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Somatic mutations in collagens are associated with a distinct tumor environment and overall survival in gastric cancer. BMC Cancer 2022; 22:139. [PMID: 35120467 PMCID: PMC8815231 DOI: 10.1186/s12885-021-09136-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 12/22/2021] [Indexed: 12/11/2022] Open
Abstract
Background Gastric cancer is a heterogeneous disease with poorly understood genetic and microenvironmental factors. Mutations in collagen genes are associated with genetic diseases that compromise tissue integrity, but their role in tumor progression has not been extensively reported. Aberrant collagen expression has been long associated with malignant tumor growth, invasion, chemoresistance, and patient outcomes. We hypothesized that somatic mutations in collagens could functionally alter the tumor extracellular matrix. Methods We used publicly available datasets including The Tumor Cancer Genome Atlas (TCGA) to interrogate somatic mutations in collagens in stomach adenocarcinomas. To demonstrate that collagens were significantly mutated above background mutation rates, we used a moderated Kolmogorov-Smirnov test along with combination analysis with a bootstrap approach to define the background accounting for mutation rates. Association between mutations and clinicopathological features was evaluated by Fisher or chi-squared tests. Association with overall survival was assessed by Kaplan-Meier and the Cox-Proportional Hazards Model. Gene Set Enrichment Analysis was used to interrogate pathways. Immunohistochemistry and in situ hybridization tested expression of COL7A1 in stomach tumors. Results In stomach adenocarcinomas, we identified individual collagen genes and sets of collagen genes harboring somatic mutations at a high frequency compared to background in both microsatellite stable, and microsatellite instable tumors in TCGA. Many of the missense mutations resemble the same types of loss of function mutations in collagenopathies that disrupt tissue formation and destabilize cells providing guidance to interpret the somatic mutations. We identified combinations of somatic mutations in collagens associated with overall survival, with a distinctive tumor microenvironment marked by lower matrisome expression and immune cell signatures. Truncation mutations were strongly associated with improved outcomes suggesting that loss of expression of secreted collagens impact tumor progression and treatment response. Germline collagenopathy variants guided interpretation of impactful somatic mutations on tumors. Conclusions These observations highlight that many collagens, expressed in non-physiologically relevant conditions in tumors, harbor impactful somatic mutations in tumors, suggesting new approaches for classification and therapy development in stomach cancer. In sum, these findings demonstrate how classification of tumors by collagen mutations identified strong links between specific genotypes and the tumor environment. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-09136-1.
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Bornert O, Hogervorst M, Nauroy P, Bischof J, Swildens J, Athanasiou I, Tufa SF, Keene DR, Kiritsi D, Hainzl S, Murauer EM, Marinkovich MP, Platenburg G, Hausser I, Wally V, Ritsema T, Koller U, Haisma EM, Nyström A. QR-313, an Antisense Oligonucleotide, Shows Therapeutic Efficacy for Treatment of Dominant and Recessive Dystrophic Epidermolysis Bullosa: A Preclinical Study. J Invest Dermatol 2020; 141:883-893.e6. [PMID: 32946877 DOI: 10.1016/j.jid.2020.08.018] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 07/21/2020] [Accepted: 08/12/2020] [Indexed: 02/06/2023]
Abstract
Dystrophic epidermolysis bullosa (DEB) is a blistering skin disease caused by mutations in the gene COL7A1 encoding collagen VII. DEB can be inherited as recessive DEB (RDEB) or dominant DEB (DDEB) and is associated with a high wound burden. Perpetual cycles of wounding and healing drive fibrosis in DDEB and RDEB, as well as the formation of a tumor-permissive microenvironment. Prolonging wound-free episodes by improving the quality of wound healing would therefore confer substantial benefit for individuals with DEB. The collagenous domain of collagen VII is encoded by 82 in-frame exons, which makes splice-modulation therapies attractive for DEB. Indeed, antisense oligonucleotide-based exon skipping has shown promise for RDEB. However, the suitability of antisense oligonucleotides for treatment of DDEB remains unexplored. Here, we developed QR-313, a clinically applicable, potent antisense oligonucleotide specifically targeting exon 73. We show the feasibility of topical delivery of QR-313 in a carbomer-composed gel for treatment of wounds to restore collagen VII abundance in human RDEB skin. Our data reveal that QR-313 also shows direct benefit for DDEB caused by exon 73 mutations. Thus, the same topically applied therapeutic could be used to improve the wound healing quality in RDEB and DDEB.
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Affiliation(s)
- Olivier Bornert
- Department of Dermatology, Medical Faculty, Medical Center - University of Freiburg, Freiburg, Germany
| | | | - Pauline Nauroy
- Department of Dermatology, Medical Faculty, Medical Center - University of Freiburg, Freiburg, Germany
| | - Johannes Bischof
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University Salzburg, Salzburg, Austria
| | - Jim Swildens
- ProQR Therapeutics N.V., Leiden, The Netherlands
| | - Ioannis Athanasiou
- Department of Dermatology, Medical Faculty, Medical Center - University of Freiburg, Freiburg, Germany
| | - Sara F Tufa
- Micro-Imaging Center, Shriners Hospital for Children, Portland, Oregon, USA
| | - Douglas R Keene
- Micro-Imaging Center, Shriners Hospital for Children, Portland, Oregon, USA
| | - Dimitra Kiritsi
- Department of Dermatology, Medical Faculty, Medical Center - University of Freiburg, Freiburg, Germany
| | - Stefan Hainzl
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University Salzburg, Salzburg, Austria
| | - Eva M Murauer
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University Salzburg, Salzburg, Austria
| | - M Peter Marinkovich
- Department of Dermatology, Stanford University School of Medicine, Stanford, California, USA; Dermatology, Veteran's Affairs Medical Center, Palo Alto, California, USA
| | | | - Ingrid Hausser
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Verena Wally
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University Salzburg, Salzburg, Austria
| | - Tita Ritsema
- ProQR Therapeutics N.V., Leiden, The Netherlands
| | - Ulrich Koller
- EB House Austria, Research Program for Molecular Therapy of Genodermatoses, Department of Dermatology and Allergology, University Hospital of the Paracelsus Medical University Salzburg, Salzburg, Austria
| | | | - Alexander Nyström
- Department of Dermatology, Medical Faculty, Medical Center - University of Freiburg, Freiburg, Germany.
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