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  • 1.
    Bersani, Cinzia
    et al.
    Karolinska Inst, Dept Oncol Pathol, Stockholm, Sweden..
    Sivars, Lars
    Karolinska Inst, Dept Oncol Pathol, Stockholm, Sweden..
    Haeggblom, Linnea
    Karolinska Inst, Dept Oncol Pathol, Stockholm, Sweden..
    DiLorenzo, Sebastian
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Mints, Michael
    Karolinska Inst, Dept Med, Stockholm, Sweden.;Umea Univ, Dept Surg & Perioperat Sci, Umea, Sweden..
    Ährlund-Richter, Andreas
    Karolinska Inst, Dept Oncol Pathol, Stockholm, Sweden..
    Tertipis, Nikolaos
    Karolinska Inst, Dept Oncol Pathol, Stockholm, Sweden..
    Munck-Wikland, Eva
    Karolinska Inst, Dept Clin Sci & Technol, Stockholm, Sweden.;Karolinska Univ Hosp, Dept Otorhinolaryngol Head & Neck Surg, Stockholm, Sweden..
    Näsman, Anders
    Karolinska Inst, Dept Oncol Pathol, Stockholm, Sweden..
    Ramqvist, Torbjörn
    Karolinska Inst, Dept Oncol Pathol, Stockholm, Sweden..
    Dalianis, Tina
    Karolinska Inst, Dept Oncol Pathol, Stockholm, Sweden..
    Targeted sequencing of tonsillar and base of tongue cancer and human papillomavirus positive unknown primary of the head and neck reveals prognostic effects of mutated FGFR32017In: Oncotarget, E-ISSN 1949-2553, Vol. 8, no 21, p. 35339-35350Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: Human papillomavirus positive (HPV+) tonsillar cancer (TSCC), base of tongue cancer (BOTSCC) and unknown primary cancer of the head and neck (HNCUP) have better outcome than corresponding HPV- cancers. To find predictive markers for response to treatment, and correlations and differences in mutated oncogenes and suppressor genes between HPV+ TSCC/BOTSSCC and HPV+ HNCUP and HPV- TSCC/BOTSCC targeted next-generation sequencing was performed of frequently mutated regions in 50 cancer related genes.

    PATIENTS AND METHODS: DNA from 348 TSCC/BOTSCC and 20 HNCUP from patients diagnosed 2000-2011, was sequenced by the Ion Proton sequencing platform using the Ion AmpliSeq Cancer Hotspot Panel v2 to identify frequently mutated regions in 50 cancer related genes. Ion Torrent Variant Caller software was used to call variants.

    RESULTS: 279 HPV+ TSCC/BOTSCC, 46 HPV- TSCC/BOTSCC and 19 HPV+ HNCUP samples qualified for further analysis. Mutations/tumor were fewer in HPV+ TSCC/BOTSCC and HNCUP, compared to HPV- tumors (0.92 vs. 1.32 vs. 1.68). Differences in mutation frequency of TP53 and PIK3CA were found between HPV+ TSCC/BOTSCC and HNCUP and HPV- TSCC/BOTSCC. In HPV+ TSCC/BOTSCC presence of FGFR3 mutations correlated to worse prognosis. Other correlations to survival within the groups were not disclosed.

    CONCLUSIONS: In HPV+ TSCC/BOTSCC mutation of PIK3CA was most frequently observed, while TP53 mutations dominated in HPV- TSCC/BOTSCC. In HPV+ TSCC/ BOTSCC and HNCUP, mutations/tumor were similar in frequency and fewer compared to that in HPV- TSCC/BOTSCC. Notably, FGFR3 mutations in HPV+ TSCC/BOTSCC indicated worse prognosis.

