When Finland was lost. Background, Course of Events and Reactions.

Since 1809 the loss of Finland has been discussed in different ways in Swedish history research. In the early 20th century the burst of the state was seen in a nationalistic perspective. It was said that the people in Sweden, or the “public opinion”, with despair and in a “nationalistic trauma” received the news bulletins from the peace agreement in Fredrikshamn 1809, which was interpreted the worst defeat ever in Swedish history. Nowadays researchers argue whether the loss of Finland really was seen as a nationalistic trauma in the early 19th century. The article first summarises the background of the war and the most important war episodes and then discusses the apprehension of a Sweden in national chock after the burst of the state

Bioinformatic Identification of Genomic Alterations in Breast Cancer

Cancer is a disease characterized by the continuous accumulation of somatic cellular aberrations, whether in the DNA or epigenetic changes. During the last decade, many different techniques, including high resolution microarrays as well as exome- and whole genome sequencing, have been developed to comprehensively characterize these changes in cancer cells. In parallel with the development of laboratory techniques, a large variety of bioinformatic methods to analyze data from these have been developed. However, many of these concentrate on the analysis of data from only one laboratory technique, while it is becoming clear that advances in cancer research increasingly depend on integration of multiple different data types for the same tumors. Simultaneously, the recent explosive growth in sequencing data requires the development of new analythical methods. The aim of this thesis was to further characterize the genomic changes in breast cancer, with an emphasis on the development and application of bioinformatic methods to analyze and integrate data from different high throughput analysis techniques. In the first part of this work, the Gene Identification by Nonsense Inhibition method was applied to identify potential tumor suppressor genes in breast cancer. The integration of steady state gene expression, transcript stabilization and array comparative genomic hybridization data for six breast cancer cell lines led to the identification of a nonsense mutation in the RIC8A gene located at 11p15, a region deleted in ~15% of breast tumors. Taken together, our results suggest loss of RIC8A expression may be important in a subgroup of aggressive breast cancers. In study II, we developed a bioinformatic method for highly specific fusion gene identification from paired-end RNA-seq data. Application of the bioinformatic pipeline to data from four breast cancer cell lines led to the identification of 24 novel and three previously published fusion genes, with 95% specificity. In addition to showing that fusion genes are more prevalent in breast cancer than previously thought, several biological characteristics of fusion genes were identified. Most prominently, fusion genes were frequently associated with DNA copy number transitions, particularly high level amplifications, suggesting that most of them are not generated by balanced rearrangements. siRNA knock-down studies furthermore provided evidence for the functional importance of the VAPB-IKZF3 fusion gene in the BT-474 cell line. In the final study, we used aCGH to characterize the size distribution of the ERBB2 amplicon across 71 amplicon carrying tumors and 10 cell lines. To study the possible contribution to cancer of other coamplified genes in the amplicon, 23 genes amplified in 60% of tumors were selected for siRNA screening in two trastuzumab sensitive, two insensitive and one control cell line. In addition to single gene siRNA silencing experiments, five amplicon genes were knocked-down together with ERBB2 to identify synergistic effects. Our results suggest that cancer cells may be dependent on a number of genes in the ERBB2 amplicon besides the primary driver oncogene, a phenomenon termed non-oncogene addiction.Käytännössä kaikissa syövissä esiintyy mutaatioita, eli muutoksia syöpäsolujen DNA:ssa. Viimeksi kuluneen vuosikymmenen aikana on kehitetty useita eri laboratoriomenetelmiä, joilla syöpäkasvaimessa tapahtuneita geneettisiä muutoksia voidaan mitata suuressa laajuudessa, tuottaen kymmeniä- tai satojatuhansia mittaustuloksia yhdestä kasvaimesta. Näiden menetelmien tuottamien laajojen datamäärien analysoimiseen ja tulkitsemiseen on kehitetty lukuisia bioinformatiivisia menetelmiä, mutta etenkin eri mittausmenetelmien tuottaman tiedon yhtistämiseen ei kuitenkaan usein ole olemassa sopivia menetelmiä. Tämän tutkimuksen tavoitteena oli kehittää uusia bioinformatiivisia menetelmiä eri mittausmenetelmien tulosten analysoimiseen ja yhdistämiseen, sekä etenkin soveltaa näitä menetelmiä rintasyövän tutkimukseen. Syövässä mutatoituvat geenit jaetaan yleensä kahteen pääkategoriaan; onkogeeneihin ja kasvunrajoitegeeneihin. Onkogeeneihin osuvat mutaatiot lisäävät geenin tuottaman proteiinin aktiivisuutta, ja tämä lisääntynyt aktiivisuus edistää syövän syntyä. Toimiessaan normaalisti, kasvunrajoitegeenit vuorostaan suojaavat solua syöpään liittyviltä muutoksilta. Ensimmäisessä osatyössä tavoitteena oli löytää uusia kasvunrajoitegeenejä rintasyöpäsolulinjoista, hyödyntäen mikrosiruihin pohjautuvia mentelmiä. Osatyössä löydettiin mutaatio RIC8A geenistä yhdessä solulinjassa, mikä yhdistettynä tutkimuksen muihin tuloksiin tukee teoriaa, että RIC8A:n vähentynyt aktiivisuus voi olla tärkeää osajoukossa agressiivisia rintasyöpiä. Fuusiogeenit ovat onkogeenien alatyyppi, jossa mutaation seurauksena syntyy uusi proteiini, joka koostuu kahden eri geenin osista. Fuusiogeenit ovat keskeisiä tekijöitä esimerkiksi leukemioiden synnyssä, mutta viimeisen parin vuoden aikana näitä on löytynyt myös kiinteistä kasvaimista, kuten eturauhassyövästä. Osatyön kaksi tavoitteena oli kehittää laboratorio- ja bioinformatiivisiä menetelmiä fuusiogeenien löytämiseksi syöpäkasvaimista käyttäen toisen sukupolven RNA-sekvensointi menetelmiä. Lisäksi tavoitteena oli selvittää missä määrin fuusiogeenejä esiintyy rintasyövässä. Tutkimuksen tuloksena syntyi aikaisemmin julkaistuja lähestymistapoja huomattavasti tarkempi menetelmä fuusiogeenien löytämiseksi. Tätä hyödyntäen pystyimme myös m.m. osoittamaan, että fuusiogeenejä esiintyy rintasyövässä selvästi useammin kuin aikaisemmin oletettiin ja että jotkin näistä voivat toimia onkogeeneina. Viimeisessä osatyössä tutkimuksen kohteena oli rintasyövässä esiintyvä ERBB2 onkogeenin monistuma. Monistuman seurauksena soluun syntyy useita ylimääräisiä kopioita ERBB2 geenistä, johtaen sen liialliseen aktivoitumiseen. ERBB2:n oheessa monistuu yleensä myös muita sen lähellä sijaitsevia geenejä, mutta näiden mahdollista merkitystä rintasyövälle ei kuitenkaan tunneta kovin hyvin. Tutkimuksessa selvitettiin ensin mitkä geenit useimmiten monistuvat yhdessä ERBB2:n kanssa. Lisäksi pystyimme RNA-interferenssi menetelmällä osoittamaan, että syöpäsolut voivat olla riippuvaisia muista ERBB2 monistumassa sijaitsevista geeneistä kuin ERBB2:sta itsestään

