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van Elsas MJ, Middelburg J, Labrie C, Roelands J, Schaap G, Sluijter M, Tonea R, Ovcinnikovs V, Lloyd K, Schuurman J, Riesenfeld SJ, Gajewski TF, de Miranda NFCC, van Hall T, van der Burg SH. Immunotherapy-activated T cells recruit and skewlate-stage activated M1-like macrophagesthat are critical for therapeutic efficacy. Cancer Cell 2024:S1535-6108(24)00135-1. [PMID: 38759656 DOI: 10.1016/j.ccell.2024.04.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 02/23/2024] [Accepted: 04/24/2024] [Indexed: 05/19/2024]
Abstract
Total tumor clearance through immunotherapy is associated with a fully coordinated innate and adaptive immune response, but knowledge on the exact contribution of each immune cell subset is limited. We show that therapy-induced intratumoral CD8+ T cells recruited and skewed late-stage activated M1-like macrophages, which were critical for effective tumor control in two different murine models of cancer immunotherapy. The activated CD8+ T cells summon these macrophages into the tumor and their close vicinity via CCR5 signaling. Exposure of non-polarized macrophages to activated T cell supernatant and tumor lysate recapitulates the late-stage activated and tumoricidal phenotype in vitro. The transcriptomic signature of these macrophages is also detected in a similar macrophage population present in human tumors and coincides with clinical response to immune checkpoint inhibitors. The requirement of a functional co-operation between CD8+ T cells and effector macrophages for effective immunotherapy gives warning to combinations with broad macrophage-targeting strategies.
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Affiliation(s)
- Marit J van Elsas
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden 2333ZA, the Netherlands
| | - Jim Middelburg
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden 2333ZA, the Netherlands
| | - Camilla Labrie
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden 2333ZA, the Netherlands
| | - Jessica Roelands
- Department of Pathology, Leiden University Medical Center, Leiden 2333ZA, the Netherlands
| | - Gaby Schaap
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden 2333ZA, the Netherlands
| | - Marjolein Sluijter
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden 2333ZA, the Netherlands
| | - Ruxandra Tonea
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA; Pritzker School of Molecular Engineering, Chicago, IL 60637, USA
| | | | | | | | | | - Thomas F Gajewski
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA
| | - Noel F C C de Miranda
- Department of Pathology, Leiden University Medical Center, Leiden 2333ZA, the Netherlands
| | - Thorbald van Hall
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden 2333ZA, the Netherlands
| | - Sjoerd H van der Burg
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden 2333ZA, the Netherlands.
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2
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de Miranda NFCC, Scheeren FA. Immunogenetic Diversity and Cancer Immunotherapy Disparities. Cancer Discov 2024; 14:585-588. [PMID: 38571423 DOI: 10.1158/2159-8290.cd-23-1536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
SUMMARY The success of checkpoint blockade cancer immunotherapies has unequivocally confirmed the critical role of T cells in cancer immunity and boosted the development of immunotherapeutic strategies targeting specific antigens on cancer cells. The vast immunogenetic diversity of human leukocyte antigen (HLA) class I alleles across populations is a key factor influencing the advancement of HLA class I-restricted therapies and related research and diagnostic tools.
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Affiliation(s)
| | - Ferenc A Scheeren
- Department of Dermatology, Leiden University Medical Center, Leiden, the Netherlands
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3
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Lei X, de Groot DC, Welters MJP, de Wit T, Schrama E, van Eenennaam H, Santegoets SJ, Oosenbrug T, van der Veen A, Vos JL, Zuur CL, de Miranda NFCC, Jacobs H, van der Burg SH, Borst J, Xiao Y. CD4 + T cells produce IFN-I to license cDC1s for induction of cytotoxic T-cell activity in human tumors. Cell Mol Immunol 2024; 21:374-392. [PMID: 38383773 PMCID: PMC10978876 DOI: 10.1038/s41423-024-01133-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 01/05/2024] [Indexed: 02/23/2024] Open
Abstract
CD4+ T cells can "help" or "license" conventional type 1 dendritic cells (cDC1s) to induce CD8+ cytotoxic T lymphocyte (CTL) anticancer responses, as proven in mouse models. We recently identified cDC1s with a transcriptomic imprint of CD4+ T-cell help, specifically in T-cell-infiltrated human cancers, and these cells were associated with a good prognosis and response to PD-1-targeting immunotherapy. Here, we delineate the mechanism of cDC1 licensing by CD4+ T cells in humans. Activated CD4+ T cells produce IFNβ via the STING pathway, which promotes MHC-I antigen (cross-)presentation by cDC1s and thereby improves their ability to induce CTL anticancer responses. In cooperation with CD40 ligand (L), IFNβ also optimizes the costimulatory and other functions of cDC1s required for CTL response induction. IFN-I-producing CD4+ T cells are present in diverse T-cell-infiltrated cancers and likely deliver "help" signals to CTLs locally, according to their transcriptomic profile and colocalization with "helped/licensed" cDCs and tumor-reactive CD8+ T cells. In agreement with this scenario, the presence of IFN-I-producing CD4+ T cells in the TME is associated with overall survival and the response to PD-1 checkpoint blockade in cancer patients.
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Affiliation(s)
- Xin Lei
- Department of Immunology, Leiden University Medical Center, Leiden, The Netherlands
- Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Daniël C de Groot
- Department of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Marij J P Welters
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Tom de Wit
- Department of Immunology, Leiden University Medical Center, Leiden, The Netherlands
- Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Ellen Schrama
- Department of Immunology, Leiden University Medical Center, Leiden, The Netherlands
- Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Saskia J Santegoets
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Timo Oosenbrug
- Department of Immunology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Joris L Vos
- Division of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Charlotte L Zuur
- Division of Medical Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Otorhinolaryngology Leiden University Medical Center, Leiden, The Netherlands
| | | | - Heinz Jacobs
- Department of Tumor Biology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Sjoerd H van der Burg
- Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Jannie Borst
- Department of Immunology, Leiden University Medical Center, Leiden, The Netherlands.
- Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands.
| | - Yanling Xiao
- Department of Immunology, Leiden University Medical Center, Leiden, The Netherlands.
- Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands.
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4
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Trimaglio G, Sneperger T, Raymond BBA, Gilles N, Näser E, Locard-Paulet M, Ijsselsteijn ME, Brouwer TP, Ecalard R, Roelands J, Matsumoto N, Colom A, Habch M, de Miranda NFCC, Vergnolle N, Devaud C, Neyrolles O, Rombouts Y. The C-type lectin DCIR contributes to the immune response and pathogenesis of colorectal cancer. Sci Rep 2024; 14:7199. [PMID: 38532110 DOI: 10.1038/s41598-024-57941-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 03/22/2024] [Indexed: 03/28/2024] Open
Abstract
Development and progression of malignancies are accompanied and influenced by alterations in the surrounding immune microenvironment. Understanding the cellular and molecular interactions between immune cells and cancer cells has not only provided important fundamental insights into the disease, but has also led to the development of new immunotherapies. The C-type lectin Dendritic Cell ImmunoReceptor (DCIR) is primarily expressed by myeloid cells and is an important regulator of immune homeostasis, as demonstrated in various autoimmune, infectious and inflammatory contexts. Yet, the impact of DCIR on cancer development remains largely unknown. Analysis of available transcriptomic data of colorectal cancer (CRC) patients revealed that high DCIR gene expression is associated with improved patients' survival, immunologically "hot" tumors and high immunologic constant of rejection, thus arguing for a protective and immunoregulatory role of DCIR in CRC. In line with these correlative data, we found that deficiency of DCIR1, the murine homologue of human DCIR, leads to the development of significantly larger tumors in an orthotopic murine model of CRC. This phenotype is accompanied by an altered phenotype of tumor-associated macrophages (TAMs) and a reduction in the percentage of activated effector CD4+ and CD8+ T cells in CRC tumors of DCIR1-deficient mice. Overall, our results show that DCIR promotes antitumor immunity in CRC, making it an attractive target for the future development of immunotherapies to fight the second deadliest cancer in the world.
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Affiliation(s)
- Giulia Trimaglio
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Tamara Sneperger
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Benjamin B A Raymond
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Nelly Gilles
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Emmanuelle Näser
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Marie Locard-Paulet
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | | | - Thomas P Brouwer
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Romain Ecalard
- INSERM US006 ANEXPLO/CREFRE, Purpan Hospital, Toulouse, France
| | - Jessica Roelands
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Naoki Matsumoto
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - André Colom
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Myriam Habch
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | | | - Nathalie Vergnolle
- Institut de Recherche en Santé Digestive, IRSD, Université de Toulouse, INSERM, INRAe, ENVT, UPS, Toulouse, France
| | - Christel Devaud
- Institut de Recherche en Santé Digestive, IRSD, Université de Toulouse, INSERM, INRAe, ENVT, UPS, Toulouse, France
| | - Olivier Neyrolles
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Yoann Rombouts
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France.
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5
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Verschoor YL, van de Haar J, van den Berg JG, van Sandick JW, Kodach LL, van Dieren JM, Balduzzi S, Grootscholten C, IJsselsteijn ME, Veenhof AAFA, Hartemink KJ, Vollebergh MA, Jurdi A, Sharma S, Spickard E, Owers EC, Bartels-Rutten A, den Hartog P, de Miranda NFCC, van Leerdam ME, Haanen JBAG, Schumacher TN, Voest EE, Chalabi M. Author Correction: Neoadjuvant atezolizumab plus chemotherapy in gastric and gastroesophageal junction adenocarcinoma: the phase 2 PANDA trial. Nat Med 2024:10.1038/s41591-024-02898-8. [PMID: 38448792 DOI: 10.1038/s41591-024-02898-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Affiliation(s)
- Yara L Verschoor
- Department of Gastrointestinal Oncology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Joris van de Haar
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
- Oncode Institute, Amsterdam, the Netherlands
| | - José G van den Berg
- Department of Pathology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Johanna W van Sandick
- Department of Surgery, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Liudmila L Kodach
- Department of Pathology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Jolanda M van Dieren
- Department of Gastrointestinal Oncology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Sara Balduzzi
- Biometrics department, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Cecile Grootscholten
- Department of Gastrointestinal Oncology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | | | - Alexander A F A Veenhof
- Department of Surgery, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Koen J Hartemink
- Department of Surgery, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Marieke A Vollebergh
- Department of Gastrointestinal Oncology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
- Department of Medical Oncology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | | | | | | | - Emilia C Owers
- Department of Nuclear Medicine, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Annemarieke Bartels-Rutten
- Department of Radiology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Peggy den Hartog
- Department of Gastrointestinal Oncology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | | | - Monique E van Leerdam
- Department of Gastrointestinal Oncology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, the Netherlands
| | - John B A G Haanen
- Department of Medical Oncology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
- Department of Medical Oncology, Leiden University Medical Center, Leiden, the Netherlands
- Oncology Service, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Ton N Schumacher
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
- Oncode Institute, Amsterdam, the Netherlands
- Department of Hematology, Leiden University Medical Center, Leiden, the Netherlands
| | - Emile E Voest
- Department of Gastrointestinal Oncology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
- Oncode Institute, Amsterdam, the Netherlands
| | - Myriam Chalabi
- Department of Gastrointestinal Oncology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands.
- Department of Medical Oncology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands.
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6
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Zhu H, Roelands J, Ahmed EI, Stouten I, Hoorntje R, van Vlierberghe RLP, Ijsselsteijn ME, Lei X, de Miranda NFCC, Tollenaar RAEM, Vahrmeijer AL, Bedognetti D, Hendrickx WRL, Kuppen PJK. Location matters: spatial dynamics of tumor-infiltrating T cell subsets is prognostic in colon cancer. Front Immunol 2024; 15:1293618. [PMID: 38375478 PMCID: PMC10875018 DOI: 10.3389/fimmu.2024.1293618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 01/16/2024] [Indexed: 02/21/2024] Open
Abstract
Background Colon cancer is a heterogeneous disease and consists of various molecular subtypes. Despite advances in high-throughput expression profiling, limitations remain in predicting clinical outcome and assigning specific treatment to individual cases. Tumor-immune interactions play a critical role, with tumors that activate the immune system having better outcome for the patient. The localization of T cells within tumor epithelium, to enable direct contact, is essential for antitumor function, but bulk DNA/RNA sequencing data lacks spatial distribution information. In this study, we provide spatial T cell tumor distribution and connect these data with previously determined genomic data in the AC-ICAM colon cancer patient cohort. Methods Colon cancer patients (n=90) with transcriptome data available were selected. We used a custom multiplex immunofluorescence assay on colon tumor tissue sections for quantifying T cell subsets spatial distribution in the tumor microenvironment, in terms of cell number, location, mutual distance, and distance to tumor cells. Statistical analyses included the previously determined Immunologic Constant of Rejection (ICR) transcriptome correlation and patient survival, revealing potential prognostic value in T cell spatial distribution. Results T cell phenotypes were characterized and CD3+CD8-FoxP3- T cells were found to be the predominant tumor-infiltrating subtype while CD3+FoxP3+ T cells and CD3+CD8+ T cells showed similar densities. Spatial distribution analysis elucidated that proliferative T cells, characterized by Ki67 expression, and Granzyme B-expressing T cells were predominantly located within the tumor epithelium. We demonstrated an increase in immune cell density and a decrease in the distance of CD3+CD8+ T cells to the nearest tumor cell, in the immune active, ICR High, immune subtypes. Higher densities of stromal CD3+FoxP3+ T cells showed enhanced survival outcomes, and patients exhibited superior clinical benefits when greater spatial distances were observed between CD3+CD8-FoxP3- or CD3+CD8+ T cells and CD3+FoxP3+ T cells. Conclusion Our study's in-depth analysis of the spatial distribution and densities of major T cell subtypes within the tumor microenvironment has provided valuable information that paves the way for further research into the intricate relationships between immune cells and colon cancer development.
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Affiliation(s)
- Hehuan Zhu
- Department of Surgery, Leiden University Medical Center, Leiden, Netherlands
| | - Jessica Roelands
- Department of Surgery, Leiden University Medical Center, Leiden, Netherlands
- Department of Pathology, Leiden University Medical Center, Leiden, Netherlands
- Translational Medicine Division, Research Branch, Sidra Medicine, Doha, Qatar
| | - Eiman I. Ahmed
- Translational Medicine Division, Research Branch, Sidra Medicine, Doha, Qatar
- Department of Biomedical Science, College of Health Sciences, Qatar University, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Imke Stouten
- Department of Surgery, Leiden University Medical Center, Leiden, Netherlands
| | - Rachel Hoorntje
- Department of Surgery, Leiden University Medical Center, Leiden, Netherlands
| | | | | | - Xin Lei
- Department of Immunology and Oncode Institute, Leiden University Medical Center, Leiden, Netherlands
| | | | | | | | - Davide Bedognetti
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
- Kite, A Gilead Company, Santa Monica, CA, United States
| | - Wouter R. L. Hendrickx
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
- Tumor Biology and Immunology Lab, Research Branch, Sidra Medicine, Doha, Qatar
| | - Peter J. K. Kuppen
- Department of Surgery, Leiden University Medical Center, Leiden, Netherlands
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7
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Abudukelimu S, de Miranda NFCC, Hawinkels LJAC. Fibroblasts in Orchestrating Colorectal Tumorigenesis and Progression. Cell Mol Gastroenterol Hepatol 2024; 17:821-826. [PMID: 38307492 PMCID: PMC10966773 DOI: 10.1016/j.jcmgh.2024.01.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 01/19/2024] [Accepted: 01/19/2024] [Indexed: 02/04/2024]
Abstract
Cancer-associated fibroblasts (CAFs) are an abundant component of the tumor microenvironment and have been shown to possess critical functions in tumor progression. Although their roles predominantly have been described as tumor-promoting, more recent findings have identified subsets of CAFs with tumor-restraining functions. Accumulating evidence underscores large heterogeneity in fibroblast subsets in which distinct subsets differentially impact the initiation, progression, and metastasis of colorectal cancer. In this review, we summarize and discuss the evolving role of CAFs in colorectal cancer, highlighting the ongoing controversies regarding their distinct origins and multifaceted functions. In addition, we explore how CAFs can confer resistance to current therapies and the challenges of developing effective CAF-directed therapies. Taken together, we believe that, in this rapidly evolving field, it is crucial first to understand CAF dynamics comprehensively, and to bridge existing knowledge gaps regarding CAF heterogeneity and plasticity before further exploring the clinical targeting of CAFs.
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Affiliation(s)
- Subinuer Abudukelimu
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Lukas J A C Hawinkels
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands.
