Methylation Dynamics of RASSF1A and Its Impact on Cancer

5-methyl cytosine (5mC) is a key epigenetic mark entwined with gene expression and the specification of cellular phenotypes. Its distribution around gene promoters sets a barrier for transcriptional enhancers or inhibitor proteins binding to their target sequences. As a result, an additional level of regulation is added to the signals that organize the access to the chromatin and its structural components. The tumor suppressor gene RASSF1A is a microtubule-associated and multitasking scaffold protein communicating with the RAS pathway, estrogen receptor signaling, and Hippo pathway. RASSF1A action stimulates mitotic arrest, DNA repair and apoptosis, and controls the cell cycle and cell migration. De novo methylation of the RASSF1A promoter has received much attention due to its increased frequency in most cancer types. RASSF1A methylation is preceded by histones modifications and could represent an early molecular event in cell transformation. Accordingly, RASSF1A methylation is proposed as an epigenetic candidate marker in many cancer types, even though an inverse correlation of methylation and expression remains to be fully ascertained. Some findings indicate that the epigenetic abrogation of RASSF1A can promote the alternative expression of the putative oncogenic isoform RASSF1C. Understanding the complexity and significance of RASSF1A methylation is instrumental for a more accurate determination of its biological and clinical role. The review covers the molecular events implicated in RASSF1A methylation and gene silencing and provides a deeper view into the significance of the RASSF1A methylation patterns in a number of gastrointestinal cancer types.

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The DAXX-SREBP axis promotes oncogenic lipogenesis and tumorigenesis

10.1101/2020.12.31.424997 ◽

2021 ◽

Author(s):

Iqbal Mahmud ◽

Guimei Tian ◽

Jia Wang ◽

Jessica Lewis ◽

Aaron Waddell ◽

...

Keyword(s):

Gene Expression ◽

Tumor Growth ◽

De Novo ◽

Lipid Synthesis ◽

De Novo Lipogenesis ◽

Recent Analysis ◽

Gene Promoters ◽

Lipogenic Gene ◽

Lipogenic Gene Expression ◽

Cancer Types

ABSTRACTDe novo lipogenesis produces lipids for membrane biosynthesis and cell signaling. Elevated lipogenesis is a major metabolic feature in cancer cells. In breast and other cancer types, genes involved in lipogenesis are highly upregulated, but the mechanisms that control their expression remain poorly understood. DAXX modulates gene expression through binding to diverse transcription factors although the functional impact of these diverse interactions remains to be defined. Our recent analysis indicates that DAXX is overexpressed in diverse cancer types. However, mechanisms underlying DAXX’s oncogenic function remains elusive. Using global integrated transcriptomic and lipidomic analyses, we show that DAXX plays a key role in lipid metabolism. DAXX depletion attenuates, while its overexpression enhances, lipogenic gene expression, lipid synthesis and tumor growth. Mechanistically, DAXX interacts with SREBP1 and SREBP2 and activates SREBP-mediated transcription. DAXX associates with lipogenic gene promoters through SREBPs. Underscoring the critical roles for the DAXX-SREBP interaction for lipogenesis, SREBP2 knockdown attenuates tumor growth in cells with DAXX overexpression, and a DAXX mutant unable to bind SREBPs are incapable of promoting lipogenesis and tumor growth. Our results identify the DAXX-SREBP axis as an important pathway for tumorigenesis.

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A121 UNDERWATER EMR FOR NON-LIFTING SESSILE COLORECTAL LESIONS

Journal of the Canadian Association of Gastroenterology ◽

10.1093/jcag/gwab002.119 ◽

2021 ◽

Vol 4 (Supplement_1) ◽

pp. 102-103

Author(s):

C Galts ◽

R Barclay ◽

D Percy

Keyword(s):

