Lyon 1, 69921 Lyon, France
| | - Marie Donzel
- Service de Pathologie Multi-Site—Site Sud, Centre Hospitalier Lyon Sud, Hospices Civils de Lyon, 69310 Lyon, France; (A.T.); (M.D.); (N.A.); (F.A.)
| | - Nadjla Alsadoun
- Service de Pathologie Multi-Site—Site Sud, Centre Hospitalier Lyon Sud, Hospices Civils de Lyon, 69310 Lyon, France; (A.T.); (M.D.); (N.A.); (F.A.)
| | - Fabienne Allias
- Service de Pathologie Multi-Site—Site Sud, Centre Hospitalier Lyon Sud, Hospices Civils de Lyon, 69310 Lyon, France; (A.T.); (M.D.); (N.A.); (F.A.)
| | - Mojgan Devouassoux-Shisheboran
- Service de Pathologie Multi-Site—Site Sud, Centre Hospitalier Lyon Sud, Hospices Civils de Lyon, 69310 Lyon, France; (A.T.); (M.D.); (N.A.); (F.A.)
- UR 3738, Centre pour l’Innovation en Cancérologie de Lyon (CICLY), Université Claude Bernard Lyon 1, 69921 Lyon, France
| |
Collapse
|
45
|
Gupta P, Arvinden VR, Thakur P, Bhoyar RC, Saravanakumar V, Gottumukkala NV, Goswami SG, Nafiz M, Iyer AR, Vignesh H, Soni R, Bhargava N, Gunda P, Jain S, Gupta V, Sivasubbu S, Scaria V, Ramalingam S. Scalable noninvasive amplicon-based precision sequencing (SNAPseq) for genetic diagnosis and screening of β-thalassemia and sickle cell disease using a next-generation sequencing platform. Front Mol Biosci 2023; 10:1244244. [PMID: 38152111 PMCID: PMC10751313 DOI: 10.3389/fmolb.2023.1244244] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 11/16/2023] [Indexed: 12/29/2023] Open
Abstract
β-hemoglobinopathies such as β-thalassemia (BT) and Sickle cell disease (SCD) are inherited monogenic blood disorders with significant global burden. Hence, early and affordable diagnosis can alleviate morbidity and reduce mortality given the lack of effective cure. Currently, Sanger sequencing is considered to be the gold standard genetic test for BT and SCD, but it has a very low throughput requiring multiple amplicons and more sequencing reactions to cover the entire HBB gene. To address this, we have demonstrated an extraction-free single amplicon-based approach for screening the entire β-globin gene with clinical samples using Scalable noninvasive amplicon-based precision sequencing (SNAPseq) assay catalyzing with next-generation sequencing (NGS). We optimized the assay using noninvasive buccal swab samples and simple finger prick blood for direct amplification with crude lysates. SNAPseq demonstrates high sensitivity and specificity, having a 100% agreement with Sanger sequencing. Furthermore, to facilitate seamless reporting, we have created a much simpler automated pipeline with comprehensive resources for pathogenic mutations in BT and SCD through data integration after systematic classification of variants according to ACMG and AMP guidelines. To the best of our knowledge, this is the first report of the NGS-based high throughput SNAPseq approach for the detection of both BT and SCD in a single assay with high sensitivity in an automated pipeline.
