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Di Candia D, Giordano G, Boracchi M, Bailo P, Primignani P, Piccinini A, Zoja R. Chemical investigation of biological trace evidence; toxicological screening of waste residues obtained from DNA extraction processes. Int J Legal Med 2024; 138:721-730. [PMID: 37968478 PMCID: PMC11003886 DOI: 10.1007/s00414-023-03119-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 10/30/2023] [Indexed: 11/17/2023]
Abstract
In a forensic scenario, if biological stains are found in very small quantities, these are usually collected for DNA analyses, considered essential for the forensic investigation and thus excluding possible investigations by other forensic disciplines as forensic toxicology. We developed an experimental study to evaluate the feasibility of analyzing DNA extraction residues obtained from DNA extraction procedures to perform toxicological analysis, with the aim to extract both genetic and toxicological information without affecting or compromising the genetic sample and/or DNA extraction. DNA extraction from four blood samples (fortified with 5 molecules of interest with a final concentrations of 1 µg/mL, 100 ng/mL, 10 ng/mL and 5 ng/mL, respectively) were analyzed with QIAGEN QIAmp® DNA Mini kit. Three waste residues collected from the DNA extraction were analyzed for the toxicological investigation via Solid-Phase Extraction and High-Performance Liquid Chromatography-Tandem Mass Spectrometry analyses (Thermo Scientific™ TSQ Fortis™ II Triple-Quadrupole Mass Spectrometer). The analytical investigation revealed that our analytes of interest were detected in two different residues of the DNA extraction procedure, allowing both genetic and toxicological analyses without affecting the DNA identification. At last, the experimental protocol was applied to a hypothetical case, with encouraging results and allowing the identification of our molecules of interest.
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Affiliation(s)
- Domenico Di Candia
- Dipartimento Di Scienze Biomediche Per La Salute, Istituto Di Medicina Legale E Delle Assicurazioni, Università Degli Studi Di Milano, 20133, Milan, Italy
| | - Gaia Giordano
- Dipartimento Di Scienze Biomediche Per La Salute, Istituto Di Medicina Legale E Delle Assicurazioni, Università Degli Studi Di Milano, 20133, Milan, Italy.
| | - Michele Boracchi
- Dipartimento Di Scienze Biomediche Per La Salute, Istituto Di Medicina Legale E Delle Assicurazioni, Università Degli Studi Di Milano, 20133, Milan, Italy
| | - Paolo Bailo
- Dipartimento Di Scienze Biomediche Per La Salute, Istituto Di Medicina Legale E Delle Assicurazioni, Università Degli Studi Di Milano, 20133, Milan, Italy
| | - Paola Primignani
- Dipartimento Di Scienze Biomediche Per La Salute, Istituto Di Medicina Legale E Delle Assicurazioni, Università Degli Studi Di Milano, 20133, Milan, Italy
| | - Andrea Piccinini
- Dipartimento Di Scienze Biomediche Per La Salute, Istituto Di Medicina Legale E Delle Assicurazioni, Università Degli Studi Di Milano, 20133, Milan, Italy
| | - Riccardo Zoja
- Dipartimento Di Scienze Biomediche Per La Salute, Istituto Di Medicina Legale E Delle Assicurazioni, Università Degli Studi Di Milano, 20133, Milan, Italy
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2
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Al-Sheboul SA, Mohammad AAR, Shboul Y, Brown B, Matalka II. A Genetic and Immunohistochemical Analysis of Helicobacter pylori Phenotypes and p27 Expression in Adenocarcinoma Patients in Jordan. J Epidemiol Glob Health 2023; 13:212-225. [PMID: 37071369 PMCID: PMC10272050 DOI: 10.1007/s44197-023-00099-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 04/04/2023] [Indexed: 04/19/2023] Open
Abstract
Stomach (gastric) cancer is one of the most prevalent and deadly cancers worldwide and most gastric cancers are adenocarcinomas. Based on prior research, there is an association between Helicobacter pylori (H. pylori) infection together with the frequency of duodenal ulcer, distal gastric adenocarcinoma, mucosa-associated lymphoid tissue (MALT) lymphoma, and antral gastritis. Helicobacter pylori virulence and toxicity factors have been identified before that significantly influence the clinical outcomes of H. pylori infection and gastric adenocarcinoma. However, it remains unclear exactly how different strains of H. pylori affect gastric adenocarcinoma. Current research suggests this involves tumor suppressor genes, like p27 but also H. pylori toxic virulence proteins. Therefore, we quantified known H. pylori genotypes within adenocarcinoma patients to establish the prevalence of known toxins that include cytotoxin-associated gene A (cagA) as well as vacuolating cytotoxin A (vacA) within patients of variable adenocarcinoma diagnosis. This analysis used gastrectomy samples validated for DNA viability. The incidence of H. pylori in adenocarcinoma patients in Jordan was established to be 54.5% positive (ureA gene positive) with cagA genotype occurrence at 57.1%, but also in this population study vacA gene ratios found to be 24.7%:22.1%:14.3%:14.3%. (vacAs1:vacAs2:vacAm1:vacAm2). Using immunohistochemistry (IHC), we confirmed with statistical significance that p27 was dysregulated and suppressed, within nearly all H. pylori vacA genotypes. In addition, within 24.6% of H. pylori samples analyzed was a different bacterial genotype, and curiously that p27 protein expression was retained in 12% of tested adenocarcinoma H. pylori samples. This is suggestive that p27 could be used as a prognostic indicator but also that an unknown genotype could be contributing to the regulatory effects of p27 protein within this bacterial and cellular environment that may include other virulence factors and unknown immune system regulatory changes.
