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Ambalaparambil A, Perumal PV, Gochhait D, Siddaraju N. Validation of a novel alcohol-free preservative solution in comparison with conventional prefixation on quality of serous body fluid smears. Diagn Cytopathol 2024; 52:633-642. [PMID: 38895827 DOI: 10.1002/dc.25369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 05/30/2024] [Accepted: 06/03/2024] [Indexed: 06/21/2024]
Abstract
BACKGROUND We describe a novel alcohol-free preservative composed of glucose, mannitol, disodium hydrogen orthophosphate, thymol, and distilled water (glucose-mannitol-disodium dihydrogen orhtophosphate-thymol [GMDT] preservative) in appropriate proportion as an alternative to alcohol prefixation (APF) of body fluids. OBJECTIVES To assess the cytomorphologic preservation and staining quality of serous body fluid smears generated by GMDT preservative and compare it with smears processed by standard 50% APF. METHODOLOGY The study comprised 151 effusion samples. Each sample was equally divided into four tubes. Equal volumes of APF and GMDT preservatives were added to the first two tubes and left at room temperature for 24 h. Similarly, the corresponding preservatives were added to the third and fourth tubes and stored for 48 h. Two smears were prepared from the centrifuged sediments of each tube (all four tubes) and stained with May-Grünwald Giemsa and Papanicolaou (Pap) stains. Using a three-tiered scoring system, the smear examination was blinded to assess the extent of cellular preservation and the staining quality by two cytotechnologists and two cytopathologists. Statistical analysis was performed by STATA 16.0. RESULTS Samples processed with the GMDT preservative at 24 h showed better cytoplasmic preservation and smear background, while nuclear features and staining quality showed no difference between the two preservatives. Mild cytoplasmic and nuclear degenerative changes were noted with the GMDT at 48 h, while all four parameters remained similar with APF at 24 and 48 h. CONCLUSIONS The newly developed alcohol-free, GMDT preservative, could be a feasible and cost-effective alternative to 50% APF, preferably when samples are processed within 24 h.
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Affiliation(s)
- Anagha Ambalaparambil
- Department of Pathology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Puducherry, India
- Department of Transfusion Medicine, Government Medical College, Kottayam, Kerala, India
| | - Prasanna Venkadesa Perumal
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Puducherry, India
| | - Debasis Gochhait
- Department of Pathology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Puducherry, India
| | - Neelaiah Siddaraju
- Department of Pathology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Puducherry, India
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Michael ARM, Amaral BC, Ball KL, Eiriksson KH, Schriemer DC. Cell fixation improves performance of in situ crosslinking mass spectrometry while preserving cellular ultrastructure. Nat Commun 2024; 15:8537. [PMID: 39358380 DOI: 10.1038/s41467-024-52844-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 09/24/2024] [Indexed: 10/04/2024] Open
Abstract
Crosslinking mass spectrometry (XL-MS) has the potential to map the interactome of the cell with high resolution and depth of coverage. However, current in vivo XL-MS methods are hampered by crosslinkers that demonstrate low cell permeability and require long reaction times. Consequently, interactome sampling is not high and long incubation times can distort the cell, bringing into question the validity any protein interactions identified by the method. We address these issues with a fast formaldehyde-based fixation method applied prior to the introduction of secondary crosslinkers. Using human A549 cells and a range of reagents, we show that 4% formaldehyde fixation with membrane permeabilization preserves cellular ultrastructure and simultaneously improves reaction conditions for in situ XL-MS. Protein labeling yields can be increased even for nominally membrane-permeable reagents, and surprisingly, high-concentration formaldehyde does not compete with conventional amine-reactive crosslinking reagents. Prefixation with permeabilization uncouples cellular dynamics from crosslinker dynamics, enhancing control over crosslinking yield and permitting the use of any chemical crosslinker.
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Affiliation(s)
- Andrew R M Michael
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, T2N-4N1, Canada
| | - Bruno C Amaral
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, T2N-4N1, Canada
| | - Kallie L Ball
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, T2N-4N1, Canada
| | - Kristen H Eiriksson
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, T2N-4N1, Canada
| | - David C Schriemer
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, T2N-4N1, Canada.
- Department of Chemistry, University of Calgary, Calgary, Alberta, T2N-4N1, Canada.
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Kropp C, Tambosco K, Chadi S, Langella P, Claus SP, Martin R. Christensenella minuta protects and restores intestinal barrier in a colitis mouse model by regulating inflammation. NPJ Biofilms Microbiomes 2024; 10:88. [PMID: 39294159 PMCID: PMC11411060 DOI: 10.1038/s41522-024-00540-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 07/23/2024] [Indexed: 09/20/2024] Open
Abstract
Christensenella minuta DSM 22607 has recently been suggested as a potential microbiome-based therapy for inflammatory bowel disease (IBD) because it displays strong anti-inflammatory effects both in vitro and in vivo. Here, we aimed to decipher the mechanism(s) underlying the DSM 22607-mediated beneficial effects on the host in a mouse model of chemically induced acute colitis. We observed that C. minuta plays a key role in the preservation of the epithelial barrier and the management of DNBS-induced inflammation by inhibiting interleukin (IL)-33 and Tumor necrosis factor receptor superfamily member 8 (Tnfrsf8) gene expression. We also showed that DSM 22607 abundance was positively correlated with Akkermansia sp. and Dubosiella sp. and modulated microbial metabolites in the cecum. These results offer new insights into the biological and molecular mechanisms underlying the beneficial effects of C. minuta DSM 22607 by protecting the intestinal barrier integrity and regulating inflammation.
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Affiliation(s)
- Camille Kropp
- Micalis Institute, AgroParisTech, INRAE, Université Paris-Saclay, 68350, Jouy-en-Josas, France
- YSOPIA Bioscience, 33076, Bordeaux, France
| | - Kevin Tambosco
- Micalis Institute, AgroParisTech, INRAE, Université Paris-Saclay, 68350, Jouy-en-Josas, France
| | - Sead Chadi
- Micalis Institute, AgroParisTech, INRAE, Université Paris-Saclay, 68350, Jouy-en-Josas, France
| | - Philippe Langella
- Micalis Institute, AgroParisTech, INRAE, Université Paris-Saclay, 68350, Jouy-en-Josas, France
| | | | - Rebeca Martin
- Micalis Institute, AgroParisTech, INRAE, Université Paris-Saclay, 68350, Jouy-en-Josas, France.
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Seki M, Satou A, Funato R, Tamaki T, Wada N, Nakada N, Matsumoto H, Nakazato I, Wada E, Sakurai K, Tsuzuki T, Karube K. Standardization of CD30 immunohistochemistry staining among three automated immunostaining platforms. Pathol Int 2024; 74:530-537. [PMID: 39171823 DOI: 10.1111/pin.13472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 07/29/2024] [Accepted: 08/02/2024] [Indexed: 08/23/2024]
Abstract
The identification of CD30 expression by immunohistochemistry is essential for the treatment of lymphomas using an antibody-drug conjugate targeting CD30. However, no standardized protocol for CD30 staining has been available. In this study, we compared three common automated immunostaining platforms {Bond III (B III), Dako Omnis (DO) and Ventana BenchMark ULTRA (VBMU)}. A primary antibody for CD30, the Ber-H2 clone, was diluted 50- to 400-fold for B III and DO, and ready-to-use antibody was used for VBMU. An enhancement step using a linker was introduced in all protocols. First, several candidate dilutions were selected for each platform by staining six cases. These candidate conditions were then confirmed with 60 cases of various types of peripheral T-cell lymphomas (PTCLs). The concordance rates of CD30 expression among platforms differed depending on cutoff values and antibody dilutions, except for anaplastic large cell lymphoma. The concordance rates among three platforms in the evaluation of "positive" or "negative" were 100% and 97% when the cutoff values were 1% and 10% respectively, if using 400-diluted antibody in B III and 100-diluted antibody in DO. This study demonstrated the feasibility of equalizing CD30 staining of PTCLs among different platforms by adjusting protocols.
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Affiliation(s)
- Masafumi Seki
- Department of Pathology and Laboratory Medicine, Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | - Akira Satou
- Department of Surgical Pathology, Aichi Medical University Hospital, Nagakute, Japan
| | - Renji Funato
- Department of Pathology and Laboratory Medicine, Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | - Tomoko Tamaki
- Department of Diagnostic Pathology, University of the Ryukyus Hospital, Okinawa, Japan
| | - Naoki Wada
- Department of Diagnostic Pathology, University of the Ryukyus Hospital, Okinawa, Japan
- Department of Pathology and Oncology, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | | | | | - Iwao Nakazato
- Department of Pathology, Okinawa Prefectural Nanbu Medical Center and Children's Medical Center, Okinawa, Japan
| | - Eriko Wada
- Department of Surgical Pathology, Aichi Medical University Hospital, Nagakute, Japan
| | - Kaneko Sakurai
- Department of Surgical Pathology, Aichi Medical University Hospital, Nagakute, Japan
| | - Toyonori Tsuzuki
- Department of Surgical Pathology, Aichi Medical University Hospital, Nagakute, Japan
| | - Kennosuke Karube
- Department of Pathology and Laboratory Medicine, Graduate School of Medicine, Nagoya University, Nagoya, Japan
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Machikhin A, Guryleva A, Chakraborty A, Khokhlov D, Selyukov A, Shuman L, Bukova V, Efremova E, Rudenko E, Burlakov A. Microscopic photoplethysmography-based evaluation of cardiotoxicity in whitefish larvae induced by acute exposure to cadmium and phenol. JOURNAL OF BIOPHOTONICS 2024:e202400111. [PMID: 39031962 DOI: 10.1002/jbio.202400111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 06/07/2024] [Accepted: 06/24/2024] [Indexed: 07/22/2024]
Abstract
Toxic environmental pollutants pose a health risk for both humans and animals. Accumulation of industrial contaminants in freshwater fish may become a significant threat to biodiversity. Comprehensive monitoring of the impact of environmental stressors on fish functional systems is important and use of non-invasive tools that can detect the presence of these toxicants in vivo is desirable. The blood circulatory system, by virtue of its sensitivity to the external stimuli, could be an informative indicator of chemical exposure. In this study, microscopic photoplethysmography-based approach was used to investigate the cardiac activity in broad whitefish larvae (Coregonus nasus) under acute exposure to cadmium and phenol. We identified contamination-induced abnormalities in the rhythms of the ventricle and atrium. Our results allow introducing additional endpoints to evaluate the cardiac dysfunction in fish larvae and contribute to the non-invasive evaluation of the toxic effects of industrial pollutants on bioaccumulation and aquatic life.
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Affiliation(s)
- Alexander Machikhin
- Scientific and Technological Center of Unique Instrumentation of Russian Academy of Sciences, Moscow, Russia
| | - Anastasia Guryleva
- Scientific and Technological Center of Unique Instrumentation of Russian Academy of Sciences, Moscow, Russia
| | - Anirban Chakraborty
- Department of Molecular Genetics & Cancer, Nitte University Centre for Science Education & Research, Nitte (Deemed to be University), Mangalore, India
| | - Demid Khokhlov
- Scientific and Technological Center of Unique Instrumentation of Russian Academy of Sciences, Moscow, Russia
| | | | - Leonid Shuman
- Tyumen State University, Laboratory AquaBioSafe, Tyumen, Russia
| | - Valeriya Bukova
- Scientific and Technological Center of Unique Instrumentation of Russian Academy of Sciences, Moscow, Russia
| | | | | | - Alexander Burlakov
- Scientific and Technological Center of Unique Instrumentation of Russian Academy of Sciences, Moscow, Russia
- Department of Ichthyology, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
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Jakowczuk T, Ren S. A comparative study of INSM1 (clone MRQ70) immunoreactivity on CytoLyt® pretreated cytology and resection specimens of pancreatic neuroendocrine tumors. Diagn Cytopathol 2024; 52:381-386. [PMID: 38655814 DOI: 10.1002/dc.25328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 04/08/2024] [Accepted: 04/12/2024] [Indexed: 04/26/2024]
Abstract
INTRODUCTION Insulinoma-associated protein 1 (INSM1) is a newly characterized sensitive and specific immunohistochemical marker for neuroendocrine (NE) tumors. Whereas more traditional NE markers, such as chromogranin A and synaptophysin, are cytoplasmic, INSM1 is uniquely nuclear and thus could serve as a useful addition to NE tumor workup. While application of immunohistochemical studies to cytology specimens is becoming increasingly relevant, knowledge of the effects of the certain fixatives as well as the pattern and intensity of immunoexpression are important considerations. METHODS Sixteen cases of pancreatic neuroendocrine tumor (PanNET) diagnosed between 2015 and 2021 underwent both fine-needle aspiration, which was subsequently prepared in CytoLyt®-fixed cytology cell block (CCB), and surgical resection, in which specimens were prepared into formalin-fixed paraffin embedded blocks (FFPE). For all samples, INSM1 immunoreactivity was classified according to staining intensity and extent, then compared between CCBs and matched FFPEs. RESULTS All 16 FFPE specimens demonstrated strong and diffuse INSM1 immunoreactivity, while only 10/16 (62.5%) CCBs were positive. Of those 10, only 2/10 (20%) demonstrated strong and diffuse reactivity. CONCLUSION The choice of fixative has a demonstrable effect on the immunoreactivity of INSM1 in PanNET. Even though the sensitivity is lower in CytoLyt®-fixed cell block specimens, the addition of INSM1 is useful, especially in challenging cases that may be negative for one or more of the traditional NE markers.