Data integration from two microarray platforms identifies bi-allelic genetic inactivation of RIC8A in a breast cancer cell line

Background: Using array comparative genomic hybridization (aCGH), a large number of deleted genomic regions have been identified in human cancers. However, subsequent efforts to identify target genes selected for inactivation in these regions have often been challenging. Methods: We integrated here genome-wide copy number data with gene expression data and non-sense mediated mRNA decay rates in breast cancer cell lines to prioritize gene candidates that are likely to be tumour suppressor genes inactivated by bi-allelic genetic events. The candidates were sequenced to identify potential mutations. Results: This integrated genomic approach led to the identification of RIC8A at 11p15 as a putative candidate target gene for the genomic deletion in the ZR-75-1 breast cancer cell line. We identified a truncating mutation in this cell line, leading to loss of expression and rapid decay of the transcript. We screened 127 breast cancers for RIC8A mutations, but did not find any pathogenic mutations. No promoter hypermethylation in these tumours was detected either. However, analysis of gene expression data from breast tumours identified a small group of aggressive tumours that displayed low levels of RIC8A transcripts. qRT-PCR analysis of 38 breast tumours showed a strong association between low RIC8A expression and the presence of TP53 mutations (P = 0.006). Conclusion: We demonstrate a data integration strategy leading to the identification of RIC8A as a gene undergoing a classical double-hit genetic inactivation in a breast cancer cell line, as well as in vivo evidence of loss of RIC8A expression in a subgroup of aggressive TP53 mutant breast cancers.Peer reviewe

