| 1. |
- Forslund, Ola, et al.
(författare)
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A novel human in vitro papillomavirus type 16 positive tonsil cancer cell line with high sensitivity to radiation and cisplatin
- 2019
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Ingår i: BMC Cancer. - : Springer Science and Business Media LLC. - 1471-2407. ; 19:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: Human papillomavirus (HPV) is an established risk factor for oropharyngeal squamous cell carcinoma (OSCC). The aim was to establish cell lines from HPV-positive tonsil carcinomas to be used for treatment development. Methods: Fresh samples from 23 HPV-positive tonsil carcinomas were cultivated in vitro. The established cell line was analyzed for viral characteristics, cell karyotype, TP53 status, and growth capabilities in nude mice. In vitro studies of sensitivities to radiation, cisplatin and cetuximab were performed. Results: After 19 months (eight passages), one cell line, LU-HNSCC-26, was established in vitro and also grew as xenografts. The tumor was from a 48 year old non-smoking man with non-keratinizing, p16 positive tonsil OSCC, stage T2N0M0 with HPV16. It contained 19.5 (CV% 3.7) HPV16 copies/cell (passage 8). The complete HPV16 genome sequence was obtained. Episomal HPV16 was present with an E2/E7 ratio of 1.1 (CV% 2.6). In addition, HPV16 mRNA specific for the intact E2 gene was detected. The viral expression manifested 1.0 (CV% 0.1) E7 mRNA copies per HPV16 genome. The karyotype was determined and the cell line demonstrated wild type TP53. The ID50 for radiation was 0.90 Gy and the IC50 for cisplatin was 0.99 μmol/L. The cell line was inhibited to a maximum of 18% by cetuximab. Conclusions: We established an in vitro tonsil carcinoma cell line containing episomal HPV16. This is an important step towards efficient treatment development.
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| 2. |
- Ku, Anson, et al.
(författare)
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A urinary extracellular vesicle microRNA biomarker discovery pipeline; from automated extracellular vesicle enrichment by acoustic trapping to microRNA sequencing
- 2019
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 14:5
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Tidskriftsartikel (refereegranskat)abstract
- Development of a robust automated platform for enrichment of extracellular vesicles from low sample volume that matches the needs for next-generation sequencing could remove major hurdles for genomic biomarker discovery. Here, we document a protocol for urinary EVs enrichment by utilizing an automated microfluidic system, termed acoustic trap, followed by next-generation sequencing of microRNAs (miRNAs) for biomarker discovery. Specifically, we compared the sequencing output from two small RNA library preparations, NEXTFlex and CATS, using only 130 pg of input total RNA. The samples prepared using NEXTflex was found to contain larger number of unique miRNAs that was the predominant RNA species whereas rRNA was the dominant RNA species in CATS prepared samples. A strong correlation was found between the miRNA expressions of the acoustic trap technical replicate in the NEXTFlex prepared samples, as well as between the acoustic trap and ultracentrifugation enrichment methods. Together, these results demonstrate a robust and automated strategy for biomarker discovery from small volumes of urine.