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Affiliation(s)
- Tiffany Jakowczuk
- Cooper Medical School of Rowan University, Camden, New Jersey, United States of America
| | - Shuyue Ren
- Department of Pathology and Laboratory Medicine, Cooper University Hospital, Camden, New Jersey, United States of America
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Wang T, Liu Y, Guo Y, Zhang C, Cai J. Retrospective evaluation of neonates with fatal congenital lung malformation: A single center 15-year forensic autopsy experience. Forensic Sci Med Pathol 2024:10.1007/s12024-024-00853-0. [PMID: 38902545 DOI: 10.1007/s12024-024-00853-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/14/2024] [Indexed: 06/22/2024]
Abstract
Congenital lung malformation (CLM) is a leading cause of infant mortality. Clinical methods for diagnosing CLM mainly rely on computed tomography, magnetic resonance imaging, ultrasonography, and Doppler. However, forensic identification of the cause of death in neonates is challenging. Unequivocal classification criteria for CLM are missing as its forensic identification is ambiguous. Therefore, we aimed to analyze neonatal death cases at our center to assist in identifying those with congenital lung malformation. This retrospective study identified and classified the causes of deaths of neonates autopsied between January 2008 and April 2023. All cases born alive and died within 28 days with a clear time of death were selected, and forensic experts reviewed their records. The manner, cause of death, and other characteristics were noted and discussed. This retrospective study reveals a steady increase in autopsy cases from 2008 to 2015, attributed to improved parental consent, heightened awareness of autopsy importance, and enhanced medical resources. However, a subsequent decline post-2015 is observed, potentially influenced by advancements in medical technology and prenatal examination protocols. The top causes of neonatal mortality include respiratory diseases, asphyxia, congenital dysplasia, and fetal distress. Congenital lung malformations, particularly bronchopulmonary malformations, constitute a significant portion of congenital anomalies. This study underscores the importance of standardized autopsies and histopathological examinations in diagnosing and understanding CLM. Future research should focus on expanding case collections and elucidating the genetic basis of CLM to improve forensic management and outcomes.
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Affiliation(s)
- Tingting Wang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Tongxinpo Road, Yuelu District Changsha City, Hunan Province, China
| | - Yishu Liu
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Tongxinpo Road, Yuelu District Changsha City, Hunan Province, China
| | - Yadong Guo
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Tongxinpo Road, Yuelu District Changsha City, Hunan Province, China
| | - Changquan Zhang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Tongxinpo Road, Yuelu District Changsha City, Hunan Province, China.
| | - Jifeng Cai
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Tongxinpo Road, Yuelu District Changsha City, Hunan Province, China.
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8
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Tian P, Yang Z, Qu C, Qi X, Zhu L, Hao G, Zhang Y. Exploration of tissue fixation methods suitable for digital pathological studies of the testis. Eur J Med Res 2024; 29:319. [PMID: 38858777 PMCID: PMC11163764 DOI: 10.1186/s40001-024-01921-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 06/05/2024] [Indexed: 06/12/2024] Open
Abstract
BACKGROUND The way of testicular tissue fixation directly affects the correlation and structural integrity between connective tissue and seminiferous tubules, which is essential for the study of male reproductive development. This study aimed to find the optimal fixative and fixation time to produce high-quality testicular histopathological sections, and provided a suitable foundation for in-depth study of male reproductive development with digital pathology technology. METHODS Testes were removed from both sides of 25 male C57BL/6 mice. Samples were fixed in three different fixatives, 10% neutral buffered formalin (10% NBF), modified Davidson's fluid (mDF), and Bouin's Fluid (BF), for 8, 12, and 24 h, respectively. Hematoxylin and eosin (H&E) staining, periodic acid Schiff-hematoxylin (PAS-h) staining, and immunohistochemistry (IHC) were used to evaluate the testicle morphology, staging of mouse seminiferous tubules, and protein preservation. Aperio ScanScope CS2 panoramic scanning was used to perform quantitative analyses. RESULTS H&E staining showed 10% NBF resulted in an approximately 15-17% reduction in the thickness of seminiferous epithelium. BF and mDF provided excellent results when staining acrosomes with PAS-h. IHC staining of synaptonemal complexes 3 (Sycp3) was superior in mDF compared to BF-fixed samples. Fixation in mDF and BF improved testis tissue morphology compared to 10% NBF. CONCLUSIONS Quantitative analysis showed that BF exhibited a very low IHC staining efficiency and revealed that mouse testes fixed for 12 h with mDF, exhibited morphological details, excellent efficiency of PAS-h staining for seminiferous tubule staging, and IHC results. In addition, the morphological damage of testis was prolonged with the duration of fixation time.
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Affiliation(s)
- Pengxiang Tian
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China
| | - Zhan Yang
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China
| | - Changbao Qu
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China
| | - Xin Qi
- Department of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Hebei Medical University, Shijiazhuang, 050017, China
| | - Linlin Zhu
- Department of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Hebei Medical University, Shijiazhuang, 050017, China
| | - Guimin Hao
- Department of Reproductive Medicine, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China.
| | - Yong Zhang
- Department of Urology, The Second Hospital of Hebei Medical University, 215 Heping W Rd, Shijiazhuang, 050000, China.
- Department of Urology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
- Department of Urology, National Cancer Center/National Clinical Research Center for Cancer/Hebei Cancer Hospital, Chinese Academy of Medical Sciences, Langfang, 065001, Hebei, China.
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Diamantino GML, Beeler-Marfisi J, Foster RA, Sears W, Defarges A, Vernau W, Bienzle D. Effects of fixation and demineralization on histomorphology and DNA amplification of canine bone marrow. Vet Pathol 2024:3009858241257920. [PMID: 38842072 DOI: 10.1177/03009858241257920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
Fixation and demineralization protocols for bone marrow (BM) across diagnostic laboratories are not standardized. How different protocols affect histomorphology and DNA amplification is incompletely understood. In this study, 2 fixatives and 3 demineralization methods were tested on canine BM samples. Twenty replicate sternal samples obtained within 24 hours of death were fixed overnight in either acetic acid-zinc-formalin (AZF) or 10% neutral-buffered formalin (NBF) and demineralized with formic acid for 12 hours. Another 53 samples were fixed in AZF and demineralized with hydrochloric acid for 1-hour, formic acid for 12 hours, or ethylenediamine tetraacetic acid (EDTA) for 24 hours. Histologic sections were scored by 4 raters as of insufficient, marginal, good, or excellent quality. In addition, DNA samples extracted from sections treated with the different fixation and demineralization methods were amplified with 3 sets of primers to conserved regions of T cell receptor gamma and immunoglobulin heavy chain genes. Amplification efficiency was graded based on review of capillary electrophoretograms. There was no significant difference in the histomorphology scores of sections fixed in AZF or NBF. However, EDTA-based demineralization yielded higher histomorphology scores than demineralization with hydrochloric or formic acid, whereas formic acid resulted in higher scores than hydrochloric acid. Demineralization with EDTA yielded DNA amplification in 29 of 36 (81%) samples, whereas demineralization with either acid yielded amplification in only 2 of 72 (3%) samples. Although slightly more time-consuming and labor-intensive, tissue demineralization with EDTA results in superior morphology and is critical for polymerase chain reaction (PCR) amplification with the DNA extraction method described in this article.
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Ewalt MD, Hsiao SJ. Molecular Methods: Clinical Utilization and Designing a Test Menu. Clin Lab Med 2024; 44:123-135. [PMID: 38821636 DOI: 10.1016/j.cll.2023.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2024]
Abstract
Pre-analytical factors in molecular oncology diagnostics are reviewed. Issues around sample collection, storage, and transport that might affect the stability of nucleic acids and the ability to perform molecular testing are addressed. In addition, molecular methods used commonly in clinical diagnostic laboratories, including newer technologies such as next-generation sequencing and digital droplet polymerase chain reaction, as well as their applications, are reviewed. Finally, we discuss considerations in designing a molecular test menu to deliver accurate and timely results in an efficient and cost-effective manner.
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Affiliation(s)
- Mark D Ewalt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, S-801C, New York, NY 10065, USA
| | - Susan J Hsiao
- Department of Pathology & Cell Biology, Columbia University Medical Center, 630 West 168th Street, P&S16-408CB, New York, NY 10032, USA.
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Kandelouei T, Zhang W, Houghton M, Knudsen B, Edgar BA. Improved Preservation of Mouse Intestinal Tissue Using a Formalin/Acetic Acid Fixative and Quantitative Histological Analysis Using QuPath. Curr Protoc 2024; 4:e1062. [PMID: 38775005 PMCID: PMC11151780 DOI: 10.1002/cpz1.1062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
The architecture and morphology of the intestinal tissue from mice or other small animals are difficult to preserve for histological and molecular analysis due to the fragile nature of this tissue. The intestinal mucosa consists of villi and crypts lined with epithelial cells. In between the epithelial folds extends the lamina propria, a loose connective tissue that contains blood and lymph vessels, fibroblasts, and immune cells. Underneath the mucosa are two layers of contractile smooth muscle and nerves. The tissue experiences significant changes during fixation, which can impair the reliability of histologic analysis. Poor-quality histologic sections are not suitable for quantitative image-based tissue analysis. This article offers a new fixative composed of neutral buffered formalin (NBF) and acetic acid, called FA. This fixative significantly improved the histology of mouse intestinal tissue compared to traditional NBF and enabled precise, reproducible histologic molecular analyses using QuPath software. Algorithmic training of QuPath allows for automated segmentation of intestinal compartments, which can be further interrogated for cellular composition and disease-related changes. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol: Improved preservation of mouse intestinal tissue using a formalin/acetic acid fixative Support Protocol: Quantitative tissue analysis using QuPath.
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Affiliation(s)
- Tahmineh Kandelouei
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, U.S.A
| | - Wei Zhang
- Department of Pathology, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, U.S.A
| | - Madeline Houghton
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, U.S.A
| | - Beatrice Knudsen
- Department of Pathology, Huntsman Cancer Institute, Institute of Scientific Computing and Imaging, University of Utah, Salt Lake City, UT, U.S.A
| | - Bruce A. Edgar
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, U.S.A
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12
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Mello MG, Westerhausen MT, Lockwood TE, Singh P, Wanagat J, Bishop DP. Immunolabelling perturbs the endogenous and antibody-conjugated elemental concentrations during immuno-mass spectrometry imaging. Anal Bioanal Chem 2024; 416:2725-2735. [PMID: 37801117 PMCID: PMC10997740 DOI: 10.1007/s00216-023-04967-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/28/2023] [Accepted: 09/19/2023] [Indexed: 10/07/2023]
Abstract
Immuno-mass spectrometry imaging uses lanthanide-conjugated antibodies to spatially quantify biomolecules via laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS). The multi-element capabilities allow for highly multiplexed analyses that may include both conjugated antibodies and endogenous metals to reveal relationships between disease and chemical composition. Sample handling is known to perturb the composition of the endogenous elements, but there has been little investigation into the effects of immunolabelling and coverslipping. Here, we used cryofixed muscle sections to examine the impact of immunolabelling steps on the concentrations of a Gd-conjugated anti-dystrophin primary antibody, and the endogenous metals Cu and Zn. Primary antibody incubation resulted in a decrease in Zn, and an increase in Cu. Zn was removed from the cytoplasm where it was hypothesised to be more labile, whereas concentrated locations of Zn remained in the cell membrane in all samples that underwent the immunostaining process. Cu increased in concentration and was found mostly in the cell membrane. The concentration of the Gd-conjugated antibody when compared to the standard air-dried sample was not significantly different when coverslipped using an organic mounting medium, whereas use of an aqueous mounting medium significantly reduced the concentration of Gd. These results build on the knowledge of how certain sample handling techniques change elemental concentrations and distributions in tissue sections. Immunolabelling steps impact the concentration of endogenous elements, and separate histological sections are required for the quantitative analysis of endogenous elements and biomolecules. Additionally, coverslipping tissue sections for complementary immunohistochemical/immunofluorescent imaging may compromise the integrity of the elemental label, and organic mounting media are recommended over aqueous mounting media.
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Affiliation(s)
- Monique G Mello
- Hyphenated Mass Spectrometry Laboratory, Faculty of Science, University of Technology Sydney, P.O. Box 123, Broadway, NSW, 2007, Australia
| | - Mika T Westerhausen
- Hyphenated Mass Spectrometry Laboratory, Faculty of Science, University of Technology Sydney, P.O. Box 123, Broadway, NSW, 2007, Australia
| | - Thomas E Lockwood
- Hyphenated Mass Spectrometry Laboratory, Faculty of Science, University of Technology Sydney, P.O. Box 123, Broadway, NSW, 2007, Australia
| | - Prashina Singh
- Hyphenated Mass Spectrometry Laboratory, Faculty of Science, University of Technology Sydney, P.O. Box 123, Broadway, NSW, 2007, Australia
| | - Jonathan Wanagat
- Division of Geriatrics, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA.
| | - David P Bishop
- Hyphenated Mass Spectrometry Laboratory, Faculty of Science, University of Technology Sydney, P.O. Box 123, Broadway, NSW, 2007, Australia.
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13
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George GV, Liu H, Jajosky AN, Oltvai ZN. Resolving Discrepancies in Idylla BRAF Mutational Assay Results Using Targeted Next-Generation Sequencing. Genes (Basel) 2024; 15:527. [PMID: 38790156 PMCID: PMC11121162 DOI: 10.3390/genes15050527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/15/2024] [Accepted: 04/20/2024] [Indexed: 05/26/2024] Open
Abstract
BRAF mutation identification is important for the diagnosis and treatment of several tumor types, both solid and hematologic. Rapid identification of BRAF mutations is required to determine eligibility for targeted BRAF inhibitor therapy. The Idylla BRAF mutation assay is a rapid, multiplex allele-specific PCR test designed to detect the most common oncogenic BRAF V600 mutations in formalin-fixed paraffin-embedded (FFPE) tissue samples. Here, we describe the validation of the Idylla BRAF mutation assay in our laboratory. During routine clinical practice, we noticed cases in which BRAF V600 mutations were identified with unusual amplification curves, with three cases displaying a delayed amplification within a double amplification pattern and two false-positive calls. We therefore initiated a quality improvement effort to systematically and retrospectively evaluate next-generation sequencing (NGS)-tested cases with BRAF mutations identified within five amino acids of BRAF codon V600 and did not identify additional false-positive cases. We hypothesize that late amplification in a double amplification pattern may represent non-specific amplification, whereas cases displaying single delayed amplification curves may stem from the presence of either non-V600 variants, very low-level V600 variants, cytosine deamination artifacts, and/or non-specific amplification by an allele-specific PCR primer. Regardless, we recommend that Idylla BRAF cases with non-classical amplification curves undergo reflex NGS testing. These findings are likely relevant for other Idylla assays interrogating hotspot mutations in genes such as EGFR, IDH1/2, KRAS, and NRAS.
