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2.
Clin Cancer Res ; 27(21): 5869-5877, 2021 11 01.
Article in English | MEDLINE | ID: mdl-34210686

ABSTRACT

PURPOSE: Almost all cervical cancers are caused by human papillomavirus (HPV) and patients with advanced stage are at high risk for relapse. Circulating HPV DNA (HPV ctDNA) may serve as a residual tumor marker at the end of chemoradiation or to predict relapse during the follow-up period. EXPERIMENTAL DESIGN: We analyzed serum samples from 94 HPV16- or HPV18-related CCs from the BioRAIDs prospective cohort. Samples were collected before and after treatment and during an 18-month follow-up period. Using digital droplet PCR (ddPCR), we assessed the relevance of circulating HPV E7 gene as a marker for residual disease compared to HPV integration site and PIK3CA mutations. Finally, the prognostic impact of circulating HPV E7 gene was assessed with its prediction value of relapse. RESULTS: HPV E7 gene was the most sensitive tumor marker, superior to both HPV integration sites and PIK3CA mutations in serum. Circulating HPV DNA (HPV ctDNA) was detected in 63% (59/94) of patients, before treatment. HPV ctDNA detection in serum sample was associated with high FIGO stage (P = 0.02) and para-aortic lymph node involvement (P = 0.01). The level of HPV ctDNA was positively correlated with HPV copy number in the tumor (R = 0.39, P < 0.001). Complete clearance of HPV ctDNA by the end of treatment was significantly associated with a longer PFS (P < 0.0001). Patients with persistent HPV ctDNA in serum relapsed with a median time of 10 months (range, 2-15) from HPV ctDNA detection. CONCLUSIONS: HPV ctDNA detection is a useful marker to predict relapse in cervical cancer.See related commentary by Wentzensen and Clarke, p. 5733.


Subject(s)
Alphapapillomavirus/genetics , Biomarkers, Tumor/blood , DNA, Viral/blood , Early Detection of Cancer , Neoplasm Recurrence, Local/blood , Neoplasm Recurrence, Local/virology , Neoplasm, Residual/blood , Neoplasm, Residual/virology , Papillomavirus Infections/blood , Uterine Cervical Neoplasms/blood , Uterine Cervical Neoplasms/virology , Adult , Aged , Aged, 80 and over , Chemoradiotherapy , Female , Humans , Middle Aged , Papillomavirus Infections/complications , Prospective Studies , Uterine Cervical Neoplasms/therapy , Young Adult
3.
Br J Cancer ; 124(4): 777-785, 2021 02.
Article in English | MEDLINE | ID: mdl-33191407

ABSTRACT

BACKGROUND: Cervical cancer (CC) remains a leading cause of gynaecological cancer-related mortality with infection by human papilloma virus (HPV) being the most important risk factor. We analysed the association between different viral integration signatures, clinical parameters and outcome in pre-treated CCs. METHODS: Different integration signatures were identified using HPV double capture followed by next-generation sequencing (NGS) in 272 CC patients from the BioRAIDs study [NCT02428842]. Correlations between HPV integration signatures and clinical, biological and molecular features were assessed. RESULTS: Episomal HPV was much less frequent in CC as compared to anal carcinoma (p < 0.0001). We identified >300 different HPV-chromosomal junctions (inter- or intra-genic). The most frequent integration site in CC was in MACROD2 gene followed by MIPOL1/TTC6 and TP63. HPV integration signatures were not associated with histological subtype, FIGO staging, treatment or PFS. HPVs were more frequently episomal in PIK3CA mutated tumours (p = 0.023). Viral integration type was dependent on HPV genotype (p < 0.0001); HPV18 and HPV45 being always integrated. High HPV copy number was associated with longer PFS (p = 0.011). CONCLUSIONS: This is to our knowledge the first study assessing the prognostic value of HPV integration in a prospectively annotated CC cohort, which detects a hotspot of HPV integration at MACROD2; involved in impaired PARP1 activity and chromosome instability.


