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Larsson, Chatarina
Publications (10 of 16) Show all publications
Glimelius, B., Melin, B., Enblad, G., Alafuzoff, I., Beskow, A. H., Ahlström, H., . . . Sjöblom, T. (2018). U-CAN: a prospective longitudinal collection of biomaterials and clinical information from adult cancer patients in Sweden.. Acta Oncologica, 57(2), 187-194
Open this publication in new window or tab >>U-CAN: a prospective longitudinal collection of biomaterials and clinical information from adult cancer patients in Sweden.
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2018 (English)In: Acta Oncologica, ISSN 0284-186X, E-ISSN 1651-226X, Vol. 57, no 2, p. 187-194Article in journal (Refereed) Published
Abstract [en]

Background: Progress in cancer biomarker discovery is dependent on access to high-quality biological materials and high-resolution clinical data from the same cases. To overcome current limitations, a systematic prospective longitudinal sampling of multidisciplinary clinical data, blood and tissue from cancer patients was therefore initiated in 2010 by Uppsala and Umeå Universities and involving their corresponding University Hospitals, which are referral centers for one third of the Swedish population.

Material and Methods: Patients with cancer of selected types who are treated at one of the participating hospitals are eligible for inclusion. The healthcare-integrated sampling scheme encompasses clinical data, questionnaires, blood, fresh frozen and formalin-fixed paraffin-embedded tissue specimens, diagnostic slides and radiology bioimaging data.

Results: In this ongoing effort, 12,265 patients with brain tumors, breast cancers, colorectal cancers, gynecological cancers, hematological malignancies, lung cancers, neuroendocrine tumors or prostate cancers have been included until the end of 2016. From the 6914 patients included during the first five years, 98% were sampled for blood at diagnosis, 83% had paraffin-embedded and 58% had fresh frozen tissues collected. For Uppsala County, 55% of all cancer patients were included in the cohort.

Conclusions: Close collaboration between participating hospitals and universities enabled prospective, longitudinal biobanking of blood and tissues and collection of multidisciplinary clinical data from cancer patients in the U-CAN cohort. Here, we summarize the first five years of operations, present U-CAN as a highly valuable cohort that will contribute to enhanced cancer research and describe the procedures to access samples and data.

National Category
Cancer and Oncology Urology and Nephrology
Identifiers
urn:nbn:se:uu:diva-325565 (URN)10.1080/0284186X.2017.1337926 (DOI)000423473200003 ()28631533 (PubMedID)
Funder
Swedish Cancer Society
Available from: 2017-06-26 Created: 2017-06-26 Last updated: 2018-03-09Bibliographically approved
Larsson, C., Ali, M. A., Djureinovic, T., Lindroth, A. M., He, L. & Sjöblom, T. (2017). Loss of DIP2C in RKO cells stimulates changes in DNA methylation and epithelial-mesenchymal transition. BMC Cancer, 17, Article ID 487.
Open this publication in new window or tab >>Loss of DIP2C in RKO cells stimulates changes in DNA methylation and epithelial-mesenchymal transition
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2017 (English)In: BMC Cancer, ISSN 1471-2407, E-ISSN 1471-2407, Vol. 17, article id 487Article in journal (Refereed) Published
Abstract [en]

Background: The disco-interacting protein 2 homolog C (DIP2C) gene is an uncharacterized gene found mutated in a subset of breast and lung cancers. To understand the role of DIP2C in tumour development we studied the gene in human cancer cells.

Methods: We engineered human DIP2C knockout cells by genome editing in cancer cells. The growth properties of the engineered cells were characterised and transcriptome and methylation analyses were carried out to identify pathways deregulated by inactivation of DIP2C. Effects on cell death pathways and epithelial-mesenchymal transition traits were studied based on the results from expression profiling.

