1
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Aerden M, De Borre M, Thienpont B. Cell-free DNA methylation-based preeclampsia prediction: A journey to improve maternal health. Prenat Diagn 2024; 44:418-421. [PMID: 38047711 DOI: 10.1002/pd.6478] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/20/2023] [Accepted: 11/20/2023] [Indexed: 12/05/2023]
Abstract
Presymptomatic prediction of preeclampsia (PE) is crucial to enable early prophylactic treatment. Current screening tools are either complex or lack predictive value. We recently demonstrated that cell-free DNA methylation can be leveraged to predict early-onset PE in 57% at a 10% false positive rate. Importantly, this minimally invasive screening test can be implemented as an add-on to current widespread noninvasive prenatal aneuploidy screening. Here, we highlight the pitfalls and promising prospects of this research.
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Affiliation(s)
- Mio Aerden
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
- Center for Human Genetics, University Hospitals Leuven, University of Leuven, Leuven, Belgium
| | - Marie De Borre
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
- Center for Human Genetics, University Hospitals Leuven, University of Leuven, Leuven, Belgium
| | - Bernard Thienpont
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
- KU Leuven Center for Single Cell Omics, Leuven, Belgium
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2
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Struys I, Velázquez C, Devriendt K, Godderis L, Segers H, Thienpont B, van Boxtel R, Van Calsteren K, Voet T, Wolters V, Lenaerts L, Amant F. Evaluating offspring Genomic and Epigenomic alterations after prenatal exposure to Cancer treatment In Pregnancy (GE-CIP): a multicentric observational study. BMJ Open 2024; 14:e081833. [PMID: 38548357 PMCID: PMC10982724 DOI: 10.1136/bmjopen-2023-081833] [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: 11/07/2023] [Accepted: 03/05/2024] [Indexed: 04/02/2024] Open
Abstract
INTRODUCTION Around 1 in 1000-2000 pregnancies are affected by a cancer diagnosis. Previous studies have shown that chemotherapy during pregnancy has reassuring cognitive and cardiac neonatal outcomes, and hence has been proposed as standard of care. However, although these children perform within normal ranges for their age, subtle differences have been identified. Given that chemotherapeutic compounds can cross the placenta, the possibility that prenatal chemotherapy exposure mutates the offspring's genome and/or epigenome, with potential deleterious effects later in life, urges to be investigated. METHODS AND ANALYSES This multicentric observational study aims to collect cord blood, meconium and neonatal buccal cells at birth, as well as peripheral blood, buccal cells and urine from infants when 6, 18 and/or 36 months of age. Using bulk and single-cell approaches, we will compare samples from chemotherapy-treated pregnant patients with cancer, pregnant patients with cancer not treated with chemotherapy and healthy pregnant women. Potential chemotherapy-related newborn genomic and/or epigenomic alterations, such as single nucleotide variants, copy number variants and DNA-methylation alterations, will be identified in mononuclear and epithelial cells, isolated from blood, buccal swabs and urine. DNA from maternal peripheral blood and paternal buccal cells will be used to determine de novo somatic mutations in the neonatal blood and epithelial cells. Additionally, the accumulated exposure of the fetus, and biological effective dose of alkylating agents, will be assessed in meconium and cord blood via mass spectrometry approaches. ETHICS AND DISSEMINATION The Ethics Committee Research of UZ/KU Leuven (EC Research) and the Medical Ethical Review Committee of University Medical Center Amsterdam have approved the study. Results of this study will be disseminated via presentations at (inter)national conferences, through peer-reviewed, open-access publications, via social media platforms aimed to inform patients and healthcare workers, and through the website of the International Network on Cancer, Infertility and Pregnancy (www.cancerinpregnancy.org).
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Affiliation(s)
- Ilana Struys
- Department of Oncology, KU Leuven, Leuven, Flanders, Belgium
| | | | - Koenraad Devriendt
- Department of Human Genetics, University Hospital Leuven, Leuven, Belgium
| | - Lode Godderis
- Department of Public Health and Primary Care, KU Leuven, Leuven, Flanders, Belgium
- External Service for Prevention and Protection at Work, Heverlee, Belgium
| | - Heidi Segers
- Department of Paediatric Oncology, University Hospital Leuven, Leuven, Belgium
| | | | - Ruben van Boxtel
- Princess Maxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Kristel Van Calsteren
- Department of Obstetrics and Gynecology, University Hospital Leuven, Leuven, Belgium
| | - Thierry Voet
- Department of Human Genetics, KU Leuven, Leuven, Flanders, Belgium
- Institute for Single Cell Omics (LISCO), KU Leuven, Leuven, Flanders, Belgium
| | - Vera Wolters
- Gynecologic Oncology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | - Frederic Amant
- Department of Oncology, KU Leuven, Leuven, Flanders, Belgium
- Department of Obstetrics and Gynecology, University Hospital Leuven, Leuven, Belgium
- Gynecologic Oncology, Netherlands Cancer Institute, Amsterdam, Netherlands
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3
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Stanley KE, Jatsenko T, Tuveri S, Sudhakaran D, Lannoo L, Van Calsteren K, de Borre M, Van Parijs I, Van Coillie L, Van Den Bogaert K, De Almeida Toledo R, Lenaerts L, Tejpar S, Punie K, Rengifo LY, Vandenberghe P, Thienpont B, Vermeesch JR. Cell type signatures in cell-free DNA fragmentation profiles reveal disease biology. Nat Commun 2024; 15:2220. [PMID: 38472221 PMCID: PMC10933257 DOI: 10.1038/s41467-024-46435-0] [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: 08/10/2023] [Accepted: 02/21/2024] [Indexed: 03/14/2024] Open
Abstract
Circulating cell-free DNA (cfDNA) fragments have characteristics that are specific to the cell types that release them. Current methods for cfDNA deconvolution typically use disease tailored marker selection in a limited number of bulk tissues or cell lines. Here, we utilize single cell transcriptome data as a comprehensive cellular reference set for disease-agnostic cfDNA cell-of-origin analysis. We correlate cfDNA-inferred nucleosome spacing with gene expression to rank the relative contribution of over 490 cell types to plasma cfDNA. In 744 healthy individuals and patients, we uncover cell type signatures in support of emerging disease paradigms in oncology and prenatal care. We train predictive models that can differentiate patients with colorectal cancer (84.7%), early-stage breast cancer (90.1%), multiple myeloma (AUC 95.0%), and preeclampsia (88.3%) from matched controls. Importantly, our approach performs well in ultra-low coverage cfDNA datasets and can be readily transferred to diverse clinical settings for the expansion of liquid biopsy.
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Affiliation(s)
- Kate E Stanley
- Department of Human Genetics, Laboratory for Cytogenetics and Genome Research, KU Leuven, Leuven, Belgium
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
| | - Tatjana Jatsenko
- Department of Human Genetics, Laboratory for Cytogenetics and Genome Research, KU Leuven, Leuven, Belgium
| | - Stefania Tuveri
- Department of Human Genetics, Laboratory for Cytogenetics and Genome Research, KU Leuven, Leuven, Belgium
| | - Dhanya Sudhakaran
- Department of Human Genetics, Laboratory for Cytogenetics and Genome Research, KU Leuven, Leuven, Belgium
| | - Lore Lannoo
- Department of Gynecology and Obstetrics, University Hospitals Leuven, Leuven, Belgium
| | - Kristel Van Calsteren
- Department of Gynecology and Obstetrics, University Hospitals Leuven, Leuven, Belgium
| | - Marie de Borre
- Department of Human Genetics, Laboratory for Functional Epigenetics, KU Leuven, Leuven, Belgium
| | - Ilse Van Parijs
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Leen Van Coillie
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | | | | | - Liesbeth Lenaerts
- Department of Oncology, Gynecological Oncology, KU Leuven, Leuven, Belgium
| | - Sabine Tejpar
- Department of Oncology, Molecular Digestive Oncology, KU Leuven, Leuven, Belgium
| | - Kevin Punie
- Multidisciplinary Breast Centre, Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium
| | - Laura Y Rengifo
- Department of Human Genetics, Laboratory of Genetics of Malignant Diseases, KU Leuven, Leuven, Belgium
| | - Peter Vandenberghe
- Department of Human Genetics, Laboratory of Genetics of Malignant Diseases, KU Leuven, Leuven, Belgium
- Department of Hematology, University Hospitals Leuven, Leuven, Belgium
| | - Bernard Thienpont
- Department of Human Genetics, Laboratory for Functional Epigenetics, KU Leuven, Leuven, Belgium
| | - Joris Robert Vermeesch
- Department of Human Genetics, Laboratory for Cytogenetics and Genome Research, KU Leuven, Leuven, Belgium.
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4
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Verdikt R, Thienpont B. Epigenetic remodelling under hypoxia. Semin Cancer Biol 2024; 98:1-10. [PMID: 38029868 DOI: 10.1016/j.semcancer.2023.10.005] [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: 08/21/2023] [Revised: 10/17/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023]
Abstract
Hypoxia is intrinsic to tumours and contributes to malignancy and metastasis while hindering the efficiency of existing treatments. Epigenetic mechanisms play a crucial role in the regulation of hypoxic cancer cell programs, both in the initial phases of sensing the decrease in oxygen levels and during adaptation to chronic lack of oxygen. During the latter, the epigenetic regulation of tumour biology intersects with hypoxia-sensitive transcription factors in a complex network of gene regulation that also involves metabolic reprogramming. Here, we review the current literature on the epigenetic control of gene programs in hypoxic cancer cells. We highlight common themes and features of such epigenetic remodelling and discuss their relevance for the development of therapeutic strategies.
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Affiliation(s)
- Roxane Verdikt
- Institute for Society and Genetics, University of California, Los Angeles, Los Angeles, CA, USA; Department of Human Genetics, KU Leuven, Leuven, Belgium; KU Leuven Institute for Single Cell Omics (LISCO), KU Leuven, Leuven, Belgium
| | - Bernard Thienpont
- Department of Human Genetics, KU Leuven, Leuven, Belgium; KU Leuven Institute for Single Cell Omics (LISCO), KU Leuven, Leuven, Belgium; KU Leuven Cancer Institute (LKI), KU Leuven, Leuven, Belgium.
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5
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Stegen S, Moermans K, Stockmans I, Thienpont B, Carmeliet G. The serine synthesis pathway drives osteoclast differentiation through epigenetic regulation of NFATc1 expression. Nat Metab 2024; 6:141-152. [PMID: 38200114 PMCID: PMC10822776 DOI: 10.1038/s42255-023-00948-y] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 11/21/2023] [Indexed: 01/12/2024]
Abstract
Bone-resorbing osteoclasts are vital for postnatal bone health, as increased differentiation or activity results in skeletal pathologies such as osteoporosis. The metabolism of mature osteoclasts differs from their progenitor cells, but whether the observed metabolic changes are secondary to the altered cell state or actively drive the process of cell differentiation is unknown. Here, we show that transient activation of the serine synthesis pathway (SSP) is essential for osteoclastogenesis, as deletion of the rate-limiting enzyme phosphoglycerate dehydrogenase in osteoclast progenitors impairs their differentiation and results in increased bone mass. In addition, pharmacological phosphoglycerate dehydrogenase inhibition abrogated bone loss in a mouse model of postmenopausal osteoporosis by blocking bone resorption. Mechanistically, SSP-derived α-ketoglutarate is necessary for histone demethylases that remove repressive histone methylation marks at the nuclear factor of activated T cells, cytoplasmic 1 (Nfatc1) gene locus, thereby inducing NFATc1 expression and consequent osteoclast maturation. Taken together, this study reveals a metabolic-epigenetic coupling mechanism that directs osteoclast differentiation and suggests that the SSP can be therapeutically targeted to prevent osteoporotic bone loss.
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Affiliation(s)
- Steve Stegen
- Laboratory of Clinical and Experimental Endocrinology, Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Karen Moermans
- Laboratory of Clinical and Experimental Endocrinology, Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Ingrid Stockmans
- Laboratory of Clinical and Experimental Endocrinology, Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Bernard Thienpont
- Laboratory of Functional Epigenetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Geert Carmeliet
- Laboratory of Clinical and Experimental Endocrinology, Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium.
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6
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Pinioti S, Sharma H, Flerin NC, Yu Q, Tzoumpa A, Cafarello ST, De Bousser E, Callewaert N, Oldenhove G, Schlenner S, Thienpont B, Garg AD, Di Matteo M, Mazzone M. A Metabolic Gene Survey Pinpoints Fucosylation as a Key Pathway Underlying the Suppressive Function of Regulatory T Cells in Cancer. Cancer Immunol Res 2023; 11:1611-1629. [PMID: 37933083 PMCID: PMC7615342 DOI: 10.1158/2326-6066.cir-22-0606] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 07/26/2022] [Revised: 02/22/2023] [Accepted: 10/18/2023] [Indexed: 11/08/2023]
Abstract
Forkhead box P3 (Foxp3)-expressing regulatory T cells (Treg) are the guardians of controlled immune reactions and prevent the development of autoimmune diseases. However, in the tumor context, their increased number suppresses antitumor immune responses, indicating the importance of understanding the mechanisms behind their function and stability. Metabolic reprogramming can affect Foxp3 regulation and, therefore, Treg suppressive function and fitness. Here, we performed a metabolic CRISPR/Cas9 screen and pinpointed novel candidate positive and negative metabolic regulators of Foxp3. Among the positive regulators, we revealed that targeting the GDP-fucose transporter Slc35c1, and more broadly fucosylation (Fuco), in Tregs compromises their proliferation and suppressive function both in vitro and in vivo, leading to alteration of the tumor microenvironment and impaired tumor progression and protumoral immune responses. Pharmacologic inhibition of Fuco dampened tumor immunosuppression mostly by targeting Tregs, thus resulting in reduced tumor growth. In order to substantiate these findings in humans, tumoral Tregs from patients with colorectal cancer were clustered on the basis of the expression of Fuco-related genes. FucoLOW Tregs were found to exhibit a more immunogenic profile compared with FucoHIGH Tregs. Furthermore, an enrichment of a FucoLOW signature, mainly derived from Tregs, correlated with better prognosis and response to immune checkpoint blockade in melanoma patients. In conclusion, Slc35c1-dependent Fuco is able to regulate the suppressive function of Tregs, and measuring its expression in Tregs might pave the way towards a useful biomarker model for patients with cancer. See related Spotlight by Silveria and DuPage, p. 1570.
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Affiliation(s)
- Sotiria Pinioti
- laboratory of Tumor Inflammation and Angiogenesis, Center for Cancer Biology, VIB, Leuven B3000, Belgium
- laboratory of Tumor Inflammation and Angiogenesis, Center for Cancer Biology, Department of Oncology, KU Leuven, Leuven B3000, Belgium
| | - Himal Sharma
- laboratory of Tumor Inflammation and Angiogenesis, Center for Cancer Biology, VIB, Leuven B3000, Belgium
- laboratory of Tumor Inflammation and Angiogenesis, Center for Cancer Biology, Department of Oncology, KU Leuven, Leuven B3000, Belgium
| | - Nina C Flerin
- laboratory of Tumor Inflammation and Angiogenesis, Center for Cancer Biology, VIB, Leuven B3000, Belgium
- laboratory of Tumor Inflammation and Angiogenesis, Center for Cancer Biology, Department of Oncology, KU Leuven, Leuven B3000, Belgium
| | - Qian Yu
- laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, Leuven B3000, Belgium
| | - Amalia Tzoumpa
- laboratory of Tumor Inflammation and Angiogenesis, Center for Cancer Biology, VIB, Leuven B3000, Belgium
- laboratory of Tumor Inflammation and Angiogenesis, Center for Cancer Biology, Department of Oncology, KU Leuven, Leuven B3000, Belgium
| | - Sarah Trusso Cafarello
- laboratory of Tumor Inflammation and Angiogenesis, Center for Cancer Biology, VIB, Leuven B3000, Belgium
- laboratory of Tumor Inflammation and Angiogenesis, Center for Cancer Biology, Department of Oncology, KU Leuven, Leuven B3000, Belgium
| | - Elien De Bousser
- Medical Biotechnology Center, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Nico Callewaert
- Medical Biotechnology Center, VIB, Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Guillaume Oldenhove
- laboratory of Immunobiology, Université Libre de Bruxelles, Gosselies, Belgium
- U-CRI (UCL Center for Research in Immunobiology), Université Libre de Bruxelles, Gosselies, Belgium
| | - Susan Schlenner
- KU Leuven-University of Leuven, Department of Microbiology, Immunology and Transplantation, Leuven B3000, Belgium
| | - Bernard Thienpont
- laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, Leuven B3000, Belgium
| | - Abhishek D Garg
- laboratory for Cell Stress & Immunity (CSI), Department for Cellular and Molecular Medicine, KU Leuven, Leuven B3000, Belgium
| | - Mario Di Matteo
- laboratory of Tumor Inflammation and Angiogenesis, Center for Cancer Biology, VIB, Leuven B3000, Belgium
- laboratory of Tumor Inflammation and Angiogenesis, Center for Cancer Biology, Department of Oncology, KU Leuven, Leuven B3000, Belgium
| | - Massimiliano Mazzone
- laboratory of Tumor Inflammation and Angiogenesis, Center for Cancer Biology, VIB, Leuven B3000, Belgium
- laboratory of Tumor Inflammation and Angiogenesis, Center for Cancer Biology, Department of Oncology, KU Leuven, Leuven B3000, Belgium
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7
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Yu Q, Van Minsel P, Galle E, Thienpont B. GiRAFR improves gRNA detection and annotation in single-cell CRISPR screens. Commun Biol 2023; 6:975. [PMID: 37741886 PMCID: PMC10518011 DOI: 10.1038/s42003-023-05351-7] [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: 05/26/2023] [Accepted: 09/12/2023] [Indexed: 09/25/2023] Open
Abstract
Novel methods that combine single cell RNA-seq with CRISPR screens enable high-throughput characterization of transcriptional changes caused by genetic perturbations. Dedicated software is however lacking to annotate CRISPR guide RNA (gRNA) libraries and associate them with single cell transcriptomes. Here, we describe a CRISPR droplet sequencing (CROP-seq) dataset. During analysis, we observed that the most commonly used method fails to detect mutant gRNAs. We therefore developed a python tool to identify and characterize intact and mutant gRNAs, called GiRAFR. We show that mutant gRNAs are dysfunctional, and failure to detect and annotate them leads to an inflated estimate of the number of untransformed cells, attenuated downregulation of target genes, as well as an underestimated multiplet frequency. These findings are mirrored in publicly available datasets, where we find that up to 35% of cells are transduced with a mutant gRNA. Applying GiRAFR hence stands to improve the annotation and quality of single cell CRISPR screens.
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Affiliation(s)
- Qian Yu
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
| | - Paulien Van Minsel
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
| | - Eva Galle
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
| | - Bernard Thienpont
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium.
- Leuven Institute for Single Cell Omics, KU Leuven, 3000, Leuven, Belgium.
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8
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De Borre M, Che H, Yu Q, Lannoo L, De Ridder K, Vancoillie L, Dreesen P, Van Den Ackerveken M, Aerden M, Galle E, Breckpot J, Van Keirsbilck J, Gyselaers W, Devriendt K, Vermeesch JR, Van Calsteren K, Thienpont B. Cell-free DNA methylome analysis for early preeclampsia prediction. Nat Med 2023; 29:2206-2215. [PMID: 37640858 DOI: 10.1038/s41591-023-02510-5] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 07/22/2023] [Indexed: 08/31/2023]
Abstract
Preeclampsia (PE) is a leading cause for peripartal morbidity, especially if developing early in gestation. To enable prophylaxis in the prevention of PE, pregnancies at risk of PE must be identified early-in the first trimester. To identify at-risk pregnancies we profiled methylomes of plasma-derived, cell-free DNA from 498 pregnant women, of whom about one-third developed early-onset PE. We detected DNA methylation differences between control and PE pregnancies that enabled risk stratification at PE diagnosis but also presymptomatically, at around 12 weeks of gestation (range 9-14 weeks). The first-trimester risk prediction model was validated in an external cohort collected from two centers (area under the curve (AUC) = 0.75) and integrated with routinely available maternal risk factors (AUC = 0.85). The combined risk score correctly predicted 72% of patients with early-onset PE at 80% specificity. These preliminary results suggest that cell-free DNA methylation profiling is a promising tool for presymptomatic PE risk assessment, and has the potential to improve treatment and follow-up in the obstetric clinic.
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Affiliation(s)
- Marie De Borre
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
- Center for Human Genetics, University Hospitals Leuven, University of Leuven, Leuven, Belgium
| | - Huiwen Che
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Qian Yu
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Lore Lannoo
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven, Belgium
| | - Kobe De Ridder
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Leen Vancoillie
- Center for Human Genetics, University Hospitals Leuven, University of Leuven, Leuven, Belgium
| | - Pauline Dreesen
- Faculty of Medicine and Life Science, Hasselt University, Hasselt, Belgium
| | - Mika Van Den Ackerveken
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Mio Aerden
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
- Center for Human Genetics, University Hospitals Leuven, University of Leuven, Leuven, Belgium
| | - Eva Galle
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Jeroen Breckpot
- Center for Human Genetics, University Hospitals Leuven, University of Leuven, Leuven, Belgium
| | | | | | - Koen Devriendt
- Center for Human Genetics, University Hospitals Leuven, University of Leuven, Leuven, Belgium
| | - Joris Robert Vermeesch
- Center for Human Genetics, University Hospitals Leuven, University of Leuven, Leuven, Belgium
| | - Kristel Van Calsteren
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven, Belgium
| | - Bernard Thienpont
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, Leuven, Belgium.
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9
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Abstract
The joint analysis of the genome, epigenome, transcriptome, proteome and/or metabolome from single cells is transforming our understanding of cell biology in health and disease. In less than a decade, the field has seen tremendous technological revolutions that enable crucial new insights into the interplay between intracellular and intercellular molecular mechanisms that govern development, physiology and pathogenesis. In this Review, we highlight advances in the fast-developing field of single-cell and spatial multi-omics technologies (also known as multimodal omics approaches), and the computational strategies needed to integrate information across these molecular layers. We demonstrate their impact on fundamental cell biology and translational research, discuss current challenges and provide an outlook to the future.
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Affiliation(s)
- Katy Vandereyken
- KU Leuven Institute for Single Cell Omics (LISCO), University of Leuven, KU Leuven, Leuven, Belgium
- Department of Human Genetics, University of Leuven, KU Leuven, Leuven, Belgium
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Alejandro Sifrim
- KU Leuven Institute for Single Cell Omics (LISCO), University of Leuven, KU Leuven, Leuven, Belgium
- Department of Human Genetics, University of Leuven, KU Leuven, Leuven, Belgium
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Bernard Thienpont
- KU Leuven Institute for Single Cell Omics (LISCO), University of Leuven, KU Leuven, Leuven, Belgium
- Department of Human Genetics, University of Leuven, KU Leuven, Leuven, Belgium
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Thierry Voet
- KU Leuven Institute for Single Cell Omics (LISCO), University of Leuven, KU Leuven, Leuven, Belgium.
