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Hermansson RS, Lillsunde-Larsson G, Helenius G, Karlsson MG, Kaliff M, Olovsson M, Lindström AK. History of HPV in HPV-positive elderly women. Eur J Obstet Gynecol Reprod Biol X 2024; 22:100297. [PMID: 38496379 PMCID: PMC10944087 DOI: 10.1016/j.eurox.2024.100297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 01/29/2024] [Accepted: 03/06/2024] [Indexed: 03/19/2024] Open
Abstract
Background The aim of this study was to examine the natural course of HPV infection in women of 60 years and older who were HPV positive at inclusion, and any association between HPV positivity in historical samples and dysplasia outcome. Methods Eighty-nine women aged 60-82 years, who tested positive for HPV between 2012 and 2016 were included. Sampling for cytology and/or histology was also performed. HPV genotyping was carried out on archived material back to 1999. Results Of the 89 HPV-positive women 16 had HSIL, 34 had LSIL and 39 were benign at inclusion. Of the women with HSIL, 50.0% had the same HPV type in the archive samples, 12.5% had another type, and 37.5% were HPV negative. Among the 34 women with LSIL, 47.1% had the same HPV type in archive samples, 5.8% had another type, and 47.1% were HPV negative. Of the 39 women without dysplasia at inclusion, 25.6% had the same HPV type in archive samples, 5.1% had another HPV type and 69.2% were HPV negative. Conclusion Surprisingly few of the elderly women thus seem to have a history with the same or any HPV infection the years before being diagnosed with an HPV infection and dysplasia. The significance of an HPV infection for dysplasia development in elderly women is still not fully understood.
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Affiliation(s)
- Ruth S. Hermansson
- Department of Women’s and Children’s Health, Uppsala University, Uppsala, Sweden
- Department of Oncology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Gabriella Lillsunde-Larsson
- Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
- School of Health Sciences, Örebro University, Örebro, Sweden
| | - Gisela Helenius
- Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Mats G. Karlsson
- Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Malin Kaliff
- Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Matts Olovsson
- Department of Women’s and Children’s Health, Uppsala University, Uppsala, Sweden
| | - Annika K. Lindström
- Department of Women’s and Children’s Health, Uppsala University, Uppsala, Sweden
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2
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Böckers A, Schurr L, Schön M, Scholl T, Böckers TM, Steinestel K, Arndt A. Predictive molecular pathology after prolonged fixation: A study on tissue from anatomical body donors. Exp Mol Pathol 2024; 137:104899. [PMID: 38761540 DOI: 10.1016/j.yexmp.2024.104899] [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: 10/16/2023] [Revised: 03/19/2024] [Accepted: 05/06/2024] [Indexed: 05/20/2024]
Abstract
Histopathological assessment of tissue samples after prolonged formalin fixation has been described previously, but currently there is only limited knowledge regarding the feasibility of molecular pathology on such tissue. In this pilot study, we tested routine molecular pathology methods (DNA isolation, DNA pyrosequencing/next-generation sequencing, DNA methylation analysis, RT-PCR, clonality analysis and fluorescence in situ hybridization) on tissue samples from 11 tumor entities as well as non-neoplastic brain tissue from 43 body donors during the gross anatomy course at Ulm University (winter semester 2019/20 and 2020/21). The mean post mortem interval until fixation was 2.5 ± 1.6 days (range, 1-6 days). Fixation was performed with aqueous formaldehyde solution (formalin, 1.5-2%). The mean storage time of body donors was 12.8 ± 5.6 months (range, 7-25 months). While most diagnostic methods were successful, samples showed significant variability in DNA quality and evaluability. DNA pyrosequencing as well as next-generation sequencing was successful in all investigated samples. Methylation analyses were partially not successful in some extend due to limited intact DNA yield for these analyses. Taken together, the use of prolonged formalin-fixed tissue samples from body donors offers new avenues in research and education, as these samples could be used for morpho-molecular studies and the establishment of biobanks, especially for tissue types that cannot be preserved and studied in vivo. Pathological ward rounds, sample collection, and histopathological and molecular workup have been integrated in the gross anatomy course in Ulm as an integral part of the curriculum, linking anatomy and pathology and providing medical students early insight into the broad field of (molecular) pathology.
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Affiliation(s)
- Anja Böckers
- Institute for Anatomy and Cell Biology, Medical Faculty, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Leon Schurr
- Institute for Anatomy and Cell Biology, Medical Faculty, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Michael Schön
- Institute for Anatomy and Cell Biology, Medical Faculty, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Tatjana Scholl
- Institute of Pathology and Molecular Pathology, Federal Army Hospital, Oberer Eselsberg 40, 89081 Ulm, Germany
| | - Tobias M Böckers
- Institute for Anatomy and Cell Biology, Medical Faculty, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Konrad Steinestel
- Institute of Pathology and Molecular Pathology, Federal Army Hospital, Oberer Eselsberg 40, 89081 Ulm, Germany
| | - Annette Arndt
- Institute of Pathology and Molecular Pathology, Federal Army Hospital, Oberer Eselsberg 40, 89081 Ulm, Germany.
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Sunitha Kumary VUN, Venters BJ, Raman K, Sen S, Estève PO, Cowles MW, Keogh MC, Pradhan S. Emerging Approaches to Profile Accessible Chromatin from Formalin-Fixed Paraffin-Embedded Sections. EPIGENOMES 2024; 8:20. [PMID: 38804369 PMCID: PMC11130958 DOI: 10.3390/epigenomes8020020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 05/06/2024] [Indexed: 05/29/2024] Open
Abstract
Nucleosomes are non-uniformly distributed across eukaryotic genomes, with stretches of 'open' chromatin strongly associated with transcriptionally active promoters and enhancers. Understanding chromatin accessibility patterns in normal tissue and how they are altered in pathologies can provide critical insights to development and disease. With the advent of high-throughput sequencing, a variety of strategies have been devised to identify open regions across the genome, including DNase-seq, MNase-seq, FAIRE-seq, ATAC-seq, and NicE-seq. However, the broad application of such methods to FFPE (formalin-fixed paraffin-embedded) tissues has been curtailed by the major technical challenges imposed by highly fixed and often damaged genomic material. Here, we review the most common approaches for mapping open chromatin regions, recent optimizations to overcome the challenges of working with FFPE tissue, and a brief overview of a typical data pipeline with analysis considerations.
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Affiliation(s)
| | - Bryan J. Venters
- EpiCypher Inc., Durham, NC 27709, USA; (V.U.N.S.K.); (B.J.V.); (M.W.C.)
| | - Karthikeyan Raman
- Genome Biology Division, New England Biolabs, Ipswich, MA 01983, USA; (K.R.); (S.S.); (P.-O.E.)
| | - Sagnik Sen
- Genome Biology Division, New England Biolabs, Ipswich, MA 01983, USA; (K.R.); (S.S.); (P.-O.E.)
| | - Pierre-Olivier Estève
- Genome Biology Division, New England Biolabs, Ipswich, MA 01983, USA; (K.R.); (S.S.); (P.-O.E.)
| | - Martis W. Cowles
- EpiCypher Inc., Durham, NC 27709, USA; (V.U.N.S.K.); (B.J.V.); (M.W.C.)
| | | | - Sriharsa Pradhan
- Genome Biology Division, New England Biolabs, Ipswich, MA 01983, USA; (K.R.); (S.S.); (P.-O.E.)
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Pruszkowska-Przybylska P, Dupont ME, Jacobsen SB, Smerup M, Tfelt-Hansen J, Morling N, Andersen JD. Evaluation of DNAmAge in paired fresh, frozen, and formalin-fixed paraffin-embedded heart tissues. PLoS One 2024; 19:e0299557. [PMID: 38718072 PMCID: PMC11078437 DOI: 10.1371/journal.pone.0299557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 02/12/2024] [Indexed: 05/12/2024] Open
Abstract
The continued development in methylome analysis has enabled a more precise assessment of DNA methylation, but treatment of target tissue prior to analysis may affect DNA analysis. Prediction of age based on methylation levels in the genome (DNAmAge) has gained much interest in disease predisposition (biological age estimation), but also in chronological donor age estimation in crime case samples. Various epigenetic clocks were designed to predict the age. However, it remains unknown how the storage of the tissues affects the DNAmAge estimation. In this study, we investigated the storage method impact of DNAmAge by the comparing the DNAmAge of the two commonly used storage methods, freezing and formalin-fixation and paraffin-embedding (FFPE) to DNAmAge of fresh tissue. This was carried out by comparing paired heart tissue samples of fresh tissue, samples stored by freezing and FFPE to chronological age and whole blood samples from the same individuals. Illumina EPIC beadchip array was used for methylation analysis and the DNAmAge was evaluated with the following epigenetic clocks: Horvath, Hannum, Levine, Horvath skin+blood clock (Horvath2), PedBE, Wu, BLUP, EN, and TL. We observed differences in DNAmAge among the storage conditions. FFPE samples showed a lower DNAmAge compared to that of frozen and fresh samples. Additionally, the DNAmAge of the heart tissue was lower than that of the whole blood and the chronological age. This highlights caution when evaluating DNAmAge for FFPE samples as the results were underestimated compared with fresh and frozen tissue samples. Furthermore, the study also emphasizes the need for a DNAmAge model based on heart tissue samples for an accurate age estimation.
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Affiliation(s)
| | - Mikkel Eriksen Dupont
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Stine Bøttcher Jacobsen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Morten Smerup
- Department of Cardiothoracic Surgery, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Jacob Tfelt-Hansen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Cardiology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jeppe Dyrberg Andersen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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5
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Ferencz B, Török K, Pipek O, Fillinger J, Csende K, Lantos A, Černeková R, Mitták M, Škarda J, Delongová P, Megyesfalvi E, Schelch K, Lang C, Solta A, Boettiger K, Brcic L, Lindenmann J, Rényi-Vámos F, Aigner C, Berta J, Megyesfalvi Z, Döme B. Expression patterns of novel immunotherapy targets in intermediate- and high-grade lung neuroendocrine neoplasms. Cancer Immunol Immunother 2024; 73:114. [PMID: 38693435 PMCID: PMC11063022 DOI: 10.1007/s00262-024-03704-7] [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: 11/06/2023] [Accepted: 04/14/2024] [Indexed: 05/03/2024]
Abstract
BACKGROUND Advancements in immunotherapeutic approaches only had a modest impact on the therapy of lung neuroendocrine neoplasms (LNENs). Our multicenter study aimed to investigate the expression patterns of novel immunotherapy targets in intermediate- and high-grade LNENs. METHODS The expressions of V-domain Ig suppressor of T cell activation (VISTA), OX40L, Glucocorticoid-induced TNF receptor (GITR), and T cell immunoglobulin and mucin domain 3 (TIM3) proteins were measured by immunohistochemistry in surgically resected tumor samples of 26 atypical carcinoid (AC), 49 large cell neuroendocrine lung cancer (LCNEC), and 66 small cell lung cancer (SCLC) patients. Tumor and immune cells were separately scored. RESULTS Tumor cell TIM3 expression was the highest in ACs (p < 0.001), whereas elevated tumor cell GITR levels were characteristic for both ACs and SCLCs (p < 0.001 and p = 0.011, respectively). OX40L expression of tumor cells was considerably lower in ACs (vs. SCLCs; p < 0.001). Tumor cell VISTA expression was consistently low in LNENs, with no significant differences across histological subtypes. ACs were the least immunogenic tumors concerning immune cell abundance (p < 0.001). Immune cell VISTA and GITR expressions were also significantly lower in these intermediate-grade malignancies than in SCLCs or in LCNECs. Immune cell TIM3 and GITR expressions were associated with borderline prognostic significance in our multivariate model (p = 0.057 and p = 0.071, respectively). CONCLUSIONS LNEN subtypes have characteristic and widely divergent VISTA, OX40L, GITR, and TIM3 protein expressions. By shedding light on the different expression patterns of these immunotherapy targets, the current multicenter study provides support for the future implementation of novel immunotherapeutic approaches.
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Affiliation(s)
- Bence Ferencz
- Department of Thoracic Surgery, Semmelweis University and National Institute of Oncology, Budapest, Hungary
- National Koranyi Institute of Pulmonology, Budapest, Hungary
| | - Klára Török
- Department of Thoracic Surgery, Semmelweis University and National Institute of Oncology, Budapest, Hungary
- National Koranyi Institute of Pulmonology, Budapest, Hungary
| | - Orsolya Pipek
- Department of Physics of Complex Systems, Eotvos Lorand University, Budapest, Hungary
| | - János Fillinger
- National Koranyi Institute of Pulmonology, Budapest, Hungary
| | - Kristóf Csende
- Department of Thoracic Surgery, Semmelweis University and National Institute of Oncology, Budapest, Hungary
| | - András Lantos
- National Koranyi Institute of Pulmonology, Budapest, Hungary
| | - Radoslava Černeková
- Department of Pulmonary Diseases and Tuberculosis, University Hospital Ostrava and Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
| | - Marcel Mitták
- Surgical Clinic, University Hospital Ostrava and Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
| | - Jozef Škarda
- Medical Faculty, Institute of Clinical and Molecular Pathology, Palacky University Olomouc, Olomouc, Czech Republic
- Department of Pathology, University Hospital Ostrava and Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
| | - Patricie Delongová
- Department of Pathology, University Hospital Ostrava and Faculty of Medicine, University of Ostrava, Ostrava, Czech Republic
| | - Evelyn Megyesfalvi
- Department of Thoracic Surgery, Semmelweis University and National Institute of Oncology, Budapest, Hungary
- Department of Clinical Pharmacology, National Institute of Oncology, Chest and Abdominal Tumors Chemotherapy "B", Budapest, Hungary
| | - Karin Schelch
- Department of Thoracic Surgery, Comprehensive Cancer Center Vienna, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Center for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Christian Lang
- Department of Thoracic Surgery, Comprehensive Cancer Center Vienna, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
- Division of Pulmonology, Department of Medicine II, Medical University of Vienna, Vienna, Austria
| | - Anna Solta
- Department of Thoracic Surgery, Comprehensive Cancer Center Vienna, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
| | - Kristiina Boettiger
- Department of Thoracic Surgery, Comprehensive Cancer Center Vienna, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
| | - Luka Brcic
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Jörg Lindenmann
- Division of Thoracic and Hyperbaric Surgery, Department of Surgery, Medical University of Graz, Graz, Austria
| | - Ferenc Rényi-Vámos
- Department of Thoracic Surgery, Semmelweis University and National Institute of Oncology, Budapest, Hungary
- National Koranyi Institute of Pulmonology, Budapest, Hungary
- National Institute of Oncology and National Tumor Biology Laboratory, Budapest, Hungary
| | - Clemens Aigner
- Department of Thoracic Surgery, Comprehensive Cancer Center Vienna, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
| | - Judit Berta
- National Koranyi Institute of Pulmonology, Budapest, Hungary.
| | - Zsolt Megyesfalvi
- Department of Thoracic Surgery, Semmelweis University and National Institute of Oncology, Budapest, Hungary
- National Koranyi Institute of Pulmonology, Budapest, Hungary
- Department of Thoracic Surgery, Comprehensive Cancer Center Vienna, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria
| | - Balázs Döme
- Department of Thoracic Surgery, Semmelweis University and National Institute of Oncology, Budapest, Hungary.
- National Koranyi Institute of Pulmonology, Budapest, Hungary.
- Department of Thoracic Surgery, Comprehensive Cancer Center Vienna, Medical University of Vienna, Waehringer Guertel 18-20, 1090, Vienna, Austria.
- Department of Translational Medicine, Lund University, Lund, Sweden.