Results: Knockout of DIP2C in RKO cells resulted in cell enlargement and growth retardation. Expression profiling revealed 780 genes for which the expression level was affected by the loss of DIP2C, including the tumour-suppressor encoding CDKN2A gene, the epithelial-mesenchymal transition (EMT) regulator-encoding ZEB1, and CD44 and CD24 that encode breast cancer stem cell markers. Analysis of DNA methylation showed more than 30,000 sites affected by differential methylation, the majority of which were hypomethylated following loss of DIP2C. Changes in DNA methylation at promoter regions were strongly correlated to changes in gene expression, and genes involved with EMT and cell death were enriched among the differentially regulated genes. The DIP2C knockout cells had higher wound closing capacity and showed an increase in the proportion of cells positive for cellular senescence markers.

Conclusions: Loss of DIP2C triggers substantial DNA methylation and gene expression changes, cellular senescence and epithelial-mesenchymal transition in cancer cells.

Place, publisher, year, edition, pages
BIOMED CENTRAL LTD, 2017
Keywords
Cancer, DIP2C, Gene knockout, rAAV-mediated gene targeting, Tumour cell biology, DNA methylation, Epithelial-mesenchymal transition (EMT)
National Category
Cancer and Oncology
Identifiers
urn:nbn:se:uu:diva-331232 (URN)10.1186/s12885-017-3472-5 (DOI)000405865300001 ()28716088 (PubMedID)
Funder
Swedish Cancer Society, 2006/2154, 2007/775, 2012/834, 2012/1235Swedish Foundation for Strategic Research , F06-0050, RBa08-0114Swedish Society for Medical Research (SSMF)
Available from: 2017-10-16 Created: 2017-10-16 Last updated: 2017-11-29Bibliographically approved
Pandzic, T., Rendo, V., Lim, J., Larsson, C., Larsson, J., Stoimenov, I., . . . Sjöblom, T. (2017). Somatic PRDM2 c.4467delA mutations in colorectal cancers control histone methylation and tumor growth. OncoTarget, 8(58), 98646-98659
Open this publication in new window or tab >>Somatic PRDM2 c.4467delA mutations in colorectal cancers control histone methylation and tumor growth
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2017 (English)In: OncoTarget, ISSN 1949-2553, E-ISSN 1949-2553, Vol. 8, no 58, p. 98646-98659Article in journal (Refereed) Published
Abstract [en]

The chromatin modifier PRDM2/RIZ1 is inactivated by mutation in several forms of cancer and is a putative tumor suppressor gene. Frameshift mutations in the C-terminal region of PRDM2, affecting (A)8 or (A)9 repeats within exon 8, are found in one third of colorectal cancers with microsatellite instability, but the contribution of these mutations to colorectal tumorigenesis is unknown. To model somatic mutations in microsatellite unstable tumors, we devised a general approach to perform genome editing while stabilizing the mutated nucleotide repeat. We then engineered isogenic cell systems where the PRDM2 c.4467delA mutation in human HCT116 colorectal cancer cells was corrected to wild-type by genome editing. Restored PRDM2 increased global histone 3 lysine 9 dimethylation and reduced migration, anchorage-independent growth and tumor growth in vivo. Gene set enrichment analysis revealed regulation of several hallmark cancer pathways, particularly of epithelial-to-mesenchymal transition (EMT), with VIM being the most significantly regulated gene. These observations provide direct evidence that PRDM2 c.4467delA is a driver mutation in colorectal cancer and confirms PRDM2 as a cancer gene, pointing to regulation of EMT as a central aspect of its tumor suppressive action.

National Category
Cancer and Oncology
Identifiers
urn:nbn:se:uu:diva-345974 (URN)10.18632/oncotarget.21713 (DOI)000419392300074 ()
Funder
Swedish Foundation for Strategic Research , F06-0050 RBa08-0114Swedish Cancer Society, 2006/2154 2007/775 2012/834
Available from: 2018-03-13 Created: 2018-03-13 Last updated: 2018-09-20Bibliographically approved
Mignardi, M., Mezger, A., Qian, X., La Fleur, L., Botling, J., Larsson, C. & Nilsson, M. (2015). Oligonucleotide gap-fill ligation for mutation detection and sequencing in situ.. Nucleic Acids Research, 43(22), Article ID e151.
Open this publication in new window or tab >>Oligonucleotide gap-fill ligation for mutation detection and sequencing in situ.
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2015 (English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 43, no 22, article id e151Article in journal (Refereed) Published
Abstract [en]

