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Barsanti S, Viana JF, Veiga A, Machado JL, Abreu DS, Dias JD, Monteiro S, Silva NA, Pinto L, Oliveira JF. Assessing Different Histological Preparations for Reconstruction of Astrocyte Tridimensional Structure. Cells 2024; 13:969. [PMID: 38891101 PMCID: PMC11171983 DOI: 10.3390/cells13110969] [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: 04/22/2024] [Revised: 05/20/2024] [Accepted: 05/31/2024] [Indexed: 06/21/2024] Open
Abstract
Astrocytes are ubiquitous in the brain and spinal cord and display a complex morphology important for the local interactions with neighboring cells, resulting in the modulation of circuit function. Thus, studies focusing on astrocyte physiology in the healthy and diseased brain generally present analyses of astrocytic structure. The labeling method used to visualize the astrocytic structure defines the morphological level to observe and may vary depending on the anatomical sub-regions. The method choice may significantly affect our understanding of their structural diversity. The main goal of this work was to identify a straightforward and efficient protocol for labeling and reconstructing a detailed astrocytic structure to apply and validate in different brain tissue preparations across laboratories. For that, we explored different tissue processing protocols before GFAP labeling to determine the most effective method for reconstructing astrocytic backbones in the mouse hippocampus. Our results show that the reconstruction of astrocytic structure in vibratome sections labeled by free-floating immunofluorescence protocol provides a more practical method to achieve a higher level of detail and arbor complexity in astrocyte backbone reconstruction. Free-floating immunofluorescence labeling is the most reliable method for obtaining better antibody penetration and more detailed astrocyte structure. Finally, we also show that introducing an antigen retrieval step appears useful for visualizing more complete structural details.
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Affiliation(s)
- Sara Barsanti
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal; (S.B.); (J.F.V.); (A.V.); (J.L.M.); (D.S.A.); (J.D.D.); (S.M.); (N.A.S.); (L.P.)
- ICVS/3B’s-PT Government Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
| | - João Filipe Viana
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal; (S.B.); (J.F.V.); (A.V.); (J.L.M.); (D.S.A.); (J.D.D.); (S.M.); (N.A.S.); (L.P.)
- ICVS/3B’s-PT Government Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
| | - Alexandra Veiga
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal; (S.B.); (J.F.V.); (A.V.); (J.L.M.); (D.S.A.); (J.D.D.); (S.M.); (N.A.S.); (L.P.)
- ICVS/3B’s-PT Government Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
| | - João Luís Machado
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal; (S.B.); (J.F.V.); (A.V.); (J.L.M.); (D.S.A.); (J.D.D.); (S.M.); (N.A.S.); (L.P.)
- ICVS/3B’s-PT Government Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
| | - Daniela Sofia Abreu
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal; (S.B.); (J.F.V.); (A.V.); (J.L.M.); (D.S.A.); (J.D.D.); (S.M.); (N.A.S.); (L.P.)
- ICVS/3B’s-PT Government Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
| | - José Duarte Dias
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal; (S.B.); (J.F.V.); (A.V.); (J.L.M.); (D.S.A.); (J.D.D.); (S.M.); (N.A.S.); (L.P.)
- ICVS/3B’s-PT Government Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
| | - Susana Monteiro
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal; (S.B.); (J.F.V.); (A.V.); (J.L.M.); (D.S.A.); (J.D.D.); (S.M.); (N.A.S.); (L.P.)
- ICVS/3B’s-PT Government Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
| | - Nuno A. Silva
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal; (S.B.); (J.F.V.); (A.V.); (J.L.M.); (D.S.A.); (J.D.D.); (S.M.); (N.A.S.); (L.P.)
- ICVS/3B’s-PT Government Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
| | - Luísa Pinto
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal; (S.B.); (J.F.V.); (A.V.); (J.L.M.); (D.S.A.); (J.D.D.); (S.M.); (N.A.S.); (L.P.)
- ICVS/3B’s-PT Government Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
| | - João Filipe Oliveira
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal; (S.B.); (J.F.V.); (A.V.); (J.L.M.); (D.S.A.); (J.D.D.); (S.M.); (N.A.S.); (L.P.)
- ICVS/3B’s-PT Government Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
- IPCA-EST-2Ai, Applied Artificial Intelligence Laboratory, Polytechnic Institute of Cávado and Ave, Campus of IPCA, 4750-810 Barcelos, Portugal
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Xu H, Usuyama N, Bagga J, Zhang S, Rao R, Naumann T, Wong C, Gero Z, González J, Gu Y, Xu Y, Wei M, Wang W, Ma S, Wei F, Yang J, Li C, Gao J, Rosemon J, Bower T, Lee S, Weerasinghe R, Wright BJ, Robicsek A, Piening B, Bifulco C, Wang S, Poon H. A whole-slide foundation model for digital pathology from real-world data. Nature 2024; 630:181-188. [PMID: 38778098 PMCID: PMC11153137 DOI: 10.1038/s41586-024-07441-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: 11/30/2023] [Accepted: 04/19/2024] [Indexed: 05/25/2024]
Abstract
Digital pathology poses unique computational challenges, as a standard gigapixel slide may comprise tens of thousands of image tiles1-3. Prior models have often resorted to subsampling a small portion of tiles for each slide, thus missing the important slide-level context4. Here we present Prov-GigaPath, a whole-slide pathology foundation model pretrained on 1.3 billion 256 × 256 pathology image tiles in 171,189 whole slides from Providence, a large US health network comprising 28 cancer centres. The slides originated from more than 30,000 patients covering 31 major tissue types. To pretrain Prov-GigaPath, we propose GigaPath, a novel vision transformer architecture for pretraining gigapixel pathology slides. To scale GigaPath for slide-level learning with tens of thousands of image tiles, GigaPath adapts the newly developed LongNet5 method to digital pathology. To evaluate Prov-GigaPath, we construct a digital pathology benchmark comprising 9 cancer subtyping tasks and 17 pathomics tasks, using both Providence and TCGA data6. With large-scale pretraining and ultra-large-context modelling, Prov-GigaPath attains state-of-the-art performance on 25 out of 26 tasks, with significant improvement over the second-best method on 18 tasks. We further demonstrate the potential of Prov-GigaPath on vision-language pretraining for pathology7,8 by incorporating the pathology reports. In sum, Prov-GigaPath is an open-weight foundation model that achieves state-of-the-art performance on various digital pathology tasks, demonstrating the importance of real-world data and whole-slide modelling.
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Affiliation(s)
- Hanwen Xu
- Microsoft Research, Redmond, WA, USA
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | | | | | | | | | | | | | | | | | - Yu Gu
- Microsoft Research, Redmond, WA, USA
| | - Yanbo Xu
- Microsoft Research, Redmond, WA, USA
| | - Mu Wei
- Microsoft Research, Redmond, WA, USA
| | | | | | - Furu Wei
- Microsoft Research, Redmond, WA, USA
| | | | | | | | | | | | - Soohee Lee
- Providence Research Network, Renton, WA, USA
| | | | | | | | - Brian Piening
- Providence Genomics, Portland, OR, USA
- Earle A. Chiles Research Institute, Providence Cancer Institute, Portland, OR, USA
| | - Carlo Bifulco
- Providence Genomics, Portland, OR, USA.
- Earle A. Chiles Research Institute, Providence Cancer Institute, Portland, OR, USA.
| | - Sheng Wang
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA.
- Department of Surgery, University of Washington, Seattle, WA, USA.
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Mulholland EJ, Leedham SJ. Redefining clinical practice through spatial profiling: a revolution in tissue analysis. Ann R Coll Surg Engl 2024; 106:305-312. [PMID: 38555868 PMCID: PMC10981989 DOI: 10.1308/rcsann.2023.0091] [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: 10/25/2023] [Indexed: 04/02/2024] Open
Abstract
Spatial biology, which combines molecular biology and advanced imaging, enhances our understanding of tissue cellular organisation. Despite its potential, spatial omics encounters challenges related to data complexity, computational requirements and standardisation of analysis. In clinical applications, spatial omics has the potential to revolutionise biomarker discovery, disease stratification and personalised treatments. It can identify disease-specific cell patterns, and could help risk stratify patients for clinical trials and disease-appropriate therapies. Although there are challenges in adopting it in clinical practice, spatial omics has the potential to significantly enhance patient outcomes. In this paper, we discuss the recent evolution of spatial biology, and its potential for improving our tissue level understanding and treatment of disease, to help advance precision and effectiveness in healthcare interventions.
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Díaz Del Arco C, Fernández Aceñero MJ, Ortega Medina L. Molecular Classifications in Gastric Cancer: A Call for Interdisciplinary Collaboration. Int J Mol Sci 2024; 25:2649. [PMID: 38473896 DOI: 10.3390/ijms25052649] [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: 01/11/2024] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024] Open
Abstract
Gastric cancer (GC) is a heterogeneous disease, often diagnosed at advanced stages, with a 5-year survival rate of approximately 20%. Despite notable technological advancements in cancer research over the past decades, their impact on GC management and outcomes has been limited. Numerous molecular alterations have been identified in GC, leading to various molecular classifications, such as those developed by The Cancer Genome Atlas (TCGA) and the Asian Cancer Research Group (ACRG). Other authors have proposed alternative perspectives, including immune, proteomic, or epigenetic-based classifications. However, molecular stratification has not yet transitioned into clinical practice for GC, and little attention has been paid to alternative molecular classifications. In this review, we explore diverse molecular classifications in GC from a practical point of view, emphasizing their relationships with clinicopathological factors, prognosis, and therapeutic approaches. We have focused on classifications beyond those of TCGA and the ACRG, which have been less extensively reviewed previously. Additionally, we discuss the challenges that must be overcome to ensure their impact on patient treatment and prognosis. This review aims to serve as a practical framework to understand the molecular landscape of GC, facilitate the development of consensus molecular categories, and guide the design of innovative molecular studies in the field.
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Affiliation(s)
- Cristina Díaz Del Arco
- Department of Legal Medicine, Psychiatry and Pathology, School of Medicine, Complutense University of Madrid, 28040 Madrid, Spain
- Department of Pathology, Hospital Clínico San Carlos, Health Research Institute of the Hospital Clínico San Carlos (IdISSC), 28040 Madrid, Spain
| | - María Jesús Fernández Aceñero
- Department of Legal Medicine, Psychiatry and Pathology, School of Medicine, Complutense University of Madrid, 28040 Madrid, Spain
- Department of Pathology, Hospital Clínico San Carlos, Health Research Institute of the Hospital Clínico San Carlos (IdISSC), 28040 Madrid, Spain
| | - Luis Ortega Medina
- Department of Legal Medicine, Psychiatry and Pathology, School of Medicine, Complutense University of Madrid, 28040 Madrid, Spain
- Department of Pathology, Hospital Clínico San Carlos, Health Research Institute of the Hospital Clínico San Carlos (IdISSC), 28040 Madrid, Spain
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Sanjai C, Hakkimane SS, Guru BR, Gaonkar SL. A comprehensive review on anticancer evaluation techniques. Bioorg Chem 2024; 142:106973. [PMID: 37984104 DOI: 10.1016/j.bioorg.2023.106973] [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] [Revised: 11/09/2023] [Accepted: 11/14/2023] [Indexed: 11/22/2023]
Abstract
The development of effective anticancer strategies and the improvement of our understanding of cancer need analytical tools. Utilizing a variety of analytical approaches while investigating anti-cancer medicines gives us a thorough understanding of the traits and mechanisms concerned to cancer cells, which enables us to develop potent treatments to combat them. The importance of anticancer research may be attributed to various analytical techniques that contributes to the identification of therapeutic targets and the assessment of medication efficacy, which are crucial things in expanding our understanding of cancer biology. The study looks at methods that are often used in cancer research, including cell viability assays, clonogenic assay, flow cytometry, 2D electrophoresis, microarray, immunofluorescence, western blot caspase activation assay, bioinformatics, etc. The fundamentals, applications, and how each technique analytical advances our understanding of cancer are briefly reviewed.
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Affiliation(s)
- Chetana Sanjai
- Department of Biotechnology, Manipal Institute of Technology Bengaluru, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Sushruta S Hakkimane
- Department of Biotechnology, Manipal Institute of Technology Bengaluru, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India.
| | - Bharath Raja Guru
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Santosh L Gaonkar
- Department of Chemistry, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India.
