bims-ectoca 2022-04-24 papers

bims-ectoca

Biomed News

on Epigenetic control of tolerance in cancer

Issue of 2022–04–24
twenty papers selected by
Ankita Daiya, Birla Institute of Technology and Science

Natural Bioactive Compounds Targeting Histone Deacetylases in Human Cancers: Recent Updates.
Can aggressive cancers be identified by the "aggressiveness" of their chromatin?
Verteporfin Inhibits the Progression of Spontaneous Osteosarcoma Caused by Trp53 and Rb1 Deficiency in Ctsk-Expressing Cells via Impeding Hippo Pathway.
HDACs and the epigenetic plasticity of cancer cells: Target the complexity.
Autophagy in cancer cell remodeling and quality control.
Preclinical Efficacy and Toxicity Analysis of the Pan-Histone Deacetylase Inhibitor Gossypol for the Therapy of Colorectal Cancer or Hepatocellular Carcinoma.
The role of extracellular vesicles in the transfer of drug resistance competences to cancer cells.
Enhancer RNAs (eRNAs) in Cancer: The Jacks of All Trades.
H3K4 demethylase KDM5B regulates cancer cell identity and epigenetic plasticity.
The regulatory mechanisms by enhancers during cancer initiation and progression.
EZH2 Inhibitors Suppress Colorectal Cancer by Regulating Macrophage Polarization in the Tumor Microenvironment.
Mitochondrial ROS Produced in Human Colon Carcinoma Associated with Cell Survival via Autophagy.
Transcription factor Runx2 changes the expression of some matricellular proteins in metastatic breast cancer cells.
Leveraging single cell sequencing to unravel intra-tumour heterogeneity and tumour evolution in human cancers.
Epigenetic Regulation in Exposome-Induced Tumorigenesis: Emerging Roles of ncRNAs.
Contribution of MicroRNAs in Chemoresistance to Cisplatin in the Top Five Deadliest Cancer: An Updated Review.
Integrated profiling of human pancreatic cancer organoids reveals chromatin accessibility features associated with drug sensitivity.
CRABP2 accelerates epithelial mesenchymal transition in serous ovarian cancer cells by promoting TRIM16 methylation via upregulating EZH2 expression.
Cross-talk between mutant p53 and p62/SQSTM1 augments cancer cell migration by promoting the degradation of cell adhesion proteins.
Continuous chromatin state feature annotation of the human epigenome.

Molecules. 2022 Apr 15. pii: 2568. [Epub ahead of print]27(8):

Natural Bioactive Compounds Targeting Histone Deacetylases in Human Cancers: Recent Updates.

Abdelhakim Bouyahya, Naoufal El Hachlafi, Tarik Aanniz, Ilhame Bourais, Hamza Mechchate, Taoufiq Benali, Mohammad Ali Shariati, Pavel Burkov, José M Lorenzo, Polrat Wilairatana, Mohammad S Mubarak, Nasreddine El Omari.

  Cancer is a complex pathology that causes a large number of deaths worldwide. Several risk factors are involved in tumor transformation, including epigenetic factors. These factors are a set of changes that do not affect the DNA sequence, while modifying the gene's expression. Histone modification is an essential mark in maintaining cellular memory and, therefore, loss of this mark can lead to tumor transformation. As these epigenetic changes are reversible, the use of molecules that can restore the functions of the enzymes responsible for the changes is therapeutically necessary. Natural molecules, mainly those isolated from medicinal plants, have demonstrated significant inhibitory properties against enzymes related to histone modifications, particularly histone deacetylases (HDACs). Flavonoids, terpenoids, phenolic acids, and alkaloids exert significant inhibitory effects against HDAC and exhibit promising epi-drug properties. This suggests that epi-drugs against HDAC could prevent and treat various human cancers. Accordingly, the present study aimed to evaluate the pharmacodynamic action of different natural compounds extracted from medicinal plants against the enzymatic activity of HDAC.

Keywords:  cancer; epidrugs; epigenetic; histone deacetylases; natural compounds

DOI:  https://doi.org/10.3390/molecules27082568
Bioessays. 2022 Apr 22. e2100212

Can aggressive cancers be identified by the "aggressiveness" of their chromatin?

Katerina Gurova.

  Phenotypic plasticity is a crucial feature of aggressive cancer, providing the means for cancer progression. Stochastic changes in tumor cell transcriptional programs increase the chances of survival under any condition. I hypothesize that unstable chromatin permits stochastic transitions between transcriptional programs in aggressive cancers and supports non-genetic heterogeneity of tumor cells as a basis for their adaptability. I present a mechanistic model for unstable chromatin which includes destabilized nucleosomes, mobile chromatin fibers and random enhancer-promoter contacts, resulting in stochastic transcription. I suggest potential markers for "unsettled" chromatin in tumors associated with poor prognosis. Although many of the characteristics of unstable chromatin have been described, they were mostly used to explain changes in the transcription of individual genes. I discuss approaches to evaluate the role of unstable chromatin in non-genetic tumor cell heterogeneity and suggest using the degree of chromatin instability and transcriptional noise in tumor cells to predict cancer aggressiveness.