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Affiliation(s)
- Suhaila A. Al-Sheboul
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, Jordan University of Science and Technology (JUST), Irbid, 22110 Jordan
| | - Ahmad Abdul-Razzak Mohammad
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, Jordan University of Science and Technology (JUST), Irbid, 22110 Jordan
| | - Yasemin Shboul
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, Jordan University of Science and Technology (JUST), Irbid, 22110 Jordan
| | | | - Ismail I. Matalka
- Department of Pathology and Microbiology, Faculty of Medicine, Jordan University of Science and Technology (JUST), Irbid, 22110 Jordan
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3
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Intarawichian P, Sangpaibool S, Prajumwongs P, Sa-Ngiamwibool P, Sangkhamanon S, Kunprom W, Thanee M, Loilome W, Khuntikeo N, Titapun A, Jareanrat A, Thanasukarn V, Srisuk T, Luvira V, Eurboonyanun K, Promsorn J, Koonmee S, Wee A, Aphivatanasiri C. Prognostic significance of tumor-infiltrating lymphocytes in predicting outcome of distal cholangiocarcinoma in Thailand. Front Oncol 2022; 12:1004220. [PMID: 36582790 PMCID: PMC9792867 DOI: 10.3389/fonc.2022.1004220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 10/28/2022] [Indexed: 12/15/2022] Open
Abstract
Patients with distal cholangiocarcinoma (dCCA) generally have poor outcomes because of late presentation and diagnosis. Therefore, prognostic factors for predicting outcomes are essential to improve therapeutic strategies and quality of life. Tumor-infiltrating lymphocytes (TILs) have been reported as a prognostic predictor in several cancers. However, their role in dCCA is still unclear. This study aimed to evaluate the association of TILs with outcome in patients with dCCA. Fifty-two patients were evaluated for the percentage rate of TILs in their cancers, and a median TIL level was used to divide the patients into two groups. Survival, multivariate, and correlation analyses were performed to determine the prognostic factors. Results showed that a low TIL level was associated with poor survival. Multivariate analysis revealed TILs as an independent factor for poor outcome. Moreover, TILs were markedly correlated with growth patterns, and both were applied to classify patients with dCCA. Subgroups of TILs with growth pattern incorporation improved stratification performance in separating good from poor patient outcomes. This study suggested that TILs could be a prognostic factor for predicting survival and for clustering patients with dCCA to improve prognostication capability. This finding may be incorporated into a new staging system for stratifying dCCA in Thailand.
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Affiliation(s)
- Piyapharom Intarawichian
- Cholangiocarcinoma Screening and Care Program (CASCAP), Khon Kaen University, Khon Kaen, Thailand,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand,Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Sirada Sangpaibool
- Cholangiocarcinoma Screening and Care Program (CASCAP), Khon Kaen University, Khon Kaen, Thailand,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand,Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Piya Prajumwongs
- Cholangiocarcinoma Screening and Care Program (CASCAP), Khon Kaen University, Khon Kaen, Thailand,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand,Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Prakasit Sa-Ngiamwibool
- Cholangiocarcinoma Screening and Care Program (CASCAP), Khon Kaen University, Khon Kaen, Thailand,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand,Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Sakkarn Sangkhamanon
- Cholangiocarcinoma Screening and Care Program (CASCAP), Khon Kaen University, Khon Kaen, Thailand,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand,Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Waritta Kunprom
- Cholangiocarcinoma Screening and Care Program (CASCAP), Khon Kaen University, Khon Kaen, Thailand,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand,Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Malinee Thanee
- Cholangiocarcinoma Screening and Care Program (CASCAP), Khon Kaen University, Khon Kaen, Thailand,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand,Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Watcharin Loilome
- Cholangiocarcinoma Screening and Care Program (CASCAP), Khon Kaen University, Khon Kaen, Thailand,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand,Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Narong Khuntikeo
- Cholangiocarcinoma Screening and Care Program (CASCAP), Khon Kaen University, Khon Kaen, Thailand,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand,Department of Surgery, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Attapol Titapun
- Cholangiocarcinoma Screening and Care Program (CASCAP), Khon Kaen University, Khon Kaen, Thailand,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand,Department of Surgery, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Apiwat Jareanrat
- Cholangiocarcinoma Screening and Care Program (CASCAP), Khon Kaen University, Khon Kaen, Thailand,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand,Department of Surgery, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Vasin Thanasukarn
- Cholangiocarcinoma Screening and Care Program (CASCAP), Khon Kaen University, Khon Kaen, Thailand,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand,Department of Surgery, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Tharatip Srisuk
- Cholangiocarcinoma Screening and Care Program (CASCAP), Khon Kaen University, Khon Kaen, Thailand,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand,Department of Surgery, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Vor Luvira
- Cholangiocarcinoma Screening and Care Program (CASCAP), Khon Kaen University, Khon Kaen, Thailand,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand,Department of Surgery, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Kulyada Eurboonyanun
- Cholangiocarcinoma Screening and Care Program (CASCAP), Khon Kaen University, Khon Kaen, Thailand,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand,Department of Radiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Julaluck Promsorn
- Cholangiocarcinoma Screening and Care Program (CASCAP), Khon Kaen University, Khon Kaen, Thailand,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand,Department of Radiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Supinda Koonmee
- Cholangiocarcinoma Screening and Care Program (CASCAP), Khon Kaen University, Khon Kaen, Thailand,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand,Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Aileen Wee
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, National University Hospital, Singapore, Singapore
| | - Chaiwat Aphivatanasiri
- Cholangiocarcinoma Screening and Care Program (CASCAP), Khon Kaen University, Khon Kaen, Thailand,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand,Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand,*Correspondence: Chaiwat Aphivatanasiri,
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4
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Sa-Ngiamwibool P, Aphivatanasiri C, Sangkhamanon S, Intarawichian P, Kunprom W, Thanee M, Prajumwongs P, Loilome W, Khuntikeo N, Titapun A, Jareanrat A, Thanasukarn V, Srisuk T, Luvira V, Eurboonyanun K, Promsorn J, Wee A, Koonmee S. Modification of the AJCC/UICC 8th edition staging system for intrahepatic cholangiocarcinoma: proposal for an alternative staging system from cholangiocarcinoma-prevalent Northeast Thailand. HPB (Oxford) 2022; 24:1944-1956. [PMID: 35810105 DOI: 10.1016/j.hpb.2022.06.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 04/18/2022] [Accepted: 06/13/2022] [Indexed: 12/12/2022]
Abstract
BACKGROUND Intrahepatic cholangiocarcinoma (iCCA) arises from bile ducts within the liver. Thailand has the highest incidence of CCA worldwide, with a high mortality rate. Early diagnosis and accurate prognostic stratification can improve overall survival. We aim to modify the AJCC/UICC 8th edition staging system for iCCA by creating the Khon Kaen University (KKU) staging system for more precise patient stratification and prognostic prediction. METHODS A total of 298 iCCA patients who underwent hepatectomy were included in this retrospective study at the Srinagarind Hospital, Khon Kaen University, Thailand. Univariate and multivariate analysis were performed to examine survival rate, hazard ratio, and prognostic factors. RESULTS Univariate and multivariate analysis of the cohort showed that growth patterns, histological type, histological grade, lymph node metastasis and distant metastasis were independent prognostic factors when compared to the respective reference groups. The 8th AJCC staging system incorporated growth patterns into the KKU staging system. This model modified AJCC stages I, II, and III for better prediction of patient survival. CONCLUSION Growth patterns were incorporated to improve the 8th AJCC staging system for prognostication of iCCA patients in Northeast Thailand. We propose the KKU staging system as an alternative model for iCCA staging to augment the accuracy of survival prognostication.