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  • 2.
    De Marchi, Tommaso
    et al.
    Lund Univ, Dept Clin Sci Lund, Div Oncol, Lund, Sweden..
    Pyl, Paul Theodor
    Natl Bioinformat Infrastruct Sweden, Dept Lab Med, Sci Life Lab, Lund, Sweden..
    Sjöström, Martin
    Lund Univ, Dept Clin Sci Lund, Div Oncol, Lund, Sweden.;Univ Calif San Francisco, Dept Radiat Oncol, San Francisco, CA USA..
    Reinsbach, Susanne Erika
    Chalmers Univ Technol, Dept Biol & Biol Engn, Sci Life Lab, Natl Bioinformat Infrastruct Sweden, Gothenburg, Sweden..
    DiLorenzo, Sebastian
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics.
    Nystedt, Björn
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Tran, Lena
    Lund Univ, Dept Clin Sci Lund, Div Oncol, Lund, Sweden..
    Pekar, Gyula
    Lund Univ, Skane Univ Hosp, Dept Clin Sci, Div Oncol & Pathol, Lund, Sweden..
    Wärnberg, Fredrik
    Univ Gothenburg, Inst Clin Sci, Dept Surg, Sahlgrenska Acad, Gothenburg, Sweden..
    Fredriksson, Irma
    Karolinska Inst, Dept Mol Med & Surg, Stockholm, Sweden.;Karolinska Univ Hosp, Dept Breast Endocrine Tumors & Sarcoma, Stockholm, Sweden..
    Malmström, Per
    Lund Univ, Dept Clin Sci Lund, Div Oncol, Lund, Sweden.;Skane Univ Hosp, Dept Haematol Oncol & Radiat Phys, Lund, Sweden..
    Fernö, Mårten
    Lund Univ, Dept Clin Sci Lund, Div Oncol, Lund, Sweden..
    Malmström, Lars
    Lund Univ, Fac Med, Dept Clin Sci Lund, Div Infect Med, Lund, Sweden..
    Malmström, Johan
    Lund Univ, Fac Med, Dept Clin Sci Lund, Div Infect Med, Lund, Sweden..
    Niméus, Emma
    Lund Univ, Dept Clin Sci Lund, Div Oncol, Lund, Sweden.;Skane Univ Hosp, Dept Surg, Lund, Sweden..
    Proteogenomics decodes the evolution of human ipsilateral breast cancer2023In: Communications Biology, E-ISSN 2399-3642, Vol. 6, no 1, article id 139Article in journal (Refereed)
    Abstract [en]

    Ipsilateral breast tumor recurrence (IBTR) is a clinically important event, where an isolated in-breast recurrence is a potentially curable event but associated with an increased risk of distant metastasis and breast cancer death. It remains unclear if IBTRs are associated with molecular changes that can be explored as a resource for precision medicine strategies. Here, we employed proteogenomics to analyze a cohort of 27 primary breast cancers and their matched IBTRs to define proteogenomic determinants of molecular tumor evolution. Our analyses revealed a relationship between hormonal receptors status and proliferation levels resulting in the gain of somatic mutations and copy number. This in turn re-programmed the transcriptome and proteome towards a highly replicating and genomically unstable IBTRs, possibly enhanced by APOBEC3B. In order to investigate the origins of IBTRs, a second analysis that included primaries with no recurrence pinpointed proliferation and immune infiltration as predictive of IBTR. In conclusion, our study shows that breast tumors evolve into different IBTRs depending on hormonal status and proliferation and that immune cell infiltration and Ki-67 are significantly elevated in primary tumors that develop IBTR. These results can serve as a starting point to explore markers to predict IBTR formation and stratify patients for adjuvant therapy.

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  • 3.
    Gunnarsson, Rebeqa
    et al.
    Lund Univ, Dept Lab Med, Div Clin Genet, Lund, Sweden.
    DiLorenzo, Sebastian
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Lundin-Ström, Kristina B.
    Lund Univ, Dept Lab Med, Div Clin Genet, Lund, Sweden.
    Olsson, Linda
    Lund Univ, Dept Lab Med, Div Clin Genet, Lund, Sweden;Dept Clin Genet & Pathol, Div Lab Med, Lund, Sweden.
    Biloglav, Andrea
    Lund Univ, Dept Lab Med, Div Clin Genet, Lund, Sweden.
    Lilljebjörn, Henrik
    Lund Univ, Dept Lab Med, Div Clin Genet, Lund, Sweden.
    Rissler, Marianne
    Lund Univ, Dept Lab Med, Div Clin Genet, Lund, Sweden.
    Wahlberg, Per
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Lundmark, Anders
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Molecular Medicine. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Castor, Anders
    Skane Univ Hosp, Dept Pediat, Lund, Sweden.
    Behrendtz, Mikael
    Linkoping Univ Hosp, Dept Pediat, Linkoping, Sweden.
    Fioretos, Thoas
    Lund Univ, Dept Lab Med, Div Clin Genet, Lund, Sweden;Dept Clin Genet & Pathol, Div Lab Med, Lund, Sweden.
    Paulsson, Kajsa
    Lund Univ, Dept Lab Med, Div Clin Genet, Lund, Sweden.
    Isaksson, Anders
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Johansson, Bertil
    Lund Univ, Dept Lab Med, Div Clin Genet, Lund, Sweden;Dept Clin Genet & Pathol, Div Lab Med, Lund, Sweden.
    Mutation, methylation, and gene expression profiles in dup(1q)-positive pediatric B-cell precursor acute lymphoblastic leukemia2018In: Leukemia, ISSN 0887-6924, E-ISSN 1476-5551, Vol. 32, no 10, p. 2117-2125Article in journal (Refereed)
    Abstract [en]

