Radiogenomics in gynecological cancer patients

Radiotherapie wordt toegepast bij ongeveer de helft van alle kankerpatiënten en vormt bijgevolg één van de belangrijkste behandelingsmethoden tegen kanker. Niettegenstaande de bestralingstechnieken de laatste jaren veel verbeterd zijn, treedt schade aan normale weefsels nog steeds op. Bovendien variëren deze stralingsgeïnduceerde complicaties sterk van patiënt tot patiënt. Door de stijgende overlevingsgraad van kankerpatiënten is de preventie of reductie van late neveneffecten ten gevolge van radiotherapie een prioriteit geworden. Met een in vitro test die de individuele radiosensitiviteit kan voorspellen vóór de radiotherapiebehandeling, zouden de behandelingsschema’s verder kunnen aangepast worden zodat stralingsgeïnduceerde toxiciteit aan normale weesfels tot een absoluut minimum beperkt wordt. Gynaecologische tumoren maken een groot deel uit van het aantal kankers in vrouwen over de hele wereld. De meeste van deze maligniteiten, in het bijzonder cervix- en endometriumkanker, worden operatief behandeld gevolgd door radiotherapie. Voor deze thesis werd een patiëntengroep bestaande uit vrouwen behandeld voor cervix- of endometriumkanker opgevolgd voor late stralingstoxiciteit. De laatste 10-tallen jaren werden verschillende in vitro testen ontwikkeld teneinde schade aan normale weefsels ten gevolge van radiotherapie te voorspellen. In het eerste deel van deze thesis werd de toepasbaarheid nagegaan van de cytogenetische G2 test op perifere bloedlymfocyten als biomerker voor late klinische radiosensitiviteit. Er kon aangetoond worden dat het gemiddeld aantal chromatidbreuken per cel significant hoger is in patiënten met late normale weefselreacties dan in patiënten zonder deze reacties. De G2 test miste echter sensitiviteit om individuele patiënten met een verhoogd risico te identificeren. Bijgevolg heeft de G2 test een beperkte bruikbaarheid bij de klinische screening voor individuele radiosensitiviteit. Momenteel wordt radiosensitiviteit van normale weefsels beschouwd als een overerfbare complexe aandoening die bepaald wordt door de interactie tussen verschillende genen of genproducten. Er wordt bijgevolg verondersteld dat klinische radiosensitiviteit voorspeld kan worden van individuele genetische profielen. DNA herstel is één van de belangrijkste mechanismen van cellen en weefsels als respons op straling. Daarom werd de associatie bestudeerd tussen acht single nucleotide polymorfismen (SNPs) in de DNA herstelgenen XRCC1, XRCC3 en OGG1 en de ontwikkeling van laattijdige radiotherapiereacties. De selectie van deze SNPs was gebaseerd op literatuurdata betreffende de mogelijke betrokkenheid van deze SNPs in kankerpredispositie en radiosensitiviteit. In dit werk werd aangetoond dat het XRCC3 IVS5-14 polymorfisme significant geassocieerd is met het risico op de ontwikkeling van laattijdige radiotherapiereacties. De overige individuele SNPs konden echter niet geassocieerd worden met een verhoogde stralingstoxiciteit. Klinische radiosensitiviteit bleek wel significant geassocieerd met een combinatie van verschillende SNPs in XRCC1 en XRCC3 op basis van een risico-allel analyse. In het tweede deel van deze thesis werd de betrokkenheid bestudeerd van drie microsatelliet polymorfismen in de DNA herstelgenen XRCC1, XRCC3 en XRCC5 bij late klinische radiosensitiviteit. Deze studie werd uitgevoerd uitgaande van veelbelovende literatuurdata die wijzen op de associatie tussen klinische radiosensitiviteit en zeldzame microsatellieten. Hoewel geen significante associatie gevonden werd tussen de lengte van één van de microsatellieten en het voorkomen van laattijdige radiotherapiereacties, kon de mogelijke betrokkenheid van korte en lange XRCC1 herhalingen niet uitgesloten worden. De laatste jaren is het duidelijk geworden dat radiosensitiviteit van normale weefsels niet enkel veroorzaakt wordt door celdood, maar het resultaat is van multicellulaire interacties tussen verscheidene celtypes in een specifiek weefsel of orgaan. De vroege activatie van cytokine cascades na stralingsblootstelling heeft een grote invloed op de respons van normale weefsels. Het profibrotische cytokine TGFβ1 speelt een cruciale rol in de ontwikkeling van stralingsgeïnduceerde late weefselreacties. Bijgevolg werd in het laatste deel van deze thesis de associatie nagegaan tussen zes polymorfismen in TGFβ1 en het voorkomen van late toxiciteit van normale weefsels. Deze studie toonde aan dat het -1.552delAGG, het -509C>T en het Leu10Pro polymorfisme sterk met elkaar geassocieerd zijn, en dat het risico op late stralingstoxiciteit gemoduleerd kan worden door deze polymorfismen. De studies uitgevoerd in deze thesis hebben bijgedragen tot het lopende onderzoek met als doel genetische profielen te identificeren die geassocieerd zijn met radiosensitiviteit van normale weefsels. Er werden indicaties gegeven dat polymorfismen in de XRCC1 en XRCC3 DNA herstelgenen en in het cytokine TGFβ1 betrokken kunnen zijn in de ontwikkeling van late radiotherapiereacties. Gelijkaardige associaties voor de TGFβ1 SNPs werden ook reeds gerapporteerd in andere onafhankelijke studies. Dit ondersteunt de mogelijke betrokkenheid van deze TGFβ1 SNPs in laattijdige radiotherapiereacties. Om tot een volledig begrip van de genetische basis van klinische radiosensitiviteit te komen en om genetische data aan te wenden in de screening naar klinische radiosensitiviteit, zijn echter grootschalige studies noodzakelijk die gebruik maken van high-troughput technologieën in een multicenter setting