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Affiliation(s)
| | | | | | - Zoltán N. Oltvai
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY 14642, USA
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14
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Sabarinath B, Suresh S, Protyusha GB, Dhanarathna S. Standardization of honey as a tissue fixative for histopathology: A morphometric study. Dent Res J (Isfahan) 2024; 21:24. [PMID: 38807662 PMCID: PMC11132230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 11/10/2023] [Accepted: 12/27/2023] [Indexed: 05/30/2024] Open
Abstract
Background Tissue fixation is a crucial step to preserve the tissues in a life-like state with minimal disruption to its cellular and chemical composition for histopathological examination. The search for an effective alternate tissue fixative to the routinely used formaldehyde has gained interest as constant exposure to formaldehyde has proven to be toxic. Honey, an organic substance with high acidity and hygroscopic nature, exhibits tissue fixative properties and has been used in the present study. The present study aimed to standardize honey as a tissue fixative for histopathology by comparing it with formalin. Materials and Methods In vitro study Oral tissue samples of goat were fixed in 10% honey and 10% formalin solution, respectively, for 24-48 h, followed by routine tissue processing and microscopic examination of 37 slides per group. 2200 epithelial cells (1100 per group) were selected for the computer-aided morphometric image analysis (Fiji-Image J) by three observers. Cell area (CA), cell perimeter (CP), nuclear area (NA), nuclear perimeter (NP), cytoplasmic area (Cyt A), and nuclear-cytoplasmic ratio were the parameters studied. Mann-Whitney U-test (STATA/IC version 16) for inter-group comparison was done and P < 0.05 was considered statistically significant. Results The probability of epithelial cells in the honey-fixed group to have greater NA, NP, and N/C ratio was about 50%-60%. The probability of epithelial cells in formalin-fixed tissues to have greater CA, CP, and Cyt A was about 70%. Conclusion Honey is a better nuclear fixative than formalin. Cytoplasmic shrinkage of epithelial cells should be taken into consideration while fixing tissues with honey.
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Affiliation(s)
- B. Sabarinath
- Department of Oral Pathology and Microbiology, Meenakshi Ammal Dental College and Hospital, Chennai, Tamil Nadu, India
| | - Shruthi Suresh
- Oral and Maxillofacial Pathologist, Chennai, Tamil Nadu, India
| | - G. B. Protyusha
- Department of Oral Pathology and Microbiology, Meenakshi Ammal Dental College and Hospital, Chennai, Tamil Nadu, India
| | - S. Dhanarathna
- Oral and Maxillofacial Pathologist, Chennai, Tamil Nadu, India
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15
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Li Y, Pillar N, Li J, Liu T, Wu D, Sun S, Ma G, de Haan K, Huang L, Zhang Y, Hamidi S, Urisman A, Keidar Haran T, Wallace WD, Zuckerman JE, Ozcan A. Virtual histological staining of unlabeled autopsy tissue. Nat Commun 2024; 15:1684. [PMID: 38396004 PMCID: PMC10891155 DOI: 10.1038/s41467-024-46077-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
Traditional histochemical staining of post-mortem samples often confronts inferior staining quality due to autolysis caused by delayed fixation of cadaver tissue, and such chemical staining procedures covering large tissue areas demand substantial labor, cost and time. Here, we demonstrate virtual staining of autopsy tissue using a trained neural network to rapidly transform autofluorescence images of label-free autopsy tissue sections into brightfield equivalent images, matching hematoxylin and eosin (H&E) stained versions of the same samples. The trained model can effectively accentuate nuclear, cytoplasmic and extracellular features in new autopsy tissue samples that experienced severe autolysis, such as COVID-19 samples never seen before, where the traditional histochemical staining fails to provide consistent staining quality. This virtual autopsy staining technique provides a rapid and resource-efficient solution to generate artifact-free H&E stains despite severe autolysis and cell death, also reducing labor, cost and infrastructure requirements associated with the standard histochemical staining.
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Affiliation(s)
- Yuzhu Li
- Electrical and Computer Engineering Department, University of California, Los Angeles, CA, 90095, USA
- Bioengineering Department, University of California, Los Angeles, CA, 90095, USA
- California NanoSystems Institute (CNSI), University of California, Los Angeles, CA, 90095, USA
| | - Nir Pillar
- Electrical and Computer Engineering Department, University of California, Los Angeles, CA, 90095, USA
- Bioengineering Department, University of California, Los Angeles, CA, 90095, USA
- California NanoSystems Institute (CNSI), University of California, Los Angeles, CA, 90095, USA
| | - Jingxi Li
- Electrical and Computer Engineering Department, University of California, Los Angeles, CA, 90095, USA
- Bioengineering Department, University of California, Los Angeles, CA, 90095, USA
- California NanoSystems Institute (CNSI), University of California, Los Angeles, CA, 90095, USA
| | - Tairan Liu
- Electrical and Computer Engineering Department, University of California, Los Angeles, CA, 90095, USA
- Bioengineering Department, University of California, Los Angeles, CA, 90095, USA
- California NanoSystems Institute (CNSI), University of California, Los Angeles, CA, 90095, USA
| | - Di Wu
- Computer Science Department, University of California, Los Angeles, CA, 90095, USA
| | - Songyu Sun
- Computer Science Department, University of California, Los Angeles, CA, 90095, USA
| | - Guangdong Ma
- Electrical and Computer Engineering Department, University of California, Los Angeles, CA, 90095, USA
- School of Physics, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China
| | - Kevin de Haan
- Electrical and Computer Engineering Department, University of California, Los Angeles, CA, 90095, USA
- Bioengineering Department, University of California, Los Angeles, CA, 90095, USA
- California NanoSystems Institute (CNSI), University of California, Los Angeles, CA, 90095, USA
| | - Luzhe Huang
- Electrical and Computer Engineering Department, University of California, Los Angeles, CA, 90095, USA
- Bioengineering Department, University of California, Los Angeles, CA, 90095, USA
- California NanoSystems Institute (CNSI), University of California, Los Angeles, CA, 90095, USA
| | - Yijie Zhang
- Electrical and Computer Engineering Department, University of California, Los Angeles, CA, 90095, USA
- Bioengineering Department, University of California, Los Angeles, CA, 90095, USA
- California NanoSystems Institute (CNSI), University of California, Los Angeles, CA, 90095, USA
| | - Sepehr Hamidi
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Anatoly Urisman
- Department of Pathology, University of California, San Francisco, CA, 94143, USA
| | - Tal Keidar Haran
- Department of Pathology, Hadassah Hebrew University Medical Center, Jerusalem, 91120, Israel
| | - William Dean Wallace
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Jonathan E Zuckerman
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Aydogan Ozcan
- Electrical and Computer Engineering Department, University of California, Los Angeles, CA, 90095, USA.
- Bioengineering Department, University of California, Los Angeles, CA, 90095, USA.
- California NanoSystems Institute (CNSI), University of California, Los Angeles, CA, 90095, USA.
- Department of Surgery, University of California, Los Angeles, CA, 90095, USA.
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16
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Monteiro TM, Cortes-Cid VO, Marceliano-Alves MFV, Campello AF, Bastos LF, Lopes RT, Siqueira JF, Alves FRF. Intracanal removal and apical extrusion of filling material after retreatment using rotary or reciprocating instruments: A new approach using human cadavers. Int Endod J 2024; 57:100-107. [PMID: 37886883 DOI: 10.1111/iej.13990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 10/10/2023] [Accepted: 10/12/2023] [Indexed: 10/28/2023]
Abstract
AIM This study compared intracanal removal of filling as well as the frequency and volume of extruded material after retreatment with either HyFlex or Reciproc instruments in mandibular teeth from cadavers. METHODOLOGY The root canals of 14 pairs of contralateral single-rooted teeth in mandibles of cadavers were instrumented with Reciproc R40 and filled using lateral compaction. The mandibles were scanned in a micro-computed tomographic (micro-CT) device before and after retreatment procedures. The contralateral teeth were assigned to two groups (n = 14) according to the retreatment protocol using either HyFlex or Reciproc instrument systems. In the HyFlex group, the HyFlex Remover instrument was worked 3 mm short of the working length (WL), followed by HyFlex CM 40.04 and 50.04 at the WL. In the Reciproc group, the R50 instrument was worked up at the coronal two thirds, followed by two more cycles until the WL was reached. Pre- and post-operative micro-CT images were analysed for extrusion and intracanal removal of filling material. RESULTS After retreatment, extrusion of filling material occurred in 11 (78%) and 14 (100%) teeth from HyFlex and Reciproc groups respectively (p > .05). A similar volume of extruded material was observed after retreatment with both systems (p > .05). A significant decrease in the intracanal filling volume was verified after retreatment with both tested systems (p < .05). However, residual filling material was found in all root canals, regardless of the system. The amount of filling material removed (HyFlex = 80.8%; Reciproc = 65.9%) and the operation time was similar between systems (p > .05). CONCLUSIONS A high frequency of filling material extrusion was observed after retreatment with the two systems in a cadaver model, with no significant difference between them. Both protocols obtained similar efficacy in filling material removal procedures, although none completely cleaned the canals.
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Affiliation(s)
- Thamyres M Monteiro
- Postgraduate Program in Dentistry, University of Grande Rio (UNIGRANRIO), Duque de Caxias, Brazil
| | - Victor O Cortes-Cid
- Postgraduate Program in Dentistry, University of Grande Rio (UNIGRANRIO), Duque de Caxias, Brazil
| | | | - Andrea F Campello
- Postgraduate Program in Dentistry, University of Grande Rio (UNIGRANRIO), Duque de Caxias, Brazil
- Department of Endodontics, Faculty of Dentistry, Iguaçu University (UNIG), Nova Iguaçu, Brazil
| | - Luan F Bastos
- Department of Nuclear Energy, Rio de Janeiro Federal University, Rio de Janeiro, Brazil
| | - Ricardo T Lopes
- Department of Nuclear Energy, Rio de Janeiro Federal University, Rio de Janeiro, Brazil
| | - José F Siqueira
- Postgraduate Program in Dentistry, University of Grande Rio (UNIGRANRIO), Duque de Caxias, Brazil
- Department of Endodontics, Faculty of Dentistry, Iguaçu University (UNIG), Nova Iguaçu, Brazil
| | - Flávio R F Alves
- Postgraduate Program in Dentistry, University of Grande Rio (UNIGRANRIO), Duque de Caxias, Brazil
- Department of Endodontics, Faculty of Dentistry, Iguaçu University (UNIG), Nova Iguaçu, Brazil
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17
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Stewart S, Stankunas K. Section Immunostaining for Protein Expression and Cell Proliferation Studies of Regenerating Fins. Methods Mol Biol 2024; 2707:235-254. [PMID: 37668917 DOI: 10.1007/978-1-0716-3401-1_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
Adult zebrafish fins fully regenerate after resection, providing a highly accessible and remarkable vertebrate model of organ regeneration. Fin injury triggers wound epidermis formation and the dedifferentiation of injury-adjacent mature cells to establish an organized blastema of progenitor cells. Balanced cell proliferation and redifferentiation along with cell movements then progressively reestablish patterned tissues and restore the fin to its original size and shape. A mechanistic understanding of these coordinated cell behaviors and transitions requires direct knowledge of proteins in their physiological context, including expression, subcellular localization, and activity. Antibody-based staining of sectioned fins facilitates such high-resolution analyses of specific, native proteins. Therefore, such methods are mainstays of comprehensive, hypothesis-driven fin regeneration studies. However, section immunostaining requires labor-intensive, empirical optimization. Here, we present detailed, multistep procedures for antibody staining and co-detecting proliferating cells using paraffin and frozen fin sections. We include suggestions to avoid common pitfalls and to streamline the development of optimized, validated protocols for new and challenging antibodies.
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Affiliation(s)
- Scott Stewart
- Institute of Molecular Biology, University of Oregon, Eugene, OR, USA.
| | - Kryn Stankunas
- Institute of Molecular Biology, University of Oregon, Eugene, OR, USA.
- Department of Biology, University of Oregon, Eugene, OR, USA.
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18
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Uzoma IC, Taiwo IA, Ugwu NI, Durosinmi MA, Akinloye O. Quality and Quantity of Nucleic Acids Extracted from Formalin-Fixed Paraffin-Embedded Lymphoma Biopsies from Nigerian Archived Biopsy. Niger J Clin Pract 2023; 26:1854-1860. [PMID: 38158353 DOI: 10.4103/njcp.njcp_389_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 08/17/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND Integrity of nucleic acids derived from archived formalin-fixed paraffin-embedded (FFPE) cancer specimens affects diagnosis, prognosis, and therapy. Several factors affect the quality and quantity of extracted nucleic acids and one of such factors is storage period. AIM We investigated the impact of storage duration on the quality and quantity of nucleic acids extracted from archived FFPE lymphoma biopsies in Nigeria. MATERIALS AND METHODS A total of 53 FFPE biopsies diagnosed as lymphoma stored over several years (2008-2019) were analyzed. They were 22 chronic lymphocytic leukemia (CLL) cases, 17 Hodgkin lymphoma (HL) cases, and 14 diffuse large B-cell lymphoma, not otherwise specified (DLBCL, NOS). DNA was extracted from all the lymphoma samples which were analyzed for integrity and amplifiability using the four pairs of control genes polymerase chain reaction (PCR) primers of BIOMED-2 protocol, whereas RNA extraction was from 6 CLL cases used for qPCR analysis of RNU43. RESULTS For CLL, the mean DNA yield was 193.6 ng/µl (range: 3.0-533.0 ng/µl), whereas the mean A260/A280 ratio was 1.7 (1.2-1.9). For DLBCL, NOS, and HL, 255.5 ng/µl (range: 32.9-605.4 ng/µl), 1.8 (1.5-2.0) and 242.7 ng/µl (range: 1.3-886.0 ng/µl), and 1.7 (0.9-1.8), respectively. The extracted DNA gave amplifiable products of at least 200bp, whereas the RNA analysis showed CT values of <38 in all the samples. The mean RNA yield was 462.2 ng/µl (range: 74.7-1082.1), whereas the mean A260/A280 was 1.7 (1.5-1.8). CONCLUSION Quantity and quality of nucleic acids from FFPE tissues stored for different time periods showed no significant difference in yield and quality.
