| 1. |
- Agarkova, Irina, et al.
(author)
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Assessing efficacy and immune-stimulatory effects of tumor-derived dendritic cell reprogramming using immuno-competent 3D tumor spheroid model
- 2023
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In: Cancer Research. - 1538-7445. ; 83:7 Supplement
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Conference paper (peer-reviewed)abstract
- Immunotherapy has brought hope for cancer treatment, but its clinical success remains limited. Recently, overexpression of the transcription factors PU.1, IRF8 and BATF3 (PIB) was shown to induce direct reprogramming of tumor cells into antigen-presenting type 1 conventional dendritic cells (cDC1s), a rare subset of immune cells with pivotal role in anti-cancer immunity. This strategy might open avenues to enhance cancer cell recognition and elimination by the immune system. However, currently existing in-vitro and in-vivo testing platforms do not qualify to reproduce all complex cell interactions essential for the approbation of this hypothesis. Here, we report the development of the InSphero 3D InSight™ Oncology Platform for in-vitro assessment of efficacy and immune-stimulatory effects of this novel cancer immunotherapy approach. The feasibility of 3D spheroid formation for several GFP-expressing tumor cell lines was evaluated by varying seeding conditions in AKURA 96 well plate. We have measured the growth (ATP content) and GFP signal overtime and analyzed the morphology of the spheroids by IHC. With this, we have established spheroid models of T98G (glioblastoma), PK59 (pancreatic cancer), and A375 (melanoma) cell lines that are growing and viable for at least 10 days. In parallel, using 2D cultures, we have identified the optimal multiplicity of infection of a lentiviral vector encoding for PIB and mCherry to enable high transduction (mCherry+ cells), reprogramming efficiency (mCherry+CD45+HLA-DR+ cells), and cell viability, quantified by flow cytometry and IHC. Then, we have demonstrated that cDC1 reprogramming progresses in the context of 3D cancer spheroids and tumor cells acquire expression of CD45+ and HLA-DR+ cells using IHC and confocal microscopy analysis. We developed an algorithm enabling automated analysis of confocal images and quantification of cDC1 reprogramming efficiency from individual image stacks calculated as a ratio of mCherry+, CD45+ and HLA-DR+ cells versus the number of DAPI+ nuclei. Using the new algorithm we have evaluated the reprogramming efficacy of the different virus dosages in all three types of 3D tumor spheroids. Lastly, we have cocultured tumor spheroids transduced with PIB with naïve or activated HLA-matched PBMCs and evaluated cytokine secretion as a readout of immune cell activation. We observed that reprogramming induces activation of T cells and correlated it to the number of reprogrammed cells in the tumor spheroid, evaluated by the HC imaging. In summary, we developed the InSphero 3D InSight™ Oncology Platform that allowed us to demonstrate the effects of direct reprogramming of tumor cells into immunogenic dendritic cells. Combined with high-content imaging analysis, this platform offers a powerful solution for preclinical translational research.
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| 2. |
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| 3. |
- C., Ellberg, et al.
(author)
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Body constitution in young healthy women from breast cancer higher risk families in relation to smoking
- 2017
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In: Cancer Research. - 1538-7445. ; 77:13
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Conference paper (peer-reviewed)abstract
- Introduction: The purpose of this study was to investigate potential associations between body composition and current smoking in young healthy women from high-risk families. Cigarette smoke contains >7000 chemicals of which 69 are established carcinogens and smoke also acts as an aromatase inhibitor. Smoking is now recognized as a carcinogen for the breast and influences both risk and prognosis. However, the underlying mechanisms need to be better elucidated. One study showed that breast cancer patients who smoked were younger, had a lower body mass index (BMI), smaller breast volumes, but a higher waist-to-hip ratio (WHR) than non-smokers. However, smoking was also associated with a higher frequency of prior oral contraceptive (OC) use. Since breast cancer development starts long before the tumor is clinically detectable, we aimed to study the impact of cigarette smoke on anthropometric factors. Material and methods: Between 1996 and 2006, 269 healthy women were included in a study on the impact of lifestyle factors in women 0.18). However, current smokers had significantly larger standardized waist circumference (78 vs 74 cm;adjP=0.02), and higher standardized WHR (0.79 vs 0.76;adjP=0.003) compared with non-smokers. Conclusion: Current smokers had significantly larger waist circumference and higher WHR, but similar BMI and breast volume compared with non-smokers, although most women had anthropometric measures within WHO's recommended limits. The difference in fat distribution towards more abdominal fat, suggests that current smoking is associated with a more inflammatory and/or androgenic profile at the age when breast cancer is initiated.
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| 4. |
- C., Ellberg, et al.