    High-throughput sequencing was applied to investigate the mutation/methylation patterns on 1q and gene expression profiles in pediatric B-cell precursor acute lymphoblastic leukemia (BCP ALL) with/without (w/wo) dup(1q). Sequencing of the breakpoint regions and all exons on 1q in seven dup(1q)-positive cases revealed non-synonymous somatic single nucleotide variants (SNVs) in BLZF1, FMN2, KCNT2, LCE1C, NES, and PARP1. Deep sequencing of these in a validation cohort w (n = 17)/wo (n = 94) dup(1q) revealed similar SNV frequencies in the two groups (47% vs. 35%; P = 0.42). Only 0.6% of the 36,259 CpGs on 1q were differentially methylated between cases w (n = 14)/wo (n = 13) dup(1q). RNA sequencing of high hyperdiploid (HeH) and t(1;19)(q23;p13)-positive cases w (n = 14)/wo (n = 52) dup(1q) identified 252 and 424 differentially expressed genes, respectively; only seven overlapped. Of the overexpressed genes in the HeH and t(1;19) groups, 23 and 31%, respectively, mapped to 1q; 60-80% of these encode nucleic acid/protein binding factors or proteins with catalytic activity. We conclude that the pathogenetically important consequence of dup(1q) in BCP ALL is a gene-dosage effect, with the deregulated genes differing between genetic subtypes, but involving similar molecular functions, biological processes, and protein classes.

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  • 4.
    Mayrhofer, Markus
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Cancer Pharmacology and Computational Medicine. Uppsala University, Science for Life Laboratory, SciLifeLab.
    DiLorenzo, Sebastian
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Isaksson, Anders
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Cancer Pharmacology and Computational Medicine. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Patchwork: allele-specific copy number analysis of whole-genome sequenced tumor tissue2013In: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 14, no 3, p. R24-Article in journal (Refereed)
    Abstract [en]

    Whole-genome sequencing of tumor tissue has the potential to provide comprehensive characterization of genomic alterations in tumor samples. We present Patchwork, a new bioinformatic tool for allele-specific copy number analysis using whole-genome sequencing data. Patchwork can be used to determine the copy number of homologous sequences throughout the genome, even in aneuploid samples with moderate sequence coverage and tumor cell content. No prior knowledge of average ploidy or tumor cell content is required. Patchwork is freely available as an R package, installable via R-Forge (http://patchwork.r-forge.r-project.org/).

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    fulltext
  • 5.
    Mesmar, Fahmi
    et al.
    Univ Houston, Dept Biol & Biochem, Ctr Nucl Receptors & Cell Signaling, Houston, TX USA;KTH Royal Inst Technol, Dept Prot Sci, Sci Life Lab, S-17121 Solna, Sweden;Indiana Univ, Sch Informat Comp & Engn, Dept Intelligent Syst Engn, Bloomington, IN USA.
    Dai, Bingbing
    Univ Texas MD Anderson Canc Ctr, Dept Surg Oncol, Houston, TX 77030 USA.
    Ibrahim, Ahmed
    KTH Royal Inst Technol, Dept Prot Sci, Sci Life Lab, S-17121 Solna, Sweden.
    Hases, Linnea
    KTH Royal Inst Technol, Dept Prot Sci, Sci Life Lab, S-17121 Solna, Sweden;Karolinska Inst, Dept Biosci & Nutr, Stockholm, Sweden.
    Jafferali, Mohammed Hakim
    KTH Royal Inst Technol, Dept Prot Sci, Sci Life Lab, S-17121 Solna, Sweden.
    Augustine, Jithesh Jose
    Univ Texas MD Anderson Canc Ctr, Dept Surg Oncol, Houston, TX 77030 USA.
    DiLorenzo, Sebastian
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Kang, Ya'an
    Univ Texas MD Anderson Canc Ctr, Dept Surg Oncol, Houston, TX 77030 USA.
    Zhao, Yang
    Univ Texas MD Anderson Canc Ctr, Dept Biointormat & Comp Sci, Houston, TX 77030 USA.
    Wang, Jing
    Univ Texas MD Anderson Canc Ctr, Dept Biointormat & Comp Sci, Houston, TX 77030 USA.
    Kim, Michael
    Univ Texas MD Anderson Canc Ctr, Dept Surg Oncol, Houston, TX 77030 USA.
    Lin, Chin-Yo
    Univ Houston, Dept Biol & Biochem, Ctr Nucl Receptors & Cell Signaling, Houston, TX USA.
    Berkenstam, Anders
    Axcentua Pharmaceut AB, Stockholm, Sweden;ABK, Stockholm, Sweden.
    Fleming, Jason
    Univ Texas MD Anderson Canc Ctr, Dept Surg Oncol, Houston, TX 77030 USA;H Lee Moffitt Canc Ctr & Res Inst, Dept Gastrointestinal Oncol, Tampa, FL USA.
    Williams, Cecilia
    KTH Royal Inst Technol, Dept Prot Sci, Sci Life Lab, S-17121 Solna, Sweden.
    Clinical candidate and genistein analogue AXP107-11 has chemoenhancing functions in pancreatic adenocarcinoma through G protein-coupled estrogen receptor signaling2019In: Cancer Medicine, E-ISSN 2045-7634, Vol. 8, no 18, p. 7705-7719Article in journal (Refereed)
    Abstract [en]