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6
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Lepore T, Macrae AI, Cantón GJ, Cantile C, Martineau HM, Palarea-Albaladejo J, Cahalan S, Underwood C, Katzer F, Chianini F. Evaluation of species-specific polyclonal antibodies to detect and differentiate between Neospora caninum and Toxoplasma gondii. J Vet Diagn Invest 2024; 36:418-427. [PMID: 38420701 PMCID: PMC11110786 DOI: 10.1177/10406387241234322] [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: 03/02/2024] Open
Abstract
Neosporosis and toxoplasmosis are major causes of abortion in livestock worldwide, leading to substantial economic losses. Detection tools are fundamental to the diagnosis and management of those diseases. Current immunohistochemistry (IHC) tests, using sera raised against whole parasite lysates, have not been able to distinguish between Toxoplasma gondii and Neospora caninum. We used T. gondii and N. caninum recombinant proteins, expressed in Escherichia coli and purified using insoluble conditions, to produce specific polyclonal rabbit antisera. We aimed to develop species-specific sera that could be used in IHC on formalin-fixed, paraffin-embedded (FFPE) tissue sections to improve the diagnosis of ruminant abortions caused by protozoa. Two polyclonal rabbit sera, raised against recombinant proteins, anti-Neospora-rNcSRS2 and anti-Toxoplasma-rTgSRS2, had specificity for the parasite they were raised against. We tested the specificity for each polyclonal serum using FFPE tissue sections known to be infected with T. gondii and N. caninum. The anti-Neospora-rNcSRS2 serum labeled specifically only N. caninum-infected tissue blocks, and the anti-Toxoplasma-rTgSRS2 serum was specific to only T. gondii-infected tissues. Moreover, tissues from 52 cattle and 19 sheep previously diagnosed by lesion profiles were tested using IHC with our polyclonal sera and PCR. The overall agreement between IHC and PCR was 90.1% for both polyclonal anti-rNcSRS2 and anti-rTgSRS2 sera. The polyclonal antisera were specific and allowed visual confirmation of protozoan parasites by IHC, but they were not as sensitive as PCR testing.
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Affiliation(s)
| | - Alastair I. Macrae
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, Scotland, UK
| | - Germán J. Cantón
- Instituto Nacional de Tecnología Agropecuaria, Balcarce, Argentina
| | | | | | | | - Stephen Cahalan
- Department of Infectious Diseases, Royal Veterinary College, London, UK
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Delhaye M, LeDue J, Robinson K, Xu Q, Zhang Q, Oku S, Zhang P, Craig AM. Adaptation of Magnified Analysis of the Proteome for Excitatory Synaptic Proteins in Varied Samples and Evaluation of Cell Type-Specific Distributions. J Neurosci 2024; 44:e1291232024. [PMID: 38360747 PMCID: PMC10993037 DOI: 10.1523/jneurosci.1291-23.2024] [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: 07/11/2023] [Revised: 02/02/2024] [Accepted: 02/07/2024] [Indexed: 02/17/2024] Open
Abstract
Growing evidence suggests a remarkable diversity and complexity in the molecular composition of synapses, forming the basis for the brain to execute complex behaviors. Hence, there is considerable interest in visualizing the spatial distribution of such molecular diversity at individual synapses within intact brain circuits. Yet this task presents significant technical challenges. Expansion microscopy approaches have revolutionized our view of molecular anatomy. However, their use to study synapse-related questions outside of the labs developing them has been limited. Here we independently adapted a version of Magnified Analysis of the Proteome (MAP) and present a step-by-step protocol for visualizing over 40 synaptic proteins in brain circuits. Surprisingly, our findings show that the advantage of MAP over conventional immunolabeling was primarily due to improved antigen recognition and secondarily physical expansion. Furthermore, we demonstrated the versatile use of MAP in brains perfused with paraformaldehyde or fresh-fixed with formalin and in formalin-fixed paraffin-embedded tissue. These tests expand the potential applications of MAP to combinations with slice electrophysiology or clinical pathology specimens. Using male and female mice expressing YFP-ChR2 exclusively in interneurons, we revealed a distinct composition of AMPA and NMDA receptors and Shank family members at synapses on hippocampal interneurons versus on pyramidal neurons. Quantitative single synapse analyses yielded comprehensive cell type distributions of synaptic proteins and their relationships. These findings exemplify the value of the versatile adapted MAP procedure presented here as an accessible tool for the broad neuroscience community to unravel the complexity of the "synaptome" across brain circuits and disease states.
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Affiliation(s)
- Mathias Delhaye
- Djavad Mowafaghian Centre for Brain Health and Department of Psychiatry, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada
| | - Jeffrey LeDue
- Djavad Mowafaghian Centre for Brain Health and Department of Psychiatry, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada
| | - Kaylie Robinson
- Djavad Mowafaghian Centre for Brain Health and Department of Psychiatry, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada
| | - Qin Xu
- Department of Neurosciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106
| | - Qian Zhang
- Department of Neurosciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106
| | - Shinichiro Oku
- Djavad Mowafaghian Centre for Brain Health and Department of Psychiatry, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada
| | - Peng Zhang
- Djavad Mowafaghian Centre for Brain Health and Department of Psychiatry, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada
- Department of Neurosciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106
| | - Ann Marie Craig
- Djavad Mowafaghian Centre for Brain Health and Department of Psychiatry, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada
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Grbavac L, Šikić A, Kostešić P, Šoštarić-Zuckermann IC, Mojčec Perko V, Boras J, Bata I, Musulin A, Kostanjšak T, Živičnjak T. Comprehensive Diagnosis, Treatment, and Outcome of Taenia crassiceps Cysticercosis in a Ring-Tailed Lemur ( Lemur catta) from a Croatian Zoo: No Longer Unusual? Pathogens 2024; 13:283. [PMID: 38668238 PMCID: PMC11055053 DOI: 10.3390/pathogens13040283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 03/19/2024] [Accepted: 03/25/2024] [Indexed: 04/29/2024] Open
Abstract
Taenia crassiceps is a zoonotic tapeworm of the genus Taenia that is distributed throughout the Northern Hemisphere. Wild and domestic carnivores are final hosts, while rodents and rabbits are primarily intermediate hosts, although many other mammals may harbour the larval stage, Cysticercus longicollis. This case report aims to describe C. longicollis infection in a lemur and molecularly characterise the isolated parasite. The excised lesion was subjected to morphological and histopathological examination, which revealed cysticerci of the tapeworm. Formalin-fixed and paraffin-embedded block (FFPEB), as well as the cysticerci fixed with formalin stored for one year, were subjected to molecular analysis, which aimed at detecting the partial mitochondrial cytochrome c oxidase subunit 1 (cox1) gene of Taenia sp. Based on the morphological characteristics, the parasite was identified as a metacestode of T. crassiceps. The presence of the cox1 gene was detected using polymerase chain reaction (PCR) in all samples. A randomly selected PCR product was sequenced and compared with other sequences from the GenBank database, confirming that the detected parasite was T. crassiceps. This article reports the first case of T. crassiceps cysticercosis in a lemur (Lemur catta) in Croatia and emphasises the potential risk of transmission from wild carnivores.
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Affiliation(s)
- Lea Grbavac
- Parasitology and Invasive Diseases Unit, Faculty of Veterinary Medicine, Heinzelova 55, 10 000 Zagreb, Croatia; (A.Š.); (T.Ž.)
| | - Ana Šikić
- Parasitology and Invasive Diseases Unit, Faculty of Veterinary Medicine, Heinzelova 55, 10 000 Zagreb, Croatia; (A.Š.); (T.Ž.)
| | - Petar Kostešić
- Clinic for Surgery, Orthopaedics and Ophthalmology, Faculty of Veterinary Medicine, Heinzelova 55, 10 000 Zagreb, Croatia; (P.K.); (A.M.)
| | | | - Vesna Mojčec Perko
- Microbiology and Infectious Diseases Unit, Faculty of Veterinary Medicine, Heinzelova 55, 10 000 Zagreb, Croatia;
| | - Jadranko Boras
- Zagreb Zoo, Fakultetsko dobro Street 1, 10 000 Zagreb, Croatia; (J.B.); (I.B.)
| | - Ingeborg Bata
- Zagreb Zoo, Fakultetsko dobro Street 1, 10 000 Zagreb, Croatia; (J.B.); (I.B.)
| | - Andrija Musulin
- Clinic for Surgery, Orthopaedics and Ophthalmology, Faculty of Veterinary Medicine, Heinzelova 55, 10 000 Zagreb, Croatia; (P.K.); (A.M.)
| | - Tara Kostanjšak
- Fitzpatrick Referrals, Halfway Lane, Eashing, Godalming GU7 2QQ, UK;
| | - Tatjana Živičnjak
- Parasitology and Invasive Diseases Unit, Faculty of Veterinary Medicine, Heinzelova 55, 10 000 Zagreb, Croatia; (A.Š.); (T.Ž.)
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Bomsztyk K, Mar D, Denisenko O, Powell S, Vishnoi M, Delegard J, Patel A, Ellenbogen RG, Ramakrishna R, Rostomily R. Analysis of gliomas DNA methylation: Assessment of pre-analytical variables. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.26.586350. [PMID: 38586048 PMCID: PMC10996653 DOI: 10.1101/2024.03.26.586350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Precision oncology is driven by molecular biomarkers. For glioblastoma multiforme (GBM), the most common malignant adult primary brain tumor, O6-methylguanine-DNA methyltransferase ( MGMT ) gene DNA promoter methylation is an important prognostic and treatment clinical biomarker. Time consuming pre-analytical steps such as biospecimen storage before fixing, sampling, and processing are major sources of errors and batch effects, that are further confounded by intra-tumor heterogeneity of MGMT promoter methylation. To assess the effect of pre-analytical variables on GBM DNA methylation, tissue storage/sampling (CryoGrid), sample preparation multi-sonicator (PIXUL) and 5-methylcytosine (5mC) DNA immunoprecipitation (Matrix MeDIP-qPCR/seq) platforms were used. MGMT promoter CpG methylation was examined in 173 surgical samples from 90 individuals, 50 of these were used for intra-tumor heterogeneity studies. MGMT promoter methylation levels in paired frozen and formalin fixed paraffin embedded (FFPE) samples were very close, confirming suitability of FFPE for MGMT promoter methylation analysis in clinical settings. Matrix MeDIP-qPCR yielded similar results to methylation specific PCR (MS-PCR). Warm ex-vivo ischemia (37°C up to 4hrs) and 3 cycles of repeated sample thawing and freezing did not alter 5mC levels at MGMT promoter, exon and upstream enhancer regions, demonstrating the resistance of DNA methylation to the most common variations in sample processing conditions that might be encountered in research and clinical settings. 20-30% of specimens exhibited intratumor heterogeneity in the MGMT DNA promoter methylation. Collectively these data demonstrate that variations in sample fixation, ischemia duration and temperature, and DNA methylation assay technique do not have significant impact on assessment of MGMT promoter methylation status. However, intratumor methylation heterogeneity underscores the need for histologic verification and value of multiple biopsies at different GBM geographic tumor sites in assessment of MGMT promoter methylation. Matrix-MeDIP-seq analysis revealed that MGMT promoter methylation status clustered with other differentially methylated genomic loci (e.g. HOXA and lncRNAs), that are likewise resilient to variation in above post-resection pre-analytical conditions. These MGMT -associated global DNA methylation patterns offer new opportunities to validate more granular data-based epigenetic GBM clinical biomarkers where the CryoGrid-PIXUL-Matrix toolbox could prove to be useful.
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10
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Eccher A, Seminati D, L’Imperio V, Casati G, Pilla D, Malapelle U, Piga I, Bindi G, Marando A, Bonoldi E, Dainese E, Riefolo M, D’Errico A, Costantini M, Lugli A, Grassi S, Scarpa A, Dei Tos AP, Pagni F. Pathology Laboratory Archives: Conservation Quality of Nucleic Acids and Proteins for NSCLC Molecular Testing. J Pers Med 2024; 14:333. [PMID: 38672960 PMCID: PMC11050929 DOI: 10.3390/jpm14040333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 03/15/2024] [Accepted: 03/20/2024] [Indexed: 04/28/2024] Open
Abstract
In the molecular era, proper archival conditions within pathology laboratories are crucial, especially for formalin-fixed paraffin-embedded (FFPE) tissue specimens retrieved years after the original diagnosis. Indeed, improper preservation can impact the integrity of nucleic acids and protein antigens. This study evaluates the quality status of stored FFPE blocks using multilevel omics approaches. FFPE blocks from 45 Non-Small Cell Lung Carcinoma (NSCLC) cases were analyzed. The blocks were collected from six different pathology archives across Italy with distinct environmental characteristics. Nucleic acids' quantity and quality, as well as protein antigens, were assessed using various techniques, including MALDI-MSI. RNA was quantitatively higher, but more fragmented, compared to DNA. DNA quantity and quality were suitable for molecular analyses in 94.4% and 62.3% of samples, respectively. RNA quantity was adequate across all samples, but it was optimal only in 22.3% of cases. DNA quality started to deteriorate after 6-8 years, whereas RNA quality diminished only after 10 years of storage. These data might suggest a particular DNA susceptibility to FFPE blocks conservation. Immunohistochemical intensity decreased significantly after 6-8 years of storage, and MALDI-MSI analysis revealed that younger tissue blocks contained more unique proteomic signals than the older ones. This study emphasizes the importance of proper FFPE archiving conditions for molecular analyses. Governance should prioritize attention to pathology archives to ensure quality preservation and optimize predictive testing. By elucidating the nuances of FFPE block storage, this research paves the way for enhanced molecular diagnostics and therapeutic insights regarding oncology and beyond.
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Affiliation(s)
- Albino Eccher
- Department of Diagnostics and Public Health, University of Modena and Reggio Emilia, 41121 Modena, Italy;
| | - Davide Seminati
- Department of Medicine and Surgery, Pathology, Fondazione IRCCS San Gerardo dei Tintori, University of Milano-Bicocca, 20900 Monza, Italy; (V.L.); (G.C.); (D.P.); (F.P.)
| | - Vincenzo L’Imperio
- Department of Medicine and Surgery, Pathology, Fondazione IRCCS San Gerardo dei Tintori, University of Milano-Bicocca, 20900 Monza, Italy; (V.L.); (G.C.); (D.P.); (F.P.)
| | - Gabriele Casati
- Department of Medicine and Surgery, Pathology, Fondazione IRCCS San Gerardo dei Tintori, University of Milano-Bicocca, 20900 Monza, Italy; (V.L.); (G.C.); (D.P.); (F.P.)
| | - Daniela Pilla
- Department of Medicine and Surgery, Pathology, Fondazione IRCCS San Gerardo dei Tintori, University of Milano-Bicocca, 20900 Monza, Italy; (V.L.); (G.C.); (D.P.); (F.P.)
| | - Umberto Malapelle
- Department of Public Health, Pathology, University of Naples Federico II, 80131 Naples, Italy;
| | - Isabella Piga
- Department of Biomedical Sciences, University of Cagliari, 09124 Cagliari, Italy;
- Proteomics and Metabolomics Unit, Department of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy;
| | - Greta Bindi
- Proteomics and Metabolomics Unit, Department of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy;
| | - Alessandro Marando
- Department of Pathology, ASST Grande Ospedale Niguarda, 20162 Milan, Italy; (A.M.); (E.B.)
| | - Emanuela Bonoldi
- Department of Pathology, ASST Grande Ospedale Niguarda, 20162 Milan, Italy; (A.M.); (E.B.)
| | - Emanuele Dainese
- Department of Pathology, ASST Valtellina e Alto Lario, 23100 Sondrio, Italy;
| | - Mattia Riefolo
- Pathology Unit, Department of Diagnostic Medicine and Prevention, Sant’Orsola-Malpighi Hospital, University of Bologna, 40138 Bologna, Italy; (M.R.); (A.D.)
| | - Antonia D’Errico
- Pathology Unit, Department of Diagnostic Medicine and Prevention, Sant’Orsola-Malpighi Hospital, University of Bologna, 40138 Bologna, Italy; (M.R.); (A.D.)
| | - Matteo Costantini
- Department of Pathology, University Hospital of Modena, 41121 Modena, Italy; (M.C.); (A.L.)
| | - Alberto Lugli
- Department of Pathology, University Hospital of Modena, 41121 Modena, Italy; (M.C.); (A.L.)
| | - Stefano Grassi
- Pathology Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy;
| | - Aldo Scarpa
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, 37126 Verona, Italy;
| | - Angelo Paolo Dei Tos
- Department of Pathology, University of Padua School of Medicine, Azienda Ospedale Università Padova, 35122 Padua, Italy;
| | - Fabio Pagni
- Department of Medicine and Surgery, Pathology, Fondazione IRCCS San Gerardo dei Tintori, University of Milano-Bicocca, 20900 Monza, Italy; (V.L.); (G.C.); (D.P.); (F.P.)