- Department of Human Genetics, University of Leuven, KU Leuven, Leuven, Belgium.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
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10
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Vande Voorde J, Steven RT, Najumudeen AK, Ford CA, Dexter A, Gonzalez-Fernandez A, Nikula CJ, Xiang Y, Ford L, Maneta Stavrakaki S, Gilroy K, Zeiger LB, Pennel K, Hatthakarnkul P, Elia EA, Nasif A, Murta T, Manoli E, Mason S, Gillespie M, Lannagan TRM, Vlahov N, Ridgway RA, Nixon C, Raven A, Mills M, Athineos D, Kanellos G, Nourse C, Gay DM, Hughes M, Burton A, Yan B, Sellers K, Wu V, De Ridder K, Shokry E, Huerta Uribe A, Clark W, Clark G, Kirschner K, Thienpont B, Li VSW, Maddocks ODK, Barry ST, Goodwin RJA, Kinross J, Edwards J, Yuneva MO, Sumpton D, Takats Z, Campbell AD, Bunch J, Sansom OJ. Metabolic profiling stratifies colorectal cancer and reveals adenosylhomocysteinase as a therapeutic target. Nat Metab 2023; 5:1303-1318. [PMID: 37580540 PMCID: PMC10447251 DOI: 10.1038/s42255-023-00857-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 02/24/2022] [Accepted: 07/06/2023] [Indexed: 08/16/2023]
Abstract
The genomic landscape of colorectal cancer (CRC) is shaped by inactivating mutations in tumour suppressors such as APC, and oncogenic mutations such as mutant KRAS. Here we used genetically engineered mouse models, and multimodal mass spectrometry-based metabolomics to study the impact of common genetic drivers of CRC on the metabolic landscape of the intestine. We show that untargeted metabolic profiling can be applied to stratify intestinal tissues according to underlying genetic alterations, and use mass spectrometry imaging to identify tumour, stromal and normal adjacent tissues. By identifying ions that drive variation between normal and transformed tissues, we found dysregulation of the methionine cycle to be a hallmark of APC-deficient CRC. Loss of Apc in the mouse intestine was found to be sufficient to drive expression of one of its enzymes, adenosylhomocysteinase (AHCY), which was also found to be transcriptionally upregulated in human CRC. Targeting of AHCY function impaired growth of APC-deficient organoids in vitro, and prevented the characteristic hyperproliferative/crypt progenitor phenotype driven by acute deletion of Apc in vivo, even in the context of mutant Kras. Finally, pharmacological inhibition of AHCY reduced intestinal tumour burden in ApcMin/+ mice indicating its potential as a metabolic drug target in CRC.
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Affiliation(s)
| | | | | | | | | | | | | | - Yuchen Xiang
- Department of Metabolism Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - Lauren Ford
- Department of Metabolism Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - Stefania Maneta Stavrakaki
- Department of Metabolism Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | | | - Lucas B Zeiger
- Cancer Research UK Beatson Institute, Glasgow, UK
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Kathryn Pennel
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | | | | | | | | | - Eftychios Manoli
- Department of Metabolism Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - Sam Mason
- Department of Metabolism Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - Michael Gillespie
- Cancer Research UK Beatson Institute, Glasgow, UK
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | | | | | | | - Colin Nixon
- Cancer Research UK Beatson Institute, Glasgow, UK
| | | | - Megan Mills
- Cancer Research UK Beatson Institute, Glasgow, UK
| | | | | | - Craig Nourse
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - David M Gay
- Cancer Research UK Beatson Institute, Glasgow, UK
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
- Københavns Universitet, BRIC, Copenhagen, Denmark
| | - Mark Hughes
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - Amy Burton
- National Physical Laboratory, London, UK
| | - Bin Yan
- National Physical Laboratory, London, UK
| | - Katherine Sellers
- The Francis Crick Institute, London, UK
- Rheos Medicines, Cambridge, MA, USA
| | - Vincen Wu
- Department of Metabolism Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - Kobe De Ridder
- Department of Human Genetics, University of Leuven, KU Leuven, Leuven, Belgium
| | - Engy Shokry
- Cancer Research UK Beatson Institute, Glasgow, UK
| | | | | | - Graeme Clark
- Cancer Research UK Beatson Institute, Glasgow, UK
| | | | - Bernard Thienpont
- Department of Human Genetics, University of Leuven, KU Leuven, Leuven, Belgium
| | | | | | - Simon T Barry
- Bioscience, Early Oncology, AstraZeneca, Cambridge, UK
| | - Richard J A Goodwin
- Imaging and Data Analytics, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, UK
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - James Kinross
- Department of Metabolism Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - Joanne Edwards
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | | | | | - Zoltan Takats
- Department of Metabolism Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
- Biological Mass Spectrometry, Rosalind Franklin Institute, Didcot, UK
| | | | - Josephine Bunch
- National Physical Laboratory, London, UK
- Department of Metabolism Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
- Biological Mass Spectrometry, Rosalind Franklin Institute, Didcot, UK
| | - Owen J Sansom
- Cancer Research UK Beatson Institute, Glasgow, UK.
- School of Cancer Sciences, University of Glasgow, Glasgow, UK.
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11
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Amoni M, Vermoortele D, Ekhteraei-Tousi S, Doñate Puertas R, Gilbert G, Youness M, Thienpont B, Willems R, Roderick HL, Claus P, Sipido KR. Heterogeneity of Repolarization and Cell-Cell Variability of Cardiomyocyte Remodeling Within the Myocardial Infarction Border Zone Contribute to Arrhythmia Susceptibility. Circ Arrhythm Electrophysiol 2023; 16:e011677. [PMID: 37128895 DOI: 10.1161/circep.122.011677] [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] [Indexed: 05/03/2023]
Abstract
BACKGROUND After myocardial infarction, the infarct border zone (BZ) is the dominant source of life-threatening arrhythmias, where fibrosis and abnormal repolarization create a substrate for reentry. We examined whether repolarization abnormalities are heterogeneous within the BZ in vivo and could be related to heterogeneous cardiomyocyte remodeling. METHODS Myocardial infarction was induced in domestic pigs by 120-minute ischemia-reperfusion injury. After 1 month, remodeling was assessed by magnetic resonance imaging, and electroanatomical mapping was performed to determine the spatial distribution of activation-recovery intervals. Cardiomyocytes were isolated and tissue samples collected from the BZ and remote regions. Optical recording allowed assessment of action potential duration (di-8-Anepps, stimulation at 1 Hz, 37 °C) of large cardiomyocyte populations while gene expression in cardiomyocytes was determined by single nuclear RNA sequencing. RESULTS In vivo, activation-recovery intervals in the BZ tended to be longer than in remote with increased spatial heterogeneity evidenced by a greater local SD (3.5±1.3 ms versus remote: 2.0±0.5 ms, P=0.036, npigs=5). Increased activation-recovery interval heterogeneity correlated with enhanced arrhythmia susceptibility. Cellular population studies (ncells=635-862 cells per region) demonstrated greater heterogeneity of action potential duration in the BZ (SD, 105.9±17.0 ms versus remote: 73.9±8.6 ms; P=0.001; npigs=6), which correlated with heterogeneity of activation-recovery interval in vivo. Cell-cell gene expression heterogeneity in the BZ was evidenced by increased Euclidean distances between nuclei of the BZ (12.1 [9.2-15.0] versus 10.6 [7.5-11.6] in remote; P<0.0001). Differentially expressed genes characterizing BZ cardiomyocyte remodeling included hypertrophy-related and ion channel-related genes with high cell-cell variability of expression. These gene expression changes were driven by stress-responsive TFs (transcription factors). In addition, heterogeneity of left ventricular wall thickness was greater in the BZ than in remote. CONCLUSIONS Heterogeneous cardiomyocyte remodeling in the BZ is driven by uniquely altered gene expression, related to heterogeneity in the local microenvironment, and translates to heterogeneous repolarization and arrhythmia vulnerability in vivo.
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Affiliation(s)
- Matthew Amoni
- Experimental Cardiology, KU Leuven, Belgium. (M.A., S.E.-T., R.D.P., G.G., M.Y., R.W., H.L.R., K.R.S.)
- Division of Cardiology, University Hospitals, Leuven, Belgium (M.A., R.W.)
| | - Dylan Vermoortele
- Imaging and Cardiovascular Dynamics, Department of Cardiovascular Sciences, KU Leuven, Belgium. (D.V., P.C.)
| | - Samaneh Ekhteraei-Tousi
- Experimental Cardiology, KU Leuven, Belgium. (M.A., S.E.-T., R.D.P., G.G., M.Y., R.W., H.L.R., K.R.S.)
| | - Rosa Doñate Puertas
- Experimental Cardiology, KU Leuven, Belgium. (M.A., S.E.-T., R.D.P., G.G., M.Y., R.W., H.L.R., K.R.S.)
| | - Guillaume Gilbert
- Experimental Cardiology, KU Leuven, Belgium. (M.A., S.E.-T., R.D.P., G.G., M.Y., R.W., H.L.R., K.R.S.)
| | - Mohamad Youness
- Experimental Cardiology, KU Leuven, Belgium. (M.A., S.E.-T., R.D.P., G.G., M.Y., R.W., H.L.R., K.R.S.)
| | - Bernard Thienpont
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, Belgium. (B.T.)
| | - Rik Willems
- Experimental Cardiology, KU Leuven, Belgium. (M.A., S.E.-T., R.D.P., G.G., M.Y., R.W., H.L.R., K.R.S.)
- Division of Cardiology, University Hospitals, Leuven, Belgium (M.A., R.W.)
| | - H Llewelyn Roderick
- Experimental Cardiology, KU Leuven, Belgium. (M.A., S.E.-T., R.D.P., G.G., M.Y., R.W., H.L.R., K.R.S.)
| | - Piet Claus
- Imaging and Cardiovascular Dynamics, Department of Cardiovascular Sciences, KU Leuven, Belgium. (D.V., P.C.)
| | - Karin R Sipido
- Experimental Cardiology, KU Leuven, Belgium. (M.A., S.E.-T., R.D.P., G.G., M.Y., R.W., H.L.R., K.R.S.)
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12
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Ekhteraeitousi S, Amoni M, Vermoortele D, Puertas RD, Youness M, Ingelaere S, Willems R, Claus P, Nagaraju CK, Thienpont B, Sipido K, Roderick HL. Altered multicellular composition and unique myocyte phenotypes characterize the arrhythmogenic infarct border zone. J Mol Cell Cardiol 2022. [DOI: 10.1016/j.yjmcc.2022.08.179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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13
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Rasking L, Roelens C, Sprangers B, Thienpont B, Nawrot TS, De Vusser K. Lupus, DNA Methylation, and Air Pollution: A Malicious Triad. Int J Environ Res Public Health 2022; 19:15050. [PMID: 36429769 PMCID: PMC9690025 DOI: 10.3390/ijerph192215050] [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] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/10/2022] [Accepted: 11/14/2022] [Indexed: 06/16/2023]
Abstract
The pathogenesis of systemic lupus erythematosus (SLE) remains elusive to this day; however, genetic, epigenetic, and environmental factors have been implicated to be involved in disease pathogenesis. Recently, it was demonstrated that in systemic lupus erythematosus (SLE) patients, interferon-regulated genes are hypomethylated in naïve CD4+ T cells, CD19+ B lymphocytes, and CD14+ monocytes. This suggests that interferon-regulated genes may have been epigenetically poised in SLE patients for rapid expression upon stimulation by different environmental factors. Additionally, environmental studies have identified DNA (hypo)methylation changes as a potential mechanism of environmentally induced health effects in utero, during childhood and in adults. Finally, epidemiologic studies have firmly established air pollution as a crucial SLE risk factor, as studies showed an association between fine particulate matter (PM2.5) and traditional SLE biomarkers related to disease flare, hospital admissions, and an increased SLEDAI score. In this review, the relationship between aberrant epigenetic regulation, the environment, and the development of SLE will be discussed.
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Affiliation(s)
- Leen Rasking
- Centre for Environmental Sciences, Hasselt University, 3590 Diepenbeek, Belgium
| | - Céline Roelens
- Depatment of Nephrology and Kidney Transplantation, University Hospital Leuven, 3000 Leuven, Belgium
| | - Ben Sprangers
- Depatment of Nephrology and Kidney Transplantation, University Hospital Leuven, 3000 Leuven, Belgium
- Department of Microbiology and Immunology, Leuven University, 3000 Leuven, Belgium
| | - Bernard Thienpont
- Department of Human Genetics, Leuven University, 3000 Leuven, Belgium
| | - Tim S. Nawrot
- Centre for Environmental Sciences, Hasselt University, 3590 Diepenbeek, Belgium
- Department of Public Health and Primary Care, Environment and Health Unit, Leuven University, 3000 Leuven, Belgium
| | - Katrien De Vusser
- Depatment of Nephrology and Kidney Transplantation, University Hospital Leuven, 3000 Leuven, Belgium
- Department of Microbiology and Immunology, Leuven University, 3000 Leuven, Belgium
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14
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de Rooij LPMH, Becker LM, Teuwen LA, Boeckx B, Jansen S, Feys S, Verleden S, Liesenborghs L, Stalder AK, Libbrecht S, Van Buyten T, Philips G, Subramanian A, Dumas SJ, Meta E, Borri M, Sokol L, Dendooven A, Truong ACK, Gunst J, Van Mol P, Haslbauer JD, Rohlenova K, Menter T, Boudewijns R, Geldhof V, Vinckier S, Amersfoort J, Wuyts W, Van Raemdonck D, Jacobs W, Ceulemans LJ, Weynand B, Thienpont B, Lammens M, Kuehnel M, Eelen G, Dewerchin M, Schoonjans L, Jonigk D, van Dorpe J, Tzankov A, Wauters E, Mazzone M, Neyts J, Wauters J, Lambrechts D, Carmeliet P. The pulmonary vasculature in lethal COVID-19 and idiopathic pulmonary fibrosis at single cell resolution. Cardiovasc Res 2022; 119:520-535. [PMID: 35998078 PMCID: PMC9452154 DOI: 10.1093/cvr/cvac139] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/18/2022] [Accepted: 08/01/2022] [Indexed: 11/30/2022] Open
Abstract
Aims SARS-CoV-2 infection causes COVID-19, which in severe cases evokes life-threatening acute respiratory distress syndrome (ARDS). Transcriptome signatures and the functional relevance of non-vascular cell types (e.g. immune and epithelial cells) in COVID-19 are becoming increasingly evident. However, despite its known contribution to vascular inflammation, recruitment/invasion of immune cells, vascular leakage and perturbed hemostasis in the lungs of severe COVID-19 patients, an in-depth interrogation of the endothelial cell (EC) compartment in lethal COVID-19 is lacking. Moreover, progressive fibrotic lung disease represents one of the complications of COVID-19 pneumonia and ARDS. Analogous features between idiopathic pulmonary fibrosis (IPF) and COVID-19 suggest partial similarities in their pathophysiology, yet, a head-to-head comparison of pulmonary cell transcriptomes between both conditions has not been implemented to date. Methods and Results We performed single nucleus RNA-seq (snRNA-seq) on frozen lungs from 7 deceased COVID-19 patients, 6 IPF explant lungs and 12 controls. The vascular fraction, comprising 38,794 nuclei, could be subclustered into 14 distinct EC subtypes. Non-vascular cell types, comprising 137,746 nuclei, were subclustered and used for EC-interactome analyses. Pulmonary ECs of deceased COVID-19 patients showed an enrichment of genes involved in cellular stress, as well as signatures suggestive of dampened immunomodulation and impaired vessel wall integrity. In addition, increased abundance of a population of systemic capillary and venous ECs was identified in COVID-19 and IPF. COVID-19 systemic ECs closely resembled their IPF counterparts, and a set of 30 genes was found congruently enriched in systemic ECs across studies. Receptor-ligand interaction analysis of ECs with non-vascular cell types in the pulmonary micro-environment revealed numerous previously unknown interactions specifically enriched/depleted in COVID-19 and/or IPF. Conclusions This study uncovered novel insights into the abundance, expression patterns and interactomes of EC subtypes in COVID-19 and IPF, relevant for future investigations into the progression and treatment of both lethal conditions. Translational perspective While assessing clinical and molecular characteristics of severe and lethal COVID-19 cases, the vasculature’s undeniable role in disease progression has been widely acknowledged. COVID-19 lung pathology moreover shares certain clinical features with late-stage IPF – yet an in-depth interrogation and direct comparison of the endothelium at single-cell level in both conditions is still lacking. By comparing the transcriptomes of ECs from lungs of deceased COVID-19 patients to those from IPF explant and control lungs, we gathered key insights the heterogeneous composition and potential roles of ECs in both lethal diseases, which may serve as a foundation for development of novel therapeutics.
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Affiliation(s)
| | | | - Laure-Anne Teuwen
- Present address: Department of Oncology, Antwerp University Hospital (UZA), Edegem 2650, Belgium
| | - Bram Boeckx
- Laboratory of Translational Genetics, Center for Cancer Biology, VIB & Department of Genetics, KU Leuven, Leuven 3000, Belgium
| | - Sander Jansen
- Laboratory of Virology & Chemotherapy, KU Leuven, Leuven 3000, Belgium
| | - Simon Feys
- Medical Intensive Care Unit, UZ Gasthuisberg & Laboratory for Clinical Infectious and Inflammatory Disorders, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven 3000, Belgium
| | - Stijn Verleden
- Present address: Department of Antwerp Surgical Training, Anatomy and Research Centre, Division of Thoracic and Vascular Surgery, University of Antwerp, Wilrijk, Belgium
| | | | - Anna K Stalder
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel 4031, Switzerland
| | - Sasha Libbrecht
- Department of Pathology, Ghent University Hospital, Ghent University, Ghent 9000, Belgium
| | - Tina Van Buyten
- Laboratory of Virology & Chemotherapy, KU Leuven, Leuven 3000, Belgium
| | - Gino Philips
- Laboratory of Translational Genetics, Center for Cancer Biology, VIB & Department of Genetics, KU Leuven, Leuven 3000, Belgium
| | - Abhishek Subramanian
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, VIB, Leuven 3000, Belgium
| | - Sébastien J Dumas
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, VIB, Leuven 3000, Belgium
| | - Elda Meta
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, VIB, Leuven 3000, Belgium
| | - Mila Borri
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, VIB, Leuven 3000, Belgium
| | - Liliana Sokol
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, VIB, Leuven 3000, Belgium
| | - Amélie Dendooven
- Department of Pathology, Ghent University Hospital, Ghent University, Ghent 9000, Belgium
- University of Antwerp, Faculty of Medicine, Wilrijk 2610, Belgium
| | - Anh-Co K Truong
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, VIB, Leuven 3000, Belgium
| | - Jan Gunst
- Laboratory of Intensive Care Medicine, Department of Cellular and Molecular Medicine, KU Leuven, Leuven 3000, Belgium
| | - Pierre Van Mol
- Laboratory of Translational Genetics, Center for Cancer Biology, VIB & Department of Genetics, KU Leuven, Leuven 3000, Belgium
| | - Jasmin D Haslbauer
- Laboratory of Tumor Inflammation and Angiogenesis, Center for Cancer Biology, VIB, Leuven 3000, Belgium
| | - Katerina Rohlenova
- Present address: Institute of Biotechnology, Czech Academy of Sciences, BIOCEV, Vestec 252 50, Czech Republic
| | - Thomas Menter
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel 4031, Switzerland
| | | | - Vincent Geldhof
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, VIB, Leuven 3000, Belgium
| | - Stefan Vinckier
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, VIB, Leuven 3000, Belgium
| | - Jacob Amersfoort
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, VIB, Leuven 3000, Belgium
| | - Wim Wuyts
- Department of Respiratory Medicine, Unit for Interstitial Lung Diseases, UZ Gasthuisberg, Leuven 3000, Belgium
| | - Dirk Van Raemdonck
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), KU Leuven, Leuven 3000, Belgium
| | - Werner Jacobs
- Medical CBRNe unit, Queen Astrid Military Hospital, Belgian Defense, Neder-Over-Heembeek 1120, Belgium
- Department of Forensic Pathology, ASTARC Antwerp University Hospital and University of Antwerp, Antwerp 2610, Belgium
| | - Laurens J Ceulemans
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), KU Leuven, Leuven 3000, Belgium
| | - Birgit Weynand
- Translational Cell & Tissue Research, Department of Imaging & Pathology, KU Leuven, Leuven 3000, Belgium
| | - Bernard Thienpont
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, Leuven 3000, Belgium
| | - Martin Lammens
- Department of Pathology Antwerp University Hospital, Edegem 2560, Belgium
- Center for Oncological Research, University of Antwerp, Antwerp 2000, Belgium
| | - Mark Kuehnel
- Medizinische Hochschule Hannover (MHH), Institut für Pathologie, D-30625 Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH) Member of the German Centre for Lung research (DZL), Hannover 30625, Germany
| | - Guy Eelen
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, VIB, Leuven 3000, Belgium
| | - Mieke Dewerchin
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, VIB, Leuven 3000, Belgium
| | - Luc Schoonjans
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, VIB, Leuven 3000, Belgium
- Laboratory of Translational Genetics, Center for Cancer Biology, VIB & Department of Genetics, KU Leuven, Leuven 3000, Belgium
| | - Danny Jonigk
- Medizinische Hochschule Hannover (MHH), Institut für Pathologie, D-30625 Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH) Member of the German Centre for Lung research (DZL), Hannover 30625, Germany
| | - Jo van Dorpe
- Department of Pathology, Ghent University Hospital, Ghent University, Ghent 9000, Belgium
| | - Alexandar Tzankov
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel 4031, Switzerland
| | - Els Wauters
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), KU Leuven, Leuven 3000, Belgium
- Respiratory Oncology Unit, University Hospital KU Leuven, Leuven 3000, Belgium
| | - Massimiliano Mazzone
- Laboratory of Tumor Inflammation and Angiogenesis, Center for Cancer Biology, VIB, Leuven 3000, Belgium
- Laboratory of Tumor Inflammation and Angiogenesis, Center for Cancer Biology, Department of Oncology, KU Leuven, Leuven 3000, Belgium
| | - Johan Neyts
- Laboratory of Virology & Chemotherapy, KU Leuven, Leuven 3000, Belgium
| | - Joost Wauters
- Medical Intensive Care Unit, UZ Gasthuisberg & Laboratory for Clinical Infectious and Inflammatory Disorders, Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven 3000, Belgium
| | - Diether Lambrechts
- Laboratory of Translational Genetics, Center for Cancer Biology, VIB & Department of Genetics, KU Leuven, Leuven 3000, Belgium
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15
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Tournaire G, Loopmans S, Stegen S, Rinaldi G, Eelen G, Torrekens S, Moermans K, Carmeliet P, Ghesquière B, Thienpont B, Fendt SM, van Gastel N, Carmeliet G. Skeletal progenitors preserve proliferation and self-renewal upon inhibition of mitochondrial respiration by rerouting the TCA cycle. Cell Rep 2022; 40:111105. [PMID: 35905715 PMCID: PMC9380255 DOI: 10.1016/j.celrep.2022.111105] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 04/13/2022] [Accepted: 06/25/2022] [Indexed: 11/25/2022] Open
Abstract
A functional electron transport chain (ETC) is crucial for supporting bioenergetics and biosynthesis. Accordingly, ETC inhibition decreases proliferation in cancer cells but does not seem to impair stem cell proliferation. However, it remains unclear how stem cells metabolically adapt. In this study, we show that pharmacological inhibition of complex III of the ETC in skeletal stem and progenitor cells induces glycolysis side pathways and reroutes the tricarboxylic acid (TCA) cycle to regenerate NAD+ and preserve cell proliferation. These metabolic changes also culminate in increased succinate and 2-hydroxyglutarate levels that inhibit Ten-eleven translocation (TET) DNA demethylase activity, thereby preserving self-renewal and multilineage potential. Mechanistically, mitochondrial malate dehydrogenase and reverse succinate dehydrogenase activity proved to be essential for the metabolic rewiring in response to ETC inhibition. Together, these data show that the metabolic plasticity of skeletal stem and progenitor cells allows them to bypass ETC blockade and preserve their self-renewal. Skeletal stem/progenitor cells can proliferate upon electron transport chain blockade Succinate dehydrogenase is reversed with fumarate functioning as electron acceptor Pyruvate and aspartate are critical for NAD+ regeneration and proliferation Metabolic changes prevent DNA demethylation and preserve self-renewal
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Affiliation(s)
- Guillaume Tournaire
- Laboratory of Clinical and Experimental Endocrinology, Department of Chronic Diseases and Metabolism, KU Leuven, O&N1bis Herestraat 49, 3000 Leuven, Belgium; Prometheus, Division of Skeletal Tissue Engineering, KU Leuven, Leuven, Belgium
| | - Shauni Loopmans
- Laboratory of Clinical and Experimental Endocrinology, Department of Chronic Diseases and Metabolism, KU Leuven, O&N1bis Herestraat 49, 3000 Leuven, Belgium; Prometheus, Division of Skeletal Tissue Engineering, KU Leuven, Leuven, Belgium
| | - Steve Stegen
- Laboratory of Clinical and Experimental Endocrinology, Department of Chronic Diseases and Metabolism, KU Leuven, O&N1bis Herestraat 49, 3000 Leuven, Belgium; Prometheus, Division of Skeletal Tissue Engineering, KU Leuven, Leuven, Belgium
| | - Gianmarco Rinaldi
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB Center for Cancer Biology, Leuven, Belgium; Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology and Leuven Cancer Institute, KU Leuven, Leuven, Belgium
| | - Guy Eelen
- Laboratory of Angiogenesis and Vascular Metabolism, VIB Center for Cancer Biology, Leuven, Belgium; Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute, KU Leuven, Leuven, Belgium
| | - Sophie Torrekens
- Laboratory of Clinical and Experimental Endocrinology, Department of Chronic Diseases and Metabolism, KU Leuven, O&N1bis Herestraat 49, 3000 Leuven, Belgium
| | - Karen Moermans
- Laboratory of Clinical and Experimental Endocrinology, Department of Chronic Diseases and Metabolism, KU Leuven, O&N1bis Herestraat 49, 3000 Leuven, Belgium
| | - Peter Carmeliet
- Laboratory of Angiogenesis and Vascular Metabolism, VIB Center for Cancer Biology, Leuven, Belgium; Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute, KU Leuven, Leuven, Belgium
| | - Bart Ghesquière
- Metabolomics Expertise Center, Department of Oncology, KU Leuven/VIB Center for Cancer Biology Leuven, Leuven, Belgium
| | - Bernard Thienpont
- Laboratory of Functional Epigenetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Sarah-Maria Fendt
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB Center for Cancer Biology, Leuven, Belgium; Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology and Leuven Cancer Institute, KU Leuven, Leuven, Belgium
| | | | - Geert Carmeliet
- Laboratory of Clinical and Experimental Endocrinology, Department of Chronic Diseases and Metabolism, KU Leuven, O&N1bis Herestraat 49, 3000 Leuven, Belgium; Prometheus, Division of Skeletal Tissue Engineering, KU Leuven, Leuven, Belgium.