Subject(s)
DNA Repair Enzymes/genetics , Hydrolases/genetics , Papillomaviridae/physiology , Papillomavirus Infections/virology , Uterine Cervical Neoplasms/virology , Virus Integration/genetics , Carcinoma, Squamous Cell/genetics , Carcinoma, Squamous Cell/virology , Class I Phosphatidylinositol 3-Kinases/genetics , Female , Humans , Kallikreins/genetics , Middle Aged , Papillomaviridae/genetics , Papillomavirus Infections/genetics , Progression-Free Survival , Prostate-Specific Antigen/genetics , Uterine Cervical Neoplasms/genetics
4.
EBioMedicine ; 61: 103049, 2020 Nov.
Article in English | MEDLINE | ID: mdl-33096476

ABSTRACT

BACKGROUND: Cervical cancer (CC) remains a leading cause of gynaecological cancer-related mortality world wide and constitutes the third most common malignancy in women. The RAIDs consortium (http://www.raids-fp7.eu/) conducted a prospective European study [BioRAIDs (NCT02428842)] with the objective to stratify CC patients for innovative treatments. A "metagene" of genomic markers in the PI3K pathway and epigenetic regulators had been previously associated with poor outcome [2]. METHODS: To detect new, more specific, targets for treatment of patients who resist standard chemo-radiation, a high-dimensional Cox model was applied to define dominant molecular variants, copy number variations, and reverse phase protein arrays (RPPA). FINDINGS: Survival analysis on 89 patients with all omics data available, suggested loss-of-function (LOF) or activating molecular alterations in nine genes to be candidate biomarkers for worse prognosis in patients treated by chemo-radiation while LOF of ATRX, MED13 as well as CASP8 were associated with better prognosis. When protein expression data by RPPA were factored in, the supposedly low molecular weight and nuclear form, of beta-catenin, phosphorylated in Ser552 (pß-Cat552), ranked highest for good prognosis, while pß-Cat675 was associated with worse prognosis. INTERPRETATION: These findings call for molecularly targeted treatments involving p53, Wnt pathway, PI3K pathway, and epigenetic regulator genes. Pß-Cat552 and pß-Cat675 may be useful biomarkers to predict outcome to chemo-radiation, which targets the DNA repair axis. FUNDING: European Union's Seventh Program for research, technological development and demonstration (agreement N°304,810), the Fondation ARC pour la recherche contre le cancer.


Subject(s)
Biomarkers, Tumor , Genetic Markers , Uterine Cervical Neoplasms/genetics , Uterine Cervical Neoplasms/metabolism , beta Catenin/genetics , beta Catenin/metabolism , Computational Biology , DNA Copy Number Variations , Disease Susceptibility , Female , Genetic Heterogeneity , Humans , Mutation , Neoplasm Staging , Phosphoproteins/genetics , Phosphoproteins/metabolism , Phosphorylation , Prognosis , Recurrence , Uterine Cervical Neoplasms/pathology , Uterine Cervical Neoplasms/therapy , Exome Sequencing
6.
Nat Commun ; 11(1): 2641, 2020 05 26.
Article in English | MEDLINE | ID: mdl-32457376

ABSTRACT

Acquired resistance to PARP inhibitors (PARPi) is a major challenge for the clinical management of high grade serous ovarian cancer (HGSOC). Here, we demonstrate CX-5461, the first-in-class inhibitor of RNA polymerase I transcription of ribosomal RNA genes (rDNA), induces replication stress and activates the DNA damage response. CX-5461 co-operates with PARPi in exacerbating replication stress and enhances therapeutic efficacy against homologous recombination (HR) DNA repair-deficient HGSOC-patient-derived xenograft (PDX) in vivo. We demonstrate CX-5461 has a different sensitivity spectrum to PARPi involving MRE11-dependent degradation of replication forks. Importantly, CX-5461 exhibits in vivo single agent efficacy in a HGSOC-PDX with reduced sensitivity to PARPi by overcoming replication fork protection. Further, we identify CX-5461-sensitivity gene expression signatures in primary and relapsed HGSOC. We propose CX-5461 is a promising therapy in combination with PARPi in HR-deficient HGSOC and also as a single agent for the treatment of relapsed disease.


Subject(s)
Benzothiazoles/pharmacology , Cystadenocarcinoma, Serous/drug therapy , DNA Damage , Naphthyridines/pharmacology , Ovarian Neoplasms/drug therapy , Animals , Cell Line, Tumor , Cystadenocarcinoma, Serous/genetics , Cystadenocarcinoma, Serous/metabolism , DNA Replication/drug effects , Drug Resistance, Neoplasm , Enzyme Inhibitors/pharmacology , Female , Heterografts , Homologous Recombination , Humans , Mice , Mice, Inbred NOD , Mice, Knockout , Mice, SCID , Models, Biological , Ovarian Neoplasms/genetics , Ovarian Neoplasms/metabolism , Poly(ADP-ribose) Polymerase Inhibitors/pharmacology , RNA Polymerase I/antagonists & inhibitors , Transcriptome
7.
Biomolecules ; 10(3)2020 03 07.
Article in English | MEDLINE | ID: mdl-32156073

