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Peeler C, Pitzer CR, Paez HG, Criswell S. Histochemical and morphological evaluation of a glyoxal acid-free fixative. Biotech Histochem 2024; 99:49-58. [PMID: 38164087 DOI: 10.1080/10520295.2023.2300797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024] Open
Abstract
The application of most chemical fixatives, such as formalin, in the anatomic pathology laboratory requires safety training and hazardous chemical monitoring due to the toxicity and health risks associated with their use. Consequently, the use of formalin has been banned in most applications in Europe; the primary exception is its use in the histology laboratory in lieu of a suitable and safer alternative. Glyoxal based solutions, several of which are available commercially, are the most promising alternative fixatives, because they are based on a mechanism of fixation similar to that of formalin. Unlike formalin, however, glyoxal based solutions do not dissociate from water and therefore do not require ventilation measures such as a fume hood. A primary barrier to the adoption of commercially available glyoxal based solutions is their low pH, which can produce undesirable morphological and antigenic tissue alterations; however, a recently available neutral pH glyoxal product (glyoxal acid free) (GAF) has been developed to mitigate the challenges of low pH. We compared the morphology and histochemistry among tissues fixed in 10% neutral buffered formalin, a commercially available acidic glyoxal product (Prefer), and GAF. Tissues fixed in formalin and Prefer exhibited similar morphology and staining properties; tissues fixed with 2% GAF exhibited deleterious effects.
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Affiliation(s)
- Chelsea Peeler
- Department of Diagnostic and Health Sciences, College of Health Professions, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Christopher R Pitzer
- Department of Physiology, College of Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Hector G Paez
- Department of Physiology, College of Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Sheila Criswell
- Department of Diagnostic and Health Sciences, College of Health Professions, University of Tennessee Health Science Center, Memphis, TN, USA
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2
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Afflerbach AK, Albers A, Appelt A, Schweizer L, Paulus W, Bockmayr M, Schüller U, Thomas C. Nanopore sequencing from formalin-fixed paraffin-embedded specimens for copy-number profiling and methylation-based CNS tumor classification. Acta Neuropathol 2024; 147:74. [PMID: 38642165 PMCID: PMC11032293 DOI: 10.1007/s00401-024-02731-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 04/22/2024]
Affiliation(s)
- Ann-Kristin Afflerbach
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
- Institute for Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anne Albers
- Institute of Neuropathology, University Hospital Münster, Pottkamp 2, 48149, Münster, Germany
| | - Anton Appelt
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
| | - Leonille Schweizer
- Institute of Neurology (Edinger Institute), University Hospital Frankfurt, Goethe University, Frankfurt Am Main, Germany
- German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, Heidelberg, Germany
- Frankfurt Cancer Institute (FCI), Frankfurt Am Main, Germany
| | - Werner Paulus
- Institute of Neuropathology, University Hospital Münster, Pottkamp 2, 48149, Münster, Germany
| | - Michael Bockmayr
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
- bAIome - Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ulrich Schüller
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christian Thomas
- Institute of Neuropathology, University Hospital Münster, Pottkamp 2, 48149, Münster, Germany.
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3
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Xavier D, Lucas N, Williams SG, Koh JMS, Ashman K, Loudon C, Reddel R, Hains PG, Robinson PJ. Heat 'n Beat: A Universal High-Throughput End-to-End Proteomics Sample Processing Platform in under an Hour. Anal Chem 2024; 96:4093-4102. [PMID: 38427620 DOI: 10.1021/acs.analchem.3c04708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2024]
Abstract
Proteomic analysis by mass spectrometry of small (≤2 mg) solid tissue samples from diverse formats requires high throughput and comprehensive proteome coverage. We developed a nearly universal, rapid, and robust protocol for sample preparation, suitable for high-throughput projects that encompass most cell or tissue types. This end-to-end workflow extends from original sample to loading the mass spectrometer and is centered on a one-tube homogenization and digestion method called Heat 'n Beat (HnB). It is applicable to most tissues, regardless of how they were fixed or embedded. Sample preparation was divided into separate challenges. The initial sample washing and final peptide cleanup steps were adapted to three tissue sources: fresh frozen (FF), optimal cutting temperature (OCT) compound embedded (FF-OCT), and formalin-fixed paraffin embedded (FFPE). Third, for core processing, tissue disruption and lysis were decreased to a 7 min heat and homogenization treatment, and reduction, alkylation, and proteolysis were optimized into a single step. The refinements produced near doubled peptide yield when compared to our earlier method ABLE delivered a consistently high digestion efficiency of 85-90%, reported by ProteinPilot, and required only 38 min for core processing in a single tube, with the total processing time being 53-63 min. The robustness of HnB was demonstrated on six organ types, a cell line, and a cancer biopsy. Its suitability for high-throughput applications was demonstrated on a set of 1171 FF-OCT human cancer biopsies, which were processed for end-to-end completion in 92 h, producing highly consistent peptide yield and quality for over 3513 MS runs.
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Affiliation(s)
- Dylan Xavier
- ProCan, Faculty of Medicine and Health, The University of Sydney, Children's Medical Research Institute, Westmead, NSW 2145, Australia
| | - Natasha Lucas
- ProCan, Faculty of Medicine and Health, The University of Sydney, Children's Medical Research Institute, Westmead, NSW 2145, Australia
| | - Steven G Williams
- ProCan, Faculty of Medicine and Health, The University of Sydney, Children's Medical Research Institute, Westmead, NSW 2145, Australia
| | - Jennifer M S Koh
- ProCan, Faculty of Medicine and Health, The University of Sydney, Children's Medical Research Institute, Westmead, NSW 2145, Australia
| | - Keith Ashman
- ProCan, Faculty of Medicine and Health, The University of Sydney, Children's Medical Research Institute, Westmead, NSW 2145, Australia
| | - Clare Loudon
- ProCan, Faculty of Medicine and Health, The University of Sydney, Children's Medical Research Institute, Westmead, NSW 2145, Australia
| | - Roger Reddel
- ProCan, Faculty of Medicine and Health, The University of Sydney, Children's Medical Research Institute, Westmead, NSW 2145, Australia
| | - Peter G Hains
- ProCan, Faculty of Medicine and Health, The University of Sydney, Children's Medical Research Institute, Westmead, NSW 2145, Australia
| | - Phillip J Robinson
- ProCan, Faculty of Medicine and Health, The University of Sydney, Children's Medical Research Institute, Westmead, NSW 2145, Australia
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4
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Meireles SI, Cruz MV, de Godoy CD, de Testagrossa L. Performance of non-formalin fixed paraffin embedded samples in hybrid capture and amplicon next-generation sequencing panels. Diagn Cytopathol 2024; 52:171-182. [PMID: 38124281 DOI: 10.1002/dc.25267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND Genomic profiling using next-generation sequencing (NGS) is fundamental for driving prognostic and therapy in cancer. Formalin-fixed paraffin embedded (FFPE) tissue is the widely used material, whereas non-FFPE may represent an alternative. However, studies comparing the NGS performance of non-FFPE materials to FFPE are still lacking in the literature. The objective of this study was to characterize in non-FFPE preparations the nucleic acid yield and NGS performance on both a capture-based and an amplicon-based NGS platform. NGS quality metrics obtained from non-FFPE preparations were compared to FFPE. METHODS We analyzed the cellularity and nucleic acid yield in 111 tumors from non-FFPE preparations. In addition, comprehensive hybrid capture panel sequencing metrics obtained from DNA and RNA libraries were compared between independent non-FFPE and FFPE samples. A paired comparison between non-FFPE and FFPE samples was performed to analyze concordance in mutant allele detection using an amplicon panel. RESULTS The mean target coverage from DNA libraries was 2× higher in non-FFPE samples than in FFPE. The detection of exogenous DNA was 2.5× higher in non-FFPE than in FFPE. Conversely, a lower performance was observed in non-FFPE RNA libraries in comparison to FFPE DNA libraries with no impact in minimum standard cutoffs. The variant allele detection in non-FFPE was found to be comparable to that of FFPE tumor samples in matched samples. CONCLUSIONS Non-FFPE was demonstrated to be a suitable material for DNA and RNA library preparations using a comprehensive NGS panel. This is the first study reporting library quality metrics according to the TSO500 analysis pipeline.
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Affiliation(s)
- Sibele Inácio Meireles
- Departamento de Anatomia Patológica e Molecular, Hospital Sírio Libanês, São Paulo, Brazil
| | - Mariana Vargas Cruz
- Departamento de Anatomia Patológica e Molecular, Hospital Sírio Libanês, São Paulo, Brazil
| | - Carla Daniele de Godoy
- Departamento de Anatomia Patológica e Molecular, Hospital Sírio Libanês, São Paulo, Brazil
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Stagg B, Foster-Smith E, Tam PCK. The diagnostic accuracy of Gram stain on formalin-fixed paraffin-embedded sections of skin tissue in the diagnosis of bacterial skin infection. J Cutan Pathol 2024; 51:246-250. [PMID: 37997440 DOI: 10.1111/cup.14563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 10/31/2023] [Accepted: 11/11/2023] [Indexed: 11/25/2023]
Abstract
BACKGROUND AND OBJECTIVE To evaluate the sensitivity, specificity, and likelihood ratios of Gram stain on formalin-fixed, paraffin-embedded (GS-FFPE) sections of skin in diagnosing bacterial skin infection. METHODS We reviewed a retrospective series of skin specimens reported at our institution wherein histopathological assessment included Gram stain and fresh tissue was concurrently submitted for microscopy and culture. The clinicopathological correlation was the reference standard, whereby the presence of infection was deduced from the final diagnosis in each patient's case notes. RESULTS Our sample included 168 cases (105 positive for infection). GS-FFPE showed a sensitivity of 0.43 (95% confidence interval 0.29, 0.57), a specificity of 0.98 (0.95, 1.01), a positive likelihood ratio of 21.50 (19.76, 23.24), and a negative likelihood ratio of 0.58 (0.41, 0.75). CONCLUSIONS GS-FFPE has poor sensitivity, and a negative result should not be used as evidence to exclude infection. In contrast, it has excellent specificity and, unless the pretest probability of infection is very low, a positive result would make infection much more likely. The value of the GS-FFPE lies in cases where sterile tissue was not submitted for microbiological studies, or sterile tissue culture was negative, and there is at least a low-to-moderate pretest probability of infection.
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Affiliation(s)
- Brendan Stagg
- Anatomical Pathology, SA Pathology, Adelaide, South Australia, Australia
- Dermatology, Flinders Medical Centre, Adelaide, South Australia, Australia
| | - Erwin Foster-Smith
- Anatomical Pathology, SA Pathology, Adelaide, South Australia, Australia
| | - Patrick Chung Kay Tam
- College of Medicine and Public Health, Flinders University, Adelaide, South Australia, Australia
- Division of Infectious Diseases, Duke University School of Medicine, Durham, North Carolina, USA
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6
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Qiu Y, Wei K, Lin H, Liu Y, Lin C, Ke R. Combined amplification-based single-molecule fluorescence in situ hybridization with immunofluorescence for simultaneous in situ detection of RNAs and proteins. Biochem Biophys Res Commun 2024; 696:149508. [PMID: 38244312 DOI: 10.1016/j.bbrc.2024.149508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 01/08/2024] [Indexed: 01/22/2024]
Abstract
We present a combined amplification-based single-molecule fluorescence in situ hybridization and immunofluorescence (asmFISH-IF) method for the detection of multiple RNAs and proteins simultaneously in cells and formaldehyde-fixed and paraffin-embedded tissue sections. We showed that performing asmFISH before immunofluorescence gives a better IF signal than the opposite. Our asmFISH-IF method could help study the interplay of RNA and protein, helping to understand their functions.
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Affiliation(s)
- Yinghui Qiu
- School of Medicine, Huaqiao University, Xiamen, Fujian, 361021, China; College of Materials Science and Engineering, Huaqiao University, Xiamen, Fujian, 361021, China
| | - Kaipeng Wei
- Department of Medical Laboratory Technology, Quanzhou Medical College, Quanzhou, Fujian, 362011, China
| | - Hui Lin
- Department of Pathology, The 910 Hospital, Quanzhou, 362000, Fujian, China
| | - Yanxiu Liu
- School of Medicine, Huaqiao University, Xiamen, Fujian, 361021, China
| | - Chen Lin
- School of Medicine, Huaqiao University, Xiamen, Fujian, 361021, China.
| | - Rongqin Ke
- School of Medicine, Huaqiao University, Xiamen, Fujian, 361021, China.
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G Jagadeeshaprasad M, Zeng J, Zheng N. LC-MS bioanalysis of protein biomarkers and protein therapeutics in formalin-fixed paraffin-embedded tissue specimens. Bioanalysis 2024; 16:245-258. [PMID: 38226835 DOI: 10.4155/bio-2023-0210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024] Open
Abstract
Formalin-fixed paraffin-embedded (FFPE) is a form of preservation and preparation for biopsy specimens. FFPE tissue specimens are readily available as part of oncology studies because they are often collected for disease diagnosis or confirmation. FFPE tissue specimens could be extremely useful for retrospective studies on protein biomarkers because the samples preserved in FFPE blocks could be stable for decades. However, LC-MS bioanalysis of FFPE tissues poses significant challenges. In this Perspective, we review the benefits and recent developments in LC-MS approach for targeted protein biomarker and protein therapeutic analysis using FFPE tissues and their clinical and translational applications. We believe that LC-MS bioanalysis of protein biomarkers in FFPE tissue specimens represents a great potential for its clinical applications.
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Affiliation(s)
| | - Jianing Zeng
- Department of Protein Sciences & Mass Spectrometry, Translational Medicine, Bristol Myers Squibb, Princeton, NJ 08543, USA
| | - Naiyu Zheng
- Department of Protein Sciences & Mass Spectrometry, Translational Medicine, Bristol Myers Squibb, Princeton, NJ 08543, USA
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8
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Gotur SP, Kamarthi N, Wadhwan V. Sirka: An alternative to the formalin fixative. INDIAN J PATHOL MICR 2024; 67:238-240. [PMID: 38358234 DOI: 10.4103/ijpm.ijpm_510_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024] Open
Abstract
Formalin fixation is the most essential step of routine histopathology practice. During the last few years, various fixatives have been developed for use in histopathology practice as an alternative to formalin, to overcome its side effects on health. Here we have demonstrated an interesting and novel idea of using sirka or sugar cane vinegar as an alternative to the formalin with the adequate result.
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Affiliation(s)
- Suhasini P Gotur
- Department of Oral Pathology and Microbiology, Subharti Dental College and Hospital, Swami Vivekanand Subharti University, Meerut, Uttar Pradesh, India Department of Oral Medicine and Radiology, Subharti Dental College and Hospital, Swami Vivekanand Subharti University, Meerut, Uttar Pradesh, India
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9
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Hsu FM, Chang YL, Chen CY, Lin SR, Cheng JCH. Hybridization Protection Reaction for Sensitive and Robust Gene Expression Profiling of Clinical Formalin-Fixed Paraffin-Embedded Samples. Clin Chem 2023; 69:1385-1395. [PMID: 37964418 DOI: 10.1093/clinchem/hvad170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 10/03/2023] [Indexed: 11/16/2023]
Abstract
BACKGROUND RNA profiling of formalin-fixed paraffin-embedded (FFPE) tumor tissues for the molecular diagnostics of disease prognosis or treatment response is often irreproducible and limited to a handful of biomarkers. This has led to an unmet need for robust multiplexed assays that can profile several RNA biomarkers of interest using a limited amount of specimen. Here, we describe hybridization protection reaction (HPR), which is a novel RNA profiling approach with high reproducibility. METHODS HPR assays were designed for multiple genes, including 10 radiosensitivity-associated genes, and compared with TaqMan assays. Performance was tested with synthetic RNA fragments, and the ability to analyze RNA was investigated in FPPE samples from 20 normal lung tissues, 40 lung cancer, and 30 esophageal cancer biopsies. RESULTS Experiments performed on 3 synthetic RNA fragments demonstrated a linear dynamic range of over 1000-fold with a replicate correlation coefficient of 0.99 and high analytical sensitivity between 3.2 to 10 000 pM. Comparison of HPR with standard quantitative reverse transcription polymerase chain reaction on FFPE specimens shows nonsignificant differences with > 99% confidence interval between 2 assays in transcript profiling of 91.7% of test transcripts. In addition, HPR was effectively applied to quantify transcript levels of 10 radiosensitivity-associated genes. CONCLUSIONS Overall, HPR is an alternative approach for RNA profiling with high sensitivity, reproducibility, robustness, and capability for molecular diagnostics in FFPE tumor biopsy specimens of lung and esophageal cancer.
