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- Brown, KM, et al.
(författare)
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cDNA Microarrays in Cancer Research.
- 2006
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Ingår i: Cancer: Principles and Practise of Oncology. - 0781774330 ; , s. 13-25
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Bokkapitel (övrigt vetenskapligt/konstnärligt)
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- Lindqvist, Breezy Malakkaran, 1978-
(författare)
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Biological signature of HER2-positive breast cancer
- 2013
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Human epidermal growth factor receptor 2 (HER2) overexpressing breast cancers (HER2+ breast cancer) are associated with an aggressive disease course. This thesis is focused on improving the understanding of the biological signature of HER2+ breast cancer.In Paper I, we identified a common deletion spanning the SLC25A43 gene which codes for a mitochondrial transport protein. Loss of heterozygosity in this gene was confirmed in an extended cohort of HER2+ breast cancer and in other types of cancers. Protein expression analysis of SLC25A43using immunohistochemistry (IHC) in HER2+ breast cancers showed that tumours with negative or low expression of SLC25A43 had lower S-phase fraction compared to tumours with medium or high expression, indicating its possible role in cell proliferation. Absence of mutations in this gene in HER2+ breast cancers led to Paper II where DNA methylation in the SLC25A43 gene was interrogated using Pyrosequencing. HER2+ breast cancer with no deletion in the SLC25A43 gene showed higher methylation in the CpG island (CGI), suggesting methylation in the CGI as an alternate mechanism for SLC25A43 gene inactivation. Methylation in the CGI and in the adjacent shores of the SLC25A43 gene was associated with negative oestrogen receptor status and positive lymph node status. In Paper III, genome-wide DNA methylation analysis of HER2+ breast cancer and normal breast tissue revealed hypermethylation in HER2+ breast cancer affecting particularly the homeobox gene family when compared to normal. We identified a total of 73 candidate genes showing differential methylation in HER2+ breast cancer and external validation of gene expression in a selected group of these genes revealed lowered mean expression in HER2+ breast cancer, warranting future clinical studies of these candidate genes. In Paper IV, we investigated expression and localisation of phosphorylated (p) Akt and FOXO3a and FOXG1 in HER2+ breast cancer using IHC. Cytoplasmic expression of pFOXO3a was associated with sentinel node metastasis while cytoplasmic expression of FOXG1 was correlated to negative progesterone receptor status. This indicates the biological and prognostic value of these proteins in HER2+ breast cancer.Thus, this thesis identified changes at the genetic, epigenetic and protein levels which add new information and improve our understanding of HER2+ breast cancer.
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| 7. |
- Martin de la Fuente, Laura, et al.
(författare)
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Copy number signatures for early diagnosis of high-grade serous ovarian carcinoma
- 2022
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- BackgroundThe detection of ovarian carcinoma-derived somatic mutations in cervical samples and uterine lavages in several studies since 2013, has brought hope for the development of new biomarkers for early detection. High-grade serous ovarian carcinoma (HGSC) is strongly dominated by copy number alterations (CNAs). These CNAs are the consequence of underlying mutational processes in HGSC. We interrogated CNAs from low coverage whole-genome sequencing (WGS) data in HGSC tumors, plasma, endometrial biopsies, and cervical samples to explore if copy number signatures can be used as a biomarker for early detection of HGSC.Methods A total of 204 samples were included from 18 patients with HGSC, four BRCA mutation carriers and seven benign controls. Estimations of ploidy and cellularity, and thus calculation of absolute copy number, were optimized through a combination of the ACE, Rascal, and ichorCNA bioinformatic tools. Mixture modelling was used to subgroup the six fundamental copy number features and non-negative matrix factorization was used to generate the signatures and cluster the samples.ResultsWe extracted six fundamental copy number features from 69 diagnostic and pre-diagnostic cervical samples from patients diagnosed with HGSC and generated six CN signatures. We found different distributions of features in benign samples compared to tumors and cervical samples from HGSC patients. We also observed different exposures to the six signatures in different patient groups.ConclusionsFurther understanding of the components and cell types contributing to each signature, and inclusion of more cervical samples into the approach, will hopefully identify a novel tumorigenic signature for early detection of HGSC in cervical samples.
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| 8. |
- Martin de la Fuente, Laura, et al.
(författare)
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Detection of Copy Number Aberration and Tumor Fraction in Archival Cervical Specimens from Ovarian Cancer Patients using Shallow Whole Genome Sequencing.