ABSTRACT

The aim of this study was to determine an optimal workflow to detect TP53 mutations in baseline and longitudinal serum cell free DNA (cfDNA) from high-grade serous ovarian carcinomas (HGSOC) patients and to define whether TP53 mutations are suitable as biomarker for disease. TP53 was investigated in tissue and archived serum from 20 HGSOC patients by a next-generation sequencing (NGS) workflow alone or combined with digital PCR (dPCR). AmpliSeq™-focused NGS panels and customized dPCR assays were used for tissue DNA and longitudinal cfDNAs, and Oncomine NGS panel with molecular barcoding was used for baseline cfDNAs. TP53 missense mutations were observed in 17 tissue specimens and in baseline cfDNA for 4/8 patients by AmpliSeq, 6/9 patients by Oncomine, and 4/6 patients by dPCR. Mutations in cfDNA were detected in 4/6 patients with residual disease and 3/4 patients with disease progression within six months, compared to 5/11 patients with no residual disease and 6/13 patients with progression after six months. Finally, mutations were detected at progression in 5/6 patients, but not during chemotherapy. NGS with molecular barcoding and dPCR were most optimal workflows to detect TP53 mutations in baseline and longitudinal serum cfDNA, respectively. TP53 mutations were undetectable in cfDNA during treatment but re-appeared at disease progression, illustrating its promise as a biomarker for disease monitoring.


Subject(s)
Biomarkers, Tumor , Circulating Tumor DNA , Mutation, Missense , Ovarian Neoplasms , Tumor Suppressor Protein p53/genetics , Adult , Aged , Biomarkers, Tumor/genetics , Biomarkers, Tumor/metabolism , Circulating Tumor DNA/blood , Circulating Tumor DNA/genetics , Female , Humans , Middle Aged , Neoplasm, Residual , Ovarian Neoplasms/blood , Ovarian Neoplasms/drug therapy , Ovarian Neoplasms/genetics
8.
Cancer Lett ; 459: 1-12, 2019 09 10.
Article in English | MEDLINE | ID: mdl-31150822

ABSTRACT

High grade serous ovarian cancer (HGSOC) is the most frequent type of ovarian cancer. Most patients have primary response to platinum-based chemotherapy but frequently relapse, which leads to patient death. A lack of well documented and characterized patient-derived HGSOC cell lines is so far a major barrier to define tumor specific therapeutic targets and to study the molecular mechanisms underlying disease progression. We established 34 patient-derived HGSOC cell lines and characterized them at cellular and molecular level. Particularly, we demonstrated that a cancer-testis antigen PRAME and Estrogen Receptor could serve as therapeutic targets. Notably, data from the cell lines did not demonstrate acquired resistance due to tumor recurrence that matched with clinical observations. Finally, we presented that all HGSOC had no or very low CDKN1A (p21) expression due to loss of wild-type TP53, suggesting that loss of cell cycle control is the determinant for tumorigenesis and progression. In conclusion, patient-derived cell lines reveal that PRAME is a potential tumor specific therapeutic target in HGSOC and counteracting the down-regulation of p21 caused by loss of wild-type TP53 might be the key to impede disease progression.


Subject(s)
Cell Line, Tumor , Cystadenocarcinoma, Serous/drug therapy , Cystadenocarcinoma, Serous/pathology , Ovarian Neoplasms/drug therapy , Ovarian Neoplasms/pathology , Adult , Aged , Aged, 80 and over , Antigens, Neoplasm/biosynthesis , Antigens, Neoplasm/genetics , Carboplatin/pharmacology , Cell Cycle , Cyclin-Dependent Kinase Inhibitor p21/biosynthesis , Cyclin-Dependent Kinase Inhibitor p21/genetics , Cystadenocarcinoma, Serous/genetics , Disease Progression , Drug Resistance, Neoplasm , Drug Screening Assays, Antitumor/methods , Female , Humans , Middle Aged , Molecular Targeted Therapy , Neoplasm Grading , Ovarian Neoplasms/genetics , Receptors, Estrogen/biosynthesis , Receptors, Estrogen/genetics , Tumor Suppressor Protein p53/deficiency , Tumor Suppressor Protein p53/genetics
9.
EBioMedicine ; 43: 253-260, 2019 May.
Article in English | MEDLINE | ID: mdl-30952619