Keywords:  3D nuclear architecture; cancer; cancer diagnostic; cancer prognosis; chromatin; enhancer-promoter interactions; unstable chromatin

DOI:  https://doi.org/10.1002/bies.202100212
Cells. 2022 Apr 16. pii: 1361. [Epub ahead of print]11(8):

Verteporfin Inhibits the Progression of Spontaneous Osteosarcoma Caused by Trp53 and Rb1 Deficiency in Ctsk-Expressing Cells via Impeding Hippo Pathway.

Yang Li, Shuting Yang, Shuying Yang.

  Osteosarcoma is the most common primary malignancy of bone in children and adolescents. Others and our previous studies have shown that Yes-associated protein (YAP)/transcriptional coactivator with PDZ-binding motif (TAZ) as core components of the Hippo pathway are crucial regulators of osteosarcoma formation and progression. Recent studies demonstrated that verteporfin (VP) is an inhibitor of YAP/TAZ signaling in xenograft osteosarcoma. However, whether VP can inhibit primary osteosarcoma in mice is unknown. Mutations of Trp53 and Rb1 occur in approximately 50~70% of human osteosarcoma. In this study, we successfully generated the Ctsk-Cre;Trp53f/f/Rb1f/f mice in which Trp53/Rb1 was ablated in Ctsk-expressing cells and found that Ctsk-Cre;Trp53f/f/Rb1f/f mice spontaneously developed osteosarcoma with increased expansive osteoid lesions in the cortical bone with aging. Loss of Trp53/Rb1 in Ctsk-expressing cells significantly promoted the expression and nuclear translocation of YAP/TAZ. Micro-CT results showed that inhibition of YAP/TAZ by VP delays osteosarcoma progression and protected against bone erosion in Ctsk-Cre;Trp53f/f/Rb1f/f mice. Importantly, the Kaplan-Meier survival curves displayed a significantly longer survival rate after VP treatment in Ctsk-Cre;Trp53f/f/Rb1f/f mice compared to non-injected groups. In vitro studies further showed that VP inhibited the proliferation, migration and invasion in Trp53/Rb1-mutant Ctsk-expressing cells. Moreover, the results from promoter luciferase activity analysis showed that the transcriptional activity of YAP/TAZ was significantly increased in osteosarcoma tissue from Ctsk-Cre;Trp53f/f/Rb1f/f mice, which was attenuated by VP treatment. Overall, these findings suggest that targeting Hippo pathway by VP may be a potential therapeutic strategy for osteosarcoma.

Keywords:  Rb1; Trp53; YAP/TAZ; osteosarcoma; verteporfin

DOI:  https://doi.org/10.3390/cells11081361
Pharmacol Ther. 2022 Apr 14. pii: S0163-7258(22)00084-5. [Epub ahead of print] 108190

HDACs and the epigenetic plasticity of cancer cells: Target the complexity.

Claudio Brancolini, Teresa Gagliano, Martina Minisini.

  Cancer cells must adapt to the hostile conditions of the microenvironment in terms of nutrition, space, and immune system attack. Mutations of DNA are the drivers of the tumorigenic process, but mutations must be able to hijack cellular functions to sustain the spread of mutant genomes. Transcriptional control is a key function in this context and is controlled by the rearrangement of the epigenome. Unlike genomic mutations, the epigenome of cancer cells can in principle be reversed. The discovery of the first epigenetic drugs triggered a contaminating enthusiasm. Unfortunately, the complexity of the epigenetic machinery has frustrated this enthusiasm. To develop efficient patient-oriented epigenetic therapies, we need to better understand the nature of this complexity. In this review, we will discuss recent advances in understanding the contribution of HDACs to the maintenance of the transformed state and the rational for their selective targeting.

Keywords:  Acetylation; Cancer; Epigenomics; HDACs; Immune-therapy; Inhibitors; Therapy

DOI:  https://doi.org/10.1016/j.pharmthera.2022.108190
Mol Cell. 2022 Apr 21. pii: S1097-2765(22)00261-1. [Epub ahead of print]82(8): 1514-1527

Autophagy in cancer cell remodeling and quality control.

Grace A Hernandez, Rushika M Perera.

