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Ma D, Ding J, Zhang L, Piao Y. Application of an in situ hybridization method for fungal diagnosis in formalin-fixed, paraffin-embedded allergic fungal rhinosinusitis tissue. Ann Diagn Pathol 2025; 77:152474. [PMID: 40121737 DOI: 10.1016/j.anndiagpath.2025.152474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2025] [Revised: 03/12/2025] [Accepted: 03/17/2025] [Indexed: 03/25/2025]
Abstract
Allergic fungal rhinosinusitis (AFRS) is a chronic inflammatory disease of the sinuses that can involve serious late complications; thus, prompt diagnosis is essential to determine the appropriate treatment. The most important diagnostic element of AFRS is the detection of noninvasive fungi within eosinophilic mucin. However, the rarity of fungal hyphae in ARFS makes it difficult to specifically identify them using histochemical staining alone. In this study, we designed a new in situ fungal detection probe for the diagnosis of fungi in formalin-fixed, paraffin-embedded AFRS tissues. Tissue sections from 49 patients with confirmed (n = 40) or suspected (n = 9) AFRS were selected for testing. A newly designed broad-spectrum probe for in situ hybridization (ISH) was compared with an anti-Aspergillus antibody in immunohistochemistry (IHC) and staining with hematoxylin and eosin and periodic acid-Schiff (PAS) to detect fungi. Hematoxylin and eosin staining had a lower detection rate (30/40 samples) than the other three methods. PAS staining led to two false-positive results in the AFRS-confirmed group and two false-negative results in the AFRS-suspected group. ISH and IHC exhibited high concordance (ĸ = 0.716); however, there was a high degree of nonspecific immunoreactivity to the anti-Aspergillus polyclonal antibody in some samples. The fungal detection rate of ISH was 95 % (38/40), with no background or nonspecific reactivity. Our novel broad-spectrum ISH probe provides more specific identification of fungi than PAS and IHC staining, exhibits no background reactivity, and may represent an essential upgrade to the in situ diagnosis of AFRS.
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Affiliation(s)
- Donglin Ma
- Department of Pathology, Beijing Tongren Hospital, Capital Medical University, Beijing, China; Beijing Key Laboratory of Head and Neck Molecular Diagnostic Pathology, Beijing, China
| | - Jing Ding
- Department of Pathology, Beijing Tongren Hospital, Capital Medical University, Beijing, China; Beijing Key Laboratory of Head and Neck Molecular Diagnostic Pathology, Beijing, China
| | - Luo Zhang
- Department of Otolaryngology, Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China; Department of Allergy, Beijing Tongren Hospital, Capital Medical University, Beijing, China.
| | - Yingshi Piao
- Department of Pathology, Beijing Tongren Hospital, Capital Medical University, Beijing, China; Beijing Key Laboratory of Head and Neck Molecular Diagnostic Pathology, Beijing, China.
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Mika J, Polanska A, Blenman KR, Pusztai L, Polanska J, Candéias S, Marczyk M. A comprehensive evaluation of diversity measures for TCR repertoire profiling. BMC Biol 2025; 23:133. [PMID: 40369611 PMCID: PMC12080070 DOI: 10.1186/s12915-025-02236-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2024] [Accepted: 05/06/2025] [Indexed: 05/16/2025] Open
Abstract
BACKGROUND T cells play a crucial role in adaptive immunity, as they monitor internal and external immunogenic signals through their specific receptors (TCRs). Using high-throughput sequencing, one can assess TCR repertoire in various clinical settings and describe it quantitatively by calculating a diversity index. Multiple diversity indices that capture the richness of TCRs and the evenness of their distribution have been proposed in the literature; however, there is no consensus on gold-standard measures and interpretation of each index is complex. Our goal was to examine the performance characteristics of 12 commonly used diversity indices in simulated and real-world data. RESULTS Simulated data were generated to evaluate how data richness and evenness affect index values using three nonparametric models. Fourteen real-world TCR datasets were obtained to examine differences in indices by analysis protocols and test their robustness to subsampling. Pielou, Basharin, d50, and Gini primarily describe evenness and highly correlate with one another. They are best suited for measuring the representation of TCR clones. Richness is best captured by S index, next Chao1 and ACE which also consider information on evenness. Shannon, Inv.Simspon, D3, D4, and Gini.Simpson measure richness and increasingly more information on evenness. More skewed TCR distributions provided more stable results in subsampling. Gini-Simpson, Pielou, and Basharin were the most robust in both simulated and experimental data. CONCLUSIONS Our results could guide investigators to select the best diversity index for their particular experimental question and draw attention to factors that can influence the accuracy and reproducibility of results.
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Affiliation(s)
- Justyna Mika
- Department of Data Science and Engineering, Silesian University of Technology, Gliwice, Poland
| | - Alicja Polanska
- Mullard Space Science Laboratory, University College London, Dorking, UK
| | - Kim Rm Blenman
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
- Department of Computer Science, School of Engineering and Applied Science, New Haven, CT, USA
| | - Lajos Pusztai
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Joanna Polanska
- Department of Data Science and Engineering, Silesian University of Technology, Gliwice, Poland
| | - Serge Candéias
- Université Grenoble Alpes, CEA, CNRS, IRIG-LCBM, Grenoble, France
| | - Michal Marczyk
- Department of Data Science and Engineering, Silesian University of Technology, Gliwice, Poland.
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA.
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Robveille C, Maggi RG, Lashnits E, Donovan TA, Linder KE, Regan DP, Woolard KD, Breitschwerdt EB. Molecular detection of Bartonella spp. DNA in dogs with hemangiosarcoma. PLoS One 2025; 20:e0321806. [PMID: 40261912 PMCID: PMC12013947 DOI: 10.1371/journal.pone.0321806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2025] [Accepted: 03/09/2025] [Indexed: 04/24/2025] Open
Abstract
INTRODUCTION The potential role of pathogens, particularly vector-transmitted infectious agents, as a cofactor or cause of neoplasia has not been intensively investigated. We previously reported a potential link between Bartonella spp. bacteremia and splenic hemangiosarcoma (HSA) in dogs living in the United States. The purpose of this study was to: 1/ further determine the prevalence of Bartonella spp. DNA in dogs with splenic HSA from throughout the United States; 2/ assess the impact of sample preservation methods on Bartonella spp. DNA amplification using characterized tissue samples from dogs diagnosed with HSA. METHODS In a blinded manner, we determined the presence of Bartonella spp. DNA in scrolls from biorepository formalin-fixed paraffin-embedded (FFPE) spleens from dogs living in three distant locations geographically transecting the United States. DNA extracted from non-lesional spleens (n = 249), nodular lymphoid hyperplasia spleens (n = 248), and splenic HSA (n = 330) were tested by quantitative polymerase chain reaction (qPCR), and droplet digital PCR (ddPCR). Subsequently, Bartonella PCR results from FFPE tissues and formalin-fixed tissues were compared using previously tested fresh frozen tissues from an additional 48 dogs with HSA. RESULTS There was no significant difference in the proportion of Bartonella PCR positive FFPE tissues from dogs diagnosed with an alesional spleen, nodular lymphoid hyperplasia, and splenic HSA. Regardless of the histological diagnosis, the most common Bartonella species identified was B. henselae (32/38). Bartonella spp. DNA was detected in a significantly larger proportion of fresh frozen tissues compared to FFPE tissues, when tested by qPCR (22/48 versus 1/48; p <0.0001) or ddPCR (19/48 versus 1/48; p <0.0001). Using ddPCR, Bartonella DNA was more often amplified from formalin-fixed tissues compared to FFPE tissues (15/39 versus 1/39; p <0.0001). The sensitivity of qPCR on FFPE samples and formalin-fixed samples, when comparing to fresh frozen samples as the reference standard, was 4.5% and 11.8%, respectively. CONCLUSION Due to decreased DNA amplification efficiency, FFPE scrolls should not be used for the detection of Bartonella infection in spleen samples from dogs with HSA. PCR testing of fresh frozen tissues substantially improves the detection of Bartonella spp. infection. If fresh frozen tissues are not available, formalin-fixed tissues should be tested with digital PCR to enhance Bartonella DNA detection.
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Affiliation(s)
- Cynthia Robveille
- Department of Clinical Sciences, Intracellular Pathogens Research Laboratory, North Carolina State University - College of Veterinary Medicine, Raleigh, North Carolina, United States of America
| | - Ricardo G. Maggi
- Department of Clinical Sciences, Intracellular Pathogens Research Laboratory, North Carolina State University - College of Veterinary Medicine, Raleigh, North Carolina, United States of America
| | - Erin Lashnits
- Department of Medical Sciences, University of Wisconsin-Madison - School of Veterinary Medicine, Madison, Wisconsin, United States of America
| | - Taryn A. Donovan
- Department of Anatomic Pathology, The Schwarzman Animal Medical Center, New York, New York, United States of America
| | - Keith E. Linder
- Department of Population Health and Pathobiology, North Carolina State University - College of Veterinary Medicine, Raleigh, North Carolina, United States of America
| | - Daniel P. Regan
- Department of Microbiology, Immunology and Pathology, Colorado State University - College of Veterinary Medicine and Biomedical Sciences, Fort Collins, Colorado, United States of America
| | - Kevin D. Woolard
- Departments of Pathology, Microbiology and Immunology, University of California-Davis - School of Veterinary Medicine, Davis, California, United States of America
| | - Edward B. Breitschwerdt
- Department of Clinical Sciences, Intracellular Pathogens Research Laboratory, North Carolina State University - College of Veterinary Medicine, Raleigh, North Carolina, United States of America
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Wang FY, Yeh YC, Lin SY, Wang SY, Chen PCH, Chou TY, Ho HL. Real-world application of targeted next-generation sequencing for identifying molecular variants in Asian non-small-cell lung cancer. BMC Cancer 2025; 25:715. [PMID: 40247220 PMCID: PMC12004552 DOI: 10.1186/s12885-025-14016-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: 01/27/2025] [Accepted: 03/25/2025] [Indexed: 04/19/2025] Open
Abstract
BACKGROUND The advent of novel therapeutic agents has advanced biomarker characterization in non-small-cell lung cancer (NSCLC), driving increased adoption of next-generation sequencing (NGS) technologies for molecular testing. However, comprehensive data addressing the clinical utility of different NGS platforms for NSCLC remains limited. METHODS This retrospective study analyzed real-world data from 478 Taiwanese NSCLC patients over five years, using the Oncomine Focus Assay (OFA) to assess genetic alterations. The evaluation focused on assay accuracy, limit of detection (LoD), sequencing performance, and the genetic landscape of NSCLC. RESULTS The OFA achieved an NGS success rate of 80.5% (385/478), with tumor cell percentage, specimen source and FFPE block age identified as key factors affecting success. Quality metrics demonstrated robust sequencing performance, including 97.0 ± 9.6% on-target alignment, 94.7 ± 6.4% uniformity, and ≥ 500 × coverage for 98.0 ± 6.6% of amplicons. Among the 385 patients analyzed, 86.8% (334/385) were found to harbor pathogenic or likely pathogenic variants, of which 78.4% (262/334) were SNVs/Indels, 41.6% (139/334) were CNVs, 2.7% (9/334) were exon skipping alterations, and 10.2% (34/334) were gene fusions. Actionable driver mutations included EGFR mutations (46.2%, 178/385), KRAS mutations (9.4%, 36/385), ERBB2 mutations (6.8%, 26/385), ALK fusions (4.4%, 17/385), MET exon 14 skipping (2.3%, 9/385), BRAF mutations (2.3%, 9/385), ROS1 and RET fusions (1.8%, 7/385 each), and NTRK1 fusions (0.5%, 2/385). Notably, KRAS G12 C mutation was detected in 2.8% (11/385) of cases. CONCLUSIONS This study demonstrates the robust performance of the OFA in identifying clinically relevant genetic alterations in NSCLC. The findings support its clinical utility in precision oncology and provide valuable insights into the genetic landscape of Asian NSCLC, enhancing personalized treatment strategies for lung cancer patients.
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Affiliation(s)
- Fang-Yu Wang
- Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, 201, Section 2, Shipai Road, Taipei, 11217, Taiwan
- Department of Biotechnology and Laboratory Science in Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Yi-Chen Yeh
- Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, 201, Section 2, Shipai Road, Taipei, 11217, Taiwan
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Shin-Ying Lin
- Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, 201, Section 2, Shipai Road, Taipei, 11217, Taiwan
| | - Shu-Ying Wang
- Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, 201, Section 2, Shipai Road, Taipei, 11217, Taiwan
| | - Paul Chih-Hsueh Chen
- Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, 201, Section 2, Shipai Road, Taipei, 11217, Taiwan
| | - Teh-Ying Chou
- Department of Pathology and Precision Medicine Research Center, Taipei Medical University Hospital, Taipei Medical University, Taipei, Taiwan
| | - Hsiang-Ling Ho
- Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, 201, Section 2, Shipai Road, Taipei, 11217, Taiwan.
- Department of Biotechnology and Laboratory Science in Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.
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Azlin SUNK, Muhammad Husairy NF, Fraser C, Zahli NIU, Akmal MN, Salleh A. Pathology of an unusual outbreak of fatal disease associated with mycobacterial and Pseudomonas aeruginosa infections and intracytoplasmic inclusion bodies in juvenile spectacled caimans (Caiman crocodilus). J Comp Pathol 2025; 218:19-25. [PMID: 40081130 DOI: 10.1016/j.jcpa.2025.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 08/29/2024] [Accepted: 02/11/2025] [Indexed: 03/15/2025]
Abstract
The spectacled caiman (Caiman crocodilus) is a common crocodilian species used for exhibition in zoos and for luxury leather and meat production. We investigated unusual mortality among juvenile spectacled caimans in a zoo in Malaysia over a 2-year period. Clinical signs included inappetence, poor body condition, dehydration and ocular lesions. Necropsy findings included integumentary, respiratory and renal abnormalities. Histopathological analyses revealed necrotic plugs and intracytoplasmic eosinophilic inclusion bodies in epidermal keratinocytes, granulomatous lesions in the lungs and liver and gout crystals in the kidneys. Acid-fast, beaded, rod-shaped bacteria were identified in the granulomatous lesions using Ziehl-Neelsen staining. Microbiological investigations identified Pseudomonas aeruginosa as the predominant pathogen, while mycobacteriosis was also detected and poxvirus infection was suspected. However, due to the lack of suitable samples, molecular diagnosis was challenging. These findings emphasize the multifactorial nature of disease in captive spectacled caimans and the need for enhanced management strategies to mitigate health risks and preserve population viability.
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Affiliation(s)
- Sufiah U N K Azlin
- Department of Veterinary Laboratory Diagnosis, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Nurul F Muhammad Husairy
- Department of Veterinary Laboratory Diagnosis, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Charisha Fraser
- Sunway Lost World Theme Park, No. 1, Persiaran Lagun Sunway 1, Sunway City Perak, Ipoh, 31159 Ipoh, Perak, Malaysia
| | - Nurul I U Zahli
- Department of Veterinary Pathology and Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Mohd N Akmal
- Department of Veterinary Preclinical Sciences, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Annas Salleh
- Department of Veterinary Laboratory Diagnosis, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; Division of Veterinary Microbiology, Department of Veterinary Science, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya, 60115, Indonesia; Laboratory of Aquatic Animal Health and Therapeutics, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia.
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Nano E, Gambella A, Paudice M, Garuti A, Pigozzi S, Valle L, Grillo F, Mastracci L. Be bold, start cold! cold formalin fixation of colorectal cancer specimens granted superior DNA and RNA quality for downstream molecular analysis. Histochem Cell Biol 2024; 162:541-550. [PMID: 39317804 PMCID: PMC11455702 DOI: 10.1007/s00418-024-02326-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/10/2024] [Indexed: 09/26/2024]
Abstract
The use of cold formalin fixation (CFF; i.e., fixating tissue samples with 4 °C precooled formalin) recently attracted further attention owing to its putative improved ability to preserve nucleic acid compared with standard room temperature formalin (SFF). In this study, we aimed to assess the effect of four formalin-based fixation protocols (SFF, CFF, delayed formalin fixation-DFF, and cold formalin hyperfixation; CFH) on both DNA and RNA quality. We collected 97 colorectal cancer (CRC) and analyzed 23 metrics of nucleic acid quantity and quality yield using a multiplatform approach by combining spectrophotometric, fluorimetric, electrophoretic, and polymerase chain reaction (PCR) assays. Following confirmation of fixation-protocol-related different effects via clustering analysis, CFF presented best metrics compared with all protocols, specifically positive coefficients of DV1000-60000, DV2/DV1, DNA λ ratio 260/230, and ABL gene expression absolute copies, and negative coefficient of DV150-1000. The SFF subgroup presented a positive coefficient of DV150-1000 and negative coefficients for DV1000-60000, DV2/DV1, RNA λ ratio 260/230, RNA QuBit concentration, DV100/200, RNA electrophoresis concentration and absolute quantity, and ABL copies. Overall, we confirmed the superior yield performances of CFF preservation for both DNA and RNA compared with the other protocols in our series of CRC samples. Pending further validations and clarification of the specific mechanisms behind these findings, our study supports the implementation of CFF in the pathology unit routine specimen management for tumor tissue molecular profiling.
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Affiliation(s)
- Ennio Nano
- Molecular Pathology Unit, IRCCS San Martino Policlinic Hospital of Genoa, Genoa, Italy
| | - Alessandro Gambella
- Pathology Unit, Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, Genoa, Italy.
| | - Michele Paudice
- Pathology Unit, Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, Genoa, Italy
- IRCCS San Martino Policlinic Hospital of Genoa, Genoa, Italy
| | - Anna Garuti
- Internal Medicine Clinic, IRCCS San Martino Policlinic Hospital of Genoa, Genoa, Italy
| | - Simona Pigozzi
- Pathology Unit, Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, Genoa, Italy
- IRCCS San Martino Policlinic Hospital of Genoa, Genoa, Italy
| | - Luca Valle
- IRCCS San Martino Policlinic Hospital of Genoa, Genoa, Italy
| | - Federica Grillo
- Pathology Unit, Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, Genoa, Italy
- IRCCS San Martino Policlinic Hospital of Genoa, Genoa, Italy
| | - Luca Mastracci
- Pathology Unit, Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, Genoa, Italy
- IRCCS San Martino Policlinic Hospital of Genoa, Genoa, Italy
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Gürel İ, Aşıcıoğlu F, Ersoy G, Bülbül Ö, Öztürk T, Filoğlu G. InDEL instability in two different tumoral tissues and its forensic significance. Forensic Sci Med Pathol 2024; 20:1241-1250. [PMID: 38568352 PMCID: PMC11790770 DOI: 10.1007/s12024-024-00808-5] [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] [Accepted: 03/22/2024] [Indexed: 02/04/2025]
Abstract
There may be cases where malignant tumor samples can be used for forensic DNA profiling studies. STRs are the first systems preferred in forensic science laboratories for identification purposes. However, genetic instability in tumoral tissues causes STR polymorphism to change, leading to erroneous results. On the other hand, insertion/deletion polymorphism (InDels) are used as genetic markers in forensic science, as they have features that make both STR and SNPs preferable. Although previous studies approved that STR instability is observed in many different tumors, there are only a few studies that have displayed the instability of InDels in tumoral tissues before. In this study, it was aimed to determine whether instability is observed in formalin-fixed paraffin-embedded breast and thyroid tumoral tissues at 36plex InDel Panel. A total of 47 cases, 26 of which were diagnosed as breast cancer and 21 as thyroid cancer, were included in the study. In 21 of 26 (80.76%) breast cancers mutational changes were observed, however only 6 of 21 (28.57%) thyroid carcinoma cases displayed instability.Moreover, in these six cases, mutations were detected at only 1 or 2 loci. The most common change in both tissues was loss of heterozygosity. These findings suggest that paraffin embedded tissues of thyroid tumor can be used in cases of forensic genetic identification, however paraffin embedded breast cancer tissues should be examined with care. In conclusion, low InDel mutation rates compared to STR instability, make InDel analysis from paraffin blocks suitable for forensic genetic identification. However, researchers should keep in mind that there may be differences between the profiles of the tumoral tissues taken as reference and the actual case. In addition, by incorporating additional markers such as SNPs and microhaplotypes with low mutation rates into the study alongside Indels, researchers can significantly enhance the discrimination power in identification processes.
