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Oganyan KA, Musaelyan AA, Lapin SV, Kupenskaya TV, Sveсhkova AA, Belyaev MA, Zakharenko AA, Orlov SV. Molecular markers as predictors of response to perioperative chemotherapy in locally advanced gastric cancer. ADVANCES IN MOLECULAR ONCOLOGY 2023. [DOI: 10.17650/2313-805x-2023-10-1-40-48] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
Abstract
Introduction. Perioperative FLOT chemotherapy has improved prognosis in patients with locally advanced resectable gastric cancer (GC). However, in 80 % of cases, the tumor is resistant to the therapy, resulting in unnecessary toxicity and delayed surgical treatment.Aim. Evaluation of clinico-morphological patterns of microsatellite instability, HER2 gene amplification, changes in gene copy number and their relationship with the response to perioperative FLOT chemotherapy in patients with locally advanced resectable GC.Materials and methods. The retrospective study included 185 patients. All tumor samples were assessed for HER2 and microsatellite instability status. Among all cases there were 45 patients with locally advanced T2–4N1–2 M0 GC, who underwent a total or subtotal gastrectomy with D2 lymphadenectomy and perioperative chemotherapy with FLOT. Microsatellite instability detection was performed using fragment analysis, HER2 gene amplification testing – fluorescent in situ hybridization. Also 19 patients were tested for copy number changes of the FGFR1, FGFR2, KRAS, MET, EGFR, CCND1, MYC genes using Multiplex ligation-dependent probe amplification. The endpoints were progression-free survival and objective response rate.Results. Microsatellite instability was detected in 4.8 % (9/185) of GC cases. Microsatellite instability was associated with advanced age (p = 0.005), low grade of differentiation (p = 0.011), presence of tumor-infiltrating lymphocytes (p = 0.0004), and high preoperative CA 72–4 levels (p = 0.025). Prevalence of HER2 amplification was 7.5 % (14/185). It was associated with low grade of differentiation (p = 0.048) and metastasis in regional lymph nodes (p = 0.037). PFS in patients with HER2-positive (HER2 – human epidermal growth factor receptor 2) GC treated with perioperative FLOT chemotherapy (4/45) was significantly lower than in patients with HER2-negative GC: the median was 156 and 317 days, respectively (hazard ratio 0.49; 95 % confidence interval 0.16–1.47; p = 0.0006). There was no correlation between the presence of the alteration and ORR (p = 1.0). Progression-free survival in GC patients with KRAS amplification (3/19) was significantly lower comparing with patients without it: the median was 98 and 327 days, respectively (hazard ratio 0.29; 95 % confidence interval 0.07–1.19; p <0.0001). There was no association between an increase in KRAS copy number and objective response rate (p = 1.0). For microsatellite instability and other studied markers no statistically significant correlation with progression-free survival and objective response rate was found (p >0.05).Conclusion. The presence of HER2 and KRAS amplification have been shown as promising predictive markers of the treatment failure in patients treated with perioperative FLOT chemotherapy for locally advanced resectable GC.
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Affiliation(s)
- K. A. Oganyan
- Pavlov First Saint Petersburg State Medical University
| | - A. A. Musaelyan
- Pavlov First Saint Petersburg State Medical University; Research Institute of Medical Primatology
| | - S. V. Lapin
- Pavlov First Saint Petersburg State Medical University
| | | | | | - M. A. Belyaev
- Pavlov First Saint Petersburg State Medical University
| | | | - S. V. Orlov
- Pavlov First Saint Petersburg State Medical University; Research Institute of Medical Primatology
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Thakore N, Norville R, Franke M, Calderon R, Lecca L, Villanueva M, Murray MB, Cooney CG, Chandler DP, Holmberg RC. Automated TruTip nucleic acid extraction and purification from raw sputum. PLoS One 2018; 13:e0199869. [PMID: 29975759 PMCID: PMC6033430 DOI: 10.1371/journal.pone.0199869] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 05/30/2018] [Indexed: 12/12/2022] Open
Abstract
Automated nucleic acid extraction from primary (raw) sputum continues to be a significant technical challenge for molecular diagnostics. In this work, we developed a prototype open-architecture, automated nucleic acid workstation that includes a mechanical homogenization and lysis function integrated with heating and TruTip purification; optimized an extraction protocol for raw sputum; and evaluated system performance on primary clinical specimens. Eight samples could be processed within 70 min. The system efficiently homogenized primary sputa and doubled nucleic acid recovery relative to an automated protocol that did not incorporate sample homogenization. Nucleic acid recovery was at least five times higher from raw sputum as compared to that of matched sediments regardless of smear or culture grade, and the automated workstation reproducibly recovered PCR-detectable DNA to at least 80 CFU mL-1 raw sputum. M. tuberculosis DNA was recovered and detected from 122/123 (99.2%) and 124/124 (100%) primary sputum and sediment extracts, respectively. There was no detectable cross-contamination across 53 automated system runs and amplification or fluorescent inhibitors (if present) were not detectable. The open fluidic architecture of the prototype automated workstation yields purified sputum DNA that can be used for any molecular diagnostic test. The ability to transfer TruTip protocols between personalized, on-demand pipetting tools and the fully automated workstation also affords public health agencies an opportunity to standardize sputum nucleic acid sample preparation procedures, reagents, and quality control across multiple levels of the health care system.