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Affiliation(s)
- Feng-Ming Hsu
- Division of Radiation Oncology, Department of Oncology, National Taiwan University Hospital, Taipei 100225, Taiwan
- Graduate Institute of Oncology and Cancer Research Center, National Taiwan University College of Medicine, Taipei 100025, Taiwan
| | - Yih-Leong Chang
- Department of Pathology, National Taiwan University Hospital, Taipei 100225, Taiwan
| | - Chung-Yung Chen
- Department of Bioscience Technology, Chung Yuan Christian University, Chungli District, Taoyuan 320314, Taiwan
- Center for Nanotechnology and Center for Biomedical Technology, Chung Yuan Christian University, Taoyuan 320314, Taiwan
| | - Shu-Rung Lin
- Department of Bioscience Technology, Chung Yuan Christian University, Chungli District, Taoyuan 320314, Taiwan
- Center for Nanotechnology and Center for Biomedical Technology, Chung Yuan Christian University, Taoyuan 320314, Taiwan
| | - Jason Chia-Hsien Cheng
- Division of Radiation Oncology, Department of Oncology, National Taiwan University Hospital, Taipei 100225, Taiwan
- Graduate Institute of Oncology and Cancer Research Center, National Taiwan University College of Medicine, Taipei 100025, Taiwan
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10
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Boottanun P, Nagai-Okatani C, Nagai M, Ungkulpasvich U, Yamane S, Yamada M, Kuno A. An improved evanescent fluorescence scanner suitable for high-resolution glycome mapping of formalin-fixed paraffin-embedded tissue sections. Anal Bioanal Chem 2023; 415:6975-6984. [PMID: 37395746 DOI: 10.1007/s00216-023-04824-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/25/2023] [Accepted: 06/21/2023] [Indexed: 07/04/2023]
Abstract
Lectin microarray (LMA) is a high-throughput platform that enables the rapid and sensitive analysis of N- and O-glycans attached to glycoproteins in biological samples, including formalin-fixed paraffin-embedded (FFPE) tissue sections. Here, we evaluated the sensitivity of the advanced scanner based on the evanescent-field fluorescence principle, which is equipped with a 1× infinity correction optical system and a high-end complementary metal-oxide semiconductor (CMOS) image sensor in digital binning mode. Using various glycoprotein samples, we estimated that the mGSR1200-CMOS scanner has at least fourfold higher sensitivity for the lower limit of linearity range than that of a previous charge-coupled device scanner (mGSR1200). A subsequent sensitivity test using HEK293T cell lysates demonstrated that cell glycomic profiling could be performed with only three cells, which has the potential for the glycomic profiling of cell subpopulations. Thus, we examined its application in tissue glycome mapping, as indicated in the online LM-GlycomeAtlas database. To achieve fine glycome mapping, we refined the laser microdissection-assisted LMA procedure to analyze FFPE tissue sections. In this protocol, it was sufficient to collect 0.1 mm2 of each of the tissue fragments from 5-μm-thick sections, which differentiated the glycomic profile between the glomerulus and renal tubules of a normal mouse kidney. In conclusion, the improved LMA enables high-resolution spatial analysis, which expands the possibilities of its application classifying cell subpopulations in clinical FFPE tissue specimens. This will be used in the discovery phase for the development of novel glyco-biomarkers and therapeutic targets, and to expand the range of target diseases.
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Affiliation(s)
- Patcharaporn Boottanun
- Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8565, Japan
| | - Chiaki Nagai-Okatani
- Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8565, Japan.
| | - Misugi Nagai
- Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8565, Japan
| | - Umbhorn Ungkulpasvich
- Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8565, Japan
| | - Shinjiro Yamane
- GlycoTechnica Ltd, 101 Hiranobiru3, 5-28-6 Utsukushigaoka, Aoba-Ku, Yokohama, Kanagawa, 225-0002, Japan
| | - Masao Yamada
- EMUKK LLC, 2-21-19, Matsunoki, Kuwana, Mie, 511-0902, Japan
| | - Atsushi Kuno
- Molecular and Cellular Glycoproteomics Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8565, Japan.
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11
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Li KYC, Dejea H, De Winne K, Bonnin A, D'Onofrio V, Cox JA, Garcia-Canadilla P, Lammens M, Cook AC, Bijnens B, Dendooven A. Feasibility and safety of synchrotron-based X-ray phase contrast imaging as a technique complementary to histopathology analysis. Histochem Cell Biol 2023; 160:377-389. [PMID: 37523091 DOI: 10.1007/s00418-023-02220-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2023] [Indexed: 08/01/2023]
Abstract
X-ray phase contrast imaging (X-PCI) is a powerful technique for high-resolution, three-dimensional imaging of soft tissue samples in a non-destructive manner. In this technical report, we assess the quality of standard histopathological techniques performed on formalin-fixed, paraffin-embedded (FFPE) human tissue samples that have been irradiated with different doses of X-rays in the context of an X-PCI experiment. The data from this study demonstrate that routine histochemical and immunohistochemical staining quality as well as DNA and RNA analyses are not affected by previous X-PCI on human FFPE samples. From these data we conclude it is feasible and acceptable to perform X-PCI on FFPE human biopsies.
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Affiliation(s)
- Kan Yan Chloe Li
- Institute of Cardiovascular Science, University College London, London, United Kingdom
| | - Hector Dejea
- Swiss Light Source, Paul Scherrer Institute, Villigen, Switzerland
- ETH Zurich, Zurich, Switzerland
- Department of Biomedical Engineering, Lund University, Lund, Sweden
- MAX IV Laboratory, Lund, Sweden
| | - Koen De Winne
- Department of Pathology, Antwerp University Hospital and University of Antwerp, Antwerp, Belgium
| | - Anne Bonnin
- Swiss Light Source, Paul Scherrer Institute, Villigen, Switzerland
| | | | - Janneke A Cox
- Faculty of Medicine and Life Sciences, Hasselt University, Hasselt, Belgium
- Department of Infectious Diseases and Immunity, Jessa Hospital, Hasselt, Belgium
| | - Patricia Garcia-Canadilla
- Interdisciplinary Cardiovascular Research Group, Sant Joan de Déu Research Institute (IRSJD), Barcelona, Spain
- BCNatal Barcelona Center for Maternal-Fetal and Neonatal Medicine, Hospital Sant Joan de Déu and Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Martin Lammens
- Department of Pathology, Antwerp University Hospital and University of Antwerp, Antwerp, Belgium
| | - Andrew C Cook
- Institute of Cardiovascular Science, University College London, London, United Kingdom
| | - Bart Bijnens
- ICREA, Barcelona, Spain
- IDIBAPS, Barcelona, Spain
| | - Amélie Dendooven
- Department of Pathology, Antwerp University Hospital and University of Antwerp, Antwerp, Belgium.
- Faculty of Medicine and Life Sciences, Hasselt University, Hasselt, Belgium.
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12
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Sounart H, Lázár E, Masarapu Y, Wu J, Várkonyi T, Glasz T, Kiss A, Borgström E, Hill A, Rezene S, Gupta S, Jurek A, Niesnerová A, Druid H, Bergmann O, Giacomello S. Dual spatially resolved transcriptomics for human host-pathogen colocalization studies in FFPE tissue sections. Genome Biol 2023; 24:237. [PMID: 37858234 PMCID: PMC10588020 DOI: 10.1186/s13059-023-03080-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 10/02/2023] [Indexed: 10/21/2023] Open
Abstract
Technologies to study localized host-pathogen interactions are urgently needed. Here, we present a spatial transcriptomics approach to simultaneously capture host and pathogen transcriptome-wide spatial gene expression information from human formalin-fixed paraffin-embedded (FFPE) tissue sections at a near single-cell resolution. We demonstrate this methodology in lung samples from COVID-19 patients and validate our spatial detection of SARS-CoV-2 against RNAScope and in situ sequencing. Host-pathogen colocalization analysis identified putative modulators of SARS-CoV-2 infection in human lung cells. Our approach provides new insights into host response to pathogen infection through the simultaneous, unbiased detection of two transcriptomes in FFPE samples.
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Affiliation(s)
- Hailey Sounart
- Department of Gene Technology, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden
| | - Enikő Lázár
- Department of Gene Technology, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Yuvarani Masarapu
- Department of Gene Technology, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden
| | - Jian Wu
- Department of Gene Technology, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden
| | - Tibor Várkonyi
- 2nd Department of Pathology, Semmelweis University, Budapest, Hungary
| | - Tibor Glasz
- 2nd Department of Pathology, Semmelweis University, Budapest, Hungary
| | - András Kiss
- 2nd Department of Pathology, Semmelweis University, Budapest, Hungary
| | | | | | - Sefanit Rezene
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Soham Gupta
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | | | - Henrik Druid
- Department of Oncology-Pathology, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Olaf Bergmann
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
- Center for Regenerative Therapies Dresden (CRTD), TU Dresden, Dresden, Germany
- Universitätsmedizin Göttingen, Institute of Pharmacology and Toxicology, Göttingen, Germany
| | - Stefania Giacomello
- Department of Gene Technology, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden.
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13
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Stelloo E, Meijers RWJ, Swennenhuis JF, Allahyar A, Hajo K, Cangiano M, de Leng WWJ, van Helvert S, Van der Meulen J, Creytens D, van Kempen LC, Cleton-Jansen AM, Bovee JVMG, de Laat W, Splinter E, Feitsma H. Formalin-Fixed, Paraffin-Embedded-Targeted Locus Capture: A Next-Generation Sequencing Technology for Accurate DNA-Based Gene Fusion Detection in Bone and Soft Tissue Tumors. J Mol Diagn 2023; 25:758-770. [PMID: 37517473 DOI: 10.1016/j.jmoldx.2023.06.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/23/2023] [Accepted: 06/28/2023] [Indexed: 08/01/2023] Open
Abstract
Chromosomal rearrangements are important drivers in cancer, and their robust detection is essential for diagnosis, prognosis, and treatment selection, particularly for bone and soft tissue tumors. Current diagnostic methods are hindered by limitations, including difficulties with multiplexing targets and poor quality of RNA. A novel targeted DNA-based next-generation sequencing method, formalin-fixed, paraffin-embedded-targeted locus capture (FFPE-TLC), has shown advantages over current diagnostic methods when applied on FFPE lymphomas, including the ability to detect novel rearrangements. We evaluated the utility of FFPE-TLC in bone and soft tissue tumor diagnostics. FFPE-TLC sequencing was successfully applied on noncalcified and decalcified FFPE samples (n = 44) and control samples (n = 19). In total, 58 rearrangements were identified in 40 FFPE tumor samples, including three previously negative samples, and none was identified in the FFPE control samples. In all five discordant cases, FFPE-TLC could identify gene fusions where other methods had failed due to either detection limits or poor sample quality. FFPE-TLC achieved a high specificity and sensitivity (no false positives and negatives). These results indicate that FFPE-TLC is applicable in cancer diagnostics to simultaneously analyze many genes for their involvement in gene fusions. Similar to the observation in lymphomas, FFPE-TLC is a good DNA-based alternative to the conventional methods for detection of rearrangements in bone and soft tissue tumors.
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Affiliation(s)
| | - Ruud W J Meijers
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Amin Allahyar
- Oncode Institute, Hubrecht Institute-Royal Netherlands Academy of Arts and Sciences, and University Medical Center Utrecht, Utrecht, the Netherlands
| | | | | | - Wendy W J de Leng
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Sjoerd van Helvert
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | | | - David Creytens
- Department of Pathology, Ghent University Hospital, Ghent, Belgium
| | - Léon C van Kempen
- Department of Pathology, University Hospital Antwerp, University of Antwerp, Antwerp, Belgium; Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | | | - Judith V M G Bovee
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Wouter de Laat
- Oncode Institute, Hubrecht Institute-Royal Netherlands Academy of Arts and Sciences, and University Medical Center Utrecht, Utrecht, the Netherlands
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14
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Samal J, Palomino TV, Chen J, Muddiman DC, Segura T. Enhanced Detection of Charged N-Glycans in the Brain by Infrared Matrix-Assisted Laser Desorption Electrospray Ionization Mass Spectrometric Imaging. Anal Chem 2023; 95:10913-10920. [PMID: 37427925 PMCID: PMC10640919 DOI: 10.1021/acs.analchem.3c00494] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
N-linked glycosylation represents a structurally diverse, complex, co- and posttranslational protein modification that bridges metabolism and cellular signaling. Consequently, aberrant protein glycosylation is a hallmark of most pathological scenarios. Due to their complex nature and non-template-driven synthesis, the analysis of glycans is faced with several challenges, underlining the need for new and improved analytical technologies. Spatial profiling of N-glycans through direct imaging on tissue sections reveals the regio-specific and/or disease pathology correlating tissue N-glycans that serve as a disease glycoprint for diagnosis. Infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) is a soft hybrid ionization technique that has been used for diverse mass spectrometry imaging (MSI) applications. Here, we report the first spatial analysis of the brain N-linked glycans by IR-MALDESI MSI, leading to a significant increase in the detection of the brain N-sialoglycans. A formalin-fixed paraffin-embedded mouse brain tissue was analyzed in negative ionization mode after tissue washing, antigen retrieval, and pneumatic application of PNGase F for enzymatic digestion of N-linked glycans. We report a comparative analysis of section thickness on the N-glycan detection using IR-MALDESI. One hundred thirty-six unique N-linked glycans were confidently identified in the brain tissue (with an additional 132 unique N-glycans, not reported in GlyConnect), where more than 50% contained sialic acid residues, which is approximately 3-fold higher than the previous reports. This work demonstrates the first application of IR-MALDESI in N-linked glycan imaging of the brain tissue, leading to a 2.5-fold increase in the in situ total brain N-glycan detection compared to the current gold standard of positive-mode matrix-assisted laser desorption/ionization mass spectrometry imaging. This is also the first report of the application of the MSI toward the identification of sulfoglycans in the rodent brain. Overall, IR-MALDESI-MSI presents a sensitive glycan detection platform to identify tissue-specific and/or disease-specific glycosignature in the brain while preserving the sialoglycans without any chemical derivatization.
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Affiliation(s)
- Juhi Samal
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708-0274, United States
| | - Tana V Palomino
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-7001, United States
| | - Judy Chen
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708-0274, United States
| | - David C Muddiman
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695-7001, United States
| | - Tatiana Segura
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708-0274, United States
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15
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Copeland-Hardin L, Paunesku T, Murley JS, Crentsil J, Antipova O, Li L, Maxey E, Jin Q, Hooper D, Lai B, Chen S, Woloschak GE. Proof of principle study: synchrotron X-ray fluorescence microscopy for identification of previously radioactive microparticles and elemental mapping of FFPE tissues. Sci Rep 2023; 13:7806. [PMID: 37179410 PMCID: PMC10183016 DOI: 10.1038/s41598-023-34890-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 05/09/2023] [Indexed: 05/15/2023] Open
Abstract
Biobanks containing formalin-fixed, paraffin-embedded (FFPE) tissues from animals and human atomic-bomb survivors exposed to radioactive particulates remain a vital resource for understanding the molecular effects of radiation exposure. These samples are often decades old and prepared using harsh fixation processes which limit sample imaging options. Optical imaging of hematoxylin and eosin (H&E) stained tissues may be the only feasible processing option, however, H&E images provide no information about radioactive microparticles or radioactive history. Synchrotron X-ray fluorescence microscopy (XFM) is a robust, non-destructive, semi-quantitative technique for elemental mapping and identifying candidate chemical element biomarkers in FFPE tissues. Still, XFM has never been used to uncover distribution of formerly radioactive micro-particulates in FFPE canine specimens collected more than 30 years ago. In this work, we demonstrate the first use of low-, medium-, and high-resolution XFM to generate 2D elemental maps of ~ 35-year-old, canine FFPE lung and lymph node specimens stored in the Northwestern University Radiobiology Archive documenting distribution of formerly radioactive micro-particulates. Additionally, we use XFM to identify individual microparticles and detect daughter products of radioactive decay. The results of this proof-of-principle study support the use of XFM to map chemical element composition in historic FFPE specimens and conduct radioactive micro-particulate forensics.