In clinical diagnostics a great need exists for targeted in situ multiplex nucleic acid analysis as the mutational status can offer guidance for effective treatment. One well-established method uses padlock probes for mutation detection and multiplex expression analysis directly in cells and tissues. Here, we use oligonucleotide gap-fill ligation to further increase specificity and to capture molecular substrates for in situ sequencing. Short oligonucleotides are joined at both ends of a padlock gap probe by two ligation events and are then locally amplified by target-primed rolling circle amplification (RCA) preserving spatial information. We demonstrate the specific detection of the A3243G mutation of mitochondrial DNA and we successfully characterize a single nucleotide variant in the ACTB mRNA in cells by in situ sequencing of RCA products generated by padlock gap-fill ligation. To demonstrate the clinical applicability of our assay, we show specific detection of a point mutation in the EGFR gene in fresh frozen and formalin-fixed, paraffin-embedded (FFPE) lung cancer samples and confirm the detected mutation by in situ sequencing. This approach presents several advantages over conventional padlock probes allowing simpler assay design for multiplexed mutation detection to screen for the presence of mutations in clinically relevant mutational hotspots directly in situ.

National Category
Clinical Laboratory Medicine Basic Medicine
Research subject
Pathology
Identifiers
urn:nbn:se:uu:diva-279075 (URN)10.1093/nar/gkv772 (DOI)000371237600003 ()26240388 (PubMedID)
Funder
Swedish Research CouncilVINNOVAEU, FP7, Seventh Framework Programme, 259796
Available from: 2016-02-29 Created: 2016-02-29 Last updated: 2018-01-10Bibliographically approved
Jiao, X., Hooper, S. D., Djureinovic, T., Larsson, C., Wärnberg, F., Tellgren-Roth, C., . . . Sjöblom, T. (2013). Gene rearrangements in hormone receptor negative breast cancers revealed by mate pair sequencing. BMC Genomics, 14, Article ID 165.
Open this publication in new window or tab >>Gene rearrangements in hormone receptor negative breast cancers revealed by mate pair sequencing
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2013 (English)In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 14, article id 165Article in journal (Refereed) Published
Abstract [en]

Background: Chromosomal rearrangements in the form of deletions, insertions, inversions and translocations are frequently observed in breast cancer genomes, and a subset of these rearrangements may play a crucial role in tumorigenesis. To identify novel somatic chromosomal rearrangements, we determined the genome structures of 15 hormone-receptor negative breast tumors by long-insert mate pair massively parallel sequencing. Results: We identified and validated 40 somatic structural alterations, including the recurring fusion between genes DDX10 and SKA3 and translocations involving the EPHA5 gene. Other rearrangements were found to affect genes in pathways involved in epigenetic regulation, mitosis and signal transduction, underscoring their potential role in breast tumorigenesis. RNA interference-mediated suppression of five candidate genes (DDX10, SKA3, EPHA5, CLTC and TNIK) led to inhibition of breast cancer cell growth. Moreover, downregulation of DDX10 in breast cancer cells lead to an increased frequency of apoptotic nuclear morphology. Conclusions: Using whole genome mate pair sequencing and RNA interference assays, we have discovered a number of novel gene rearrangements in breast cancer genomes and identified DDX10, SKA3, EPHA5, CLTC and TNIK as potential cancer genes with impact on the growth and proliferation of breast cancer cells.