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Affiliation(s)
- Nitu Thakore
- Akonni Biosystems, Inc., Frederick, Maryland, United States of America
| | - Ryan Norville
- Akonni Biosystems, Inc., Frederick, Maryland, United States of America
| | - Molly Franke
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | | | - Leonid Lecca
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- Socios En Salud Sucursal Perú, Carabayllo, Lima, Peru
| | | | - Megan B. Murray
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
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3
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Song N, Tan Y, Zhang L, Luo W, Guan Q, Yan MZ, Zuo R, Liu W, Luo FL, Zhang XL. Detection of circulating Mycobacterium tuberculosis-specific DNA by droplet digital PCR for vaccine evaluation in challenged monkeys and TB diagnosis. Emerg Microbes Infect 2018; 7:78. [PMID: 29691363 PMCID: PMC5915492 DOI: 10.1038/s41426-018-0076-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 03/02/2018] [Accepted: 03/05/2018] [Indexed: 12/29/2022]
Abstract
Mycobacterium tuberculosis (M. tb) is emerging as a more serious pathogen due to the increased multidrug-resistant TB and co-infection of human immunodeficiency virus (HIV). The development of an effective and sensitive detection method is urgently needed for bacterial load evaluation in vaccine development, early TB diagnosis, and TB treatment. Droplet digital polymerase chain reaction (ddPCR) is a newly developed sensitive PCR method for the absolute quantification of nucleic acid concentrations. Here, we used ddPCR to quantify the circulating virulent M. tb-specific CFP10 (10-kDa culture filtrate protein, Rv3874) and Rv1768 DNA copy numbers in the blood samples from Bacille Calmette-Guerin (BCG)-vaccinated and/or virulent M. tb H37Rv-challenged rhesus monkeys. We found that ddPCR was more sensitive compared to real-time fluorescence quantitative PCR (qPCR), as the detection limits of CFP10 were 1.2 copies/μl for ddPCR, but 15.8 copies/μl for qPCR. We demonstrated that ddPCR could detect CFP10 and Rv1768 DNA after 3 weeks of infection and at least two weeks earlier than qPCR in M.tb H37Rv-challenged rhesus monkey models. DdPCR could also successfully quantify CFP10 and Rv1768 DNA copy numbers in clinical TB patients’ blood samples (active pulmonary TB, extrapulmonary TB (EPTB), and infant TB). To our knowledge, this study is the first to demonstrate that ddPCR is an effective and sensitive method of measuring the circulating CFP10 and Rv1768 DNA for vaccine development, bacterial load evaluation in vivo, and early TB (including EPTB and infant TB) diagnosis as well.