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Affiliation(s)
- Prakasit Sa-Ngiamwibool
- Cholangiocarcinoma Screening and Care Program (CASCAP), Khon Kaen University, Khon Kaen, Thailand; Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand; Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Chaiwat Aphivatanasiri
- Cholangiocarcinoma Screening and Care Program (CASCAP), Khon Kaen University, Khon Kaen, Thailand; Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand; Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Sakkarn Sangkhamanon
- Cholangiocarcinoma Screening and Care Program (CASCAP), Khon Kaen University, Khon Kaen, Thailand; Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand; Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Piyapharom Intarawichian
- Cholangiocarcinoma Screening and Care Program (CASCAP), Khon Kaen University, Khon Kaen, Thailand; Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand; Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Waritta Kunprom
- Cholangiocarcinoma Screening and Care Program (CASCAP), Khon Kaen University, Khon Kaen, Thailand; Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand; Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Malinee Thanee
- Cholangiocarcinoma Screening and Care Program (CASCAP), Khon Kaen University, Khon Kaen, Thailand; Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand; Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Piya Prajumwongs
- Cholangiocarcinoma Screening and Care Program (CASCAP), Khon Kaen University, Khon Kaen, Thailand; Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand; Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Watcharin Loilome
- Cholangiocarcinoma Screening and Care Program (CASCAP), Khon Kaen University, Khon Kaen, Thailand; Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand; Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Narong Khuntikeo
- Cholangiocarcinoma Screening and Care Program (CASCAP), Khon Kaen University, Khon Kaen, Thailand; Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand; Department of Surgery, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Attapol Titapun
- Cholangiocarcinoma Screening and Care Program (CASCAP), Khon Kaen University, Khon Kaen, Thailand; Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand; Department of Surgery, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Apiwat Jareanrat
- Cholangiocarcinoma Screening and Care Program (CASCAP), Khon Kaen University, Khon Kaen, Thailand; Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand; Department of Surgery, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Vasin Thanasukarn
- Cholangiocarcinoma Screening and Care Program (CASCAP), Khon Kaen University, Khon Kaen, Thailand; Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand; Department of Surgery, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Tharatip Srisuk
- Cholangiocarcinoma Screening and Care Program (CASCAP), Khon Kaen University, Khon Kaen, Thailand; Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand; Department of Surgery, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Vor Luvira
- Cholangiocarcinoma Screening and Care Program (CASCAP), Khon Kaen University, Khon Kaen, Thailand; Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand; Department of Surgery, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Kulyada Eurboonyanun
- Cholangiocarcinoma Screening and Care Program (CASCAP), Khon Kaen University, Khon Kaen, Thailand; Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand; Department of Radiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Julaluck Promsorn
- Cholangiocarcinoma Screening and Care Program (CASCAP), Khon Kaen University, Khon Kaen, Thailand; Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand; Department of Radiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Aileen Wee
- Department of Pathology, National University Hospital, Singapore
| | - Supinda Koonmee
- Cholangiocarcinoma Screening and Care Program (CASCAP), Khon Kaen University, Khon Kaen, Thailand; Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand; Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.
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5
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Kunprom W, Aphivatanasiri C, Sa-Ngiamwibool P, Sangkhamanon S, Intarawichian P, Bamrungkit W, Thanee M, Prajumwongs P, Loilome W, Khuntikeo N, Titapun A, Jareanrat A, Thanasukarn V, Srisuk T, Luvira V, Eurboonyanun K, Promsorn J, Koonmee S. Prognostic Significance of Growth Pattern in Predicting Outcome of Opisthorchis viverrini-Associated Distal Cholangiocarcinoma in Thailand. Front Public Health 2022; 10:816028. [PMID: 35651852 PMCID: PMC9149579 DOI: 10.3389/fpubh.2022.816028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 04/26/2022] [Indexed: 11/23/2022] Open
Abstract
Distal cholangiocarcinoma (dCCA) is a rare type of CCA in Asia, even in Opisthorchis viverrini-prevalent Northeastern Thailand. The clinical ambiguity and imprecision of diagnosis surrounding this malignancy result in high mortality due often to advanced/metastatic disease on presentation. We aim to identify a prognostic factor that can improve the performance stratification and influence the outcome of dCCA patients after curative resection. A total of 79 patients who underwent curative-intended surgery for dCCA was enrolled. Possible risk factors for survival were analyzed with log-rank test, and independent factors with Cox regression model. dCCA patients were staged and classified according to the 8th edition the American Joint Committee on Cancer (AJCC) Staging Manual. Results were then compared with the revised classification employing the prognostic factor identified from multivariate analysis. Multivariate analysis revealed that growth pattern (p < 0.01) and distant metastasis (p = 0.012) were independent factors. Growth patterns comprise intraductal (ID), periductal infiltrating (PI), mass-forming (MF), and mixed types. When dCCA patients were grouped into those having good and poor outcomes (with and without ID components, respectively). The survival outcomes significantly differed among patients with and without ID components, which was better than with the 8th AJCC staging system in our cohort. Furthermore, Chi-square test showed that patterns without ID components (PI, MF, PI + MF) correlated with lymph node and distant metastasis. Therefore, classification of dCCA patients after curative-intended surgical resection based on growth pattern provides additional beneficial information for the prediction of survival in dCCA patients.