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Affiliation(s)
- I C Uzoma
- Department of Medical Laboratory Science, Faculty of Health Sciences and Technology, Molecular Hematology and Immunogenetics Laboratory, College of Medicine, University of Nigeria, Enugu Campus, Nsukka, Nigeria
| | - I A Taiwo
- Department of Cell Biology and Genetics, Faculty of Science, Genetics Laboratory, University of Lagos, Lagos, Nigeria
| | - N I Ugwu
- Department of Hematology and Immunology, Faculty of Clinical Medicine, College of Health Sciences, Ebonyi State University, Abakaliki, Nigeria
| | - M A Durosinmi
- Department of Hematology and Blood Transfusion, Obafemi Awolowo University Teaching Hospitals Complex, Ile-Ife, Nigeria
| | - O Akinloye
- Department of Medical Laboratory Science, Faculty of Basic Medical Sciences, Clinical Chemistry and Molecular Diagnostics Laboratory, College of Medicine, University of Lagos, Lagos, Nigeria
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19
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Sura GH, Tran K, Fu C, Du L, Marczyk M, Gould RE, Chen E, Tasto AM, Tinnirello AA, Symmans WF. Pre-analytical effects on whole transcriptome and targeted RNA sequencing analysis in cytology: The effects of prolonged time in storage of effusion specimens prior to preservation. Cytopathology 2023; 34:551-561. [PMID: 37712171 PMCID: PMC10592006 DOI: 10.1111/cyt.13304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/16/2023] [Accepted: 08/23/2023] [Indexed: 09/16/2023]
Abstract
OBJECTIVES To investigate the pre-analytics of the molecular testing of cytology specimens, we studied the effects of time in refrigerator storage (4°C) of malignant effusions on RNA sequencing (RNAseq) results. METHODS Ten effusion specimens were stored in a refrigerator (4°C) for different durations (day 0, 1, 4, and 7). All specimens were prepared as cytospins fixed in either Carnoy's solution or 95% ethanol (EtOH) and in an RNA preservative for a fresh frozen (FF) high-quality reference. Whole transcriptome (wt) and targeted (t)RNAseq of two multigene expression signatures were performed. We then compared transcript expression levels (including mutant allele fraction) according to pre-analytical variables using a concordance correlation coefficient (CCC) and a mixed effect model. RESULTS Sequencing results were mostly stable over increasing time in storage. Cytospins fixed in Carnoy's solution were more concordant with FF samples than cytospins fixed in 95% EtOH at all timepoints. This finding was consistent for both wtRNAseq (averages: day 0 CCC = 0.98 vs 0.91; day 7 CCC = 0.88 vs 0.78) and tRNAseq methods (averages: day 0 CCC = 0.98 vs 0.81; day 7 CCC = 0.98 vs 0.90). Cytospins fixed in Carnoy's solution did not show significant changes in expression over timepoints or between expression signatures, whereas 95% EtOH did. CONCLUSION RNAseq can be accurately performed on effusion specimens after prolonged refrigerator storage. RNA extracted from scraped cytospin slides fixed in Carnoy's solution was marginally superior to 95% EtOH fixation, but either method had comparable analytic performance to high-quality FF RNA samples.
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Affiliation(s)
- Gloria H. Sura
- Department of Pathology and Genomic Medicine, Houston Methodist, Houston, Texas, USA
| | - Kevin Tran
- Department of Pathology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Chunxiao Fu
- Department of Pathology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Lili Du
- Department of Pathology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Michał Marczyk
- Department of Data Science and Engineering, Silesian University of Technology, Gliwice, Poland
- Yale Cancer Center, Yale University, New Haven, Connecticut, USA
| | - Rebekah E. Gould
- Department of Pathology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Eveline Chen
- Department of Pathology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Amy M. Tasto
- Department of Pathology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Agata A. Tinnirello
- Department of Pathology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - W. Fraser Symmans
- Department of Pathology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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20
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Freund P, Skopnik CM, Metzke D, Goerlich N, Klocke J, Grothgar E, Prskalo L, Hiepe F, Enghard P. Addition of formaldehyde releaser imidazolidinyl urea and MOPS buffer to urine samples enables delayed processing for flow cytometric analysis of urinary cells: A simple, two step conservation method of urinary cells for flow cytometry. CYTOMETRY. PART B, CLINICAL CYTOMETRY 2023; 104:417-425. [PMID: 36880455 DOI: 10.1002/cyto.b.22117] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 02/03/2023] [Accepted: 02/13/2023] [Indexed: 03/08/2023]
Abstract
INTRODUCTION Kidney diseases are a major health concern worldwide. Currently there is a large unmet need for novel biomarkers to non-invasively diagnose and monitor kidney diseases. Urinary cells are promising biomarkers and their analysis by flow cytometry has demonstrated its utility in diverse clinical settings. However, up to date this methodology depends on fresh samples, as cellular event counts and the signal-to-noise-ratio deter over time. Here we developed an easy-to-use two-step preservation method for conservation of urine samples for subsequent flow cytometry. METHODS The protocol utilizes a combination of the formaldehyde releasing agent imidazolidinyl urea (IU) and MOPS buffer, leading to gentle fixation of urinary cells. RESULTS The preservation method increases acceptable storing time of urine samples from several hours to up to 6 days. Cellular event counts and staining properties of cells remain comparable to fresh untreated samples. OUTLOOK The hereby presented preservation method facilitates future investigations on flow cytometry of urinary cells as potential biomarkers and may enable broad implementation in clinical practice.
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Affiliation(s)
- Paul Freund
- Department of Nephrology and Medical Intensive Care, Charité - Universital Hospital Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Rheumatism Research Center Berlin (DRFZ), An Institute of the Leibniz Foundation, Berlin, Germany
| | - Christopher M Skopnik
- Department of Nephrology and Medical Intensive Care, Charité - Universital Hospital Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Rheumatism Research Center Berlin (DRFZ), An Institute of the Leibniz Foundation, Berlin, Germany
| | - Diana Metzke
- Department of Nephrology and Medical Intensive Care, Charité - Universital Hospital Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Rheumatism Research Center Berlin (DRFZ), An Institute of the Leibniz Foundation, Berlin, Germany
| | - Nina Goerlich
- Department of Nephrology and Medical Intensive Care, Charité - Universital Hospital Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Rheumatism Research Center Berlin (DRFZ), An Institute of the Leibniz Foundation, Berlin, Germany
| | - Jan Klocke
- Department of Nephrology and Medical Intensive Care, Charité - Universital Hospital Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Rheumatism Research Center Berlin (DRFZ), An Institute of the Leibniz Foundation, Berlin, Germany
| | - Emil Grothgar
- Department of Nephrology and Medical Intensive Care, Charité - Universital Hospital Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Rheumatism Research Center Berlin (DRFZ), An Institute of the Leibniz Foundation, Berlin, Germany
| | - Luka Prskalo
- Department of Nephrology and Medical Intensive Care, Charité - Universital Hospital Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Rheumatism Research Center Berlin (DRFZ), An Institute of the Leibniz Foundation, Berlin, Germany
| | - Falk Hiepe
- German Rheumatism Research Center Berlin (DRFZ), An Institute of the Leibniz Foundation, Berlin, Germany
- Department of Rheumatology and Clinical Immunology, Charite - Universital Hospital Berlin, Berlin, Germany
| | - Philipp Enghard
- Department of Nephrology and Medical Intensive Care, Charité - Universital Hospital Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Rheumatism Research Center Berlin (DRFZ), An Institute of the Leibniz Foundation, Berlin, Germany
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Grignani P, Visonà SD, Fronda MV, Borrelli P, Monti MC, Bertoglio B, Conti A, Fattorini P, Previderè C. The role of single nucleotide polymorphisms related to iron homeostasis in mesothelioma susceptibility after asbestos exposure: a genetic study on autoptic samples. Front Public Health 2023; 11:1236558. [PMID: 37942251 PMCID: PMC10628177 DOI: 10.3389/fpubh.2023.1236558] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 10/06/2023] [Indexed: 11/10/2023] Open
Abstract
Asbestos-related diseases still represent a major public health problem all over the world. Among them, malignant mesothelioma (MM) is a poor-prognosis cancer, arising from the serosal lining of the pleura, pericardium and peritoneum, triggered by asbestos exposure. Literature data suggest the key role of iron metabolism in the coating process leading to the formation of asbestos bodies, considered to be both protective and harmful. Two sample sets of individuals were taken into consideration, both residing in Broni or neighboring cities (Northwestern Italy) where an asbestos cement factory was active between 1932 and 1993. The present study aims to compare the frequency of six SNPs involved in iron trafficking, previously found to be related to protection/predisposition to MM after asbestos exposure, between 48 male subjects with documented asbestos exposure who died of MM and 48 male subjects who were exposed to asbestos but did not develop MM or other neoplastic respiratory diseases (Non-Mesothelioma Asbestos Exposed - NMAE). The same analysis was performed on 76 healthy male controls. The allelic and genotypic frequencies of a sub-group of 107 healthy Italian individuals contained in the 1000 genomes database were considered for comparison. PCR-multiplex amplification followed by SNaPshot mini-sequencing reaction was used. The findings presented in this study show that the allelic and genotypic frequencies for six SNP markers involved in iron metabolism/homeostasis and the modulation of tumor microenvironment are not significantly different between the two sample sets of MM and NMAE. Therefore, the SNPs here considered do not seem to be useful markers for individual susceptibility to mesothelioma. This finding is not in agreement with previous literature.
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Affiliation(s)
- Pierangela Grignani
- Department of Public Health, Experimental and Forensic Medicine, University of Pavia, Pavia, Italy
| | - Silvia Damiana Visonà
- Department of Public Health, Experimental and Forensic Medicine, University of Pavia, Pavia, Italy
| | - Maria Vittoria Fronda
- Department of Public Health, Experimental and Forensic Medicine, University of Pavia, Pavia, Italy
| | - Paola Borrelli
- Department of Public Health, Experimental and Forensic Medicine, University of Pavia, Pavia, Italy
- Laboratory of Biostatistics, Department of Medical, Oral and Biotechnological Sciences, G. d’Annunzio, University of Chieti, Chieti, Italy
| | - Maria Cristina Monti
- Department of Public Health, Experimental and Forensic Medicine, University of Pavia, Pavia, Italy
| | - Barbara Bertoglio
- Department of Public Health, Experimental and Forensic Medicine, University of Pavia, Pavia, Italy
| | - Adelaide Conti
- Department of Medical and Surgical Specialities, Radiological Sciences and Public Health, Forensic Medicine Unit, ASST Spedali Civili of Brescia, Brescia, Italy
| | - Paolo Fattorini
- Department of Medicine, Surgery and Health, University of Trieste, Ospedale di Cattinara, Trieste, Italy
| | - Carlo Previderè
- Department of Public Health, Experimental and Forensic Medicine, University of Pavia, Pavia, Italy
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22
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Patel D, Nguyen A, Fleeting C, Patel AB, Mumtaz M, Lucke-Wold B. Precision medicine in neurosurgery: The evolving role of theranostics. INNOSC THERANOSTICS & PHARMACOLOGICAL SCIENCES 2023; 6:417. [PMID: 37601162 PMCID: PMC10439809 DOI: 10.36922/itps.417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/22/2023]
Abstract
Theranostics in neurosurgery is a rapidly advancing field of precision medicine that combines diagnostic and therapeutic modalities to optimize patient outcomes. This approach has the potential to provide real-time feedback during therapy and diagnose a condition while simultaneously providing treatment. One such form of theranostics is focused ultrasound, which has been found to be effective in inducing neuroablation and neuromodulation and improving the efficacy of chemotherapy drugs by disrupting the blood-brain barrier. Targeted radionuclide therapy, which pairs positron emission tomography tracers with therapeutic effects and imaging modalities, is another promising form of theranostics for neurosurgery. Automated pathology analysis is yet another form of theranostics that can provide real-time feedback during the surgical resection of tumors. Electrical stimulation has also shown promise in optimizing therapies for patients with cerebral palsy. Overall, theranostics is a cost-effective way to optimize medical care for patients in neurosurgery. It is a relatively new field, but the advancements made so far show great promise for improving patient outcomes.
