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Arceneaux JS, Brockman AA, Khurana R, Chalkley MBL, Geben LC, Krbanjevic A, Vestal M, Zafar M, Weatherspoon S, Mobley BC, Ess KC, Ihrie RA. Multiparameter quantitative analyses of diagnostic cells in brain tissues from tuberous sclerosis complex. CYTOMETRY. PART B, CLINICAL CYTOMETRY 2024. [PMID: 38953209 DOI: 10.1002/cyto.b.22194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 06/05/2024] [Accepted: 06/11/2024] [Indexed: 07/03/2024]
Abstract
The advent of high-dimensional imaging offers new opportunities to molecularly characterize diagnostic cells in disorders that have previously relied on histopathological definitions. One example case is found in tuberous sclerosis complex (TSC), a developmental disorder characterized by systemic growth of benign tumors. Within resected brain tissues from patients with TSC, detection of abnormally enlarged balloon cells (BCs) is pathognomonic for this disorder. Though BCs can be identified by an expert neuropathologist, little is known about the specificity and broad applicability of protein markers for these cells, complicating classification of proposed BCs identified in experimental models of this disorder. Here, we report the development of a customized machine learning pipeline (BAlloon IDENtifier; BAIDEN) that was trained to prospectively identify BCs in tissue sections using a histological stain compatible with high-dimensional cytometry. This approach was coupled to a custom 36-antibody panel and imaging mass cytometry (IMC) to explore the expression of multiple previously proposed BC marker proteins and develop a descriptor of BC features conserved across multiple tissue samples from patients with TSC. Here, we present a modular workflow encompassing BAIDEN, a custom antibody panel, a control sample microarray, and analysis pipelines-both open-source and in-house-and apply this workflow to understand the abundance, structure, and signaling activity of BCs as an example case of how high-dimensional imaging can be applied within human tissues.
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Affiliation(s)
- Jerome S Arceneaux
- Department of Biochemistry, Cancer Biology, Neuroscience, and Pharmacology, Meharry Medical College, Nashville, Tennessee, USA
| | - Asa A Brockman
- Department of Cell & Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Rohit Khurana
- Department of Cell & Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Mary-Bronwen L Chalkley
- Department of Cell & Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Laura C Geben
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee, USA
| | - Aleksandar Krbanjevic
- Department of Pathology, Microbiology, & Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Matthew Vestal
- Duke University Children's Hospital and Health Center, Durham, North Carolina, USA
| | - Muhammad Zafar
- Duke University Children's Hospital and Health Center, Durham, North Carolina, USA
| | - Sarah Weatherspoon
- Neuroscience Institute, Le Bonheur Children's Hospital, Memphis, Tennessee, USA
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Bret C Mobley
- Department of Pathology, Microbiology, & Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Kevin C Ess
- Department of Cell & Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Neurology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Section of Child Neurology, University of Colorado Anschutz Medical Center, Aurora, Colorado, USA
| | - Rebecca A Ihrie
- Department of Cell & Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA
- Department of Neurological Surgery, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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Friedel J, Pierre S, Kolbinger A, Schäufele TJ, Aliraj B, Weigert A, Scholich K. Mast cell-derived interleukin-4 mediates activation of dendritic cell during toll-like receptor 2-mediated inflammation. Front Immunol 2024; 15:1353922. [PMID: 38745645 PMCID: PMC11091258 DOI: 10.3389/fimmu.2024.1353922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 04/17/2024] [Indexed: 05/16/2024] Open
Abstract
Introduction During an innate inflammation, immune cells form distinct pro- and anti-inflammatory regions around pathogen-containing core-regions. Mast cells are localized in an anti-inflammatory microenvironment during the resolution of an innate inflammation, suggesting antiinflammatory roles of these cells. Methods High-content imaging was used to investigated mast cell-dependent changes in the regional distribution of immune cells during an inflammation, induced by the toll-like receptor (TLR)-2 agonist zymosan. Results The distance between the zymosan-containing core-region and the anti-inflammatory region, described by M2-like macrophages, increased in mast cell-deficient mice. Absence of mast cells abolished dendritic cell (DC) activation, as determined by CD86-expression and localized the DCs in greater distance to zymosan particles. The CD86- DCs had a higher expression of the pro-inflammatory interleukins (IL)-1β and IL-12/23p40 as compared to activated CD86+ DCs. IL-4 administration restored CD86 expression, cytokine expression profile and localization of the DCs in mast cell-deficient mice. The IL-4 effects were mast cell-specific, since IL-4 reduction by eosinophil depletion did not affect activation of DCs. Discussion We found that mast cells induce DC activation selectively at the site of inflammation and thereby determine their localization within the inflammation. Overall, mast cells have antiinflammatory functions in this inflammation model and limit the size of the pro-inflammatory region surrounding the zymosan-containing core region.
