Cancer epigenetics: promises and pitfalls for cancer therapy

Lineage Plasticity and Stemness Phenotypes in Prostate Cancer: Harnessing the Power of Integrated "Omics" Approaches to Explore Measurable Metrics

Prostate cancer (PCa), the most frequent and second most lethal cancer type in men in developed countries, is a highly heterogeneous disease. PCa heterogeneity, therapy resistance, stemness, and lethal progression have been attributed to lineage plasticity, which refers to the ability of neoplastic cells to undergo phenotypic changes under microenvironmental pressures by switching between developmental cell states. What remains to be elucidated is how to identify measurements of lineage plasticity, how to implement them to inform preclinical and clinical research, and, further, how to classify patients and inform therapeutic strategies in the clinic. Recent research has highlighted the crucial role of next-generation sequencing technologies in identifying potential biomarkers associated with lineage plasticity. Here, we review the genomic, transcriptomic, and epigenetic events that have been described in PCa and highlight those with significance for lineage plasticity. We further focus on their relevance in PCa research and their benefits in PCa patient classification. Finally, we explore ways in which bioinformatic analyses can be used to determine lineage plasticity based on large omics analyses and algorithms that can shed light on upstream and downstream events. Most importantly, an integrated multiomics approach may soon allow for the identification of a lineage plasticity signature, which would revolutionize the molecular classification of PCa patients.

Opioids and opioid receptors; understanding pharmacological mechanisms as a key to therapeutic advances and mitigation of the misuse crisis

Opioids are a mainstay in acute pain management and produce their effects and side effects (e.g., tolerance, opioid-use disorder and immune suppression) by interaction with opioid receptors. I will discuss opioid pharmacology in some controversial areas of enquiry of anaesthetic relevance. The main opioid target is the µ (mu,MOP) receptor but other members of the opioid receptor family, δ (delta; DOP) and κ (kappa; KOP) opioid receptors also produce analgesic actions. These are naloxone-sensitive. There is important clinical development relating to the Nociceptin/Orphanin FQ (NOP) receptor, an opioid receptor that is not naloxone-sensitive. Better understanding of the drivers for opioid effects and side effects may facilitate separation of side effects and production of safer drugs. Opioids bind to the receptor orthosteric site to produce their effects and can engage monomer or homo-, heterodimer receptors. Some ligands can drive one intracellular pathway over another. This is the basis of biased agonism (or functional selectivity). Opioid actions at the orthosteric site can be modulated allosterically and positive allosteric modulators that enhance opioid action are in development. As well as targeting ligand-receptor interaction and transduction, modulating receptor expression and hence function is also tractable. There is evidence for epigenetic associations with different types of pain and also substance misuse. As long as the opioid narrative is defined by the 'opioid crisis' the drive to remove them could gather pace. This will deny use where they are effective, and access to morphine for pain relief in low income countries.

On the thermodynamics of DNA methylation process

DNA methylation is an epigenetic mechanism that plays important roles in various biological processes including transcriptional and post-transcriptional regulation, genomic imprinting, aging, and stress response to environmental changes and disease. Consistent with thermodynamic principles acting within living systems and the application of maximum entropy principle, we propose a theoretical framework to understand and decode the DNA methylation process. A central tenet of this argument is that the probability density function of DNA methylation information-divergence summarizes the statistical biophysics underlying spontaneous methylation background and implicitly bears on the channel capacity of molecular machines conforming to Shannon's capacity theorem. On this theoretical basis, contributions from the molecular machine (enzyme) logical operations to Gibb entropy (S) and Helmholtz free energy (F) are intrinsic. Application to the estimations of S on datasets from Arabidopsis thaliana suggests that, as a thermodynamic state variable, individual methylome entropy is completely determined by the current state of the system, which in biological terms translates to a correspondence between estimated entropy values and observable phenotypic state. In patients with different types of cancer, results suggest that a significant information loss occurs in the transition from differentiated (healthy) tissues to cancer cells. This type of analysis may have important implications for early-stage diagnostics. The analysis of entropy fluctuations on experimental datasets revealed existence of restrictions on the magnitude of genome-wide methylation changes originating by organismal response to environmental changes. Only dysfunctional stages observed in the Arabidopsis mutant met1 and in cancer cells do not conform to these rules.

