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van Rijthoven M, Obahor S, Pagliarulo F, van den Broek M, Schraml P, Moch H, van der Laak J, Ciompi F, Silina K. Multi-resolution deep learning characterizes tertiary lymphoid structures and their prognostic relevance in solid tumors. Commun Med (Lond) 2024; 4:5. [PMID: 38182879 PMCID: PMC10770129 DOI: 10.1038/s43856-023-00421-7] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 11/30/2023] [Indexed: 01/07/2024] Open
Abstract
BACKGROUND Tertiary lymphoid structures (TLSs) are dense accumulations of lymphocytes in inflamed peripheral tissues, including cancer, and are associated with improved survival and response to immunotherapy in various solid tumors. Histological TLS quantification has been proposed as a novel predictive and prognostic biomarker, but lack of standardized methods of TLS characterization hampers assessment of TLS densities across different patients, diseases, and clinical centers. METHODS We introduce an approach based on HookNet-TLS, a multi-resolution deep learning model, for automated and unbiased TLS quantification and identification of germinal centers in routine hematoxylin and eosin stained digital pathology slides. We developed HookNet-TLS using n = 1019 manually annotated TCGA slides from clear cell renal cell carcinoma, muscle-invasive bladder cancer, and lung squamous cell carcinoma. RESULTS Here we show that HookNet-TLS automates TLS quantification across multiple cancer types achieving human-level performance and demonstrates prognostic associations similar to visual assessment. CONCLUSIONS HookNet-TLS has the potential to be used as a tool for objective quantification of TLS in routine H&E digital pathology slides. We make HookNet-TLS publicly available to promote its use in research.
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Affiliation(s)
- Mart van Rijthoven
- Pathology Department, Radboud University Medical Center, Nijmegen, Netherlands.
| | - Simon Obahor
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Fabio Pagliarulo
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | | | - Peter Schraml
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
- Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | - Jeroen van der Laak
- Pathology Department, Radboud University Medical Center, Nijmegen, Netherlands
| | - Francesco Ciompi
- Pathology Department, Radboud University Medical Center, Nijmegen, Netherlands
| | - Karina Silina
- Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology, Zurich, Switzerland
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2
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Angori S, Banaei-Esfahani A, Mühlbauer K, Bolck HA, Kahraman A, Karakulak T, Poyet C, Feodoroff M, Potdar S, Kallioniemi O, Pietiäinen V, Schraml P, Moch H. Ex Vivo Drug Testing in Patient-derived Papillary Renal Cancer Cells Reveals EGFR and the BCL2 Family as Therapeutic Targets. Eur Urol Focus 2023; 9:751-759. [PMID: 36933996 DOI: 10.1016/j.euf.2023.03.005] [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: 12/09/2022] [Revised: 02/13/2023] [Accepted: 03/01/2023] [Indexed: 03/18/2023]
Abstract
BACKGROUND Immune checkpoint inhibitors and antiangiogenic agents are used for first-line treatment of advanced papillary renal cell carcinoma (pRCC) but pRCC response rates to these therapies are low. OBJECTIVE To generate and characterise a functional ex vivo model to identify novel treatment options in advanced pRCC. DESIGN, SETTING, AND PARTICIPANTS We established patient-derived cell cultures (PDCs) from seven pRCC samples from patients and characterised them via genomic analysis and drug profiling. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS Comprehensive molecular characterisation in terms of copy number analysis and whole-exome sequencing confirmed the concordance of pRCC PDCs with the original tumours. We evaluated their sensitivity to novel drugs by generating drug scores for each PDC. RESULTS AND LIMITATIONS PDCs confirmed pRCC-specific copy number variations such as gains in chromosomes 7, 16, and 17. Whole-exome sequencing revealed that PDCs retained mutations in pRCC-specific driver genes. We performed drug screening with 526 novel and oncological compounds. Whereas exposure to conventional drugs showed low efficacy, the results highlighted EGFR and BCL2 family inhibition as the most effective targets in our pRCC PDCs. CONCLUSIONS High-throughput drug testing on newly established pRCC PDCs revealed that inhibition of EGFR and BCL2 family members could be a therapeutic strategy in pRCC. PATIENT SUMMARY We used a new approach to generate patient-derived cells from a specific type of kidney cancer. We showed that these cells have the same genetic background as the original tumour and can be used as models to study novel treatment options for this type of kidney cancer.
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Affiliation(s)
- Silvia Angori
- Department of Pathology and Molecular Pathology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Amir Banaei-Esfahani
- Department of Pathology and Molecular Pathology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Katharina Mühlbauer
- Department of Pathology and Molecular Pathology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Hella A Bolck
- Department of Pathology and Molecular Pathology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Abdullah Kahraman
- School for Life Sciences, Institute for Chemistry and Bioanalytics, University of Applied Sciences Northwestern Switzerland, Muttenz, Switzerland
| | - Tülay Karakulak
- Department of Pathology and Molecular Pathology, University Hospital Zurich and University of Zurich, Zurich, Switzerland; Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland; Swiss Informatics Institute, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Cédric Poyet
- Department of Urology, University Hospital Zurich, Zurich, Switzerland
| | - Michaela Feodoroff
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland; Laboratory of Immunovirotherapy, Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland; Translational Immunology Research Program, University of Helsinki, Helsinki, Uusimaa, Finland
| | - Swapnil Potdar
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Olli Kallioniemi
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland; Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, Solna, Sweden
| | - Vilja Pietiäinen
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Peter Schraml
- Department of Pathology and Molecular Pathology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University Hospital Zurich and University of Zurich, Zurich, Switzerland.
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Batavia AA, Rutishauser D, Sobottka B, Schraml P, Beerenwinkel N, Moch H. Biallelic ELOC-Inactivated Renal Cell Carcinoma: Molecular Features Supporting Classification as a Distinct Entity. Mod Pathol 2023; 36:100194. [PMID: 37088333 DOI: 10.1016/j.modpat.2023.100194] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 03/28/2023] [Accepted: 04/16/2023] [Indexed: 04/25/2023]
Abstract
Approximately 70% of clear cell renal cell carcinoma (ccRCC) is characterized by the biallelic inactivation of von Hippel-Lindau (VHL) on chromosome 3p. ELOC-mutated (Elongin C-mutated) renal cell carcinoma containing biallelic ELOC inactivations with chromosome 8q deletions is considered a novel subtype of renal cancer possessing a morphologic overlap with ccRCC, renal cell carcinoma (RCC) with fibromyomatous stroma exhibiting Tuberous Sclerosis Complex (TSC)/mammalian Target of Rapamycin (mTOR) mutations, and clear cell papillary tumor. However, the frequency and consequences of ELOC alterations in wild-type VHL and mutated VHL RCC are unclear. In this study, we characterize 123 renal tumors with clear cell morphology and known VHL mutation status to assess the morphologic and molecular consequences of ELOC inactivation. Using OncoScan and whole-exome sequencing, we identify 18 ELOC-deleted RCCs, 3 of which contain ELOC mutations resulting in the biallelic inactivation of ELOC. Biallelic ELOC and biallelic VHL aberrations were mutually exclusive; however, 2 ELOC-mutated RCCs showed monoallelic VHL alterations. Furthermore, no mutations in TSC1, TSC2, or mTOR were identified in ELOC-mutated RCC with biallelic ELOC inactivation. Using High Ambiguity Driven biomolecular DOCKing, we report a novel ELOC variant containing a duplication event disrupting ELOC-VHL interaction alongside the frequently seen Y79C alteration. Using hyper reaction monitoring mass spectrometry, we show RCCs with biallelic ELOC alterations have significantly reduced ELOC expression but similar carbonic anhydrase 9 and vascular endothelial growth factor A expression compared with classical ccRCC with biallelic VHL inactivation. The absence of biallelic VHL and TSC1, TSC2, or mTOR inactivation in RCC with biallelic ELOC inactivation (ELOC mutation in combination with ELOC deletions on chromosome 8q) supports the notion of a novel, molecularly defined tumor entity.
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Affiliation(s)
- Aashil A Batavia
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland; Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Dorothea Rutishauser
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Bettina Sobottka
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Peter Schraml
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.
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Krishnan A, Spegg V, Dettwiler S, Schraml P, Moch H, Dedes K, Varga Z, Altmeyer M. Analysis of the PARP1, ADP-Ribosylation, and TRIP12 Triad With Markers of Patient Outcome in Human Breast Cancer. Mod Pathol 2023; 36:100167. [PMID: 36990278 DOI: 10.1016/j.modpat.2023.100167] [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: 09/14/2022] [Revised: 03/15/2023] [Accepted: 03/21/2023] [Indexed: 03/29/2023]
Abstract
PARP inhibitors (PARPi) are increasingly used in breast cancer therapy, including high-grade triple-negative breast cancer (TNBC) treatment. Varying treatment responses and PARPi resistance with relapse currently pose limitations to the efficacy of PARPi therapy. The pathobiological reasons why individual patients respond differently to PARPi are poorly understood. In this study, we analyzed expression of PARP1, the main target of PARPi, in normal breast tissue, breast cancer, and its precursor lesions using human breast cancer tissue microarrays covering a total of 824 patients, including more than 100 TNBC cases. In parallel, we analyzed nuclear adenosine diphosphate (ADP)-ribosylation as a marker of PARP1 activity and TRIP12, an antagonist of PARPi-induced PARP1 trapping. Although we found PARP1 expression to be generally increased in invasive breast cancer, PARP1 protein levels and nuclear ADP-ribosylation were lower in higher tumor grade and TNBC samples than non-TNBCs. Cancers with low levels of PARP1 and low levels of nuclear ADP-ribosylation were associated with significantly reduced overall survival. This effect was even more pronounced in cases with high levels of TRIP12. These results indicate that PARP1-dependent DNA repair capacity may be compromised in aggressive breast cancers, potentially fueling enhanced accumulation of mutations. Moreover, the results revealed a subset of breast cancers with low PARP1, low nuclear ADP-ribosylation, and high TRIP12 levels, which may compromise their response to PARPi, suggesting a combination of markers for PARP1 abundance, enzymatic activity, and trapping capabilities might aid patient stratification for PARPi therapy.
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Affiliation(s)
- Aswini Krishnan
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Vincent Spegg
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Susanne Dettwiler
- Department of Pathology and Molecular Pathology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Peter Schraml
- Department of Pathology and Molecular Pathology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Konstantin Dedes
- Department of Gynecology, University Hospital of Zurich, Zurich, Switzerland
| | - Zsuzsanna Varga
- Department of Pathology and Molecular Pathology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Matthias Altmeyer
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland.
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Schraml P, Aimi F, Zoche M, Aguilera-Garcia D, Arnold F, Moch H, Hottiger MO. Altered cytoplasmic and nuclear ADP-ribosylation levels analyzed with an improved ADP-ribose binder are a prognostic factor in renal cell carcinoma. J Pathol Clin Res 2023. [PMID: 36999983 DOI: 10.1002/cjp2.320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 02/03/2023] [Accepted: 03/10/2023] [Indexed: 04/01/2023]
Abstract
ADP-ribosylation (ADPR) of proteins is catalyzed by ADP-ribosyltransferases, which are targeted by inhibitors (i.e. poly(ADP-ribose) polymerase inhibitors [PARPi]). Although renal cell carcinoma (RCC) cells are sensitive in vitro to PARPi, studies on the association between ADPR levels and somatic loss of function mutations in DNA damage repair genes are currently missing. Here we observed, in two clear cell RCC (ccRCC) patient cohorts (n = 257 and n = 241) stained with an engineered ADP-ribose binding macrodomain (eAf1521), that decreased cytoplasmic ADPR (cyADPR) levels significantly correlated with late tumor stage, high-ISUP (the International Society of Urological Pathology) grade, presence of necrosis, dense lymphocyte infiltration, and worse patient survival (p < 0.01 each). cyADPR proved to be an independent prognostic factor (p = 0.001). Comparably, absence of nuclear ADPR staining in ccRCC correlated with absence of PARP1 staining (p < 0.01) and worse patient outcome (p < 0.05). In papillary RCC the absence of cyADPR was also significantly associated with tumor progression and worse patient outcome (p < 0.05 each). To interrogate whether the ADPR status could be associated with genetic alterations in DNA repair, chromatin remodeling, and histone modulation, we performed DNA sequence analysis and identified a significant association of increased ARID1A mutations in ccRCCcyADPR+++/PARP1+ compared with ccRCCcyADPR-/PARP1- (31% versus 4%; p < 0.05). Collectively, our data suggest the prognostic value of nuclear and cytoplasmic ADPR levels in RCC that might be further influenced by genetic alterations.
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Affiliation(s)
- Peter Schraml
- Department of Pathology and Molecular Pathology, University Hospital Zurich (USZ), Zurich, Switzerland
| | - Fabio Aimi
- Department of Pathology and Molecular Pathology, University Hospital Zurich (USZ), Zurich, Switzerland
- Department of Molecular Mechanism of Disease (DMMD), University of Zurich (UZH), Zurich, Switzerland
| | - Martin Zoche
- Department of Pathology and Molecular Pathology, University Hospital Zurich (USZ), Zurich, Switzerland
| | - Domingo Aguilera-Garcia
- Department of Pathology and Molecular Pathology, University Hospital Zurich (USZ), Zurich, Switzerland
| | - Fabian Arnold
- Department of Pathology and Molecular Pathology, University Hospital Zurich (USZ), Zurich, Switzerland
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University Hospital Zurich (USZ), Zurich, Switzerland
| | - Michael O Hottiger
- Department of Molecular Mechanism of Disease (DMMD), University of Zurich (UZH), Zurich, Switzerland
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Fischer JR, Jackson HW, de Souza N, Varga Z, Schraml P, Moch H, Bodenmiller B. Multiplex imaging of breast cancer lymph node metastases identifies prognostic single-cell populations independent of clinical classifiers. Cell Rep Med 2023; 4:100977. [PMID: 36921599 PMCID: PMC10040454 DOI: 10.1016/j.xcrm.2023.100977] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 09/29/2022] [Accepted: 02/21/2023] [Indexed: 03/15/2023]
Abstract
Although breast cancer mortality is largely caused by metastasis, clinical decisions are based on analysis of the primary tumor and on lymph node involvement but not on the phenotype of disseminated cells. Here, we use multiplex imaging mass cytometry to compare single-cell phenotypes of primary breast tumors and matched lymph node metastases in 205 patients. We observe extensive phenotypic variability between primary and metastatic sites and that disseminated cell phenotypes frequently deviate from the clinical disease subtype. We identify single-cell phenotypes and spatial organizations of disseminated tumor cells that are associated with patient survival and a weaker survival association for high-risk phenotypes in the primary tumor. We show that p53 and GATA3 in lymph node metastases provide prognostic information beyond clinical classifiers and can be measured with standard methods. Molecular characterization of disseminated tumor cells is an untapped source of clinically applicable prognostic information for breast cancer.
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Affiliation(s)
- Jana Raja Fischer
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland; Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland; Life Science Zurich Graduate School, ETH Zurich and University of Zurich, Zurich, Switzerland
| | | | - Natalie de Souza
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland; Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland; Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Zsuzsanna Varga
- Department of Pathology and Molecular Pathology, University and University Hospital Zurich, Zurich, Switzerland
| | - Peter Schraml
- Department of Pathology and Molecular Pathology, University and University Hospital Zurich, Zurich, Switzerland
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University and University Hospital Zurich, Zurich, Switzerland
| | - Bernd Bodenmiller
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland; Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland.
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7
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Erlmeier F, Sun N, Shen J, Feuchtinger A, Buck A, Prade VM, Kunzke T, Schraml P, Moch H, Autenrieth M, Weichert W, Hartmann A, Walch A. Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging: Diagnostic Pathways and Metabolites for Renal Tumor Entities. Oncology 2022; 101:126-133. [PMID: 36198279 DOI: 10.1159/000526436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 07/20/2022] [Indexed: 11/19/2022]
Abstract
BACKGROUND Correct tumor subtyping of primary renal tumors is essential for treatment decision in daily routine. Most of the tumors can be classified based on morphology alone. Nevertheless, some diagnoses are difficult, and further investigations are needed for correct tumor subtyping. Besides histochemical investigations, high-mass-resolution matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) can detect new diagnostic biomarkers and hence improve the diagnostic. PATIENTS AND METHODS Formalin-fixed paraffin embedded tissue specimens from clear cell renal cell carcinoma (ccRCC, n = 552), papillary renal cell carcinoma (pRCC, n = 122), chromophobe renal cell carcinoma (chRCC, n = 108), and renal oncocytoma (rO, n = 71) were analyzed by high-mass-resolution MALDI fourier-transform ion cyclotron resonance (FT-ICR) MSI. The SPACiAL pipeline was executed for automated co-registration of histological and molecular features. Pathway enrichment and pathway topology analysis were performed to determine significant differences between RCC subtypes. RESULTS We discriminated the four histological subtypes (ccRCC, pRCC, chRCC, and rO) and established the subtype-specific pathways and metabolic profiles. rO showed an enrichment of pentose phosphate, taurine and hypotaurine, glycerophospholipid, amino sugar and nucleotide sugar, fructose and mannose, glycine, serine, and threonine pathways. ChRCC is defined by enriched pathways including the amino sugar and nucleotide sugar, fructose and mannose, glycerophospholipid, taurine and hypotaurine, glycine, serine, and threonine pathways. Pyrimidine, amino sugar and nucleotide sugar, glycerophospholipids, and glutathione pathways are enriched in ccRCC. Furthermore, we detected enriched phosphatidylinositol and glycerophospholipid pathways in pRCC. CONCLUSION In summary, we performed a classification system with a mean accuracy in tumor discrimination of 85.13%. Furthermore, we detected tumor-specific biomarkers for the four most common primary renal tumors by MALDI-MSI. This method is a useful tool in differential diagnosis and biomarker detection.