ABSTRACT

BACKGROUND: There is a lack of information as to which molecular processes, present at diagnosis, favor tumour escape from standard-of-care treatments in cervical cancer (CC). RAIDs consortium (www.raids-fp7.eu), conducted a prospectively monitored trial, [BioRAIDs (NCT02428842)] with the objectives to generate high quality samples and molecular assessments to stratify patient populations and to identify molecular patterns associated with poor outcome. METHODS: Between 2013 and 2017, RAIDs collected a prospective CC sample and clinical dataset involving 419 participant patients from 18 centers in seven EU countries. Next Generation Sequencing has so far been carried out on a total of 182 samples from 377 evaluable (48%) patients, allowing to define dominant genetic alterations. Reverse phase protein expression arrays (RPPA) was applied to group patients into clusters. Activation of key genetic pathways and protein expression signatures were tested for associations with outcome. FINDINGS: At a median follow up (FU) of 22 months, progression-free survival rates of this FIGO stage IB1-IV population, treated predominantly (87%) by chemoradiation, were65•4% [CI95%: 60•2-71.1]. Dominant oncogenic alterations were seen in PIK3CA (40%), while dominant suppressor gene alterations were seen in KMT2D (15%) and KMT2C (16%). Cumulative frequency of loss-of-function (LOF) mutations in any epigenetic modulator gene alteration was 47% and it was associated with PIK3CA gene alterations in 32%. Patients with tumours harboring alterations in both pathways had a significantly poorer PFS. A new finding was the detection of a high frequency of gains of TLR4 gene amplifications (10%), as well as amplifications, mutations, and non-frame-shift deletions of Androgen receptor (AR) gene in 7% of patients. Finally, RPPA protein expression analysis defined three expression clusters. INTERPRETATION: Our data suggests that patient population may be stratified into four different treatment strategies based on molecular markers at the outset. FUND: European Union's Seventh Program grant agreement No 304810.


Subject(s)
Biomarkers, Tumor , Class I Phosphatidylinositol 3-Kinases/genetics , Epigenesis, Genetic , Uterine Cervical Neoplasms/genetics , Adult , Aged , Combined Modality Therapy , Computational Biology/methods , Female , Gene Expression Profiling , Humans , Middle Aged , Neoplasm Metastasis , Neoplasm Staging , Prognosis , Treatment Outcome , Uterine Cervical Neoplasms/mortality , Uterine Cervical Neoplasms/pathology , Uterine Cervical Neoplasms/therapy , Exome Sequencing
10.
Oncogene ; 37(14): 1869-1884, 2018 04.
Article in English | MEDLINE | ID: mdl-29353882

ABSTRACT

Antiestrogen resistance in estrogen receptor positive (ER+) breast cancer is associated with increased expression and activity of insulin-like growth factor 1 receptor (IGF1R). Here, a kinome siRNA screen has identified 10 regulators of IGF1R-mediated antiestrogen with clinical significance. These include the tamoxifen resistance suppressors BMPR1B, CDK10, CDK5, EIF2AK1, and MAP2K5, and the tamoxifen resistance inducers CHEK1, PAK2, RPS6KC1, TTK, and TXK. The p21-activated kinase 2, PAK2, is the strongest resistance inducer. Silencing of the tamoxifen resistance inducing genes, particularly PAK2, attenuates IGF1R-mediated resistance to tamoxifen and fulvestrant. High expression of PAK2 in ER+ metastatic breast cancer patients is correlated with unfavorable outcome after first-line tamoxifen monotherapy. Phospho-proteomics has defined PAK2 and the PAK-interacting exchange factors PIXα/ß as downstream targets of IGF1R signaling, which are independent from PI3K/ATK and MAPK/ERK pathways. PAK2 and PIXα/ß modulate IGF1R signaling-driven cell scattering. Targeting PIXα/ß entirely mimics the effect of PAK2 silencing on antiestrogen re-sensitization. These data indicate PAK2/PIX as an effector pathway in IGF1R-mediated antiestrogen resistance.


Subject(s)
Antineoplastic Agents, Hormonal/therapeutic use , Breast Neoplasms/drug therapy , Drug Resistance, Neoplasm/genetics , Estrogen Antagonists/therapeutic use , Receptors, Somatomedin/physiology , Rho Guanine Nucleotide Exchange Factors/metabolism , p21-Activated Kinases/metabolism , Breast Neoplasms/genetics , Breast Neoplasms/metabolism , Breast Neoplasms/pathology , Cell Line, Tumor , Female , Gene Expression Regulation, Enzymologic/drug effects , Gene Expression Regulation, Neoplastic/drug effects , HEK293 Cells , High-Throughput Screening Assays , Humans , MCF-7 Cells , RNA, Small Interfering/pharmacology , Receptor, IGF Type 1 , Receptors, Somatomedin/genetics , Rho Guanine Nucleotide Exchange Factors/genetics , Signal Transduction/drug effects , Signal Transduction/physiology , Tamoxifen/therapeutic use , p21-Activated Kinases/genetics
11.
Clin Cancer Res ; 23(24): 7621-7632, 2017 Dec 15.
Article in English | MEDLINE | ID: mdl-28972047