  As one of the two highly conserved cellular degradation systems, autophagy plays a critical role in regulation of protein, lipid, and organelle quality control and cellular homeostasis. This evolutionarily conserved pathway singles out intracellular substrates for elimination via encapsulation within a double-membrane vesicle and delivery to the lysosome for degradation. Multiple cancers disrupt normal regulation of autophagy and hijack its degradative ability to remodel their proteome, reprogram their metabolism, and adapt to environmental challenges, making the autophagy-lysosome system a prime target for anti-cancer interventions. Here, we discuss the roles of autophagy in tumor progression, including cancer-specific mechanisms of autophagy regulation and the contribution of tumor and host autophagy in metabolic regulation, immune evasion, and malignancy. We further discuss emerging proteomics-based approaches for systematic profiling of autophagosome-lysosome composition and contents. Together, these approaches are uncovering new features and functions of autophagy, leading to more effective strategies for targeting this pathway in cancer.

Keywords:  autophagy; cancer; lysosome; quality control; remodeling

DOI:  https://doi.org/10.1016/j.molcel.2022.03.023
Pharmaceuticals (Basel). 2022 Apr 01. pii: 438. [Epub ahead of print]15(4):

Preclinical Efficacy and Toxicity Analysis of the Pan-Histone Deacetylase Inhibitor Gossypol for the Therapy of Colorectal Cancer or Hepatocellular Carcinoma.

Mascha Mayer, Alexander Berger, Christian Leischner, Olga Renner, Markus Burkard, Alexander Böcker, Seema Noor, Timo Weiland, Thomas S Weiss, Christian Busch, Ulrich M Lauer, Stephan C Bischoff, Sascha Venturelli.

  Gossypol, a sesquiterpenoid found in cotton seeds, exerts anticancer effects on several tumor entities due to inhibition of DNA synthesis and other mechanisms. In clinical oncology, histone deacetylase inhibitors (HDACi) are applied as anticancer compounds. In this study, we examined whether gossypol harbors HDAC inhibiting activity. In vitro analyses showed that gossypol inhibited class I, II, and IV HDAC, displaying the capability to laterally interact with the respective catalytic center and is, therefore, classified as a pan-HDAC inhibitor. Next, we studied the effects of gossypol on human-derived hepatoma (HepG2) and colon carcinoma (HCT-116) cell lines and found that gossypol induced hyperacetylation of histone protein H3 and/or tubulin within 6 h. Furthermore, incubation with different concentrations of gossypol (5-50 µM) over a time period of 96 h led to a prominent reduction in cellular viability and proliferation of hepatoma (HepG2, Hep3B) and colon carcinoma (HCT-116, HT-29) cells. In-depth analysis of underlying mechanisms showed that gossypol induced apoptosis via caspase activation. For pre-clinical evaluation, toxicity analyses showed toxic effects of gossypol in vitro toward non-malignant primary hepatocytes (PHH), the colon-derived fibroblast cell line CCD-18Co, and the intestinal epithelial cell line CCD 841 CoN at concentrations of ≥5 µM, and embryotoxicity in chicken embryos at ≥2.5 µM. In conclusion, the pronounced inhibitory capacity of gossypol on cancer cells was characterized, and pan-HDACi activity was detected in silico, in vitro, by inhibiting individual HDAC isoenzymes, and on protein level by determining histone acetylation. However, for clinical application, further chemical optimization is required to decrease cellular toxicity.

Keywords:  AT-101; colon cancer; epigenetics; gossypol; histone deacetylase; liver cancer

DOI:  https://doi.org/10.3390/ph15040438
Drug Resist Updat. 2022 Apr 05. pii: S1368-7646(22)00032-2. [Epub ahead of print]62 100833

The role of extracellular vesicles in the transfer of drug resistance competences to cancer cells.

Cristina P R Xavier, Dimas Carolina Belisario, Rita Rebelo, Yehuda G Assaraf, Elisa Giovannetti, Joanna Kopecka, M Helena Vasconcelos.

  Drug resistance remains a major hurdle to successful cancer treatment, being accountable for approximately 90% of cancer-related deaths. In the past years, increasing attention has been given to the role of extracellular vesicles (EVs) in the horizontal transfer of drug resistance in cancer. Indeed, many studies have described the dissemination of therapy resistance traits mediated by EVs, which may be transferred from drug resistant tumor cells to their drug sensitive counterparts. Importantly, different key players of drug resistance have been identified in the cargo of those EVs, such as drug efflux pumps, oncoproteins, antiapoptotic proteins, or microRNAs, among others. Interestingly, the EVs-mediated crosstalk between cells from the tumor microenvironment (TME) and tumor cells has emerged as another important mechanism that leads to cancer cells drug resistance. Recently, the cargo of the TME-derived EVs responsible for the transfer of drug resistance traits has also become a focus of attention. In addition, the possible mechanisms involved in drug sequestration by EVs, likely to contribute to cancer drug resistance, are also described and discussed herein. Despite the latest scientific advances in the field of EVs, this is still a challenging area of research, particularly in the clinical setting. Therefore, further investigation is needed to assess the relevance of EVs to the failure of cancer patients to drug treatment, to identify biomarkers of drug resistance in the EV's cargo, and to develop effective therapeutic strategies to surmount drug resistance. This up-to-date review summarizes relevant literature on the role of EVs in the transfer of drug resistance competences to cancer cells, and the relevance of tumor cells and of TME cells in this process. Finally, this knowledge is integrated with a discussion of possible future clinical applications of EVs as biomarkers of drug resistance.