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| 3. |
- Ravi, Naveen
(författare)
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Genetic Characterization and Identification of Novel Treatment Targets in Anaplastic Thyroid Carcinoma
- 2019
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Anaplastic thyroid cancer (ATC) is a rare and highly aggressive thyroid malignancy, usually resistant to conventional therapeutic strategies. The prognosis of ATC is extremely poor with a median survival rate of 6 months. Current treatment therapy includes surgical resection in combination with external radiotherapy and chemotherapy. The underlying mechanisms involved in ATC tumorigenesis is understudied. In this thesis, we have focused on genomic characterization of ATC that could possibly lead to identification of novel treatment strategies in ATC.Article I & III highlights the genomic heterogeneity in ATC cell lines and primary cases. ATC displayed massive aneuploidy with frequent variations in copy number. Additionally, we found frequent mutations in TP53, TERT, BRAF and RAS family genes. Furthermore, the most frequent mutational signature in ATC cell lines and primary cases was increased activity of the cytidine deaminase apolipoprotein B editing complex (APOBEC). Moreover, we found interstitial deletions in NEGR1, resulting in aberrant splicing, which could possibly be a driver event in ATC. Furthermore, we detected amplifications in CCNE1, CDK6 and TWIST1; these patients could be treated with targeted therapy. In Article II, we investigated the tumor initiation, progression and clonal evolution of papillary thyroid cancer in a conditional mouse model. Stochastic activation of mutant Braf leads to development of multifocal microtumors that are oligoclonal in nature. Furthermore, we identified additional mutations at low frequencies, highlighting the presence of subclones that might be associated with tumor progression. In article IV, we studied the genome-wide methylation profile in primary ATC cases. Global hypomethylation was common in ATC, while hypermethylation was noticed in promoters and CpG islands. Furthermore, aberrant DNA methylation in MTOR and NOTCH1 genes was associated with increased expression. Alternatively, hypomethylation in thyroid related genes including TSHR and SLC26A7 was associated with decreased expression in gene body regions. Moreover, we found that processes related to the cell cycle were upregulated, while TP53-regulated genes and thyroid-related pathways were downregulated in ATC.Taken together, this thesis provides a better understanding of the complex processes involved in ATC tumorigenesis. Furthermore, a substantial proportion of ATC patients could be suitable for personalized treatment, including CDK and TWIST1 inhibition therapy.
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| 4. |
- Ravi, Naveen, et al.
(författare)
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Identification of targetable lesions in anaplastic thyroid cancer by genome profiling
- 2019
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Ingår i: Cancers. - : MDPI AG. - 2072-6694. ; 11:3
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Tidskriftsartikel (refereegranskat)abstract
- Anaplastic thyroid cancer (ATC) is a rare and extremely malignant tumor with no available cure. The genetic landscape of this malignancy has not yet been fully explored. In this study, we performed whole exome sequencing and the RNA-sequencing of fourteen cases of ATC to delineate copy number changes, fusion gene events, and somatic mutations. A high frequency of genomic amplifications was seen, including 29% of cases having amplification of CCNE1 and 9% of CDK6; these events may be targetable by cyclin dependent kinase (CDK) inhibition. Furthermore, 9% harbored amplification of TWIST1, which is also a potentially targetable lesion. A total of 21 fusion genes in five cases were seen, none of which were recurrent. Frequent mutations included TP53 (55%), the TERT promoter (36%), and ATM (27%). Analyses of mutational signatures showed an involvement of processes that are associated with normal aging, defective DNA mismatch repair, activation induced cytidine deaminase (AID)/apolipoprotein B editing complex (APOBEC) activity, failure of DNA double-strand break repair, and tobacco exposure. Taken together, our results shed new light on the tumorigenesis of ATC and show that a relatively large proportion (36%) of ATCs harbor genetic events that make them candidates for novel therapeutic approaches. When considering that ATC today has a mortality rate of close to 100%, this is highly relevant from a clinical perspective.
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| 5. |
- Yang, Minjun, et al.
(författare)
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Proteogenomics and Hi-C reveal transcriptional dysregulation in high hyperdiploid childhood acute lymphoblastic leukemia
- 2019
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- Hyperdiploidy, i.e. gain of whole chromosomes, is one of the most common genetic features of childhood acute lymphoblastic leukemia (ALL), but its pathogenetic impact is poorly understood. Here, we report a proteogenomic analysis on matched datasets from genomic profiling, RNA-sequencing, and mass spectrometry-based analysis of >8,000 genes and proteins as well as Hi-C of primary patient samples from hyperdiploid and ETV6/RUNX1-positive pediatric ALL. We show that CTCF and cohesin, which are master regulators of chromatin architecture, display low expression in hyperdiploid ALL. In line with this, a general genome-wide dysregulation of gene expression in relation to topologically associating domain (TAD) borders were seen in the hyperdiploid group. Furthermore, Hi-C of a limited number of hyperdiploid childhood ALL cases revealed that 2/4 cases displayed a clear loss of TAD boundary strength and 3/4 showed reduced insulation at TAD borders, with putative leukemogenic effects.
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