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Affiliation(s)
- İpek Gürel
- Department of Science, Institute of Forensic Sciences and Legal Medicine, İstanbul University- Cerrahpaşa, İstanbul, Türkiye
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Haliç University, İstanbul, Türkiye
| | - Faruk Aşıcıoğlu
- Department of Medical Sciences, Institute of Forensic Sciences and Legal Medicine, İstanbul University-Cerrahpaşa, İstanbul, Türkiye.
| | - Gökhan Ersoy
- Department of Medical Sciences, Institute of Forensic Sciences and Legal Medicine, İstanbul University-Cerrahpaşa, İstanbul, Türkiye
| | - Özlem Bülbül
- Department of Science, Institute of Forensic Sciences and Legal Medicine, İstanbul University- Cerrahpaşa, İstanbul, Türkiye
| | - Tülin Öztürk
- Department of Medical Pathology, Cerrahpaşa Faculty of Medicine, İstanbul University- Cerrahpaşa, İstanbul, Türkiye
| | - Gönül Filoğlu
- Department of Science, Institute of Forensic Sciences and Legal Medicine, İstanbul University- Cerrahpaşa, İstanbul, Türkiye
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Truong TT, Crawford K, Wang-McGuire I, Jensen K, Mushtaq A, Lieberman NAP, Buckner FS, Van Voorhis WC, Cookson BT, Salipante SJ, Lieberman JA. Descriptive and molecular epidemiology of leishmaniasis diagnosed from clinical samples in the United States, 2021-2022. Microbiol Spectr 2024; 12:e0105524. [PMID: 39248481 PMCID: PMC11448060 DOI: 10.1128/spectrum.01055-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 08/06/2024] [Indexed: 09/10/2024] Open
Abstract
Leishmaniasis is a rare disease in the United States, with an estimated annual incidence of dozens of cases occurring primarily in travelers, migrants, and military personnel. True disease incidence is unknown, since leishmaniasis is not a nationally notifiable condition. Here, we describe the results of molecular leishmaniasis over a 1-year interval (September 2021 to August 2022) when our laboratory served as the primary national reference laboratory for molecular diagnosis of civilian leishmaniasis. We tested 218 specimens submitted from 36 states yielding 94 of the 186 (50.5%) positive cases with species or species complex-level identification and 18 novel mini-exon alleles. Most species belonged to subgenus Viannia (75.6%) and associated with cutaneous or mucocutaneous disease. Cases were associated with recent travel (18.1%), travel timing unspecified (7.4%), migration (7.4%), remote travel (2.1%), military (1.1%), or unknown history (63.8%). These data illustrate the clinical utility of molecular testing for leishmaniasis and provide unique insight into disease epidemiology. IMPORTANCE Leishmaniasis is a disfiguring, neglected parasitic infection endemic to the Southern United States and the Americas. Despite significant populations at risk-travelers, military and foreign service members, and migrating persons-the epidemiology of the disease in the United States is poorly understood. Moreover, few clinical laboratories in the United States can test for the disease. Here, we present results from 1 year of testing for this disease at a major reference laboratory. These findings are particularly relevant because they coincide with a temporary "pause" on all clinical testing at the CDC. Our findings suggest at least several hundred cases occur each year in the United States. In particular, mucosal leishmaniasis may be more common than previously reported. We also highlight greater genetic diversity in Leishmania species endemic to the Americas than has been previously sampled, with implications for diagnostic specificity.
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Affiliation(s)
- Thao T. Truong
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Karissa Crawford
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Ichih Wang-McGuire
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Kendal Jensen
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Aisha Mushtaq
- Center for Emerging and Re-emerging Infectious Diseases (CERID), Division of Allergy & Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Nicole A. P. Lieberman
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Frederick S. Buckner
- Center for Emerging and Re-emerging Infectious Diseases (CERID), Division of Allergy & Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Wesley C. Van Voorhis
- Center for Emerging and Re-emerging Infectious Diseases (CERID), Division of Allergy & Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, Washington, USA
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Brad T. Cookson
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Stephen J. Salipante
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Joshua A. Lieberman
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
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von Ammon JL, Machado GJR, da Matta RRC, Telles AC, Carrijo F, dos Santos BAF, Brandão JCD, da Silva TM, Hecht F, Colozza-Gama GA, Tezzei JH, Cerutti JM, Ramos HE. Follicular cell-derived thyroid carcinomas harboring novel genetic BRAFNON-V600E mutations: real-world data obtained using a multigene panel. ARCHIVES OF ENDOCRINOLOGY AND METABOLISM 2024; 68:e240067. [PMID: 39420942 PMCID: PMC11460960 DOI: 10.20945/2359-4292-2024-0067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 05/08/2024] [Indexed: 10/19/2024]
Abstract
Objectives To assess the molecular profile of follicular cell-derived thyroid carcinomas (FCDTCs) and correlate the identified mutations with the clinical and pathological features of the affected patients. Materials and methods Cross-sectional study of tumor samples from 100 adult patients diagnosed with FCDTC between 2010 and 2019. The patients' clinical and pathological data were collected. Genomic DNA was extracted from formalin-fixed, paraffin-embedded (FFPE) tumors using the ReliaPrep FFPE gDNA Miniprep System. Genotyping of target genomic regions (KRAS, NRAS, BRAF, EGFR, and PIK3CA) was performed using the AmpliSeq panel, while sequencing was performed on the iSeq 100 platform. Results The patients' mean age was 39 years. In all, 82% of the tumors were classic papillary thyroid carcinomas. Overall, 54 (54%) tumor samples yielded satisfactory results on next-generation sequencing (NGS), of which 31 harbored mutations. BRAF gene mutations were the most frequent, with the BRAF V600E mutation present in 10 tumors. Seven tumors had BRAF NON-V600E mutations not previously described in FCDTCs (G464E, G464R, G466E, S467L, G469E, G596D, and the T599Ifs*10 deletion) but described in other types of cancer (i.e., skin/melanoma, lung, colorectal, and others). One tumor had a previously reported BRAF A598V mutation. EGFR gene mutations were found in 16 (29%) and KRAS or NRAS alterations in 8 (14%) of the 54 tumors analyzed. Conclusion We described herein seven non-hotspot/novel variants in the BRAF gene, highlighting their potential role in expanding our understanding of FCDTC genetics.
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Affiliation(s)
- Juliana Lima von Ammon
- Universidade Federal da BahiaInstituto de Ciências da SaúdePrograma de Pós-graduação em Processos Interativos de Órgãos e SistemasSalvadorBABrasilPrograma de Pós-graduação em Processos Interativos de Órgãos e Sistemas, Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, BA, Brasil
| | - Gabriel Jeferson Rodríguez Machado
- Universidade Federal da BahiaInstituto de Ciências da SaúdePrograma de Pós-graduação em Processos Interativos de Órgãos e SistemasSalvadorBABrasilPrograma de Pós-graduação em Processos Interativos de Órgãos e Sistemas, Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, BA, Brasil
| | - Rafael Reis Campos da Matta
- Universidade Federal da BahiaInstituto de Ciências da SaúdePrograma de Pós-graduação em Processos Interativos de Órgãos e SistemasSalvadorBABrasilPrograma de Pós-graduação em Processos Interativos de Órgãos e Sistemas, Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, BA, Brasil
| | - Ana Clara Telles
- Universidade Federal da BahiaInstituto de Ciências da SaúdePrograma de Pós-graduação em Processos Interativos de Órgãos e SistemasSalvadorBABrasilPrograma de Pós-graduação em Processos Interativos de Órgãos e Sistemas, Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, BA, Brasil
| | - Fabiane Carrijo
- Universidade Federal da BahiaInstituto de Ciências da SaúdePrograma de Pós-graduação em Processos Interativos de Órgãos e SistemasSalvadorBABrasilPrograma de Pós-graduação em Processos Interativos de Órgãos e Sistemas, Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, BA, Brasil
| | - Bruno Alexsander França dos Santos
- Universidade Federal da BahiaInstituto de Ciências da SaúdeDepartamento de BiorregulaçãoSalvadorBABrasilDepartamento de Biorregulação, Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, BA, Brasil
| | - Juliana Cabral Duarte Brandão
- Serviço de Patologia do Hospital Aristides MaltezSalvadorBABrasilServiço de Patologia do Hospital Aristides Maltez, Salvador, BA, Brasil
| | - Thiago Magalhães da Silva
- Universidade Estadual do Sudoeste da BahiaDepartamento de Ciências BiológicasJequiéBABrasilDepartamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia, Jequié, BA, Brasil
| | - Fabio Hecht
- Universidade Federal do Rio de JaneiroInstituto de Biofísica Carlos Chagas FilhoRio de JaneiroRJBrasilInstituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - Gabriel Avela Colozza-Gama
- Universidade Federal de São PauloDepartamento de Morfologia e GenéticaLaboratório de Bases Genéticas de Tumores de TireoideSão PauloSPBrasilLaboratório de Bases Genéticas de Tumores de Tireoide, Divisão de Genética, Departamento de Morfologia e Genética, Universidade Federal de São Paulo, São Paulo, SP, Brasil
| | - Julia Helena Tezzei
- Universidade Federal de São PauloDepartamento de Morfologia e GenéticaLaboratório de Bases Genéticas de Tumores de TireoideSão PauloSPBrasilLaboratório de Bases Genéticas de Tumores de Tireoide, Divisão de Genética, Departamento de Morfologia e Genética, Universidade Federal de São Paulo, São Paulo, SP, Brasil
| | - Janete Maria Cerutti
- Universidade Federal de São PauloDepartamento de Morfologia e GenéticaLaboratório de Bases Genéticas de Tumores de TireoideSão PauloSPBrasilLaboratório de Bases Genéticas de Tumores de Tireoide, Divisão de Genética, Departamento de Morfologia e Genética, Universidade Federal de São Paulo, São Paulo, SP, Brasil
| | - Helton Estrela Ramos
- Universidade Federal da BahiaInstituto de Ciências da SaúdePrograma de Pós-graduação em Processos Interativos de Órgãos e SistemasSalvadorBABrasilPrograma de Pós-graduação em Processos Interativos de Órgãos e Sistemas, Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, BA, Brasil
- Universidade Federal da BahiaInstituto de Ciências da SaúdeDepartamento de BiorregulaçãoSalvadorBABrasilDepartamento de Biorregulação, Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, BA, Brasil
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10
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Quesada J, Alfaro-Segura P, Mata-Somarribas C, Alger J, Toledo M, Ramos de Souza J, Mora J, Graeff-Teixeira C, Solano-Barquero A, Rojas A. Real-time qPCR coupled with high-resolution melting curve analysis for the detection of the internal transcribed spacer 1 of Angiostrongylus costaricensis. Parasitol Res 2024; 123:312. [PMID: 39218957 DOI: 10.1007/s00436-024-08327-6] [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: 05/06/2024] [Accepted: 08/14/2024] [Indexed: 09/04/2024]
Abstract
Abdominal angiostrongyliasis (AA) is a zoonotic and severe parasitic infection caused by Angiostrongylus costaricensis. AA is currently diagnosed by the observation of A. costaricensis-compatible structures in biopsies or the detection of antibodies in serological tests. However, molecular methods targeting homologous sequences of A. costaricensis have not been designed before, and therefore, an HRM-coupled qPCR was developed to detect the internal transcribed spacer 1 (ITS1) of the parasite. The present assay successfully amplified DNA of A. costaricensis obtained from different hosts and identified slight sequence differences through the HRM analysis. The detection limit of the HRM-qPCR was 0.00036 ng/µL, 1.0 ng/µL, and 0.1 ng/µL when A. costaricensis DNA was diluted in nuclease-free water, whole blood, and sera, respectively, which highlights its potential use for cell-free DNA detection. Moreover, the reaction did not cross-amplify DNA of Angiostrongylus cantonensis, Strongyloides stercoralis, and other nematodes, thus emphasizing its specificity. Additionally, the assay tested positive in formalin-fixed paraffin embedded biopsies with visible A. costaricensis adults or eggs, but not in samples without evident parasites or a low number of larvae, which suggests that the reaction is useful for confirming the presence of the nematode in clinical samples. Finally, DNA of sera from patients with AA was evaluated with the HRM-qPCR but none tested positive, possibly due to long storage periods of the samples which could have led to cfDNA degradation. These results indicate that this assay may be useful in the confirmation of AA and its prospection for cell-free DNA detection protocols.
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Affiliation(s)
- Joban Quesada
- Laboratory of Helminthology, Faculty of Microbiology, University of Costa Rica, San José, Costa Rica
| | - Paula Alfaro-Segura
- Laboratory of Helminthology, Faculty of Microbiology, University of Costa Rica, San José, Costa Rica
| | - Carlos Mata-Somarribas
- Centro Nacional de Referencia de Parasitología, Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud, Cartago, Costa Rica
| | - Jackeline Alger
- Departamento de Laboratorio Clínico, Hospital Escuela, Tegucigalpa, Honduras
| | - Mazlova Toledo
- Departamento de Patología, Hospital Escuela, Tegucigalpa, Honduras
| | - Jucicleide Ramos de Souza
- National Reference Laboratory for Schistosomiasis and Malacology, Instituto Oswaldo Cruz-Fiocruz, Rio de Janeiro, Brazil
| | - Javier Mora
- Laboratory of Helminthology, Faculty of Microbiology, University of Costa Rica, San José, Costa Rica
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Carlos Graeff-Teixeira
- Laboratorio de Enfermedades Infecciosas, Centro de Ciências da Saúde, Universidad Federal de Espíritu Santo, Vitória, Brazil
| | - Alberto Solano-Barquero
- Laboratory of Helminthology, Faculty of Microbiology, University of Costa Rica, San José, Costa Rica
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Alicia Rojas
- Laboratory of Helminthology, Faculty of Microbiology, University of Costa Rica, San José, Costa Rica.
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica.
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11
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Chicaud M, Vergara R, Théate I, Lesne P, Rullier A, le Teap P. [Recycled formalin: A new environmental mitigation tool in pathology?]. Ann Pathol 2024; 44:346-352. [PMID: 38965024 DOI: 10.1016/j.annpat.2024.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/07/2024] [Accepted: 06/19/2024] [Indexed: 07/06/2024]
Abstract
Formalin is the international gold-standard fixative in pathology laboratories. However it is not the ideal one considering its deleterious effects on individuals and the environment. Complete formalin removal or even substitution does not seem possible in the near future. In this update, we present various tools allowing to integrate the use of formalin into an ecocare approach. Among them, formalin recycling according to the protocol developed by the University Hospital of Bordeaux is simple to implement and delivers rapid and significant results, allowing pathology professionals to meet the sustainable development objectives included in the France 2030 agenda.
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Affiliation(s)
- Matthieu Chicaud
- Service d'anatomie & cytologie pathologiques, hôpital Simone-Veil, 14, rue de Saint-Prix, 95600 Eaubonne, France.
| | - Rémi Vergara
- Service de pathologie, hôpital du Haut Lévêque, CHU de Bordeaux, 33600 Pessac, France
| | - Ivan Théate
- Service de pathologie, CHU UCL Namur, site Godinne, avenue G.-Thérasse, 1-5530 Yvoir, Belgique
| | - Perrine Lesne
- Service d'anatomie & cytologie pathologiques, hôpital Simone-Veil, 14, rue de Saint-Prix, 95600 Eaubonne, France
| | - Anne Rullier
- Service de pathologie, hôpital Pellegrin, CHU de Bordeaux, 33076 Bordeaux, France
| | - Pour le Teap
- Groupe français pour la transformation écologique en anatomo-cyto-pathologie, France
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12
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Jin W, Qifu C, Hong Y, Hua H, Xuelin L, Xiaomin W, Shuihua L, Mutong F. Intracranial tuberculomas diagnosed with Xpert MTB/RIF Ultra assay of formalin-fixed paraffin-embedded brain tissues and treated with an optimized antituberculosis regimen: A case report. Heliyon 2024; 10:e32462. [PMID: 38961962 PMCID: PMC11219345 DOI: 10.1016/j.heliyon.2024.e32462] [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: 12/29/2023] [Revised: 05/07/2024] [Accepted: 06/04/2024] [Indexed: 07/05/2024] Open
Abstract
Diagnosis of intracranial tuberculoma remains a challenge due to its rarity, non-specific clinical presentation, and radiological findings. Herein, we describe a case of intracranial tuberculomas in a male diabetic patient who presented headache and vomiting on admission. Neuroimaging findings indicated multiple ring contrast-enhanced lesions with extensive perilesional edema. However, a cerebrospinal fluid (CSF) examination was normal. When a biopsy of brain lesions was performed, pathological characteristics of tuberculosis were absent and acid-fast staining was negative. A tuberculosis diagnosis was subsequently obtained from an Xpert MTB/RIF Ultra assay of formalin-fixed paraffin-embedded brain tissue. The patient was treated with an optimized anti-tuberculosis regimen which included high-dose intravenous administration of rifampicin and isoniazid, and oral administration of linezolid. The patient recovered well and exhibited marked clinical improvement. This case report demonstrates that when CSF analysis does not indicate the presence of intracranial tuberculomas, analysis of formalin-fixed paraffin-embedded brain tissue specimens with the Xpert MTB/RIF Ultra assay may be able to confirm a diagnosis. Furthermore, a high dose of rifampicin and isoniazid plus linezolid may improve patient outcome.