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Affiliation(s)
- Letonia Copeland-Hardin
- Department of Radiation Oncology and Department of Radiology, Feinberg School of Medicine, Northwestern University, 300 E. Superior St., Tarry 4-713, Chicago, IL, 60611, USA
| | - Tatjana Paunesku
- Department of Radiation Oncology and Department of Radiology, Feinberg School of Medicine, Northwestern University, 300 E. Superior St., Tarry 4-713, Chicago, IL, 60611, USA
| | - Jeffrey S Murley
- Department of Radiation Oncology and Department of Radiology, Feinberg School of Medicine, Northwestern University, 300 E. Superior St., Tarry 4-713, Chicago, IL, 60611, USA
| | - Jasson Crentsil
- Department of Radiation Oncology and Department of Radiology, Feinberg School of Medicine, Northwestern University, 300 E. Superior St., Tarry 4-713, Chicago, IL, 60611, USA
| | - Olga Antipova
- X-Ray Science Division, Advanced Photon Source, Argonne National Laboratory, Lemont, IL, USA
| | - LuXi Li
- X-Ray Science Division, Advanced Photon Source, Argonne National Laboratory, Lemont, IL, USA
| | - Evan Maxey
- X-Ray Science Division, Advanced Photon Source, Argonne National Laboratory, Lemont, IL, USA
| | - Qiaoling Jin
- X-Ray Science Division, Advanced Photon Source, Argonne National Laboratory, Lemont, IL, USA
| | - David Hooper
- Nuclear Nonproliferation Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Barry Lai
- X-Ray Science Division, Advanced Photon Source, Argonne National Laboratory, Lemont, IL, USA
| | - Si Chen
- X-Ray Science Division, Advanced Photon Source, Argonne National Laboratory, Lemont, IL, USA
| | - Gayle E Woloschak
- Department of Radiation Oncology and Department of Radiology, Feinberg School of Medicine, Northwestern University, 300 E. Superior St., Tarry 4-713, Chicago, IL, 60611, USA.
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16
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Trecourt A, Rabodonirina M, Mauduit C, Traverse-Glehen A, Devouassoux-Shisheboran M, Meyronet D, Dijoud F, Ginevra C, Chapey-Picq E, Josse E, Martins-Simoes P, Bentaher A, Dupont D, Miossec C, Persat F, Wallon M, Ferry T, Pham F, Simon B, Menotti J. Fungal Integrated Histomolecular Diagnosis Using Targeted Next-Generation Sequencing on Formalin-Fixed Paraffin-Embedded Tissues. J Clin Microbiol 2023; 61:e0152022. [PMID: 36809009 PMCID: PMC10035294 DOI: 10.1128/jcm.01520-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/30/2023] [Indexed: 02/23/2023] Open
Abstract
Histopathology is the gold standard for fungal infection (FI) diagnosis, but it does not provide a genus and/or species identification. The objective of the present study was to develop targeted next-generation sequencing (NGS) on formalin-fixed tissue samples (FTs) to achieve a fungal integrated histomolecular diagnosis. Nucleic acid extraction was optimized on a first group of 30 FTs with Aspergillus fumigatus or Mucorales infection by macrodissecting the microscopically identified fungal-rich area and comparing Qiagen and Promega extraction methods through DNA amplification by A. fumigatus and Mucorales primers. Targeted NGS was developed on a second group of 74 FTs using three primer pairs (ITS-3/ITS-4, MITS-2A/MITS-2B, and 28S-12-F/28S-13-R) and two databases (UNITE and RefSeq). A prior fungal identification of this group was established on fresh tissues. Targeted NGS and Sanger sequencing results on FTs were compared. To be valid, the molecular identifications had to be compatible with the histopathological analysis. In the first group, the Qiagen method yielded a better extraction efficiency than the Promega method (100% and 86.7% of positive PCRs, respectively). In the second group, targeted NGS allowed fungal identification in 82.4% (61/74) of FTs using all primer pairs, in 73% (54/74) using ITS-3/ITS-4, in 68.9% (51/74) using MITS-2A/MITS-2B, and in 23% (17/74) using 28S-12-F/28S-13-R. The sensitivity varied according to the database used (81% [60/74] using UNITE compared to 50% [37/74] using RefSeq [P = 0.000002]). The sensitivity of targeted NGS (82.4%) was higher than that of Sanger sequencing (45.9%; P < 0.00001). To conclude, fungal integrated histomolecular diagnosis using targeted NGS is suitable on FTs and improves fungal detection and identification.
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Affiliation(s)
- Alexis Trecourt
- Service de Pathologie Multi-Site—Site Sud, Hospices Civils de Lyon, Centre Hospitalier Lyon Sud, Lyon, France
- Faculté de Médecine Lyon-Sud Charles Mérieux, UR 3738–CICLY–Equipe Inflammation et Immunité de L’épithélium Respiratoire, Université Claude Bernard Lyon 1, Lyon, France
| | - Meja Rabodonirina
- Institut des Agents Infectieux, Service de Parasitologie et Mycologie Médicale, Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
- Faculté de Médecine Lyon Sud Charles Mérieux, Université Claude Bernard Lyon 1, Lyon, France
| | - Claire Mauduit
- Service de Pathologie Multi-Site—Site Sud, Hospices Civils de Lyon, Centre Hospitalier Lyon Sud, Lyon, France
- Faculté de Médecine Lyon Sud Charles Mérieux, Université Claude Bernard Lyon 1, Lyon, France
- Centre Méditerranéen de Médecine Moléculaire (C3M), Unité 1065, Institut National de la Santé et de la Recherche Médicale, Nice, France
| | - Alexandra Traverse-Glehen
- Service de Pathologie Multi-Site—Site Sud, Hospices Civils de Lyon, Centre Hospitalier Lyon Sud, Lyon, France
- Faculté de Médecine Lyon Sud Charles Mérieux, Université Claude Bernard Lyon 1, Lyon, France
- Faculté de Médecine Lyon Sud Charles Mérieux, Centre de Recherche en Cancérologie de Lyon, INSERM U1052-CNRS UMR5286, Université Claude Bernard Lyon 1, Lyon, France
| | - Mojgan Devouassoux-Shisheboran
- Service de Pathologie Multi-Site—Site Sud, Hospices Civils de Lyon, Centre Hospitalier Lyon Sud, Lyon, France
- Faculté de Médecine Lyon Est, Université Claude Bernard Lyon 1, Lyon, France
| | - David Meyronet
- Faculté de Médecine Lyon Est, Université Claude Bernard Lyon 1, Lyon, France
- Service de Pathologie Multi-site—Site Est, Hospices Civils de Lyon, Centre Hospitalier Lyon Est, Lyon, France
| | - Frédérique Dijoud
- Faculté de Médecine Lyon Est, Université Claude Bernard Lyon 1, Lyon, France
- Service de Pathologie Multi-site—Site Est, Hospices Civils de Lyon, Centre Hospitalier Lyon Est, Lyon, France
| | - Christophe Ginevra
- Institut des Agents Infectieux, Génomique Épidémiologique des Maladies Infectieuses (GENEPII), Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
- Institut des Agents Infectieux, Centre National de Référence des Légionelles, Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
| | - Emmanuelle Chapey-Picq
- Institut des Agents Infectieux, Service de Parasitologie et Mycologie Médicale, Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
- Faculté de Médecine Lyon Sud Charles Mérieux, Université Claude Bernard Lyon 1, Lyon, France
| | - Emilie Josse
- Institut des Agents Infectieux, Service de Parasitologie et Mycologie Médicale, Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
| | - Patricia Martins-Simoes
- Institut des Agents Infectieux, Génomique Épidémiologique des Maladies Infectieuses (GENEPII), Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
- Institut des Agents Infectieux, Centre National de Référence des Staphyloccoques, Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
| | - Abderrazzak Bentaher
- Faculté de Médecine Lyon-Sud Charles Mérieux, UR 3738–CICLY–Equipe Inflammation et Immunité de L’épithélium Respiratoire, Université Claude Bernard Lyon 1, Lyon, France
- Faculté de Médecine Lyon Sud Charles Mérieux, Université Claude Bernard Lyon 1, Lyon, France
| | - Damien Dupont
- Institut des Agents Infectieux, Service de Parasitologie et Mycologie Médicale, Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
- Faculté de Médecine Lyon Est, Université Claude Bernard Lyon 1, Lyon, France
| | - Charline Miossec
- Institut des Agents Infectieux, Service de Parasitologie et Mycologie Médicale, Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
| | - Florence Persat
- Faculté de Médecine Lyon-Sud Charles Mérieux, UR 3738–CICLY–Equipe Inflammation et Immunité de L’épithélium Respiratoire, Université Claude Bernard Lyon 1, Lyon, France
- Institut des Agents Infectieux, Service de Parasitologie et Mycologie Médicale, Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
- Faculté de Médecine Lyon Est, Université Claude Bernard Lyon 1, Lyon, France
| | - Martine Wallon
- Institut des Agents Infectieux, Service de Parasitologie et Mycologie Médicale, Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
- Faculté de Médecine Lyon Sud Charles Mérieux, Université Claude Bernard Lyon 1, Lyon, France
| | - Tristan Ferry
- Faculté de Médecine Lyon Est, Université Claude Bernard Lyon 1, Lyon, France
- Service de Maladies Infectieuses et Tropicales, Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
| | - Félix Pham
- Service de Dermatologie, Hospices Civils de Lyon, Centre Hospitalier Lyon Sud, Lyon, France
| | - Bruno Simon
- Institut des Agents Infectieux, Génomique Épidémiologique des Maladies Infectieuses (GENEPII), Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
- Institut des Agents Infectieux, Service de Virologie, Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
| | - Jean Menotti
- Faculté de Médecine Lyon-Sud Charles Mérieux, UR 3738–CICLY–Equipe Inflammation et Immunité de L’épithélium Respiratoire, Université Claude Bernard Lyon 1, Lyon, France
- Institut des Agents Infectieux, Service de Parasitologie et Mycologie Médicale, Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
- Faculté de Médecine Lyon Est, Université Claude Bernard Lyon 1, Lyon, France
- Institut des Agents Infectieux, Génomique Épidémiologique des Maladies Infectieuses (GENEPII), Hospices Civils de Lyon, Hôpital Croix-Rousse, Lyon, France
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17
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Fink JL, Jaradi B, Stone N, Anderson L, Leo PJ, Marshall M, Ellis J, Waring PM, O'Byrne K. Minimizing Sample Failure Rates for Challenging Clinical Tumor Samples. J Mol Diagn 2023; 25:263-273. [PMID: 36773702 DOI: 10.1016/j.jmoldx.2023.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 01/04/2023] [Accepted: 01/19/2023] [Indexed: 02/11/2023] Open
Abstract
Identification of somatic variants in cancer by high-throughput sequencing has become common clinical practice, largely because many of these variants may be predictive biomarkers for targeted therapies. However, there can be high sample quality control (QC) failure rates for some tests that prevent the return of results. Stem-loop inhibition mediated amplification (SLIMamp) is a patented technology that has been incorporated into commercially available cancer next-generation sequencing testing kits. The claimed advantage is that these kits can interrogate challenging formalin-fixed, paraffin-embedded tissue samples with low tumor purity, poor-quality DNA, and/or low-input DNA, resulting in a high sample QC pass rate. The study aimed to substantiate that claim using Pillar Biosciences oncoReveal Solid Tumor Panel. Forty-eight samples that had failed one or more preanalytical QC sample parameters for whole-exome sequencing from the Australian Translational Genomics Center's ISO15189-accredited diagnostic genomics laboratory were acquired. XING Genomic Services performed an exploratory data analysis to characterize the samples and then tested the samples in their ISO15189-accredited laboratory. Clinical reports could be generated for 37 (77%) samples, of which 29 (60%) contained clinically actionable or significant variants that would not otherwise have been identified. Eleven samples were deemed unreportable, and the sequencing data were likely dominated by artifacts. A novel postsequencing QC metric was developed that can discriminate between clinically reportable and unreportable samples.
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Affiliation(s)
- J Lynn Fink
- XING Genomic Services, Sinnamon Park, Queensland, Australia; Australian Translational Genomics Centre, Queensland University of Technology, Woolloongabba, Queensland, Australia; The University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, Queensland, Australia.
| | - Binny Jaradi
- XING Genomic Services, Sinnamon Park, Queensland, Australia
| | - Nathan Stone
- XING Genomic Services, Sinnamon Park, Queensland, Australia
| | - Lisa Anderson
- Australian Translational Genomics Centre, Queensland University of Technology, Woolloongabba, Queensland, Australia; Princess Alexandra Hospital, Woolloongabba, Queensland, Australia
| | - Paul J Leo
- Australian Translational Genomics Centre, Queensland University of Technology, Woolloongabba, Queensland, Australia; Princess Alexandra Hospital, Woolloongabba, Queensland, Australia
| | - Mhairi Marshall
- Australian Translational Genomics Centre, Queensland University of Technology, Woolloongabba, Queensland, Australia; Princess Alexandra Hospital, Woolloongabba, Queensland, Australia
| | - Jonathan Ellis
- Australian Translational Genomics Centre, Queensland University of Technology, Woolloongabba, Queensland, Australia; Princess Alexandra Hospital, Woolloongabba, Queensland, Australia
| | - Paul M Waring
- XING Genomic Services, Sinnamon Park, Queensland, Australia
| | - Kenneth O'Byrne
- Australian Translational Genomics Centre, Queensland University of Technology, Woolloongabba, Queensland, Australia; The University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, Queensland, Australia; Princess Alexandra Hospital, Woolloongabba, Queensland, Australia
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18
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Chung JY, Kim K, Ylaya K, Walker-Bawa KE, Perry C, Star RA, Hewitt SM. The Application of Guanidinium to Improve Biomolecule Quality in Fixed, Paraffin-embedded Tissue. J Histochem Cytochem 2023; 71:87-101. [PMID: 36869703 PMCID: PMC10088100 DOI: 10.1369/00221554231159451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 01/31/2023] [Indexed: 03/05/2023] Open
Abstract
Neutral buffered formalin (NBF) is the most common fixative in clinical applications. However, NBF damages proteins and nucleic acids, limiting the quality of proteomic and nucleic acid-based assays. Prior studies have demonstrated that BE70, a fixative of buffered 70% ethanol, has many benefits over NBF but the degradation of proteins and nucleic acids in archival paraffin blocks remain a challenge. Thus, we evaluated the addition of guanidinium salts to BE70 with the hypothesis that this may protect RNA and protein. Guanidinium salt supplemented BE70 (BE70G)-fixed tissue is comparable with that of BE70 via histology and immunohistochemistry. Western blot analysis also revealed that HSP70, AKT, and glyceraldehyde 3-phosphate dehydrogenase (GAPDH) expression signals in BE70G-fixed tissue were higher than those in BE70-fixed tissue. The quality of nucleic acids extracted from BE70G-fixed, paraffin-embedded tissue was also superior, and BE70G provides improved protein and RNA quality at shorter fixation times than its predecessors. The degradation of proteins, AKT and GAPDH, in archival tissue blocks is also decreased with the addition of guanidinium salt to BE70. In conclusion, BE70G fixative improves the quality of molecular analysis with more rapid fixation of tissue and enhanced long-term storage of paraffin blocks at room temperature for evaluation of protein epitopes.
