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- Almstedt, Elin, 1988-
(författare)
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New targeted therapies for malignant neural tumors : From systematic discovery to zebrafish models
- 2020
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Cancers in the neural system presents a major health challenge. The most aggressive brain tumor in adults, glioblastoma, has a median survival of 15 months and few therapeutic options. High-risk neuroblastoma, a childhood tumor originating in the sympathetic nervous system, has a 5-year survival under 50%, despite extensive therapy. Molecular characterization of these tumors has had some, but so far limited, clinical impact. In neuroblastoma, patients with ALK mutated tumors can benefit from treatment with ALK inhibitors. In glioblastoma, molecular subgroups have not yet revealed any subgroup-specific gene dependencies due to tumor heterogeneity and plasticity. In this thesis, we identify novel treatment candidates for neuroblastoma and glioblastoma. In paper I, we discover novel drug targets for high-risk neuroblastoma by integrating patient data, large-scale pharmacogenomic profiles, and drug-protein interaction maps. Using a novel algorithm, TargetTranslator, we identify more than 80 targets for this patient group. Activation of cannabinoid receptor 2 (CNR2) or inhibition of mitogen-activated protein kinase 8 (MAPK8) reduces tumor growth in zebrafish and mice models of neuroblastoma, establishing TargetTranslator as a useful tool for target discovery in cancer. In paper II, we screen approximately 1500 compounds across 100 molecularly characterized cell lines from patients to uncover heterogeneous responses to drugs in glioblastoma. We identify several connections between pathway activities and drug response. Sensitivity to proteasome inhibition is linked to oxidative stress response and p53 activity in cells, and can be predicted using a gene signature. We also discover sigma receptors as novel drug targets for glioblastoma and find a synergistic vulnerability in targeting cholesterol homeostasis.In paper III, we systematically explore novel targets for glioblastoma using an siRNA screen. Downregulation of ZBTB16 decreases cell cycle-related proteins and transcripts in patient-derived glioblastoma cells. Using a zebrafish assay, we find that ZBTB16 promotes glioblastoma invasion in vivo. In paper IV, we characterized the growth of seven patient-derived glioblastoma cell lines in orthotopic zebrafish xenografts. Using automated longitudinal imaging, we find that tumor engraftment strongly correlates with tumor initiation capacity in mice xenografts and that the heterogeneous response to proteasome inhibitors is maintained in vivo. In summary, this thesis identifies novel targets for glioblastoma and neuroblastoma using systematic approaches. Treatment candidates are evaluated in novel zebrafish xenograft models that are developed for high-throughput glioblastoma and neuroblastoma drug evaluation. Together, this thesis provides promising evidence of new therapeutic options for malignant neural tumors.
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| 3. |
- Backman, Samuel, 1994-
(författare)
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Molecular studies of endocrine tumors : Insights from genetics and epigenetics
- 2020
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Endocrine tumors may be benign or malignant and may occur in any of the hormone producing tissues. They share several biological characteristics, including a low mutation-burden, and may co-occur in several hereditary tumor syndromes. The aim of this thesis was to identify genetic and epigenetic aberrations in endocrine tumors.In paper I we performed a comprehensive DNA methylation analysis of 39 pheochromocytomas/paragangliomas as well as 4 normal adrenal medullae on the HumanMethylation27 BeadChip array. We validated two previously described clusters based on DNA methylation with distinct genetic associations.In Paper II we performed a transcriptomic analysis of 15 aldosterone producing adenomas. CTNNB1-mutated tumors were found to form a distinct subgroup based on gene expression and to share gene expression similarities with non-aldosterone producing adrenocortical tumors with CTNNB1 mutations, including overexpression of AFF3 and ISM1.In paper III we used whole genome sequencing to identify germline genetic variants in 14 patients with Multiple Endocrine Neoplasia type 1 previously found to be wildtype for the MEN1 gene on routine clinical testing. Three patients were found to carry previously undetected MEN1 mutations. Two patients were confirmed to have phenocopies caused by variants affecting CASR or CDC73. In total 9/14 patients were not found to have a disease-causing germline variant, suggesting that the syndrome may in some cases be due to chance co-occurrence of several sporadic tumors.In paper IV RNA-Seq and whole genome sequencing of a cohort of SI-NETs selected on the basis of unusually short or long survival was performed in order to identify disease causing genes and potential prognostic factors. We confirmed known genetic aberrations and found rare variants in known cancer driver genes. Based on gene expression two clusters that differ in prognosis were detected. Moreover, through integration of copy number variation data and gene expression, we identied novel potential disease causing genes.