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16
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Che H, Thienpont B. More of less: Novel multi-ome profiling of single human neurons. Cell Genom 2022; 2:100110. [PMID: 36777334 PMCID: PMC9903744 DOI: 10.1016/j.xgen.2022.100110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Epigenetic modifications to DNA and chromatin interact to influence gene expression and cellular phenotypes, but defining these omics layers in complex tissues is a daunting task. In this issue of Cell Genomics, Luo et al. describe a novel single-cell multi-omic method, simultaneously profiling transcriptome, DNA methylome, and chromatin accessibility, to shed light on human neurons.
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Affiliation(s)
- Huiwen Che
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, Leuven 3000, Belgium,Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Bernard Thienpont
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, Leuven 3000, Belgium,Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA,KU Leuven Institute for Single Cell Omics (LISCO), KU Leuven, Leuven 3000, Belgium,Corresponding author
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17
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Struys I, Lenaerts L, Thienpont B, Amant F. Novel next-generation sequencing-based methodologies to characterize the mutational consequences of (prenatal) chemotherapy exposure in noncancerous tissue. Curr Opin Oncol 2021; 33:476-484. [PMID: 34038918 DOI: 10.1097/cco.0000000000000755] [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: 11/25/2022]
Abstract
PURPOSE OF REVIEW Although chemotherapeutics are considered as genotoxins for decades, their exact mutagenic impact on the genome of cancerous and normal cells of cancer patients was unknown for a long time. However, this knowledge is necessary to understand the long-term side effects of chemotherapy. A particular condition represents pregnant cancer patients being treated with chemotherapy. Since certain chemotherapeutics can cross the placenta, concerns exist about possible mutational effects on the fetus' genome with potential long-term health consequences. RECENT FINDINGS Recent advances of next-generation sequencing (NGS) techniques have opened possibilities to explore the exact mutational footprint of chemotherapies in healthy tissue from treated cancer patients. However, the ultra-low frequency of chemotherapy-induced mutations, introduction of technical artefacts, and inaccessibility of normal tissue has posed important limitations. This review discusses five state-of-the-art approaches that were recently designed to overcome these drawbacks. SUMMARY Results of the latest investigations give valuable insights into the genome-wide genotoxicity profile of frequently applied chemotherapies, with most of these drugs being associated with a signature of random base substitutions and small indels. Though these findings still might be limited to extrapolate to healthy tissue, they pave the way for studies on the origin of long-term chemotherapy-related adverse health effects.
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Affiliation(s)
| | | | | | - Frédéric Amant
- Department of Oncology
- Gynecologic Oncology, Netherlands Cancer Institute
- Gynecologic Oncology, Amsterdam University Medical Centers, Amsterdam, The Netherlands
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18
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Audain E, Wilsdon A, Breckpot J, Izarzugaza JMG, Fitzgerald TW, Kahlert AK, Sifrim A, Wünnemann F, Perez-Riverol Y, Abdul-Khaliq H, Bak M, Bassett AS, Benson DW, Berger F, Daehnert I, Devriendt K, Dittrich S, Daubeney PE, Garg V, Hackmann K, Hoff K, Hofmann P, Dombrowsky G, Pickardt T, Bauer U, Keavney BD, Klaassen S, Kramer HH, Marshall CR, Milewicz DM, Lemaire S, Coselli JS, Mitchell ME, Tomita-Mitchell A, Prakash SK, Stamm K, Stewart AFR, Silversides CK, Siebert R, Stiller B, Rosenfeld JA, Vater I, Postma AV, Caliebe A, Brook JD, Andelfinger G, Hurles ME, Thienpont B, Larsen LA, Hitz MP. Correction: Integrative analysis of genomic variants reveals new associations of candidate haploinsufficient genes with congenital heart disease. PLoS Genet 2021; 17:e1009809. [PMID: 34547032 PMCID: PMC8454942 DOI: 10.1371/journal.pgen.1009809] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
[This corrects the article DOI: 10.1371/journal.pgen.1009679.].
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19
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Audain E, Wilsdon A, Breckpot J, Izarzugaza JMG, Fitzgerald TW, Kahlert AK, Sifrim A, Wünnemann F, Perez-Riverol Y, Abdul-Khaliq H, Bak M, Bassett AS, Benson WD, Berger F, Daehnert I, Devriendt K, Dittrich S, Daubeney PEF, Garg V, Hackmann K, Hoff K, Hofmann P, Dombrowsky G, Pickardt T, Bauer U, Keavney BD, Klaassen S, Kramer HH, Marshall CR, Milewicz DM, Lemaire S, Coselli JS, Mitchell ME, Tomita-Mitchell A, Prakash SK, Stamm K, Stewart AFR, Silversides CK, Siebert R, Stiller B, Rosenfeld JA, Vater I, Postma AV, Caliebe A, Brook JD, Andelfinger G, Hurles ME, Thienpont B, Larsen LA, Hitz MP. Integrative analysis of genomic variants reveals new associations of candidate haploinsufficient genes with congenital heart disease. PLoS Genet 2021; 17:e1009679. [PMID: 34324492 PMCID: PMC8354477 DOI: 10.1371/journal.pgen.1009679] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 08/10/2021] [Accepted: 06/23/2021] [Indexed: 11/18/2022] Open
Abstract
Numerous genetic studies have established a role for rare genomic variants in Congenital Heart Disease (CHD) at the copy number variation (CNV) and de novo variant (DNV) level. To identify novel haploinsufficient CHD disease genes, we performed an integrative analysis of CNVs and DNVs identified in probands with CHD including cases with sporadic thoracic aortic aneurysm. We assembled CNV data from 7,958 cases and 14,082 controls and performed a gene-wise analysis of the burden of rare genomic deletions in cases versus controls. In addition, we performed variation rate testing for DNVs identified in 2,489 parent-offspring trios. Our analysis revealed 21 genes which were significantly affected by rare CNVs and/or DNVs in probands. Fourteen of these genes have previously been associated with CHD while the remaining genes (FEZ1, MYO16, ARID1B, NALCN, WAC, KDM5B and WHSC1) have only been associated in small cases series or show new associations with CHD. In addition, a systems level analysis revealed affected protein-protein interaction networks involved in Notch signaling pathway, heart morphogenesis, DNA repair and cilia/centrosome function. Taken together, this approach highlights the importance of re-analyzing existing datasets to strengthen disease association and identify novel disease genes and pathways.
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Affiliation(s)
- Enrique Audain
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital of Schleswig-Holstein, Kiel, Germany
- German Center for Cardiovascular Research (DZHK), Kiel, Germany
| | - Anna Wilsdon
- School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Jeroen Breckpot
- Centre for Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
| | | | - Tomas W. Fitzgerald
- European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, United Kingdom
| | - Anne-Karin Kahlert
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital of Schleswig-Holstein, Kiel, Germany
- German Center for Cardiovascular Research (DZHK), Kiel, Germany
- Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Alejandro Sifrim
- Department of Human Genetics, University of Leuven, KU Leuven, Leuven, Belgium
- Sanger Institute-EBI Single-Cell Genomics Centre, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | | | - Yasset Perez-Riverol
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Hashim Abdul-Khaliq
- Clinic for Pediatric Cardiology—University Hospital of Saarland, Homburg (Saar), Germany
| | - Mads Bak
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Anne S. Bassett
- Toronto Congenital Cardiac Centre for Adults, and Division of Cardiology, Department of Medicine, University Health Network, Toronto, Canada
- Department of Psychiatry, University of Toronto, Toronto, Canada
| | - Woodrow D. Benson
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Felix Berger
- Department of Congenital Heart Disease—Pediatric Cardiology, German Heart Center Berlin, Berlin, Germany
| | - Ingo Daehnert
- Department of Pediatric Cardiology and Congenital Heart Disease, Heart Center, University of Leipzig, Leipzig, Germany
| | - Koenraad Devriendt
- Centre for Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Sven Dittrich
- Department of Pediatric Cardiology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Piers EF Daubeney
- Division of Paediatric Cardiology, Royal Brompton Hospital, London, United Kingdom
| | - Vidu Garg
- The Heart Center, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, United States of America
- Center for Cardiovascular Research, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
- Department of Pediatrics, The Ohio State University, Columbus, Ohio, United States of America
| | - Karl Hackmann
- Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Kirstin Hoff
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital of Schleswig-Holstein, Kiel, Germany
- German Center for Cardiovascular Research (DZHK), Kiel, Germany
| | - Philipp Hofmann
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital of Schleswig-Holstein, Kiel, Germany
- German Center for Cardiovascular Research (DZHK), Kiel, Germany
| | - Gregor Dombrowsky
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital of Schleswig-Holstein, Kiel, Germany
- German Center for Cardiovascular Research (DZHK), Kiel, Germany
| | - Thomas Pickardt
- Competence Network for Congenital Heart Defects, Berlin, Germany
| | - Ulrike Bauer
- Competence Network for Congenital Heart Defects, Berlin, Germany
| | - Bernard D. Keavney
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
- Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Sabine Klaassen
- Experimental and Clinical Research Center (ECRC), a joint cooperation between the Charité Medical Faculty and the Max-Delbrück-Center for Molecular Medicine (MDC), Berlin, Germany
- Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Pediatric Cardiology, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Berlin, Germany
| | - Hans-Heiner Kramer
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital of Schleswig-Holstein, Kiel, Germany
- German Center for Cardiovascular Research (DZHK), Kiel, Germany
| | - Christian R. Marshall
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Canada
- Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Dianna M. Milewicz
- Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Scott Lemaire
- Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, Texas, United States of America
| | - Joseph S. Coselli
- Department of Surgery, Division of Cardiothoracic Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Michael E. Mitchell
- Department of Surgery, Division of Cardiothoracic Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Aoy Tomita-Mitchell
- Department of Surgery, Division of Cardiothoracic Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Siddharth K. Prakash
- Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Karl Stamm
- Department of Surgery, Division of Cardiothoracic Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Alexandre F. R. Stewart
- Ruddy Canadian Cardiovascular Genetics Centre, University of Ottawa Heart Institute, Ottawa, Canada
| | - Candice K. Silversides
- Toronto Congenital Cardiac Centre for Adults, and Division of Cardiology, Department of Medicine, University Health Network, Toronto, Canada
| | - Reiner Siebert
- Institute of Human Genetics, University Hospital Ulm, Ulm, Germany
- Department of Human Genetics, University Medical Center Schleswig-Holstein (UKSH), Kiel, Germany
| | - Brigitte Stiller
- Department of Congenital Heart Disease and Pediatric Cardiology, University Heart Center Freiburg—Bad Krozingen, Freiburg, Germany
| | - Jill A. Rosenfeld
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Inga Vater
- Department of Human Genetics, University Medical Center Schleswig-Holstein (UKSH), Kiel, Germany
| | - Alex V. Postma
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Almuth Caliebe
- Department of Human Genetics, University Medical Center Schleswig-Holstein (UKSH), Kiel, Germany
| | - J. David Brook
- School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Gregor Andelfinger
- Cardiovascular Genetics, Department of Pediatrics, Centre Hospitalier Universitaire Saint-Justine Research Centre, Université de Montréal, Montreal, Canada
| | - Matthew E. Hurles
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Bernard Thienpont
- Centre for Human Genetics, Katholieke Universiteit Leuven, Leuven, Belgium
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Lars Allan Larsen
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Marc-Phillip Hitz
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital of Schleswig-Holstein, Kiel, Germany
- German Center for Cardiovascular Research (DZHK), Kiel, Germany
- Department of Human Genetics, University Medical Center Schleswig-Holstein (UKSH), Kiel, Germany
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
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20
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Bartoccetti M, van der Veer BK, Luo X, Khoueiry R, She P, Bajaj M, Xu J, Janiszewski A, Thienpont B, Pasque V, Koh KP. Regulatory Dynamics of Tet1 and Oct4 Resolve Stages of Global DNA Demethylation and Transcriptomic Changes in Reprogramming. Cell Rep 2021; 30:2150-2169.e9. [PMID: 32075734 DOI: 10.1016/j.celrep.2020.01.065] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 03/22/2019] [Revised: 12/12/2019] [Accepted: 01/21/2020] [Indexed: 01/05/2023] Open
Abstract
Reprogramming somatic cells into induced pluripotent stem cells (iPSCs) involves the reactivation of endogenous pluripotency genes and global DNA demethylation, but temporal resolution of these events using existing markers is limited. Here, we generate murine transgenic lines harboring reporters for the 5-methylcytosine dioxygenase Tet1 and for Oct4. By monitoring dual reporter fluorescence during pluripotency entry, we identify a sequential order of Tet1 and Oct4 activation by proximal and distal regulatory elements. Full Tet1 activation marks an intermediate stage that accompanies predominantly repression of somatic genes, preceding full Oct4 activation, and distinguishes two waves of global DNA demethylation that target distinct genomic features but are uncoupled from transcriptional changes. Tet1 knockout shows that TET1 contributes to both waves of demethylation and activates germline regulatory genes in reprogramming intermediates but is dispensable for Oct4 reactivation. Our dual reporter system for time-resolving pluripotency entry thus refines the molecular roadmap of iPSC maturation.
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Affiliation(s)
- Michela Bartoccetti
- Department of Development and Regeneration, Stem Cell Institute Leuven, KU Leuven, 3000 Leuven, Belgium
| | - Bernard K van der Veer
- Department of Development and Regeneration, Stem Cell Institute Leuven, KU Leuven, 3000 Leuven, Belgium
| | - Xinlong Luo
- Department of Development and Regeneration, Stem Cell Institute Leuven, KU Leuven, 3000 Leuven, Belgium
| | - Rita Khoueiry
- Department of Development and Regeneration, Stem Cell Institute Leuven, KU Leuven, 3000 Leuven, Belgium
| | - Pinyi She
- Department of Development and Regeneration, Stem Cell Institute Leuven, KU Leuven, 3000 Leuven, Belgium
| | - Manmohan Bajaj
- Department of Development and Regeneration, Stem Cell Institute Leuven, KU Leuven, 3000 Leuven, Belgium
| | - Jiayi Xu
- Department of Development and Regeneration, Stem Cell Institute Leuven, KU Leuven, 3000 Leuven, Belgium
| | - Adrian Janiszewski
- Department of Development and Regeneration, Stem Cell Institute Leuven, KU Leuven, 3000 Leuven, Belgium
| | - Bernard Thienpont
- Department of Human Genetics, Laboratory for Functional Epigenetics, KU Leuven, 3000 Leuven, Belgium
| | - Vincent Pasque
- Department of Development and Regeneration, Stem Cell Institute Leuven, KU Leuven, 3000 Leuven, Belgium
| | - Kian Peng Koh
- Department of Development and Regeneration, Stem Cell Institute Leuven, KU Leuven, 3000 Leuven, Belgium.
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21
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Horvath L, Thienpont B, Zhao L, Wolf D, Pircher A. Overcoming immunotherapy resistance in non-small cell lung cancer (NSCLC) - novel approaches and future outlook. Mol Cancer 2020; 19:141. [PMID: 32917214 PMCID: PMC7488475 DOI: 10.1186/s12943-020-01260-z] [Citation(s) in RCA: 129] [Impact Index Per Article: 32.3] [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: 05/31/2020] [Accepted: 09/04/2020] [Indexed: 12/16/2022] Open
Abstract
Immunotherapy (IO) has revolutionized the therapy landscape of non-small cell lung cancer (NSCLC), significantly prolonging the overall survival (OS) of advanced stage patients. Over the recent years IO therapy has been broadly integrated into the first-line setting of non-oncogene driven NSCLC, either in combination with chemotherapy, or in selected patients with PD-L1high expression as monotherapy. Still, a significant proportion of patients suffer from disease progression. A better understanding of resistance mechanisms depicts a central goal to avoid or overcome IO resistance and to improve patient outcome.We here review major cellular and molecular pathways within the tumor microenvironment (TME) that may impact the evolution of IO resistance. We summarize upcoming treatment options after IO resistance including novel IO targets (e.g. RIG-I, STING) as well as interesting combinational approaches such as IO combined with anti-angiogenic agents or metabolic targets (e.g. IDO-1, adenosine signaling, arginase). By discussing the fundamental mode of action of IO within the TME, we aim to understand and manage IO resistance and to seed new ideas for effective therapeutic IO concepts.
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MESH Headings
- Arginase/genetics
- B7-H1 Antigen/antagonists & inhibitors
- B7-H1 Antigen/genetics
- B7-H1 Antigen/immunology
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/immunology
- Carcinoma, Non-Small-Cell Lung/therapy
- DEAD Box Protein 58/antagonists & inhibitors
- DEAD Box Protein 58/genetics
- DEAD Box Protein 58/immunology
- Drug Resistance, Neoplasm/genetics
- Drug Resistance, Neoplasm/immunology
- Humans
- Immunotherapy/adverse effects
- Indoleamine-Pyrrole 2,3,-Dioxygenase/genetics
- Membrane Proteins/antagonists & inhibitors
- Membrane Proteins/genetics
- Membrane Proteins/immunology
- Receptors, Immunologic/antagonists & inhibitors
- Receptors, Immunologic/genetics
- Receptors, Immunologic/immunology
- Tumor Microenvironment/drug effects
- Tumor Microenvironment/immunology
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Affiliation(s)
- Lena Horvath
- Internal Medicine V, Department of Hematology and Oncology, Medical University Innsbruck, Anichstraße 35, 6020, Innsbruck, Austria
| | - Bernard Thienpont
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Liyun Zhao
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Dominik Wolf
- Internal Medicine V, Department of Hematology and Oncology, Medical University Innsbruck, Anichstraße 35, 6020, Innsbruck, Austria
- Medical Clinic III, Department of Oncology, Hematology, Immunoncology and Rheumatology, University Hospital Bonn (UKB), Sigmund-Freud-Street 25, 53127, Bonn, Germany
| | - Andreas Pircher
- Internal Medicine V, Department of Hematology and Oncology, Medical University Innsbruck, Anichstraße 35, 6020, Innsbruck, Austria.
