DNA methylation of imprinted gene control regions in the regression of low-grade cervical lesions

Abstract BACKGROUND The diagnosis of intracranial tumors relies on tissue specimens obtained by invasive surgery. Non-invasive diagnostic approaches, particularly for patients with brain tumours, provide an opportunity to avoid surgery and mitigate unnecessary risk to patients. We reasoned that DNA methylation profiles of circulating tumor DNA in blood can be used as a clinically useful biomarker for patients with brain tumors, given the specificity of DNA methylation profiles for cell-of-origin. METHODS We generated methylation profiles on the plasma of 608 patients with cancer (219 intracranial, 388 extracranial) and 60 healthy controls using a cell-free methylated DNA immunoprecipitation combined with deep sequencing (cfMeDIP-seq) approach. Using machine-learning approaches we generated and evaluated models to distinguish brain tumors from extracranial cancers that may metastasize to the brain, as well as additional models to discriminate common brain tumors included in the differential diagnosis of solitary extra-axial and intra-axial tumors. RESULTS We observed high sensitivity and discriminative capacity for our models to distinguish gliomas from other cancerous and healthy patients (AUC=0.99, 95%CI 0.96–1), with similar performance in IDH mutant and wildtype gliomas as well as in lower- and high-grade gliomas. Excluding non-malignant contributors to plasma methylation did not change model performance (AUC=0.982, 95%CI 0.93–1). Models generated to discriminate intracranial tumors from each other also demonstrated high accuracy for common extra-axial tumors (AUCmeningioma=0.89, 95%CI 0.80–0.97; AUChemangiopericytoma=0.95, 95%CI 0.73–1) as well as intra-axial tumors ranging from low-grade indolent glial-neuronal tumors (AUC 0.93, 95%CI 0.80 – 1) to diffuse intra-axial gliomas with distinct molecular composition (AUCIDH-mutant glioma = 0.82, 95%CI 0.66 -0.98; AUCIDH-wildtype-glioma = 0.71, 95%CI 0.53 – 0.9). Plasma cfMeDIP-seq signals originated from corresponding tumor tissue DNA methylation signals (r=0.37, p< 2.2e-16). CONCLUSIONS These results demonstrate the potential for cfMeDIP-seq profiles to not only detect circulating tumor DNA, but to accurately discriminate common intracranial tumors that share cell-of-origin lineages.

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A urine-based DNA methylation assay to facilitate early detection and risk stratification of bladder cancer

Clinical Epigenetics ◽

10.1186/s13148-021-01073-x ◽

2021 ◽

Vol 13 (1) ◽

Author(s):

Weimei Ruan ◽

Xu Chen ◽

Ming Huang ◽

Hong Wang ◽

Jiaxin Chen ◽

...

Keyword(s):

Dna Methylation ◽

Bladder Cancer ◽

Risk Stratification ◽

Early Stage ◽

Operative Risk ◽

Low Grade ◽

Single Center ◽

Detection Model ◽

Methylation Assay ◽

Muscle Invasive

Abstract Background Current non-invasive tests have limited sensitivities and lack capabilities of pre-operative risk stratification for bladder cancer (BC) diagnosis. We aimed to develop and validate a urine-based DNA methylation assay as a clinically feasible test for improving BC detection and enabling pre-operative risk stratifications. Methods A urine-based DNA methylation assay was developed and validated by retrospective single-center studies in patients of suspected BC in Cohort 1 (n = 192) and Cohort 2 (n = 98), respectively. In addition, a prospective single-center study in hematuria patient group (Cohort 3, n = 174) was used as a second validation of the model. Results The assay with a dual-marker detection model showed 88.1% and 91.2% sensitivities, 89.7% and 85.7% specificities in validation Cohort 2 (patients of suspected BC) and Cohort 3 (patients of hematuria), respectively. Furthermore, this assay showed improved sensitivities over cytology and FISH on detecting low-grade tumor (66.7–77.8% vs. 0.0–22.2%, 0.0–22.2%), Ta tumor (83.3% vs. 22.2–41.2%, 44.4–52.9%) and non-muscle invasive BC (NMIBC) (80.0–89.7% vs. 51.5–52.0%, 59.4–72.0%) in both cohorts. The assay also had higher accuracies (88.9–95.8%) in diagnosing cases with concurrent genitourinary disorders as compared to cytology (55.6–70.8%) and FISH (72.2–77.8%). Meanwhile, the assay with a five-marker stratification model identified high-risk NMIBC and muscle invasive BC with 90.5% sensitivity and 86.8% specificity in Cohort 2. Conclusions The urine-based DNA methylation assay represents a highly sensitive and specific approach for BC early-stage detection and risk stratification. It has a potential to be used as a routine test to improve diagnosis and prognosis of BC in clinic.