In situ sequence-specific visualization of single methylated cytosine on tissue sections using ICON probe and rolling-circle amplification

Since epigenetic modifications differ from cell to cell, detecting the DNA methylation status of individual cells is requisite. Therefore, it is important to conduct "morphology-based epigenetics research", in which the sequence-specific DNA methylation status is observed while maintaining tissue architecture. Here we demonstrate a novel histochemical technique that efficiently shows the presence of a single methylated cytosine in a sequence-dependent manner by applying ICON (interstrand complexation with osmium for nucleic acids) probes. By optimizing the concentration and duration of potassium osmate treatment, ICON probes selectively hybridize to methylated cytosine on tissue sections. Since the elongation process by rolling-circle amplification through the padlock probe and synchronous amplification by the hyperbranching reaction at a constant temperature efficiently amplifies the reaction, it is possible to specifically detect the presence of a single methylated cytosine. Since the ICON probe is cross-linked to the nuclear or mitochondrial DNA of the target cell, subsequent elongation and multiplication reactions proceed like a tree growing in soil with its roots firmly planted, thus facilitating the demonstration of methylated cytosine in situ. Using this novel ICON-mediated histochemical method, detection of the methylation of DNA in the regulatory region of the RANK gene in cultured cells and of mitochondrial DNA in paraffin sections of mouse cerebellar tissue was achievable. This combined ICON and rolling-circle amplification method is the first that shows evidence of the presence of a single methylated cytosine in a sequence-specific manner in paraffin sections, and is foreseen as applicable to a wide range of epigenetic studies.

PROTACs in Epigenetic Cancer Therapy: Current Status and Future Opportunities

The epigenetic regulation of gene functions has been proven to be strongly associated with the development and progression of cancer. Reprogramming the cancer epigenome landscape is one of the most promising target therapies in both treatments and in reversing drug resistance. Proteolytic targeted chimeras (PROTACs) are an emerging therapeutic modality for selective degradation via the native ubiquitin-proteasome system. Rapid advances in PROTACs have facilitated the exploration of targeting epigenetic proteins, a lot of PROTAC degraders have already been designed in the field of epigenetic cancer therapy, and PROTACs targeting epigenetic proteins can better exploit target druggability and improve the mechanistic understanding of the epigenetic regulation of cancer. Thus, this review focuses on the progress made in the development of PROTAC degraders and PROTAC drugs targeting epigenetics in cancer and discusses challenges and future opportunities for the field.

Targeting Epigenetic Mechanisms: A Boon for Cancer Immunotherapy

Immunotherapy is rapidly emerging as a promising approach against cancer. In the last decade, various immunological mechanisms have been targeted to induce an increase in the immune response against cancer cells. However, despite promising results, many patients show partial response, resistance, or serious toxicities. A promising way to overcome this is the use of immunotherapeutic approaches, in combination with other potential therapeutic approaches. Aberrant epigenetic modifications play an important role in carcinogenesis and its progression, as well as in the functioning of immune cells. Thus, therapeutic approaches targeting aberrant epigenetic mechanisms and the immune response might provide an effective antitumor effect. Further, the recent development of potent epigenetic drugs and immunomodulators gives hope to this combinatorial approach. In this review, we summarize the synergy mechanism between epigenetic therapies and immunotherapy for the treatment of cancer, and discuss recent advancements in the translation of this approach.

The FEBS Journal in 2023: building back better

The FEBS Journal publishes high impact research on diverse topics in the life sciences, with a focus on molecular mechanisms underpinning biological processes. Here, Editor-in-Chief Seamus Martin discusses highlights of the journal from the past year and gives a glimpse into what's in store for 2023.

Genome-wide screening for differentially methylated long noncoding RNAs identifies LIFR-AS1 as an epigenetically regulated lncRNA that inhibits the progression of colorectal cancer

Background

Aberrant DNA methylation is an epigenetic marker that has been linked to the pathogenesis of colorectal cancer (CRC). Long noncoding RNAs (lncRNAs) have been increasingly identified to be associated with tumorigenic processes of CRC. Identifying epigenetically dysregulated lncRNAs and characterizing their effects during carcinogenesis are focuses of cancer research.