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Affiliation(s)
- Franziska Erlmeier
- Institute of Pathology, University Hospital Erlangen-Nuernberg, Erlangen, Germany
| | - Na Sun
- Research Unit Analytical Pathology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Jian Shen
- Research Unit Analytical Pathology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Annette Feuchtinger
- Research Unit Analytical Pathology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Achim Buck
- Research Unit Analytical Pathology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Verena M Prade
- Research Unit Analytical Pathology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Thomas Kunzke
- Research Unit Analytical Pathology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Peter Schraml
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Michael Autenrieth
- Department of Urology, Rechts der Isar Medical Center, Technical University of Munich, Munich, Germany
| | - Wilko Weichert
- Institute of Pathology, Technical University Munich, Munich, Germany
| | - Arndt Hartmann
- Institute of Pathology, University Hospital Erlangen-Nuernberg, Erlangen, Germany
| | - Axel Walch
- Research Unit Analytical Pathology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
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Erlmeier F, Sun N, Shen J, Feuchtinger A, Buck A, Prade VM, Kunzke T, Schraml P, Moch H, Autenrieth M, Weichert W, Hartmann A, Walch A. MALDI Mass Spectrometry Imaging-Prognostic Pathways and Metabolites for Renal Cell Carcinomas. Cancers (Basel) 2022; 14:cancers14071763. [PMID: 35406537 PMCID: PMC8996951 DOI: 10.3390/cancers14071763] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/24/2022] [Accepted: 03/24/2022] [Indexed: 01/27/2023] Open
Abstract
Simple Summary Renal cell carcinoma (RCC) is the seventh most common cancer type and accounts for more than 80% of all renal tumors. Nevertheless, prognostic biomarkers for RCC are still missing. Therefore, we analyzed a large, multicenter cohort including the three most common RCC subtypes (clear cell RCC (ccRCC), papillary RCC (pRCC) and chromophobe RCC (chRCC)) by high mass resolution matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) for prognostic biomarker detection. This is a suitable method for biomarker detection for several tumor entities. We detected several pathways and metabolites with prognostic power for RCC in general and also for different RCC subtypes. Abstract High mass resolution matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) is a suitable method for biomarker detection for several tumor entities. Renal cell carcinoma (RCC) is the seventh most common cancer type and accounts for more than 80% of all renal tumors. Prognostic biomarkers for RCC are still missing. Therefore, we analyzed a large, multicenter cohort including the three most common RCC subtypes (clear cell RCC (ccRCC), papillary RCC (pRCC) and chromophobe RCC (chRCC)) by MALDI for prognostic biomarker detection. MALDI-Fourier-transform ion cyclotron resonance (FT-ICR)-MSI analysis was performed for renal carcinoma tissue sections from 782 patients. SPACiAL pipeline was integrated for automated co-registration of histological and molecular features. Kaplan–Meier analyses with overall survival as endpoint were executed to determine the metabolic features associated with clinical outcome. We detected several pathways and metabolites with prognostic power for RCC in general and also for different RCC subtypes.
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Affiliation(s)
- Franziska Erlmeier
- Institute of Pathology, University Hospital Erlangen-Nuremberg, 91054 Erlangen, Germany;
- Correspondence: (F.E.); (N.S.)
| | - Na Sun
- Research Unit Analytical Pathology, Helmholtz Zentrum München–German Research Center for Environmental Health, 85764 Neuherberg, Germany; (J.S.); (A.F.); (A.B.); (V.M.P.); (T.K.); (A.W.)
- Correspondence: (F.E.); (N.S.)
| | - Jian Shen
- Research Unit Analytical Pathology, Helmholtz Zentrum München–German Research Center for Environmental Health, 85764 Neuherberg, Germany; (J.S.); (A.F.); (A.B.); (V.M.P.); (T.K.); (A.W.)
| | - Annette Feuchtinger
- Research Unit Analytical Pathology, Helmholtz Zentrum München–German Research Center for Environmental Health, 85764 Neuherberg, Germany; (J.S.); (A.F.); (A.B.); (V.M.P.); (T.K.); (A.W.)
| | - Achim Buck
- Research Unit Analytical Pathology, Helmholtz Zentrum München–German Research Center for Environmental Health, 85764 Neuherberg, Germany; (J.S.); (A.F.); (A.B.); (V.M.P.); (T.K.); (A.W.)
| | - Verena M. Prade
- Research Unit Analytical Pathology, Helmholtz Zentrum München–German Research Center for Environmental Health, 85764 Neuherberg, Germany; (J.S.); (A.F.); (A.B.); (V.M.P.); (T.K.); (A.W.)
| | - Thomas Kunzke
- Research Unit Analytical Pathology, Helmholtz Zentrum München–German Research Center for Environmental Health, 85764 Neuherberg, Germany; (J.S.); (A.F.); (A.B.); (V.M.P.); (T.K.); (A.W.)
| | - Peter Schraml
- Department of Pathology and Molecular Pathology, University Hospital Zurich, 8091 Zurich, Switzerland; (P.S.); (H.M.)
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University Hospital Zurich, 8091 Zurich, Switzerland; (P.S.); (H.M.)
| | - Michael Autenrieth
- Department of Urology, Rechts der Isar Medical Center, Technical University of Munich, 81675 Munich, Germany;
| | - Wilko Weichert
- Institute of Pathology, Technical University Munich, 81675 Munich, Germany;
| | - Arndt Hartmann
- Institute of Pathology, University Hospital Erlangen-Nuremberg, 91054 Erlangen, Germany;
| | - Axel Walch
- Research Unit Analytical Pathology, Helmholtz Zentrum München–German Research Center for Environmental Health, 85764 Neuherberg, Germany; (J.S.); (A.F.); (A.B.); (V.M.P.); (T.K.); (A.W.)
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Prade VM, Sun N, Shen J, Feuchtinger A, Kunzke T, Buck A, Schraml P, Moch H, Schwamborn K, Autenrieth M, Gschwend JE, Erlmeier F, Hartmann A, Walch A. The synergism of spatial metabolomics and morphometry improves machine learning‐based renal tumour subtype classification. Clin Transl Med 2022; 12:e666. [PMID: 35184396 PMCID: PMC8858620 DOI: 10.1002/ctm2.666] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 11/11/2021] [Accepted: 11/17/2021] [Indexed: 12/14/2022] Open
Affiliation(s)
- Verena M. Prade
- Research Unit Analytical Pathology Helmholtz Zentrum München – German Research Center for Environmental Health Neuherberg Germany
| | - Na Sun
- Research Unit Analytical Pathology Helmholtz Zentrum München – German Research Center for Environmental Health Neuherberg Germany
| | - Jian Shen
- Research Unit Analytical Pathology Helmholtz Zentrum München – German Research Center for Environmental Health Neuherberg Germany
| | - Annette Feuchtinger
- Research Unit Analytical Pathology Helmholtz Zentrum München – German Research Center for Environmental Health Neuherberg Germany
| | - Thomas Kunzke
- Research Unit Analytical Pathology Helmholtz Zentrum München – German Research Center for Environmental Health Neuherberg Germany
| | - Achim Buck
- Research Unit Analytical Pathology Helmholtz Zentrum München – German Research Center for Environmental Health Neuherberg Germany
| | - Peter Schraml
- Institute of Pathology and Molecular Pathology University Hospital Zurich Zurich Switzerland
| | - Holger Moch
- Institute of Pathology and Molecular Pathology University Hospital Zurich Zurich Switzerland
| | | | | | | | - Franziska Erlmeier
- Institute of Pathology, University Hospital Erlangen Friedrich‐Alexander‐University Erlangen‐Nürnberg Erlangen Germany
- Comprehensive Cancer Center Erlangen‐EMN (CCC ER‐EMN) Erlangen Germany
| | - Arndt Hartmann
- Institute of Pathology, University Hospital Erlangen Friedrich‐Alexander‐University Erlangen‐Nürnberg Erlangen Germany
- Comprehensive Cancer Center Erlangen‐EMN (CCC ER‐EMN) Erlangen Germany
| | - Axel Walch
- Research Unit Analytical Pathology Helmholtz Zentrum München – German Research Center for Environmental Health Neuherberg Germany
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10
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Kuett L, Catena R, Özcan A, Plüss A, Schraml P, Moch H, de Souza N, Bodenmiller B. Three-dimensional imaging mass cytometry for highly multiplexed molecular and cellular mapping of tissues and the tumor microenvironment. Nat Cancer 2022; 3:122-133. [PMID: 35121992 PMCID: PMC7613779 DOI: 10.1038/s43018-021-00301-w] [Citation(s) in RCA: 64] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 11/03/2021] [Indexed: 11/22/2022]
Abstract
A holistic understanding of tissue and organ structure and function requires the detection of molecular constituents in their original three-dimensional (3D) context. Imaging mass cytometry (IMC) enables simultaneous detection of up to 40 antigens and transcripts using metal-tagged antibodies but has so far been restricted to two-dimensional imaging. Here we report the development of 3D IMC for multiplexed 3D tissue analysis at single-cell resolution and demonstrate the utility of the technology by analysis of human breast cancer samples. The resulting 3D models reveal cellular and microenvironmental heterogeneity and cell-level tissue organization not detectable in two dimensions. 3D IMC will prove powerful in the study of phenomena occurring in 3D space such as tumor cell invasion and is expected to provide invaluable insights into cellular microenvironments and tissue architecture.
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Affiliation(s)
- Laura Kuett
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
- Institute of Molecular Health Sciences, ETH Zurich, Zürich, Switzerland
| | - Raúl Catena
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
- Leica Geosystems part of Hexagon, Heerbrugg, St. Gallen, Switzerland
| | - Alaz Özcan
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
- Department of Immunology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Alex Plüss
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Peter Schraml
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Natalie de Souza
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
- Institute of Molecular Systems Biology, ETH Zurich, Zürich, Switzerland
| | - Bernd Bodenmiller
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland.
- Institute of Molecular Health Sciences, ETH Zurich, Zürich, Switzerland.
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11
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Kuipers J, Moore AL, Jahn K, Schraml P, Wang F, Morita K, Futreal PA, Takahashi K, Beisel C, Moch H, Beerenwinkel N. Statistical tests for intra-tumour clonal co-occurrence and exclusivity. PLoS Comput Biol 2021; 17:e1009036. [PMID: 34910733 PMCID: PMC8716063 DOI: 10.1371/journal.pcbi.1009036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 04/28/2021] [Revised: 12/29/2021] [Accepted: 11/19/2021] [Indexed: 12/31/2022] Open
Abstract
Tumour progression is an evolutionary process in which different clones evolve over time, leading to intra-tumour heterogeneity. Interactions between clones can affect tumour evolution and hence disease progression and treatment outcome. Intra-tumoural pairs of mutations that are overrepresented in a co-occurring or clonally exclusive fashion over a cohort of patient samples may be suggestive of a synergistic effect between the different clones carrying these mutations. We therefore developed a novel statistical testing framework, called GeneAccord, to identify such gene pairs that are altered in distinct subclones of the same tumour. We analysed our framework for calibration and power. By comparing its performance to baseline methods, we demonstrate that to control type I errors, it is essential to account for the evolutionary dependencies among clones. In applying GeneAccord to the single-cell sequencing of a cohort of 123 acute myeloid leukaemia patients, we find 1 clonally co-occurring and 8 clonally exclusive gene pairs. The clonally exclusive pairs mostly involve genes of the key signalling pathways. Tumours typically display high levels of heterogeneity, not only between different tumours but also within a single one. Intra-tumour heterogeneity results from an evolutionary process, giving rise to different populations of cancer cells known as clones. How clones interact may affect tumour evolution, which in turn determines disease progression and treatment outcome. In practice, we may observe pairs of mutations that co-occur in clones or exclude each other more often than we would expect for a given cohort of patient samples. Exclusive pairs are suggestive that clones carrying one or the other mutation may cooperate in the evolutionary process. Targeting only one of them may then suffice to alter the tumour evolution. Therefore it is critical to have statistical methods which allow us to identify such pairs. GeneAccord is a novel statistical testing framework we developed especially to identify pairs of genes altered in distinct clones of the same tumour. Accounting for the evolutionary dependencies among clones emerged as critical to adequately control testing errors. In a cohort of 123 acute myeloid leukaemia patients, GeneAccord identified one clonally co-occurring and eight clonally exclusive gene pairs. The latter predominantly involved genes of key signalling pathways.
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Affiliation(s)
- Jack Kuipers
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Ariane L. Moore
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Katharina Jahn
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Peter Schraml
- Department of Pathology and Molecular Pathology, University and University Hospital Zurich, Zurich, Switzerland
| | - Feng Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Kiyomi Morita
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - P. Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Koichi Takahashi
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Christian Beisel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University and University Hospital Zurich, Zurich, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
- * E-mail:
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12
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Bolis M, Bossi D, Vallerga A, Ceserani V, Cavalli M, Impellizzieri D, Di Rito L, Zoni E, Mosole S, Elia AR, Rinaldi A, Pereira Mestre R, D’Antonio E, Ferrari M, Stoffel F, Jermini F, Gillessen S, Bubendorf L, Schraml P, Calcinotto A, Corey E, Moch H, Spahn M, Thalmann G, Kruithof-de Julio M, Rubin MA, Theurillat JPP. Dynamic prostate cancer transcriptome analysis delineates the trajectory to disease progression. Nat Commun 2021; 12:7033. [PMID: 34857732 PMCID: PMC8640014 DOI: 10.1038/s41467-021-26840-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 10/20/2021] [Indexed: 12/13/2022] Open
Abstract
Comprehensive genomic studies have delineated key driver mutations linked to disease progression for most cancers. However, corresponding transcriptional changes remain largely elusive because of the bias associated with cross-study analysis. Here, we overcome these hurdles and generate a comprehensive prostate cancer transcriptome atlas that describes the roadmap to tumor progression in a qualitative and quantitative manner. Most cancers follow a uniform trajectory characterized by upregulation of polycomb-repressive-complex-2, G2-M checkpoints, and M2 macrophage polarization. Using patient-derived xenograft models, we functionally validate our observations and add single-cell resolution. Thereby, we show that tumor progression occurs through transcriptional adaption rather than a selection of pre-existing cancer cell clusters. Moreover, we determine at the single-cell level how inhibition of EZH2 - the top upregulated gene along the trajectory - reverts tumor progression and macrophage polarization. Finally, a user-friendly web-resource is provided enabling the investigation of dynamic transcriptional perturbations linked to disease progression.