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Affiliation(s)
- Joon-Yong Chung
- Laboratory of Pathology, Center for Cancer
Research, National Cancer Institute, National Institutes of Health,
Bethesda, Maryland
| | - Kyungeun Kim
- Laboratory of Pathology, Center for Cancer
Research, National Cancer Institute, National Institutes of Health,
Bethesda, Maryland
- Department of Pathology, School of Medicine,
Kangbuk Samsung Hospital, Sungkyunkwan University, Seoul, Republic of
Korea
| | - Kris Ylaya
- Laboratory of Pathology, Center for Cancer
Research, National Cancer Institute, National Institutes of Health,
Bethesda, Maryland
| | - Katharine E. Walker-Bawa
- Laboratory of Pathology, Center for Cancer
Research, National Cancer Institute, National Institutes of Health,
Bethesda, Maryland
| | - Candice Perry
- Antibody Characterization Laboratory, Advanced
Technology Program, Leidos Biomedical Research, Inc., Frederick,
Maryland
| | - Robert A. Star
- Renal Diagnostics and Therapeutics Unit,
National Institutes of Diabetes and Digestive and Kidney Disease, National
Institutes of Health, Bethesda, Maryland
| | - Stephen M. Hewitt
- Laboratory of Pathology, Center for Cancer
Research, National Cancer Institute, National Institutes of Health,
Bethesda, Maryland
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19
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Pu J, Xue C, Huo S, Shen Q, Qu Y, Yang X, An B, Angel TE, Chen Z, Mehl JT, Tang H, Yang E, Sikorski TW, Qu J. Highly Accurate and Robust Absolute Quantification of Target Proteins in Formalin-Fixed Paraffin-Embedded (FFPE) Tissues by LC-MS. Anal Chem 2023; 95:924-934. [PMID: 36534410 PMCID: PMC10581745 DOI: 10.1021/acs.analchem.2c03473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Accurate, absolute liquid chromatography-mass spectrometry (LC-MS)-based quantification of target proteins in formalin-fixed paraffin-embedded (FFPE) tissues would greatly expand sample availability for pharmaceutical/clinical investigations but remains challenging owing to the following issues: (i) efficient/quantitative recovery of target signature peptides from FFPE tissues is essential but an optimal procedure for targeted, absolute quantification is lacking; (ii) most FFPE samples are long-term-stored; severe immunohistochemistry (IHC) signal losses of target proteins during storage were widely reported, while the effect of storage on LC-MS-based methods was unknown; and (iii) the proper strategy to prepare calibration/quality-control samples to ensure accurate targeted protein analysis in FFPE tissues remained elusive. Using targeted quantification of monoclonal antibody (mAb), antigen, and 40 tissue markers in FFPE tissues as a model system, we extensively investigate those issues and develope an LC-MS-based strategy enabling accurate and precise targeted protein quantification in FFPE samples. First, we demonstrated a surfactant cocktail-based procedure (f-SEPOD), providing high/reproducible recovery of target signature peptides from FFPE tissues. Second, a heat-accelerated degradation study within a roughly estimated 5 year storage period recapitulated the loss of protein IHC signals while LC-MS signals of all targets remained constant. This indicates that the storage of FFPE tissues mainly causes decreased immunoreactivity but unlikely chemical degradation of proteins, which strongly suggests that the storage of FFPE tissues does not cause significant quantitative bias for LC-MS-based methods. Third, while a conventional spike-and-extract approach for calibration caused substantial negative biases, a novel approach, using FFPE-treated calibration standards, enabled accurate and precise quantification. With the pipeline, we conducted the first-ever pharmacokinetics measurement of mAb and its target in FFPE tissues, where time courses by FFPE vs fresh tissues showed excellent correlation.
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Affiliation(s)
- Jie Pu
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
| | - Chao Xue
- Department of Chemical and Biological Engineering, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
| | - Shihan Huo
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
| | - Qingqing Shen
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
| | - Yang Qu
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States; New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York 14203, United States
| | - Xinxin Yang
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
| | - Bo An
- Bioanalysis, Immunogenicity & Biomarkers, In-Vitro/In-Vivo Translation, R&D Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Thomas E. Angel
- Bioanalysis, Immunogenicity & Biomarkers, In-Vitro/In-Vivo Translation, R&D Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Zhuo Chen
- Bioanalysis, Immunogenicity & Biomarkers, In-Vitro/In-Vivo Translation, R&D Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - John T. Mehl
- Bioanalysis, Immunogenicity & Biomarkers, In-Vitro/In-Vivo Translation, R&D Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Huaping Tang
- Bioanalysis, Immunogenicity & Biomarkers, In-Vitro/In-Vivo Translation, R&D Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Eric Yang
- Bioanalysis, Immunogenicity & Biomarkers, In-Vitro/In-Vivo Translation, R&D Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Timothy W. Sikorski
- Bioanalysis, Immunogenicity & Biomarkers, In-Vitro/In-Vivo Translation, R&D Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States; Phone: (610) 270-4978
| | - Jun Qu
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States; New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York 14203, United States
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20
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Kanda M, Terashima M, Kinoshita T, Yabusaki H, Tokunaga M, Kodera Y. A multi-institutional study to evaluate the feasibility of next-generation sequencing and genomic analysis using formalin-fixed, paraffin-embedded biopsies of gastric cancer. Gastric Cancer 2023; 26:108-115. [PMID: 36369312 DOI: 10.1007/s10120-022-01351-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 11/03/2022] [Indexed: 11/13/2022]
Abstract
BACKGROUND Formalin-fixed, paraffin-embedded (FFPE) samples acquired and preserved adequately are expected to faithfully maintain tumor characteristics. Endoscopic biopsy tissues represent an attractive resource for identifying predictive biomarkers to evaluate pretreatment responses of patients with advanced gastric cancer (GC). However, whether genomic profiles obtained through next-generation sequencing (NGS) using biopsy samples match well with those gained from surgical FFPE samples remains a concern. METHODS We collected 50 FFPE samples (26 biopsies and 24 surgical samples) from patients with GC who participated in phase III clinical trial JCOG1509. The quality and quantity of FFPE samples were determined for deep sequencing using NGS. We queried a 435-gene panel CANCERPLEX-JP to generate comprehensive genomic profiling data including the tumor mutation burden (TMB). RESULTS The median DNA yields and NGS success rates of biopsy samples compared with surgical samples were 879 ng and 80.8% vs 8523 ng and 100%, respectively. Epstein-Barr virus and microsatellite instability-high were detected in 9.5% of biopsy samples. Comparing the genomic profiles of 18 paired samples for which NGS data were available, we detected identical somatic mutations in paired biopsy and surgical samples (kappa coefficient, 0.8692). TMB positively correlated between paired biopsy and surgical samples (correlation coefficient, 0.6911). CONCLUSIONS NGS is applicable to the analysis of FFPE samples of GC acquired by the endoscopic biopsy, and the data were highly concordant with those obtained from surgical specimens of the same patients.
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Affiliation(s)
- Mitsuro Kanda
- Department of Gastroenterological Surgery, Nagoya University Graduate School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan.
| | | | - Takahiro Kinoshita
- Department of Gastric Surgery, National Cancer Center Hospital East, Kashiwa, Japan
| | - Hiroshi Yabusaki
- Department of Gastroenterological Surgery, Niigata Cancer Center Hospital, Niigata, Japan
| | - Masanori Tokunaga
- Department of Gastrointestinal Surgery, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yasuhiro Kodera
- Department of Gastroenterological Surgery, Nagoya University Graduate School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan
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21
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Nayak D, Weadick B, Govindarajan R. Combination of Tissue Microarray Profiling and Multiplexed IHC Approaches to Investigate Transport Mechanism of Nucleoside Analog Drug Resistance. Methods Mol Biol 2023; 2660:95-121. [PMID: 37191793 PMCID: PMC10311792 DOI: 10.1007/978-1-0716-3163-8_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Nucleoside analogs (NAs) are an established class of anticancer agents being used clinically for the treatment of diverse cancers, either as monotherapy or in combination with other established anticancer or pharmacological agents. To date, nearly a dozen anticancer NAs are approved by the FDA, and several novel NAs are being tested in preclinical and clinical trials for future applications. However, improper delivery of NAs into tumor cells because of alterations in expression of one or more drug carrier proteins (e.g., solute carrier (SLC) transporters) within tumor cells or cells surrounding the tumor microenvironment stands as one of the primary reasons for therapeutic drug resistance. The combination of tissue microarray (TMA) and multiplexed immunohistochemistry (IHC) is an advanced, high-throughput approach over conventional IHC that enables researchers to effectively investigate alterations to numerous such chemosensitivity determinants simultaneously in hundreds of tumor tissues derived from patients. In this chapter, taking an example of a TMA from pancreatic cancer patients treated with gemcitabine (a NA chemotherapeutic agent), we describe the step-by-step procedure of performing multiplexed IHC, imaging of TMA slides, and quantification of expression of some relevant markers in these tissue sections as optimized in our laboratory and discuss considerations while designing and carrying out this experiment.
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Affiliation(s)
- Debasis Nayak
- Division of Pharmaceutics and Pharmacology, The Ohio State University College of Pharmacy, Columbus, OH, USA
| | - Brenna Weadick
- Division of Pharmaceutics and Pharmacology, The Ohio State University College of Pharmacy, Columbus, OH, USA
| | - Rajgopal Govindarajan
- Division of Pharmaceutics and Pharmacology, The Ohio State University College of Pharmacy, Columbus, OH, USA.
- Translational Therapeutics, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA.
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22
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Barroux M, Horstmann J, Fricke L, Schömig L, Werner M, Kraynova E, Kamarádová K, Fléjou JF, Maerkel B, Kumarasinghe MP, Vieth M, Westerhoff M, Patil DT, Steiger K, Becker KF, Weichert W, Schmid RM, Quante M, Slotta-Huspenina J. Histological evaluation of PAXgene tissue fixation in Barrett’s esophagus and esophageal adenocarcinoma diagnostics. Virchows Arch 2022; 482:887-898. [PMID: 36527466 PMCID: PMC10156762 DOI: 10.1007/s00428-022-03471-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/01/2022] [Accepted: 11/30/2022] [Indexed: 12/23/2022]
Abstract
Abstract
The dysplasia grading of Barrett’s esophagus (BE), based on the histomorphological assessment of formalin-fixed, paraffin-embedded (FFPE) tissue, suffers from high interobserver variability leading to an unsatisfactory prediction of cancer risk. Thus, pre-analytic preservation of biological molecules, which could improve risk prediction in BE enabling molecular and genetic analysis, is needed. We aimed to evaluate such a molecular pre-analytic fixation tool, PAXgene-fixed paraffin-embedded (PFPE) biopsies, and their suitability for histomorphological BE diagnostics in comparison to FFPE. In a ring trial, 9 GI pathologists evaluated 116 digital BE slides of non-dysplastic BE (NDBE), low-grade dysplasia (LGD), high-grade dysplasia (HGD), and esophageal adenocarcinomas (EAC) using virtual microscopy. Overall quality, cytological and histomorphological parameters, dysplasia criteria, and diagnosis were analyzed. PFPE showed better preservation of nuclear details as chromatin and nucleoli, whereas overall quality and histomorphologic parameters as visibility of basal lamina, goblet cells, and presence of artifacts were scored as equal to FFPE. The interobserver reproducibility with regard to the diagnosis was best for NDBE and EAC (κF = 0.72–0.75) and poor for LGD and HGD (κF = 0.13–0.3) in both. In conclusion, our data suggest that PFPE allows equally confident histomorphological diagnosis of BE and EAC, introducing a novel tool for molecular analysis and parallel histomorphological evaluation.
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Affiliation(s)
- Melissa Barroux
- Klinikum Rechts Der Isar, Medical Clinic and Polyclinic II, Technical University of Munich, Munich, Germany.
| | - Julia Horstmann
- Klinikum Rechts Der Isar, Medical Clinic and Polyclinic II, Technical University of Munich, Munich, Germany
| | - Lisa Fricke
- Klinikum Rechts Der Isar, Medical Clinic and Polyclinic II, Technical University of Munich, Munich, Germany
| | - Linus Schömig
- Department of Medicine II, Universitaetsklinikum Freiburg, Freiburg, Germany
| | - Martin Werner
- Institute for Surgical Pathology, Medical Center-University of Freiburg and Faculty of Medicine, University of Freiburg, 79106, Freiburg, Germany
| | - Ekaterina Kraynova
- Department of Pathology, Yaroslavl Regional Cancer Hospital, Yaroslavl, Russian Federation
| | - Katerina Kamarádová
- The Fingerland Department of Pathology, Faculty of Medicine and University Hospital, Charles University, Hradec Králové, Czech Republic
| | - Jean-François Fléjou
- Service d'Anatomie Pathologique, AP-HP, Faculté de Médecine Sorbonne, Hôpital Saint-Antoine, Université, 75012, Paris, France
| | - Bruno Maerkel
- Institute of Pathology and Molecular Diagnostics, University Medical Center Augsburg, Augsburg, Germany
| | - M Priyanthi Kumarasinghe
- Department of Pathology, PathWest Laboratory-University of Western Australia, WA, Perth, Australia
| | - Michael Vieth
- Institute for Pathology, Friedrich-Alexander-University Erlangen-Nuremberg, Klinikum Bayreuth, Bayreuth, Germany
| | | | - Deepa T Patil
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, USA
| | - Katja Steiger
- Institute of Pathology, Technical University of Munich, Munich, Germany
| | | | - Wilko Weichert
- Institute of Pathology, Technical University of Munich, Munich, Germany
| | - Roland M Schmid
- Klinikum Rechts Der Isar, Medical Clinic and Polyclinic II, Technical University of Munich, Munich, Germany
| | - Michael Quante
- Klinikum Rechts Der Isar, Medical Clinic and Polyclinic II, Technical University of Munich, Munich, Germany
- Department of Medicine II, Universitaetsklinikum Freiburg, Freiburg, Germany
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23
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Guo Q, Lakatos E, Bakir IA, Curtius K, Graham TA, Mustonen V. The mutational signatures of formalin fixation on the human genome. Nat Commun 2022; 13:4487. [PMID: 36068219 PMCID: PMC9448750 DOI: 10.1038/s41467-022-32041-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 07/14/2022] [Indexed: 12/02/2022] Open
Abstract
Clinical archives of patient material near-exclusively consist of formalin-fixed and paraffin-embedded (FFPE) blocks. The ability to precisely characterise mutational signatures from FFPE-derived DNA has tremendous translational potential. However, sequencing of DNA derived from FFPE material is known to be riddled with artefacts. Here we derive genome-wide mutational signatures caused by formalin fixation. We show that the FFPE-signature is highly similar to signature 30 (the signature of Base Excision Repair deficiency due to NTHL1 mutations), and chemical repair of DNA lesions leads to a signature highly similar to signature 1 (clock-like signature due to spontaneous deamination of methylcytosine). We demonstrate that using uncorrected mutational catalogues of FFPE samples leads to major mis-assignment of signature activities. To correct for this, we introduce FFPEsig, a computational algorithm to rectify the formalin-induced artefacts in the mutational catalogue. We demonstrate that FFPEsig enables accurate mutational signature analysis both in simulated and whole-genome sequenced FFPE cancer samples. FFPEsig thus provides an opportunity to unlock additional clinical potential of archival patient tissues.
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Affiliation(s)
- Qingli Guo
- Organismal and Evolutionary Biology Research Programme, Department of Computer Science, University of Helsinki, Helsinki, Finland
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Eszter Lakatos
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Genomics and Evolutionary Dynamics Laboratory, Centre for Evolution and Cancer, Institute of Cancer Research, London, UK
| | - Ibrahim Al Bakir
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Kit Curtius
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Trevor A Graham
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK.
- Genomics and Evolutionary Dynamics Laboratory, Centre for Evolution and Cancer, Institute of Cancer Research, London, UK.
| | - Ville Mustonen
- Organismal and Evolutionary Biology Research Programme, Department of Computer Science, University of Helsinki, Helsinki, Finland.
- Institute of Biotechnology, Helsinki Institute for Information Technology, University of Helsinki, Helsinki, Finland.