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Affiliation(s)
- Waritta Kunprom
- Cholangiocarcinoma Screening and Care Program (CASCAP), Khon Kaen University, Khon Kaen, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand.,Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Chaiwat Aphivatanasiri
- Cholangiocarcinoma Screening and Care Program (CASCAP), Khon Kaen University, Khon Kaen, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand.,Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Prakasit Sa-Ngiamwibool
- Cholangiocarcinoma Screening and Care Program (CASCAP), Khon Kaen University, Khon Kaen, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand.,Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Sakkarn Sangkhamanon
- Cholangiocarcinoma Screening and Care Program (CASCAP), Khon Kaen University, Khon Kaen, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand.,Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Piyapharom Intarawichian
- Cholangiocarcinoma Screening and Care Program (CASCAP), Khon Kaen University, Khon Kaen, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand.,Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Walailak Bamrungkit
- Cholangiocarcinoma Screening and Care Program (CASCAP), Khon Kaen University, Khon Kaen, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand.,Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Malinee Thanee
- Cholangiocarcinoma Screening and Care Program (CASCAP), Khon Kaen University, Khon Kaen, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand.,Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Piya Prajumwongs
- Cholangiocarcinoma Screening and Care Program (CASCAP), Khon Kaen University, Khon Kaen, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand.,Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Watcharin Loilome
- Cholangiocarcinoma Screening and Care Program (CASCAP), Khon Kaen University, Khon Kaen, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand.,Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Narong Khuntikeo
- Cholangiocarcinoma Screening and Care Program (CASCAP), Khon Kaen University, Khon Kaen, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand.,Department of Surgery, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Attapol Titapun
- Cholangiocarcinoma Screening and Care Program (CASCAP), Khon Kaen University, Khon Kaen, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand.,Department of Surgery, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Apiwat Jareanrat
- Cholangiocarcinoma Screening and Care Program (CASCAP), Khon Kaen University, Khon Kaen, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand.,Department of Surgery, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Vasin Thanasukarn
- Cholangiocarcinoma Screening and Care Program (CASCAP), Khon Kaen University, Khon Kaen, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand.,Department of Surgery, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Tharatip Srisuk
- Cholangiocarcinoma Screening and Care Program (CASCAP), Khon Kaen University, Khon Kaen, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand.,Department of Surgery, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Vor Luvira
- Cholangiocarcinoma Screening and Care Program (CASCAP), Khon Kaen University, Khon Kaen, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand.,Department of Surgery, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Kulyada Eurboonyanun
- Cholangiocarcinoma Screening and Care Program (CASCAP), Khon Kaen University, Khon Kaen, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand.,Department of Radiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Julaluck Promsorn
- Cholangiocarcinoma Screening and Care Program (CASCAP), Khon Kaen University, Khon Kaen, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand.,Department of Radiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Supinda Koonmee
- Cholangiocarcinoma Screening and Care Program (CASCAP), Khon Kaen University, Khon Kaen, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand.,Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
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6
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Luiz RLF, Menezes RC, Pereira SA, de Oliveira RDVC, Oliveira MME. Nested PCR for the Diagnosis of Feline Sporotrichosis From Formalin-Fixed and Paraffin-Embedded Samples Using Different DNA Extraction Protocols. Front Vet Sci 2022; 8:755897. [PMID: 35071377 PMCID: PMC8766819 DOI: 10.3389/fvets.2021.755897] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 12/13/2021] [Indexed: 12/25/2022] Open
Abstract
Sporotrichosis is a chronic, cosmopolitan granulomatous mycosis that affects humans and animals. The infection is caused by the dimorphic fungi Sporothrix sp. The aims of the present study were to evaluate, standardize and validate a nested PCR technique using two DNA purification kits for the extraction of DNA from formalin fixed and paraffin-embedded tissues (FFPE) for Sporothrix sp. detection. FFPE mycological culture pellet samples of different Sporothrix species (S. chilensis, S. mexicana, S. pallida, S. globosa, S. brasiliensis and S. schenckii) were used as positive controls and clinical FFPE tissue samples of animals positive for Cryptococcus sp., Leishmania infantum and Histoplasma sp. were used as negative controls. Ten clinical FFPE skin samples from cats with sporotrichosis were used to validate the nested PCR. These samples were cut into two distinct paraffin sectioning protocols (5 and 16 μm thick). The paraffin sections were subjected to two different DNA extraction kits (chemical and thermal extractions). A nested PCR was performed on the extracted DNA to identify the genus Sporothrix. The chemical extraction protocol with the 5 μm thick paraffin section was more effective in extracting DNA from Sporothrix sp. from FFPE samples and the nested PCR technique showed the highest sensitivities (100% in the positive controls and of 50% in the skin samples of cats) and specificity (100%). Therefore, the nested PCR using this protocol has great potential to be applied in Sporothrix sp. diagnosis in FFPE samples of cats.
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Affiliation(s)
- Raul Leal Faria Luiz
- Laboratory of Taxonomy, Biochemistry and Bioprospecting of Fungi, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Rodrigo Caldas Menezes
- Laboratory of Clinical Research on Dermatozoonoses in Domestic Animals, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Sandro Antonio Pereira
- Laboratory of Clinical Research on Dermatozoonoses in Domestic Animals, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
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7
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Di Candia D, Boracchi M, Gentile G, Giordano G, Zoja R. Histological paraffin-embedded block: a good alternative specimen to detect the use of opiates at least 20 years ago. Forensic Toxicol 2022; 40:302-311. [PMID: 36454408 PMCID: PMC9715498 DOI: 10.1007/s11419-022-00614-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 02/09/2022] [Indexed: 01/26/2023]
Abstract
PURPOSE Since the solely certain remnants of a performed autopsy are formalin-fixed paraffin-embedded (FFPE) samples, stored in the archives of every institute of legal medicine, we managed to extract molecules of toxicological interest from these specimens. METHODS We assessed the analysis of ten fresh liver samples collected from heroin-related deaths and then histologically processed the same samples. The embedded blocks were then extracted by means of a new extracting method and the eluates were measured. We also selected five toxicological cases of heroin-related fatalities that were examined 20 years ago, collected the toxicological result documents of the analysis that were carried out at the time and then processed the corresponding FFPE liver samples that were stored in the archives. RESULTS We managed to isolate heroine-related metabolites from 20-year-old paraffin-embedded blocks and calculated ratios to evaluate the performance of our new extraction. CONCLUSIONS According to our study, it is feasible to carry out a toxicological examination on old histological samples and, therefore, this matrix can be considered as a new alternative specimen for chemical-analytical evaluations of past cases or when fresh samples are not available anymore. The new extractive method was evaluated as efficient in treating these complex, paraffin-embedded samples. It was surprising that the target compounds could be quantitated from FFPE bocks created as long as 20 years ago.