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11
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G Jagadeeshaprasad M, Zeng J, Zheng N. LC-MS bioanalysis of protein biomarkers and protein therapeutics in formalin-fixed paraffin-embedded tissue specimens. Bioanalysis 2024; 16:245-258. [PMID: 38226835 DOI: 10.4155/bio-2023-0210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024] Open
Abstract
Formalin-fixed paraffin-embedded (FFPE) is a form of preservation and preparation for biopsy specimens. FFPE tissue specimens are readily available as part of oncology studies because they are often collected for disease diagnosis or confirmation. FFPE tissue specimens could be extremely useful for retrospective studies on protein biomarkers because the samples preserved in FFPE blocks could be stable for decades. However, LC-MS bioanalysis of FFPE tissues poses significant challenges. In this Perspective, we review the benefits and recent developments in LC-MS approach for targeted protein biomarker and protein therapeutic analysis using FFPE tissues and their clinical and translational applications. We believe that LC-MS bioanalysis of protein biomarkers in FFPE tissue specimens represents a great potential for its clinical applications.
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Affiliation(s)
| | - Jianing Zeng
- Department of Protein Sciences & Mass Spectrometry, Translational Medicine, Bristol Myers Squibb, Princeton, NJ 08543, USA
| | - Naiyu Zheng
- Department of Protein Sciences & Mass Spectrometry, Translational Medicine, Bristol Myers Squibb, Princeton, NJ 08543, USA
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12
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Begum NF, Ramalingam K, Ramani P. Storage, Retention, and Use of Leftover Pathology Specimens: The Underestimated Treasures. Cureus 2024; 16:e53025. [PMID: 38410328 PMCID: PMC10895552 DOI: 10.7759/cureus.53025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/26/2024] [Indexed: 02/28/2024] Open
Abstract
The proper regulations for storage, retention, and use of archived specimens in pathology laboratories and academic institutions are yet to be established. These specimens could be used appropriately for research purposes. Ideal storage and retention in a controlled environment is necessary, and there is a lack of established rules regarding the ownership of the tissue specimens, paraffin blocks, and slides. Though there are numerous uses of formalin-fixed tissue specimens, blocks, and slides, there are also problems in archiving them that hinder their use. This review article addresses the above issues and proposes simple guidelines for the effective use of archived specimens.
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Affiliation(s)
- N Fazulunnisa Begum
- Oral Pathology and Microbiology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, IND
| | - Karthikeyan Ramalingam
- Oral Pathology and Microbiology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, IND
| | - Pratibha Ramani
- Oral Pathology and Microbiology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, IND
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13
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Mar D, Babenko IM, Zhang R, Noble WS, Denisenko O, Vaisar T, Bomsztyk K. A High-Throughput PIXUL-Matrix-Based Toolbox to Profile Frozen and Formalin-Fixed Paraffin-Embedded Tissues Multiomes. J Transl Med 2024; 104:100282. [PMID: 37924947 PMCID: PMC10872585 DOI: 10.1016/j.labinv.2023.100282] [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: 08/29/2023] [Revised: 10/23/2023] [Accepted: 10/27/2023] [Indexed: 11/06/2023] Open
Abstract
Large-scale high-dimensional multiomics studies are essential to unravel molecular complexity in health and disease. We developed an integrated system for tissue sampling (CryoGrid), analytes preparation (PIXUL), and downstream multiomic analysis in a 96-well plate format (Matrix), MultiomicsTracks96, which we used to interrogate matched frozen and formalin-fixed paraffin-embedded (FFPE) mouse organs. Using this system, we generated 8-dimensional omics data sets encompassing 4 molecular layers of intracellular organization: epigenome (H3K27Ac, H3K4m3, RNA polymerase II, and 5mC levels), transcriptome (messenger RNA levels), epitranscriptome (m6A levels), and proteome (protein levels) in brain, heart, kidney, and liver. There was a high correlation between data from matched frozen and FFPE organs. The Segway genome segmentation algorithm applied to epigenomic profiles confirmed known organ-specific superenhancers in both FFPE and frozen samples. Linear regression analysis showed that proteomic profiles, known to be poorly correlated with transcriptomic data, can be more accurately predicted by the full suite of multiomics data, compared with using epigenomic, transcriptomic, or epitranscriptomic measurements individually.
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Affiliation(s)
- Daniel Mar
- UW Medicine South Lake Union, University of Washington, Seattle, Washington; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington
| | - Ilona M Babenko
- Diabetes Institute, University of Washington, Seattle, Washington
| | - Ran Zhang
- Department of Genome Sciences, University of Washington, Seattle, Washington
| | - William Stafford Noble
- Department of Genome Sciences, University of Washington, Seattle, Washington; Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington
| | - Oleg Denisenko
- UW Medicine South Lake Union, University of Washington, Seattle, Washington
| | - Tomas Vaisar
- Diabetes Institute, University of Washington, Seattle, Washington
| | - Karol Bomsztyk
- UW Medicine South Lake Union, University of Washington, Seattle, Washington; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington; Matchstick Technologies, Inc, Kirkland, Washington.
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14
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Duivenvoorden AM, Claes BSR, van der Vloet L, Lubbers T, Glunde K, Olde Damink SWM, Heeren RMA, Lenaerts K. Lipidomic Phenotyping Of Human Small Intestinal Organoids Using Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging. Anal Chem 2023; 95:18443-18450. [PMID: 38060464 PMCID: PMC10733903 DOI: 10.1021/acs.analchem.3c03543] [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: 08/08/2023] [Revised: 10/29/2023] [Accepted: 11/06/2023] [Indexed: 12/20/2023]
Abstract
In the past decade, interest in organoids for biomedical research has surged, resulting in a higher demand for advanced imaging techniques. Traditional specimen embedding methods pose challenges, such as analyte delocalization and histological assessment. Here, we present an optimized sample preparation approach utilizing an Epredia M-1 cellulose-based embedding matrix, which preserves the structural integrity of fragile small intestinal organoids (SIOs). Additionally, background interference (delocalization of analytes, nonspecific (histological) staining, matrix ion clusters) was minimized, and we demonstrate the compatibility with matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI). With our approach, we can conduct label-free lipid imaging at the single-cell level, thereby yielding insights into the spatial distribution of lipids in both positive and negative ion modes. Moreover, M-1 embedding allows for an improved coregistration with histological and immunohistochemical (IHC) stainings, including MALDI-IHC, facilitating combined untargeted and targeted spatial information. Applying this approach, we successfully phenotyped crypt-like (CL) and villus-like (VL) SIOs, revealing that PE 36:2 [M - H]- (m/z 742.5) and PI 38:4 [M - H]- (m/z 885.5) display higher abundance in CL organoids, whereas PI 36:1 [M - H]- (m/z 863.6) was more prevalent in VL organoids. Our findings demonstrate the utility of M-1 embedding for advancing organoid research and unraveling intricate biological processes within these in vitro models.
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Affiliation(s)
- Annet
A. M. Duivenvoorden
- Department
of Surgery, NUTRIM School of Nutrition and Translational Research
in Metabolism, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Britt S. R. Claes
- The
Maastricht MultiModal Molecular Imaging (M4i) Institute, Division
of Imaging Mass Spectrometry (IMS), Maastricht
University, 6229 ER Maastricht, The Netherlands
| | - Laura van der Vloet
- The
Maastricht MultiModal Molecular Imaging (M4i) Institute, Division
of Imaging Mass Spectrometry (IMS), Maastricht
University, 6229 ER Maastricht, The Netherlands
| | - Tim Lubbers
- Department
of Surgery, Maastricht University Medical
Center+ (MUMC+), 6229 HX Maastricht, The Netherlands
- GROW
– School for Oncology and Developmental Biology, Maastricht University Medical Center+ (MUMC+), 6229 HX Maastricht, The Netherlands
| | - Kristine Glunde
- The
Russell H. Morgan Department of Radiology and Radiological Science,
Division of Cancer Imaging Research, The
Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States
- The
Sidney
Kimmel Comprehensive Cancer Center, The
Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States
- Department
of Biological Chemistry, The Johns Hopkins
School of Medicine, Baltimore, Maryland 21205, United States
| | - Steven W. M. Olde Damink
- Department
of Surgery, NUTRIM School of Nutrition and Translational Research
in Metabolism, Maastricht University, 6229 ER Maastricht, The Netherlands
- Department
of Surgery, Maastricht University Medical
Center+ (MUMC+), 6229 HX Maastricht, The Netherlands
- Department
of General, Gastrointestinal, Hepatobiliary and Transplant Surgery, RWTH Aachen University Hospital, 52074 Aachen, Germany
| | - Ron M. A. Heeren
- The
Maastricht MultiModal Molecular Imaging (M4i) Institute, Division
of Imaging Mass Spectrometry (IMS), Maastricht
University, 6229 ER Maastricht, The Netherlands
| | - Kaatje Lenaerts
- Department
of Surgery, NUTRIM School of Nutrition and Translational Research
in Metabolism, Maastricht University, 6229 ER Maastricht, The Netherlands
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15
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Afonso CL, Afonso AM. Next-Generation Sequencing for the Detection of Microbial Agents in Avian Clinical Samples. Vet Sci 2023; 10:690. [PMID: 38133241 PMCID: PMC10747646 DOI: 10.3390/vetsci10120690] [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: 10/13/2023] [Revised: 11/24/2023] [Accepted: 11/29/2023] [Indexed: 12/23/2023] Open
Abstract
Direct-targeted next-generation sequencing (tNGS), with its undoubtedly superior diagnostic capacity over real-time PCR (RT-PCR), and direct-non-targeted NGS (ntNGS), with its higher capacity to identify and characterize multiple agents, are both likely to become diagnostic methods of choice in the future. tNGS is a rapid and sensitive method for precise characterization of suspected agents. ntNGS, also known as agnostic diagnosis, does not require a hypothesis and has been used to identify unsuspected infections in clinical samples. Implemented in the form of multiplexed total DNA metagenomics or as total RNA sequencing, the approach produces comprehensive and actionable reports that allow semi-quantitative identification of most of the agents present in respiratory, cloacal, and tissue samples. The diagnostic benefits of the use of direct tNGS and ntNGS are high specificity, compatibility with different types of clinical samples (fresh, frozen, FTA cards, and paraffin-embedded), production of nearly complete infection profiles (viruses, bacteria, fungus, and parasites), production of "semi-quantitative" information, direct agent genotyping, and infectious agent mutational information. The achievements of NGS in terms of diagnosing poultry problems are described here, along with future applications. Multiplexing, development of standard operating procedures, robotics, sequencing kits, automated bioinformatics, cloud computing, and artificial intelligence (AI) are disciplines converging toward the use of this technology for active surveillance in poultry farms. Other advances in human and veterinary NGS sequencing are likely to be adaptable to avian species in the future.
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16
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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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17
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Pankiw M, Brezden-Masley C, Charames GS. Comprehensive genomic profiling for oncological advancements by precision medicine. Med Oncol 2023; 41:1. [PMID: 37993657 DOI: 10.1007/s12032-023-02228-x] [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: 06/14/2023] [Accepted: 10/25/2023] [Indexed: 11/24/2023]
Abstract
Considerable advancements in next generation sequencing (NGS) techniques have sparked the use of comprehensive genomic profiling (CGP) as a guiding tool for precision-centered oncological treatments. The past two decades have seen the completion of the human genome project, and the consequential invention of NGS. High-throughput sequencing technologies support the discovery and commonplace use of individualized cancer treatments, specifically immune-centered checkpoint inhibitor therapies, and oncogene and tumor suppressor gene targeted therapies. Nevertheless, CGP is not commonly used in all clinical settings. This review investigates the clinically relevant applications of CGP. Studies published between the years 2000-2023 have shown substantial evidence of the benefits of integrating CGP into routine care practice, while also making important comparisons to current-standard oncological treatment strategies. Findings of a comprehensive genomic profile includes predictive, prognostic, and diagnostic biomarkers, together with somatic mutation identification which can indicate the efficacy of immunotherapies and molecularly guided therapies. This review highlights the importance of CGP in identifying driver mutations in tumors that subsequently can be effectively targeted with molecular therapeutics and lead to drug discovery, allowing for increased precision in treating tumors selectively based on their specific genetic mutations, thereby improving patient outcomes.
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Affiliation(s)
- Maya Pankiw
- Department of Medicine, Mount Sinai Hospital, Toronto, ON, Canada
- Department of Pathology and Lab Medicine, Mount Sinai Hospital, Toronto, ON, Canada
| | - Christine Brezden-Masley
- Department of Medicine, Mount Sinai Hospital, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
- Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - George S Charames
- Department of Pathology and Lab Medicine, Mount Sinai Hospital, Toronto, ON, Canada.
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada.
- Department of Lab Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.
- Mount Sinai Services, Toronto, ON, Canada.
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18
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Li KYC, Dejea H, De Winne K, Bonnin A, D'Onofrio V, Cox JA, Garcia-Canadilla P, Lammens M, Cook AC, Bijnens B, Dendooven A. Feasibility and safety of synchrotron-based X-ray phase contrast imaging as a technique complementary to histopathology analysis. Histochem Cell Biol 2023; 160:377-389. [PMID: 37523091 DOI: 10.1007/s00418-023-02220-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2023] [Indexed: 08/01/2023]
Abstract
X-ray phase contrast imaging (X-PCI) is a powerful technique for high-resolution, three-dimensional imaging of soft tissue samples in a non-destructive manner. In this technical report, we assess the quality of standard histopathological techniques performed on formalin-fixed, paraffin-embedded (FFPE) human tissue samples that have been irradiated with different doses of X-rays in the context of an X-PCI experiment. The data from this study demonstrate that routine histochemical and immunohistochemical staining quality as well as DNA and RNA analyses are not affected by previous X-PCI on human FFPE samples. From these data we conclude it is feasible and acceptable to perform X-PCI on FFPE human biopsies.