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Affiliation(s)
- Marco Bolis
- Faculty of Biomedical Sciences, Institute of Oncology Research, USI, Bellinzona, TI, 6500, Switzerland. .,Computational Oncology Unit, Department of Oncology, Istituto di Richerche Farmacologiche 'Mario Negri' IRCCS, 20156, Milano, Italy. .,Bioinformatics Core Unit, Swiss Institute of Bioinformatics, TI, 6500, Bellinzona, Switzerland.
| | - Daniela Bossi
- grid.29078.340000 0001 2203 2861Faculty of Biomedical Sciences, Institute of Oncology Research, USI, Bellinzona, TI 6500 Switzerland
| | - Arianna Vallerga
- grid.29078.340000 0001 2203 2861Faculty of Biomedical Sciences, Institute of Oncology Research, USI, Bellinzona, TI 6500 Switzerland ,grid.419765.80000 0001 2223 3006Bioinformatics Core Unit, Swiss Institute of Bioinformatics, TI 6500 Bellinzona, Switzerland
| | - Valentina Ceserani
- grid.29078.340000 0001 2203 2861Faculty of Biomedical Sciences, Institute of Oncology Research, USI, Bellinzona, TI 6500 Switzerland
| | - Manuela Cavalli
- grid.29078.340000 0001 2203 2861Faculty of Biomedical Sciences, Institute of Oncology Research, USI, Bellinzona, TI 6500 Switzerland
| | - Daniela Impellizzieri
- grid.29078.340000 0001 2203 2861Faculty of Biomedical Sciences, Institute of Oncology Research, USI, Bellinzona, TI 6500 Switzerland
| | - Laura Di Rito
- grid.4527.40000000106678902Computational Oncology Unit, Department of Oncology, Istituto di Richerche Farmacologiche ‘Mario Negri’ IRCCS, 20156 Milano, Italy
| | - Eugenio Zoni
- grid.5734.50000 0001 0726 5157Department of Biomedical Research, University of Bern, 3008 Bern, Switzerland
| | - Simone Mosole
- grid.29078.340000 0001 2203 2861Faculty of Biomedical Sciences, Institute of Oncology Research, USI, Bellinzona, TI 6500 Switzerland
| | - Angela Rita Elia
- grid.29078.340000 0001 2203 2861Faculty of Biomedical Sciences, Institute of Oncology Research, USI, Bellinzona, TI 6500 Switzerland
| | - Andrea Rinaldi
- grid.29078.340000 0001 2203 2861Faculty of Biomedical Sciences, Institute of Oncology Research, USI, Bellinzona, TI 6500 Switzerland
| | - Ricardo Pereira Mestre
- grid.419922.5Oncology Institute of Southern Switzerland, Bellinzona, TI 6500 Switzerland
| | - Eugenia D’Antonio
- grid.419922.5Oncology Institute of Southern Switzerland, Bellinzona, TI 6500 Switzerland
| | - Matteo Ferrari
- grid.469433.f0000 0004 0514 7845Urology Department, Ente Ospedaliero Cantonale, Bellinzona, TI Switzerland
| | - Flavio Stoffel
- grid.469433.f0000 0004 0514 7845Urology Department, Ente Ospedaliero Cantonale, Bellinzona, TI Switzerland
| | - Fernando Jermini
- grid.469433.f0000 0004 0514 7845Urology Department, Ente Ospedaliero Cantonale, Bellinzona, TI Switzerland
| | - Silke Gillessen
- grid.419922.5Oncology Institute of Southern Switzerland, Bellinzona, TI 6500 Switzerland ,grid.29078.340000 0001 2203 2861Faculty of Biomedical Sciences, University of Southern Switzerland (USI), TI 6900 Lugano, Switzerland
| | - Lukas Bubendorf
- grid.410567.1Institute of Surgical Pathology, University Hospital Basel, 4031 Basel, Switzerland
| | - Peter Schraml
- grid.412004.30000 0004 0478 9977Department of Pathology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Arianna Calcinotto
- grid.29078.340000 0001 2203 2861Faculty of Biomedical Sciences, Institute of Oncology Research, USI, Bellinzona, TI 6500 Switzerland
| | - Eva Corey
- grid.34477.330000000122986657Department of Urology, University of Washington, Seattle, WA 98195 USA
| | - Holger Moch
- grid.412004.30000 0004 0478 9977Department of Pathology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Martin Spahn
- grid.415941.c0000 0004 0509 4333Lindenhofspital Bern, Prostate Center Bern, 3012 Bern, Switzerland
| | - George Thalmann
- grid.5734.50000 0001 0726 5157Department of Biomedical Research, University of Bern, 3008 Bern, Switzerland ,grid.411656.10000 0004 0479 0855Department of Urology, Inselspital, Bern University Hospital, 3010 Bern, Switzerland
| | - Marianna Kruithof-de Julio
- grid.5734.50000 0001 0726 5157Department of Biomedical Research, University of Bern, 3008 Bern, Switzerland ,grid.411656.10000 0004 0479 0855Department of Urology, Inselspital, Bern University Hospital, 3010 Bern, Switzerland
| | - Mark A. Rubin
- grid.5734.50000 0001 0726 5157Department of Biomedical Research, University of Bern, 3008 Bern, Switzerland ,grid.5734.50000 0001 0726 5157Bern Center for Precision Medicine, University of Bern and Inselspital, 3012 Bern, Switzerland
| | - Jean-Philippe P. Theurillat
- grid.29078.340000 0001 2203 2861Faculty of Biomedical Sciences, Institute of Oncology Research, USI, Bellinzona, TI 6500 Switzerland
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13
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Fomitcheva-Khartchenko A, Rapsomaniki MA, Sobottka B, Schraml P, Kaigala GV. Spatial protein heterogeneity analysis in frozen tissues to evaluate tumor heterogeneity. PLoS One 2021; 16:e0259332. [PMID: 34797831 PMCID: PMC8604290 DOI: 10.1371/journal.pone.0259332] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 07/24/2021] [Accepted: 10/19/2021] [Indexed: 11/19/2022] Open
Abstract
A new workflow for protein-based tumor heterogeneity probing in tissues is here presented. Tumor heterogeneity is believed to be key for therapy failure and differences in prognosis in cancer patients. Comprehending tumor heterogeneity, especially at the protein level, is critical for tracking tumor evolution, and showing the presence of different phenotypical variants and their location with respect to tissue architecture. Although a variety of techniques is available for quantifying protein expression, the heterogeneity observed in the tissue is rarely addressed. The proposed method is validated in breast cancer fresh-frozen tissues derived from five patients. Protein expression is quantified on the tissue regions of interest (ROI) with a resolution of up to 100 μm in diameter. High heterogeneity values across the analyzed patients in proteins such as cytokeratin 7, β-actin and epidermal growth factor receptor (EGFR) using a Shannon entropy analysis are observed. Additionally, ROIs are clustered according to their expression levels, showing their location in the tissue section, and highlighting that similar phenotypical variants are not always located in neighboring regions. Interestingly, a patient with a phenotype related to increased aggressiveness of the tumor presents a unique protein expression pattern. In summary, a workflow for the localized extraction and protein analysis of regions of interest from frozen tissues, enabling the evaluation of tumor heterogeneity at the protein level is presented.
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Affiliation(s)
| | | | - Bettina Sobottka
- Department of Pathology and Molecular Pathology, University Hospital Zurich and University Zurich, Zurich, Switzerland
| | - Peter Schraml
- Department of Pathology and Molecular Pathology, University Hospital Zurich and University Zurich, Zurich, Switzerland
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14
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Voith von Voithenberg L, Kashyap A, Opitz L, Aquino C, Sykes T, Nieser M, Petrini LFT, Enrriquez Casimiro N, van Kooten XF, Biskup S, Schlapbach R, Schraml P, Kaigala GV. Mapping Spatial Genetic Landscapes in Tissue Sections through Microscale Integration of Sampling Methodology into Genomic Workflows. Small 2021; 17:e2007901. [PMID: 33852760 DOI: 10.1002/smll.202007901] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/12/2021] [Indexed: 06/12/2023]
Abstract
In cancer research, genomic profiles are often extracted from homogenized macrodissections of tissues, with the histological context lost and a large fraction of material underutilized. Pertinently, the spatial genomic landscape provides critical complementary information in deciphering disease heterogeneity and progression. Microscale sampling methods such as microdissection to obtain such information are often destructive to a sizeable fraction of the biopsy sample, thus showing limited multiplexability and adaptability to different assays. A modular microfluidic technology is here implemented to recover cells at the microscale from tumor tissue sections, with minimal disruption of unsampled areas and tailored to interface with genome profiling workflows, which is directed here toward evaluating intratumoral genomic heterogeneity. The integrated workflow-GeneScape-is used to evaluate heterogeneity in a metastatic mammary carcinoma, showing distinct single nucleotide variants and copy number variations in different tumor tissue regions, suggesting the polyclonal origin of the metastasis as well as development driven by multiple location-specific drivers.
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Affiliation(s)
| | - Aditya Kashyap
- IBM Research Europe, Säumerstrasse 4, Rüschlikon, CH-8803, Switzerland
| | - Lennart Opitz
- Functional Genomics Center Zurich, Winterthurerstr. 190, Zurich, CH-8057, Switzerland
| | - Catharine Aquino
- Functional Genomics Center Zurich, Winterthurerstr. 190, Zurich, CH-8057, Switzerland
| | - Timothy Sykes
- Functional Genomics Center Zurich, Winterthurerstr. 190, Zurich, CH-8057, Switzerland
| | - Maike Nieser
- Center for Genomics and Transcriptomics, Paul-Ehrlich-Str. 23, 72076, Tübingen, Germany
| | | | | | | | - Saskia Biskup
- Center for Genomics and Transcriptomics, Paul-Ehrlich-Str. 23, 72076, Tübingen, Germany
| | - Ralph Schlapbach
- Functional Genomics Center Zurich, Winterthurerstr. 190, Zurich, CH-8057, Switzerland
| | - Peter Schraml
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Schmelzbergstr. 12, Zurich, CH-8091, Switzerland
| | - Govind V Kaigala
- IBM Research Europe, Säumerstrasse 4, Rüschlikon, CH-8803, Switzerland
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15
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Khartchenko AF, Schraml P, Kaigala GV. Abstract PO-086: Local quantification of protein expression on frozen tissue sections to evaluate tumor heterogeneity. Cancer Res 2020. [DOI: 10.1158/1538-7445.tumhet2020-po-086] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The discernment of intra-tumor heterogeneity is critical to understand therapy failure and differences of prognosis between patients with similar disease states. Part of the heterogeneity can be appreciated at the protein level, where quantitation can aid the elucidation of complex biological processes. We propose a workflow to quantify protein expression on a “local” level on frozen breast tumor tissue sections, providing a measure and easy visualization of the phenotypical heterogeneity present in the tissue. In this workflow, we extract 8-10 regions of interest (ROIs) of ~100 µm in diameter from frozen tissue sections of 5 patients using a microfluidic probe (MFP). The MFP is a microfluidic scanning probe device that confines a biochemical on a selected region of a tissue, with the capacity of working in liquid environments, and which allows the extraction of individual regions (footprints) in less than 3 min. The rapid extraction together with the liquid environment in which the tissue is present are key for minimizing protein degradation. The extracted proteins are analyzed through an antibody microarray with a panel of 13 proteins that aids a proteomic-based classification of molecular subtypes of breast cancer. Protein expression is quantified based on the greyscale intensity of the corresponding spot in the microarray and normalized by the area of the extracted region. Further analysis determines the presence and extension of phenotypical clusters. Using local protein expression, we generated an expression map of the 13 analyzed proteins. We observe large variations of protein concentrations in the case of beta-actin, estrogen receptor (ER) and EGFR. Cytokeratins (CK)5, CK8, CK17, progesterone receptor and GAPDH presented lower variations in concentration between the analyzed regions in this set of patients. We then evaluated whether the observed differences were statistically significant using Cohen size D effect, showing higher heterogeneity among some proteins (beta-actin, ER, or androgen receptor) and some patients (Patient 1). Finally, we performed a hierarchical clustering analysis across the patients to understand the presence and distribution of phenotypical variants. Patients 3 and 5 presented one single phenotypical variant, while the other patients had up to four. Quantitative methods to describe heterogeneity on the proteomic level are essential to improve our comprehension of tumor biology and thus develop more precise cancer diagnostic approaches. Techniques such as the one presented here can advance our understanding of the spatial location of phenotypical variants within the tumor mass, hinting towards a more accurate choice of treatment modalities.
Citation Format: Anna Fomitcheva Khartchenko, Peter Schraml, Govind V. Kaigala. Local quantification of protein expression on frozen tissue sections to evaluate tumor heterogeneity [abstract]. In: Proceedings of the AACR Virtual Special Conference on Tumor Heterogeneity: From Single Cells to Clinical Impact; 2020 Sep 17-18. Philadelphia (PA): AACR; Cancer Res 2020;80(21 Suppl):Abstract nr PO-086.
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Affiliation(s)
| | - Peter Schraml
- 2Institute for Surgical Pathology, University Hospital Zurich, Zurich, Switzerland,
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16
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Lakshminarayanan H, Rutishauser D, Schraml P, Moch H, Bolck HA. Liquid Biopsies in Renal Cell Carcinoma-Recent Advances and Promising New Technologies for the Early Detection of Metastatic Disease. Front Oncol 2020; 10:582843. [PMID: 33194717 PMCID: PMC7656014 DOI: 10.3389/fonc.2020.582843] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 09/29/2020] [Indexed: 12/21/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) displays a highly varying clinical progression, from slow growing localized tumors to very aggressive metastatic disease (mRCC). Almost a third of all patients with ccRCC show metastatic dissemination at presentation while another third develop metastasis during the course of the disease. Survival rates of mRCC patients remain low despite the development of novel targeted treatment regimens. Biomarkers indicating disease progression could help to define its aggressive potential and thus guide patient management. However, molecular markers that can reliably assess metastatic dissemination and disease recurrence in ccRCC have not been recommended for clinical practice to date. Liquid biopsies could provide an attractive and non-invasive method to determine the risk of recurrence or metastatic dissemination during follow-up and thus assist the search for surveillance biomarkers in ccRCC tumors. A wide spectrum of circulating molecules have already shown considerable potential for ccRCC diagnosis and prognostication. In this review, we outline state of the art of the key circulating analytes such as cfDNA, cfRNA, proteins, and exosomes that may serve as biomarkers for the longitudinal monitoring of ccRCC progression to metastasis. Moreover, we address some of the prevailing limitations in the past approaches and present promising adoptable technologies that could help to pursue the implementation of liquid biopsies as a prognostic tool for mRCC.
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Affiliation(s)
| | | | | | - Holger Moch
- Department of Pathology and Molecular Pathology, University of Zurich and University Hospital Zurich, Zurich, Switzerland
| | - Hella A. Bolck
- Department of Pathology and Molecular Pathology, University of Zurich and University Hospital Zurich, Zurich, Switzerland
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17
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Orjuela S, Menigatti M, Schraml P, Kambakamba P, Robinson MD, Marra G. The DNA hypermethylation phenotype of colorectal cancer liver metastases resembles that of the primary colorectal cancers. BMC Cancer 2020; 20:290. [PMID: 32252665 PMCID: PMC7137338 DOI: 10.1186/s12885-020-06777-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 03/23/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Identifying molecular differences between primary and metastatic colorectal cancers-now possible with the aid of omics technologies-can improve our understanding of the biological mechanisms of cancer progression and facilitate the discovery of novel treatments for late-stage cancer. We compared the DNA methylomes of primary colorectal cancers (CRCs) and CRC metastases to the liver. Laser microdissection was used to obtain epithelial tissue (10 to 25 × 106 μm2) from sections of fresh-frozen samples of primary CRCs (n = 6), CRC liver metastases (n = 12), and normal colon mucosa (n = 3). DNA extracted from tissues was enriched for methylated sequences with a methylCpG binding domain (MBD) polypeptide-based protocol and subjected to deep sequencing. The performance of this protocol was compared with that of targeted enrichment for bisulfite sequencing used in a previous study of ours. RESULTS MBD enrichment captured a total of 322,551 genomic regions (249.5 Mb or ~ 7.8% of the human genome), which included over seven million CpG sites. A few of these regions were differentially methylated at an expected false discovery rate (FDR) of 5% in neoplastic tissues (primaries: 0.67%, i.e., 2155 regions containing 279,441 CpG sites; liver metastases: 1%, i.e., 3223 regions containing 312,723 CpG sites) as compared with normal mucosa samples. Most of the differentially methylated regions (DMRs; 94% in primaries; 70% in metastases) were hypermethylated, and almost 80% of these (1882 of 2396) were present in both lesion types. At 5% FDR, no DMRs were detected in liver metastases vs. primary CRC. However, short regions of low-magnitude hypomethylation were frequent in metastases but rare in primaries. Hypermethylated DMRs were far more abundant in sequences classified as intragenic, gene-regulatory, or CpG shelves-shores-island segments, whereas hypomethylated DMRs were equally represented in extragenic (mainly, open-sea) and intragenic (mainly, gene bodies) sequences of the genome. Compared with targeted enrichment, MBD capture provided a better picture of the extension of CRC-associated DNA hypermethylation but was less powerful for identifying hypomethylation. CONCLUSIONS Our findings demonstrate that the hypermethylation phenotype in CRC liver metastases remains similar to that of the primary tumor, whereas CRC-associated DNA hypomethylation probably undergoes further progression after the cancer cells have migrated to the liver.
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Affiliation(s)
- Stephany Orjuela
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.,Institute of Molecular Life Sciences, University of Zurich and SIB Swiss Institute of Bioinformatics, Zürich, Switzerland
| | - Mirco Menigatti
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Peter Schraml
- Department of Pathology and Molecular Pathology, University of Zurich, Zürich, Switzerland
| | - Patryk Kambakamba
- Division of Surgical Research, University of Zurich, Zürich, Switzerland
| | - Mark D Robinson
- Institute of Molecular Life Sciences, University of Zurich and SIB Swiss Institute of Bioinformatics, Zürich, Switzerland
| | - Giancarlo Marra
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
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18
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Ohashi R, Martignoni G, Hartmann A, Caliò A, Segala D, Stöhr C, Wach S, Erlmeier F, Weichert W, Autenrieth M, Schraml P, Rupp NJ, Ohe C, Otsuki Y, Kawasaki T, Kobayashi H, Kobayashi K, Miyazaki T, Shibuya H, Usuda H, Umezu H, Fujishima F, Furusato B, Osakabe M, Sugai T, Kuroda N, Tsuzuki T, Nagashima Y, Ajioka Y, Moch H. Correction to: Multi-institutional re-evaluation of prognostic factors in chromophobe renal cell carcinoma: proposal of a novel two-tiered grading scheme. Virchows Arch 2020; 476:419-422. [PMID: 32157467 DOI: 10.1007/s00428-020-02786-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The legends of Figs. 1 and 3 in the published original version of the above article are incorrect.