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Affiliation(s)
- Wang Jin
- Division of Pulmonary Diseases Department, The Third People's Hospital of Shenzhen, Southern University of Science and Technology, Shenzhen, Guangdong, China
- National Clinical Research Center for Infectious Disease, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Chen Qifu
- Department of Neurosurgery, The Third People's Hospital of Shenzhen, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Yu Hong
- Department of Pathology, The Third People's Hospital of Shenzhen, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Huang Hua
- Department of Radiology, The Third People's Hospital of Shenzhen, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Li Xuelin
- Department of Clinical Laboratory, The Third People's Hospital of Shenzhen, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Wang Xiaomin
- National Clinical Research Center for Infectious Disease, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Lu Shuihua
- Division of Pulmonary Diseases Department, The Third People's Hospital of Shenzhen, Southern University of Science and Technology, Shenzhen, Guangdong, China
- National Clinical Research Center for Infectious Disease, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Fang Mutong
- Division of Pulmonary Diseases Department, The Third People's Hospital of Shenzhen, Southern University of Science and Technology, Shenzhen, Guangdong, China
- National Clinical Research Center for Infectious Disease, Southern University of Science and Technology, Shenzhen, Guangdong, China
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13
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Sunitha Kumary VUN, Venters BJ, Raman K, Sen S, Estève PO, Cowles MW, Keogh MC, Pradhan S. Emerging Approaches to Profile Accessible Chromatin from Formalin-Fixed Paraffin-Embedded Sections. EPIGENOMES 2024; 8:20. [PMID: 38804369 PMCID: PMC11130958 DOI: 10.3390/epigenomes8020020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 05/06/2024] [Indexed: 05/29/2024] Open
Abstract
Nucleosomes are non-uniformly distributed across eukaryotic genomes, with stretches of 'open' chromatin strongly associated with transcriptionally active promoters and enhancers. Understanding chromatin accessibility patterns in normal tissue and how they are altered in pathologies can provide critical insights to development and disease. With the advent of high-throughput sequencing, a variety of strategies have been devised to identify open regions across the genome, including DNase-seq, MNase-seq, FAIRE-seq, ATAC-seq, and NicE-seq. However, the broad application of such methods to FFPE (formalin-fixed paraffin-embedded) tissues has been curtailed by the major technical challenges imposed by highly fixed and often damaged genomic material. Here, we review the most common approaches for mapping open chromatin regions, recent optimizations to overcome the challenges of working with FFPE tissue, and a brief overview of a typical data pipeline with analysis considerations.
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Affiliation(s)
| | - Bryan J. Venters
- EpiCypher Inc., Durham, NC 27709, USA; (V.U.N.S.K.); (B.J.V.); (M.W.C.)
| | - Karthikeyan Raman
- Genome Biology Division, New England Biolabs, Ipswich, MA 01983, USA; (K.R.); (S.S.); (P.-O.E.)
| | - Sagnik Sen
- Genome Biology Division, New England Biolabs, Ipswich, MA 01983, USA; (K.R.); (S.S.); (P.-O.E.)
| | - Pierre-Olivier Estève
- Genome Biology Division, New England Biolabs, Ipswich, MA 01983, USA; (K.R.); (S.S.); (P.-O.E.)
| | - Martis W. Cowles
- EpiCypher Inc., Durham, NC 27709, USA; (V.U.N.S.K.); (B.J.V.); (M.W.C.)
| | | | - Sriharsa Pradhan
- Genome Biology Division, New England Biolabs, Ipswich, MA 01983, USA; (K.R.); (S.S.); (P.-O.E.)
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14
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Evans M, Kendall T. Practical considerations for pathological diagnosis and molecular profiling of cholangiocarcinoma: an expert review for best practices. Expert Rev Mol Diagn 2024; 24:393-408. [PMID: 38752560 DOI: 10.1080/14737159.2024.2353696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 05/07/2024] [Indexed: 05/22/2024]
Abstract
INTRODUCTION Advances in precision medicine have expanded access to targeted therapies and demand for molecular profiling of cholangiocarcinoma (CCA) patients in routine clinical practice. However, pathologists face challenges in establishing a definitive intrahepatic CCA (iCCA) diagnosis while preserving sufficient tissue for molecular profiling. Additionally, they frequently face challenges in optimal tissue handling to preserve nucleic acid integrity. AREAS COVERED This article first identifies the challenges in establishing a definitive diagnosis of iCCA in a lesional liver biopsy while preserving sufficient tissue for molecular profiling. Then, the authors explore the clinical value of molecular profiling, the basic principles of single gene and next-generation sequencing (NGS) techniques, and the challenges in tissue sampling for genomic testing. They also propose an algorithm for best practice in tissue management for molecular profiling of CCA. EXPERT OPINION Several practical challenges face pathologists during tissue sampling and processing for molecular profiling. Optimized tissue processing, careful tissue handling, and selection of appropriate approaches to molecular testing are essential to ensure that the highest possible quality of diagnostic information is provided in the greatest proportion of cases.
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Affiliation(s)
- Matt Evans
- Cellular Pathologist, University Hospital Southampton NHS Foundation Trust, Southampton, UK
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15
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Silva RG, Kiupel M, Langohr IM, Wise A, Pereira SA, Gonçalves NP, da Conceição GMS, Ferreira LC, de Campos MP, Miranda LDFC, Figueiredo FB, de Oliveira RDVC, Keidel L, Menezes RC. Comparative Study of Colorimetric In Situ Hybridization and Quantitative Real-Time Polymerase Chain Reaction for Diagnosis of Infection by Leishmania infantum in Dogs in Formalin-Fixed and Paraffin-Embedded Skin. Trop Med Infect Dis 2024; 9:91. [PMID: 38668552 PMCID: PMC11054412 DOI: 10.3390/tropicalmed9040091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/18/2024] [Accepted: 04/18/2024] [Indexed: 04/29/2024] Open
Abstract
The zoonotic visceral leishmaniasis is caused by the protozoan Leishmania infantum and dogs are reservoirs for this parasite. For the diagnosis of Leishmania at the species level in dogs in formalin-fixed, paraffin-embedded skin (FFPES) samples, colorimetric in situ hybridization (CISH) and quantitative real-time polymerase chain reaction (qPCR) are options, but their sensitivities are not well established. Therefore, the aim of this study was to determine the sensitivity of these two techniques in FFPES for the diagnosis of the L. infantum infection in dogs using culture as the reference standard. The FFPES of 48 dogs with cutaneous infection by L. infantum confirmed by culture and by multilocus enzyme electrophoresis were examined by CISH and qPCR using specific probes for L. infantum. The sensitivities of qPCR, CISH and their combination were, respectively, 77.0%, 58.0% and 83.3%. The sensitivities of qPCR in dogs with and without clinical signs were, respectively, 74.2% and 82.4%. The sensitivities of CISH in dogs with and without clinical signs were, respectively, 61.3% and 52.9%. The CISH and qPCR showed satisfactory sensitivities for the diagnosis of L. infantum in the FFPES of dogs, even in dogs without clinical signs, and their combination increases the sensitivity for this diagnosis.
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Affiliation(s)
- Ricardo Gonçalves Silva
- Laboratory of Clinical Research on Dermatozoonoses in Domestic Animals, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Av. Brasil, 4365, Rio de Janeiro 21040-360, Brazil; (R.G.S.); (S.A.P.); (L.C.F.); (L.K.)
| | - Matti Kiupel
- Veterinary Diagnostic Laboratory, Michigan State University, 4125 Beaumont Road, Lansing, MI 48910, USA; (M.K.); (A.W.)
| | - Ingeborg Maria Langohr
- Sanofi, Global Discovery Pathology, Translational Models Research Platform, 350 Water Street, Cambridge, MA 02141, USA;
| | - Annabel Wise
- Veterinary Diagnostic Laboratory, Michigan State University, 4125 Beaumont Road, Lansing, MI 48910, USA; (M.K.); (A.W.)
| | - Sandro Antonio Pereira
- Laboratory of Clinical Research on Dermatozoonoses in Domestic Animals, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Av. Brasil, 4365, Rio de Janeiro 21040-360, Brazil; (R.G.S.); (S.A.P.); (L.C.F.); (L.K.)
| | - Natália Pedra Gonçalves
- Bio-Manguinhos, Oswaldo Cruz Foundation, Av. Brasil, 4365, Rio de Janeiro 21040-360, Brazil; (N.P.G.); (G.M.S.d.C.)
| | | | - Luiz Cláudio Ferreira
- Laboratory of Clinical Research on Dermatozoonoses in Domestic Animals, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Av. Brasil, 4365, Rio de Janeiro 21040-360, Brazil; (R.G.S.); (S.A.P.); (L.C.F.); (L.K.)
| | - Monique Paiva de Campos
- Carlos Chagas Institute, Oswaldo Cruz Foundation, Rua Prof. Algacyr Munhoz Mader, 3775, Curitiba 81350-010, Brazil; (M.P.d.C.); (F.B.F.)
| | - Luciana de Freitas Campos Miranda
- Laboratory of Clinical Research and Surveillance of Leishmaniasis, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Av. Brasil, 4365, Rio de Janeiro 21040-360, Brazil;
| | - Fabiano Borges Figueiredo
- Carlos Chagas Institute, Oswaldo Cruz Foundation, Rua Prof. Algacyr Munhoz Mader, 3775, Curitiba 81350-010, Brazil; (M.P.d.C.); (F.B.F.)
| | | | - Lucas Keidel
- Laboratory of Clinical Research on Dermatozoonoses in Domestic Animals, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Av. Brasil, 4365, Rio de Janeiro 21040-360, Brazil; (R.G.S.); (S.A.P.); (L.C.F.); (L.K.)
| | - Rodrigo Caldas Menezes
- Laboratory of Clinical Research on Dermatozoonoses in Domestic Animals, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Av. Brasil, 4365, Rio de Janeiro 21040-360, Brazil; (R.G.S.); (S.A.P.); (L.C.F.); (L.K.)
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16
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Hoshino A, Oana Y, Ohi Y, Maeda Y, Omori M, Takada Y, Ikeda T, Sotome K, Maeda H, Yanagisawa T, Takeuchi O, Kuronuma S, Sangai T, Shibahara Y, Murakumo Y, Saegusa M, Kanomata N, Nagasawa S, Yamaguchi R, Yoshida M, Kozuka Y, Matsumoto H, Tsugawa K, Maeda I. Using the DNA Integrity Number to Analyze DNA Quality in Specimens Collected from Liquid-Based Cytology after Fine-Needle Aspiration of Breast Tumors and Lesions. Acta Cytol 2024; 68:145-152. [PMID: 38555634 DOI: 10.1159/000538071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 02/25/2024] [Indexed: 04/02/2024]
Abstract
INTRODUCTION Cancer genome analysis using next-generation sequencing requires adequate and high-quality DNA samples. Genomic analyses were conventionally performed using formalin-fixed paraffin-embedded sections rather than cytology samples such as cell block or smear specimens. Specimens collected from liquid-based cytology (LBC) have the potential to be sources of high-quality DNA suitable for genetic analysis even after long-term storage. METHODS We collected breast tumor/lesion fractions from 92 residual LBC specimens using fine-needle aspiration (FNA) biopsy, including breast carcinoma (1 invasive carcinoma and 4 ductal carcinomas in situ), papillomatous lesion (5 intraductal papillomas), and fibroepithelial lesion (19 phyllodes tumors and 53 fibroadenomas) samples, and others (1 ductal adenoma, 1 hamartoma, 1 fibrocystic disease, and 7 unknown). DNA was extracted from all samples and subjected to DNA integrity number (DIN) score analysis. RESULTS Average DIN score collected from 92 LBC specimens was significantly higher score. In addition, high-quality DNA with high DIN values (7.39 ± 0.80) was successfully extracted more than 12 months after storage of residual LBC specimens. CONCLUSION Residual LBC specimens collected from FNA of the breast were verified to carry high-quality DNA and could serve as an alternate source for genetic analysis.
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Affiliation(s)
- Akiyoshi Hoshino
- Department of Diagnostic Pathology, Kitasato University Kitasato Institute Hospital, Tokyo, Japan,
- Department of Pathology, Kitasato University School of Medicine, Tokyo, Japan,
| | - Yoshiyasu Oana
- Department of Diagnostic Pathology, Kitasato University Kitasato Institute Hospital, Tokyo, Japan
| | - Yasuyo Ohi
- Department of Pathology, Sagara Hospital, Kagoshima City, Kagoshima, Japan
| | - Yukari Maeda
- Department of Pathology, Sagara Hospital, Kagoshima City, Kagoshima, Japan
| | - Masako Omori
- Department of Pathology, Kurashiki Medical Center, Kurashiki City, Okayama, Japan
| | - Yuki Takada
- Department of Pathology, Kurashiki Medical Center, Kurashiki City, Okayama, Japan
| | - Tadashi Ikeda
- Department of Surgery, Kitasato University Kitasato Institute Hospital, Tokyo, Japan
| | - Keiichi Sotome
- Department of Surgery, Kitasato University Kitasato Institute Hospital, Tokyo, Japan
| | - Hinako Maeda
- Department of Surgery, Kitasato University Kitasato Institute Hospital, Tokyo, Japan
| | - Takako Yanagisawa
- Department of Surgery, Kitasato University Kitasato Institute Hospital, Tokyo, Japan
| | - Osamu Takeuchi
- Biomedical Laboratory, Kitasato University Kitasato Institute Hospital, Tokyo, Japan
| | - Satoshi Kuronuma
- Biomedical Laboratory, Kitasato University Kitasato Institute Hospital, Tokyo, Japan
| | - Takafumi Sangai
- Department of Surgery, Kitasato University Hospital, Sagamihara City, Sagamihara, Japan
| | - Yukiko Shibahara
- Department of Pathology, Kitasato University Hospital, Sagamihara City, Sagamihara, Japan
| | - Yoshiki Murakumo
- Department of Pathology, Kitasato University Hospital, Sagamihara City, Sagamihara, Japan
| | - Makoto Saegusa
- Department of Pathology, Kitasato University Hospital, Sagamihara City, Sagamihara, Japan
| | - Naoki Kanomata
- Department of Pathology, St. Lukes International Hospital, Tokyo, Japan
| | - Satoi Nagasawa
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa City, Chiba, Japan
| | - Rin Yamaguchi
- Department of Pathology, Nagasaki University Hospital, Nagasaki City, Nagasaki, Japan
| | - Masayuki Yoshida
- Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan
| | - Yuji Kozuka
- Department of Pathology, Mie University Hospital, Tsu, Japan
| | | | - Koichiro Tsugawa
- Divison of Breast and Endocrine Surgery, Department of Surgery, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Ichiro Maeda
- Department of Diagnostic Pathology, Kitasato University Kitasato Institute Hospital, Tokyo, Japan
- Department of Pathology, Kitasato University School of Medicine, Tokyo, Japan
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Ivorová S, Kopčaková A, Pristaš P, Kišidayová S. Morphometric and Molecular Analysis of Five-Spine Epidinium Morphotypes Taken from the Rumen of European Bison, Bison bonasus. Life (Basel) 2023; 13:2350. [PMID: 38137951 PMCID: PMC10744686 DOI: 10.3390/life13122350] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
An important feature of ruminal ciliates is their phenotypic plasticity, which makes their identification difficult. The common manifestation of the phenotypic plasticity in rumen ciliates is a change in their cell size and caudal spination. We analyzed various morphotypes of Epidinium with five caudal processes (spines) taken from the rumen of European bison (Bison bonasus). In the study, the cluster analysis and K-means analysis of morphometric data could not distinguish very similar morphotypes of Epidinium with five caudal processes. However, the morphotype of E. parvicaudatum prevailed (70%). The DNA of four individual E. parvicaudatum was isolated successfully from formaldehyde-preserved samples. The partial 18S rDNA gene sequences (about 350-400 bp) were identical to Epidinium sequences in GenBank (E. caudatum, a one-spine morphotype, and E. cattanei, a five-spine morphotype). It can be assumed that these short sequences cannot distinguish the differences between the Epidinium morphospecies. Complete gene sequences from various hosts and various molecular markers are necessary to reveal the validity of the Epidinium five-spine species. In conclusion, classical morphology should be supplemented with molecular data when more morphotypes of the rumen ciliate species are present in samples.
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Affiliation(s)
| | | | | | - Svetlana Kišidayová
- Institute of Animal Physiology, Centre of Biosciences, Slovak Academy of Sciences, 04001 Košice, Slovakia; (S.I.); (A.K.); (P.P.)
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18
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Vucevic DD, Seidman MA, Mesaki K, Guan Z, Juvet S, Liu M, Keshavjee S, Murphy K. A Novel Tissue Preservation and Transport Solution as a Substitute for Formalin. J Transl Med 2023; 103:100198. [PMID: 37321542 DOI: 10.1016/j.labinv.2023.100198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/31/2023] [Accepted: 06/05/2023] [Indexed: 06/17/2023] Open
Abstract
Formalin, a common laboratory fixative, is a type 1 carcinogen; a biohazard with risks, environmental, disposal, and legal costs; and a chemical modifier of protein epitopes in tissues. A less-toxic tissue preservation method is therefore badly needed. We have developed a novel tissue preservation medium, Amber, composed of low-potassium dextran glucose, 10% honey, and 1% coconut oil. This study investigates Amber as compared with formalin with respect to the following aspects: (1) histologic preservation, (2) epitope integrity with immunohistochemistry (IHC) and immunofluorescence (IF), and (3) integrity of tissue RNA. Rat and human lung, liver, kidney, and heart tissues were collected and stored for 24 hours at 4 °C in Amber or formalin. The tissues were evaluated with hematoxylin and eosin; IHC: thyroid transcription factor, muscle-specific actin, hepatocyte-specific antigen, and common acute lymphoblastic leukemia antigen; and IF: VE-cadherin, vimentin, and muscle-specific actin. RNA quality upon extraction was also assessed. Amber demonstrated superior and/or noninferior performance in rat and human tissue evaluation with respect to standard techniques of histology, IHC, IF, and extracted RNA quality. Amber maintains high-quality morphology without compromising the ability to perform IHC and nucleic acid extraction. As such, Amber could be a safer and superior substitute to formalin for clinical tissue preservation for contemporary pathological examination.
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Affiliation(s)
- Diana D Vucevic
- Biomedical Engineering Institute, University of Toronto, Toronto, Ontario, Canada; Division of Thoracic Surgery and Latner Thoracic Research Laboratories, Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Michael A Seidman
- Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada; Department of Laboratory Medicine & Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Kumi Mesaki
- Division of Thoracic Surgery and Latner Thoracic Research Laboratories, Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Zehong Guan
- Division of Thoracic Surgery and Latner Thoracic Research Laboratories, Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Stephen Juvet
- Biomedical Engineering Institute, University of Toronto, Toronto, Ontario, Canada; Division of Thoracic Surgery and Latner Thoracic Research Laboratories, Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada; Department of Surgery, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada; Institute of Medical Science, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Mingyao Liu
- Division of Thoracic Surgery and Latner Thoracic Research Laboratories, Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada; Department of Surgery, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada; Institute of Medical Science, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Shaf Keshavjee
- Biomedical Engineering Institute, University of Toronto, Toronto, Ontario, Canada; Division of Thoracic Surgery and Latner Thoracic Research Laboratories, Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada; Department of Surgery, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada; Institute of Medical Science, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Kieran Murphy
- Joint Department of Medical Imaging, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.
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Rao W, Guo L, Ling Y, Dong L, Li W, Ying J, Li W. Developing an effective quality evaluation strategy of next-generation sequencing for accurate detecting non-small cell lung cancer samples with variable characteristics: a real-world clinical practice. J Cancer Res Clin Oncol 2023; 149:4889-4897. [PMID: 36305947 DOI: 10.1007/s00432-022-04388-1] [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: 07/10/2022] [Accepted: 09/29/2022] [Indexed: 10/31/2022]
Abstract
PURPOSE Next-generation sequencing (NGS) has been widely used in determining molecular profiling of non-small cell lung cancer (NSCLC). However, low-quality sequencing data may be generated with formalin-fixed and paraffin-embedded (FFPE) samples that have passed pre-sequencing quality control (QC). Therefore, quality evaluation of sequencing data is also critical for accurate tissue genotyping. Herein, we aimed to developed a grading QC algorithm, and provide a recommendation to refine and optimize NGS-based molecular diagnostic strategies. METHODS We interrogated 1260 NSCLC samples using hybrid capture-based targeted DNA NGS, and quantified the sequencing data as high, medium and low quality, according to a grading QC algorithm. Then, we explored the relationship between sequencing quality and sample characteristics, and compared the concordance rates of results between NGS and conventional molecular tests for FFPE samples with variable characteristics. RESULTS We found that high-quality data were associated with samples with shorter storage time and lower DNA degradation in resection samples, and were associated with intra-hospital samples, adequate DNA quantity, and lower DNA degradation in biopsy samples. Moreover, accurate NGS results can be achieved in samples with high-quality data, but not samples with medium-quality data, especially for rearrangements detection. CONCLUSION Our study demonstrates that the real-world clinical adoption of an effective QC strategy for NGS is necessary to ensure accurate results from FFPE samples of NSCLC with variable characteristics. Validation of actionable alterations by additional methods is highly recommended in cases with low QC score, particularly for the detection of rearrangements.