Keywords:  Cancer drug resistance; Extracellular vesicles; Intercellular transfer of drug resistance competences; Tumor microenvironment

DOI:  https://doi.org/10.1016/j.drup.2022.100833
Cancers (Basel). 2022 Apr 14. pii: 1978. [Epub ahead of print]14(8):

Enhancer RNAs (eRNAs) in Cancer: The Jacks of All Trades.

Sara Napoli, Nicolas Munz, Francesca Guidetti, Francesco Bertoni.

  Enhancer RNAs (eRNAs) are non-coding RNAs (ncRNAs) transcribed in enhancer regions. They play an important role in transcriptional regulation, mainly during cellular differentiation. eRNAs are tightly tissue- and cell-type specific and are induced by specific stimuli, activating promoters of target genes in turn. eRNAs usually have a very short half-life but in some cases, once activated, they can be stably expressed and acquire additional functions. Due to their critical role, eRNAs are often dysregulated in cancer and growing number of interactions with chromatin modifiers, transcription factors, and splicing machinery have been described. Enhancer activation and eRNA transcription have particular relevance also in inflammatory response, placing the eRNAs at the interplay between cancer and immune cells. Here, we summarize all the possible molecular mechanisms recently reported in association with eRNAs activity.

Keywords:  cancer; eRNA; enhancer; immune response; ncRNA; transcriptional regulation

DOI:  https://doi.org/10.3390/cancers14081978
Oncogene. 2022 Apr 19.

H3K4 demethylase KDM5B regulates cancer cell identity and epigenetic plasticity.

Runsheng He, Besa Xhabija, Lijin K Gopi, Jiji T Kurup, Zhishan Xu, Zhe Liu, Benjamin L Kidder.

The H3K4 demethylase KDM5B is overexpressed in multiple cancer types, and elevated expression levels of KDM5B is associated with decreased survival. However, the underlying mechanistic contribution of dysregulated expression of KDM5B and H3K4 demethylation in cancer is poorly understood. Our results show that loss of KDM5B in multiple types of cancer cells leads to increased proliferation and elevated expression of cancer stem cell markers. In addition, we observed enhanced tumor formation following KDM5B depletion in a subset of representative cancer cell lines. Our findings also support a role for KDM5B in regulating epigenetic plasticity, where loss of KDM5B in cancer cells with elevated KDM5B expression leads to alterations in activity of chromatin states, which facilitate activation or repression of alternative transcriptional programs. In addition, we define KDM5B-centric epigenetic and transcriptional patterns that support cancer cell plasticity, where KDM5B depleted cancer cells exhibit altered epigenetic and transcriptional profiles resembling a more primitive cellular state. This study also provides a resource for evaluating associations between alterations in epigenetic patterning upon depletion of KDM5B and gene expression in a diverse set of cancer cells.

DOI: https://doi.org/10.1038/s41388-022-02311-z
Yi Chuan. 2022 Apr 20. 44(4): 275-288

The regulatory mechanisms by enhancers during cancer initiation and progression.

Si-Han Qi, Qi-Lin Wang, Jun-You Zhang, Qian Liu, Chun-Yan Li.

  Enhancer is a DNA sequence, and mainly acts in cis to regulate gene transcription. Due to the uncertainty in both location and distance between enhancers and their target genes, it is more complex and difficult to study the underlying regulatory mechanism of enhancers. Accumulating evidences indicate that enhancers are closely associated with the occurrence and development of diseases, such as cancer. Therefore, the studies of enhancers in cancer will be helpful to deeply unravel cancer pathogenesis and to promote the development of antitumor drugs. The related research is with great social significance and economic value. Currently, the identification of enhancers is insufficient. The regulatory mechanisms by enhancers during the initiation and progression of cancer and other diseases have not been fully delineated. In this review, we provide an overview of enhancers, super enhancers and their properties, followed by a description of enhancer prediction and identification at the genome-wide level. Finally, we summarize the regulatory roles of enhancers during diseases such as cancer in recent years, thereby providing a reference for the future exploration on enhancer regulatory mechanisms as well as cancer diagnosis and treatment.