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Affiliation(s)
- Riuko Ohashi
- Histopathology Core Facility, Niigata University Faculty of Medicine, 1-757 Asahimachi-dori, Chuo-ku, Niigata, 951-8510, Japan.,Department of Pathology and Molecular Pathology, University and University Hospital Zurich, Schmelzbergstrasse 12, CH-8091, Zurich, Switzerland.,Division of Molecular and Diagnostic Pathology, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata, 951-8510, Japan
| | - Guido Martignoni
- Department of Diagnostic and Public Health, University of Verona, Piazzale Ludovico Antonio Scuro 10, 37134, Verona, Italy.,Department of Pathology, Pederzoli Hospital, Via Monte Baldo 24, 37019, Peschiera del Garda, Italy
| | - Arndt Hartmann
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Krankenhausstrasse 8-10, 91054, Erlangen, Germany
| | - Anna Caliò
- Department of Diagnostic and Public Health, University of Verona, Piazzale Ludovico Antonio Scuro 10, 37134, Verona, Italy
| | - Diego Segala
- Department of Pathology, Pederzoli Hospital, Via Monte Baldo 24, 37019, Peschiera del Garda, Italy
| | - Christine Stöhr
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Krankenhausstrasse 8-10, 91054, Erlangen, Germany
| | - Sven Wach
- Department of Urology and Pediatric Urology, University Hospital Erlangen, Friedrich Alexander-University Erlangen-Nürnberg, Krankenhausstrasse 12, 91054, Erlangen, Germany
| | - Franziska Erlmeier
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Krankenhausstrasse 8-10, 91054, Erlangen, Germany.,Institute of Pathology, Technical University Munich, Trogerstrasse 18, 81675, Munich, Germany
| | - Wilko Weichert
- Institute of Pathology, Technical University Munich, Trogerstrasse 18, 81675, Munich, Germany
| | - Michael Autenrieth
- Department of Urology, Technical University Munich, Klinikum rechts der Isar, Ismaninger Strasse 22, 81675, Munich, Germany
| | - Peter Schraml
- Department of Pathology and Molecular Pathology, University and University Hospital Zurich, Schmelzbergstrasse 12, CH-8091, Zurich, Switzerland
| | - Niels J Rupp
- Department of Pathology and Molecular Pathology, University and University Hospital Zurich, Schmelzbergstrasse 12, CH-8091, Zurich, Switzerland
| | - Chisato Ohe
- Department of Pathology and Laboratory Medicine, Kansai Medical University, 2-5-1 Shin-machi, Hirakata, 573-1010, Japan
| | - Yoshiro Otsuki
- Department of Pathology, Seirei Hamamatsu General Hospital, 2-12-12 Sumiyoshi, Naka-ku, Hamamatsu, 430-8558, Japan
| | - Takashi Kawasaki
- Department of Pathology, Niigata Cancer Center Hospital, 2-15-3 Kawagishi-cho, Chuo-ku, Niigata, 951-8566, Japan
| | - Hiroshi Kobayashi
- Department of Pathology, Tachikawa General Hospital, 1-24 Asahioka, Nagaoka, 940-8621, Japan
| | - Kazuhiro Kobayashi
- Department of Pathology, Gifu University Hospital, 1-1 Yanagido, Gifu, 501-1194, Japan
| | - Tatsuhiko Miyazaki
- Department of Pathology, Gifu University Hospital, 1-1 Yanagido, Gifu, 501-1194, Japan
| | - Hiroyuki Shibuya
- Department of Pathology, Niigata City General Hospital, 463-7 Shumoku, Chuo-ku, Niigata, 950-1197, Japan
| | - Hiroyuki Usuda
- Department of Diagnostic Pathology, Nagaoka Red Cross Hospital, 2-297-1 Sensyu, Nagaoka, 940-2085, Japan
| | - Hajime Umezu
- Division of Pathology, Niigata University Medical & Dental Hospital, 1-754 Asahimachi-dori, Chuo-ku, Niigata, 951-8520, Japan
| | - Fumiyoshi Fujishima
- Department of Anatomic Pathology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8575, Japan
| | - Bungo Furusato
- Cancer Genomics Unit, Clinical Genomics Center, Nagasaki University Hospital, 1-7-1, Sakamoto, Nagasaki, 852-8501, Japan.,Department of Pathology, Nagasaki University Graduate School of Biomedical Sciences, 1-7-1, Sakamoto, Nagasaki, 852-8501, Japan
| | - Mitsumasa Osakabe
- Department of Molecular Diagnostic Pathology, School of Medicine, Iwate Medical University, 2-1-1, Idai-dori, Yahaba-cho, Shiwa-gun, Iwate, 028-3695, Japan
| | - Tamotsu Sugai
- Department of Molecular Diagnostic Pathology, School of Medicine, Iwate Medical University, 2-1-1, Idai-dori, Yahaba-cho, Shiwa-gun, Iwate, 028-3695, Japan
| | - Naoto Kuroda
- Department of Diagnostic Pathology, Kochi Red Cross Hospital, 1-4-63-11 hadaminamimachi, Kochi, Kochi, 780-8562, Japan
| | - Toyonori Tsuzuki
- Department of Surgical Pathology, Aichi Medical University Hospital, 1-1 Yazakokarimata, Nagakute, 480-1195, Japan
| | - Yoji Nagashima
- Department of Surgical Pathology, Tokyo Women's Medical University Hospital, 8-1 Kawada-cho, Shinjuku-ku, Tokyo, 162-8666, Japan
| | - Yoichi Ajioka
- Histopathology Core Facility, Niigata University Faculty of Medicine, 1-757 Asahimachi-dori, Chuo-ku, Niigata, 951-8510, Japan.,Division of Molecular and Diagnostic Pathology, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata, 951-8510, Japan
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University and University Hospital Zurich, Schmelzbergstrasse 12, CH-8091, Zurich, Switzerland.
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19
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Voith von Voithenberg L, Fomitcheva Khartchenko A, Huber D, Schraml P, Kaigala GV. Spatially multiplexed RNA in situ hybridization to reveal tumor heterogeneity. Nucleic Acids Res 2020; 48:e17. [PMID: 31853536 PMCID: PMC7026647 DOI: 10.1093/nar/gkz1151] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 11/20/2019] [Accepted: 12/03/2019] [Indexed: 02/07/2023] Open
Abstract
Multiplexed RNA in situ hybridization for the analysis of gene expression patterns plays an important role in investigating development and disease. Here, we present a method for multiplexed RNA-ISH to detect spatial tumor heterogeneity in tissue sections. We made use of a microfluidic chip to deliver ISH-probes locally to regions of a few hundred micrometers over time periods of tens of minutes. This spatial multiplexing method can be combined with ISH-approaches based on signal amplification, with bright field detection and with the commonly used format of formalin-fixed paraffin-embedded tissue sections. By using this method, we analyzed the expression of HER2 with internal positive and negative controls (ActB, dapB) as well as predictive biomarker panels (ER, PgR, HER2) in a spatially multiplexed manner on single mammary carcinoma sections. We further demonstrated the applicability of the technique for subtype differentiation in breast cancer. Local analysis of HER2 revealed medium to high spatial heterogeneity of gene expression (Cohen effect size r = 0.4) in equivocally tested tumor tissues. Thereby, we exemplify the importance of using such a complementary approach for the analysis of spatial heterogeneity, in particular for equivocally tested tumor samples. As the method is compatible with a range of ISH approaches and tissue samples, it has the potential to find broad applicability in the context of molecular analysis of human diseases.
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Affiliation(s)
| | | | - Deborah Huber
- IBM Research Zürich, Säumerstrasse 4, CH-8803 Rüschlikon, Switzerland
| | - Peter Schraml
- University Hospital Zurich, Department of Pathology and Molecular Pathology, Schmelzbergstr. 12, CH-8091 Zurich, Switzerland
| | - Govind V Kaigala
- IBM Research Zürich, Säumerstrasse 4, CH-8803 Rüschlikon, Switzerland
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20
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Bolck HA, Pauli C, Göbel E, Mühlbauer K, Dettwiler S, Moch H, Schraml P. Cancer Sample Biobanking at the Next Level: Combining Tissue With Living Cell Repositories to Promote Precision Medicine. Front Cell Dev Biol 2019; 7:246. [PMID: 31696117 PMCID: PMC6817465 DOI: 10.3389/fcell.2019.00246] [Citation(s) in RCA: 15] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 10/07/2019] [Indexed: 12/24/2022] Open
Abstract
Biorespositories of formalin-fixed and paraffin-embedded (FFPE) or fresh frozen human tissues from malignant diseases generated as integral part of the diagnostic workup in many pathology departments have been pivotal resources for translational cancer studies. However, such tissue biobanks have traditionally contained only non-viable specimens and thus cannot enable functional assays for the discovery and validation of therapeutic targets or the assessment of drug responses and resistance to treatment. To overcome these limitations, we have developed a next-generation comprehensive biobanking platform that includes the generation of patient-derived in vitro cell models from colorectal, pancreatic and kidney cancers among others. As such patient-derived cell (PDC) models retain important features of the original human tumors, they have emerged as relevant tools for more dynamic clinical and experimental analyses of cancer. Here, we describe details of the complex processes of acquisition and processing of patient-derived samples, propagation, annotation, characterization and distribution of resulting cell models and emphasize the requirements of quality assurance, organizational considerations and investment into resources. Taken together, we show how clinical tissue collections can be taken to the next level thus promising major new opportunities for understanding and treating cancer in the context of precision medicine.
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Affiliation(s)
- Hella A Bolck
- Department of Pathology and Molecular Pathology, University Hospital of Zürich, Zurich, Switzerland
| | - Chantal Pauli
- Department of Pathology and Molecular Pathology, University Hospital of Zürich, Zurich, Switzerland
| | - Elisabeth Göbel
- Department of Pathology and Molecular Pathology, University Hospital of Zürich, Zurich, Switzerland
| | - Katharina Mühlbauer
- Department of Pathology and Molecular Pathology, University Hospital of Zürich, Zurich, Switzerland
| | - Susanne Dettwiler
- Department of Pathology and Molecular Pathology, University Hospital of Zürich, Zurich, Switzerland
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University Hospital of Zürich, Zurich, Switzerland
| | - Peter Schraml
- Department of Pathology and Molecular Pathology, University Hospital of Zürich, Zurich, Switzerland
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21
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Bolck HA, Corrò C, Kahraman A, von Teichman A, Toussaint NC, Kuipers J, Chiovaro F, Koelzer VH, Pauli C, Moritz W, Bode PK, Rechsteiner M, Beerenwinkel N, Schraml P, Moch H. Tracing Clonal Dynamics Reveals that Two- and Three-dimensional Patient-derived Cell Models Capture Tumor Heterogeneity of Clear Cell Renal Cell Carcinoma. Eur Urol Focus 2019; 7:152-162. [PMID: 31266731 DOI: 10.1016/j.euf.2019.06.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [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: 03/15/2019] [Revised: 05/16/2019] [Accepted: 06/13/2019] [Indexed: 12/20/2022]
Abstract
BACKGROUND Extensive DNA sequencing has led to an unprecedented view of the diversity of individual genomes and their evolution among patients with clear cell renal cell carcinoma (ccRCC). OBJECTIVE To understand subclonal architecture and dynamics of patient-derived two-dimensional (2D) and three-dimensional (3D) ccRCC models in vitro, in order to determine whether they mirror ccRCC inter- and intratumor heterogeneity. DESIGN, SETTING, AND PARTICIPANTS We have established a comprehensive platform of living renal cancer cell models from ccRCC surgical specimens. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS We confirmed the concordance of 2D and 3D patient-derived cell (PDC) models with the original tumor tissue in terms of histology, biomarker expression, cancer driver mutations, and copy number alterations. We addressed inter- and intrapatient heterogeneity by analyzing clonal dynamics during serial passaging. RESULTS AND LIMITATIONS In-depth genetic characterization verified the presence of heterogeneous cell populations, and revealed a high degree of similarity between subclonal compositions of monolayer and organoid cell cultures and the corresponding parental ccRCCs. Clonal dynamics were evident during serial passaging of cells in vitro, suggesting that PDC cultures can offer insights into evolutionary potential and treatment susceptibility of ccRCC subclones in vivo. Proof-of-concept drug profiling using selected ccRCC-targeted therapy agents highlighted patient-specific vulnerabilities in PDC models that could not be anticipated by interrogating commercially available cell lines. CONCLUSIONS We demonstrate that PDC models mirror inter- and intratumor heterogeneity of ccRCC in vitro. Based on our findings, we envision that the use of these models will advance our understanding of the trajectories that cause genetic diversity and their consequences for treatment on an individual level. PATIENT SUMMARY In this study, we developed two- and three-dimensional patient-derived models from clear cell renal cell carcinoma (ccRCC) as "mini-tumors in a dish." We show that these cell models retain important features of the human ccRCCs such as the profound tumor heterogeneity, thus highlighting their importance for cancer research and precision medicine.
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Affiliation(s)
- Hella A Bolck
- Department of Pathology and Molecular Pathology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Claudia Corrò
- Department of Pathology and Molecular Pathology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Abdullah Kahraman
- Department of Pathology and Molecular Pathology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Adriana von Teichman
- Department of Pathology and Molecular Pathology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Nora C Toussaint
- NEXUS Personalized Health Technologies, ETH Zurich, Zurich, Switzerland; SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Jack Kuipers
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland; Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | | | - Viktor H Koelzer
- Department of Pathology and Molecular Pathology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Chantal Pauli
- Department of Pathology and Molecular Pathology, University Hospital and University of Zurich, Zurich, Switzerland
| | | | - Peter K Bode
- Department of Pathology and Molecular Pathology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Markus Rechsteiner
- Department of Pathology and Molecular Pathology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Niko Beerenwinkel
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland; Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Peter Schraml
- Department of Pathology and Molecular Pathology, University Hospital and University of Zurich, Zurich, Switzerland.
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University Hospital and University of Zurich, Zurich, Switzerland
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22
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Dimitrakopoulos C, Vrugt B, Flury R, Schraml P, Knippschild U, Wild P, Hoerstrup S, Henne-Bruns D, Wuerl P, Graf R, Breitenstein S, Bond G, Beerenwinkel N, Grochola LF. Identification and Validation of a Biomarker Signature in Patients With Resectable Pancreatic Cancer via Genome-Wide Screening for Functional Genetic Variants. JAMA Surg 2019; 154:e190484. [PMID: 30942874 DOI: 10.1001/jamasurg.2019.0484] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Importance Surgery currently offers the only chance for a cure in pancreatic ductal adenocarcinoma (PDAC), but it carries a significant morbidity and mortality risk and results in varying oncologic outcomes. At present, to our knowledge, there are no tests available before surgical resection to identify tumors with an aggressive biological phenotype that could guide personalized treatment strategies. Objective Identification of noninvasive genetic biomarkers that could direct therapy in patients whose cases are amenable to pancreatic cancer resection. Design, Setting, and Participants This multicenter study combined a prospective European cohort of patients with PDAC who underwent pancreatic resection (from University Hospital of Zurich, Zurich, Switzerland; Cantonal Hospital of Winterthur, Winterthur, Switzerland; and University Clinic of Ulm, Ulm, Germany) with data from the Cancer Genome Atlas database in the United States, which includes prospectively registered patients with PDAC. A genome-wide screening for functional single-nucleotide polymorphisms (SNPs) that affect PDAC survival was conducted using the European cohort for identification and the Cancer Genome Atlas cohort for validation. We used Cox proportional hazards models to screen for high-frequency polymorphic variants that are associated with allelic differences in tumor-associated survival and either result in an altered protein structure and function or reside in known regulatory noncoding genomic regions. The false-discovery rate method was applied for multiple hypothesis-testing corrections. Data analysis occurred from November 2017 to May 2018. Exposures Pancreatic resection. Main Outcomes and Measures Tumor-associated survival. Results A total of 195 patients in the European cohort were included, as well as 136 patients in the Cancer Genome Atlas cohort (overall median [range] age, 66 [19-87] years; 156 [47.1%] were women, and 175 [52.9%] were men). Two SNPs in noncoding, functional regions of genes that regulate cancer progression, invasion, and metastasis were identified (CHI3L2 SNP rs684559 and CD44 SNP rs353630). These were associated with survival after PDAC resection; patients who carry the risk alleles at 1 of both SNP loci had a 2.63-fold increased risk for tumor-associated death compared with those with protective genotypes (hazard ratio for survival, 0.38 [95% CI, 0.27-0.53]; P = 1.0 × 10-8). Conclusions and Relevance The identified polymorphisms may serve as a noninvasive biomarker signature of prospective survival after pancreatic resection that is readily available at the time of PDAC diagnosis. This signature can be used to identify a subset of high-risk patients with PDAC with very low survival probability who might be eligible for inclusion in clinical trials of new therapeutic strategies, including neoadjuvant chemotherapy protocols. In addition, the biological knowledge about these SNPs could help guide the development of individualized genomic strategies for PDAC therapies.