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8
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Özkan A, van den Bos F, Mooijaart SP, Slingerland M, Kapiteijn E, de Miranda NFCC, Portielje JEA, de Glas NA. Geriatric predictors of response and adverse events in older patients with cancer treated with immune checkpoint inhibitors: A systematic review. Crit Rev Oncol Hematol 2024; 194:104259. [PMID: 38199430 DOI: 10.1016/j.critrevonc.2024.104259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 11/13/2023] [Accepted: 01/04/2024] [Indexed: 01/12/2024] Open
Abstract
BACKGROUND Immunotherapy with checkpoint inhibitors (ICI) has improved cancer treatment in recent years. Older and frail patients are frequently treated with ICIs, but since they have been underrepresented in previous clinical trials, the real impact of ICI in this patient group is not well defined. The aim of this systematic review was to evaluate the evidence for associations between geriatric impairments and treatment outcomes in older patients with advanced and metastatic cancer treated with ICIs. METHODS A systematic search was conducted in PubMed, Cochrane Library, Embase, and Web of Science for relevant articles published before June 2022. Studies investigating the association between impairments in at least two geriatric domains and treatment outcome were considered eligible. Data extraction and risk of bias assessment using the QUIPS tool was performed independently by two investigators. RESULTS A total of nine studies were included. Median sample size of the studies was 92 patients (interquartile range (IQR) 47-113), with a median of 26 frail patients (IQR 21-35). Five studies investigated disease-related and survival outcomes, and two of them found a statistically significant association between geriatric impairments and either survival or disease progression. Eight studies investigated toxicity outcomes, and two of them showed a statistically significant association between geriatric impairments and immune-related adverse events (irAEs). Few studies suggested a relation between geriatric impairments and worse clinical outcomes. CONCLUSIONS Only a few studies have investigated the association between geriatric impairments and treatment outcomes and these studies were small. Older patients with geriatric impairments seem to be more likely to experience irAEs, but larger studies that include frail patients and use geriatric screening tools are required to confirm this association. These studies will be essential to improve the development of specific strategies to deal with frail patients.
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Affiliation(s)
- Asli Özkan
- Department of Medical Oncology, Leiden University Medical Center, Leiden, the Netherlands
| | - Frederiek van den Bos
- Department of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, the Netherlands
| | - Simon P Mooijaart
- Department of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, the Netherlands; Center for Medicine for Older People, Leiden University Medical Center, Leiden, the Netherlands
| | - Marije Slingerland
- Department of Medical Oncology, Leiden University Medical Center, Leiden, the Netherlands
| | - Ellen Kapiteijn
- Department of Medical Oncology, Leiden University Medical Center, Leiden, the Netherlands
| | | | | | - Nienke A de Glas
- Department of Medical Oncology, Leiden University Medical Center, Leiden, the Netherlands.
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9
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Verschoor YL, van de Haar J, van den Berg JG, van Sandick JW, Kodach LL, van Dieren JM, Balduzzi S, Grootscholten C, IJsselsteijn ME, Veenhof AAFA, Hartemink KJ, Vollebergh MA, Jurdi A, Sharma S, Spickard E, Owers EC, Bartels-Rutten A, den Hartog P, de Miranda NFCC, van Leerdam ME, Haanen JBAG, Schumacher TN, Voest EE, Chalabi M. Neoadjuvant atezolizumab plus chemotherapy in gastric and gastroesophageal junction adenocarcinoma: the phase 2 PANDA trial. Nat Med 2024; 30:519-530. [PMID: 38191613 PMCID: PMC10878980 DOI: 10.1038/s41591-023-02758-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 12/07/2023] [Indexed: 01/10/2024]
Abstract
Gastric and gastroesophageal junction (G/GEJ) cancers carry a poor prognosis, and despite recent advancements, most patients die of their disease. Although immune checkpoint blockade became part of the standard-of-care for patients with metastatic G/GEJ cancers, its efficacy and impact on the tumor microenvironment (TME) in early disease remain largely unknown. We hypothesized higher efficacy of neoadjuvant immunotherapy plus chemotherapy in patients with nonmetastatic G/GEJ cancer. In the phase 2 PANDA trial, patients with previously untreated resectable G/GEJ tumors (n = 21) received neoadjuvant treatment with one cycle of atezolizumab monotherapy followed by four cycles of atezolizumab plus docetaxel, oxaliplatin and capecitabine. Treatment was well tolerated. There were grade 3 immune-related adverse events in two of 20 patients (10%) but no grade 4 or 5 immune-related adverse events, and all patients underwent resection without treatment-related delays, meeting the primary endpoint of safety and feasibility. Tissue was obtained at multiple time points, allowing analysis of the effects of single-agent anti-programmed cell death ligand 1 (PD-L1) and the subsequent combination with chemotherapy on the TME. Twenty of 21 patients underwent surgery and were evaluable for secondary pathologic response and survival endpoints, and 19 were evaluable for exploratory translational analyses. A major pathologic response (≤10% residual viable tumor) was observed in 14 of 20 (70%, 95% confidence interval 46-88%) patients, including 9 (45%, 95% confidence interval 23-68%) pathologic complete responses. At a median follow-up of 47 months, 13 of 14 responders were alive and disease-free, and five of six nonresponders had died as a result of recurrence. Notably, baseline anti-programmed cell death protein 1 (PD-1)+CD8+ T cell infiltration was significantly higher in responders versus nonresponders, and comparison of TME alterations following anti-PD-L1 monotherapy versus the subsequent combination with chemotherapy showed an increased immune activation on single-agent PD-1/L1 axis blockade. On the basis of these data, monotherapy anti-PD-L1 before its combination with chemotherapy warrants further exploration and validation in a larger cohort of patients with nonmetastatic G/GEJ cancer. ClinicalTrials.gov registration: NCT03448835 .
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Affiliation(s)
- Yara L Verschoor
- Department of Gastrointestinal Oncology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Joris van de Haar
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
- Oncode Institute, Amsterdam, the Netherlands
| | - José G van den Berg
- Department of Pathology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Johanna W van Sandick
- Department of Surgery, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Liudmila L Kodach
- Department of Pathology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Jolanda M van Dieren
- Department of Gastrointestinal Oncology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Sara Balduzzi
- Biometrics department, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Cecile Grootscholten
- Department of Gastrointestinal Oncology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | | | - Alexander A F A Veenhof
- Department of Surgery, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Koen J Hartemink
- Department of Surgery, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Marieke A Vollebergh
- Department of Gastrointestinal Oncology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
- Department of Medical Oncology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | | | | | | | - Emilia C Owers
- Department of Nuclear Medicine, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Annemarieke Bartels-Rutten
- Department of Radiology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Peggy den Hartog
- Department of Gastrointestinal Oncology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | | | - Monique E van Leerdam
- Department of Gastrointestinal Oncology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, the Netherlands
| | - John B A G Haanen
- Department of Medical Oncology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
- Department of Medical Oncology, Leiden University Medical Center, Leiden, the Netherlands
- Oncology Service, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Ton N Schumacher
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
- Oncode Institute, Amsterdam, the Netherlands
- Department of Hematology, Leiden University Medical Center, Leiden, the Netherlands
| | - Emile E Voest
- Department of Gastrointestinal Oncology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
- Oncode Institute, Amsterdam, the Netherlands
| | - Myriam Chalabi
- Department of Gastrointestinal Oncology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands.
- Department of Medical Oncology, Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands.
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10
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van Oost S, Meijer DM, Ijsselsteijn ME, Roelands JP, van den Akker BEMW, van der Breggen R, Briaire-de Bruijn IH, van der Ploeg M, Wijers-Koster PM, Polak SB, Peul WC, van der Wal RJP, de Miranda NFCC, Bovee JVMG. Multimodal profiling of chordoma immunity reveals distinct immune contextures. J Immunother Cancer 2024; 12:e008138. [PMID: 38272563 PMCID: PMC10824073 DOI: 10.1136/jitc-2023-008138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/02/2024] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND Chordomas are rare cancers from the axial skeleton which present a challenging clinical management with limited treatment options due to their anatomical location. In recent years, a few clinical trials demonstrated that chordomas can respond to immunotherapy. However, an in-depth portrayal of chordoma immunity and its association with clinical parameters is still lacking. METHODS We present a comprehensive characterization of immunological features of 76 chordomas through application of a multimodal approach. Transcriptomic profiling of 20 chordomas was performed to inform on the activity of immune-related genes through the immunologic constant of rejection (ICR) signature. Multidimensional immunophenotyping through imaging mass cytometry was applied to provide insights in the different immune contextures of 32 chordomas. T cell infiltration was further evaluated in all 76 patients by means of multispectral immunofluorescence and then associated with clinical parameters through univariate and multivariate Cox proportional hazard models as well as Kaplan-Meier estimates. Moreover, distinct expression patterns of human leukocyte antigen (HLA) class I were assessed by immunohistochemical staining in all 76 patients. Finally, clonal enrichment of the T cell receptor (TCR) was sought through profiling of the variable region of TCRB locus of 24 patients. RESULTS Chordomas generally presented an immune "hot" microenvironment in comparison to other sarcomas, as indicated by the ICR transcriptional signature. We identified two distinct groups of chordomas based on T cell infiltration which were independent from clinical parameters. The highly infiltrated group was further characterized by high dendritic cell infiltration and the presence of multicellular immune aggregates in tumors, whereas low T cell infiltration was associated with lower overall cell densities of immune and stromal cells. Interestingly, patients with higher T cell infiltration displayed a more pronounced clonal enrichment of the TCR repertoire compared with those with low T cell counts. Furthermore, we observed that the majority of chordomas maintained HLA class I expression. CONCLUSION Our findings shed light on the natural immunity against chordomas through the identification of distinct immune contextures. Understanding their immune landscape could guide the development and application of immunotherapies in a tailored manner, ultimately leading to an improved clinical outcome for patients with chordoma.
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Affiliation(s)
- Siddh van Oost
- Department of Pathology, Leiden University Medical Center, Leiden, Netherlands
- Leiden Center for Computational Oncology, Leiden University Medical Center, Leiden, Netherlands
| | - Debora M Meijer
- Department of Pathology, Leiden University Medical Center, Leiden, Netherlands
- Leiden Center for Computational Oncology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Jessica P Roelands
- Department of Pathology, Leiden University Medical Center, Leiden, Netherlands
| | | | | | | | - Manon van der Ploeg
- Department of Pathology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Samuel B Polak
- University Neurosurgical Center Holland, Leiden University Medical Center, Leiden, Zuid-Holland, Netherlands
| | - Wilco C Peul
- University Neurosurgical Center Holland, Leiden University Medical Center, Leiden, Zuid-Holland, Netherlands
| | - Robert J P van der Wal
- Department of Orthopaedic Surgery, Leiden University Medical Center, Leiden, Netherlands
| | - Noel F C C de Miranda
- Department of Pathology, Leiden University Medical Center, Leiden, Netherlands
- Leiden Center for Computational Oncology, Leiden University Medical Center, Leiden, Netherlands
| | - Judith V M G Bovee
- Department of Pathology, Leiden University Medical Center, Leiden, Netherlands
- Leiden Center for Computational Oncology, Leiden University Medical Center, Leiden, Netherlands
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11
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van Eijck CWF, Mustafa DAM, Vadgama D, de Miranda NFCC, Groot Koerkamp B, van Tienhoven G, van der Burg SH, Malats N, van Eijck CHJ. Enhanced antitumour immunity following neoadjuvant chemoradiotherapy mediates a favourable prognosis in women with resected pancreatic cancer. Gut 2024; 73:311-324. [PMID: 37709493 PMCID: PMC10850691 DOI: 10.1136/gutjnl-2023-330480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 08/01/2023] [Indexed: 09/16/2023]
Abstract
BACKGROUND This study investigates sex disparities in clinical outcomes and tumour immune profiles in patients with pancreatic ductal adenocarcinoma (PDAC) who underwent upfront resection or resection preceded by gemcitabine-based neoadjuvant chemoradiotherapy (nCRT). METHODS Patients originated from the PREOPANC randomised controlled trial. Upfront surgery was performed in 82 patients, and 66 received nCRT before resection. The impact of sex on overall survival (OS) was investigated using Cox proportional hazards models. The immunological landscape within the tumour microenvironment (TME) was mapped using transcriptomic and spatial proteomic profiling. RESULTS The 5-year OS rate differed between the sexes following resection preceded by nCRT, with 43% for women compared with 22% for men. In multivariate analysis, the female sex was a favourable independent prognostic factor for OS only in the nCRT group (HR 0.19; 95% CI 0.07 to 0.52). Multivariate heterogeneous treatment effects analysis revealed a significant interaction between sex and treatment, implying increased nCRT efficacy among women with resected PDAC. The TME of women contained fewer protumoural CD163+MRC1+M2 macrophages than that of men after nCRT, as indicated by transcriptomic and validated using spatial proteomic profiling. CONCLUSION PDAC tumours of women are more sensitive to gemcitabine-based nCRT, resulting in longer OS after resection compared with men. This may be due to enhanced immunity impeding the infiltration of protumoral M2 macrophages into the TME. Our findings highlight the importance of considering sex disparities and mitigating immunosuppressive macrophage polarisation for personalised PDAC treatment.
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Affiliation(s)
- Casper W F van Eijck
- Department of Surgery, Erasmus Medical Center, Rotterdam, The Netherlands
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre, and CIBERONC, Madrid, Spain
| | - Dana A M Mustafa
- Department of Pathology, Tumour-Immuno Pathology Laboratory, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Disha Vadgama
- Department of Pathology, Tumour-Immuno Pathology Laboratory, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Bas Groot Koerkamp
- Department of Surgery, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Sjoerd H van der Burg
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Núria Malats
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre, and CIBERONC, Madrid, Spain
| | - Casper H J van Eijck
- Department of Surgery, Erasmus Medical Center, Rotterdam, The Netherlands
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre, and CIBERONC, Madrid, Spain
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12
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Luk SJ, Schoppmeyer R, Ijsselsteijn ME, Somarakis A, Acem I, Remst DFG, Cox DT, van Bergen CAM, Briaire-de Bruijn I, Grönloh MLB, van der Meer WJ, Hawinkels LJAC, Koning RI, Bos E, Bovée JVMG, de Miranda NFCC, Szuhai K, van Buul JD, Falkenburg JHF, Heemskerk MHM. VISTA Expression on Cancer-Associated Endothelium Selectively Prevents T-cell Extravasation. Cancer Immunol Res 2023; 11:1480-1492. [PMID: 37695550 DOI: 10.1158/2326-6066.cir-22-0759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 04/14/2023] [Accepted: 09/01/2023] [Indexed: 09/12/2023]
Abstract
Cancers evade T-cell immunity by several mechanisms such as secretion of anti-inflammatory cytokines, down regulation of antigen presentation machinery, upregulation of immune checkpoint molecules, and exclusion of T cells from tumor tissues. The distribution and function of immune checkpoint molecules on tumor cells and tumor-infiltrating leukocytes is well established, but less is known about their impact on intratumoral endothelial cells. Here, we demonstrated that V-domain Ig suppressor of T-cell activation (VISTA), a PD-L1 homolog, was highly expressed on endothelial cells in synovial sarcoma, subsets of different carcinomas, and immune-privileged tissues. We created an ex vivo model of the human vasculature and demonstrated that expression of VISTA on endothelial cells selectively prevented T-cell transmigration over endothelial layers under physiologic flow conditions, whereas it does not affect migration of other immune cell types. Furthermore, endothelial VISTA correlated with reduced infiltration of T cells and poor prognosis in metastatic synovial sarcoma. In endothelial cells, we detected VISTA on the plasma membrane and in recycling endosomes, and its expression was upregulated by cancer cell-secreted factors in a VEGF-A-dependent manner. Our study reveals that endothelial VISTA is upregulated by cancer-secreted factors and that it regulates T-cell accessibility to cancer and healthy tissues. This newly identified mechanism should be considered when using immunotherapeutic approaches aimed at unleashing T cell-mediated cancer immunity.