Keywords:  cancer; enhancers; regulatory mechanisms; super enhancers

DOI:  https://doi.org/10.16288/j.yczz.21-440
Front Immunol. 2022 ;13 857808

EZH2 Inhibitors Suppress Colorectal Cancer by Regulating Macrophage Polarization in the Tumor Microenvironment.

Chen Li, Jiagui Song, Zhengyang Guo, Yueqing Gong, Tengrui Zhang, Jiaqi Huang, Rui Cheng, Xiaotong Yu, Yanfang Li, Li Chen, Xiaojuan Ma, Yan Sun, Yan Wang, Lixiang Xue.

  EZH2 inhibitors (EZH2i), a class of small-molecule inhibitors that target EZH2 to exert anti-tumor functions, have just been approved by the US Food and Drug Administration (FDA) in treatment of adults and adolescents with locally advanced or metastatic epithelioid sarcoma. The application of EZH2i in several solid tumors is still in different stages of clinical trials and needs to be further validated. As a key epigenetic regulator, besides its role in controlling the proliferation of tumor cells, EZH2 has been implicated in the regulation of various immune cells including macrophages. But there are still controversial research results at present. Colorectal cancer (CRC) is a common malignant tumor that highly expresses EZH2, which has the third highest incidence and is the second leading cause of cancer-related death worldwide. Studies have shown that the numbers of M2-type tumor-associated macrophages (TAMs) are highly associated with the progression and metastasis of CRC. In the current study, we aim to investigate how EZH2 modulates the polarization of macrophages in the tumor microenvironment (TME) of CRC, and compare the role of two different EZH2 inhibitors, EPZ6438 and GSK126. We applied a 3D culture method to demonstrate that EZH2i did indeed suppress the proliferation of CRC cells in vitro. In vivo, we found that the percentage of CD206+ macrophages of the TME was decreased under the treatment of EPZ6438, but it increased upon GSK126 treatment. Besides, in the co-culture system of macrophages and CRC cells, EPZ6438 led to significant elevation of M1 markers and reduction of M2 markers. Furthermore, mechanistic studies validated by ChIP-qPCR demonstrated that EZH2i inhibit EZH2-mediated H3K27me3 levels on the promoters of STAT3, an essential transcription factor for M1 macrophage polarization. Therefore, our data suggested that EZH2i not only suppress CRC cell proliferation directly, but also regulate macrophage by skewing M2 into effector M1 macrophage to exert a tumor suppressive effect. Moreover, our study provided new insight for better understanding of the role of two kinds of EZH2i: EPZ6438 and GSK126, which may pave the way in treating CRC by targeting cancer cells and immune cells via this epigenetic approach in the future.

Keywords:  EZH2; EZH2 inhibitor; colorectal cancer; macrophage; tumor microenvironment

DOI:  https://doi.org/10.3389/fimmu.2022.857808
Cancers (Basel). 2022 Apr 08. pii: 1883. [Epub ahead of print]14(8):

Mitochondrial ROS Produced in Human Colon Carcinoma Associated with Cell Survival via Autophagy.

Eun Ji Gwak, Dasol Kim, Hui-Yun Hwang, Ho Jeong Kwon.

  Human colon carcinomas, including HCT116 cells, often exhibit high autophagic flux under nutrient deprivation or hypoxic conditions. Mitochondrial ROS (mROS) is known as a 'molecular switch' for regulating the autophagic pathway, which is critical for directing cancer cell survival or death. In early tumorigenesis, autophagy plays important roles in maintaining cellular homeostasis and contributes to tumor growth. However, the relationships between mROS and the autophagic capacities of HCT116 cells are poorly understood. Ubiquinol cytochrome c reductase binding protein (UQCRB) has been reported as a biomarker of colorectal cancer, but its role in tumor growth has not been clarified. Here, we showed that UQCRB is overexpressed in HCT116 cells compared to CCD18co cells, a normal colon fibroblast cell line. Pharmacological inhibition of UQCRB reduced mROS levels, autophagic flux, and the growth of HCT116 tumors in a xenograft mouse model. We further investigated mutant UQCRB-overexpressing cell lines to identify functional links in UQCRB-mROS-autophagy. Notably, an increasing level of mROS caused by UQCRB overexpression released Ca2+ by the activation of lysosomal transient receptor potential mucolipin 1 (TRPML1) channels. This activation induced transcription factor EB (TFEB) nuclear translocation and lysosome biogenesis, leading to autophagy flux. Collectively, our study showed that increasing levels of mROS caused by the overexpression of UQCRB in human colon carcinoma HCT116 cells could be linked to autophagy for cell survival.

Keywords:  UQCRB; autophagy; colorectal cancer; lysosome; mROS

DOI:  https://doi.org/10.3390/cancers14081883
Mol Biol Rep. 2022 Apr 19.