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| 4. |
- Hayden, Jane M.
(författare)
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The effect of intra-abdominal local anaesthetics following major gynaecological surgery. Clinical and experimental studies
- 2020
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Background: Local anaesthetics (LA), in addition to inhibition of pain signalling, also have anti-inflammatory properties. In vitro studies have demonstrated anti-proliferative and cytotoxic effect of LAs on cancer cells when administered in therapeutic concentrations. Intraperitoneal administrated LA is shown to reduce pain, improve surgical recovery and to blunt the postsurgical inflammatory response. Retrospective studies have indicated beneficial oncological outcome of regional anaesthesia on cancer recurrence when used in cancer surgery. Abdominal hysterectomy causes moderate to severe pain, and assessing new tools for pain treatment is crucial. The postoperative period of extensive surgery for advanced ovarian cancer is associated with high morbidity. When the patients have recovered from cancer surgery, chemotherapy can be initiated. New therapeutic approaches to enhanced recovery with reduced postoperative pain and inflammation is of great interest. Methods and aim: The thesis aimed to evaluate the efficacy of intra-abdominal local anaesthetics on pain, inflammatory response, serum concentration of LA and patient recovery after gynaecological surgery (study I, II and III). The aim of study IV was to determine the effects of LA on ovarian cancer cells in vitro. The clinical studies were prospective, double blind, randomized and placebo-controlled. In study I, women scheduled for abdominal hysterectomy, were randomised to local infiltration analgesia (Group LIA) or placebo (group C). Rescue analgesic consumption and opioid related side effects were analysed. In study II and III, women undergoing cytoreductive surgery for advanced ovarian cancer were randomised to receive either intraperitoneal ropivacaine (Group IPLA) or saline (Group Control) peroperatively. Inflammatory markers in serum, LA concentrations (study II), and objective measures of patient comfort, postoperative complications, pain, home readiness and time to initiation of chemotherapy (study III) were analysed. In study IV proliferation and migration in two ovarian cancer cell lines, exposed to LA in concentrations corresponding to doses used in study II and III, were analysed. Analysis of cancer stem cells (CSC) phenotypes were performed. Results: The median supplemental requirements of morphine during 0–24 hours after abdominal hysterectomy was significantly lower in group LIA compared to group C (18 mg vs. 27 mg, p = 0.028) and the median time to first analgesic injection was significantly longer in group LIA (40 min vs. 20 min, p = 0.005) (Study I). Perioperative intraperitoneal LA resulted in significantly decreased serum cortisol levels. Serum concentrations of ropivacaine were well below toxic concentrations (study II). Time to initiation of chemotherapy was significantly shorter in group IPLA (Median 21, IQR 19-29 vs. 29 days, IQR 21-40, p = 0.021). No differences in standardised recovery endpoints were found between the groups (Study III) . The laboratory study showed a significantly reduced cell number and an inhibited cell migration. Cell size were significantly increased and CSC phenotype analysis showed a reduction in all cells by up to 50% (Study IV). Discussion: Local infiltration analgesia results in a significantly lower rescue morphine consumption following abdominal hysterectomy. Intraperitoneal local anestetics can be administered in ovarian cancer cytoreductive surgery safely, without achieving toxic doses. Although IPLA do not provide further anti-inflammatory effects, the stress response is briefly blunted and there might be positive effects such as earlier start of chemotherapy. LA reduce the ability of cancer cells to metastasise. Intra-abdominal LA offers a potential to have beneficial effects on pain, recovery and circulating tumour cells after gynaecological surgery.
