Reversible Epigenetic Alterations Regulate Class I HLA Loss in Prostate Cancer

Abstract Downregulation of HLA class I (HLA-I) impairs immune recognition and surveillance in prostate cancer and may underlie the ineffectiveness of checkpoint blockade. However, the molecular mechanisms regulating HLA-I loss in prostate cancer have not been fully explored. Here, we conducted a comprehensive analysis of HLA-I genomic, epigenomic and gene expression alterations in primary and metastatic human prostate cancer. Loss of HLA-I gene expression was associated with repressive chromatin states including DNA methylation, histone H3 tri-methylation at lysine 27, and reduced chromatin accessibility. Pharmacological DNMT and HDAC inhibition decreased DNA methylation and increased H3 lysine 27 acetylation and resulted in re-expression of HLA-I on the surface of tumor cells. Re-expression of HLA-I on LNCaP cells by DNMT and HDAC inhibition increased activation of co-cultured PSMA27-38-specific CD8+ T-cells. Methylated HLA-I was detected in HLA-Ilow circulating tumor cells (CTCs), which may serve as a biomarker for identifying patients who would benefit from epigenetic targeted therapies.

Download Full-text

Prognostic Significance of Gene Expression and DNA Methylation Markers in Circulating Tumor Cells and Paired Plasma Derived Exosomes in Metastatic Castration Resistant Prostate Cancer

Cancers ◽

10.3390/cancers13040780 ◽

2021 ◽

Vol 13 (4) ◽

pp. 780

Author(s):

Martha Zavridou ◽

Areti Strati ◽

Evangelos Bournakis ◽

Stavroula Smilkou ◽

Victoria Tserpeli ◽

...

Keyword(s):

Gene Expression ◽

Prostate Cancer ◽

Dna Methylation ◽

Tumor Cells ◽

Liquid Biopsy ◽

Prognostic Significance ◽

Comparison Study ◽

Castration Resistant Prostate Cancer ◽

Castration Resistant ◽

First Time

Liquid biopsy, based on the analysis of circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA), provides non-invasive real-time monitoring of tumor evolution and therapeutic efficacy. We performed for the first time a direct comparison study on gene expression and DNA methylation markers in CTCs and paired plasma-derived exosomes and evaluated their prognostic significance in metastatic castration resistant prostate cancer. This prospective liquid biopsy (LB) study was based on a group of 62 metastatic castration resistant prostate cancer (mCRPC) patients and 10 healthy donors (HD) as controls. Identical blood draws were used to: (a) enumerate CTC and tumor-derived extracellular vesicles (tdEVs) using CellSearch (CS) and (b) analyze CTCs and paired plasma-derived exosomes at the gene expression and DNA methylation level. CTCs were enumerated using CellSearch in 57/62 patients, with values ranging from 5 to 854 cells/7.5 mL PB. Our results revealed for the first time a significantly higher positivity of gene expression markers (CK-8, CK-18, TWIST1, PSMA, AR-FL, AR-V7, AR-567 and PD-L1 mRNA) in EpCAM-positive CTCs compared to plasma-derived exosomes. GSTP1, RASSF1A and SCHLAFEN were methylated both in CTC and exosomes. In CTCs, Kaplan–Meier analysis revealed that CK-19 (p = 0.009), PSMA (p = 0.001), TWIST1 (p = 0.001) expression and GSTP1 (p = 0.001) methylation were correlated with OS, while in exosomes GSTP1 (p = 0.007) and RASSF1A (p = 0.001) methylation was correlated with OS. Our direct comparison study of CTCs and exosomes at gene expression and DNA methylation level, revealed for the first time a significantly higher positivity in EpCAM-positive CTCs compared to plasma-derived exosomes. Future perspective of this study should be the evaluation of clinical utility of molecular biomarkers in CTCs and exosomes on independent multicentric cohorts with mCRPC patients.

Download Full-text

Frequent HLA class I alterations in human prostate cancer: molecular mechanisms and clinical relevance

Cancer Immunology Immunotherapy ◽

10.1007/s00262-015-1774-5 ◽

2015 ◽

Vol 65 (1) ◽

pp. 47-59 ◽

Cited By ~ 15

Author(s):

Francisco Javier Carretero ◽

Ana Belen del Campo ◽

Jose Francisco Flores-Martín ◽

Rosa Mendez ◽

Cesar García-Lopez ◽

...