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Affiliation(s)
- Domenico Di Candia
- Dipartimento di Scienze Biomediche per la Salute-Sezione di Medicina Legale e delle Assicurazioni, Università degli Studi di Milano, Via L. Mangiagalli 37, 20133 Milan, Italy
| | - Michele Boracchi
- Dipartimento di Scienze Biomediche per la Salute-Sezione di Medicina Legale e delle Assicurazioni, Università degli Studi di Milano, Via L. Mangiagalli 37, 20133 Milan, Italy
| | - Guendalina Gentile
- Dipartimento di Scienze Biomediche per la Salute-Sezione di Medicina Legale e delle Assicurazioni, Università degli Studi di Milano, Via L. Mangiagalli 37, 20133 Milan, Italy
| | - Gaia Giordano
- Dipartimento di Scienze Biomediche per la Salute-Sezione di Medicina Legale e delle Assicurazioni, Università degli Studi di Milano, Via L. Mangiagalli 37, 20133 Milan, Italy
| | - Riccardo Zoja
- Dipartimento di Scienze Biomediche per la Salute-Sezione di Medicina Legale e delle Assicurazioni, Università degli Studi di Milano, Via L. Mangiagalli 37, 20133 Milan, Italy
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8
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Ibrahim S, Lan C, Chabot C, Mitsa G, Buchanan M, Aguilar-Mahecha A, Elchebly M, Poetz O, Spatz A, Basik M, Batist G, Zahedi RP, Borchers CH. Precise Quantitation of PTEN by Immuno-MRM: A Tool To Resolve the Breast Cancer Biomarker Controversy. Anal Chem 2021; 93:10816-10824. [PMID: 34324311 DOI: 10.1021/acs.analchem.1c00975] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The tumor suppressor PTEN is the main negative regulator of PI3K/AKT/mTOR signaling and is commonly found downregulated in breast cancer (BC). Conflicting data from conventional immunoassays such as immunohistochemistry (IHC) has sparked controversy about PTEN's role as a prognostic and predictive biomarker in BC, which can be largely attributed to the lack of specificity, sensitivity, and interlaboratory standardization. Here, we present a fully standardized, highly sensitive, robust microflow immuno-MRM (iMRM) assay that enables precise quantitation of PTEN concentrations in cells and fresh frozen (FF) and formalin-fixed paraffin-embedded (FFPE) tissues, down to 0.1 fmol/10 μg of extracted protein, with high interday and intraday precision (CV 6.3%). PTEN protein levels in BC PDX samples that were determined by iMRM correlate well with semiquantitative IHC and WB data. iMRM, however, allowed the precise quantitation of PTEN-even in samples that were deemed to be PTEN negative by IHC or western blot (WB)-while requiring substantially less tumor tissue than WB. This is particularly relevant because the extent of PTEN downregulation in tumors has been shown to correlate with severity. Our standardized and robust workflow includes an 11 min microflow LC-MRM analysis on a triple-quadrupole MS and thus provides a much needed tool for the study of PTEN as a potential biomarker for BC.
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Affiliation(s)
- Sahar Ibrahim
- Division of Experimental Medicine, McGill University, Montréal, Quebec H4A 3J1 Canada.,Clinical Pathology Department, Menoufia University, Shebeen, El Kom 32511, Egypt.,Segal Cancer Proteomics Centre, McGill University, Montréal, Quebec H3T 1E2, Canada
| | - Cathy Lan
- Segal Cancer Centre, McGill University, Montréal, Quebec H3T 1E2, Canada
| | - Catherine Chabot
- Segal Cancer Centre, McGill University, Montréal, Quebec H3T 1E2, Canada
| | - Georgia Mitsa
- Division of Experimental Medicine, McGill University, Montréal, Quebec H4A 3J1 Canada.,Segal Cancer Proteomics Centre, McGill University, Montréal, Quebec H3T 1E2, Canada
| | | | | | - Mounib Elchebly
- Segal Cancer Centre, McGill University, Montréal, Quebec H3T 1E2, Canada
| | - Oliver Poetz
- University of Tuebingen, Reutlingen 72770, Germany.,SIGNATOPE GmbH, Reutlingen 72770, Germany
| | - Alan Spatz
- Division of Experimental Medicine, McGill University, Montréal, Quebec H4A 3J1 Canada.,Segal Cancer Centre, McGill University, Montréal, Quebec H3T 1E2, Canada.,Department of Pathology, McGill University, Montréal, Quebec H3A 2B4, Canada.,OPTILAB-McGill University Health Centre, Montréal, Quebec H4A 3J1, Canada
| | - Mark Basik
- Division of Experimental Medicine, McGill University, Montréal, Quebec H4A 3J1 Canada.,Segal Cancer Centre, McGill University, Montréal, Quebec H3T 1E2, Canada.,Gerald Bronfman Department of Oncology, McGill University, Montréal, Quebec H3T 1E2, Canada
| | - Gerald Batist
- Segal Cancer Centre, McGill University, Montréal, Quebec H3T 1E2, Canada.,Gerald Bronfman Department of Oncology, McGill University, Montréal, Quebec H3T 1E2, Canada
| | - René P Zahedi
- Segal Cancer Proteomics Centre, McGill University, Montréal, Quebec H3T 1E2, Canada.,Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Christoph H Borchers
- Segal Cancer Proteomics Centre, McGill University, Montréal, Quebec H3T 1E2, Canada.,Gerald Bronfman Department of Oncology, McGill University, Montréal, Quebec H3T 1E2, Canada.,Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
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9
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Smith CC, Bixby LM, Miller KL, Selitsky SR, Bortone DS, Hoadley KA, Vincent BG, Serody JS. Using RNA Sequencing to Characterize the Tumor Microenvironment. Methods Mol Biol 2020; 2055:245-272. [PMID: 31502156 DOI: 10.1007/978-1-4939-9773-2_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
RNA sequencing (RNA-seq) is an integral tool in immunogenomics, allowing for interrogation of the transcriptome of a tumor and its microenvironment. Analytical methods to deconstruct the genomics data can then be applied to infer gene expression patterns associated with the presence of various immunocyte populations. High quality RNA-seq is possible from formalin-fixed, paraffin-embedded (FFPE), fresh-frozen, and fresh tissue, with a wide variety of sequencing library preparation methods, sequencing platforms, and downstream bioinformatics analyses currently available. Selection of an appropriate library preparation method is largely determined by tissue type, quality of RNA, and quantity of RNA. Downstream of sequencing, many analyses can be applied to the data, including differential gene expression analysis, immune gene signature analysis, gene pathway analysis, T/B-cell receptor inference, HLA inference, and viral transcript quantification. In this chapter, we will describe our workflow for RNA-seq from bulk tissue to evaluable data, including extraction of RNA, library preparation methods, sequencing of libraries, alignment and quality assurance of data, and initial downstream analyses of RNA-seq data to extract relevant immunogenomics features. Systems biology methods that draw additional insights by integrating these features are covered further in Chapters 28 - 30 .