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Affiliation(s)
- Neng Song
- State Key Laboratory of Virology and Medical Research Institute, Hubei Province Key Laboratory of Allergy and Immunology and Department of Immunology, Wuhan University School of Basic Medical Sciences, Wuhan, 430071, China
| | - Yang Tan
- State Key Laboratory of Virology and Medical Research Institute, Hubei Province Key Laboratory of Allergy and Immunology and Department of Immunology, Wuhan University School of Basic Medical Sciences, Wuhan, 430071, China
| | - Lingyun Zhang
- State Key Laboratory of Virology and Medical Research Institute, Hubei Province Key Laboratory of Allergy and Immunology and Department of Immunology, Wuhan University School of Basic Medical Sciences, Wuhan, 430071, China
| | - Wei Luo
- State Key Laboratory of Virology and Medical Research Institute, Hubei Province Key Laboratory of Allergy and Immunology and Department of Immunology, Wuhan University School of Basic Medical Sciences, Wuhan, 430071, China
| | - Qing Guan
- State Key Laboratory of Virology and Medical Research Institute, Hubei Province Key Laboratory of Allergy and Immunology and Department of Immunology, Wuhan University School of Basic Medical Sciences, Wuhan, 430071, China
| | - Ming-Zhe Yan
- Wuhan Medical Treatment Center, Wuhan, 430071, China
| | - Ruiqi Zuo
- State Key Laboratory of Virology and Medical Research Institute, Hubei Province Key Laboratory of Allergy and Immunology and Department of Immunology, Wuhan University School of Basic Medical Sciences, Wuhan, 430071, China
| | - Weixiang Liu
- State Key Laboratory of Virology and Medical Research Institute, Hubei Province Key Laboratory of Allergy and Immunology and Department of Immunology, Wuhan University School of Basic Medical Sciences, Wuhan, 430071, China
| | - Feng-Ling Luo
- State Key Laboratory of Virology and Medical Research Institute, Hubei Province Key Laboratory of Allergy and Immunology and Department of Immunology, Wuhan University School of Basic Medical Sciences, Wuhan, 430071, China.
| | - Xiao-Lian Zhang
- State Key Laboratory of Virology and Medical Research Institute, Hubei Province Key Laboratory of Allergy and Immunology and Department of Immunology, Wuhan University School of Basic Medical Sciences, Wuhan, 430071, China.
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Mo Y, Cui F, Li D, Dai Y, Li X, Zhang X, Qiu Y, Yin Y, Zhang X, Xu W. Establishment of a rapid and sensitive method based on recombinase polymerase amplification to detect mts90, a new molecular target of Mycobacterium tuberculosis. RSC Adv 2017. [DOI: 10.1039/c7ra09999a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The paper is about rapid screening of tuberculosis for detecting mts90, a new molecular target ofMycobacterium tuberculosis.
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5
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Ferguson TM, Weigel KM, Lakey Becker A, Ontengco D, Narita M, Tolstorukov I, Doebler R, Cangelosi GA, Niemz A. Pilot study of a rapid and minimally instrumented sputum sample preparation method for molecular diagnosis of tuberculosis. Sci Rep 2016; 6:19541. [PMID: 26785769 PMCID: PMC4726292 DOI: 10.1038/srep19541] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 11/16/2015] [Indexed: 11/23/2022] Open
Abstract
Nucleic acid amplification testing (NAAT) enables rapid and sensitive diagnosis of tuberculosis (TB), which facilitates treatment and mitigates transmission. Nucleic acid extraction from sputum constitutes the greatest technical challenge in TB NAAT for near-patient settings. This report presents preliminary data for a semi-automated sample processing method, wherein sputum is disinfected and liquefied, followed by PureLyse® mechanical lysis and solid-phase nucleic acid extraction in a miniaturized, battery-operated bead blender. Sputum liquefaction and disinfection enabled a >104 fold reduction in viable load of cultured Mycobacterium tuberculosis (M.tb) spiked into human sputum, which mitigates biohazard concerns. Sample preparation via the PureLyse® method and a clinically validated manual method enabled positive PCR-based detection for sputum spiked with 104 and 105 colony forming units (cfu)/mL M.tb. At 103 cfu/mL sputum, four of six and two of six samples amplified using the comparator and PureLyse® method, respectively. For clinical specimens from TB cases and controls, the two methods provided 100% concordant results for samples with 1 mL input volume (N = 41). The semi-automated PureLyse® method therefore performed similarly to a validated manual comparator method, but is faster, minimally instrumented, and can be integrated into TB molecular diagnostic platforms designed for near-patient low-resource settings.