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Affiliation(s)
- Kan Yan Chloe Li
- Institute of Cardiovascular Science, University College London, London, United Kingdom
| | - Hector Dejea
- Swiss Light Source, Paul Scherrer Institute, Villigen, Switzerland
- ETH Zurich, Zurich, Switzerland
- Department of Biomedical Engineering, Lund University, Lund, Sweden
- MAX IV Laboratory, Lund, Sweden
| | - Koen De Winne
- Department of Pathology, Antwerp University Hospital and University of Antwerp, Antwerp, Belgium
| | - Anne Bonnin
- Swiss Light Source, Paul Scherrer Institute, Villigen, Switzerland
| | | | - Janneke A Cox
- Faculty of Medicine and Life Sciences, Hasselt University, Hasselt, Belgium
- Department of Infectious Diseases and Immunity, Jessa Hospital, Hasselt, Belgium
| | - Patricia Garcia-Canadilla
- Interdisciplinary Cardiovascular Research Group, Sant Joan de Déu Research Institute (IRSJD), Barcelona, Spain
- BCNatal Barcelona Center for Maternal-Fetal and Neonatal Medicine, Hospital Sant Joan de Déu and Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Martin Lammens
- Department of Pathology, Antwerp University Hospital and University of Antwerp, Antwerp, Belgium
| | - Andrew C Cook
- Institute of Cardiovascular Science, University College London, London, United Kingdom
| | - Bart Bijnens
- ICREA, Barcelona, Spain
- IDIBAPS, Barcelona, Spain
| | - Amélie Dendooven
- Department of Pathology, Antwerp University Hospital and University of Antwerp, Antwerp, Belgium.
- Faculty of Medicine and Life Sciences, Hasselt University, Hasselt, Belgium.
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19
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Abbas ZN, Al-Saffar AZ, Jasim SM, Sulaiman GM. Comparative analysis between 2D and 3D colorectal cancer culture models for insights into cellular morphological and transcriptomic variations. Sci Rep 2023; 13:18380. [PMID: 37884554 PMCID: PMC10603139 DOI: 10.1038/s41598-023-45144-w] [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: 05/05/2023] [Accepted: 10/16/2023] [Indexed: 10/28/2023] Open
Abstract
Drug development is a time-consuming and expensive process, given the low success rate of clinical trials. Now, anticancer drug developments have shifted to three-dimensional (3D) models which are more likely to mimic tumor behavior compared to traditional two-dimensional (2D) cultures. A comparative study among different aspects was conducted between 2D and 3D cultures using colorectal cancer (CRC) cell lines, in addition, Formalin-Fixed Paraffin-Embedded (FFPE) block samples of patients with CRC were used for evaluation. Compared to the 2D culture, cells grown in 3D displayed significant (p < 0.01) differences in the pattern of cell proliferation over time, cell death phase profile, expression of tumorgenicity-related genes, and responsiveness to 5-fluorouracil, cisplatin, and doxorubicin. Epigenetically, 3D cultures and FFPE shared the same methylation pattern and microRNA expression, while 2D cells showed elevation in methylation rate and altered microRNA expression. Lastly, transcriptomic study depending on RNA sequencing and thorough bioinformatic analyses showed significant (p-adj < 0.05) dissimilarity in gene expression profile between 2D and 3D cultures involving thousands of genes (up/down-regulated) of multiple pathways for each cell line. Taken together, the study provides insights into variations in cellular morphologies between cells cultured in 2D and 3D models.
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Affiliation(s)
- Zaid Nsaif Abbas
- Department of Molecular and Medical Biotechnology, College of Biotechnology, Al-Nahrain University, Jadriya, Baghdad, Iraq
| | - Ali Z Al-Saffar
- Department of Molecular and Medical Biotechnology, College of Biotechnology, Al-Nahrain University, Jadriya, Baghdad, Iraq.
| | - Saba Mahdi Jasim
- Oncology Teaching Hospital, Medical City, Ministry of Health, Baghdad, Iraq
| | - Ghassan M Sulaiman
- Division of Biotechnology, Department of Applied Sciences, University of Technology, Baghdad, Iraq
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20
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Eccher A, Dei Tos AP, Scarpa A, L'Imperio V, Munari E, Troncone G, Naccarato AG, Seminati D, Pagni F. Cost analysis of archives in the pathology laboratories: from safety to management. J Clin Pathol 2023; 76:659-663. [PMID: 37532289 PMCID: PMC10511949 DOI: 10.1136/jcp-2023-209035] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 07/26/2023] [Indexed: 08/04/2023]
Abstract
CONTEXT Despite the reluctance to invest and the challenging estimation of necessary supporting costs, optimising the archives seems to be one of the hottest topics in the future management of the pathology laboratories. Historically, archives were only partially designed to securely store and organise tissue specimens, and tracking systems were often flawed, posing significant risks to patients' health and legal ramifications for pathologists. OBJECTIVE The current review explores the available data from the literature on archives' management in pathology, including comprehensive business plans, structure setup, outfit, inventories, ongoing conservation and functional charges. DATA SOURCES Electronic searches in PubMed-MEDLINE and Embase were made to extract pertinent articles from the literature. Works about the archiving process and storage were included and analysed to extract information. Prepublication servers were ignored. Italian Institutional Regional databases for public competitive bidding processes were queried too. CONCLUSIONS A new emergent feeling in the pathology laboratory is growing for archives management; the digital pathology era is a great opportunity to apply innovation to tracking systems and samples preservation. The main aim is a critical evaluation of the return of investment in developing automatic and tracked archiving processes for improving not only quality, efficacy and efficiency of the labs but also patients' healthcare.
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Affiliation(s)
- Albino Eccher
- Department of Diagnostics and Public Health, Università degli Studi di Verona, Verona, Italy
| | | | - Aldo Scarpa
- Department of Diagnostics and Public Health, Università degli Studi di Verona, Verona, Italy
| | - Vincenzo L'Imperio
- Department of Medicine and Surgery, Pathology, University of Milan-Bicocca, Milano, Italy
| | - Enrico Munari
- Department of Pathology, University of Brescia, Brescia, Italy
| | - Giancarlo Troncone
- Public Health, University of Naples Federico II School of Medicine and Surgery, Napoli, Italy
| | | | - Davide Seminati
- Department of Medicine and Surgery, Pathology, University of Milan-Bicocca, Milano, Italy
| | - Fabio Pagni
- Department of Medicine and Surgery, Pathology, University of Milan-Bicocca, Milano, Italy
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21
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Dupont ME, Jacobsen SB, Christiansen SNN, Tfelt-Hansen J, Smerup MH, Andersen JD, Morling N. Fresh and frozen cardiac tissue are comparable in DNA methylation array β-values, but formalin-fixed, paraffin-embedded tissue may overestimate DNA methylation levels. Sci Rep 2023; 13:16381. [PMID: 37773256 PMCID: PMC10541404 DOI: 10.1038/s41598-023-43788-2] [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: 08/09/2023] [Accepted: 09/28/2023] [Indexed: 10/01/2023] Open
Abstract
Untreated fresh cardiac tissue is the optimal tissue material for investigating DNA methylation patterns of cardiac biology and diseases. However, fresh tissue is difficult to obtain. Therefore, tissue stored as frozen or formalin-fixed, paraffin-embedded (FFPE) is widely used for DNA methylation studies. It is unknown whether storage conditions alter the DNA methylation in cardiac tissue. In this study, we compared the DNA methylation patterns of fresh, frozen, and FFPE cardiac tissue to investigate if the storage method affected the DNA methylation results. We used the Infinium MethylationEPIC assay to obtain genome-wide methylation levels in fresh, frozen, and FFPE tissues from nine individuals. We found that the DNA methylation levels of 21.4% of the examined CpG sites were overestimated in the FFPE samples compared to that of fresh and frozen tissue, whereas 5.7% were underestimated. Duplicate analyses of the DNA methylation patterns showed high reproducibility (precision) for frozen and FFPE tissues. In conclusion, we found that frozen and FFPE tissues gave reproducible DNA methylation results and that frozen and fresh tissues gave similar results.
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Affiliation(s)
- Mikkel Eriksen Dupont
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Stine Bøttcher Jacobsen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Steffan Noe Niikanoff Christiansen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Jacob Tfelt-Hansen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Cardiology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Morten Holdgaard Smerup
- Department of Cardiothoracic Surgery, Rigshospitalet Copenhagen University Hospital, Copenhagen, Denmark
| | - Jeppe Dyrberg Andersen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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22
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Zhang S, He S, Zhu X, Wang Y, Xie Q, Song X, Xu C, Wang W, Xing L, Xia C, Wang Q, Li W, Zhang X, Yu J, Ma S, Shi J, Gu H. DNA methylation profiling to determine the primary sites of metastatic cancers using formalin-fixed paraffin-embedded tissues. Nat Commun 2023; 14:5686. [PMID: 37709764 PMCID: PMC10502058 DOI: 10.1038/s41467-023-41015-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 08/18/2023] [Indexed: 09/16/2023] Open
Abstract
Identifying the primary site of metastatic cancer is critical to guiding the subsequent treatment. Approximately 3-9% of metastatic patients are diagnosed with cancer of unknown primary sites (CUP) even after a comprehensive diagnostic workup. However, a widely accepted molecular test is still not available. Here, we report a method that applies formalin-fixed, paraffin-embedded tissues to construct reduced representation bisulfite sequencing libraries (FFPE-RRBS). We then generate and systematically evaluate 28 molecular classifiers, built on four DNA methylation scoring methods and seven machine learning approaches, using the RRBS library dataset of 498 fresh-frozen tumor tissues from primary cancer patients. Among these classifiers, the beta value-based linear support vector (BELIVE) performs the best, achieving overall accuracies of 81-93% for identifying the primary sites in 215 metastatic patients using top-k predictions (k = 1, 2, 3). Coincidentally, BELIVE also successfully predicts the tissue of origin in 81-93% of CUP patients (n = 68).
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Affiliation(s)
- Shirong Zhang
- Translational Medicine Research Center, Hangzhou First People's Hospital, 310006, Hangzhou, Zhejiang Province, China
- Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Hangzhou First People's Hospital, 310006, Hangzhou, Zhejiang Province, China
| | - Shutao He
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 200031, Shanghai, China
- Institute of Biotechnology and Health, Beijing Academy of Science and Technology, 100089, Beijing, China
| | - Xin Zhu
- Key Laboratory of Head & Neck Cancer Translational Research of Zhejiang Province, Zhejiang Cancer Hospital, 310022, Hangzhou, Zhejiang Province, China
| | - Yunfei Wang
- Zhejiang ShengTing Biotech Co. Ltd, 310018, Hangzhou, Zhejiang Province, China
| | - Qionghuan Xie
- Zhejiang ShengTing Biotech Co. Ltd, 310018, Hangzhou, Zhejiang Province, China
| | - Xianrang Song
- Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, 250117, Jinan, Shandong Province, China
| | - Chunwei Xu
- Department of Respiratory Medicine, Jinling Hospital, Nanjing University School of Medicine, 210002, Nanjing, Jiangshu Province, China
| | - Wenxian Wang
- Key Laboratory of Head & Neck Cancer Translational Research of Zhejiang Province, Zhejiang Cancer Hospital, 310022, Hangzhou, Zhejiang Province, China
| | - Ligang Xing
- Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, 250117, Jinan, Shandong Province, China
| | - Chengqing Xia
- Zhejiang ShengTing Biotech Co. Ltd, 310018, Hangzhou, Zhejiang Province, China
| | - Qian Wang
- Department of Respiratory Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, 210029, Nanjing, Jiangshu Province, China
| | - Wenfeng Li
- Department of Medical Oncology, The First Affiliated Hospital of Wenzhou Medical University, 325000, Wenzhou, Zhejiang Province, China
| | - Xiaochen Zhang
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, 310006, Hangzhou, Zhejiang Province, China
| | - Jinming Yu
- Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, 250117, Jinan, Shandong Province, China
| | - Shenglin Ma
- Translational Medicine Research Center, Hangzhou First People's Hospital, 310006, Hangzhou, Zhejiang Province, China.
- Department of Oncology, Hangzhou Cancer Hospital, 310006, Hangzhou, Zhejiang Province, China.
| | - Jiantao Shi
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 200031, Shanghai, China.
| | - Hongcang Gu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, 230031, Hefei, Anhui Province, China.
- Hefei Cancer Hospital, Chinese Academy of Sciences, 230031, Hefei, Anhui Province, China.
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23
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Plummer JT, George SHL. Challenges and Opportunities in Building a Global Representative Single-Cell and Spatial Atlas in Cancer. Cancer Discov 2023; 13:1969-1972. [PMID: 37671469 DOI: 10.1158/2159-8290.cd-23-0810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2023]
Abstract
SUMMARY Cancer health disparities are complex and a mixture of factors that need to be accounted for in both our planning, implementation, and execution across all researchers, especially in single-cell and spatial technologies, which have a higher burden for adoption in low- and middle-income countries. This commentary tackles the hurdles these technologies face in creating a diverse, representative atlas of cancer and is a call to arms for a strategic plan toward inclusivity across all global populations.
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Affiliation(s)
- Jasmine T Plummer
- Center for Spatial Omics, St. Jude Children's Research Hospital, Memphis, Tennessee
- Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, Tennessee
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee
- Department of Cellular and Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Sophia H L George
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Miami Miller School of Medicine, Miami, Florida
- Sylvester Comprehensive Cancer Center, UHealth Medical Systems, University of Miami Miller School of Medicine, Miami, Florida
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24
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Wang K, Kumar T, Wang J, Minussi DC, Sei E, Li J, Tran TM, Thennavan A, Hu M, Casasent AK, Xiao Z, Bai S, Yang L, King LM, Shah V, Kristel P, van der Borden CL, Marks JR, Zhao Y, Zurita AJ, Aparicio A, Chapin B, Ye J, Zhang J, Gibbons DL, Sawyer E, Thompson AM, Futreal A, Hwang ES, Wesseling J, Lips EH, Navin NE. Archival single-cell genomics reveals persistent subclones during DCIS progression. Cell 2023; 186:3968-3982.e15. [PMID: 37586362 DOI: 10.1016/j.cell.2023.07.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 05/09/2023] [Accepted: 07/17/2023] [Indexed: 08/18/2023]
Abstract
Ductal carcinoma in situ (DCIS) is a common precursor of invasive breast cancer. Our understanding of its genomic progression to recurrent disease remains poor, partly due to challenges associated with the genomic profiling of formalin-fixed paraffin-embedded (FFPE) materials. Here, we developed Arc-well, a high-throughput single-cell DNA-sequencing method that is compatible with FFPE materials. We validated our method by profiling 40,330 single cells from cell lines, a frozen tissue, and 27 FFPE samples from breast, lung, and prostate tumors stored for 3-31 years. Analysis of 10 patients with matched DCIS and cancers that recurred 2-16 years later show that many primary DCIS had already undergone whole-genome doubling and clonal diversification and that they shared genomic lineages with persistent subclones in the recurrences. Evolutionary analysis suggests that most DCIS cases in our cohort underwent an evolutionary bottleneck, and further identified chromosome aberrations in the persistent subclones that were associated with recurrence.
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Affiliation(s)
- Kaile Wang
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Tapsi Kumar
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA; MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA; Department of Genomic Medicine, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Junke Wang
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA; MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Darlan Conterno Minussi
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA; MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Emi Sei
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jianzhuo Li
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Tuan M Tran
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Aatish Thennavan
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Min Hu
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Anna K Casasent
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zhenna Xiao
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Shanshan Bai
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lei Yang
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA; MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Lorraine M King
- Department of Surgery, Duke University School of Medicine, Durham, NC 27707, USA
| | - Vandna Shah
- School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, Guy's Cancer Centre, King's College London, London WC2R 2LS, UK
| | - Petra Kristel
- Division of Molecular Pathology, the Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Carolien L van der Borden
- Division of Molecular Pathology, the Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Jeffrey R Marks
- Department of Surgery, Duke University School of Medicine, Durham, NC 27707, USA
| | - Yuehui Zhao
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Amado J Zurita
- Department of Genitourinary Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Ana Aparicio
- Department of Genitourinary Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Brian Chapin
- Department of Urology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jie Ye
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA; MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA; Department of Thoracic/Head and Neck Medical Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jianjun Zhang
- Department of Genomic Medicine, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Thoracic/Head and Neck Medical Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Don L Gibbons
- Department of Thoracic/Head and Neck Medical Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ellinor Sawyer
- School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, Guy's Cancer Centre, King's College London, London WC2R 2LS, UK
| | - Alastair M Thompson
- Department of Surgery, Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Andrew Futreal
- Department of Genomic Medicine, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - E Shelley Hwang
- Department of Surgery, Duke University School of Medicine, Durham, NC 27707, USA
| | - Jelle Wesseling
- Department of Pathology, the Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam 1066 CX, the Netherlands; Department of Pathology, Leiden University Medical Center, Leiden 2333 ZC, the Netherlands
| | - Esther H Lips
- Department of Pathology, the Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam 1066 CX, the Netherlands; Department of Pathology, Leiden University Medical Center, Leiden 2333 ZC, the Netherlands
| | - Nicholas E Navin
- Department of Systems Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genetics, UT MD Anderson Cancer Center, Houston, TX 77030, USA; MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA; Department of Bioinformatics, UT MD Anderson Cancer Center, Houston, TX 77030, USA.