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24
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Sachdeva A, Hart CA, Carey CD, Vincent AE, Greaves LC, Heer R, Oliveira P, Brown MD, Clarke NW, Turnbull DM. Automated quantitative high-throughput multiplex immunofluorescence pipeline to evaluate OXPHOS defects in formalin-fixed human prostate tissue. Sci Rep 2022; 12:6660. [PMID: 35459777 PMCID: PMC9033818 DOI: 10.1038/s41598-022-10588-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 04/01/2022] [Indexed: 11/09/2022] Open
Abstract
Advances in multiplex immunofluorescence (mIF) and digital image analysis has enabled simultaneous assessment of protein defects in electron transport chain components. However, current manual methodology is time consuming and labour intensive. Therefore, we developed an automated high-throughput mIF workflow for quantitative single-cell level assessment of formalin fixed paraffin embedded tissue (FFPE), leveraging tyramide signal amplification on a Ventana Ultra platform coupled with automated multispectral imaging on a Vectra 3 platform. Utilising this protocol, we assessed the mitochondrial oxidative phosphorylation (OXPHOS) protein alterations in a cohort of benign and malignant prostate samples. Mitochondrial OXPHOS plays a critical role in cell metabolism, and OXPHOS perturbation is implicated in carcinogenesis. Marked inter-patient, intra-patient and spatial cellular heterogeneity in OXPHOS protein abundance was observed. We noted frequent Complex IV loss in benign prostate tissue and Complex I loss in age matched prostate cancer tissues. Malignant regions within prostate cancer samples more frequently contained cells with low Complex I & IV and high mitochondrial mass in comparison to benign-adjacent regions. This methodology can now be applied more widely to study the frequency and distribution of OXPHOS alterations in formalin-fixed tissues, and their impact on long-term clinical outcomes.
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Affiliation(s)
- Ashwin Sachdeva
- Genito Urinary Cancer Research Group, Division of Cancer Sciences, Oglesby Cancer Research Building, University of Manchester, Manchester, M20 4GJ, UK.
- Belfast-Manchester Movember FASTMAN Prostate Cancer Centre of Excellence, Manchester, UK.
- Department of Surgery, The Christie NHS Foundation Trust, Manchester, M20 4BX, UK.
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle-upon-Tyne, UK.
| | - Claire A Hart
- Genito Urinary Cancer Research Group, Division of Cancer Sciences, Oglesby Cancer Research Building, University of Manchester, Manchester, M20 4GJ, UK
- Belfast-Manchester Movember FASTMAN Prostate Cancer Centre of Excellence, Manchester, UK
| | - Christopher D Carey
- Translational and Clinical Research Institute, Newcastle University, Newcastle-upon-Tyne, UK
- NovoPath, Cellular Pathology, Newcastle-upon-Tyne NHS Foundation Trust, Newcastle-upon-Tyne, UK
| | - Amy E Vincent
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle-upon-Tyne, UK
| | - Laura C Greaves
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle-upon-Tyne, UK
| | - Rakesh Heer
- Translational and Clinical Research Institute, Newcastle University, Newcastle-upon-Tyne, UK
| | - Pedro Oliveira
- Department of Pathology, The Christie NHS Foundation Trust, Manchester, M20 4BX, UK
| | - Michael D Brown
- Genito Urinary Cancer Research Group, Division of Cancer Sciences, Oglesby Cancer Research Building, University of Manchester, Manchester, M20 4GJ, UK
- Belfast-Manchester Movember FASTMAN Prostate Cancer Centre of Excellence, Manchester, UK
| | - Noel W Clarke
- Genito Urinary Cancer Research Group, Division of Cancer Sciences, Oglesby Cancer Research Building, University of Manchester, Manchester, M20 4GJ, UK
- Belfast-Manchester Movember FASTMAN Prostate Cancer Centre of Excellence, Manchester, UK
- Department of Surgery, The Christie NHS Foundation Trust, Manchester, M20 4BX, UK
- Department of Urology, Salford Royal NHS Foundation Trust, Salford, M6 8HD, UK
| | - Doug M Turnbull
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle-upon-Tyne, UK
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25
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Quy PN, Fukuyama K, Kanai M, Kou T, Kondo T, Yoshioka M, Matsubara J, Sakuma T, Minamiguchi S, Matsumoto S, Muto M. Inter-assay variability of next-generation sequencing-based gene panels. BMC Med Genomics 2022; 15:86. [PMID: 35428255 PMCID: PMC9013031 DOI: 10.1186/s12920-022-01230-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 04/04/2022] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Tumor heterogeneity has been known to cause inter-assay discordance among next-generation sequencing (NGS) results. However, whether preclinical factors such as sample type, sample quality and analytical features of gene panel can affect the concordance between two different assays remains largely unexplored. METHODS Replicate sets of DNA samples extracted from formalin-fixed paraffin-embedded tissues (FFPE) (n = 20) and fresh frozen (FF) tissues (n = 10) were herein analyzed using a tumor-only (TO) and paired tumor-normal (TN) gene panel in laboratories certified by the Clinical Laboratory Improvement Amendment. Reported variants from the TO and TN panels were then compared. Furthermore, additional FFPE samples were sequentially sliced from the same FFPE block and submitted to another TN panel assay. RESULTS Substantial discordance (71.8%) was observed between the results of the two panels despite using identical DNA samples, with the discordance rate being significantly higher for FFPE samples (p < 0.05). Among the 99 variants reported only in the TO panel, 32.3% were consistent with germline variants, which were excluded in the TN panel, while 30.3% had an allele frequency of less than 5%, some of which were highly likely to be artificial calls. The comparison of two independent TN panel assay results from the same FFPE block also showed substantial discordance rate (55.3%). CONCLUSIONS In the context of clinical settings, our comparative analysis revealed that inter-NGS assay discordance commonly occurred due to sample types and the different analytical features of each panel.
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Affiliation(s)
- Pham Nguyen Quy
- Department of Therapeutic Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Keita Fukuyama
- Department of Therapeutic Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Real World Data Research and Development, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masashi Kanai
- Department of Therapeutic Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
| | - Tadayuki Kou
- Department of Therapeutic Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tomohiro Kondo
- Department of Therapeutic Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masahiro Yoshioka
- Department of Therapeutic Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Junichi Matsubara
- Department of Therapeutic Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tomohiro Sakuma
- Biomedical Department, Mitsui Knowledge Industry Co., Ltd., Tokyo, Japan
| | - Sachiko Minamiguchi
- Department of Diagnostic Pathology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shigemi Matsumoto
- Department of Therapeutic Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Real World Data Research and Development, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Manabu Muto
- Department of Therapeutic Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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26
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Mandarano M, Pelliccia C, Gianatti A, Sidoni A. On the Need of a Suitable Immunohistochemical Test for Demonstration of SARS-CoV-2 on Formalin-fixed and Paraffin-embedded Tissues. Appl Immunohistochem Mol Morphol 2022; 30:e30-e31. [PMID: 35384883 PMCID: PMC8989606 DOI: 10.1097/pai.0000000000001013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Martina Mandarano
- Section of Anatomic Pathology and Histology, Department of Medicine and Surgery, University of Perugia, Perugia Italy
| | - Cristina Pelliccia
- Section of Anatomic Pathology and Histology, Department of Medicine and Surgery, University of Perugia, Perugia Italy
| | | | - Angelo Sidoni
- Section of Anatomic Pathology and Histology, Department of Medicine and Surgery, University of Perugia, Perugia Italy
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27
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Wągrodzki M, Tysarowski A, Seliga K, Wojnowska A, Stepaniuk M, Castañeda Wysocka P, Makuła D, Pieńkowski A, Szostakowski B, Zub R, Rutkowski P. Diagnostic Utility of Genetic and Immunohistochemical H3-3A Mutation Analysis in Giant Cell Tumour of Bone. Int J Mol Sci 2022; 23:ijms23020969. [PMID: 35055156 PMCID: PMC8778699 DOI: 10.3390/ijms23020969] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 01/09/2022] [Accepted: 01/14/2022] [Indexed: 02/06/2023] Open
Abstract
To validate the reliability and implementation of an objective diagnostic method for giant cell tumour of bone (GCTB). H3-3A gene mutation testing was performed using two different methods, Sanger sequencing and immunohistochemical (IHC) assays. A total of 214 patients, including 120 with GCTB and 94 with other giant cell-rich bone lesions, participated in the study. Sanger sequencing and IHC with anti-histone H3.3 G34W and G34V antibodies were performed on formalin-fixed, paraffin-embedded tissues, which were previously decalcified in EDTA if needed. The sensitivity and specificity of the molecular method was 100% (95% CI: 96.97–100%) and 100% (95% CI: 96.15–100%), respectively. The sensitivity and specificity of IHC was 94.32% (95% CI: 87.24–98.13%) and 100% (95% CI: 93.94–100.0%), respectively. P.G35 mutations were discovered in 2/9 (22.2%) secondary malignant GCTBs and 9/13 (69.2%) GCTB after denosumab treatment. We confirmed in a large series of patients that evaluation of H3-3A mutational status using direct sequencing is a reliable tool for diagnosing GCTB, and it should be incorporated into the diagnostic algorithm. Additionally, we discovered IHC can be used as a screening tool. Proper tissue processing and decalcification are necessary. The presence of the H3-3A mutation did not exclude malignant GCTB. Denosumab did not eradicate the neoplastic cell population of GCTB.
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Affiliation(s)
- Michał Wągrodzki
- Department of Pathology and Laboratory Diagnostics, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
- Correspondence: ; Tel.: +48-537484741
| | - Andrzej Tysarowski
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (A.T.); (K.S.); (A.W.); (R.Z.)
| | - Katarzyna Seliga
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (A.T.); (K.S.); (A.W.); (R.Z.)
| | - Aneta Wojnowska
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (A.T.); (K.S.); (A.W.); (R.Z.)
| | - Maria Stepaniuk
- Department of Pathology, The Children’s Memorial Health Institute, 04-730 Warsaw, Poland;
| | - Patrycja Castañeda Wysocka
- Department of Radiology, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (P.C.W.); (D.M.)
| | - Donata Makuła
- Department of Radiology, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (P.C.W.); (D.M.)
| | - Andrzej Pieńkowski
- Department of Bone/Soft Tissue Sarcoma and Melanoma, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (A.P.); (B.S.); (P.R.)
| | - Bartłomiej Szostakowski
- Department of Bone/Soft Tissue Sarcoma and Melanoma, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (A.P.); (B.S.); (P.R.)
| | - Renata Zub
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (A.T.); (K.S.); (A.W.); (R.Z.)
| | - Piotr Rutkowski
- Department of Bone/Soft Tissue Sarcoma and Melanoma, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (A.P.); (B.S.); (P.R.)
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28
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Wang Y, Ruan Y, Du B, Li J, Ebendorff-Heidepriem H, Wang X. Real-time Raman analysis of the hydrolysis of formaldehyde oligomers for enhanced collagen fixation. Spectrochim Acta A Mol Biomol Spectrosc 2022; 264:120285. [PMID: 34455375 DOI: 10.1016/j.saa.2021.120285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 08/09/2021] [Accepted: 08/11/2021] [Indexed: 06/13/2023]
Abstract
Formaldehyde (FA) is widely applied as a fixative for proteins such as collagen. Current studies have confirmed that the reversible oligomer-to-monomer equilibrium of FA in aqueous solution and the proportion of FA monomer is a significant factor affecting tissue fixation. Since the hydrolysis of FA oligomers is a dynamic process affected jointly by different factors, its real time monitoring has proved to be challenging. In this work, by utilizing the well-established Raman technique as an analytical platform, we identified the factors affecting the hydrolysis of FA oligomers by rationally examining the νs (OCO) and νas (OCO) modes with varying conditions, such as time, pH, temperature, and FA concentration. The optimized conditions of the highest hydrolysis rate of oligomers into monomers for fixation on collagen and tissues have been found to be relatively low FA concentration (≤5%) in phosphate-buffered saline at pH 9.0 in room temperature. In order to compare the fixation quality of the optimized conditions to that of the conventional conditions used by current medical practices (4% FA concentration in tap water under room temperature), Raman spectroscopy and chemical derivatization methods with o-phthalaldehyde and fluorescent probe FAP-1 have been investigated, and our results revealed that the FA molecules under our optimized conditions have reacted with at least 15% more amino groups within collagen compared to those under the conventional conditions mentioned above. This study provides direct evidence of the FA equilibrium in solution by Raman spectroscopy, which could be applied for the optimal use of FA in medicine, even at an industrial scale.
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Affiliation(s)
- Yansong Wang
- College of Chemistry and Chemical Engineering, Shaanxi University of Science & Technology, Xi'an 710021, China; Institute for Photonics and Advanced Sensing (IPAS), School of Physical Sciences, and ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP), The University of Adelaide, Adelaide 5005, Australia
| | - Yinlan Ruan
- School of Electronic Engineering and Automation, Guilin University of Electronic Technology, Guilin 541004, China; Institute for Photonics and Advanced Sensing (IPAS), School of Physical Sciences, and ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP), The University of Adelaide, Adelaide 5005, Australia.
| | - Bobo Du
- Institute for Photonics and Advanced Sensing (IPAS), School of Physical Sciences, and ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP), The University of Adelaide, Adelaide 5005, Australia; The Key Laboratory of Physical Electronics and Devices of Ministry of Education, School of Electronic Science and Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Ji Li
- Institute of Biomass & Functional Materials (IBFM), College of Bioresources Chemical and Materials Engineering, Shaanxi University of Science & Technology, Xi'an 710021, China
| | - Heike Ebendorff-Heidepriem
- Institute for Photonics and Advanced Sensing (IPAS), School of Physical Sciences, and ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP), The University of Adelaide, Adelaide 5005, Australia
| | - Xuechuan Wang
- College of Chemistry and Chemical Engineering, Shaanxi University of Science & Technology, Xi'an 710021, China; Institute of Biomass & Functional Materials (IBFM), College of Bioresources Chemical and Materials Engineering, Shaanxi University of Science & Technology, Xi'an 710021, China.
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29
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Nagai-Okatani C, Zou X, Matsuda A, Itakura Y, Toyoda M, Zhang Y, Kuno A. Tissue Glycome Mapping: Lectin Microarray-Based Differential Glycomic Analysis of Formalin-Fixed Paraffin-Embedded Tissue Sections. Methods Mol Biol 2022; 2460:161-180. [PMID: 34972936 DOI: 10.1007/978-1-0716-2148-6_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Lectin microarray (LMA) is a high-sensitive glycan analysis technology used to obtain global glycomic profiles of both N- and O-glycans attached not only to purified glycoproteins but also to crude glycoprotein samples. Through additional use of laser microdissection (LMD) for tissue collection, we developed an LMA-based glycomic profiling technique for a specific type of cells in a tiny area of formalin-fixed paraffin-embedded (FFPE) tissue sections. This LMD-LMA method makes it possible to obtain reproducible tissue glycomic profiles that can be compared with each other, using a unified protocol for all procedures, including FFPE tissue preparation, tissue staining, protein extraction and labeling, and LMA analysis. Here, we describe the standardized LMD-LMA procedure for a "tissue glycome mapping" approach, which facilitates an in-depth understanding of region- and tissue-specific protein glycosylation. We also describe potential applications of the spatial tissue glycomic profiles, including histochemical analysis for evaluating distribution of lectin ligands and a fluorescence LMD-LMA method for cell type-selective glycomic profiling using a cell type-specific probe, composed of a lectin and an antibody. The protocols presented here will accelerate the effective utilization of FFPE tissue specimens by providing tissue glycome maps for the discovery of the biological roles and disease-related alterations of protein glycosylation.
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Affiliation(s)
- Chiaki Nagai-Okatani
- Glycoscience and Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan.
| | - Xia Zou
- Glycoscience and Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
- Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Atsushi Matsuda
- Glycoscience and Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
- Department of Biochemistry, School of Medicine, Keio University, Tokyo, Japan
| | - Yoko Itakura
- Department of Geriatric Medicine (Vascular Medicine), Tokyo Metropolitan Institute of Gerontology, Tokyo, Japan
| | - Masashi Toyoda
- Department of Geriatric Medicine (Vascular Medicine), Tokyo Metropolitan Institute of Gerontology, Tokyo, Japan
| | - Yan Zhang
- Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Atsushi Kuno
- Glycoscience and Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan.