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Kim J, Dwivedi G, Boughton BA, Sharma A, Lee S. Advances in cellular and tissue-based imaging techniques for sarcoid granulomas. Am J Physiol Cell Physiol 2024; 326:C10-C26. [PMID: 37955119 DOI: 10.1152/ajpcell.00507.2023] [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: 10/05/2023] [Revised: 11/06/2023] [Accepted: 11/08/2023] [Indexed: 11/14/2023]
Abstract
Sarcoidosis embodies a complex inflammatory disorder spanning multiple systems, with its origin remaining elusive. It manifests as the infiltration of inflammatory cells that coalesce into distinctive noncaseous granulomas within afflicted organs. Unraveling this disease necessitates the utilization of cellular or tissue-based imaging methods to both visualize and characterize the biochemistry of these sarcoid granulomas. Although hematoxylin and eosin stain, standard in routine use alongside cytological stains have found utility in diagnosis within clinical contexts, special stains such as Masson's trichrome, reticulin, methenamine silver, and Ziehl-Neelsen provide additional varied perspectives of sarcoid granuloma imaging. Immunohistochemistry aids in pinpointing specific proteins and gene expressions further characterizing these granulomas. Finally, recent advances in spatial transcriptomics promise to divulge profound insights into their spatial orientation and three-dimensional (3-D) molecular mapping. This review focuses on a range of preexisting imaging methods employed for visualizing sarcoid granulomas at the cellular level while also exploring the potential of the latest cutting-edge approaches like spatial transcriptomics and matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI), with the overarching goal of shedding light on the trajectory of sarcoidosis research.
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Affiliation(s)
- Junwoo Kim
- Department of Advanced Clinical and Translational Cardiovascular Imaging, Harry Perkins Institute of Medical Research, Murdoch, Western Australia, Australia
- School of Medicine, The University of Western Australia, Perth, Western Australia, Australia
| | - Girish Dwivedi
- Department of Advanced Clinical and Translational Cardiovascular Imaging, Harry Perkins Institute of Medical Research, Murdoch, Western Australia, Australia
- School of Medicine, The University of Western Australia, Perth, Western Australia, Australia
- Department of Cardiology, Fiona Stanley Hospital, Murdoch, Western Australia, Australia
| | - Berin A Boughton
- Australian National Phenome Centre, Murdoch University, Murdoch, Western Australia, Australia
| | - Ankur Sharma
- Onco-Fetal Ecosystem Laboratory, Harry Perkins Institute of Medical Research, Nedlands, Western Australia, Australia
- Curtin Medical School, Curtin University, Perth, Western Australia, Australia
| | - Silvia Lee
- Department of Advanced Clinical and Translational Cardiovascular Imaging, Harry Perkins Institute of Medical Research, Murdoch, Western Australia, Australia
- School of Medicine, The University of Western Australia, Perth, Western Australia, Australia
- Curtin Medical School, Curtin University, Perth, Western Australia, Australia
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Gurnani B, Kaur K. Molecular and epigenetic mechanisms governing ocular surface squamous neoplasia: opportunities for diagnostics. Expert Rev Mol Diagn 2023:1-15. [PMID: 38131180 DOI: 10.1080/14737159.2023.2298681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 12/20/2023] [Indexed: 12/23/2023]
Abstract
INTRODUCTION Ocular surface squamous neoplasia (OSSN) is the most common ocular malignancy; the pathophysiology is influenced by molecular, genetic, and epigenetic mechanisms. The incidence of OSSN is associated with the anatomy and physiology of the ocular surface, limbal stem cell configuration, limbal vulnerability, cancer stem cells, dysplasia, neoplasia, angiogenesis, invasion, and metastasis. The key etiological factors involved are human papillomavirus (HPV), human immunodeficiency virus (HIV), immunosuppression, p53 tumor suppressor gene, hypovitaminosis A, and failure of Deoxyribonucleic acid (DNA) repair mechanisms. AREAS COVERED This special report is a focussed attempt to understand the molecular mechanism, genetic and epigenetic mechanism, and diagnostic modalities for OSSN. EXPERT OPINION While these mechanisms contribute to genome instability, promoter-specific hypermethylation might facilitate and promote tumor formation by silencing tumor suppressor genes. OSSN understanding has improved with increased literature available on various genetic, molecular, and epigenetic mechanisms, although the exact genetic and epigenetic mechanisms still need to be elucidated. It is important to note that the molecular mechanisms of OSSN can vary among individuals, and further research is required to elucidate the underlying processes fully. Understanding these mechanisms is crucial for the development of targeted therapies and improved management of OSSN.
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Affiliation(s)
- Bharat Gurnani
- Cataract, Cornea, Refractive Services, Trauma, External Diseases, Contact Lens and Ocular Surface, Sadguru Netra Chikitsalya, Shri Sadguru Seva Sangh Trust, Chitrakoot, India
| | - Kirandeep Kaur
- Children Eye Care Centre, Department of Pediatric Ophthalmology and Strabismus, Sadguru Netra Chikitsalya, Shri Sadguru Seva Sangh Trust, Janaki Kund, Chitrakoot, India
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Di Tucci C, Muzii L. Chronic Pelvic Pain, Vulvar Pain Disorders, and Proteomics Profiles: New Discoveries, New Hopes. Biomedicines 2023; 12:1. [PMID: 38275362 PMCID: PMC10813718 DOI: 10.3390/biomedicines12010001] [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: 11/08/2023] [Revised: 12/13/2023] [Accepted: 12/14/2023] [Indexed: 01/27/2024] Open
Abstract
Chronic pelvic pain (CPP) is generally defined as non-cyclic pain perceived in the pelvic area that has persisted from three to six months or longer and is unrelated to pregnancy. The etiology of CPP is complex, multifactorial, with heterogeneous presentation, and includes several diseases such as endometriosis, adenomyosis, and interstitial cystitis/bladder pain syndrome. It may also be associated with sexual dysfunction, musculoskeletal disorders, and comorbid psychiatric symptoms. Vulvar pain disorders (VPDs) are typically categorized separately from chronic pelvic pain; among all VPDs, vulvodynia is a chronic vulvar pain of unknown etiology, lasting at least 3 months and that might be associated with other potentially linked factors. Proteomics represents a useful approach to study the proteome profiles of clinical samples. In this review, we have considered a selection of articles that have analyzed the protein abundance and novel protein species from various biological samples, including eutopic/ectopic endometrium, urine, serum, follicular, peritoneal fluid, and cervical mucus, potentially involved in the pathogenesis and progression of CPP and VPDs. These findings could represent valuable targets for paving the way for the differential diagnosis and therapeutic management of CPP and VDPs, thereby optimizing both the prevention and treatment of these conditions.
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Affiliation(s)
- Chiara Di Tucci
- Department of Obstetrics and Gynecology, “Sapienza” University, 00185 Rome, Italy;
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Witt BL, Tollefsbol TO. Molecular, Cellular, and Technical Aspects of Breast Cancer Cell Lines as a Foundational Tool in Cancer Research. Life (Basel) 2023; 13:2311. [PMID: 38137912 PMCID: PMC10744609 DOI: 10.3390/life13122311] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/30/2023] [Accepted: 12/02/2023] [Indexed: 12/24/2023] Open
Abstract
Breast cancer comprises about 30% of all new female cancers each year and is the most common malignant cancer in women in the United States. Breast cancer cell lines have been harnessed for many years as a foundation for in vitro analytic studies to understand the use of cancer prevention and therapy. There has yet to be a compilation of works to analyze the pitfalls, novel discoveries, and essential techniques for breast cancer cell line studies in a scientific context. In this article, we review the history of breast cancer cell lines and their origins, as well as analyze the molecular pathways that pharmaceutical drugs apply to breast cancer cell lines in vitro and in vivo. Controversies regarding the origins of certain breast cancer cell lines, the benefits of utilizing Patient-Derived Xenograft (PDX) versus Cell-Derived Xenograft (CDX), and 2D versus 3D cell culturing techniques will be analyzed. Novel outcomes from epigenetic discovery with dietary compound usage are also discussed. This review is intended to create a foundational tool that will aid investigators when choosing a breast cancer cell line to use in multiple expanding areas such as epigenetic discovery, xenograft experimentation, and cancer prevention, among other areas.
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Affiliation(s)
- Brittany L. Witt
- Department of Biology, University of Alabama at Birmingham, 902 14th Street, Birmingham, AL 35228, USA;
| | - Trygve O. Tollefsbol
- Department of Biology, University of Alabama at Birmingham, 902 14th Street, Birmingham, AL 35228, USA;
- Integrative Center for Aging Research, University of Alabama at Birmingham, 1530 3rd Avenue South, Birmingham, AL 35294, USA
- O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, 1802 6th Avenue South, Birmingham, AL 35294, USA
- Nutrition Obesity Research Center, University of Alabama at Birmingham, 1675 University Boulevard, Birmingham, AL 35294, USA
- Comprehensive Diabetes Center, University of Alabama at Birmingham, 1825 University Boulevard, Birmingham, AL 35294, USA
- University Wide Microbiome Center, University of Alabama at Birmingham, 845 19th Street South, Birmingham, AL 35294, USA
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Menotti L, Silvello G, Atzori M, Boytcheva S, Ciompi F, Di Nunzio GM, Fraggetta F, Giachelle F, Irrera O, Marchesin S, Marini N, Müller H, Primov T. Modelling digital health data: The ExaMode ontology for computational pathology. J Pathol Inform 2023; 14:100332. [PMID: 37705689 PMCID: PMC10495665 DOI: 10.1016/j.jpi.2023.100332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 07/14/2023] [Accepted: 08/16/2023] [Indexed: 09/15/2023] Open
Abstract
Computational pathology can significantly benefit from ontologies to standardize the employed nomenclature and help with knowledge extraction processes for high-quality annotated image datasets. The end goal is to reach a shared model for digital pathology to overcome data variability and integration problems. Indeed, data annotation in such a specific domain is still an unsolved challenge and datasets cannot be steadily reused in diverse contexts due to heterogeneity issues of the adopted labels, multilingualism, and different clinical practices. Material and methods This paper presents the ExaMode ontology, modeling the histopathology process by considering 3 key cancer diseases (colon, cervical, and lung tumors) and celiac disease. The ExaMode ontology has been designed bottom-up in an iterative fashion with continuous feedback and validation from pathologists and clinicians. The ontology is organized into 5 semantic areas that defines an ontological template to model any disease of interest in histopathology. Results The ExaMode ontology is currently being used as a common semantic layer in: (i) an entity linking tool for the automatic annotation of medical records; (ii) a web-based collaborative annotation tool for histopathology text reports; and (iii) a software platform for building holistic solutions integrating multimodal histopathology data. Discussion The ontology ExaMode is a key means to store data in a graph database according to the RDF data model. The creation of an RDF dataset can help develop more accurate algorithms for image analysis, especially in the field of digital pathology. This approach allows for seamless data integration and a unified query access point, from which we can extract relevant clinical insights about the considered diseases using SPARQL queries.