Collapse
Affiliation(s)
- Pragya Gupta
- CSIR- Institute for Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - V. R. Arvinden
- CSIR- Institute for Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Priya Thakur
- CSIR- Institute for Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Rahul C. Bhoyar
- CSIR- Institute for Genomics and Integrative Biology, New Delhi, India
| | | | | | - Sangam Giri Goswami
- CSIR- Institute for Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Mehwish Nafiz
- CSIR- Institute for Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Aditya Ramdas Iyer
- CSIR- Institute for Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Harie Vignesh
- CSIR- Institute for Genomics and Integrative Biology, New Delhi, India
| | - Rajat Soni
- CSIR- Institute for Genomics and Integrative Biology, New Delhi, India
| | - Nupur Bhargava
- CSIR- Institute for Genomics and Integrative Biology, New Delhi, India
| | - Padma Gunda
- Thalassemia and Sickle Cell Society, Hyderabad, India
| | - Suman Jain
- Thalassemia and Sickle Cell Society, Hyderabad, India
| | - Vivek Gupta
- Government Institute of Medical Sciences (GIMS), Greater Noida, India
| | - Sridhar Sivasubbu
- CSIR- Institute for Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Vinod Scaria
- CSIR- Institute for Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Sivaprakash Ramalingam
- CSIR- Institute for Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| |
Collapse
|
46
|
Li M, Jin X, Jiang Q, Wei H, Deng A, Mao Z, Wang Y, Zeng Z, Wu Y, Liu S, Kim J, Wang X, Liu Y, Liu J, Lv W, Huang L, Liao Q, Huang G, Zhang L. Loop-Mediated Isothermal Amplification (LAMP): Potential Point-of-Care Testing for Vulvovaginal Candidiasis. J Fungi (Basel) 2023; 9:1159. [PMID: 38132760 PMCID: PMC10744362 DOI: 10.3390/jof9121159] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/24/2023] [Accepted: 11/28/2023] [Indexed: 12/23/2023] Open
Abstract
PURPOSE The aim of this study is to establish a loop-mediated isothermal amplification (LAMP) method for the rapid detection of vulvovaginal candidiasis (VVC). METHODS We developed and validated a loop-mediated isothermal amplification (LAMP) method for detecting the most common Candida species associated with VVC, including C. albicans, N. glabratus, C. tropicalis, and C. parapsilosis. We evaluated the specificity, sensitivity, positive predictive value (PPV), negative predictive value (NPV), and Kappa value of the LAMP method to detect different Candida species, using the conventional culture method and internal transcribed spacer (ITS) sequencing as gold standards and smear Gram staining and real-time Rolymerase Chain Reaction (PCR) as controls. RESULTS A total of 202 cases were enrolled, of which 88 were VVC-positive and 114 were negative. Among the 88 positive patients, the fungal culture and ITS sequencing results showed that 67 cases (76.14%) were associated with C. albicans, 13 (14.77%) with N. glabratus, 5 (5.68%) with C. tropicalis, and 3 (3.41%) with other species. Regarding the overall detection rate, the LAMP method presented sensitivity, specificity, PPV, NPV, and Kappa values of 90.91%, 100%, 100%, 93.4%, and 0.919, respectively. Moreover, the LAMP had a specificity of 100% for C. albicans, N. glabratus, and C. tropicalis, with a sensitivity of 94.03%, 100%, and 80%, respectively. Moreover, the microscopy evaluation had the highest sensitivity, while the real-time PCR was less specific for C. albicans than LAMP. In addition, CHROMagar Candida was inferior to LAMP in detecting non-albicans Candida (NAC) species. CONCLUSIONS Based on the cost-effective, rapid, and inexpensive characteristics of LAMP, coupled with the high sensitivity and specificity of our VVC-associated Candida detection method, we provided a possibility for the point-of-care testing (POCT) of VVC, especially in developing countries and some laboratories with limited resources.
Collapse
Affiliation(s)
- Meng Li
- School of Clinical Medicine, Tsinghua University, Beijing 100084, China; (M.L.)
- Department of Obstetrics and Gynecology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing 102218, China
| | - Xiangyu Jin
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China; (X.J.)
| | - Qingyun Jiang
- School of Clinical Medicine, Tsinghua University, Beijing 100084, China; (M.L.)
- Department of Obstetrics and Gynecology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing 102218, China
| | - Hongbo Wei
- Beijing Institute of Spacecraft System Engineering, China Academy of Space Technology, Beijing 100094, China
| | - Anni Deng
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China; (X.J.)
| | - Zeyin Mao
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China; (X.J.)
| | - Ying Wang
- Department of Obstetrics and Gynecology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing 102218, China
| | - Zhen Zeng
- Department of Obstetrics and Gynecology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing 102218, China
| | - Yifan Wu
- School of Clinical Medicine, Tsinghua University, Beijing 100084, China; (M.L.)
- Department of Obstetrics and Gynecology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing 102218, China
| | - Shuai Liu
- School of Clinical Medicine, Tsinghua University, Beijing 100084, China; (M.L.)
- Department of Obstetrics and Gynecology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing 102218, China
| | - Juhyun Kim
- School of Clinical Medicine, Tsinghua University, Beijing 100084, China; (M.L.)