Keyword(s):

Prostate Cancer ◽

Clinical Relevance ◽

Molecular Mechanisms ◽

Hla Class I ◽

Class I ◽

Human Prostate ◽

Human Prostate Cancer

Download Full-text

Distinct Contribution of DNA Methylation and Histone Acetylation to the Genomic Occupancy of Transcription Factors

10.1101/670307 ◽

2019 ◽

Cited By ~ 1

Author(s):

Martin Cusack ◽

Hamish W. King ◽

Paolo Spingardi ◽

Benedikt M. Kessler ◽

Robert J. Klose ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Transcription Factor ◽

Transcription Factors ◽

Embryonic Stem ◽

Transcription Factor Binding ◽

Chromatin Accessibility ◽

Histone Deacetylation ◽

Hdac Inhibition ◽

Factor Binding

AbstractEpigenetic modifications on chromatin play important roles in regulating gene expression. While chromatin states are often governed by multi-layered structure, how individual pathways contribute to gene expression remains poorly understood. For example, DNA methylation is known to regulate transcription factor binding but also to recruit methyl-CpG binding proteins that affect chromatin structure through the activity of histone deacetylase complexes (HDACs). Both of these mechanisms can potentially affect gene expression, but the importance of each, and whether these activities are integrated to achieve appropriate gene regulation, remains largely unknown. To address this important question, we measured gene expression, chromatin accessibility, and transcription factor occupancy in wild-type or DNA methylation-deficient mouse embryonic stem cells following HDAC inhibition. Interestingly, we observe widespread increases in chromatin accessibility at repeat elements when HDACs are inhibited, and this is magnified when cells also lack DNA methylation. A subset of these elements have elevated binding of the YY1 and GABPA transcription factors and increased expression. The pronounced additive effect of HDAC inhibition in DNA methylation deficient cells demonstrate that DNA methylation and histone deacetylation act largely independently to suppress transcription factor binding and gene expression.

Download Full-text

Network effects of the neuropsychiatric 15q13.3 microdeletion on the transcriptome and epigenome in human induced neurons

10.1101/772541 ◽

2019 ◽

Author(s):

Siming Zhang ◽

Xianglong Zhang ◽

Shining Ma ◽

Carolin Purmann ◽

Kasey Davis ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Ribosome Biogenesis ◽

Molecular Mechanisms ◽

Association Studies ◽

Neuropsychiatric Disorders ◽

Chromatin Accessibility ◽

Gene Copy ◽

Genome Wide ◽

Induced Neurons

AbstractHeterozygous deletions in the 15q13.3 region are associated with several neuropsychiatric disorders including autism, schizophrenia, and attention deficit hyperactivity disorder. Several genes within the 15q13.3 deletion region may play a role in neuronal dysfunction, based on association studies in humans and functional studies in mice, but the intermediate molecular mechanisms remain unknown. We analyzed the genome-wide effects of the 15q13.3 microdeletion on the transcriptome and epigenome. Induced pluripotent stem cell (iPSC) lines from three patients with the typical heterozygous 15q13.3 microdeletion and three sex-matched controls were generated and converted into induced neurons (iNs) using the neurogenin-2 induction method. We analyzed genome-wide gene expression using RNA-Seq, genome-wide DNA methylation using SeqCap-Epi, and genome-wide chromatin accessibility using ATAC-Seq, in both iPSCs and iNs. In both cell types, gene copy number change within the 15q13.3 microdeletion was accompanied by significantly decreased gene expression and no compensatory changes in DNA methylation or chromatin accessibility, supporting the model that haploinsufficiency of genes within the deleted region drives the disorder. Further, we observed global effects of the deletion on the transcriptome and epigenome, with the effects being cell type specific and occurring at discrete loci. Several genes and pathways associated with neuropsychiatric disorders and neuronal development were significantly altered, including Wnt signaling, ribosome biogenesis, DNA binding, and clustered protocadherins. This molecular systems analysis of a large neuropsychiatric microdeletion can also be applied to other brain relevant chromosomal aberrations to further our etiological understanding of neuropsychiatric disorders.

Download Full-text

Mapping chromatin accessibility and active regulatory elements reveals pathological mechanisms in human gliomas

Nature Communications ◽

10.1038/s41467-021-23922-2 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Karolina Stępniak ◽

Magdalena A. Machnicka ◽

Jakub Mieczkowski ◽

Anna Macioszek ◽

Bartosz Wojtaś ◽

...