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Affiliation(s)
- Joschua Friedel
- Institute of Clinical Pharmacology, Goethe University, Frankfurt, Germany
| | - Sandra Pierre
- Institute of Clinical Pharmacology, Goethe University, Frankfurt, Germany
| | - Anja Kolbinger
- Institute of Clinical Pharmacology, Goethe University, Frankfurt, Germany
| | - Tim J. Schäufele
- Institute of Clinical Pharmacology, Goethe University, Frankfurt, Germany
| | - Blerina Aliraj
- Institute of Biochemistry I, Faculty of Medicine, Goethe University, Frankfurt, Germany
| | - Andreas Weigert
- Institute of Biochemistry I, Faculty of Medicine, Goethe University, Frankfurt, Germany
| | - Klaus Scholich
- Institute of Clinical Pharmacology, Goethe University, Frankfurt, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Frankfurt, Germany
- Fraunhofer Cluster of Excellence for Immune-Mediated Diseases CIMD, Frankfurt, Germany
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de Souza N, Zhao S, Bodenmiller B. Multiplex protein imaging in tumour biology. Nat Rev Cancer 2024; 24:171-191. [PMID: 38316945 DOI: 10.1038/s41568-023-00657-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/08/2023] [Indexed: 02/07/2024]
Abstract
Tissue imaging has become much more colourful in the past decade. Advances in both experimental and analytical methods now make it possible to image protein markers in tissue samples in high multiplex. The ability to routinely image 40-50 markers simultaneously, at single-cell or subcellular resolution, has opened up new vistas in the study of tumour biology. Cellular phenotypes, interaction, communication and spatial organization have become amenable to molecular-level analysis, and application to patient cohorts has identified clinically relevant cellular and tissue features in several cancer types. Here, we review the use of multiplex protein imaging methods to study tumour biology, discuss ongoing attempts to combine these approaches with other forms of spatial omics, and highlight challenges in the field.
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Affiliation(s)
- Natalie de Souza
- University of Zurich, Department of Quantitative Biomedicine, Zurich, Switzerland
- ETH Zurich, Institute of Molecular Systems Biology, Zurich, Switzerland
- ETH Zurich, Institute of Molecular Health Sciences, Zurich, Switzerland
| | - Shan Zhao
- University of Zurich, Department of Quantitative Biomedicine, Zurich, Switzerland
- ETH Zurich, Institute of Molecular Health Sciences, Zurich, Switzerland
| | - Bernd Bodenmiller
- University of Zurich, Department of Quantitative Biomedicine, Zurich, Switzerland.
- ETH Zurich, Institute of Molecular Health Sciences, Zurich, Switzerland.