Surgical Resection ◽

De Novo ◽

Lesion Size ◽

Colorectal Polyps ◽

Invasive Cancer ◽

Previous Attempt ◽

Tubular Adenoma ◽

En Bloc ◽

Clinical Role ◽

Submucosal Injection

Abstract Background Sessile colorectal lesions which do not elevate with submucosal injection — “non-lifting” lesions — are considered poor candidates for EMR due to concerns of possible invasive cancer and increased procedural risk. However, a non-lifting sign is an unreliable predictor of malignancy, relegating many benign lesions to surgical resection. Underwater EMR (UEMR), which obviates submucosal injection, is effective for sessile colorectal polyps but has not been evaluated specifically for non-lifting lesions. Aims The aim of this study was to assess the efficacy of UEMR for “non-lifting” large sessile colorectal lesions with the hypothesis that UEMR may have a clinical role in managing complex lesions. Methods We reviewed our database from 2016 to 2019 for patients referred for large (≥ 20 mm) non-lifting colorectal lesions without overt signs of invasive cancer, who subsequently underwent UEMR. Results Thirty-two cases were successfully treated with single session UEMR. 18 (56%) were de novo lesions whereas the remainder had undergone previous attempt(s) at conventional EMR. The mean lesion size was 37 ± 17 mm. 4 cases (13%) were resected en bloc; the remainder piecemeal. Final pathology was T1 adenocarcinoma, N=3 (9%); tubulovillous adenoma, N=15 (47%); tubular adenoma, N=8 (25%); sessile serrated, N=6 (19%); high-grade dysplasia, N=2 (6%). One patient with cancer underwent surgical resection (T1N0); the remainder had endoscopic follow-up over 8 ± 3 months with benign recurrent/residual lesions in 8%, all amenable to UEMR. There were no procedural complications. Conclusions In this series of large sessile non-lifting colorectal lesions, UEMR was effective for both de novo and previously treated lesions, obviating surgery in the majority of cases. Funding Agencies None

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De novo methylation of tumor suppressor gene p16/INK4a is a frequent finding in multiple myeloma patients at diagnosis

Leukemia ◽

10.1038/sj.leu.2401617 ◽

2000 ◽

Vol 14 (1) ◽

pp. 183-187 ◽

Cited By ~ 43

Author(s):

M González ◽

MV Mateos ◽

R García-Sanz ◽

A Balanzategui ◽

R López-Pérez ◽

...

Keyword(s):

Multiple Myeloma ◽

Tumor Suppressor ◽

Tumor Suppressor Gene ◽

De Novo ◽

Suppressor Gene ◽

Frequent Finding ◽

P16 Ink4a ◽

De Novo Methylation

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Application of recurrence plot analysis to characterise whole chamber propagation of atrial fibrillation

EP Europace ◽

10.1093/europace/euab116.120 ◽

2021 ◽

Vol 23 (Supplement_3) ◽

Author(s):

M Pope ◽

P Kuklik ◽

A Briosa E Gala ◽

M Leo ◽

J Paisey ◽

...

Keyword(s):

Atrial Fibrillation ◽

Catheter Ablation ◽

Charge Density ◽

De Novo ◽

Inverse Correlation ◽

Right Atrial ◽

Research Centre ◽

Activation Patterns ◽

Density Mapping ◽

Distance Matrices

Abstract Funding Acknowledgements Type of funding sources: Public hospital(s). Main funding source(s): Oxford Biomedical Research Centre Introduction Non-contact charge density mapping allows visualisation of whole chamber propagation during atrial fibrillation (AF). The identification of regions with repetitive or, conversely, more complex patterns of wavefront propagation may provide clues to mechanisms responsible for AF maintenance and lead to improved outcomes from catheter ablation. Our novel mapping approach based on signal recurrence plots has never been applied to whole chamber, bi-atrial recording of atrial fibrillation. Purpose To apply recurrence analysis to characterise whole chamber bi-atrial AF propagation. Methods Non-contact dipole signals from left and right atrial maps were obtained during simultaneous bi-atrial charge density mapping of AF. Signals were converted to phase and mean phase coherence calculated for the generation of recurrence distance matrices for the whole chamber and each anatomical region (6x LA and 4x RA) over the 30-second recording duration, where a value of 1 (purple, see figure panel A) represents uniform repetitive conduction, and 0 (red), irregular, non-repetitive activity. Whole chamber and regional mean recurrence values were calculated and correlated with the frequency of wavefronts of localised irregular activation patterns. Results Maps were obtained prior to ablation in 21 patients (5 paroxysmal (pAF), 16 persistent AF (persAF)) undergoing de-novo catheter ablation procedures. Whole chamber recurrence was higher in patients with pAF (0.40 ± 0.08) than persAF (0.34 ± 0.05), p < 0.0005. There was an inverse correlation between regional recurrence values and the number of localised irregular activations detected (-0.7021, p < 0.0005, figure panel B) with the lateral LA and anterior RA demonstrating the highest recurrence values in each chamber (figure panel C). Conclusion Use of recurrence distance matrices characterises global AF propagation phenotypes. Regional values are inversely correlated with the frequency of localised irregular activation patterns identified demonstrating an anatomic dependence in the level of AF propagation complexity, greatest in the anterior LA and septal RA. Comparison of strategies targeting regions with maximal vs. minimal values during catheter ablation may define an optimal approach to treatment of persistent AF. Abstract Figure. Recurrence abstract figure

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Identification and characterization of de novo TP53 mutation carriers in Li-Fraumeni syndrome families: A single institution experience.