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22
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D'Anna F, Van Dyck L, Xiong J, Zhao H, Berrens RV, Qian J, Bieniasz-Krzywiec P, Chandra V, Schoonjans L, Matthews J, De Smedt J, Minnoye L, Amorim R, Khorasanizadeh S, Yu Q, Zhao L, De Borre M, Savvides SN, Simon MC, Carmeliet P, Reik W, Rastinejad F, Mazzone M, Thienpont B, Lambrechts D. DNA methylation repels binding of hypoxia-inducible transcription factors to maintain tumor immunotolerance. Genome Biol 2020; 21:182. [PMID: 32718321 PMCID: PMC7384226 DOI: 10.1186/s13059-020-02087-z] [Citation(s) in RCA: 24] [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] [Received: 01/23/2020] [Accepted: 06/29/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Hypoxia is pervasive in cancer and other diseases. Cells sense and adapt to hypoxia by activating hypoxia-inducible transcription factors (HIFs), but it is still an outstanding question why cell types differ in their transcriptional response to hypoxia. RESULTS We report that HIFs fail to bind CpG dinucleotides that are methylated in their consensus binding sequence, both in in vitro biochemical binding assays and in vivo studies of differentially methylated isogenic cell lines. Based on in silico structural modeling, we show that 5-methylcytosine indeed causes steric hindrance in the HIF binding pocket. A model wherein cell-type-specific methylation landscapes, as laid down by the differential expression and binding of other transcription factors under normoxia, control cell-type-specific hypoxia responses is observed. We also discover ectopic HIF binding sites in repeat regions which are normally methylated. Genetic and pharmacological DNA demethylation, but also cancer-associated DNA hypomethylation, expose these binding sites, inducing HIF-dependent expression of cryptic transcripts. In line with such cryptic transcripts being more prone to cause double-stranded RNA and viral mimicry, we observe low DNA methylation and high cryptic transcript expression in tumors with high immune checkpoint expression, but not in tumors with low immune checkpoint expression, where they would compromise tumor immunotolerance. In a low-immunogenic tumor model, DNA demethylation upregulates cryptic transcript expression in a HIF-dependent manner, causing immune activation and reducing tumor growth. CONCLUSIONS Our data elucidate the mechanism underlying cell-type-specific responses to hypoxia and suggest DNA methylation and hypoxia to underlie tumor immunotolerance.
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Affiliation(s)
- Flora D'Anna
- Center for Cancer Biology, VIB, 3000, Leuven, Belgium
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
| | - Laurien Van Dyck
- Center for Cancer Biology, VIB, 3000, Leuven, Belgium
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
| | - Jieyi Xiong
- Center for Cancer Biology, VIB, 3000, Leuven, Belgium
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
| | - Hui Zhao
- Center for Cancer Biology, VIB, 3000, Leuven, Belgium
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
| | - Rebecca V Berrens
- Epigenetics Programme, Babraham Institute, Cambridge, CB22 3AT, UK
- The Old Schools, University of Cambridge, Trinity Lane Cambridge, CB2 1TN, UK
| | - Junbin Qian
- Center for Cancer Biology, VIB, 3000, Leuven, Belgium
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
| | - Pawel Bieniasz-Krzywiec
- Center for Cancer Biology, VIB, 3000, Leuven, Belgium
- Laboratory of Tumor Inflammation and Angiogenesis, Department of Oncology, KU Leuven, 3000, Leuven, Belgium
| | - Vikas Chandra
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Luc Schoonjans
- Center for Cancer Biology, VIB, 3000, Leuven, Belgium
- State Key Laboratory of Ophthalmology, Zhongsan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, Leuven Cancer Institute, KU Leuven, 3000, Leuven, Belgium
| | - Jason Matthews
- Institute of Basic Medical Sciences, University of Oslo, 0372, Oslo, Norway
| | - Julie De Smedt
- Laboratory of Dermatology, Department of Oncology, KU Leuven, 3000, Leuven, Belgium
| | - Liesbeth Minnoye
- Center for Cancer Biology, VIB, 3000, Leuven, Belgium
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
| | - Ricardo Amorim
- Center for Cancer Biology, VIB, 3000, Leuven, Belgium
- Laboratory of Tumor Inflammation and Angiogenesis, Department of Oncology, KU Leuven, 3000, Leuven, Belgium
| | - Sepideh Khorasanizadeh
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Qian Yu
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
| | - Liyun Zhao
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
| | - Marie De Borre
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
| | - Savvas N Savvides
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, 9052, Ghent, Belgium
- VIB Center for Inflammation Research, 9052, Ghent, Belgium
| | - M Celeste Simon
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Peter Carmeliet
- Center for Cancer Biology, VIB, 3000, Leuven, Belgium
- State Key Laboratory of Ophthalmology, Zhongsan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, Leuven Cancer Institute, KU Leuven, 3000, Leuven, Belgium
| | - Wolf Reik
- Epigenetics Programme, Babraham Institute, Cambridge, CB22 3AT, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, CB2 3EG, UK
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3EG, UK
| | - Fraydoon Rastinejad
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Clinical and Experimental Endocrinology, Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, 3000, Leuven, Belgium
| | - Massimiliano Mazzone
- Center for Cancer Biology, VIB, 3000, Leuven, Belgium
- Laboratory of Tumor Inflammation and Angiogenesis, Department of Oncology, KU Leuven, 3000, Leuven, Belgium
| | - Bernard Thienpont
- Center for Cancer Biology, VIB, 3000, Leuven, Belgium.
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium.
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium.
| | - Diether Lambrechts
- Center for Cancer Biology, VIB, 3000, Leuven, Belgium.
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium.
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23
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Griffiths CD, Bilawchuk LM, McDonough JE, Jamieson KC, Elawar F, Cen Y, Duan W, Lin C, Song H, Casanova JL, Ogg S, Jensen LD, Thienpont B, Kumar A, Hobman TC, Proud D, Moraes TJ, Marchant DJ. IGF1R is an entry receptor for respiratory syncytial virus. Nature 2020; 583:615-619. [PMID: 32494007 DOI: 10.1038/s41586-020-2369-7] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [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: 05/14/2019] [Accepted: 03/25/2020] [Indexed: 11/09/2022]
Abstract
Pneumonia resulting from infection is one of the leading causes of death worldwide. Pulmonary infection by the respiratory syncytial virus (RSV) is a large burden on human health, for which there are few therapeutic options1. RSV targets ciliated epithelial cells in the airways, but how viruses such as RSV interact with receptors on these cells is not understood. Nucleolin is an entry coreceptor for RSV2 and also mediates the cellular entry of influenza, the parainfluenza virus, some enteroviruses and the bacterium that causes tularaemia3,4. Here we show a mechanism of RSV entry into cells in which outside-in signalling, involving binding of the prefusion RSV-F glycoprotein with the insulin-like growth factor-1 receptor, triggers the activation of protein kinase C zeta (PKCζ). This cellular signalling cascade recruits nucleolin from the nuclei of cells to the plasma membrane, where it also binds to RSV-F on virions. We find that inhibiting PKCζ activation prevents the trafficking of nucleolin to RSV particles on airway organoid cultures, and reduces viral replication and pathology in RSV-infected mice. These findings reveal a mechanism of virus entry in which receptor engagement and signal transduction bring the coreceptor to viral particles at the cell surface, and could form the basis of new therapeutics to treat RSV infection.
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Affiliation(s)
- Cameron D Griffiths
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta, Canada
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
| | - Leanne M Bilawchuk
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta, Canada
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
| | - John E McDonough
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Kyla C Jamieson
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Farah Elawar
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta, Canada
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
| | - Yuchen Cen
- Program of Translational Medicine, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Wenming Duan
- Program of Translational Medicine, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Cindy Lin
- Program of Translational Medicine, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Haeun Song
- Program of Translational Medicine, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Jean-Laurent Casanova
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Imagine Institute, Paris Descartes University, Paris, France
- Pediatric Immunology-Hematology Unit, Necker Hospital for Sick Children, Paris, France
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Steven Ogg
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta, Canada
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
| | - Lionel Dylan Jensen
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta, Canada
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
| | - Bernard Thienpont
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Anil Kumar
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta, Canada
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
| | - Tom C Hobman
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta, Canada
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
| | - David Proud
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Theo J Moraes
- Program of Translational Medicine, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
- Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - David J Marchant
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta, Canada.
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada.
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24
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Qian J, Olbrecht S, Boeckx B, Vos H, Laoui D, Etlioglu E, Wauters E, Pomella V, Verbandt S, Busschaert P, Bassez A, Franken A, Bempt MV, Xiong J, Weynand B, van Herck Y, Antoranz A, Bosisio FM, Thienpont B, Floris G, Vergote I, Smeets A, Tejpar S, Lambrechts D. A pan-cancer blueprint of the heterogeneous tumor microenvironment revealed by single-cell profiling. Cell Res 2020; 30:745-762. [PMID: 32561858 PMCID: PMC7608385 DOI: 10.1038/s41422-020-0355-0] [Citation(s) in RCA: 300] [Impact Index Per Article: 75.0] [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: 10/09/2019] [Accepted: 05/05/2020] [Indexed: 12/16/2022] Open
Abstract
The stromal compartment of the tumor microenvironment consists of a heterogeneous set of tissue-resident and tumor-infiltrating cells, which are profoundly moulded by cancer cells. An outstanding question is to what extent this heterogeneity is similar between cancers affecting different organs. Here, we profile 233,591 single cells from patients with lung, colorectal, ovary and breast cancer (n = 36) and construct a pan-cancer blueprint of stromal cell heterogeneity using different single-cell RNA and protein-based technologies. We identify 68 stromal cell populations, of which 46 are shared between cancer types and 22 are unique. We also characterise each population phenotypically by highlighting its marker genes, transcription factors, metabolic activities and tissue-specific expression differences. Resident cell types are characterised by substantial tissue specificity, while tumor-infiltrating cell types are largely shared across cancer types. Finally, by applying the blueprint to melanoma tumors treated with checkpoint immunotherapy and identifying a naïve CD4+ T-cell phenotype predictive of response to checkpoint immunotherapy, we illustrate how it can serve as a guide to interpret scRNA-seq data. In conclusion, by providing a comprehensive blueprint through an interactive web server, we generate the first panoramic view on the shared complexity of stromal cells in different cancers.
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Affiliation(s)
- Junbin Qian
- VIB Center for Cancer Biology, Leuven, Belgium.,Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Siel Olbrecht
- VIB Center for Cancer Biology, Leuven, Belgium.,Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium.,Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven, Belgium
| | - Bram Boeckx
- VIB Center for Cancer Biology, Leuven, Belgium.,Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Hanne Vos
- Department of Oncology, KU Leuven, Surgical Oncology, University Hospitals Leuven, Leuven, Belgium
| | - Damya Laoui
- Lab of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium.,Myeloid Cell Immunology Lab, VIB Center for Inflammation Research, Brussels, Belgium
| | - Emre Etlioglu
- Laboratory of Molecular Digestive Oncology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Els Wauters
- Respiratory Oncology Unit (Pneumology) and Leuven Lung Cancer Group, University Hospital KU Leuven, Leuven, Belgium.,Laboratory of Pneumology, Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, Leuven, Belgium
| | - Valentina Pomella
- Laboratory of Molecular Digestive Oncology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Sara Verbandt
- Laboratory of Molecular Digestive Oncology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Pieter Busschaert
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven, Belgium
| | - Ayse Bassez
- VIB Center for Cancer Biology, Leuven, Belgium.,Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Amelie Franken
- VIB Center for Cancer Biology, Leuven, Belgium.,Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Marlies Vanden Bempt
- VIB Center for Cancer Biology, Leuven, Belgium.,Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Jieyi Xiong
- VIB Center for Cancer Biology, Leuven, Belgium.,Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Birgit Weynand
- Department of Imaging and Pathology, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, KU Leuven-University of Leuven, B-3000, Leuven, Belgium
| | | | - Asier Antoranz
- Department of Imaging and Pathology, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, KU Leuven-University of Leuven, B-3000, Leuven, Belgium
| | - Francesca Maria Bosisio
- Department of Imaging and Pathology, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, KU Leuven-University of Leuven, B-3000, Leuven, Belgium
| | - Bernard Thienpont
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Giuseppe Floris
- Department of Imaging and Pathology, Laboratory of Translational Cell & Tissue Research and University Hospitals Leuven, Department of Pathology, KU Leuven-University of Leuven, B-3000, Leuven, Belgium
| | - Ignace Vergote
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven, Belgium
| | - Ann Smeets
- Department of Oncology, KU Leuven, Surgical Oncology, University Hospitals Leuven, Leuven, Belgium
| | - Sabine Tejpar
- Laboratory of Molecular Digestive Oncology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Diether Lambrechts
- VIB Center for Cancer Biology, Leuven, Belgium. .,Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium.
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25
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Stegen S, Rinaldi G, Loopmans S, Stockmans I, Moermans K, Thienpont B, Fendt SM, Carmeliet P, Carmeliet G. Glutamine Metabolism Controls Chondrocyte Identity and Function. Dev Cell 2020; 53:530-544.e8. [DOI: 10.1016/j.devcel.2020.05.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 04/20/2020] [Accepted: 05/01/2020] [Indexed: 12/31/2022]
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26
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Jariani A, Vermeersch L, Cerulus B, Perez-Samper G, Voordeckers K, Van Brussel T, Thienpont B, Lambrechts D, Verstrepen KJ. A new protocol for single-cell RNA-seq reveals stochastic gene expression during lag phase in budding yeast. eLife 2020; 9:e55320. [PMID: 32420869 PMCID: PMC7259953 DOI: 10.7554/elife.55320] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [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] [Received: 01/20/2020] [Accepted: 05/15/2020] [Indexed: 12/17/2022] Open
Abstract
Current methods for single-cell RNA sequencing (scRNA-seq) of yeast cells do not match the throughput and relative simplicity of the state-of-the-art techniques that are available for mammalian cells. In this study, we report how 10x Genomics' droplet-based single-cell RNA sequencing technology can be modified to allow analysis of yeast cells. The protocol, which is based on in-droplet spheroplasting of the cells, yields an order-of-magnitude higher throughput in comparison to existing methods. After extensive validation of the method, we demonstrate its use by studying the dynamics of the response of isogenic yeast populations to a shift in carbon source, revealing the heterogeneity and underlying molecular processes during this shift. The method we describe opens new avenues for studies focusing on yeast cells, as well as other cells with a degradable cell wall.
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Affiliation(s)
- Abbas Jariani
- Laboratory for Systems Biology, VIB-KU Leuven Center for MicrobiologyLeuvenBelgium
- Laboratory of Genetics and Genomics, CMPG, Department M2S, KU LeuvenLeuvenBelgium
| | - Lieselotte Vermeersch
- Laboratory for Systems Biology, VIB-KU Leuven Center for MicrobiologyLeuvenBelgium
- Laboratory of Genetics and Genomics, CMPG, Department M2S, KU LeuvenLeuvenBelgium
| | - Bram Cerulus
- Laboratory for Systems Biology, VIB-KU Leuven Center for MicrobiologyLeuvenBelgium
- Laboratory of Genetics and Genomics, CMPG, Department M2S, KU LeuvenLeuvenBelgium
| | - Gemma Perez-Samper
- Laboratory for Systems Biology, VIB-KU Leuven Center for MicrobiologyLeuvenBelgium
- Laboratory of Genetics and Genomics, CMPG, Department M2S, KU LeuvenLeuvenBelgium
| | - Karin Voordeckers
- Laboratory for Systems Biology, VIB-KU Leuven Center for MicrobiologyLeuvenBelgium
- Laboratory of Genetics and Genomics, CMPG, Department M2S, KU LeuvenLeuvenBelgium
| | - Thomas Van Brussel
- Laboratory for Translational Genetics, Department of Human Genetics, KU LeuvenLeuvenBelgium
- VIB Center for Cancer Biology, VIBLeuvenBelgium
| | - Bernard Thienpont
- Laboratory for Translational Genetics, Department of Human Genetics, KU LeuvenLeuvenBelgium
- VIB Center for Cancer Biology, VIBLeuvenBelgium
- Laboratory for Functional Epigenetics, Department of Genetics, KU LeuvenLeuvenBelgium
| | - Diether Lambrechts
- Laboratory for Translational Genetics, Department of Human Genetics, KU LeuvenLeuvenBelgium
- VIB Center for Cancer Biology, VIBLeuvenBelgium
| | - Kevin J Verstrepen
- Laboratory for Systems Biology, VIB-KU Leuven Center for MicrobiologyLeuvenBelgium
- Laboratory of Genetics and Genomics, CMPG, Department M2S, KU LeuvenLeuvenBelgium
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27
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Rohlenova K, Goveia J, García-Caballero M, Subramanian A, Kalucka J, Treps L, Falkenberg KD, de Rooij LPMH, Zheng Y, Lin L, Sokol L, Teuwen LA, Geldhof V, Taverna F, Pircher A, Conradi LC, Khan S, Stegen S, Panovska D, De Smet F, Staal FJT, Mclaughlin RJ, Vinckier S, Van Bergen T, Ectors N, De Haes P, Wang J, Bolund L, Schoonjans L, Karakach TK, Yang H, Carmeliet G, Liu Y, Thienpont B, Dewerchin M, Eelen G, Li X, Luo Y, Carmeliet P. Single-Cell RNA Sequencing Maps Endothelial Metabolic Plasticity in Pathological Angiogenesis. Cell Metab 2020; 31:862-877.e14. [PMID: 32268117 DOI: 10.1016/j.cmet.2020.03.009] [Citation(s) in RCA: 136] [Impact Index Per Article: 34.0] [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: 07/11/2019] [Revised: 12/20/2019] [Accepted: 03/09/2020] [Indexed: 01/22/2023]
Abstract
Endothelial cell (EC) metabolism is an emerging target for anti-angiogenic therapy in tumor angiogenesis and choroidal neovascularization (CNV), but little is known about individual EC metabolic transcriptomes. By single-cell RNA sequencing 28,337 murine choroidal ECs (CECs) and sprouting CNV-ECs, we constructed a taxonomy to characterize their heterogeneity. Comparison with murine lung tumor ECs (TECs) revealed congruent marker gene expression by distinct EC phenotypes across tissues and diseases, suggesting similar angiogenic mechanisms. Trajectory inference predicted that differentiation of venous to angiogenic ECs was accompanied by metabolic transcriptome plasticity. ECs displayed metabolic transcriptome heterogeneity during cell-cycle progression and in quiescence. Hypothesizing that conserved genes are important, we used an integrated analysis, based on congruent transcriptome analysis, CEC-tailored genome-scale metabolic modeling, and gene expression meta-analysis in cross-species datasets, followed by in vitro and in vivo validation, to identify SQLE and ALDH18A1 as previously unknown metabolic angiogenic targets.
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Affiliation(s)
- Katerina Rohlenova
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB, Department of Oncology, Leuven Cancer Institute, KU Leuven, Leuven 3000, Belgium
| | - Jermaine Goveia
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB, Department of Oncology, Leuven Cancer Institute, KU Leuven, Leuven 3000, Belgium
| | - Melissa García-Caballero
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB, Department of Oncology, Leuven Cancer Institute, KU Leuven, Leuven 3000, Belgium
| | - Abhishek Subramanian
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB, Department of Oncology, Leuven Cancer Institute, KU Leuven, Leuven 3000, Belgium
| | - Joanna Kalucka
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB, Department of Oncology, Leuven Cancer Institute, KU Leuven, Leuven 3000, Belgium
| | - Lucas Treps
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB, Department of Oncology, Leuven Cancer Institute, KU Leuven, Leuven 3000, Belgium
| | - Kim D Falkenberg
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB, Department of Oncology, Leuven Cancer Institute, KU Leuven, Leuven 3000, Belgium
| | - Laura P M H de Rooij
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB, Department of Oncology, Leuven Cancer Institute, KU Leuven, Leuven 3000, Belgium
| | - Yingfeng Zheng
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510060, Guangdong, China
| | - Lin Lin
- Department of Biomedicine, Aarhus University, Aarhus 8000, Denmark; Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China
| | - Liliana Sokol
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB, Department of Oncology, Leuven Cancer Institute, KU Leuven, Leuven 3000, Belgium
| | - Laure-Anne Teuwen
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB, Department of Oncology, Leuven Cancer Institute, KU Leuven, Leuven 3000, Belgium; Translational Cancer Research Unit, GZA Hospitals Sint-Augustinus, Antwerp 2610, Belgium; Center for Oncological Research, University of Antwerp, Antwerp 2000, Belgium
| | - Vincent Geldhof
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB, Department of Oncology, Leuven Cancer Institute, KU Leuven, Leuven 3000, Belgium
| | - Federico Taverna
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB, Department of Oncology, Leuven Cancer Institute, KU Leuven, Leuven 3000, Belgium
| | - Andreas Pircher
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB, Department of Oncology, Leuven Cancer Institute, KU Leuven, Leuven 3000, Belgium
| | - Lena-Christin Conradi
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB, Department of Oncology, Leuven Cancer Institute, KU Leuven, Leuven 3000, Belgium
| | - Shawez Khan
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB, Department of Oncology, Leuven Cancer Institute, KU Leuven, Leuven 3000, Belgium
| | - Steve Stegen
- Laboratory of Clinical and Experimental Endocrinology, Department of Chronic Diseases, Metabolism and Aging, KU Leuven, Leuven 3000, Belgium
| | - Dena Panovska
- Laboratory for Precision Cancer Medicine, Translational Cell & Tissue Research, Department of Imaging & Pathology, KU Leuven, Leuven 3000, Belgium
| | - Frederik De Smet
- Laboratory for Precision Cancer Medicine, Translational Cell & Tissue Research, Department of Imaging & Pathology, KU Leuven, Leuven 3000, Belgium
| | - Frank J T Staal
- Department of Immunology and Blood Transfusion, Leiden University Medical Center, Leiden 2300 RC, the Netherlands
| | - Rene J Mclaughlin
- Department of Immunology and Blood Transfusion, Leiden University Medical Center, Leiden 2300 RC, the Netherlands
| | - Stefan Vinckier
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB, Department of Oncology, Leuven Cancer Institute, KU Leuven, Leuven 3000, Belgium
| | | | - Nadine Ectors
- Laboratory for Precision Cancer Medicine, Translational Cell & Tissue Research, Department of Imaging & Pathology, KU Leuven, Leuven 3000, Belgium
| | | | - Jian Wang
- BGI-Shenzhen, Shenzhen 518083, China; China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Lars Bolund
- Department of Biomedicine, Aarhus University, Aarhus 8000, Denmark; Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China
| | - Luc Schoonjans
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB, Department of Oncology, Leuven Cancer Institute, KU Leuven, Leuven 3000, Belgium; State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510060, Guangdong, China
| | - Tobias K Karakach
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB, Department of Oncology, Leuven Cancer Institute, KU Leuven, Leuven 3000, Belgium
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen 518083, China; China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Geert Carmeliet
- Laboratory of Clinical and Experimental Endocrinology, Department of Chronic Diseases, Metabolism and Aging, KU Leuven, Leuven 3000, Belgium
| | - Yizhi Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510060, Guangdong, China
| | - Bernard Thienpont
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, Leuven 3000, Belgium
| | - Mieke Dewerchin
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB, Department of Oncology, Leuven Cancer Institute, KU Leuven, Leuven 3000, Belgium
| | - Guy Eelen
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB, Department of Oncology, Leuven Cancer Institute, KU Leuven, Leuven 3000, Belgium
| | - Xuri Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510060, Guangdong, China.
| | - Yonglun Luo
- Department of Biomedicine, Aarhus University, Aarhus 8000, Denmark; Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China; BGI-Shenzhen, Shenzhen 518083, China; China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China.
| | - Peter Carmeliet
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB, Department of Oncology, Leuven Cancer Institute, KU Leuven, Leuven 3000, Belgium; State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510060, Guangdong, China.