ABSTRACT

Purpose: Most high-grade serous ovarian cancer (HGSOC) patients develop recurrent disease after first-line treatment, frequently with fatal outcome. This work aims at studying the molecular biology of both primary and recurrent HGSOC.Experimental Design: Gene expression profiles of matched primary and recurrent fresh-frozen tumor tissues from 66 HGSOC patients were obtained by RNA sequencing. Clustering analyses and pairwise comparison of the profiles between matched samples and subsequent functional alignment were used for the identification of molecular characteristics of HGSOC.Results: Both primary and recurrent HGSOC samples presented predominant gene expression differences in their microenvironment, determined by a panel of genes covering all major pathways of immune activation together with a number of genes involved in the remodeling of extracellular matrix and adipose tissues. Stratifying tumor tissues into immune active and silent groups, we further discovered that although some recurrent tumors shared the same immune status as their primary counterparts, others switched the immune status, either from silent to active or active to silent. Interestingly, genes belonging to the B7-CD28 immune checkpoint family, known for their major role as negative regulators of the immune response, were overexpressed in the immune active tumors. Searching for potential tumor antigens, CEACAM21, a member of the carcinoembryonic antigen family, was found to be significantly overexpressed in immune active tissues in comparison with the silent ones.Conclusions: The results illustrate the complexity of the tumor microenvironment in HGSOC and reveal the molecular relationship between primary and recurrent tumors, which have multiple therapeutic implications. Clin Cancer Res; 23(24); 7621-32. ©2017 AACR.


Subject(s)
Antigens, Neoplasm/genetics , Cystadenocarcinoma, Serous/genetics , Ovarian Neoplasms/genetics , Tumor Microenvironment/genetics , Adult , Aged , Antigens, Neoplasm/immunology , Cell Line, Tumor , Cystadenocarcinoma, Serous/immunology , Cystadenocarcinoma, Serous/pathology , Female , Gene Expression Regulation, Neoplastic , Humans , Middle Aged , Neoplasm Grading , Neoplasm Recurrence, Local/genetics , Neoplasm Recurrence, Local/pathology , Ovarian Neoplasms/immunology , Ovarian Neoplasms/pathology , Sequence Analysis, RNA , Tumor Microenvironment/immunology
12.
Transl Oncol ; 10(5): 854-866, 2017 Oct.
Article in English | MEDLINE | ID: mdl-28886403

ABSTRACT

INTRODUCTION: While mutations in PIK3CA are most frequently (45%) detected in luminal breast cancer, downstream PI3K/AKT/mTOR pathway activation is predominantly observed in the basal subtype. The aim was to identify proteins activated in PIK3CA mutated luminal breast cancer and the clinical relevance of such a protein in breast cancer patients. MATERIALS AND METHODS: Expression levels of 171 signaling pathway (phospho-)proteins established by The Cancer Genome Atlas (TCGA) using reverse phase protein arrays (RPPA) were in silico examined in 361 breast cancers for their relation with PIK3CA status. MAPK1/3 phosphorylation was evaluated with immunohistochemistry on tissue microarrays (TMA) containing 721 primary breast cancer core biopsies to explore the relationship with metastasis-free survival. RESULTS: In silico analyses revealed increased phosphorylation of MAPK1/3, p38 and YAP, and decreased expression of p70S6K and 4E-BP1 in PIK3CA mutated compared to wild-type luminal breast cancer. Augmented MAPK1/3 phosphorylation was most significant, i.e. in luminal A for both PIK3CA exon 9 and 20 mutations and in luminal B for exon 9 mutations. In 290 adjuvant systemic therapy naïve lymph node negative (LNN) breast cancer patients with luminal cancer, high MAPK phosphorylation in nuclei (HR=0.49; 95% CI, 0.25-0.95; P=.036) and in tumor cells (HR=0.37; 95% CI, 0.18-0.79; P=.010) was related with favorable metastasis-free survival in multivariate analyses including traditional prognostic factors. CONCLUSION: Enhanced MAPK1/3 phosphorylation in luminal breast cancer is related to PIK3CA exon-specific mutations and correlated with favorable prognosis especially when located in the nuclei of tumor cells.