- Department of Obstetrics and Gynecology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing 102218, China
| | - Xiaoqian Wang
- Department of Obstetrics and Gynecology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing 102218, China
| | - Ying Liu
- Department of Obstetrics and Gynecology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing 102218, China
| | - Jun Liu
- Department of Obstetrics and Gynecology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing 102218, China
| | - Wenqi Lv
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China; (X.J.)
| | - Leyang Huang
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China; (X.J.)
| | - Qinping Liao
- Department of Obstetrics and Gynecology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing 102218, China
| | - Guoliang Huang
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China; (X.J.)
| | - Lei Zhang
- Department of Obstetrics and Gynecology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing 102218, China
| |
Collapse
|
47
|
Kim D, Jeon J, Kim M, Jeong J, Heo YM, Lee DG, Yon DK, Han K. Comparison of microbial molecular diagnosis efficiency within unstable template metagenomic DNA samples between qRT-PCR and chip-based digital PCR platforms. Genomics Inform 2023; 21:e52. [PMID: 38224719 PMCID: PMC10788361 DOI: 10.5808/gi.23068] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 10/03/2023] [Accepted: 10/11/2023] [Indexed: 01/17/2024] Open
Abstract
Accurate and efficient microbial diagnosis is crucial for effective molecular diagnostics, especially in the field of human healthcare. The gold standard equipment widely employed for detecting specific microorganisms in molecular diagnosis is quantitative real-time polymerase chain reaction (qRT-PCR). However, its limitations in low metagenomic DNA yield samples necessitate exploring alternative approaches. Digital PCR, by quantifying the number of copies of the target sequence, provides absolute quantification results for the bacterial strain. In this study, we compared the diagnostic efficiency of qRT-PCR and digital PCR in detecting a particular bacterial strain (Staphylococcus aureus), focusing on skin-derived DNA samples. Experimentally, specific primer for S. aureus were designed at transcription elongation factor (greA) gene and the target amplicon were cloned and sequenced to validate efficiency of specificity to the greA gene of S. aureus. To quantify the absolute amount of microorganisms present on the skin, the variable region 5 (V5) of the 16S rRNA gene was used, and primers for S. aureus identification were used to relative their amount in the subject's skin. The findings demonstrate the absolute convenience and efficiency of digital PCR in microbial diagnostics. We suggest that the high sensitivity and precise quantification provided by digital PCR could be a promising tool for detecting specific microorganisms, especially in skin-derived DNA samples with low metagenomic DNA yields, and that further research and implementation is needed to improve medical practice and diagnosis.
Collapse
Affiliation(s)
- Dongwan Kim
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan 31116, Korea
| | - Junhyeon Jeon
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan 31116, Korea
| | - Minseo Kim
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan 31116, Korea
| | - Jinuk Jeong
- Department of Bioconvergence Engineering, Dankook University, Jukjeon 16890, Korea
| | | | - Dong-Geol Lee
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan 31116, Korea
- R&I Center, COSMAX BTI, Seongnam 13486, Korea
| | - Dong Keon Yon
- Center for Digital Health, Medical Science Research Institute, Kyung Hee University Medical Center, Kyung Hee University College of Medicine, Seoul 02447, Korea
- Department of Pediatrics, Kyung Hee University College of Medicine, Seoul 02447, Korea
| | - Kyudong Han
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan 31116, Korea
- Department of Bioconvergence Engineering, Dankook University, Jukjeon 16890, Korea
- HuNbiome Co., Ltd, R&D Center, Seoul 08503, Korea
| |
Collapse
|
48
|
de Nattes T, Kaveri R, Farce F, François A, Guerrot D, Hanoy M, Laurent C, Candon S, Bertrand D. Daratumumab for antibody-mediated rejection: Is it time to target the real culprit? Am J Transplant 2023; 23:1990-1994. [PMID: 37414251 DOI: 10.1016/j.ajt.2023.06.018] [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: 04/06/2023] [Revised: 06/26/2023] [Accepted: 06/28/2023] [Indexed: 07/08/2023]
Abstract
We report the case of a sensitized woman who underwent successful transplantation after a desensitization protocol, with an optically normal 8-day biopsy. At 3 months, she developed active antibody-mediated rejection (AMR) due to preformed donor-specific antibodies. It was decided to treat the patient with daratumumab, an anti-CD38 monoclonal antibody. The mean fluorescence intensity of donor-specific antibodies decreased, pathologic signs of AMR regressed, and kidney function returned to normal. A molecular assessment of biopsies was retrospectively performed. By doing so, regression of the molecular signature of AMR was evidenced between the second and third biopsies. Interestingly, the first biopsy revealed a gene expression profile of AMR, which helped retrospectively classify this biopsy as AMR, illustrating the relevance of molecular phenotyping of biopsy in high-risk situations such as desensitization.