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Yadav S, Zhou S, He B, Du Y, Garmire LX. Deep learning and transfer learning identify breast cancer survival subtypes from single-cell imaging data. COMMUNICATIONS MEDICINE 2023; 3:187. [PMID: 38114659 PMCID: PMC10730890 DOI: 10.1038/s43856-023-00414-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 11/23/2023] [Indexed: 12/21/2023] Open
Abstract
BACKGROUND Single-cell multiplex imaging data have provided new insights into disease subtypes and prognoses recently. However, quantitative models that explicitly capture single-cell resolution cell-cell interaction features to predict patient survival at a population scale are currently missing. METHODS We quantified hundreds of single-cell resolution cell-cell interaction features through neighborhood calculation, in addition to cellular phenotypes. We applied these features to a neural-network-based Cox-nnet survival model to identify survival-associated features. We used non-negative matrix factorization (NMF) to identify patient survival subtypes. We identified atypical subpopulations of triple-negative breast cancer (TNBC) patients with moderate prognosis and Luminal A patients with poor prognosis and validated these subpopulations by label transferring using the UNION-COM method. RESULTS The neural-network-based Cox-nnet survival model using all cellular phenotype and cell-cell interaction features is highly predictive of patient survival in the test data (Concordance Index > 0.8). We identify seven survival subtypes using the top survival features, presenting distinct profiles of epithelial, immune, and fibroblast cells and their interactions. We reveal atypical subpopulations of TNBC patients with moderate prognosis (marked by GATA3 over-expression) and Luminal A patients with poor prognosis (marked by KRT6 and ACTA2 over-expression and CDH1 under-expression). These atypical subpopulations are validated in TCGA-BRCA and METABRIC datasets. CONCLUSIONS This work provides an approach to bridge single-cell level information toward population-level survival prediction.
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Affiliation(s)
- Shashank Yadav
- Department of Computational Medicine and Bioinformatics, University of Michigan, Michigan, MI, 48105, USA
| | - Shu Zhou
- Department of Computational Medicine and Bioinformatics, University of Michigan, Michigan, MI, 48105, USA
| | - Bing He
- Department of Computational Medicine and Bioinformatics, University of Michigan, Michigan, MI, 48105, USA
| | - Yuheng Du
- Department of Computational Medicine and Bioinformatics, University of Michigan, Michigan, MI, 48105, USA
| | - Lana X Garmire
- Department of Computational Medicine and Bioinformatics, University of Michigan, Michigan, MI, 48105, USA.
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Li T, Zhang WH, Liu J, Mao YL, Liu S. Isolated axillary tumor deposit consistent with primary breast carcinoma: A case report. World J Clin Cases 2023; 11:7718-7723. [DOI: 10.12998/wjcc.v11.i31.7718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/08/2023] [Accepted: 10/16/2023] [Indexed: 11/06/2023] Open
Abstract
BACKGROUND We all know that lymph-node metastasis is an important factor for poor clinical outcome in breast cancer prognosis. Tumor deposit refers to a discrete collection of cancer cells that is found in the lymph nodes or other tissues adjacent to the primary tumor site. These tumor deposits are separate from the primary tumor and are often considered as a manifestation of lymph node metastasis. In gastric and colorectal cancer, tumor deposits in the lymph node drainage area have been included as independent prognostic factors. The question arises whether tumor deposits should also be considered as prognostic factors in breast cancer patients. This article aims to provoke some thoughts on this matter through a case study and literature review.
CASE SUMMARY A 70-year-old female patient was found to have a right breast lump for over 2 years. On January 3, 2023, a core needle biopsy of the right breast lump was performed, and the pathology report indicated invasive carcinoma. Subsequently, on January 17, 2023, the patient underwent right breast-conserving surgery, sentinel lymph node biopsy, and right axillary lymph node dissection. The postoperative pathological staging was determined as stage IIB. The patient received chemotherapy, radiotherapy, and endocrine therapy. At present, nearly one year after the surgery, no obvious signs of metastasis have been observed in the follow-up examinations, but the long-term prognosis is still unknown.
CONCLUSION There is a need for increased focus on the matter of tumor deposits in the lymph node drainage region, as well as a requirement for further clinical investigation to ascertain the relevance of tumor deposits in the prognosis of individuals with breast carcinoma.