(author)
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Smoking impacts endogenous estradiol and testosterone levels in young healthy women
- 2017
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In: Cancer Research. - 1538-7445. ; 77:13 Suppl
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Conference paper (peer-reviewed)abstract
- Introduction: The purpose of the study was to elucidate the association between smoking and estradiol (E2) and testosterone (T) levels in young healthy women from highrisk families. Cigarette smoke contains multiple carcinogens and is considered a risk factor for breast cancer. However, tobacco also contains aromatase inhibiting substances, but the impact on hormonal levels in young women at the age when breast cancer is initiated is unclear and needs further elucidation. Material and methods Between 1996 and 2002, 258 healthy women from high-risk breast cancer families in Sweden were enrolled in a study on the impact of lifestyle factors in women
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| 5. |
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| 6. |
- H.L., Olsson
(author)
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With increasing age at tumor diagnosis in families with cancer, cancer is limited to fewer organs
- 2016
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In: Cancer Research. - 1538-7445. ; 76:14 Suppl
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Conference paper (peer-reviewed)abstract
- Hereditary cancer that has monogenic inheritance affects every tenth patient, on average, who is diagnosed with cancer, and it has been suggested based on twin studies, that approximately 30% of all cancer patients have a genetic predisposition to developing cancer. The author posited that familial syndromes become more organ specific with increasing age at tumour presentation to the point that very late in life, only a few organs are affected by tumours disease. The reason for this could be that the tumour originates from a more differentiated, organ-specific progenitor/stem cell later in life, while the progenitor/stem cell might be involved in organogenesis in different organs earlier in life. Examples are given for skin cancer and breast cancer. Summary: Patients with familial cancer who present with cancer at an older age at tumour presentation have a more organ restricted disease. This could be because the tumor has a more differentiated progenitor/stem cell origin. Examples are given for families with breast cancer, melanoma, and non-melanoma skin cancer.
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| 7. |
- Schrijver, L, et al.
(author)
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Oral contraceptive use and breast cancer risk: A cohort study of BRCA1 and BRCA2 mutation carriers
- 2017
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In: Cancer Research. - 1538-7445. ; 77:13 Suppl 1
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Conference paper (peer-reviewed)abstract
- Background: BRCA1 and BRCA2 mutation carriers are at high risk of breast and ovarian cancer. Oral contraceptive preparations (OCPs) may reduce ovarian cancer risk, but its effect on breast cancer risk remains unclear. Methods: Combined data from three cohorts of 5705 BRCA1 and 3521 BRCA2 mutation carriers (IBCCS, BCFR and kConFab) were analyzed using age-dependent Cox regression models stratified for study and birth cohort. We conducted the first prospective analyses on this topic. Our additional main retrospective analyses were leftcensored 5 years preceding date of baseline questionnaire to control for survival bias. The full-cohort retrospective analyses, without left-censoring, was performed to compare results with the literature. Prospective analyses were considered most valid, while retrospective analyses were most powerful. Results: For BRCA1 mutation carriers we found no association between ever OCP use and risk of breast cancer in the prospective analyses (HR=1.08, 95% CI 0.75-1.56), but 23% and 27% increased risks for ever OCP use in the left-censored and full retrospective analyses, respectively. Retrospectively, an increasing trend for longer duration of use, especially before first full-term pregnancy (FFTP) was found (left-censored analyses: 10 years HR 1.41 (95%CI 1.10-1.813), p-trend=0.001 for duration of use before FFTP). For BRCA2 mutation carriers we found a positive association between ever OCP use and risk of breast cancer prospectively (HR=1.75, 95% CI 1.03-2.97), but retrospectively findings were inconsistent (HR=1.06, 95% CI 0.85-1.33 and HR=1.52, 95% CI 1.28-1.81 for the left-censored and full analyses, respectively). Conclusion: For BRCA1 mutation carriers the discrepancy between results of prospective and retrospective analyses may be explained by time since last OCP use before FFTP. Thus, a temporal increased risk of breast cancer following longer duration of OCP use before FFTP cannot be ruled out. The discordant findings between prospective and retrospective analyses for BRCA2 carriers could not be explained. Because of the lack of scientific clarity it is too early to give an unequivocal advice on OCP use with respect to breast cancer risk to BRCA1 and BRCA2 mutation carriers.
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| 9. |
- Ullmark, Tove, et al.
(author)
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Global binding pattern of the Wilms' tumor gene 1 (WT1) +17AA -KTS isoform in leukemic cells
- 2016
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In: Cancer Research. - 1538-7445. ; 76:14 Suppl.
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Conference paper (peer-reviewed)abstract
- The aim of this study was to investigate the global DNA-binding pattern of Wilms' tumor gene 1 (WT1) in leukemic cells. Clinical and preclinical data indicate the zinc finger transcription factor WT1 as an oncogene, but the full target gene repertoire of WT1 in leukemic cells has not been previously characterized. The -KTS isoforms (excluding the three amino acid (KTS) insert between zinc finger three and four) are considered as the most efficient DNA-binders. Among these, the 17AA isoform (including 17 amino acids encoded by exon 5) is the most abundant one. To specifically analyze the DNA-binding of WT1(+17AA/-KTS) in leukemic cells, we generated a K562 clone that stably expressed BIO-tagged WT1(+17AA/-KTS), as well as the biotinylating enzyme Bir A. From the cells chromatin immunoprecipitation (ChIP) by streptavidin capture was performed followed by sequencing with a minimum of 50 million reads per sample. After alignment to the genome and peak calling, peaks were characterized and compared to available K562 tracks in the ENCODE database. We found that 45% of identified WT1(+17AA/-KTS) peaks are in the proximity of transcription start sites (promoter area, first exon or first intron) of target genes, whereas only 11% of randomized peaks were found here. Within the peaks we show strong enrichment for three different previously published WT1-binding motifs. Comparison to ENCODE tracks showed that WT1(+17AA/-KTS) peaks are in close proximity to binding sites of other transcription factors, to histone marks for actively transcribed genes, and to binding sites of chromatin modifiers. Considering peaks within promoters and gene bodies only (for safe assignment to a target gene), Gene Ontology (GO) analysis revealed enrichment of GO groups important for proliferation, cell death, embryonic development, and cell motility. In conclusion, WT1(+17AA/-KTS) binds close to transcription start sites in areas of active transcription. The target genes implicated in proliferation, cell death, cell signaling and motility adds to the growing evidence of WT1 as an effector gene in leukemia.