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Affiliation(s)
- Christos Dimitrakopoulos
- Computational Biology Group, Department of Biosystems Science and Engineering, ETH Zurich, Zurich, Switzerland.,Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Bart Vrugt
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Renata Flury
- Institute for Pathology, Cantonal Hospital of Winterthur, Winterthur, Switzerland
| | - Peter Schraml
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Uwe Knippschild
- Department of General and Visceral Surgery, Ulm University Hospital, Ulm, Germany
| | - Peter Wild
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland.,Senckenberg Institute for Pathology, Goethe University Hospital Frankfurt, Frankfurt, Germany
| | - Simon Hoerstrup
- Institute for Regenerative Medicine, University of Zurich, Zurich, Switzerland
| | - Doris Henne-Bruns
- Department of General and Visceral Surgery, Ulm University Hospital, Ulm, Germany
| | - Peter Wuerl
- Department of General, Visceral and Thoracic Surgery, Klinikum Dessau, Dessau, Germany
| | - Rolf Graf
- Department of Visceral and Transplantation Surgery, University Hospital Zurich, Zurich, Switzerland
| | - Stefan Breitenstein
- Department of Visceral and Thoracic Surgery, Cantonal Hospital of Winterthur, Winterthur, Switzerland
| | - Gareth Bond
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, United Kingdom
| | - Niko Beerenwinkel
- Computational Biology Group, Department of Biosystems Science and Engineering, ETH Zurich, Zurich, Switzerland.,Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Lukasz Filip Grochola
- Institute for Regenerative Medicine, University of Zurich, Zurich, Switzerland.,Department of Visceral and Thoracic Surgery, Cantonal Hospital of Winterthur, Winterthur, Switzerland
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23
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Ohashi R, Schraml P, Batavia A, Angori S, Simmler P, Rupp N, Ajioka Y, Oliva E, Moch H. Allele Loss and Reduced Expression of CYCLOPS Genes is a Characteristic Feature of Chromophobe Renal Cell Carcinoma. Transl Oncol 2019; 12:1131-1137. [PMID: 31200327 PMCID: PMC6563336 DOI: 10.1016/j.tranon.2019.05.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 05/08/2019] [Indexed: 12/14/2022] Open
Abstract
Copy-number alterations Yielding Cancer Liabilities Owing to Partial losS (CYCLOPS) genes have been recently identified as the most enriched class of copy-number associated gene dependencies in human cancer. These genes are cell essential and render tumor cells highly sensitive to the expression of the remaining copy. Chromophobe renal cell carcinoma (chRCC) is characterized by frequent chromosomal deletions, but the relevance of CYCLOPS genes in this tumor subtype is unclear. We found 39 (31%) of 124 recently published candidate CYCLOPS genes (B. Paolella et al., eLife 2017;6:e23268) located on 7 autosomes that are frequently lost in chRCC. GISTIC and RNA-seq data obtained from the TCGA-KICH database showed that 62% of these CYCLOPS genes had significantly lower expression levels in samples with deletion of the respective gene. As copy number (CN) loss of the CYCLOPS gene SF3B1 (Splicing factor 3B subunit 1) has been recently reported in 71% chRCC, we explored the relevance of SF3B1 CN alteration and SF3B1 expression in a set of chRCC and additional oncocytic renal neoplasms. The frequency of SF3B1 CN loss (65%) was similar to that obtained from the TCGA-KICH database and correlated significantly with both lower SF3B1 mRNA (P < .05) and protein expression (P < .001). Other tumor subtypes with oncocytic cytoplasm had normal SF3B1 CN and displayed strong SF3B1 protein expression. These results suggest that CN loss of CYCLOPS genes is a characteristic feature in chRCC. Since many CYCLOPS genes code for components of proteasomes and transcriptional regulation, their alteration could make chRCC vulnerable to targeted drugs.
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Affiliation(s)
- Riuko Ohashi
- Histopathology Core Facility, 1-757 Asahimachi-dori, Niigata University Faculty of Medicine, Chuo-ku, 951-8510 Niigata, Japan; Department of Pathology and Molecular Pathology, Schmelzbergstrasse 12, University and University Hospital Zurich, CH-8091 Zurich, Switzerland.
| | - Peter Schraml
- Department of Pathology and Molecular Pathology, Schmelzbergstrasse 12, University and University Hospital Zurich, CH-8091 Zurich, Switzerland.
| | - Aashil Batavia
- Department of Pathology and Molecular Pathology, Schmelzbergstrasse 12, University and University Hospital Zurich, CH-8091 Zurich, Switzerland.
| | - Silvia Angori
- Department of Pathology and Molecular Pathology, Schmelzbergstrasse 12, University and University Hospital Zurich, CH-8091 Zurich, Switzerland.
| | - Patrik Simmler
- Department of Biology, Institute of Molecular Health Sciences, Otto-Stern-Weg 7, ETH Zurich, CH-8093 Zurich, Switzerland.
| | - Niels Rupp
- Department of Pathology and Molecular Pathology, Schmelzbergstrasse 12, University and University Hospital Zurich, CH-8091 Zurich, Switzerland.
| | - Yoichi Ajioka
- Histopathology Core Facility, 1-757 Asahimachi-dori, Niigata University Faculty of Medicine, Chuo-ku, 951-8510 Niigata, Japan; Division of Molecular and Diagnostic Pathology, Niigata University Graduate School of Medical and Dental Sciences, 757 Ichibancho, Asahimachi-dori, Chuo Ward, 951-8510 Niigata, Japan.
| | - Esther Oliva
- Department of Pathology, Warren Building, 55 Fruit Street, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
| | - Holger Moch
- Department of Pathology and Molecular Pathology, Schmelzbergstrasse 12, University and University Hospital Zurich, CH-8091 Zurich, Switzerland.
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24
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Corrò C, Healy ME, Engler S, Bodenmiller B, Li Z, Schraml P, Weber A, Frew IJ, Rechsteiner M, Moch H. IL-8 and CXCR1 expression is associated with cancer stem cell-like properties of clear cell renal cancer. J Pathol 2019; 248:377-389. [PMID: 30883740 PMCID: PMC6618115 DOI: 10.1002/path.5267] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 02/25/2019] [Accepted: 03/13/2019] [Indexed: 12/28/2022]
Abstract
Recent studies suggest that clear cell renal cell carcinoma (ccRCC) possesses a rare population of cancer stem cells (CSCs) that might contribute to tumor heterogeneity, metastasis and therapeutic resistance. Nevertheless, their relevance for renal cancer is still unclear. In this study, we successfully isolated CSCs from established human ccRCC cell lines. CSCs displayed high expression of the chemokine IL‐8 and its receptor CXCR1. While recombinant IL‐8 significantly increased CSC number and properties in vitro, CXCR1 inhibition using an anti‐CXCR1 antibody or repertaxin significantly reduced these features. After injection into immune‐deficient mice, CSCs formed primary tumors that metastasized to the lung and liver. All xenografted tumors in mice expressed high levels of IL‐8 and CXCR1. Furthermore, IL‐8/CXCR1 expression significantly correlated with decreased overall survival in ccRCC patients. These results suggest that the IL‐8/CXCR1 phenotype is associated with CSC‐like properties in renal cancer. © 2019 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Claudia Corrò
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland.,Life Science Zurich Graduate School, ETH and University of Zurich, Zurich, Switzerland
| | - Marc E Healy
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Stefanie Engler
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Bernd Bodenmiller
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Zhe Li
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Peter Schraml
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Achim Weber
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Ian J Frew
- Clinic of Internal Medicine I, Faculty of Medicine, Medical Center - University of Freiburg, Freiburg im Breisgau, Germany
| | - Markus Rechsteiner
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
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25
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Batavia AA, Schraml P, Moch H. Clear cell renal cell carcinoma with wild-type von Hippel-Lindau gene: a non-existent or new tumour entity? Histopathology 2019; 74:60-67. [PMID: 30565303 DOI: 10.1111/his.13749] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 08/30/2018] [Indexed: 01/01/2023]
Abstract
The current World Health Organisation (WHO) classification of renal tumours is based on characteristic histological features or specific molecular alterations. von Hippel-Lindau (VHL) alteration is the hallmark of clear cell renal cell carcinoma (RCC). After identification of the MiT translocation family of tumours, clear cell papillary renal cancer and others, the group of ccRCC with wild-type VHL is small. TCEB1 mutation combined with chromosome 8q loss is an emerging tumour entity with wild-type VHL. Inactivation of TCEB1 increases HIF stabilisation via the same mechanism as VHL inactivation. Importantly, recent molecular analyses suggest the existence of another 'VHL wild-type' evolutionary subtype of clear cell RCC in addition to TCEB1 mutated RCC and clear cell papillary renal cancer. These tumours are characterised by an aggressive behaviour, high tumour cell proliferation rate, elevated chromosomal instability and frequent presence of sarcomatoid differentiation. Future clinicopathological studies will have to provide data to determine whether TCEB1 tumours and clear cell RCC with wild-type VHL are separate tumour entities or represent variants of a clear cell RCC tumour family.
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Affiliation(s)
- Aashil A Batavia
- Department of Pathology and Molecular Pathology, University and University Hospital Zurich, Zurich, Switzerland
| | - Peter Schraml
- Department of Pathology and Molecular Pathology, University and University Hospital Zurich, Zurich, Switzerland
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University and University Hospital Zurich, Zurich, Switzerland
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26
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Bihr S, Ohashi R, Moore AL, Rüschoff JH, Beisel C, Hermanns T, Mischo A, Corrò C, Beyer J, Beerenwinkel N, Moch H, Schraml P. Expression and Mutation Patterns of PBRM1, BAP1 and SETD2 Mirror Specific Evolutionary Subtypes in Clear Cell Renal Cell Carcinoma. Neoplasia 2019; 21:247-256. [PMID: 30660076 PMCID: PMC6355619 DOI: 10.1016/j.neo.2018.12.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [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: 10/31/2018] [Revised: 12/14/2018] [Accepted: 12/22/2018] [Indexed: 12/16/2022] Open
Abstract
Bi-allelic inactivation of the VHL gene on chromosome 3p is the characteristic feature in most clear cell renal cell carcinomas (ccRCC). Frequent gene alterations were also identified in SETD2, BAP1 and PBRM1, all of which are situated on chromosome 3p and encode histone/chromatin regulators. The relationship between gene mutation, loss of protein expression and the correlations with clinicopathological parameters is important for the understanding of renal cancer progression. We analyzed PBRM1 and BAP1 protein expression as well as the tri-methylation state of H3K36 as a surrogate marker for SETD2 activity in more than 700 RCC samples. In ccRCC loss of nuclear PBRM1 (68%), BAP1 (40%) and H3K36me3 (47%) expression was significantly correlated with each other, advanced tumor stage, poor tumor differentiation (P < .0001 each), and necrosis (P < .005) Targeted next generation sequencing of 83 ccRCC samples demonstrated a significant association of genetic mutations in PBRM1, BAP1, and SETD2 with absence of PBRM1, BAP1, and HEK36me3 protein expression (P < .05, each). By assigning the protein expression patterns to evolutionary subtypes, we revealed similar clinical phenotypes as suggested by TRACERx Renal. Given their important contribution to tumor suppression, we conclude that combined functional inactivation of PBRM1, BAP1, SETD2 and pVHL is critical for ccRCC progression.
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Affiliation(s)
- Svenja Bihr
- Department of Oncology, University Hospital Zurich and University Zurich, Zurich, Switzerland
| | - Riuko Ohashi
- Histopathology Core Facility, Niigata University Faculty of Medicine, Niigata, Japan
| | - Ariane L Moore
- Department of Biosystems Science and Engineering, ETH, Zurich, Basel, Switzerland
| | - Jan H Rüschoff
- Department of Pathology and Molecular Pathology, University Hospital Zurich and University Zurich, Zurich, Switzerland
| | - Christian Beisel
- Department of Biosystems Science and Engineering, ETH, Zurich, Basel, Switzerland
| | - Thomas Hermanns
- Department of Urology, University Hospital Zurich and University Zurich, Zurich, Switzerland
| | - Axel Mischo
- Department of Oncology, University Hospital Zurich and University Zurich, Zurich, Switzerland
| | - Claudia Corrò
- Department of Pathology and Molecular Pathology, University Hospital Zurich and University Zurich, Zurich, Switzerland
| | - Jörg Beyer
- Department of Oncology, University Hospital Zurich and University Zurich, Zurich, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH, Zurich, Basel, Switzerland
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University Hospital Zurich and University Zurich, Zurich, Switzerland
| | - Peter Schraml
- Department of Pathology and Molecular Pathology, University Hospital Zurich and University Zurich, Zurich, Switzerland.
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27
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Velagapudi S, Schraml P, Yalcinkaya M, Bolck HA, Rohrer L, Moch H, von Eckardstein A. Scavenger receptor BI promotes cytoplasmic accumulation of lipoproteins in clear-cell renal cell carcinoma. J Lipid Res 2018; 59:2188-2201. [PMID: 30173145 PMCID: PMC6210910 DOI: 10.1194/jlr.m083311] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 06/21/2018] [Indexed: 01/01/2023] Open
Abstract
Clear-cell renal cell carcinomas (ccRCCs) are characterized by inactivation of the von Hippel-Lindau (VHL) gene and intracellular lipid accumulation by unknown pathomechanisms. The immunochemical analysis of 356 RCCs revealed high abundance of apoA-I and apoB, as well as scavenger receptor BI (SR-BI) in the ccRCC subtype. Given the characteristic loss of VHL function in ccRCC, we used VHL-defective and VHL-proficient cells to study the potential influence of VHL on lipoprotein uptake. VHL-defective patient-derived ccRCC cells and cell lines (786O and RCC4) showed enhanced uptake as well as less resecretion and degradation of radio-iodinated HDL and LDL (125I-HDL and 125I-LDL, respectively) compared with the VHL-proficient cells. The ccRCC cells showed enhanced vascular endothelial growth factor (VEGF) and SR-BI expression compared with normal kidney epithelial cells. Uptake of 125I-HDL and 125I-LDL by patient-derived normal kidney epithelial cells as well as the VHL-reexpressing ccRCC cell lines, 786-O-VHL and RCC4-O-VHL cells, was strongly enhanced by VEGF treatment. The knockdown of the VEGF coreceptor, neuropilin-1 (NRP1), as well as blocking of SR-BI significantly reduced the uptake of lipoproteins into ccRCC cells in vitro. LDL stimulated proliferation of 786-O cells more potently than 786-O-VHL cells in a NRP1- and SR-BI-dependent manner. In conclusion, enhanced lipoprotein uptake due to increased activities of VEGF/NRP1 and SR-BI promotes lipid accumulation and proliferation of VHL-defective ccRCC cells.
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Affiliation(s)
- Srividya Velagapudi
- Institute of Clinical Chemistry University of Zurich and University Hospital of Zurich, Zurich, Switzerland
| | - Peter Schraml
- Department of Pathology and Molecular Pathology, University of Zurich and University Hospital of Zurich, Zurich, Switzerland
| | - Mustafa Yalcinkaya
- Institute of Clinical Chemistry University of Zurich and University Hospital of Zurich, Zurich, Switzerland
| | - Hella A Bolck
- Department of Pathology and Molecular Pathology, University of Zurich and University Hospital of Zurich, Zurich, Switzerland
| | - Lucia Rohrer
- Institute of Clinical Chemistry University of Zurich and University Hospital of Zurich, Zurich, Switzerland
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University of Zurich and University Hospital of Zurich, Zurich, Switzerland
| | - Arnold von Eckardstein
- Institute of Clinical Chemistry University of Zurich and University Hospital of Zurich, Zurich, Switzerland
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28
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Razafinjatovo CF, Stiehl D, Deininger E, Rechsteiner M, Moch H, Schraml P. VHL missense mutations in the p53 binding domain show different effects on p53 signaling and HIFα degradation in clear cell renal cell carcinoma. Oncotarget 2018; 8:10199-10212. [PMID: 28052007 PMCID: PMC5354652 DOI: 10.18632/oncotarget.14372] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 12/15/2016] [Indexed: 11/25/2022] Open
Abstract
Clear cell Renal Cell Carcinoma (ccRCC) formation is connected to functional loss of the von Hippel-Lindau (VHL) gene. Recent data identified its gene product, pVHL, as a multifunctional adaptor protein which interacts with HIFα subunits but also with the tumor suppressor p53. p53 is hardly expressed and rarely mutated in most ccRCC. We showed that low and absent p53 expression correlated with the severity of VHL mutations in 262 analyzed ccRCC tissues. In contrast to nonsense and frameshift mutations which abrogate virtually all pVHL functions, missense mutations may rather influence one or few functions. Therefore, we focused on four VHL missense mutations, which affect the overlapping pVHL binding sites of p53 and Elongin C, by investigating their impact on HIFα degradation, p53 expression and signaling, as well as on cellular behavior using ccRCC cell lines and tissues. TP53 mRNA and its effector targets p21, Bax and Noxa, were altered both in engineered cell lines and in tumor tissues which carried the same missense mutations. Two of these mutations were not able to degrade HIFα whereas the remaining two mutations led to HIFα downregulation, suggesting the latter are p53 binding site-specific. The selected VHL missense mutations further enhanced tumor cell survival, but had no effects on cell proliferation. Whereas Sunitinib was able to efficiently reduce cell proliferation, Camptothecin was additionally able to increase apoptotic activity of the tumor cells. It is concluded that systematic characterization of the VHL mutation status may help optimizing targeted therapy for patients with metastatic ccRCC.