Journal of Clinical Oncology ◽

10.1200/jco.2021.39.15_suppl.10538 ◽

2021 ◽

Vol 39 (15_suppl) ◽

pp. 10538-10538

Author(s):

Carlos Christian Vera Recio ◽

Jessica Corredor ◽

Elissa Dodd-Eaton ◽

Angelica M. Gutierrez-Barrera ◽

Najat C. Daw ◽

...

Keyword(s):

Tp53 Mutation ◽

De Novo ◽

De Novo Mutation ◽

Brier Score ◽

Li Fraumeni Syndrome ◽

Mutation Carriers ◽

Cancer Types ◽

Li Fraumeni ◽

Identification And Characterization

10538 Background: Li-Fraumeni syndrome (LFS) is an inherited cancer syndrome mainly caused by a deleterious mutation in TP53. An estimated 48% of LFS patients present due to a deleterious de novo mutation (DNM) in TP53. The knowledge of DNM status, DNM or familial mutation (FM), of an LFS patient requires genetic testing of both parents which is often inaccessible, making de novo LFS patients an understudied population. Famdenovo.TP53 is a Mendelian Risk prediction model used to predict DNM status of TP53 mutation carriers based on the cancer-family history and several input genetic parameters, including disease-gene penetrance. The good predictive performance of Famdenovo.TP53 was demonstrated using data collected from four historical US cohorts. We hypothesize that by incorporating penetrance estimates that are specific for different types of cancers diagnosed in family members, we can develop a model with further improved calibration, accuracy and prediction. Methods: We present Famdenovo.CS, which uses cancer-specific penetrance estimates that were derived previously using a Bayesian semi-parametric competing risk model, to calculate the DNM probability. We use our model to analyze 101 families recently collected from the Clinical Cancer Genetic program at MD Anderson Cancer Center (CCG-TP53) that includes 20 families with known DNM status and 81 families with unknown DNM status. We used the concordance index (AUC), observed:expected ratios (OE) and Brier score (BS) to measure our model’s discrimination, calibration and accuracy, respectively. We estimate the proportion of probands that present a DNM and compare DNM to FM carriers in several areas including: cancer types diagnosed, age at diagnosis, number of primary cancers diagnosed, sex, amino acid change caused by mutation in TP53. Results: Famdenovo.CS showed equally good discrimination and calibration performance to Famdenovo.TP53, while improving the overall accuracy, demonstrated by a decrease in the Brier score of -0.09 (95% CI: [-0.02, -0.19]). Of the 101 probands in the CCG-TP53 cohort, we predict 39 to be DNMs and 62 to be FMs. The cancer types and ages of diagnosis observed in FMs and DNMs are similarly distributed. Conclusions: Famdenovo.CS shows improved model accuracy in the CCG cohort. DNMs in TP53 are a prevalent cause of LFS and we did not find differences in the clinical characteristics of DNM and FM carriers. Our model allows for a systematic identification and characterization of TP53 DNM carriers.

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Multi-omic data helps improve prediction of personalised tumor suppressors and oncogenes

10.1101/2022.01.13.476163 ◽

2022 ◽

Author(s):

Malvika Sudhakar ◽

Raghunathan Rengaswamy ◽

Karthik Raman

Keyword(s):

Tumour Progression ◽

Suppressor Gene ◽

Tumour Suppressor Gene ◽

Driver Mutations ◽

Cancer Type ◽

Expression Data ◽

Multiple Cancer ◽

Driver Genes ◽

Cancer Types ◽

Omic Data

The progression of tumorigenesis starts with a few mutational and structural driver events in the cell. Various cohort-based computational tools exist to identify driver genes but require a large number of samples to produce reliable results. Many studies use different methods to identify driver mutations/genes from mutations that have no impact on tumour progression; however, a small fraction of patients show no mutational events in any known driver genes. Current unsupervised methods map somatic and expression data onto a network to identify the perturbation in the network. Our method is the first machine learning model to classify genes as tumour suppressor gene (TSG), oncogene (OG) or neutral, thus assigning the functional impact of the gene in the patient. In this study, we develop a multi-omic approach, PIVOT (Personalised Identification of driVer OGs and TSGs), to train on experimentally or computationally validated mutational and structural driver events. Given the lack of any gold standards for the identification of personalised driver genes, we label the data using four strategies and, based on classification metrics, show gene-based labelling strategies perform best. We build different models using SNV, RNA, and multi-omic features to be used based on the data available. Our models trained on multi-omic data improved predictions compared to mutation and expression data, achieving an accuracy >0.99 for BRCA, LUAD and COAD datasets. We show network and expression-based features contribute the most to PIVOT. Our predictions on BRCA, COAD and LUAD cancer types reveal commonly altered genes such as TP53, and PIK3CA, which are predicted drivers for multiple cancer types. Along with known driver genes, our models also identify new driver genes such as PRKCA, SOX9 and PSMD4. Our multi-omic model labels both CNV and mutations with a more considerable contribution by CNV alterations. While predicting labels for genes mutated in multiple samples, we also label rare driver events occurring in as few as one sample. We also identify genes with dual roles within the same cancer type. Overall, PIVOT labels personalised driver genes as TSGs and OGs and also identifies rare driver genes. PIVOT is available at https://github.com/RamanLab/PIVOT.