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Affiliation(s)
- Laura Menotti
- Department of Information Engineering, University of Padua, Padova, Italy
| | - Gianmaria Silvello
- Department of Information Engineering, University of Padua, Padova, Italy
| | - Manfredo Atzori
- Information Systems Institute, University of Applied Sciences Western Switzerland, Delémont, Switzerland
- Department of Neuroscience, University of Padua, Padova, Italy
| | | | - Francesco Ciompi
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | | | - Fabio Giachelle
- Department of Information Engineering, University of Padua, Padova, Italy
| | - Ornella Irrera
- Department of Information Engineering, University of Padua, Padova, Italy
| | - Stefano Marchesin
- Department of Information Engineering, University of Padua, Padova, Italy
| | - Niccolò Marini
- Information Systems Institute, University of Applied Sciences Western Switzerland, Delémont, Switzerland
| | - Henning Müller
- Information Systems Institute, University of Applied Sciences Western Switzerland, Delémont, Switzerland
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11
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Cheun JH, Kim HK, Moon HG, Han W, Lee HB. Locoregional Recurrence Patterns in Patients With Different Molecular Subtypes of Breast Cancer. JAMA Surg 2023; 158:841-852. [PMID: 37342035 PMCID: PMC10285677 DOI: 10.1001/jamasurg.2023.2150] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 03/15/2023] [Indexed: 06/22/2023]
Abstract
Importance While numerous studies have consistently reported that the molecular subtypes of breast cancer (BC) are associated with different patterns of distant metastasis, few studies have investigated the association of tumor subtypes with locoregional recurrence. Objective To investigate the patterns of ipsilateral breast tumor recurrence (IBTR), regional recurrence (RR), and contralateral BC (CBC) according to tumor subtypes. Design, Setting, and Participants This retrospective cohort study used the clinical records of patients who underwent BC surgery at a single institution in South Korea between January 2000 and December 2018. Data were analyzed from May 1, 2019, to February 20, 2023. Exposures Ipsilateral breast tumor recurrence, RR, and CBC events. Main Outcomes and Measures The primary outcome was differences in annual incidence patterns of IBTR, RR, and CBC according to tumor subtypes. Hormone receptor (HR) status was assessed by immunohistochemical staining assay, and ERBB2 status was evaluated according to American Society of Clinical Oncology and College of American Pathologists guidelines. Results A total of 16 462 female patients were included in the analysis (median age at time of operation, 49.0 years [IQR, 43.0-57.0 years]). The 10-year IBTR-, RR-, and CBC-free survival rates were 95.9%, 96.1%, and 96.5%, respectively. On univariate analysis, HR-/ERBB2+ tumors had the worst IBTR-free survival (vs HR+/ERBB2- subtype: adjusted hazard ratio, 2.95; 95% CI, 2.15-4.06), while the HR-/ERBB2- subtype had the worst RR- and CBC-free survival among all subtypes (vs HR+/ERBB2- subtype, RR: adjusted hazard ratio, 2.95; 95% CI, 2.37-3.67; CBC: adjusted hazard ratio, 2.12; 95% CI, 1.64-2.75). Subtype remained significantly associated with recurrence events in Cox proportional hazards regression analysis. Regarding the annual recurrence pattern, the IBTR patterns of HR-/ERBB2+ and HR-/ERBB2- subtypes showed double peaks, while HR+/ERBB2- tumors showed a steadily increasing pattern without distinguishable peaks. Additionally, the HR+/ERBB2- subtype seemed to have a steady RR pattern, but other subtypes showed the highest RR incidence at 1 year following surgery, which then gradually decreased. The annual recurrence incidence of CBC gradually increased among all subtypes, and patients with the HR-/ERBB2- subtype had a higher incidence than patients with other subtypes over 10 years. Younger patients (age ≤40 years) had greater differences in IBTR, RR, and CBC patterns between subtypes than did older patients. Conclusions and Relevance In this study, locoregional recurrence occurred with different patterns according to BC subtypes, with younger patients having greater differences in patterns among subtypes than older patients. The findings suggest that tailoring surveillance should be recommended regarding differences in locoregional recurrence patterns according to tumor subtypes, particularly for younger patients.
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Affiliation(s)
- Jong-Ho Cheun
- Seoul Metropolitan Government–Seoul National University Boramae Medical Center, Seoul, South Korea
| | - Hong-Kyu Kim
- Department of Surgery, Seoul National University College of Medicine, Seoul, South Korea
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
| | - Hyeong-Gon Moon
- Department of Surgery, Seoul National University College of Medicine, Seoul, South Korea
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
| | - Wonshik Han
- Department of Surgery, Seoul National University College of Medicine, Seoul, South Korea
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
| | - Han-Byoel Lee
- Department of Surgery, Seoul National University College of Medicine, Seoul, South Korea
- Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
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12
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Shafique A, Babaie M, Gonzalez R, Batten A, Sikdar S, Tizhoosh HR. Composite Biomarker Image for Advanced Visualization in Histopathology. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2023; 2023:1-4. [PMID: 38083181 DOI: 10.1109/embc40787.2023.10340335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Immunohistochemistry (IHC) biomarkers are essential tools for reliable cancer diagnosis and subtyping. It requires cross-staining comparison among Whole Slide Images (WSIs) of IHCs and hematoxylin and eosin (H&E) slides. Currently, pathologists examine the visually co-localized areas across IHC and H&E glass slides for a final diagnosis, which is a tedious and challenging task. Moreover, visually inspecting different IHC slides back and forth to analyze local co-expressions is inherently subjective and prone to error, even when carried out by experienced pathologists. Relying on digital pathology, we propose "Composite Biomarker Image" (CBI) in this work. CBI is a single image that can be composed using different filtered IHC biomarker images for better visualization. We present a CBI image produced in two steps by the proposed solution for better visualization and hence more efficient clinical workflow. In the first step, IHC biomarker images are aligned with the H&E images using one coordinate system and orientation. In the second step, the positive or negative IHC regions from each biomarker image (based on the pathologists' recommendation) are filtered and combined into one image using a fuzzy inference system. For evaluation, the resulting CBI images, from the proposed system, were evaluated qualitatively by the expert pathologists. The CBI concept helps the pathologists to identify the suspected target tissues more easily, which could be further assessed by examining the actual WSIs at the same suspected regions.
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13
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Shafique A, Babaie M, Gonzalez R, Tizhoosh HR. Immunohistochemistry Biomarkers-Guided Image Search for Histopathology. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2023; 2023:1-5. [PMID: 38082577 DOI: 10.1109/embc40787.2023.10340099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Medical practitioners use a number of diagnostic tests to make a reliable diagnosis. Traditionally, Haematoxylin and Eosin (H&E) stained glass slides have been used for cancer diagnosis and tumor detection. However, recently a variety of immunohistochemistry (IHC) stained slides can be requested by pathologists to examine and confirm diagnoses for determining the subtype of a tumor when this is difficult using H&E slides only. Deep learning (DL) has received a lot of interest recently for image search engines to extract features from tissue regions, which may or may not be the target region for diagnosis. This approach generally fails to capture high-level patterns corresponding to the malignant or abnormal content of histopathology images. In this work, we are proposing a targeted image search approach, inspired by the pathologists' workflow, which may use information from multiple IHC biomarker images when available. These IHC images could be aligned, filtered, and merged together to generate a composite biomarker image (CBI) that could eventually be used to generate an attention map to guide the search engine for localized search. In our experiments, we observed that an IHC-guided image search engine can retrieve relevant data more accurately than a conventional (i.e., H&E-only) search engine without IHC guidance. Moreover, such engines are also able to accurately conclude the subtypes through majority votes.
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14
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Nayerpour dizaj T, Jafari-Gharabaghlou D, Farhoudi Sefidan Jadid M, Jahanban R, Rahimi M, Farajollahi MM, Mohsenzadegan M, Zarghami N. Fabrication of Antibody Conjugated Super Magnetic Oxide Nanoparticles for Early Detection of Prostate Cancer. Asian Pac J Cancer Prev 2023; 24:2089-2097. [PMID: 37378940 PMCID: PMC10505892 DOI: 10.31557/apjcp.2023.24.6.2089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND Prostate cancer is one of the most widespread cancers in the world. Early diagnosis is the most important factor in treatment efficiency. Furthermore, new methods for early diagnosis and treatment play an important role. In this study, we designed targeted conjugation of antibodies with iron nanoparticles and evaluated the binding properties of antibodies to prostate cancers and benign tissues. This method in addition to having a lower cost has high sensitivity and specificity. METHODS Anti- PSCA antibodies were purified and conjugated to super magnetic oxide nanoparticles (SPION). Then, iron staining on prostate adenocarcinoma tissues was performed. At the same time, immunohistochemically staining was performed on similar tissues to compare the results. In addition, benign prostatic hyperplasia (BPH) samples were used as a control sample. RESULTS In adenocarcinoma tissues with iron staining, many blue spots are seen compared to benign tissues, and the number of these spots increases with increasing tumor grade. CONCLUSION These findings indicate the characteristic of iron staining as a conjugate antibody to iron can be an appropriate approach to specific staining of tumor markers in cancer tissues and can be used to diagnose prostate cancer due to its safety, low cost, sensitivity, and specificity.
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Affiliation(s)
- Tina Nayerpour dizaj
- Department of Biotechnology, Faculty of Advanced Medical Science, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Davoud Jafari-Gharabaghlou
- Department of Clinical Biochemistry and Laboratory Medicine, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Mahdi Farhoudi Sefidan Jadid
- Department of Clinical Biochemistry and Laboratory Medicine, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Rana Jahanban
- Department of Biotechnology, Faculty of Advanced Medical Science, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Mandana Rahimi
- Department of Pathology, Hasheminejad Kidney center, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.
| | | | - Monireh Mohsenzadegan
- Department of Medical Laboratory sciences, Faculty of Allied Medical sciences, Iran University of Medical Sciences, Tehran, Iran.
| | - Nosratollah Zarghami
- Department of Clinical Biochemistry and Laboratory Medicine, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
- Department of Medical Biochemistry, Faculty of Medicine, Istanbul Aydin University, Istanbul, Turkey.
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15
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Gu J, Jian H, Wei C, Shiu J, Ganesan A, Zhao W, Hedde PN. A Low-Cost Modular Imaging System for Rapid, Multiplexed Immunofluorescence Detection in Clinical Tissues. Int J Mol Sci 2023; 24:7008. [PMID: 37108170 PMCID: PMC10138925 DOI: 10.3390/ijms24087008] [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: 02/25/2023] [Revised: 04/03/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
To image 4-plex immunofluorescence-stained tissue samples at a low cost with cellular level resolution and sensitivity and dynamic range required to detect lowly and highly abundant targets, here we describe a robust, inexpensive (<$9000), 3D printable portable imaging device (Tissue Imager). The Tissue Imager can immediately be deployed on benchtops for in situ protein detection in tissue samples. Applications for this device are broad, ranging from answering basic biological questions to clinical pathology, where immunofluorescence can detect a larger number of markers than the standard H&E or chromogenic immunohistochemistry (CIH) staining, while the low cost also allows usage in classrooms. After characterizing our platform's specificity and sensitivity, we demonstrate imaging of a 4-plex immunology panel in human cutaneous T-cell lymphoma (CTCL) formalin-fixed paraffin-embedded (FFPE) tissue samples. From those images, positive cells were detected using CellProfiler, a popular open-source software package, for tumor marker profiling. We achieved a performance on par with commercial epifluorescence microscopes that are >10 times more expensive than our Tissue Imager. This device enables rapid immunofluorescence detection in tissue sections at a low cost for scientists and clinicians and can provide students with a hands-on experience to understand engineering and instrumentation. We note that for using the Tissue Imager as a medical device in clinical settings, a comprehensive review and approval processes would be required.
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Affiliation(s)
- Joshua Gu
- Department of Biological Chemistry, University of California, Irvine, CA 92697, USA
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, CA 92697, USA
| | - Hannah Jian
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
| | - Christine Wei
- Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697, USA
| | - Jessica Shiu
- Department of Dermatology, University of California, Irvine, CA 92697, USA
| | - Anand Ganesan
- Department of Biological Chemistry, University of California, Irvine, CA 92697, USA
- Department of Dermatology, University of California, Irvine, CA 92697, USA
- Chao Family Comprehensive Cancer Center, University of California, Irvine, CA 92697, USA
| | - Weian Zhao
- Department of Biological Chemistry, University of California, Irvine, CA 92697, USA
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, CA 92697, USA
- Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697, USA
- Chao Family Comprehensive Cancer Center, University of California, Irvine, CA 92697, USA
- Edwards Life Sciences Center for Advanced Cardiovascular Technology, University of California, Irvine, CA 92697, USA
- Department of Biomedical Engineering, University of California, Irvine, CA 92697, USA
- Institute for Immunology, University of California, Irvine, CA 92697, USA
| | - Per Niklas Hedde
- Beckman Laser Institute and Medical Clinic, University of California, Irvine, CA 92697, USA
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16
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Al Deleemy M, Huynh B, Waters KA, Machaalani R. Immunohistochemistry for acetylcholinesterase and butyrylcholinesterase in the dorsal motor nucleus of the vagus (DMNV) of formalin-fixed, paraffin-embedded tissue: comparison with reported literature. Histochem Cell Biol 2023; 159:247-262. [PMID: 36422707 DOI: 10.1007/s00418-022-02164-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/01/2022] [Indexed: 11/27/2022]
Abstract
The majority of research regarding the expression of acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) in the brain has been conducted using histochemistry to identify enzymatic activity in frozen fixed tissue. However, retrospective human neurochemistry studies are generally restricted to formalin-fixed, paraffin-embedded (FFPE) tissues that are not suitable for histochemical procedures. The availability of commercially available antibody formulations provides the means to study such tissues by immunohistochemistry (IHC). In this study, we optimised IHC conditions for evaluating the expression of AChE and BuChE in the brainstem, focusing on the dorsal motor nucleus of the vagus, in human and piglet FFPE tissues, using commercially available antibodies. Our results were compared to published reports of histochemically determined AChE and BuChE expression. We varied antibody concentrations and antigen retrieval methods, and evaluated different detection systems, with the overall aim to optimise immunohistochemical staining. The primary findings, consistent across both species, are: (1) AChE and BuChE expression dominated in the neuronal somata, specifically in the neuronal cytoplasm; and (2) no change in the protocol resulted in axonal/neuropil expression of AChE. These results indicate that IHC is a suitable tool to detect AChE and BuChE in FFPE tissue using commercial antibodies, albeit the staining patterns obtained differed from those using histochemistry in frozen tissue. The underlying cause(s) for these differences are discussed in detail and may be associated with the principal components of the staining method, the antibody protein target and/or limitations to the detection of epitopes by tissue fixation.
