In recent years, digitalization and computer-based technologies have greatly revolutionized the field of bioinformatics. Advance research and development of computer-based programs have enhanced various DNA sequencing technologies. This advancement has significantly broadened our understanding of genomic evolution and has widely contributed to the application of clinical genomics. Cancer has been one of the major causes of death across the world. Cancer is mainly caused due to the damage or changes in DNA that affect the function of genes which contain a set of instructions that control various functions of cells. This damage in genes that maintain DNA repair mechanism may lead towards genome instability allowing rapid growth of cancer.   Microsatellite instability (MSI) is one such condition characterized due to genomic alteration leading towards the failure of DNA repair mechanism in cancerous cells. MSI is found in various types of cancer but is most often found in colorectal cancer, gastric cancer, and endometrial cancer. Hence, detection of this MSI can greatly contribute towards cancer therapies and enable to plan for the best treatment. This study mainly focuses on evaluating the performance of MSI calling algorithms using targeted sequencing methods.   The literature provides a detailed outline of various topics related to MSI detection. Moreover, different computational methods like MSIsensor, MSIsensor-ct, MSIsensor-pro, MSings, MiMSI, and MSIsensor2 were used in this study for the detection of MSI in selected samples are thoroughly discussed in the methodology section. Finally, the findings of this study conclude that the MSI calling algorithms mentioned above provide accurate detection of MSI in the chosen samples. Also, these algorithms enable us to determine the MSI status of the chosen samples more precisely

Bakgrund: Ordet cancer kan vara ett väldigt laddat ord för många människor, cancer hos barn är ännu mer laddat eftersom det gäller just ett barn. Då ett barn får diagnosen cancer är det inte bara barnet som drabbas, utan även familjen och stora delar av omgivningen såsom skola och kompisar. Idag finns det goda chanser att barn överlever sin cancersjukdom och det finns välgjorda riktlinjer för hur vården ska bedrivas under aktiv behandling och hur uppföljningen av barnet ska ske efter avslutad behandling. Men finns det någon plan för att uppföljning av föräldrarna och hur är deras mående tas omhand efter en påfrestande tid som denna? Syfte: Syftet var att undersöka föräldrars erfarenheter av livet efter att barnet har avslutat en lyckad cancerbehandling. Metod: En litteraturstudie genomfördes och resultatet baseras på åtta vetenskapliga kvalitativa och kvantitativa artiklar. Resultat: Fyra övergripande kategorier identifierades: Erfarenhet av känslomässiga reaktioner; Erfarenhet av påverkan på livet; Betydelsen av stöd och relationer; Att återgå till det normala. Slutsats: Resultat i studien visade att många föräldrar upplever ständig närvaro av oro, ångest eller depression även efter barnets avslutade behandling. De föräldrar som uppfattar sina barn som mer sårbara och bräckliga blir mer påverkade av den negativa stress som sjukdomen och dess behandling har utgjort. Vidare gick att utläsa att den ständiga jakten efter eventuella symtom blir ett stresspåslag och utgör en påminnelse i det vardagliga livet. Allt detta bidrar till okontrollerbara tankar om återfall eller död vilket leder till ett hinder för familjen att bearbeta det de varit med om och gå vidare. En förlorad nära kontakt med vårdpersonal efter avslutad behandling får vissa föräldrar att känna ångest.

Introduction: Rituximab is a monoclonal antibody used to treat hematological malignancies. The antibody depletes CD20+ B cells via cytotoxic immune mechanisms, such as complement-dependent cytotoxicity (CDC) and antibody-dependent cell-mediated cytotoxicity (ADCC), which is mainly induced by natural killer (NK) cells. Rituximab is mostly well-tolerated but has been reported to induce the release of large amounts of cytokines in blood, thus causing systemic inflammatory response. Aim: To study rituximab-induced B cell depletion and cytokine release in blood from healthy volunteers and how this was affected by Fc modified versions of the antibody. Methods and materials: Fresh blood from healthy donors (n=3) was incubated with rituximab and Fc modified versions that influence the antibody’s target functions, namely ADCC and CDC, for 4 hours in a blood loop system. Results were measured using multicolor flow cytometry, except for cytokine release in plasma which was measured by enzyme-linked immunosorbent assay (ELISA). Results: Of all treatments, rituximab wild type (WT) showed superior B cell depletion than Fc mutant rituximab. The C1q knock-out variant (rituximab-P331S) and the variant with improved affinity to Fc receptor CD16 (rituximab-GASDALIE) did not differ in depletion. A cytokine release was not detected with the treatments, however, a cytokine stimulation in NK cells was observed. Rituximab-GASDALIE had the most prominent cytokine stimulation and CD107a (marker of NK cell functional activity) expression on NK cells. Rituximab-WT and rituximab-P331S had a minor and similar cytokine stimulation and CD107a expression between each other. Rituximab-IgG2 had minimal B cell depletion, CD107a expression and cytokine stimulation. Conclusions: Rituximab depleted B cells without inducing measurable cytokine release for healthy individuals. Among the treatments, Fc mutant rituximab seem to induce less B cell depletion. Moreover, rituximab-GASDALIE appear to elicit an enhanced NK cell activation. Further studies should include more donors as supplement and the results should be interpreted as complementary data to future data analyzed by performing the loop experiment using blood from patients.