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28
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Bartoccetti M, van der Veer BK, Luo X, Khoueiry R, She P, Bajaj M, Xu J, Janiszewski A, Thienpont B, Pasque V, Koh KP. Regulatory Dynamics of Tet1 and Oct4 Resolve Stages of Global DNA Demethylation and Transcriptomic Changes in Reprogramming. Cell Rep 2020; 30:3948. [PMID: 32187561 DOI: 10.1016/j.celrep.2020.03.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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29
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Goveia J, Rohlenova K, Taverna F, Treps L, Conradi LC, Pircher A, Geldhof V, de Rooij LPMH, Kalucka J, Sokol L, García-Caballero M, Zheng Y, Qian J, Teuwen LA, Khan S, Boeckx B, Wauters E, Decaluwé H, De Leyn P, Vansteenkiste J, Weynand B, Sagaert X, Verbeken E, Wolthuis A, Topal B, Everaerts W, Bohnenberger H, Emmert A, Panovska D, De Smet F, Staal FJT, Mclaughlin RJ, Impens F, Lagani V, Vinckier S, Mazzone M, Schoonjans L, Dewerchin M, Eelen G, Karakach TK, Yang H, Wang J, Bolund L, Lin L, Thienpont B, Li X, Lambrechts D, Luo Y, Carmeliet P. An Integrated Gene Expression Landscape Profiling Approach to Identify Lung Tumor Endothelial Cell Heterogeneity and Angiogenic Candidates. Cancer Cell 2020; 37:421. [PMID: 32183954 DOI: 10.1016/j.ccell.2020.03.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Galle E, Thienpont B, Cappuyns S, Venken T, Busschaert P, Van Haele M, Van Cutsem E, Roskams T, van Pelt J, Verslype C, Dekervel J, Lambrechts D. DNA methylation-driven EMT is a common mechanism of resistance to various therapeutic agents in cancer. Clin Epigenetics 2020; 12:27. [PMID: 32059745 PMCID: PMC7023776 DOI: 10.1186/s13148-020-0821-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [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: 09/24/2019] [Accepted: 01/30/2020] [Indexed: 01/06/2023] Open
Abstract
Background Overcoming therapeutic resistance is one of the major hurdles in cancer care. One mechanism contributing to therapeutic resistance is a process in which epithelial cells switch to a mesenchymal state (epithelial-to-mesenchymal transition or EMT). The precise mechanisms driving EMT-mediated therapeutic resistance have, however, not been elucidated. Results Here, we study ten cell line pairs, for which parental cell lines were made resistant to either a targeted or chemotherapy-based treatment. First, we show by miRNA-200 overexpression that treatment resistance is driven by EMT. Next, we demonstrate that DNA methylation changes occur within each cell line pair and show that exposure to 5-azacytidine or knock down of DNA methyltransferases (DNMTs), both of which globally demethylate cells, result in EMT reversal and increased therapeutic sensitivity. This suggests DNA methylation to causally underlie EMT and treatment resistance. We also observe significant overlap in methylation profiles between resistant lines, suggesting a common epigenetic mechanism to cause resistance to therapy. In line with this hypothesis, cross-resistance to other targeted and chemotherapies is observed, while importantly, this is lost upon demethylation of the cells. Finally, we clinically validate that DNA methylation changes drive EMT-mediated resistance to sorafenib in patients with advanced hepatocellular carcinoma (HCC). Specifically, we develop a capture-based protocol to interrogate DNA methylation in low amounts of circulating tumor DNA (ctDNA). By interrogating the methylation status in liquid biopsies, longitudinally collected during sorafenib treatment, we assess whether DNA methylation changes also drive EMT and therapy resistance in a clinical setting. Particularly, by monitoring methylation changes in EMT genes, we are able to predict tumor response and acquired resistance to sorafenib. Conclusions We propose methylation changes underlying EMT to constitute a common resistance mechanism to cancer therapies. This process can be reversed pharmacologically and monitored non-invasively in ctDNA to predict resistance to treatment.
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Affiliation(s)
- Eva Galle
- Centre for Cancer Biology, VIB, 3000, Leuven, Belgium.,Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium.,Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
| | - Bernard Thienpont
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
| | - Sarah Cappuyns
- Centre for Cancer Biology, VIB, 3000, Leuven, Belgium.,Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium.,Clinical Digestive Oncology, Department of Oncology, KU Leuven and University Hospitals Leuven, 3000, Leuven, Belgium
| | - Tom Venken
- Centre for Cancer Biology, VIB, 3000, Leuven, Belgium.,Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
| | - Pieter Busschaert
- Centre for Cancer Biology, VIB, 3000, Leuven, Belgium.,Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
| | - Matthias Van Haele
- Department of Imaging and Pathology, Translational Cell and Tissue Research, KU Leuven and University Hospitals Leuven, 3000, Leuven, Belgium
| | - Eric Van Cutsem
- Clinical Digestive Oncology, Department of Oncology, KU Leuven and University Hospitals Leuven, 3000, Leuven, Belgium
| | - Tania Roskams
- Department of Imaging and Pathology, Translational Cell and Tissue Research, KU Leuven and University Hospitals Leuven, 3000, Leuven, Belgium
| | - Jos van Pelt
- Laboratory of Clinical Digestive Oncology, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), 3000, Leuven, Belgium
| | - Chris Verslype
- Clinical Digestive Oncology, Department of Oncology, KU Leuven and University Hospitals Leuven, 3000, Leuven, Belgium
| | - Jeroen Dekervel
- Clinical Digestive Oncology, Department of Oncology, KU Leuven and University Hospitals Leuven, 3000, Leuven, Belgium.
| | - Diether Lambrechts
- Centre for Cancer Biology, VIB, 3000, Leuven, Belgium. .,Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium.
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Kalucka J, de Rooij LP, Goveia J, Rohlenova K, Dumas SJ, Meta E, Conchinha NV, Taverna F, Teuwen LA, Veys K, García-Caballero M, Khan S, Geldhof V, Sokol L, Chen R, Treps L, Borri M, de Zeeuw P, Dubois C, Karakach TK, Falkenberg KD, Parys M, Yin X, Vinckier S, Du Y, Fenton RA, Schoonjans L, Dewerchin M, Eelen G, Thienpont B, Lin L, Bolund L, Li X, Luo Y, Carmeliet P. Single-Cell Transcriptome Atlas of Murine Endothelial Cells. Cell 2020; 180:764-779.e20. [DOI: 10.1016/j.cell.2020.01.015] [Citation(s) in RCA: 284] [Impact Index Per Article: 71.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 11/21/2019] [Accepted: 01/09/2020] [Indexed: 12/29/2022]
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32
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Goveia J, Rohlenova K, Taverna F, Treps L, Conradi LC, Pircher A, Geldhof V, de Rooij LPMH, Kalucka J, Sokol L, García-Caballero M, Zheng Y, Qian J, Teuwen LA, Khan S, Boeckx B, Wauters E, Decaluwé H, De Leyn P, Vansteenkiste J, Weynand B, Sagaert X, Verbeken E, Wolthuis A, Topal B, Everaerts W, Bohnenberger H, Emmert A, Panovska D, De Smet F, Staal FJT, Mclaughlin RJ, Impens F, Lagani V, Vinckier S, Mazzone M, Schoonjans L, Dewerchin M, Eelen G, Karakach TK, Yang H, Wang J, Bolund L, Lin L, Thienpont B, Li X, Lambrechts D, Luo Y, Carmeliet P. An Integrated Gene Expression Landscape Profiling Approach to Identify Lung Tumor Endothelial Cell Heterogeneity and Angiogenic Candidates. Cancer Cell 2020; 37:21-36.e13. [PMID: 31935371 DOI: 10.1016/j.ccell.2019.12.001] [Citation(s) in RCA: 186] [Impact Index Per Article: 46.5] [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: 05/24/2019] [Revised: 08/30/2019] [Accepted: 12/06/2019] [Indexed: 12/20/2022]
Abstract
Heterogeneity of lung tumor endothelial cell (TEC) phenotypes across patients, species (human/mouse), and models (in vivo/in vitro) remains poorly inventoried at the single-cell level. We single-cell RNA (scRNA)-sequenced 56,771 endothelial cells from human/mouse (peri)-tumoral lung and cultured human lung TECs, and detected 17 known and 16 previously unrecognized phenotypes, including TECs putatively regulating immune surveillance. We resolved the canonical tip TECs into a known migratory tip and a putative basement-membrane remodeling breach phenotype. Tip TEC signatures correlated with patient survival, and tip/breach TECs were most sensitive to vascular endothelial growth factor blockade. Only tip TECs were congruent across species/models and shared conserved markers. Integrated analysis of the scRNA-sequenced data with orthogonal multi-omics and meta-analysis data across different human tumors, validated by functional analysis, identified collagen modification as a candidate angiogenic pathway.
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Affiliation(s)
- Jermaine Goveia
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Katerina Rohlenova
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Federico Taverna
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Lucas Treps
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Lena-Christin Conradi
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Andreas Pircher
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Vincent Geldhof
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Laura P M H de Rooij
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Joanna Kalucka
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Liliana Sokol
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Melissa García-Caballero
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Yingfeng Zheng
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510060, Guangdong, China
| | - Junbin Qian
- Laboratory of Translational Genetics, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Laure-Anne Teuwen
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Shawez Khan
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Bram Boeckx
- Laboratory of Translational Genetics, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Els Wauters
- Respiratory Oncology Unit (Respiratory Medicine) and Leuven Lung Cancer Group, University Hospitals Leuven, Leuven 3000, Belgium
| | - Herbert Decaluwé
- Respiratory Oncology Unit (Respiratory Medicine) and Leuven Lung Cancer Group, University Hospitals Leuven, Leuven 3000, Belgium; Department of Thoracic Surgery, University Hospitals Leuven, Leuven 3000, Belgium
| | - Paul De Leyn
- Respiratory Oncology Unit (Respiratory Medicine) and Leuven Lung Cancer Group, University Hospitals Leuven, Leuven 3000, Belgium; Department of Thoracic Surgery, University Hospitals Leuven, Leuven 3000, Belgium
| | - Johan Vansteenkiste
- Respiratory Oncology Unit (Respiratory Medicine) and Leuven Lung Cancer Group, University Hospitals Leuven, Leuven 3000, Belgium
| | - Birgit Weynand
- Translational Cell & Tissue Research, Department of Imaging & Pathology, KU Leuven, Leuven 3000, Belgium
| | - Xavier Sagaert
- Translational Cell & Tissue Research, Department of Imaging & Pathology, KU Leuven, Leuven 3000, Belgium
| | - Erik Verbeken
- Translational Cell & Tissue Research, Department of Imaging & Pathology, KU Leuven, Leuven 3000, Belgium
| | - Albert Wolthuis
- Department of Abdominal Surgery, University Hospitals Leuven, Leuven 3000, Belgium
| | - Baki Topal
- Department of Abdominal Surgery, University Hospitals Leuven, Leuven 3000, Belgium
| | - Wouter Everaerts
- Laboratory for Experimental Urology, Department of Development and Regeneration, KU Leuven, Leuven 3000, Belgium; Department of Urology, University Hospitals Leuven, Leuven 3000, Belgium
| | | | - Alexander Emmert
- Department of Thoracic and Cardiovascular Surgery, University Medical Center, Göttingen 37075, Germany
| | - Dena Panovska
- Laboratory for Precision Cancer Medicine, Translational Cell & Tissue Research, Department of Imaging & Pathology, KU Leuven, Leuven 3000, Belgium
| | - Frederik De Smet
- Laboratory for Precision Cancer Medicine, Translational Cell & Tissue Research, Department of Imaging & Pathology, KU Leuven, Leuven 3000, Belgium
| | - Frank J T Staal
- Department of Immunology and Blood Transfusion, Leiden University Medical Center, Leiden 2300 RC, the Netherlands
| | - Rene J Mclaughlin
- Department of Immunology and Blood Transfusion, Leiden University Medical Center, Leiden 2300 RC, the Netherlands
| | - Francis Impens
- VIB Proteomics Core and VIB Center for Medical Biotechnology, Ghent 9000, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent 9000, Belgium
| | - Vincenzo Lagani
- Institute of Chemical Biology, Ilia State University, Tbilisi 0162, Georgia; Gnosis Data Analysis PC, Heraklion GR-700 13, Greece
| | - Stefan Vinckier
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Massimiliano Mazzone
- Laboratory of Tumor Inflammation and Angiogenesis, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Luc Schoonjans
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Mieke Dewerchin
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Guy Eelen
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Tobias K Karakach
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen 518083, China; China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen 518083, China; China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Lars Bolund
- Department of Biomedicine, Aarhus University, Aarhus 8000, Denmark; Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China
| | - Lin Lin
- Department of Biomedicine, Aarhus University, Aarhus 8000, Denmark; Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China
| | - Bernard Thienpont
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, Leuven 3000, Belgium
| | - Xuri Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510060, Guangdong, China.
| | - Diether Lambrechts
- Laboratory of Translational Genetics, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, Leuven 3000, Belgium
| | - Yonglun Luo
- BGI-Shenzhen, Shenzhen 518083, China; China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China; Department of Biomedicine, Aarhus University, Aarhus 8000, Denmark; Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China.
| | - Peter Carmeliet
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, VIB Center for Cancer Biology, Leuven 3000, Belgium; State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 510060, Guangdong, China.
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Balikova I, Postelmans L, Pasteels B, Coquelet P, Catherine J, Efendic A, Hosoda Y, Miyake M, Yamashiro K, Thienpont B, Lambrechts D. Genetic biomarkers in the VEGF pathway predicting response to anti-VEGF therapy in age-related macular degeneration. BMJ Open Ophthalmol 2020; 4:e000273. [PMID: 31909188 PMCID: PMC6936450 DOI: 10.1136/bmjophth-2019-000273] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 01/14/2019] [Revised: 10/18/2019] [Accepted: 11/11/2019] [Indexed: 11/17/2022] Open
Abstract
Objective Age-related macular degeneration (ARMD) is a leading cause of visual impairment.
Intravitreal injections of anti-vascular endothelial growth factor (VEGF) are the
standard treatment for wet ARMD. There is however, variability in patient responses,
suggesting patient-specific factors influencing drug efficacy. We tested whether single
nucleotide polymorphisms (SNPs) in genes encoding VEGF pathway members contribute to
therapy response. Methods and analysis A retrospective cohort of 281 European wet ARMD patients treated with anti-VEGF was
genotyped for 138 tagging SNPs in the VEGF pathway. Per patient, we collected best
corrected visual acuity at baseline, after three loading injections and at 12 months. We
also registered the injection number and changes in retinal morphology after three
loading injections (central foveal thickness (CFT), intraretinal cysts and serous
neuroepithelium detachment). Changes in CFT after 3 months were our primary outcome
measure. Association of SNPs to response was assessed by binomial logistic regression.
Replication was attempted by associating visual acuity changes to genotypes in an
independent Japanese cohort. Results Association with treatment response was detected for seven SNPs, including in FLT4
(rs55667289: OR=0.746, 95% CI 0.63 to 0.88, p=0.0005) and KDR (rs7691507:
OR=1.056, 95% CI 1.02 to 1.10, p=0.005; and rs2305945: OR=0.963, 95% CI
0.93 to 1.00, p=0.0472). Only association with rs55667289 in FLT4 survived multiple
testing correction. This SNP was unavailable for testing in the replication cohort. Of
six SNPs tested for replication, one was significant although not after multiple testing
correction. Conclusion Identifying genetic variants that define treatment response can help to develop
individualised therapeutic approaches for wet ARMD patients and may point towards new
targets in non-responders.
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Affiliation(s)
- Irina Balikova
- Department of Ophthalmology, Ghent University Hospital, Ghent University, Ghent, Belgium.,Ophthalmology, University Hospital Brugmann, Université Libre de Bruxelles, Brussels, Belgium
| | - Laurence Postelmans
- Ophthalmology, University Hospital Brugmann, Université Libre de Bruxelles, Brussels, Belgium
| | - Brigitte Pasteels
- Ophthalmology, University Hospital Brugmann, Université Libre de Bruxelles, Brussels, Belgium
| | - Pascale Coquelet
- Ophthalmology, University Hospital Brugmann, Université Libre de Bruxelles, Brussels, Belgium
| | - Janet Catherine
- Ophthalmology, University Hospital Brugmann, Université Libre de Bruxelles, Brussels, Belgium
| | - Azra Efendic
- Ophthalmology, University Hospital Brugmann, Université Libre de Bruxelles, Brussels, Belgium
| | - Yoshikatsu Hosoda
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Masahiro Miyake
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Kenji Yamashiro
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, Kyoto, Japan.,Department of Ophthalmology, Otsu Red Cross Hospital, Otsu, Japan
| | | | - Bernard Thienpont
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium.,Laboratory of Functional Epigenetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Diether Lambrechts
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium.,VIB Center for Cancer Biology, Leuven, Belgium
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Kalucka J, Bierhansl L, Conchinha NV, Missiaen R, Elia I, Brüning U, Scheinok S, Treps L, Cantelmo AR, Dubois C, de Zeeuw P, Goveia J, Zecchin A, Taverna F, Morales-Rodriguez F, Brajic A, Conradi LC, Schoors S, Harjes U, Vriens K, Pilz GA, Chen R, Cubbon R, Thienpont B, Cruys B, Wong BW, Ghesquière B, Dewerchin M, De Bock K, Sagaert X, Jessberger S, Jones EAV, Gallez B, Lambrechts D, Mazzone M, Eelen G, Li X, Fendt SM, Carmeliet P. Quiescent Endothelial Cells Upregulate Fatty Acid β-Oxidation for Vasculoprotection via Redox Homeostasis. Cell Metab 2018; 28:881-894.e13. [PMID: 30146488 DOI: 10.1016/j.cmet.2018.07.016] [Citation(s) in RCA: 144] [Impact Index Per Article: 24.0] [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: 08/14/2017] [Revised: 06/09/2018] [Accepted: 07/28/2018] [Indexed: 01/15/2023]
Abstract
Little is known about the metabolism of quiescent endothelial cells (QECs). Nonetheless, when dysfunctional, QECs contribute to multiple diseases. Previously, we demonstrated that proliferating endothelial cells (PECs) use fatty acid β-oxidation (FAO) for de novo dNTP synthesis. We report now that QECs are not hypometabolic, but upregulate FAO >3-fold higher than PECs, not to support biomass or energy production but to sustain the tricarboxylic acid cycle for redox homeostasis through NADPH regeneration. Hence, endothelial loss of FAO-controlling CPT1A in CPT1AΔEC mice promotes EC dysfunction (leukocyte infiltration, barrier disruption) by increasing endothelial oxidative stress, rendering CPT1AΔEC mice more susceptible to LPS and inflammatory bowel disease. Mechanistically, Notch1 orchestrates the use of FAO for redox balance in QECs. Supplementation of acetate (metabolized to acetyl-coenzyme A) restores endothelial quiescence and counters oxidative stress-mediated EC dysfunction in CPT1AΔEC mice, offering therapeutic opportunities. Thus, QECs use FAO for vasculoprotection against oxidative stress-prone exposure.