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| 10. |
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| 11. |
- Brueffer, Christian, et al.
(author)
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Abstract P4-09-03: On the development and clinical value of RNA-sequencing-based classifiers for prediction of the five conventional breast cancer biomarkers: A report from the population-based multicenter SCAN-B study
- 2018
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In: Cancer research. Supplement. - 1538-7445. ; 78:4
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Conference paper (peer-reviewed)abstract
- Background:In early breast cancer, five histopathological biomarkers are part of current clinical routines and used for determining prognosis and treatment: estrogen receptor (ER), progesterone receptor (PgR), human epidermal growth factor receptor 2 (ERBB2/HER2), Ki67, and Nottingham histological grade (NHG). We aimed to develop classifiers for these biomarkers based on tumor mRNA-sequencing (RNA-seq), compare classification performance to conventional histopathology, and test whether RNA-seq-based predictors could add value for patient risk-stratification.Patients and Methods:In total, 3678 breast tumors were studied. For 405 breast tumors in the training cohort, a comprehensive histopathological biomarker evaluation was performed by three pathology readings to estimate inter-pathologist variability on the original diagnostic slides as well as on repeat immunostains for this study, and the consensus biomarker status for all five conventional biomarkers was determined. Whole transcriptome gene expression profiling was performed by RNA-sequencing on the Illumina platform. Using RNA-seq-derived tumor gene expression data as input, single-gene classifiers (SGC) and multi-gene classifiers (MGC) were trained on the consensus pathology biomarker labels. The trained classifiers were tested on an independent prospective population-based series of 3273 primary breast cancer cases from the multicenter SCAN-B study with median 41 months follow-up (ClinicalTrials.gov identifier NCT02306096), and classifications were evaluated by agreement statistics and by Kaplan-Meier and Cox regression survival analyses.Results:For the histopathological evaluation, pathologist evaluation concordance was high for ER, PgR, and HER2 (average kappa values of .920, .891, and .899, respectively), but moderate for Ki67 and NHG (.734 and .581). Classification concordance between RNA-seq classifiers and histopathology for the independent 3273-cohort was similar to that within histopathology assessments, with SGCs slightly outperforming MGCs. Importantly, patients with discordant results, classified as hormone responsive (HoR+) by histopathology but non-hormone responsive by MGC, presented with significantly inferior overall survival compared to patients with concordant results. These results extended to patients with no adjuvant systemic therapy (hazard ratio, HR, 4.54; 95% confidence interval, CI, 1.42-14.5), endocrine therapy alone (HR 3.46; 95% CI, 2.01-5.95), or receiving chemotherapy (HR 2.57; 95% CI 1.13-5.86). For HoR+ cases receiving endocrine therapy alone, the MGC HoR classifier remained significant after multivariable adjustment (HR 3.14; 95% CI, 1.75-5.65).Conclusions:RNA-seq-based classifiers for the five key early breast cancer biomarkers were generally equivalent to conventional histopathology with regards to classification error rate. However, when benchmarked using overall survival, our RNA-seq classifiers provided added clinical value in particular for cases that are determined by histopathology to be hormone-responsive but by RNA-seq appear hormone-insensitive and have a significantly poorer outcome when treated with endocrine therapy alone
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| 12. |
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| 14. |
- Loman, Niklas, et al.