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Constitutional de novo deletion CNV encompassing REST predisposes to diffuse hyperplastic perilobar nephroblastomatosis (HPLN)

Journal of Medical Genetics ◽

10.1136/jmedgenet-2020-107087 ◽

2020 ◽

pp. jmedgenet-2020-107087

Author(s):

Zerin Hyder ◽

Adele Fairclough ◽

Mike Groom ◽

Joan Getty ◽

Elizabeth Alexander ◽

...

Keyword(s):

Developmental Disorders ◽

De Novo ◽

Suppressor Gene ◽

Tumour Suppressor Gene ◽

Cancer Predisposition ◽

Tumour Suppressor ◽

Comparative Genomic Hybridisation ◽

Comparative Genomic ◽

Predisposition Genes ◽

Work Up

BackgroundNephroblastomatosis is a recognised precursor for the development of Wilms tumour (WT), the most common childhood renal tumour. While the majority of WT is sporadic in origin, germline intragenic mutations of predisposition genes such as WT1, REST and TRIM28 have been described in apparently isolated (non-familial) WT.Despite constitutional CNVs being a well-studied cause of developmental disorders, their role in cancer predisposition is less well defined, so that the interpretation of cancer risks associated with specific CNVs can be complex.ObjectiveTo highlight the role of a constitutional deletion CNV (delCNV) encompassing the REST tumour suppressor gene in diffuse hyperplastic perilobar nephroblastomatosis (HPLN).Methods/resultsArray comparative genomic hybridisation in an infant presenting with apparently sporadic diffuse HPLN revealed a de novo germline CNV, arr[GRCh37] 4q12(57,385,330–57,947,405)x1. The REST tumour suppressor gene is located at GRCh37 chr4:57,774,042–57,802,010.ConclusionThis delCNV encompassing REST is associated with nephroblastomatosis. Deletion studies should be included in the molecular work-up of inherited predisposition to WT/nephroblastomatosis. Detection of delCNVs involving known cancer predisposition genes can yield insights into the relationship between underlying genomic architecture and associated tumour risk.

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Heat Shock Proteins Are Essential Components in Transformation and Tumor Progression: Cancer Cell Intrinsic Pathways and Beyond

International Journal of Molecular Sciences ◽

10.3390/ijms20184507 ◽

2019 ◽

Vol 20 (18) ◽

pp. 4507 ◽

Cited By ~ 13

Author(s):

Lang ◽

Guerrero-Giménez ◽

Prince ◽

Ackerman ◽

Bonorino ◽

...

Keyword(s):

Heat Shock ◽

Cancer Cells ◽

Stress Proteins ◽

De Novo ◽

Human Cancer ◽

Essential Components ◽

Wide Range ◽

Cancer Types ◽

Shock Proteins

Heat shock protein (HSP) synthesis is switched on in a remarkably wide range of tumor cells, in both experimental animal systems and in human cancer, in which these proteins accumulate in high levels. In each case, elevated HSP concentrations bode ill for the patient, and are associated with a poor outlook in terms of survival in most cancer types. The significance of elevated HSPs is underpinned by their essential roles in mediating tumor cell intrinsic traits such as unscheduled cell division, escape from programmed cell death and senescence, de novo angiogenesis, and increased invasion and metastasis. An increased HSP expression thus seems essential for tumorigenesis. Perhaps of equal significance is the pronounced interplay between cancer cells and the tumor milieu, with essential roles for intracellular HSPs in the properties of the stromal cells, and their roles in programming malignant cells and in the release of HSPs from cancer cells to influence the behavior of the adjacent tumor and infiltrating the normal cells. These findings of a triple role for elevated HSP expression in tumorigenesis strongly support the targeting of HSPs in cancer, especially given the role of such stress proteins in resistance to conventional therapies.