Factors modifying the risk for developing acute skin toxicity after whole-breast intensity modulated radiotherapy

Background: After breast-conserving radiation therapy most patients experience acute skin toxicity to some degree. This may impair patients' quality of life, cause pain and discomfort. In this study, we investigated treatment and patient-related factors, including genetic polymorphisms, that can modify the risk for severe radiation-induced skin toxicity in breast cancer patients. Methods: We studied 377 patients treated at Ghent University Hospital and at ST.-Elisabeth Clinic and Maternity in Namur, with adjuvant intensity modulated radiotherapy (IMRT) after breast-conserving surgery for breast cancer. Women were treated in a prone or supine position with normofractionated (25 x 2 Gy) or hypofractionated (15 x 2.67 Gy) IMRT alone or in combination with other adjuvant therapies. Patient-and treatment-related factors and genetic markers in regulatory regions of radioresponsive genes and in LIG3, MLH1 and XRCC3 genes were considered as variables. Acute dermatitis was scored using the CTCAEv3.0 scoring system. Desquamation was scored separately on a 3-point scale (0-none, 1-dry, 2-moist). Results: Two-hundred and twenty patients (58%) developed G2+ dermatitis whereas moist desquamation occurred in 56 patients (15%). Normofractionation (both p = D (p = 0.001 and p = 0.043) and concurrent hormone therapy (p = 0.001 and p = 0.037) were significantly associated with occurrence of acute dermatitis and moist desquamation, respectively. Additional factors associated with an increased risk of acute dermatitis were the genetic variation in MLH1 rs1800734 (p=0.008), smoking during RT (p = 0.010) and supine IMRT (p = 0.004). Patients receiving trastuzumab showed decreased risk of acute dermatitis (p < 0.001). Conclusions: The normofractionation schedule, supine IMRT, concomitant hormone treatment and patient related factors (high BMI, large breast, smoking during treatment and the genetic variation in MLH1 rs1800734) were associated with increased acute skin toxicity in patients receiving radiation therapy after breast-conserving surgery. Trastuzumab seemed to be protective