Cancer is a global health issue and is estimated to be the second leading cause of death worldwide. Within cancer treatment, it has become attractive to introduce precision medicine to harness the body’s own immune system to fight cancer. Personalised peptide cancer vaccine can activate the immune system and elicit an immune response by using the patient’s own blood and tumour cells.   The aim of this study was to gather information to better understand the production of individual-specific peptides and the challenges when producing these peptides with focus from a GMP perspective. The methodology for conducting this study and retrieve information for the result was gathered by three different data bases; EMA, European Commission and FDA, and by qualitative semi-structured interviews.   The findings show that these personalised peptides should be manufactured by using solid-phase peptide synthesis, cleavage from the resin, HPLC purification, and final salt exchange. The traditional GMP requirements must be used as a basis to build a pragmatic program. In terms of delivery time, the peptides can be delivered within a few weeks. The main challenges will be to manufacture successful peptides since the peptide sequences vary from patient to patient and due to that fact have different production efficacy, deliver within the set timeframe, and have flexibility in the manufacture process.   Multiple guidelines need to be followed in order to set up a process that consistently delivers the intended product. When producing oncology drugs on-demand it is essential to keep the timeline since the patients are severely ill. However, further studies are needed to determine how the manufacture of personalised peptides could be performed to harmonise with regulatory guidelines.

BAKGRUND: I Sverige är cancer en av de vanligaste sjukdomarna. Bröstcancer är den vanligaste cancersjukdomen hos kvinnor. Bröstcancer kan sprida sig i kroppen och bilda en sekundär cancer som kallas metastas. Transformerande tillväxtfaktor-β-receptorer (TGF-β-receptorer) har en viktig roll i tumörutveckling. SYFTE: Syftet med denna studie är att studera rollen av TGF-β-receptorer i cancer, särskild bröstcancer med fokus på metastaserna. METOD: Den är en litteraturstudie, som är baserad på sex vetenskapliga artiklar. Dessa artiklar hämtas från databas PubMed genom användning av olika specifika sökord. RESULTAT: Resultat visar att TGF-β-receptorer har två motsatta rollar i cancerutveckling. Första fungerar TGF-β-receptorer som en tumörundertryckare i början av cancerutveckling. Däremot bidrar TGF-β-receptorer till utveckling av maligna celler lite senare under cancerutveckling. Det gör det genom att förbättra metastatiska potential samt undertrycka antitumörimmunitet. Metastaser bildas via Epithelial to mesenchymal transition med hjälp av vissa andra faktorer såsom cancerassocierade fibroblaster. Epithelial to mesenchymal transition och andel av cancerassocierade fibroblaster kan stimuleras av TGF-β-receptorer, som kan i sin tur leda till ökning av metastaseringen. Ett exempel på metastas är skelettcancer. DISKUSSION: Transformerande tillväxtfaktor-β receptorer, som kan påverka cancer, betraktas som ett bra fynd i läkemedelsutveckling mot cancer. TGF-β-receptorer har en viktig roll i tumörutveckling, särskilt sekundär cancer. Sekundär cancer/metastas är farligare än primär cancer, därför är det bättre att försöka förstå hela mekanismen bakom TGF-β-receptorer på ett tydligt sätt, för att kunna behandla patienter i god tid. SLUTSATS: Transformerande tillväxtfaktor- β -receptorer är en av de viktigaste parametrarna för att få den optimala effekten av medicineringen mot cancer.