Transcription factor Runx2 changes the expression of some matricellular proteins in metastatic breast cancer cells.

Sevgi Binay, Engin Kaptan.

   BACKGROUND: Runx2 is one of the runt-related genes that are overexpressed in human cancers and contribute to metastasis. The cancer cell metastasis requires modifications of the extracellular matrix (ECM) and reduction in ECM-cell interaction. This process is performed by various enzymes and proteins secreted by cancer and surrounding cells. This study aimed to investigate the effect of the Runx2 transcription factor on the expression of matricellular proteins such as HPA1, LOX, SPARC, and OPN, which have important roles in ECM modification and ECM-cell interaction in human breast cancer. Also, the changes in their associated oncogenic pathways including Akt, Erk, FAK activities, and c-jun protein expression were investigated.
METHODS AND RESULTS: Runx2 knockdown model was created using runx2 siRNA in MDA-MB-231 human metastatic breast cancer cells. The changes in the mRNA and protein expressions of ECM proteins were shown by the qPCR and Western blotting, respectively. The results showed that there was a decrease in both mRNA and protein expressions of HPA1, SPARC, and LOX, whereas there was no change in those of OPN. Phosphorylated Akt, Erk, FAK levels, and protein expression of c-jun, however, decreased in the cells.
CONCLUSION: Our results revealed that Runx2 affected matricellular protein expression, which is important for metastasis and invasion of breast cancer. Hence, we have concluded that runx2 appears to be efficient for regulating breast cancer metastasis through an expression of matricellular proteins.

Keywords:  Breast cancer; Heparanase; LOX; Osteopontin; Runx2; SPARC

DOI:  https://doi.org/10.1007/s11033-022-07457-3
J Pathol. 2022 Apr 19.

Leveraging single cell sequencing to unravel intra-tumour heterogeneity and tumour evolution in human cancers.

Amy Bowes, Maxime Tarabichi, Nischalan Pillay, Peter Van Loo.

  Intra-tumour heterogeneity and tumour evolution are well-documented phenomena in human cancers. While the advent of next-generation sequencing technologies has facilitated the large-scale capture of genomic data, the field of single cell genomics is nascent but rapidly advancing and generating many new insights into the complex molecular mechanisms of tumour biology. In this review, we provide an overview of current single cell DNA sequencing technologies, exploring how recent methodological advancements have enumerated new insights into intra-tumour heterogeneity and tumour evolution. Areas highlighted include the potential power of single cell genome sequencing studies to explore evolutionary dynamics contributing to tumourigenesis through to progression, metastasis and therapy resistance. We also explore the use of in-situ sequencing technologies to study intra-tumour heterogeneity in a spatial context, as well as examining the use of single cell genomics to perform lineage tracing in both normal and malignant tissues. Finally, we consider the use of multi-modal single cell sequencing technologies. Taken together, it is hoped that these many facets of single cell genome sequencing will improve our understanding of tumourigenesis, progression and lethality in cancer leading to the development of novel therapies. This article is protected by copyright. All rights reserved.

Keywords:  clone; copy number aberrations (CNAs); intra-tumour heterogeneity (ITH); single cell DNA sequencing; subclone; tumour evolution; tumour phylogeny

DOI:  https://doi.org/10.1002/path.5914
Biomolecules. 2022 Mar 28. pii: 513. [Epub ahead of print]12(4):

Epigenetic Regulation in Exposome-Induced Tumorigenesis: Emerging Roles of ncRNAs.

Miguel Ángel Olmedo-Suárez, Ivonne Ramírez-Díaz, Andrea Pérez-González, Alejandro Molina-Herrera, Miguel Ángel Coral-García, Sagrario Lobato, Pouya Sarvari, Guillermo Barreto, Karla Rubio.

  Environmental factors, including pollutants and lifestyle, constitute a significant role in severe, chronic pathologies with an essential societal, economic burden. The measurement of all environmental exposures and assessing their correlation with effects on individual health is defined as the exposome, which interacts with our unique characteristics such as genetics, physiology, and epigenetics. Epigenetics investigates modifications in the expression of genes that do not depend on the underlying DNA sequence. Some studies have confirmed that environmental factors may promote disease in individuals or subsequent progeny through epigenetic alterations. Variations in the epigenetic machinery cause a spectrum of different disorders since these mechanisms are more sensitive to the environment than the genome, due to the inherent reversible nature of the epigenetic landscape. Several epigenetic mechanisms, including modifications in DNA (e.g., methylation), histones, and noncoding RNAs can change genome expression under the exogenous influence. Notably, the role of long noncoding RNAs in epigenetic processes has not been well explored in the context of exposome-induced tumorigenesis. In the present review, our scope is to provide relevant evidence indicating that epigenetic alterations mediate those detrimental effects caused by exposure to environmental toxicants, focusing mainly on a multi-step regulation by diverse noncoding RNAs subtypes.