(author)
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Abstract P2-02-09: Breast cancer subtype distribution and circulating tumor DNA in response to neoadjuvant chemotherapy: Experiences from a preoperative cohort within SCAN-B
- 2018
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In: Cancer research. Supplement. - 1538-7445. ; 78:4
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Conference paper (peer-reviewed)abstract
- Introduction: Preoperative chemotherapy in early breast cancer increases the rate of breast preservation and provides prognostic information. In the case of residual disease, a change in subtypes may be observed. Sensitive and reproducible biomarkers predicting treatment response early during the treatment course are needed in order to better exploit the potential benefit of an individualized preoperative treatment.Material and Methods: In an ongoing prospective study within the population-based SCAN-B project (NCT02306096), patients undergoing preoperative chemotherapy for early or locally recurrent breast cancer have been treated with iv Epirubicin and Cyclophosphamide q3w x 3 in sequence with either Docetaxel q3w x 3 or Paclitaxel q1w x 9 with a preoperative intent. HER2-positive cases also received HER2-directed treatment. At baseline, patients were staged using sentinel node biopsy for clinically node-negative patients and CT scan for cytologically confirmed node-positive cases. A clinical core needle biopsy as well as tissue from the surgical specimen was collected for determination of conventional biomarkers including ER, PgR, HER2 and Ki67. Tumor biopsies for biomolecule-extraction and RNA-sequencing were taken using ultrasound guidance and collected fresh in RNAlater at baseline, after 2 treatment cycles, as well as at surgery. Blood plasma samples were collected at baseline, after one-, three-, and six- 3w treatment cycles, and post-surgery. Using RNA-sequencing data, somatic mutations were identified in the tumor biopsies and personalized analyses for circulating tumor DNA (ctDNA) were performed. A pathological complete remission (pCR) was defined as the complete disappearance of invasive breast cancer in the breast and axilla at time of definitive surgery. Subtyping was performed using modified St Gallen criteria (2013).Results: Thus far, 45 patients aged 24-74 years have been included, of which 34 (76 %) were clinical stage 2 and 11 (24%) were stage 3. The subtype distribution at baseline was five Luminal A-like (11 %), 21 Luminal B-like (HER2 negative) (47 %), 8 HER2-positive (18 %) and 11 Triple-negative (ductal) (24 %). The rates of pCR in 38 operated cases to date were 0/3 Luminal A-like, 3/19 Luminal B-like (HER2 negative), 2/8 HER2-positive, and 4/7 Triple-negative (overall 24 % pCR rate). One patient did not undergo surgery due to clinically progressive disease. In 25 cases with evaluable residual disease at surgery, there was a shift in the subtype in 13 (52 %), the majority of which represented a transition from Luminal B to Luminal A. No Triple-negative cases underwent a change in subtype during treatment. Results of the ctDNA analyses will be presented at the meeting.Discussion: We have established an infrastructure allowing for an extensive evaluation of preoperative chemotherapy in early breast cancer. The goal is to develop methods to refine response-guided treatment in early breast cancer using molecular responses in the tumor as well as in the blood circulation. The patients continue to be prospectively monitored with iterative ctDNA analyses during follow-up.
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| 15. |
- Morgan, G, et al.
(author)
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Abstract P3-02-02: Concordance between immunohistochemical and gene-expression based subtyping of early breast cancer using core needle biopsies and surgical specimens - experices from SCAN-B
- 2018
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In: Cancer research. Supplement. - 1538-7445. ; 78:4
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Conference paper (peer-reviewed)abstract
- Introduction: Preoperative chemotherapy in early breast cancer increases the rate of breast preservation and provides prognostic information. Treatment decisions in these cases rely on biomarker assessments and subtyping from tissue acquired through core needle biopsies. Tumor heterogeneity and representativity are pit-falls when limited tissue is available. Biomarker expression may change considerably as a result of preoperative chemotherapy, and in a subset of cases a complete pathological response at time of surgery may even preclude any further assessment. Therefore, the reliability and reproducibility of biomarkers in base-line core biopsies are of utmost importance for patients treated with preoperative chemotherapy.Material and Methods: In an ongoing population-based study of early breast cancer, the SCAN-B (NCT02306096), patients were identified for whom an ultra-sound guided core needle biopsy was analyzed for biomarkers during primary clinical work-up and the patient was offered primary surgery as initial treatment. Clinical biomarker profiles including immunohistochemical (IHC) determinations of ER, PgR, HER2 and Ki67 were translated to subtypes according to modified St Gallen criteria (2013) and compared with paired samples from surgical specimens. In addition, tumor specimens for biomolecule extraction and RNA sequencing were collected fresh in RNAlater.Results: IHC data was available from 51 paired samples. The subtype distribution in core needle biopsies was DCIS in 1 case (2 %), LCIS in 1 case (2 %) Luminal A-like in 16 cases (31 %), Luminal B-like (HER2 negative) in 26 cases (51 %), Luminal B-HER2-like (HER2 positive) in 4 cases (8 %), HER2-positive (non-luminal) in 1 case (2 %) and triple negative (ductal) breast cancer in 2 cases (4 %). The subtype distribution in surgical specimens was DCIS in 0 case (0 %), LCIS in 1 case (2 %) Luminal A-like in 18 cases (35 %), Luminal B-like (HER2negative) in 23 cases (45 %), Luminal B--like (HER2 positive) in 6 cases (12 %), HER2-positive (non-luminal) in 1 case (2 %) and triple negative (ductal) breast cancer in 2 cases (4 %). Notably, 5/16 cases classified as Luminal A-like in the core needle biopsy were reclassified as Luminal B-like (HER2-negative) in the surgical specimen, whereas 9/26 cases classified as Luminal B-like (HER2-negative) in the core needle biopsy were reclassified as either Luminal A-like (7 cases) or Luminal B-like (HER2 positive) (2 cases) in the surgical specimen. In all instances, except one, transition between Luminal A-like and Luminal B-like was due to recorded Ki67 expression. One case that was classified as a DCIS in the core needle was reclassified as Luminal B-like (HER2 negative) at time of surgery.Discussion: In this limited material, discordance between evaluations regarding Luminal A-like and Luminal B-like was considerable. Especially the misclassification of primary HER2-positive breast cancer needs further evaluation. These findings may be caused by tumor heterogeneity, and highlight the risk of both over- and under-treatment upon biomarker assessment from core needle biopsies. Data from gene expression based subtype classifications will be presented during the meeting.