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Affiliation(s)
- Drashti Patel
- Department of Neurosurgery, University of Florida, College of Medicine, Gainesville, Florida, USA
| | - Andrew Nguyen
- Department of Neurosurgery, University of Florida, College of Medicine, Gainesville, Florida, USA
| | - Chance Fleeting
- Department of Neurosurgery, University of Florida, College of Medicine, Gainesville, Florida, USA
| | - Anjali B. Patel
- Department of Neurosurgery, University of Florida, College of Medicine, Gainesville, Florida, USA
| | - Mohammed Mumtaz
- Department of Neurosurgery, University of Florida, College of Medicine, Gainesville, Florida, USA
| | - Brandon Lucke-Wold
- Department of Neurosurgery, University of Florida, College of Medicine, Gainesville, Florida, USA
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23
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Markus MA, Ferrari DP, Alves F, Ramos-Gomes F. Effect of tissue fixation on the optical properties of structural components assessed by non-linear microscopy imaging. BIOMEDICAL OPTICS EXPRESS 2023; 14:3988-4002. [PMID: 37799688 PMCID: PMC10549744 DOI: 10.1364/boe.488453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/20/2023] [Accepted: 04/25/2023] [Indexed: 10/07/2023]
Abstract
Fixation methods such as formalin are commonly used for the preservation of tissue with the aim of keeping their structure as close as possible to the native condition. However, fixatives chemically interact with tissue molecules, such as collagen in the extracellular matrix (ECM) or myosin, and may thus modify their structure. Taking advantage of the second- and third-harmonic generation (SHG and THG) emission capabilities of such components, we used nonlinear two-photon microscopy (NL2PM) to evaluate the effect that preservation methods, such as chemical fixatives, have on the nonlinear capabilities of protein components within mouse tissues. Our results show that depending on the preservation technique used, the nonlinear capabilities of collagen, lipid droplets and myosin microarchitecture are strongly affected. Parameters of collagen fibers, such as density and branch points, especially in collagen-sparse regions, e.g., in kidneys, were found to be altered upon formalin fixation. Moreover, cryo-freezing drastically reduced SHG signals from myosin. Our findings provide valuable information to select the best tissue fixation method for visualization and quantification of structural proteins, such as collagen and myosin by advanced NL2PM imaging techniques. This may advance the interpretation of the role these proteins play in disease.
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Affiliation(s)
- M. Andrea Markus
- Translational Molecular Imaging Group,
Max-Planck Institute for Multidisciplinary Sciences, Hermann-Rein-Str. 3, 37075 Göttingen, Germany
| | - Daniele P. Ferrari
- Translational Molecular Imaging Group,
Max-Planck Institute for Multidisciplinary Sciences, Hermann-Rein-Str. 3, 37075 Göttingen, Germany
| | - Frauke Alves
- Translational Molecular Imaging Group,
Max-Planck Institute for Multidisciplinary Sciences, Hermann-Rein-Str. 3, 37075 Göttingen, Germany
- Clinic of Haematology and Medical Oncology, Institute of Interventional and Diagnostic Radiology, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075 Göttingen, Germany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC), Robert-Koch-Str. 40, 37075 Göttingen, Germany
| | - Fernanda Ramos-Gomes
- Translational Molecular Imaging Group,
Max-Planck Institute for Multidisciplinary Sciences, Hermann-Rein-Str. 3, 37075 Göttingen, Germany
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24
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Erber WN, Hui HYL, Mincherton TI, Harms M, Clarke S, Fuller KA. Enhanced multi-FISH analysis of immunophenotyped plasma cells by imaging flow cytometry. J Hum Genet 2023:10.1038/s10038-023-01155-z. [PMID: 37161034 DOI: 10.1038/s10038-023-01155-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 05/11/2023]
Affiliation(s)
- Wendy N Erber
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia.
- PathWest Laboratory Medicine, Nedlands, WA, Australia.
| | - Henry Y L Hui
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Thomas I Mincherton
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Matthew Harms
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
- Medical School, The University of Western Australia, Crawley, WA, Australia
| | - Sarah Clarke
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Kathy A Fuller
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
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25
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Gros R, Rodríguez-Núñez O, Felger L, Moriconi S, McKinley R, Pierangelo A, Novikova T, Vassella E, Schucht P, Hewer E, Maragkou T. Effects of formalin fixation on polarimetric properties of brain tissue: fresh or fixed? NEUROPHOTONICS 2023; 10:025009. [PMID: 37234458 PMCID: PMC10207713 DOI: 10.1117/1.nph.10.2.025009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/16/2023] [Accepted: 05/01/2023] [Indexed: 05/28/2023]
Abstract
Significance Imaging Mueller polarimetry (IMP) appears as a promising technique for real-time delineation of healthy and neoplastic tissue during neurosurgery. The training of machine learning algorithms used for the image post-processing requires large data sets typically derived from the measurements of formalin-fixed brain sections. However, the success of the transfer of such algorithms from fixed to fresh brain tissue depends on the degree of alterations of polarimetric properties induced by formalin fixation (FF). Aim Comprehensive studies were performed on the FF induced changes in fresh pig brain tissue polarimetric properties. Approach Polarimetric properties of pig brain were assessed in 30 coronal thick sections before and after FF using a wide-field IMP system. The width of the uncertainty region between gray and white matter was also estimated. Results The depolarization increased by 5% in gray matter and remained constant in white matter following FF, whereas the linear retardance decreased by 27% in gray matter and by 28% in white matter after FF. The visual contrast between gray and white matter and fiber tracking remained preserved after FF. Tissue shrinkage induced by FF did not have a significant effect on the uncertainty region width. Conclusions Similar polarimetric properties were observed in both fresh and fixed brain tissues, indicating a high potential for transfer learning.
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Affiliation(s)
- Romain Gros
- University of Bern, Institute of Tissue Medicine and Pathology, Bern, Switzerland
- University of Bern, Graduate School for Cellular and Biomedical Sciences, Bern, Switzerland
| | - Omar Rodríguez-Núñez
- Bern University Hospital, University of Bern, Department of Neurosurgery, Inselspital, Bern, Switzerland
| | - Leonard Felger
- Bern University Hospital, University of Bern, Department of Neurosurgery, Inselspital, Bern, Switzerland
| | - Stefano Moriconi
- University of Bern, Inselspital, Bern University Hospital, University Institute of Diagnostic and Interventional Radiology, Support Center for Advanced Neuroimaging, Bern, Switzerland
| | - Richard McKinley
- University of Bern, Inselspital, Bern University Hospital, University Institute of Diagnostic and Interventional Radiology, Support Center for Advanced Neuroimaging, Bern, Switzerland
| | | | | | - Erik Vassella
- University of Bern, Institute of Tissue Medicine and Pathology, Bern, Switzerland
| | - Philippe Schucht
- Bern University Hospital, University of Bern, Department of Neurosurgery, Inselspital, Bern, Switzerland
| | - Ekkehard Hewer
- Lausanne University Hospital and University of Lausanne, Institute of Pathology, Lausanne, Switzerland
| | - Theoni Maragkou
- University of Bern, Institute of Tissue Medicine and Pathology, Bern, Switzerland
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26
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Danusso R, Rosati R, Possenti L, Lombardini E, Gigli F, Costantino ML, Ferrazzi E, Casagrande G, Lattuada D. Human umbilical cord blood cells suffer major modification by fixatives and anticoagulants. Front Physiol 2023; 14:1070474. [PMID: 37008002 PMCID: PMC10050555 DOI: 10.3389/fphys.2023.1070474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 02/28/2023] [Indexed: 03/17/2023] Open
Abstract
Introduction: Developing techniques for the tagless isolation of homogeneous cell populations in physiological-like conditions is of great interest in medical research. A particular case is Gravitational Field-Flow Fractionation (GrFFF), which can be run avoiding cell fixation, and that was already used to separate viable cells. Cell dimensions have a key role in this process. However, their dimensions under physiological-like conditions are not easily known since the most diffused measurement techniques are performed on fixed cells, and the fixation used to preserve tissues can alter the cell size. This work aims to obtain and compare cell size data under physiological-like conditions and in the presence of a fixative.Methods: We developed a new protocol that allows the analysis of blood cells in different conditions. Then, we applied it to obtain a dataset of human cord blood cell dimensions from 32 subjects, comparing two tubes with anticoagulants (EDTA and Citrate) and two tubes with different preservatives (CellRescue and CellSave). We analyzed a total of 2071 cells by using confocal microscopy via bio-imaging to assess dimensions (cellular and nuclear) and morphology.Results: Cell diameter measured does not differ when using the different anticoagulants, except for the increase reported for monocyte in the presence of citrate. Instead, cell dimensions differ when comparing anticoagulants and cell preservative tubes, with a few exceptions. Cells characterized by high cytoplasm content show a reduction in their size, while morphology appears always preserved. In a subgroup of cells, 3D reconstruction was performed. Cell and nucleus volumes were estimated using different methods (specific 3D tool or reconstruction from 2D projection).Discussion: We found that some cell types benefit from a complete 3D analysis because they contain non-spherical structures (mainly for cells characterized by poly-lobated nucleus). Overall, we showed the effect of the preservatives mixture on cell dimensions. Such an effect must be considered when dealing with problems highly dependent on cell size, such as GrFFF. Additionally, such information is crucial in computational models increasingly being employed to simulate biological events.
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Affiliation(s)
- Roberta Danusso
- Department of Women-Child-Newborn, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milano, Italy
- Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Riccardo Rosati
- Department of Women-Child-Newborn, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - Luca Possenti
- LaBS, Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, Milan, Italy
| | - Elena Lombardini
- Department of Women-Child-Newborn, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - Francesca Gigli
- Department of Women-Child-Newborn, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - Maria Laura Costantino
- LaBS, Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, Milan, Italy
| | - Enrico Ferrazzi
- Department of Women-Child-Newborn, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - Giustina Casagrande
- Department of Women-Child-Newborn, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milano, Italy
- LaBS, Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, Milan, Italy
| | - Debora Lattuada
- Department of Women-Child-Newborn, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milano, Italy
- *Correspondence: Debora Lattuada,
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27
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Moreira JD, Gower AC, Xue L, Alekseyev Y, Smith KK, Choi SH, Ayalon N, Farb MG, Tenan K, LeClerc A, Levy D, Benjamin EJ, Lenburg ME, Mitchell RN, Padera RF, Fetterman JL, Gopal DM. Systematic dissection, preservation, and multiomics in whole human and bovine hearts. Cardiovasc Pathol 2023; 63:107495. [PMID: 36334690 PMCID: PMC10031913 DOI: 10.1016/j.carpath.2022.107495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/22/2022] [Accepted: 10/27/2022] [Indexed: 11/07/2022] Open
Abstract
OBJECTIVES We sought to develop a rigorous, systematic protocol for the dissection and preservation of human hearts for biobanking that expands previous success in postmortem transcriptomics to multiomics from paired tissue. BACKGROUND Existing cardiac biobanks consist largely of biopsy tissue or explanted hearts in select diseases and are insufficient for correlating whole organ phenotype with clinical data. METHODS We demonstrate optimal conditions for multiomics interrogation (ribonucleic acid (RNA) sequencing, untargeted metabolomics) in hearts by evaluating the effect of technical variables (storage solution, temperature) and simulated postmortem interval (PMI) on RNA and metabolite stability. We used bovine (n=3) and human (n=2) hearts fixed in PAXgene or snap-frozen with liquid nitrogen. RESULTS Using a paired Wald test, only two of the genes assessed were differentially expressed between left ventricular samples from bovine hearts stored in PAXgene at 0 and 12 hours PMI (FDR q<0.05). We obtained similar findings in human left ventricular samples, suggesting stability of RNA transcripts at PMIs up to 12 hours. Different library preparation methods (mRNA poly-A capture vs. rRNA depletion) resulted in similar quality metrics with both library preparations achieving >95% of reads properly aligning to the reference genomes across all PMIs for bovine and human hearts. PMI had no effect on RNA Integrity Number or quantity of RNA recovered at the time points evaluated. Of the metabolites identified (855 total) using untargeted metabolomics of human left ventricular tissue, 503 metabolites remained stable across PMIs (0, 4, 8, 12 hours). Most metabolic pathways retained several stable metabolites. CONCLUSIONS Our data demonstrate a technically rigorous, reproducible protocol that will enhance cardiac biobanking practices and facilitate novel insights into human CVD. CONDENSED ABSTRACT Cardiovascular disease (CVD) is the leading cause of mortality worldwide. Current biobanking practices insufficiently capture both the diverse array of phenotypes present in CVDs and the spatial heterogeneity across cardiac tissue sites. We have developed a rigorous and systematic protocol for the dissection and preservation of human cardiac biospecimens to enhance the availability of whole organ tissue for multiple applications. When combined with longitudinal clinical phenotyping, our protocol will enable multiomics in hearts to deepen our understanding of CVDs.
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Affiliation(s)
- Jesse D Moreira
- Evans Department of Medicine and The Whitaker Cardiovascular Institute, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Adam C Gower
- Department of Medicine, Section of Computational Biomedicine, and Clinical and Translational Science Institute, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Liying Xue
- Evans Department of Medicine and The Whitaker Cardiovascular Institute, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Yuriy Alekseyev
- Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Karan K Smith
- Evans Department of Medicine and The Whitaker Cardiovascular Institute, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Seung H Choi
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nir Ayalon
- Cardiovascular Medicine Section, Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Melissa G Farb
- Evans Department of Medicine and The Whitaker Cardiovascular Institute, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Kenneth Tenan
- BU Microarray and Sequencing Resource, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Ashley LeClerc
- BU Microarray and Sequencing Resource, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Daniel Levy
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA; Department of Medicine, Preventive Medicine & Epidemiology Section, Boston University Chobanian & Avedisian School of Medicine, Boston University and the National Heart, Lung and Blood Institute's Framingham Heart Study, Framingham, MA, USA
| | - Emelia J Benjamin
- Department of Medicine, Preventive Medicine & Epidemiology Section, Boston University Chobanian & Avedisian School of Medicine, Boston University and the National Heart, Lung and Blood Institute's Framingham Heart Study, Framingham, MA, USA; Section of Cardiovascular Medicine, Boston Medical Center/Boston University Chobanian & Avedisian School of Medicine and Department of Epidemiology Boston University School of Public Health, Boston, MA, USA
| | - Marc E Lenburg
- Department of Medicine, Section of Computational Biomedicine, and Clinical and Translational Science Institute, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Richard N Mitchell
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Robert F Padera
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jessica L Fetterman
- Evans Department of Medicine and The Whitaker Cardiovascular Institute, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA.
| | - Deepa M Gopal
- Evans Department of Medicine and The Whitaker Cardiovascular Institute, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA; Cardiovascular Medicine Section, Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA.