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Affiliation(s)
| | - Kris M Weigel
- University of Washington, Department of Environmental and Occupational Health Sciences, Seattle, WA.,Seattle Biomedical Research Institute, Seattle, WA
| | - Annie Lakey Becker
- University of Washington, Department of Environmental and Occupational Health Sciences, Seattle, WA.,Seattle Biomedical Research Institute, Seattle, WA
| | - Delia Ontengco
- Seattle Biomedical Research Institute, Seattle, WA.,University of Santo Tomas Graduate School, Manila, Philippines
| | - Masahiro Narita
- Public Health - Seattle &King County, TB Control Program, Seattle, WA
| | | | | | - Gerard A Cangelosi
- University of Washington, Department of Environmental and Occupational Health Sciences, Seattle, WA.,Seattle Biomedical Research Institute, Seattle, WA
| | - Angelika Niemz
- Keck Graduate Institute of Applied Life Sciences, Claremont, CA
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Rapid detection of Mycobacterium tuberculosis complex by real-time PCR in sputum samples and its use in the routine diagnosis in a reference laboratory. J Med Microbiol 2015; 64:1040-1045. [DOI: 10.1099/jmm.0.000121] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Lyra JMAD, Maruza M, Verza M, Carneiro MM, Albuquerque MDFMD, Rossetti ML, Ximenes R, Braga MC, Lucena-Silva N. Evaluation of four molecular methods for the diagnosis of tuberculosis in pulmonary and blood samples from immunocompromised patients. Mem Inst Oswaldo Cruz 2014; 109:805-13. [PMID: 25317709 PMCID: PMC4238774 DOI: 10.1590/0074-0276130542] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Accepted: 06/20/2014] [Indexed: 11/21/2022] Open
Abstract
The present study analysed the concordance among four different molecular diagnostic
methods for tuberculosis (TB) in pulmonary and blood samples from immunocompromised
patients. A total of 165 blood and 194 sputum samples were collected from 181 human
immunodeficiency virus (HIV)-infected patients with upper respiratory complaints,
regardless of suspicious for TB. The samples were submitted for smear microscopy,
culture and molecular tests: a laboratory-developed conventional polymerase chain
reaction (PCR) and real-time quantitative PCR (qPCR) and the Gen-Probe and Detect-TB
Ampligenix kits. The samples were handled blindly by all the technicians involved,
from sample processing to results analysis. For sputum, the sensitivity and
specificity were 100% and 96.7% for qPCR, 81.8% and 94.5% for Gen-Probe and 100% and
66.3% for Detect-TB, respectively. qPCR presented the best concordance with sputum
culture [kappa (k) = 0.864)], followed by Gen-Probe (k = 0.682). For blood samples,
qPCR showed 100% sensitivity and 92.3% specificity, with a substantial correlation
with sputum culture (k = 0.754) and with the qPCR results obtained from sputum of the
corresponding patient (k = 0.630). Conventional PCR demonstrated the worst results
for sputa and blood, with a sensitivity of 100% vs. 88.9% and a specificity of 46.3%
vs. 32%, respectively. Commercial or laboratory-developed molecular assays can
overcome the difficulties in the diagnosis of TB in paucibacillary patients using
conventional methods available in most laboratories.
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Affiliation(s)
| | - Magda Maruza
- Hospital Correia Picanço, Secretaria do Estado de Pernambuco, Recife, PE, Brasil
| | - Mirela Verza
- Fundação Estadual de Produção e Pesquisa em Saúde, Porto Alegre, RS, Brasil
| | | | | | | | - Ricardo Ximenes
- Departamento de Medicina Tropical, Universidade Federal de Pernambuco, Recife, PE, Brasil
| | - Maria Cynthia Braga
- Departamento de Parasitologia, Centro de Pesquisas Aggeu Magalhães-Fiocruz, Recife, PE, Brasil
| | - Norma Lucena-Silva
- Departamento de Imunologia, Centro de Pesquisas Aggeu Magalhães-Fiocruz, Recife, PE, Brasil
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Medrano BA, Salinas G, Sanchez C, Miramontes R, Restrepo BI, Haddad MB, Lambert LA. A missed tuberculosis diagnosis resulting in hospital transmission. Infect Control Hosp Epidemiol 2014; 35:534-7. [PMID: 24709722 PMCID: PMC5019171 DOI: 10.1086/675833] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
OBJECTIVE To find the source of tuberculin skin test conversions among 38 hospital employees on 1 floor during routine testing January-February 2010. METHODS Record review of patients at a private hospital during September-December 2009 and interviews with hospital employees. Names of patients from the state tuberculosis (TB) registry were cross-referenced with hospital records for admissions. Mycobacterium tuberculosis genotype results in the county and adjacent counties were examined, and contacts were evaluated for TB infection and disease. RESULTS One of the 38 employees, a nurse, was diagnosed with pulmonary TB with a matching M. tuberculosis genotype and drug resistance pattern (isoniazid monoresistant) to those of a county jail inmate also recently diagnosed with pulmonary TB. The nurse had no known contact with that inmate; however, another inmate in his 20's from the same jail had been hospitalized under that nurse's care in October 2009. That young man died, and a postmortem examination result subsequently confirmed TB, which had not been suspected. Exposure to this man with undiagnosed TB could explain the transmission: 87 (27%) of the 318 hospital-based contacts without previous positive tuberculin skin test results were infected, and 9 contacts had active TB. CONCLUSIONS This investigation demonstrated M. tuberculosis transmission in a hospital due to a missed diagnosis and nonadherence to national TB infection control guidelines. Routine TB screening of employees allowed early detection of this missed TB diagnosis, facilitating prompt evaluation of contacts. Healthcare providers should suspect TB in symptomatic persons and adhere to TB control policies.