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| 16. |
- Nielsen, Torsten O, et al.
(author)
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Abstract P2-03-01: Analytical validation of a standardized scoring protocol for Ki67 assessed on breast excision whole sections: An international multicenter collaboration
- 2018
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In: Cancer research. Supplement. - 1538-7445. ; 78:4
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Conference paper (peer-reviewed)abstract
- Aims: (i) Determine whether between-observer reproducibility for Ki67 when assessed on whole sections according to a standardized scoring protocol is adequate for clinical application. (ii) Compare between-observer reproducibility of Ki67 scores assessed on hot-spots to scores using a global method that averages across a tissue section.Background: The nuclear proliferation biomarker Ki67 has multiple potential roles in breast cancer, including aiding decisions based on prognosis, but unacceptable levels of between-laboratory variability have been observed. The International Ki67 in Breast Cancer Working Group has undertaken a systematic program to determine whether Ki67 measurement can be analytically validated and standardized across labs. In phase 1, variability in visual interpretation was identified as an important source of variability. Phases 2 and 3a showed that adherence to defined scoring methods substantially improved reproducibility in scoring tissue microarrays and core-cut biopsies. We now assess whether acceptable reproducibility can be achieved on whole sections.Methods: Adjacent sections from 30 primary ER+ breast cancers were centrally stained for Ki67 to assemble 4 sets of 30 stained tumor sections, circulated around 23 labs in 12 countries. Ki67 was scored by 2 methods by all labs: (a) global: 4 fields of 100 tumor cells each were selected to reflect observed heterogeneity in nuclear staining (b) hot-spot: the field with highest Ki67 percentage of tumor cells with nuclear staining was selected and up to 500 cells scored. Ki67 scores were log2-transformed for statistical analyses and back-transformed for presentation. The primary objective was to assess whether either method could achieve an intraclass correlation coefficient (ICC) significantly greater than 0.8, considered substantial to almost-perfect reproducibility. Secondary objectives were to assess which method had highest observed ICC and to assess whether observers identified the same “hot-spots”.Results: ICC for the global method was 0.87 (95%CI: 0.799-0.93), marginally meeting the prespecified success criterion. The ICC for the hot-spot method was 0.83 (95%CI: 0.74-0.90) and had a CI extending below the success criterion. Across the 23 labs, geometric mean value of the 30 scores ranged from 8.5 to 19.6 for the global method and from 12.8 to 30.3 for the hot-spot method. The overall mean (95% CI) of these values was 12.9 (11.9-14.0) and 20.9 (19.1-22.8), respectively. Visually, between-laboratory agreement in location of selected hot-spot varies between cases. The median times for scoring were 9 and 6 minutes for global and hot-spot methods respectively.Conclusions: The global method marginally met the prespecified criterion of success; it should now be evaluated for clinical validity in appropriate cohorts of cases. The hot-spot method was observed to have slightly less reproducibility between labs. The time taken for scoring by either method is practical using counting software we are making publicly available. Establishment of external quality assessment schemes is likely to improve the reproducibility between labs further
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| 18. |
- Staaf, Johan, et al.
(author)
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Abstract P1-06-01: Putting multigene signatures to the test: Prognostic assessment in population-based contemporary clinical breast cancer
- 2018
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In: Cancer research. Supplement. - 1538-7445. ; 78:4
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Conference paper (peer-reviewed)abstract
- Background Gene expression signatures hold promise for a molecularly driven division of primary breast cancer with clinical implications. A gap still remains in the application/validation of such signatures in actual clinical treatment groups from unselected, population-based, primary breast cancer receiving current standard of care therapy. We analyzed classification proportions and overall survival (OS) of 14 reported gene expression phenotypes (GEPs) and risk predictors (RPs) in seven clinical treatments groups from an 3273-sample breast cancer cohort representative of population-based disease in the South Swedish healthcare region. Patients and methods Between 2010-09-01 to 2015-03-31, 5101 (87%) of 5892 patients with invasive primary disease in the healthcare region were included in the SCAN-B study (ClinicalTrials.gov ID: NCT02306096). Inclusion criteria included no generalized/prior contralateral disease and known surgery/treatment status (neo- or adjuvant). 3273 tumors were profiled by RNA sequencing and matched to clinicopathological patient data from the National Breast Cancer Register, with distribution of clinicopathological characteristics reflecting proportions in the catchment region. RNA profiles were classified according to 14 reported gene signatures featuring both GEPs (PAM50, IC10, CIT, TNBCtype) and specific risk predictors (e.g. Oncotype Dx, 70-gene, 76-gene, ROR-variants, genomic grade index). Classifications were investigated for association with patient OS by univariate and multivariate analyses in seven adjuvant clinical treatment groups: TNBC-ACT (adjuvant chemotherapy, n=228), TNBC-untreated (n=83), HER2+/ER- with trastuzumab + ACT treatment (n=101), HER2+/ER+ with trastuzumab + ACT + endocrine treatment (n=210), ER+/HER2- with endocrine treatment (n=1477), ER+/HER2- with endocrine + ACT treatment (n=637), and ER+/HER2- untreated (n=216). Results For the majority of signatures, analysis of classification demonstrated prognostic value limited to ER+/HER2- tumors given follow-up time. Several signatures (including Oncotype Dx, 70-gene, ROR-variants) showed strong predictive value in identifying a subset of ER+/HER2- patients receiving a combination of endocrine and ACT therapy with excellent overall survival (>96%), indicating appropriate therapy selection. In addition, for both ER+/HER2- treatment groups signature analysis identified high-risk groups of patients in clear need of additional treatment beyond standard therapeutic regimes, even with less than 5-years of follow-up. Conclusions Our results support the prognostic association of gene expression signatures in large unselected population-based primary breast cancer cohorts even with a short follow-up of OS.Importantly, prognostic associations are limited to specific subgroups for different classifiers and in population-based breast cancer some clinically important subgroups constitute a small proportion of cases. In this context, continued population-based inclusion and broad transcriptional profiling of breast cancer patients provides an opportunity for application to broader patient groups (e.g. TNBC and HER2+), and for consensus classification of individual risk assessments that could potentially provide more stable predictions.
