Recent advance in single-cell epigenomics

Progress in multifactorial single-cell chromatin profiling methods

Chromatin states play a key role in shaping overall cellular states and fates. Building a complete picture of the functional state of chromatin in cells requires the co-detection of several distinct biochemical aspects. These span DNA methylation, chromatin accessibility, chromosomal conformation, histone posttranslational modifications, and more. While this certainly presents a challenging task, over the past few years many new and creative methods have been developed that now enable co-assay of these different aspects of chromatin at single cell resolution. This field is entering an exciting phase, where a confluence of technological improvements, decreased sequencing costs, and computational innovation are presenting new opportunities to dissect the diversity of chromatin states present in tissues, and how these states may influence gene regulation. In this review, I discuss the spectrum of current experimental approaches for multifactorial chromatin profiling, highlight some of the experimental and analytical challenges, as well as some areas for further innovation.

How single-cell techniques help us look into lung cancer heterogeneity and immunotherapy

Lung cancer patients tend to have strong intratumoral and intertumoral heterogeneity and complex tumor microenvironment, which are major contributors to the efficacy of and drug resistance to immunotherapy. From a new perspective, single-cell techniques offer an innovative way to look at the intricate cellular interactions between tumors and the immune system and help us gain insights into lung cancer and its response to immunotherapy. This article reviews the application of single-cell techniques in lung cancer, with focuses directed on the heterogeneity of lung cancer and the efficacy of immunotherapy. This review provides both theoretical and experimental information for the future development of immunotherapy and personalized treatment for the management of lung cancer.

How do plants reprogramme the fate of differentiated cells?

Being able to change cell fate after differentiation highlights the remarkable developmental plasticity of plant cells. Recent studies show that phytohormones, such as auxin and cytokinin, promote cell cycle reactivation, a critical first step to reprogramme mitotically inactive, differentiated cells into organogenic stem cells. Accumulating evidence suggests that wounding provides an additional cue to convert the identity of differentiated cells by promoting the loss of existing cell fate and/or acquisition of new cell fate. Differentiated cells can also alter cell fate without undergoing cell division and in this case, wounding and phytohormones induce master regulators that can directly assign new cell fate.

Epigenetic regulation of nuclear processes in fungal plant pathogens

Through the association of protein complexes to DNA, the eukaryotic nuclear genome is broadly organized into open euchromatin that is accessible for enzymes acting on DNA and condensed heterochromatin that is inaccessible. Chemical and physical alterations to chromatin may impact its organization and functionality and are therefore important regulators of nuclear processes. Studies in various fungal plant pathogens have uncovered an association between chromatin organization and expression of in planta-induced genes that are important for pathogenicity. This review discusses chromatin-based regulation mechanisms as determined in the fungal plant pathogen Verticillium dahliae and relates the importance of epigenetic transcriptional regulation and other nuclear processes more broadly in fungal plant pathogens.

Epigenetic analytical approaches in ecotoxicological aquatic research

Environmental epigenetics has become a key research focus in global climate change studies and environmental pollutant investigations impacting aquatic ecosystems. Specifically, triggered by environmental stress conditions, intergenerational DNA methylation changes contribute to biological adaptive responses and survival of organisms to increase their tolerance towards these conditions. To critically review epigenetic analytical approaches in ecotoxicological aquatic research, we evaluated 78 publications reported over the past five years (2016-2021) that applied these methods to investigate the responses of aquatic organisms to environmental changes and pollution. The results show that DNA methylation appears to be the most robust epigenetic regulatory mark studied in aquatic animals. As such, multiple DNA methylation analysis methods have been developed in aquatic organisms, including enzyme restriction digestion-based and methyl-specific immunoprecipitation methods, and bisulfite (in)dependent sequencing strategies. In contrast, only a handful of aquatic studies, i.e. about 15%, have been focusing on histone variants and post-translational modifications due to the lack of species-specific affinity based immunological reagents, such as specific antibodies for chromatin immunoprecipitation applications. Similarly, ncRNA regulation remains as the least popular method used in the field of environmental epigenetics. Insights into the opportunities and challenges of the DNA methylation and histone variant analysis methods as well as decreasing costs of next generation sequencing approaches suggest that large-scale epigenetic environmental studies in model and non-model organisms will soon become available in the near future. Moreover, antibody-dependent and independent methods, such as mass spectrometry-based methods, can be used as an alternative epigenetic approach to characterize global changes of chromatin histone modifications in future aquatic research. Finally, a systematic guide for DNA methylation and histone variant methods is offered for ecotoxicological aquatic researchers to select the most relevant epigenetic analytical approach in their research.