13.
Clin Chem Lab Med ; 55(9): 1291-1304, 2017 Aug 28.
Article in English | MEDLINE | ID: mdl-28157690

ABSTRACT

BACKGROUND: Proteogenomics is an emerging field at the intersection of genomics and proteomics. Many variant peptides corresponding to single nucleotide variations (SNVs) are associated with specific diseases. The aim of this study was to demonstrate the feasibility of proteogenomic-based variant peptide detection in disease models and clinical specimens. METHODS: We sought to detect p53 single amino acid variant (SAAV) peptides in breast cancer tumor samples that have been previously subjected to sequencing analysis. Initially, two cancer cell lines having a cellular tumor antigen p53 (TP53) mutation and one wild type for TP53 were analyzed by selected reaction monitoring (SRM) assays as controls. One pool of wild type and one pool of mutated for TP53 cytosolic extracts were assayed with a shotgun proteogenomic workflow. Furthermore, 18 individual samples having a mutation in TP53 were assayed by SRM. RESULTS: Two mutant p53 peptides were successfully detected in two cancer cell lines as expected from their DNA sequence. Wild type p53 peptides were detected in both cytosolic pools, however, none of the mutant p53 peptides were identified. Mutations at the protein level were detected in two cytosolic extracts and whole tumor lysates from the same patients by SRM analysis. Six thousand and six hundred and twenty eight non-redundant proteins were identified in the two cytosolic pools, thus greatly improving a previously reported cytosolic proteome. CONCLUSIONS: In the current study we show the great potential of using proteogenomics for the direct identification of cancer-associated mutations in clinical samples and we discuss current limitations and future perspectives.


Subject(s)
Peptides/analysis , Peptides/genetics , Proteogenomics , Tumor Suppressor Protein p53/genetics , Cell Line, Tumor , Chromatography, Liquid , Cytosol/chemistry , Enzyme-Linked Immunosorbent Assay , Humans , Mass Spectrometry , Mutation , Neoplasms/genetics , Peptides/chemistry , Reproducibility of Results , Tandem Mass Spectrometry , Tumor Suppressor Protein p53/analysis , Tumor Suppressor Protein p53/chemistry , Validation Studies as Topic
14.
Clin Cancer Res ; 23(9): 2213-2222, 2017 May 01.
Article in English | MEDLINE | ID: mdl-27663594

ABSTRACT

Purpose: DNA damage repair can lead to epigenetic changes. DNA mismatch repair proteins bind to platinum DNA adducts and at sites of DNA damage can recruit the DNA methylating enzyme DNMT1, resulting in aberrant methylation. We hypothesised that DNA damage repair during platinum-based chemotherapy may cause aberrant DNA methylation in normal tissues of patients such as blood.Experimental Design: We used Illumina 450k methylation arrays and bisulphite pyrosequencing to investigate methylation at presentation and relapse in blood DNA from patients with ovarian cancer enrolled in the SCOTROC1 trial (n = 247) and in a cohort of ovarian tumor DNA samples collected at first relapse (n = 46). We used an ovarian cancer cell line model to investigate the role of the DNA mismatch repair gene MLH1 in platinum-induced methylation changes.Results: Specific CpG methylation changes in blood at relapse are observed following platinum-based chemotherapy and are associated with patient survival, independent of other clinical factors [hazard ratio, 3.7; 95% confidence interval, 1.8-7.6, P = 2.8 × 10-4]. Similar changes occur in ovarian tumors at relapse, also associated with patient survival (hazard ratio, 2.6; 95% confidence interval, 1.0-6.8, P = 0.048). Using an ovarian cancer cell line model, we demonstrate that functional mismatch repair increases the frequency of platinum-induced methylation.Conclusions: DNA methylation in blood at relapse following chemotherapy, and not at presentation, is informative regarding survival of patients with ovarian cancer. Functional DNA mismatch repair increases the frequency of DNA methylation changes induced by platinum. DNA methylation in blood following chemotherapy could provide a noninvasive means of monitoring patients' epigenetic responses to treatment without requiring a tumor biopsy. Clin Cancer Res; 23(9); 2213-22. ©2016 AACR.