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| 5. |
- Rosenblatt, Robert, 1982-
(författare)
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Neoadjuvant chemotherapy in muscle-invasive urinary bladder cancer : studies on treatment response, tumor draining lymph nodes and blood transfusion
- 2020
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Muscle-invasive urinary bladder cancer is a deadly disease. Mortality rates remained unchanged for decades despite radical surgery.After several randomized trials, we today know that cisplatin based chemotherapy given prior to cystectomy, improves survival for every tenth patient. Markers that predict responsiveness to chemotherapy would spare unnecessary treatment to the majority of patients. In the search for signs of chemosensitivity, we performed a retrospective analysis of the Nordic cystectomy trials 1 & 2: Chemo treated patients had an almost doubled increase in tumor downstaging compared to the controls. More importantly, this group presented with a reduced absolute risk of death of more than 30% compared to the rest of the patients. These results were presented in paper I.Many cancers spread through the lymphatic system. Usually, there is at least one tumor draining lymph node, referred to as the sentinel node. If this node is free of metastases, there is no lymphatic spread of the disease, and consequently, no use of excavating all neighboring lymph nodes.Sentinel node detection, is an established method in breast cancer, penile cancer and malignant melanoma. Based on the same principles, members of our group developed a similar detection technique in bladder cancer. Unfortunately, sensitivity and specificity were too low to rely on this method as a diagnostic tool for lymphatic spread. Instead, it turned out in recent years that sentinel nodes in muscle invasive bladder cancer are valuable for translational research-lines - mainly in tumor immunology. As for example, sentinel nodes contain tumor specific T cells that are useful in adoptive immunotherapy.In paper II, we set out to test whether sentinel node detection was feasible after chemotherapy and/or tumor downstaging. In a prospective cohort of patients, we saw no difference in detection rates between the groups. Thus, we concluded, neither chemotherapy nor downstaging appeared to hamper the identification of sentinel nodes.The concept was expanded in paper III. After recruiting more patients to the cohort mentioned above, the average numbers of sentinel nodes in different categories of patients were compared. We saw a pattern of decreased number of sentinel nodes in those with locally advanced tumors. It seemed that the number of sentinel nodes had prognostic implications.In the last study, published in paper IV, we wanted to widen our knowledge on the clinical effects of blood transfusion. Mounting data suggests that perioperative blood products have a negative impact on long term survival after cancer surgery. How much allogenic blood was given during the chemotherapy prior to surgery ? It turned out that one third of the bladder cancer patients received blood, and these patients demonstrated a significantly worse overall survival.Neoadjuvant chemotherapy has added a new beneficial dimension to the treatment of muscle invasive bladder cancer. In these four studies, we addressed the effects of chemotherapy on pathoanatomical outcomes, on tumor lymphatics and further; we are suggesting consequences of neoadjuvant chemotherapy in conjunction with blood transfusion. It appears that the immune system is involved in all aspects investigated above. Most likely, an improved scientific understanding of the immune system will be crucial for future bladder cancer treatment options.
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| 7. |
- Lindström, Jonathan
(författare)
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Modelling the evolution of treatment-induced resistance in Ph+ leukaemias
- 2020
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Targeted therapies are a mainstay of modern cancer treatments. Rather than harming rapidly dividing cells in general, targeted therapies work by directly interfering with oncogenic molecular pathways present in a tumour. Consequently, a targeted therapy typically has less severe side effects. However, specificity comes at a price as comparatively small changes to the target can render the treatment ineffective. Much like the natural selection among plants and animals, individual cancer cells compete with one another for space and resources. Hence, if a single cancer cell acquires a resistance adaptation, the forces of evolution can turn that advantage in a single cell into an untreatable resistant cancer.This thesis is principally concerned with chronic myeloid leukaemia (CML), characterized by a chromosomal translocation called the Philadelphia chromosome which creates the constitutively active tyrosine kinase Bcr-Abl1. The discovery of tyrosine kinase inhibitors (TKIs) targeting Bcr-Abl1 greatly improved treatment outcomes. Eventually however, resistance emerges. An important mechanism in CML is mutations in the kinase domain of Bcr-Abl1 that affect how well the drugs bind. A number of drugs have been developed that target the mutated kinase to varying degrees, but it is still desirable to prevent drug resistance from occurring in the first place, as the accumulation of multiple mutations is almost certain to create untreatable resistance.The fitness effects of a drug resistance adaptation depend on the drug treatment, so it may be possible to alter the fitness landscape by modifying the treatment. This work examines different approaches, mainly in CML, to delay or prevent the onset of resistance through modifying the treatment protocol.Periodically switching between different TKIs, i.e. drug rotations, was shown through modelling to increase the expected time to resistance and seems to have some protective benefits in vitro. Also apparently promising were drug combinations involving a novel inhibitor asciminib, currently in phase III trials, which can reduce overall drug burden while also being seemingly effective against known resistance mutations. Finally, a model of the interaction between resistance mutations and less potent alternate resistance mechanisms revealed how a drug holiday may have resensitizing, or even beneficial effects.