Focus on 16p13.3 Locus in colon cancer

Background : With one million new cases of colorectal cancer (CRC) diagnosed annually in the world, CRC is the third most commonly diagnosed cancer in the Western world. Patients with stage I-III CRC can be cured with surgery but are at risk for recurrence. Colorectal cancer is characterized by the presence of chromosomal deletions and gains. Large genomic profiling studies have however not been conducted in this disease. The number of a specific genetic aberration in a tumour sample could correlate with recurrence-free survival or overall survival, possibly leading to its use as biomarker for therapeutic decisions. At this point there are not sufficient markers for prediction of disease recurrence in colorectal cancer, which can be used in the clinic to discriminate between stage II patients who will benefit from adjuvant chemotherapy. For instance, the benefit of adjuvant chemotherapy has been most clearly demonstrated in stage III disease with an approximately 30 percent relative reduction in the risk of disease recurrence. The benefits of adjuvant chemotherapy in stage II disease are less certain, the risk for relapse is much smaller in the overall group and the specific patients at risk are hard to identify. Materials and Methods : In this study, array-comparative genomic hybridization analysis (array-CGH) was applied to study high-resolution DNA copy number alterations in 93 colon carcinoma samples. These genomic data were combined with parameters like KRAS mutation status, microsatellite status and clinicopathological characteristics. Results : Both large and small chromosomal losses and gains were identified in our sample cohort. Recurrent gains were found for chromosome 1q, 7, 8q, 13 and 20 and losses were mostly found for 1p, 4, 8p, 14, 15, 17p, 18, 21 and 22. Data analysis demonstrated that loss of chromosome 4 is linked to a worse prognosis in our patients series. Besides these alterations, two interesting small regions of overlap were identified, which could be associated with disease recurrence. Gain of the 16p13.3 locus (including the RNA binding protein, fox-1 homolog gene, RBFOX1) was linked with a worse recurrence-free survival in our patient cohort. On the other hand, loss of RBFOX1 was only found in patients without disease recurrence. Most interestingly, above mentioned characteristics were also found in stage II patients, for whom there is a high medical need for the identification of new prognostic biomarkers. Conclusions : In conclusion, copy number variation of the 16p13.3 locus seems to be an important parameter for prediction of disease recurrence in colon cancer

A SARS-CoV-2 sequence submission tool for the European Nucleotide Archive

Abstract Summary Many aspects of the global response to the COVID-19 pandemic are enabled by the fast and open publication of SARS-CoV-2 genetic sequence data. The European Nucleotide Archive (ENA) is the European recommended open repository for genetic sequences. In this work, we present a tool for submitting raw sequencing reads of SARS-CoV-2 to ENA. The tool features a single-step submission process, a graphical user interface, tabular-formatted metadata and the possibility to remove human reads prior to submission. A Galaxy wrap of the tool allows users with little or no bioinformatic knowledge to do bulk sequencing read submissions. The tool is also packed in a Docker container to ease deployment. Availability CLI ENA upload tool is available at github.com/usegalaxy-eu/ena-upload-cli (DOI 10.5281/zenodo.4537621); Galaxy ENA upload tool at toolshed.g2.bx.psu.edu/view/iuc/ena_upload/382518f24d6d and https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload (development) and; ENA upload Galaxy container at github.com/ELIXIR-Belgium/ena-upload-container (DOI 10.5281/zenodo.4730785) </jats:sec

Large-Scale Meta-GWAS Reveals Common Genetic Factors Linked to Radiation-Induced Acute Toxicities across Cancers

BACKGROUND: This study was designed to identify common genetic susceptibility and shared genetic variants associated with acute radiation-induced toxicity (RIT) across four cancer types (prostate, head and neck, breast, and lung).METHODS: A GWAS meta-analysis was performed using 19 cohorts including 12,042 patients. Acute standardized total average toxicity (rSTATacute) was modelled using a generalized linear regression model for additive effect of genetic variants adjusted for demographic and clinical covariates. LD score regression estimated shared SNP-based heritability of rSTATacute in all patients and for each cancer type.RESULTS: Shared SNP-based heritability of STATacute among all cancer types was estimated at 10% (se = 0.02), and was higher for prostate (17%, se = 0.07), head and neck (27%, se = 0.09), and breast (16%, se = 0.09) cancers. We identified 130 suggestive associated SNPs with rSTATacute (5.0x10-8&lt;P-value&lt;1.0x10-5) across 25 genomic regions. rs142667902 showed the strongest association (effect allele A; effect size -0.17; P-value=1.7x10-7), which is located near DPPA4, encoding a protein involved in pluripotency in stem cells, which are essential for repair of radiation-induced tissue injury. Gene-set enrichment analysis identified 'RNA splicing via endonucleolytic cleavage and ligation' (P = 5.1 x10-6, Pcorrected =0.079) as the top gene set associated with rSTATacute among all patients. In-silico gene expression analysis showed the genes associated with rSTATacute were statistically significantly up-regulated in skin (not sun exposed Pcorrected=0.004; sun exposed Pcorrected=0.026).CONCLUSIONS: There is shared SNP-based heritability for acute RIT across and within individual cancer sites. Future meta-GWAS among large radiotherapy patient cohorts are worthwhile to identify the common causal variants for acute radiotoxicity across cancer types.</p

Identification of Novel Susceptibility Loci and Genes for Prostate Cancer Risk: A Transcriptome-Wide Association Study in over 140,000 European Descendants