Subject(s)
DNA Methylation/genetics , DNA, Neoplasm/blood , Ovarian Neoplasms/drug therapy , Platinum/administration & dosage , Aged , Cell Line, Tumor , DNA Adducts/genetics , DNA Damage/drug effects , DNA Methylation/drug effects , DNA Repair/drug effects , DNA, Neoplasm/genetics , Drug Resistance, Neoplasm/genetics , Female , Gene Expression Regulation, Neoplastic/drug effects , Humans , Middle Aged , Neoplasm Recurrence, Local/drug therapy , Neoplasm Recurrence, Local/genetics , Neoplasm Recurrence, Local/pathology , Ovarian Neoplasms/genetics , Ovarian Neoplasms/pathology , Platinum/adverse effects , Promoter Regions, Genetic
15.
Br J Cancer ; 115(12): 1575-1583, 2016 Dec 06.
Article in English | MEDLINE | ID: mdl-27875525

ABSTRACT

BACKGROUND: Cervical cancer (CC) remains a leading cause of gynaecological cancer-related mortality worldwide. CC pathogenesis is triggered when human papillomavirus (HPV) inserts into the genome, resulting in tumour suppressor gene inactivation and oncogene activation. Collecting tumour and blood samples is critical for identifying these genetic alterations. METHODS: BIO-RAIDs is the first prospective molecular profiling clinical study to include a substantial biobanking effort that used uniform high-quality standards and control of samples. In this European Union (EU)-funded study, we identified the challenges that were impeding the effective implementation of such a systematic and comprehensive biobanking effort. RESULTS: The challenges included a lack of uniform international legal and ethical standards, complexities in clinical and molecular data management, and difficulties in determining the best technical platforms and data analysis techniques. Some difficulties were encountered by all investigators, while others affected only certain institutions, regions, or countries. CONCLUSIONS: The results of the BIO-RAIDs programme highlight the need to facilitate and standardise regulatory procedures, and we feel that there is also a need for international working groups that make recommendations to regulatory bodies, governmental funding agencies, and academic institutions to achieve a proficient biobanking programme throughout EU countries. This represents the first step in precision medicine.


Subject(s)
Biological Specimen Banks , Uterine Cervical Neoplasms/pathology , Female , Humans
16.
Mol Oncol ; 10(8): 1363-73, 2016 10.
Article in English | MEDLINE | ID: mdl-27491861

ABSTRACT

BACKGROUND: PIK3CA is the most frequent somatic mutated oncogene in estrogen receptor (ER) positive breast cancer. We previously observed an association between PIK3CA genotype and aromatase inhibitors (AI) treatment outcome. This study now evaluates whether expression of mRNAs and miRs are linked to PIK3CA genotype and are independently related to AI therapy response in order to define potential expressed biomarkers for treatment outcome. MATERIALS AND METHODS: The miR and mRNA expression levels were evaluated for their relationship with the PIK3CA genotype in two breast tumor datasets, i.e. 286 luminal cancers from the TCGA consortium and our set of 84 ER positive primary tumors of metastatic breast cancer patients who received first line AI. BRB Array tools class comparison was performed to define miRs and mRNAs whose expression associate with PIK3CA exon 9 and 20 status. Spearman correlations established miR-mRNA pairs and mRNAs with related expression. Next, a third dataset of 25 breast cancer patients receiving neo-adjuvant letrozole was evaluated, to compare expression levels of identified miRs and mRNAs in biopsies before and after treatment. Finally, to identify potential biomarkers miR and mRNA levels were related with overall survival (OS) and progression free survival (PFS) after first-line AI therapy. RESULTS: Expression of 3 miRs (miR-449a, miR-205-5p, miR-301a-3p) and 9 mRNAs (CCNO, FAM81B, LRG1, NEK10, PLCL1, PGR, SERPINA3, SORBS2, VTCN1) was related to the PIK3CA status in both datasets. All except miR-301a-3p had an increased expression in tumors with PIK3CA mutations. Validation in a publicly available dataset showed that LRG1, PGR, and SERPINA3 levels were decreased after neo-adjuvant AI-treatment. Six miR-mRNA pairs correlated significantly and stepdown analysis of all 12 factors revealed 3 mRNAs (PLCL1, LRG1, FAM81B) related to PFS. Further analyses showed LRG1 and PLCL1 expression to be unrelated with luminal subtype and to associate with OS and with PFS, the latter independent from traditional predictive factors. CONCLUSION: We showed in two datasets of ER positive and luminal breast tumors that the expression of 3 miRs and 9 mRNAs associate with the PIK3CA status. Expression of LRG1 is independent of luminal (A or B) subtype, decreased after neo-adjuvant AI-treatment, and is proposed as potential biomarker for AI therapy outcome.