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Affiliation(s)
- C C Smith
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - L M Bixby
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - K L Miller
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - S R Selitsky
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - D S Bortone
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - K A Hoadley
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - B G Vincent
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Division of Hematology/Oncology, Department of Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - J S Serody
- Department of Microbiology and Immunology, UNC School of Medicine, Chapel Hill, NC, USA. .,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. .,Division of Hematology/Oncology, Department of Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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10
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Rivenson Y, Liu T, Wei Z, Zhang Y, de Haan K, Ozcan A. PhaseStain: the digital staining of label-free quantitative phase microscopy images using deep learning. LIGHT, SCIENCE & APPLICATIONS 2019; 8:23. [PMID: 30728961 PMCID: PMC6363787 DOI: 10.1038/s41377-019-0129-y] [Citation(s) in RCA: 145] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 01/05/2019] [Accepted: 01/11/2019] [Indexed: 05/03/2023]
Abstract
Using a deep neural network, we demonstrate a digital staining technique, which we term PhaseStain, to transform the quantitative phase images (QPI) of label-free tissue sections into images that are equivalent to the brightfield microscopy images of the same samples that are histologically stained. Through pairs of image data (QPI and the corresponding brightfield images, acquired after staining), we train a generative adversarial network and demonstrate the effectiveness of this virtual-staining approach using sections of human skin, kidney, and liver tissue, matching the brightfield microscopy images of the same samples stained with Hematoxylin and Eosin, Jones' stain, and Masson's trichrome stain, respectively. This digital-staining framework may further strengthen various uses of label-free QPI techniques in pathology applications and biomedical research in general, by eliminating the need for histological staining, reducing sample preparation related costs and saving time. Our results provide a powerful example of some of the unique opportunities created by data-driven image transformations enabled by deep learning.
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Affiliation(s)
- Yair Rivenson
- Electrical and Computer Engineering Department, University of California, Los Angeles, CA 90095 USA
- Bioengineering Department, University of California, Los Angeles, CA 90095 USA
- California NanoSystems Institute (CNSI), University of California, Los Angeles, CA 90095 USA
| | - Tairan Liu
- Electrical and Computer Engineering Department, University of California, Los Angeles, CA 90095 USA
- Bioengineering Department, University of California, Los Angeles, CA 90095 USA
- California NanoSystems Institute (CNSI), University of California, Los Angeles, CA 90095 USA
| | - Zhensong Wei
- Electrical and Computer Engineering Department, University of California, Los Angeles, CA 90095 USA
- Bioengineering Department, University of California, Los Angeles, CA 90095 USA
- California NanoSystems Institute (CNSI), University of California, Los Angeles, CA 90095 USA
| | - Yibo Zhang
- Electrical and Computer Engineering Department, University of California, Los Angeles, CA 90095 USA
- Bioengineering Department, University of California, Los Angeles, CA 90095 USA
- California NanoSystems Institute (CNSI), University of California, Los Angeles, CA 90095 USA
| | - Kevin de Haan
- Electrical and Computer Engineering Department, University of California, Los Angeles, CA 90095 USA
- Bioengineering Department, University of California, Los Angeles, CA 90095 USA
- California NanoSystems Institute (CNSI), University of California, Los Angeles, CA 90095 USA
| | - Aydogan Ozcan
- Electrical and Computer Engineering Department, University of California, Los Angeles, CA 90095 USA
- Bioengineering Department, University of California, Los Angeles, CA 90095 USA
- California NanoSystems Institute (CNSI), University of California, Los Angeles, CA 90095 USA
- Department of Surgery, David Geffen School of Medicine, University of California, Los Angeles, CA 90095 USA
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11
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Carlsson J, Davidsson S, Fridfeldt J, Giunchi F, Fiano V, Grasso C, Zelic R, Richiardi L, Andrén O, Pettersson A, Fiorentino M, Akre O. Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies. BMC Med Res Methodol 2018; 18:161. [PMID: 30518332 PMCID: PMC6280346 DOI: 10.1186/s12874-018-0628-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 11/26/2018] [Indexed: 01/10/2023] Open
Abstract
Background In Sweden, human tissue samples obtained from diagnostic and surgical procedures have for decades been routinely stored in a formalin-fixed, paraffin-embedded, form. Through linkage with nationwide registers, these samples are available for molecular studies to identify biomarkers predicting mortality even in slow-progressing prostate cancer. However, tissue fixation causes modifications of nucleic acids, making it challenging to extract high-quality nucleic acids from formalin fixated tissues. Methods In this study, the efficiency of five commercial nucleic acid extraction kits was compared on 30 prostate biopsies with normal histology, and the quantity and quality of the products were compared using spectrophotometry and Agilent’s BioAnalyzer. Student’s t-test’s and Bland-Altman analyses were performed in order to investigate differences in nucleic acid quantity and quality between the five kits. The best performing extraction kits were subsequently tested on an additional 84 prostate tumor tissues. A Spearman’s correlation test and linear regression analyses were performed in order to investigate the impact of tissue age and amount of tissue on nucleic acid quantity and quality. Results Nucleic acids extracted with RNeasy® FFPE and QIAamp® DNA FFPE Tissue kit had the highest quantity and quality, and was used for extraction from 84 tumor tissues. Nucleic acids were successfully extracted from all biopsies, and the amount of tumor (in millimeter) was found to have the strongest association with quantity and quality of nucleic acids. Conclusions To conclude, this study shows that the choice of nucleic acid extraction kit affects the quantity and quality of extracted products. Furthermore, we show that extraction of nucleic acids from archival formalin-fixed prostate biopsies is possible, allowing molecular studies to be performed on this valuable sample collection.