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Affiliation(s)
- Sietse J Luk
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Rouven Schoppmeyer
- Molecular Cell Biology Lab, Department of Molecular Hematology, Sanquin Research, Amsterdam, the Netherlands
- Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
- Leeuwenhoek Centre for Advanced Microscopy, Molecular Cytology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | | | - Antonios Somarakis
- Department of Radiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Ibtissam Acem
- Department of Orthopedic Surgery, Leiden University Medical Center, Leiden, the Netherlands
- Department of Oncological and Gastrointestinal Surgery, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Dennis F G Remst
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Daan T Cox
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | | | | | - Max L B Grönloh
- Molecular Cell Biology Lab, Department of Molecular Hematology, Sanquin Research, Amsterdam, the Netherlands
- Leeuwenhoek Centre for Advanced Microscopy, Molecular Cytology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Werner J van der Meer
- Molecular Cell Biology Lab, Department of Molecular Hematology, Sanquin Research, Amsterdam, the Netherlands
- Leeuwenhoek Centre for Advanced Microscopy, Molecular Cytology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | - Lukas J A C Hawinkels
- Department of Gastroenterology-Hepatology, Leiden University Medical Center, Leiden, the Netherlands
| | - Roman I Koning
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Erik Bos
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Judith V M G Bovée
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Karoly Szuhai
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Jaap D van Buul
- Molecular Cell Biology Lab, Department of Molecular Hematology, Sanquin Research, Amsterdam, the Netherlands
- Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
- Leeuwenhoek Centre for Advanced Microscopy, Molecular Cytology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands
| | | | - Mirjam H M Heemskerk
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
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13
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Ijsselsteijn ME, de Miranda NFCC. Advancing multiplexed imaging for enhanced tissue complexity analysis. Nat Methods 2023; 20:1280-1281. [PMID: 37653119 DOI: 10.1038/s41592-023-01935-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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14
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Roelands J, Kuppen PJK, Ahmed EI, Mall R, Masoodi T, Singh P, Monaco G, Raynaud C, de Miranda NFCC, Ferraro L, Carneiro-Lobo TC, Syed N, Rawat A, Awad A, Decock J, Mifsud W, Miller LD, Sherif S, Mohamed MG, Rinchai D, Van den Eynde M, Sayaman RW, Ziv E, Bertucci F, Petkar MA, Lorenz S, Mathew LS, Wang K, Murugesan S, Chaussabel D, Vahrmeijer AL, Wang E, Ceccarelli A, Fakhro KA, Zoppoli G, Ballestrero A, Tollenaar RAEM, Marincola FM, Galon J, Khodor SA, Ceccarelli M, Hendrickx W, Bedognetti D. An integrated tumor, immune and microbiome atlas of colon cancer. Nat Med 2023; 29:1273-1286. [PMID: 37202560 PMCID: PMC10202816 DOI: 10.1038/s41591-023-02324-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 03/28/2023] [Indexed: 05/20/2023]
Abstract
The lack of multi-omics cancer datasets with extensive follow-up information hinders the identification of accurate biomarkers of clinical outcome. In this cohort study, we performed comprehensive genomic analyses on fresh-frozen samples from 348 patients affected by primary colon cancer, encompassing RNA, whole-exome, deep T cell receptor and 16S bacterial rRNA gene sequencing on tumor and matched healthy colon tissue, complemented with tumor whole-genome sequencing for further microbiome characterization. A type 1 helper T cell, cytotoxic, gene expression signature, called Immunologic Constant of Rejection, captured the presence of clonally expanded, tumor-enriched T cell clones and outperformed conventional prognostic molecular biomarkers, such as the consensus molecular subtype and the microsatellite instability classifications. Quantification of genetic immunoediting, defined as a lower number of neoantigens than expected, further refined its prognostic value. We identified a microbiome signature, driven by Ruminococcus bromii, associated with a favorable outcome. By combining microbiome signature and Immunologic Constant of Rejection, we developed and validated a composite score (mICRoScore), which identifies a group of patients with excellent survival probability. The publicly available multi-omics dataset provides a resource for better understanding colon cancer biology that could facilitate the discovery of personalized therapeutic approaches.
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Affiliation(s)
- Jessica Roelands
- Translational Medicine Division, Research Branch, Sidra Medicine, Doha, Qatar
- Department of Surgery, Leiden University Medical Center, Leiden, The Netherlands
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter J K Kuppen
- Department of Surgery, Leiden University Medical Center, Leiden, The Netherlands
| | - Eiman I Ahmed
- Translational Medicine Division, Research Branch, Sidra Medicine, Doha, Qatar
| | - Raghvendra Mall
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Biotechnology Research Center, Technology Innovation Institute, Abu Dhabi, United Arab Emirates
| | - Tariq Masoodi
- Translational Medicine Division, Research Branch, Sidra Medicine, Doha, Qatar
| | - Parul Singh
- Translational Medicine Division, Research Branch, Sidra Medicine, Doha, Qatar
| | - Gianni Monaco
- Institute for Transfusion Medicine and Gene Therapy, Medical Center-University of Freiburg, Freiburg, Germany
- Neuropathology, Medical Center-University of Freiburg, Freiburg, Germany
- BIOGEM Institute of Molecular Biology and Genetics, Ariano Irpino, Italy
| | - Christophe Raynaud
- Translational Medicine Division, Research Branch, Sidra Medicine, Doha, Qatar
| | | | - Luigi Ferraro
- BIOGEM Institute of Molecular Biology and Genetics, Ariano Irpino, Italy
- Department of Electrical Engineering and Information Technology (DIETI), University of Naples Federico II, Naples, Italy
| | | | - Najeeb Syed
- Integrated Genomics Services, Research Branch, Sidra Medicine, Doha, Qatar
| | - Arun Rawat
- Translational Medicine Division, Research Branch, Sidra Medicine, Doha, Qatar
| | - Amany Awad
- Translational Medicine Division, Research Branch, Sidra Medicine, Doha, Qatar
| | - Julie Decock
- Translational Cancer and Immunity Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - William Mifsud
- Department of Pathology, Sidra Medicine, Doha, Qatar
- Weill-Cornell Medicine Qatar, Doha, Qatar
| | - Lance D Miller
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Shimaa Sherif
- Translational Medicine Division, Research Branch, Sidra Medicine, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - Mahmoud G Mohamed
- Translational Medicine Division, Research Branch, Sidra Medicine, Doha, Qatar
- Women's Wellness and Research Center, Hamad Medical Corporation, Doha, Qatar
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, Genoa, Italy
| | - Darawan Rinchai
- Translational Medicine Division, Research Branch, Sidra Medicine, Doha, Qatar
- Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY, USA
| | - Marc Van den Eynde
- Institut Roi Albert II, Cliniques Universitaires Saint-Luc, UCLouvain, Brussels, Belgium
| | - Rosalyn W Sayaman
- Department of Laboratory Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Elad Ziv
- Department of Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Francois Bertucci
- Laboratory of Predictive Oncology, Centre de Recherche en Cancérologie de Marseille, Institut Paoli-Calmettes, Aix-Marseille Université, Inserm UMR1068, CNRS UMR725, Marseille, France
- Department of Medical Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Mahir Abdulla Petkar
- Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha, Qatar
| | - Stephan Lorenz
- Integrated Genomics Services, Research Branch, Sidra Medicine, Doha, Qatar
| | - Lisa Sara Mathew
- Integrated Genomics Services, Research Branch, Sidra Medicine, Doha, Qatar
| | - Kun Wang
- Integrated Genomics Services, Research Branch, Sidra Medicine, Doha, Qatar
| | | | - Damien Chaussabel
- Translational Medicine Division, Research Branch, Sidra Medicine, Doha, Qatar
- Computational Sciences Department, The Jackson Laboratory, Farmington, CT, USA
| | | | - Ena Wang
- Translational Medicine Division, Research Branch, Sidra Medicine, Doha, Qatar
- Nurix Therapeutics, San Francisco, CA, USA
| | - Anna Ceccarelli
- Medical Oncology, Fondazione Policlinico Universitario Agostino Gemelli IRCCS- Università Cattolica del Sacro Cuore, Rome, Italy
| | - Khalid A Fakhro
- Translational Medicine Division, Research Branch, Sidra Medicine, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
- Weill-Cornell Medicine Qatar, Doha, Qatar
| | - Gabriele Zoppoli
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, Genoa, Italy
- IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Alberto Ballestrero
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, Genoa, Italy
- IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Rob A E M Tollenaar
- Department of Surgery, Leiden University Medical Center, Leiden, The Netherlands
| | - Francesco M Marincola
- Translational Medicine Division, Research Branch, Sidra Medicine, Doha, Qatar
- Sonata Therapeutics, Watertown, MA, USA
| | - Jérôme Galon
- Inserm, Laboratory of Integrative Cancer Immunology, Equipe Labellisée Ligue Contre Le Cancer, Centre de Recherche de Cordeliers, Université de Paris, Sorbonne Université, Paris, France
| | - Souhaila Al Khodor
- Translational Medicine Division, Research Branch, Sidra Medicine, Doha, Qatar
| | - Michele Ceccarelli
- BIOGEM Institute of Molecular Biology and Genetics, Ariano Irpino, Italy
- Department of Electrical Engineering and Information Technology (DIETI), University of Naples Federico II, Naples, Italy
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Wouter Hendrickx
- Translational Medicine Division, Research Branch, Sidra Medicine, Doha, Qatar.
- College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar.
| | - Davide Bedognetti
- Translational Medicine Division, Research Branch, Sidra Medicine, Doha, Qatar.
- College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar.
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, Genoa, Italy.
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15
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Dang H, Harryvan TJ, Liao CY, Danen EHJ, Spalburg VNLN, Kielbasa SM, Mei H, Goeman JJ, de Jonge-Muller ES, Janson SGT, van der Reijden JJ, Crobach S, Hardwick JCH, Boonstra JJ, de Miranda NFCC, Hawinkels LJAC. Cancer-associated fibroblasts are key determinants of cancer cell invasion in the earliest stage of colorectal cancer. Cell Mol Gastroenterol Hepatol 2023; 16:107-131. [PMID: 37085135 DOI: 10.1016/j.jcmgh.2023.04.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 04/09/2023] [Accepted: 04/10/2023] [Indexed: 04/23/2023]
Abstract
BACKGROUND AND AIMS Improving clinical management of early-stage colorectal cancers (T1CRCs) requires a better understanding of their underlying biology. Accumulating evidence shows that cancer-associated fibroblasts (CAFs) are important determinants of tumor progression in advanced colorectal cancer (CRC), but their role in the initial stages of CRC tumorigenesis is unknown. Therefore, we investigated the contribution of T1CAFs to early CRC progression. METHODS Primary T1CAFs and patient-matched normal fibroblasts (NFs) were isolated from endoscopic biopsies of histologically confirmed T1CRCs and normal mucosa, respectively. The impact of T1CAFs and NFs on tumor behavior was studied using 3D co-culture systems with primary T1CRC organoids and extracellular matrix (ECM) remodeling assays. Whole transcriptome sequencing and gene silencing were used to pinpoint mediators of T1CAF functions. RESULTS In 3D multicellular cultures, matrix invasion of T1CRC organoids was induced by T1CAFs, but not by matched NFs. Enhanced T1CRC invasion was accompanied by T1CAF-induced ECM remodeling and upregulation of CD44 in epithelial cells. RNA sequencing of 10 NF-T1CAF pairs revealed 404 differentially expressed genes, with significant enrichment for ECM-related pathways in T1CAFs. Cathepsin H, a cysteine-type protease that was specifically upregulated in T1CAFs but not in fibroblasts from pre-malignant lesions or advanced CRCs, was identified as a key factor driving matrix remodeling by T1CAFs. Finally, we showed high abundance of Cathepsin H-expressing T1CAFs at the invasive front of primary T1CRC sections. CONCLUSION Already in the earliest stage of CRC, cancer cell invasion is promoted by CAFs via direct interactions with epithelial cancer cells and stage-specific, Cathepsin H-dependent ECM remodeling.
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Affiliation(s)
- Hao Dang
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Tom J Harryvan
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Chen-Yi Liao
- Division of Drug Discovery and Safety, Leiden Academic Centre of Drug Research, Leiden University, Leiden, the Netherlands
| | - Erik H J Danen
- Division of Drug Discovery and Safety, Leiden Academic Centre of Drug Research, Leiden University, Leiden, the Netherlands
| | - Vienna N L N Spalburg
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Szymon M Kielbasa
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Hailiang Mei
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Jelle J Goeman
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Eveline S de Jonge-Muller
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Stefanus G T Janson
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Johan J van der Reijden
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Stijn Crobach
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - James C H Hardwick
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Jurjen J Boonstra
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Lukas J A C Hawinkels
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands.
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16
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van der Sluis TC, Beyrend G, van der Gracht ETI, Abdelaal T, Jochems SP, Belderbos RA, Wesselink TH, van Duikeren S, van Haften FJ, Redeker A, Ouboter LF, Beyranvand Nejad E, Camps M, Franken KLMC, Linssen MM, Hohenstein P, de Miranda NFCC, Mei H, Bins AD, Haanen JBAG, Aerts JG, Ossendorp F, Arens R. OX40 agonism enhances PD-L1 checkpoint blockade by shifting the cytotoxic T cell differentiation spectrum. Cell Rep Med 2023; 4:100939. [PMID: 36796366 PMCID: PMC10040386 DOI: 10.1016/j.xcrm.2023.100939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 10/07/2022] [Accepted: 01/20/2023] [Indexed: 02/17/2023]
Abstract
Immune checkpoint therapy (ICT) has the power to eradicate cancer, but the mechanisms that determine effective therapy-induced immune responses are not fully understood. Here, using high-dimensional single-cell profiling, we interrogate whether the landscape of T cell states in the peripheral blood predict responses to combinatorial targeting of the OX40 costimulatory and PD-1 inhibitory pathways. Single-cell RNA sequencing and mass cytometry expose systemic and dynamic activation states of therapy-responsive CD4+ and CD8+ T cells in tumor-bearing mice with expression of distinct natural killer (NK) cell receptors, granzymes, and chemokines/chemokine receptors. Moreover, similar NK cell receptor-expressing CD8+ T cells are also detected in the blood of immunotherapy-responsive cancer patients. Targeting the NK cell and chemokine receptors in tumor-bearing mice shows the functional importance of these receptors for therapy-induced anti-tumor immunity. These findings provide a better understanding of ICT and highlight the use and targeting of dynamic biomarkers on T cells to improve cancer immunotherapy.
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Affiliation(s)
- Tetje C van der Sluis
- Department of Immunology, Leiden University Medical Center, 2333ZA Leiden, the Netherlands
| | - Guillaume Beyrend
- Department of Immunology, Leiden University Medical Center, 2333ZA Leiden, the Netherlands
| | | | - Tamim Abdelaal
- Department of Radiology, Leiden University Medical Center, 2333ZA Leiden, the Netherlands; Systems and Biomedical Engineering Department, Faculty of Engineering, Cairo University, Giza 12613, Egypt; Pattern Recognition and Bioinformatics, Delft University of Technology, 2628XE Delft, the Netherlands
| | - Simon P Jochems
- Department of Parasitology, Leiden University Center for Infectious Diseases, Leiden University Medical Center, 2333ZA Leiden, the Netherlands
| | - Robert A Belderbos
- Department of Pulmonary Diseases, Erasmus Medical Center, 3015GD Rotterdam, the Netherlands
| | - Thomas H Wesselink
- Department of Immunology, Leiden University Medical Center, 2333ZA Leiden, the Netherlands
| | - Suzanne van Duikeren
- Department of Immunology, Leiden University Medical Center, 2333ZA Leiden, the Netherlands
| | - Floortje J van Haften
- Department of Immunology, Leiden University Medical Center, 2333ZA Leiden, the Netherlands
| | - Anke Redeker
- Department of Immunology, Leiden University Medical Center, 2333ZA Leiden, the Netherlands
| | - Laura F Ouboter
- Department of Immunology, Leiden University Medical Center, 2333ZA Leiden, the Netherlands
| | - Elham Beyranvand Nejad
- Department of Immunology, Leiden University Medical Center, 2333ZA Leiden, the Netherlands
| | - Marcel Camps
- Department of Immunology, Leiden University Medical Center, 2333ZA Leiden, the Netherlands
| | - Kees L M C Franken
- Department of Immunology, Leiden University Medical Center, 2333ZA Leiden, the Netherlands
| | - Margot M Linssen
- Central Animal and Transgenic Facility, Leiden University Medical Center, 2333ZA Leiden, the Netherlands
| | - Peter Hohenstein
- Central Animal and Transgenic Facility, Leiden University Medical Center, 2333ZA Leiden, the Netherlands
| | - Noel F C C de Miranda
- Department of Pathology, Leiden University Medical Center, 2333ZA Leiden, the Netherlands
| | - Hailiang Mei
- Department of Biomedical Data Sciences, Sequencing Analysis Support Core, Leiden University Medical Center, 2333ZA Leiden, the Netherlands
| | - Adriaan D Bins
- Department of Internal Medicine, Amsterdam University Medical Center, 1105AZ Amsterdam, the Netherlands
| | - John B A G Haanen
- Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Joachim G Aerts
- Department of Pulmonary Diseases, Erasmus Medical Center, 3015GD Rotterdam, the Netherlands
| | - Ferry Ossendorp
- Department of Immunology, Leiden University Medical Center, 2333ZA Leiden, the Netherlands
| | - Ramon Arens
- Department of Immunology, Leiden University Medical Center, 2333ZA Leiden, the Netherlands.
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17
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Guo N, Li N, Jia L, Jiang Q, Schreurs M, van Unen V, de Sousa Lopes SMC, Vloemans AA, Eggermont J, Lelieveldt B, Staal FJT, de Miranda NFCC, Pascutti MF, Koning F. Immune subset-committed proliferating cells populate the human foetal intestine throughout the second trimester of gestation. Nat Commun 2023; 14:1318. [PMID: 36899020 PMCID: PMC10006174 DOI: 10.1038/s41467-023-37052-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 03/01/2023] [Indexed: 03/12/2023] Open
Abstract
The intestine represents the largest immune compartment in the human body, yet its development and organisation during human foetal development is largely unknown. Here we show the immune subset composition of this organ during development, by longitudinal spectral flow cytometry analysis of human foetal intestinal samples between 14 and 22 weeks of gestation. At 14 weeks, the foetal intestine is mainly populated by myeloid cells and three distinct CD3-CD7+ ILC, followed by rapid appearance of adaptive CD4+, CD8+ T and B cell subsets. Imaging mass cytometry identifies lymphoid follicles from week 16 onwards in a villus-like structure covered by epithelium and confirms the presence of Ki-67+ cells in situ within all CD3-CD7+ ILC, T, B and myeloid cell subsets. Foetal intestinal lymphoid subsets are capable of spontaneous proliferation in vitro. IL-7 mRNA is detected within both the lamina propria and the epithelium and IL-7 enhances proliferation of several subsets in vitro. Overall, these observations demonstrate the presence of immune subset-committed cells capable of local proliferation in the developing human foetal intestine, likely contributing to the development and growth of organized immune structures throughout most of the 2nd trimester, which might influence microbial colonization upon birth.