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| 19. |
- Ali, Zaheer, et al.
(author)
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Abstract 6124 : Translation of zebrafish tumor-derived xenograft-models for improved diagnosis and treatment planning in urinary bladder cancer patients
- 2020
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In: Cancer Research. - : American Association for Cancer Research. - 0008-5472 .- 1538-7445. ; 80:6 Supplement, s. 6124-6124
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Journal article (peer-reviewed)abstract
- Precision medicine in oncology aims to identify the most effective treatment for any given patient based on individualized analyses of patient material. Currently, precision medicine relies on sequencing of DNA or RNA to identify patient tumor-specific mutational profiles that may be coupled to drug response. These techniques, however, fail to reveal actionable mutations in approximately 85% of the cancer patients, and have not been established at all for many commonly used drugs including cisplatin-based treatments used in urinary bladder cancer. While mouse-PDX models can determine drug response rates with high accuracy in most patients and for most drugs, such techniques are too slow and expensive to be relevant for first line treatment planning. Urinary bladder cancer patients are often treated with cisplatin-containing combination therapy, with the hope of down-staging tumors before surgery. 60%, however, do not respond or even progress on this treatment, and these patients would benefit from immediate surgery upon diagnosis. To help identify non-responding patients, we show here that patient-derived tumor xenograft models can be established in zebrafish larvae (ZTX models) and that the resulting tumors exhibit differential responses to the two main cisplatin-containing treatments GC and MVAC.Preliminary results from the first 19 patients are presented. Two tumor biopsies were destroyed during transport and two did not allow isolation of sufficient viable cells for implantation. From the remaining 15 samples an average of 2,6 million cells with average viability of 53% were isolated and used to implant at least 60 2-days old larvae. All 15 samples implanted in the larvae and survived and/or grew exhibiting varying degrees of metastatic dissemination (average between 2 and 13 metastasized cells per embryo and model) within only three days from implantation. Four ZTX models exhibited different responses to GC and MVAC demonstrating that these treatments are not equally effective in all patients. Non-response in ZTX models was associated with tumors having re-appeared in the bladder upon radical cystectomy in all patients undergoing surgery prior to Dec. 5th 2019 (n=3). GC inhibited metastasis in all models (average 69% inhibition), whereas MVAC inhibited metastasis in 40% of the models (average 36% inhibition).In conclusion: The ZTX urinary bladder cancer platform presented here overcome limitations associated with long assay time and high cost of other functional models within precision medicine as well as the low hit-rate of actionable mutations associated with genomic techniques. ZTX models will therefore likely become a powerful method for functional precision medicine within oncology, in the near future.
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| 20. |
- Arroyo, Vidal M., et al.