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Affiliation(s)
- Jessica Carlsson
- Department of Urology, Faculty of Medicine and Health, University Hospital in Örebro, Örebro University, Södra Grevrosengatan, 70185, Örebro, Sweden.
| | - Sabina Davidsson
- Department of Urology, Faculty of Medicine and Health, University Hospital in Örebro, Örebro University, Södra Grevrosengatan, 70185, Örebro, Sweden
| | - Jonna Fridfeldt
- Department of Urology, Faculty of Medicine and Health, University Hospital in Örebro, Örebro University, Södra Grevrosengatan, 70185, Örebro, Sweden
| | - Francesca Giunchi
- Department of Pathology, F. Addari Institute of Oncology S. Orsola Hospital, Bologna, Italy
| | - Valentina Fiano
- Cancer Epidemiology Unit-CERMS, Department of Medical Sciences, University of Turin and CPO-Piemonte, Turin, Italy
| | - Chiara Grasso
- Cancer Epidemiology Unit-CERMS, Department of Medical Sciences, University of Turin and CPO-Piemonte, Turin, Italy
| | - Renata Zelic
- Clinical Epidemiology Unit, Department of Medicine Solna, Karolinska Institute, Stockholm, Sweden
| | - Lorenzo Richiardi
- Cancer Epidemiology Unit-CERMS, Department of Medical Sciences, University of Turin and CPO-Piemonte, Turin, Italy
| | - Ove Andrén
- Department of Urology, Faculty of Medicine and Health, University Hospital in Örebro, Örebro University, Södra Grevrosengatan, 70185, Örebro, Sweden
| | - Andreas Pettersson
- Clinical Epidemiology Unit, Department of Medicine Solna, Karolinska Institute, Stockholm, Sweden
| | | | - Olof Akre
- Department of Medicine Solna, Karolinska Institute, and Department of Urology, Karolinska University Hospital, Stockholm, Sweden
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12
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Rosa-Rosa JM, Caniego-Casas T, Leskela S, Muñoz G, Del Castillo F, Garrido P, Palacios J. Modified SureSelect QXT Target Enrichment Protocol for Illumina Multiplexed Sequencing of FFPE Samples. Biol Proced Online 2018; 20:19. [PMID: 30337841 PMCID: PMC6182866 DOI: 10.1186/s12575-018-0084-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 09/20/2018] [Indexed: 12/18/2022] Open
Abstract
Background Personalised medicine is nowadays a major objective in oncology. Molecular characterization of tumours through NGS offers the possibility to find possible therapeutic targets in a time- and cost-effective way. However, the low quality and complexity of FFPE DNA samples bring a series of disadvantages for massive parallel sequencing techniques compared to high-quality DNA samples (from blood cells, cell cultures, etc.). Results We performed several experiments to understand the behaviour of FFPE DNA samples during the construction of SureSelectQXT libraries. First, we designed a quality checkpoint for FFPE DNA samples based on the quantification of their amplification capability (qcPCR). We observed that FFPE DNA samples can be classified according to DIN value and qcPCR concentration into unusable, or low-quality (LQ) and good-quality (GQ) DNA. For GQ samples, we increased the amount of input DNA to 150 ng and the digestion time to 30 min, whereas for LQ samples, we used 50 ng of DNA as input but we decreased the digestion time to 1 min. In all cases, we increased the cycles of the pre-hyb PCR to 10 but decreased the cycles of the post-hyb PCR to 8. In addition, we confirmed that using half of the volume of reagents can be beneficial. Finally, in order to obtain better results, we designed a decision flow-chart to achieve a seeding concentration of 12–14 pM for MiSeq Reagent Kit v2. Conclusions Our experiments allowed us to unveil the behaviour of low-quality FFPE DNA samples during the construction of SureSelectQXT libraries. Sequencing results showed that, using our modified SureSelectQXT protocol, the final percentage of usable reads for low-quality samples was increased more than three times allowing to reach median depth/million reads values of 76.35. This value is equivalent to ~ 0.9 and ~ 0.7 of the values obtained for good-quality FFPE and high-quality DNA respectively. Electronic supplementary material The online version of this article (10.1186/s12575-018-0084-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- J M Rosa-Rosa
- 1CIBER-ONC, Instituto de Salud Carlos III, Madrid, Spain
| | - T Caniego-Casas
- 2Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
| | - S Leskela
- 1CIBER-ONC, Instituto de Salud Carlos III, Madrid, Spain.,2Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
| | - G Muñoz
- 2Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
| | - F Del Castillo
- 2Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain.,3Servicio de Genética, Hospital Universitario Ramón y Cajal, Madrid, Spain.,4CIBER-ER, Instituto de Salud Carlos III, Madrid, Spain
| | - P Garrido
- 2Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain.,5Medical Oncology Department, Hospital Universitario Ramón y Cajal, Madrid, Spain.,6Facultad de Medicina, Universidad de Alcalá de Henares, Madrid, Spain
| | - J Palacios
- 1CIBER-ONC, Instituto de Salud Carlos III, Madrid, Spain.,2Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain.,6Facultad de Medicina, Universidad de Alcalá de Henares, Madrid, Spain.,7Servicio de Anatomía Patológica, Hospital Ramón y Cajal, Ctra. Colmenar Viejo km 9,100, 28034 Madrid, Spain
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13
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Chun SM, Sung CO, Jeon H, Kim TI, Lee JY, Park H, Kim Y, Kim D, Jang SJ. Next-Generation Sequencing Using S1 Nuclease for Poor-Quality Formalin-Fixed, Paraffin-Embedded Tumor Specimens. J Mol Diagn 2018; 20:802-811. [PMID: 30055350 DOI: 10.1016/j.jmoldx.2018.06.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 05/15/2018] [Accepted: 06/21/2018] [Indexed: 12/30/2022] Open
Abstract
Next-generation sequencing (NGS) testing of formalin-fixed, paraffin-embedded (FFPE) tissues is widely used in clinical diagnosis. However, the failure of high-quality DNA library construction, a critical step for NGS, often limits NGS application for FFPE tissues, particularly for old FFPE tissues. The aim was to develop a high-quality DNA library construction method optimized for NGS of FFPE specimens. DNA library construction was developed for FFPE specimens by using S1 nuclease and compared with the Covaris method-the widely accepted DNA library construction protocol. The Covaris method includes a DNA shearing step with sonication to generate shortened DNA fragments. DNA shearing was found to be unnecessary, and S1 nuclease treatment only during genomic DNA extraction significantly improved the success rate of library construction from FFPE tissues. Moreover, poor-quality FFPE tissues that failed the Covaris method were rescued with the S1 method. Higher complexity was observed in DNA libraries constructed by the S1 method. Among 223 FFPE specimens, DNA libraries were successfully constructed for 134 cases with the Covaris method (60.0% success rate), whereas the success rate was 86.5% (193 of 223) with the S1 method (P = 5.255e-10). Furthermore, we were able to rescue 59 samples, including 25 primary lung cancers, from the 89 failed Covaris method cases. In conclusion, the S1 method is optimal for NGS testing of poor-quality FFPE specimens.