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30
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Aros CJ. Indirect Immunofluorescence of Tissue Sections. Methods Mol Biol 2022; 2386:17-26. [PMID: 34766262 DOI: 10.1007/978-1-0716-1771-7_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Immunofluorescence (IF) on tissue sections allows for the detection of protein species subcellular localization. IF studies further offer the ability to achieve this understanding at the level of single cell granularity. Here, we describe the processes by which tissue is fixed, embedded, sectioned, and subsequently utilized for conducting indirect IF assays. We raise potential opportunities for troubleshooting and optimization at varying stages of the protocol.
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Affiliation(s)
- Cody J Aros
- UCLA Department of Molecular Biology Interdepartmental Program, UCLA, Los Angeles, CA, USA.
- UCLA Medical Scientist Training Program, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
- UCLA Children's Discovery and Innovation Institute, Mattel Children's Hospital UCLA, Department of Pediatrics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
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31
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Abstract
Immunohistochemistry (IHC) offers a valuable method for determining the spatial distribution of proteins in cells and tissues. Fixation of tissues prior IHC enables their long-term stability and preserves tissue morphology; however, downstream analysis of protein localization within fixed samples can be complicated by cross-links formed between proteins during formalin fixation which mask target epitopes. Antigen Retrieval (AR) is a process introduced to reverse such cross-links, improving the sensitivity of antibody-based protein detection, and can be performed using protease- or heat-based approaches. Even following AR, low abundance target proteins may require additional amplification for sensitive visualization. The development of amplification approaches such as the use of biotinylated secondary antibodies with avidin-biotin complex and tyramide signal amplification greatly improve the sensitivity of IHC, enabling a wider range of epitopes to be detected when coupled with AR.
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Affiliation(s)
- Logan Dunkenberger
- Neurological Cancer Research, Louisiana Cancer Research Center, Louisiana State University Health Sciences Center, New Orleans, LA, USA
| | - Luis Del Valle
- Department of Pathology and Medicine & Louisiana Cancer Research Center, Louisiana State University Health Sciences Center, New Orleans, LA, USA.
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32
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Abstract
The basic goal of all histological techniques is the identification of tissue components, both normal and pathologic. In the case of any immunodetection technique we expect: specific detection of the antigen with a mark strong enough to be easily detected; and a clear preservation of histological and cytological details of the environment. To achieve these expectations the technical procedures employed must be clearly understood so we can control the previous methodological steps, avoiding any failure and/or complication that could seriously affect the results of our study. In this chapter, we review the basic concepts related to representability of the sample, fixation process, and all procedures carried out before performing the immunohistochemical technique on paraffin sections, which constitute what we know as sample preparation. We describe and analyze the key events so the pathologist and/or the researcher can control the variables in order to obtain the best results in an immunodetection procedure.
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Abstract
Tissue processing is the technique by which fixed tissues are made suitable for embedding within a supportive medium such as paraffin, and consists of three sequential steps: dehydration, clearing, and infiltration. In most clinical and research settings, tissue processing is accomplished using an automated tissue processor, with or without microwave-assistance. To ensure high-quality results, processing protocols should be tailored to tissue size and composition by modifying variables such as reagents used and the timing of the various steps. Herein, we provide an overview of tissue processing theory and outline a basic tissue processing method for use with a conventional automated fluid transfer/enclosed processor. The principles described will assist readers in optimizing tissue processing for their own projects.
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Affiliation(s)
- Sarah J Aziz
- Department of Pathology and Laboratory Medicine, Western University and London Health Sciences Centre, London, ON, Canada
| | - Cady E Zeman-Pocrnich
- Department of Pathology and Laboratory Medicine, Western University and London Health Sciences Centre, London, ON, Canada.
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34
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Kunder R, Shirsat NV. Real-Time PCR Assays on Formalin-Fixed, Paraffin-Embedded Medulloblastomas. Methods Mol Biol 2022; 2423:15-25. [PMID: 34978684 DOI: 10.1007/978-1-0716-1952-0_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Real-time PCR technology has been instrumental in contributing toward biomarker discovery, classification of tumors as well as risk stratification of patients. However, much of its success depends on the quality and quantity of the starting material used for RNA extraction. Clinical samples are most often provided as formalin-fixed and paraffin-embedded, wherein the RNA is extensively degraded, affecting sensitivity. Here, we describe a real-time PCR based assay developed for molecular subgrouping of medulloblastomas that is particularly useful for formalin-fixed, paraffin-embedded (FFPE) samples.
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Affiliation(s)
- Ratika Kunder
- Advanced Centre for Treatment, Research & Education in Cancer, Tata Memorial Centre, Navi Mumbai, Maharashtra, India.
| | - Neelam Vishwanath Shirsat
- Advanced Centre for Treatment, Research & Education in Cancer, Tata Memorial Centre, Navi Mumbai, Maharashtra, India
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35
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Abstract
Immunofluorescence is an important immunochemical technique that utilizes fluorescence-labeled antibodies to detect specific target antigens. It is used widely in both scientific research and clinical laboratories. Immunofluorescence allows for excellent sensitivity and amplification of signal in comparison to immunohistochemistry. However, analysis of samples labeled with fluorescence-labeled antibodies has to be performed using a fluorescence microscope or other type of fluorescence imaging. There are two methods available: direct (primary) and indirect (secondary) immunofluorescence. Here, we describe the principle of immunofluorescence methods as well as the preparation of fresh-frozen and formalin-fixed, paraffin embedded tissues for both direct and indirect immunofluorescence labeling.
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Affiliation(s)
| | | | - Sergio Piña-Oviedo
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
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36
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Kotnala A, Anderson DM, Patterson NH, Cantrell LS, Messinger JD, Curcio CA, Schey KL. Tissue fixation effects on human retinal lipid analysis by MALDI imaging and LC-MS/MS technologies. J Mass Spectrom 2021; 56:e4798. [PMID: 34881479 PMCID: PMC8711642 DOI: 10.1002/jms.4798] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 10/09/2021] [Accepted: 11/04/2021] [Indexed: 06/13/2023]
Abstract
Imaging mass spectrometry (IMS) allows the location and abundance of lipids to be mapped across tissue sections of human retina. For reproducible and accurate information, sample preparation methods need to be optimized. Paraformaldehyde fixation of a delicate multilayer structure like human retina facilitates the preservation of tissue morphology by forming methylene bridge crosslinks between formaldehyde and amine/thiols in biomolecules; however, retina sections analyzed by IMS are typically fresh-frozen. To determine if clinically significant inferences could be reliably based on fixed tissue, we evaluated the effect of fixation on analyte detection, spatial localization, and introduction of artifactual signals. Hence, we assessed the molecular identity of lipids generated by matrix-assisted laser desorption ionization (MALDI-IMS) and liquid chromatography coupled tandem mass spectrometry (LC-MS/MS) for fixed and fresh-frozen retina tissues in positive and negative ion modes. Based on MALDI-IMS analysis, more lipid signals were observed in fixed compared with fresh-frozen retina. More potassium adducts were observed in fresh-frozen tissues than fixed as the fixation process caused displacement of potassium adducts to protonated and sodiated species in ion positive ion mode. LC-MS/MS analysis revealed an overall decrease in lipid signals due to fixation that reduced glycerophospholipids and glycerolipids and conserved most sphingolipids and cholesteryl esters. The high quality and reproducible information from untargeted lipidomics analysis of fixed retina informs on all major lipid classes, similar to fresh-frozen retina, and serves as a steppingstone towards understanding of lipid alterations in retinal diseases.
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Affiliation(s)
- Ankita Kotnala
- Department of Biochemistry and Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, Birmingham, AL
| | - David M.G. Anderson
- Department of Biochemistry and Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN
| | - Nathan Heath Patterson
- Department of Biochemistry and Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN
| | - Lee S. Cantrell
- Department of Biochemistry and Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN
| | - Jeffrey D. Messinger
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, Birmingham, AL
| | - Christine A. Curcio
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, Birmingham, AL
| | - Kevin L. Schey
- Department of Biochemistry and Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN
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37
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Ching J, Osborne A, Eva R, Prudent J, Yu-Wai-Man P. Quantifying inter-organelle membrane contact sites using proximity ligation assay in fixed optic nerve sections. Exp Eye Res 2021; 213:108793. [PMID: 34656549 PMCID: PMC8683748 DOI: 10.1016/j.exer.2021.108793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 10/02/2021] [Accepted: 10/12/2021] [Indexed: 10/25/2022]
Abstract
Membrane contact sites (MCS) play crucial roles in cell physiology with dysfunction in several MCS proteins being linked with neurological and optic nerve diseases. Although there have been significant advances in imaging these interactions over the past two decades with advanced electron microscopy techniques, super-resolution imaging and proximity-dependent fluorescent reporters, a technique to observe and quantify MCS in mammalian optic nerve tissues has not yet been reported. We demonstrate for the first time that proximity ligation assay (PLA), a technique already used in mammalian cell lines, can be used as an efficient method of quantifying inter-organelle contact sites, namely mitochondria-endoplasmic reticulum (ER) and mitochondria-late-endosomes, in mammalian optic nerve tissues treated with adeno-associated virus (AAV) gene therapy with wild-type or phosphomimetic (active) protrudin. PLA utilises complementary single-stranded DNA oligomers bound to secondary antibodies that hybridise and complete a circular piece of DNA when the primary antibodies of interest interact. These interactions can be detected by amplifying the circular DNA and adding fluorescent probes. We show that PLA is a useful method that can be used to quantify MCS in optic nerve tissues. We have found that upregulation of protrudin with gene therapy significantly increases the number of mitochondria-ER and mitochondria-Rab7-late endosomes contact sites in optic nerves.
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Affiliation(s)
- Jared Ching
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK; Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK; Department of Ophthalmology, Addenbrooke's Hospital, Cambridge, UK.
| | - Andrew Osborne
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK; Ikarovec Ltd, Norwich Innovation Centre, Norwich, UK
| | - Richard Eva
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Julien Prudent
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Patrick Yu-Wai-Man
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK; Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK; Department of Ophthalmology, Addenbrooke's Hospital, Cambridge, UK; Moorfields Eye Hospital, London, UK; UCL Institute of Ophthalmology, University College London, London, UK
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38
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Wu Y, Han X, Su Y, Glidewell M, Daniels JS, Liu J, Sengupta T, Rey-Suarez I, Fischer R, Patel A, Combs C, Sun J, Wu X, Christensen R, Smith C, Bao L, Sun Y, Duncan LH, Chen J, Pommier Y, Shi YB, Murphy E, Roy S, Upadhyaya A, Colón-Ramos D, La Riviere P, Shroff H. Multiview confocal super-resolution microscopy. Nature 2021; 600:279-284. [PMID: 34837071 PMCID: PMC8686173 DOI: 10.1038/s41586-021-04110-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 10/07/2021] [Indexed: 12/31/2022]
Abstract
Confocal microscopy1 remains a major workhorse in biomedical optical microscopy owing to its reliability and flexibility in imaging various samples, but suffers from substantial point spread function anisotropy, diffraction-limited resolution, depth-dependent degradation in scattering samples and volumetric bleaching2. Here we address these problems, enhancing confocal microscopy performance from the sub-micrometre to millimetre spatial scale and the millisecond to hour temporal scale, improving both lateral and axial resolution more than twofold while simultaneously reducing phototoxicity. We achieve these gains using an integrated, four-pronged approach: (1) developing compact line scanners that enable sensitive, rapid, diffraction-limited imaging over large areas; (2) combining line-scanning with multiview imaging, developing reconstruction algorithms that improve resolution isotropy and recover signal otherwise lost to scattering; (3) adapting techniques from structured illumination microscopy, achieving super-resolution imaging in densely labelled, thick samples; (4) synergizing deep learning with these advances, further improving imaging speed, resolution and duration. We demonstrate these capabilities on more than 20 distinct fixed and live samples, including protein distributions in single cells; nuclei and developing neurons in Caenorhabditis elegans embryos, larvae and adults; myoblasts in imaginal disks of Drosophila wings; and mouse renal, oesophageal, cardiac and brain tissues.
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Affiliation(s)
- Yicong Wu
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA.
| | - Xiaofei Han
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
- Department of Automation, Tsinghua University, Beijing, China
| | - Yijun Su
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
- Leica Microsystems, Buffalo Grove, IL, USA
- SVision, Bellevue, WA, USA
| | | | | | - Jiamin Liu
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD, USA
| | - Titas Sengupta
- Department of Neuroscience and Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Ivan Rey-Suarez
- Institute for Physical Science and Technology, University of Maryland, College Park, MD, USA
| | - Robert Fischer
- Cell and Developmental Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Akshay Patel
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
| | - Christian Combs
- NHLBI Light Microscopy Facility, National Institutes of Health, Bethesda, MD, USA
| | - Junhui Sun
- Laboratory of Cardiac Physiology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Xufeng Wu
- NHLBI Light Microscopy Facility, National Institutes of Health, Bethesda, MD, USA
| | - Ryan Christensen
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
| | - Corey Smith
- Department of Radiology, University of Chicago, Chicago, IL, USA
| | - Lingyu Bao
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Yilun Sun
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, National Institutes of Health, Bethesda, MD, USA
| | - Leighton H Duncan
- Department of Neuroscience and Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Jiji Chen
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD, USA
| | - Yves Pommier
- Laboratory of Molecular Pharmacology, Developmental Therapeutics Branch, Center for Cancer Research, National Institutes of Health, Bethesda, MD, USA
| | - Yun-Bo Shi
- Section on Molecular Morphogenesis, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Elizabeth Murphy
- Laboratory of Cardiac Physiology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sougata Roy
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
| | - Arpita Upadhyaya
- Institute for Physical Science and Technology, University of Maryland, College Park, MD, USA
- Department of Physics, University of Maryland, College Park, MD, USA
| | - Daniel Colón-Ramos
- Department of Neuroscience and Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Marine Biological Laboratory, Woods Hole, MA, USA
- Instituto de Neurobiología, Recinto de Ciencias Médicas, Universidad de Puerto Rico, San Juan, Puerto Rico
| | - Patrick La Riviere
- Department of Radiology, University of Chicago, Chicago, IL, USA
- Marine Biological Laboratory, Woods Hole, MA, USA
| | - Hari Shroff
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA
- Advanced Imaging and Microscopy Resource, National Institutes of Health, Bethesda, MD, USA
- Marine Biological Laboratory, Woods Hole, MA, USA
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García-Pérez O, Melgar-Vilaplana L, Córdoba-Lanús E, Fernández-de-Misa R. Gene Expression Studies in Formalin-Fixed Paraffin-Embedded Samples of Cutaneous Cancer: The Need for Reference Genes. Curr Issues Mol Biol 2021; 43:2167-2176. [PMID: 34940125 PMCID: PMC8928935 DOI: 10.3390/cimb43030151] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/27/2021] [Accepted: 11/29/2021] [Indexed: 01/02/2023] Open
Abstract
Formalin-fixed paraffin-embedded (FFPE) tumour samples may provide crucial data regarding biomarkers for neoplasm progression. Analysis of gene expression is frequently used for this purpose. Therefore, mRNA expression needs to be normalized through comparison to reference genes. In this study, we establish which of the usually reported reference genes is the most reliable one in cutaneous malignant melanoma (MM) and cutaneous squamous cell carcinoma (CSCC). ACTB, TFRC, HPRT1 and TBP expression was quantified in 123 FFPE samples (74 MM and 49 CSCC biopsies) using qPCR. Expression stability was analysed by NormFinder and Bestkeeper softwares, and the direct comparison method between means and SD. The in-silico analysis with BestKeeper indicated that HPRT1 was more stable than ACTB and TFRC in MM (1.85 vs. 2.15) and CSCC tissues (2.09 vs. 2.33). The best option to NormFinder was ACTB gene (0.56) in MM and TFRC (0.26) in CSCC. The direct comparison method showed lower SD means of ACTB expression in MM (1.17) and TFRC expression in CSCC samples (1.00). When analysing the combination of two reference genes for improving stability, NormFinder indicated HPRT1 and ACTB to be the best for MM samples, and HPRT1 and TFRC genes for CSCC. In conclusion, HPRT1 and ACTB genes in combination are the most appropriate choice for normalization in gene expression studies in MM FFPE tissue, while the combination of HPRT1 and TFRC genes are the best option in analysing CSCC FFPE samples. These may be used consistently in forthcoming studies on gene expression in both tumours.