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Affiliation(s)
- Masarra Al Deleemy
- Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Benjamin Huynh
- Brain and Mind Centre, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, Australia
| | - Karen A Waters
- Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Rita Machaalani
- Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Camperdown, NSW, 2006, Australia.
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17
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Goyal D, Kumar H. In Vivo and 3D Imaging Technique(s) for Spatiotemporal Mapping of Pathological Events in Experimental Model(s) of Spinal Cord Injury. ACS Chem Neurosci 2023; 14:809-819. [PMID: 36787542 DOI: 10.1021/acschemneuro.2c00643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023] Open
Abstract
Endothelial damage, astrogliosis, microgliosis, and neuronal degeneration are the most common events after spinal cord injury (SCI). Studies highlighted that studying the spatiotemporal profile of these events might provide a deeper understanding of the pathophysiology of SCI. For imaging of these events, available conventional techniques such as 2-dimensional histology and immunohistochemistry (IHC) are well established and frequently used to visualize and detect the altered expression of the protein of interest involved in these events. However, the technique requires the physical sectioning of the tissue, and results are also open to misinterpretation. Currently, researchers are focusing more attention toward the advanced tools for imaging the spinal cord's various physiological and pathological parameters. The tools include two-photon imaging, light sheet fluorescence microscopy, in vivo imaging system with fluorescent probes, and in vivo chemical and fluorescent protein-expressing viral-tracers. These techniques outperform the limitations associated with conventional techniques in various aspects, such as optical sectioning of tissue, 3D reconstructed imaging, and imaging of particular planes of interest. In addition to this, these techniques are minimally invasive and less time-consuming. In this review, we will discuss the various advanced imaging methodologies that will evolve in the future to explore the fundamental mechanisms after SCI.
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Affiliation(s)
- Divya Goyal
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER)-Ahmedabad, Gandhinagar, Gujarat India, 382355
| | - Hemant Kumar
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER)-Ahmedabad, Gandhinagar, Gujarat India, 382355
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18
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Molnar A, Monroe H, Basri Aydin H, Arslan ME, Lightle A, Lee H, El Jabbour T. Tumors of the Digestive System: Comprehensive Review of Ancillary Testing and Biomarkers in the Era of Precision Medicine. Curr Oncol 2023; 30:2388-2404. [PMID: 36826143 PMCID: PMC9954843 DOI: 10.3390/curroncol30020182] [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: 01/26/2023] [Revised: 02/13/2023] [Accepted: 02/15/2023] [Indexed: 02/18/2023] Open
Abstract
Immunotherapy has remained at the vanguard of promising cancer therapeutic regimens due to its exceptionally high specificity for tumor cells and potential for significantly improved treatment-associated quality of life compared to other therapeutic approaches such as surgery and chemoradiation. This is especially true in the digestive system, where high rates of mutation give rise to a host of targetable tumor-specific antigens. Many patients, however, do not exhibit measurable improvements under immunotherapy due to intrinsic or acquired resistance, making predictive biomarkers necessary to determine which patients will benefit from this line of treatment. Many of these biomarkers are assessed empirically by pathologists according to nuanced scoring criteria and algorithms. This review serves to inform clinicians and pathologists of extant and promising upcoming biomarkers predictive of immunotherapeutic efficacy among digestive system malignancies and the ancillary testing required for interpretation by pathologists according to tumor site of origin.
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Affiliation(s)
- Attila Molnar
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10025, USA
| | - Hunter Monroe
- Department of Pathology, West Virginia University, Morgantown, WV 26506, USA
| | - Hasan Basri Aydin
- Department of Pathology, Albany Medical Center, Albany, NY 12208, USA
| | - Mustafa Erdem Arslan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Andrea Lightle
- Department of Pathology, Albany Medical Center, Albany, NY 12208, USA
| | - Hwajeong Lee
- Department of Pathology, Albany Medical Center, Albany, NY 12208, USA
| | - Tony El Jabbour
- Department of Pathology, West Virginia University, Morgantown, WV 26506, USA
- Correspondence:
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19
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Deep-learning based breast cancer detection for cross-staining histopathology images. Heliyon 2023; 9:e13171. [PMID: 36755605 PMCID: PMC9900267 DOI: 10.1016/j.heliyon.2023.e13171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 01/13/2023] [Accepted: 01/19/2023] [Indexed: 01/23/2023] Open
Abstract
Hematoxylin and eosin (H&E) staining is the gold standard for tissue characterization in routine pathological diagnoses. However, these visible light dyes do not exclusively label the nuclei and cytoplasm, making clear-cut segmentation of staining signals challenging. Currently, fluorescent staining technology is much more common in clinical research for analyzing tissue morphology and protein distribution owing to its advantages of channel independence, multiplex labeling, and the possibility of enabling 3D tissue labeling. Although both H&E and fluorescent dyes can stain the nucleus and cytoplasm for representative tissue morphology, color variation between these two staining technologies makes cross-analysis difficult, especially with computer-assisted artificial intelligence (AI) algorithms. In this study, we applied color normalization and nucleus extraction methods to overcome the variation between staining technologies. We also developed an available workflow for using an H&E-stained segmentation AI model in the analysis of fluorescent nucleic acid staining images in breast cancer tumor recognition, resulting in 89.6% and 80.5% accuracy in recognizing specific tumor features in H&E- and fluorescent-stained pathological images, respectively. The results show that the cross-staining inference maintained the same precision level as the proposed workflow, providing an opportunity for an expansion of the application of current pathology AI models.
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20
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Meta-Analysis of MS-Based Proteomics Studies Indicates Interferon Regulatory Factor 4 and Nucleobindin1 as Potential Prognostic and Drug Resistance Biomarkers in Diffuse Large B Cell Lymphoma. Cells 2023; 12:cells12010196. [PMID: 36611989 PMCID: PMC9818977 DOI: 10.3390/cells12010196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/20/2022] [Accepted: 12/26/2022] [Indexed: 01/06/2023] Open
Abstract
The prognosis of diffuse large B cell lymphoma (DLBCL) is inaccurately predicted using clinical features and immunohistochemistry (IHC) algorithms. Nomination of a panel of molecules as the target for therapy and predicting prognosis in DLBCL is challenging because of the divergences in the results of molecular studies. Mass spectrometry (MS)-based proteomics in the clinic represents an analytical tool with the potential to improve DLBCL diagnosis and prognosis. Previous proteomics studies using MS-based proteomics identified a wide range of proteins. To achieve a consensus, we reviewed MS-based proteomics studies and extracted the most consistently significantly dysregulated proteins. These proteins were then further explored by analyzing data from other omics fields. Among all significantly regulated proteins, interferon regulatory factor 4 (IRF4) was identified as a potential target by proteomics, genomics, and IHC. Moreover, annexinA5 (ANXA5) and nucleobindin1 (NUCB1) were two of the most up-regulated proteins identified in MS studies. Functional enrichment analysis identified the light zone reactions of the germinal center (LZ-GC) together with cytoskeleton locomotion functions as enriched based on consistent, significantly dysregulated proteins. In this study, we suggest IRF4 and NUCB1 proteins as potential biomarkers that deserve further investigation in the field of DLBCL sub-classification and prognosis.
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Abstract
Immunohistochemistry (IHC) is one of the most widely used protein detection techniques. The principle of this technique is based on the binding of a specific antibody to a matching specific antigen in tissue. The bound antigen-antibody complex then is visualized using a range of detection techniques. IHC uses a number of different enzymatic labels, such as peroxidase and alkaline phosphatase, for the detection of the antigens of interest whereas immunofluorescence (IF) uses a fluorescent signal. In this chapter, IHC will be described using the peroxidase label. Both IHC and IF can be used on formalin-fixed paraffin-embedded (FFPE) or appropriately processed fresh tissues. IHC/IF can be multiplexed to detect more than one antigen at a time, or may be sequentially stained to detect multiple targets. These techniques are routinely used in diagnostic pathology laboratories, not just for diagnostic purposes but many biomarkers are used for patient staging, treatment allocation, and prognostication. Immunofluorescence is routinely used for the detection of antibodies and antigens in freshly biopsied tissues, particularly for immune-mediated and vesiculobullous lesions. In this chapter, the principles of IHC are reviewed followed by examples of IHC and IF staining using readily available antibodies. Steps and processes involved in IHC/IF double staining are also described.
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Affiliation(s)
| | - Benedict Seo
- School of Dentistry, University of Otago, Dunedin, New Zealand
| | - Alison M Rich
- School of Dentistry, University of Otago, Dunedin, New Zealand
- School of Medicine, University of Otago, Dunedin, New Zealand
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22
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Zhong X, Chen R. Detection of Ferroptosis by Immunohistochemistry and Immunofluorescence. Methods Mol Biol 2023; 2712:211-222. [PMID: 37578709 DOI: 10.1007/978-1-0716-3433-2_19] [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: 08/15/2023]
Abstract
Ferroptosis is a type of regulated cell death driven by oxidative damage, characterized by iron overload and lipid peroxidation, and regulated by a network of distinct molecules and organelles. Impaired ferroptotic response is implicated in multiple physiological and pathological processes, including tumorigenesis, neurodegeneration, and ischemia-reperfusion damage. Classical techniques of immunohistochemistry (IHC) and immunofluorescence (IF) can be employed to exhibit antigen expression and location in tissues observed with microscopy, making them powerful tools in studying the ferroptosis process. In this chapter, we introduce commonly used protocols and summarize typical markers used in IHC and IF to monitor ferroptosis.
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Affiliation(s)
- Xiao Zhong
- Department of Infectious Diseases, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Viral Hepatitis, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Ruochan Chen
- Department of Infectious Diseases, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Viral Hepatitis, Xiangya Hospital, Central South University, Changsha, Hunan, China
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23
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Muacevic A, Adler JR, Vezhavendhan N, Sivaramakrishnan M, Santhanam VL, Suganya R. Expression of Matrix Metalloproteinase-21 in Oral Squamous Cell Carcinoma. Cureus 2023; 15:e34256. [PMID: 36855499 PMCID: PMC9968393 DOI: 10.7759/cureus.34256] [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: 01/26/2023] [Indexed: 01/28/2023] Open
Abstract
Introduction Oral squamous cell carcinoma (OSCC) is one of the most common cancer with increasing morbidity and mortality due to regional invasion, metastasis, and secondary malignancy along with associated medical complications. The degradation of matrix metalloproteinases (MMPs) is essential for the progression of carcinoma, hence MMPs are implicated in cancer invasion and metastasis as a biomarker. Objective The primary objective of this study was to find the expression of MMP-21 between oral squamous cell carcinoma and healthy tissue. Materials and methods In this retrospective study, banked pathology was used to observe the expression of MMP-21 in oral squamous cell carcinoma. MMP-21 protein expression was assessed in 50 cases of OSCC by immunohistochemistry assay. Statistical analysis was performed to evaluate the relation of MMP-21 expression. Results There was increased expression of MMP-21 in OSCC, and this was statistically significant (p<0.0001). Conclusion This result suggests the potential role in tumor progression and as a potent marker in diagnosing OSCC. In the future, it might also be a novel tool in therapeutic intervention.
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Imperatore R, Cristino L. Assessing CB 1 Expression in the Brain by Immunohistochemical Methods: Light, Confocal, and Electron Microscopy. Methods Mol Biol 2023; 2576:407-424. [PMID: 36152206 DOI: 10.1007/978-1-0716-2728-0_34] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Conventional techniques to reveal the neuroanatomical distribution of type 1 cannabinoid receptor (CB1) in the brain, at the cellular and subcellular level, are mainly represented by light, confocal, and electron microscopy. By using immunoperoxidase and immunofluorescence methods, it is possible to reveal CB1 distribution and localization in the brain and its changes under pathological conditions. Moreover, by using electron microscopy, we can define the ultrastructural localization at the level of subcellular structures and organelles. Here, we describe immunoperoxidase, immunofluorescence, and electron microscopy protocols used to get information about CB1 spatial distribution and localization in the brain. Preparation of reagents, resin embedding, preparation for an endogenous activity-blocking step, and background counterstaining and revelation of CB1 by using specific labeled secondary antibodies will be presented. The methods here discussed are highly sensitive and specific multistep processes, where each step is critical to finally obtain an optimum signal.