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Affiliation(s)
- Nannan Guo
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Na Li
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands.,State Key Laboratory of Zoonotic Diseases, Institute of Zoonoses, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Li Jia
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Qinyue Jiang
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Mette Schreurs
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Vincent van Unen
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands.,Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | | | | | - Jeroen Eggermont
- Department of Radiology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Frank J T Staal
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | | | - M Fernanda Pascutti
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands.
| | - Frits Koning
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands.
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18
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van den Bulk J, van der Ploeg M, Ijsselsteijn ME, Ruano D, van der Breggen R, Duhen R, Peeters KCMJ, Fariña-Sarasqueta A, Verdegaal EME, van der Burg SH, Duhen T, de Miranda NFCC. CD103 and CD39 coexpression identifies neoantigen-specific cytotoxic T cells in colorectal cancers with low mutation burden. J Immunother Cancer 2023; 11:jitc-2022-005887. [PMID: 36792124 PMCID: PMC9933759 DOI: 10.1136/jitc-2022-005887] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/13/2023] [Indexed: 02/17/2023] Open
Abstract
BACKGROUND Expression of CD103 and CD39 has been found to pinpoint tumor-reactive CD8+ T cells in a variety of solid cancers. We aimed to investigate whether these markers specifically identify neoantigen-specific T cells in colorectal cancers (CRCs) with low mutation burden. EXPERIMENTAL DESIGN Whole-exome and RNA sequencing of 11 mismatch repair-proficient (MMR-proficient) CRCs and corresponding healthy tissues were performed to determine the presence of putative neoantigens. In parallel, tumor-infiltrating lymphocytes (TILs) were cultured from the tumor fragments and, in parallel, CD8+ T cells were flow-sorted from their respective tumor digests based on single or combined expression of CD103 and CD39. Each subset was expanded and subsequently interrogated for neoantigen-directed reactivity with synthetic peptides. Neoantigen-directed reactivity was determined by flow cytometric analyses of T cell activation markers and ELISA-based detection of IFN-γ and granzyme B release. Additionally, imaging mass cytometry was applied to investigate the localization of CD103+CD39+ cytotoxic T cells in tumors. RESULTS Neoantigen-directed reactivity was only encountered in bulk TIL populations and CD103+CD39+ (double positive, DP) CD8+ T cell subsets but never in double-negative or single-positive subsets. Neoantigen-reactivity detected in bulk TIL but not in DP CD8+ T cells could be attributed to CD4+ T cells. CD8+ T cells that were located in direct contact with cancer cells in tumor tissues were enriched for CD103 and CD39 expression. CONCLUSION Coexpression of CD103 and CD39 is characteristic of neoantigen-specific CD8+ T cells in MMR-proficient CRCs with low mutation burden. The exploitation of these subsets in the context of adoptive T cell transfer or engineered T cell receptor therapies is a promising avenue to extend the benefits of immunotherapy to an increasing number of CRC patients.
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Affiliation(s)
- Jitske van den Bulk
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Manon van der Ploeg
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Dina Ruano
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ruud van der Breggen
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Rebekka Duhen
- Basic Immunology Lab, Earle A Chiles Research Institute, Portland, Oregon, USA
| | - Koen C M J Peeters
- Department of Surgery, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Els M E Verdegaal
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Sjoerd H van der Burg
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Thomas Duhen
- Anti-Cancer Immune Response Lab, Earle A Chiles Research Institute, Portland, Oregon, USA
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19
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Roelands J, van der Ploeg M, Ijsselsteijn ME, Dang H, Boonstra JJ, Hardwick JCH, Hawinkels LJAC, Morreau H, de Miranda NFCC. Transcriptomic and immunophenotypic profiling reveals molecular and immunological hallmarks of colorectal cancer tumourigenesis. Gut 2022:gutjnl-2022-327608. [PMID: 36442992 DOI: 10.1136/gutjnl-2022-327608] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 11/12/2022] [Indexed: 11/29/2022]
Abstract
OBJECTIVE Biological insights into the stepwise development and progression of colorectal cancer (CRC) are imperative to develop tailored approaches for early detection and optimal clinical management of this disease. Here, we aimed to dissect the transcriptional and immunologic alterations that accompany malignant transformation in CRC and to identify clinically relevant biomarkers through spatial profiling of pT1 CRC samples. DESIGN We employed digital spatial profiling (GeoMx) on eight pT1 CRCs to study gene expression in the epithelial and stromal segments across regions of distinct histology, including normal mucosa, low-grade and high-grade dysplasia and cancer. Consecutive histology sections were profiled by imaging mass cytometry to reveal immune contextures. Finally, publicly available single-cell RNA-sequencing data was analysed to determine the cellular origin of relevant transcripts. RESULTS Comparison of gene expression between regions within pT1 CRC samples identified differentially expressed genes in the epithelium (n=1394 genes) and the stromal segments (n=1145 genes) across distinct histologies. Pathway analysis identified an early onset of inflammatory responses during malignant transformation, typified by upregulation of gene signatures such as innate immune sensing. We detected increased infiltration of myeloid cells and a shift in macrophage populations from pro-inflammatory HLA-DR+CD204- macrophages to HLA-DR-CD204+ immune-suppressive subsets from normal tissue through dysplasia to cancer, accompanied by the upregulation of the CD47/SIRPα 'don't eat me signal'. CONCLUSION Spatial profiling revealed the molecular and immunological landscape of CRC tumourigenesis at early disease stage. We identified biomarkers with strong association with disease progression as well as targetable immune processes that are exploitable in a clinical setting.
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Affiliation(s)
- Jessica Roelands
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Manon van der Ploeg
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Hao Dang
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Jurjen J Boonstra
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | - James C H Hardwick
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Lukas J A C Hawinkels
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Hans Morreau
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
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20
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Abdulrahman Z, Hendriks N, J Kruse A, Somarakis A, J M van de Sande A, J van Beekhuizen H, M J Piek J, de Miranda NFCC, Kooreman LFS, F M Slangen B, van der Burg SH, de Vos van Steenwijk PJ, van Esch EMG. Immune-based biomarker accurately predicts response to imiquimod immunotherapy in cervical high-grade squamous intraepithelial lesions. J Immunother Cancer 2022; 10:jitc-2022-005288. [PMID: 36323430 PMCID: PMC9639137 DOI: 10.1136/jitc-2022-005288] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/13/2022] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND The complete response rate of cervical high-grade squamous intraepithelial lesion (cHSIL) patients to imiquimod immunotherapy is approximately 60%. Consequently, many patients are exposed to unnecessary adverse effects of imiquimod. On the other hand, conventional surgical large loop excision therapy is associated with increased risk of premature births in subsequent pregnancies. An in-depth analysis of the cHSIL immune microenvironment was performed in order to identify and develop a predictive biomarker for response to imiquimod, to maximize therapy efficacy and to avoid adverse effects in patients unlikely to respond. METHODS Biopsies of 35 cHSIL patients, before and 10 weeks on imiquimod treatment, were analyzed by two multispectral seven-color immunofluorescence panels for T cell and myeloid cell composition in relation to treatment response. Based on these results a simplified immunohistochemical detection protocol was developed. Samples were scanned with the Vectra multispectral imaging system and cells were automatically identified using machine learning. RESULTS The immune microenvironment of complete responders (CR) is characterized by a strong and coordinated infiltration by T helper cells (activated PD1+/type 1 Tbet+), M1-like macrophages (CD68+CD163-) and dendritic cells (CD11c+) prior to imiquimod. The lesions of non-responders (NRs) displayed a high infiltration by CD3+FOXP3+ regulatory T cells. At 10 weeks on imiquimod, a strong influx of intraepithelial and stromal CD4+ T cells was observed in CR but not NR patients. A steep decrease in macrophages occurred both in CR and NR patients, leveling the pre-existing differences in myeloid cell composition between the two groups. Based on the pre-existing immune composition differences, the sum of intraepithelial CD4 T cell, macrophage and dendritic cell counts was used to develop a quantitative simplified one color immunohistochemical biomarker, the CHSIL immune biomarker for imiquimod (CIBI), which can be automatically and unbiasedly quantified and has an excellent predictive capacity (receiver operating characteristic area under the curve 0.95, p<0.0001). CONCLUSION The capacity of cHSIL patients to respond to imiquimod is associated with a pre-existing coordinated local immune process, fostering an imiquimod-mediated increase in local T cell infiltration. The CIBI immunohistochemical biomarker has strong potential to select cHSIL patients with a high likelihood to experience a complete response to imiquimod immunotherapy.
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Affiliation(s)
- Ziena Abdulrahman
- Leiden University Medical Center, Leiden, The Netherlands,Oncode Institute, Utrecht, The Netherlands
| | - Natasja Hendriks
- Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Arnold J Kruse
- Maastricht University Medical Centre+, Maastricht, The Netherlands
| | | | | | | | | | | | | | | | - Sjoerd H van der Burg
- Leiden University Medical Center, Leiden, The Netherlands,Oncode Institute, Utrecht, The Netherlands
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21
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Kumar S, Schoonderwoerd MJA, Kroonen JS, de Graaf IJ, Sluijter M, Ruano D, González-Prieto R, Verlaan-de Vries M, Rip J, Arens R, de Miranda NFCC, Hawinkels LJAC, van Hall T, Vertegaal ACO. Targeting pancreatic cancer by TAK-981: a SUMOylation inhibitor that activates the immune system and blocks cancer cell cycle progression in a preclinical model. Gut 2022; 71:2266-2283. [PMID: 35074907 PMCID: PMC9554032 DOI: 10.1136/gutjnl-2021-324834] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 12/29/2021] [Indexed: 12/27/2022]
Abstract
OBJECTIVE Pancreatic ductal adenocarcinoma (PDAC) has the characteristics of high-density desmoplastic stroma, a distinctive immunosuppressive microenvironment and is profoundly resistant to all forms of chemotherapy and immunotherapy, leading to a 5-year survival rate of 9%. Our study aims to add novel small molecule therapeutics for the treatment of PDAC. DESIGN We have studied whether TAK-981, a novel highly selective and potent small molecule inhibitor of the small ubiquitin like modifier (SUMO) activating enzyme E1 could be used to treat a preclinical syngeneic PDAC mouse model and we have studied the mode of action of TAK-981. RESULTS We found that SUMOylation, a reversible post-translational modification required for cell cycle progression, is increased in PDAC patient samples compared with normal pancreatic tissue. TAK-981 decreased SUMOylation in PDAC cells at the nanomolar range, thereby causing a G2/M cell cycle arrest, mitotic failure and chromosomal segregation defects. TAK-981 efficiently limited tumour burden in the KPC3 syngeneic mouse model without evidence of systemic toxicity. In vivo treatment with TAK-981 enhanced the proportions of activated CD8 T cells and natural killer (NK) cells but transiently decreased B cell numbers in tumour, peripheral blood, spleen and lymph nodes. Single cell RNA sequencing revealed activation of the interferon response on TAK-981 treatment in lymphocytes including T, B and NK cells. TAK-981 treatment of CD8 T cells ex vivo induced activation of STAT1 and interferon target genes. CONCLUSION Our findings indicate that pharmacological inhibition of the SUMO pathway represents a potential strategy to target PDAC via a dual mechanism: inhibiting cancer cell cycle progression and activating anti-tumour immunity by inducing interferon signalling.
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Affiliation(s)
- Sumit Kumar
- Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Jessie S Kroonen
- Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ilona J de Graaf
- Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Marjolein Sluijter
- Department of Medical Oncology, Leiden University Medical Center, Leiden, The Netherlands
| | - Dina Ruano
- Pathology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Román González-Prieto
- Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Jasper Rip
- Immunology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ramon Arens
- Immunology, Leiden University Medical Center, Leiden, The Netherlands
| | | | | | - Thorbald van Hall
- Department of Medical Oncology, Leiden University Medical Center, Leiden, The Netherlands
| | - Alfred C O Vertegaal
- Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
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22
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Brouwer TP, van der Zanden SY, van der Ploeg M, van Eendenburg JDH, Bonsing BA, de Miranda NFCC, Neefjes JJ, Vahrmeijer AL. The identification of the anthracycline aclarubicin as an effective cytotoxic agent for pancreatic cancer. Anticancer Drugs 2022; 33:614-621. [PMID: 35324522 PMCID: PMC9281511 DOI: 10.1097/cad.0000000000001283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 01/28/2022] [Indexed: 12/02/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal types of cancer, mainly due to its delayed diagnosis and lack of effective therapeutic options. Therefore, it is imperative to find novel treatment options for PDAC. Here, we tested a series of conventional chemotherapeutics together with anthracycline compounds as single agents or in combination, determining their effectivity against established commercial and patient-derived, low-passage PDAC cell lines. Proliferation and colony formation assays were performed to determine the anticancer activity of anthracyclines; aclarubicin and doxorubicin, on commercial and patient-derived, low-passage PDAC cell lines. In addition, the effect of standard-of-care drugs gemcitabine and individual components of FOLFIRINOX were also investigated. To evaluate which mechanisms of cell death were involved in drug response, cleavage of poly(ADP-ribose)polymerase was evaluated by western blot. Aclarubicin showed superior antitumor activity compared to other anthracyclines and standard of care drugs (gemcitabine and individual components of FOLFIRINOX) in a patient-derived, low-passage PDAC cell line and in commercial cell lines. Importantly, the combination of gemcitabine and aclarubicin showed a synergistic effect at a dose range where the single agents by themselves were ineffective. In parallel, evaluation of the antitumor activity of aclarubicin demonstrated an apoptotic effect in all PDAC cell lines. Aclarubicin is cytotoxic for commercial and patient-derived low-passage PDAC cell lines, at doses lower than peak serum concentrations for patient treatment. Our findings support a (re)consideration of aclarubicin as a backbone of new combination regimens for pancreatic cancer patients.
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Affiliation(s)
| | | | | | | | | | | | - Jacques J Neefjes
- Cell and Chemical Biology, Leiden University Medical Center, Leiden
- Oncode Institute, The Netherlands
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23
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Brouwer TP, de Vries NL, Abdelaal T, Krog RT, Li Z, Ruano D, Fariña A, Lelieveldt BPF, Morreau H, Bonsing BA, Vahrmeijer AL, Koning F, de Miranda NFCC. Local and systemic immune profiles of human pancreatic ductal adenocarcinoma revealed by single-cell mass cytometry. J Immunother Cancer 2022; 10:e004638. [PMID: 35793870 PMCID: PMC9260840 DOI: 10.1136/jitc-2022-004638] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/09/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal malignancy in need of effective (immuno)therapeutic treatment strategies. For the optimal application and development of cancer immunotherapies, a comprehensive understanding of local and systemic immune profiles in patients with PDAC is required. Here, our goal was to decipher the interplay between local and systemic immune profiles in treatment-naïve patients with PDAC. METHODS The immune composition of PDAC, matched non-malignant pancreatic tissue, regional lymph nodes, spleen, portal vein blood, and peripheral blood samples (collected before and after surgery) from 11 patients with PDAC was assessed by measuring 41 immune cell markers by single-cell mass cytometry. Furthermore, the activation potential of tumor-infiltrating lymphocytes as determined by their ability to produce cytokines was investigated by flow cytometry. In addition, the spatial localization of tumor-infiltrating innate lymphocytes in the tumor microenvironment was confirmed by multispectral immunofluorescence. RESULTS We found that CD103+CD8+ T cells with cytotoxic potential are infrequent in the PDAC immune microenvironment and lack the expression of activation markers and checkpoint blockade molecule programmed cell death protein-1 (PD-1). In contrast, PDAC tissues showed a remarkable increased relative frequency of B cells and regulatory T cells as compared with non-malignant pancreatic tissues. Besides, a previously unappreciated innate lymphocyte cell (ILC) population (CD127-CD103+CD39+CD45RO+ ILC1-like) was discovered in PDAC tissues. Strikingly, the increased relative frequency of B cells and regulatory T cells in pancreatic cancer samples was reflected in matched portal vein blood samples but not in peripheral blood, suggesting a regional enrichment of immune cells that infiltrate the PDAC microenvironment. After surgery, decreased frequencies of myeloid dendritic cells were found in peripheral blood. CONCLUSIONS Our work demonstrates an immunosuppressive landscape in PDAC tissues, generally deprived of cytotoxic T cells and enriched in regulatory T cells and B cells. The antitumor potential of ILC1-like cells in PDAC may be exploited in a therapeutic setting. Importantly, immune profiles detected in blood isolated from the portal vein reflected the immune cell composition of the PDAC microenvironment, suggesting that this anatomical location could be a source of tumor-associated immune cell subsets.