National Category
Medical Genetics
Identifiers
urn:nbn:se:uu:diva-182312 (URN)10.1186/1471-2164-14-165 (DOI)000316207800001 ()23496902 (PubMedID)
Funder
Swedish Cancer Society
Available from: 2012-10-09 Created: 2012-10-09 Last updated: 2018-01-12Bibliographically approved
Weibrecht, I., Lundin, E., Kiflemariam, S., Mignardi, M., Grundberg, I., Larsson, C., . . . Söderberg, O. (2013). In situ detection of individual mRNA molecules and protein complexes or post-translational modifications using padlock probes combined with the in situ proximity ligation assay. Nature Protocols, 8(2), 355-372
Open this publication in new window or tab >>In situ detection of individual mRNA molecules and protein complexes or post-translational modifications using padlock probes combined with the in situ proximity ligation assay
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2013 (English)In: Nature Protocols, ISSN 1754-2189, E-ISSN 1750-2799, Vol. 8, no 2, p. 355-372Article in journal (Refereed) Published
Abstract [en]

Analysis at the single-cell level is essential for the understanding of cellular responses in heterogeneous cell populations, but it has been difficult to perform because of the strict requirements put on detection methods with regard to selectivity and sensitivity (i.e., owing to the cross-reactivity of probes and limited signal amplification). Here we describe a 1.5-d protocol for enumerating and genotyping mRNA molecules in situ while simultaneously obtaining information on protein interactions or post-translational modifications; this is achieved by combining padlock probes with in situ proximity ligation assays (in situ PLA). In addition, we provide an example of how to design padlock probes and how to optimize staining conditions for fixed cells and tissue sections. Both padlock probes and in situ PLA provide the ability to directly visualize single molecules by standard microscopy in fixed cells or tissue sections, and these methods may thus be valuable for both research and diagnostic purposes.

National Category
Medical and Health Sciences
Identifiers
urn:nbn:se:uu:diva-199740 (URN)10.1038/nprot.2013.006 (DOI)000317109900009 ()
Available from: 2013-05-13 Created: 2013-05-13 Last updated: 2017-12-06Bibliographically approved
Larsson, C., Grundberg, I., Söderberg, O. & Nilsson, M. (2010). In situ detection and genotyping of individual mRNA molecules. Nature Methods, 7(5), 395-397
Open this publication in new window or tab >>In situ detection and genotyping of individual mRNA molecules
2010 (English)In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 7, no 5, p. 395-397Article in journal (Refereed) Published
Abstract [en]

Increasing knowledge about the heterogeneity of mRNA expression within cell populations highlights the need to study transcripts at the level of single cells. We present a method for detection and genotyping of individual transcripts based on padlock probes and in situ target-primed rolling-circle amplification. We detect a somatic point mutation, differentiate between members of a gene family and perform multiplex detection of transcripts in human and mouse cells and tissue.

National Category
Medical and Health Sciences
Identifiers
urn:nbn:se:uu:diva-137786 (URN)10.1038/NMETH.1448 (DOI)000277175100023 ()20383134 (PubMedID)
Note

De 2 första författarna delar förstaförfattarskapet.

Available from: 2010-12-15 Created: 2010-12-15 Last updated: 2017-12-11Bibliographically approved
Larsson, C. (2009). Single-molecule Detection in situ. (Doctoral dissertation). Uppsala: Acta Universitatis Upsaliensis
Open this publication in new window or tab >>Single-molecule Detection in situ
2009 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The human body contains a variety of different cell types that share a common genome, but differ in how they use the information encoded therein. Variation in molecular content exists even at the level of individual cells, and to provide deeper insight into complex cellular processes methods that permit analysis of each cell on its own are needed. This thesis presents molecular methods for localized detection of individual nucleic acid molecules. The developed methods are based on padlock probes and target-primed rolling circle amplification. Single-molecule detection sensitivity in combination with single-nucleotide genotyping selectivity enables detection of allelic DNA variants and closely related target sequences directly in cells. Padlock probes further enable multiplex detection of targets, and in combination with image analysis quantitative molecular data for individual cells can be acquired for large cell populations at a resolution that no other in situ detection method can provide at present.