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Long-term outcomes of patients with advanced-stage cutaneous T-cell lymphoma and large cell transformation

Blood ◽

10.1182/blood-2008-05-154609 ◽

2008 ◽

Vol 112 (8) ◽

pp. 3082-3087 ◽

Cited By ~ 103

Author(s):

Suzanne O. Arulogun ◽

H. Miles Prince ◽

Jonathan Ng ◽

Stephen Lade ◽

Gail F. Ryan ◽

...

Keyword(s):

De Novo ◽

Cell Transformation ◽

Early Stage ◽

Large Cell ◽

Tumor Stage ◽

Advanced Stage ◽

Long Term Outcomes ◽

Stage Disease ◽

Large Cell Transformation

Abstract Although mycosis fungoides (MF) is typically an indolent disease, patients with advanced-stage disease (stages IIB-IVB), including Sézary syndrome (SS), often have a poor outcome. A 31-year, retrospective analysis of our cutaneous lymphoma database, of 297 patients with MF and SS, was undertaken to study long-term outcomes and identify clinical predictors of outcome in patients with advanced-stage disease (ASD, n = 92) and large cell transformation (LCT, n = 22). Two-thirds of patients with ASD presented with de novo ASD. The median overall survival (OS) for ASD was 5 years with a 10-year predicted OS of 32%. Age at initial diagnosis (P = .01), tumor stage (P = .01), and clinical stage (P = .001) were found to be significant predictors of outcome. Patients who presented with de novo ASD demonstrated better outcomes that were not statistically significant than those with a prior diagnosis of early-stage MF (P = .25). Transformation developed in 22 of the 297 MF/SS patients (7.4%), with a transformation rate of only 1.4% in patients with early-stage disease, compared with stage IIB (27%) and stage IV (56%-67%) disease. The median OS from diagnosis of LCT was 2 years. We confirm that the incidence of LCT is strongly dependent on tumor stage at diagnosis, and we demonstrate a much lower overall risk of LCT than previously reported.

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Efficient and accurate determination of genome-wide DNA methylation patterns in Arabidopsis thaliana with enzymatic methyl sequencing

Epigenetics & Chromatin ◽

10.1186/s13072-020-00361-9 ◽

2020 ◽

Vol 13 (1) ◽

Cited By ~ 1

Author(s):

Suhua Feng ◽

Zhenhui Zhong ◽

Ming Wang ◽

Steven E. Jacobsen

Keyword(s):

Dna Methylation ◽

Bisulfite Sequencing ◽

Accurate Determination ◽

Gc Content ◽

Epigenetic Mark ◽

Whole Genome ◽

Whole Genome Bisulfite Sequencing ◽

Genome Wide ◽

A Genome ◽

Genome Bisulfite Sequencing

Abstract Background 5′ methylation of cytosines in DNA molecules is an important epigenetic mark in eukaryotes. Bisulfite sequencing is the gold standard of DNA methylation detection, and whole-genome bisulfite sequencing (WGBS) has been widely used to detect methylation at single-nucleotide resolution on a genome-wide scale. However, sodium bisulfite is known to severely degrade DNA, which, in combination with biases introduced during PCR amplification, leads to unbalanced base representation in the final sequencing libraries. Enzymatic conversion of unmethylated cytosines to uracils can achieve the same end product for sequencing as does bisulfite treatment and does not affect the integrity of the DNA; enzymatic methylation sequencing may, thus, provide advantages over bisulfite sequencing. Results Using an enzymatic methyl-seq (EM-seq) technique to selectively deaminate unmethylated cytosines to uracils, we generated and sequenced libraries based on different amounts of Arabidopsis input DNA and different numbers of PCR cycles, and compared these data to results from traditional whole-genome bisulfite sequencing. We found that EM-seq libraries were more consistent between replicates and had higher mapping and lower duplication rates, lower background noise, higher average coverage, and higher coverage of total cytosines. Differential methylation region (DMR) analysis showed that WGBS tended to over-estimate methylation levels especially in CHG and CHH contexts, whereas EM-seq detected higher CG methylation levels in certain highly methylated areas. These phenomena can be mostly explained by a correlation of WGBS methylation estimation with GC content and methylated cytosine density. We used EM-seq to compare methylation between leaves and flowers, and found that CHG methylation level is greatly elevated in flowers, especially in pericentromeric regions. Conclusion We suggest that EM-seq is a more accurate and reliable approach than WGBS to detect methylation. Compared to WGBS, the results of EM-seq are less affected by differences in library preparation conditions or by the skewed base composition in the converted DNA. It may therefore be more desirable to use EM-seq in methylation studies.

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