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Affiliation(s)
- Joanna Kalucka
- Laboratory of Angiogenesis and Vascular Metabolism, VIB Center for Cancer Biology (CCB), VIB, 3000 Leuven, Belgium; State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 51006, Guangdong, P.R. China; Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, 3000 Leuven, Belgium
| | - Laura Bierhansl
- Laboratory of Angiogenesis and Vascular Metabolism, VIB Center for Cancer Biology (CCB), VIB, 3000 Leuven, Belgium; Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, 3000 Leuven, Belgium
| | - Nadine Vasconcelos Conchinha
- Laboratory of Angiogenesis and Vascular Metabolism, VIB Center for Cancer Biology (CCB), VIB, 3000 Leuven, Belgium; Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, 3000 Leuven, Belgium
| | - Rindert Missiaen
- Laboratory of Angiogenesis and Vascular Metabolism, VIB Center for Cancer Biology (CCB), VIB, 3000 Leuven, Belgium; Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, 3000 Leuven, Belgium
| | - Ilaria Elia
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, 3000 Leuven, Belgium; Laboratory of Cellular Metabolism and Metabolic Regulation, VIB Center for Cancer Biology, Center for Cancer Biology (CCB), VIB, 3000 Leuven, Belgium
| | - Ulrike Brüning
- Laboratory of Angiogenesis and Vascular Metabolism, VIB Center for Cancer Biology (CCB), VIB, 3000 Leuven, Belgium; Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, 3000 Leuven, Belgium
| | - Samantha Scheinok
- Université Catholique de Louvain, Louvain Drug Research Institute, Biomedical Magnetic Resonance Research Group, 1200 Brussels, Belgium
| | - Lucas Treps
- Laboratory of Angiogenesis and Vascular Metabolism, VIB Center for Cancer Biology (CCB), VIB, 3000 Leuven, Belgium; Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, 3000 Leuven, Belgium
| | - Anna Rita Cantelmo
- Laboratory of Angiogenesis and Vascular Metabolism, VIB Center for Cancer Biology (CCB), VIB, 3000 Leuven, Belgium; Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, 3000 Leuven, Belgium
| | - Charlotte Dubois
- Laboratory of Angiogenesis and Vascular Metabolism, VIB Center for Cancer Biology (CCB), VIB, 3000 Leuven, Belgium; Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, 3000 Leuven, Belgium
| | - Pauline de Zeeuw
- Laboratory of Angiogenesis and Vascular Metabolism, VIB Center for Cancer Biology (CCB), VIB, 3000 Leuven, Belgium; Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, 3000 Leuven, Belgium
| | - Jermaine Goveia
- Laboratory of Angiogenesis and Vascular Metabolism, VIB Center for Cancer Biology (CCB), VIB, 3000 Leuven, Belgium; Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, 3000 Leuven, Belgium
| | - Annalisa Zecchin
- Laboratory of Angiogenesis and Vascular Metabolism, VIB Center for Cancer Biology (CCB), VIB, 3000 Leuven, Belgium; Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, 3000 Leuven, Belgium
| | - Federico Taverna
- Laboratory of Angiogenesis and Vascular Metabolism, VIB Center for Cancer Biology (CCB), VIB, 3000 Leuven, Belgium; Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, 3000 Leuven, Belgium
| | - Francisco Morales-Rodriguez
- Laboratory of Angiogenesis and Vascular Metabolism, VIB Center for Cancer Biology (CCB), VIB, 3000 Leuven, Belgium; Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, 3000 Leuven, Belgium
| | - Aleksandra Brajic
- Laboratory of Angiogenesis and Vascular Metabolism, VIB Center for Cancer Biology (CCB), VIB, 3000 Leuven, Belgium; Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, 3000 Leuven, Belgium
| | - Lena-Christin Conradi
- Laboratory of Angiogenesis and Vascular Metabolism, VIB Center for Cancer Biology (CCB), VIB, 3000 Leuven, Belgium; Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, 3000 Leuven, Belgium
| | - Sandra Schoors
- Laboratory of Angiogenesis and Vascular Metabolism, VIB Center for Cancer Biology (CCB), VIB, 3000 Leuven, Belgium; Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, 3000 Leuven, Belgium
| | - Ulrike Harjes
- Laboratory of Angiogenesis and Vascular Metabolism, VIB Center for Cancer Biology (CCB), VIB, 3000 Leuven, Belgium; Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, 3000 Leuven, Belgium
| | - Kim Vriens
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, 3000 Leuven, Belgium; Laboratory of Cellular Metabolism and Metabolic Regulation, VIB Center for Cancer Biology, Center for Cancer Biology (CCB), VIB, 3000 Leuven, Belgium
| | - Gregor-Alexander Pilz
- Brain Research Institute, Faculty of Medicine and Science, University of Zurich, Zurich 8057, Switzerland
| | - Rongyuan Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 51006, Guangdong, P.R. China
| | - Richard Cubbon
- Division of Cardiovascular and Diabetes Research, Multidisciplinary Cardiovascular Research Centre, University of Leeds, Leeds LS2 9JT, UK
| | - Bernard Thienpont
- Laboratory of Translational Genetics, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, 3000 Leuven, Belgium; Laboratory of Translational Genetics, VIB Center for Cancer Biology (CCB), VIB, 3000 Leuven, Belgium
| | - Bert Cruys
- Laboratory of Angiogenesis and Vascular Metabolism, VIB Center for Cancer Biology (CCB), VIB, 3000 Leuven, Belgium; Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, 3000 Leuven, Belgium
| | - Brian W Wong
- Laboratory of Angiogenesis and Vascular Metabolism, VIB Center for Cancer Biology (CCB), VIB, 3000 Leuven, Belgium; Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, 3000 Leuven, Belgium
| | - Bart Ghesquière
- Metabolomics Expertise Center, VIB Center for Cancer Biology (CCB), VIB, 3000 Leuven, Belgium; Metabolomics Expertise Center, Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Mieke Dewerchin
- Laboratory of Angiogenesis and Vascular Metabolism, VIB Center for Cancer Biology (CCB), VIB, 3000 Leuven, Belgium; Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, 3000 Leuven, Belgium
| | - Katrien De Bock
- Laboratory of Angiogenesis and Vascular Metabolism, VIB Center for Cancer Biology (CCB), VIB, 3000 Leuven, Belgium; Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, 3000 Leuven, Belgium
| | - Xavier Sagaert
- Translational Cell & Tissue Research, Department of Imaging & Pathology, KU Leuven, 3000 Leuven, Belgium
| | - Sebastian Jessberger
- Brain Research Institute, Faculty of Medicine and Science, University of Zurich, Zurich 8057, Switzerland
| | - Elizabeth A V Jones
- Department of Cardiovascular Sciences, KU Leuven, UZ Herestraat 49, Box 911, 3000 Leuven, Belgium; Centre for Molecular and Vascular Biology, KU Leuven, UZ Herestraat 49, Box 911, 3000 Leuven, Belgium
| | - Bernard Gallez
- Université Catholique de Louvain, Louvain Drug Research Institute, Biomedical Magnetic Resonance Research Group, 1200 Brussels, Belgium
| | - Diether Lambrechts
- Laboratory of Translational Genetics, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, 3000 Leuven, Belgium; Laboratory of Translational Genetics, VIB Center for Cancer Biology (CCB), VIB, 3000 Leuven, Belgium
| | - Massimiliano Mazzone
- Laboratory of Tumor Inflammation and Angiogenesis, VIB Center for Cancer Biology (CCB), VIB, 3000 Leuven, Belgium; Laboratory of Tumor Inflammation and Angiogenesis, Department of Oncology, University of Leuven, 3000 Leuven, Belgium
| | - Guy Eelen
- Laboratory of Angiogenesis and Vascular Metabolism, VIB Center for Cancer Biology (CCB), VIB, 3000 Leuven, Belgium; Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, 3000 Leuven, Belgium
| | - Xuri Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 51006, Guangdong, P.R. China.
| | - Sarah-Maria Fendt
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, 3000 Leuven, Belgium; Laboratory of Cellular Metabolism and Metabolic Regulation, VIB Center for Cancer Biology, Center for Cancer Biology (CCB), VIB, 3000 Leuven, Belgium
| | - Peter Carmeliet
- Laboratory of Angiogenesis and Vascular Metabolism, VIB Center for Cancer Biology (CCB), VIB, 3000 Leuven, Belgium; State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou 51006, Guangdong, P.R. China; Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, 3000 Leuven, Belgium.
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35
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McDonough JE, Kaminski N, Thienpont B, Hogg JC, Vanaudenaerde BM, Wuyts WA. Gene correlation network analysis to identify regulatory factors in idiopathic pulmonary fibrosis. Thorax 2018; 74:132-140. [PMID: 30366970 PMCID: PMC6467239 DOI: 10.1136/thoraxjnl-2018-211929] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [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: 04/12/2018] [Revised: 09/21/2018] [Accepted: 09/24/2018] [Indexed: 12/31/2022]
Abstract
BACKGROUND Idiopathic pulmonary fibrosis (IPF) is a severe lung disease characterised by extensive pathological changes. The objective for this study was to identify the gene network and regulators underlying disease pathology in IPF and its association with lung function. METHODS Lung Tissue Research Consortium dataset with 262 IPF and control subjects (GSE47460) was randomly divided into two non-overlapping groups for cross-validated differential gene expression analysis. Consensus weighted gene coexpression network analysis identified overlapping coexpressed gene modules between both IPF groups. Modules were correlated with lung function (diffusion capacity, DLCO; forced expiratory volume in 1 s, FEV1; forced vital capacity, FVC) and enrichment analyses used to identify biological function and transcription factors. Module correlation with miRNA data (GSE72967) identified associated regulators. Clinical relevance in IPF was assessed in a peripheral blood gene expression dataset (GSE93606) to identify modules related to survival. RESULTS Correlation network analysis identified 16 modules in IPF. Upregulated modules were associated with cilia, DNA replication and repair, contractile fibres, B-cell and unfolded protein response, and extracellular matrix. Downregulated modules were associated with blood vessels, T-cell and interferon responses, leucocyte activation and degranulation, surfactant metabolism, and cellular metabolic and catabolic processes. Lung function correlated with nine modules (eight with DLCO, five with FVC). Intermodular network of transcription factors and miRNA showed clustering of fibrosis, immune response and contractile modules. The cilia-associated module was able to predict survival (p=0.0097) in an independent peripheral blood IPF cohort. CONCLUSIONS We identified a correlation gene expression network with associated regulators in IPF that provides novel insight into the pathological process of this disease.
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Affiliation(s)
- John E McDonough
- Laboratory of Respiratory Diseases, Department of Chronic Diseases, Metabolism, and Ageing, KU Leuven, Leuven, Belgium
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale University, New Haven, Connecticut, USA
| | - Bernard Thienpont
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - James C Hogg
- Centre for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Bart M Vanaudenaerde
- Laboratory of Respiratory Diseases, Department of Chronic Diseases, Metabolism, and Ageing, KU Leuven, Leuven, Belgium
| | - Wim A Wuyts
- Laboratory of Respiratory Diseases, Department of Chronic Diseases, Metabolism, and Ageing, KU Leuven, Leuven, Belgium
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36
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Lambrechts D, Wauters E, Boeckx B, Aibar S, Nittner D, Burton O, Bassez A, Decaluwé H, Pircher A, Van den Eynde K, Weynand B, Verbeken E, De Leyn P, Liston A, Vansteenkiste J, Carmeliet P, Aerts S, Thienpont B. Phenotype molding of stromal cells in the lung tumor microenvironment. Nat Med 2018; 24:1277-1289. [PMID: 29988129 DOI: 10.1038/s41591-018-0096-5] [Citation(s) in RCA: 906] [Impact Index Per Article: 151.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 05/16/2018] [Indexed: 02/07/2023]
Abstract
Cancer cells are embedded in the tumor microenvironment (TME), a complex ecosystem of stromal cells. Here, we present a 52,698-cell catalog of the TME transcriptome in human lung tumors at single-cell resolution, validated in independent samples where 40,250 additional cells were sequenced. By comparing with matching non-malignant lung samples, we reveal a highly complex TME that profoundly molds stromal cells. We identify 52 stromal cell subtypes, including novel subpopulations in cell types hitherto considered to be homogeneous, as well as transcription factors underlying their heterogeneity. For instance, we discover fibroblasts expressing different collagen sets, endothelial cells downregulating immune cell homing and genes coregulated with established immune checkpoint transcripts and correlating with T-cell activity. By assessing marker genes for these cell subtypes in bulk RNA-sequencing data from 1,572 patients, we illustrate how these correlate with survival, while immunohistochemistry for selected markers validates them as separate cellular entities in an independent series of lung tumors. Hence, in providing a comprehensive catalog of stromal cells types and by characterizing their phenotype and co-optive behavior, this resource provides deeper insights into lung cancer biology that will be helpful in advancing lung cancer diagnosis and therapy.
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Affiliation(s)
- Diether Lambrechts
- VIB Center for Cancer Biology, Leuven, Belgium. .,Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium.
| | - Els Wauters
- Respiratory Oncology Unit (Pneumology) and Leuven Lung Cancer Group, University Hospitals KU Leuven, Leuven, Belgium.,Laboratory of Pneumology, Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, Leuven, Belgium
| | - Bram Boeckx
- VIB Center for Cancer Biology, Leuven, Belgium.,Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Sara Aibar
- Laboratory for Computational Biology, Department of Human Genetics, KU Leuven, Leuven, Belgium.,VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium
| | - David Nittner
- Histopathology Expertise Center, VIB Leuven Center for Cancer Biology, VIB, Leuven, Belgium.,Department of Oncology, KU Leuven, Leuven, Belgium
| | - Oliver Burton
- VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,Laboratory of Genetics of Autoimmunity, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | - Ayse Bassez
- VIB Center for Cancer Biology, Leuven, Belgium.,Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Herbert Decaluwé
- Department of Thoracic Surgery, University Hospitals KU Leuven, Leuven, Belgium.,Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, Leuven, Belgium
| | - Andreas Pircher
- VIB Center for Cancer Biology, Leuven, Belgium.,Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Kathleen Van den Eynde
- Translational Cell & Tissue Research, Department of Imaging & Pathology, KU Leuven, Leuven, Belgium
| | - Birgit Weynand
- Translational Cell & Tissue Research, Department of Imaging & Pathology, KU Leuven, Leuven, Belgium
| | - Erik Verbeken
- Translational Cell & Tissue Research, Department of Imaging & Pathology, KU Leuven, Leuven, Belgium
| | - Paul De Leyn
- Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, Leuven, Belgium
| | - Adrian Liston
- VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.,Laboratory of Genetics of Autoimmunity, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | - Johan Vansteenkiste
- Respiratory Oncology Unit (Pneumology) and Leuven Lung Cancer Group, University Hospitals KU Leuven, Leuven, Belgium.,Laboratory of Pneumology, Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, Leuven, Belgium
| | - Peter Carmeliet
- VIB Center for Cancer Biology, Leuven, Belgium.,Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, KU Leuven, Leuven, Belgium.,State Key Laboratory of Ophthalmology, Zhongsan Ophthalmic Center, SunYat-Sen University, Guangzhou, China
| | - Stein Aerts
- Laboratory for Computational Biology, Department of Human Genetics, KU Leuven, Leuven, Belgium.,VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium
| | - Bernard Thienpont
- VIB Center for Cancer Biology, Leuven, Belgium. .,Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, Leuven, Belgium.
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37
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Davie K, Janssens J, Koldere D, De Waegeneer M, Pech U, Kreft Ł, Aibar S, Makhzami S, Christiaens V, Bravo González-Blas C, Poovathingal S, Hulselmans G, Spanier KI, Moerman T, Vanspauwen B, Geurs S, Voet T, Lammertyn J, Thienpont B, Liu S, Konstantinides N, Fiers M, Verstreken P, Aerts S. A Single-Cell Transcriptome Atlas of the Aging Drosophila Brain. Cell 2018; 174:982-998.e20. [PMID: 29909982 PMCID: PMC6086935 DOI: 10.1016/j.cell.2018.05.057] [Citation(s) in RCA: 407] [Impact Index Per Article: 67.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 03/30/2018] [Accepted: 05/25/2018] [Indexed: 02/06/2023]
Abstract
The diversity of cell types and regulatory states in the brain, and how these change during aging, remains largely unknown. We present a single-cell transcriptome atlas of the entire adult Drosophila melanogaster brain sampled across its lifespan. Cell clustering identified 87 initial cell clusters that are further subclustered and validated by targeted cell-sorting. Our data show high granularity and identify a wide range of cell types. Gene network analyses using SCENIC revealed regulatory heterogeneity linked to energy consumption. During aging, RNA content declines exponentially without affecting neuronal identity in old brains. This single-cell brain atlas covers nearly all cells in the normal brain and provides the tools to study cellular diversity alongside other Drosophila and mammalian single-cell datasets in our unique single-cell analysis platform: SCope (http://scope.aertslab.org). These results, together with SCope, allow comprehensive exploration of all transcriptional states of an entire aging brain. A single-cell atlas of the adult fly brain during aging Network inference reveals regulatory states related to oxidative phosphorylation Cell identity is retained during aging despite exponential decline of gene expression SCope: An online tool to explore and compare single-cell datasets across species
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Affiliation(s)
- Kristofer Davie
- VIB Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium; Department of Human Genetics KU Leuven, Leuven 3000, Belgium
| | - Jasper Janssens
- VIB Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium; Department of Human Genetics KU Leuven, Leuven 3000, Belgium
| | - Duygu Koldere
- VIB Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium; Department of Human Genetics KU Leuven, Leuven 3000, Belgium
| | - Maxime De Waegeneer
- VIB Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium; Department of Human Genetics KU Leuven, Leuven 3000, Belgium
| | - Uli Pech
- VIB Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium; Department of Neurosciences, KU Leuven, Leuven 3000, Belgium
| | - Łukasz Kreft
- VIB Bioinformatics Core, VIB, Ghent 9052, Belgium
| | - Sara Aibar
- VIB Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium; Department of Human Genetics KU Leuven, Leuven 3000, Belgium
| | - Samira Makhzami
- VIB Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium; Department of Human Genetics KU Leuven, Leuven 3000, Belgium
| | - Valerie Christiaens
- VIB Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium; Department of Human Genetics KU Leuven, Leuven 3000, Belgium
| | - Carmen Bravo González-Blas
- VIB Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium; Department of Human Genetics KU Leuven, Leuven 3000, Belgium
| | | | - Gert Hulselmans
- VIB Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium; Department of Human Genetics KU Leuven, Leuven 3000, Belgium
| | - Katina I Spanier
- VIB Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium; Department of Human Genetics KU Leuven, Leuven 3000, Belgium
| | - Thomas Moerman
- ESAT, KU Leuven, Leuven 3001, Belgium; Smart Applications and Innovation Services, IMEC, Leuven 3001, Belgium
| | | | - Sarah Geurs
- Department of Human Genetics KU Leuven, Leuven 3000, Belgium
| | - Thierry Voet
- Department of Human Genetics KU Leuven, Leuven 3000, Belgium
| | | | | | - Sha Liu
- VIB Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium; Department of Neurosciences, KU Leuven, Leuven 3000, Belgium
| | | | - Mark Fiers
- VIB Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium; Department of Neurosciences, KU Leuven, Leuven 3000, Belgium
| | - Patrik Verstreken
- VIB Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium; Department of Neurosciences, KU Leuven, Leuven 3000, Belgium
| | - Stein Aerts
- VIB Center for Brain & Disease Research, KU Leuven, Leuven 3000, Belgium; Department of Human Genetics KU Leuven, Leuven 3000, Belgium.
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Ghoussaini M, Edwards SL, Michailidou K, Nord S, Cowper-Sal Lari R, Desai K, Kar S, Hillman KM, Kaufmann S, Glubb DM, Beesley J, Dennis J, Bolla MK, Wang Q, Dicks E, Guo Q, Schmidt MK, Shah M, Luben R, Brown J, Czene K, Darabi H, Eriksson M, Klevebring D, Bojesen SE, Nordestgaard BG, Nielsen SF, Flyger H, Lambrechts D, Thienpont B, Neven P, Wildiers H, Broeks A, Van't Veer LJ, Rutgers EJT, Couch FJ, Olson JE, Hallberg E, Vachon C, Chang-Claude J, Rudolph A, Seibold P, Flesch-Janys D, Peto J, Dos-Santos-Silva I, Gibson L, Nevanlinna H, Muranen TA, Aittomäki K, Blomqvist C, Hall P, Li J, Liu J, Humphreys K, Kang D, Choi JY, Park SK, Noh DY, Matsuo K, Ito H, Iwata H, Yatabe Y, Guénel P, Truong T, Menegaux F, Sanchez M, Burwinkel B, Marme F, Schneeweiss A, Sohn C, Wu AH, Tseng CC, Van Den Berg D, Stram DO, Benitez J, Pilar Zamora M, Perez JIA, Menéndez P, Shu XO, Lu W, Gao YT, Cai Q, Cox A, Cross SS, Reed MWR, Andrulis IL, Knight JA, Glendon G, Tchatchou S, Sawyer EJ, Tomlinson I, Kerin MJ, Miller N, Haiman CA, Henderson BE, Schumacher F, Le Marchand L, Lindblom A, Margolin S, Teo SH, Yip CH, Lee DSC, Wong TY, Hooning MJ, Martens JWM, Collée JM, van Deurzen CHM, Hopper JL, Southey MC, Tsimiklis H, Kapuscinski MK, Shen CY, Wu PE, Yu JC, Chen ST, Alnæs GG, Borresen-Dale AL, Giles GG, Milne RL, McLean C, Muir K, Lophatananon A, Stewart-Brown S, Siriwanarangsan P, Hartman M, Miao H, Buhari SABS, Teo YY, Fasching PA, Haeberle L, Ekici AB, Beckmann MW, Brenner H, Dieffenbach AK, Arndt V, Stegmaier C, Swerdlow A, Ashworth A, Orr N, Schoemaker MJ, García-Closas M, Figueroa J, Chanock SJ, Lissowska J, Simard J, Goldberg MS, Labrèche F, Dumont M, Winqvist R, Pylkäs K, Jukkola-Vuorinen A, Brauch H, Brüning T, Koto YD, Radice P, Peterlongo P, Bonanni B, Volorio S, Dörk T, Bogdanova NV, Helbig S, Mannermaa A, Kataja V, Kosma VM, Hartikainen JM, Devilee P, Tollenaar RAEM, Seynaeve C, Van Asperen CJ, Jakubowska A, Lubinski J, Jaworska-Bieniek K, Durda K, Slager S, Toland AE, Ambrosone CB, Yannoukakos D, Sangrajrang S, Gaborieau V, Brennan P, McKay J, Hamann U, Torres D, Zheng W, Long J, Anton-Culver H, Neuhausen SL, Luccarini C, Baynes C, Ahmed S, Maranian M, Healey CS, González-Neira A, Pita G, Rosario Alonso M, Álvarez N, Herrero D, Tessier DC, Vincent D, Bacot F, de Santiago I, Carroll J, Caldas C, Brown MA, Lupien M, Kristensen VN, Pharoah PDP, Chenevix-Trench G, French JD, Easton DF, Dunning AM. Publisher Correction: Evidence that breast cancer risk at the 2q35 locus is mediated through IGFBP5 regulation. Nat Commun 2018; 9:16193. [PMID: 29633761 PMCID: PMC5898457 DOI: 10.1038/ncomms16193] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
This corrects the article DOI: 10.1038/ncomms5999.
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Heylen L, Thienpont B, Naesens M, Busschaert P, Depreeuw J, Smeets D, Jochmans I, Monbaliu D, Pirenne J, Lerut E, Ghesquiere B, Kuypers D, Lambrechts D, Sprangers B. Ischemia-Induced DNA Hypermethylation during Kidney Transplant Predicts Chronic Allograft Injury. J Am Soc Nephrol 2018; 29:1566-1576. [PMID: 29610404 DOI: 10.1681/asn.2017091027] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [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: 09/26/2017] [Accepted: 02/26/2018] [Indexed: 12/28/2022] Open
Abstract
Background Ischemia during kidney transplant causes chronic allograft injury and adversely affects outcome, but the underlying mechanisms are incompletely understood. In tumors, oxygen shortage reduces the DNA demethylating activity of the ten-11 translocation (TET) enzymes, yielding hypermethylated genomes that promote tumor progression. We investigated whether ischemia similarly induces DNA hypermethylation in kidney transplants and contributes to chronic injury.Methods We profiled genome-wide DNA methylation in three cohorts of brain-dead donor kidney allograft biopsy specimens: a longitudinal cohort with paired biopsy specimens obtained at allograft procurement (preischemia; n=13), after implantation and reperfusion (postischemia; n=13), and at 3 or 12 months after transplant (n=5 each); a cross-sectional cohort with preimplantation biopsy specimens (n=82); and a cross-sectional cohort with postreperfusion biopsy specimens (n=46).Results Analysis of the paired preischemia and postischemia specimens revealed that methylation increased drastically in all allografts on ischemia. Hypermethylation was caused by loss of 5-hydroxymethylcytosine, the product of TET activity, and it was stable 1 year after transplant. In the preimplantation cohort, CpG hypermethylation directly correlated with ischemia time and for some CpGs, increased 2.6% per additional hour of ischemia. Hypermethylation preferentially affected and reduced the expression of genes involved in suppressing kidney injury and fibrosis. Moreover, CpG hypermethylation in preimplantation specimens predicted chronic injury, particularly fibrosis and glomerulosclerosis, 1 year after transplant. This finding was validated in the independent postreperfusion cohort, in which hypermethylation also predicted reduced allograft function 1 year after transplant, outperforming established clinical variables.Conclusions We highlight a novel epigenetic basis for ischemia-induced chronic allograft injury with biomarker potential.