Collapse
Affiliation(s)
- Tristan de Nattes
- Univ Rouen Normandie, INSERM U1234, CHU Rouen, Service de Néphrologie, Rouen, France.
| | - Rangolie Kaveri
- EFS Hauts de France-Normandie, Service d'Histocompatibilité, Rouen, France
| | - Fabienne Farce
- EFS Hauts de France-Normandie, Service d'Histocompatibilité, Rouen, France
| | | | - Dominique Guerrot
- Univ Rouen Normandie, INSERM U1096, CHU Rouen, CIC-CRB 1404, Service de Néphrologie, Rouen, France
| | | | | | - Sophie Candon
- Univ Rouen Normandie, INSERM U1234, CHU Rouen, Service d'Immunologie et de Biothérapies, Rouen, France
| | | |
Collapse
|
49
|
Israr F, Masood Ul Hasan S, Hussain M, Qazi FUR, Hasan A. Investigating In Situ Expression of Neurotrophic Factors and Partner Proteins in Irreversible Pulpitis. J Endod 2023; 49:1668-1675. [PMID: 37660765 DOI: 10.1016/j.joen.2023.08.017] [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: 04/09/2023] [Revised: 07/30/2023] [Accepted: 08/26/2023] [Indexed: 09/05/2023]
Abstract
INTRODUCTION In situ assessments of neurotrophic factors and their associated molecular partners have not been explored to date, particularly in humans. The present investigation aimed to explore the expressional dysregulation of neurotrophic factors (nerve growth factor [NGF], brain derived neurotrophic factor [BDNF], and NT4/5), their receptors (TrkA and TrkB), and their modulators (USP36 and Nedd4-2) directly in irreversibly inflamed human pulp tissues. METHODS Forty samples each of healthy and irreversibly inflamed pulp were extirpated for the study. Immunohistochemical examinations were carried out for the anatomic changes and expression of neurotrophic factors and partner proteins. Expression was digitally quantified using the IHC profiler module of ImageJ and deduced as optical density. Statistical analyses were carried out by GraphPad Prism. RESULTS Decrease in nuclear and vessel diameters was observed in irreversibly inflamed pulp tissues. NGF and BDNF were found to be significantly upregulated in symptomatic irreversible pulpitis (SIP), whereas no significant difference was observed in the expression of TrkA and TrkB. Expression of Nedd4-2, USP36, and TrkA was found positively correlated with the NGF in healthy pulp tissues. However, in SIP, positive correlation was only observed between the expression of USP36 and NGF. Among the ligands, BDNF expression was found positively correlated with NGF in healthy pulp but not with NT4/5. In the case of SIP, no correlation was observed between any neurotrophic factors. CONCLUSIONS Upregulation of NGF, BDNF, USP36 and Nedd4-2 in SIP indicates dysregulation in the molecular events underlying the disease biology and could be exploited as potential markers for the disease diagnosis.
Collapse
Affiliation(s)
- Fatima Israr
- Dr Ishrat ul Ebad Khan Institute of Oral Health Sciences, Dow University of Health Sciences, Karachi, Pakistan; Bioinformatics and Molecular Medicine Research Group, Dow Research Institute of Biotechnology and Biomedical Sciences, Dow College of Biotechnology, Dow University of Health Sciences, Karachi, Pakistan
| | - Syed Masood Ul Hasan
- Dr Ishrat ul Ebad Khan Institute of Oral Health Sciences, Dow University of Health Sciences, Karachi, Pakistan; Bioinformatics and Molecular Medicine Research Group, Dow Research Institute of Biotechnology and Biomedical Sciences, Dow College of Biotechnology, Dow University of Health Sciences, Karachi, Pakistan
| | - Mushtaq Hussain
- Bioinformatics and Molecular Medicine Research Group, Dow Research Institute of Biotechnology and Biomedical Sciences, Dow College of Biotechnology, Dow University of Health Sciences, Karachi, Pakistan.