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Affiliation(s)
- Thomas P Brouwer
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Surgery, Leiden University Medical Center, Leiden, The Netherlands
| | - Natasja L de Vries
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Immunology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Tamim Abdelaal
- Pattern recognition and Bioinformatics, Delft University of Technology, Delft, The Netherlands
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands
| | - Ricki T Krog
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Zheng Li
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Dina Ruano
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Arantza Fariña
- Department of Pathology, Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Boudewijn P F Lelieveldt
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands
| | - Hans Morreau
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Bert A Bonsing
- Department of Surgery, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Frits Koning
- Department of Immunology, Leiden University Medical Centre, Leiden, The Netherlands
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24
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Rademaker E, Bastiaannet E, Oosting J, Dekker-Ensink NG, Kuppen PJK, de Miranda NFCC, Liefers GJ. Revising the Role of Integrin Subunit β4 Expression in Colon Cancer Progression and Survival. J Gastrointest Cancer 2022; 54:147-154. [PMID: 35112314 PMCID: PMC10182939 DOI: 10.1007/s12029-021-00787-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2021] [Indexed: 11/29/2022]
Abstract
PURPOSE Integrin subunit β4 (β4) has been proposed to play an important role in colon cancer progression through its involvement in hemidesmosome disassembly processes and tumor cell migration. However, the association between β4 expression and clinicopathological outcomes in colon cancer remains unclear. METHODS Expression of β4 was assessed by immunohistochemistry in a large cohort of 651 colon cancer patients, the largest colon cancer cohort so far. Chi-squared tests were used to study the association between β4 expression and clinicopathological features. Overall and disease-free survival were assessed by Cox proportional hazard models. RESULTS Loss of β4 expression was associated with local tumor invasion. Only 17.9% of the pT1 tumors displayed weak β4 expression level versus 28.1% of pT4 tumors, and 25.0% of the pT1 tumors had a high expression level versus 8.6% of the pT4 tumors (p = 0.012). No association between β4 expression and overall (p = 0.845) or disease-free survival (p = 0.767) was encountered, which disputes the role of β4 as a biomarker of malignant behavior in colon cancer. CONCLUSION Contradictory reports have suggested opposite roles for β4 expression in (colon) cancer progression. In the present large cohort of colon cancer patients, we found that β4 expression was not associated with worse clinical prognosis, but decreased with advanced pathological tumor stage. Future studies should establish whether loss of β4 expression promotes invasive characteristics of colon cancer cells.
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Affiliation(s)
- Eva Rademaker
- Department of Surgical Oncology, Leiden University Medical Center, P.O. Box 9600, Leiden, 2300 RC, The Netherlands. .,Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands.
| | - Esther Bastiaannet
- Department of Surgical Oncology, Leiden University Medical Center, P.O. Box 9600, Leiden, 2300 RC, The Netherlands
| | - Jan Oosting
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Neeltje G Dekker-Ensink
- Department of Surgical Oncology, Leiden University Medical Center, P.O. Box 9600, Leiden, 2300 RC, The Netherlands
| | - Peter J K Kuppen
- Department of Surgical Oncology, Leiden University Medical Center, P.O. Box 9600, Leiden, 2300 RC, The Netherlands
| | | | - Gerrit J Liefers
- Department of Surgical Oncology, Leiden University Medical Center, P.O. Box 9600, Leiden, 2300 RC, The Netherlands
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25
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Abdulrahman Z, Santegoets SJ, Sturm G, Charoentong P, Ijsselsteijn ME, Somarakis A, Höllt T, Finotello F, Trajanoski Z, van Egmond SL, Mustafa DAM, Welters MJP, de Miranda NFCC, van der Burg SH. Tumor-specific T cells support chemokine-driven spatial organization of intratumoral immune microaggregates needed for long survival. J Immunother Cancer 2022; 10:e004346. [PMID: 35217577 PMCID: PMC8883276 DOI: 10.1136/jitc-2021-004346] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The composition of the tumor immune microenvironment (TIME) associated with good prognosis generally also predicts the success of immunotherapy, and both entail the presence of pre-existing tumor-specific T cells. Here, the blueprint of the TIME associated with such an ongoing tumor-specific T-cell response was dissected in a unique prospective oropharyngeal squamous cell carcinoma (OPSCC) cohort, in which tumor-specific tumor-infiltrating T cells were detected (immune responsiveness (IR+)) or not (lack of immune responsiveness (IR-)). METHODS A comprehensive multimodal, high-dimensional strategy was applied to dissect the TIME of treatment-naive IR+ and IR- OPSCC tissue, including bulk RNA sequencing (NanoString), imaging mass cytometry (Hyperion) for phenotyping and spatial interaction analyses of immune cells, and combined single-cell gene expression profiling and T-cell receptor (TCR) sequencing (single-cell RNA sequencing (scRNAseq)) to characterize the transcriptional states of clonally expanded tumor-infiltrating T cells. RESULTS IR+ patients had an excellent survival during >10 years follow-up. The tumors of IR+ patients expressed higher levels of genes strongly related to interferon gamma signaling, T-cell activation, TCR signaling, and mononuclear cell differentiation, as well as genes involved in several immune signaling pathways, than IR- patients. The top differently overexpressed genes included CXCL12 and LTB, involved in ectopic lymphoid structure development. Moreover, scRNAseq not only revealed that CD4+ T cells were the main producers of LTB but also identified a subset of clonally expanded CD8+ T cells, dominantly present in IR+ tumors, which secreted the T cell and dendritic cell (DC) attracting chemokine CCL4. Indeed, immune cell infiltration in IR+ tumors is stronger, highly coordinated, and has a distinct spatial phenotypical signature characterized by intratumoral microaggregates of CD8+CD103+ and CD4+ T cells with DCs. In contrast, the IR- TIME comprised spatial interactions between lymphocytes and various immunosuppressive myeloid cell populations. The impact of these chemokines on local immunity and clinical outcome was confirmed in an independent The Cancer Genome Atlas OPSCC cohort. CONCLUSION The production of lymphoid cell attracting and organizing chemokines by tumor-specific T cells in IR+ tumors constitutes a positive feedback loop to sustain the formation of the DC-T-cell microaggregates and identifies patients with excellent survival after standard therapy.
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Affiliation(s)
- Ziena Abdulrahman
- Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Saskia J Santegoets
- Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Gregor Sturm
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | - Pornpimol Charoentong
- Medical Oncology and National Center for Tumor diseases, University Hospital Heidelberg, German Cancer Research Center, Heidelberg, Germany
| | | | | | - Thomas Höllt
- Radiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Francesca Finotello
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innsbruck, Austria
| | | | | | - Dana A M Mustafa
- Pathology, Tumor Immuno-Pathology Laboratory, Leiden University Medical Center, Leiden, The Netherlands
| | - Marij J P Welters
- Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Sjoerd H van der Burg
- Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
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Krog RT, de Miranda NFCC, Vahrmeijer AL, Kooreman NG. The Potential of Induced Pluripotent Stem Cells to Advance the Treatment of Pancreatic Ductal Adenocarcinoma. Cancers (Basel) 2021; 13:cancers13225789. [PMID: 34830945 PMCID: PMC8616212 DOI: 10.3390/cancers13225789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/12/2021] [Accepted: 11/13/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Despite improvements in the treatment of several cancer types, the extremely poor prognosis of pancreatic cancer patients has remained unchanged over the last decades. Therefore, new therapeutic regimens for pancreatic cancer are highly needed. In this review, we will discuss the potential of induced pluripotent stem cells (iPSCs) to generate representative pancreatic cancer models that can aid the development of novel diagnostics and therapeutic strategies. Furthermore, the potential of iPSCs as pancreatic cancer vaccines or as a basis for cellular therapies will be discussed. With promising preclinical results and ongoing clinical trials, the potential of iPSCs to further the treatment of pancreatic cancer is being explored and, in turn, will hopefully provide additional therapies to increase the poor survival rates of this patient population. Abstract Advances in the treatment of pancreatic ductal adenocarcinoma (PDAC) using neoadjuvant chemoradiotherapy, chemotherapy, and immunotherapy have had minimal impact on the overall survival of patients. A general lack of immunogenic features and a complex tumor microenvironment (TME) are likely culprits for therapy refractoriness in PDAC. Induced pluripotent stem cells (iPSCs) should be explored as a means to advance the treatment options for PDAC, by providing representative in vitro models of pancreatic cancer development. In addition, iPSCs could be used for tailor-made cellular immunotherapies or as a source of tumor-associated antigens in the context of vaccination.
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Affiliation(s)
- Ricki T. Krog
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (R.T.K.); (A.L.V.)
- Department of Pathology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands;
| | | | - Alexander L. Vahrmeijer
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (R.T.K.); (A.L.V.)
| | - Nigel G. Kooreman
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (R.T.K.); (A.L.V.)
- Correspondence:
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27
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van Oost S, Meijer DM, Kuijjer ML, Bovée JVMG, de Miranda NFCC. Linking Immunity with Genomics in Sarcomas: Is Genomic Complexity an Immunogenic Trigger? Biomedicines 2021; 9:1048. [PMID: 34440251 PMCID: PMC8391750 DOI: 10.3390/biomedicines9081048] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/14/2021] [Accepted: 08/16/2021] [Indexed: 11/16/2022] Open
Abstract
Sarcomas comprise a collection of highly heterogeneous malignancies that can be grossly grouped in the categories of sarcomas with simple or complex genomes. Since the outcome for most sarcoma patients has barely improved in the last decades, there is an urgent need for improved therapies. Immunotherapy, and especially T cell checkpoint blockade, has recently been a game-changer in cancer therapy as it produced significant and durable treatment responses in several cancer types. Currently, only a small fraction of sarcoma patients benefit from immunotherapy, supposedly due to a general lack of somatically mutated antigens (neoantigens) and spontaneous T cell immunity in most cancers. However, genomic events resulting from chromosomal instability are frequent in sarcomas with complex genomes and could drive immunity in those tumors. Improving our understanding of the mechanisms that shape the immune landscape of sarcomas will be crucial to overcoming the current challenges of sarcoma immunotherapy. This review focuses on what is currently known about the tumor microenvironment in sarcomas and how this relates to their genomic features. Moreover, we discuss novel therapeutic strategies that leverage the tumor microenvironment to increase the clinical efficacy of immunotherapy, and which could provide new avenues for the treatment of sarcomas.
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Affiliation(s)
- Siddh van Oost
- Department of Pathology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (S.v.O.); (D.M.M.); (M.L.K.); (N.F.C.C.d.M.)
| | - Debora M. Meijer
- Department of Pathology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (S.v.O.); (D.M.M.); (M.L.K.); (N.F.C.C.d.M.)
| | - Marieke L. Kuijjer
- Department of Pathology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (S.v.O.); (D.M.M.); (M.L.K.); (N.F.C.C.d.M.)
- Centre for Molecular Medicine Norway (NCMM), Faculty of Medicine, University of Oslo, 0318 Oslo, Norway
| | - Judith V. M. G. Bovée
- Department of Pathology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (S.v.O.); (D.M.M.); (M.L.K.); (N.F.C.C.d.M.)
| | - Noel F. C. C. de Miranda
- Department of Pathology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (S.v.O.); (D.M.M.); (M.L.K.); (N.F.C.C.d.M.)
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28
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Ijsselsteijn ME, Somarakis A, Lelieveldt BPF, Höllt T, de Miranda NFCC. Semi-automated background removal limits data loss and normalizes imaging mass cytometry data. Cytometry A 2021; 99:1187-1197. [PMID: 34196108 PMCID: PMC9542015 DOI: 10.1002/cyto.a.24480] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 06/14/2021] [Accepted: 06/25/2021] [Indexed: 12/16/2022]
Abstract
Imaging mass cytometry (IMC) allows the detection of multiple antigens (approximately 40 markers) combined with spatial information, making it a unique tool for the evaluation of complex biological systems. Due to its widespread availability and retained tissue morphology, formalin‐fixed, paraffin‐embedded (FFPE) tissues are often a material of choice for IMC studies. However, antibody performance and signal to noise ratios can differ considerably between FFPE tissues as a consequence of variations in tissue processing, including fixation. In contrast to batch effects caused by differences in the immunodetection procedure, variations in tissue processing are difficult to control. We investigated the effect of immunodetection‐related signal intensity fluctuations on IMC analysis and phenotype identification, in a cohort of 12 colorectal cancer tissues. Furthermore, we explored different normalization strategies and propose a workflow to normalize IMC data by semi‐automated background removal, using publicly available tools. This workflow can be directly applied to previously acquired datasets and considerably improves the quality of IMC data, thereby supporting the analysis and comparison of multiple samples.
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Affiliation(s)
| | - Antonios Somarakis
- Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Thomas Höllt
- Computer Graphics and Visualization, EEMCS, TU Delft, Delft, The Netherlands.,Leiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands
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29
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Lam SW, Kostine M, de Miranda NFCC, Schöffski P, Lee CJ, Morreau H, Bovée JVMG. Mismatch repair deficiency is rare in bone and soft tissue tumors. Histopathology 2021; 79:509-520. [PMID: 33825202 PMCID: PMC8518745 DOI: 10.1111/his.14377] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 03/25/2021] [Accepted: 03/30/2021] [Indexed: 12/19/2022]
Abstract
Introduction There has been an increased demand for mismatch repair (MMR) status testing in sarcoma patients after the success of immune checkpoint inhibition (ICI) in MMR deficient tumors. However, data on MMR deficiency in bone and soft tissue tumors is sparse, rendering it unclear if routine screening should be applied. Hence, we aimed to study the frequency of MMR deficiency in bone and soft tissue tumors after we were prompted by two (potential) Lynch syndrome patients developing sarcomas. Methods Immunohistochemical expression of MLH1, PMS2, MSH2 and MSH6 was assessed on tissue micro arrays (TMAs), and included 353 bone and 539 soft tissue tumors. Molecular data was either retrieved from reports or microsatellite instability (MSI) analysis was performed. In MLH1 negative cases, additional MLH1 promoter hypermethylation analysis followed. Furthermore, a systematic literature review on MMR deficiency in bone and soft tissue tumors was conducted. Results Eight MMR deficient tumors were identified (1%), which included four leiomyosarcoma, two rhabdomyosarcoma, one malignant peripheral nerve sheath tumor and one radiation‐associated sarcoma. Three patients were suspected for Lynch syndrome. Literature review revealed 30 MMR deficient sarcomas, of which 33% were undifferentiated/unclassifiable sarcomas. 57% of the patients were genetically predisposed. Conclusion MMR deficiency is rare in bone and soft tissue tumors. Screening focusing on tumors with myogenic differentiation, undifferentiated/unclassifiable sarcomas and in patients with a genetic predisposition / co‐occurrence of other malignancies can be helpful in identifying patients potentially eligible for ICI.
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Affiliation(s)
- Suk Wai Lam
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Marie Kostine
- Department of Rheumatology, Centre Hospitalier Universitaire de Bordeaux Groupe hospitalier Pellegrin, Bordeaux, France
| | | | - Patrick Schöffski
- Department of General Medical Oncology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium.,Department of Oncology, KU Leuven, Laboratory of Experimental Oncology, Leuven, Belgium
| | - Che-Jui Lee
- Department of General Medical Oncology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium.,Department of Oncology, KU Leuven, Laboratory of Experimental Oncology, Leuven, Belgium
| | - Hans Morreau
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Judith V M G Bovée
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
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30
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Abstract
BACKGROUND Checkpoint blockade immunotherapy has had a significant impact on the survival of a subset of patients with advanced cancers. It has been particularly effective in immunogenic cancer types that present large numbers of somatic mutations in their genomes. To date, all conventional immunotherapies have failed to produce significant clinical benefits for patients diagnosed with pancreatic cancer, probably due to its poor immunogenic properties, including low numbers of neoantigens and highly immune-suppressive microenvironments. CONCLUSIONS Herein, we discuss advances that have recently been made in cancer immunotherapy and the potential of this field to deliver effective treatment options for pancreatic cancer patients. Preclinical investigations, combining different types of therapies, highlight possibilities to enhance anti-tumor immunity and to generate meaningful clinical responses in pancreatic cancer patients. Results from completed and ongoing (pre)clinical trials are discussed.
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Affiliation(s)
- Thomas P Brouwer
- Department of Surgery, Leiden University Medical Center, Leiden, The Netherlands.,Department of Pathology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands, PO Box 9600, 2300 RC
| | | | - Noel F C C de Miranda
- Department of Pathology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands, PO Box 9600, 2300 RC.
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31
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Kenkhuis B, Somarakis A, de Haan L, Dzyubachyk O, IJsselsteijn ME, de Miranda NFCC, Lelieveldt BPF, Dijkstra J, van Roon-Mom WMC, Höllt T, van der Weerd L. Iron loading is a prominent feature of activated microglia in Alzheimer's disease patients. Acta Neuropathol Commun 2021; 9:27. [PMID: 33597025 PMCID: PMC7887813 DOI: 10.1186/s40478-021-01126-5] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 01/30/2021] [Indexed: 12/19/2022] Open
Abstract
Brain iron accumulation has been found to accelerate disease progression in amyloid-β(Aβ) positive Alzheimer patients, though the mechanism is still unknown. Microglia have been identified as key players in the disease pathogenesis, and are highly reactive cells responding to aberrations such as increased iron levels. Therefore, using histological methods, multispectral immunofluorescence and an automated in-house developed microglia segmentation and analysis pipeline, we studied the occurrence of iron-accumulating microglia and the effect on its activation state in human Alzheimer brains. We identified a subset of microglia with increased expression of the iron storage protein ferritin light chain (FTL), together with increased Iba1 expression, decreased TMEM119 and P2RY12 expression. This activated microglia subset represented iron-accumulating microglia and appeared morphologically dystrophic. Multispectral immunofluorescence allowed for spatial analysis of FTL+Iba1+-microglia, which were found to be the predominant Aβ-plaque infiltrating microglia. Finally, an increase of FTL+Iba1+-microglia was seen in patients with high Aβ load and Tau load. These findings suggest iron to be taken up by microglia and to influence the functional phenotype of these cells, especially in conjunction with Aβ.