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Affiliation(s)
- Wei Rao
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17 Panjiayuan Nanli, Beijing, 100021, China
| | - Lei Guo
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17 Panjiayuan Nanli, Beijing, 100021, China
| | - Yun Ling
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17 Panjiayuan Nanli, Beijing, 100021, China
| | - Lin Dong
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17 Panjiayuan Nanli, Beijing, 100021, China
| | - Wenbin Li
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17 Panjiayuan Nanli, Beijing, 100021, China
| | - Jianming Ying
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17 Panjiayuan Nanli, Beijing, 100021, China
| | - Weihua Li
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 17 Panjiayuan Nanli, Beijing, 100021, China.
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20
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Kato A, Kondo N, Wanifuchi-Endo Y, Fujita T, Asano T, Hisada T, Uemoto Y, Terada M, Kato H, Komura M, Okuda K, Takahashi S, Toyama T. Low TINAGL1 expression is a marker for poor prognosis in breast cancer. J Cancer Res Clin Oncol 2023; 149:4771-4782. [PMID: 36229542 DOI: 10.1007/s00432-022-04394-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 10/04/2022] [Indexed: 11/25/2022]
Abstract
PURPOSE Tubulointerstitial nephritis antigen-like 1 (TINAGL1) was reported to suppress tumor metastasis and growth in triple-negative (TN) breast cancer. We aimed to determine the associations of TINAGL1 expression with clinicopathological factors and prognosis in breast cancer patients with long-term follow-up. METHODS A total of 599 consecutive primary invasive breast cancer patients with available tissue specimens from surgery in our hospital were included in the study. TINAGL1 mRNA expression was examined in all 599 tissue specimens using a TaqMan real-time PCR system. TINAGL1 protein expression was further examined in 299 patients with available tissue specimens for immunohistochemical staining. Survival analyses were performed using the Kaplan-Meier method and Cox proportional hazards models. RESULTS The median follow-up period was 12.0 years. In the total patients, low TINAGL1 mRNA expression was associated with significantly shorter disease-free survival (DFS) and overall survival than high expression (P = 0.003 and P = 0.01, respectively). Furthermore, hormone receptor-positive/human epidermal growth factor receptor 2-negative breast cancer patients with low TINAGL1 mRNA expression had a worse prognosis. Multivariate analysis identified low TINAGL1 mRNA expression, combined with lymph node positivity, as an independent poor prognostic factor for DFS in invasive breast cancer patients (HR 1.41; 95% CI 1.02-1.96; P = 0.036). TINAGL1 mRNA expression also varied with menopausal status, with low TINAGL1 mRNA expression being positively associated with poor prognosis in premenopausal patients, but not in postmenopausal patients. CONCLUSION Our findings demonstrate that TINAGL1 may be a promising candidate biomarker and therapeutic target in breast cancer patients.
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Affiliation(s)
- Akiko Kato
- Department of Breast Surgery, Nagoya City University Graduate School of Medical Sciences, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya, 467-8601, Japan
| | - Naoto Kondo
- Department of Breast Surgery, Nagoya City University Graduate School of Medical Sciences, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya, 467-8601, Japan
| | - Yumi Wanifuchi-Endo
- Department of Breast Surgery, Nagoya City University Graduate School of Medical Sciences, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya, 467-8601, Japan
| | - Takashi Fujita
- Department of Breast Surgery, Nagoya City University Graduate School of Medical Sciences, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya, 467-8601, Japan
| | - Tomoko Asano
- Department of Breast Surgery, Nagoya City University Graduate School of Medical Sciences, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya, 467-8601, Japan
| | - Tomoka Hisada
- Department of Breast Surgery, Nagoya City University Graduate School of Medical Sciences, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya, 467-8601, Japan
| | - Yasuaki Uemoto
- Department of Breast Surgery, Nagoya City University Graduate School of Medical Sciences, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya, 467-8601, Japan
| | - Mitsuo Terada
- Department of Breast Surgery, Nagoya City University Graduate School of Medical Sciences, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya, 467-8601, Japan
| | - Hiroyuki Kato
- Department of Experimental Pathology and Tumor Biology, Nagoya City University Graduate School of Medical Sciences, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya, 467-8601, Japan
| | - Masayuki Komura
- Department of Experimental Pathology and Tumor Biology, Nagoya City University Graduate School of Medical Sciences, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya, 467-8601, Japan
| | - Katsuhiro Okuda
- Department of Oncology, Immunology and Surgery, Nagoya City University Graduate School of Medical Sciences, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya, 467-8601, Japan
| | - Satoru Takahashi
- Department of Experimental Pathology and Tumor Biology, Nagoya City University Graduate School of Medical Sciences, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya, 467-8601, Japan
| | - Tatsuya Toyama
- Department of Breast Surgery, Nagoya City University Graduate School of Medical Sciences, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya, 467-8601, Japan.
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21
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Bontoux C, Marcovich A, Goffinet S, Pesce F, Tanga V, Bohly D, Salah M, Washetine K, Messaoudi Z, Felix JM, Bonnetaud C, Wang L, Menon G, Berthet JP, Cohen C, Benzaquen J, Marquette CH, Lassalle S, Long-Mira E, Hofman V, Xerri L, Ilié M, Hofman P. The Need to Set up a Biobank Dedicated to Lymphoid Malignancies: Experience of a Single Center (Laboratory of Clinical and Experimental Pathology, University Côte d'Azur, Nice, France). J Pers Med 2023; 13:1076. [PMID: 37511690 PMCID: PMC10381579 DOI: 10.3390/jpm13071076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
Several therapies to improve the management of lymphoma are currently being investigated, necessitating the development of new biomarkers. However, this requires high-quality and clinically annotated biological material. Therefore, we established a lymphoma biobank including all available biological material (tissue specimens and matched biological resources) along with associated clinical data for lymphoma patients diagnosed, according to the WHO classification, between 2005 and 2022 in the Laboratory of Clinical and Experimental Pathology, Nice, France. We retrospectively included selected cases in a new collection at the Côte d'Azur Biobank, which contains 2150 samples from 363 cases (351 patients). The male/female ratio was 1.3, and the median age at diagnosis was 58 years. The most common lymphoma types were classical Hodgkin lymphoma, diffuse large B-cell lymphoma, and extra-nodal marginal zone lymphoma of MALT tissue. The main sites of lymphoma were the mediastinum, lymph node, Waldeyer's ring, and lung. The Côte d'Azur Biobank is ISO 9001 and ISO 20387 certified and aims to provide high quality and diverse biological material to support translational research projects into lymphoma. The clinico-pathological data generated by this collection should aid the development of new biomarkers to enhance the survival of patients with lymphoid malignancies.
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Affiliation(s)
- Christophe Bontoux
- Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- Team 4, Institute of Research on Cancer and Aging of Nice (IRCAN), Inserm U1081, CNRS UMR7284, Université Côte d'Azur, CHU de Nice, CEDEX 2, 06107 Nice, France
- FHU OncoAge, Université Côte d'Azur, CEDEX 1, 06001 Nice, France
- Institut Hospitalo-Universitaire (IHU), RespirERA, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
| | - Aubiège Marcovich
- Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- FHU OncoAge, Université Côte d'Azur, CEDEX 1, 06001 Nice, France
- Institut Hospitalo-Universitaire (IHU), RespirERA, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
| | - Samantha Goffinet
- Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- FHU OncoAge, Université Côte d'Azur, CEDEX 1, 06001 Nice, France
- Institut Hospitalo-Universitaire (IHU), RespirERA, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
| | - Florian Pesce
- Department of Biopathology and Tumor Immunology, Institut Paoli-Calmettes, Centre de Recherche en Cancérologie de Marseille, INSERM U1068, Centre National de la Recherche Scientifique UMR 7258, Aix-Marseille University, UM105, CEDEX 9, 13273 Marseille, France
| | - Virginie Tanga
- Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- FHU OncoAge, Université Côte d'Azur, CEDEX 1, 06001 Nice, France
- Institut Hospitalo-Universitaire (IHU), RespirERA, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
| | - Doriane Bohly
- Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- FHU OncoAge, Université Côte d'Azur, CEDEX 1, 06001 Nice, France
- Institut Hospitalo-Universitaire (IHU), RespirERA, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
| | - Myriam Salah
- Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- FHU OncoAge, Université Côte d'Azur, CEDEX 1, 06001 Nice, France
- Institut Hospitalo-Universitaire (IHU), RespirERA, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
| | - Kevin Washetine
- Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- FHU OncoAge, Université Côte d'Azur, CEDEX 1, 06001 Nice, France
- Institut Hospitalo-Universitaire (IHU), RespirERA, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
| | - Zeineb Messaoudi
- Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- FHU OncoAge, Université Côte d'Azur, CEDEX 1, 06001 Nice, France
| | - Jean-Marc Felix
- Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- FHU OncoAge, Université Côte d'Azur, CEDEX 1, 06001 Nice, France
- Institut Hospitalo-Universitaire (IHU), RespirERA, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
| | - Christelle Bonnetaud
- Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- FHU OncoAge, Université Côte d'Azur, CEDEX 1, 06001 Nice, France
- Institut Hospitalo-Universitaire (IHU), RespirERA, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
| | - Lihui Wang
- Haemato-Oncology Diagnostic Service, Cheshire & Merseyside Cancer Network, Liverpool University Hospitals NHS Foundation Trust, CSSB Building Level 4, Vernon Street, Liverpool L7 8YE, UK
| | - Geetha Menon
- Haemato-Oncology Diagnostic Service, Cheshire & Merseyside Cancer Network, Liverpool University Hospitals NHS Foundation Trust, CSSB Building Level 4, Vernon Street, Liverpool L7 8YE, UK
| | - Jean-Philippe Berthet
- Institut Hospitalo-Universitaire (IHU), RespirERA, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- Department of Thoracic Surgery, FHU OncoAge, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
| | - Charlotte Cohen
- Institut Hospitalo-Universitaire (IHU), RespirERA, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- Department of Thoracic Surgery, FHU OncoAge, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
| | - Jonathan Benzaquen
- FHU OncoAge, Université Côte d'Azur, CEDEX 1, 06001 Nice, France
- Institut Hospitalo-Universitaire (IHU), RespirERA, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- Department of Pneumology, FHU OncoAge, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
| | - Charles-Hugo Marquette
- FHU OncoAge, Université Côte d'Azur, CEDEX 1, 06001 Nice, France
- Institut Hospitalo-Universitaire (IHU), RespirERA, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- Department of Pneumology, FHU OncoAge, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
| | - Sandra Lassalle
- Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- Team 4, Institute of Research on Cancer and Aging of Nice (IRCAN), Inserm U1081, CNRS UMR7284, Université Côte d'Azur, CHU de Nice, CEDEX 2, 06107 Nice, France
- FHU OncoAge, Université Côte d'Azur, CEDEX 1, 06001 Nice, France
- Institut Hospitalo-Universitaire (IHU), RespirERA, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
| | - Elodie Long-Mira
- Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- Team 4, Institute of Research on Cancer and Aging of Nice (IRCAN), Inserm U1081, CNRS UMR7284, Université Côte d'Azur, CHU de Nice, CEDEX 2, 06107 Nice, France
- FHU OncoAge, Université Côte d'Azur, CEDEX 1, 06001 Nice, France
- Institut Hospitalo-Universitaire (IHU), RespirERA, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
| | - Veronique Hofman
- Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- Team 4, Institute of Research on Cancer and Aging of Nice (IRCAN), Inserm U1081, CNRS UMR7284, Université Côte d'Azur, CHU de Nice, CEDEX 2, 06107 Nice, France
- FHU OncoAge, Université Côte d'Azur, CEDEX 1, 06001 Nice, France
- Institut Hospitalo-Universitaire (IHU), RespirERA, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
| | - Luc Xerri
- Department of Biopathology and Tumor Immunology, Institut Paoli-Calmettes, Centre de Recherche en Cancérologie de Marseille, INSERM U1068, Centre National de la Recherche Scientifique UMR 7258, Aix-Marseille University, UM105, CEDEX 9, 13273 Marseille, France
| | - Marius Ilié
- Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- Team 4, Institute of Research on Cancer and Aging of Nice (IRCAN), Inserm U1081, CNRS UMR7284, Université Côte d'Azur, CHU de Nice, CEDEX 2, 06107 Nice, France
- FHU OncoAge, Université Côte d'Azur, CEDEX 1, 06001 Nice, France
- Institut Hospitalo-Universitaire (IHU), RespirERA, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
| | - Paul Hofman
- Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- Team 4, Institute of Research on Cancer and Aging of Nice (IRCAN), Inserm U1081, CNRS UMR7284, Université Côte d'Azur, CHU de Nice, CEDEX 2, 06107 Nice, France
- FHU OncoAge, Université Côte d'Azur, CEDEX 1, 06001 Nice, France
- Institut Hospitalo-Universitaire (IHU), RespirERA, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
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22
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Rasmussen M, Sowter P, Gallon R, Durhuus JA, Hayes C, Andersen O, Nilbert M, Schejbel L, Høgdall E, Santibanez-Koref M, Jackson MS, Burn J, Therkildsen C. Mismatch repair deficiency testing in Lynch syndrome-associated urothelial tumors. Front Oncol 2023; 13:1147591. [PMID: 37143941 PMCID: PMC10151563 DOI: 10.3389/fonc.2023.1147591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 03/23/2023] [Indexed: 05/06/2023] Open
Abstract
Introduction Lynch syndrome-associated cancer develops due to germline pathogenic variants in one of the mismatch repair (MMR) genes, MLH1, MSH2, MSH6 or PMS2. Somatic second hits in tumors cause MMR deficiency, testing for which is used to screen for Lynch syndrome in colorectal cancer and to guide selection for immunotherapy. Both MMR protein immunohistochemistry and microsatellite instability (MSI) analysis can be used. However, concordance between methods can vary for different tumor types. Therefore, we aimed to compare methods of MMR deficiency testing in Lynch syndrome-associated urothelial cancers. Methods Ninety-seven urothelial (61 upper tract and 28 bladder) tumors diagnosed from 1980 to 2017 in carriers of Lynch syndrome-associated pathogenic MMR variants and their first-degree relatives (FDR) were analyzed by MMR protein immunohistochemistry, the MSI Analysis System v1.2 (Promega), and an amplicon sequencing-based MSI assay. Two sets of MSI markers were used in sequencing-based MSI analysis: a panel of 24 and 54 markers developed for colorectal cancer and blood MSI analysis, respectively. Results Among the 97 urothelial tumors, 86 (88.7%) showed immunohistochemical MMR loss and 68 were successfully analyzed by the Promega MSI assay, of which 48 (70.6%) were MSI-high and 20 (29.4%) were MSI-low/microsatellite stable. Seventy-two samples had sufficient DNA for the sequencing-based MSI assay, of which 55 (76.4%) and 61 (84.7%) scored as MSI-high using the 24-marker and 54-marker panels, respectively. The concordance between the MSI assays and immunohistochemistry was 70.6% (p = 0.003), 87.5% (p = 0.039), and 90.3% (p = 1.00) for the Promega assay, the 24-marker assay, and the 54-marker assay, respectively. Of the 11 tumors with retained MMR protein expression, four were MSI-low/MSI-high or MSI-high by the Promega assay or one of the sequencing-based assays. Conclusion Our results show that Lynch syndrome-associated urothelial cancers frequently had loss of MMR protein expression. The Promega MSI assay was significantly less sensitive, but the 54-marker sequencing-based MSI analysis showed no significant difference compared to immunohistochemistry. Data from this study alongside previous studies, suggest that universal MMR deficiency testing of newly diagnosed urothelial cancers, using immunohistochemistry and/or sequencing-based MSI analysis of sensitive markers, offer a potentially useful approach to identification of Lynch syndrome cases.
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Affiliation(s)
- Maria Rasmussen
- Department of Clinical Research, Copenhagen University Hospital - Amager and Hvidovre, Copenhagen, Denmark
| | - Peter Sowter
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Richard Gallon
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jon Ambæk Durhuus
- Department of Clinical Research, Copenhagen University Hospital - Amager and Hvidovre, Copenhagen, Denmark
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Christine Hayes
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Ove Andersen
- Department of Clinical Research, Copenhagen University Hospital - Amager and Hvidovre, Copenhagen, Denmark
| | - Mef Nilbert
- Institute of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Lone Schejbel
- Molecular Unit, Department of Pathology, Copenhagen University Hospital - Herlev and Gentofte, Copenhagen, Denmark
| | - Estrid Høgdall
- Molecular Unit, Department of Pathology, Copenhagen University Hospital - Herlev and Gentofte, Copenhagen, Denmark
| | - Mauro Santibanez-Koref
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Michael S Jackson
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - John Burn
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Christina Therkildsen
- The Danish HNPCC Register, Gastro Unit, Copenhagen University Hospital - Amager and Hvidovre, Copenhagen, Denmark
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23
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Butter R, Halfwerk H, Radonic T, Lissenberg-Witte B, Thunnissen E. The impact of impaired tissue fixation in resected non-small-cell lung cancer on protein deterioration and DNA degradation. Lung Cancer 2023; 178:108-115. [PMID: 36812759 DOI: 10.1016/j.lungcan.2023.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 01/25/2023] [Accepted: 02/08/2023] [Indexed: 02/13/2023]
Abstract
OBJECTIVES The objective is to assess the impact of the quality of tissue fixation in surgical pathology on immunohistochemical (IHC) staining and DNA degradation. MATERIALS AND METHODS Twenty-five non-small cell lung cancer (NSCLC) resection specimens were analyzed. After resection, all tumors were processed according to the protocols in our center. In haematoxylin and eosin (H&E) stained tissue slides, adequately- and inadequately fixed tumor areas were microscopically demarcated, based on basement membrane detachment. In 10 IHC stains ALK (clone 5A4), PD-L (clone 22C3), CAM5.2, CK7, c-Met, KER-MNF116, NapsinA, p40, ROS1, TTF1) the immunoreactivity in H-scores was determined in adequately- and inadequately fixed, and necrotic tumor areas. From the same areas DNA was isolated, and DNA fragmentation in base pairs (bp) was measured. RESULTS H-scores were significantly higher in H&E adequately fixed tumor areas in IHC stains KER-MNF116 (H-score 256 vs 15, p=0.001) and p40 (H-score 293 vs 248, p=0.028). All other stains showed a trend towards higher immunoreactivity in H&E adequately fixed areas. Independent of H&E adequatelty- or inadequately fixed areas, all IHC stains showed significant different IHC staining intensity within tumors, suggesting heterogeneous immunoreactivity (H-scores: PD-L1 123 vs 6, p = 0.001; CAM5.2 242 vs 101, p=<0.001; CK7 242 vs 128, p=<0.001; c-MET 99 vs 20, p=<0.001; KER-MNF116 281 vs 120, p=<0.001; Napsin A 268 vs 130, p = 0.005; p40 292 vs 166, p = 0.008; TTF1 199 vs 63, p=<0.001). DNA fragments rarely exceeded a length of 300 bp, independent of adequate fixation. However, DNA fragments of 300 and 400 bp had higher concentrations in tumors with short fixation delay (<6 h vs >16 h) and short fixation time (<24 h vs >24 h). CONCLUSIONS Impaired tissue fixation of resected lung tumors results in decreased IHC staining intensity in some parts of the tumor. This may impact the reliability of IHC analysis.