Array-based gene expression, CGH and tissue data defines a 12q24 gain in neuroblastic tumors with prognostic implication

Neuroblastoma has successfully served as a model system for the identification of neuroectoderm-derived oncogenes. However, in spite of various efforts, only a few clinically useful prognostic markers have been found. Here, we present a framework, which integrates DNA, RNA and tissue data to identify and prioritize genetic events that represent clinically relevant new therapeutic targets and prognostic biomarkers for neuroblastoma.Peer reviewe

A method for finding putative causes of gene expression variation

The majority of microarray studies evaluate gene ex- pression differences between various specimens or con- ditions. However, the causes of this variability often re- main unknown. Our aim is to identify underlying causes of these patterns, a process that would eventually enable a mechanistic understanding of the deregulation of gene expression in cancer. The procedure consists of three phases: pre-processing, data integration and statistical analysis. We have applied the strategy to identify genes that are overexpressed due to amplification in breast cancer. The data were obtained from 14 breast cancer cell lines, which were subjected to cDNA microarray based copy number and expression experiments. The re- sult of the analysis was a list that consisted of 92 genes. This set includes several genes that are known to be both overexpressed and amplified in breast cancer. The com- plete study was published in Journal of the Franklin In- stitute 2004, and in this paper we focus on the main issues of the study

Identification of fusion genes in breast cancer by paired-end RNA-sequencing

Background Until recently, chromosomal translocations and fusion genes have been an underappreciated class of mutations in solid tumors. Next-generation sequencing technologies provide an opportunity for systematic characterization of cancer cell transcriptomes, including the discovery of expressed fusion genes resulting from underlying genomic rearrangements. Results We applied paired-end RNA-seq to identify 24 novel and 3 previously known fusion genes in breast cancer cells. Supported by an improved bioinformatic approach, we had a 95% success rate of validating gene fusions initially detected by RNA-seq. Fusion partner genes were found to contribute promoters (5' UTR), coding sequences and 3' UTRs. Most fusion genes were associated with copy number transitions and were particularly common in high-level DNA amplifications. This suggests that fusion events may contribute to the selective advantage provided by DNA amplifications and deletions. Some of the fusion partner genes, such as GSDMB in the TATDN1-GSDMB fusion and IKZF3 in the VAPB-IKZF3 fusion, were only detected as a fusion transcript, indicating activation of a dormant gene by the fusion event. A number of fusion gene partners have either been previously observed in oncogenic gene fusions, mostly in leukemias, or otherwise reported to be oncogenic. RNA interference-mediated knock-down of the VAPB-IKZF3 fusion gene indicated that it may be necessary for cancer cell growth and survival. Conclusions In summary, using RNA-sequencing and improved bioinformatic stratification, we have discovered a number of novel fusion genes in breast cancer, and identified VAPB-IKZF3 as a potential fusion gene with importance for the growth and survival of breast cancer cells