Background: Neuroblastoma (NB) is a pediatric tumor in infants and young children. The survival rate is only around 50 percent for high-risk NB despite advanced and intense multi-modal therapy. Current research aims to find new effective treatment additional to modern therapy to improve prognosis of high-risk NB in children. As such, SU11248 may be a valuable approach for improving treatment and survival as growth factors have crucial roles in tumor growth, angiogenesis, and metastasis. Aim: The aim of this investigation was to examine tissues from SU11248 treated and nontreated tumor-bearing animals on the abundance of tumor-associated macrophages (TAMs) in metastases found on vital organs. Our hypothesis is that if SU11248 could cause “deactivation” or “silencing” of the stroma of metastases particularly by acting on stromal immune cells such as TAMs. Methods: Paraffin-embedded metastases developed in an orthotopic xenograft model in beige SCID mice were stained with a monoclonal rat anti-mouse antibody as a marker of TAMs. Morphological analysis of tissue slides, and macrophage quantification was performed using a microscope. Statistical analysis was achieved using an unpaired two tailed t-test.  Results: Macrophages were stained nicely, but the number of macrophages in the metastases were not statistically different between the vehicle treated controls and SU11248 treated metastases. Conclusion: In patients with high-risk NB, SU11248 may be a useful therapeutic supplement. We believe that further research into mechanisms that target critical factors for angiogenesis and metastasis in NB, such as TAMs, is an important step toward improving patient outcomes in high-risk NB.

Background: As a nurse, when caring for children with cancer, you need to offer the best care for the child and in the meantime focus on family centered care in order to meet the thoughts and wishes the family carries. Caring for children with cancer might contain many obstacles and difficulties. Communication, education and to understand one's role as a nurse is important when caring for these children. Aim: To identify nursing experience when caring for children with cancer. Method: A literature overview has been done and ten studies were gathered through the databases PubMed and Cinahl. The analysis of these studies created four categories with associated subcategories. Results: It came through those nurses faced difficulties in pediatric care in different situations. These situations created categories which were: Ethical issues, Education, Cooperation with the family and Nurses emotions and support. Conclusion: Factors found in this study were nurses' experience of lacking the necessary preparation, the need of emotional support and the importance of working close to the families. It is found that nurses felt unprepared for their work and dealing with tough situations. The relationship between the nurse and the patient's family is important to provide high quality care. Nurses expressed the need for support from colleagues and family members in order to grow as a nurse and as a person.

Rhabdomyosarcoma (RMS) is a type of soft tissue sarcoma that mainly occurs in children. RMS can be divided into two subtypes embryonal (ERMS) and alveolar (ARMS). The ARMS subtype can be especially aggressive when a balanced chromosomal translocation is present. This translocation results in the expression of a PAX3/7-FOXO1 fusion protein, an oncogenic transcription factor. PAX3-FOXO1 positive RMS has an especially bad prognosis and survival rate. In the cell painting assay relevant organelles are stained and morphological features are extracted on a cellular level. Based on these features, morphological profiles of each cell type and a similarity score can be calculated. The morphological profiles of ERMS cell lines RD and RD18 as well as the ARMS cell lines RH30 and CW9019 were obtained. RD and RD18 are most similar to each other followed by RH30. CW9019 has a very different profile from the other cell lines. Since ERMS is associated with a better survival rate a drug that reprograms the phenotype from ARMS to a more ERMS-like phenotype might sensitize the cells to the standard treatment of RMS. ARMS patients might then benefit from a combination therapy of such a drug and the standard treatment. To find such a drug a drug screen was conducted. Drugs were selected for the screen that either target fusion-protein stability or overexpressed targets of the fusion protein. Phenotypic reference compounds were included to get a first idea of the mechanisms and involved organelles of the screened drugs. In total, 30 compounds and 9 phenotypic reference compounds were screened for changing morphological profiles of RMS cell lines with the cell painting assay. 15 compounds were identified that change the phenotype of the ARMS cell line RH30. In addition, 7 of these compounds shift the phenotype of RH30 towards an ERMS-like phenotype. If that morphological resemblance of RH30 cells to ERMS cells translates into a change of a more ERMS-like behavior and sensitizes the cells for the standard treatment of RMS remains to be investigated. The reprogramming hits showed high similarity with phenotypic reference compounds that increase nucleus size which might suggest changed behavior of the fusion protein. Especially, Bosutinib, Midostaurin and Alisertib are promising new compounds for ARMS treatment. They shifted the ARMS phenotype towards an ERMS-like phenotype in the drug screen. This shift is likely a result of the interaction with PLK1 or Aurora-kinase A that are shown to have an influence on fusion-protein stability.