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Affiliation(s)
- Rogier Butter
- Department of Pathology, Cancer Center Amsterdam, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Hans Halfwerk
- Department of Pathology, Cancer Center Amsterdam, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Teodora Radonic
- Department of Pathology, Cancer Center Amsterdam, Amsterdam University Medical Centers, VU University Amsterdam, Amsterdam, The Netherlands
| | - Birgit Lissenberg-Witte
- Department of Epidemiology and Data Science, Amsterdam University Medical Centers, VU University Amsterdam, Amsterdam, The Netherlands
| | - Erik Thunnissen
- Department of Pathology, Cancer Center Amsterdam, Amsterdam University Medical Centers, VU University Amsterdam, Amsterdam, The Netherlands.
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24
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Kohabir KAV, Nooi LO, Brink A, Brakenhoff RH, Sistermans EA, Wolthuis RMF. In Vitro CRISPR-Cas12a-Based Detection of Cancer-Associated TP53 Hotspot Mutations Beyond the crRNA Seed Region. CRISPR J 2023; 6:127-139. [PMID: 36637878 PMCID: PMC10123810 DOI: 10.1089/crispr.2022.0077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Cost-effective and time-efficient detection of oncogenic mutations supports improved presymptomatic cancer diagnostics and post-treatment disease monitoring. Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas12a is an RNA-guided endonuclease that, upon protospacer adjacent motif (PAM)-dependent recognition of target DNA in cis, exhibits indiscriminate ssDNase activity in trans, which can be harnessed for diagnostics. TP53, one of the most frequently mutated tumor suppressor genes in cancer, displays recurring point mutations at so-called "hotspots." In this study, we optimized Cas12a-based assay conditions for in vitro detection of six TP53 hotspot mutations at the codon for p.R273, located outside the Cas12a seed region, and evaluated the specificities of four commercial Cas12a variants. We found that nonengineered LbCas12a significantly outperformed the other tested nucleases specifically in distinguishing mutant p.R273 codons in synthetic DNA, mock cell-free DNA, and tissue biopsies, despite the suboptimal PAM-distal positioning of the corresponding mutations. Future clinical Cas12a-based applications may include point-of-care tumor analysis, cost-effective mutation screening, and improved monitoring of individual cancer patients.
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Affiliation(s)
- Kavish A V Kohabir
- Department of Human Genetics, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Embryonic & Fetal Development, Amsterdam Reproduction & Development, Amsterdam, The Netherlands.,Imaging and Biomarkers, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Lars O Nooi
- Department of Human Genetics, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Arjen Brink
- Cancer Biology and Immunology, Cancer Center Amsterdam, Amsterdam, The Netherlands.,Department of Otolaryngology/Head and Neck Surgery, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Ruud H Brakenhoff
- Imaging and Biomarkers, Cancer Center Amsterdam, Amsterdam, The Netherlands.,Cancer Biology and Immunology, Cancer Center Amsterdam, Amsterdam, The Netherlands.,Department of Otolaryngology/Head and Neck Surgery, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Erik A Sistermans
- Department of Human Genetics, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Embryonic & Fetal Development, Amsterdam Reproduction & Development, Amsterdam, The Netherlands
| | - Rob M F Wolthuis
- Department of Human Genetics, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Cancer Biology and Immunology, Cancer Center Amsterdam, Amsterdam, The Netherlands
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25
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Xing X, Karlow JA, Li D, Jang HS, Lee HJ, Wang T. Capture Methylation-Sensitive Restriction Enzyme Sequencing (Capture MRE-Seq) for Methylation Analysis of Highly Degraded DNA Samples. Methods Mol Biol 2023; 2621:73-89. [PMID: 37041441 DOI: 10.1007/978-1-0716-2950-5_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Understanding the impact of DNA methylation within different disease contexts often requires accurate assessment of these modifications in a genome-wide fashion. Frequently, patient-derived tissues stored in long-term hospital tissue banks have been preserved using formalin-fixation paraffin-embedding (FFPE). While these samples can comprise valuable resources for studying disease, the fixation process ultimately compromises the DNA's integrity and leads to degradation. Degraded DNA can complicate CpG methylome profiling using traditional techniques, particularly when performing methylation-sensitive restriction enzyme sequencing (MRE-seq), yielding high backgrounds and resulting in lowered library complexity. Here, we describe Capture MRE-seq, a new MRE-seq protocol tailored to preserving unmethylated CpG information when using samples with highly degraded DNA. The results using Capture MRE-seq correlate well (0.92) with traditional MRE-seq calls when profiling non-degraded samples, and can recover unmethylated regions in highly degraded samples when traditional MRE-seq fails, which we validate using bisulfite sequencing-based data (WGBS) as well as methylated DNA immunoprecipitation followed by sequencing (MeDIP-seq).
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Affiliation(s)
- Xiaoyun Xing
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Jennifer A Karlow
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Daofeng Li
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Hyo Sik Jang
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Hyung Joo Lee
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- Pin Pharmaceuticals, South San Francisco, CA, USA
| | - Ting Wang
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
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26
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Jacobsen SB, Tfelt-Hansen J, Smerup MH, Andersen JD, Morling N. Comparison of whole transcriptome sequencing of fresh, frozen, and formalin-fixed, paraffin-embedded cardiac tissue. PLoS One 2023; 18:e0283159. [PMID: 36989279 PMCID: PMC10058139 DOI: 10.1371/journal.pone.0283159] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 03/02/2023] [Indexed: 03/30/2023] Open
Abstract
The use of fresh tissue for molecular studies is preferred but often impossible. Instead, frozen or formalin-fixed, paraffin-embedded (FFPE) tissues are widely used and constitute valuable resources for retrospective studies. We assessed the utility of cardiac tissue stored in different ways for gene expression analyses by whole transcriptome sequencing of paired fresh, frozen, and FFPE tissues. RNA extracted from FFPE was highly degraded. Sequencing of RNA from FFPE tissues yielded higher proportions of intronic and intergenic reads compared to RNA from fresh and frozen tissues. The global gene expression profiles varied with the storage conditions, particularly mitochondrial and long non-coding RNAs. However, we observed high correlations among protein-coding transcripts (ρ > 0.94) with the various storage conditions. We did not observe any significant storage effect on the allele-specific gene expression. However, FFPE had statistically significantly (p < 0.05) more discordant variant calls compared to fresh and frozen tissue. In conclusion, we found that frozen and FFPE tissues can be used for reliable gene expression analyses, provided that proper quality control is performed and caution regarding the technical variability is withheld.
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Affiliation(s)
- Stine Bøttcher Jacobsen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jacob Tfelt-Hansen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Cardiology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Morten Holdgaard Smerup
- Department of Cardiothoracic Surgery, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Jeppe Dyrberg Andersen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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27
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Gonzálvez M, Ruiz de Ybáñez R, Rodríguez-Caro RC, Maíz-García A, Gómez L, Giménez A, Graciá E. Assessing DESS solution for the long-term preservation of nematodes from faecal samples. Res Vet Sci 2022; 153:45-48. [PMID: 36308790 DOI: 10.1016/j.rvsc.2022.10.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 10/06/2022] [Accepted: 10/11/2022] [Indexed: 11/09/2022]
Abstract
Preservation of biological samples is a relevant issue for many scientific disciplines. Although traditional preservers, such as formaldehyde or ethanol, imply major disadvantages related to health risks, DNA degradation and distortion of structures, they are widely used. Hence, the search for viable alternatives preserving morphometry and genetics seems necessary. Here we assess the suitability of DESS solution to preserve adult nematodes and their eggs in faeces. Concretely, faecal samples of terrestrial tortoises with oxyurids were used to: (i) compare the 1-month storage efficacy of eggs from different conservation protocols (faeces without preserver at -20 °C, faeces with DESS solution at room temperature, faeces with DESS solution at -20 °C and faeces with ethanol 70% at room temperature); (ii) address morphological nematode identification after 2 years of storage with DESS. We also corroborated that nematode DNA remained viable after 2 years. Overall, our results showed that DESS solution at room temperature is an advisable alternative to conserve both parasite eggs and adult nematodes for morphological identification and genetic purposes. It also offers the advantages of being low-cost, safe and suitable for fieldwork conditions and shipments without refrigeration for nematode preservation.
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Affiliation(s)
- M Gonzálvez
- Departamento de Sanidad Animal, Facultad de Veterinaria, Campus de Excelencia Internacional Regional "Campus Mare Nostrum", Universidad de Murcia, 30100 Murcia, Spain; Área de Ecología, Departamento de Biología Aplicada, Universidad Miguel Hernández, Av. de la Universidad, 03202 Elche, Spain
| | - R Ruiz de Ybáñez
- Departamento de Sanidad Animal, Facultad de Veterinaria, Campus de Excelencia Internacional Regional "Campus Mare Nostrum", Universidad de Murcia, 30100 Murcia, Spain.
| | - R C Rodríguez-Caro
- Área de Ecología, Departamento de Biología Aplicada, Universidad Miguel Hernández, Av. de la Universidad, 03202 Elche, Spain; Department of Zoology, Oxford University, 11a Mansfield Road, OX1 3SZ, Oxford, England, UK; Department of Ecology, University of Alicante, Road. San Vicente del Raspeig, 03690 Alicante, Spain
| | - A Maíz-García
- Área de Ecología, Departamento de Biología Aplicada, Universidad Miguel Hernández, Av. de la Universidad, 03202 Elche, Spain
| | - L Gómez
- Departamento de Sanidad Animal, Facultad de Veterinaria, Campus de Excelencia Internacional Regional "Campus Mare Nostrum", Universidad de Murcia, 30100 Murcia, Spain
| | - A Giménez
- Área de Ecología, Departamento de Biología Aplicada, Universidad Miguel Hernández, Av. de la Universidad, 03202 Elche, Spain; Centro de Investigación e Innovación Agroalimentaria y Agroambiental (CIAGRO-UMH), Universidad Miguel Hernández, Elche, Spain
| | - E Graciá
- Área de Ecología, Departamento de Biología Aplicada, Universidad Miguel Hernández, Av. de la Universidad, 03202 Elche, Spain; Centro de Investigación e Innovación Agroalimentaria y Agroambiental (CIAGRO-UMH), Universidad Miguel Hernández, Elche, Spain
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28
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HPV-Associated Breast Cancer: Myth or Fact? Pathogens 2022; 11:pathogens11121510. [PMID: 36558844 PMCID: PMC9786769 DOI: 10.3390/pathogens11121510] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/01/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
Some estimates place the proportion of human malignancies attributable to viruses at between 15 and 20 percent. Viruses including the human papillomavirus are considered an interesting but controversial etiological risk factor for breast cancer. HPV infection is anticipated to be an early trigger in breast cancer carcinogenesis, followed by cumulative alterations over time ("hit and run" mechanism) through synergy with other environmental factors. The association between HPV and breast cancer has not yet been verified. There are very conflicting data on the presence of HPV DNA in breast cancer samples, and we lack a clarified, exact mode of HPV transmission to the breast. In our review article we analyzed the up-to-date knowledge about the association of HPV and breast cancer. Furthermore, we summarized the available original research published since 2010. In conclusion, the complexity and inconsistency of the available results together with the relatively low prevalence of HPV infection requires extensive research with much larger studies and exact and unified diagnostic methods are required to better understand the role of the HPV in breast carcinogenesis.
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29
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Favre L, Sako N, Tarfi S, Quang VT, Joy C, Dupuy A, Guillerm E, Gaulard P, Wagner‐Ballon O, Pujals A, Sloma I. Evaluation of two new highly multiplexed PCR assays as an alternative to next-generation sequencing for IDH1/2 mutation detection. Mol Oncol 2022; 16:3916-3926. [PMID: 36062346 PMCID: PMC9718115 DOI: 10.1002/1878-0261.13311] [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: 02/24/2022] [Revised: 06/20/2022] [Accepted: 09/02/2022] [Indexed: 12/24/2022] Open
Abstract
IDH1 and IDH2 somatic mutations have been identified in solid tumors and blood malignancies. The development of inhibitors of mutant IDH1 and IDH2 in the past few years has prompted the development of a fast and sensitive assay to detect IDH1R132 , IDH2R140 and IDH2R172 mutations to identify patients eligible for these targeted therapies. This study aimed to compare two new multiplexed PCR assays - an automated quantitative PCR (qPCR) on the PGX platform and a droplet digital PCR (ddPCR) with next-generation sequencing (NGS) for IDH1/2 mutation detection. These assays were evaluated on 102 DNA extracted from patient peripheral blood, bone marrow and formalin-fixed paraffin-embedded tissue samples with mutation allelic frequency ranging from 0.6% to 45.6%. The ddPCR assay had better analytical performances than the PGX assay with 100% specificity, 100% sensitivity and a detection limit down to 0.5% on IDH1R132 , IDH2R140 and IDH2R172 codons, and a high correlation with NGS results. Therefore, the new highly multiplexed ddPCR is a fast and cost-effective assay that meets most clinical needs to identify and follow cancer patients in the era of anti-IDH1/2-targeted therapies.
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Affiliation(s)
- Loetitia Favre
- Department of PathologyAP‐HP, Henri Mondor University HospitalCreteilFrance,Univ Paris Est Creteil, INSERM, IMRBFrance
| | - Nouhoum Sako
- Department of PathologyAP‐HP, Henri Mondor University HospitalCreteilFrance
| | - Sihem Tarfi
- Univ Paris Est Creteil, INSERM, IMRBFrance,Hematology and Immunology DepartmentAP‐HP, Henri Mondor University HospitalCreteilFrance
| | - Violaine Tran Quang
- Univ Paris Est Creteil, INSERM, IMRBFrance,Hematology and Immunology DepartmentAP‐HP, Henri Mondor University HospitalCreteilFrance
| | - Corine Joy
- Hematology and Immunology DepartmentAP‐HP, Henri Mondor University HospitalCreteilFrance
| | | | - Erell Guillerm
- Genetic DepartmentAP‐HP, University Hospital Pitié SalpêtrièreParisFrance
| | - Philippe Gaulard
- Department of PathologyAP‐HP, Henri Mondor University HospitalCreteilFrance,Univ Paris Est Creteil, INSERM, IMRBFrance
| | - Orianne Wagner‐Ballon
- Univ Paris Est Creteil, INSERM, IMRBFrance,Hematology and Immunology DepartmentAP‐HP, Henri Mondor University HospitalCreteilFrance
| | - Anaïs Pujals
- Department of PathologyAP‐HP, Henri Mondor University HospitalCreteilFrance,Univ Paris Est Creteil, INSERM, IMRBFrance
| | - Ivan Sloma
- Univ Paris Est Creteil, INSERM, IMRBFrance,Hematology and Immunology DepartmentAP‐HP, Henri Mondor University HospitalCreteilFrance
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30
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Muñoz-Barrera A, Rubio-Rodríguez LA, Díaz-de Usera A, Jáspez D, Lorenzo-Salazar JM, González-Montelongo R, García-Olivares V, Flores C. From Samples to Germline and Somatic Sequence Variation: A Focus on Next-Generation Sequencing in Melanoma Research. Life (Basel) 2022; 12:1939. [PMID: 36431075 PMCID: PMC9695713 DOI: 10.3390/life12111939] [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: 10/28/2022] [Revised: 11/12/2022] [Accepted: 11/16/2022] [Indexed: 11/24/2022] Open
Abstract
Next-generation sequencing (NGS) applications have flourished in the last decade, permitting the identification of cancer driver genes and profoundly expanding the possibilities of genomic studies of cancer, including melanoma. Here we aimed to present a technical review across many of the methodological approaches brought by the use of NGS applications with a focus on assessing germline and somatic sequence variation. We provide cautionary notes and discuss key technical details involved in library preparation, the most common problems with the samples, and guidance to circumvent them. We also provide an overview of the sequence-based methods for cancer genomics, exposing the pros and cons of targeted sequencing vs. exome or whole-genome sequencing (WGS), the fundamentals of the most common commercial platforms, and a comparison of throughputs and key applications. Details of the steps and the main software involved in the bioinformatics processing of the sequencing results, from preprocessing to variant prioritization and filtering, are also provided in the context of the full spectrum of genetic variation (SNVs, indels, CNVs, structural variation, and gene fusions). Finally, we put the emphasis on selected bioinformatic pipelines behind (a) short-read WGS identification of small germline and somatic variants, (b) detection of gene fusions from transcriptomes, and (c) de novo assembly of genomes from long-read WGS data. Overall, we provide comprehensive guidance across the main methodological procedures involved in obtaining sequencing results for the most common short- and long-read NGS platforms, highlighting key applications in melanoma research.
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Affiliation(s)
- Adrián Muñoz-Barrera
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
| | - Luis A. Rubio-Rodríguez
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
| | - Ana Díaz-de Usera
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, 38010 Santa Cruz de Tenerife, Spain
| | - David Jáspez
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
| | - José M. Lorenzo-Salazar
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
| | - Rafaela González-Montelongo
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
| | - Víctor García-Olivares
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
| | - Carlos Flores
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, 38010 Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Facultad de Ciencias de la Salud, Universidad Fernando de Pessoa Canarias, 35450 Las Palmas de Gran Canaria, Spain
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31
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Ferreira LC, Quintella LP, Schubach ADO, Miranda LDFC, Madeira MDF, Pimentel MIF, Vasconcellos ÉDCFE, Lyra MR, de Oliveira RDVC, Menezes RC. Comparison between Colorimetric In Situ Hybridization, Histopathology, and Immunohistochemistry for the Diagnosis of New World Cutaneous Leishmaniasis in Human Skin Samples. Trop Med Infect Dis 2022; 7:344. [PMID: 36355886 PMCID: PMC9695648 DOI: 10.3390/tropicalmed7110344] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/25/2022] [Accepted: 10/27/2022] [Indexed: 09/16/2024] Open
Abstract
New world cutaneous leishmaniasis (NWCL) is an anthropozoonosis caused by different species of the protozoan Leishmania. Colorimetric in situ hybridization (CISH) was shown to satisfactorily detect amastigote forms of Leishmania spp. in animal tissues, yet it was not tested for the diagnosis of human NWCL. The aim of this study was to compare CISH, histopathology (HP), and immunohistochemistry (IHC) techniques to diagnose NWCL in human cutaneous lesions. The sample comprised fifty formalin-fixed, paraffin-embedded skin biopsy specimens from patients with NWCL caused by L. (V.) braziliensis. These specimens were analyzed by CISH, using a generic probe for Leishmania, IHC, and HP to assess the sensitivity of these methods by using a parasitological culture as a standard reference. Additional specimens from three patients diagnosed with cutaneous mycoses were also included to evaluate cross-reactions between CISH and IHC. The sensitivities of IHC, CISH, and HP for detecting amastigotes was 66%, 54%, and 50%, respectively. IHC, unlike CISH, cross-reacted with different species of fungi. Together, these results demonstrate that CISH may be a complementary assay for the detection of amastigote in the laboratorial diagnosis routine of human NWCL caused by L. (V.) braziliensis.