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Affiliation(s)
- Roberta Imperatore
- Department of Sciences and Technologies, University of Sannio, Benevento, Italy
| | - Luigia Cristino
- Endocannabinoid Research Group, Institute of Biomolecular Chemistry, National Research Council, Pozzuoli, NA, Italy.
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25
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Elevated expression of receptors for EGF, PDGF, transferrin and folate within murine and human lupus nephritis kidneys. Clin Immunol 2023; 246:109188. [PMID: 36396012 DOI: 10.1016/j.clim.2022.109188] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022]
Abstract
OBJECTIVE Systemic lupus erythematosus (SLE) is a chronic autoimmune disease where the body's immune system targets cells and tissue in numerous organs, including the kidneys. Lupus nephritis (LN) is a highly heterogeneous disease, and diagnosis is difficult because clinical manifestations vary widely among patients. Comprehensive proteomic studies reported recently in LN have identified several urinary proteins which are also cell-surface receptors. If indeed these receptor proteins are also hyper-expressed within the kidneys, ligands to these receptors may be useful for drug targeting. METHODS scRNA sequence data analysis and immunohistochemistry were performed on LN kidneys for expression of four implicated receptors, EGFR, FOL2R2, PDGF-RB, and TFRC. RESULTS In reported scRNA sequencing studies from 21 LN patients and 3 healthy control renal biopsies or renal-infiltrating immune cells from 24 LN biopsies, EGFR, FOLR2, PDGF-Rb, and TFRC were all hyper expressed within LN kidneys in comparison to healthy kidneys, either within resident renal cells or infiltrating leukocytes. Immunohistochemistry staining of murine lupus renal biopsies from lupus mice revealed EGFR, FOLR2, TFRC and PDGF-RB were elevated in LN kidneys. Immunohistochemistry staining of human Class II, Class III, and Class IV kidney tissue sections revealed EGFR, TFRC, and PDGF-RB were significantly elevated in proliferative LN kidneys. CONCLUSION These findings underscore the potential of EGFR, TFRC, FOLR2, and PDGF-RB as promising receptors for potential drug-targeting in LN.
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Chen K, Yong J, Zauner R, Wally V, Whitelock J, Sajinovic M, Kopecki Z, Liang K, Scott KF, Mellick AS. Chondroitin Sulfate Proteoglycan 4 as a Marker for Aggressive Squamous Cell Carcinoma. Cancers (Basel) 2022; 14:cancers14225564. [PMID: 36428658 PMCID: PMC9688099 DOI: 10.3390/cancers14225564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 10/27/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
Chondroitin sulfate (CS) proteoglycan 4 (CSPG4) is a cell surface proteoglycan that is currently under investigation as a marker of cancer malignancy, and as a potential target of anticancer drug treatment. CSPG4 acts as a driver of tumourigenesis by regulating turnover of the extracellular matrix (ECM) to promote tumour cell invasion, migration as well as inflammation and angiogenesis. While CSPG4 has been widely studied in certain malignancies, such as melanoma, evidence is emerging from global gene expression studies, which suggests a role for CSPG4 in squamous cell carcinoma (SCC). While relatively treatable, lack of widely agreed upon diagnostic markers for SCCs is problematic, especially for clinicians managing certain patients, including those who are aged or infirm, as well as those with underlying conditions such as epidermolysis bullosa (EB), for which a delayed diagnosis is likely lethal. In this review, we have discussed the structure of CSPG4, and quantitatively analysed CSPG4 expression in the tissues and pathologies where it has been identified to determine the usefulness of CSPG4 expression as a diagnostic marker and therapeutic target in management of malignant SCC.
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Affiliation(s)
- Kathryn Chen
- Ingham Institute for Applied Medical Research, Medicine, University of New South Wales, Liverpool, NSW 2170, Australia
- School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia
| | - Joel Yong
- Ingham Institute for Applied Medical Research, Medicine, University of New South Wales, Liverpool, NSW 2170, Australia
- School of Chemical Engineering, University of New South Wales, Kensington, NSW 2033, Australia
| | - Roland Zauner
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology & Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria
| | - Verena Wally
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology & Allergology, University Hospital of the Paracelsus Medical University, 5020 Salzburg, Austria
| | - John Whitelock
- Ingham Institute for Applied Medical Research, Medicine, University of New South Wales, Liverpool, NSW 2170, Australia
- Graduate School of Biomedical Engineering, University of New South Wales, Kensington, NSW 2033, Australia
| | - Mila Sajinovic
- Ingham Institute for Applied Medical Research, Medicine, University of New South Wales, Liverpool, NSW 2170, Australia
| | - Zlatko Kopecki
- Future Industries Institute, University of South Australia, Mawson Lakes, SA 5095, Australia
| | - Kang Liang
- Ingham Institute for Applied Medical Research, Medicine, University of New South Wales, Liverpool, NSW 2170, Australia
- School of Chemical Engineering, University of New South Wales, Kensington, NSW 2033, Australia
| | - Kieran Francis Scott
- Ingham Institute for Applied Medical Research, Medicine, University of New South Wales, Liverpool, NSW 2170, Australia
- School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia
| | - Albert Sleiman Mellick
- Ingham Institute for Applied Medical Research, Medicine, University of New South Wales, Liverpool, NSW 2170, Australia
- Graduate School of Biomedical Engineering, University of New South Wales, Kensington, NSW 2033, Australia
- Correspondence:
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27
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Proteomics-Based Identification of Dysregulated Proteins in Breast Cancer. Proteomes 2022; 10:proteomes10040035. [PMID: 36278695 PMCID: PMC9590004 DOI: 10.3390/proteomes10040035] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/10/2022] [Accepted: 10/18/2022] [Indexed: 11/18/2022] Open
Abstract
Immunohistochemistry (IHC) is still widely used as a morphology-based assay for in situ analysis of target proteins as specific tumor antigens. However, as a very heterogeneous collection of neoplastic diseases, breast cancer (BC) requires an accurate identification and characterization of larger panels of candidate biomarkers, beyond ER, PR, and HER2 proteins, for diagnosis and personalized treatment, without the limited availability of antibodies that are required to identify specific proteins. Top-down, middle-down, and bottom-up mass spectrometry (MS)-based proteomics approaches complement traditional histopathological tissue analysis to examine expression, modification, and interaction of hundreds to thousands of proteins simultaneously. In this review, we discuss the proteomics-based identification of dysregulated proteins in BC that are essential for the following issues: discovery and validation of new biomarkers by analysis of solid and liquid/non-invasive biopsies, cell lines, organoids and xenograft models; identification of panels of biomarkers for early detection and accurate discrimination between cancer, benign and normal tissues; identification of subtype-specific and stage-specific protein expression profiles in BC grading and measurement of disease progression; characterization of new subtypes of BC; characterization and quantitation of post-translational modifications (PTMs) and aberrant protein-protein interactions (PPI) involved in tumor development; characterization of the global remodeling of BC tissue homeostasis, diagnosis and prognostic information; and deciphering of molecular functions, biological processes and mechanisms through which the dysregulated proteins cause tumor initiation, invasion, and treatment resistance.
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Prabakaran RC, Rachel JB, Rao GN, Vennila AA, Fathima SD, Keerthik Lavanya MK. Expression sites of immunohistochemistry markers in oral diseases - A scoping review. J Oral Maxillofac Pathol 2022; 26:524-533. [PMID: 37082070 PMCID: PMC10112098 DOI: 10.4103/jomfp.jomfp_364_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/03/2022] [Accepted: 09/08/2022] [Indexed: 04/22/2023] Open
Abstract
Introduction Immunohistochemistry (IHC) has not always been an easy field for the research beginners like postgraduates, research fellows and scientists. Meaningful interpretation of IHC positivity needs expertise. This could be made easier for beginners by developing a conceptual framework of markers. The literature review revealed a lack of qualitative evidence on the hitherto IHC studies on oral diseases about the overall expression of IHC markers and its comparison with pathology and normal tissues. Aim This scoping review aimed to examine the literature and classify the various immunohistochemistry markers of oral diseases based on the tissue, cell and site of expression. Materials and Methods The review was in accordance with Preferred Reporting Items for scoping reviews (PRISMA -ScR). Electronic databases such as PubMed and Cochrane were searched for relevant articles till 2021. Results We included 43 articles. We found five different possibilities of the site of expression of a marker in a cell. They are the nucleus, cytoplasm, cell membrane, extracellular matrix or any of the above combinations. Based on the tissue of expression, we also mapped the markers expressed in oral diseases to their tissue of origin as ectoderm, endoderm, mesoderm and markers with multiple tissues of expression. Based on our results, we derived two classifications that give an overview of the expression of IHC markers in oral diseases. Conclusion This scoping review derived new insight into the classification of IHC markers based on cell lineage, tissue and site of expression. This would enable a beginner to better understand a marker with its application and the interpretation of the staining in research. This could also serve as a beginner's guide for any researcher to thrive and explore the IHC world.
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Affiliation(s)
- Rebekah C. Prabakaran
- Department of Oral and Maxillofacial Pathology, C. S. I. College of Dental Sciences and Research, Madurai, Tamil Nadu, India
| | - J Beryl Rachel
- Department of Oral and Maxillofacial Pathology, C. S. I. College of Dental Sciences and Research, Madurai, Tamil Nadu, India
| | - Gururaj N. Rao
- Department of Oral and Maxillofacial Pathology, C. S. I. College of Dental Sciences and Research, Madurai, Tamil Nadu, India
| | - Alagu A Vennila
- Department of Oral and Maxillofacial Pathology, C. S. I. College of Dental Sciences and Research, Madurai, Tamil Nadu, India
| | - S Deenul Fathima
- Department of Oral and Maxillofacial Pathology, C. S. I. College of Dental Sciences and Research, Madurai, Tamil Nadu, India
| | - M. K Keerthik Lavanya
- Department of Oral and Maxillofacial Pathology, C. S. I. College of Dental Sciences and Research, Madurai, Tamil Nadu, India
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29
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Wang Y, Hu J, Sun Y, Song B, Zhang Y, Lu Y, Ma H. Metformin Synergizes with PD-L1 Monoclonal Antibody Enhancing Tumor Immune Response in Treating Non-Small Cell Lung Cancer and Its Molecular Mechanism Investigation. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2022; 2022:5983959. [PMID: 36199547 PMCID: PMC9527407 DOI: 10.1155/2022/5983959] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/04/2022] [Accepted: 07/06/2022] [Indexed: 12/02/2022]
Abstract
Despite non-small cell lung cancer (NSCLC) treatment is proved to be effective using PD-L1 monoclonal antibody (PD-L1 MAb), it is commonly seen in immune-related adverse events reported. We aimed to explore metformin synergized with PD-L1 MAb in treating NSCLC and its potential molecular mechanism. In mice, the transplantable lung cancer models were established and a co-culture system of CD8+T cells and LLC cells was constructed. The anti-tumor effect was assessed by xenograft tumor growth, proliferation signal Ki67 expression, and MTT assays. Immunohistochemistry and western blot assays were also conducted to determine tumor immune response as well as mechanism investigation. The results indicated that tumor volume and cell proliferation were markedly inhibited following metformin synergized with PD-L1 MAb which was more effective than either single metformin or PD-L1 MAb. The cytokines TNF-α, IL-2, and IFN-γ secretion in CD8+ T cells was significantly increased, and the immune response was enhanced by metformin synergized with PD-L1 MAb. Further, the WB results implied that metformin synergized with PD-L1 MAb could activate the AMPK pathway and inhibit mTOR. AMPK inhibitor (Compound C) was added, and the results showed that the anti-tumor effect was reduced in metformin + PD-L1 MAb + CC than in metformin + PD-L1 MAb which indicates the metformin synergized with PD-L1 MAb efficacy was AMPK pathway dependent. In conclusion, metformin synergized with PD-L1 MAb has better efficacy against NSCLC than metformin or PD-L1 MAb alone in an AMPK-dependent way and facilitates increasing CD8+ T cell infiltration and enhancing tumor immune response.