Keyword(s):

Gene Expression ◽

Chromatin Structure ◽

Molecular Mechanisms ◽

Genome Mapping ◽

Malignant Gliomas ◽

Regulatory Elements ◽

Chromatin Accessibility ◽

Multiple Tumor ◽

Genes Encoding ◽

Methylation Patterns

AbstractChromatin structure and accessibility, and combinatorial binding of transcription factors to regulatory elements in genomic DNA control transcription. Genetic variations in genes encoding histones, epigenetics-related enzymes or modifiers affect chromatin structure/dynamics and result in alterations in gene expression contributing to cancer development or progression. Gliomas are brain tumors frequently associated with epigenetics-related gene deregulation. We perform whole-genome mapping of chromatin accessibility, histone modifications, DNA methylation patterns and transcriptome analysis simultaneously in multiple tumor samples to unravel epigenetic dysfunctions driving gliomagenesis. Based on the results of the integrative analysis of the acquired profiles, we create an atlas of active enhancers and promoters in benign and malignant gliomas. We explore these elements and intersect with Hi-C data to uncover molecular mechanisms instructing gene expression in gliomas.

Download Full-text

Leveraging epigenetics to enhance the efficacy of immunotherapy

Clinical Epigenetics ◽

10.1186/s13148-021-01100-x ◽

2021 ◽

Vol 13 (1) ◽

Author(s):

Jonathan D. Licht ◽

Richard L. Bennett

Keyword(s):

Gene Expression ◽

Clinical Trials ◽

Antigen Presentation ◽

Tumor Cells ◽

Immune Evasion ◽

Regulatory Elements ◽

Chromatin Accessibility ◽

Epigenetic Modifications ◽

Main Body ◽

Epigenetic Mechanisms

Abstract Background Epigenetic mechanisms regulate chromatin accessibility patterns that govern interaction of transcription machinery with genes and their cis-regulatory elements. Mutations that affect epigenetic mechanisms are common in cancer. Because epigenetic modifications are reversible many anticancer strategies targeting these mechanisms are currently under development and in clinical trials. Main body Here we review evidence suggesting that epigenetic therapeutics can deactivate immunosuppressive gene expression or reprogram tumor cells to activate antigen presentation mechanisms. In addition, the dysregulation of epigenetic mechanisms commonly observed in cancer may alter the immunogenicity of tumor cells and effectiveness of immunotherapies. Conclusions Therapeutics targeting epigenetic mechanisms may be helpful to counter immune evasion and improve the effectiveness of immunotherapies.

Download Full-text

Cell–cell coupling and DNA methylation abnormal phenotypes in the after-hours mice

Epigenetics & Chromatin ◽

10.1186/s13072-020-00373-5 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Federico Tinarelli ◽

Elena Ivanova ◽

Ilaria Colombi ◽

Erica Barini ◽

Edoardo Balzani ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Neuronal Networks ◽

Molecular Mechanisms ◽

Ex Vivo ◽

Neuronal Cultures ◽

Functional Impairments ◽

After Hours ◽

The Impact

Abstract Background DNA methylation has emerged as an important epigenetic regulator of brain processes, including circadian rhythms. However, how DNA methylation intervenes between environmental signals, such as light entrainment, and the transcriptional and translational molecular mechanisms of the cellular clock is currently unknown. Here, we studied the after-hours mice, which have a point mutation in the Fbxl3 gene and a lengthened circadian period. Methods In this study, we used a combination of in vivo, ex vivo and in vitro approaches. We measured retinal responses in Afh animals and we have run reduced representation bisulphite sequencing (RRBS), pyrosequencing and gene expression analysis in a variety of brain tissues ex vivo. In vitro, we used primary neuronal cultures combined to micro electrode array (MEA) technology and gene expression. Results We observed functional impairments in mutant neuronal networks, and a reduction in the retinal responses to light-dependent stimuli. We detected abnormalities in the expression of photoreceptive melanopsin (OPN4). Furthermore, we identified alterations in the DNA methylation pathways throughout the retinohypothalamic tract terminals and links between the transcription factor Rev-Erbα and Fbxl3. Conclusions The results of this study, primarily represent a contribution towards an understanding of electrophysiological and molecular phenotypic responses to external stimuli in the Afh model. Moreover, as DNA methylation has recently emerged as a new regulator of neuronal networks with important consequences for circadian behaviour, we discuss the impact of the Afh mutation on the epigenetic landscape of circadian biology.