 

In this thesis, the in situ target-primed rolling circle amplification technique was first used for genotyping of a point mutation in the mitochondrial genome with padlock probes. This displayed mitochondrial DNA heterogeneity in cell populations. Application of the method on comet assay preparations showed that mitochondrial genomes are lost from these samples prior to analysis. Nuclear DNA targets, however, can be efficiently detected in corresponding samples. Padlock probes and rolling circle amplification are thus an attractive alternative to FISH analysis for localized DNA detection in comet assay samples. A method was also developed for localized detection of individual mRNA molecules with padlock probes and rolling circle amplification. This method provides unique possibilities to genotype allelic variants of transcripts in situ. mRNA expression is associated with substantial cell-to-cell variation and our presented method permits simultaneous visualization of multiple transcripts directly in complex tissue samples. Application of the methods presented in this thesis will enable new types of studies of biological samples from both normal and disease states.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2009. p. 49
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine, ISSN 1651-6206 ; 431
National Category
Cell and Molecular Biology
Research subject
Molecular Medicine
Identifiers
urn:nbn:se:uu:diva-98538 (URN)978-91-554-7442-3 (ISBN)
Public defence
2009-04-09, Rudbecksalen, Rudbecklaboratoriet, Dag Hammarskjölds väg 20, Uppsala, 09:15 (English)
Opponent
Supervisors
Available from: 2009-03-19 Created: 2009-02-25 Last updated: 2018-01-13Bibliographically approved
Wählby, C., Karlsson, P., Henriksson, S., Larsson, C., Nilsson, M. & Bengtsson, E. (2008). Finding cells, finding molecules, finding patterns. International Journal of Signal and Imaging Systems Engineering, 1(1), 11-17
Open this publication in new window or tab >>Finding cells, finding molecules, finding patterns
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2008 (English)In: International Journal of Signal and Imaging Systems Engineering, ISSN 1748-0698, Vol. 1, no 1, p. 11-17Article in journal (Refereed) Published
Abstract [en]

Many modern molecular labelling techniques result in bright point signals. Signals from molecules that are detected directly inside a cell can be captured by fluorescence microscopy. Signals representing different types of molecules may be randomly distributed in the cells or show systematic patterns, indicating that the corresponding molecules have specific, non-random localisations and functions in the cell. Assessing this information requires high speed robust image segmentation followed by signal detection, and finally, pattern analysis. We present and discuss these types of methods and show an example of how the distribution of different variants of mitochondrial DNA can be analysed.

Keywords
mass data analysis, image analysis, cytometry, single molecule detection, padlock probes, pattern analysis
National Category
Computer Vision and Robotics (Autonomous Systems)
Research subject
Computerized Image Analysis
Identifiers
urn:nbn:se:uu:diva-97427 (URN)10.1504/IJSISE.2008.017768 (DOI)
Available from: 2008-08-29 Created: 2008-08-29 Last updated: 2018-01-13Bibliographically approved
Melin, J., Jarvius, J., Larsson, C., Söderberg, O., Landegren, U. & Nilsson, M. (2008). Ligation-based molecular tools for lab-on-a-chip devices. New Biotechnology, 25(1), 42-8
Open this publication in new window or tab >>Ligation-based molecular tools for lab-on-a-chip devices
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2008 (English)In: New Biotechnology, ISSN 1871-6784, Vol. 25, no 1, p. 42-8Article in journal (Refereed) Published
Abstract [en]

Molecular diagnostics can offer early detection of disease, improved diagnostic accuracy, and qualified follow-up. Moreover, the use of microfluidic devices can in principle render these analyses quickly and user-friendly, placing them within the reach of the general practitioner and maybe even in households. However, the progress launching such devices has been limited so far. We propose that an important limiting factor has been the difficulty of establishing molecular assays suitable for microfabricated formats. The assays should be capable of monitoring a wide range of molecules, including genomic DNA, RNA and proteins with secondary modifications and interaction partners, and they must exhibit excellent sensitivity and specificity. We discuss these problems and describe a series of molecular tools that may present new opportunities for lab-on-a-chip devices at the point-of-care.

National Category
Medical and Health Sciences
Identifiers
urn:nbn:se:uu:diva-16651 (URN)10.1016/j.nbt.2008.02.003 (DOI)000259343400018 ()18504018 (PubMedID)
Available from: 2008-06-02 Created: 2008-06-02Bibliographically approved
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