Subject(s)
Aromatase Inhibitors/therapeutic use , Breast Neoplasms/drug therapy , Breast Neoplasms/genetics , Class I Phosphatidylinositol 3-Kinases/genetics , Glycoproteins/genetics , Aromatase Inhibitors/pharmacology , Biomarkers, Tumor/metabolism , Class I Phosphatidylinositol 3-Kinases/metabolism , Disease-Free Survival , Female , Gene Expression Profiling , Gene Expression Regulation, Neoplastic/drug effects , Genotype , Glycoproteins/metabolism , Humans , MicroRNAs/genetics , MicroRNAs/metabolism , Mutation/genetics , RNA, Messenger/genetics , RNA, Messenger/metabolism , Transcriptome/genetics , Treatment Outcome
17.
Oncotarget ; 7(28): 43412-43418, 2016 Jul 12.
Article in English | MEDLINE | ID: mdl-27270325

ABSTRACT

The aim was to identify mutations in serum cell-free DNA (cfDNA) associated with disease progression on tamoxifen treatment in metastatic breast cancer (MBC). Sera available at start of therapy, during therapy and at disease progression were selected from 10 estrogen receptor (ER)-positive breast cancer patients. DNA from primary tumor and normal tissue and cfDNA from minute amounts of sera were analyzed by targeted next generation sequencing (NGS) of 45 genes (1,242 exons). At disease progression, stop-gain single nucleotide variants (SNVs) for CREBBP (1 patient) and SMAD4 (1 patient) and non-synonymous SNVs for AKAP9 (1 patient), PIK3CA (2 patients) and TP53 (2 patients) were found. Mutations in CREBBP and SMAD4 have only been occasionally reported in breast cancer. All mutations, except for AKAP9, were also present in the primary tumor but not detected in all blood specimens preceding progression. More sensitive detection by deeper re-sequencing and digital PCR confirmed the occurrence of circulating tumor DNA (ctDNA) and these biomarkers in blood specimens.


Subject(s)
Antineoplastic Agents, Hormonal/therapeutic use , Breast Neoplasms/genetics , Cell-Free Nucleic Acids/genetics , DNA, Neoplasm/genetics , Tamoxifen/therapeutic use , A Kinase Anchor Proteins/genetics , Biomarkers, Tumor/blood , Biomarkers, Tumor/genetics , Breast/pathology , Breast Neoplasms/blood , Breast Neoplasms/drug therapy , Breast Neoplasms/pathology , CREB-Binding Protein/genetics , Cell-Free Nucleic Acids/blood , Cell-Free Nucleic Acids/isolation & purification , Class I Phosphatidylinositol 3-Kinases/genetics , Cytoskeletal Proteins/genetics , DNA, Neoplasm/blood , DNA, Neoplasm/isolation & purification , Disease Progression , Exons/genetics , Female , High-Throughput Nucleotide Sequencing , Humans , Middle Aged , Polymorphism, Single Nucleotide , Sequence Analysis, DNA , Smad4 Protein/genetics , Tumor Suppressor Protein p53/genetics
18.
Am J Cancer Res ; 6(2): 270-84, 2016.
Article in English | MEDLINE | ID: mdl-27186402

ABSTRACT

Our previous study demonstrated that high mRNA levels for Seven in Absentia Homolog 2 (SIAH2) correlated with high Estrogen Receptor (ER) mRNA levels and with longer progression-free survival (PFS) after first-line tamoxifen. Others showed high SIAH2 protein levels in ER-negative breast cancer associated with an unfavorable relapse-free survival. In the current study, we investigated SIAH2 protein expression to clarify the discrepancy between protein and mRNA findings and to determine its diagnostic value in breast cancer patients. Tissue microarrays (TMAs) containing core specimens of primary breast tumors were immunohistochemically stained for SIAH2 protein. The TMAs analyzed a cohort of 746 patients with primary breast cancer (PBC) and a cohort of 245 patients with ER-positive metastatic breast cancer (MBC) treated with first-line tamoxifen. SIAH2 staining was scored for intensity and proportion of positive tumor cells and evaluated for its relationship with metastasis-free survival (MFS) and PFS. Multivariate survival analyses included traditional prognostic or predictive factors, respectively. The PBC-cohort had 263 patients with high SIAH2 protein expression and decreased expression of ER protein and mRNA levels (P = 0.005 and P = 0.003, respectively). High SIAH2 levels correlated with significant unfavorable MFS in lymph node negative, ER-positive breast cancer patients. The MBC-cohort had 86 patients with increased SIAH2 protein expression. High SIAH2 expression was associated with an unfavorable PFS after first-line tamoxifen in multivariate analyses (HR = 1.45; 95% CI, 1.07-1.96; P = 0.015). In conclusion, SIAH2 protein expression is especially observed in ER-negative tumors. Its prognostic value in breast cancer does not add to current prognostic markers. The proportion of SIAH2-positive cells can be used as biomarker to predict tamoxifen treatment failure in MBC patients.

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