(author)
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Soft tissue sarcoma clinical presentation, treatment, and survival in adolescents and young adults compared to older adults : A report from the Scandinavian Sarcoma Group
- 2018
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In: Cancer Research. - : American Association for Cancer Research. - 0008-5472 .- 1538-7445. ; 78:13
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Journal article (other academic/artistic)abstract
- Background: Five-year survival rates for those diagnosed with soft tissue sarcoma (STS) have improved significantly among children and older adults (OAs), but these same trends have not been observed for adolescents and young adults (AYAs). While these disparities could be due to differences in biology or treatment, few studies have evaluated STS occurrence and outcome in AYAs. Therefore, the purpose of this study was to evaluate differences between adolescents and young adults (AYAs) and older adults (OAs) diagnosed with STS by stratifying analysis by: (1) clinical presentation; (2) treatment; and (3) survival.Methods: Data were obtained from the Scandinavian Sarcoma Group (SSG) Central Register, which includes information on 5,747 patients from Sweden and Norway, diagnosed with a STS during 1986-2011. Variables included: age at diagnosis, metastasis at diagnosis, tumor size, histology, adjuvant treatment, date of death or last follow-up. AYAs were defined as those diagnosed ages 15-39 years. Categorical variables were analyzed using chi-square tests, and continuous variables were analyzed using t-tests. Overall survival (OS) and recurrence-free survival (RFS) were compared between AYAs and OAs using Kaplan-Meier estimates and log-rank tests. All analyses were conducted overall and by common STS subtypes.Results: Overall and by STS subtype, there were significant differences between AYAs and OAs on presentation, treatment, and survival. The distribution of STS subtypes was different between OAs and AYAs. For example, OAs were more likely to be diagnosed with leiomyosarcoma compared to AYAs (18% vs. 10%, p<0.001), whereas AYAs were more likely to be diagnosed with malignant peripheral nerve sheath tumor (MPNST, 9% vs. 4%, p<0.001). OAs were also more likely to have larger tumors (>5 cm, 67% vs. 52%, p<0.001) and higher malignancy grade (grade IV, 45% vs. 31%, p<0.001). Interestingly, AYAs were more likely to be treated with radiotherapy and chemotherapy compared to OAs (12% vs. 5%, p<0.001). There were also differences within STS subtypes. For example, OAs were more likely to have metastasis compared to AYAs if diagnosed with leiomyosarcoma (18% vs. 10%, p=0.04). In most scenarios AYAs had significantly better OS and RFS compared to OAs, other than for MPNST (OS: p=0.19, RFS: p=0.28).Conclusions: There were several differences between AYAs and OAs on STS presentation, treatment, and outcome. AYAs not only had differences in terms of STS subtypes but also tumor size and malignancy grade within subtypes. Additional work is needed to characterize the biology underlying these differences, which will inform future treatment strategies for both AYAs and OAs with STS.
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- Harrison, Tabitha A., et al.
(author)
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Genome-wide association study by colorectal carcinoma subtype
- 2018
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In: Cancer Research. - : American Association for Cancer Research. - 0008-5472 .- 1538-7445. ; 78:13
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Journal article (other academic/artistic)abstract
- Over 50 genetic variants have been associated with colorectal cancer (CRC) risk through genome-wide association studies (GWAS), yet these variants represent only a fraction of the total estimated heritability. CRC is a heterogenous disease with diverse tumor etiology. Assessing genetic risk in molecular subtypes may help to identify novel loci and characterize genetic risk among tumor subtypes. We used microsatellite instability (MSI), an established CRC classifier with etiological and therapeutic relevance, to define CRC subtypes for GWAS analyses. We conducted a case-case analysis to estimate odds ratios (OR) and 95% confidence intervals (CI) for association of genome-wide variants with microsatellite stable (MSS) versus unstable (MSI) carcinomas. We ran an inverse-variance weighted fixed-effects meta-analysis across GWAS in a discovery set of 4,163 population-based CRC cases with harmonized microsatellite instability (MSI) marker and imputed genotype data. For each analysis, we used log-additive logistic regression, adjusting for age, sex, and principal components to account for population substructure. We then followed up with replication of 102 SNPs that reached p-values less than 5x10-6 in 1,698 cases. A total of 845 (20.3%) cancer cases were microsatellite unstable in the discovery population and 174 (10.2%) were unstable in the replication population. No variants reached the genome-wide significance level of 5x10-8 in the discovery set. However, we identified two variants that reached a Bonferroni corrected p-value of 4.0x10-4 in the replication set. This included one variant in MLH1 (Replication: OR=1.74, 95% CI=1.53-1.98, p=1.63x10-5; Discovery+Replication: OR=1.45, 95% CI=1.37-1.54, p=9.76x10-11) and one variant in LOC105377645 (Replication: OR=1.70, 95% CI=1.49-1.94, p=5.13x10-5; Discovery+Replication: OR=1.45, 95% CI=1.37-1.54, p=9.76 x 10-11). The MLH1 gene is a DNA mismatch repair gene implicated in Lynch Syndrome, the hallmark of which is microsatellite instability. This is the first genome-wide scan to identify a common variant in MLH1 that is associated with CRC. This variant (minor allele frequency, MAF = 23% in this all European ancestry population) is located in the 5'-untranslated region of MLH1 and is thought to act as a long-range regulator of DCLK3, a potential tumor driver gene. The second variant, located in LOC105377645 with an MAF of 22%, is in an uncharacterized region of the genome and has not previously been implicated in cancer development. These findings suggest that accounting for molecular heterogeneity is important for discovery and characterization of genetic variants associated with CRC risk. We plan to run polytomous regression analyses, increase our sample size, and further investigate CRC subtypes by CIMP, BRAF mutation, KRAS mutation status.
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- Jacobs, Daniel I., et al.