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25
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Hoboth P, Sztacho M, Quaas A, Akgül B, Hozák P. Quantitative super-resolution microscopy reveals the differences in the nanoscale distribution of nuclear phosphatidylinositol 4,5-bisphosphate in human healthy skin and skin warts. Front Cell Dev Biol 2023; 11:1217637. [PMID: 37484912 PMCID: PMC10361526 DOI: 10.3389/fcell.2023.1217637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 06/22/2023] [Indexed: 07/25/2023] Open
Abstract
Introduction: Imaging of human clinical formalin-fixed paraffin-embedded (FFPE) tissue sections provides insights into healthy and diseased states and therefore represents a valuable resource for basic research, as well as for diagnostic and clinical purposes. However, conventional light microscopy does not allow to observe the molecular details of tissue and cell architecture due to the diffraction limit of light. Super-resolution microscopy overcomes this limitation and provides access to the nanoscale details of tissue and cell organization. Methods: Here, we used quantitative multicolor stimulated emission depletion (STED) nanoscopy to study the nanoscale distribution of the nuclear phosphatidylinositol 4,5-bisphosphate (nPI(4,5)P2) with respect to the nuclear speckles (NS) marker SON. Results: Increased nPI(4,5)P2 signals were previously linked to human papillomavirus (HPV)-mediated carcinogenesis, while NS-associated PI(4,5)P2 represents the largest pool of nPI(4,5)P2 visualized by staining and microscopy. The implementation of multicolor STED nanoscopy in human clinical FFPE skin and wart sections allowed us to provide here the quantitative evidence for higher levels of NS-associated PI(4,5)P2 in HPV-induced warts compared to control skin. Discussion: These data expand the previous reports of HPV-induced increase of nPI(4,5)P2 levels and reveal for the first time the functional, tissue-specific localization of nPI(4,5)P2 within NS in clinically relevant samples. Moreover, our approach is widely applicable to other human clinical FFPE tissues as an informative addition to the classical histochemistry.
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Affiliation(s)
- Peter Hoboth
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Martin Sztacho
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Alexander Quaas
- Institute of Pathology, Medical Faculty and University Hospital Cologne, Cologne, Germany
| | - Baki Akgül
- Institute of Virology, University of Cologne, Medical Faculty and University Hospital Cologne, Cologne, Germany
| | - Pavel Hozák
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
- Microscopy Centre, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
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26
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Muniz Partida C, Walters E. A novel immunohistochemical protocol for paraffin embedded tissue sections using free-floating techniques. Front Neuroanat 2023; 17:1154568. [PMID: 37235185 PMCID: PMC10206034 DOI: 10.3389/fnana.2023.1154568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 04/24/2023] [Indexed: 05/28/2023] Open
Abstract
Immunohistochemistry (IHC) is a well-established and widely used protocol used to visualize tissue architecture, protein expression and localization. Free-floating methods for IHC employ tissue sections that are cut from a cryostat or vibratome. The limitations of these tissue sections are tissue fragility, poor morphology, and the need to use sections of 20-50 μm. In addition, there is a void of information regarding the use of free floating immunohistochemical techniques on paraffin embedded tissue. To address this, we developed a free-float IHC protocol with paraffin embedded tissue (PFFP) that saves time, resources, and tissues. PFFP localized GFAP, olfactory marker protein, tyrosine hydroxylase, and Nestin expression in mouse hippocampal, olfactory bulb, striatum, and cortical tissue. Successful localization of these antigens was achieved using PFFP with and without antigen retrieval, with subsequent chromogenic DAB (3,3'-diaminobenzidine) development and immunofluorescence detection methods. The application of the PFFP in combination with methodologies of in situ hybridization, protein/protein interactions, laser capture dissection, and pathological diagnosis expands the versatility of paraffin embedded tissues.
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27
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Brožová K, Hantusch B, Kenner L, Kratochwill K. Spatial Proteomics for the Molecular Characterization of Breast Cancer. Proteomes 2023; 11:17. [PMID: 37218922 PMCID: PMC10204503 DOI: 10.3390/proteomes11020017] [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: 02/20/2023] [Revised: 03/30/2023] [Accepted: 04/23/2023] [Indexed: 05/24/2023] Open
Abstract
Breast cancer (BC) is a major global health issue, affecting a significant proportion of the female population and contributing to high rates of mortality. One of the primary challenges in the treatment of BC is the disease's heterogeneity, which can lead to ineffective therapies and poor patient outcomes. Spatial proteomics, which involves the study of protein localization within cells, offers a promising approach for understanding the biological processes that contribute to cellular heterogeneity within BC tissue. To fully leverage the potential of spatial proteomics, it is critical to identify early diagnostic biomarkers and therapeutic targets, and to understand protein expression levels and modifications. The subcellular localization of proteins is a key factor in their physiological function, making the study of subcellular localization a major challenge in cell biology. Achieving high resolution at the cellular and subcellular level is essential for obtaining an accurate spatial distribution of proteins, which in turn can enable the application of proteomics in clinical research. In this review, we present a comparison of current methods of spatial proteomics in BC, including untargeted and targeted strategies. Untargeted strategies enable the detection and analysis of proteins and peptides without a predetermined molecular focus, whereas targeted strategies allow the investigation of a predefined set of proteins or peptides of interest, overcoming the limitations associated with the stochastic nature of untargeted proteomics. By directly comparing these methods, we aim to provide insights into their strengths and limitations and their potential applications in BC research.
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Affiliation(s)
- Klára Brožová
- Core Facility Proteomics, Medical University of Vienna, 1090 Vienna, Austria
- Department of Pathology, Medical University of Vienna, 1090 Vienna, Austria
- Division of Molecular and Structural Preclinical Imaging, Department of Biomedical Imaging and Image-Guided Therapy, Medical University of Vienna, 1210 Vienna, Austria
- Unit of Laboratory Animal Pathology, University of Veterinary Medicine, 1090 Vienna, Austria
| | - Brigitte Hantusch
- Department of Pathology, Medical University of Vienna, 1090 Vienna, Austria
| | - Lukas Kenner
- Department of Pathology, Medical University of Vienna, 1090 Vienna, Austria
- Unit of Laboratory Animal Pathology, University of Veterinary Medicine, 1090 Vienna, Austria
- CBmed GmbH—Center for Biomarker Research in Medicine, 8010 Graz, Austria
- Christian Doppler Laboratory for Applied Metabolomics, Medical University of Vienna, 1090 Vienna, Austria
| | - Klaus Kratochwill
- Core Facility Proteomics, Medical University of Vienna, 1090 Vienna, Austria
- Christian Doppler Laboratory for Molecular Stress Research in Peritoneal Dialysis, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, 1090 Vienna, Austria
- Division of Pediatric Nephrology and Gastroenterology, Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria
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Imazato H, Takahashi N, Hirakawa Y, Yamaguchi Y, Hiyoshi M, Tajima T, Chosa E, Sawaguchi A. Three-dimensional fine structures in deep fascia revealed by combined use of cryo-fixed histochemistry and low-vacuum scanning microscopy. Sci Rep 2023; 13:6352. [PMID: 37072465 PMCID: PMC10113183 DOI: 10.1038/s41598-023-33479-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 04/13/2023] [Indexed: 05/03/2023] Open
Abstract
Recent physiological studies have shown that the deep fascia has received much attention concerning clinical medicine; however, histological examination of the deep fascia has not been well established. In this study, we aimed to clarify and visualize the structure of the deep fascia by taking advantage of cryofixation techniques and low-vacuum scanning electron microscopy. As a result, the ultrastructural observations revealed three-dimensional stratification of the deep fascia composed of three layers: the first superficial layer consisting of collagen fibers extending in various directions with blood vessels and peripheral nerves; the second intermediate layer formed by single straight and thick collagen fibers with flexibility; and the third deepest layer, consisting of relatively straight and thin collagen fibers. We explored the use of two hooks to hold a piece of deep fascia in place through the course of cryo-fixation. A comparative observation with or without the hook-holding procedure would indicate the morphological adaptation to physiological stretch and contraction of the deep fascia. The present morphological approach paves the way to visualize three-dimensional ultrastructures for future biomedical studies including clinical pathophysiology.
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Affiliation(s)
- Hiroyuki Imazato
- Division of Orthopaedic Surgery, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki, 889-1692, Japan
| | - Nobuyasu Takahashi
- Department of Anatomy, Ultrastructural Cell Biology, Faculty of Medicine, University of Miyazaki, Miyazaki, 889-1692, Japan.
| | - Yusuke Hirakawa
- Division of Orthopaedic Surgery, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki, 889-1692, Japan
| | - Yoichiro Yamaguchi
- Division of Orthopaedic Surgery, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki, 889-1692, Japan
| | - Masaru Hiyoshi
- Division of Orthopaedic Surgery, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki, 889-1692, Japan
| | - Takuya Tajima
- Division of Orthopaedic Surgery, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki, 889-1692, Japan
| | - Etsuo Chosa
- Division of Orthopaedic Surgery, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki, 889-1692, Japan
| | - Akira Sawaguchi
- Department of Anatomy, Ultrastructural Cell Biology, Faculty of Medicine, University of Miyazaki, Miyazaki, 889-1692, Japan
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29
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Hellinger R, Sigurdsson A, Wu W, Romanova EV, Li L, Sweedler JV, Süssmuth RD, Gruber CW. Peptidomics. NATURE REVIEWS. METHODS PRIMERS 2023; 3:25. [PMID: 37250919 PMCID: PMC7614574 DOI: 10.1038/s43586-023-00205-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/09/2023] [Indexed: 05/31/2023]
Abstract
Peptides are biopolymers, typically consisting of 2-50 amino acids. They are biologically produced by the cellular ribosomal machinery or by non-ribosomal enzymes and, sometimes, other dedicated ligases. Peptides are arranged as linear chains or cycles, and include post-translational modifications, unusual amino acids and stabilizing motifs. Their structure and molecular size render them a unique chemical space, between small molecules and larger proteins. Peptides have important physiological functions as intrinsic signalling molecules, such as neuropeptides and peptide hormones, for cellular or interspecies communication, as toxins to catch prey or as defence molecules to fend off enemies and microorganisms. Clinically, they are gaining popularity as biomarkers or innovative therapeutics; to date there are more than 60 peptide drugs approved and more than 150 in clinical development. The emerging field of peptidomics comprises the comprehensive qualitative and quantitative analysis of the suite of peptides in a biological sample (endogenously produced, or exogenously administered as drugs). Peptidomics employs techniques of genomics, modern proteomics, state-of-the-art analytical chemistry and innovative computational biology, with a specialized set of tools. The complex biological matrices and often low abundance of analytes typically examined in peptidomics experiments require optimized sample preparation and isolation, including in silico analysis. This Primer covers the combination of techniques and workflows needed for peptide discovery and characterization and provides an overview of various biological and clinical applications of peptidomics.
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Affiliation(s)
- Roland Hellinger
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Arnar Sigurdsson
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Wenxin Wu
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Elena V Romanova
- Department of Chemistry, University of Illinois, Urbana, IL, USA
| | - Lingjun Li
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | | | | | - Christian W Gruber
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
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Mar D, Babenko IM, Zhang R, Noble WS, Denisenko O, Vaisar T, Bomsztyk K. MultiomicsTracks96: A high throughput PIXUL-Matrix-based toolbox to profile frozen and FFPE tissues multiomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.16.533031. [PMID: 36993219 PMCID: PMC10055122 DOI: 10.1101/2023.03.16.533031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Background The multiome is an integrated assembly of distinct classes of molecules and molecular properties, or "omes," measured in the same biospecimen. Freezing and formalin-fixed paraffin-embedding (FFPE) are two common ways to store tissues, and these practices have generated vast biospecimen repositories. However, these biospecimens have been underutilized for multi-omic analysis due to the low throughput of current analytical technologies that impede large-scale studies. Methods Tissue sampling, preparation, and downstream analysis were integrated into a 96-well format multi-omics workflow, MultiomicsTracks96. Frozen mouse organs were sampled using the CryoGrid system, and matched FFPE samples were processed using a microtome. The 96-well format sonicator, PIXUL, was adapted to extract DNA, RNA, chromatin, and protein from tissues. The 96-well format analytical platform, Matrix, was used for chromatin immunoprecipitation (ChIP), methylated DNA immunoprecipitation (MeDIP), methylated RNA immunoprecipitation (MeRIP), and RNA reverse transcription (RT) assays followed by qPCR and sequencing. LC-MS/MS was used for protein analysis. The Segway genome segmentation algorithm was used to identify functional genomic regions, and linear regressors based on the multi-omics data were trained to predict protein expression. Results MultiomicsTracks96 was used to generate 8-dimensional datasets including RNA-seq measurements of mRNA expression; MeRIP-seq measurements of m6A and m5C; ChIP-seq measurements of H3K27Ac, H3K4m3, and Pol II; MeDIP-seq measurements of 5mC; and LC-MS/MS measurements of proteins. We observed high correlation between data from matched frozen and FFPE organs. The Segway genome segmentation algorithm applied to epigenomic profiles (ChIP-seq: H3K27Ac, H3K4m3, Pol II; MeDIP-seq: 5mC) was able to recapitulate and predict organ-specific super-enhancers in both FFPE and frozen samples. Linear regression analysis showed that proteomic expression profiles can be more accurately predicted by the full suite of multi-omics data, compared to using epigenomic, transcriptomic, or epitranscriptomic measurements individually. Conclusions The MultiomicsTracks96 workflow is well suited for high dimensional multi-omics studies - for instance, multiorgan animal models of disease, drug toxicities, environmental exposure, and aging as well as large-scale clinical investigations involving the use of biospecimens from existing tissue repositories.
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Lapini A, Caffo O, Conti GN, Pappagallo G, Del Re M, D'Angelillo RM, Capoluongo ED, Castiglione F, Brunelli M, Iacovelli R, De Giorgi U, Bracarda S. Matching BRCA and prostate cancer in a public health system: Report of the Italian Society for Uro-Oncology (SIUrO) consensus project. Crit Rev Oncol Hematol 2023; 184:103959. [PMID: 36921782 DOI: 10.1016/j.critrevonc.2023.103959] [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: 12/08/2022] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 03/16/2023] Open
Abstract
The recent approval of PARP inhibitors for the treatment of metastatic -castration-resistant prostate cancer (mCRPC) patients with BRCA mutations firstly introduced the possibility of proposing a targeted treatment in this disease. However, the availability of this therapeutic option raises a number of questions concerning the management of prostate cancer in everyday clinical practice: the timing and method of detecting BRCA mutations, the therapeutic implications of the detection, and the screening of the members of the family of a prostate cancer patient with a BRCA alteration. These challenging issues led the Italian Society for Uro-Oncology (SIUrO) to organise a Consensus Conference aimed to develop suggestions capable of supporting clinicians managing prostate cancer patients. The present paper described the development of the statements discussed during the consensus, which involved all of the most important Italian scientific societies engaged in the multi-disciplinary and multi-professional management of the disease.