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Affiliation(s)
- Tian Li
- Department of Breast Surgery, Shanghai Baoshan Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai 201900, China
| | - Wei-Hong Zhang
- Department of Breast Surgery, Shanghai Baoshan Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai 201900, China
| | - Juan Liu
- Department of Pathology, Shanghai Baoshan Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai 201900, China
| | - Yi-Ling Mao
- Department of Radiology, Shanghai Baoshan Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai 201900, China
| | - Sheng Liu
- Graduate School, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
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Massa C, Seliger B. Combination of multiple omics techniques for a personalized therapy or treatment selection. Front Immunol 2023; 14:1258013. [PMID: 37828984 PMCID: PMC10565668 DOI: 10.3389/fimmu.2023.1258013] [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: 07/13/2023] [Accepted: 09/05/2023] [Indexed: 10/14/2023] Open
Abstract
Despite targeted therapies and immunotherapies have revolutionized the treatment of cancer patients, only a limited number of patients have long-term responses. Moreover, due to differences within cancer patients in the tumor mutational burden, composition of the tumor microenvironment as well as of the peripheral immune system and microbiome, and in the development of immune escape mechanisms, there is no "one fit all" therapy. Thus, the treatment of patients must be personalized based on the specific molecular, immunologic and/or metabolic landscape of their tumor. In order to identify for each patient the best possible therapy, different approaches should be employed and combined. These include (i) the use of predictive biomarkers identified on large cohorts of patients with the same tumor type and (ii) the evaluation of the individual tumor with "omics"-based analyses as well as its ex vivo characterization for susceptibility to different therapies.
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Affiliation(s)
- Chiara Massa
- Institute for Translational Immunology, Brandenburg Medical School Theodor Fontane, Brandenburg an der Havel, Germany
| | - Barbara Seliger
- Institute for Translational Immunology, Brandenburg Medical School Theodor Fontane, Brandenburg an der Havel, Germany
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle, Germany
- Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
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Yadav S, Zhou S, He B, Du Y, Garmire LX. Deep-learning and transfer learning identify new breast cancer survival subtypes from single-cell imaging data. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.14.23295578. [PMID: 37745392 PMCID: PMC10516066 DOI: 10.1101/2023.09.14.23295578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Quantitative models that explicitly capture single-cell resolution cell-cell interaction features to predict patient survival at population scale are currently missing. Here, we computationally extracted hundreds of features describing single-cell based cell-cell interactions and cellular phenotypes from a large, published cohort of cyto-images of breast cancer patients. We applied these features to a neural-network based Cox-nnet survival model and obtained high accuracy in predicting patient survival in test data (Concordance Index > 0.8). We identified seven survival subtypes using the top survival features, which present distinct profiles of epithelial, immune, fibroblast cells, and their interactions. We identified atypical subpopulations of TNBC patients with moderate prognosis (marked by GATA3 over-expression) and Luminal A patients with poor prognosis (marked by KRT6 and ACTA2 over-expression and CDH1 under-expression). These atypical subpopulations are validated in TCGA-BRCA and METABRIC datasets. This work provides important guidelines on bridging single-cell level information towards population-level survival prediction. STATEMENT OF TRANSLATIONAL RELEVANCE Our findings from a breast cancer population cohort demonstrate the clinical utility of using the single-cell level imaging mass cytometry (IMC) data as a new type of patient prognosis prediction marker. Not only did the prognosis prediction achieve high accuracy with a Concordance index score greater than 0.8, it also enabled the discovery of seven survival subtypes that are more distinguishable than the molecular subtypes. These new subtypes present distinct profiles of epithelial, immune, fibroblast cells, and their interactions. Most importantly, this study identified and validated atypical subpopulations of TNBC patients with moderate prognosis (GATA3 over-expression) and Luminal A patients with poor prognosis (KRT6 and ACTA2 over-expression and CDH1 under-expression), using multiple large breast cancer cohorts.
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Abstract
Lymph node metastasis in breast cancer depends in part on the acquisition of an IFN-dependent, MHC-II+ state that induces regulatory T cell expansion and local immune suppression (Lei et al. 2023. J. Exp. Med.https://doi.org/10.1084/jem.20221847).
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Affiliation(s)
- Amanda W. Lund
- Ronald O. Perelman Department of Dermatology, Department of Pathology, NYU Grossman School of Medicine, Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
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