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Affiliation(s)
- Yifan Wang
- The First Affiliated Hospital of Soochow University, Department of Thoracic Surgery, Suzhou 215006, China
- Affiliated Hospital of Chengdu University, Department of Thoracic Surgery, Chengdu 610081, China
| | - Jingguo Hu
- Affiliated Hospital of Chengdu University, Department of Thoracic Surgery, Chengdu 610081, China
| | - Yu Sun
- Affiliated Hospital of Chengdu University, Department of Thoracic Surgery, Chengdu 610081, China
| | - Bo Song
- Affiliated Hospital of Chengdu University, Department of Thoracic Surgery, Chengdu 610081, China
| | - Yan Zhang
- Affiliated Hospital of Chengdu University, Department of Thoracic Surgery, Chengdu 610081, China
| | - Yusong Lu
- Affiliated Hospital of Chengdu University, Department of Thoracic Surgery, Chengdu 610081, China
| | - Haitao Ma
- The First Affiliated Hospital of Soochow University, Department of Thoracic Surgery, Suzhou 215006, China
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30
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Boys EL, Liu J, Robinson PJ, Reddel RR. Clinical applications of mass spectrometry-based proteomics in cancer: where are we? Proteomics 2022; 23:e2200238. [PMID: 35968695 DOI: 10.1002/pmic.202200238] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 08/07/2022] [Accepted: 08/09/2022] [Indexed: 11/12/2022]
Abstract
Tumor tissue processing methodologies in combination with data-independent acquisition mass spectrometry (DIA-MS) have emerged that can comprehensively analyze the proteome of multiple tumor samples accurately and reproducibly. Increasing recognition and adoption of these technologies has resulted in a tranche of studies providing novel insights into cancer classification systems, functional tumor biology, cancer biomarkers, treatment response and drug targets. Despite this, with some limited exceptions, MS-based proteomics has not yet been implemented in routine cancer clinical practice. Here, we summarize the use of DIA-MS in studies that may pave the way for future clinical cancer applications, and highlight the role of alternative MS technologies and multi-omic strategies. We discuss limitations and challenges of studies in this field to date and propose steps for integrating proteomic data into the cancer clinic. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Emma L Boys
- ProCan®, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
| | - Jia Liu
- ProCan®, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia.,The Kinghorn Cancer Centre, St Vincent's Hospital, Darlinghurst, NSW, Australia.,School of Clinical Medicine, St Vincent's Campus, University of New South Wales, Sydney, NSW, Australia
| | - Phillip J Robinson
- ProCan®, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
| | - Roger R Reddel
- ProCan®, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
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31
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Garg T, Weiss CR, Sheth RA. Techniques for Profiling the Cellular Immune Response and Their Implications for Interventional Oncology. Cancers (Basel) 2022; 14:3628. [PMID: 35892890 PMCID: PMC9332307 DOI: 10.3390/cancers14153628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 12/07/2022] Open
Abstract
In recent years there has been increased interest in using the immune contexture of the primary tumors to predict the patient's prognosis. The tumor microenvironment of patients with cancers consists of different types of lymphocytes, tumor-infiltrating leukocytes, dendritic cells, and others. Different technologies can be used for the evaluation of the tumor microenvironment, all of which require a tissue or cell sample. Image-guided tissue sampling is a cornerstone in the diagnosis, stratification, and longitudinal evaluation of therapeutic efficacy for cancer patients receiving immunotherapies. Therefore, interventional radiologists (IRs) play an essential role in the evaluation of patients treated with systemically administered immunotherapies. This review provides a detailed description of different technologies used for immune assessment and analysis of the data collected from the use of these technologies. The detailed approach provided herein is intended to provide the reader with the knowledge necessary to not only interpret studies containing such data but also design and apply these tools for clinical practice and future research studies.
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Affiliation(s)
- Tushar Garg
- Division of Vascular and Interventional Radiology, Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; (T.G.); (C.R.W.)
| | - Clifford R. Weiss
- Division of Vascular and Interventional Radiology, Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; (T.G.); (C.R.W.)
| | - Rahul A. Sheth
- Department of Interventional Radiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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32
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Gyanchandani A, Shukla S, Vagha S, Acharaya S, Kadu RP. Diagnostic Utility of Cytokeratin 17 Expression in Oral Squamous Cell Carcinoma: A Review. Cureus 2022; 14:e27041. [PMID: 35989819 PMCID: PMC9389021 DOI: 10.7759/cureus.27041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 07/19/2022] [Indexed: 11/21/2022] Open
Abstract
One of the most common oral malignancies is oral squamous cell carcinoma (OSCC). Although the prevalence of oral cancer varies worldwide, it is generally agreed that the oral cavity is a common anatomical site for cancer, depending primarily on the country (and even particular region in some countries) and gender of the patients. Finding diagnostic markers for OSCC is critical for early diagnosis and personalised treatment of patients. Because they are overexpressed in OSCC relative to normal mucosa, cytokeratins (CKs), intermediate filaments of the cytoskeletons, are possibilities for diagnostic markers of OSCC. CK17 should be targeted as a diagnostic marker for OSCC among the CKs, as multiple other CKs have been linked to the disease. This study aims to assess the immuno-histochemistry expression of CK17 and to investigate whether there is a link between CK17 and OSCC differentiation.
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33
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Prospective role and immunotherapeutic targets of sideroflexin protein family in lung adenocarcinoma: evidence from bioinformatics validation. Funct Integr Genomics 2022; 22:1057-1072. [DOI: 10.1007/s10142-022-00883-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 07/08/2022] [Accepted: 07/08/2022] [Indexed: 11/27/2022]
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34
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Simultaneous Visualization of MiRNA-221 and Caspase-3 in Cancer Cells for Investigating the Feasibility of MiRNA-Targeted Therapy with a Dual-Color Fluorescent Nanosensor. BIOSENSORS 2022; 12:bios12070444. [PMID: 35884247 PMCID: PMC9312853 DOI: 10.3390/bios12070444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/16/2022] [Accepted: 06/20/2022] [Indexed: 11/22/2022]
Abstract
MiRNA-targeted therapy holds great promise for precision cancer therapy. It is important to investigate the effect of changes in miRNA expression on apoptosis in order to evaluate miRNA-targeted therapy and achieve personalized therapy. In this study, we designed a dual-color fluorescent nanosensor consisting of grapheme oxide modified with a molecular beacon and peptide. The nanosensor can simultaneously detect and image miRNA-221 and apoptotic protein caspase-3 in living cells. Intracellular experiments showed that the nanosensor could be successfully applied for in situ monitoring of the effect of miRNA-221 expression changes on apoptosis by dual-color imaging. The current strategy could provide new avenues for investigating the feasibility of miRNA-targeted therapy, screening new anti-cancer drugs targeting miRNA and developing personalized treatment plans.
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35
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Cheng TW, Ahern MC, Giubellino A. The Spectrum of Spitz Melanocytic Lesions: From Morphologic Diagnosis to Molecular Classification. Front Oncol 2022; 12:889223. [PMID: 35747831 PMCID: PMC9209745 DOI: 10.3389/fonc.2022.889223] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 04/26/2022] [Indexed: 11/17/2022] Open
Abstract
Spitz tumors represent a distinct subtype of melanocytic lesions with characteristic histopathologic features, some of which are overlapping with melanoma. More common in the pediatric and younger population, they can be clinically suspected by recognizing specific patterns on dermatoscopic examination, and several subtypes have been described. We now classify these lesions into benign Spitz nevi, intermediate lesions identified as “atypical Spitz tumors” (or Spitz melanocytoma) and malignant Spitz melanoma. More recently a large body of work has uncovered the molecular underpinning of Spitz tumors, including mutations in the HRAS gene and several gene fusions involving several protein kinases. Here we present an overarching view of our current knowledge and understanding of Spitz tumors, detailing clinical, histopathological and molecular features characteristic of these lesions.
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Affiliation(s)
- Tiffany W. Cheng
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, United States
| | - Madeline C. Ahern
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, United States
| | - Alessio Giubellino
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, United States
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States
- *Correspondence: Alessio Giubellino,
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36
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Singh DK, Cole J, Escobedo RA, Alfson KJ, Singh B, Lee TH, Alvarez X, Ganatra SR, Carrion R, Kaushal D. Animal Models of COVID-19: Nonhuman Primates. Methods Mol Biol 2022; 2452:227-258. [PMID: 35554911 DOI: 10.1007/978-1-0716-2111-0_15] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
With the advent of the novel SARS-CoV-2, the entire world has been thrown into chaos with severe disruptions from a normal life. While the entire world was going chaotic, the researchers throughout the world were struggling to contribute to the best of their capabilities to advance the understanding of this new pandemic and fast track the development of novel therapeutics and vaccines. While various animal models have helped a lot to understand the basic physiology, nonhman primates have been promising and much more successful in modelling human diseases compared to other available clinical models. Here we describe the different aspects of modelling the SARS-CoV-2 infection in NHPs along with the associated methods used in NHP immunology.
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Affiliation(s)
- Dhiraj K Singh
- Southwest National Primate Research Center, San Antonio, TX, USA
- Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Journey Cole
- Southwest National Primate Research Center, San Antonio, TX, USA
- Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Ruby A Escobedo
- Southwest National Primate Research Center, San Antonio, TX, USA
- Texas Biomedical Research Institute, San Antonio, TX, USA
| | | | - Bindu Singh
- Southwest National Primate Research Center, San Antonio, TX, USA
- Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Tae-Hyung Lee
- Southwest National Primate Research Center, San Antonio, TX, USA
- Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Xavier Alvarez
- Southwest National Primate Research Center, San Antonio, TX, USA
- Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Shashank R Ganatra
- Southwest National Primate Research Center, San Antonio, TX, USA
- Texas Biomedical Research Institute, San Antonio, TX, USA
| | | | - Deepak Kaushal
- Southwest National Primate Research Center, San Antonio, TX, USA.
- Texas Biomedical Research Institute, San Antonio, TX, USA.
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37
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Cifci D, Foersch S, Kather JN. Artificial intelligence to identify genetic alterations in conventional histopathology. J Pathol 2022; 257:430-444. [PMID: 35342954 DOI: 10.1002/path.5898] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 03/09/2022] [Accepted: 03/23/2022] [Indexed: 11/10/2022]
Abstract
Precision oncology relies on the identification of targetable molecular alterations in tumor tissues. In many tumor types, a limited set of molecular tests is currently part of standard diagnostic workflows. However, universal testing for all targetable alterations, especially rare ones, is limited by the cost and availability of molecular assays. From 2017 to 2021, multiple studies have shown that artificial intelligence (AI) methods can predict the probability of specific genetic alterations directly from conventional hematoxylin and eosin (H&E) tissue slides. Although these methods are currently less accurate than gold-standard testing (e.g. immunohistochemistry, polymerase chain reaction or next-generation sequencing), they could be used as pre-screening tools to reduce the workload of genetic analyses. In this systematic literature review, we summarize the state of the art in predicting molecular alterations from H&E using AI. We found that AI methods perform reasonably well across multiple tumor types, although few algorithms have been broadly validated. In addition, we found that genetic alterations in FGFR, IDH, PIK3CA, BRAF, TP53 and DNA repair pathways are predictable from H&E in multiple tumor types, while many other genetic alterations have rarely been investigated or were only poorly predictable. Finally, we discuss the next steps for the implementation of AI-based surrogate tests in diagnostic workflows. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Didem Cifci
- Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany
| | - Sebastian Foersch
- Institute of Pathology, University Medical Center of the Johannes Gutenberg-University, Mainz, Germany
| | - Jakob Nikolas Kather
- Department of Medicine III, University Hospital RWTH Aachen, Aachen, Germany.,Pathology and Data Analytics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK.,Medical Oncology, National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany
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38
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McGuigan A, Whitworth J, Andreou A, Hearn T, Tischkowitz M, Maher ER. Multilocus Inherited Neoplasia Allele Syndrome (MINAS): an update. Eur J Hum Genet 2022; 30:265-270. [PMID: 34983940 PMCID: PMC8904543 DOI: 10.1038/s41431-021-01013-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 10/14/2021] [Accepted: 11/15/2021] [Indexed: 12/21/2022] Open
Abstract
Multi-locus Inherited Neoplasia Allele Syndrome (MINAS) refers to individuals with germline pathogenic variants in two or more cancer susceptibility genes(CSGs). With increased use of exome/genome sequencing it would be predicted that detection of MINAS would become more frequent. Here we review recent progress in knowledge of MINAS. A systematic literature search for reports of individuals with germline pathogenic variants in 2 or more of 94 CSGs was performed. In addition, participants with multiple primary tumours who underwent genome sequencing as part of the Rare Disease arm of the UK 100,000 Genomes Project were interrogated to detect additional cases. We identified 385 MINAS cases (211 reported in the last 5 years, 6 from 100,000 genomes participants). Most (287/385) cases contained at least one pathogenic variant in either BRCA1 or BRCA2. 108/385 MINAS cases had multiple primary tumours at presentation and a subset of cases presented unusual multiple tumour phenotypes. We conclude that, as predicted, increasing numbers of individuals with MINAS are being have been reported but, except for individuals with BRCA1/BRCA2 MINAS, individual CSG combinations are generally rare. In many cases it appears that the clinical phenotype is that which would be expected from the effects of the constituent CSG variants acting independently. However, in some instances the presence of unusual tumour phenotypes and/or multiple primary tumours suggests that there may be complex interactions between the relevant MINAS CSGs. Systematic reporting of MINAS cases in a MINAS database (e.g. https://databases.lovd.nl/shared/diseases/04296 ) will facilitate more accurate prognostic predictions for specific CSG combinations.