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PCR to detect Mycobacterium tuberculosis in respiratory tract samples: evaluation of clinical data. Epidemiol Infect 2013; 142:1517-23. [PMID: 24107314 DOI: 10.1017/s0950268813002598] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Tuberculosis (TB) remains as an important public health problem worldwide. Therefore, the rapid detection of M. tuberculosis is of primary importance to effectively reduce transmission in patients. The aims of this study were to evaluate two in-house molecular tests: nested PCR (nPCR) and real-time PCR (rtPCR) to detect M. tuberculosis complex directly from clinical samples. The results were compared to the culture results and to the culture results plus clinical data of patients. The rtPCR and nPCR presented high sensitivity (Se) and specificity (Sp) (rtPCR 97·6% and 91·5%, nPCR 85·7% and 92·7%, respectively) compared to culture. When the results of the molecular tests were compared to the culture plus clinical data the Se and Sp were 90·2% and 97·3% for rtPCR and 80·4% and 98·6% for the nPCR, respectively. The results demonstrated that molecular assays of M. tuberculosis can provide a sensitive and rapid diagnostic of TB, and when used in addition to the clinical data of TB patients will help to improve the Sp of the diagnosis of pulmonary TB.
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Niemz A, Boyle DS. Nucleic acid testing for tuberculosis at the point-of-care in high-burden countries. Expert Rev Mol Diagn 2013; 12:687-701. [PMID: 23153237 DOI: 10.1586/erm.12.71] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Early diagnosis of tuberculosis (TB) facilitates appropriate treatment initiation and can limit the spread of this highly contagious disease. However, commonly used TB diagnostic methods are slow, often insensitive, cumbersome and inaccessible to most patients in TB endemic countries that lack necessary resources. This review discusses nucleic acid amplification technologies, which are being developed for rapid near patient TB diagnosis, that are in the market or undergoing clinical evaluation. They are based on PCR or isothermal methods and are implemented as manual assays or partially/fully integrated instrument systems, with associated tradeoffs between clinical performance, cost, robustness, quality assurance and usability in remote settings by minimally trained personnel. Unmet needs prevail for the identification of drug-resistant TB and for TB diagnosis in HIV-positive and pediatric patients.
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Affiliation(s)
- Angelika Niemz
- Keck Graduate Institute of Applied Life Sciences, 535 Watson Drive, Claremont, CA 91711, USA.
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Validation of Mycobacterium tuberculosis Rv1681 protein as a diagnostic marker of active pulmonary tuberculosis. J Clin Microbiol 2013; 51:1367-73. [PMID: 23390284 DOI: 10.1128/jcm.03192-12] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The development of an accurate antigen detection assay for the diagnosis of active tuberculosis (TB) would represent a major clinical advance. Here, we demonstrate that the Mycobacterium tuberculosis Rv1681 protein is a biomarker for active TB with potential diagnostic utility. We initially identified, by mass spectroscopy, peptides from the Rv1681 protein in urine specimens from 4 patients with untreated active TB. Rabbit IgG anti-recombinant Rv1681 detected Rv1681 protein in lysates and culture filtrates of M. tuberculosis and immunoprecipitated it from pooled urine specimens from two TB patients. An enzyme-linked immunosorbent assay formatted with these antibodies detected Rv1681 protein in unconcentrated urine specimens from 11/25 (44%) TB patients and 1/21 (4.8%) subjects in whom TB was initially clinically suspected but then ruled out by conventional methods. Rv1681 protein was not detected in urine specimens from 10 subjects with Escherichia coli-positive urine cultures, 26 subjects with confirmed non-TB tropical diseases (11 with schistosomiasis, 5 with Chagas' disease, and 10 with cutaneous leishmaniasis), and 14 healthy subjects. These results provide strong validation of Rv1681 protein as a promising biomarker for TB diagnosis.
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Endsley JJ, Actor JK. Texas Tuberculosis Research Symposium 2011: collaborative efforts within the State of Texas toward elimination of TB. Tuberculosis (Edinb) 2011; 91 Suppl 1:S1-2. [PMID: 22192869 DOI: 10.1016/j.tube.2011.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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