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EPCO-17. METHYLATION ANALYSIS OF MATCHED PRIMARY AND RECURRENT IDHmt ASTROCYTOMA; AN UPDATE FROM THE GLIOMA LONGITUDINAL ANALYSIS NL (GLASS-NL) CONSORTIUM

Neuro-Oncology ◽

10.1093/neuonc/noab196.016 ◽

2021 ◽

Vol 23 (Supplement_6) ◽

pp. vi5-vi5

Author(s):

Wies Vallentgoed ◽

Anneke Niers ◽

Karin van Garderen ◽

Martin van den Bent ◽

Kaspar Draaisma ◽

...

Keyword(s):

Dna Methylation ◽

Surgical Resection ◽

Molecular Mechanisms ◽

Relative Proportion ◽

Low Grade ◽

High Grade ◽

Primary Tumors ◽

Genome Wide ◽

Dna Methylation Profiling ◽

Methylation Profiling

Abstract The GLASS-NL consortium, was initiated to gain insight into the molecular mechanisms underlying glioma evolution and to identify markers of progression in IDH-mutant astrocytomas. Here, we present the first results of genome-wide DNA-methylation profiling of GLASS-NL samples. 110 adult patients were identified with an IDH-mutant astrocytoma at first diagnosis. All patients underwent a surgical resection of the tumor at least twice, separated by at least 6 months (median 40.9 months (IQR: 24.0, 64.7). In 37% and 18% of the cases, patients were treated with radiotherapy or chemotherapy respectively, before surgical resection of the recurrent tumor. DNA-methylation profiling was done on 235 samples from 103 patients (102 1st, 101 2nd, 29 3rd, and 3 4th resection). Copy number variations were also extracted from these data. Methylation classes were determined according to Capper et al. Overall survival (OS) was measured from date of first surgery. Of all primary tumors, the methylation-classifier assigned 85 (87%) to the low grade subclass and 10 (10%) to the high grade subclass. The relative proportion of high grade tumors increased ~three-fold at tumor recurrence (32/101, 32%) and even further in the second recurrence (15/29, 52%). Methylation classes were prognostic, both in primary and recurrent tumors. The overall DNA-methylation levels of recurrent samples was lower than that of primary samples. This difference is explained by the increased number of high grade samples at recurrence, since near identical DNA-methylation levels were observed in samples that remained low grade. In an unsupervised analysis, DNA-methylation data derived from primary and first recurrence samples of individual patients mostly (79%) cluster together. Recurrent samples that do not cluster with their primary tumor, form a separate group with relatively low genome-wide DNA-methylation. Our data demonstrate that methylation profiling identifies a shift towards a higher grade at tumor progression coinciding with reduced genome-wide DNA-methylation levels.

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Prevalence and type distribution of human papillomavirus infection among women with different degrees of cervical cytological abnormalities in Sicily (Italy)

Microbiologia Medica ◽

10.4081/mm.2016.5018 ◽

2016 ◽

Vol 31 (2) ◽

Author(s):

Concetta Franchina ◽

Carmela M. Costanzo ◽

Raffaela Russo ◽

Concetta I. Palermo ◽

Guido Scalia

Keyword(s):

Pap Smear ◽

Blot Hybridization ◽

Human Papillomaviruses ◽

Multiple Infections ◽

Low Grade ◽

Genotype Distribution ◽

Cervical Lesions ◽

Hpv Dna ◽

Papillomavirus Infection ◽

Hpv Genotypes

Human papillomaviruses (HPVs) are etiological agents of cervical cancer. In the absence of Pap smear alterations, high-risk HPV DNA can be detected in cervical samples. The prevalence of papillomavirus infection and their genotype distribution varies greatly across populations. The aims of this study were: i) to assess the prevalences of HPV genotypes in people living in Eastern Sicily (Italy) and the frequency of HPV multiple infections; ii) to evaluate the association between HPV genotypes and cervical lesions in order to improve the epidemiological knowledge useful for monitoring or treating infected women. Nested PCR and reverse dot/blot hybridization were used for the detection and typing of HPV DNA in 315 women who had had an abnormal PAP-smear. HPV DNA test was positive in 70.5% cases; the prevalence was 50% in atypical squamous cells of undetermined significance (ASCUS), 80.8% in low grade-, and 76.2% in high grade-squamous intraepithelial lesion (H-SIL). The genotype distribution showed a predominance of HPV-16 (56.7%) followed by HPV-18 (12.2%), HPV-31 (9.5%) and HPV-6 (9.5%). Multiple infections were detected in 35.1% of the infected patients. High frequency of positive results for HPV was confirmed and, even in case of ASCUS, patients should be taken into account for genotyping. Our data indicate that multiple infections are consistent in women with low-grade lesions while they are less frequent in women with H-SIL. This could reinforce the theory of the multi-stage cancer model, by which one HPV type becomes predominant along with the progression of cervical lesion severity.