Fluorescerande protein kan användas som reportrar i genetiska kretsar för att identifiera framgångsrikt modifierade celler. Med hjälp av syntetisk biologi kan genetiska kretsar, som är en sammansättning gener som kodar för protein, skapas. Genetiska kretsar möjliggör modifiering av celler och har haft stor framgång, vid immunterapi av cancer. Chimeric antigen receptor (CAR) T-celler är en genetisk krets där T-celler modifieras till att eliminera tumörceller baserat på en utvald ytmarkör. Med hjälp av fluorescerande proteiner kan olika komponenter i genetiska kretsar märkas in och därmed tydligt följas vid modifieringen av celler, ofta används Blue fluorescent protein (BFP) eller Green fluorescent protein (GFP). För att utveckla mer komplexa genetiska kretsar med flera komponenter krävs fler fluorescerande proteiner som kan kombineras med BFP och GFP, såsom sådana i det röda spektrumet. I denna studie undersöktes rödfluorescerade proteinerna E2Crimson, TagRFP657, mNeptune2.5, mKelly2, mKate2, mCardinal och Katushka2S. Med hjälp av klonade vektorer för respektive protein kan lentivirus produceras för att transducera Jurkat celler. Flödescytometri användes för att identifiera proteinernas fluorescensintensitet i det röda spektrumet, samt deras läckage i BFP och GFP spektrat. Proteinerna med högst fluorescensintensitet i det röda spektrumet samt minst läckage i BFP och GFP spektrat var E2Crimson samt mCardinal. E2Crimson har enligt tidigare studie låg toxicitet och god ljusstyrka samt hade i denna studie högst fluorescensintensitet i det röda spektrumet. E2Crimson anses därför vara optimal att kombinera med BFP och GFP i genetiska kretsar med flera komponenter. / Fluorescent protein can be used as reporters in genetic circuits to identify successfully modified cells. Using synthetic biology, genetic circuits, which are an assembly of genes that code for protein, can be created. Genetic circuits enable the modification of cells and have had great success in immunotherapy of cancer. Chimeric antigen receptor (CAR) T cells are a genetic circuit which modifies T cells to eliminate tumor cells based on a selected surface marker. With the help of the fluorescent protein, various components of genetic circuits can be marked and thus followed during the modification of cells, Blue fluorescent protein (BFP) or Green fluorescent protein (GFP) are often used as reporters. When developing complex genetic circuits with multiple components more fluorescent proteins that can combine with BFP and GFP are required, such as those in the red spectrum. In this study, the far-red fluorescent proteins E2Crimson, TagRFP657, mNeptune2.5, mKelly2, mKate2, mCardinal and Katushka2S were included. Using cloned vectors for each protein, lentiviruses can be produced to transduce Jurkat cells. Flow cytometry was used to identify the proteins fluorescence intensity in the red spectrum, as well as their leakage in the BFP and GFP spectra. The proteins with the highest fluorescence intensity in the red spectrum and the least leakage in the BFP and GFP spectra were E2Crimson and mCardinal. E2Crimson has according to other studies low toxicity and good brightness and in this study E2Crimson showed the highest fluorescence intensity in the red spectrum. E2Crimson is therefore considered optimal to combine with BFP and GFP in multicomponent genetic circuits.

Background: Prostate cancer is the most prevalent form of cancer affecting men.In case of biochemical recurrence, positron emission tomography (PET) targeting prostate-specific membrane antigen (PSMA) on prostate tumor cells is primarily used, in combination with computed tomography (CT), for detection and localization of recurrence. Research for optimizing a PSMA-ligand with high affinity for tumor cells and minimal excretion to the urinary bladder is constantly ongoing, in order to allow better evaluation of the prostate and nearby regions. One such ligand is 18F-PSMA-1007, which was expected to be excreted in the urinary bladder at a rate of 5-10%. However, after switching from diagnostic to low-dose CT, the elimination of 18F-PSMA-1007 in the bladder was higher than expected. Purpose: To evaluate whether hydration during the accumulation period could affect the activity concentration in the bladder. Materials and Methods: The study involved analyzing PET-CT scans obtained from two prostate cancer patient groups who underwent 18F-PSMA-1007-PET with low-dose CT. The groups consisted of 20 participants each, with one group hydrating during the tracer’s accumulation time, while scans from the comparison group were obtained from a time point where patients did not receive instructions about water intake. The amount of radioactivity was measured by placing a standardized 3.00 cm Volume of Interest (VOI) on the bladder, which was then adjusted based on the individual size and shape of the patients' bladder. From the VOI, a standardized uptake value (SUV) was determined, which can be represented as either SUVmean or SUVmax. These values represent the average tracer concentration within a VOI and the highest concentration of the tracer in the urinary bladder, respectively. Results: SUV in the urinary bladder was lower for the hydrated group, where the SUVmean was 1,55 vs 4,5 (p=0,011) for the non-hydrated group. Similar values were obtained for SUVmax, 2,3 vs 6,65 (p< 0,003). Conclusion: This retrospective study suggests that water intake during the accumulation period leads to significantly lower activity concentration in the bladder among these patients, which benefits the detection of recurrences in adjacent areas.