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Affiliation(s)
| | - Daniel Stiehl
- Institute of Physiology and Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, Zurich, Switzerland
| | - Eva Deininger
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Markus Rechsteiner
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Peter Schraml
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
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29
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Lukamowicz-Rajska M, Mittmann C, Prummer M, Zhong Q, Bedke J, Hennenlotter J, Stenzl A, Mischo A, Bihr S, Schmidinger M, Vogl U, Blume I, Karlo C, Schraml P, Moch H. MiR-99b-5p expression and response to tyrosine kinase inhibitor treatment in clear cell renal cell carcinoma patients. Oncotarget 2018; 7:78433-78447. [PMID: 27738339 PMCID: PMC5346651 DOI: 10.18632/oncotarget.12618] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 09/18/2016] [Indexed: 11/25/2022] Open
Abstract
A number of treatments targeting VEGF or mTOR pathways have been approved for metastatic clear cell Renal Cell Carcinoma (ccRCC), but the majority of patients show disease progression after first line therapy with a very low rate of complete or long-term responders. It has been shown that miRs may play a role in prediction of treatment response in various cancer types. The aim of our study was to identify a miR signature predictive for RCC patients' response to antiangiogenic tyrosine kinase inhibitor (TKI) treatment in the first line therapy. Sequencing of 40 paired normal/tumor formalin fixed and paraffin embedded ccRCC tissues revealed separate clustering via unsupervised dendrograms. With supervised analysis, the strongest differential expression was obtained with miR-99b-5p, which was significantly lower in patients with short progression free survival (<8 months) and TKI non-responders (progressive disease patients according to RECIST) (p<0.0001, each). Validation using RTqPCR and a second patient cohort compiled from three different hospitals (n=65) showed higher expression of miR-99b-5p in complete responders, but this trend did not reach statistical significance. It is concluded that low miR-99b-5p expression analyzed with sequencing methodology may correlate with tumor progression in TKI-treated ccRCC patients.
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Affiliation(s)
| | - Christiane Mittmann
- Institute of Surgical Pathology, University Hospital Zürich, Zurich, Switzerland
| | - Michael Prummer
- NEXUS Personalized Health Technologies, ETH Zürich, Zürich, Switzerland
| | - Qing Zhong
- Institute of Surgical Pathology, University Hospital Zürich, Zurich, Switzerland
| | - Jens Bedke
- Department of Urology, University Tübingen, Tübingen, Germany
| | | | - Arnulf Stenzl
- Department of Urology, University Tübingen, Tübingen, Germany
| | - Axel Mischo
- Oncology Department, University Hospital Zürich, Zürich, Switzerland
| | - Svenja Bihr
- Oncology Department, University Hospital Zürich, Zürich, Switzerland
| | - Manuela Schmidinger
- Department of Internal Medicine I, Division of Oncology & Comprehensive Cancer Center Vienna, Medical University of Vienna, Vienna, Austria
| | - Ursula Vogl
- Department of Internal Medicine I, Division of Oncology & Comprehensive Cancer Center Vienna, Medical University of Vienna, Vienna, Austria
| | - Iris Blume
- Institute for diagnostic and interventional Radiology, University Hospital Zurich, Zürich, Switzerland
| | - Christoph Karlo
- Institute for diagnostic and interventional Radiology, University Hospital Zurich, Zürich, Switzerland
| | - Peter Schraml
- Institute of Surgical Pathology, University Hospital Zürich, Zurich, Switzerland
| | - Holger Moch
- Institute of Surgical Pathology, University Hospital Zürich, Zurich, Switzerland
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30
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Posch F, Silina K, Leibl S, Mündlein A, Moch H, Siebenhüner A, Samaras P, Riedl J, Stotz M, Szkandera J, Stöger H, Pichler M, Stupp R, van den Broek M, Schraml P, Gerger A, Petrausch U, Winder T. Maturation of tertiary lymphoid structures and recurrence of stage II and III colorectal cancer. Oncoimmunology 2017; 7:e1378844. [PMID: 29416939 PMCID: PMC5798199 DOI: 10.1080/2162402x.2017.1378844] [Citation(s) in RCA: 165] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 09/07/2017] [Accepted: 09/08/2017] [Indexed: 12/18/2022] Open
Abstract
Tertiary lymphoid structures (TLS) are associated with favorable outcome in non-metastatic colorectal carcinoma (nmCRC), but the dynamics of TLS maturation and its association with effective anti-tumor immune surveillance in nmCRC are unclear. Here, we hypothesized that not only the number of TLS but also their composition harbors information on recurrence risk in nmCRC. In a comprehensive molecular, tissue, laboratory, and clinical analysis of 109 patients with stage II/III nmCRC, we assessed TLS numbers and degree of maturation in surgical specimens by multi-parameter immunofluorescence of follicular dendritic cell (FDC) and germinal center (GC) markers. TLS formed in most tumors and were significantly more prevalent in highly-microsatellite-instable (MSI-H) and/or BRAF-mutant nmCRC. We could distinguish three sequential TLS maturation stages which were characterized by increasing prevalence of FDCs and mature B-cells: [1] Early TLS, composed of dense lymphocytic aggregates without FDCs, [2] Primary follicle-like TLS, having FDCs but no GC reaction, and [3] Secondary follicle-like TLS, having an active GC reaction. A simple integrated TLS immunoscore reflecting these parameters identified a large subgroup of nmCRC patients with a very low risk of recurrence independently of clinical co-variables such as ECOG performance status, age, stage, and adjuvant chemotherapy. We conclude that (1) mismatch repair and BRAF mutation status are associated with the formation of TLS in nmCRC, (2) TLS formation in nmCRC follows sequential maturation steps, culminating in germinal center formation, and (3) this maturation process harbors important prognostic information on the risk of disease recurrence.
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Affiliation(s)
- Florian Posch
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Auenbruggerplatz 15, Graz, Austria
| | - Karina Silina
- Tumor Immunology Research Unit, Institute of Experimental Immunology, University of Zurich, Winterthurerstrasse 190, Zurich, Switzerland
| | - Sebastian Leibl
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Schmelzbergstrasse 12, Zürich, Switzerland
| | - Axel Mündlein
- Vorarlberg Institute for Vascular Investigation and Treatment (VIVIT), Carinagasse 47, Feldkirch, Austria
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Schmelzbergstrasse 12, Zürich, Switzerland
| | - Alexander Siebenhüner
- Department of Oncology, University Hospital Zurich, Rämistrasse 100, Zürich, Switzerland
| | - Panagiotis Samaras
- Department of Oncology, University Hospital Zurich, Rämistrasse 100, Zürich, Switzerland
| | - Jakob Riedl
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Auenbruggerplatz 15, Graz, Austria
| | - Michael Stotz
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Auenbruggerplatz 15, Graz, Austria
| | - Joanna Szkandera
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Auenbruggerplatz 15, Graz, Austria
| | - Herbert Stöger
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Auenbruggerplatz 15, Graz, Austria
| | - Martin Pichler
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Auenbruggerplatz 15, Graz, Austria.,Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Roger Stupp
- Department of Oncology, University Hospital Zurich, Rämistrasse 100, Zürich, Switzerland
| | - Maries van den Broek
- Tumor Immunology Research Unit, Institute of Experimental Immunology, University of Zurich, Winterthurerstrasse 190, Zurich, Switzerland
| | - Peter Schraml
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Schmelzbergstrasse 12, Zürich, Switzerland
| | - Armin Gerger
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Auenbruggerplatz 15, Graz, Austria
| | - Ulf Petrausch
- Department of Oncology, University Hospital Zurich, Rämistrasse 100, Zürich, Switzerland.,Swiss Tumor Immunology Institute, OnkoZentrum Zürich, Seestrasse 259, Zürich, Switzerland
| | - Thomas Winder
- Vorarlberg Institute for Vascular Investigation and Treatment (VIVIT), Carinagasse 47, Feldkirch, Austria.,Department of Oncology, University Hospital Zurich, Rämistrasse 100, Zürich, Switzerland
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31
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Janouskova H, El Tekle G, Bellini E, Udeshi ND, Rinaldi A, Ulbricht A, Bernasocchi T, Civenni G, Losa M, Svinkina T, Bielski CM, Kryukov GV, Cascione L, Napoli S, Enchev RI, Mutch DG, Carney ME, Berchuck A, Winterhoff BJN, Broaddus RR, Schraml P, Moch H, Bertoni F, Catapano CV, Peter M, Carr SA, Garraway LA, Wild PJ, Theurillat JPP. Opposing effects of cancer-type-specific SPOP mutants on BET protein degradation and sensitivity to BET inhibitors. Nat Med 2017; 23:1046-1054. [PMID: 28805821 PMCID: PMC5592092 DOI: 10.1038/nm.4372] [Citation(s) in RCA: 130] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 06/16/2017] [Indexed: 12/12/2022]
Abstract
It is generally assumed that recurrent mutations within a given cancer driver gene elicit similar drug responses. Cancer genome studies have identified recurrent but divergent missense mutations in the substrate recognition domain of the ubiquitin ligase adaptor SPOP in endometrial and prostate cancer. Their therapeutic implications remain incompletely understood. Here, we analyzed changes in the ubiquitin landscape induced by endometrial cancer-associated SPOP mutations and identified BRD2, BRD3 and BRD4 proteins (BETs) as SPOP-CUL3 substrates that are preferentially degraded by endometrial SPOP mutants. The resulting reduction of BET protein levels sensitized cancer cells to BET inhibitors. Conversely, prostate cancer-specific SPOP mutants impaired degradation of BETs, promoting resistance against their pharmacologic inhibition. These results uncover an oncogenomics paradox, whereby mutations within the same domain evoke opposing drug susceptibilities. Specifically, we provide a molecular rationale for the use of BET inhibitors to treat endometrial but not prostate cancer patients with SPOP mutations.
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Affiliation(s)
- Hana Janouskova
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland.,Faculty of Biomedical Science, Università della Svizzera Italiana, Lugano, Switzerland
| | - Geniver El Tekle
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland.,Faculty of Biomedical Science, Università della Svizzera Italiana, Lugano, Switzerland.,Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
| | - Elisa Bellini
- Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Namrata D Udeshi
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Anna Rinaldi
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland.,Faculty of Biomedical Science, Università della Svizzera Italiana, Lugano, Switzerland
| | - Anna Ulbricht
- Department of Biochemistry, Eidgenössische Technische Hochschule, Zurich, Switzerland
| | - Tiziano Bernasocchi
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland.,Faculty of Biomedical Science, Università della Svizzera Italiana, Lugano, Switzerland.,Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
| | - Gianluca Civenni
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland.,Faculty of Biomedical Science, Università della Svizzera Italiana, Lugano, Switzerland
| | - Marco Losa
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland.,Faculty of Biomedical Science, Università della Svizzera Italiana, Lugano, Switzerland
| | - Tanya Svinkina
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Craig M Bielski
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.,Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | | | - Luciano Cascione
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland.,Faculty of Biomedical Science, Università della Svizzera Italiana, Lugano, Switzerland
| | - Sara Napoli
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland.,Faculty of Biomedical Science, Università della Svizzera Italiana, Lugano, Switzerland
| | - Radoslav I Enchev
- Department of Biochemistry, Eidgenössische Technische Hochschule, Zurich, Switzerland
| | - David G Mutch
- Division of Gynecologic Oncology, Washington University, St. Louis, Missouri, USA
| | - Michael E Carney
- Department of Obstetrics, Gynecology and Women’s Health, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, USA
| | - Andrew Berchuck
- Division of Gynecologic Oncology, Duke Cancer Center, Durham, North Carolina, USA
| | - Boris J N Winterhoff
- Division of Gynecologic Oncology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Russell R Broaddus
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Peter Schraml
- Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Holger Moch
- Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Francesco Bertoni
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland.,Faculty of Biomedical Science, Università della Svizzera Italiana, Lugano, Switzerland
| | - Carlo V Catapano
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland.,Faculty of Biomedical Science, Università della Svizzera Italiana, Lugano, Switzerland.,Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
| | - Matthias Peter
- Department of Biochemistry, Eidgenössische Technische Hochschule, Zurich, Switzerland
| | - Steven A Carr
- Department of Biochemistry, Eidgenössische Technische Hochschule, Zurich, Switzerland
| | - Levi A Garraway
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.,Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA.,Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Peter J Wild
- Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Jean-Philippe P Theurillat
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland.,Faculty of Biomedical Science, Università della Svizzera Italiana, Lugano, Switzerland.,Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
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32
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Posch F, Silina K, Petrausch U, Leibl S, Muendlein A, Moch H, Siebenhuener AR, Pestalozzi BC, Riedl JM, Stotz M, Szkandera J, Stoger H, Pichler M, Stupp R, Schraml P, Gerger A, Winder T. The maturation stage of tumoral tertiary lymphoid structures to predict recurrence risk in localized colorectal cancer. J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.15_suppl.e15083] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
e15083 Background: The tumor immune infiltrate and organized lymphocytic aggregates within the tumor microenvironment, known as tertiary lymphoid structures (TLS), play a critical role in cancer. We hypothesize that the maturation stage of TLS harbors prognostic information on recurrence risk in patients (pts) with non-metastatic colorectal cancer (nmCRC). Methods: In a comprehensive immunofluorescence and clinical analysis of 111 pts with UICC stage II & III nmCRC (median age: 65 yrs; female: n = 53 (48%); stage III: n = 69 (62%)), we quantified the number and maturation status of tumor-associated TLS in baseline surgical specimens:[1] Early TLS (E-TLS, composed of dense lymphocytic aggregates without follicular dendritic cells (FDCs), [2] Primary follicle-like TLS (PFL-TLS, having FDCs but no germinal center (GC) reaction), and [3] Secondary follicle-like TLS (SFL-TLS, having an active GC reaction). The 3-year incidence of recurrence was the primary endpoint of this study, which occurred in 19 pts (3-year recurrence risk = 18.3%). Results: Most TLS formed in tissue adjacent to the tumor. The median number of TLS/mm of tumor perimeter was 1.0 [25th-75th percentile: 0.5-1.7]. The average proportions of different TLS maturation stages were 56% of E-TLS [40-78], 20% of PFL-TLS [6-37], and 16% of SFL-TLS [0-32]. A structural equation model was fitted to summarize the TLS counts and maturation stages into a TLS maturation immunoscore for predicting recurrence. 3-year recurrence risks were 31.7% (95%CI: 17.2-47.3), 15.9% (5.7-30.5), and 9.4% (2.4-22.4) in pts in the 1st, 2nd, and 3rd tertile of the score (Gray’s test p = 0.05). A higher score was significantly associated with a lower recurrence risk (Hazard ratio (HR) for 10 units increase = 0.76, 95%CI: 0.59-0.97, p = 0.03), and this association prevailed in multivariable analysis adjusting for age, ECOG performance status, stage, and adjuvant chemotherapy (Adjusted HR = 0.73, 0.54-0.99, p = 0.05). Conclusions: Tumors of nmCRC pts with a very low risk of recurrence are characterized by an increased fraction of mature TLS comprising FDCs and GCs. If confirmed prospectively, adjuvant chemotherapy may be avoided in nmCRC pts with a high TLS maturation score.
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Affiliation(s)
- Florian Posch
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Karina Silina
- Institute of Experimental Immunology, University Hospital Zurich, Zurich, Switzerland
| | | | - Sebastian Leibl
- Department of Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Axel Muendlein
- Vorarlberg Institute for Vascular Investigation and Treatment, Feldkirch, Austria
| | - Holger Moch
- Department of Pathology, University Hospital Zurich, Zurich, Switzerland
| | | | | | - Jakob M. Riedl
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Michael Stotz
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Joanna Szkandera
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Herbert Stoger
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Martin Pichler
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Roger Stupp
- Department of Oncology, University Hospital Zurich, Zurich, Switzerland
| | - Peter Schraml
- Department of Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Armin Gerger
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
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Varga Z, Lebeau A, Bu H, Hartmann A, Penault-Llorca F, Guerini-Rocco E, Schraml P, Symmans F, Stoehr R, Teng X, Turzynski A, von Wasielewski R, Gürtler C, Laible M, Schlombs K, Joensuu H, Keller T, Sinn P, Sahin U, Bartlett J, Viale G. An international reproducibility study validating quantitative determination of ERBB2, ESR1, PGR, and MKI67 mRNA in breast cancer using MammaTyper®. Breast Cancer Res 2017; 19:55. [PMID: 28490348 PMCID: PMC5426065 DOI: 10.1186/s13058-017-0848-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 04/27/2017] [Indexed: 02/05/2023] Open
Abstract
Background Accurate determination of the predictive markers human epidermal growth factor receptor 2 (HER2/ERBB2), estrogen receptor (ER/ESR1), progesterone receptor (PgR/PGR), and marker of proliferation Ki67 (MKI67) is indispensable for therapeutic decision making in early breast cancer. In this multicenter prospective study, we addressed the issue of inter- and intrasite reproducibility using the recently developed reverse transcription-quantitative real-time polymerase chain reaction-based MammaTyper® test. Methods Ten international pathology institutions participated in this study and determined messenger RNA expression levels of ERBB2, ESR1, PGR, and MKI67 in both centrally and locally extracted RNA from formalin-fixed, paraffin-embedded breast cancer specimens with the MammaTyper® test. Samples were measured repeatedly on different days within the local laboratories, and reproducibility was assessed by means of variance component analysis, Fleiss’ kappa statistics, and interclass correlation coefficients (ICCs). Results Total variations in measurements of centrally and locally prepared RNA extracts were comparable; therefore, statistical analyses were performed on the complete dataset. Intersite reproducibility showed total SDs between 0.21 and 0.44 for the quantitative single-marker assessments, resulting in ICC values of 0.980–0.998, demonstrating excellent agreement of quantitative measurements. Also, the reproducibility of binary single-marker results (positive/negative), as well as the molecular subtype agreement, was almost perfect with kappa values ranging from 0.90 to 1.00. Conclusions On the basis of these data, the MammaTyper® has the potential to substantially improve the current standards of breast cancer diagnostics by providing a highly precise and reproducible quantitative assessment of the established breast cancer biomarkers and molecular subtypes in a decentralized workup. Electronic supplementary material The online version of this article (doi:10.1186/s13058-017-0848-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zsuzsanna Varga
- Institute of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland.