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Affiliation(s)
- Alberto Lapini
- Department of Urology, University of Florence, University Hospital of Florence, Largo Brambilla, 3, 50134 Florence, Italy
| | - Orazio Caffo
- Department of Medical Oncology, Santa Chiara Hospital, Largo Medaglie d'Oro, 38122 Trento, Italy.
| | - Giario Natale Conti
- Italian Society for Uro-Oncology (SIURO), Via Dante 17, 40125 Bologna, Italy
| | - Giovanni Pappagallo
- IRCCS "Sacro Cuore - Don Calabria", Viale Luigi Rizzardi, 4, 37024 Negrar di Valpolicella, Italy
| | - Marzia Del Re
- Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University of Pisa, Via Roma, 67, 56126 Pisa, Italy
| | - Rolando Maria D'Angelillo
- Radiation Oncology, Department of Biomedicine and Prevention University of Rome "Tor Vergata", Viale Oxford 81, 00133 Rome, Italy
| | - Ettore Domenico Capoluongo
- Department of Molecular Medicine and Medical Biotechnologies, University Federico II, Via Pansini 5, 80131 Naples, Italy; Department of Clinical Pathology and Genomics, Azienda Ospedaliera per L'Emergenza Cannizzaro, Via Messina 829, 95126 Catania, Italy
| | - Francesca Castiglione
- Department of Pathology, University of Florence, Largo Brambilla, 3, 50134 Florence, Italy
| | - Matteo Brunelli
- Unit of Pathology, Department of Diagnostics and Public Health, University of Verona, P.le L.A. Scuro 10, 37134 Verona, Italy
| | - Roberto Iacovelli
- Medical Oncology Unit, Fondazione Policlinico Universitario A. Gemelli IRCCS, Largo Agostino Gemelli 8, 00168 Rome, Italy
| | - Ugo De Giorgi
- Unit of Medical Oncology, IRCCS-Istituto Romagnolo per lo Studio dei Tumori (IRST) 'Dino Amadori', Via Maroncelli 40, 47014 Meldola, Italy
| | - Sergio Bracarda
- Medical and Translational Oncology, Department of Oncology, Azienda Ospedaliera Santa Maria, Viale Tristano di Joannuccio, 05100 Terni, Italy
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32
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Jerome K, Sattar S, Mehedi M. Simultaneous detection and quantification of spike mRNA and protein in SARS-CoV-2 infected airway epithelium .. MethodsX 2023; 10:102050. [PMID: 36779029 PMCID: PMC9894770 DOI: 10.1016/j.mex.2023.102050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Visualizing and quantifying mRNA and its corresponding protein provides a unique perspective of gene expression at a single-molecule level. Here, we describe a method for differentiating primary cells for making airway epithelium and detecting SARS-CoV-2 Spike (S) mRNA and S protein in the paraformaldehyde-fixed paraffin-embedded severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infected airway epithelium. For simultaneous detection of mRNA and protein in the same cell, we combined two protocols: 1. RNA fluorescence-based in situ hybridization (RNA-FISH) based mRNA detection and 2. fluorescence-based immunohistochemistry (IHC) based protein detection. The detection of mRNA and proteins in the same cell also allows for quantifying them using the open-source software QuPath, which provides an accurate and more straightforward fluorescent-based quantification of mRNA and protein in the microscopic images of the infected cells. Additionally, we can achieve the subcellular distribution of both S mRNA and S protein. This method identifies SARS-CoV-2 S gene products' (mRNA and protein) degree of expression and their subcellular localization in the infected airway epithelium. Advantages of this method include: •Simultaneous detection and quantification of mRNA and protein in the same cell.•Universal use due to the ability to use mRNA-specific primer-probe and protein-specific antibodies.•An open-source software QuPath provides a straightforward fluorescent-based quantification.
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Affiliation(s)
| | | | - Masfique Mehedi
- Department of Biomedical Sciences, University of North Dakota School of Medicine & Health Sciences, Grand Forks, ND 58202, USA
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33
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Unkovič A, Boštjančič E, Belič A, Perše M. Selection and Evaluation of mRNA and miRNA Reference Genes for Expression Studies (qPCR) in Archived Formalin-Fixed and Paraffin-Embedded (FFPE) Colon Samples of DSS-Induced Colitis Mouse Model. BIOLOGY 2023; 12:biology12020190. [PMID: 36829468 PMCID: PMC9952917 DOI: 10.3390/biology12020190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/21/2023] [Accepted: 01/25/2023] [Indexed: 01/28/2023]
Abstract
The choice of appropriate reference genes is essential for correctly interpreting qPCR data and results. However, the majority of animal studies use a single reference gene without any prior evaluation. Therefore, many qPCR results from rodent studies can be misleading, affecting not only reproducibility but also translatability. In this study, the expression stability of reference genes for mRNA and miRNA in archived FFPE samples of 117 C57BL/6JOlaHsd mice (males and females) from 9 colitis experiments (dextran sulfate sodium; DSS) were evaluated and their expression analysis was performed. In addition, we investigated whether normalization reduced/neutralized the influence of inter/intra-experimental factors which we systematically included in the study. Two statistical algorithms (NormFinder and Bestkeeper) were used to determine the stability of reference genes. Multivariate analysis was made to evaluate the influence of normalization with different reference genes on target gene expression in regard to inter/intra-experimental factors. Results show that archived FFPE samples are a reliable source of RNA and imply that the FFPE procedure does not change the ranking of stability of reference genes obtained in fresh tissues. Multivariate analysis showed that the histological picture is an important factor affecting the expression levels of target genes.
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Affiliation(s)
- Ana Unkovič
- Medical Experimental Centre, Institute of Pathology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Emanuela Boštjančič
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Aleš Belič
- Statistics and Modelling, Technical Development Biologics, Novartis Technical Research & Development, Lek Pharmaceuticals d.d., 1000 Ljubljana, Slovenia
| | - Martina Perše
- Medical Experimental Centre, Institute of Pathology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
- Correspondence:
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34
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Van Haver D, Dendooven A, Impens F. Proteomics-Based Analysis and Diagnosis of Formalin-Fixed Paraffin-Embedded Amyloidosis Samples. Methods Mol Biol 2023; 2718:213-233. [PMID: 37665462 DOI: 10.1007/978-1-0716-3457-8_12] [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: 09/05/2023]
Abstract
Amyloidosis is a group of rare pathologies characterized by abnormal folding and deposition of susceptible proteins in tissues and organs. Diagnosis of amyloidosis often relies on immunohistochemistry of formalin-fixed paraffin-embedded (FFPE) patient samples; however, dependency on antibodies for protein staining is one of the major pitfalls of this approach, especially for the detection of rare amyloidosis types. In recent years, mass spectrometry-based proteomics has emerged as a promising alternative for adequate detection and amyloid typing, despite the fact that preparing FFPE samples for proteomics remains a challenging task. Major hurdles are removal of formalin-induced protein cross-links and water-insoluble paraffin prior to mass spectrometry analysis. With the recent development of the suspension trapping protocol, enabling the use of high concentrations of SDS, these obstacles can be overcome. In this chapter, we describe the implementation of suspension trapping for FFPE sample processing and its application to analyze human amyloidosis samples, comparing a standard procedure with probe sonication with a more advanced workflow based on ultrasonication.
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Affiliation(s)
- Delphi Van Haver
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- VIB Proteomics Core, Ghent, Belgium
| | - Amélie Dendooven
- Department of Pathology, Ghent University Hospital, Ghent, Belgium
- Laboratory for Experimental Medicine and Pediatrics, Antwerp University, Edegem, Belgium
| | - Francis Impens
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium.
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
- VIB Proteomics Core, Ghent, Belgium.
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35
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Xing S, Hu K, Wang Y. Tumor Immune Microenvironment and Immunotherapy in Non-Small Cell Lung Cancer: Update and New Challenges. Aging Dis 2022; 13:1615-1632. [PMID: 36465180 PMCID: PMC9662266 DOI: 10.14336/ad.2022.0407] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 04/07/2022] [Indexed: 08/03/2023] Open
Abstract
Non-small cell lung cancer (NSCLC) is a serious threat to the health of older adults. Despite the significant progress in immunotherapy, effective treatments for NSCLC remain limited. The development of tumors indicates failure in immune surveillance and the successful immune escape of tumor cells. Research on the tumor immune microenvironment (TIME) revealed these opposing immune processes and contributed to the discovery of new methods to suppress the immune escape and restore the immune surveillance functions. This paper aimed to provide updates on the current findings regarding the relevance of TIME in NSCLC treatment. It also aimed to introduce the TIME, immune editing, cancer immunotherapy, and new challenges. Based on the clinical data, the combination of neoadjuvant chemotherapy and immune checkpoint inhibitor (ICI) therapy is suitable for patients with NSCLC who are not eligible to undergo surgery. Combined ICI therapy after epidermal growth factor receptor (EGFR)/tyrosine kinase inhibitor (TKI) therapy should be considered in patients with EGFR mutations. Chemoradiotherapy may increase the density of CD8+ lymphocytes, which is significantly associated with better prognosis. For older patients and those with advanced-stage disease, regional tumor treatments, such as stereotactic radiation therapy and percutaneous cryoablation, may be more suitable, but further studies are needed to confirm this. In conclusion, restoring immune surveillance is as important as removing cancerous tissues; further studies that include the use of combined treatment methods, individualized treatment plans, and immunonutrition are warranted.
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Affiliation(s)
- Shuqin Xing
- Department of Oncology, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China.
| | - Kaiwen Hu
- Department of Oncology, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China.
| | - Yafei Wang
- Department of Orthopedics, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China.
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36
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Bapat PR, Epari S, Joshi PV, Dhanavade DS, Rumde RH, Gurav MY, Shetty OA, Desai SB. Comparative Assessment of DNA Extraction Techniques From Formalin-Fixed, Paraffin-Embedded Tumor Specimens and Their Impact on Downstream Analysis. Am J Clin Pathol 2022; 158:739-749. [PMID: 36197908 DOI: 10.1093/ajcp/aqac122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 09/05/2022] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES Good-quality nucleic acid extraction from formalin-fixed, paraffin-embedded (FFPE) specimens remains a challenge in molecular-oncopathology practice. This study evaluates the efficacy of an in-house developed FFPE extraction buffer compared with other commercially available kits. METHODS Eighty FFPE specimens processed in different surgical pathology laboratories formed the study sample. DNA extraction was performed using three commercial kits and the in-house developed FFPE extraction buffer. DNA yield was quantified by a NanoDrop spectrophotometer and Qubit Fluorometer, and its purity was measured by the 260/280-nm ratio. A fragment analyzer system was used for accurate sizing of DNA fragments of FFPE DNA. The downstream effects of all extraction methods were evaluated by polymerase chain reaction (PCR) and Sanger sequencing. RESULTS In comparison with the commercial kits, the in-house buffer yielded higher DNA quantity and quality number (P < .0001). In addition, DNA integrity and fragment size were preserved in a significantly greater number of samples isolated with the in-house buffer (P < .05). The target PCR amplification rate with the in-house buffer extracted samples was also significantly higher, with 98% of the samples showing interpretable sequencing results. CONCLUSIONS The in-house developed FFPE extraction buffer performed superior to other methods in terms of suitability for downstream applications, time, cost-efficiency, and ease of performance.
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Affiliation(s)
- Prachi R Bapat
- Molecular Pathology, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, India
| | - Sridhar Epari
- Molecular Pathology, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, India
| | - Pradnya V Joshi
- Molecular Pathology, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, India
| | - Dipika S Dhanavade
- Molecular Pathology, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, India
| | - Rachna H Rumde
- Molecular Pathology, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, India
| | - Mamta Y Gurav
- Molecular Pathology, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, India
| | - Omshree A Shetty
- Molecular Pathology, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, India
| | - Sangeeta B Desai
- Molecular Pathology, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, India
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van Ineveld RL, Collot R, Román MB, Pagliaro A, Bessler N, Ariese HCR, Kleinnijenhuis M, Kool M, Alieva M, Chuva de Sousa Lopes SM, Wehrens EJ, Rios AC. Multispectral confocal 3D imaging of intact healthy and tumor tissue using mLSR-3D. Nat Protoc 2022; 17:3028-3055. [PMID: 36180532 DOI: 10.1038/s41596-022-00739-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 06/16/2022] [Indexed: 11/09/2022]
Abstract
Revealing the 3D composition of intact tissue specimens is essential for understanding cell and organ biology in health and disease. State-of-the-art 3D microscopy techniques aim to capture tissue volumes on an ever-increasing scale, while also retaining sufficient resolution for single-cell analysis. Furthermore, spatial profiling through multi-marker imaging is fast developing, providing more context and better distinction between cell types. Following these lines of technological advance, we here present a protocol based on FUnGI (fructose, urea and glycerol clearing solution for imaging) optical clearing of tissue before multispectral large-scale single-cell resolution 3D (mLSR-3D) imaging, which implements 'on-the-fly' linear unmixing of up to eight fluorophores during a single acquisition. Our protocol removes the need for repetitive illumination, thereby allowing larger volumes to be scanned with better image quality in less time, also reducing photo-bleaching and file size. To aid in the design of multiplex antibody panels, we provide a fast and manageable intensity equalization assay with automated analysis to design a combination of markers with balanced intensities suitable for mLSR-3D. We demonstrate effective mLSR-3D imaging of various tissues, including patient-derived organoids and xenografted tumors, and, furthermore, describe an optimized workflow for mLSR-3D imaging of formalin-fixed paraffin-embedded samples. Finally, we provide essential steps for 3D image data processing, including shading correction that does not require pre-acquired shading references and 3D inhomogeneity correction to correct fluorescence artefacts often afflicting 3D datasets. Together, this provides a one-week protocol for eight-fluorescent-marker 3D visualization and exploration of intact tissue of various origins at single-cell resolution.
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Affiliation(s)
- Ravian L van Ineveld
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Oncode Institute, Utrecht, the Netherlands
| | - Raphaël Collot
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Oncode Institute, Utrecht, the Netherlands
| | - Mario Barrera Román
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Oncode Institute, Utrecht, the Netherlands
| | - Anna Pagliaro
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Oncode Institute, Utrecht, the Netherlands
| | - Nils Bessler
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Oncode Institute, Utrecht, the Netherlands
| | - Hendrikus C R Ariese
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Oncode Institute, Utrecht, the Netherlands
| | - Michiel Kleinnijenhuis
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Oncode Institute, Utrecht, the Netherlands
| | - Marcel Kool
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Division of Pediatric Neurooncology, German Cancer Research Center DKFZ and German Cancer Consortium DKTK, Heidelberg, Germany
| | - Maria Alieva
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Oncode Institute, Utrecht, the Netherlands
| | | | - Ellen J Wehrens
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.,Oncode Institute, Utrecht, the Netherlands
| | - Anne C Rios
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands. .,Oncode Institute, Utrecht, the Netherlands.