- 2021
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Ovarian cancer, often called the silent killer due to its diffuse symptoms at early stage, poor prognosis after treatments and high mortality, is also a heterogeneous disease consisting of different histological subtypes with potentially different origins. About 90% of all cases derive from epithelial cells and high-grade serous ovarian carcinoma (HGSOC) is the most common and aggressive form of epithelial ovarian cancer. Recent data indicate the p53 signature lesions and serous tubal intraepithelial carcinomas (STICs) in the fallopian tube are likely to be the common origin of HGSOC, and neoplastic cells containing TP53 somatic mutations could be detected in the cervical specimens collected from 20 months to 6 years before the diagnosis. Our ongoing project is to validate pre-diagnostic cervical specimens from HGSOC by using shallow whole genome sequencing (sWGS), which can detect copy number aberrations (CNAs) even in preserved tumor DNA samples with advantages of low cost, high multiplex and easy data handling. The sWGS will be performed on Illumina sequencing platforms and the sequencing data will be processed with BWA (alignment), SAMtools (cleanup), Picardtools (duplicate) and gatk (BQSR). QDNAseq will be used for the downstream copy number analysis, and GISTIC2.0 for identifying focal gain and loss region. It will be a challenge to estimate the tumor purity and ploidy on the scarce amount of ovarian tumorigenic precursors in the cervical specimens, and we will need to use a probabilistic graphical model without a priori information from normal fallopian tissue to estimate tumor fraction, corrected CNAs as well as tumorigenic copy number signatures. We hope the sWGS approach will allow us to study and detect the early onset of ovarian cancers on large population based cervical screening in a non-invasive and cost-efficient manner.
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- Veerla, Srinivas, et al.
(författare)
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Deciphering the normal-like molecular subtype of breast cancer
- 2023
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- The normal-like molecular subtype of breast cancer has not been well characterized and is currently not included in the clinically approved PAM50 molecular subtype classification. Tumors classified as normallike display high expression of basal epithelial genes and low expression of luminal epithelial genes, but also high expression of genes expressed by non-epithelial cell types including adipocytes [1]. The normal-like subtype has been suggested to represent tumors with low invasive tumor cell content, hence challenging its legitimacy as an intrinsic subtype. To clarify this issue we aimed to characterize the features of early breast cancers classified as normal-like using RNA sequencing and immunohistochemistry (IHC). Using a consecutive series of 14,000 early breast cancers from the population-based multi-center observational Sweden Cancerome Analysis Network – Breast (SCAN-B)and a recently published RNAseq-based single-sample molecular subtype predictor [2] the subtype distribution was: 39% luminal A, 25% luminal B, 12% HER2-enriched, 9% basal and 15% normal-like. The median tumor size did not differ significantly between the subtypes, while tumor cellularity assessedon H&E slides was lower among normal-like breast cancers (median 20%) compared to the other subtypes (median range 40-70%). Using a version of the classifier that excludes the normal-like subtype, i.e. akin to clinical PAM50 subtyping, 67.5% of the tumors classified as normal-like were reclassifiedas luminal A, with the remaining cases re-classified as either basal (17.5%) or HER2-enriched (14.9%). The distribution of hallmark features among normal-like tumors was 75% ER+, 67% PR+, 20% Ki67 high and 10% HER2 positive by IHC/CISH. IHC further revealed loss of E-cadherin in 30% of normal-like breast cancers, in line with 30% lobular histology. Significantly differentially expressed genes between lobular and non-lobular normal-like breast cancers included CDH1, PGC, CPB1, SERPINA6, TRH, MSLN, MMP1 and AKR1B15. The lobular normal-like breast cancers were enriched for the ER+/HER2- /node negative clinical subgroup (58%). Mutation calling using the SCAN-B MutationExplorer application [3] revealed enrichment of PIK3CA (46% vs. 18%), CDH1 (37% vs. 18%), TP53 (7% vs 0%) and ESR1 (6% vs. 0%) mutations in normal-like lobular vs. luminal lobular breast cancers. Finally, overall survival within the normal-like group was significantly different from all other subtypes and was intermediatebetween the luminal A and B groups (p<0.05 for pairwise comparisons). To conclude, the normal-like subgroup is enriched for lobular breast cancers and displays downregulation of genes involved in cell adhesion and hormone regulation. Normal-like breast cancers are primarily classified as luminal A tumorswith current clinical subtype classification algorithms, but the inferior survival and distinct features of these tumors do not preclude that this may be a true intrinsic subtype, thus warranting further investigation of the normal-like subtype.
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