Keywords:  biomarkers; environment-related toxicants; epigenetic reprogramming; exposome; noncoding RNAs; tumorigenesis

DOI:  https://doi.org/10.3390/biom12040513
Front Pharmacol. 2022 ;13 831099

Contribution of MicroRNAs in Chemoresistance to Cisplatin in the Top Five Deadliest Cancer: An Updated Review.

Pía Loren, Nicolás Saavedra, Kathleen Saavedra, Nadine De Godoy Torso, Marília Berlofa Visacri, Patricia Moriel, Luis A Salazar.

  Cisplatin (DDP) is a well-known anticancer drug used for the treatment of numerous human cancers in solid organs, including bladder, breast, cervical, head and neck squamous cell, ovarian, among others. Its most important mode of action is the DNA-platinum adducts formation, inducing DNA damage response, silencing or activating several genes to induce apoptosis; these mechanisms result in genetics and epigenetics modifications. The ability of DDP to induce tumor cell death is often challenged by the presence of anti-apoptotic regulators, leading to chemoresistance, wherein many patients who have or will develop DDP-resistance. Cancer cells resist the apoptotic effect of chemotherapy, being a problem that severely restricts the successful results of treatment for many human cancers. In the last 30 years, researchers have discovered there are several types of RNAs, and among the most important are non-coding RNAs (ncRNAs), a class of RNAs that are not involved in protein production, but they are implicated in gene expression regulation, and representing the 98% of the human genome non-translated. Some ncRNAs of great interest are long ncRNAs, circular RNAs, and microRNAs (miRs). Accumulating studies reveal that aberrant miRs expression can affect the development of chemotherapy drug resistance, by modulating the expression of relevant target proteins. Thus, identifying molecular mechanisms underlying chemoresistance development is fundamental for setting strategies to improve the prognosis of patients with different types of cancer. Therefore, this review aimed to identify and summarize miRs that modulate chemoresistance in DDP-resistant in the top five deadliest cancer, both in vitro and in vivo human models.

Keywords:  cancer; cisplatin; drug-resistance; microRNA; sensitivity

DOI:  https://doi.org/10.3389/fphar.2022.831099
Nat Commun. 2022 Apr 21. 13(1): 2169

Integrated profiling of human pancreatic cancer organoids reveals chromatin accessibility features associated with drug sensitivity.

Xiaohan Shi, Yunguang Li, Qiuyue Yuan, Shijie Tang, Shiwei Guo, Yehan Zhang, Juan He, Xiaoyu Zhang, Ming Han, Zhuang Liu, Yiqin Zhu, Suizhi Gao, Huan Wang, Xiongfei Xu, Kailian Zheng, Wei Jing, Luonan Chen, Yong Wang, Gang Jin, Dong Gao.

Chromatin accessibility plays an essential role in controlling cellular identity and the therapeutic response of human cancers. However, the chromatin accessibility landscape and gene regulatory network of pancreatic cancer are largely uncharacterized. Here, we integrate the chromatin accessibility profiles of 84 pancreatic cancer organoid lines with whole-genome sequencing data, transcriptomic sequencing data and the results of drug sensitivity analysis of 283 epigenetic-related chemicals and 5 chemotherapeutic drugs. We identify distinct transcription factors that distinguish molecular subtypes of pancreatic cancer, predict numerous chromatin accessibility peaks associated with gene regulatory networks, discover regulatory noncoding mutations with potential as cancer drivers, and reveal the chromatin accessibility signatures associated with drug sensitivity. These results not only provide the chromatin accessibility atlas of pancreatic cancer but also suggest a systematic approach to comprehensively understand the gene regulatory network of pancreatic cancer in order to advance diagnosis and potential personalized medicine applications.

DOI: https://doi.org/10.1038/s41467-022-29857-6
Environ Toxicol. 2022 Apr 20.

CRABP2 accelerates epithelial mesenchymal transition in serous ovarian cancer cells by promoting TRIM16 methylation via upregulating EZH2 expression.

Tingting Xie, Minghua Tan, Yang Gao, Hong Yang.