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Affiliation(s)
- Anthony McGuigan
- Department of Medical Genetics, University of Cambridge and Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK.
| | - James Whitworth
- Department of Medical Genetics, University of Cambridge and Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Avgi Andreou
- Department of Medical Genetics, University of Cambridge and Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Timothy Hearn
- Department of Medical Genetics, University of Cambridge and Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | | | - Marc Tischkowitz
- Department of Medical Genetics, University of Cambridge and Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Eamonn R Maher
- Department of Medical Genetics, University of Cambridge and Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK.
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Lee S, Kim M, Hong S, Kim EJ, Kim JH, Sohn Y, Jung HS. Effects of Sparganii Rhizoma on Osteoclast Formation and Osteoblast Differentiation and on an OVX-Induced Bone Loss Model. Front Pharmacol 2022; 12:797892. [PMID: 35058781 PMCID: PMC8764242 DOI: 10.3389/fphar.2021.797892] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 12/06/2021] [Indexed: 12/31/2022] Open
Abstract
Postmenopausal osteoporosis is caused by an imbalance between osteoclasts and osteoblasts and causes severe bone loss. Osteoporotic medicines are classified into bone resorption inhibitors and bone formation promoters according to the mechanism of action. Long-term use of bisphosphonate and selective estrogen receptor modulators (SERMs) can cause severe side effects in postmenopausal osteoporosis patients. Therefore, it is important to find alternative natural products that reduce osteoclast activity and increase osteoblast formation. Sparganii Rhizoma (SR) is the dried tuberous rhizome of Sparganium stoloniferum Buchanan-Hamilton and is called “samreung” in Korea. However, to date, the effect of SR on osteoclast differentiation and the ovariectomized (OVX)-induced bone loss model has not been reported. In vitro, tartrate-resistant acid phosphatase (TRAP) staining, western blots, RT-PCR and other methods were used to examine the effect of SR on osteoclast differentiation and osteoblasts. In vivo, we confirmed the effect of SR in a model of OVX-induced postmenopausal osteoporosis. SR inhibited osteoclast differentiation and decreased the expression of TNF receptor-associated factor 6 (TRAF6), nuclear factor of activated T cells 1 (NFATc1) and c-Fos pathway. In addition, SR stimulates osteoblast differentiation and increased protein expression of the bone morphogenetic protein 2 (BMP-2)/SMAD signaling pathway. Moreover, SR protected against bone loss in OVX-induced rats. Our results appear to advance our knowledge of SR and successfully demonstrate its potential role as a osteoclastogenesis-inhibiting and osteogenesis-promoting herbal medicine for the treatment of postmenopausal osteoporosis.
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Affiliation(s)
- Sungyub Lee
- Department of Anatomy, College of Korean Medicine, Kyung Hee University, Seoul, South Korea
| | - Minsun Kim
- Department of Anatomy, College of Korean Medicine, Kyung Hee University, Seoul, South Korea
| | - Sooyeon Hong
- Department of Anatomy, College of Korean Medicine, Kyung Hee University, Seoul, South Korea
| | - Eom Ji Kim
- Department of Anatomy, College of Korean Medicine, Kyung Hee University, Seoul, South Korea
| | - Jae-Hyun Kim
- Department of Anatomy, College of Korean Medicine, Kyung Hee University, Seoul, South Korea
| | - Youngjoo Sohn
- Department of Anatomy, College of Korean Medicine, Kyung Hee University, Seoul, South Korea
| | - Hyuk-Sang Jung
- Department of Anatomy, College of Korean Medicine, Kyung Hee University, Seoul, South Korea
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Evaluating Dengue Virus Pathogenesis in Mice and Humans by Histological and Immunohistochemistry Approaches. Methods Mol Biol 2022; 2409:259-269. [PMID: 34709648 DOI: 10.1007/978-1-0716-1879-0_18] [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: 12/14/2022]
Abstract
The analysis of dengue virus (DENV) infected tissues in mice experimental model and in human biopsies/autopsies may support the pathogenesis studies. Through such models, it is possible to investigate possible histopathological changes caused by the infection and detections of different targets of interest, such as viral antigens, immune cells, and cytokines. In this chapter, we showed a brief review of how histological and immunohistochemistry approaches may improve the knowledge in this field.
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Neumann EK, Patterson NH, Rivera ES, Allen JL, Brewer M, deCaestecker MP, Caprioli RM, Fogo AB, Spraggins JM. Highly multiplexed immunofluorescence of the human kidney using co-detection by indexing. Kidney Int 2022; 101:137-143. [PMID: 34619231 PMCID: PMC8741652 DOI: 10.1016/j.kint.2021.08.033] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 08/24/2021] [Accepted: 08/26/2021] [Indexed: 01/03/2023]
Abstract
The human kidney is composed of many cell types that vary in their abundance and distribution from normal to diseased organ. As these cell types perform unique and essential functions, it is important to confidently label each within a single tissue to accurately assess tissue architecture and microenvironments. Towards this goal, we demonstrate the use of co-detection by indexing (CODEX) multiplexed immunofluorescence for visualizing 23 antigens within the human kidney. Using CODEX, many of the major cell types and substructures, such as collecting ducts, glomeruli, and thick ascending limb, were visualized within a single tissue section. Of these antibodies, 19 were conjugated in-house, demonstrating the flexibility and utility of this approach for studying the human kidney using custom and commercially available antibodies. We performed a pilot study that compared both fresh frozen and formalin-fixed paraffin-embedded healthy non-neoplastic and diabetic nephropathy kidney tissues. The largest cellular differences between the two groups was observed in cells labeled with aquaporin 1, cytokeratin 7, and α-smooth muscle actin. Thus, our data show the power of CODEX multiplexed immunofluorescence for surveying the cellular diversity of the human kidney and the potential for applications within pathology, histology, and building anatomical atlases.
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Affiliation(s)
- Elizabeth K. Neumann
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA 37232,Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA 37232
| | - Nathan Heath Patterson
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA 37232,Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA 37232
| | - Emilio S. Rivera
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA 37232,Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA 37232
| | - Jamie L. Allen
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA 37232,Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA 37232
| | - Maya Brewer
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN USA 37232
| | - Mark P. deCaestecker
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN USA 37232
| | - Richard M. Caprioli
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA 37232,Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA 37232.,Department of Chemistry, Vanderbilt University, Nashville, TN, USA 37232
| | - Agnes B. Fogo
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN USA 37232,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN USA 37232.,Departments of Medicine and Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA 37232
| | - Jeffrey M. Spraggins
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA 37232.,Department of Chemistry, Vanderbilt University, Nashville, TN, USA 37232,Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA 37232
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Pawlak M, Reszka K, Moskal Ł, Stępień M. Importance of immunohistochemical staining in differential diagnosis of extramammary Paget and Bowen's diseases located in female anogenital region - a case report. J OBSTET GYNAECOL 2021; 42:1580-1582. [PMID: 34906025 DOI: 10.1080/01443615.2021.1981270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Martyna Pawlak
- Department of Oncology, Wroclaw Medical University, Wroclaw, Poland
| | - Konrad Reszka
- Department of Oncology, Wroclaw Medical University, Wroclaw, Poland
| | - Łukasz Moskal
- Department of Oncology, Wroclaw Medical University, Wroclaw, Poland
| | - Marcin Stępień
- Department of Oncology, Gynaecological Oncology Clinic, Wroclaw Medical University, Wroclaw, Poland.,Clinical Department of Gynecological Radiotherapy, Lower Silesian Cancer Center, Wroclaw, Poland
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Stagner AM, Tahan SR, Nazarian RM. Changing Trends in Dermatopathology Case Complexity: A 9-Year Academic Center Experience. Arch Pathol Lab Med 2021; 145:1144-1147. [PMID: 33290514 DOI: 10.5858/arpa.2020-0458-oa] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/24/2020] [Indexed: 11/06/2022]
Abstract
CONTEXT.— Pathology case volume and complexity impact clinical service burden, staffing, and reimbursement, particularly in an academic setting. OBJECTIVE.— To investigate dermatopathology case complexity by using indicators of challenging cases, which require increased clinical service effort. DESIGN.— A retrospective review was performed of dermatopathology cases during a 9-year period at a tertiary care academic center. A subset of cases was analyzed for which extractable data were available. Cases requiring the following metrics of complexity were identified: rush processing, consensus agreement, performance of immunohistochemistry, use of special histochemical stains, use of immunofluorescence, examination of additional tissue levels, review of a prior case, addition of an explanatory note, presence of multiple specimen parts, and use of intradepartmental consultation. RESULTS.— A total of 8173 cases were reviewed. During the same 3-month period of the year, there was a statistically significant increase in use of rush processing/interpretation, consensus review, number of cases requiring immunostains, special stains, levels, and an explanatory note, and cases reviewed by other subspecialists in the department from 2010 to 2019. CONCLUSIONS.— This study shows an increasing trend in dermatopathology case complexity, suggesting that overall clinical service efforts have increased. These findings may inform clinical service staffing and reimbursement.
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Affiliation(s)
- Anna M Stagner
- From the Department of Pathology, Massachusetts General Hospital, Boston (Stagner, Nazarian).,David G. Cogan Laboratory of Ophthalmic Pathology, Massachusetts Eye and Ear, Boston (Stagner)
| | - Steven R Tahan
- The Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts (Tahan)
| | - Rosalynn M Nazarian
- From the Department of Pathology, Massachusetts General Hospital, Boston (Stagner, Nazarian)
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da Cunha IW, de Almeida Coudry R, de Macedo MP, de Assis EACP, Stefani S, Soares FA. A call to action: molecular pathology in Brazil. SURGICAL AND EXPERIMENTAL PATHOLOGY 2021. [DOI: 10.1186/s42047-021-00096-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Abstract
Background
Adoption of molecular pathology in Brazil is currently very limited. Of note, there are no programs for training new molecular pathologists in the country; thus, documents compiling nationally applicable information on molecular pathology are few.
Methods
A selected panel of Brazilian experts in fields related to molecular pathology were provided with a series of relevant questions to address prior to the multi-day conference. Within this conference, each narrative was discussed and edited by the entire group, through numerous drafts and rounds of discussion until a consensus was achieved.
Results
The panel proposes specific and realistic recommendations for implementing molecular pathology in cancer care in Brazil. In creating these recommendations, the authors strived to address all barriers to the widespread use and impediments to access mentioned previously within this manuscript.
Conclusion
This manuscript provides a review of molecular pathology principles as well as the current state of molecular pathology in Brazil. Additionally, the panel proposes practical and actionable recommendations for the implementation of molecular pathology throughout the country in order to increase awareness of the importance molecular pathology in Brazil.
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Chen Z, Na H, Wu A. ImmuCellDB: An Indicative Database of Immune Cell Composition From Different Tissues and Disease Conditions in Mouse and Human. Front Immunol 2021; 12:670070. [PMID: 34456903 PMCID: PMC8387820 DOI: 10.3389/fimmu.2021.670070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 07/27/2021] [Indexed: 11/13/2022] Open
Abstract
Immune cell composition is highly divergent across different tissues and diseases. A comprehensive resource of tissue immune cells across different conditions in mouse and human will thus provide great understanding of the immune microenvironment of many diseases. Recently, computational methods for estimating immune cell abundance from tissue transcriptome data have been developed and are now widely used. Using these computational tools, large-scale estimation of immune cell composition across tissues and conditions should be possible using gene expression data collected from public databases. In total, 266 tissue types and 706 disease types in humans, as well as 143 tissue types and 61 disease types, and 206 genotypes in mouse had been included in a database we have named ImmuCellDB (http://wap-lab.org:3200/ImmuCellDB/). In ImmuCellDB, users can search and browse immune cell proportions based on tissues, disease or genotype in mouse or humans. Additionally, the variation and correlation of immune cell abundance and gene expression level between different conditions can be compared and viewed in this database. We believe that ImmuCellDB provides not only an indicative view of tissue-dependent or disease-dependent immune cell profiles, but also represents an easy way to pre-determine immune cell abundance and gene expression profiles for specific situations.