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Affiliation(s)
- Boyd Kenkhuis
- Department of Human Genetics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands.
- Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands.
| | - Antonios Somarakis
- Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Lorraine de Haan
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Oleh Dzyubachyk
- Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | | | | | | | - Jouke Dijkstra
- Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Willeke M C van Roon-Mom
- Department of Human Genetics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Thomas Höllt
- Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Intelligent Systems, Delft University of Technology, Delft, The Netherlands
| | - Louise van der Weerd
- Department of Human Genetics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
- Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
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32
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Somarakis A, Ijsselsteijn ME, Luk SJ, Kenkhuis B, de Miranda NFCC, Lelieveldt BPF, Hollt T. Visual cohort comparison for spatial single-cell omics-data. IEEE Trans Vis Comput Graph 2021; 27:733-743. [PMID: 33112747 DOI: 10.1109/tvcg.2020.3030336] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Spatially-resolved omics-data enable researchers to precisely distinguish cell types in tissue and explore their spatial interactions, enabling deep understanding of tissue functionality. To understand what causes or deteriorates a disease and identify related biomarkers, clinical researchers regularly perform large-scale cohort studies, requiring the comparison of such data at cellular level. In such studies, with little a-priori knowledge of what to expect in the data, explorative data analysis is a necessity. Here, we present an interactive visual analysis workflow for the comparison of cohorts of spatially-resolved omics-data. Our workflow allows the comparative analysis of two cohorts based on multiple levels-of-detail, from simple abundance of contained cell types over complex co-localization patterns to individual comparison of complete tissue images. As a result, the workflow enables the identification of cohort-differentiating features, as well as outlier samples at any stage of the workflow. During the development of the workflow, we continuously consulted with domain experts. To show the effectiveness of the workflow, we conducted multiple case studies with domain experts from different application areas and with different data modalities.
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33
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Rocha S, Basto AP, Ijsselsteijn ME, Teles SP, Azevedo MM, Gonçalves G, Gullo I, Almeida GM, Maqueda JJ, Oliveira MI, Carneiro F, Barata JT, Graça L, de Miranda NFCC, Carvalho J, Oliveira C. Immunophenotype of Gastric Tumors Unveils a Pleiotropic Role of Regulatory T Cells in Tumor Development. Cancers (Basel) 2021; 13:cancers13030421. [PMID: 33498681 PMCID: PMC7865950 DOI: 10.3390/cancers13030421] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 01/26/2023] Open
Abstract
Gastric cancer (GC) patients display increased regulatory T cell (Tregs) numbers in peripheral blood and among tumor-infiltrating lymphocytes. Nevertheless, the role of Tregs in GC progression remains controversial. Here, we sought to explore the impact of Tregs in GCs with distinct histology, and whether Tregs can directly influence tumor cell behavior and GC development. We performed a comprehensive immunophenotyping of 82 human GC cases, through an integrated analysis of multispectral immunofluorescence detection of T cells markers and patient clinicopathological data. Moreover, we developed 3D in vitro co-cultures with Tregs and tumor cells that were followed by high-throughput and light-sheet imaging, and their biological features studied with conventional/imaging flow cytometry and Western blotting. We showed that Tregs located at the tumor nest were frequent in intestinal-type GCs but did not associate with increased levels of effector T cells. Our in vitro results suggested that Tregs preferentially infiltrated intestinal-type GC spheroids, induced the expression of IL2Rα and activation of MAPK signaling pathway in tumor cells, and promoted spheroid growth. Accumulation of Tregs in intestinal-type GCs was increased at early stages of the stomach wall invasion and in the absence of vascular and perineural invasion. In this study, we proposed a non-immunosuppressive mechanism through which Tregs might directly modulate GC cells and thereby promote tumor growth. Our findings hold insightful implications for therapeutic strategies targeting intestinal-type GCs and other tumors with similar immune context.
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Affiliation(s)
- Sara Rocha
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (S.R.); (S.P.T.); (M.M.A.); (I.G.); (G.M.A.); (J.J.M.); (F.C.); (J.C.)
- Ipatimup—Institute of Molecular Pathology and Immunology of University of Porto, 4200-135 Porto, Portugal
- Doctoral Program on Cellular and Molecular Biotechnology Applied to Health Sciences, ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
| | - Afonso P Basto
- iMM—Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, 1649-028 Lisbon, Portugal; (A.P.B.); (J.T.B.); (L.G.)
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| | - Marieke E Ijsselsteijn
- Department of Pathology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (M.E.I.); (N.F.C.C.d.M.)
| | - Sara P Teles
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (S.R.); (S.P.T.); (M.M.A.); (I.G.); (G.M.A.); (J.J.M.); (F.C.); (J.C.)
- Ipatimup—Institute of Molecular Pathology and Immunology of University of Porto, 4200-135 Porto, Portugal
| | - Maria M Azevedo
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (S.R.); (S.P.T.); (M.M.A.); (I.G.); (G.M.A.); (J.J.M.); (F.C.); (J.C.)
| | - Gilza Gonçalves
- Department of Pathology, Faculty of Medicine of the University of Porto (FMUP), 4200-319 Porto, Portugal;
| | - Irene Gullo
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (S.R.); (S.P.T.); (M.M.A.); (I.G.); (G.M.A.); (J.J.M.); (F.C.); (J.C.)
- Ipatimup—Institute of Molecular Pathology and Immunology of University of Porto, 4200-135 Porto, Portugal
- Department of Pathology, Faculty of Medicine of the University of Porto (FMUP), 4200-319 Porto, Portugal;
- Department of Pathology, Centro Hospitalar Universitário de São João, 4200-319 Porto, Portugal
| | - Gabriela M Almeida
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (S.R.); (S.P.T.); (M.M.A.); (I.G.); (G.M.A.); (J.J.M.); (F.C.); (J.C.)
- Ipatimup—Institute of Molecular Pathology and Immunology of University of Porto, 4200-135 Porto, Portugal
- Department of Pathology, Faculty of Medicine of the University of Porto (FMUP), 4200-319 Porto, Portugal;
| | - Joaquín J Maqueda
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (S.R.); (S.P.T.); (M.M.A.); (I.G.); (G.M.A.); (J.J.M.); (F.C.); (J.C.)
- Ipatimup—Institute of Molecular Pathology and Immunology of University of Porto, 4200-135 Porto, Portugal
| | - Marta I Oliveira
- International Iberian Nanotechnology Laboratory, 4715-330 Braga, Portugal;
| | - Fátima Carneiro
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (S.R.); (S.P.T.); (M.M.A.); (I.G.); (G.M.A.); (J.J.M.); (F.C.); (J.C.)
- Ipatimup—Institute of Molecular Pathology and Immunology of University of Porto, 4200-135 Porto, Portugal
- Department of Pathology, Faculty of Medicine of the University of Porto (FMUP), 4200-319 Porto, Portugal;
- Department of Pathology, Centro Hospitalar Universitário de São João, 4200-319 Porto, Portugal
| | - João T Barata
- iMM—Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, 1649-028 Lisbon, Portugal; (A.P.B.); (J.T.B.); (L.G.)
| | - Luís Graça
- iMM—Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, 1649-028 Lisbon, Portugal; (A.P.B.); (J.T.B.); (L.G.)
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| | - Noel F C C de Miranda
- Department of Pathology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (M.E.I.); (N.F.C.C.d.M.)
| | - Joana Carvalho
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (S.R.); (S.P.T.); (M.M.A.); (I.G.); (G.M.A.); (J.J.M.); (F.C.); (J.C.)
- Ipatimup—Institute of Molecular Pathology and Immunology of University of Porto, 4200-135 Porto, Portugal
| | - Carla Oliveira
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (S.R.); (S.P.T.); (M.M.A.); (I.G.); (G.M.A.); (J.J.M.); (F.C.); (J.C.)
- Ipatimup—Institute of Molecular Pathology and Immunology of University of Porto, 4200-135 Porto, Portugal
- Department of Pathology, Faculty of Medicine of the University of Porto (FMUP), 4200-319 Porto, Portugal;
- Correspondence: ; Tel.: +351-225-570-785
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Beyranvand Nejad E, Labrie C, Abdulrahman Z, van Elsas MJ, Rademaker E, Kleinovink JW, van der Sluis TC, van Duikeren S, Teunisse AFAS, Jochemsen AG, Oosting J, de Miranda NFCC, Van Hall T, Arens R, van der Burg SH. Lack of myeloid cell infiltration as an acquired resistance strategy to immunotherapy. J Immunother Cancer 2020; 8:jitc-2020-001326. [PMID: 32873723 PMCID: PMC7467529 DOI: 10.1136/jitc-2020-001326] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Immunotherapy of cancer is successful but tumor regression often is incomplete and followed by escape. Understanding the mechanisms underlying this acquired resistance will aid the development of more effective treatments. METHODS We exploited a mouse model where tumor-specific therapeutic vaccination results in tumor regression, followed by local recurrence and resistance. In depth studies on systemic, local and tumor intrinsic changes were performed with flow and mass cytometry, immunohistochemistry, transcriptomics and several perturbation studies with inhibitors or agonistic antibodies in mice. Main findings were recapitulated in vaccinated patients. RESULTS Full tumor regression and cure of tumor-bearing mice is dependent on the magnitude of the vaccine-induced T-cell response. Recurrence of tumors did not involve classical immune escape mechanisms, such as antigen-presentation alterations, immune checkpoint expression, resistance to killing or local immune suppression. However, the recurrent tumors displayed a changed transcriptome with alterations in p53, tumor necrosis factor-α and transforming growth factor-β signaling pathways and they became immunologically cold. Remarkably, ex vivo cell-sorted recurrent tumors, directly reinjected in naïve hosts retained their resistance to vaccination despite a strong infiltration with tumor-specific CD8+ T cells, similar to that of vaccine-responsive tumors. The influx of inflammatory mature myeloid effector cells in the resistant tumors, however, was impaired and this turned out to be the underlying mechanisms as restoration of inflammatory myeloid cell infiltration reinstated the sensitivity of these refractory tumors to vaccination. Notably, impaired myeloid cell infiltration after vaccination was also associated with vaccine resistance in patients. CONCLUSION An immunotherapy-induced disability of tumor cells to attract innate myeloid effector cells formed a major mechanism underlying immune escape and acquired resistance. These data not only stresses the importance of myeloid effector cells during immunotherapy but also demands for new studies to harness their tumoricidal activities.
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Affiliation(s)
- Elham Beyranvand Nejad
- Oncode institute, Medical Oncology, Leiden University Medical Center, Leiden, The Netherlands
| | - Camilla Labrie
- Oncode institute, Medical Oncology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ziena Abdulrahman
- Oncode institute, Medical Oncology, Leiden University Medical Center, Leiden, The Netherlands
| | - Marit J van Elsas
- Oncode institute, Medical Oncology, Leiden University Medical Center, Leiden, The Netherlands
| | - Eva Rademaker
- Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Jan Willem Kleinovink
- Oncode institute, Medical Oncology, Leiden University Medical Center, Leiden, The Netherlands
| | - Tetje C van der Sluis
- Immunohematology and Bloodtransfusion, Leiden Universitair Medisch Centrum, Leiden, The Netherlands
| | - Suzanne van Duikeren
- Immunohematology and Bloodtransfusion, Leiden Universitair Medisch Centrum, Leiden, The Netherlands
| | - Amina F A S Teunisse
- Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Aart G Jochemsen
- Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Jan Oosting
- Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Thorbald Van Hall
- Oncode institute, Medical Oncology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ramon Arens
- Immunohematology and Bloodtransfusion, Leiden Universitair Medisch Centrum, Leiden, The Netherlands
| | - Sjoerd H van der Burg
- Oncode institute, Medical Oncology, Leiden University Medical Center, Leiden, The Netherlands
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35
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de Vries NL, Mahfouz A, Koning F, de Miranda NFCC. Unraveling the Complexity of the Cancer Microenvironment With Multidimensional Genomic and Cytometric Technologies. Front Oncol 2020; 10:1254. [PMID: 32793500 PMCID: PMC7390924 DOI: 10.3389/fonc.2020.01254] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/17/2020] [Indexed: 12/26/2022] Open
Abstract
Cancers are characterized by extensive heterogeneity that occurs intratumorally, between lesions, and across patients. To study cancer as a complex biological system, multidimensional analyses of the tumor microenvironment are paramount. Single-cell technologies such as flow cytometry, mass cytometry, or single-cell RNA-sequencing have revolutionized our ability to characterize individual cells in great detail and, with that, shed light on the complexity of cancer microenvironments. However, a key limitation of these single-cell technologies is the lack of information on spatial context and multicellular interactions. Investigating spatial contexts of cells requires the incorporation of tissue-based techniques such as multiparameter immunofluorescence, imaging mass cytometry, or in situ detection of transcripts. In this Review, we describe the rise of multidimensional single-cell technologies and provide an overview of their strengths and weaknesses. In addition, we discuss the integration of transcriptomic, genomic, epigenomic, proteomic, and spatially-resolved data in the context of human cancers. Lastly, we will deliberate on how the integration of multi-omics data will help to shed light on the complex role of cell types present within the human tumor microenvironment, and how such system-wide approaches may pave the way toward more effective therapies for the treatment of cancer.
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Affiliation(s)
- Natasja L. de Vries
- Pathology, Leiden University Medical Center, Leiden, Netherlands
- Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
| | - Ahmed Mahfouz
- Human Genetics, Leiden University Medical Center, Leiden, Netherlands
- Delft Bioinformatics Laboratory, Delft University of Technology, Delft, Netherlands
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, Netherlands
| | - Frits Koning
- Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
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36
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Guo N, van Unen V, Ijsselsteijn ME, Ouboter LF, van der Meulen AE, Chuva de Sousa Lopes SM, de Miranda NFCC, Koning F, Li N. A 34-Marker Panel for Imaging Mass Cytometric Analysis of Human Snap-Frozen Tissue. Front Immunol 2020; 11:1466. [PMID: 32765508 PMCID: PMC7381123 DOI: 10.3389/fimmu.2020.01466] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 06/05/2020] [Indexed: 12/13/2022] Open
Abstract
Imaging mass cytometry (IMC) is able to quantify the expression of dozens of markers at sub-cellular resolution on a single tissue section by combining a novel laser ablation system with mass cytometry. As such, it allows us to gain spatial information and antigen quantification in situ, and can be applied to both snap-frozen and formalin-fixed, paraffin-embedded (FFPE) tissue sections. Herein, we have developed and optimized the immunodetection conditions for a 34-antibody panel for use on human snap-frozen tissue sections. For this, we tested the performance of 80 antibodies. Moreover, we compared tissue drying times, fixation procedures and antibody incubation conditions. We observed that variations in the drying times of tissue sections had little impact on the quality of the images. Fixation with methanol for 5 min at -20°C or 1% paraformaldehyde (PFA) for 5 min at room temperature followed by methanol for 5 min at -20°C were superior to fixation with acetone or PFA only. Finally, we observed that antibody incubation overnight at 4°C yielded more consistent results as compared to staining at room temperature for 5 h. Finally, we used the optimized method for staining of human fetal and adult intestinal tissue samples. We present the tissue architecture and spatial distribution of the stromal cells and immune cells in these samples visualizing blood vessels, the epithelium and lamina propria based on the expression of α-smooth muscle actin (α-SMA), E-Cadherin and Vimentin, while simultaneously revealing the colocalization of T cells, innate lymphoid cells (ILCs), and various myeloid cell subsets in the lamina propria of the human fetal intestine. We expect that this work can aid the scientific community who wish to improve IMC data quality.
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Affiliation(s)
- Nannan Guo
- Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
| | - Vincent van Unen
- Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands.,Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, United States
| | | | - Laura F Ouboter
- Gastroenterology, Leiden University Medical Center, Leiden, Netherlands
| | | | | | | | - Frits Koning
- Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
| | - Na Li
- Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands.,Key Laboratory of Zoonoses Research, Ministry of Education, Institute of Zoonoses, College of Veterinary Medicine, Jilin University, Changchun, China
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37
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Schubert SA, Morreau H, de Miranda NFCC, van Wezel T. The missing heritability of familial colorectal cancer. Mutagenesis 2020; 35:221-231. [PMID: 31605533 PMCID: PMC7352099 DOI: 10.1093/mutage/gez027] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 09/05/2019] [Indexed: 02/06/2023] Open
Abstract
Pinpointing heritability factors is fundamental for the prevention and early detection of cancer. Up to one-quarter of colorectal cancers (CRCs) occur in the context of familial aggregation of this disease, suggesting a strong genetic component. Currently, only less than half of the heritability of CRC can be attributed to hereditary syndromes or common risk loci. Part of the missing heritability of this disease may be explained by the inheritance of elusive high-risk variants, polygenic inheritance, somatic mosaicism, as well as shared environmental factors, among others. A great deal of the missing heritability in CRC is expected to be addressed in the coming years with the increased application of cutting-edge next-generation sequencing technologies, routine multigene panel testing and tumour-focussed germline predisposition screening approaches. On the other hand, it will be important to define the contribution of environmental factors to familial aggregation of CRC incidence. This review provides an overview of the known genetic causes of familial CRC and aims at providing clues that explain the missing heritability of this disease.