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28
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Butter R, Halfwerk H, Radonic T, Lissenberg-Witte B, Thunnissen E. The impact of impaired tissue fixation in resected non-small-cell lung cancer on protein deterioration and DNA degradation. Lung Cancer 2023; 178:108-115. [PMID: 36812759 DOI: 10.1016/j.lungcan.2023.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 01/25/2023] [Accepted: 02/08/2023] [Indexed: 02/13/2023]
Abstract
OBJECTIVES The objective is to assess the impact of the quality of tissue fixation in surgical pathology on immunohistochemical (IHC) staining and DNA degradation. MATERIALS AND METHODS Twenty-five non-small cell lung cancer (NSCLC) resection specimens were analyzed. After resection, all tumors were processed according to the protocols in our center. In haematoxylin and eosin (H&E) stained tissue slides, adequately- and inadequately fixed tumor areas were microscopically demarcated, based on basement membrane detachment. In 10 IHC stains ALK (clone 5A4), PD-L (clone 22C3), CAM5.2, CK7, c-Met, KER-MNF116, NapsinA, p40, ROS1, TTF1) the immunoreactivity in H-scores was determined in adequately- and inadequately fixed, and necrotic tumor areas. From the same areas DNA was isolated, and DNA fragmentation in base pairs (bp) was measured. RESULTS H-scores were significantly higher in H&E adequately fixed tumor areas in IHC stains KER-MNF116 (H-score 256 vs 15, p=0.001) and p40 (H-score 293 vs 248, p=0.028). All other stains showed a trend towards higher immunoreactivity in H&E adequately fixed areas. Independent of H&E adequatelty- or inadequately fixed areas, all IHC stains showed significant different IHC staining intensity within tumors, suggesting heterogeneous immunoreactivity (H-scores: PD-L1 123 vs 6, p = 0.001; CAM5.2 242 vs 101, p=<0.001; CK7 242 vs 128, p=<0.001; c-MET 99 vs 20, p=<0.001; KER-MNF116 281 vs 120, p=<0.001; Napsin A 268 vs 130, p = 0.005; p40 292 vs 166, p = 0.008; TTF1 199 vs 63, p=<0.001). DNA fragments rarely exceeded a length of 300 bp, independent of adequate fixation. However, DNA fragments of 300 and 400 bp had higher concentrations in tumors with short fixation delay (<6 h vs >16 h) and short fixation time (<24 h vs >24 h). CONCLUSIONS Impaired tissue fixation of resected lung tumors results in decreased IHC staining intensity in some parts of the tumor. This may impact the reliability of IHC analysis.
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Affiliation(s)
- Rogier Butter
- Department of Pathology, Cancer Center Amsterdam, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Hans Halfwerk
- Department of Pathology, Cancer Center Amsterdam, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Teodora Radonic
- Department of Pathology, Cancer Center Amsterdam, Amsterdam University Medical Centers, VU University Amsterdam, Amsterdam, The Netherlands
| | - Birgit Lissenberg-Witte
- Department of Epidemiology and Data Science, Amsterdam University Medical Centers, VU University Amsterdam, Amsterdam, The Netherlands
| | - Erik Thunnissen
- Department of Pathology, Cancer Center Amsterdam, Amsterdam University Medical Centers, VU University Amsterdam, Amsterdam, The Netherlands.
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29
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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] [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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30
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Marini N, Otalora S, Wodzinski M, Tomassini S, Dragoni AF, Marchand-Maillet S, Morales JPD, Duran-Lopez L, Vatrano S, Müller H, Atzori M. Data-driven color augmentation for H&E stained images in computational pathology. J Pathol Inform 2023; 14:100183. [PMID: 36687531 PMCID: PMC9852546 DOI: 10.1016/j.jpi.2022.100183] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/28/2022] [Accepted: 12/28/2022] [Indexed: 01/05/2023] Open
Abstract
Computational pathology targets the automatic analysis of Whole Slide Images (WSI). WSIs are high-resolution digitized histopathology images, stained with chemical reagents to highlight specific tissue structures and scanned via whole slide scanners. The application of different parameters during WSI acquisition may lead to stain color heterogeneity, especially considering samples collected from several medical centers. Dealing with stain color heterogeneity often limits the robustness of methods developed to analyze WSIs, in particular Convolutional Neural Networks (CNN), the state-of-the-art algorithm for most computational pathology tasks. Stain color heterogeneity is still an unsolved problem, although several methods have been developed to alleviate it, such as Hue-Saturation-Contrast (HSC) color augmentation and stain augmentation methods. The goal of this paper is to present Data-Driven Color Augmentation (DDCA), a method to improve the efficiency of color augmentation methods by increasing the reliability of the samples used for training computational pathology models. During CNN training, a database including over 2 million H&E color variations collected from private and public datasets is used as a reference to discard augmented data with color distributions that do not correspond to realistic data. DDCA is applied to HSC color augmentation, stain augmentation and H&E-adversarial networks in colon and prostate cancer classification tasks. DDCA is then compared with 11 state-of-the-art baseline methods to handle color heterogeneity, showing that it can substantially improve classification performance on unseen data including heterogeneous color variations.
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Affiliation(s)
- Niccolò Marini
- Information Systems Institute, University of Applied Sciences Western Switzerland (HES-SO Valais), Sierre, Switzerland
- Centre Universitaire d'Informatique, University of Geneva, Geneva, Switzerland
| | - Sebastian Otalora
- Support Center for Advanced Neuroimaging, University Institute of Diagnostic and Interventional Neuroradiology, Bern, Switzerland
| | - Marek Wodzinski
- Information Systems Institute, University of Applied Sciences Western Switzerland (HES-SO Valais), Sierre, Switzerland
- Department of Measurement and Electronics, AGH University of Science and Technology, Krakow, Poland
| | - Selene Tomassini
- Department of Information Engineering, Engineering Faculty, Università Politecnica delle Marche, Ancona, Italy
| | - Aldo Franco Dragoni
- Department of Information Engineering, Engineering Faculty, Università Politecnica delle Marche, Ancona, Italy
| | | | - Juan Pedro Dominguez Morales
- Robotics and Technology of Computers Lab., ETSII-EPS, Universidad de Sevilla, Sevilla, Spain
- SCORE Lab, I3US, Universidad de Sevilla, Spain
| | - Lourdes Duran-Lopez
- Robotics and Technology of Computers Lab., ETSII-EPS, Universidad de Sevilla, Sevilla, Spain
- SCORE Lab, I3US, Universidad de Sevilla, Spain
| | - Simona Vatrano
- Pathology Unit, Gravina Hospital Caltagirone ASP, Catania, Italy
| | - Henning Müller
- Information Systems Institute, University of Applied Sciences Western Switzerland (HES-SO Valais), Sierre, Switzerland
- Medical Faculty, University of Geneva, Geneva, Switzerland
| | - Manfredo Atzori
- Information Systems Institute, University of Applied Sciences Western Switzerland (HES-SO Valais), Sierre, Switzerland
- Department of Neurosciences, University of Padua, Padua, Italy
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31
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Dumigan A, Gonzalez RC, Morris B, Sá-Pessoa J. Visualisation of Host-Pathogen Communication. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1406:19-39. [PMID: 37016109 DOI: 10.1007/978-3-031-26462-7_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/06/2023]
Abstract
The core of biomedical science is the use of laboratory techniques to support the diagnosis and treatment of disease in clinical settings. Despite tremendous advancement in our understanding of medicine in recent years, we are still far from having a complete understanding of human physiology in homeostasis, let alone the pathology of disease states. Indeed medical advances over the last two hundred years would not have been possible without the invention of and continuous development of visualisation techniques available to research scientists and clinicians. As we have all learned from the recent COVID pandemic, despite advances in modern medicine we still have much to learn regarding infection biology. Indeed antimicrobial resistant (AMR) bacteria are a global threat to human health, meaning research into bacterial pathogenesis is vital. In this chapter, we will briefly describe the nature of microbes and host immune responses before delving into some of the visualisation techniques utilised in the field of biomedical research with a focus on host-pathogen interactions. We will give a brief overview of commonly used techniques from gold standard staining methods, in situ hybridisation, microscopy, western blotting, microbial characterisation, to cutting-edge image flow cytometry and mass spectrometry. Specifically, we will focus on techniques utilised to visualise interactions between the host, our own bodies, and invading organisms including bacteria. We will touch on in vitro and ex vivo modelling methodology with examples utilised to delineate pathogenicity in disease. A better understanding of bacterial biology, immunology and how these fields interact (host-pathogen communications) in biomedical research is integral to developing novel therapeutic approaches which circumvent the need for antibiotics, an important issue as we enter a post-antibiotic era.
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Affiliation(s)
- Amy Dumigan
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK.
| | | | - Brenda Morris
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
| | - Joana Sá-Pessoa
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, UK
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32
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Decruyenaere P, Verniers K, Poma-Soto F, Van Dorpe J, Offner F, Vandesompele J. RNA Extraction Method Impacts Quality Metrics and Sequencing Results in Formalin-Fixed, Paraffin-Embedded Tissue Samples. J Transl Med 2023; 103:100027. [PMID: 37039153 DOI: 10.1016/j.labinv.2022.100027] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/19/2022] [Accepted: 11/03/2022] [Indexed: 01/11/2023] Open
Abstract
Archived formalin-fixed, paraffin-embedded (FFPE) tissue samples are being increasingly used in molecular cancer research. Compared with fresh-frozen tissue, the nucleic acid analysis of FFPE tissue is technically more challenging. This study aimed to compare the impact of 3 different RNA extraction methods on yield, quality, and sequencing-based gene expression results in FFPE samples. RNA extraction was performed in 16 FFPE tumor specimens from patients with diffuse large B-cell lymphoma and in reference FFPE material from microsatellite-stable and microsatellite-instable cell lines (3 replicates each) using 2 silica-based procedures (A, miRNeasy FFPE; C, iCatcher FFPE Tissue RNA) and 1 isotachophoresis-based procedure (B, Ionic FFPE to Pure RNA). The RNA yield; RNA integrity, as reflected by the distribution value 200; and RNA purity, as reflected by the 260/280 and the 260/230 nm absorbance ratios, were determined. The RNA was sequenced on the NovaSeq 6000 instrument using the TruSeq RNA Exome and SMARTer Stranded Total RNA-Seq Pico v3 library preparations kits. Our results highlight the impact of RNA extraction methodology on both preanalytical and sequencing-based gene expression results. Overall, methods B and C outperformed method A because these showed significantly higher fractions of uniquely mapped reads, an increased number of detectable genes, a lower fraction of duplicated reads, and better representation of the B-cell receptor repertoire. Differences among the extraction methods were generally more explicit for the total RNA sequencing method than for the exome-capture sequencing method. Importantly, the predicative value of quality metrics varies among extraction kits, and caution should be applied when comparing and interpreting results obtained using different methods.
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33
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Yaneva Z, Ivanova D, Nikolova N, Toneva M. Organic dyes in contemporary medicinal chemistry and biomedicine. I. From the chromophore to the bioimaging/bioassay agent. BIOTECHNOL BIOTEC EQ 2022. [DOI: 10.1080/13102818.2022.2039077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Zvezdelina Yaneva
- Department of Pharmacology, Animal Physiology, Biochemistry and Chemistry, Faculty of Veterinary Medicine, Trakia University, Stara Zagora, Bulgaria
| | - Donika Ivanova
- Department of Pharmacology, Animal Physiology, Biochemistry and Chemistry, Faculty of Veterinary Medicine, Trakia University, Stara Zagora, Bulgaria
| | - Nevena Nikolova
- Ecology Unit, Department of Pharmacology, Animal Physiology, Biochemistry and Chemistry, Faculty of Veterinary Medicine, Trakia University, Stara Zagora, Bulgaria
| | - Monika Toneva
- Department of Pharmacology, Animal Physiology, Biochemistry and Chemistry, Faculty of Veterinary Medicine, Trakia University, Stara Zagora, Bulgaria
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34
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Begić V, Sertić Perić M, Hančić S, Marchiotti I, Gabud T, Šestak Panižić I, Radanović I, Korać P. Effectiveness of five different solutions for preserving aquatic insects commonly used in morphological and stream ecology studies. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01298-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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35
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De Martino E, Medeot C, D'Amico L, Stanta G, Bonin S. Impact of standardization in tissue processing: the performance of different fixatives. N Biotechnol 2022; 71:30-36. [PMID: 35878783 DOI: 10.1016/j.nbt.2022.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 07/21/2022] [Accepted: 07/21/2022] [Indexed: 10/31/2022]
Abstract
Most tissues in clinical practice are formalin-fixed and paraffin-embedded for histological as well as molecular analyses. The reproducibility and uniformity of molecular analyses is strictly dependent on the quality of the biomolecules, which is highly influenced by pre-analytical processes. In this study, the effect of different fixatives was compared, including formalin, Bouin's solution, RCL2® and TAG-1™ fixatives, by stringent application of ISO standards in mouse liver tissue processing, including formalin-free transport of tissues and tissue grossing in a refrigerated environment. The effect of fixatives was studied in terms of nucleic acid quality at the time of tissue processing and after one year of tissue storage at room temperature in the dark. Furthermore, a microcomputed tomography (CT) scan analysis was applied to investigate the paraffin embedding. The results show that the application of ISO standards in tissue processing allows analysis of 400 bases amplicons from RNA and 1000 bases from DNA, even in extracts from formalin-fixed and paraffin-embedded tissues. However, after one year storage at room temperature in the dark, a degradation of the nucleic acids was observed. Nevertheless, extracts can still be analyzed, but for metachronous tests it is highly recommended to repeat the quantitation of housekeeping genes in order to standardize the extent of nucleic acid degradation.
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Affiliation(s)
| | - Caterina Medeot
- Department of Medical Sciences, University of Trieste, Trieste, Italy
| | - Lorenzo D'Amico
- Department of Physics, University of Trieste, Trieste, Italy; Elettra-Sincrotrone Trieste S.C.p.A., Area Science Park, Trieste, Italy
| | - Giorgio Stanta
- Department of Medical Sciences, University of Trieste, Trieste, Italy
| | - Serena Bonin
- Department of Medical Sciences, University of Trieste, Trieste, Italy.