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Mukherjee A, Ghosh S, Biswas D, Rao A, Shetty P, Epari S, Moiyadi A, Srivastava S. Clinical Proteomics for Meningioma: An Integrated Workflow for Quantitative Proteomics and Biomarker Validation in Formalin-Fixed Paraffin-Embedded Tissue Samples. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2022; 26:512-520. [PMID: 36036964 DOI: 10.1089/omi.2022.0082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Clinical proteomics is a rapidly emerging frontier in laboratory medicine. High-throughput proteomic investigations of biopsy tissues provide mechanistic insights into complex human diseases. For large-scale proteomics, formalin-fixed and paraffin-embedded (FFPE) tissue samples offer a viable alternative to fresh-frozen (FF) tissues that have restricted availability. In this context, meningioma is one of the most common primary brain tumors where innovation in diagnostics and therapeutic targets can benefit from clinical proteomics. We present here an integrated workflow for quantitative proteomics and biomarker validation of meningioma FFPE tissues. Applying label-free quantitative (LFQ) proteomics, we reproducibly (Pearson's correlation: 0.84-0.91) obtained an in-depth proteome coverage (nearly 4000 proteins per sample) from 120 min gradient of single unfractionated mass spectrometry run. Furthermore, building upon LFQ data and literature curated set of meningioma-associated proteins, we validated VIM, AHNAK, and CLU from FFPE tissues using selected reaction monitoring (SRM) assay and compared its performance with FF tissues. This study illustrates how knowledge from label-free proteomics can be integrated for selecting peptides for targeted validation and suggests that FFPE tissues are comparable to FF tissues for SRM assays. This quantitative clinical proteomics workflow is scalable for large-scale clinical diagnostics studies in the future, for example, utilizing the global repository of FFPE tissues in meningioma and possibly in other cancers.
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Affiliation(s)
- Arijit Mukherjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Susmita Ghosh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Deeptarup Biswas
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Aishwarya Rao
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | | | | | | | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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39
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Cumulative dialytic glucose exposure is a risk factor for peritoneal fibrosis and angiogenesis in pediatric patients undergoing peritoneal dialysis using neutral-pH fluids. Kidney Int Rep 2022; 7:2431-2445. [DOI: 10.1016/j.ekir.2022.08.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 08/12/2022] [Accepted: 08/15/2022] [Indexed: 11/21/2022] Open
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40
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Walsh EM, Halushka MK. A Comparison of Tissue Dissection Techniques for Diagnostic, Prognostic, and Theragnostic Analysis of Human Disease. Pathobiology 2022; 90:199-208. [PMID: 35952628 PMCID: PMC9918608 DOI: 10.1159/000525979] [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: 04/20/2022] [Accepted: 07/05/2022] [Indexed: 11/19/2022] Open
Abstract
Histopathology has historically been the critical technique for the diagnosis and treatment of human disease. Today, genomics, transcriptomics, and proteomics from specific cells, rather than bulk tissue, have become key to understanding underlying disease mechanisms and rendering useful diagnostic information. Extraction of desired analytes, i.e., nucleic acids or proteins, from easily accessible formalin-fixed paraffin-embedded tissues allows for clinically relevant activities, such as sequencing biomarker mutations or typing amyloidogenic proteins. Genetic profiling has become routine for cancers as varied as non-small cell lung cancer and prostatic carcinoma. The five main tissue dissection techniques that have been developed thus far include: bulk scraping, manual macrodissection, manual microdissection, laser-capture microdissection, and expression microdissection. In this review, we discuss the importance of tissue dissection in clinical practice and research, the basic methods, applications, as well as some advantages and disadvantages for each modality.
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Affiliation(s)
- Elise M. Walsh
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Marc K. Halushka
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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41
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Nwosu AJ, Misal SA, Truong T, Carson RH, Webber KGI, Axtell NB, Liang Y, Johnston SM, Virgin KL, Smith EG, Thomas GV, Morgan T, Price JC, Kelly RT. In-Depth Mass Spectrometry-Based Proteomics of Formalin-Fixed, Paraffin-Embedded Tissues with a Spatial Resolution of 50-200 μm. J Proteome Res 2022; 21:2237-2245. [PMID: 35916235 PMCID: PMC9767749 DOI: 10.1021/acs.jproteome.2c00409] [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: 11/29/2022]
Abstract
Formalin-fixed, paraffin-embedded (FFPE) tissues are banked in large repositories to cost-effectively preserve valuable specimens for later study. With the rapid growth of spatial proteomics, FFPE tissues can serve as a more accessible alternative to more commonly used frozen tissues. However, extracting proteins from FFPE tissues is challenging due to cross-links formed between proteins and formaldehyde. Here, we have adapted the nanoPOTS sample processing workflow, which was previously applied to single cells and fresh-frozen tissues, to profile protein expression from FFPE tissues. Following the optimization of extraction solvents, times, and temperatures, we identified an average of 1312 and 3184 high-confidence master proteins from 10 μm thick FFPE-preserved mouse liver tissue squares having lateral dimensions of 50 and 200 μm, respectively. The observed proteome coverage for FFPE tissues was on average 88% of that achieved for similar fresh-frozen tissues. We also characterized the performance of our fully automated sample preparation and analysis workflow, termed autoPOTS, for FFPE spatial proteomics. This modified nanodroplet processing in one pot for trace samples (nanoPOTS) and fully automated processing in one pot for trace sample (autoPOTS) workflows provides the greatest coverage reported to date for high-resolution spatial proteomics applied to FFPE tissues. Data are available via ProteomeXchange with identifier PXD029729.
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Affiliation(s)
- Andikan J Nwosu
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Santosh A Misal
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Thy Truong
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Richard H Carson
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Kei G I Webber
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Nathaniel B Axtell
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Yiran Liang
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - S Madisyn Johnston
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Kenneth L Virgin
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Ethan G Smith
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - George V Thomas
- Knight Cancer Center, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Terry Morgan
- Department of Pathology, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - John C Price
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Ryan T Kelly
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
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42
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Wang F, Ugai T, Haruki K, Wan Y, Akimoto N, Arima K, Zhong R, Twombly TS, Wu K, Yin K, Chan AT, Giannakis M, Nowak JA, Meyerhardt JA, Liang L, Song M, Smith‐Warner SA, Zhang X, Giovannucci EL, Willett WC, Ogino S. Healthy and unhealthy plant-based diets in relation to the incidence of colorectal cancer overall and by molecular subtypes. Clin Transl Med 2022; 12:e893. [PMID: 35998061 PMCID: PMC9398226 DOI: 10.1002/ctm2.893] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 04/30/2022] [Accepted: 05/09/2022] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Plant-based foods have been recommended for health. However, not all plant foods are healthy, and little is known about the association between plant-based diets and specific molecular subtypes of colorectal cancer (CRC). We examined the associations of healthy and unhealthy plant-based diets with the incidence of CRC and its molecular subtypes. METHODS While 123 773 participants of the Nurses' Health Study and the Health Professionals Follow-up Study had been followed up (3 143 158 person-years), 3077 of them had developed CRC. Healthy and unhealthy plant-based diet indices (hPDI and uPDI, respectively) were calculated using repeated food frequency questionnaire data. We determined the tumoural status of microsatellite instability (MSI), CpG island methylator phenotype (CIMP), and BRAF and KRAS mutations. RESULTS Higher hPDI was associated with lower CRC incidence (multivariable hazard ratio [HR] comparing extreme quartiles, 0.86, 95% confidence interval [CI]: 0.77, 0.96; P-trend = .04), whereas higher uPDI was associated with higher CRC incidence (multivariable HR comparing extreme quartiles, 1.16, 95% CI: 1.04, 1.29; P-trend = .005). The association of hPDI significantly differed by KRAS status (P-heterogeneity = .003) but not by other tumour markers. The hPDI was associated with lower incidence of KRAS-wildtype CRC (multivariable HR comparing extreme quartiles, 0.74, 95% CI: 0.57, 0.96; P-trend = .004) but not KRAS-mutant CRC (P-trend = .22). CONCLUSIONS While unhealthy plant-based diet enriched with refined grains and sugar is associated with higher CRC incidence, healthy plant-based diet rich in whole grains, fruits and vegetables is associated with lower incidence of CRC, especially KRAS-wildtype CRC.
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43
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Niewold P, Ijsselsteijn ME, Verreck FAW, Ottenhoff THM, Joosten SA. An imaging mass cytometry immunophenotyping panel for non-human primate tissues. Front Immunol 2022; 13:915157. [PMID: 35911721 PMCID: PMC9334813 DOI: 10.3389/fimmu.2022.915157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 06/28/2022] [Indexed: 11/16/2022] Open
Abstract
It has recently become clear that spatial organization contributes to cellular function and that expanding our knowledge on cellular organization is essential to further our understanding of processes in health and disease. Imaging mass cytometry enables high dimensional imaging of tissue while preserving spatial context and is therefore a suitable tool to unravel spatial relationships between cells. As availability of human tissue collected over the course of disease or infection is limited, preclinical models are a valuable source of such material. Non-human primate models are used for translational research as their anatomy, physiology and immune system closely resemble those of humans due to close evolutionary proximity. Tissue from non-human primate studies is often preserved large archives encompassing a range of conditions and organs. However, knowledge on antibody clones suitable for FFPE tissue of non-human primate origin is very limited. Here, we present an imaging mass cytometry panel development pipeline which enables the selection and incorporation of antibodies for imaging of non-human primate tissue. This has resulted in an 18-marker backbone panel which enables visualization of a broad range of leukocyte subsets in rhesus and cynomolgus macaque tissues. This high-dimensional imaging mass cytometry panel can be used to increase our knowledge of cellular organization within tissues and its effect on outcome of disease.
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Affiliation(s)
- Paula Niewold
- Department of Infectious Diseases, Leiden University Medical Centre, Leiden, Netherlands
| | | | - Frank A. W. Verreck
- Section of Tuberculosis (TB) Research and Immunology, Department of Parasitology, Biomedical Primate Research Centre, Rijswijk, Netherlands
| | - Tom H. M. Ottenhoff
- Department of Infectious Diseases, Leiden University Medical Centre, Leiden, Netherlands
| | - Simone A. Joosten
- Department of Infectious Diseases, Leiden University Medical Centre, Leiden, Netherlands
- *Correspondence: Simone A. Joosten,
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44
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Mund A, Coscia F, Kriston A, Hollandi R, Kovács F, Brunner AD, Migh E, Schweizer L, Santos A, Bzorek M, Naimy S, Rahbek-Gjerdrum LM, Dyring-Andersen B, Bulkescher J, Lukas C, Eckert MA, Lengyel E, Gnann C, Lundberg E, Horvath P, Mann M. Deep Visual Proteomics defines single-cell identity and heterogeneity. Nat Biotechnol 2022; 40:1231-1240. [PMID: 35590073 PMCID: PMC9371970 DOI: 10.1038/s41587-022-01302-5] [Citation(s) in RCA: 131] [Impact Index Per Article: 65.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 03/30/2022] [Indexed: 02/07/2023]
Abstract
Despite the availabilty of imaging-based and mass-spectrometry-based methods for spatial proteomics, a key challenge remains connecting images with single-cell-resolution protein abundance measurements. Here, we introduce Deep Visual Proteomics (DVP), which combines artificial-intelligence-driven image analysis of cellular phenotypes with automated single-cell or single-nucleus laser microdissection and ultra-high-sensitivity mass spectrometry. DVP links protein abundance to complex cellular or subcellular phenotypes while preserving spatial context. By individually excising nuclei from cell culture, we classified distinct cell states with proteomic profiles defined by known and uncharacterized proteins. In an archived primary melanoma tissue, DVP identified spatially resolved proteome changes as normal melanocytes transition to fully invasive melanoma, revealing pathways that change in a spatial manner as cancer progresses, such as mRNA splicing dysregulation in metastatic vertical growth that coincides with reduced interferon signaling and antigen presentation. The ability of DVP to retain precise spatial proteomic information in the tissue context has implications for the molecular profiling of clinical samples. Deep Visual Proteomics combines machine learning, automated image analysis and single-cell proteomics.
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Affiliation(s)
- Andreas Mund
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Fabian Coscia
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Spatial Proteomics Group, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - András Kriston
- Synthetic and Systems Biology Unit, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary.,Single-Cell Technologies Ltd., Szeged, Hungary
| | - Réka Hollandi
- Synthetic and Systems Biology Unit, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
| | - Ferenc Kovács
- Synthetic and Systems Biology Unit, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary.,Single-Cell Technologies Ltd., Szeged, Hungary
| | - Andreas-David Brunner
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Ede Migh
- Synthetic and Systems Biology Unit, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
| | - Lisa Schweizer
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Alberto Santos
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Center for Health Data Science, University of Copenhagen, Copenhagen, Denmark.,Big Data Institute, Li-Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Michael Bzorek
- Department of Pathology, Zealand University Hospital, Roskilde, Denmark
| | - Soraya Naimy
- Department of Pathology, Zealand University Hospital, Roskilde, Denmark
| | - Lise Mette Rahbek-Gjerdrum
- Department of Pathology, Zealand University Hospital, Roskilde, Denmark.,Institute for Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Beatrice Dyring-Andersen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Dermatology and Allergy, Herlev and Gentofte Hospital, University of Copenhagen, Hellerup, Denmark.,Leo Foundation Skin Immunology Research Center, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jutta Bulkescher
- Protein Imaging Platform, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Claudia Lukas
- Protein Imaging Platform, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mark Adam Eckert
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL, USA
| | - Ernst Lengyel
- Department of Obstetrics and Gynecology/Section of Gynecologic Oncology, University of Chicago, Chicago, IL, USA
| | - Christian Gnann
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Emma Lundberg
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden.,Department of Bioengineering, Stanford University, Stanford, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Peter Horvath
- Synthetic and Systems Biology Unit, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary. .,Single-Cell Technologies Ltd., Szeged, Hungary. .,Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.
| | - Matthias Mann
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. .,Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.