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Affiliation(s)
- Stephanie A Schubert
- Department of Pathology, Leiden University Medical Center, Leiden University, Leiden, The Netherlands
| | - Hans Morreau
- Department of Pathology, Leiden University Medical Center, Leiden University, Leiden, The Netherlands
| | - Noel F C C de Miranda
- Department of Pathology, Leiden University Medical Center, Leiden University, Leiden, The Netherlands
| | - Tom van Wezel
- Department of Pathology, Leiden University Medical Center, Leiden University, Leiden, The Netherlands
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38
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Abdulrahman Z, de Miranda NFCC, Hellebrekers BWJ, de Vos van Steenwijk PJ, van Esch EMG, van der Burg SH, van Poelgeest MIE. A pre-existing coordinated inflammatory microenvironment is associated with complete response of vulvar high-grade squamous intraepithelial lesions to different forms of immunotherapy. Int J Cancer 2020; 147:2914-2923. [PMID: 32574376 PMCID: PMC7540004 DOI: 10.1002/ijc.33168] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/12/2020] [Accepted: 06/08/2020] [Indexed: 12/11/2022]
Abstract
Immunotherapy of vulvar high-grade squamous intraepithelial lesion (vHSIL) is investigated as an alternative for surgery, because of high comorbidity and risk of recurrence. Limited evidence exists on the role and composition of the immune microenvironment in current immunotherapeutic approaches for vHSIL. The vHSIL of 29 patients biopsied before treatment with imiquimod were analyzed by two multiplex seven-color immunofluorescence panels to investigate the pre-existing T-cell and myeloid cell composition in relation to treatment response. The samples were scanned with the Vectra multispectral imaging system. Cells were automatically phenotyped and counted with inForm advanced image analysis software. Cell counts and composition were compared to that of vHSIL patients before therapeutic vaccination (n = 29) and to healthy vulva (n = 27). Our data show that the immune microenvironment of complete responders (CR) to imiquimod resembled the coordinated infiltration with type 1 CD4+ and CD8+ T cells and CD14+ inflammatory myeloid cells also found in healthy vulva. However, more CD8+ T cells and FoxP3+ regulatory T cells were present in CR. The lesions of partial responders (PR) lacked such a coordinated response and displayed an impaired influx of CD14+ inflammatory myeloid cells. Importantly, complete responses after imiquimod or therapeutic vaccination showed the same dependency on a pre-existing coordinated type 1 T-cell and CD14+ myeloid cell infiltration. In conclusion, a good clinical outcome after two different forms of immunotherapy for vHSIL is associated with the presence of a primary inflammatory process resulting in the coordinated influx of several types of immune cells which is then amplified.
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Affiliation(s)
- Ziena Abdulrahman
- Department of Gynaecology, Leiden University Medical Center, Leiden, The Netherlands.,Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands.,Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | | | | | | | - Edith M G van Esch
- Department of Gynaecology, Catharina Hospital, Eindhoven, The Netherlands
| | - Sjoerd H van der Burg
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
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39
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Schubert SA, Ruano D, Tiersma Y, Drost M, de Wind N, Nielsen M, van Hest LP, Morreau H, de Miranda NFCC, van Wezel T. Digenic inheritance of MSH6 and MUTYH variants in familial colorectal cancer. Genes Chromosomes Cancer 2020; 59:697-701. [PMID: 32615015 PMCID: PMC7689793 DOI: 10.1002/gcc.22883] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 06/25/2020] [Accepted: 06/29/2020] [Indexed: 12/15/2022] Open
Abstract
We describe a family severely affected by colorectal cancer (CRC) where whole-exome sequencing identified the coinheritance of the germline variants encoding MSH6 p.Thr1100Met and MUTYH p.Tyr179Cys in, at least, three CRC patients diagnosed before 60 years of age. Digenic inheritance of monoallelic MSH6 variants of uncertain significance and MUTYH variants has been suggested to predispose to Lynch syndrome-associated cancers; however, cosegregation with disease in the familial setting has not yet been established. The identification of individuals carrying multiple potential cancer risk variants is expected to rise with the increased application of whole-genome sequencing and large multigene panel testing in clinical genetic counseling of familial cancer patients. Here we demonstrate the coinheritance of monoallelic variants in MSH6 and MUTYH consistent with cosegregation with CRC, further supporting a role for digenic inheritance in cancer predisposition.
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Affiliation(s)
| | - Dina Ruano
- Department of PathologyLeiden University Medical CenterLeidenThe Netherlands
| | - Yvonne Tiersma
- Department of Human GeneticsLeiden University Medical CenterLeidenThe Netherlands
| | - Mark Drost
- Department of Human GeneticsLeiden University Medical CenterLeidenThe Netherlands
| | - Niels de Wind
- Department of Human GeneticsLeiden University Medical CenterLeidenThe Netherlands
| | - Maartje Nielsen
- Department of Clinical GeneticsLeiden University Medical CenterLeidenThe Netherlands
| | - Liselotte P. van Hest
- Department of Clinical GeneticsAmsterdam UMC, Vrije Universiteit AmsterdamAmsterdamThe Netherlands
| | - Hans Morreau
- Department of PathologyLeiden University Medical CenterLeidenThe Netherlands
| | | | - Tom van Wezel
- Department of PathologyLeiden University Medical CenterLeidenThe Netherlands
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40
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de Vries NL, van Unen V, Ijsselsteijn ME, Abdelaal T, van der Breggen R, Farina Sarasqueta A, Mahfouz A, Peeters KCMJ, Höllt T, Lelieveldt BPF, Koning F, de Miranda NFCC. High-dimensional cytometric analysis of colorectal cancer reveals novel mediators of antitumour immunity. Gut 2020; 69:691-703. [PMID: 31270164 PMCID: PMC7063399 DOI: 10.1136/gutjnl-2019-318672] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 05/17/2019] [Accepted: 06/12/2019] [Indexed: 02/07/2023]
Abstract
OBJECTIVE A comprehensive understanding of anticancer immune responses is paramount for the optimal application and development of cancer immunotherapies. We unravelled local and systemic immune profiles in patients with colorectal cancer (CRC) by high-dimensional analysis to provide an unbiased characterisation of the immune contexture of CRC. DESIGN Thirty-six immune cell markers were simultaneously assessed at the single-cell level by mass cytometry in 35 CRC tissues, 26 tumour-associated lymph nodes, 17 colorectal healthy mucosa and 19 peripheral blood samples from 31 patients with CRC. Additionally, functional, transcriptional and spatial analyses of tumour-infiltrating lymphocytes were performed by flow cytometry, single-cell RNA-sequencing and multispectral immunofluorescence. RESULTS We discovered that a previously unappreciated innate lymphocyte population (Lin-CD7+CD127-CD56+CD45RO+) was enriched in CRC tissues and displayed cytotoxic activity. This subset demonstrated a tissue-resident (CD103+CD69+) phenotype and was most abundant in immunogenic mismatch repair (MMR)-deficient CRCs. Their presence in tumours was correlated with the infiltration of tumour-resident cytotoxic, helper and γδ T cells with highly similar activated (HLA-DR+CD38+PD-1+) phenotypes. Remarkably, activated γδ T cells were almost exclusively found in MMR-deficient cancers. Non-activated counterparts of tumour-resident cytotoxic and γδ T cells were present in CRC and healthy mucosa tissues, but not in lymph nodes, with the exception of tumour-positive lymph nodes. CONCLUSION This work provides a blueprint for the understanding of the heterogeneous and intricate immune landscape of CRC, including the identification of previously unappreciated immune cell subsets. The concomitant presence of tumour-resident innate and adaptive immune cell populations suggests a multitargeted exploitation of their antitumour properties in a therapeutic setting.
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Affiliation(s)
- Natasja L de Vries
- Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands,TECObiosciences GmbH, Landshut, Germany
| | - Vincent van Unen
- Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
| | | | - Tamim Abdelaal
- Pattern Recognition and Bioinformatics, Delft University of Technology, Delft, The Netherlands,Leiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands
| | | | | | - Ahmed Mahfouz
- Pattern Recognition and Bioinformatics, Delft University of Technology, Delft, The Netherlands,Leiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Thomas Höllt
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands,Computer Graphics and Visualization, Delft University of Technology, Delft, The Netherlands
| | - Boudewijn P F Lelieveldt
- Pattern Recognition and Bioinformatics, Delft University of Technology, Delft, The Netherlands,LKEB Radiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Frits Koning
- Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
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41
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van den Bulk J, Verdegaal EME, Ruano D, Ijsselsteijn ME, Visser M, van der Breggen R, Duhen T, van der Ploeg M, de Vries NL, Oosting J, Peeters KCMJ, Weinberg AD, Farina-Sarasqueta A, van der Burg SH, de Miranda NFCC. Neoantigen-specific immunity in low mutation burden colorectal cancers of the consensus molecular subtype 4. Genome Med 2019; 11:87. [PMID: 31888734 PMCID: PMC6938004 DOI: 10.1186/s13073-019-0697-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 11/20/2019] [Indexed: 12/30/2022] Open
Abstract
Background The efficacy of checkpoint blockade immunotherapies in colorectal cancer is currently restricted to a minority of patients diagnosed with mismatch repair-deficient tumors having high mutation burden. However, this observation does not exclude the existence of neoantigen-specific T cells in colorectal cancers with low mutation burden and the exploitation of their anti-cancer potential for immunotherapy. Therefore, we investigated whether autologous neoantigen-specific T cell responses could also be observed in patients diagnosed with mismatch repair-proficient colorectal cancers. Methods Whole-exome and transcriptome sequencing were performed on cancer and normal tissues from seven colorectal cancer patients diagnosed with mismatch repair-proficient tumors to detect putative neoantigens. Corresponding neo-epitopes were synthesized and tested for recognition by in vitro expanded T cells that were isolated from tumor tissues (tumor-infiltrating lymphocytes) and from peripheral mononuclear blood cells stimulated with tumor material. Results Neoantigen-specific T cell reactivity was detected to several neo-epitopes in the tumor-infiltrating lymphocytes of three patients while their respective cancers expressed 15, 21, and 30 non-synonymous variants. Cell sorting of tumor-infiltrating lymphocytes based on the co-expression of CD39 and CD103 pinpointed the presence of neoantigen-specific T cells in the CD39+CD103+ T cell subset. Strikingly, the tumors containing neoantigen-reactive TIL were classified as consensus molecular subtype 4 (CMS4), which is associated with TGF-β pathway activation and worse clinical outcome. Conclusions We have detected neoantigen-targeted reactivity by autologous T cells in mismatch repair-proficient colorectal cancers of the CMS4 subtype. These findings warrant the development of specific immunotherapeutic strategies that selectively boost the activity of neoantigen-specific T cells and target the TGF-β pathway to reinforce T cell reactivity in this patient group.
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Affiliation(s)
| | | | - Dina Ruano
- Pathology, LUMC, Postbus 9600, 2300 RC, Leiden, The Netherlands
| | | | - Marten Visser
- Medical Oncology, Oncode Institute, LUMC, Leiden, The Netherlands
| | | | | | | | | | - Jan Oosting
- Pathology, LUMC, Postbus 9600, 2300 RC, Leiden, The Netherlands
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Ijsselsteijn ME, van der Breggen R, Farina Sarasqueta A, Koning F, de Miranda NFCC. A 40-Marker Panel for High Dimensional Characterization of Cancer Immune Microenvironments by Imaging Mass Cytometry. Front Immunol 2019; 10:2534. [PMID: 31736961 PMCID: PMC6830340 DOI: 10.3389/fimmu.2019.02534] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 10/11/2019] [Indexed: 11/13/2022] Open
Abstract
Multiplex immunophenotyping technologies are indispensable for a deeper understanding of biological systems. Until recently, high-dimensional cellular analyses implied the loss of tissue context as they were mostly performed in single-cell suspensions. The advent of imaging mass cytometry introduced the possibility to simultaneously detect a multitude of cellular markers in tissue sections. This technique can be applied to various tissue sources including snap-frozen and formalin-fixed, paraffin-embedded (FFPE) tissues. However, a number of methodological challenges must be overcome when developing large antibody panels in order to preserve signal intensity and specificity of antigen detection. We report the development of a 40-marker panel for imaging mass cytometry on FFPE tissues with a particular focus on the study of cancer immune microenvironments. It comprises a variety of immune cell markers including lineage and activation markers as well as surrogates of cancer cell states and tissue-specific markers (e.g., stroma, epithelium, vessels) for cellular contextualization within the tissue. Importantly, we developed an optimized workflow for maximum antibody performance by separating antibodies into two distinct incubation steps, at different temperatures and incubation times, shown to significantly improve immunodetection. Furthermore, we provide insight into the antibody validation process and discuss why some antibodies and/or cellular markers are not compatible with the technique. This work is aimed at supporting the implementation of imaging mass cytometry in other laboratories by describing methodological procedures in detail. Furthermore, the panel described here is an excellent immune monitoring tool that can be readily applied in the context of cancer research.
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Affiliation(s)
| | | | | | - Frits Koning
- Department of Pathology, Leiden University Medical Center, Leiden, Netherlands.,Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
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43
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Beyrend G, van der Gracht E, Yilmaz A, van Duikeren S, Camps M, Höllt T, Vilanova A, van Unen V, Koning F, de Miranda NFCC, Arens R, Ossendorp F. PD-L1 blockade engages tumor-infiltrating lymphocytes to co-express targetable activating and inhibitory receptors. J Immunother Cancer 2019; 7:217. [PMID: 31412943 PMCID: PMC6694641 DOI: 10.1186/s40425-019-0700-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 07/31/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The clinical benefit of immunotherapeutic approaches against cancer has been well established although complete responses are only observed in a minority of patients. Combination immunotherapy offers an attractive avenue to develop more effective cancer therapies by improving the efficacy and duration of the tumor-specific T-cell response. Here, we aimed at deciphering the mechanisms governing the response to PD-1/PD-L1 checkpoint blockade to support the rational design of combination immunotherapy. METHODS Mice bearing subcutaneous MC-38 tumors were treated with blocking PD-L1 antibodies. To establish high-dimensional immune signatures of immunotherapy-specific responses, the tumor microenvironment was analyzed by CyTOF mass cytometry using 38 cellular markers. Findings were further examined and validated by flow cytometry and by functional in vivo experiments. Immune profiling was extended to the tumor microenvironment of colorectal cancer patients. RESULTS PD-L1 blockade induced selectively the expansion of tumor-infiltrating CD4+ and CD8+ T-cell subsets, co-expressing both activating (ICOS) and inhibitory (LAG-3, PD-1) molecules. By therapeutically co-targeting these molecules on the TAI cell subsets in vivo by agonistic and antagonist antibodies, we were able to enhance PD-L1 blockade therapy as evidenced by an increased number of TAI cells within the tumor micro-environment and improved tumor protection. Moreover, TAI cells were also found in the tumor-microenvironment of colorectal cancer patients. CONCLUSIONS This study shows the presence of T cell subsets in the tumor micro-environment expressing both activating and inhibitory receptors. These TAI cells can be targeted by combined immunotherapy leading to improved survival.
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Affiliation(s)
- Guillaume Beyrend
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Albinusdreef 2, 2333, ZA, Leiden, The Netherlands
| | - Esmé van der Gracht
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Albinusdreef 2, 2333, ZA, Leiden, The Netherlands
| | - Ayse Yilmaz
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Albinusdreef 2, 2333, ZA, Leiden, The Netherlands
| | - Suzanne van Duikeren
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Albinusdreef 2, 2333, ZA, Leiden, The Netherlands
| | - Marcel Camps
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Albinusdreef 2, 2333, ZA, Leiden, The Netherlands
| | - Thomas Höllt
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands
- Department of Computer Graphics and Visualization Group, Delft, the Netherlands
| | - Anna Vilanova
- Computer Graphics and Visualization Group, faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Delft, the Netherlands
| | - Vincent van Unen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Albinusdreef 2, 2333, ZA, Leiden, The Netherlands
| | - Frits Koning
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Albinusdreef 2, 2333, ZA, Leiden, The Netherlands
| | | | - Ramon Arens
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Albinusdreef 2, 2333, ZA, Leiden, The Netherlands.
| | - Ferry Ossendorp
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Albinusdreef 2, 2333, ZA, Leiden, The Netherlands.
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Affiliation(s)
- Noel F C C de Miranda
- Department of Pathology, Leiden University Medical Centre, Albinusdreef, 2333 ZA, Leiden, The Netherlands.
| | - Zlatko Trajanoski
- Biocenter, Institute of Bioinformatics, Medical University of Innsbruck, Innrain, 6020, Innsbruck, Austria.