| | - Fazal Ur Rehman Qazi
- Dr Ishrat ul Ebad Khan Institute of Oral Health Sciences, Dow University of Health Sciences, Karachi, Pakistan
| | - Arshad Hasan
- Dow Dental College, Dow University of Health Sciences, Karachi, Pakistan
| |
Collapse
|
50
|
Deng Y, Ma Z, Su B, Bai G, Pan J, Wang Q, Cai L, Song Y, Shang Y, Ma P, Li J, Zhou Q, Mulati G, Fan D, Li S, Tan Y, Pang Y. Accuracy of the InnowaveDX MTB/RIF test for detection of Mycobacterium tuberculosis and rifampicin resistance: a prospective multicentre study. Emerg Microbes Infect 2023; 12:2151382. [PMID: 36416478 DOI: 10.1080/22221751.2022.2151382] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Early and accurate diagnosis of tuberculosis (TB) is necessary to initiate proper therapy for the benefit of the patients and to prevent disease transmission in the community. In this study, we developed the InnowaveDX MTB/RIF (InnowaveDX) to detect Mycobacterium tuberculosis (MTB) and rifampicin resistance simultaneously. A prospective multicentre study was conducted to evaluate the diagnostic performance of InnowaveDX for the detection MTB in sputum samples as compared with Xpert and culture. The calculated limit of detection (LOD) for InnowaveDX was 9.6 CFU/ml for TB detection and 374.9 CFU/ml for RIF susceptibility. None of the other bacteria tested produced signals that fulfilled the positive TB criteria, demonstrating a species-specificity of InnowaveDX. Then 951 individuals were enrolled at 7 hospitals, of which 607 were definite TB cases with positive culture and/or Xpert results, including 354 smear-positive and 253 smear-negative cases. InnowaveDX sensitivity was 92.7% versus bacteriologically TB standard. Further follow-up revealed that 61 (91.0%) out of 67 false-positive patients with no bacteriological evidence met the criteria of clinically diagnosed TB. Among 125 RIF-resistant TB patients diagnosed by Xpert, 108 cases were correctly identified by InnowaveDX, yielding a sensitivity of 86.4%. Additionally, the proportion of very low bacterial load in the discordant susceptibility group was significantly higher than in the concordant susceptibility group (P = 0.029). To conclude, we have developed a novel molecular diagnostic with promising detection capabilities of TB and RIF susceptibility. In addition, the discordant RIF susceptibility results between InnowaveDX and Xpert are more frequently observed in samples with very low bacterial load.
Collapse
Affiliation(s)
- Yunfeng Deng
- Katharine Hsu International Research Center of Human Infectious Diseases, Shandong Public Health Clinical Center Affiliated to Shandong University, Jinan, People's Republic of China
| | - Zichun Ma
- Department of Bacteriology and Immunology, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing, People's Republic of China
| | - Biyi Su
- Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou, People's Republic of China
| | - Guanghong Bai
- Department of Clinical Laboratory, Shanxi Provincial Tuberculosis Hospital, Xi'an, People's Republic of China
| | - Jianhua Pan
- Department of Clinical Laboratory, Changsha Central Hospital, Changsha, People's Republic of China
| | - Quan Wang
- Department of Clinical Laboratory, The Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, People's Republic of China
| | - Long Cai
- Department of Clinical Laboratory, Hangzhou Red Cross Hospital, Hangzhou, People's Republic of China
| | - Yanhua Song
- Department of Tuberculosis, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing, People's Republic of China
| | - Yuanyuan Shang
- Department of Bacteriology and Immunology, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing, People's Republic of China
| | - Pinyun Ma
- Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou, People's Republic of China
| | - Jing Li
- Department of Clinical Laboratory, Shanxi Provincial Tuberculosis Hospital, Xi'an, People's Republic of China
| | - Qianxuan Zhou
- Department of Clinical Laboratory, Changsha Central Hospital, Changsha, People's Republic of China
| | - Gulibike Mulati
- Department of Clinical Laboratory, The Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, People's Republic of China
| | - Dapeng Fan
- Department of Clinical Laboratory, Hangzhou Red Cross Hospital, Hangzhou, People's Republic of China
| | - Shanshan Li
- Department of Bacteriology and Immunology, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing, People's Republic of China
| | - Yaoju Tan
- Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou, People's Republic of China
| | - Yu Pang
- Department of Bacteriology and Immunology, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing, People's Republic of China
| |
Collapse
|