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Affiliation(s)
- Ziyi Chen
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Suzhou Institute of Systems Medicine, Suzhou, Suzhou, China.,Department of Infectious Diseases, The Second Hospital of Nanjing, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Han Na
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Suzhou Institute of Systems Medicine, Suzhou, Suzhou, China
| | - Aiping Wu
- Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.,Suzhou Institute of Systems Medicine, Suzhou, Suzhou, China
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Huebner T, Scholl C, Steffens M. Cytogenetic and Biochemical Genetic Techniques for Personalized Drug Therapy in Europe. Diagnostics (Basel) 2021; 11:diagnostics11071169. [PMID: 34206978 PMCID: PMC8303692 DOI: 10.3390/diagnostics11071169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/18/2021] [Accepted: 06/23/2021] [Indexed: 11/16/2022] Open
Abstract
For many authorized drugs, accumulating scientific evidence supports testing for predictive biomarkers to apply personalized therapy and support preventive measures regarding adverse drug reactions and treatment failure. Here, we review cytogenetic and biochemical genetic testing methods that are available to guide therapy with drugs centrally approved in the European Union (EU). We identified several methods and combinations of techniques registered in the Genetic Testing Registry (GTR), which can be used to guide therapy with drugs for which pharmacogenomic-related information is provided in the European public assessment reports. Although this registry provides information on genetic tests offered worldwide, we identified limitations regarding standard techniques applied in clinical practice and the information on test validity rarely provided in the according sections.
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Madheswaran S, Mungra N, Biteghe FAN, De la Croix Ndong J, Arowolo AT, Adeola HA, Ramamurthy D, Naran K, Khumalo NP, Barth S. Antibody-Based Targeted Interventions for the Diagnosis and Treatment of Skin Cancers. Anticancer Agents Med Chem 2021; 21:162-186. [PMID: 32723261 DOI: 10.2174/1871520620666200728123006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 03/19/2020] [Accepted: 04/30/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Cutaneous malignancies most commonly arise from skin epidermal cells. These cancers may rapidly progress from benign to a metastatic phase. Surgical resection represents the gold standard therapeutic treatment of non-metastatic skin cancer while chemo- and/or radiotherapy are often used against metastatic tumors. However, these therapeutic treatments are limited by the development of resistance and toxic side effects, resulting from the passive accumulation of cytotoxic drugs within healthy cells. OBJECTIVE This review aims to elucidate how the use of monoclonal Antibodies (mAbs) targeting specific Tumor Associated Antigens (TAAs) is paving the way to improved treatment. These mAbs are used as therapeutic or diagnostic carriers that can specifically deliver cytotoxic molecules, fluorophores or radiolabels to cancer cells that overexpress specific target antigens. RESULTS mAbs raised against TAAs are widely in use for e.g. differential diagnosis, prognosis and therapy of skin cancers. Antibody-Drug Conjugates (ADCs) particularly show remarkable potential. The safest ADCs reported to date use non-toxic photo-activatable Photosensitizers (PSs), allowing targeted Photodynamic Therapy (PDT) resulting in targeted delivery of PS into cancer cells and selective killing after light activation without harming the normal cell population. The use of near-infrared-emitting PSs enables both diagnostic and therapeutic applications upon light activation at the specific wavelengths. CONCLUSION Antibody-based approaches are presenting an array of opportunities to complement and improve current methods employed for skin cancer diagnosis and treatment.
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Affiliation(s)
- Suresh Madheswaran
- Medical Biotechnology & Immunotherapy Research Unit, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Neelakshi Mungra
- Medical Biotechnology & Immunotherapy Research Unit, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Fleury A N Biteghe
- Department of Radiation Oncology and Biomedical Sciences, Cedars-Sinai Medical, 8700 Beverly Blvd, Los Angeles, CA, United States
| | - Jean De la Croix Ndong
- Department of Orthopedic Surgery, New York University Langone Orthopedic Hospital, 301 East 17th Street, New York, NY, United States
| | - Afolake T Arowolo
- The Hair and Skin Research Lab, Division of Dermatology, Department of Medicine, Faculty of Health Sciences, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa
| | - Henry A Adeola
- The Hair and Skin Research Lab, Division of Dermatology, Department of Medicine, Faculty of Health Sciences, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa
| | - Dharanidharan Ramamurthy
- Medical Biotechnology & Immunotherapy Research Unit, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Krupa Naran
- Medical Biotechnology & Immunotherapy Research Unit, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Nonhlanhla P Khumalo
- The Hair and Skin Research Lab, Division of Dermatology, Department of Medicine, Faculty of Health Sciences, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa
| | - Stefan Barth
- Medical Biotechnology & Immunotherapy Research Unit, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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Cieśla S, Lisiecki R, Ławnicka A, Kudliński B, Ostrowska P, Davì A, Veroux M, Murawa D. Clinical Significance of Peritoneal Fluid Examination for Free Cancer Cells in Patients Qualified for Surgery for Gastric Cancer. Front Surg 2021; 8:685868. [PMID: 34235174 PMCID: PMC8255366 DOI: 10.3389/fsurg.2021.685868] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 05/24/2021] [Indexed: 12/27/2022] Open
Abstract
Background: Peritoneal lavage cytology in patients with gastric cancer may correlate with an unfavorable prognosis. This study evaluated the presence of free cancer cells in the peritoneal lavage of a population of patients with gastric cancer and its correlation with the outcome of surgical treatment. Methods: One hundred patients diagnosed with gastric or gastrointestinal junction adenocarcinoma underwent surgery. In all patients, a cytological and immunohistochemical analysis of peritoneal lavage was performed. Based on the presence of free cancer cells (fcc) at the cytological and immunohistochemical examination of peritoneal lavage, patients undergoing surgery for gastric cancer were divided into two groups: fcc (+) and fcc (–). Results: A total of 100 patients, 37 women, and 63 men with a median age of 65 years were included in the study. In the entire study group, 16 (16%) patients were positive for the presence of free cancer cells (fcc +) at peritoneal lavage examination. However, in the group of patients who underwent gastrectomy, fcc (+) was found in 10 out of 77 (13%) patients. The presence of cancer cells in peritoneal lavage was a strong predictive factor in an unfavorable outcome after surgery, and 1-year and 2-year patient survival was 34 and 0% in fcc (+) patients and 79 and 59% in fcc (–), respectively. Moreover, the presence of free cancer cells was associated with a five-fold increased risk of death within 2 years after surgery. When analyzing the group of patients undergoing R0/R1 surgery, this difference was even more significant (p < 0.0001). Conclusions: The presence of free cancer cells in peritoneal lavage may significantly affect the outcome of patients with gastric cancer. Radical surgery in patients with free cancer cells in the peritoneal lavage did not result in a survival advantage. Identification of free cancer cells could help for a better stratification of gastric cancer patients, identifying those patients who could better benefit from a radical surgical treatment, finally improving long-term survival.
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Affiliation(s)
- Sławomir Cieśla
- General and Oncological Surgery Clinic of the K. Marcinkowski University Hospital in Zielona Góra, Zielona Góra, Poland
| | - Radosław Lisiecki
- Department of General and Oncological Surgery of the Medical Centre in Pleszew, Pleszew, Poland
| | - Agnieszka Ławnicka
- General and Oncological Surgery Clinic of the K. Marcinkowski University Hospital in Zielona Góra, Zielona Góra, Poland
| | - Bartosz Kudliński
- Department of Anaesthesiology, Intensive Care and Emergency Medicine at Collegium Medicum of the University of Zielona Góra, Zielona Góra, Poland
| | - Paulina Ostrowska
- Department of Oncology of the Medical Centre in Pleszew, Pleszew, Poland
| | - Alberto Davì
- Vascular and Endovascular Surgery Unit, Cuneo, Italy
| | - Massimiliano Veroux
- General Surgery Unit, Department of Medical and Surgical Sciences and Advanced Technologies University Hospital of Catania, Catania, Italy
| | - Dawid Murawa
- General and Oncological Surgery Clinic of the K. Marcinkowski University Hospital in Zielona Góra, Zielona Góra, Poland.,Department of Surgery and Oncology, Faculty of Medicine and Health Sciences of the University of Zielona Góra, Zielona Góra, Poland
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49
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Detection of Human Cytomegalovirus Proteins in Paraffin-Embedded Breast Cancer Tissue Specimens-A Novel, Automated Immunohistochemical Staining Protocol. Microorganisms 2021; 9:microorganisms9051059. [PMID: 34068349 PMCID: PMC8153275 DOI: 10.3390/microorganisms9051059] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 05/02/2021] [Accepted: 05/07/2021] [Indexed: 12/24/2022] Open
Abstract
Emerging evidence supports a significant association between human cytomegalovirus (HCMV) and human malignancies, suggesting HCMV as a human oncomodulatory virus. HCMV gene products are found in >90% of breast cancer tumors and seem to be correlated with more aggressive disease. The definitive diagnosis of HCMV relies on identification of virus inclusions and/or viral proteins by different techniques including immunohistochemical staining. In order to reduce biases and improve clinical value of HCMV diagnostics in oncological pathology, automation of the procedure is needed and this was the purpose of this study. Tumor specimens from 115 patients treated for primary breast cancer at Akershus University Hospital in Norway were available for the validation of the staining method in this retrospective study. We demonstrate that our method is highly sensitive and delivers excellent reproducibility for staining of HCMV late antigen (LA), which makes this method useful for future routine diagnostics and scientific applications.
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50
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Bagchi A, Madaj Z, Engel KB, Guan P, Rohrer DC, Valley DR, Wolfrum E, Feenstra K, Roche N, Hostetter G, Moore HM, Jewell SD. Impact of Preanalytical Factors on the Measurement of Tumor Tissue Biomarkers Using Immunohistochemistry. J Histochem Cytochem 2021; 69:297-320. [PMID: 33641490 DOI: 10.1369/0022155421995600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Analysis of formalin-fixed paraffin-embedded (FFPE) tissue by immunohistochemistry (IHC) is commonplace in clinical and research laboratories. However, reports suggest that IHC results can be compromised by biospecimen preanalytical factors. The National Cancer Institute's Biospecimen Preanalytical Variables Program conducted a systematic study to examine the potential effects of delay to fixation (DTF) and time in fixative (TIF) on IHC using 24 cancer biomarkers. Differences in IHC staining, relative to controls with a DTF of 1 hr, were observed in FFPE kidney tumor specimens after a DTF of ≥2 hr. Reductions in H-score and/or staining intensity were observed for c-MET, p53, PAX2, PAX8, pAKT, and survivin, whereas increases were observed for RCC1, EGFR, and CD10. Prolonged TIF of 72 hr resulted in significantly reduced H-scores of CD44 and c-Met in kidney tumor specimens, compared with controls with 12-hr TIF. An elevated probability of altered staining intensity due to DTF was observed for nine antigens, whereas for prolonged TIF an elevated probability was observed for one antigen. Results reported here and elsewhere across tumor types and antigens support limiting DTF to ≤1 hr when possible and fixing tissues in formalin for 12-24 hr to avoid confounding effects of these preanalytical factors on IHC.
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Affiliation(s)
- Aditi Bagchi
- Pathology and Biorepository Core, Van Andel Institute, Grand Rapids, Michigan.,Spectrum Health Helen DeVos Children's Hospital, Grand Rapids, Michigan.,St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Zachary Madaj
- Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, Michigan
| | | | - Ping Guan
- Biorepositories and Biospecimen Research Branch, National Cancer Institute, Bethesda, Maryland
| | | | | | - Emily Wolfrum
- Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, Michigan
| | - Kristin Feenstra
- Pathology and Biorepository Core, Van Andel Institute, Grand Rapids, Michigan
| | - Nancy Roche
- Leidos Biomedical Research, Inc., Frederick, Maryland
| | - Galen Hostetter
- Pathology and Biorepository Core, Van Andel Institute, Grand Rapids, Michigan
| | - Helen M Moore
- Biorepositories and Biospecimen Research Branch, National Cancer Institute, Bethesda, Maryland
| | - Scott D Jewell
- Pathology and Biorepository Core, Van Andel Institute, Grand Rapids, Michigan
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