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| 8. |
- Semenas, Julius, 1987-
(författare)
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Targeted therapeutic strategies for prostate cancer treatment using novel lipid kinase inhibitors in combination with current drugs
- 2020
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Prostate cancer (PCa) is one of the most common cancer types and the fifth cancer-related cause of death among Western world men. The sex steroid hormone, androgen and androgen receptor (AR) play important roles in PCa progression. Herewith, androgen deprivation therapy (ADT) is used as a regimen for PCa, but inevitably leads to development of castration-resistant PCa (CRPC) and distant metastasis. No effective treatment for metastatic PCa currently exists. Furthermore, it remains poorly understood whether and how the steroid hormone signaling in cooperation with multiple pathways that control proliferation, survival and invasion of cancer cells may contribute to metastatic dissemination and growth.The aims of my PhD thesis focused on: (i) studying the clinical importance of estrogen- and androgen-related signaling pathways in promoting homing and metastatic growth of PCa cells in bone, (ii) gaining deeper understanding of the underlying mechanisms that facilitate PCa metastasis and treatment resistance, with focus on phosphatidylinositol-4-phosphate 5-kinase type-1 alpha (PIP5K1α), estrogen- and androgen receptor signaling, (iii) testing and characterizing the therapeutic potential of PIP5K1α inhibitor in combination with anti-estrogen or anti-androgen agents to improve treatment and overcome treatment resistance in CRPC.In my thesis work we have shown that key biomarker genes exhibited unique expression profiles and signatures in PCa subtypes within large patient cohorts. Alterations in androgen- and estrogen-related biomarkers and PIP5K1α/Akt pathways were associated with poor patient outcome. We further discovered that CRPC cells and cancer stem-like cells utilized estrogen-associated factors including aromatase and estrogen receptor alpha (ERα), as well as cyclin A1, a key cell cycle regulator, to gain proliferative advantage, and to survive and metastasize to distant organs.We found that the interaction between PIP5K1α and AR splice variant AR-V7 contributed to enzalutamide resistance. In series of in vivo treatment experiments using tumor xenograft mice, we demonstrated that ISA-2011B alone or in combination with enzalutamide had great therapeutic potential to suppress growth of tumors that had elevated levels of PI3K/Akt and AR-V7, and that were resistant to enzalutamide monotherapy.We further showed that combination treatment using tamoxifen together with ISA-2011B selectively blocked elevated ERα/cyclin D1 and PIP5K1α/Akt, leading to tumor regression and had superior inhibitory effect over monotherapy in xenograft mice.My studies therefore suggest that steroid hormone receptors, PIP5K1α signaling cascade and multiple cellular pathways cooperatively promote PCa progression. Taken together, the reported findings are the first to suggest a new therapeutic potential to inhibit or utilize the mechanisms related to ERα and PIP5K1α/Akt network, and provide a new therapeutic strategy to treat castration-resistant ER-positive subtype of tumors with metastatic potential.
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| 9. |
- Saba, Karim
(författare)
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Genomic and Transcriptomic Analyses of Osteogenic Tumours of Bone
- 2020
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Primary tumours of bone are heterogenous and infrequent neoplasms. Distinguishing between benign, intermediate and malignant entities can in some instances pose a clinical challenge. For some tumour types, there is still much to be learned about the genetic mechanisms that give rise to and drive these tumours forward. With the hope of improving diagnostic accuracy and treatment outcomes on the longer term, this thesis will deal with the genetic mutational mechanisms that characterise the primary osteogenic neoplasms osteoblastoma and osteosarcoma.In Article I, we show that a subgroup of non-FOS-rearranged, preferentially epithelioid osteoblastomas harbour homozygous loss of the NF2 gene. Additionally, we find a lower proportion of FOS-rearranged cases than previously reported and a high normal cell content.In Article II, we genetically characterise a rare chondroblastoma-like osteosarcoma/malignant phosphaturic mesenchymal tumour of bone. We detect a potentially targetable FN1-FGFR1 gene fusion and homozygous loss of the CDKN2A and DMD genes.In Article III, an RNA-sequencing screen of conventional osteosarcomas reveals that NTRK fusions are rare and most likely non-functional events.In Article IV, we demonstrate, for the first time, the existence of a recurrent gain-of-function mechanism involving the promoter region of the TP53 tumour suppressor gene in a subset of conventional osteosarcoma. We show that structural variants abrogate TP53 expression but also relocate its promoter region. By responding to ongoing DNA damage, it in turn leads to upregulation of known or putative oncogenes erroneously translocated into its vicinity.In Article V, we subdivide 12q-amplified osteosarcomas into four distinct groups and show that recurrent promoter swapping events involving the FRS2 and PLEKHA5 regulatory regions occur in many high-grade and dedifferentiated osteosarcomas with CDK4 and MDM2 amplification.In conclusion, this thesis will highlight the role chromosome remodelling plays in the development of primary osteogenic tumours of bone.