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Affiliation(s)
- Sung-Min Chun
- Department of Pathology, Asan Institute for Life Science, University of Ulsan College of Medicine, Asan Medical Center, Seoul, South Korea.
| | - Chang Ohk Sung
- Department of Pathology, Asan Institute for Life Science, University of Ulsan College of Medicine, Asan Medical Center, Seoul, South Korea; Center for Cancer Genome Discovery, Asan Institute for Life Science, University of Ulsan College of Medicine, Asan Medical Center, Seoul, South Korea
| | - Hyejoon Jeon
- Center for Cancer Genome Discovery, Asan Institute for Life Science, University of Ulsan College of Medicine, Asan Medical Center, Seoul, South Korea
| | - Tae-Im Kim
- Center for Cancer Genome Discovery, Asan Institute for Life Science, University of Ulsan College of Medicine, Asan Medical Center, Seoul, South Korea
| | - Ji-Young Lee
- Center for Cancer Genome Discovery, Asan Institute for Life Science, University of Ulsan College of Medicine, Asan Medical Center, Seoul, South Korea
| | - Hwan Park
- Center for Cancer Genome Discovery, Asan Institute for Life Science, University of Ulsan College of Medicine, Asan Medical Center, Seoul, South Korea
| | - Yujin Kim
- Center for Cancer Genome Discovery, Asan Institute for Life Science, University of Ulsan College of Medicine, Asan Medical Center, Seoul, South Korea
| | - Deokhoon Kim
- Department of Pathology, Asan Institute for Life Science, University of Ulsan College of Medicine, Asan Medical Center, Seoul, South Korea; Center for Cancer Genome Discovery, Asan Institute for Life Science, University of Ulsan College of Medicine, Asan Medical Center, Seoul, South Korea
| | - Se Jin Jang
- Department of Pathology, Asan Institute for Life Science, University of Ulsan College of Medicine, Asan Medical Center, Seoul, South Korea; Center for Cancer Genome Discovery, Asan Institute for Life Science, University of Ulsan College of Medicine, Asan Medical Center, Seoul, South Korea.
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14
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Patel PG, Selvarajah S, Guérard KP, Bartlett JMS, Lapointe J, Berman DM, Okello JBA, Park PC. Reliability and performance of commercial RNA and DNA extraction kits for FFPE tissue cores. PLoS One 2017. [PMID: 28640876 PMCID: PMC5480995 DOI: 10.1371/journal.pone.0179732] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Cancer biomarker studies often require nucleic acid extraction from limited amounts of formalin-fixed, paraffin-embedded (FFPE) tissues, such as histologic sections or needle cores. A major challenge is low quantity and quality of extracted nucleic acids, which can limit our ability to perform genetic analyses, and have a significant influence on overall study design. This study was aimed at identifying the most reliable and reproducible method of obtaining sufficient high-quality nucleic acids from FFPE tissues. We compared the yield and quality of nucleic acids from 0.6-mm FFPE prostate tissue cores across 16 DNA and RNA extraction protocols, using 14 commercially available kits. Nucleic acid yield was determined by fluorometry, and quality was determined by spectrophotometry. All protocols yielded nucleic acids in quantities that are compatible with downstream molecular applications. However, the protocols varied widely in the quality of the extracted RNA and DNA. Four RNA and five DNA extraction protocols, including protocols from two kits for dual-extraction of RNA and DNA from the same tissue source, were prioritized for further quality assessment based on the yield and purity of their products. Specifically, their compatibility with downstream reactions was assessed using both NanoString nCounter gene expression assays and reverse-transcriptase real-time PCR for RNA, and methylation-specific PCR assays for DNA. The kit deemed most suitable for FFPE tissue was the AllPrep kit by Qiagen because of its yield, quality, and ability to purify both RNA and DNA from the same sample, which would be advantageous in biomarker studies.
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Affiliation(s)
- Palak G. Patel
- Department of Pathology & Molecular Medicine, Queen’s University, Kingston, Ontario, Canada
- Division of Cancer Biology & Genetics, Queen’s Cancer Research Institute, Queen’s University, Kingston, Ontario, Canada
| | - Shamini Selvarajah
- Department of Pathology & Molecular Medicine, Queen’s University, Kingston, Ontario, Canada
| | - Karl-Philippe Guérard
- Department of Surgery, Division of Urology, McGill University and the Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - John M. S. Bartlett
- Diagnostic Development Program, Ontario Institute for Cancer Research (OICR), Toronto, Ontario, Canada
| | - Jacques Lapointe
- Department of Surgery, Division of Urology, McGill University and the Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - David M. Berman
- Department of Pathology & Molecular Medicine, Queen’s University, Kingston, Ontario, Canada
- Division of Cancer Biology & Genetics, Queen’s Cancer Research Institute, Queen’s University, Kingston, Ontario, Canada
| | - John B. A. Okello
- Department of Pathology & Molecular Medicine, Queen’s University, Kingston, Ontario, Canada
- Division of Cancer Biology & Genetics, Queen’s Cancer Research Institute, Queen’s University, Kingston, Ontario, Canada
| | - Paul C. Park
- Department of Pathology & Molecular Medicine, Queen’s University, Kingston, Ontario, Canada
- * E-mail: ,
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