| | - Annette Lebeau
- Private Group Practice for Pathology and PathoPlan GbR, Lübeck, Germany
| | - Hong Bu
- Department of Pathology and Laboratory of Pathology, West China Hospital, Sichuan University, Chengdu, China
| | - Arndt Hartmann
- Institute of Pathology, University Erlangen-Nürnberg, Erlangen, Germany
| | | | | | - Peter Schraml
- Institute of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Fraser Symmans
- University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Robert Stoehr
- Institute of Pathology, University Erlangen-Nürnberg, Erlangen, Germany
| | - Xiaodong Teng
- Department of Pathology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Andreas Turzynski
- Private Group Practice for Pathology and PathoPlan GbR, Lübeck, Germany
| | | | | | | | | | - Heikki Joensuu
- Department of Oncology, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | | | - Peter Sinn
- Department of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Ugur Sahin
- BioNTech Diagnostics GmbH, Mainz, Germany
| | - John Bartlett
- Transformative Pathology, Ontario Institute for Cancer Research (OICR), Toronto, ON, Canada
| | - Giuseppe Viale
- European Institute of Oncology, University of Milan, Milan, Italy
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34
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Murakami A, Wang L, Kalhorn S, Schraml P, Rathmell WK, Tan AC, Nemenoff R, Stenmark K, Jiang BH, Reyland ME, Heasley L, Hu CJ. Context-dependent role for chromatin remodeling component PBRM1/BAF180 in clear cell renal cell carcinoma. Oncogenesis 2017; 6:e287. [PMID: 28092369 PMCID: PMC5294252 DOI: 10.1038/oncsis.2016.89] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [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: 08/16/2016] [Revised: 11/16/2016] [Accepted: 11/30/2016] [Indexed: 12/11/2022] Open
Abstract
A subset of clear cell renal cell carcinoma (ccRCC) tumors exhibit a HIF1A gene mutation, yielding two ccRCC tumor types, H1H2 type expressing both HIF1α and HIF2α, and H2 type expressing HIF2α, but not functional HIF1α protein. However, it is unclear how the H1H2 type ccRCC tumors escape HIF1's tumor-suppressive activity. The polybromo-1 (PBRM1) gene coding for the BAF180 protein, a component of the SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodeling complex, is inactivated in 40% ccRCCs, the function and mechanism of BAF180 mutation is unknown. Our previous study indicates that BAF180-containing SWI/SNF chromatin remodeling complex is a co-activator for transcription factor HIF to induce HIF target genes. Thus, our questions are if BAF180 is involved in HIF-mediated hypoxia response and if PBRM1/BAF180 mutation has any association with the HIF1A retention in H1H2 type ccRCC. We report here that BAF180 is mutated in H1H2 ccRCC cell lines and tumors, and BAF180 re-expression in H1H2 ccRCC cell lines reduced cell proliferation/survival, indicating that BAF180 has tumor-suppressive role in these cells. However, BAF180 is expressed in HIF1-deficient H2 ccRCC cell lines and tumors, and BAF180 knockdown in H2 type ccRCC cell lines reduced cell proliferation/survival, indicating that BAF180 has tumor-promoting activity in these cells. In addition, our data show that BAF180 functions as co-activator for HIF1- and HIF2-mediated transcriptional response, and BAF180's tumor-suppressive and -promoting activity in ccRCC cell lines depends on co-expression of HIF1 and HIF2, respectively. Thus, our studies reveal that BAF180 function in ccRCC is context dependent, and that mutation of PBRM1/BAF180 serves as an alternative strategy for ccRCC tumors to reduce HIF1 tumor-suppressive activity in H1H2 ccRCC tumors. Our studies define distinct functional subgroups of ccRCCs based on expression of BAF180, and suggest that BAF180 inhibition may be a novel therapeutic target for patients with H2, but not H1H2, ccRCC tumors.
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Affiliation(s)
- A Murakami
- Molecular Biology Graduate Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - L Wang
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - S Kalhorn
- Doctor of Dental Surgery Program, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - P Schraml
- Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland
| | - W K Rathmell
- Division of Hematology/Oncology, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - A C Tan
- Division of Medical Oncology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - R Nemenoff
- Division of Renal and Hypertension, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - K Stenmark
- Departments of Pediatrics, Medicine, and Anesthesiology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - B-H Jiang
- Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - M E Reyland
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - L Heasley
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - C-J Hu
- Molecular Biology Graduate Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.,Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
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Hofmann AL, Behr J, Singer J, Kuipers J, Beisel C, Schraml P, Moch H, Beerenwinkel N. Detailed simulation of cancer exome sequencing data reveals differences and common limitations of variant callers. BMC Bioinformatics 2017; 18:8. [PMID: 28049408 PMCID: PMC5209852 DOI: 10.1186/s12859-016-1417-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 12/10/2016] [Indexed: 12/30/2022] Open
Abstract
Background Next-generation sequencing of matched tumor and normal biopsy pairs has become a technology of paramount importance for precision cancer treatment. Sequencing costs have dropped tremendously, allowing the sequencing of the whole exome of tumors for just a fraction of the total treatment costs. However, clinicians and scientists cannot take full advantage of the generated data because the accuracy of analysis pipelines is limited. This particularly concerns the reliable identification of subclonal mutations in a cancer tissue sample with very low frequencies, which may be clinically relevant. Results Using simulations based on kidney tumor data, we compared the performance of nine state-of-the-art variant callers, namely deepSNV, GATK HaplotypeCaller, GATK UnifiedGenotyper, JointSNVMix2, MuTect, SAMtools, SiNVICT, SomaticSniper, and VarScan2. The comparison was done as a function of variant allele frequencies and coverage. Our analysis revealed that deepSNV and JointSNVMix2 perform very well, especially in the low-frequency range. We attributed false positive and false negative calls of the nine tools to specific error sources and assigned them to processing steps of the pipeline. All of these errors can be expected to occur in real data sets. We found that modifying certain steps of the pipeline or parameters of the tools can lead to substantial improvements in performance. Furthermore, a novel integration strategy that combines the ranks of the variants yielded the best performance. More precisely, the rank-combination of deepSNV, JointSNVMix2, MuTect, SiNVICT and VarScan2 reached a sensitivity of 78% when fixing the precision at 90%, and outperformed all individual tools, where the maximum sensitivity was 71% with the same precision. Conclusions The choice of well-performing tools for alignment and variant calling is crucial for the correct interpretation of exome sequencing data obtained from mixed samples, and common pipelines are suboptimal. We were able to relate observed substantial differences in performance to the underlying statistical models of the tools, and to pinpoint the error sources of false positive and false negative calls. These findings might inspire new software developments that improve exome sequencing pipelines and further the field of precision cancer treatment. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1417-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ariane L Hofmann
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstr, Basel, 26, 4058, Switzerland.,Swiss Institute of Bioinformatics, Mattenstr, Basel, 26, 4058, Switzerland
| | - Jonas Behr
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstr, Basel, 26, 4058, Switzerland.,Swiss Institute of Bioinformatics, Mattenstr, Basel, 26, 4058, Switzerland
| | - Jochen Singer
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstr, Basel, 26, 4058, Switzerland.,Swiss Institute of Bioinformatics, Mattenstr, Basel, 26, 4058, Switzerland
| | - Jack Kuipers
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstr, Basel, 26, 4058, Switzerland.,Swiss Institute of Bioinformatics, Mattenstr, Basel, 26, 4058, Switzerland
| | - Christian Beisel
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstr, Basel, 26, 4058, Switzerland
| | - Peter Schraml
- Institute for Surgical Pathology, University Hospital Zurich, Schmelzbergstrasse 12, Zurich, 8091, Switzerland
| | - Holger Moch
- Institute for Surgical Pathology, University Hospital Zurich, Schmelzbergstrasse 12, Zurich, 8091, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstr, Basel, 26, 4058, Switzerland. .,Swiss Institute of Bioinformatics, Mattenstr, Basel, 26, 4058, Switzerland.
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Stracquadanio G, Vrugt B, Flury R, Schraml P, Würl P, Müller TH, Knippschild U, Henne-Bruns D, Breitenstein S, Clavien PA, Graf R, Bond GL, Grochola LF. CD44 SNPrs187115: A Novel Biomarker Signature that Predicts Survival in Resectable Pancreatic Ductal Adenocarcinoma. Clin Cancer Res 2016; 22:6069-6077. [PMID: 27283965 DOI: 10.1158/1078-0432.ccr-16-0058] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [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: 01/11/2016] [Revised: 05/19/2016] [Accepted: 05/19/2016] [Indexed: 11/16/2022]
Abstract
PURPOSE Although pancreatic ductal adenocarcinoma (PDAC) is an aggressive tumor, like other common cancers, it displays a wide range of biology. However, at present, there are no reliable tests to predict patients' cancer-specific outcomes and guide personalized treatment decisions. In this study, we aim to identify such biomarkers in resectable PDAC by studying SNPs in the CD44 gene, which drives the progression of pancreatic cancer. EXPERIMENTAL DESIGN A total of 348 PDAC patients from three independent cohorts [Switzerland, Germany, The Cancer Genome Atlas (TCGA)] who underwent pancreatic resection are included in the study. Information on the haplotype structure of the CD44 gene is obtained using 1000 Genomes Project data, and the genotypes of the respective tagging SNPs are determined. Cox proportional hazards models are utilized to analyze the impact of SNP genotype on patients' survival. RESULTS We identify an SNP in the CD44 gene (SNPrs187115) that independently associates with allelic differences in prognosis in all study cohorts. Specifically, in 121 Swiss patients, we observe an up to 2.38-fold (P = 0.020) difference in tumor-related death between the genotypes of SNPrs187115 We validate those results in both the German (HR = 2.32, P = 0.044, 101 patients) and the TCGA cohort (HR = 2.36, P = 0.044, 126 patients). CONCLUSIONS CD44 SNPrs187115 can serve as a novel biomarker readily available at the time of PDAC diagnosis that identifies patients at risk for faster tumor progression and guide personalized treatment decisions. It has the potential to significantly expand the pool of patients that would benefit from tumor resection. Clin Cancer Res; 22(24); 6069-77. ©2016 AACR.
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Affiliation(s)
| | - Bart Vrugt
- Institute for Surgical Pathology, University Hospital of Zurich, Zurich, Switzerland
| | - Renata Flury
- Institute for Pathology, Cantonal Hospital of Winterthur, Winterthur, Switzerland
| | - Peter Schraml
- Institute for Surgical Pathology, University Hospital of Zurich, Zurich, Switzerland
| | - Peter Würl
- Department of General and Visceral Surgery, Diakoniekrankenhaus Halle, Halle, Germany
| | - Thomas H Müller
- German Red Cross Blood Transfusion Service NSTOB, Springe, Germany
| | - Uwe Knippschild
- Department of General and Visceral Surgery, Ulm University Hospital, Ulm, Germany
| | - Doris Henne-Bruns
- Department of General and Visceral Surgery, Ulm University Hospital, Ulm, Germany
| | - Stefan Breitenstein
- Department of Visceral- and Thoracic Surgery, Cantonal Hospital of Winterthur, Winterthur, Switzerland
| | - Pierre-Alain Clavien
- Department of Visceral and Transplantation Surgery, University Hospital of Zurich, Zurich, Switzerland
| | - Rolf Graf
- Department of Visceral and Transplantation Surgery, University Hospital of Zurich, Zurich, Switzerland
| | - Gareth L Bond
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, United Kingdom
| | - Lukasz F Grochola
- Department of Visceral and Transplantation Surgery, University Hospital of Zurich, Zurich, Switzerland.
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Beleut M, Soeldner R, Egorov M, Guenther R, Dehler S, Morys-Wortmann C, Moch H, Henco K, Schraml P. Discretization of Gene Expression Data Unmasks Molecular Subgroups Recurring in Different Human Cancer Types. PLoS One 2016; 11:e0161514. [PMID: 27537329 PMCID: PMC4990327 DOI: 10.1371/journal.pone.0161514] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [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: 01/18/2016] [Accepted: 08/05/2016] [Indexed: 12/21/2022] Open
Abstract
Despite the individually different molecular alterations in tumors, the malignancy associated biological traits are strikingly similar. Results of a previous study using renal cell carcinoma (RCC) as a model pointed towards cancer-related features, which could be visualized as three groups by microarray based gene expression analysis. In this study, we used a mathematic model to verify the presence of these groups in RCC as well as in other cancer types. We developed an algorithm for gene-expression deviation profiling for analyzing gene expression data of a total of 8397 patients with 13 different cancer types and normal tissues. We revealed three common Cancer Transcriptomic Profiles (CTPs) which recurred in all investigated tumors. Additionally, CTPs remained robust regardless of the functions or numbers of genes analyzed. CTPs may represent common genetic fingerprints, which potentially reflect the closely related biological traits of human cancers.
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Affiliation(s)
- Manfred Beleut
- Qlaym Healthcare AG, Hans-Adolf-Krebs Weg 1, 37077 Goettingen, Germany
- * E-mail: (MB); (PS)
| | - Robert Soeldner
- Qlaym Healthcare AG, Hans-Adolf-Krebs Weg 1, 37077 Goettingen, Germany
| | - Mark Egorov
- Qlaym Healthcare AG, Hans-Adolf-Krebs Weg 1, 37077 Goettingen, Germany
| | - Rolf Guenther
- Qlaym Healthcare AG, Hans-Adolf-Krebs Weg 1, 37077 Goettingen, Germany
| | - Silvia Dehler
- Cancer Registry Zurich and Zug, University Hospital Zurich, Zurich, Switzerland
| | | | - Holger Moch
- Institute of Surgical Pathology, University Hospital Zurich, Schmelzbergstrasse 12, 8091 Zurich, Switzerland
| | - Karsten Henco
- Qlaym Healthcare AG, Hans-Adolf-Krebs Weg 1, 37077 Goettingen, Germany
| | - Peter Schraml
- Institute of Surgical Pathology, University Hospital Zurich, Schmelzbergstrasse 12, 8091 Zurich, Switzerland
- * E-mail: (MB); (PS)
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38
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Razafinjatovo C, Bihr S, Mischo A, Vogl U, Schmidinger M, Moch H, Schraml P. Characterization of VHL missense mutations in sporadic clear cell renal cell carcinoma: hotspots, affected binding domains, functional impact on pVHL and therapeutic relevance. BMC Cancer 2016; 16:638. [PMID: 27530247 PMCID: PMC4987997 DOI: 10.1186/s12885-016-2688-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 08/08/2016] [Indexed: 12/18/2022] Open
Abstract
Background The VHL protein (pVHL) is a multiadaptor protein that interacts with more than 30 different binding partners involved in many oncogenic processes. About 70 % of clear cell renal cell carcinoma (ccRCC) have VHL mutations with varying impact on pVHL function. Loss of pVHL function leads to the accumulation of Hypoxia Inducible Factor (HIF), which is targeted by current targeted treatments. In contrast to nonsense and frameshift mutations that highly likely nullify pVHL multipurpose functions, missense mutations may rather specifically influence the binding capability of pVHL to its partners. The affected pathways may offer predictive clues to therapy and response to treatment. In this study we focused on the VHL missense mutation pattern in ccRCC, and studied their potential effects on pVHL protein stability and binding partners and discussed treatment options. Methods We sequenced VHL in 360 sporadic ccRCC FFPE samples and compared observed and expected frequency of missense mutations in 32 different binding domains. The prediction of the impact of those mutations on protein stability and function was assessed in silico. The response to HIF-related, anti-angiogenic treatment of 30 patients with known VHL mutation status was also investigated. Results We identified 254 VHL mutations (68.3 % of the cases) including 89 missense mutations (35 %). Codons Ser65, Asn78, Ser80, Trp117 and Leu184 represented hotspots and missense mutations in Trp117 and Leu 184 were predicted to highly destabilize pVHL. About 40 % of VHL missense mutations were predicted to cause severe protein malfunction. The pVHL binding domains for HIF1AN, BCL2L11, HIF1/2α, RPB1, PRKCZ, aPKC-λ/ι, EEF1A1, CCT-ζ-2, and Cullin2 were preferentially affected. These binding partners are mainly acting in transcriptional regulation, apoptosis and ubiquitin ligation. There was no correlation between VHL mutation status and response to treatment. Conclusions VHL missense mutations may exert mild, moderate or strong impact on pVHL stability. Besides the HIF binding domain, other pVHL binding sites seem to be non-randomly altered by missense mutations. In contrast to LOF mutations that affect all the different pathways normally controlled by pVHL, missense mutations may be rather appropriate for designing tailor-made treatment strategies for ccRCC. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2688-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Svenja Bihr
- Oncology Clinic, University Hospital Zurich, Zurich, Switzerland
| | - Axel Mischo
- Oncology Clinic, University Hospital Zurich, Zurich, Switzerland
| | - Ursula Vogl
- Department of Medicine, St. Joseph Hospital Vienna, Vienna, Austria
| | - Manuela Schmidinger
- Department of Medicine I, Clinical Division of Oncology and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Holger Moch
- Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Peter Schraml
- Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland
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39
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Ruf M, Moch H, Schraml P. PD-L1 expression is regulated by hypoxia inducible factor in clear cell renal cell carcinoma. Int J Cancer 2016; 139:396-403. [PMID: 26945902 DOI: 10.1002/ijc.30077] [Citation(s) in RCA: 137] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 02/29/2016] [Indexed: 12/13/2022]
Abstract
In our study, we demonstrate that ccRCC cell lines with impaired function of pVHL to degrade HIFα express elevated levels of PD-L1. In vitro analysis provided evidence that both reconstitution of pVHL and silencing of HIF2α, but not of HIF1α, lead to reduced PD-L1 expression. The strong correlation of expression between the HIF2α-specific HIF target Glut1 and PD-L1 confirmed this finding in ccRCC cell lines and tissue. Soluble PD-L1 levels remained constant in the sera of ccRCC patients regardless of the PD-L1 expression status in their tumors. In conclusion, our data suggest PD-L1 as HIF2α target, which is upregulated in pVHL deficient ccRCC. The combination of PD-L1 targeting drugs with HIF inhibiting agents may be an additional option for the treatment of ccRCC.