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Affiliation(s)
- Line Heylen
- Departments of Nephrology.,Laboratories of Experimental Transplantation.,Laboratory for Translational Genetics, Department of Human Genetics, and
| | - Bernard Thienpont
- Laboratory for Translational Genetics, Department of Human Genetics, and.,VIB Center for Cancer Biology, VIB, Leuven, Belgium
| | | | - Pieter Busschaert
- VIB Center for Cancer Biology, VIB, Leuven, Belgium.,Division of Gynaecological Oncology, Leuven Cancer Institute, University of Leuven, Belgium; and
| | - Jeroen Depreeuw
- VIB Center for Cancer Biology, VIB, Leuven, Belgium.,Division of Gynaecological Oncology, Leuven Cancer Institute, University of Leuven, Belgium; and
| | - Dominiek Smeets
- Laboratory for Translational Genetics, Department of Human Genetics, and.,VIB Center for Cancer Biology, VIB, Leuven, Belgium
| | - Ina Jochmans
- Abdominal Transplantation, Department of Microbiology and Immunology.,Abdominal Transplant Surgery, and
| | - Diethard Monbaliu
- Abdominal Transplantation, Department of Microbiology and Immunology.,Abdominal Transplant Surgery, and
| | - Jacques Pirenne
- Abdominal Transplantation, Department of Microbiology and Immunology.,Abdominal Transplant Surgery, and
| | - Evelyne Lerut
- Pathology, University Hospitals Leuven, Leuven, Belgium
| | | | | | - Diether Lambrechts
- Laboratory for Translational Genetics, Department of Human Genetics, and .,VIB Center for Cancer Biology, VIB, Leuven, Belgium
| | - Ben Sprangers
- Departments of Nephrology.,Laboratories of Experimental Transplantation
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40
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Spans L, Van den Broeck T, Smeets E, Prekovic S, Thienpont B, Lambrechts D, Karnes RJ, Erho N, Alshalalfa M, Davicioni E, Helsen C, Gevaert T, Tosco L, Haustermans K, Lerut E, Joniau S, Claessens F. Genomic and epigenomic analysis of high-risk prostate cancer reveals changes in hydroxymethylation and TET1. Oncotarget 2017; 7:24326-38. [PMID: 27014907 PMCID: PMC5029704 DOI: 10.18632/oncotarget.8220] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 03/04/2016] [Indexed: 11/25/2022] Open
Abstract
The clinical heterogeneity of prostate cancer (PCa) makes it difficult to identify those patients that could benefit from more aggressive treatments. As a contribution to a better understanding of the genomic changes in the primary tumor that are associated with the development of high-risk disease, we performed exome sequencing and copy number determination of a clinically homogeneous cohort of 47 high-risk PCas. We confirmed recurrent mutations in SPOP, PTEN and TP53 among the 850 point mutations we detected. In seven cases, we discovered genomic aberrations in the TET1 (Ten-Eleven Translocation 1) gene which encodes a DNA hydroxymethylase than can modify methylated cytosines in genomic DNA and thus is linked with gene expression changes. TET1 protein levels were reduced in tumor versus non-tumor prostate tissue in 39 of 40 cases. The clinical relevance of changes in TET1 levels was demonstrated in an independent PCa cohort, in which low TET1 mRNA levels were significantly associated with worse metastases-free survival. We also demonstrate a strong reduction in hydroxymethylated DNA in tumor tissue in 27 of 41 cases. Furthermore, we report the first exploratory (h)MeDIP-Seq analyses of eight high-risk PCa samples. This reveals a large heterogeneity in hydroxymethylation changes in tumor versus non-tumor genomes which can be linked with cell polarity.
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Affiliation(s)
- Lien Spans
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, University of Leuven, Campus Gasthuisberg, Leuven, Belgium.,Current address: Laboratory for Genetics of Malignant Disorders, Department of Human Genetics, University of Leuven, Campus Gasthuisberg, Leuven, Belgium
| | - Thomas Van den Broeck
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, University of Leuven, Campus Gasthuisberg, Leuven, Belgium.,Department of Urology, University Hospitals Leuven, Campus Gasthuisberg, Leuven, Belgium
| | - Elien Smeets
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, University of Leuven, Campus Gasthuisberg, Leuven, Belgium
| | - Stefan Prekovic
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, University of Leuven, Campus Gasthuisberg, Leuven, Belgium
| | - Bernard Thienpont
- Vesalius Research Center, VIB, Leuven, Belgium.,Laboratory of Translational Genetics, Department of Oncology, University of Leuven, Campus Gasthuisberg, Leuven, Belgium
| | - Diether Lambrechts
- Vesalius Research Center, VIB, Leuven, Belgium.,Laboratory of Translational Genetics, Department of Oncology, University of Leuven, Campus Gasthuisberg, Leuven, Belgium
| | | | - Nicholas Erho
- Research and Development, GenomeDx Biosciences, Inc., Vancouver, BC, Canada
| | | | - Elai Davicioni
- Research and Development, GenomeDx Biosciences, Inc., Vancouver, BC, Canada
| | - Christine Helsen
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, University of Leuven, Campus Gasthuisberg, Leuven, Belgium
| | - Thomas Gevaert
- Organ Systems, Department of Development and Regeneration, University of Leuven, Campus Gasthuisberg, Leuven, Belgium
| | - Lorenzo Tosco
- Department of Urology, University Hospitals Leuven, Campus Gasthuisberg, Leuven, Belgium
| | - Karin Haustermans
- Laboratory of Experimental Radiotherapy, Department of Oncology, University of Leuven, Campus Gasthuisberg, Leuven, Belgium
| | - Evelyne Lerut
- Translational Cell & Tissue Research, Department of Imaging and Pathology, University Hospitals Leuven, Leuven, Belgium.,PEARL Consortium
| | - Steven Joniau
- Department of Urology, University Hospitals Leuven, Campus Gasthuisberg, Leuven, Belgium
| | - Frank Claessens
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, University of Leuven, Campus Gasthuisberg, Leuven, Belgium
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41
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Abstract
In a new report in Nature, Tian and colleagues (2017) describe that T cell activation in tumors induces blood vessel normalization. Because abnormal vasculature in tumors is known to reduce chemotherapy effectiveness and T lymphocyte infiltration and to increase metastasis, this suggests an exciting novel angle for checkpoint immunotherapy.
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Affiliation(s)
- Bernard Thienpont
- Center for Cancer Biology, VIB, 3000 Leuven, Belgium; Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium.
| | - Diether Lambrechts
- Center for Cancer Biology, VIB, 3000 Leuven, Belgium; Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium.
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42
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Olvedy M, Tisserand JC, Luciani F, Boeckx B, Wouters J, Lopez S, Rambow F, Aibar S, Thienpont B, Barra J, Köhler C, Radaelli E, Tartare-Deckert S, Aerts S, Dubreuil P, van den Oord JJ, Lambrechts D, De Sepulveda P, Marine JC. Comparative oncogenomics identifies tyrosine kinase FES as a tumor suppressor in melanoma. J Clin Invest 2017; 127:2310-2325. [PMID: 28463229 DOI: 10.1172/jci91291] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 03/02/2017] [Indexed: 01/11/2023] Open
Abstract
Identification and functional validation of oncogenic drivers are essential steps toward advancing cancer precision medicine. Here, we have presented a comprehensive analysis of the somatic genomic landscape of the widely used BRAFV600E- and NRASQ61K-driven mouse models of melanoma. By integrating the data with publically available genomic, epigenomic, and transcriptomic information from human clinical samples, we confirmed the importance of several genes and pathways previously implicated in human melanoma, including the tumor-suppressor genes phosphatase and tensin homolog (PTEN), cyclin dependent kinase inhibitor 2A (CDKN2A), LKB1, and others. Importantly, this approach also identified additional putative melanoma drivers with prognostic and therapeutic relevance. Surprisingly, one of these genes encodes the tyrosine kinase FES. Whereas FES is highly expressed in normal human melanocytes, FES expression is strongly decreased in over 30% of human melanomas. This downregulation correlates with poor overall survival. Correspondingly, engineered deletion of Fes accelerated tumor progression in a BRAFV600E-driven mouse model of melanoma. Together, these data implicate FES as a driver of melanoma progression and demonstrate the potential of cross-species oncogenomic approaches combined with mouse modeling to uncover impactful mutations and oncogenic driver alleles with clinical importance in the treatment of human cancer.
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Affiliation(s)
- Michael Olvedy
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, Vlaams Instituut voor Biotechnologie (VIB), Leuven, Belgium.,Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Julie C Tisserand
- INSERM, Aix Marseille University, CNRS, Institut Paoli-Calmettes, CRCM, Equipe Labellisée Ligue Contre le Cancer, Marseille, France
| | - Flavie Luciani
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, Vlaams Instituut voor Biotechnologie (VIB), Leuven, Belgium.,Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Bram Boeckx
- Laboratory for Translational Genetics, Center for Cancer Biology, VIB, Leuven, Belgium.,Laboratory for Translational Genetics, and
| | - Jasper Wouters
- Laboratory of Computational Biology, Department of Human Genetics, KU Leuven, Leuven, Belgium.,Laboratory of Computational Biology, and
| | - Sophie Lopez
- INSERM, Aix Marseille University, CNRS, Institut Paoli-Calmettes, CRCM, Equipe Labellisée Ligue Contre le Cancer, Marseille, France
| | - Florian Rambow
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, Vlaams Instituut voor Biotechnologie (VIB), Leuven, Belgium.,Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Sara Aibar
- Laboratory of Computational Biology, Department of Human Genetics, KU Leuven, Leuven, Belgium.,Laboratory of Computational Biology, and
| | - Bernard Thienpont
- Laboratory for Translational Genetics, Center for Cancer Biology, VIB, Leuven, Belgium.,Laboratory for Translational Genetics, and
| | - Jasmine Barra
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, Vlaams Instituut voor Biotechnologie (VIB), Leuven, Belgium.,Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Corinna Köhler
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, Vlaams Instituut voor Biotechnologie (VIB), Leuven, Belgium.,Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Enrico Radaelli
- Mouse Histopathology Core Facility, VIB Center for Brain & Disease Research, Leuven, Belgium
| | - Sophie Tartare-Deckert
- Centre Méditerranéen de Médecine Moléculaire (C3M), INSERM, U1065, Université Côte d'Azur, Nice, France
| | - Stein Aerts
- Laboratory of Computational Biology, Department of Human Genetics, KU Leuven, Leuven, Belgium.,Laboratory of Computational Biology, and
| | - Patrice Dubreuil
- INSERM, Aix Marseille University, CNRS, Institut Paoli-Calmettes, CRCM, Equipe Labellisée Ligue Contre le Cancer, Marseille, France
| | - Joost J van den Oord
- Laboratory of Translational Cell and Tissue Research, Department of Pathology, KU Leuven and UZ Leuven, Leuven, Belgium
| | - Diether Lambrechts
- Laboratory for Translational Genetics, Center for Cancer Biology, VIB, Leuven, Belgium.,Laboratory for Translational Genetics, and
| | - Paulo De Sepulveda
- INSERM, Aix Marseille University, CNRS, Institut Paoli-Calmettes, CRCM, Equipe Labellisée Ligue Contre le Cancer, Marseille, France
| | - Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, Vlaams Instituut voor Biotechnologie (VIB), Leuven, Belgium.,Laboratory for Molecular Cancer Biology, Department of Oncology, KU Leuven, Leuven, Belgium
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43
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Heylen L, Thienpont B, Naesens M, Busschaert P, Depreeuw J, Jochmans I, Monbaliu D, Pirenne J, Kuypers D, Lerut E, Lambrechts D, Sprangers B. SO009ISCHEMIA IN KIDNEY TRANSPLANTATION CAUSES DNA HYPERMETHYLATION AND PREDICTS GRAFT FIBROSIS: AN EPIGENOME-WIDE ASSOCIATION STUDY. Nephrol Dial Transplant 2017. [DOI: 10.1093/ndt/gfx101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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44
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Heylen L, Sprangers B, Thienpont B, Moisse M, Kuypers D, Lambrechts D, Naesens M. SO013AGING IS ASSOCIATED WITH EPIGENETIC CHANGES IN GENES INVOLVED IN FIBROSIS IN THE KIDNEY: AN EPIGENOME-WIDE STUDY. Nephrol Dial Transplant 2017. [DOI: 10.1093/ndt/gfx101.so013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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45
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Abstract
DNA hypermethylation is pervasive in tumors, but the factors triggering this modification are largely unknown. We recently demonstrated that the activity of 10-11-translocation methylcytosine dioxygenases, initiators of DNA demethylation, is compromised in hypoxic tumors. The resultant accumulation of methylation inactivates associated genes, linking the tumor microenvironment to epigenetic changes in cancer cells.
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Affiliation(s)
- Bernard Thienpont
- Vesalius Research Center, VIB, Leuven, Belgium; Laboratory of Translational Genetics, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Laurien Van Dyck
- Vesalius Research Center, VIB, Leuven, Belgium; Laboratory of Translational Genetics, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Diether Lambrechts
- Vesalius Research Center, VIB, Leuven, Belgium; Laboratory of Translational Genetics, Department of Oncology, KU Leuven, Leuven, Belgium
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46
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Cantelmo AR, Conradi LC, Brajic A, Goveia J, Kalucka J, Pircher A, Chaturvedi P, Hol J, Thienpont B, Teuwen LA, Schoors S, Boeckx B, Vriens J, Kuchnio A, Veys K, Cruys B, Finotto L, Treps L, Stav-Noraas TE, Bifari F, Stapor P, Decimo I, Kampen K, De Bock K, Haraldsen G, Schoonjans L, Rabelink T, Eelen G, Ghesquière B, Rehman J, Lambrechts D, Malik AB, Dewerchin M, Carmeliet P. Inhibition of the Glycolytic Activator PFKFB3 in Endothelium Induces Tumor Vessel Normalization, Impairs Metastasis, and Improves Chemotherapy. Cancer Cell 2016; 30:968-985. [PMID: 27866851 PMCID: PMC5675554 DOI: 10.1016/j.ccell.2016.10.006] [Citation(s) in RCA: 406] [Impact Index Per Article: 50.8] [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: 06/06/2015] [Revised: 06/30/2016] [Accepted: 10/04/2016] [Indexed: 01/01/2023]
Abstract
Abnormal tumor vessels promote metastasis and impair chemotherapy. Hence, tumor vessel normalization (TVN) is emerging as an anti-cancer treatment. Here, we show that tumor endothelial cells (ECs) have a hyper-glycolytic metabolism, shunting intermediates to nucleotide synthesis. EC haplo-deficiency or blockade of the glycolytic activator PFKFB3 did not affect tumor growth, but reduced cancer cell invasion, intravasation, and metastasis by normalizing tumor vessels, which improved vessel maturation and perfusion. Mechanistically, PFKFB3 inhibition tightened the vascular barrier by reducing VE-cadherin endocytosis in ECs, and rendering pericytes more quiescent and adhesive (via upregulation of N-cadherin) through glycolysis reduction; it also lowered the expression of cancer cell adhesion molecules in ECs by decreasing NF-κB signaling. PFKFB3-blockade treatment also improved chemotherapy of primary and metastatic tumors.
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Affiliation(s)
- Anna Rita Cantelmo
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, KU Leuven, Leuven 3000, Belgium; Laboratory of Angiogenesis and Vascular Metabolism, Vesalius Research Center, VIB, Leuven 3000, Belgium
| | - Lena-Christin Conradi
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, KU Leuven, Leuven 3000, Belgium; Laboratory of Angiogenesis and Vascular Metabolism, Vesalius Research Center, VIB, Leuven 3000, Belgium
| | - Aleksandra Brajic
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, KU Leuven, Leuven 3000, Belgium; Laboratory of Angiogenesis and Vascular Metabolism, Vesalius Research Center, VIB, Leuven 3000, Belgium
| | - Jermaine Goveia
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, KU Leuven, Leuven 3000, Belgium; Laboratory of Angiogenesis and Vascular Metabolism, Vesalius Research Center, VIB, Leuven 3000, Belgium
| | - Joanna Kalucka
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, KU Leuven, Leuven 3000, Belgium; Laboratory of Angiogenesis and Vascular Metabolism, Vesalius Research Center, VIB, Leuven 3000, Belgium
| | - Andreas Pircher
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, KU Leuven, Leuven 3000, Belgium; Laboratory of Angiogenesis and Vascular Metabolism, Vesalius Research Center, VIB, Leuven 3000, Belgium
| | - Pallavi Chaturvedi
- Department of Pharmacology, University of Illinois College of Medicine, Chicago, IL 60612, USA
| | - Johanna Hol
- Department of Pathology, K.G. Jebsen Inflammation Research Center, Oslo University Hospital, University of Oslo, Oslo 0424, Norway
| | - Bernard Thienpont
- Laboratory for Translational Genetics, Vesalius Research Center, VIB, Leuven 3000, Belgium; Laboratory for Translational Genetics, Department of Oncology, KU Leuven, Leuven 3000, Belgium
| | - Laure-Anne Teuwen
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, KU Leuven, Leuven 3000, Belgium; Laboratory of Angiogenesis and Vascular Metabolism, Vesalius Research Center, VIB, Leuven 3000, Belgium
| | - Sandra Schoors
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, KU Leuven, Leuven 3000, Belgium; Laboratory of Angiogenesis and Vascular Metabolism, Vesalius Research Center, VIB, Leuven 3000, Belgium
| | - Bram Boeckx
- Laboratory for Translational Genetics, Vesalius Research Center, VIB, Leuven 3000, Belgium; Laboratory for Translational Genetics, Department of Oncology, KU Leuven, Leuven 3000, Belgium
| | - Joris Vriens
- Laboratory of Ion Channel Research and TRP Research Platform Leuven (TRPLe), KU Leuven, Leuven 3000, Belgium
| | - Anna Kuchnio
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, KU Leuven, Leuven 3000, Belgium; Laboratory of Angiogenesis and Vascular Metabolism, Vesalius Research Center, VIB, Leuven 3000, Belgium
| | - Koen Veys
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, KU Leuven, Leuven 3000, Belgium; Laboratory of Angiogenesis and Vascular Metabolism, Vesalius Research Center, VIB, Leuven 3000, Belgium
| | - Bert Cruys
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, KU Leuven, Leuven 3000, Belgium; Laboratory of Angiogenesis and Vascular Metabolism, Vesalius Research Center, VIB, Leuven 3000, Belgium
| | - Lise Finotto
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, KU Leuven, Leuven 3000, Belgium; Laboratory of Angiogenesis and Vascular Metabolism, Vesalius Research Center, VIB, Leuven 3000, Belgium
| | - Lucas Treps
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, KU Leuven, Leuven 3000, Belgium; Laboratory of Angiogenesis and Vascular Metabolism, Vesalius Research Center, VIB, Leuven 3000, Belgium
| | - Tor Espen Stav-Noraas
- Department of Pathology, K.G. Jebsen Inflammation Research Center, Oslo University Hospital, University of Oslo, Oslo 0424, Norway
| | - Francesco Bifari
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, KU Leuven, Leuven 3000, Belgium; Laboratory of Angiogenesis and Vascular Metabolism, Vesalius Research Center, VIB, Leuven 3000, Belgium
| | - Peter Stapor
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, KU Leuven, Leuven 3000, Belgium; Laboratory of Angiogenesis and Vascular Metabolism, Vesalius Research Center, VIB, Leuven 3000, Belgium
| | - Ilaria Decimo
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, KU Leuven, Leuven 3000, Belgium; Laboratory of Angiogenesis and Vascular Metabolism, Vesalius Research Center, VIB, Leuven 3000, Belgium
| | - Kim Kampen
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, KU Leuven, Leuven 3000, Belgium; Laboratory of Angiogenesis and Vascular Metabolism, Vesalius Research Center, VIB, Leuven 3000, Belgium
| | - Katrien De Bock
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, KU Leuven, Leuven 3000, Belgium; Laboratory of Angiogenesis and Vascular Metabolism, Vesalius Research Center, VIB, Leuven 3000, Belgium
| | - Guttorm Haraldsen
- Department of Pathology, K.G. Jebsen Inflammation Research Center, Oslo University Hospital, University of Oslo, Oslo 0424, Norway
| | - Luc Schoonjans
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, KU Leuven, Leuven 3000, Belgium; Laboratory of Angiogenesis and Vascular Metabolism, Vesalius Research Center, VIB, Leuven 3000, Belgium
| | - Ton Rabelink
- Department of Nephrology, Einthoven Laboratory for Vascular Medicine, LUMC, Leiden University Medical Center, Leiden 2300 RC, the Netherlands
| | - Guy Eelen
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, KU Leuven, Leuven 3000, Belgium; Laboratory of Angiogenesis and Vascular Metabolism, Vesalius Research Center, VIB, Leuven 3000, Belgium
| | - Bart Ghesquière
- Metabolomics Core Facility, Department of Oncology, KU Leuven, Leuven 3000, Belgium; Metabolomics Core Facility, Vesalius Research Center, VIB, Leuven 3000, Belgium
| | - Jalees Rehman
- Department of Pharmacology, University of Illinois College of Medicine, Chicago, IL 60612, USA; Section of Cardiology, Department of Medicine, University of Illinois College of Medicine, Chicago, IL 60612, USA
| | - Diether Lambrechts
- Laboratory for Translational Genetics, Vesalius Research Center, VIB, Leuven 3000, Belgium; Laboratory for Translational Genetics, Department of Oncology, KU Leuven, Leuven 3000, Belgium
| | - Asrar B Malik
- Department of Pharmacology, University of Illinois College of Medicine, Chicago, IL 60612, USA
| | - Mieke Dewerchin
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, KU Leuven, Leuven 3000, Belgium; Laboratory of Angiogenesis and Vascular Metabolism, Vesalius Research Center, VIB, Leuven 3000, Belgium
| | - Peter Carmeliet
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, KU Leuven, Leuven 3000, Belgium; Laboratory of Angiogenesis and Vascular Metabolism, Vesalius Research Center, VIB, Leuven 3000, Belgium.
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47
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Thienpont B, Aronsen JM, Robinson EL, Okkenhaug H, Loche E, Ferrini A, Brien P, Alkass K, Tomasso A, Agrawal A, Bergmann O, Sjaastad I, Reik W, Roderick HL. The H3K9 dimethyltransferases EHMT1/2 protect against pathological cardiac hypertrophy. J Clin Invest 2016; 127:335-348. [PMID: 27893464 DOI: 10.1172/jci88353] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 10/17/2016] [Indexed: 11/17/2022] Open
Abstract
Cardiac hypertrophic growth in response to pathological cues is associated with reexpression of fetal genes and decreased cardiac function and is often a precursor to heart failure. In contrast, physiologically induced hypertrophy is adaptive, resulting in improved cardiac function. The processes that selectively induce these hypertrophic states are poorly understood. Here, we have profiled 2 repressive epigenetic marks, H3K9me2 and H3K27me3, which are involved in stable cellular differentiation, specifically in cardiomyocytes from physiologically and pathologically hypertrophied rat hearts, and correlated these marks with their associated transcriptomes. This analysis revealed the pervasive loss of euchromatic H3K9me2 as a conserved feature of pathological hypertrophy that was associated with reexpression of fetal genes. In hypertrophy, H3K9me2 was reduced following a miR-217-mediated decrease in expression of the H3K9 dimethyltransferases EHMT1 and EHMT2 (EHMT1/2). miR-217-mediated, genetic, or pharmacological inactivation of EHMT1/2 was sufficient to promote pathological hypertrophy and fetal gene reexpression, while suppression of this pathway protected against pathological hypertrophy both in vitro and in mice. Thus, we have established a conserved mechanism involving a departure of the cardiomyocyte epigenome from its adult cellular identity to a reprogrammed state that is accompanied by reexpression of fetal genes and pathological hypertrophy. These results suggest that targeting miR-217 and EHMT1/2 to prevent H3K9 methylation loss is a viable therapeutic approach for the treatment of heart disease.