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Affiliation(s)
- Luiz Cláudio Ferreira
- Anatomic Pathology Service, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Av. Brasil, 4365, Rio de Janeiro 21040-360, Brazil
| | - Leonardo Pereira Quintella
- Anatomic Pathology Service, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Av. Brasil, 4365, Rio de Janeiro 21040-360, Brazil
| | - Armando de Oliveira Schubach
- Laboratory of Clinical Research and Surveillance of Leishmaniasis, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Av. Brasil, 4365, Rio de Janeiro 21040-360, Brazil
| | - Luciana de Freitas Campos Miranda
- Laboratory of Clinical Research and Surveillance of Leishmaniasis, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Av. Brasil, 4365, Rio de Janeiro 21040-360, Brazil
| | - Maria de Fátima Madeira
- Laboratory of Clinical Research and Surveillance of Leishmaniasis, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Av. Brasil, 4365, Rio de Janeiro 21040-360, Brazil
| | - Maria Inês Fernandes Pimentel
- Laboratory of Clinical Research and Surveillance of Leishmaniasis, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Av. Brasil, 4365, Rio de Janeiro 21040-360, Brazil
| | | | - Marcelo Rosandiski Lyra
- Laboratory of Clinical Research and Surveillance of Leishmaniasis, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Av. Brasil, 4365, Rio de Janeiro 21040-360, Brazil
| | | | - Rodrigo Caldas Menezes
- Laboratory of Clinical Research on Dermatozoonoses in Domestic Animals, Evandro Chagas National Institute of Infectious Diseases, Oswaldo Cruz Foundation, Av. Brasil, 4365, Rio de Janeiro 21040-360, Brazil
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Favre L, Cohen J, Calderaro J, Pécriaux A, Nguyen C, Bourgoin R, Larnaudie L, Dupuy A, Ollier M, Lechapt E, Sloma I, Tournigand C, Rousseau B, Pujals A. High prevalence of unusual KRAS, NRAS, and BRAF mutations in POLE-hypermutated colorectal cancers. Mol Oncol 2022; 16:3055-3065. [PMID: 35624529 PMCID: PMC9441000 DOI: 10.1002/1878-0261.13257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 04/05/2022] [Accepted: 05/25/2022] [Indexed: 12/04/2022] Open
Abstract
Exonucleasic domain POLE (edPOLE) mutations, which are responsible for a hypermutated tumor phenotype, occur in 1-2% of colorectal cancer (CRC) cases. These alterations represent an emerging biomarker for response to immune checkpoint blockade. This study aimed to assess the molecular characteristics of edPOLE-mutated tumors to facilitate patient screening. Based on opensource data analysis, we compared the prevalence of edPOLE mutations in a control group of unselected CRC patients (n = 222) vs a group enriched for unusual BRAF/RAS mutations (n = 198). Tumor mutational burden (TMB) and immune infiltrate of tumors harboring edPOLE mutations were then analyzed. In total, 420 CRC patients were analyzed: 11 edPOLE-mutated tumors were identified, most frequently in microsatellite (MMR)-proficient young (< 70 years) male patients, with left-sided tumors harboring noncodon 12 KRAS mutation. The prevalence of edPOLE-mutated tumors in the control vs the experimental screening group was, respectively, 0.45% (n = 1) vs 5.0% (n = 10). Among the 11 edPOLE-mutated cases, two had a low TMB, three were hypermutated, and six were ultramutated. EdPOLE-mutated cases had a high CD8+ tumor-infiltrating lymphocyte (TIL) infiltration. These clinicopathological and molecular criteria may help to identify edPOLE mutations associated with a high TMB in CRC, and improve the selection of patients who could benefit from immunotherapy.
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Affiliation(s)
- Loetitia Favre
- Département de PathologieAP‐HP, Centre Hospitalier Universitaire Henri MondorCréteilFrance
- INSERM, IMRBUniv Paris Est CreteilFrance
| | - Justine Cohen
- Département de PathologieAP‐HP, Centre Hospitalier Universitaire Henri MondorCréteilFrance
| | - Julien Calderaro
- Département de PathologieAP‐HP, Centre Hospitalier Universitaire Henri MondorCréteilFrance
- INSERM, IMRBUniv Paris Est CreteilFrance
| | - Adrien Pécriaux
- Département de PathologieAP‐HP, Centre Hospitalier Universitaire Henri MondorCréteilFrance
| | | | - Rémi Bourgoin
- Département de PathologieAP‐HP, Centre Hospitalier Universitaire Henri MondorCréteilFrance
| | - Laura Larnaudie
- Département de PathologieAP‐HP, Centre Hospitalier Universitaire Henri MondorCréteilFrance
| | | | - Marie Ollier
- Département de PathologieAP‐HP, Centre Hospitalier Universitaire Henri MondorCréteilFrance
| | - Emmanuèle Lechapt
- Département de PathologieAP‐HP, Centre Hospitalier Universitaire Henri MondorCréteilFrance
- INSERM, IMRBUniv Paris Est CreteilFrance
| | - Ivan Sloma
- INSERM, IMRBUniv Paris Est CreteilFrance
- Département d'Hématologie BiologiqueAP‐HP, Centre Hospitalier Universitaire Henri MondorCréteilFrance
| | - Christophe Tournigand
- INSERM, IMRBUniv Paris Est CreteilFrance
- Service d'Oncologie MédicaleAP‐HP, Centre Hospitalier Universitaire Henri MondorCréteilFrance
| | - Benoit Rousseau
- Service d'Oncologie MédicaleAP‐HP, Centre Hospitalier Universitaire Henri MondorCréteilFrance
- Mortimer B. Zuckerman Research CenterMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Anaïs Pujals
- Département de PathologieAP‐HP, Centre Hospitalier Universitaire Henri MondorCréteilFrance
- INSERM, IMRBUniv Paris Est CreteilFrance
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Voigtlaender M, Edler C, Gerling M, Schädler J, Ondruschka B, Schröder AS, Sperhake J, Ehrhardt S, Wang L, Haddad M, Kiencke V, Renné T, Roedl K, Kluge S, Wichmann D, Langer F. Thromboembolic events in deceased patients with proven SARS-CoV-2 infection: Frequency, characteristics and risk factors. Thromb Res 2022; 218:171-176. [PMID: 36057167 PMCID: PMC9420077 DOI: 10.1016/j.thromres.2022.08.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 08/11/2022] [Accepted: 08/19/2022] [Indexed: 11/15/2022]
Abstract
BACKGROUND Infection with the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) results in respiratory syndromes but also in vascular complications such as thromboembolism (TE). In this regard, immunothrombosis, resulting from inflammation in SARS-CoV-2 infected tissues, has been described. Data on TE in COVID-19 are mainly based on clinical observational and/or incomplete autopsy studies. The true burden of TE and the relevance of genetic predisposition, however, have not been resolved. OBJECTIVES Here, we report on a consecutive cohort of 100 fully autopsied patients deceased by SARS-CoV-2 infections during the first wave of the pandemic (March to April 2020). We investigated the localization of TE, potential clinical risk factors, and the prothrombotic gene mutations, factor V Leiden and prothrombin G20210A, in postmortem blood or tissue samples. RESULTS TE was found in 43/100 autopsies. 93 % of TE events were venous occlusions, with 23 patients having pulmonary thromboembolism (PT) with or without lower-extremity deep vein thrombosis. Of these, 70 % showed PT restricted to (sub)segmental arteries, consistent with in situ immunothrombosis. Patients with TE had a significantly higher BMI and died more frequently at an intensive care unit. Hereditary thrombophilia factors were not associated with TE. CONCLUSIONS Our autopsy results show that a significant proportion of SARS-CoV-2 infected patients suffer from TE, affecting predominantly the venous system. Orthotopic peripheral PT was the most frequent finding. Hereditary thrombophilia appears not to be a determinant for TE in COVID-19. However, obesity and the need for intensive care increase the risk of TE in these patients.
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Affiliation(s)
- Minna Voigtlaender
- II. Medical Department - Oncology, Hematology, Bone Marrow Transplantation and Pneumology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Carolin Edler
- Institute of Legal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Moritz Gerling
- Institute of Legal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Julia Schädler
- Institute of Legal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Benjamin Ondruschka
- Institute of Legal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ann Sophie Schröder
- Institute of Legal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jan Sperhake
- Institute of Legal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stephan Ehrhardt
- Bloomberg School of Public Health, Department of Epidemiology, Johns Hopkins University Baltimore, Baltimore, USA
| | - Lin Wang
- Bloomberg School of Public Health, Department of Epidemiology, Johns Hopkins University Baltimore, Baltimore, USA
| | - Munif Haddad
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Verena Kiencke
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Thomas Renné
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; Irish Centre for Vascular Biology, School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland; Center for Thrombosis and Hemostasis (CTH), Johannes Gutenberg University Medical Center, Mainz, Germany
| | - Kevin Roedl
- Department of Intensive Care Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Kluge
- Department of Intensive Care Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Dominic Wichmann
- Department of Intensive Care Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Florian Langer
- II. Medical Department - Oncology, Hematology, Bone Marrow Transplantation and Pneumology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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Fujii T, Takeda M, Uchiyama T, Nitta Y, Maebou K, Terada C, Okada F, Matsuoka M, Sugimoto S, Sasaki S, Morita K, Itami H, Miyake M, Takeda M, Sawabata N, Fujimoto K, Ohbayashi C. Identification of fusion transcripts in sarcoma from archival formalin-fixed paraffin-embedded tissues: A next-generation sequencing approach. Pathol Int 2022; 72:444-456. [PMID: 35975909 DOI: 10.1111/pin.13265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 07/21/2022] [Indexed: 11/30/2022]
Abstract
Most sarcomas are highly aggressive, and cause necrosis and hemorrhage. The diagnosis of sarcoma is challenging because of the lack of specificity of immunohistochemical staining; however, molecular biological approaches, such as genetic mutation, chromosomal translocation, and gene amplification, are promising. In this study, we extracted RNA from formalin-fixed paraffin-embedded (FFPE) tissue derived from surgically resected specimens of sarcoma stored for various periods and performed next-generation sequencing (NGS) analysis by MiniSeq using the Archer Fusion-Plex Sarcoma Panel. RNA was extracted from 63 FFPE tissue samples, and the degree of RNA degradation was assessed. The number of reads and fragment lengths were evaluated by NGS analysis. RNA extraction and cDNA synthesis were successful in 56 cases and library preparation was possible. Fusion genes were detected in 16 of 63 archived FFPE tissue samples in this study. However, in 18 cases, fragmentation was strong, and high-quality libraries could not be obtained. Nevertheless, comprehensive analysis of fusion genes with high sequence specificity by NGS can be a powerful alternative to reverse transcription-polymerase chain reaction and fluorescence in situ hybridization methods.
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Affiliation(s)
- Tomomi Fujii
- Department of Diagnostic Pathology, Nara Medical University School of Medicine, Nara, Japan
| | - Maiko Takeda
- Department of Diagnostic Pathology, Nara Medical University School of Medicine, Nara, Japan
| | - Tomoko Uchiyama
- Department of Diagnostic Pathology, Nara Medical University School of Medicine, Nara, Japan
| | - Yuji Nitta
- Department of Diagnostic Pathology, Nara Medical University School of Medicine, Nara, Japan
| | - Katsuya Maebou
- Department of Diagnostic Pathology, Nara Medical University School of Medicine, Nara, Japan
| | - Chiyoko Terada
- Department of Diagnostic Pathology, Nara Medical University School of Medicine, Nara, Japan
| | - Fumi Okada
- Department of Diagnostic Pathology, Nara Medical University School of Medicine, Nara, Japan
| | - Minami Matsuoka
- Department of Diagnostic Pathology, Nara Medical University School of Medicine, Nara, Japan
| | - Sumire Sugimoto
- Department of Diagnostic Pathology, Nara Medical University School of Medicine, Nara, Japan
| | - Shoh Sasaki
- Department of Diagnostic Pathology, Nara Medical University School of Medicine, Nara, Japan
| | - Kohei Morita
- Department of Diagnostic Pathology, Nara Medical University School of Medicine, Nara, Japan
| | - Hiroe Itami
- Department of Diagnostic Pathology, Nara Medical University School of Medicine, Nara, Japan
| | - Makito Miyake
- Department of Urology, Nara Medical University School of Medicine, Nara, Japan
| | - Masayuki Takeda
- Department of Cancer Genomics and Medical Oncology, Nara Medical University School of Medicine, Nara, Japan
| | - Noriyoshi Sawabata
- Department of Thoracic and Cardiovascular Surgery, Nara Medical University School of Medicine, Nara, Japan
| | - Kiyohide Fujimoto
- Department of Urology, Nara Medical University School of Medicine, Nara, Japan
| | - Chiho Ohbayashi
- Department of Diagnostic Pathology, Nara Medical University School of Medicine, Nara, Japan
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35
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De Martino E, Medeot C, D'Amico L, Stanta G, Bonin S. Impact of standardization in tissue processing: the performance of different fixatives. N Biotechnol 2022; 71:30-36. [PMID: 35878783 DOI: 10.1016/j.nbt.2022.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 07/21/2022] [Accepted: 07/21/2022] [Indexed: 10/31/2022]
Abstract
Most tissues in clinical practice are formalin-fixed and paraffin-embedded for histological as well as molecular analyses. The reproducibility and uniformity of molecular analyses is strictly dependent on the quality of the biomolecules, which is highly influenced by pre-analytical processes. In this study, the effect of different fixatives was compared, including formalin, Bouin's solution, RCL2® and TAG-1™ fixatives, by stringent application of ISO standards in mouse liver tissue processing, including formalin-free transport of tissues and tissue grossing in a refrigerated environment. The effect of fixatives was studied in terms of nucleic acid quality at the time of tissue processing and after one year of tissue storage at room temperature in the dark. Furthermore, a microcomputed tomography (CT) scan analysis was applied to investigate the paraffin embedding. The results show that the application of ISO standards in tissue processing allows analysis of 400 bases amplicons from RNA and 1000 bases from DNA, even in extracts from formalin-fixed and paraffin-embedded tissues. However, after one year storage at room temperature in the dark, a degradation of the nucleic acids was observed. Nevertheless, extracts can still be analyzed, but for metachronous tests it is highly recommended to repeat the quantitation of housekeeping genes in order to standardize the extent of nucleic acid degradation.
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Affiliation(s)
| | - Caterina Medeot
- Department of Medical Sciences, University of Trieste, Trieste, Italy
| | - Lorenzo D'Amico
- Department of Physics, University of Trieste, Trieste, Italy; Elettra-Sincrotrone Trieste S.C.p.A., Area Science Park, Trieste, Italy
| | - Giorgio Stanta
- Department of Medical Sciences, University of Trieste, Trieste, Italy
| | - Serena Bonin
- Department of Medical Sciences, University of Trieste, Trieste, Italy.
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36
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Yu IS, Aubin F, Goodwin R, Loree JM, Mather C, Sheffield BS, Snow S, Gill S. Tumor Biomarker Testing for Metastatic Colorectal Cancer: a Canadian Consensus Practice Guideline. Ther Adv Med Oncol 2022; 14:17588359221111705. [PMID: 35898967 PMCID: PMC9310231 DOI: 10.1177/17588359221111705] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 06/17/2022] [Indexed: 11/17/2022] Open
Abstract
The systemic therapy management of metastatic colorectal cancer (mCRC) has evolved from primarily cytotoxic chemotherapies to now include targeted agents given alone or in combination with chemotherapy, and immune checkpoint inhibitors. A better understanding of the pathogenesis and molecular drivers of colorectal cancer not only aided the development of novel targeted therapies but led to the discovery of tumor mutations which act as predictive biomarkers for therapeutic response. Mutational status of the KRAS gene became the first genomic biomarker to be established as part of standard of care molecular testing, where KRAS mutations within exons 2, 3, and 4 predict a lack of response to anti- epidermal growth factor receptor therapies. Since then, several other biomarkers have become relevant to inform mCRC treatment; however, there are no published Canadian guidelines which reflect the current standards for biomarker testing. This guideline was developed by a pan-Canadian advisory group to provide contemporary, evidence-based recommendations on the minimum acceptable standards for biomarker testing in mCRC, and to describe additional biomarkers for consideration.
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Affiliation(s)
- Irene S. Yu
- Department of Medical Oncology, BC Cancer
Surrey, Surrey, BC, Canada
| | - Francine Aubin
- Division of Hematology and Oncology, Department
of Medicine, Centre Hospitalier de l’Université de Montréal, Montreal, QC,
Canada
| | - Rachel Goodwin
- Division of Medical Oncology, Department of
Medicine, Ottawa Hospital Cancer Centre, Ottawa, ON, Canada
| | - Jonathan M. Loree
- Department of Medical Oncology, BC Cancer
Agency - Vancouver Centre, Vancouver, BC, Canada
| | - Cheryl Mather
- Department of Laboratory Medicine and
Pathology, University of Alberta, Edmonton, AB, Canada
| | - Brandon S. Sheffield
- Division of Advanced Diagnostics, William Osler
Health System, Brampton, ON, Canada
| | - Stephanie Snow
- Department of Medicine, Queen Elizabeth II
Health Sciences Centre, Halifax, NS, Canada
| | - Sharlene Gill
- Department of Medical Oncology, BC Cancer
Agency – Vancouver Centre, 600 W 10th Ave, Vancouver, BC, V5Z 4E6,
Canada
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Hatano K, Nonomura N. Genomic Profiling of Prostate Cancer: An Updated Review. World J Mens Health 2022; 40:368-379. [PMID: 34448375 PMCID: PMC9253799 DOI: 10.5534/wjmh.210072] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/02/2021] [Accepted: 06/13/2021] [Indexed: 12/24/2022] Open
Abstract
Understanding the genomic profiling of prostate cancer is crucial, owing to the emergence of precision medicine to guide therapeutic approaches. Over the last decade, integrative genomic profiling of prostate tumors has provided insights that improve the understanding and treatment of the disease. Minimally invasive liquid biopsy procedures have emerged to investigate cancer-related molecules with the advantage of detecting heterogeneity as well as acquired resistance in cancer. The metastatic castration-resistant prostate cancer (mCRPC) tumors have a highly complex genomic landscape compared to primary prostate tumors; a number of mCRPC harbor clinically actionable molecular alterations, including DNA damage repair (e.g., BRCA1/2 and ATM) and PTEN/phosphoinositide 3-kinase signaling. Heterogeneity in the genomic landscape of prostate cancer has become apparent and genomic alterations of TP53, RB1, AR, and cell cycle pathway are associated with poor clinical outcomes in patients. Prostate cancer with mutant SPOP shows a distinct pattern of genomic alterations, associating with better clinical outcomes. Several genomic profiling tests, which can be used in the clinic, are approved by the U.S. Food and Drug Administration, including MSK-IMPACT, FoundationOne CDx, and FoundationOne Liquid CDx. Here, we review emerging evidence for genomic profiling of prostate cancer, especially focusing on associations between genomic alteration and clinical outcome, liquid biopsy, and actionable molecular alterations.