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Grolleman JE, de Voer RM, Elsayed FA, Nielsen M, Weren RDA, Palles C, Ligtenberg MJL, Vos JR, Ten Broeke SW, de Miranda NFCC, Kuiper RA, Kamping EJ, Jansen EAM, Vink-Börger ME, Popp I, Lang A, Spier I, Hüneburg R, James PA, Li N, Staninova M, Lindsay H, Cockburn D, Spasic-Boskovic O, Clendenning M, Sweet K, Capellá G, Sjursen W, Høberg-Vetti H, Jongmans MC, Neveling K, Geurts van Kessel A, Morreau H, Hes FJ, Sijmons RH, Schackert HK, Ruiz-Ponte C, Dymerska D, Lubinski J, Rivera B, Foulkes WD, Tomlinson IP, Valle L, Buchanan DD, Kenwrick S, Adlard J, Dimovski AJ, Campbell IG, Aretz S, Schindler D, van Wezel T, Hoogerbrugge N, Kuiper RP. Mutational Signature Analysis Reveals NTHL1 Deficiency to Cause a Multi-tumor Phenotype. Cancer Cell 2019; 35:256-266.e5. [PMID: 30753826 DOI: 10.1016/j.ccell.2018.12.011] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 09/17/2018] [Accepted: 12/26/2018] [Indexed: 01/01/2023]
Abstract
Biallelic germline mutations affecting NTHL1 predispose carriers to adenomatous polyposis and colorectal cancer, but the complete phenotype is unknown. We describe 29 individuals carrying biallelic germline NTHL1 mutations from 17 families, of which 26 developed one (n = 10) or multiple (n = 16) malignancies in 14 different tissues. An unexpected high breast cancer incidence was observed in female carriers (60%). Mutational signature analysis of 14 tumors from 7 organs revealed that NTHL1 deficiency underlies the main mutational process in all but one of the tumors (93%). These results reveal NTHL1 as a multi-tumor predisposition gene with a high lifetime risk for extracolonic cancers and a typical mutational signature observed across tumor types, which can assist in the recognition of this syndrome.
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Affiliation(s)
- Judith E Grolleman
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Richarda M de Voer
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands.
| | - Fadwa A Elsayed
- Department of Pathology, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Maartje Nielsen
- Department of Clinical Genetics, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Robbert D A Weren
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Claire Palles
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Marjolijn J L Ligtenberg
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands; Department of Pathology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Janet R Vos
- Department of Human Genetics, Radboud Institute for Health Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Sanne W Ten Broeke
- Department of Clinical Genetics, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Noel F C C de Miranda
- Department of Pathology, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Renske A Kuiper
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Eveline J Kamping
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Erik A M Jansen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - M Elisa Vink-Börger
- Department of Pathology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Isabell Popp
- Department of Human Genetics, University of Würzburg, 97074 Würzburg, Germany
| | - Alois Lang
- Vorarlberg Cancer Registry, Agency for Preventive and Social Medicine, Bregenz 6900, Austria
| | - Isabel Spier
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; Center for Hereditary Tumor Syndromes, University of Bonn, 53127 Bonn, Germany
| | - Robert Hüneburg
- Center for Hereditary Tumor Syndromes, University of Bonn, 53127 Bonn, Germany; Department of Internal Medicine I, University of Bonn, 53127 Bonn, Germany
| | - Paul A James
- Familial Cancer Centre, Peter MacCallum Cancer Centre, Melbournem, VIC 3000, Australia
| | - Na Li
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Marija Staninova
- Center for Biomolecular Pharmaceutical Analyzes, UKIM Faculty of Pharmacy, 1000 Skopje, Republic of Macedonia
| | - Helen Lindsay
- Leeds Genetics Laboratory, Leeds Teaching Hospitals NHS Trust, Leeds LS9 7TF, UK
| | - David Cockburn
- Leeds Genetics Laboratory, Leeds Teaching Hospitals NHS Trust, Leeds LS9 7TF, UK
| | | | - Mark Clendenning
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, VIC 3010, Australia; University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC 3010, Australia
| | - Kevin Sweet
- Division of Human Genetics, Ohio State University Medical Centre, Columbus, OH 43221, USA
| | - Gabriel Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, CIBERONC, Hospitalet de Llobregat, Barcelona 08908, Spain
| | - Wenche Sjursen
- Department of Medical Genetics, St Olavs University Hospital, 7030 Trondheim, Norway; Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
| | - Hildegunn Høberg-Vetti
- Western Norway Familial Cancer Center, Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, 5021 Bergen, Norway
| | - Marjolijn C Jongmans
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Kornelia Neveling
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Ad Geurts van Kessel
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Hans Morreau
- Department of Pathology, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Frederik J Hes
- Department of Clinical Genetics, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Rolf H Sijmons
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands
| | - Hans K Schackert
- Department of Surgical Research, Universitätsklinikum Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
| | - Clara Ruiz-Ponte
- Fundación Pública Galega de Medicina Xenómica (FPGMX)-SERGAS, Grupo de Medicina Xenómica-USC, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Galicia 15706, Spain
| | - Dagmara Dymerska
- Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - Jan Lubinski
- Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - Barbara Rivera
- Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H3A 0G4, Canada
| | - William D Foulkes
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada
| | - Ian P Tomlinson
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; Oxford National Institute for Health Research (NIHR) Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Laura Valle
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, CIBERONC, Hospitalet de Llobregat, Barcelona 08908, Spain
| | - Daniel D Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, VIC 3010, Australia; University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC 3010, Australia; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC 3010, Australia; Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, VIC 3010, Australia
| | - Sue Kenwrick
- East Anglian Medical Genetics Service, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Julian Adlard
- Yorkshire Regional Genetics Service and University of Leeds, Leeds LS7 4SA, UK
| | - Aleksandar J Dimovski
- Center for Biomolecular Pharmaceutical Analyzes, UKIM Faculty of Pharmacy, 1000 Skopje, Republic of Macedonia
| | - Ian G Campbell
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Stefan Aretz
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; Center for Hereditary Tumor Syndromes, University of Bonn, 53127 Bonn, Germany
| | - Detlev Schindler
- Department of Human Genetics, University of Würzburg, 97074 Würzburg, Germany
| | - Tom van Wezel
- Department of Pathology, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Nicoline Hoogerbrugge
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Roland P Kuiper
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands; Princess Máxima Center for Pediatric Oncology, 3584 CT Utrecht, The Netherlands.
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Li N, van Unen V, Abdelaal T, Guo N, Kasatskaya SA, Ladell K, McLaren JE, Egorov ES, Izraelson M, Chuva de Sousa Lopes SM, Höllt T, Britanova OV, Eggermont J, de Miranda NFCC, Chudakov DM, Price DA, Lelieveldt BPF, Koning F. Memory CD4 + T cells are generated in the human fetal intestine. Nat Immunol 2019; 20:301-312. [PMID: 30664737 PMCID: PMC6420108 DOI: 10.1038/s41590-018-0294-9] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 12/04/2018] [Indexed: 12/31/2022]
Abstract
The fetus is thought to be protected from exposure to foreign antigens,
yet CD45RO+ T cells reside in the fetal intestine. Here we combined
functional assays with mass cytometry, single-cell RNA-sequencing and
high-throughput T cell antigen receptor (TCR) sequencing to characterize the
CD4+ T cell compartment in the human fetal intestine. We
identified 22 CD4+ T cell clusters, including naive-like,
regulatory-like and memory-like subpopulations, which were confirmed and further
characterized at the transcriptional level. Memory-like CD4+ T cells
had high expression of Ki-67, indicative of cell division, and CD5, a surrogate
marker of TCR avidity, and produced the cytokines IFN-γ and IL-2. Pathway
analysis revealed a differentiation trajectory associated with cellular
activation and proinflammatory effector functions, and TCR repertoire analysis
indicated clonal expansions, distinct repertoire characteristics and
interconnections between subpopulations of memory-like CD4+ T cells.
Imaging-mass cytometry indicated that memory-like CD4+ T cells
colocalized with antigen-presenting cells. Collectively, these results provide
evidence for the generation of memory-like CD4+ T cells in the human
fetal intestine that is consistent with exposure to foreign antigens.
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Affiliation(s)
- Na Li
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
| | - Vincent van Unen
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
| | - Tamim Abdelaal
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, the Netherlands.,Department of Pattern Recognition and Bioinformatics Group, Delft University of Technology, Delft, the Netherlands
| | - Nannan Guo
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
| | - Sofya A Kasatskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Centre for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Kristin Ladell
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - James E McLaren
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | - Evgeny S Egorov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Mark Izraelson
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | | | - Thomas Höllt
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, the Netherlands.,Computer Graphics and Visualization Group, Delft University of Technology, Delft, the Netherlands
| | - Olga V Britanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Jeroen Eggermont
- Department of Radiology, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Dmitriy M Chudakov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Centre for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia.,Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Molecular Technologies, Pirogov Russian National Research Medical University, Moscow, Russia.,MiLaboratory LLC, Skolkovo Innovation Centre, Moscow, Russia.,Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - David A Price
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK.,Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, UK
| | - Boudewijn P F Lelieveldt
- Department of Pattern Recognition and Bioinformatics Group, Delft University of Technology, Delft, the Netherlands.,Department of Radiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Frits Koning
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands.
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de Miranda NFCC, van Dinther M, van den Akker BEWM, van Wezel T, ten Dijke P, Morreau H. Transforming Growth Factor β Signaling in Colorectal Cancer Cells With Microsatellite Instability Despite Biallelic Mutations in TGFBR2. Gastroenterology 2015; 148:1427-37.e8. [PMID: 25736321 DOI: 10.1053/j.gastro.2015.02.052] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 02/24/2015] [Accepted: 02/26/2015] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Most colorectal cancer (CRC) cells with high levels of microsatellite instability (MSI-H) accumulate mutations at a microsatellite sequence in the gene encoding transforming growth factor β receptor II (TGFBR2). TGFβ signaling therefore is believed to be defective in these tumors, although CRC cells with TGFBR2 mutations have been reported to remain sensitive to TGFβ. We investigated how TGFβ signaling might continue in MSI-H CRC cells. METHODS We sequenced the 10-adenines microsatellite sequence in the TGFBR2 gene of 32 MSI-H colon cancer tissues and 6 cell lines (HCT116, LS180, LS411N, RKO, SW48, and SW837). Activation of TGFβ signaling was detected by SMAD2 phosphorylation and through use of a TGFβ-responsive reporter construct in all CRC cell lines. Transcripts of TGFBR2 were knocked-down in CRC cells using short hairpin RNA. Full-length and mutant forms of TGFBR2 were expressed in LS411N cells, which do not respond to TGFβ, and their activities were measured. RESULTS SMAD2 was phosphorylated in most MSI-H CRC tissues (strong detection in 44% and weak detection in 34% of MSI-H tumors). Phosphorylation of SMAD2 in MSI-H cells required TGFBR2—even the form encoding a frameshift mutation. Transcription and translation of TGFBR2 with a 1-nucleotide deletion at its microsatellite sequence still produced a full-length TGFBR2 protein. However, protein expression required preservation of the TGFBR2 microsatellite sequence; cells in which this sequence was replaced with a synonymous nonmicrosatellite sequence did not produce functional TGFBR2 protein. CONCLUSION TGFβ signaling remains active in some MSI-H CRC cells despite the presence of frameshift mutations in the TGFBR2 gene because the mutated gene still expresses a functional protein. Strategies to reactivate TGFβ signaling in colorectal tumors might not be warranted, and the functional effects of mutations at other regions of microsatellite instability should be evaluated.
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Affiliation(s)
| | - Maarten van Dinther
- Department of Molecular Cell Biology, Cancer Genomics Centre Netherlands, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Tom van Wezel
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter ten Dijke
- Department of Molecular Cell Biology, Cancer Genomics Centre Netherlands, Leiden University Medical Center, Leiden, The Netherlands; Ludwig Institute for Cancer Research, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
| | - Hans Morreau
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands.
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48
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de Miranda NFCC, Peng R, Georgiou K, Wu C, Falk Sörqvist E, Berglund M, Chen L, Gao Z, Lagerstedt K, Lisboa S, Roos F, van Wezel T, Teixeira MR, Rosenquist R, Sundström C, Enblad G, Nilsson M, Zeng Y, Kipling D, Pan-Hammarström Q. DNA repair genes are selectively mutated in diffuse large B cell lymphomas. ACTA ACUST UNITED AC 2013; 210:1729-42. [PMID: 23960188 PMCID: PMC3754869 DOI: 10.1084/jem.20122842] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
DNA repair mechanisms are fundamental for B cell development, which relies on the somatic diversification of the immunoglobulin genes by V(D)J recombination, somatic hypermutation, and class switch recombination. Their failure is postulated to promote genomic instability and malignant transformation in B cells. By performing targeted sequencing of 73 key DNA repair genes in 29 B cell lymphoma samples, somatic and germline mutations were identified in various DNA repair pathways, mainly in diffuse large B cell lymphomas (DLBCLs). Mutations in mismatch repair genes (EXO1, MSH2, and MSH6) were associated with microsatellite instability, increased number of somatic insertions/deletions, and altered mutation signatures in tumors. Somatic mutations in nonhomologous end-joining (NHEJ) genes (DCLRE1C/ARTEMIS, PRKDC/DNA-PKcs, XRCC5/KU80, and XRCC6/KU70) were identified in four DLBCL tumors and cytogenetic analyses revealed that translocations involving the immunoglobulin-heavy chain locus occurred exclusively in NHEJ-mutated samples. The novel mutation targets, CHEK2 and PARP1, were further screened in expanded DLBCL cohorts, and somatic as well as novel and rare germline mutations were identified in 8 and 5% of analyzed tumors, respectively. By correlating defects in a subset of DNA damage response and repair genes with genomic instability events in tumors, we propose that these genes play a role in DLBCL lymphomagenesis.
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Affiliation(s)
- Noel F C C de Miranda
- Clinical Immunology, Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital, Huddinge, Sweden
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Hermsen IGC, Haak HR, de Krijger RR, Kerkhofs TMA, Feelders RA, de Herder WW, Wilmink H, Smit JWA, Gelderblom H, de Miranda NFCC, van Eijk R, van Wezel T, Morreau H. Mutational analyses of epidermal growth factor receptor and downstream pathways in adrenocortical carcinoma. Eur J Endocrinol 2013; 169:51-8. [PMID: 23585556 DOI: 10.1530/eje-13-0093] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
BACKGROUND Adrenocortical carcinoma (ACC) is a rare disease with a poor prognosis and limited therapeutic options. Mitotane is considered the standard first-line therapy with only 30% of the patients showing objective tumour response. Defining predictive factors for response is therefore of clinical importance. The epidermal growth factor receptor (EGFR) has been implicated in the development of one-third of all malignancies. EGFR pathway members in ACC have been investigated, however, without available clinical data and relation to survival. METHODS In this study, mutation status of EGFR and downstream signalling pathways was evaluated in 47 ACC patients on mitotane using direct sequencing, a TaqMan allele-specific assay and immunohistochemistry. Archival formalin-fixed paraffin-embedded tumour tissue was used for all analyses. Patient data were obtained anonymously, after coupling with the collected tumour tissue. RESULTS One BRAF, two EGFR TK domain (c.2590> A, p.864A>T) and 11 TP53, but no PIK3CA or KRAS, mutations were found. No relationship was found between mutation status, immunostaining and mitotane response or survival. CONCLUSION In conclusion, our data suggest that the role of EGFR tyrosine kinase inhibitors in ACC is limited. Treatment with EGFR monoclonal antibodies on the other hand might be beneficial for a larger group of patients. The possible efficacy of this therapy in ACC should be evaluated in future trials.
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Affiliation(s)
- Ilse G C Hermsen
- Department of Internal Medicine, Máxima Medical Centre, PO Box 90052, 5600 PD Eindhoven, The Netherlands.
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de Miranda NFCC, Goudkade D, Jordanova ES, Tops CMJ, Hes FJ, Vasen HFA, van Wezel T, Morreau H. Infiltration of Lynch colorectal cancers by activated immune cells associates with early staging of the primary tumor and absence of lymph node metastases. Clin Cancer Res 2012; 18:1237-45. [PMID: 22261803 DOI: 10.1158/1078-0432.ccr-11-1997] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
PURPOSE Lynch syndrome colorectal cancers often lose human leukocyte antigen (HLA) class I expression. The outgrowth of clones with immune evasive phenotypes is thought to be positively selected by the action of cytotoxic T cells that target HLA class I-positive cancer cells. To investigate this hypothesis, we related the type and density of tumor lymphocytic infiltrate in Lynch colorectal cancers with their HLA class I phenotype and clinicopathologic stage. EXPERIMENTAL DESIGN HLA class I expression was assessed by means of immunohistochemistry. Characterization of tumor-infiltrating lymphocytes was carried out by using a triple immunofluorescence procedure that allowed the simultaneous detection of CD3-, CD8-, and granzyme B (GZMB)-positive cells. Additional markers were also used for further characterization of an elusive CD3(-)/CD8(-)/GZMB(+) cell population. RESULTS We discovered that high tumor infiltration by activated CD8(+) T cells correlated with aberrant HLA class I expression and associated with early tumor stages (P < 0.05). CD8(+) T cells were most abundant in HLA class I heterogeneous tumors (P = 0.02) and frequent in HLA class I-negative cases (P = 0.04) when compared with HLA class I-positive carcinomas. An elusive immune cell population (CD45(+)/CD8(-)/CD56(-)/GZMB(+)) was characteristic for HLA class I-negative tumors lacking lymph node metastases (P < 0.01). CONCLUSIONS The immune system assumes an important role in counteracting the progression of Lynch colorectal cancers and in selecting abnormal HLA class I phenotypes. Our findings support the development of clinical strategies that explore the natural antitumor immune responses occurring in Lynch syndrome carriers.
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