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48
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Bifari F, Decimo I, Pino A, Llorens-Bobadilla E, Zhao S, Lange C, Panuccio G, Boeckx B, Thienpont B, Vinckier S, Wyns S, Bouché A, Lambrechts D, Giugliano M, Dewerchin M, Martin-Villalba A, Carmeliet P. Neurogenic Radial Glia-like Cells in Meninges Migrate and Differentiate into Functionally Integrated Neurons in the Neonatal Cortex. Cell Stem Cell 2016; 20:360-373.e7. [PMID: 27889318 DOI: 10.1016/j.stem.2016.10.020] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [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: 02/06/2016] [Revised: 10/08/2016] [Accepted: 10/27/2016] [Indexed: 12/13/2022]
Abstract
Whether new neurons are added in the postnatal cerebral cortex is still debated. Here, we report that the meninges of perinatal mice contain a population of neurogenic progenitors formed during embryonic development that migrate to the caudal cortex and differentiate into Satb2+ neurons in cortical layers II-IV. The resulting neurons are electrically functional and integrated into local microcircuits. Single-cell RNA sequencing identified meningeal cells with distinct transcriptome signatures characteristic of (1) neurogenic radial glia-like cells (resembling neural stem cells in the SVZ), (2) neuronal cells, and (3) a cell type with an intermediate phenotype, possibly representing radial glia-like meningeal cells differentiating to neuronal cells. Thus, we have identified a pool of embryonically derived radial glia-like cells present in the meninges that migrate and differentiate into functional neurons in the neonatal cerebral cortex.
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Affiliation(s)
- Francesco Bifari
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, KU Leuven, 3000 Leuven, Belgium; Laboratory of Angiogenesis and Vascular Metabolism, Vesalius Research Center, VIB, 3000 Leuven, Belgium
| | - Ilaria Decimo
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, KU Leuven, 3000 Leuven, Belgium; Laboratory of Angiogenesis and Vascular Metabolism, Vesalius Research Center, VIB, 3000 Leuven, Belgium; Department of Diagnostics and Public Health, University of Verona, 37134 Verona, Italy
| | - Annachiara Pino
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, KU Leuven, 3000 Leuven, Belgium; Laboratory of Angiogenesis and Vascular Metabolism, Vesalius Research Center, VIB, 3000 Leuven, Belgium; Department of Diagnostics and Public Health, University of Verona, 37134 Verona, Italy
| | | | - Sheng Zhao
- Molecular Neurobiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Christian Lange
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, KU Leuven, 3000 Leuven, Belgium; Laboratory of Angiogenesis and Vascular Metabolism, Vesalius Research Center, VIB, 3000 Leuven, Belgium
| | - Gabriella Panuccio
- Theoretical Neurobiology and Neuroengineering Laboratory, Department of Biomedical Sciences, Antwerp University, 2610 Wilrijk, Belgium
| | - Bram Boeckx
- Laboratory for Translational Genetics, Vesalius Research Center, VIB, 3000 Leuven, Belgium; Laboratory for Translational Genetics, Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Bernard Thienpont
- Laboratory for Translational Genetics, Vesalius Research Center, VIB, 3000 Leuven, Belgium; Laboratory for Translational Genetics, Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Stefan Vinckier
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, KU Leuven, 3000 Leuven, Belgium; Laboratory of Angiogenesis and Vascular Metabolism, Vesalius Research Center, VIB, 3000 Leuven, Belgium
| | - Sabine Wyns
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, KU Leuven, 3000 Leuven, Belgium; Laboratory of Angiogenesis and Vascular Metabolism, Vesalius Research Center, VIB, 3000 Leuven, Belgium
| | - Ann Bouché
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, KU Leuven, 3000 Leuven, Belgium; Laboratory of Angiogenesis and Vascular Metabolism, Vesalius Research Center, VIB, 3000 Leuven, Belgium
| | - Diether Lambrechts
- Laboratory for Translational Genetics, Vesalius Research Center, VIB, 3000 Leuven, Belgium; Laboratory for Translational Genetics, Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Michele Giugliano
- Theoretical Neurobiology and Neuroengineering Laboratory, Department of Biomedical Sciences, Antwerp University, 2610 Wilrijk, Belgium; Brain Mind Institute, Swiss Federal Institute of Technology, 1015 Lausanne, Switzerland; Department of Computer Science, University of Sheffield, Sheffield S10 2TN, UK
| | - Mieke Dewerchin
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, KU Leuven, 3000 Leuven, Belgium; Laboratory of Angiogenesis and Vascular Metabolism, Vesalius Research Center, VIB, 3000 Leuven, Belgium.
| | - Ana Martin-Villalba
- Molecular Neurobiology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
| | - Peter Carmeliet
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology, KU Leuven, 3000 Leuven, Belgium; Laboratory of Angiogenesis and Vascular Metabolism, Vesalius Research Center, VIB, 3000 Leuven, Belgium.
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Thienpont B, Galle E, Lambrechts D. TET enzymes as oxygen-dependent tumor suppressors: exciting new avenues for cancer management. Epigenomics 2016; 8:1445-1448. [PMID: 27733058 DOI: 10.2217/epi-2016-0126] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Bernard Thienpont
- Vesalius Research Center, VIB, 3000 Leuven, Belgium.,Department of Oncology, Laboratory of Translational Genetics, KU Leuven, 3000 Leuven, Belgium
| | - Eva Galle
- Vesalius Research Center, VIB, 3000 Leuven, Belgium.,Department of Oncology, Laboratory of Translational Genetics, KU Leuven, 3000 Leuven, Belgium
| | - Diether Lambrechts
- Vesalius Research Center, VIB, 3000 Leuven, Belgium.,Department of Oncology, Laboratory of Translational Genetics, KU Leuven, 3000 Leuven, Belgium
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Shi J, Zhang Y, Zheng W, Michailidou K, Ghoussaini M, Bolla MK, Wang Q, Dennis J, Lush M, Milne RL, Shu XO, Beesley J, Kar S, Andrulis IL, Anton-Culver H, Arndt V, Beckmann MW, Zhao Z, Guo X, Benitez J, Beeghly-Fadiel A, Blot W, Bogdanova NV, Bojesen SE, Brauch H, Brenner H, Brinton L, Broeks A, Brüning T, Burwinkel B, Cai H, Canisius S, Chang-Claude J, Choi JY, Couch FJ, Cox A, Cross SS, Czene K, Darabi H, Devilee P, Droit A, Dork T, Fasching PA, Fletcher O, Flyger H, Fostira F, Gaborieau V, García-Closas M, Giles GG, Guenel P, Haiman CA, Hamann U, Hartman M, Miao H, Hollestelle A, Hopper JL, Hsiung CN, Ito H, Jakubowska A, Johnson N, Torres D, Kabisch M, Kang D, Khan S, Knight JA, Kosma VM, Lambrechts D, Li J, Lindblom A, Lophatananon A, Lubinski J, Mannermaa A, Manoukian S, Le Marchand L, Margolin S, Marme F, Matsuo K, McLean C, Meindl A, Muir K, Neuhausen SL, Nevanlinna H, Nord S, Børresen-Dale AL, Olson JE, Orr N, van den Ouweland AM, Peterlongo P, Putti TC, Rudolph A, Sangrajrang S, Sawyer EJ, Schmidt MK, Schmutzler RK, Shen CY, Hou MF, Shrubsole MJ, Southey MC, Swerdlow A, Teo SH, Thienpont B, Toland AE, Tollenaar RA, Tomlinson I, Truong T, Tseng CC, Wen W, Winqvist R, Wu AH, Yip CH, Zamora PM, Zheng Y, Floris G, Cheng CY, Hooning MJ, Martens JW, Seynaeve C, Kristensen VN, Hall P, Pharoah PD, Simard J, Chenevix-Trench G, Dunning AM, Antoniou AC, Easton DF, Cai Q, Long J. Fine-scale mapping of 8q24 locus identifies multiple independent risk variants for breast cancer. Int J Cancer 2016; 139:1303-1317. [PMID: 27087578 PMCID: PMC5110427 DOI: 10.1002/ijc.30150] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [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: 07/31/2015] [Revised: 01/11/2016] [Accepted: 01/19/2016] [Indexed: 02/03/2023]
Abstract
Previous genome-wide association studies among women of European ancestry identified two independent breast cancer susceptibility loci represented by single nucleotide polymorphisms (SNPs) rs13281615 and rs11780156 at 8q24. A fine-mapping study across 2.06 Mb (chr8:127,561,724-129,624,067, hg19) in 55,540 breast cancer cases and 51,168 controls within the Breast Cancer Association Consortium was conducted. Three additional independent association signals in women of European ancestry, represented by rs35961416 (OR = 0.95, 95% CI = 0.93-0.97, conditional p = 5.8 × 10(-6) ), rs7815245 (OR = 0.94, 95% CI = 0.91-0.96, conditional p = 1.1 × 10(-6) ) and rs2033101 (OR = 1.05, 95% CI = 1.02-1.07, conditional p = 1.1 × 10(-4) ) were found. Integrative analysis using functional genomic data from the Roadmap Epigenomics, the Encyclopedia of DNA Elements project, the Cancer Genome Atlas and other public resources implied that SNPs rs7815245 in Signal 3, and rs1121948 in Signal 5 (in linkage disequilibrium with rs11780156, r(2) = 0.77), were putatively functional variants for two of the five independent association signals. The results highlighted multiple 8q24 variants associated with breast cancer susceptibility in women of European ancestry.
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Affiliation(s)
- Jiajun Shi
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Yanfeng Zhang
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Kyriaki Michailidou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Maya Ghoussaini
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Manjeet K. Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Michael Lush
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Roger L. Milne
- Cancer Epidemiology Centre, The Cancer Council Victoria, Melbourne, Victoria 3053, Australia
- Centre for Epidemiology and Biostatistics, School of Population and Global health, The University of Melbourne, Melbourne, Victoria 3053, Australia
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Jonathan Beesley
- Department of Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Siddhartha Kar
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Irene L. Andrulis
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Hoda Anton-Culver
- Department of Epidemiology, University of California Irvine, Irvine, CA 92697, USA
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg 69120, Germany
| | - Matthias W. Beckmann
- Department of Gynaecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen 91054, Germany
| | - Zhiguo Zhao
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Xingyi Guo
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Javier Benitez
- Human Cancer Genetics Program, Spanish National Cancer Research Centre, Madrid 28029, Spain
- Centro de Investigación en Red de Enfermedades Raras, Valencia, Spain
| | - Alicia Beeghly-Fadiel
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - William Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
- International Epidemiology Institute, Rockville, MD 20850, USA
| | - Natalia V. Bogdanova
- Department of Radiation Oncology, Hannover Medical School, Hannover 30625, Germany
| | - Stig E. Bojesen
- Copenhagen General Population Study, Herlev Hospital, 2730 Herlev, Denmark
- Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, 2730 Herlev, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Hiltrud Brauch
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart 70376, Germany
- University of Tübingen, Tübingen 72074, Germany
- German Cancer Consortium, German Cancer Research Center(DKFZ), Heidelberg 69120, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg 69120, Germany
- German Cancer Consortium, German Cancer Research Center(DKFZ), Heidelberg 69120, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Louise Brinton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20850, USA
| | - Annegien Broeks
- Netherlands Cancer Institute, Antoni van Leeuwenhoek hospital, Amsterdam 1066 CX, The Netherlands
| | - Thomas Brüning
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Bochum 44789, Germany
| | - Barbara Burwinkel
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg 69120, Germany
- Molecular Epidemiology Group, German Cancer Research Center, Heidelberg 69120, Germany
| | - Hui Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Sander Canisius
- Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, 1066 CX Amsterdam, the Netherlands
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center, Heidelberg 69120, Germany
| | - Ji-Yeob Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 110-799, Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul 110-799, Korea
| | - Fergus J. Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Angela Cox
- Sheffield Cancer Research Centre, Department of Oncology, University of Sheffield, Sheffield S10 2RX, UK
| | - Simon S. Cross
- Academic Unit of Pathology, Department of Neuroscience, University of Sheffield, Sheffield S10 2HQ, UK
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm SE-17177, Sweden
| | - Hatef Darabi
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm SE-17177, Sweden
| | - Peter Devilee
- Separtment of Pathology, Leiden University Medical Center, Leiden 2333 ZC, The Netherlands
- Department of Human Genetics, Leiden University Medical Center, Leiden 2333 ZC, The Netherlands
| | - Arnaud Droit
- Centre Hospitalier Universitaire de Québec Research Center, Laval University, Québec City G1V 4G2, Canada
| | - Thilo Dork
- Gynaecology Research Unit, Hannover Medical School, Hannover 30625, Germany
| | - Peter A. Fasching
- Department of Gynaecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen 91054, Germany
- David Geffen School of Medicine, Department of Medicine Division of Hematology and Oncology, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Olivia Fletcher
- Division of Cancer Studies, Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London SW3 6JB, UK
| | - Henrik Flyger
- Department of Breast Surgery, Herlev Hospital, Copenhagen University Hospital, 2730 Herlev, Denmark
| | - Florentia Fostira
- Molecular Diagnostics Laboratory, IRRP, National Centre for Scientific Research "Demokritos", 153 10 Athens, Greece
| | | | - Montserrat García-Closas
- Division of Cancer Studies, Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London SW3 6JB, UK
- Division of Genetics and Epidemiology, Institute of Cancer Research, London SW7 3RP, UK
| | - Graham G. Giles
- Cancer Epidemiology Centre, The Cancer Council Victoria, Melbourne, Victoria 3053, Australia
- Centre for Epidemiology and Biostatistics, School of Population and Global health, The University of Melbourne, Melbourne, Victoria 3053, Australia
| | - Mervi Grip
- Department of Surgery, Oulu University Hospital and University of Oulu, Oulu FI-90220, Finland
| | - Pascal Guenel
- Environmental Epidemiology of Cancer, Center for Research in Epidemiology and Population Health, INSERM, Villejuif 94807, France
- University Paris-Sud, Villejuif 94807, France
| | - Christopher A. Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Mikael Hartman
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore 119077, Singapore
- Department of Surgery, National University Health System, Singapore 117597
| | - Hui Miao
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore 119077, Singapore
| | - Antoinette Hollestelle
- Department of Medical Oncology, Erasmus MC Cancer Institute, 3015 CN Rotterdam, The Netherlands
| | - John L. Hopper
- Division of Gynaecology and Obstetrics, Technische Universität München, Munich 81675, Germany
| | - Chia-Ni Hsiung
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - kConFab Investigators
- Peter MacCallum Cancer Centre, The University of Melbourne, East Melbourne, VIC 3002, Australi
| | - Hidemi Ito
- Division of Epidemiology and Prevention, Aichi Cancer Center Research Institute, Aichi 464-8681, Japan
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin 70-115, Poland
| | - Nichola Johnson
- Division of Cancer Studies, Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London SW3 6JB, UK
| | - Diana Torres
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
- Institute of Human Genetics, Pontificia Universidad Javeriana, Bogota 12362, Colombi
| | - Maria Kabisch
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Daehee Kang
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 110-799, Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul 110-799, Korea
- Department of Obstetrics and Gynecology, Helsinki University Central Hospital, University of Helsinki, Helsinki, FI-00029 HUS, Finland
| | - Sofia Khan
- Department of Obstetrics and Gynecology, Helsinki University Central Hospital, University of Helsinki, Helsinki, FI-00029 HUS, Finland
| | - Julia A. Knight
- Prosserman Centre for Health Research, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
- Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Veli-Matti Kosma
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine and Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finlan
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio 70210, Finland
| | - Diether Lambrechts
- Vesalius Research Center, Leuven 3000, Belgium
- Laboratory for Translational Genetics, Department of Oncology, University of Leuven, Leuven 3000, Belgium
| | - Jingmei Li
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm SE-17177, Sweden
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm SE-17177, Sweden
| | - Artitaya Lophatananon
- Division of Health Sciences, Warwick Medical School, Warwick University, Coventry CV4 7AL, UK
| | - Jan Lubinski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin 70-115, Poland
| | - Arto Mannermaa
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine and Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finlan
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio 70210, Finland
| | - Siranoush Manoukian
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milan 20133, Italy
| | | | - Sara Margolin
- Department of Oncology - Pathology, Karolinska Institutet, Stockholm SE-17177, Sweden
| | - Frederik Marme
- National Center for Tumor Diseases, University of Heidelberg, Heidelberg 69120, Germany
- Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg 69120, Germany
| | - Keitaro Matsuo
- Department of Preventive Medicine, Kyushu University Faculty of Medical Sciences, Fukuoka, Japan
| | - Catriona McLean
- Anatomical Pathology, The Alfred Hospital, Melbourne, , Victoria 3004, Australia
| | - Alfons Meindl
- Division of Gynaecology and Obstetrics, Technische Universität München, Munich 81675, Germany
| | - Kenneth Muir
- Division of Health Sciences, Warwick Medical School, Warwick University, Coventry CV4 7AL, UK
- Institute of Population Health, University of Manchester, Manchester M13 9PL, UK
| | | | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, Helsinki University Central Hospital, University of Helsinki, Helsinki, FI-00029 HUS, Finland
| | - Silje Nord
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, Radiumhospitalet, Ullernchausseen 70, N-0310 Oslo, Norway
- K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Kirkeveien 166, 0450 Oslo, Norway
| | - Anne-Lise Børresen-Dale
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, Radiumhospitalet, Ullernchausseen 70, N-0310 Oslo, Norway
- K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Kirkeveien 166, 0450 Oslo, Norway
| | - Janet E. Olson
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Nick Orr
- Division of Breast Cancer Research, Institute of Cancer Research, London, UK; Cancer Research, Institute of Cancer Research, London SW3 6JB, UK
| | - Ans M.W. van den Ouweland
- Department of Clinical Genetics, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Paolo Peterlongo
- IFOM, the FIRC Institute of Molecular Oncology, Milan 20139, Italy
| | | | - Anja Rudolph
- Division of Cancer Epidemiology, German Cancer Research Center, Heidelberg 69120, Germany
| | | | - Elinor J. Sawyer
- Research Oncology, Guy’s Hospital, King's College London, London SE1 9RT, UK
| | - Marjanka K. Schmidt
- Netherlands Cancer Institute, Antoni van Leeuwenhoek hospital, Amsterdam 1066 CX, The Netherlands
| | - Rita K. Schmutzler
- Division of Molecular Gyneco-Oncology, Department of Gynaecology and Obstetrics, University Hospital of Cologne, Cologne 50931, Germany
- Center for Integrated Oncology, University Hospital of Cologne, Cologne 50931, Germany
- Center for Molecular Medicine, University Hospital of Cologne, Cologne 50931, Germany
- Center of Familial Breast and Ovarian Cancer, University Hospital of Cologne, Cologne 50931, Germany
| | - Chen-Yang Shen
- School of Public Health, China Medical University, Taichung 404, Taiwan
- Taiwan Biobank, Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Ming-Feng Hou
- Cancer Center and Department of Surgery, Chung-Ho Memorial Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Matha J Shrubsole
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Melissa C. Southey
- Department of Pathology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Anthony Swerdlow
- Division of Genetics and Epidemiology and Division of Breast Cancer Research, Institute of Cancer Research, London SW7 3RP, UK
| | - Soo Hwang Teo
- Cancer Research Initiatives Foundation, 47500 Subang Jaya, Selangor, Malaysia
- Breast Cancer Research Unit, Cancer Research Institute, University Malaya Medical Centre, 59100 KualaLumpur, Malaysia
| | - Bernard Thienpont
- Vesalius Research Center, Leuven 3000, Belgium
- Laboratory for Translational Genetics, Department of Oncology, University of Leuven, Leuven 3000, Belgium
| | - Amanda E. Toland
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Robert A.E.M. Tollenaar
- Department of Surgical Oncology, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands
| | - Ian Tomlinson
- Wellcome Trust Centre for Human Genetics and Oxford Biomedical Research Centre, University of Oxford, Oxford OX3 7BN, UK
| | - Therese Truong
- Environmental Epidemiology of Cancer, Center for Research in Epidemiology and Population Health, INSERM, Villejuif 94807, France
- University Paris-Sud, Villejuif 94807, France
| | - Chiu-chen Tseng
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Wanqing Wen
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Robert Winqvist
- Laboratory of Cancer Genetics and Tumor Biology, Department of Clinical Chemistry, University of Oulu, Oulu FI-90220, Finland
- Laboratory of Cancer Genetics and Tumor Biology, Northern Finland Laboratory Centre NordLab, Oulu FI-90220, Finland
| | - Anna H. Wu
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Cheng Har Yip
- Breast Cancer Research Unit, Cancer Research Institute, University Malaya Medical Centre, 59100 KualaLumpur, Malaysia
| | - Pilar M. Zamora
- Servicio de Oncología Médica, Hospital Universitario La Paz, Madrid 28046, Spain
| | - Ying Zheng
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, 200336, PR China
| | | | - Ching-Yu Cheng
- Singapore Eye Research Institute, National University of Singapore, Singapore, Singapore
| | - Maartje J. Hooning
- Department of Medical Oncology, Erasmus MC Cancer Institute, 3015 CN Rotterdam, The Netherlands
| | - John W.M. Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, 3015 CN Rotterdam, The Netherlands
| | - Caroline Seynaeve
- Department of Medical Oncology, Erasmus MC Cancer Institute, 3015 CN Rotterdam, The Netherlands
| | - Vessela N. Kristensen
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, Radiumhospitalet, Ullernchausseen 70, N-0310 Oslo, Norway
- K.G. Jebsen Center for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Kirkeveien 166, 0450 Oslo, Norway
- Department of Clinical Molecular Biology (EpiGen), Akershus University Hospital, University of Oslo (UiO), Oslo, Norway
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm SE-17177, Sweden
| | - Paul D.P. Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Jacques Simard
- Centre Hospitalier Universitaire de Québec Research Center, Laval University, Québec City G1V 4G2, Canada
| | - Georgia Chenevix-Trench
- Department of Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- Peter MacCallum Cancer Centre, The University of Melbourne, East Melbourne, VIC 3002, Australi
| | - Alison M. Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Antonis C. Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Douglas F. Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
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