Change search
ReferencesLink to record
Permanent link

Direct link
In situ sequencing identifies TMPRSS2-ERG fusion transcripts, somatic point mutations and gene expression levels in prostate cancers
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
Show others and affiliations
2014 (English)In: Journal of Pathology, ISSN 0022-3417, E-ISSN 1096-9896, Vol. 234, no 2, 253-261 p.Article in journal (Refereed) Published
Abstract [en]

Translocations contribute to the genesis and progression of epithelial tumours and in particular to prostate cancer development. To better understand the contribution of fusion transcripts and visualize the clonal composition of multifocal tumours, we have developed a technology for multiplex in situ detection and identification of expressed fusion transcripts. When compared to immunohistochemistry, TMPRSS2-ERG fusion-negative and fusion-positive prostate tumours were correctly classified. The most prevalent TMPRSS2-ERG fusion variants were visualized, identified, and quantitated in human prostate cancer tissues, and the ratio of the variant fusion transcripts could for the first time be directly determined by in situ sequencing. Further, we demonstrate concurrent in situ detection of gene expression, point mutations, and gene fusions of the prostate cancer relevant targets AMACR, AR, TP53, and TMPRSS2-ERG. This unified approach to in situ analyses of somatic mutations can empower studies of intra-tumoural heterogeneity and future tissue-based diagnostics of mutations and translocations.

Place, publisher, year, edition, pages
2014. Vol. 234, no 2, 253-261 p.
Keyword [en]
TMPRSS2-ERG, padlock probes, in situ sequencing, prostate cancer, somatic mutations
National Category
Cancer and Oncology Biological Sciences
URN: urn:nbn:se:su:diva-109002DOI: 10.1002/path.4392ISI: 000342976700013OAI: diva2:768858


Available from: 2014-12-05 Created: 2014-11-10 Last updated: 2014-12-05Bibliographically approved
In thesis
1. In situ Sequencing: Methods for spatially-resolved transcriptome analysis
Open this publication in new window or tab >>In situ Sequencing: Methods for spatially-resolved transcriptome analysis
2014 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

It is well known that cells in tissues display a large heterogeneity in gene expression due to differences in cell lineage origin and variation in the local environment at different sites in the tissue, a heterogeneity that is difficult to study by analyzing bulk RNA extracts from tissue. Recently, genome-wide transcriptome analysis technologies have enabled the analysis of this variation with single-cell resolution. In order to link the heterogeneity observed at molecular level with the morphological context of tissues, new methods are needed which achieve an additional level of information, such as spatial resolution.

In this thesis I describe the development and application of padlock probes and rolling circle amplification (RCA) as molecular tools for spatially-resolved transcriptome analysis. Padlock probes allow in situ detection of individual mRNA molecules with single nucleotide resolution, visualizing the molecular information directly in the cell and tissue context. Detection of clinically relevant point mutations in tumor samples is achieved by using padlock probes in situ, allowing visualization of intra-tumor heterogeneity. To resolve more complex gene expression patterns, we developed in situ sequencing of RCA products combining padlock probes and next-generation sequencing methods. We demonstrated the use of this new method by, for the first time, sequencing short stretches of transcript molecules directly in cells and tissue. By using in situ sequencing as read-out for multiplexed padlock probe assays, we measured the expression of tens of genes in hundreds of thousands of cells, including point mutations, fusions transcripts and gene expression level.

These molecular tools can complement genome-wide transcriptome analyses adding spatial resolution to the molecular information. This level of resolution is important for the understanding of many biological processes and potentially relevant for the clinical management of cancer patients.

Place, publisher, year, edition, pages
Stockholm: Department of Biochemistry and Biophysics, Stockholm University, 2014. 49 p.
Padlock probes, rolling circle amplification, in situ sequencing, spatially-resolved transcriptomics, molecular diagnostics
National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Research subject
urn:nbn:se:su:diva-110057 (URN)978-91-7649-066-2 (ISBN)
Public defence
2015-01-23, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 16 B, Stockholm, 10:00 (English)

At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 4: Manuscript.

Available from: 2014-12-29 Created: 2014-12-05 Last updated: 2014-12-15Bibliographically approved

Open Access in DiVA

No full text

Other links

Publisher's full text

Search in DiVA

By author/editor
Mignardi, MarcoNilsson, Mats
By organisation
Department of Biochemistry and Biophysics
In the same journal
Journal of Pathology
Cancer and OncologyBiological Sciences

Search outside of DiVA

GoogleGoogle Scholar
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

Altmetric score

Total: 16 hits
ReferencesLink to record
Permanent link

Direct link