Download Full-text

Selective Histocompatibility Leukocyte Antigen (Hla)-A2 Loss Caused by Aberrant Pre-mRNA Splicing in 624mel28 Melanoma Cells

Journal of Experimental Medicine ◽

10.1084/jem.190.2.205 ◽

1999 ◽

Vol 190 (2) ◽

pp. 205-216 ◽

Cited By ~ 71

Author(s):

Zhigang Wang ◽

Francesco M. Marincola ◽

Licia Rivoltini ◽

Giorgio Parmiani ◽

Soldano Ferrone

Keyword(s):

Hla Class I ◽

Melanoma Cells ◽

Class I ◽

Splice Donor Site ◽

Immune Recognition ◽

Translation Efficiency ◽

Exon 2 ◽

Leukocyte Antigen ◽

Allele Loss ◽

Intron 2

Histocompatibility leukocyte antigen (HLA)-A2 is used as a restricting element to present several melanoma-associated antigen (MAA)-derived peptides to cytotoxic T lymphocytes (CTLs). HLA-A2 antigen is selectively lost in primary melanoma lesions and more frequently in metastases. Only scanty information is available about the molecular mechanisms underlying this abnormality, in spite of its potentially negative impact on the clinical course of the disease and on the outcome of T cell–based immunotherapy. Therefore, in this study we have shown that the selective HLA-A2 antigen loss in melanoma cells 624MEL28 is caused by a splicing defect of HLA-A2 pre-mRNA because of a base substitution at the 5′ splice donor site of intron 2 of the HLA-A2 gene. As a result, HLA-A2 transcripts are spliced to two aberrant forms, one with exon 2 skipping and the other with intron 2 retention. The latter is not translated because of an early premature stop codon in the retained intron. In contrast, the transcript with exon 2 skipping is translated to a truncated HLA-A2 heavy chain without the α1 domain. Such a polypeptide is synthesized in vitro but is not detectable in cells, probably because of the low steady state level of the corresponding mRNA and the low translation efficiency. These results indicate that a single mutational event in an HLA class I gene is sufficient for loss of the corresponding allele. This may account, at least in part, for the high frequency of selective HLA class I allele loss in melanoma cells. Our conclusion emphasizes the need to implement active specific immunotherapy with a combination of peptides presented by various HLA class I alleles. This strategy may counteract the ability of melanoma cells with selective HLA class I allele loss to escape from immune recognition.

Download Full-text

Repurposing of KLF5 activates a cell cycle signature during the progression from a precursor state to Oesophageal Adenocarcinoma

10.1101/2020.02.10.941872 ◽

2020 ◽

Author(s):

Connor Rogerson ◽

Samuel Ogden ◽

Edward Britton ◽

Yeng Ang ◽

Andrew D. Sharrocks ◽

...

Keyword(s):

Gene Expression ◽

Cell Cycle ◽

Molecular Mechanisms ◽

Target Genes ◽

Prognostic Significance ◽

Gene Expression Signature ◽

Chromatin Accessibility ◽

Oesophageal Adenocarcinoma ◽

Cell Cycle Gene ◽

A Cell

AbstractOesophageal adenocarcinoma (OAC) is one of the most common causes of cancer deaths and yet compared to other common cancers, we know relatively little about the underlying molecular mechanisms. Barrett’s oesophagus (BO) is the only known precancerous precursor to OAC, but our understanding about the specific events leading to OAC development is limited. Here, we have integrated gene expression and chromatin accessibility profiles of human biopsies of BO and OAC and identified a strong cell cycle gene expression signature in OAC compared to BO. Through analysing associated chromatin accessibility changes, we have implicated the transcription factor KLF5 in the transition from BO to OAC. Importantly, we show that KLF5 expression is unchanged during this transition, but instead, KLF5 is redistributed across chromatin in OAC cells to directly regulate cell cycle genes specifically in OAC. Our findings have potential prognostic significance as the survival of patients with high expression of KLF5 target genes is significantly lower. We have provided new insights into the gene expression networks in OAC and the mechanisms behind progression to OAC, chiefly the repurposing of KLF5 for novel regulatory activity in OAC.

Download Full-text