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45
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Megyesfalvi Z, Barany N, Lantos A, Valko Z, Pipek O, Lang C, Schwendenwein A, Oberndorfer F, Paku S, Ferencz B, Dezso K, Fillinger J, Lohinai Z, Moldvay J, Galffy G, Szeitz B, Rezeli M, Rivard C, Hirsch FR, Brcic L, Popper H, Kern I, Kovacevic M, Skarda J, Mittak M, Marko-Varga G, Bogos K, Renyi-Vamos F, Hoda MA, Klikovits T, Hoetzenecker K, Schelch K, Laszlo V, Dome B. Expression patterns and prognostic relevance of subtype-specific transcription factors in surgically resected small cell lung cancer: an international multicenter study. J Pathol 2022; 257:674-686. [PMID: 35489038 PMCID: PMC9541929 DOI: 10.1002/path.5922] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 04/10/2022] [Accepted: 04/27/2022] [Indexed: 11/17/2022]
Abstract
The tissue distribution and prognostic relevance of subtype‐specific proteins (ASCL1, NEUROD1, POU2F3, YAP1) present an evolving area of research in small‐cell lung cancer (SCLC). The expression of subtype‐specific transcription factors and P53 and RB1 proteins were measured by immunohistochemistry (IHC) in 386 surgically resected SCLC samples. Correlations between subtype‐specific proteins and in vitro efficacy of various therapeutic agents were investigated by proteomics and cell viability assays in 26 human SCLC cell lines. Besides SCLC‐A (ASCL1‐dominant), SCLC‐AN (combined ASCL1/NEUROD1), SCLC‐N (NEUROD1‐dominant), and SCLC‐P (POU2F3‐dominant), IHC and cluster analyses identified a quadruple‐negative SCLC subtype (SCLC‐QN). No unique YAP1‐subtype was found. The highest overall survival rates were associated with non‐neuroendocrine subtypes (SCLC‐P and SCLC‐QN) and the lowest with neuroendocrine subtypes (SCLC‐A, SCLC‐N, SCLC‐AN). In univariate analyses, high ASCL1 expression was associated with poor prognosis and high POU2F3 expression with good prognosis. Notably, high ASCL1 expression influenced survival outcomes independently of other variables in a multivariate model. High POU2F3 and YAP1 protein abundances correlated with sensitivity and resistance to standard‐of‐care chemotherapeutics, respectively. Specific correlation patterns were also found between the efficacy of targeted agents and subtype‐specific protein abundances. In conclusion, we investigated the clinicopathological relevance of SCLC molecular subtypes in a large cohort of surgically resected specimens. Differential IHC expression of ASCL1, NEUROD1, and POU2F3 defines SCLC subtypes. No YAP1‐subtype can be distinguished by IHC. High POU2F3 expression is associated with improved survival in a univariate analysis, whereas elevated ASCL1 expression is an independent negative prognosticator. Proteomic and cell viability assays of human SCLC cell lines revealed distinct vulnerability profiles defined by transcription regulators. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Zsolt Megyesfalvi
- Department of Thoracic Surgery, Semmelweis University and National Institute of Oncology, Budapest, Hungary.,National Koranyi Institute of Pulmonology, Budapest, Hungary.,Department of Thoracic Surgery, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Nandor Barany
- National Koranyi Institute of Pulmonology, Budapest, Hungary.,Department of Thoracic Surgery, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria.,1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Andras Lantos
- National Koranyi Institute of Pulmonology, Budapest, Hungary
| | - Zsuzsanna Valko
- National Koranyi Institute of Pulmonology, Budapest, Hungary.,Department of Thoracic Surgery, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Orsolya Pipek
- Department of Physics of Complex Systems, Eotvos Lorand University, Budapest, Hungary
| | - Christian Lang
- Department of Thoracic Surgery, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Anna Schwendenwein
- Department of Thoracic Surgery, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | | | - Sandor Paku
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Bence Ferencz
- Department of Thoracic Surgery, Semmelweis University and National Institute of Oncology, Budapest, Hungary.,National Koranyi Institute of Pulmonology, Budapest, Hungary
| | - Katalin Dezso
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Janos Fillinger
- National Koranyi Institute of Pulmonology, Budapest, Hungary
| | - Zoltan Lohinai
- National Koranyi Institute of Pulmonology, Budapest, Hungary
| | - Judit Moldvay
- National Koranyi Institute of Pulmonology, Budapest, Hungary.,MTA-SE NAP, Brain Metastasis Research Group, Hungarian Academy of Sciences, Budapest, Hungary
| | - Gabriella Galffy
- Torokbalint County Institute of Pulmonology, Torokbalint, Hungary
| | - Beata Szeitz
- Division of Oncology, Department of Internal Medicine and Oncology, Semmelweis University, Budapest, Hungary
| | - Melinda Rezeli
- Department of Biomedical Engineering, Lund University, Lund, Sweden
| | - Christopher Rivard
- Division of Medical Oncology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Fred R Hirsch
- Division of Medical Oncology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.,Tisch Cancer Institute, Center for Thoracic Oncology, Mount Sinai Health System, New York, NY, USA
| | - Luka Brcic
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Helmut Popper
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Izidor Kern
- University Clinic for Respiratory and Allergic Diseases Golnik, Golnik, Slovenia
| | - Mile Kovacevic
- University Clinic for Respiratory and Allergic Diseases Golnik, Golnik, Slovenia
| | - Jozef Skarda
- Institute of Clinical and Molecular Pathology, Medical Faculty, Palacky University Olomouc, Olomouc, Czech Republic.,Department of Pathology, University Hospital Ostrava and Faculty of Medicine University of Ostrava, Ostrava, Czech Republic
| | - Marcel Mittak
- Department of Surgery, University Hospital Ostrava and Faculty of Medicine University of Ostrava, Ostrava, Czech Republic
| | | | - Krisztina Bogos
- National Koranyi Institute of Pulmonology, Budapest, Hungary
| | - Ferenc Renyi-Vamos
- Department of Thoracic Surgery, Semmelweis University and National Institute of Oncology, Budapest, Hungary.,National Koranyi Institute of Pulmonology, Budapest, Hungary
| | - Mir Alireza Hoda
- Department of Thoracic Surgery, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Thomas Klikovits
- Department of Thoracic Surgery, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria.,Department of Thoracic Surgery, Klinik Floridsdorf, Vienna, Austria
| | - Konrad Hoetzenecker
- Department of Thoracic Surgery, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Karin Schelch
- Department of Thoracic Surgery, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Viktoria Laszlo
- Department of Thoracic Surgery, Semmelweis University and National Institute of Oncology, Budapest, Hungary.,Department of Thoracic Surgery, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Balazs Dome
- Department of Thoracic Surgery, Semmelweis University and National Institute of Oncology, Budapest, Hungary.,National Koranyi Institute of Pulmonology, Budapest, Hungary.,Department of Thoracic Surgery, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
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46
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Ineveld RL, Vliet EJ, Wehrens EJ, Alieva M, Rios AC. 3D imaging for driving cancer discovery. EMBO J 2022; 41:e109675. [PMID: 35403737 PMCID: PMC9108604 DOI: 10.15252/embj.2021109675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 03/09/2022] [Accepted: 03/09/2022] [Indexed: 11/09/2022] Open
Abstract
Our understanding of the cellular composition and architecture of cancer has primarily advanced using 2D models and thin slice samples. This has granted spatial information on fundamental cancer biology and treatment response. However, tissues contain a variety of interconnected cells with different functional states and shapes, and this complex organization is impossible to capture in a single plane. Furthermore, tumours have been shown to be highly heterogenous, requiring large-scale spatial analysis to reliably profile their cellular and structural composition. Volumetric imaging permits the visualization of intact biological samples, thereby revealing the spatio-phenotypic and dynamic traits of cancer. This review focuses on new insights into cancer biology uniquely brought to light by 3D imaging and concomitant progress in cancer modelling and quantitative analysis. 3D imaging has the potential to generate broad knowledge advance from major mechanisms of tumour progression to new strategies for cancer treatment and patient diagnosis. We discuss the expected future contributions of the newest imaging trends towards these goals and the challenges faced for reaching their full application in cancer research.
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Affiliation(s)
- Ravian L Ineveld
- Princess Máxima Center for Pediatric Oncology Utrecht The Netherlands
- Oncode Institute Utrecht The Netherlands
| | - Esmée J Vliet
- Princess Máxima Center for Pediatric Oncology Utrecht The Netherlands
- Oncode Institute Utrecht The Netherlands
| | - Ellen J Wehrens
- Princess Máxima Center for Pediatric Oncology Utrecht The Netherlands
- Oncode Institute Utrecht The Netherlands
| | - Maria Alieva
- Princess Máxima Center for Pediatric Oncology Utrecht The Netherlands
- Oncode Institute Utrecht The Netherlands
| | - Anne C Rios
- Princess Máxima Center for Pediatric Oncology Utrecht The Netherlands
- Oncode Institute Utrecht The Netherlands
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47
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Cintron-Diaz YL, Gomez-Hernandez ME, Verhaert MMHA, Verhaert PDEM, Fernandez-Lima F. Spatially Resolved Neuropeptide Characterization from Neuropathological Formalin-Fixed, Paraffin-Embedded Tissue Sections by a Combination of Imaging MALDI FT-ICR Mass Spectrometry Histochemistry and Liquid Extraction Surface Analysis-Trapped Ion Mobility Spectrometry-Tandem Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:681-687. [PMID: 35258288 PMCID: PMC9390806 DOI: 10.1021/jasms.1c00376] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
To make the vast collections of well-documented human clinical samples archived in biobanks accessible for mass spectrometry imaging (MSI), recent developments have focused on the label-free top-down MS analysis of neuropeptides in sections of formalin-fixed, paraffin-embedded (FFPE) tissues. In analogy to immunohistochemistry (IHC), this variant of MSI has been designated MSHC (mass spectrometry histochemistry). Besides the detection and localization of neuropeptide and other biomolecular MS signals in these FFPE samples, there is great interest in their molecular identification and full characterization. We here used matrix assisted laser desorption ionization (MALDI) MSI employing ultrahigh-resolution FT-ICR MS on 2,5-dihydroxybenzoic acid (DHB) coated five-micron sections of human FFPE pituitary to demonstrate clear isotope patterns and elemental composition assignment of neuropeptides (with ∼1 ppm mass accuracy). Besides tandem MS fragmentation pattern analysis to deduce or confirm amino acid sequence information (Arg-vasopressin for the case presented here), there is a need for orthogonal primary structure characterization of the peptide-like MS signals of biomolecules desorbed directly off FFPE tissue sections. In the present work, we performed liquid extraction surface analysis (LESA) extractions on consecutive (uncoated) tissue slices. This enables the successful characterization by ion mobility MS of vasopressin present in FFPE material. Differences in sequence coverage are discussed on the basis of the mobility selected collision induced dissociation (CID), electron capture dissociation (ECD), and UV photodissociation (UVPD) MS/MS. Using Arg-vasopressin as model case (a peptide with a disulfide bridged ring structure), we illustrate the use of LESA in combination with a reduction agent for effective sequencing using mobility selected CID, ECD, and UVPD MS/MS.
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Affiliation(s)
- Yarixa L Cintron-Diaz
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, AHC4-233, Miami, Florida 33199, United States
| | - Mario E Gomez-Hernandez
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, AHC4-233, Miami, Florida 33199, United States
| | - Marthe M H A Verhaert
- ProteoFormiX, JLABS@BE, Janssen Pharmaceutica Campus, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Peter D E M Verhaert
- ProteoFormiX, JLABS@BE, Janssen Pharmaceutica Campus, Turnhoutseweg 30, B-2340 Beerse, Belgium
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, AHC4-233, Miami, Florida 33199, United States
- Biomolecular Science Institute, Florida International University, 11200 SW 8th Street, AHC4-233, Miami, Florida 33199, United States
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Case study: Targeted RNA-sequencing of aged formalin-fixed paraffin-embedded samples for understanding chemical mode of action. Toxicol Rep 2022; 9:883-894. [DOI: 10.1016/j.toxrep.2022.04.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 04/12/2022] [Accepted: 04/13/2022] [Indexed: 11/19/2022] Open
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Teyssonneau D, Thiery-Vuillemin A, Dariane C, Barret E, Beauval JB, Brureau L, Créhange G, Fiard G, Fromont G, Gauthé M, Ruffion A, Renard-Penna R, Mathieu R, Sargos P, Rouprêt M, Ploussard G, Roubaud G. PARP Inhibitors as Monotherapy in Daily Practice for Advanced Prostate Cancers. J Clin Med 2022; 11:jcm11061734. [PMID: 35330059 PMCID: PMC8952857 DOI: 10.3390/jcm11061734] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/07/2022] [Accepted: 03/14/2022] [Indexed: 02/05/2023] Open
Abstract
Despite recent improvements in survival, metastatic castration-resistant prostate cancers (mCRPCs) remain lethal. Alterations in genes involved in the homologous recombination repair (HRR) pathway are associated with poor prognosis. Poly-ADP-ribose polymerase (PARP) inhibitors (PARPis) have demonstrated anti-tumoral effects by synthetic lethality in patients with mCRPCs harboring HRR gene alterations, in particular BRCA2. While both olaparib and rucaparib have obtained government approvals for use, the selection of eligible patients as well as the prescription of these treatments within the clinical urology community are challenging. This review proposes a brief review of the rationale and outcomes of PARPi treatment, then a pragmatic vision of PARPi use in terms of prescription and the selection of patients based on molecular screening, which can involve potential genetic counseling in the case of associated germinal alterations.
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Affiliation(s)
- Diego Teyssonneau
- Department of Medical Oncology, Institut Bergonié, 33000 Bordeaux, France;
- Correspondence:
| | - Antoine Thiery-Vuillemin
- Department of Medical Oncology, Centre Hospitalier Universitaire Besançon, 25000 Besançon, France;
| | - Charles Dariane
- Department of Urology, Hôpital Européen Georges-Pompidou, AP-HP, Paris University, 75005 Paris, France;
| | - Eric Barret
- Department of Urology, Institut Mutualiste Montsouris, 75014 Paris, France;
| | - Jean-Baptiste Beauval
- Department of Urology, La Croix du Sud Hôpital, Quint Fonsegrives, 31000 Toulouse, France; (J.-B.B.); (G.P.)
| | - Laurent Brureau
- Department of Urology, CHU de Pointe-à-Pitre, University of Antilles, 97110 Pointe-à-Pitre, France;
| | - Gilles Créhange
- Department of Urology, Grenoble Alpes University Hospital, Université Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, 38400 Grenoble, France;
| | - Gaëlle Fiard
- Department of Radiation Oncology, Curie Institute, 75005 Paris, France;
| | - Gaëlle Fromont
- Department of Pathology, CHRU Tours, 37000 Tours, France;
| | - Mathieu Gauthé
- Department of Nuclear Medicine, Scintep, 38000 Grenoble, France;
| | - Alain Ruffion
- Service d’Urologie Centre Hospitalier Lyon Sud, Hospices Civils de Lyon, 69000 Lyon, France;
- Equipe 2, Centre d’Innovation en Cancérologie de Lyon (EA 3738 CICLY), Faculté de Médecine Lyon Sud, Université Lyon 1, 69000 Lyon, France
| | - Raphaële Renard-Penna
- Department of Radiology, Sorbonne University, AP-HP, Radiology, Pitie-Salpetriere Hospital, 75013 Paris, France;
| | - Romain Mathieu
- Department of Urology, University of Rennes, 35000 Rennes, France;
- Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail), University of Rennes, 35000 Rennes, France
| | - Paul Sargos
- Department of Radiotherapy, Institut Bergonié, 33000 Bordeaux, France;
| | - Morgan Rouprêt
- Department of Urology, Sorbonne University, GRC 5 Predictive Onco-Uro, AP-HP, Urology, Pitie-Salpetriere Hospital, 75013 Paris, France;
| | - Guillaume Ploussard
- Department of Urology, La Croix du Sud Hôpital, Quint Fonsegrives, 31000 Toulouse, France; (J.-B.B.); (G.P.)
| | - Guilhem Roubaud
- Department of Medical Oncology, Institut Bergonié, 33000 Bordeaux, France;
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50
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Mohammad Yousof S, Erfan H, Mohamed Hosny M, Shehata SA, El-sayed K. Subacute Toxic Effects of Silver Nanoparticles oral Administration and Withdrawal on the Structure and Function of Adult Albino Rats’ Hepatic Tissue. Saudi J Biol Sci 2022; 29:3890-3898. [PMID: 35844407 PMCID: PMC9280256 DOI: 10.1016/j.sjbs.2022.02.054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 02/26/2022] [Accepted: 02/28/2022] [Indexed: 11/30/2022] Open
Abstract
Products containing Silver nanoparticles (Ag NPs) are becoming vastly used in our daily life. The widespread increased introduction of Ag NPs in many aspects of life has raised researchers' concerns regarding their safety and toxicity for biological and environmental life in the past few years. The current study aimed to explore the subsequent effects of Ag NPs withdrawal, following short-term oral administration. Eighteen rats were assigned randomly into three groups (control group "1" and AG NPs treated groups "2" and "3"; 6 animals each). The control group received normal food and tap water while groups 2 & 3 received 0.5 ml of a solution containing 25 ppm Ag NPs for 14 days. Group 2 rats were sacrificed on day 14 whereas group 3 was left for another 14 days of particle cessation followed by euthanasia on day 28. Functional assessment was done by liver enzyme assays, hydrogen peroxide activity, hepatic Bdnf expression, and P53 immunoreactivity. Hepatic tissue structural assessment was done via hematoxylin and eosin, periodic acid-Schiff as well as Masson's trichrome stains. The results revealed a significant elevation of Hydrogen peroxide in group 2 only compared to the control group. Hepatic Bdnf and liver enzymes were both insignificantly affected. Structural abnormalities and enhanced apoptosis in hepatic tissue were found 14 days after ceasing the nanoparticles. In conclusion: Structural and functional insults following Ag NPs oral administration continues after particle withdrawal, and interestingly they do not necessitate apparent reflection on liver enzyme assays.
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