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36
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Thomas S, Sadanandan J, Blackburn SL, McBride DW, Dienel A, Hong S, Zeineddine HA, Thankamani PK. Glyoxal Fixation Is Optimal for Immunostaining of Brain Vessels, Pericytes and Blood-Brain Barrier Proteins. Int J Mol Sci 2022; 23:7776. [PMID: 35887131 PMCID: PMC9317650 DOI: 10.3390/ijms23147776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/07/2022] [Accepted: 07/12/2022] [Indexed: 12/02/2022] Open
Abstract
Brain vascular staining is very important for understanding cerebrovascular pathologies. 4% paraformaldehyde is considered the gold standard fixation technique for immunohistochemistry and it revolutionized the examination of proteins in fixed tissues. However, this fixation technique produces inconsistent immunohistochemical staining results due to antigen masking. Here, we test a new fixation protocol using 3% glyoxal and demonstrate that this method improves the staining of the brain vasculature, pericytes, and tight junction proteins compared to 4% paraformaldehyde. Use of this new fixation technique will provide more detailed information about vascular protein expressions, their distributions, and colocalizations with other proteins at the molecular level in the brain vasculature.
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Affiliation(s)
| | | | | | | | | | | | | | - Peeyush Kumar Thankamani
- The Vivian L. Smith Department of Neurosurgery, University of Texas Health Science Center, 6431 Fannin St. MSB 7.147, Houston, TX 77030, USA; (S.T.); (J.S.); (S.L.B.); (D.W.M.); (A.D.); (S.H.); (H.A.Z.)
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37
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Murphy PR, Narayanan D, Kumari S. Methods to Identify Immune Cells in Tissues With a Focus on Skin as a Model. Curr Protoc 2022; 2:e485. [PMID: 35822855 DOI: 10.1002/cpz1.485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The skin protects our body from external challenges, insults, and pathogens and consists of two layers, epidermis and dermis. The immune cells of the skin are an integral part of protecting the body and essential for mediating skin immune homeostasis. They are distributed in the epidermal and dermal layers of the skin. Under homeostatic conditions, the mouse and human skin epidermis harbors immune cells such as Langerhans cells and CD8+ T cells, whereas the dermis contains dendritic cells (DCs), mast cells, macrophages, T cells, and neutrophils. Skin immune homeostasis is maintained through communication between epidermal and dermal cells and soluble factors. This communication is important for proper recruitment of immune cells in the skin to mount immune responses during infection/injury or in response to external/internal insults that alter the local cellular milieu. Imbalance in this crosstalk that occurs in association with inflammatory skin disorders such as psoriasis and atopic dermatitis can lead to alterations in the number and type of immune cells contributing to pathological manifestation in these disorders. Profiling changes in the immune cell type, localization, and number can provide important information about disease mechanisms and help design interventional therapeutic strategies. Toward this end, skin cells can be detected and characterized using basic techniques like immunofluorescence, immunohistochemistry, and flow cytometry, and recently developed methods of multiplexing. This article provides an overview on the basic techniques that are widely accessible to researchers to characterize immune cells of the skin. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC.
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Affiliation(s)
- Peter R Murphy
- The University of Queensland Diamantina Institute, Faculty of Medicine, Translational Research Institute, Brisbane, Queensland, Australia
| | - Divyaa Narayanan
- The University of Queensland Diamantina Institute, Faculty of Medicine, Translational Research Institute, Brisbane, Queensland, Australia
| | - Snehlata Kumari
- The University of Queensland Diamantina Institute, Faculty of Medicine, Translational Research Institute, Brisbane, Queensland, Australia
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38
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Prostate cancer histopathology using label-free multispectral deep-UV microscopy quantifies phenotypes of tumor aggressiveness and enables multiple diagnostic virtual stains. Sci Rep 2022; 12:9329. [PMID: 35665770 PMCID: PMC9167293 DOI: 10.1038/s41598-022-13332-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 05/23/2022] [Indexed: 12/20/2022] Open
Abstract
Identifying prostate cancer patients that are harboring aggressive forms of prostate cancer remains a significant clinical challenge. Here we develop an approach based on multispectral deep-ultraviolet (UV) microscopy that provides novel quantitative insight into the aggressiveness and grade of this disease, thus providing a new tool to help address this important challenge. We find that UV spectral signatures from endogenous molecules give rise to a phenotypical continuum that provides unique structural insight (i.e., molecular maps or “optical stains") of thin tissue sections with subcellular (nanoscale) resolution. We show that this phenotypical continuum can also be applied as a surrogate biomarker of prostate cancer malignancy, where patients with the most aggressive tumors show a ubiquitous glandular phenotypical shift. In addition to providing several novel “optical stains” with contrast for disease, we also adapt a two-part Cycle-consistent Generative Adversarial Network to translate the label-free deep-UV images into virtual hematoxylin and eosin (H&E) stained images, thus providing multiple stains (including the gold-standard H&E) from the same unlabeled specimen. Agreement between the virtual H&E images and the H&E-stained tissue sections is evaluated by a panel of pathologists who find that the two modalities are in excellent agreement. This work has significant implications towards improving our ability to objectively quantify prostate cancer grade and aggressiveness, thus improving the management and clinical outcomes of prostate cancer patients. This same approach can also be applied broadly in other tumor types to achieve low-cost, stain-free, quantitative histopathological analysis.
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39
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Fulcheri E, Buffelli F, Fiore C, Izzotti A, Piccardo MT, Chiozza MB, Petralia P, Ciliberti R, Bonsignore A. Considerations about the burial of foetuses of less than 20-weeks gestational age. Pathologica 2022; 114:238-240. [PMID: 35775710 PMCID: PMC9248242 DOI: 10.32074/1591-951x-773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 04/20/2022] [Indexed: 11/30/2022] Open
Affiliation(s)
- Ezio Fulcheri
- Section of Pathology, Department of Surgical and Diagnostic Sciences (DISC), University of Genova, Genova, Italy.,Fetal and Perinatal Pathology Unit, IRCCS - Istituto Giannina Gaslini, Genova, Italy
| | - Francesca Buffelli
- Fetal and Perinatal Pathology Unit, IRCCS - Istituto Giannina Gaslini, Genova, Italy
| | | | - Alberto Izzotti
- Department of Experimental Medicine (DIMES), University of Genova, Genova, Italy.,Mutagenesis & Cancer Prevention Unit, IRCCS Policlinico San Martino, Teaching Hospital, Genova, Italy
| | - Maria Teresa Piccardo
- Mutagenesis & Cancer Prevention Unit, IRCCS Policlinico San Martino, Teaching Hospital, Genova, Italy
| | | | - Paolo Petralia
- General Direction of the Local Health Authority ASL4, Liguria Region, Italy
| | - Rosagemma Ciliberti
- Section of Bioethics and History of Medicine, Department of Health Sciences (DISSAL), University of Genova, Genova, Italy
| | - Alessandro Bonsignore
- Section of Legal and Forensic Medicine, Department of Health Sciences (DISSAL), University of Genova, Genova, Italy.,IRCCS Policlinico San Martino, Teaching Hospital, Genova, Italy
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40
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Snyder JM, Radaelli E, Goeken A, Businga T, Boyden AW, Karandikar NJ, Gibson-Corley KN. Perfusion with 10% neutral-buffered formalin is equivalent to 4% paraformaldehyde for histopathology and immunohistochemistry in a mouse model of experimental autoimmune encephalomyelitis. Vet Pathol 2022; 59:498-505. [PMID: 35130806 PMCID: PMC9364762 DOI: 10.1177/03009858221075588] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Intravascular (IV) perfusion of tissue fixative is commonly used in the field of neuroscience as the central nervous system tissues are exquisitely sensitive to handling and fixation artifacts which can affect downstream microscopic analysis. Both 10% neutral-buffered formalin (NBF) and 4% paraformaldehyde (PFA) are used, although IV perfusion with PFA is most commonly referenced. The study objective was to compare the severity of handling and fixation artifacts, semiquantitative scores of inflammatory and neurodegenerative changes, and quantitative immunohistochemistry following terminal IV perfusion of mice with either 10% NBF or 4% PFA in a model of experimental autoimmune encephalitis (EAE). The study included 24 mice; 12 were control animals not immunized and an additional 12 were immunized with PLP139-151 subcutaneously, harvested at day 20, and fixed in the same fashion. Equal numbers (4 per group) were perfused with 10% NBF or 4% PFA, and 4 were immersion-fixed in 10% NBF. NBF-perfused mice had less severe dark neuron artifact than PFA-perfused mice (P < .001). Immersion-fixed animals had significantly higher scores for oligodendrocyte halos, dark neuron artifact, and perivascular clefts than perfusion-fixed animals. Histopathology scores in EAE mice for inflammation, demyelination, and necrosis did not differ among fixation methods. Also, no significant differences in quantitative immunohistochemistry for CD3 and Iba-1 were observed in immunized animals regardless of the method of fixation. These findings indicate that IV perfusion of mice with 10% NBF and 4% PFA are similar and adequate fixation techniques in this model.
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Affiliation(s)
| | - Enrico Radaelli
- University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA
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41
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Buszewska-Forajta M, Rafińska K, Buszewski B. Tissue sample preparations for preclinical research determined by molecular imaging mass spectrometry using MALDI. J Sep Sci 2022; 45:1345-1361. [PMID: 35122386 DOI: 10.1002/jssc.202100578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 01/25/2022] [Accepted: 01/26/2022] [Indexed: 11/09/2022]
Abstract
Matrix-assisted laser desorption/ionization - imaging mass spectrometry is an alternative tool, which can be implemented in order to obtain and visualize the "omic" signature of tissue samples. Its application to clinical study enables simultaneous imaging-based morphological observations and mass spectrometry analysis. Application of fully informative material like tissue, allows to obtain the complex and unique profile of analyzed samples. This knowledge leads to diagnose disease, study the mechanism of cancer development, select the potential biomarkers as well as correlating obtained image with prognosis. Nevertheless, it is worth to notice that this method is found to be objective but the result of analysis is mainly influenced by the sample preparation protocol, included collection of biological material, its preservation and processing. However, application of this approach requires a special sample preparation procedure. The main goal of the study is to present the current knowledge on the clinical application of matrix-assisted laser desorption/ionization - imaging mass spectrometry in cancer research, with particular emphasis on the sample preparation step. For this purpose, several protocols based on cryosections and formalin-fixed paraffin embedded tissue were compiled and compared, taking into account the measured metabolites of potential diagnostic importance for a given type of cancer. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Magdalena Buszewska-Forajta
- Institute of Veterinary Medicine, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Lwowska 1, Toruń, 87-100, Poland
| | - Katarzyna Rafińska
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarina Str., Torun, 87-100, Poland
| | - Boguslaw Buszewski
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarina Str., Torun, 87-100, Poland.,Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Torun, 4 Wileńska Str., Torun, 87-100, Poland
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42
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Silva H, Tassone C, Ross EG, Lee JT, Zhou W, Nelson D. Collagen Fibril Orientation in Tissue Specimens From Atherosclerotic Plaque Explored Using Small Angle X-Ray Scattering. J Biomech Eng 2022; 144:024505. [PMID: 34529040 PMCID: PMC10782870 DOI: 10.1115/1.4052432] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 08/22/2021] [Indexed: 01/12/2023]
Abstract
Atherosclerotic plaques can gradually develop in certain arteries. Disruption of fibrous tissue in plaques can result in plaque rupture and thromboembolism, leading to heart attacks and strokes. Collagen fibrils are important tissue building blocks and tissue strength depends on how fibrils are oriented. Fibril orientation in plaque tissue may potentially influence vulnerability to disruption. While X-ray scattering has previously been used to characterize fibril orientations in soft tissues and bones, it has never been used for characterization of human atherosclerotic plaque tissue. This study served to explore fibril orientation in specimens from human plaques using small angle X-ray scattering (SAXS). Plaque tissue was extracted from human femoral and carotid arteries, and each tissue specimen contained a region of calcified material. Three-dimensional (3D) collagen fibril orientation was determined along scan lines that started away from and then extended toward a given calcification. Fibrils were found to be oriented mainly in the circumferential direction of the plaque tissue at the majority of locations away from calcifications. However, in a number of cases, the dominant fibril direction differed near a calcification, changing from circumferential to longitudinal or thickness (radial) directions. Further study is needed to elucidate how these fibril orientations may influence plaque tissue stress-strain behavior and vulnerability to rupture.
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Affiliation(s)
- Herbert Silva
- NASA, 2101 NASA Parkway Building 13 R 208, Houston, TX 77058
| | - Christopher Tassone
- Stanford Synchrotron Radiation Lightsource, 2575 Sand Hill Road, Menlo Park, CA 94025
| | - Elsie Gyang Ross
- Division of Vascular Surgery, Stanford Medical Center, 300 Pasteur Drive, Stanford, CA 94305
| | - Jason T. Lee
- Division of Vascular Surgery, Stanford Medical Center, 300 Pasteur Drive, Stanford, CA 94305
| | - Wei Zhou
- Vascular Surgery Division, College of Medicine, University of Arizona, Tucson, AZ 85724
| | - Drew Nelson
- Mechanical Engineering Department, Stanford University, Stanford, CA 94305
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43
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Edechi CA, Amini M, Hamedani MK, Terceiro LE, Nickel BE, Leygue E, Myal Y. Comparison of Fixation Methods for the Detection of Claudin 1 and E-Cadherin in Breast Cancer Cell Lines by Immunofluorescence. J Histochem Cytochem 2022; 70:181-187. [PMID: 34715746 PMCID: PMC8777374 DOI: 10.1369/00221554211055240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The tight junction membrane protein claudin 1 and the adherens junction protein E-cadherin play critical roles in cell-cell communication and in cell signaling. As a result, their protein levels and distribution in cancer have been a focus of cancer researchers in recent years. The loss of sensitivity to contact inhibition and the establishment of invasive properties in cancer are thought to be a result of the mislocalization of these membrane proteins to the cytoplasm. However, reports on their distribution and levels have been inconsistent. It is therefore critical that the techniques used to determine the cellular localization of these proteins be both consistent and reliable. This study was undertaken to determine the optimal fixation method, methanol or formalin, for the detection of claudin 1 and E-cadherin by immunofluorescence in five different human breast cancer cell lines. Both methods exhibited staining of the cell membrane and cytoplasm, but the strongest and most distinct signals were obtained using methanol fixation. Interestingly, cell-specific differences were also observed that appeared to be associated with levels of claudin 1 and E-cadherin as seen by Western blotting. Therefore, when evaluating cellular localization of the junction proteins claudin 1 and E-cadherin, expression level and cell type differences must be considered.