  Recently, it was covered that cellular retinoic acid-binding protein 2 (CRABP2) is upregulated in ovarian cancer and participates in tumor progression, however, the specific mechanism remains to be explored. The pcDNA-CRABP2 or si-CRABP2 was transfected into SKOV3 and OVCAR3 ovarian cancer cells, respectively, and we observed that overexpression of CRABP2 inhibited cell apoptosis, promoted cell invasion and expression of epithelial mesenchymal transition (EMT) marker proteins, and transfection of si-CRABP2 had the opposite effect. Furthermore, we predicted that EZH2 interacted with CRABP2, and overexpression of CRABP2 promoted EZH2 expression, knockdown of CRABP2 inhibited EZH2 expression, and co-immunoprecipitation assay confirmed their binding relationship. The SKOV3 and OVCAR3 cells were then incubated with pcDNA-CRABP2 alone together with si-EZH2, and we found that si-EZH2 reversed the effect of pcDNA-CRABP2 on promotion of EZH2 expression, cell invasion and EMT maker protein levels. Next, we found that EZH2 could bind to DNMT1, and overexpression of EZH2 inhibited TRIM16 expression and knockdown of EZH2 promoted TRIM16 expression. Moreover, the promoter of TRIM16 contains the CpG island, and ChIP assay observed enriched DNMT1 on the promoter of TRIM16, and overexpression of EZH2 increased the promoter methylation level of TRIM16 and knockdown of EZH2 suppressed the methylation. The SKOV3 cells were incubated with si-EZH2 alone or combined with si-TRIM16, and we found that si-TRIM16 reversed the effect of si-EZH2. In vivo studies showed that knockdown of CRABP2 inhibited tumor volume and weight, suppressed the expression of EZH2 and EMT related proteins vimentin and snail, and increased the expression of TRIM16 and E-cadherin.

Keywords:  CRABP2; EZH2; TRIM16; epithelial mesenchymal transition; ovarian cancer

DOI:  https://doi.org/10.1002/tox.23542
Proc Natl Acad Sci U S A. 2022 Apr 26. 119(17): e2119644119

Cross-talk between mutant p53 and p62/SQSTM1 augments cancer cell migration by promoting the degradation of cell adhesion proteins.

Saptaparna Mukherjee, Martino Maddalena, YiQing Lü, Sebastien Martinez, Nishanth Belugali Nataraj, Ashish Noronha, Sansrity Sinha, Katie Teng, Victoria Cohen-Kaplan, Tamar Ziv, Sharathchandra Arandkar, Ori Hassin, Rishita Chatterjee, Anna-Chiara Pirona, Michal Shreberk-Shaked, Anat Gershoni, Yael Aylon, Zvulun Elazar, Yosef Yarden, Daniel Schramek, Moshe Oren.

  SignificanceMissense mutations in the TP53 gene, encoding the p53 tumor suppressor, are very frequent in human cancer. Some of those mutations, particularly the more common ("hotspot") ones, not only abrogate p53's tumor suppressor activities but also endow the mutant protein with oncogenic gain of function (GOF). We report that p53R273H, the most common p53 mutant in pancreatic cancer, interacts with the SQSTM1/p62 protein to accelerate the degradation of cell adhesion proteins. This enables pancreatic cancer cells to detach from the epithelial sheet and engage in individualized cell migration, probably augmenting metastatic spread. By providing insights into mechanisms that underpin mutant p53 GOF, this study may suggest ways to interfere with the progression of cancers bearing particular p53 mutants.

Keywords:  cell adhesion; migration; mutant p53; p62; protein–protein interaction

DOI:  https://doi.org/10.1073/pnas.2119644119
Bioinformatics. 2022 Apr 22. pii: btac283. [Epub ahead of print]

Continuous chromatin state feature annotation of the human epigenome.

Habib Daneshpajouh, Bowen Chen, Neda Shokraneh, Shohre Masoumi, Kay C Wiese, Maxwell W Libbrecht.

MOTIVATION: Segmentation and genome annotation (SAGA) algorithms are widely used to understand genome activity and gene regulation. These methods take as input a set of sequencing-based assays of epigenomic activity, such as ChIP-seq measurements of histone modification and transcription factor binding. They output an annotation of the genome that assigns a chromatin state label to each genomic position. Existing SAGA methods have several limitations caused by the discrete annotation framework: such annotations cannot easily represent varying strengths of genomic elements, and they cannot easily represent combinatorial elements that simultaneously exhibit multiple types of activity. To remedy these limitations, we propose an annotation strategy that instead outputs a vector of chromatin state features at each position rather than a single discrete label. Continuous modeling is common in other fields, such as in topic modeling of text documents. We propose a method, epigenome-ssm-nonneg, that uses a non-negative state space model to efficiently annotate the genome with chromatin state features. We also propose several measures of the quality of a chromatin state feature annotation and we compare the performance of several alternative methods according to these quality measures.
RESULTS: We show that chromatin state features from epigenome-ssm-nonneg are more useful for several downstream applications than both continuous and discrete alternatives, including their ability to identify expressed genes and enhancers. Therefore, we expect that these continuous chromatin state features will be valuable reference annotations to be used in visualization and downstream analysis.
AVAILABILITY: Source code for epigenome-ssm is available at https://github.com/habibdanesh/epigenome-ssm.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

DOI: https://doi.org/10.1093/bioinformatics/btac283