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Affiliation(s)
- Koji Hatano
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Japan.
| | - Norio Nonomura
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Japan
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38
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Walker M, Uranga C, Levy SHS, Kelly C, Edlund A. Thrombus-associated microbiota in acute ischemic stroke patients. Surg Neurol Int 2022; 13:247. [PMID: 35855159 PMCID: PMC9282817 DOI: 10.25259/sni_104_2022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 05/25/2022] [Indexed: 11/18/2022] Open
Abstract
Background: Despite a reduction in stroke incidence and age-standardized death rates, stroke remains a leading cause of death and disability worldwide. Significant interest in recent years has focused on the microbiota-host interaction because accumulating evidence has revealed myriad ways in which bacteria may contribute to risk of stroke and adverse outcomes after stroke. The emergence of endovascular thrombectomy as a treatment provides a unique opportunity to utilize thrombus retrieved from cerebral arteries to fill knowledge gaps about the influence of bacteria on stroke pathophysiology. While bacterial signatures have been confirmed in cerebral thrombi, the exact nature of the pathogenesis has not been established. Methods: Thrombi were obtained from a cohort of adult ischemic stroke patients during standard of care thrombectomy. After DNA extraction and quantification, thrombi underwent 16S rRNA amplicon-based metagenomic sequencing, followed by bioinformatics processing. Taxonomic identification of bacterial colonies isolated on Agar plates from plated suspension was performed using DNA extraction and full length 16S Sanger sequencing. Results: A broad diversity of bacterial signatures was identified in specimens, primarily of cariogenic origin. Conclusion: In this small study, we demonstrate proof of concept and technical feasibility for amplicon-based metagenomic sequencing of arterial thrombi and briefly discuss preliminary findings, challenges, and near-term translational opportunities for thrombus genomics.
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Affiliation(s)
- Melanie Walker
- Department of Neurological Surgery, University of Washington, Seattle, Washington, United States
| | - Carla Uranga
- Genomic Medicine Group, J. Craig Venter Institute, La Jolla, California, United States
| | - Samuel HS Levy
- Department of Neurological Surgery, University of Washington, Seattle, Washington, United States
| | - Cory Kelly
- Department of Neurological Surgery, University of Washington, Seattle, Washington, United States
| | - Anna Edlund
- Genomic Medicine Group, J. Craig Venter Institute, La Jolla, California, United States
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39
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Grantzau T, Toft BG, Melchior LC, Elversang J, Stormoen DR, Omland LH, Pappot H. PD-L1 expression and FGFR-mutations among Danish patients diagnosed with metastatic urothelial carcinoma: A retrospective and descriptive study. APMIS 2022; 130:498-506. [PMID: 35616216 PMCID: PMC9545015 DOI: 10.1111/apm.13249] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 05/22/2022] [Indexed: 12/19/2022]
Abstract
Checkpoint inhibitors have changed the treatment landscape of advanced urothelial carcinoma (mUC), and recently, a fibroblast-growth-factor-receptor (FGFR) inhibitor has been introduced. This study aimed at estimating programmed death-ligand 1 (PD-L1) expression in primary tumors (PTs) and the PD-L1 expression concordance between PTs and paired metastases in 100 patients with UC managed in the real-world setting. Further, the aim was to investigate FGFR1-3 aberrations and the correlation between FGFR1-3 aberrations and PD-L1 expression. PD-L1 immunohistochemistry was performed on 100 formalin-fixed paraffin-embedded archival primary UC samples and 55 matched metastases using the 22C3 PD-L1 assay. PD-L1 expression was determined by the combined positive score, considered positive at ≥10. Targeted next-generation sequencing on the S5+/Prime System with the Oncomine Comprehensive Assay version 3 was used to detect FGFR1-3 aberrations in PTs. We found that 29 of 100 PTs had positive PD-L1 expression. The PD-L1 concordance rate was 71%. FGFR1-3 aberrations were observed in 18% of PTs, most frequently FGFR3 amplifications or mutations. We found no association between FGFR1-3 aberrations and PT PD-L1 expression (p = 0.379). Our data emphasize the need for further studies in predictive biomarkers.
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Affiliation(s)
- Trine Grantzau
- Department of Pathology, Rigshospitalet, Copenhagen, Denmark
| | | | | | | | - Dag Rune Stormoen
- Department of Oncology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Lise Høj Omland
- Department of Oncology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Helle Pappot
- Department of Oncology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
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40
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Shimizu T, Fujita T, Fujii H. Oligoribonucleotide interference-PCR: principles and applications. BIOLOGY METHODS AND PROTOCOLS 2022; 7:bpac010. [PMID: 35664805 PMCID: PMC9154734 DOI: 10.1093/biomethods/bpac010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/07/2022] [Accepted: 04/19/2022] [Indexed: 11/29/2022]
Abstract
Polymerase chain reaction (PCR) amplification of multiple templates using common primers is used widely for molecular biological research and clinical diagnosis. However, amplifying a specific DNA sequence harboring a mutation that is present in a small number of mutant cells within a large population of normal cells (e.g., as in cancer) in a tissue is difficult using the original PCR protocol. Thus, some measures are necessary to suppress amplification of background signals. To achieve this, we developed the oligoribonucleotide (ORN) interference-PCR (ORNi-PCR) technology in which an ORN (short RNA) hybridizes with a complementary DNA sequence to inhibit PCR amplification across the specific target sequence. ORNs can be prepared inexpensively, and ORNi-PCR can be carried out easily by adding ORNs to the PCR reaction mixture. Suppressing amplification of target sequences by ORNi-PCR is useful for detecting target sequence mutations. We showed that ORNi-PCR can discriminate single-nucleotide mutations in cancer cells and indel mutations introduced by genome editing. We also showed that ORNi-PCR can identify the CpG methylation status of a target sequence within bisulfite-treated DNA, and can enrich DNA sequences of interest from a DNA mixture by suppressing amplification of unwanted sequences. Thus, ORNi-PCR has many potential applications in various fields, including medical diagnosis and molecular biology. In this review, we outline the principles of the ORNi-PCR method and its use to detect nucleotide mutations in a variety of specimens.
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Affiliation(s)
- Takeshi Shimizu
- Department of Biochemistry and Genome Biology, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki, 036-8562, Aomori, Japan
| | - Toshitsugu Fujita
- Department of Biochemistry and Genome Biology, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki, 036-8562, Aomori, Japan
| | - Hodaka Fujii
- Department of Biochemistry and Genome Biology, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki, 036-8562, Aomori, Japan
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41
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Cappello F, Angerilli V, Munari G, Ceccon C, Sabbadin M, Pagni F, Fusco N, Malapelle U, Fassan M. FFPE-Based NGS Approaches into Clinical Practice: The Limits of Glory from a Pathologist Viewpoint. J Pers Med 2022; 12:750. [PMID: 35629172 PMCID: PMC9146170 DOI: 10.3390/jpm12050750] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/29/2022] [Accepted: 05/03/2022] [Indexed: 01/02/2023] Open
Abstract
The introduction of next-generation sequencing (NGS) in the molecular diagnostic armamentarium is deeply changing pathology practice and laboratory frameworks. NGS allows for the comprehensive molecular characterization of neoplasms, in order to provide the best treatment to oncologic patients. On the other hand, NGS raises technical issues and poses several challenges in terms of education, infrastructures and costs. The aim of this review is to give an overview of the main NGS sequencing platforms that can be used in current molecular diagnostics and gain insights into the clinical applications of NGS in precision oncology. Hence, we also focus on the preanalytical, analytical and interpretative issues raised by the incorporation of NGS in routine pathology diagnostics.
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Affiliation(s)
- Filippo Cappello
- Department of Medicine (DIMED), University of Padua, 35128 Padua, Italy; (F.C.); (V.A.); (C.C.)
| | - Valentina Angerilli
- Department of Medicine (DIMED), University of Padua, 35128 Padua, Italy; (F.C.); (V.A.); (C.C.)
| | - Giada Munari
- Veneto Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), 35128 Padua, Italy; (G.M.); (M.S.)
| | - Carlotta Ceccon
- Department of Medicine (DIMED), University of Padua, 35128 Padua, Italy; (F.C.); (V.A.); (C.C.)
| | - Marianna Sabbadin
- Veneto Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), 35128 Padua, Italy; (G.M.); (M.S.)
| | - Fabio Pagni
- Department of Medicine and Surgery, Pathology, University Milan Bicocca, 20900 Milan, Italy;
| | - Nicola Fusco
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy;
- Division of Pathology, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, 80131 Naples, Italy;
| | - Matteo Fassan
- Department of Medicine (DIMED), University of Padua, 35128 Padua, Italy; (F.C.); (V.A.); (C.C.)
- Veneto Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), 35128 Padua, Italy; (G.M.); (M.S.)
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42
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Zhang JJ, Xie YX, Luo LL, Yang XT, Wang YX, Cao Y, Long ZB, Wang WP. A comparison of capillary electrophoresis and next-generation sequencing in the detection of immunoglobulin heavy chain H and light chain κ gene rearrangements in the diagnosis of classic hodgkin’s lymphoma. Bioengineered 2022; 13:5868-5879. [PMID: 35220891 PMCID: PMC8973983 DOI: 10.1080/21655979.2022.2038901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
This study aimed to compare the application value of capillary electrophoresis and next-generation sequencing for immunoglobulin (IG) gene rearrangement in the diagnosis of classic Hodgkin’s lymphoma. Twenty paraffin-embedded specimens from patients with classic Hodgkin’s lymphoma were screened. For gene rearrangement detection, the ABI 3500 Genetic Analyzer and ABI Ion GeneStudio S5 Plus sequencing system were used, respectively, and the results were compared. Five cases with monoclonal rearrangements (25%, 5/20) were detected by Capillary Electrophoresis, and positivity for the FR1, FR2, FR3, and IGк loci was 5%, 10%, 10%, and 15%, respectively; 12 cases with monoclonal rearrangements (60%, 12/20) were detected by Next-generation Sequencing where the positivity of the above corresponding loci were 35%, 45%, 50%, and 30%, respectively. Among the 20 samples, 6 IGк clonal rearrangements were detected, and the usage frequency (66.7%) of IGкJ4 was the highest in the IGкJ subgroup. The usage frequency of IGкV1 and IGкV3 in the GкV sub-group was 33.3% and 33.3%, respectively. Twelve immunoglobulin heavy chain (IGH) clonal rearrangements were detected among the 20 samples, and the order of usage frequency in the IGH joining region J (IGHJ) subgroup was IGHJ4 > IGHJ5 > IGHJ6 > IGHJ3. The gene with the highest usage frequency in the IGH variable (IGHV) subgroup was IGHV3 (50%) and the percentage of IGHV mutations ranged from 0% ± 11.45% with an average frequency of 3.34%. Compared with Capillary Electrophoresis, Next-generation Sequencing showed a higher positivity in the detection of gene clonal rearrangements, was more accurate in the interpretation of results.
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Affiliation(s)
- Juan-Juan Zhang
- Department of Pathology, The First People’s Hospital of Yunnan Province
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Yu-Xin Xie
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Li-Lin Luo
- Department of Pathology, The First People’s Hospital of Yunnan Province
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Xuan-Tao Yang
- Department of Pathology, The First People’s Hospital of Yunnan Province
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Yi-Xing Wang
- Department of Pathology, The First People’s Hospital of Yunnan Province
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Yue Cao
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Zheng-Bo Long
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Wan-Pu Wang
- Department of Pathology, The First People’s Hospital of Yunnan Province
- The Affiliated Hospital of Kunming University of Science and Technology, Kunming, Yunnan, China
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43
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Knapp J, Lallemand S, Monnien F, Felix S, Valmary-Degano S, Courquet S, Demonmerot F, Heyd B, Turco C, Doussot A, Bourgeois L, Bresson-Hadni S, Richou C, Millon L. Molecular diagnosis of alveolar echinococcosis in patients based on frozen and formalin-fixed paraffin-embedded tissue samples. Parasite 2022; 29:4. [PMID: 35113014 PMCID: PMC8812296 DOI: 10.1051/parasite/2022004] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 01/14/2022] [Indexed: 11/14/2022] Open
Abstract
Confirmed diagnosis of alveolar echinococcosis (AE) is based on pathological criteria and molecular evidence. This parasite-borne disease, caused by the cestode Echinococcus multilocularis, sparingly involves humans as a dead-end host. In humans, the parasite mainly colonizes the liver but can colonize any organ and cause atypical forms, often difficult to characterize clinically. Moreover, molecular methods may be suitable to make the diagnosis of AE in cases of atypical forms, extra-hepatic localizations, or immunosuppressed patients. The aim of this study was to determine the most relevant published PCR techniques, for diagnosis of AE in patients and adopt the best strategy for molecular diagnosis depending on the nature of the tested sample. In this study, we evaluated nine end-point PCR assays and one real-time PCR assay (qPCR), targeting mitochondrial genes, using a total of 89 frozen or formalin-fixed paraffin-embedded (FFPE) samples from either 48 AE or 9 cystic echinococcosis patients. Targeted fragment-genes ranged from 84 to 529 bp. Six PCR assays were able to amplify the DNA of 100% of the frozen AE-samples and for one PCR, 69.8% of the FFPE AE-samples. The 16S rrnL PCR (84 bp) was positive in PCR for 77% of the AE samples and in qPCR for 86.5%. The sensitivity of the PCR assays was higher for fresh samples and FFPE samples stored for less than 5 years. The qPCR assay further increased sensitivity for the tested samples, confirming the need for the development of an Echinococcus spp. qPCR to improve the molecular diagnosis of echinococcoses.
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Affiliation(s)
- Jenny Knapp
- Department of Parasitology-Mycology, National Reference Centre for Echinococcoses, University Hospital of Besançon, 25030 Besançon, France - UMR CNRS 6249 Laboratoire Chrono-environnement, Université Bourgogne-Franche-Comté, 16 Route de Gray, 25030 Besançon, France
| | - Séverine Lallemand
- Department of Parasitology-Mycology, National Reference Centre for Echinococcoses, University Hospital of Besançon, 25030 Besançon, France
| | - Franck Monnien
- Department of Pathology, University Hospital of Besançon, 25030 Besançon, France
| | - Sophie Felix
- Department of Pathology, University Hospital of Besançon, 25030 Besançon, France
| | - Séverine Valmary-Degano
- Department of Pathology, University Hospital of Besançon, 25030 Besançon, France - Department of Pathology, University Hospital of Grenoble-Alps, 38043 Grenoble, France
| | - Sandra Courquet
- Department of Parasitology-Mycology, National Reference Centre for Echinococcoses, University Hospital of Besançon, 25030 Besançon, France - UMR CNRS 6249 Laboratoire Chrono-environnement, Université Bourgogne-Franche-Comté, 16 Route de Gray, 25030 Besançon, France
| | - Florent Demonmerot
- Department of Parasitology-Mycology, National Reference Centre for Echinococcoses, University Hospital of Besançon, 25030 Besançon, France
| | - Bruno Heyd
- Visceral, Digestive and Cancer Surgery, Hepatic Transplantation Unit, University Hospital of Besançon, 25030 Besançon, France
| | - Celia Turco
- Department of Digestive Surgery, Hepato-Biliary-Pancreatic and Liver Transplantation, AP-HP Pitié-Salpêtrière Hospital - Charles-Foix, 75651 Paris, France
| | - Alexandre Doussot
- Visceral, Digestive and Cancer Surgery, Hepatic Transplantation Unit, University Hospital of Besançon, 25030 Besançon, France
| | - Lucie Bourgeois
- Department of Pathology, University Hospital of Besançon, 25030 Besançon, France
| | - Solange Bresson-Hadni
- Department of Parasitology-Mycology, National Reference Centre for Echinococcoses, University Hospital of Besançon, 25030 Besançon, France - UMR CNRS 6249 Laboratoire Chrono-environnement, Université Bourgogne-Franche-Comté, 16 Route de Gray, 25030 Besançon, France
| | - Carine Richou
- Department of Hepatology, University Hospital of Besançon, 25030 Besançon, France
| | - Laurence Millon
- Department of Parasitology-Mycology, National Reference Centre for Echinococcoses, University Hospital of Besançon, 25030 Besançon, France - UMR CNRS 6249 Laboratoire Chrono-environnement, Université Bourgogne-Franche-Comté, 16 Route de Gray, 25030 Besançon, France
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44
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Vo TTL, Nguyen TN, Nguyen TT, Pham ATD, Vuong DL, Ta VT, Ho VS. SHOX2 methylation in Vietnamese patients with lung cancer. Mol Biol Rep 2022; 49:3413-3421. [PMID: 35088378 DOI: 10.1007/s11033-022-07172-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 01/19/2022] [Indexed: 10/19/2022]
Abstract
BACKGROUND DNA methylation on cytosine in the CpG dinucleotides is one of the most common epigenetic perturbations taking place during cancer initiation, progression, occurrence and resistance therapy. DNA methylation seems to be sufficiently stable epigenetic modification to be utilized as a cancer biomarker in in vitro diagnostic (IVD) settings. Nowadays, the SHOX2 methylation (mSHOX2) is one of the most valuable DNA methylation biomarkers of lung cancer that is the leading cause of cancer death. It is being continuously validated across ethnicities, lifestyles and lifespan. This study focused on characteristics of mSHOX2 in Vietnamese patients with lung cancer since a lack of investigation and evidence of its utility in this country. METHODS The probe and primer sets were designed according to the MethyLight method for quantitative assessment of the mSHOX2 in 214 formalin-fixed paraffin-embedded (FFPE) lung tissues and 57 plasma samples. RESULTS mSHOX2 in FFPE tissues allowed discriminating benign and malignant lung diseases with 60% (95% CI 50.7-68.8%) sensitivity and 90.4% (95% CI 82.6-95.5%) specificity. Importantly, based on mSHOX2 in plasma, lung cancer could be detected with 83.3% (95% CI 65.3-94.4%) sensitivity and 92.6% (95% CI 75.7-99.1%) specificity, respectively. There were insignificant associations between mSHOX2 with age, cancer stage, EGFR mutation and serum CEA, CYFRA21-1 concentrations except for that gender. CONCLUSION Our study indicated that mSHOX2 was satisfactory for distinguishing malignant from benign lung tissue and noninvasively detecting lung cancer.