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Affiliation(s)
- Omar García-Pérez
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Ctra. Gral. del Rosario, 145, 38010 Santa Cruz de Tenerife, Spain;
- Universidad de La Laguna, Calle Padre Herrera, s/n, 38200 San Cristóbal de La Laguna, Spain
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (IUETSPC), 38296 San Cristóbal de La Laguna, Spain
| | - Leticia Melgar-Vilaplana
- Pathology Department, Hospital Universitario Nuestra Señora de Candelaria, Ctra. Gral. del Rosario, 145, 38010 Santa Cruz de Tenerife, Spain;
| | - Elizabeth Córdoba-Lanús
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Ctra. Gral. del Rosario, 145, 38010 Santa Cruz de Tenerife, Spain;
- Universidad de La Laguna, Calle Padre Herrera, s/n, 38200 San Cristóbal de La Laguna, Spain
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (IUETSPC), 38296 San Cristóbal de La Laguna, Spain
- Correspondence: (E.C.-L.); (R.F.-d.-M.)
| | - Ricardo Fernández-de-Misa
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Ctra. Gral. del Rosario, 145, 38010 Santa Cruz de Tenerife, Spain;
- Universidad de La Laguna, Calle Padre Herrera, s/n, 38200 San Cristóbal de La Laguna, Spain
- Dermatology Department, Hospital Universitario Nuestra Señora de Candelaria, Ctra. Gral. del Rosario, 145, 38010 Santa Cruz de Tenerife, Spain
- Correspondence: (E.C.-L.); (R.F.-d.-M.)
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40
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Meng S, Xia W, Xia L, Zhou L, Xu J, Pan X, Meng L. A Pilot Study of Rare Renal Amyloidosis Based on FFPE Proteomics. Molecules 2021; 26:molecules26237234. [PMID: 34885818 PMCID: PMC8659071 DOI: 10.3390/molecules26237234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 11/25/2021] [Accepted: 11/25/2021] [Indexed: 11/21/2022] Open
Abstract
Renal amyloidosis typically manifests albuminuria, nephrotic-range proteinuria, and ultimately progresses to end-stage renal failure if diagnosed late. Different types of renal amyloidosis have completely different treatments and outcomes. Therefore, amyloidosis typing is essential for disease prognosis, genetic counseling and treatment. Thirty-six distinct proteins currently known to cause amyloidosis that have been described as amyloidogenic precursors, immunohistochemistry (IHC) or immunofluorescence (IF), can be challenging for amyloidosis typing especially in rare or hereditary amyloidosis in clinical practice. We made a pilot study that optimized the proteomics pre-processing procedures for trace renal amyloidosis formalin-fixed paraffin-embedded (FFPE) tissue samples, combined with statistical and bioinformatics analysis to screen out the amyloidosis-related proteins to accurately type or subtype renal amyloidosis in order to achieve individual treatment. A sensitive, specific and reliable FFPE-based proteomics analysis for trace sample manipulation was developed for amyloidosis typing. Our results not only underlined the great promise of traditional proteomics and bioinformatics analysis using FFPE tissues for amyloidosis typing, but also proved that retrospective diagnosis and analysis of previous cases laid a solid foundation for personalized treatment.
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Affiliation(s)
- Shuang Meng
- Department of Core Facility of Basic Medical Sciences, Shanghai Jiao Tong University School of Basic Medicine, Shanghai 200025, China; (S.M.); (L.X.); (L.Z.)
| | - Wenwen Xia
- Department of Pathology, Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China;
| | - Li Xia
- Department of Core Facility of Basic Medical Sciences, Shanghai Jiao Tong University School of Basic Medicine, Shanghai 200025, China; (S.M.); (L.X.); (L.Z.)
| | - Li Zhou
- Department of Core Facility of Basic Medical Sciences, Shanghai Jiao Tong University School of Basic Medicine, Shanghai 200025, China; (S.M.); (L.X.); (L.Z.)
| | - Jing Xu
- Department of Nephrology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China;
| | - Xiaoxia Pan
- Department of Nephrology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China;
- Correspondence: (X.P.); (L.M.); Tel.: +86-21-64370045 (X.P.); +86-21-63846590 (L.M.)
| | - Liyuan Meng
- Department of Core Facility of Basic Medical Sciences, Shanghai Jiao Tong University School of Basic Medicine, Shanghai 200025, China; (S.M.); (L.X.); (L.Z.)
- Correspondence: (X.P.); (L.M.); Tel.: +86-21-64370045 (X.P.); +86-21-63846590 (L.M.)
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Verma G, Aggarwal N, Chhakara S, Tyagi A, Vishnoi K, Jadli M, Singh T, Goel A, Pandey D, Sharma A, Agarwal K, Sarkar U, Doval DC, Sharma S, Mehrotra R, Singh SM, Bharti AC. Detection of human papillomavirus infection in oral cancers reported at dental facility: assessing the utility of FFPE tissues. Med Oncol 2021; 39:13. [PMID: 34792663 DOI: 10.1007/s12032-021-01608-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 11/02/2021] [Indexed: 12/24/2022]
Abstract
Incidence of human papillomavirus (HPV)-associated oral cancers is on the rise. However, epidemiological data of this subset of cancers are limited. Dental hospital poses a unique advantage in detection of HPV-positive oral malignancies. We assessed the utility of formalin-fixed paraffin-embedded (FFPE) tissues, which are readily available, for evaluation of high-risk HPV infection in oral cancer. For protocol standardization, we used 20 prospectively collected paired FFPE and fresh tissues of histopathologically confirmed oral cancer cases reported in Oral Medicine department of a dental hospital for comparative study. Only short PCRs (~ 200 bp) of DNA isolated using a modified xylene-free method displayed a concordant HPV result. For HPV analysis, we used additional 30 retrospectively collected FFPE tissues. DNA isolated from these specimens showed an overall 23.4% (11/47) HPV positivity with detection of HPV18. Comparison of HPV positivity from dental hospital FFPE specimens with overall HPV positivity of freshly collected oral cancer specimens (n = 55) from three cancer care hospitals of the same region showed notable difference (12.7%; 7/55). Further, cancer hospital specimens showed HPV16 positivity and displayed a characteristic difference in reported sub-sites and patient spectrum. Overall, using a xylene-free FFPE DNA isolation method clubbed with short amplicon PCR, we showed detection of HPV-positive oral cancer in dental hospitals.
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Affiliation(s)
- Gaurav Verma
- Division of Molecular Oncology, ICMR- National Institute of Cancer Prevention and Research, Noida, Uttar Pradesh, India
- School of Biotechnology, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Nikita Aggarwal
- Molecular Oncology Laboratory, Department of Zoology, University of Delhi, New Delhi, 110007, India
| | - Suhail Chhakara
- Molecular Oncology Laboratory, Department of Zoology, University of Delhi, New Delhi, 110007, India
| | - Abhishek Tyagi
- Division of Molecular Oncology, ICMR- National Institute of Cancer Prevention and Research, Noida, Uttar Pradesh, India
- Department of Cancer Biology, Wake Forest University of Medicine, Winston-Salem, NC, USA
| | - Kanchan Vishnoi
- Division of Molecular Oncology, ICMR- National Institute of Cancer Prevention and Research, Noida, Uttar Pradesh, India
- School of Biotechnology, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Mohit Jadli
- Molecular Oncology Laboratory, Department of Zoology, University of Delhi, New Delhi, 110007, India
| | - Tejveer Singh
- Molecular Oncology Laboratory, Department of Zoology, University of Delhi, New Delhi, 110007, India
| | - Ankit Goel
- Subharti Dental College, Meerut, Uttar Pradesh, India
| | - Durgatosh Pandey
- Department of Oncosurgery, Dr. Bheem Rao Ambedkar Institute-Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | | | | | - Urmi Sarkar
- Rajiv Gandhi Cancer Institute & Research Centre, New Delhi, India
| | | | - Shashi Sharma
- Division of Molecular Oncology, ICMR- National Institute of Cancer Prevention and Research, Noida, Uttar Pradesh, India
| | - Ravi Mehrotra
- Division of Molecular Oncology, ICMR- National Institute of Cancer Prevention and Research, Noida, Uttar Pradesh, India
| | - Sukh Mahendra Singh
- School of Biotechnology, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Alok Chandra Bharti
- Division of Molecular Oncology, ICMR- National Institute of Cancer Prevention and Research, Noida, Uttar Pradesh, India.
- Molecular Oncology Laboratory, Department of Zoology, University of Delhi, New Delhi, 110007, India.
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Chen YL, Chen WL, Cheng YC, Lin MC, Yang SC, Tsai HW, Lin C, Su WC, Chow NH, Ho CL. Development of a novel ALK rearrangement screening test for non-small cell lung cancers. PLoS One 2021; 16:e0257152. [PMID: 34559836 PMCID: PMC8462717 DOI: 10.1371/journal.pone.0257152] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 08/24/2021] [Indexed: 11/18/2022] Open
Abstract
Approximately 5–7% of non–small cell lung cancer (NSCLC) cases harbor an anaplastic lymphoma kinase (ALK) fusion gene and may benefit from ALK inhibitor therapy. To detect ALK fusion genes, we developed a novel test using reverse transcription polymerase chain reaction (RT-PCR) for the ALK kinase domain (KD). Since ALK expression is mostly silenced in the adult with the exception of neuronal tissue, the normal lung tissue, mesothelial lining, and inflammatory cells are devoid of ALK transcript, making ALK KD RT-PCR an ideal surrogate test for ALK fusion transcripts in lung or pleural effusion. The test was designed with a short PCR product (197 bp) to work for both malignant pleural effusion (MPE) and formalin-fixed, paraffin-embedded (FFPE) NSCLC samples. Using ALK IHC as a reference, the sensitivity of the test was 100% for both MPE and FFPE. The specificity was 97.6% for MPE and 97.4% for FFPE. Two false positive cases were found. One was a metastatic brain lesion which should be avoided in the future due to intrinsic ALK expression in the neuronal tissue. The other one resulted from ALK gene amplification. Due to potential false positivity, subsequent confirmation tests such as fluorescence in situ hybridization or multiplex PCR would be preferable. Nevertheless, the test is simple and inexpensive with no false negativity, making it a desirable screening test. It also offers an advantage over multiplex RT-PCR with the capability to detect novel ALK fusions. Indeed through the screening test, we found a novel ALK fusion partner (sperm antigen with calponin homology and coiled-coil domains 1 like gene, SPECC1L) with increased sensitivity to crizotinib in vitro. In summary, a novel RNA-based ALK KD analysis was developed for ALK rearrangement screening in MPE and FFPE specimens of NSCLC. This simple inexpensive test can be implemented as routine diagnostics.
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Affiliation(s)
- Yi-Lin Chen
- Molecular Diagnosis Laboratory, Department of Pathology, National Cheng Kung University Hospital, Tainan, Taiwan
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Molecular Medicine Core Laboratory, Research center of Clinical Medicine, National Cheng Kung University Hospital, Tainan, Taiwan
- Associations of Medical Technologists, Tainan, Taiwan
| | - Wan-Li Chen
- Molecular Diagnosis Laboratory, Department of Pathology, National Cheng Kung University Hospital, Tainan, Taiwan
- Molecular Medicine Core Laboratory, Research center of Clinical Medicine, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Yi-Chia Cheng
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ming-Ching Lin
- Molecular Diagnosis Laboratory, Department of Pathology, National Cheng Kung University Hospital, Tainan, Taiwan
- Molecular Medicine Core Laboratory, Research center of Clinical Medicine, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Shu-Ching Yang
- Molecular Diagnosis Laboratory, Department of Pathology, National Cheng Kung University Hospital, Tainan, Taiwan
- Molecular Medicine Core Laboratory, Research center of Clinical Medicine, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Hung-Wen Tsai
- Molecular Diagnosis Laboratory, Department of Pathology, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Chien‐Chung Lin
- Department of Internal Medicine, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Wu-Chou Su
- Department of Internal Medicine, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Nan-Haw Chow
- Molecular Diagnosis Laboratory, Department of Pathology, National Cheng Kung University Hospital, Tainan, Taiwan
- Molecular Medicine Core Laboratory, Research center of Clinical Medicine, National Cheng Kung University Hospital, Tainan, Taiwan
- The Institute of Molecular Medical, College of Medicine, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Chung-Liang Ho
- Molecular Diagnosis Laboratory, Department of Pathology, National Cheng Kung University Hospital, Tainan, Taiwan
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Molecular Medicine Core Laboratory, Research center of Clinical Medicine, National Cheng Kung University Hospital, Tainan, Taiwan
- The Institute of Molecular Medical, College of Medicine, National Cheng Kung University Hospital, Tainan, Taiwan
- * E-mail:
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Wei L, Dugas M, Sandmann S. SimFFPE and FilterFFPE: improving structural variant calling in FFPE samples. Gigascience 2021; 10:giab065. [PMID: 34553214 PMCID: PMC8458033 DOI: 10.1093/gigascience/giab065] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 07/19/2021] [Accepted: 09/06/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Artifact chimeric reads are enriched in next-generation sequencing data generated from formalin-fixed paraffin-embedded (FFPE) samples. Previous work indicated that these reads are characterized by erroneous split-read support that is interpreted as evidence of structural variants. Thus, a large number of false-positive structural variants are detected. To our knowledge, no tool is currently available to specifically call or filter structural variants in FFPE samples. To overcome this gap, we developed 2 R packages: SimFFPE and FilterFFPE. RESULTS SimFFPE is a read simulator, specifically designed for next-generation sequencing data from FFPE samples. A mixture of characteristic artifact chimeric reads, as well as normal reads, is generated. FilterFFPE is a filtration algorithm, removing artifact chimeric reads from sequencing data while keeping real chimeric reads. To evaluate the performance of FilterFFPE, we performed structural variant calling with 3 common tools (Delly, Lumpy, and Manta) with and without prior filtration with FilterFFPE. After applying FilterFFPE, the mean positive predictive value improved from 0.27 to 0.48 in simulated samples and from 0.11 to 0.27 in real samples, while sensitivity remained basically unchanged or even slightly increased. CONCLUSIONS FilterFFPE improves the performance of SV calling in FFPE samples. It was validated by analysis of simulated and real data.
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Affiliation(s)
- Lanying Wei
- Institute of Medical Informatics, University of Münster, Münster 48149, Germany
| | - Martin Dugas
- Institute of Medical Informatics, University of Münster, Münster 48149, Germany
- Institute of Medical Informatics, Heidelberg University Hospital, Heidelberg 69120, Germany
| | - Sarah Sandmann
- Institute of Medical Informatics, University of Münster, Münster 48149, Germany
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Sato H, Norimatsu Y, Irino S, Nishikawa T. Efficacy of the Antigenicity-Retaining Ability of Fixative Solutions for Liquid-Based Cytology: Immunocytochemistry of Long-Term Storage. Acta Cytol 2021; 65:510-521. [PMID: 34535585 DOI: 10.1159/000518452] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 07/11/2021] [Indexed: 11/19/2022]
Abstract
INTRODUCTION/OBJECTIVE Liquid-based cytology (LBC) is advantageous as multiple stained specimens can be prepared and used for additional assays such as immunocytochemical and molecular-pathological investigations. Two types of preservative-fixative solutions (fixatives) are used for nongynecologic specimens used in the BD SurePath-LBC (SP-LBC) method, and their components vary. However, few studies have evaluated the differences in antigen-retaining ability between these fixatives. Therefore, we investigated and compared the antigen-retaining ability of the fixatives in immunocytochemical staining (ICC) under long-term storage conditions. MATERIALS AND METHODS Sediments of cultured RAJI cells (derived from Burkitt's lymphoma) were added to each fixative (red and blue) and stored at room temperature for a specified period (1 h; 1 week; and 1, 3, and 6 months). The specimens were then prepared using the SP-LBC method and subjected to ICC. Positivity rate was calculated using the specimens fixed at room temperature for 1 h as a control. Antibodies against Ki67 expressed in the nucleus and against CD20 and leukocyte common antigen (LCA) expressed on the cell membrane were used. RESULTS For CD20 and LCA, the positivity rate increased with time in the red fixative compared with that in the control. In the blue fixative, the positivity rate was highest at 1 h and was maintained at a high level throughout the storage period. In contrast, the Ki67 positivity rate was highest at 1 h in both red and blue fixatives and markedly decreased with time. Therefore, although refrigerated (8°C) storage was used, no improvement was noted. CONCLUSIONS Long-term storage is possible for cell membrane antigens at room temperature; however, it is unsuitable for intranuclear antigens. Therefore, we conclude that suitable fixative type and storage temperature differ based on antigen location. Further investigation is warranted.