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Affiliation(s)
- Melanie Ruf
- Institute of Surgical Pathology, University Hospital Zurich, Switzerland
| | - Holger Moch
- Institute of Surgical Pathology, University Hospital Zurich, Switzerland
| | - Peter Schraml
- Institute of Surgical Pathology, University Hospital Zurich, Switzerland
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40
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Ruf M, Mittmann C, Nowicka AM, Hartmann A, Hermanns T, Poyet C, van den Broek M, Sulser T, Moch H, Schraml P. pVHL/HIF-regulated CD70 expression is associated with infiltration of CD27+ lymphocytes and increased serum levels of soluble CD27 in clear cell renal cell carcinoma. Clin Cancer Res 2015; 21:889-98. [PMID: 25691774 DOI: 10.1158/1078-0432.ccr-14-1425] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE CD70, a member of the TNF ligand superfamily, has been shown frequently overexpressed in clear cell renal cell carcinoma (ccRCC). The mechanisms of CD70's upregulation and its role in ccRCC are unknown. EXPERIMENTAL DESIGN CD70 expression was immunohistochemically analyzed in 667 RCCs and RCC metastases. Von Hippel-Lindau gene (VHL) mutations, expression patterns of VHL protein (pVHL), hypoxia-inducible factor (HIF) α, and several HIF targets were studied in tissues and cell lines and correlated with CD70 overexpression. Gene promoter analysis was performed to confirm CD70 as HIF target gene. Consecutive tissue sections were immunostained to reveal the relation between CD70-expressing RCCs and tumor-infiltrating lymphocytes positive for the CD70 receptor (CD27). CD70-mediated release of soluble CD27 in RCC was assessed by coculture experiments and sera analysis of patients with RCC. RESULTS Elevated CD70 expression was seen in 80% of primary tumors and metastases of ccRCC and correlated with dysregulation of the pVHL/HIF pathway. In vitro analyses demonstrated that CD70 upregulation is driven by HIF. Furthermore, CD27(+) lymphocytes preferentially infiltrate CD70-expressing ccRCCs. CD70-dependent release of soluble CD27 in cocultures may explain the high CD27 levels observed in sera of patients with CD70-expressing ccRCC. The combination of lymphocyte infiltration and CD70 expression in RCC was associated with worse patient outcome. CONCLUSION Our findings demonstrate that in ccRCC, CD70 expression is regulated by HIF as a consequence of pVHL inactivation. Increased serum levels of CD27 suggest the existence of CD70-expressing ccRCC, thus representing a potential serum marker for patients suffering from this disease.
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Affiliation(s)
- Melanie Ruf
- Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland.
| | - Christiane Mittmann
- Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Anna M Nowicka
- Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Arndt Hartmann
- Institute of Pathology, University Hospital Erlangen, Erlangen, Germany
| | - Thomas Hermanns
- Department of Urology, University Hospital Zurich, Zurich, Switzerland
| | - Cédric Poyet
- Department of Urology, University Hospital Zurich, Zurich, Switzerland
| | | | - Tullio Sulser
- Department of Urology, University Hospital Zurich, Zurich, Switzerland
| | - Holger Moch
- Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Peter Schraml
- Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland.
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41
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Nowicka AM, Häuselmann I, Borsig L, Bolduan S, Schindler M, Schraml P, Heikenwalder M, Moch H. A novel pVHL-independent but NEMO-driven pathway in renal cancer promotes HIF stabilization. Oncogene 2015; 35:3125-38. [PMID: 26500060 DOI: 10.1038/onc.2015.400] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Revised: 07/22/2015] [Accepted: 08/14/2015] [Indexed: 12/11/2022]
Abstract
Activation of hypoxia-inducible factor (HIF) is due to loss of von Hippel-Lindau protein (pVHL) function in most clear cell renal cell carcinomas (ccRCCs). Here we describe a novel pVHL-independent mechanism of HIF regulation and identify nuclear factor (NF)-κB essential modulator (NEMO) as a hitherto unknown oncogenic factor influencing human ccRCC progression. Over 60% of human ccRCCs (n=157) have negative or weak NEMO protein expression by immunohistochemistry. Moderate/strong NEMO protein expression is more frequent in VHL wild-type ccRCCs. We show that NEMO stabilizes HIFα via direct interaction and independently of NF-κB signaling in vitro. NEMO prolongs tumor cell survival via regulation of apoptosis and activation of epithelial-to-mesenchymal transition, facilitating tumor metastasis. Our findings suggest that NEMO-driven HIF activation is involved in progression of ccRCC. Therefore, NEMO may represent a clinically relevant link between NF-κB and the VHL/HIF pathways. Targeting NEMO with specific inhibitors in patients with metastatic ccRCC could be a novel treatment approach in patients with ccRCC expressing functional pVHL.
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Affiliation(s)
- A M Nowicka
- Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland
| | - I Häuselmann
- Institute of Physiology, Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland
| | - L Borsig
- Institute of Physiology, Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland
| | - S Bolduan
- Institute of Virology, Technische Universität München/Helmholtz Zentrum München, Munich, Germany
| | - M Schindler
- Institute of Virology, Technische Universität München/Helmholtz Zentrum München, Munich, Germany
| | - P Schraml
- Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland
| | - M Heikenwalder
- Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland.,Institute of Virology, Technische Universität München/Helmholtz Zentrum München, Munich, Germany.,Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ) Heidelberg, Heidelberg, Germany
| | - H Moch
- Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland
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Ruf M, Moch H, Schraml P. Interaction of tumor cells with infiltrating lymphocytes via CD70 and CD27 in clear cell renal cell carcinoma. Oncoimmunology 2015; 4:e1049805. [PMID: 26587319 DOI: 10.1080/2162402x.2015.1049805] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [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: 05/04/2015] [Accepted: 05/04/2015] [Indexed: 10/23/2022] Open
Abstract
CD70 upregulation by hypoxia-inducible factor and CD27+ lymphocyte tumor infiltration are associated with worse survival in von Hippel-Lindau gene (VHL) mutated clear cell renal cell carcinoma (ccRCC). CD70/CD27 interaction is accompanied by high soluble CD27 levels in the sera of ccRCC patients suggesting that soluble CD27 is a potential predictive tool for anti-CD70 therapy.
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Affiliation(s)
- Melanie Ruf
- Institute of Surgical Pathology; University Hospital Zürich ; Zürich, Switzerland
| | - Holger Moch
- Institute of Surgical Pathology; University Hospital Zürich ; Zürich, Switzerland
| | - Peter Schraml
- Institute of Surgical Pathology; University Hospital Zürich ; Zürich, Switzerland
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Eppler E, Janas E, Link K, Weidmann L, Bischofberger H, Wenger M, Tinguely M, Schraml P, Moch H, Fellbaum C. Insulin-like growth factor I is expressed in classical and nodular lymphocyte-predominant Hodgkin’s lymphoma tumour and microenvironmental cells. Cell Tissue Res 2014; 359:841-51. [DOI: 10.1007/s00441-014-2052-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 10/27/2014] [Indexed: 12/29/2022]
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Dannenmann SR, Thielicke J, Stöckli M, Matter C, von Boehmer L, Cecconi V, Hermanns T, Hefermehl L, Schraml P, Moch H, Knuth A, van den Broek M. Tumor-associated macrophages subvert T-cell function and correlate with reduced survival in clear cell renal cell carcinoma. Oncoimmunology 2014; 2:e23562. [PMID: 23687622 PMCID: PMC3655740 DOI: 10.4161/onci.23562] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Although malignant cells can be recognized and controlled by the immune system, in patients with clinically apparent cancer immunosurveillance has failed. To better understand local immunoregulatory processes that impact on cancer progression, we correlated intratumoral immunological profiles with the survival of patients affected by primary clear cell renal cell carcinoma (ccRCC). A retrospective analysis of 54 primary ccRCC samples for 31 different immune response-related transcripts, revealed a negative correlation of CD68 (a marker of tumor-associated macrophages, TAMs) and FOXP3 (a marker of regulatory T cells, Tregs) with survival. The subsequent analysis of 12 TAM-related transcripts revealed an association between the genes coding for CD163, interferon regulatory factor 4 (IRF4) and fibronectin 1 (FN1), all of which have been linked to the M2 TAM phenotype, with reduced survival and increased tumor stage, whereas the opposite was the case for the M1-associated gene coding for inducible nitric oxide synthetase (iNOS). The M2 signature of (CD68+) TAMs was found to correlate with CD163 expression, as determined in prospectively collected fresh ccRCC tissue samples. Upon co-culture with autologous tumor cells, CD11b+ cells isolated from paired blood samples expressed CD163 and other M2-associated proteins, suggesting that the malignant cells promote the accumulation of M2 TAMs. Furthermore, the tumor-associated milieu as well as isolated TAMs induced the skewing of autologous, blood-derived CD4+ T cells toward a more immunosuppressive phenotype, as shown by decreased production of effector cytokines, increased production of interleukin-10 (IL-10) and enhanced expression of the co-inhibitory molecules programmed death 1 (PD-1) and T-cell immunoglobulin mucin 3 (TIM-3). Taken together, our data suggest that ccRCC progressively attracts macrophages and induces their skewing into M2 TAMs, in turn subverting tumor-infiltrating T cells such that immunoregulatory functions are increased at the expense of effector functions.
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Matter MS, Schwarz E, Marafioti T, Schraml P, Moch H. Immunohistochemical detection of CD3 in T-cell lymphomas: superior sensitivity of rabbit monoclonal 2GV6 antibody compared to mouse monoclonal F7·2·38 antibody. J Histotechnol 2013. [DOI: 10.1179/2046023612y.0000000017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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Dannenmann SR, Hermanns T, Bransi A, Matter C, von Boehmer L, Stevanovic S, Schraml P, Moch H, Knuth A, van den Broek M. Spontaneous peripheral T-cell responses toward the tumor-associated antigen cyclin D1 in patients with clear cell renal cell carcinoma. Cancer Immunol Res 2013; 1:288-95. [PMID: 24777966 DOI: 10.1158/2326-6066.cir-13-0113] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Renal cell carcinoma (RCC) is a heterogeneous group of kidney cancers with clear cell RCC (ccRCC) as the major subgroup. To expand the number of clinically relevant tumor-associated antigens (TAA) that can be targeted by immunotherapy, we analyzed samples from 23 patients with primary ccRCC for the expression and immunogenicity of various TAAs. We found high-frequency expression of MAGE-A9 and NY-ESO-1 in 36% and 55% of samples, respectively, and overexpression of PRAME, RAGE-1, CA-IX, Cyclin D1, ADFP, C-MET, and RGS-5 in many of the tumor samples. We analyzed the blood of patients with HLA-A2(+) ccRCC for the presence of CD8(+) T cells specific for TAA-derived HLA-A2-restricted peptides and found spontaneous responses to cyclin D1 in 5 of 6 patients with Cyclin D1-positive tumors. Cyclin D1-specific CD8(+) T cells secreted TNF-α, IFN-γ, and interleukin-2 (IL-2), and degranulated, indicating the presence of polyfunctional tumor-specific CD8(+) T cells in the blood of these patients with ccRCC. The high frequency (43%) of Cyclin D1 overexpression and the presence of functional cyclin D1-specific T cells in 83% of these patients with ccRCC suggest that cyclin D1 may be a target for immunotherapeutic strategies.
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Affiliation(s)
- Stefanie R Dannenmann
- Authors' Affiliations: Departments of Department of Immunology, Interfaculty Institute for Cell Biology, University of Tubingen, Tubingen, Germany
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Vogetseder A, Thies S, Ingold B, Roth P, Weller M, Schraml P, Goodman SL, Moch H. αv-Integrin isoform expression in primary human tumors and brain metastases. Int J Cancer 2013; 133:2362-71. [PMID: 23661241 DOI: 10.1002/ijc.28267] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [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: 04/06/2013] [Accepted: 04/17/2013] [Indexed: 11/12/2022]
Abstract
UNLABELLED To determine whether metastasis to brain is associated with altered expression patterns of integrins, we investigated the expression of αvβ3, αvβ5, αvβ6 and αvβ8 integrins in primary malignancies and metastases to brain of breast, lung and renal carcinomas and in malignant melanoma. Inhibitors of αv integrins are currently in clinical trials for glioblastoma. The role of integrins in the process of brain metastasis from other human tumors is unknown. Immunohistochemistry with novel integrin subtype specific rabbit monoclonal antibodies was performed on tissue microarrays of archival material of surgical biopsies taken from primary tumors and brain metastases. Integrin αvβ3 expression was increased in brain metastases compared to primary tumors of breast adenocarcinoma, non-small cell lung cancer, renal clear cell cancer and malignant cutaneous melanoma (all p < 0.01). Similarly, integrin αvβ8 expression was increased in brain metastases compared to primary tumors of breast cancer (p < 0.0001), lung cancer (p < 0.01) and renal cancer (p < 0.0001), with a similar trend in metastatic melanoma. Integrin αvβ5 was expressed in most primary tumors (98% breast cancer; 67% lung cancer; 90% renal cancer; 89% melanoma) and showed a stronger expression in brain metastases compared to primary tumors from lung cancer and melanoma (p < 0.05). Also integrin αvβ6 expression was increased in brain metastases compared to primary breast cancer (p < 0.001). CONCLUSIONS The stronger αv-integrin expression in brain metastases, especially of αvβ3 and αvβ8 integrins, suggests that certain αv integrin are involved in the process of brain metastasis. αv Integrins may be therapeutic targets for patients with metastatic cancer in brain.
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Affiliation(s)
- Alexander Vogetseder
- Department of Pathology, Institute for Surgical Pathology, University Hospital Zurich, Switzerland
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Kaufmann MR, Schraml P, Hermanns T, Wenger RH, Camenisch G. Onconeuronal antigen Cdr2 correlates with HIF prolyl-4-hydroxylase PHD1 and worse prognosis in renal cell carcinoma. Exp Mol Pathol 2013; 94:453-7. [DOI: 10.1016/j.yexmp.2013.03.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 03/13/2013] [Indexed: 12/18/2022]
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Rechsteiner M, von Teichman A, Rüschoff JH, Fankhauser N, Pestalozzi B, Schraml P, Weber A, Wild P, Zimmermann D, Moch H. KRAS, BRAF, and TP53 Deep Sequencing for Colorectal Carcinoma Patient Diagnostics. J Mol Diagn 2013; 15:299-311. [DOI: 10.1016/j.jmoldx.2013.02.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 01/07/2013] [Accepted: 02/07/2013] [Indexed: 12/12/2022] Open
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Albers J, Rajski M, Schönenberger D, Harlander S, Schraml P, von Teichman A, Georgiev S, Wild PJ, Moch H, Krek W, Frew IJ. Combined mutation of Vhl and Trp53 causes renal cysts and tumours in mice. EMBO Mol Med 2013; 5:949-64. [PMID: 23606570 PMCID: PMC3779454 DOI: 10.1002/emmm.201202231] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [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: 11/02/2012] [Revised: 03/08/2013] [Accepted: 03/12/2013] [Indexed: 12/03/2022] Open
Abstract
The combinations of genetic alterations that cooperate with von Hippel–Lindau (VHL) mutation to cause clear cell renal cell carcinoma (ccRCC) remain poorly understood. We show that the TP53 tumour suppressor gene is mutated in approximately 9% of human ccRCCs. Combined deletion of Vhl and Trp53 in primary mouse embryo fibroblasts causes proliferative dysregulation and high rates of aneuploidy. Deletion of these genes in the epithelium of the kidney induces the formation of simple cysts, atypical cysts and neoplasms, and deletion in the epithelia of the genital urinary tract leads to dysplasia and tumour formation. Kidney cysts display a reduced frequency of primary cilia and atypical cysts and neoplasms exhibit a pro-proliferative signature including activation of mTORC1 and high expression of Myc, mimicking several cellular and molecular alterations seen in human ccRCC and its precursor lesions. As the majority of ccRCC is associated with functional inactivation of VHL, our findings suggest that for a subset of ccRCC, loss of p53 function represents a critical event in tumour development.
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Affiliation(s)
- Joachim Albers
- Institute of Physiology, University of Zurich, Zurich, Switzerland
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