    Despite advances in cancer therapeutics, pancreatic cancer remains difficult to treat and often develops resistance to chemotherapies. We have evaluated a bioavailable genistein analogue, AXP107-11 which has completed phase Ib clinical trial, as an approach to sensitize tumor cells to chemotherapy. Using organotypic cultures of 14 patient-derived xenografts (PDX) of pancreatic ductal adenocarcinoma, we found that addition of AXP107-11 indeed sensitized 57% of cases to gemcitabine treatment. Results were validated using PDX models in vivo. Further, RNA-Seq from responsive and unresponsive tumors proposed a 41-gene treatment-predictive signature. Functional and molecular assays were performed in cell lines and demonstrated that the effect was synergistic. Transcriptome analysis indicated activation of G-protein-coupled estrogen receptor (GPER1) as the main underlying mechanism of action, which was corroborated using GPER1-selective agonists and antagonists. GPER1 expression in pancreatic tumors was indicative of survival, and our study proposes that activation of GPER1 may constitute a new avenue for pancreatic cancer therapeutics.

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  • 6.
    Paulsson, Johan O.
    et al.
    Karolinska Inst, Dept Oncol Pathol, S-17164 Solna, Sweden..
    Rafati, Nima
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    DiLorenzo, Sebastian
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics.
    Chen, Yi
    Karolinska Inst, Dept Oncol Pathol, S-17164 Solna, Sweden..
    Haglund, Felix
    Karolinska Inst, Dept Oncol Pathol, S-17164 Solna, Sweden.;Karolinska Univ Hosp, Dept Pathol & Cytol, S-17176 Stockholm, Sweden..
    Zedenius, Jan
    Karolinska Univ Hosp, Dept Breast Endocrine Tumors & Sarcoma, S-17176 Stockholm, Sweden.;Karolinska Inst, Dept Mol Med & Surg, S-17176 Stockholm, Sweden..
    Juhlin, C. Christofer
    Karolinska Inst, Dept Oncol Pathol, S-17164 Solna, Sweden.;Karolinska Univ Hosp, Dept Pathol & Cytol, S-17176 Stockholm, Sweden..
    Whole-genome Sequencing of Follicular Thyroid Carcinomas Reveal Recurrent Mutations in MicroRNA Processing Subunit DGCR82021In: Journal of Clinical Endocrinology and Metabolism, ISSN 0021-972X, E-ISSN 1945-7197, Vol. 106, no 11, p. 3265-3282Article in journal (Refereed)
    Abstract [en]

    Background: The genomic and transcriptomic landscape of widely invasive follicular thyroid carcinomas (wiFTCs) and Hurthle cell carcinoma (HCC) are poorly characterized, and subsets of these tumors lack information on genetic driver events.

    Objective: The aim of this study was to bridge this gap.

    Methods: We performed whole-genome and RNA sequencing and subsequent bioinformatic analyses of 11 wiFTCs and 2 HCCs with a particularly poor prognosis, and matched normal tissue.

    Results: All wiFTCs exhibited one or several mutations in established thyroid cancer genes, including TERT (n=4), NRAS (n=3), HRAS, KRAS, AKT, PTEN, PIK3CA, MUTYH, TSHR, and MEN1 (n=1 each). MutSig2CV analysis revealed recurrent somatic mutations in FAM72D (n=3, in 2 wiFTCs and in a single HCC), TP53 (n=3, in 2 wiFTCs and a single HCC), and EIF1AX (n=3), with DGCR8 (n=2) as borderline significant. The DGCR8 mutations were recurrent p.E518K missense alterations, known to cause familial multinodular goiter via disruption of microRNA (miRNA) processing. Expression analyses showed reduced DGCR8 messenger RNA expression in FTCs in general, and the 2 DGCR8 mutants displayed a distinct miRNA profile compared to DGCR8 wild-types. Copy number analyses revealed recurrent gains on chromosomes 4, 6, and 10, and fusion gene analyses revealed 27 high-quality events. Both HCCs displayed hyperploidy, which was fairly unusual in the FTC cohort. Based on the transcriptome data, tumors amassed in 2 principal clusters.

    Conclusion: We describe the genomic and transcriptomic landscape in wiFTCs and HCCs and identify novel recurrent mutations and copy number alterations with possible driver properties and lay the foundation for future studies.

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