(author)
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Elucidating the molecular pathogenesis of familial glioma
- 2018
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In: Cancer Research. - : American Association for Cancer Research. - 0008-5472 .- 1538-7445. ; 78:13
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Journal article (other academic/artistic)abstract
- In recent years, the molecular characterization of sporadically arising diffuse gliomas has identified recurrent driving alterations and delineated molecularly and clinically distinct subclasses of disease. However, less is known about the molecular nature of gliomas that are familial in origin. To address this question, we integrated germline and somatic genomic data to characterize the molecular pathogenesis of 20 tumors arising in unrelated individuals with a family history of glioma collected through the Gliogene International Consortium. METHODS: FFPE tumor specimens were sectioned and reviewed to localize neoplastic tissue for DNA extraction. Library preparation, exome plus targeted capture, and paired-end sequencing on the Illumina HiSeq 2000 platform was performed at the Baylor College of Medicine Human Genome Sequencing Center. Single-nucleotide variants and indels were called with respect to germline DNA sequencing data for each case using MuTect2. Copy number profiling was performed on the Illumina HumanOmniExpress BeadChip and analyzed using GenomeStudio v2.0. Genotypes at known glioma risk polymorphisms were determined from germline DNA profiled on the Illumina Infinium OncoArray and rare, predicted deleterious germline mutations were identified from germline whole-exome sequencing data. RESULTS: Tumor exome sequencing was completed at an average read depth of 116X and we detected a median of 54 non-silent somatic mutations per tumor across the 20 tumors profiled. All three molecular subtypes of sporadic glioma were represented, including IDH-mutant, 1p/19q codeleted (n=3), IDH-mutant, 1p/19q intact (n=7), and IDH-wildtype tumors (n=10). Characteristic subtype-specific mutations and copy number alterations (e.g., TP53 and ATRX mutations among IDH-mutant, 1p/19q intact tumors) were observed, and the frequencies of recurrent alterations were comparable to sporadic glioma cases analyzed by The Cancer Genome Atlas. Notably, all 20 cases had alterations in genes regulating telomere length; 17 had acquired mutations in ATRX or the TERT promoter as typically seen in sporadic glioma, while three instead had germline mutations in telomere shelterin complex genes POT1 or TERF2. Frequencies of known common glioma risk alleles were similar to those among sporadic cases and correlations between risk alleles and specific somatic mutations were not observed. CONCLUSIONS: This study illustrates: 1) the complementarity of inherited and acquired alterations in driving gliomagenesis in some individuals with a familial predisposition to the disease; and 2) that the molecular characteristics of familial tumors profiled largely recapitulate what is known about sporadic glioma. In the majority of cases, the source of germline genetic susceptibility is not known but does not appear to be conferred by common risk polymorphisms.
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- Ostrom, Quinn T., et al.
(author)
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Evaluating glioma risk associated with extent of European admixture in African-Americans and Latinos
- 2018
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In: Cancer Research. - : American Association for Cancer Research. - 0008-5472 .- 1538-7445. ; 78:13
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Journal article (other academic/artistic)abstract
- Glioma incidence is highest in non-Hispanic Whites, where it occurs ~2x as frequently compared with other race/ethnicity groups. Glioma GWAS to date have included European ancestry populations only, and it is unknown whether variants identified by these analyses are associated with glioma in non- European ancestry populations. African Americans and Hispanics are admixed populations with varying proportions of European ancestry. While global ancestry may be similar within admixed groups, the proportion of European ancestry at each allele can vary across the genome. As glioma is more common in European ancestry populations, the presence of increased local European ancestry in these admixed populations could be used to identify glioma risk loci. Here we assessed whether excess European ancestry at established risk loci (Melin et al, Nature Genetics, 2017) was associated with glioma risk in non-European ancestry populations. Global ancestry was estimated using fastStructure, and local ancestry was estimated using RFMix. Both methods used 1,000 genomes project reference populations (African: YRI; European: CEU; East Asian: CHB/JPT; and Native American: CLM/PEL/MXL). We evaluated differences in local European ancestry between cases and controls using logistic regression conditioned on global European ancestry within 500kb of 25 previously identified risk variants among individuals with ≥50% African ancestry, and ≥30% Native American ancestry for all gliomas, and for grade IV glioblastoma (GBM) and grade II-III non-GBM. There were 347 individuals (184 cases and 163 controls) with ≥50% global African ancestry, and 277 individuals (153 cases and 124 controls) with ≥30% global American ancestry. There was no significant difference in proportion of global European ancestry between cases and controls with ≥50% global African ancestry (cases: 18.2%, controls: 17.7%, p=0.6834), and no significant difference in proportion of global European ancestry between cases and controls with ≥30% global American ancestry (cases: 51.1%, controls: 49.0%, p=0.2123). Among individuals with >50% African ancestry, we observed a nominally significant association between all glioma and increased local European ancestry at 7p11.2 (EGFR, pmin=0.0070) and between GBM and increased local European ancestry at 22q13.1 (CSNK1E, pmin=0.0098), both near SNPs previously associated with glioblastoma in majority European-ancestry populations. The dataset used for this analysis represents the largest collection of genotyped non-European glioma cases. These results suggest that glioma risk in African Americans may be associated with an increased local European ancestry variants at glioma risk loci previously identified in majority European ancestry populations (7p11.2 and 22q13.1).
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