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Affiliation(s)
| | | | | | | | - Barbara E. Nickel
- Institute of Cardiovascular Sciences, St.
Boniface Hospital Albrechtsen Research Centre, Winnipeg, MB, Canada
| | - Etienne Leygue
- Department of Biochemistry,Max Rady College of Medicine, University of
Manitoba, Winnipeg, MB, Canada, CancerCare Manitoba Research Institute,
Winnipeg, MB, Canada
| | - Yvonne Myal
- Yvonne Myal, Department of Pathology, Max
Rady College of Medicine, University of Manitoba, 401 Brodie Centre, 727
McDermot Avenue, Winnipeg, MB R3E 3P5, Canada. E-mail:
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44
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An R, Robbins D, Rey FE, Thibeault SL. Vocal fold mucus layer: Comparison of histological protocols for visualization in mice. Laryngoscope Investig Otolaryngol 2022; 7:444-453. [PMID: 35434350 PMCID: PMC9008169 DOI: 10.1002/lio2.743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 01/06/2022] [Accepted: 01/11/2022] [Indexed: 11/07/2022] Open
Affiliation(s)
- Ran An
- Department of Surgery, School of Medicine and Public Health University of Wisconsin‐Madison Madison Wisconsin USA
| | - Daniel Robbins
- Department of Surgery, School of Medicine and Public Health University of Wisconsin‐Madison Madison Wisconsin USA
| | - Federico E. Rey
- Department of Bacteriology, College of Agricultural and Life Sciences University of Wisconsin‐Madison Madison Wisconsin USA
| | - Susan L. Thibeault
- Department of Surgery, School of Medicine and Public Health University of Wisconsin‐Madison Madison Wisconsin USA
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45
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Tendler BC, Qi F, Foxley S, Pallebage-Gamarallage M, Menke RAL, Ansorge O, Hurley SA, Miller KL. A method to remove the influence of fixative concentration on postmortem T 2 maps using a kinetic tensor model. Hum Brain Mapp 2021; 42:5956-5972. [PMID: 34541735 PMCID: PMC8596944 DOI: 10.1002/hbm.25661] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 08/06/2021] [Accepted: 08/30/2021] [Indexed: 12/20/2022] Open
Abstract
Formalin fixation has been shown to substantially reduce T2 estimates, primarily driven by the presence of fixative in tissue. Prior to scanning, post‐mortem samples are often placed into a fluid that has more favourable imaging properties. This study investigates whether there is evidence for a change in T2 in regions close to the tissue surface due to fixative outflux into this surrounding fluid. Furthermore, we investigate whether a simulated spatial map of fixative concentration can be used as a confound regressor to reduce T2 inhomogeneity. To achieve this, T2 maps and diffusion tensor estimates were obtained in 14 whole, formalin‐fixed post‐mortem brains placed in Fluorinert approximately 48 hr prior to scanning. Seven brains were fixed with 10% formalin and seven brains were fixed with 10% neutral buffered formalin (NBF). Fixative outflux was modelled using a proposed kinetic tensor (KT) model, which incorporates voxelwise diffusion tensor estimates to account for diffusion anisotropy and tissue‐specific diffusion coefficients. Brains fixed with 10% NBF revealed a spatial T2 pattern consistent with modelled fixative outflux. Confound regression of fixative concentration reduced T2 inhomogeneity across both white and grey matter, with the greatest reduction attributed to the KT model versus simpler models of fixative outflux. No such effect was observed in brains fixed with 10% formalin. Correlations between the transverse relaxation rate R2 and ferritin/myelin proteolipid protein (PLP) histology lead to an increased similarity for the relationship between R2 and PLP for the two fixative types after KT correction.
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Affiliation(s)
- Benjamin C Tendler
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford
| | - Feng Qi
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford
| | - Sean Foxley
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford.,Department of Radiology, University of Chicago, Chicago, Illinois, USA
| | | | - Ricarda A L Menke
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford
| | - Olaf Ansorge
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Samuel A Hurley
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford.,Department of Radiology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Karla L Miller
- Wellcome Centre for Integrative Neuroimaging, FMRIB, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford
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Nishikawa T, Suzuki H, Takeuchi M, Tatsumi S, Tachibana Y, Ohbayashi C, Kobayashi TK, Norimatsu Y. A study on preserving endometrial glandular architecture during preparation using BD SurePath™ liquid-based cytology reagents: Cellular fixation with preservative fluid requires at least 18 h. Cytopathology 2021; 33:357-361. [PMID: 34882854 DOI: 10.1111/cyt.13087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/23/2021] [Accepted: 12/06/2021] [Indexed: 11/30/2022]
Abstract
INTRODUCTION This study aimed to determine the causes of disruption of the three-dimensional architecture of endometrial glands prepared using BD SurePath™ liquid-based cytology (SP-LBC) reagents. One sample preparation method for endometrial cytology is presented in which this three-dimensional architecture can be retained. METHODS SP-LBC specimens were prepared by the following three methods: (1) using the BD PrepMateTM (PrepMate) System after cellular fixation for 1-6 h (method A); (2) without using the PrepMate System after cellular fixation for 1-6 h (method B); and (3) using the PrepMate System after cellular fixation for at least 18 h (method C). Size and numbers of endometrial cell clusters and numbers of solitary scattered cells were then evaluated. RESULTS Significantly higher numbers of cell clusters with a major axis of 200 μm or more were yielded by method C (71.3 ± 57.2) than methods A (9.3 ± 5.9, P < 0.001) or B (44.3 ± 28.8, P < 0.05). Method B yielded significantly higher numbers of cell clusters than method A (P < 0.001). Method A (132.2 ± 107.7, p < 0.001) yielded significantly higher numbers of solitary scattered cells than methods B (29.1 ± 14.8) and C (35.7 ± 23.3). No significant difference in solitary cell numbers was found between methods B and C. CONCLUSIONS Retention of endometrial glandular architecture is rendered possible by allowing sample fixation times of 18 h or more when preparing specimens using the PrepMate System.
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Affiliation(s)
- Takeshi Nishikawa
- Department of Pathology, Nara Medical University Hospital, Nara, Japan
| | - Hisae Suzuki
- Department of Pathology, Nara Medical University Hospital, Nara, Japan
| | - Mao Takeuchi
- Department of Pathology, Nara Medical University Hospital, Nara, Japan
| | - Shigenobu Tatsumi
- Department of Pathology, Nara Medical University Hospital, Nara, Japan
| | - Yuma Tachibana
- Department of Medical Technology, Yamatotakada Municipal Hospital, Nara, Japan
| | - Chiho Ohbayashi
- Department of Diagnostic Pathology, Nara Medical University School of Medicine, Nara, Japan
| | - Tadao K Kobayashi
- Cancer Education and Research Center, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Yoshiaki Norimatsu
- Departments of Medical Technology, Faculty of Health Sciences, Ehime Prefectural University of Health Sciences, Ehime, Japan
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[Expert Consensus on Tumor Mutational Burden for Immunotherapy in Lung Cancer]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2021; 24:743-752. [PMID: 34802204 PMCID: PMC8607287 DOI: 10.3779/j.issn.1009-3419.2021.101.40] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Lung cancer is one of the malignant tumors with the highest morbidity and mortality in the world. Immune checkpoint inhibitors (ICIs), including programmed cell death 1 (PD-1) antibody, programmed cell death ligand 1 (PD-L1) antibody, and cytotoxic T lymphocyte associated protein 4 (CTLA-4) antibody. It has brought significant survival benefits to some patients with advanced lung cancer and changed the treatment pattern of advanced lung cancer. Previous studies have shown that the objective response rate of PD-1/PD-L1 antibody in advanced non-small cell lung cancer (NSCLC) is only about 20%. So reliable biomarkers are urgently needed to screen out the potential benefit population of ICIs and improve the clinical response rate. Tumor mutational burden (TMB) is an emerging biomarker of immunotherapy in addition to PD-L1 expression. There is little correlation between PD-L1 expression and TMB in lung cancer. It is estimated that TMB can expand the benefit population of immunotherapy. However, in clinical practice, the detection of TMB, the determination of cut-off value and the clinical guidance strategy are still not standardized. This consensus will give guiding suggestions on the detection and application scenarios of TMB, so as to promote the standardization of TMB application for immunotherapy in lung cancer.
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Fomitcheva-Khartchenko A, Rapsomaniki MA, Sobottka B, Schraml P, Kaigala GV. Spatial protein heterogeneity analysis in frozen tissues to evaluate tumor heterogeneity. PLoS One 2021; 16:e0259332. [PMID: 34797831 PMCID: PMC8604290 DOI: 10.1371/journal.pone.0259332] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 10/19/2021] [Indexed: 11/19/2022] Open
Abstract
A new workflow for protein-based tumor heterogeneity probing in tissues is here presented. Tumor heterogeneity is believed to be key for therapy failure and differences in prognosis in cancer patients. Comprehending tumor heterogeneity, especially at the protein level, is critical for tracking tumor evolution, and showing the presence of different phenotypical variants and their location with respect to tissue architecture. Although a variety of techniques is available for quantifying protein expression, the heterogeneity observed in the tissue is rarely addressed. The proposed method is validated in breast cancer fresh-frozen tissues derived from five patients. Protein expression is quantified on the tissue regions of interest (ROI) with a resolution of up to 100 μm in diameter. High heterogeneity values across the analyzed patients in proteins such as cytokeratin 7, β-actin and epidermal growth factor receptor (EGFR) using a Shannon entropy analysis are observed. Additionally, ROIs are clustered according to their expression levels, showing their location in the tissue section, and highlighting that similar phenotypical variants are not always located in neighboring regions. Interestingly, a patient with a phenotype related to increased aggressiveness of the tumor presents a unique protein expression pattern. In summary, a workflow for the localized extraction and protein analysis of regions of interest from frozen tissues, enabling the evaluation of tumor heterogeneity at the protein level is presented.
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Affiliation(s)
| | | | - Bettina Sobottka
- Department of Pathology and Molecular Pathology, University Hospital Zurich and University Zurich, Zurich, Switzerland
| | - Peter Schraml
- Department of Pathology and Molecular Pathology, University Hospital Zurich and University Zurich, Zurich, Switzerland
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Wagner A, Teufl M, Gold L, Lehner M, Obinger C, Sykacek P, Traxlmayr MW. PhosphoFlowSeq - A High-throughput Kinase Activity Assay for Screening Drug Resistance Mutations in EGFR. J Mol Biol 2021; 433:167210. [PMID: 34499921 DOI: 10.1016/j.jmb.2021.167210] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/29/2021] [Accepted: 08/14/2021] [Indexed: 12/30/2022]
Abstract
Drug resistance poses a major challenge for targeted cancer therapy. To be able to functionally screen large randomly mutated target gene libraries for drug resistance mutations, we developed a biochemically defined high-throughput assay termed PhosphoFlowSeq. Instead of selecting for proliferation or resistance to apoptosis, PhosphoFlowSeq directly analyzes the enzymatic activities of randomly mutated kinases, thereby reducing the dependency on the signaling network in the host cell. Moreover, simultaneous analysis of expression levels enables compensation for expression-based biases on a single cell level. Using EGFR and its kinase inhibitor erlotinib as a model system, we demonstrate that the clinically most relevant resistance mutation T790M is reproducibly detected at high frequencies after four independent PhosphoFlowSeq selection experiments. Moreover, upon decreasing the selection pressure, also mutations which only confer weak resistance were identified, including T854A and L792H. We expect that PhosphoFlowSeq will be a valuable tool for the prediction and functional screening of drug resistance mutations in kinases.
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Affiliation(s)
- Anja Wagner
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Austria; Department of Biotechnology, Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Magdalena Teufl
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Lukas Gold
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Manfred Lehner
- St. Anna Children's Cancer Research Institute, Vienna, Austria; Department of Pediatrics, St. Anna Kinderspital, Medical University of Vienna, Vienna, Austria
| | - Christian Obinger
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Peter Sykacek
- Department of Biotechnology, Institute for Computational Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Michael W Traxlmayr
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Austria.
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da Cunha IW, de Almeida Coudry R, de Macedo MP, de Assis EACP, Stefani S, Soares FA. A call to action: molecular pathology in Brazil. SURGICAL AND EXPERIMENTAL PATHOLOGY 2021. [DOI: 10.1186/s42047-021-00096-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Abstract
Background
Adoption of molecular pathology in Brazil is currently very limited. Of note, there are no programs for training new molecular pathologists in the country; thus, documents compiling nationally applicable information on molecular pathology are few.
Methods
A selected panel of Brazilian experts in fields related to molecular pathology were provided with a series of relevant questions to address prior to the multi-day conference. Within this conference, each narrative was discussed and edited by the entire group, through numerous drafts and rounds of discussion until a consensus was achieved.
Results
The panel proposes specific and realistic recommendations for implementing molecular pathology in cancer care in Brazil. In creating these recommendations, the authors strived to address all barriers to the widespread use and impediments to access mentioned previously within this manuscript.
Conclusion
This manuscript provides a review of molecular pathology principles as well as the current state of molecular pathology in Brazil. Additionally, the panel proposes practical and actionable recommendations for the implementation of molecular pathology throughout the country in order to increase awareness of the importance molecular pathology in Brazil.
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