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| 10. |
- Kvarnbrink, Samuel, 1981-
(författare)
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LRIG1 in lung cancer : prognostic effects and mechanistic studies
- 2020
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Lung cancer is the leading cause of cancer-related death worldwide as well as in Sweden. Non-small cell lung cancer (NSCLC) is the predominant form, which is largely subdivided into adenocarcinomas and squamous cell carcinomas. A small minority of NSCLC cases that present with localized small tumors are curable with surgery alone, but adjuvant chemotherapy is recommended in most cases that are treated with surgery, even though it only increases the chance of cure by less than 5%. Therefore, additional biomarkers are needed to guide the clinical decision making in early-stage disease.The leucine-rich repeats and immunoglobulin-like (LRIG) family of proteins consists of three paralogous transmembrane proteins that are involved in the regulation of growth factor signaling. Of these proteins, LRIG1 is the most studied and it interacts with a wide variety of growth factor receptors and related proteins, including the epidermal growth factor (EGFR) and several others. High levels of LRIG1 have been associated with better survival in a multitude of malignant diseases, including (but not limited to) breast cancer, bladder cancer, cervical cancer, glioma and melanoma. The aim of this thesis was to investigate whether LRIG1 was a prognostic factor in NSCLC as well, and to further characterize the biological role of LRIG proteins in this disease.To investigate the prognostic impact of LRIG proteins in NSCLC, we stained a tissue microarray (TMA) containing tumor samples from 347 surgically treated early-stage NSCLC patients for LRIG1, LRIG2 and LRIG3. LRIG1 high-expressing adenocarcinoma cases had a large and statistically significant survival benefit of 33 months compared to negative cases. Similarly, an in silico analysis of a large gene expression dataset from the Oncomine database showed that high LRIG1 mRNA expression was linked to better survival as well. Differences in survival persisted even when adjusting for known prognostic factors, meaning that LRIG1 was an independent positive prognostic marker for survival in NSCLC.A yeast two-hybrid screen was performed to search for proteins interacting with a conserved cytosolic peptide shared between all three mammalian LRIG proteins. This screen yielded hits for the paralogous proteins LIM domain only protein 7 (LMO7) and LIM and calponin homology domains-containing protein 1 (LIMCH1). LRIG1 and LRIG3 were both found to physically interact with LMO7 and LIMCH1 as assessed through immunoprecipitation techniques on overexpressed proteins. For LMO7, this could also be confirmed at endogenous protein levels using the proximity ligation assay. The 347 samples in the previously mentioned TMA were stained for LMO7. In our survival analysis, we observed no significant survival differences when looking at LMO7 alone, but the survival benefit observed for high LRIG1 was found to be limited to the subgroup that also was negative for LMO7. This means that the observed physical interaction between LRIG1 and LMO7 appears to translate to differences in patient survival.To investigate possible mechanisms underlying the observed association between high LRIG1 expression and a favorable patient survival, a panel of NSCLC cell lines was modified to overexpress LRIG1. Broadly, LRIG1 overexpression resulted in minor decreases in cellular proliferation rates and no effects on chemosensitivity or radiosensitivity. Looking across the panel of NSCLC cell lines, no clear pattern was observed regarding the effects of LRIG1 overexpression on cellular motility. However, LRIG1 overexpression significantly decreased the clonogenic potential in most cell lines. The only cell line in the panel, H1299, that formed hematogenous disseminated disease in immunodeficient mice was used to establish a mixed-population primary tumor of tagged LRIG1 overexpressing cells and control cells. The LRIG1 transduced cells were was found to be enriched in the injected primary tumor, but no significant changes in their relative abundance was observed between the metastatic sites and their corresponding primary tumors.In summary, we found that LRIG1 was an independent positive prognostic factor in early-stage NSCLC. We identified LMO7 and LIMCH1 as interaction partners for LRIG proteins and showed that the interaction between LMO7 and LRIG1 had implications for the clinical outcome in NSCLC. Furthermore, our mechanistic studies on the effects of LRIG1 overexpression on NSCLC cells suggested that the survival benefit conferred by high LRIG1 expression may be due to differences in metastatic potential. Taken together, the findings in this thesis suggest an important biological role for LRIG proteins in NSCLC.
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