Genome-wide association study–identified prostate cancer risk variants explain only a relatively small fraction of its familial relative risk, and the genes responsible for many of these identified associations remain unknown. To discover novel prostate cancer genetic loci and possible causal genes at previously identified risk loci, we performed a transcriptome-wide association study in 79,194 cases and 61,112 controls of European ancestry. Using data from the Genotype-Tissue Expression Project, we established genetic models to predict gene expression across the transcriptome for both prostate models and cross-tissue models and evaluated model performance using two independent datasets. We identified significant associations for 137 genes at P < 2.61 × 10−6, a Bonferroni-corrected threshold, including nine genes that remained significant at P < 2.61 × 10−6 after adjusting for all known prostate cancer risk variants in nearby regions. Of the 128 remaining associated genes, 94 have not yet been reported as potential target genes at known loci. We silenced 14 genes and many showed a consistent effect on viability and colony-forming efficiency in three cell lines. Our study provides substantial new information to advance our understanding of prostate cancer genetics and biology. SIGNIFICANCE: This study identifies novel prostate cancer genetic loci and possible causal genes, advancing our understanding of the molecular mechanisms that drive prostate cancer

Spontaneous and radiation-induced chromosomal instability and persistence of chromosome aberrations after radiotherapy in lymphocytes from prostate cancer patients

The aim of the study was to compare the spontaneous and ex vivo radiation-induced chromosomal damage in lymphocytes of untreated prostate cancer patients and age-matched healthy donors, and to evaluate the chromosomal damage, induced by radiotherapy, and its persistence. Blood samples from 102 prostate cancer patients were obtained before radiotherapy to investigate the excess acentric fragments and dicentric chromosomes. In addition, in a subgroup of ten patients, simple exchanges in chromosomes 2 and 4 were evaluated by fluorescent in situ hybridization (FISH), before the onset of therapy, in the middle and at the end of therapy, and 1 year later. Data were compared to blood samples from ten age-matched healthy donors. We found that spontaneous yields of acentric chromosome fragments and simple exchanges were significantly increased in lymphocytes of patients before onset of therapy, indicating chromosomal instability in these patients. Ex vivo radiation-induced aberrations were not significantly increased, indicating proficient repair of radiation-induced DNA double-strand breaks in lymphocytes of these patients. As expected, the yields of dicentric and acentric chromosomes, and the partial yields of simple exchanges, were increased after the onset of therapy. Surprisingly, yields after 1 year were comparable to those directly after radiotherapy, indicating persistence of chromosomal instability over this time. Our results indicate that prostate cancer patients are characterized by increased spontaneous chromosomal instability. This instability seems to result from defects other than a deficient repair of radiation-induced DNA double-strand breaks. Radiotherapy-induced chromosomal damage persists 1 year after treatment

A Bioinformatics Filtering Strategy for Identifying Radiation Response Biomarker Candidates

The number of biomarker candidates is often much larger than the number of clinical patient data points available, which motivates the use of a rational candidate variable filtering methodology. The goal of this paper is to apply such a bioinformatics filtering process to isolate a modest number (<10) of key interacting genes and their associated single nucleotide polymorphisms involved in radiation response, and to ultimately serve as a basis for using clinical datasets to identify new biomarkers. In step 1, we surveyed the literature on genetic and protein correlates to radiation response, in vivo or in vitro, across cellular, animal, and human studies. In step 2, we analyzed two publicly available microarray datasets and identified genes in which mRNA expression changed in response to radiation. Combining results from Step 1 and Step 2, we identified 20 genes that were common to all three sources. As a final step, a curated database of protein interactions was used to generate the most statistically reliable protein interaction network among any subset of the 20 genes resulting from Steps 1 and 2, resulting in identification of a small, tightly interacting network with 7 out of 20 input genes. We further ranked the genes in terms of likely importance, based on their location within the network using a graph-based scoring function. The resulting core interacting network provides an attractive set of genes likely to be important to radiation response

Genome-wide association study identifies susceptibility loci for B-cell childhood acute lymphoblastic leukemia.

Genome-wide association studies (GWAS) have advanced our understanding of susceptibility to B-cell precursor acute lymphoblastic leukemia (BCP-ALL); however, much of the heritable risk remains unidentified. Here, we perform a GWAS and conduct a meta-analysis with two existing GWAS, totaling 2442 cases and 14,609 controls. We identify risk loci for BCP-ALL at 8q24.21 (rs28665337, P = 3.86 × 10-9, odds ratio (OR) = 1.34) and for ETV6-RUNX1 fusion-positive BCP-ALL at 2q22.3 (rs17481869, P = 3.20 × 10-8, OR = 2.14). Our findings provide further insights into genetic susceptibility to ALL and its biology