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Affiliation(s)
- Hiaki Sato
- Department of Medical Technology and Clinical Engineering, Faculty of Health and Medical Sciences, Hokuriku University, Kanazawa, Japan
| | - Yoshiaki Norimatsu
- Department of Medical Technology, Faculty of Health Sciences, Ehime Prefectural University of Health Sciences, Tobe, Japan
| | - Satoshi Irino
- Department of Nursing, Ehime Prefectural University of Health Sciences, Tobe, Japan
| | - Takeshi Nishikawa
- Department of Pathology, Nara Medical University Hospital, Nara, Japan
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Alperstein AM, Molnar KS, Dicke SS, Farrell KM, Makley LN, Zanni MT, Andley UP. Analysis of amyloid-like secondary structure in the Cryab-R120G knock-in mouse model of hereditary cataracts by two-dimensional infrared spectroscopy. PLoS One 2021; 16:e0257098. [PMID: 34520490 PMCID: PMC8439473 DOI: 10.1371/journal.pone.0257098] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 08/23/2021] [Indexed: 11/18/2022] Open
Abstract
αB-crystallin is a small heat shock protein that forms a heterooligomeric complex with αA-crystallin in the ocular lens. It is also widely distributed in tissues throughout the body and has been linked with neurodegenerative diseases such as Alzheimer's, where it is associated with amyloid fibrils. Crystallins can form amorphous aggregates in cataracts as well as more structured amyloid-like fibrils. The arginine 120 to glycine (R120G) mutation in αB-crystallin (Cryab-R120G) results in high molecular weight crystallin protein aggregates and loss of the chaperone activity of the protein in vitro, and it is associated with human hereditary cataracts and myopathy. Characterizing the amorphous (unstructured) versus the highly ordered (amyloid fibril) nature of crystallin aggregates is important in understanding their role in disease and important to developing pharmacological treatments for cataracts. We investigated protein secondary structure in wild-type (WT) and Cryab-R120G knock-in mutant mouse lenses using two-dimensional infrared (2DIR) spectroscopy, which has been used to detect amyloid-like fibrils in human lenses and measure UV radiation-induced changes in porcine lenses. Our goal was to compare the aggregated proteins in this mouse lens model to human lenses and evaluate the protein structural relevance of the Cryab-R120G knock-in mouse model to general age-related cataract disease. In the 2DIR spectra, amide I diagonal peak frequencies were red-shifted to smaller wavenumbers in mutant mouse lenses as compared to WT mouse lenses, consistent with an increase in ordered secondary structure. The cross peak frequency and intensity indicated the presence of amyloid in the mutant mouse lenses. While the diagonal and cross peak changes in location and intensity from the 2DIR spectra indicated significant structural differences between the wild type and mutant mouse lenses, these differences were smaller than those found in human lenses; thus, the Cryab-R120G knock-in mouse lenses contain less amyloid-like secondary structure than human lenses. The results of the 2DIR spectroscopy study confirm the presence of amyloid-like secondary structure in Cryab-R120G knock-in mice with cataracts and support the use of this model to study age-related cataract.
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Affiliation(s)
- Ariel M. Alperstein
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Kathleen S. Molnar
- ViewPoint Therapeutics, San Francisco, California, United States of America
| | - Sidney S. Dicke
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Kieran M. Farrell
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Leah N. Makley
- ViewPoint Therapeutics, San Francisco, California, United States of America
| | - Martin T. Zanni
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Usha P. Andley
- Washington University School of Medicine, Department of Ophthalmology and Visual Sciences St. Louis, St. Louis, Missouri, United States of America
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Li Z, Ungerer M, Faßbender J, Wenhart C, Holthoff HP, Muench G. Tissue block staining and domestic adhesive tape yield qualified integral sections of adult mouse orbits and eyeballs. PLoS One 2021; 16:e0255363. [PMID: 34347814 PMCID: PMC8336840 DOI: 10.1371/journal.pone.0255363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 07/14/2021] [Indexed: 11/27/2022] Open
Abstract
The standard histological processing procedure, which produces excellent staining of sections for most tissues, fails to yield satisfactory results in adult mouse orbits or eyeballs. Here, we show that a protocol using tissue block staining and domestic adhesive tapes resulted in qualified integral serial cryo-sections of whole orbits or eyeballs, and the fine structures were well preserved. The histological processing protocol comprises paraformaldehyde fixation, ethylenediaminetetraacetic acid decalcification, tissue block staining with hematoxylin and eosin, embedding, adhesive tape aided sectioning, and water-soluble mounting. This protocol was proved to be the best in comparison with seven other related existing histological traditional or non-traditional processing methods, according to the staining slice quality. We observed a hundred percent success rate in sectioning, collection, and mounting with this method. The reproducibility tested on qualified section success rates and slice quality scores confirmed that the technique is reliable. The feasibility of the method to detect target molecules in orbits was verified by successful trial tests on block immunostaining and adhesive tape-aided sectioning. Application of this protocol in joints, brains, and so on,—the challenging integral sectioning tissues, also generated high-quality histological staining sections.
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Affiliation(s)
- Zhongmin Li
- Advancecor GmbH, Martinsried, Germany
- * E-mail:
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Alenda C, Rojas E, Valor LM. FFPE samples from cavitational ultrasonic surgical aspirates are suitable for RNA profiling of gliomas. PLoS One 2021; 16:e0255168. [PMID: 34293049 PMCID: PMC8297856 DOI: 10.1371/journal.pone.0255168] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 07/11/2021] [Indexed: 01/18/2023] Open
Abstract
During surgical procedures for gliomas, tissue material obtained from cavitational ultrasonic surgical aspirators (CUSAs) is generally discarded but can actually exceed the amount and quality of certain tumour core resections (TCRs). Despite reports indicating the suitability of CUSA-derived material for diagnosis and research, its use is still marginal. We extended these conclusions to formalin-fixed, paraffin-embedded (FFPE) samples, the most common format for archival tumour tissue in anatomical pathology departments, by conducting for the first time RNA-seq analysis in CUSA aspirates. We compared the molecular diagnosis of somatic mutations used in the clinical routine and the gene expression profiles of fixed solid material from CUSA aspirates and TCRs from the same patients in selected gliomas encompassing grades II to IV. Despite the characteristic heterogeneity of gliomas, we found substantial similarities between the corresponding aspirates and TCRs that included transcriptional signatures associated with glioma subtypes. Based on these results, we confirmed that CUSA-fixed biomaterials from glioma surgeries are appropriate for downstream applications and biomarkers screening.
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Affiliation(s)
- Cristina Alenda
- Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL), Alicante, Spain
- Departamento de Patología, Hospital General Universitario de Alicante, Alicante, Spain
| | - Estefanía Rojas
- Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL), Alicante, Spain
- Departamento de Patología, Hospital General Universitario de Alicante, Alicante, Spain
| | - Luis M. Valor
- Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL), Alicante, Spain
- Laboratorio de Apoyo a la Investigación, Hospital General Universitario de Alicante, Alicante, Spain
- * E-mail:
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Baker JE, Plaska SW, Qin Z, Liu CJ, Rege J, Rainey WE, Udager AM. Targeted RNA sequencing of adrenal zones using immunohistochemistry-guided capture of formalin-fixed paraffin-embedded tissue. Mol Cell Endocrinol 2021; 530:111296. [PMID: 33915228 PMCID: PMC8456741 DOI: 10.1016/j.mce.2021.111296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/05/2021] [Accepted: 04/20/2021] [Indexed: 10/21/2022]
Abstract
Adequate access to fresh or frozen normal adrenal tissue has been a primary limitation to the enhanced characterization of the adrenal zones via RNA sequencing (RNAseq). Herein, we describe the application of targeted RNAseq to formalin-fixed paraffin-embedded (FFPE) normal adrenal gland specimens. Immunohistochemistry (IHC) was used to visualize and guide the capture of the adrenocortical zones and medulla. Following IHC-based tissue capture and isolation of RNA, high-throughput targeted RNAseq highlighted clear transcriptomic differences and identified differentially expressed genes among the adrenal zones. Our data demonstrate the ability to capture FFPE adrenal zone tissue for targeted transcriptomic analyses. Future comparison of normal adrenal zones will improve our understanding of transcriptomic patterns and help identify potential novel pathways controlling zone-specific steroid production.
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Affiliation(s)
- Jessica E Baker
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Samuel W Plaska
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Zhaoping Qin
- Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Chia-Jen Liu
- Michigan Center for Translational Pathology, Ann Arbor, MI, USA
| | - Juilee Rege
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - William E Rainey
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA; Department of Internal Medicine, Division of Metabolism, Endocrine, and Diabetes, University of Michigan Medical School, Ann Arbor, MI, USA.
| | - Aaron M Udager
- Michigan Center for Translational Pathology, Ann Arbor, MI, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.
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Lahiri P, Mukherjee S, Ghosh B, Das D, Lahiri B, Varshney SK, Pal M, Paul RR, Chatterjee J. Comprehensive Evaluation of PAXgene Fixation on Oral Cancer Tissues Using Routine Histology, Immunohistochemistry, and FTIR Microspectroscopy. Biomolecules 2021; 11:biom11060889. [PMID: 34203873 PMCID: PMC8232633 DOI: 10.3390/biom11060889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/06/2021] [Accepted: 06/10/2021] [Indexed: 11/25/2022] Open
Abstract
The choice of tissue fixation is critical for preserving the morphology and biochemical information of tissues. Fragile oral tissues with lower tensile strength are challenging to process for histological applications as they are prone to processing damage, such as tissue tear, wrinkling, and tissue fall-off from slides. This leads to loss of morphological information and unnecessary delay in experimentation. In this study, we have characterized the new PAXgene tissue fixation system on oral buccal mucosal tissue of cancerous and normal pathology for routine histological and immunohistochemical applications. We aimed to minimize the processing damage of tissues and improve the quality of histological experiments. We also examined the preservation of biomolecules by PAXgene fixation using FTIR microspectroscopy. Our results demonstrate that the PAXgene-fixed tissues showed significantly less tissue fall-off from slides. Hematoxylin and Eosin staining showed comparable morphology between formalin-fixed and PAXgene-fixed tissues. Good quality and slightly superior immunostaining for cancer-associated proteins p53 and CK5/6 were observed in PAXgene-fixed tissues without antigen retrieval than formalin-fixed tissues. Further, FTIR measurements revealed superior preservation of glycogen, fatty acids, and amide III protein secondary structures in PAXgene-fixed tissues. Overall, we present the first comprehensive evaluation of the PAXgene tissue fixation system in oral tissues. This study concludes that the PAXgene tissue fixation system can be applied to oral tissues to perform diagnostic molecular pathology experiments without compromising the quality of the morphology or biochemistry of biomolecules.
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Affiliation(s)
- Pooja Lahiri
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India; (S.M.); (B.G.); (D.D.); (J.C.)
- Correspondence:
| | - Suranjana Mukherjee
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India; (S.M.); (B.G.); (D.D.); (J.C.)
| | - Biswajoy Ghosh
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India; (S.M.); (B.G.); (D.D.); (J.C.)
| | - Debnath Das
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India; (S.M.); (B.G.); (D.D.); (J.C.)
| | - Basudev Lahiri
- Department of Electronics and Electrical Communication Engineering, Indian Institute of Technology Kharagpur, Kharagpur 721302, India; (B.L.); (S.K.V.)
| | - Shailendra Kumar Varshney
- Department of Electronics and Electrical Communication Engineering, Indian Institute of Technology Kharagpur, Kharagpur 721302, India; (B.L.); (S.K.V.)
| | - Mousumi Pal
- Guru Nanak Institute of Dental Sciences and Research (GNIDSR), Kolkata 700114, India;
| | - Ranjan Rashmi Paul
- Department of Oral & Dental Sciences, JIS University, Kolkata 700109, India;
| | - Jyotirmoy Chatterjee
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur 721302, India; (S.M.); (B.G.); (D.D.); (J.C.)
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50
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Paasila PJ, Fok SYY, Flores‐Rodriguez N, Sajjan S, Svahn AJ, Dennis CV, Holsinger RMD, Kril JJ, Becker TS, Banati RB, Sutherland GT, Graeber MB. Ground state depletion microscopy as a tool for studying microglia-synapse interactions. J Neurosci Res 2021; 99:1515-1532. [PMID: 33682204 PMCID: PMC8251743 DOI: 10.1002/jnr.24819] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 02/02/2021] [Accepted: 02/06/2021] [Indexed: 01/09/2023]
Abstract
Ground state depletion followed by individual molecule return microscopy (GSDIM) has been used in the past to study the nanoscale distribution of protein co-localization in living cells. We now demonstrate the successful application of GSDIM to archival human brain tissue sections including from Alzheimer's disease cases as well as experimental tissue samples from mouse and zebrafish larvae. Presynaptic terminals and microglia and their cell processes were visualized at a resolution beyond diffraction-limited light microscopy, allowing clearer insights into their interactions in situ. The procedure described here offers time and cost savings compared to electron microscopy and opens the spectrum of molecular imaging using antibodies and super-resolution microscopy to the analysis of routine formalin-fixed paraffin sections of archival human brain. The investigation of microglia-synapse interactions in dementia will be of special interest in this context.
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Affiliation(s)
- Patrick Jarmo Paasila
- Faculty of Medicine and HealthCharles Perkins Centre and School of Medical SciencesThe University of SydneyCamperdownNSWAustralia
| | - Sandra Y. Y. Fok
- Biomedical Imaging FacilityMark Wainwright Analytical CentreUniversity of New South Wales SydneyKensingtonNSWAustralia
| | - Neftali Flores‐Rodriguez
- Charles Perkins CentreSydney Microscopy and MicroanalysisThe University of SydneyCamperdownNSWAustralia
| | - Sujata Sajjan
- Faculty of Medicine and HealthBrain and Mind CentreThe University of SydneyCamperdownNSWAustralia
| | - Adam J. Svahn
- Faculty of Medicine and HealthBrain and Mind CentreThe University of SydneyCamperdownNSWAustralia
| | - Claude V. Dennis
- Faculty of Medicine and HealthCharles Perkins Centre and School of Medical SciencesThe University of SydneyCamperdownNSWAustralia
| | - R. M. Damian Holsinger
- Faculty of Medicine and HealthBrain and Mind CentreThe University of SydneyCamperdownNSWAustralia
| | - Jillian J. Kril
- Faculty of Medicine and HealthCharles Perkins Centre and School of Medical SciencesThe University of SydneyCamperdownNSWAustralia
| | - Thomas S. Becker
- Faculty of Medicine and HealthBrain and Mind CentreThe University of SydneyCamperdownNSWAustralia
| | - Richard B. Banati
- Faculty of Medicine and HealthBrain and Mind CentreThe University of SydneyCamperdownNSWAustralia
- Life SciencesAustralian Nuclear Science and Technology OrganisationKirraweeNSWAustralia
| | - Greg T. Sutherland
- Faculty of Medicine and HealthCharles Perkins Centre and School of Medical SciencesThe University of SydneyCamperdownNSWAustralia
| | - Manuel B. Graeber
- Faculty of Medicine and HealthBrain and Mind CentreThe University of SydneyCamperdownNSWAustralia
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