Integrin trafficking regulated by Rab21 is necessary for cytokinesis

Adherent cells undergo remarkable changes in shape during cell division. However, the functional interplay between cell adhesion turnover and the mitotic machinery is poorly understood. The endo/exocytic trafficking of integrins is regulated by the small GTPase Rab21, which associates with several integrin alpha subunits. Here, we show that targeted trafficking of integrins to and from the cleavage furrow is required for successful cytokinesis, and that this is regulated by Rab21. Rab21 activity, integrin-Rab21 association, and integrin endocytosis are all necessary for normal cytokinesis, which becomes impaired when integrin-mediated adhesion at the cleavage furrow fails. We also describe a chromosomal deletion and loss of Rab21 gene expression in human cancer, which leads to the accumulation of multinucleate cells. Importantly, reintroduction of Rab21 rescued this phenotype. In conclusion, Rab21-regulated integrin trafficking is essential for normal cell division, and its defects may contribute to multinucleation and genomic instability, which are hallmarks of cancer.Adherent cells undergo remarkable changes in shape during cell division. However, the functional interplay between cell adhesion turnover and the mitotic machinery is poorly understood. The endo/exocytic trafficking of integrins is regulated by the small GTPase Rab21, which associates with several integrin alpha subunits. Here, we show that targeted trafficking of integrins to and from the cleavage furrow is required for successful cytokinesis, and that this is regulated by Rab21. Rab21 activity, integrin-Rab21 association, and integrin endocytosis are all necessary for normal cytokinesis, which becomes impaired when integrin-mediated adhesion at the cleavage furrow fails. We also describe a chromosomal deletion and loss of Rab21 gene expression in human cancer, which leads to the accumulation of multinucleate cells. Importantly, reintroduction of Rab21 rescued this phenotype. In conclusion, Rab21-regulated integrin trafficking is essential for normal cell division, and its defects may contribute to multinucleation and genomic instability, which are hallmarks of cancer.Adherent cells undergo remarkable changes in shape during cell division. However, the functional interplay between cell adhesion turnover and the mitotic machinery is poorly understood. The endo/exocytic trafficking of integrins is regulated by the small GTPase Rab21, which associates with several integrin alpha subunits. Here, we show that targeted trafficking of integrins to and from the cleavage furrow is required for successful cytokinesis, and that this is regulated by Rab21. Rab21 activity, integrin-Rab21 association, and integrin endocytosis are all necessary for normal cytokinesis, which becomes impaired when integrin-mediated adhesion at the cleavage furrow fails. We also describe a chromosomal deletion and loss of Rab21 gene expression in human cancer, which leads to the accumulation of multinucleate cells. Importantly, reintroduction of Rab21 rescued this phenotype. In conclusion, Rab21-regulated integrin trafficking is essential for normal cell division, and its defects may contribute to multinucleation and genomic instability, which are hallmarks of cancer.Peer reviewe

Integrative functional genomics analysis of sustained polyploidy phenotypes in breast cancer cells identifies an oncogenic profile for GINS2

Aneuploidy is among the most obvious differences between normal and cancer cells. However, mechanisms contributing to development and maintenance of aneuploid cell growth are diverse and incompletely understood. Functional genomics analyses have shown that aneuploidy in cancer cells is correlated with diffuse gene expression signatures and that aneuploidy can arise by a variety of mechanisms, including cytokinesis failures, DNA endoreplication and possibly through polyploid intermediate states. Here, we used a novel cell spot microarray technique to identify genes with a loss-of-function effect inducing polyploidy and/or allowing maintenance of polyploid cell growth of breast cancer cells. Integrative genomics profiling of candidate genes highlighted GINS2 as a potential oncogene frequently overexpressed in clinical breast cancers as well as in several other cancer types. Multivariate analysis indicated GINS2 to be an independent prognostic factor for breast cancer outcome (p = 0.001). Suppression of GINS2 expression effectively inhibited breast cancer cell growth and induced polyploidy. In addition, protein level detection of nuclear GINS2 accurately distinguished actively proliferating cancer cells suggesting potential use as an operational biomarker.Peer reviewe

Systematic drug screening reveals specific vulnerabilities and co-resistance patterns in endocrine-resistant breast cancer

Abstract Background The estrogen receptor (ER) inhibitor tamoxifen reduces breast cancer mortality by 31 % and has served as the standard treatment for ER-positive breast cancers for decades. However, 50 % of advanced ER-positive cancers display de novo resistance to tamoxifen, and acquired resistance evolves in 40 % of patients who initially respond. Mechanisms underlying resistance development remain poorly understood and new therapeutic opportunities are urgently needed. Here, we report the generation and characterization of seven tamoxifen-resistant breast cancer cell lines from four parental strains. Methods Using high throughput drug sensitivity and resistance testing (DSRT) with 279 approved and investigational oncology drugs, exome-sequencing and network analysis, we for the first time, systematically determine the drug response profiles specific to tamoxifen resistance. Results We discovered emerging vulnerabilities towards specific drugs, such as ERK1/2-, proteasome- and BCL-family inhibitors as the cells became tamoxifen-resistant. Co-resistance to other drugs such as the survivin inhibitor YM155 and the chemotherapeutic agent paclitaxel also occurred. Conclusion This study indicates that multiple molecular mechanisms dictate endocrine resistance, resulting in unexpected vulnerabilities to initially ineffective drugs, as well as in emerging co-resistances. Thus, combatting drug-resistant tumors will require patient-tailored strategies in order to identify new drug vulnerabilities, and to understand the associated co-resistance patterns