Methods

Differentially methylated loci and expressed lncRNAs were identified by integrating DNA methylome and transcriptome analyses using The Cancer Genome Atlas database. Bisulfite sequencing PCR (BSP) was performed to analyze LIFR-AS1 promoter methylation status. The functional roles of LIFR-AS1 in CRC were determined by in vitro and in vivo experiments.

Results

We identified a novel hypermethylated lncRNA, LIFR-AS1, that was downregulated and associated with tumorigenesis, metastasis, and poor prognosis in CRC. High methylation burden of LIFR-AS1 indicated a poor survival of CRC patients. Promoter hypermethylation of LIFR-AS1 in tumor tissues was confirmed by BSP. Functional assays revealed that LIFR-AS1 could competitively bind to hsa-miR-29b-3p, and repressed colon cancer cell proliferation, colony formation and invasion. LIFR-AS1 also inhibited tumor growth in a mouse xenograft model of CRC.

Conclusions

Our results showed that the identified DNA methylation-dysregulated lncRNAs may be potential biomarkers and highlighted a role for LIFR-AS1 as a tumor suppressor in CRC.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13148-022-01361-0.

A critical review of datasets and computational suites for improving cancer theranostics and biomarker discovery

Cancer has been constantly evolving and so is the research pertaining to cancer diagnosis and therapeutic regimens. Early detection and specific therapeutics are the key features of modern cancer therapy. These requirements can only be fulfilled with the integration of diverse high-throughput technologies. Integration of advanced omics methodology involving genomics, epigenomics, proteomics, and transcriptomics provide a clear understanding of multi-faceted cancer. In the past few years, tremendous high-throughput data have been generated from cancer genomics and epigenomic analyses, which on further methodological analyses can yield better biological insights. The major epigenetic alterations reported in cancer are DNA methylation levels, histone post-translational modifications, and epi-miRNA regulating the oncogenes and tumor suppressor genes. While the genomic analyses like gene expression profiling, cancer gene prediction, and genome annotation divulge the genetic alterations in oncogenes or tumor suppressor genes. Also, systems biology approach using biological networks is being extensively used to identify novel cancer biomarkers. Therefore, integration of these multi-dimensional approaches will help to identify potential diagnostic and therapeutic biomarkers. Here, we reviewed the critical databases and tools dedicated to various epigenomic and genomic alterations in cancer. The review further focuses on the multi-omics resources available for further validating the identified cancer biomarkers. We also highlighted the tools for cancer biomarker discovery using a systems biology approach utilizing genomic and epigenomic data. Biomarkers predicted using such integrative approaches are shown to be more clinically relevant.

Epigenetic and epitranscriptomic mechanisms of chromium carcinogenesis

Hexavalent chromium [Cr(VI)], a Group I carcinogen classified by the International Agency for Research on Cancer (IARC), represents one of the most common occupational and environmental pollutants. The findings from human epidemiological and laboratory animal studies show that long-term exposure to Cr(VI) causes lung cancer and other cancer. Although Cr(VI) is a well-recognized carcinogen, the mechanism of Cr(VI) carcinogenesis has not been well understood. Due to the fact that Cr(VI) undergoes a series of metabolic reductions once entering cells to generate reactive Cr metabolites and reactive oxygen species (ROS) causing genotoxicity, Cr(VI) is generally considered as a genotoxic carcinogen. However, more and more studies have demonstrated that acute or chronic Cr(VI) exposure also causes epigenetic dysregulations including changing DNA methylation, histone posttranslational modifications and regulatory non-coding RNA (microRNA and long non-coding RNA) expressions. Moreover, emerging evidence shows that Cr(VI) exposure is also capable of altering cellular epitranscriptome. Given the increasingly recognized importance of epigenetic and epitranscriptomic dysregulations in cancer initiation and progression, it is believed that Cr(VI) exposure-caused epigenetic and epitranscriptomic changes could play important roles in Cr(VI) carcinogenesis. The goal of this chapter is to review the epigenetic and epitranscriptomic effects of Cr(VI) exposure and discuss their roles in Cr(VI) carcinogenesis. Better understanding the mechanism of Cr(VI) carcinogenesis may identify new molecular targets for more efficient prevention and treatment of cancer resulting from Cr(VI) exposure.