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High-risk HPV genotypes and cervical lesions association in postmenopausal women

European Journal of Public Health ◽

10.1093/eurpub/ckab120.044 ◽

2021 ◽

Vol 31 (Supplement_2) ◽

Author(s):

Ana Rita Fernandes Miranda da Costa ◽

Cláudia Sousa ◽

Erica Isidoro ◽

Regina Silva ◽

Cristiana Mourato

Keyword(s):

Cervical Cancer ◽

High Risk ◽

Postmenopausal Women ◽

Age Groups ◽

Low Grade ◽

High Grade ◽

Cervical Lesions ◽

Intraepithelial Lesion ◽

The Bethesda System ◽

High Risk Hpv

Abstract Background Persistent infection by high-risk Human Papillomavirus (hrHPV) are the major cause of cervical cancer. Studies report disparities in the incidence of infection and the various genotypes of this virus in different age groups, suggesting a higher frequency of hrHPV in young women and low-risk subtypes being predominant in older women. This study aimed to investigate the incidence and distribution of hrHPV genotypes in postmenopausal women as well as the correlation with the cytological findings. Methods 16 859 women, aged 50–64 years, performed cervical cancer screening test in Friuri Venezia Giulia region, Italy. The infection was evaluated by the Polymerase Chain Reaction methodology and the positive samples were evaluated by Liquid Based Cytology according to the Bethesda System from 2014. A statistical analysis was performed to study the molecular and cytological data of this population. Results hrHPV infection were found in 5.8% of the women and 78.3% of these were caused by hrHPV other than HPV16 and HPV18 (). Also, 65.7% of the positive samples were negative for intraepithelial lesion or malignancy while low grade squamous intraepithelial lesion was the most frequent (22.4%). There was an increase in the number of high-grade intraepithelial lesions in the presence of HPV16 compared to that recorded when this genotype was absent (20.8% vs. 8.5%). No cervical cancers were detected. Conclusions Infection with hrHPV is uncommon in postmenopausal women and it is mostly caused by subtypes less associated with the development of cervical cancer. Yet, HPV16 infection triggers the development of high-grade lesions.

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Systematic identification of non-coding somatic single nucleotide variants associated with altered transcription and DNA methylation in adult and pediatric cancers

NAR Cancer ◽

10.1093/narcan/zcab001 ◽

2021 ◽

Vol 3 (1) ◽

Author(s):

Fengju Chen ◽

Yiqun Zhang ◽

Chad J Creighton

Keyword(s):

Dna Methylation ◽

Brain Tumor ◽

Low Grade ◽

Single Nucleotide Variants ◽

Multiple Cancer ◽

Single Nucleotide ◽

Altered Expression ◽

Wide Range ◽

Mutational Hotspots ◽

Cancer Types

Abstract Whole-genome sequencing combined with transcriptomics can reveal impactful non-coding single nucleotide variants (SNVs) in cancer. Here, we developed an integrative analytical approach that, as a first step, identifies genes altered in expression or DNA methylation in association with nearby somatic SNVs, in contrast to alternative approaches that first identify mutational hotspots. Using genomic datasets from the Pan-Cancer Analysis of Whole Genomes (PCAWG) consortium and the Children's Brain Tumor Tissue Consortium (CBTTC), we identified hundreds of genes and associated CpG islands for which the nearby presence of a non-coding somatic SNV recurrently associated with altered expression or DNA methylation, respectively. Genomic regions upstream or downstream of genes, gene introns and gene untranslated regions were all involved. The PCAWG adult cancer cohort yielded different significant SNV-expression associations from the CBTTC pediatric brain tumor cohort. The SNV-expression associations involved a wide range of cancer types and histologies, as well as potential gain or loss of transcription factor binding sites. Notable genes with SNV-associated increased expression include TERT, COPS3, POLE2 and HDAC2—involving multiple cancer types—MYC, BCL2, PIM1 and IGLL5—involving lymphomas—and CYHR1—involving pediatric low-grade gliomas. Non-coding somatic SNVs show a major role in shaping the cancer transcriptome, not limited to mutational hotspots.