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Affiliation(s)
- Thi Thuong Lan Vo
- Faculty of Biology, University of Science, Vietnam National University, Hanoi, Vietnam.
| | - Thuy Ngan Nguyen
- Faculty of Biology, University of Science, Vietnam National University, Hanoi, Vietnam
| | - Thu Trang Nguyen
- Faculty of Biology, University of Science, Vietnam National University, Hanoi, Vietnam
| | - Anh Thuy Duong Pham
- Faculty of Biology, University of Science, Vietnam National University, Hanoi, Vietnam
| | - Dieu Linh Vuong
- Pathology and Molecular Biology Center, Vietnam National Cancer Hospital, Hanoi, Vietnam
| | - Van To Ta
- Pathology and Molecular Biology Center, Vietnam National Cancer Hospital, Hanoi, Vietnam
| | - Van Son Ho
- Department of Chemistry, 175 Hospital, Ho Chi Minh City, Vietnam
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45
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Kazdal D, Hofman V, Christopoulos P, Ilié M, Stenzinger A, Hofman P. Fusion-positive non-small cell lung carcinoma: Biological principles, clinical practice, and diagnostic implications. Genes Chromosomes Cancer 2022; 61:244-260. [PMID: 34997651 DOI: 10.1002/gcc.23022] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/26/2021] [Accepted: 12/27/2021] [Indexed: 12/11/2022] Open
Abstract
Based on superior efficacy and tolerability, targeted therapy is currently preferred over chemotherapy and/or immunotherapy for actionable gene fusions that occur in late-stage non-small cell lung carcinoma (NSCLC). Consequently, current clinical practice guidelines mandate testing for ALK, ROS1, NTRK, and RET gene fusions in all patients with newly diagnosed advanced non-squamous NSCLC (NS-NSCLC). Gene fusions can be detected using different approaches, but today RNA next-generation sequencing (NGS) or combined DNA/RNA NGS is the method of choice. The discovery of other gene fusions (involving, eg, NRG1, NUT, FGFR1, FGFR2, MET, BRAF, EGFR, SMARC fusions) and their partners has increased progressively in recent years, leading to the development of new and promising therapies and mandating the development and implementation of comprehensive detection methods. The purpose of this review is to focus on recent data concerning the main gene fusions identified in NSCLC, followed by the discussion of major challenges in this domain.
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Affiliation(s)
- Daniel Kazdal
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,Translational Lung Research Center (TLRC) Heidelberg, Heidelberg, Germany.,German Center for Lung Research (DZL), Heidelberg, Germany
| | - Véronique Hofman
- Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, Université Côte d'Azur, FHU OncoAge, Nice, France.,Centre Antoine Lacassagne Cancer Center, Université Côte d'Azur, CNRS, INSERM, IRCAN, FHU OncoAge, Nice, France.,Hospital-Integrated Biobank BB-0033-00025, Université Côte d'Azur, CHU Nice, FHU OncoAge, Nice, France
| | - Petros Christopoulos
- Translational Lung Research Center (TLRC) Heidelberg, Heidelberg, Germany.,German Center for Lung Research (DZL), Heidelberg, Germany.,Thoraxklinik and National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Marius Ilié
- Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, Université Côte d'Azur, FHU OncoAge, Nice, France.,Centre Antoine Lacassagne Cancer Center, Université Côte d'Azur, CNRS, INSERM, IRCAN, FHU OncoAge, Nice, France.,Hospital-Integrated Biobank BB-0033-00025, Université Côte d'Azur, CHU Nice, FHU OncoAge, Nice, France
| | - Albrecht Stenzinger
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,German Center for Lung Research (DZL), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Paul Hofman
- Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, Université Côte d'Azur, FHU OncoAge, Nice, France.,Centre Antoine Lacassagne Cancer Center, Université Côte d'Azur, CNRS, INSERM, IRCAN, FHU OncoAge, Nice, France.,Hospital-Integrated Biobank BB-0033-00025, Université Côte d'Azur, CHU Nice, FHU OncoAge, Nice, France
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46
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Emser SV, Schaschl H, Millesi E, Steinborn R. Extension of Mitogenome Enrichment Based on Single Long-Range PCR: mtDNAs and Putative Mitochondrial-Derived Peptides of Five Rodent Hibernators. Front Genet 2021; 12:685806. [PMID: 35027919 PMCID: PMC8749263 DOI: 10.3389/fgene.2021.685806] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 11/10/2021] [Indexed: 12/14/2022] Open
Abstract
Enriching mitochondrial DNA (mtDNA) for sequencing entire mitochondrial genomes (mitogenomes) can be achieved by single long-range PCR. This avoids interference from the omnipresent nuclear mtDNA sequences (NUMTs). The approach is currently restricted to the use of samples collected from humans and ray-finned fishes. Here, we extended the use of single long-range PCR by introducing back-to-back oligonucleotides that target a sequence of extraordinary homology across vertebrates. The assay was applied to five hibernating rodents, namely alpine marmot, Arctic and European ground squirrels, and common and garden dormice, four of which have not been fully sequenced before. Analysis of the novel mitogenomes focussed on the prediction of mitochondrial-derived peptides (MDPs) providing another level of information encoded by mtDNA. The comparison of MOTS-c, SHLP4 and SHLP6 sequences across vertebrate species identified segments of high homology that argue for future experimentation. In addition, we evaluated four candidate polymorphisms replacing an amino acid in mitochondrially encoded subunits of the oxidative phosphorylation (OXPHOS) system that were reported in relation to cold-adaptation. No obvious pattern was found for the diverse sets of mammalian species that either apply daily or multiday torpor or otherwise cope with cold. In summary, our single long-range PCR assay applying a pair of back-to-back primers that target a consensus sequence motif of Vertebrata has potential to amplify (intact) mitochondrial rings present in templates from a taxonomically diverse range of vertebrates. It could be promising for studying novel mitogenomes, mitotypes of a population and mitochondrial heteroplasmy in a sensitive, straightforward and flexible manner.
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Affiliation(s)
- Sarah V. Emser
- Genomics Core Facility, VetCore, University of Veterinary Medicine, Vienna, Austria
- Department of Behavioral and Cognitive Biology, University of Vienna, Vienna, Austria
| | - Helmut Schaschl
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Eva Millesi
- Department of Behavioral and Cognitive Biology, University of Vienna, Vienna, Austria
| | - Ralf Steinborn
- Genomics Core Facility, VetCore, University of Veterinary Medicine, Vienna, Austria
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47
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Le TN, Handt O, Henry J, Linacre A. A novel approach for rapid cell assessment to estimate DNA recovery from human bone tissue. Forensic Sci Med Pathol 2021; 17:649-659. [PMID: 34633584 DOI: 10.1007/s12024-021-00428-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/18/2021] [Indexed: 11/26/2022]
Abstract
We report on the use of a DNA staining dye to locate and record nucleated osteocytes and other bone-related cells within sections of archived formalin-fixed and paraffin-embedded human tibia from which informative DNA profiles were obtained. Eleven of these archived tibia samples were sectioned at a thickness of 5 µm. Diamond™ Nucleic Acid Dye was applied to the sections and cells within the matrix of the bone fluoresced so that their location and number of cells could be photographed. DNA was isolated from these 11 samples using a standard extraction process and the yields were quantified by real-time PCR. Complete STR profiles were generated from ten bone extracts where low-level inhibition was recorded with an incomplete STR profile obtained from one sample with higher inhibition. The stained image of this sample showed that few cells were present. There was a significant relationship between the number of DD-stained cells and the number of alleles obtained (p < 0.05). Staining cells to determine the prevalence of bone cell nuclei allows a triage of samples prior to any subsequent DNA profiling.
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Affiliation(s)
- Thien Ngoc Le
- College of Science and Engineering, Flinders University, Flinders, SA, 5042, Australia
| | - Oliva Handt
- College of Science and Engineering, Flinders University, Flinders, SA, 5042, Australia
- Forensic Science SA, PO Box 2790, Adelaide, SA, 5001, Australia
| | - Julianne Henry
- College of Science and Engineering, Flinders University, Flinders, SA, 5042, Australia
- Forensic Science SA, PO Box 2790, Adelaide, SA, 5001, Australia
| | - Adrian Linacre
- College of Science and Engineering, Flinders University, Flinders, SA, 5042, Australia.
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48
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Salvo M, González-Feliú E, Toro J, Gallegos I, Maureira I, Miranda-González N, Barajas O, Bustamante E, Ahumada M, Colombo A, Armisén R, Villamán C, Ibañez C, Bravo ML, Sanhueza V, Spencer ML, de Toro G, Morales E, Bizama C, García P, Carrasco AM, Gutiérrez L, Bermejo JL, Verdugo RA, Marcelain K. Validation of an NGS Panel Designed for Detection of Actionable Mutations in Tumors Common in Latin America. J Pers Med 2021; 11:jpm11090899. [PMID: 34575676 PMCID: PMC8472524 DOI: 10.3390/jpm11090899] [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: 07/07/2021] [Revised: 08/29/2021] [Accepted: 09/03/2021] [Indexed: 12/24/2022] Open
Abstract
Next-generation sequencing (NGS) is progressively being used in clinical practice. However, several barriers preclude using this technology for precision oncology in most Latin American countries. To overcome some of these barriers, we have designed a 25-gene panel that contains predictive biomarkers for most current and near-future available therapies in Chile and Latin America. Library preparation was optimized to account for low DNA integrity observed in formalin-fixed paraffin-embedded tissue. The workflow includes an automated bioinformatic pipeline that accounts for the underrepresentation of Latin Americans in genome databases. The panel detected small insertions, deletions, and single nucleotide variants down to allelic frequencies of 0.05 with high sensitivity, specificity, and reproducibility. The workflow was validated in 272 clinical samples from several solid tumor types, including gallbladder (GBC). More than 50 biomarkers were detected in these samples, mainly in BRCA1/2, KRAS, and PIK3CA genes. In GBC, biomarkers for PARP, EGFR, PIK3CA, mTOR, and Hedgehog signaling inhibitors were found. Thus, this small NGS panel is an accurate and sensitive method that may constitute a more cost-efficient alternative to multiple non-NGS assays and costly, large NGS panels. This kind of streamlined assay with automated bioinformatics analysis may facilitate the implementation of precision medicine in Latin America.
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Affiliation(s)
- Mauricio Salvo
- Department of Basic and Clinical Oncology, Faculty of Medicine, Universidad de Chile, Santiago 8330015, Chile; (M.S.); (E.G.-F.); (J.T.); (I.G.); (I.M.); (N.M.-G.); (O.B.); (M.A.); (A.C.); (C.V.)
| | - Evelin González-Feliú
- Department of Basic and Clinical Oncology, Faculty of Medicine, Universidad de Chile, Santiago 8330015, Chile; (M.S.); (E.G.-F.); (J.T.); (I.G.); (I.M.); (N.M.-G.); (O.B.); (M.A.); (A.C.); (C.V.)
| | - Jessica Toro
- Department of Basic and Clinical Oncology, Faculty of Medicine, Universidad de Chile, Santiago 8330015, Chile; (M.S.); (E.G.-F.); (J.T.); (I.G.); (I.M.); (N.M.-G.); (O.B.); (M.A.); (A.C.); (C.V.)
| | - Iván Gallegos
- Department of Basic and Clinical Oncology, Faculty of Medicine, Universidad de Chile, Santiago 8330015, Chile; (M.S.); (E.G.-F.); (J.T.); (I.G.); (I.M.); (N.M.-G.); (O.B.); (M.A.); (A.C.); (C.V.)
- Department of Pathology, Hospital Clínico de la Universidad de Chile, Santiago 8380456, Chile
| | - Ignacio Maureira
- Department of Basic and Clinical Oncology, Faculty of Medicine, Universidad de Chile, Santiago 8330015, Chile; (M.S.); (E.G.-F.); (J.T.); (I.G.); (I.M.); (N.M.-G.); (O.B.); (M.A.); (A.C.); (C.V.)
- Department of Medical Technology, Faculty of Medicine, Universidad de Chile, Santiago 8330015, Chile
| | - Nicolás Miranda-González
- Department of Basic and Clinical Oncology, Faculty of Medicine, Universidad de Chile, Santiago 8330015, Chile; (M.S.); (E.G.-F.); (J.T.); (I.G.); (I.M.); (N.M.-G.); (O.B.); (M.A.); (A.C.); (C.V.)
| | - Olga Barajas
- Department of Basic and Clinical Oncology, Faculty of Medicine, Universidad de Chile, Santiago 8330015, Chile; (M.S.); (E.G.-F.); (J.T.); (I.G.); (I.M.); (N.M.-G.); (O.B.); (M.A.); (A.C.); (C.V.)
- Department of Internal Medicine, Hospital Clínico Universidad de Chile, Santiago 8380456, Chile
- Fundación Arturo López Pérez, Santiago 7500921, Chile; (E.B.); (A.M.C.)
| | - Eva Bustamante
- Fundación Arturo López Pérez, Santiago 7500921, Chile; (E.B.); (A.M.C.)
| | - Mónica Ahumada
- Department of Basic and Clinical Oncology, Faculty of Medicine, Universidad de Chile, Santiago 8330015, Chile; (M.S.); (E.G.-F.); (J.T.); (I.G.); (I.M.); (N.M.-G.); (O.B.); (M.A.); (A.C.); (C.V.)
- Department of Internal Medicine, Hospital Clínico Universidad de Chile, Santiago 8380456, Chile
| | - Alicia Colombo
- Department of Basic and Clinical Oncology, Faculty of Medicine, Universidad de Chile, Santiago 8330015, Chile; (M.S.); (E.G.-F.); (J.T.); (I.G.); (I.M.); (N.M.-G.); (O.B.); (M.A.); (A.C.); (C.V.)
- Department of Pathology, Hospital Clínico de la Universidad de Chile, Santiago 8380456, Chile
| | - Ricardo Armisén
- Center for Genetics and Genomics, Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago 8320000, Chile;
| | - Camilo Villamán
- Department of Basic and Clinical Oncology, Faculty of Medicine, Universidad de Chile, Santiago 8330015, Chile; (M.S.); (E.G.-F.); (J.T.); (I.G.); (I.M.); (N.M.-G.); (O.B.); (M.A.); (A.C.); (C.V.)
| | - Carolina Ibañez
- Department of Hematology & Oncology, Faculty of Medicine, Pontificia Universidad Católica de Chile (PUC), Santiago 3580000, Chile; (C.I.); (M.L.B.)
| | - María Loreto Bravo
- Department of Hematology & Oncology, Faculty of Medicine, Pontificia Universidad Católica de Chile (PUC), Santiago 3580000, Chile; (C.I.); (M.L.B.)
| | - Verónica Sanhueza
- Department of Pathology, Hospital Padre Hurtado, Santiago 8710022, Chile;
| | - M. Loreto Spencer
- Department of Pathology, Hospital Clínico Regional Guillermo Grant Benavente, Concepción 4070038, Chile;
| | - Gonzalo de Toro
- School of Medical Technology, Universidad Austral de Chile at Puerto Montt, Puerto Montt 5110566, Chile;
| | - Erik Morales
- Department of Pathology, Hospital Regional de Talca, Talca 3460000, Chile;
- Department of Preclinical Sciences, Faculty of Medicine, Universidad Católica del Maule, Talca 3460000, Chile
| | - Carolina Bizama
- Department of Pathology, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago 3580000, Chile; (C.B.); (P.G.)
| | - Patricia García
- Department of Pathology, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago 3580000, Chile; (C.B.); (P.G.)
| | | | - Lorena Gutiérrez
- Department of Pathology, Hospital San Juan de Dios, Santiago 8320000, Chile;
| | | | - Ricardo A. Verdugo
- Department of Basic and Clinical Oncology, Faculty of Medicine, Universidad de Chile, Santiago 8330015, Chile; (M.S.); (E.G.-F.); (J.T.); (I.G.); (I.M.); (N.M.-G.); (O.B.); (M.A.); (A.C.); (C.V.)
- Human Genetics Program, ICBM, Faculty of Medicine, Universidad de Chile, Santiago 8330015, Chile
- Correspondence: (R.A.V.); (K.M.); Tel.: +56-22978-9527 (R.A.V.); +56-22978-9562 (K.M.)
| | - Katherine Marcelain
- Department of Basic and Clinical Oncology, Faculty of Medicine, Universidad de Chile, Santiago 8330015, Chile; (M.S.); (E.G.-F.); (J.T.); (I.G.); (I.M.); (N.M.-G.); (O.B.); (M.A.); (A.C.); (C.V.)
- Correspondence: (R.A.V.); (K.M.); Tel.: +56-22978-9527 (R.A.V.); +56-22978-9562 (K.M.)
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Hur JY, Lee KY. Characteristics and Clinical Application of Extracellular Vesicle-Derived DNA. Cancers (Basel) 2021; 13:3827. [PMID: 34359729 PMCID: PMC8345206 DOI: 10.3390/cancers13153827] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/25/2021] [Accepted: 07/27/2021] [Indexed: 02/06/2023] Open
Abstract
Extracellular vesicles (EVs) carry RNA, proteins, lipids, and diverse biomolecules for intercellular communication. Recent studies have reported that EVs contain double-stranded DNA (dsDNA) and oncogenic mutant DNA. The advantage of EV-derived DNA (EV DNA) over cell-free DNA (cfDNA) is the stability achieved through the encapsulation in the lipid bilayer of EVs, which protects EV DNA from degradation by external factors. The existence of DNA and its stability make EVs a useful source of biomarkers. However, fundamental research on EV DNA remains limited, and many aspects of EV DNA are poorly understood. This review examines the known characteristics of EV DNA, biogenesis of DNA-containing EVs, methylation, and next-generation sequencing (NGS) analysis using EV DNA for biomarker detection. On the basis of this knowledge, this review explores how EV DNA can be incorporated into diagnosis and prognosis in clinical settings, as well as gene transfer of EV DNA and its therapeutic potential.
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Affiliation(s)
- Jae Young Hur
- Precision Medicine Lung Cancer Center, Konkuk University Medical Center, Seoul 05030, Korea;
- Department of Pathology, Konkuk University Medical Center, Seoul 05030, Korea
| | - Kye Young Lee
- Precision Medicine Lung Cancer Center, Konkuk University Medical Center, Seoul 05030, Korea;
- Department of Pulmonary Medicine, Konkuk University School of Medicine, Seoul 05030, Korea
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50
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Hulaniuk ML, Corach D, Trinks J, Caputo M. A simple and rapid approach for human herpesvirus type 8 subtype characterization using single base extension. Lett Appl Microbiol 2021; 73:308-317. [PMID: 34048079 DOI: 10.1111/lam.13515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 11/28/2022]
Abstract
Sequence analysis of the ORFK1 of human herpesvirus type 8 (HHV-8) allows the identification of six major subtypes (A-F), which are related to human migrations and the clinical progression of Kaposi's sarcoma. Sequencing and subsequent phylogenetic analysis of ORFK1 is considered to be the most reliable method for HHV-8 genotyping. However, it exhibits challenges and limitations. Herein, we designed and validated a single base extension (SBE) protocol for characterization of HHV-8 ORFK1 subtypes. A nested polymerase chain reaction (PCR) protocol was carried out to amplify a small 294-bp PCR product encompassing four single nucleotide polymorphisms at positions 360, 406, 465 and 527 of the HHV-8 genome. Finally, a multiplex SBE technique was developed and validated in 20 samples previously genotyped by phylogenetic analysis. The patterns obtained in this reaction could successfully discriminate between ORFK1 subtypes. The typing results obtained completely matched with those of the 'gold standard' method in all analysed samples. This method can reliably identify HHV-8 subtypes A, B and C, which are the most prevalent ones worldwide, and the remaining subtypes (D, E and F). SBE can be useful as an efficient, rapid and low-cost screening method for viral genotyping in a single tube, particularly samples with low-quality DNA, and with easy data interpretation.
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Affiliation(s)
- M L Hulaniuk
- Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB), CONICET, Instituto Universitario del Hospital Italiano (IUHI), Hospital Italiano (HIBA), Buenos Aires, Argentina
| | - D Corach
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.,Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética, Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas, Buenos Aires, Argentina
| | - J Trinks
- Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB), CONICET, Instituto Universitario del Hospital Italiano (IUHI), Hospital Italiano (HIBA), Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - M Caputo
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.,Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Microbiología, Inmunología, Biotecnología y Genética, Cátedra de Genética Forense y Servicio de Huellas Digitales Genéticas, Buenos Aires, Argentina
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