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High prevalence of Human Papillomavirus (HPV) type 66 in low-grade cervical lesions of Mexican women

10.1101/2020.01.07.20016857 ◽

2020 ◽

Author(s):

Karina Juárez-González ◽

Vladimir Paredes-Cervantes ◽

Silvia Gordillo-Rodríguez ◽

Saúl González-Guzmán ◽

Xochilt Moncayo-Valencia ◽

...

Keyword(s):

Risk Factors ◽

Cervical Cancer ◽

Transmitted Disease ◽

Low Grade ◽

Mexican Women ◽

Cervical Lesions ◽

Hpv 16 ◽

High Prevalence ◽

Hpv Types ◽

Intraepithelial Lesions

AbstractBackgroundHPV-16 infections constitute the highest risk for developing uterine cervix cancer. However, the role of other high-risk types is still controversial.ObjectiveTo analyze HR-HPV prevalence and its possible associations between HPV and risk factors related to cervical lesions among Mexican women.MethodsCross sectional study using 362 cervical samples collected between 2016 and 2017. Fourteen HR-HPV types (16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66 and 68) were detected by highly sensitive PCR amplification followed by reverse hybridization. Bivariate and multivariate analyses were performed to investigate the association between HPV types and risk factors among lesions.ResultsMost samples were HR-HPV positive (83.43%). HPV-16 was the most prevalent infection among negative for intraepithelial lesions or malignancy (78.6%), high-grade squamous intraepithelial lesions (50%), and cervical cancer (58.2%). HPV-66 showed an unexpected high prevalence in atypical squamous cells of undetermined significance (50%), low-grade squamous intraepithelial (45.7%), and only found in 3.6% of cervical cancers. HPV-16 was significantly prevalent among women between 30-39 years, whereas types 66 and 52 were significantly associated when previously sexually transmitted disease had occurred (p< 0.05).ConclusionsHPV-66 either in single or co-infection with other HR-HPV types (excluding 16 and 18) might be indicative of non-progressive cancer lesions. HPV-66 prevalence was unusually high in low-grade cervical lesions, predominantly in co-infection with HPV-51, and very low among cervical cancer. This should be addressed to interpret results obtained by methods that group type 66 with other HR-types.

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Abnormal colposcopic images in patients with preinvasive cervical lesions

Journal of Health Sciences ◽

10.17532/jhsci.2013.71 ◽

2013 ◽

Vol 3 (2) ◽

pp. 98-102

Author(s):

Adnan Babović ◽

Dženita Ljuca ◽

Gordana Bogdanović ◽

Lejla Muminhodžić

Keyword(s):

Intraepithelial Neoplasia ◽

Control Group ◽

Low Grade ◽

High Grade ◽

Cervical Lesions ◽

Cytological Examination ◽

Chi Square ◽

Chi Square Test ◽

Intraepithelial Lesion ◽

Experimental Group

Introduction: The objective of the study was to determine frequency and to compare frequency of the abnormal colposcopic images in patients with low and high grade pre-invasive lesions of cervix.Methods: Study includes 259 patients, whom colposcopic and cytological examination of cervix was done. The experimental group of patients consisted of patents with pre-invasive low grade squamousintraepithelial lesion (LSIL) and high grade squamous intraepithelial lesion (HSIL), and the control group consisted of patients without cervical intraepithelial neoplasia (CIN).Results: In comparison to the total number of satisfactory fi ndings (N=259), pathological findings were registered in N=113 (43.6 %) and abnormal colposcopic fi ndings in N=128 (49.4%). The study did notinclude patients with unsatisfactory fi nding N=22 (8.5%). Abnormal colposcopic image is present most frequently in older patients but there are no statistically important difference between age categories(Pearson Chi-Square 0.47, df -3, p=0.923). Frequency of abnormal colposcopic fi ndings (N=128) is the biggest in pathological cytological (N=113) and HSIL 58 (45.3%), LSIL 36 (28.1%). There is statisticallysignifi cant difference in frequency of abnormal colposcopic images in patients with low-grade in comparison to patients with high-grade pre-invasive cervix lesions (Chi-Square test, Pearson Chi-Square 117.14,df-12 p<0.0001).Conclusion: Thanks to characteristic colposcopic images, abnormal epithelium is successfully recognized, but the severity grade of intraepithelial lesion cannot be determined.

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