New Method for Counting and Picking Out Single Circulating Tumor Cells from Microliter-Volume Samples for Tumor Progression Surveillance and Single-Cell Heterogeneity Analysis

Circulating tumor cells (CTCs) are crucial in tumor progression and metastasis, but the knowledge of their roles grows slowly at single-cell levels. Characterizing the rarity and fragility of CTCs by nature, highly stable and efficient single-CTC sampling methods are still lacking, which impedes the development of single-CTC analysis. Herein, an improved, capillary-based single-cell sampling (SiCS) method, the so-called bubble-glue single-cell sampling (bubble-glue SiCS), is introduced. Benefiting from the characteristic that the cells tend to adhere to air bubbles in the solution, single cells can be sampled with bubbles as low as 20 pL with a self-designed microbubble-volume-controlled system. Benefiting from the excellent maneuverability, single CTCs are sampled directly from 10 μL volume of real blood samples after fluorescent labeling. Meanwhile, over 90% of the CTCs obtained survived and well proliferated after the bubble-glue SiCS process, which showed considerable superiority for downstream single-CTC profiling. Furthermore, a highly metastatic breast cancer model of the 4T1 cell line in vivo was employed for the real blood sample analysis. Increases in CTC numbers were observed during the tumor progression process, and significant heterogeneities among individual CTCs were discovered. In all, we propose a novel avenue for target SiCS and provide an alternative technique route for CTC separation and analysis.

Pioneer factor ASCL1 cooperates with the mSWI/SNF complex at distal regulatory elements to regulate human neural differentiation

Pioneer transcription factors are thought to play pivotal roles in developmental processes by binding nucleosomal DNA to activate gene expression, though mechanisms through which pioneer transcription factors remodel chromatin remain unclear. Here, using single-cell transcriptomics, we show that endogenous expression of neurogenic transcription factor ASCL1, considered a classical pioneer factor, defines a transient population of progenitors in human neural differentiation. Testing ASCL1's pioneer function using a knockout model to define the unbound state, we found that endogenous expression of ASCL1 drives progenitor differentiation by cis-regulation both as a classical pioneer factor and as a nonpioneer remodeler, where ASCL1 binds permissive chromatin to induce chromatin conformation changes. ASCL1 interacts with BAF SWI/SNF chromatin remodeling complexes, primarily at targets where it acts as a nonpioneer factor, and we provide evidence for codependent DNA binding and remodeling at a subset of ASCL1 and SWI/SNF cotargets. Our findings provide new insights into ASCL1 function regulating activation of long-range regulatory elements in human neurogenesis and uncover a novel mechanism of its chromatin remodeling function codependent on partner ATPase activity.

GAGAM v1.2: An Improvement on Peak Labeling and Genomic Annotated Gene Activity Matrix Construction

Single-cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq) is rapidly becoming a powerful technology for assessing the epigenetic landscape of thousands of cells. However, the sparsity of the resulting data poses significant challenges to their interpretability and informativeness. Different computational methods are available, proposing ways to generate significant features from accessibility data and process them to obtain meaningful results. Foremost among them is the peak calling, which interprets the raw scATAC-seq data generating the peaks as features. However, scATAC-seq data are not trivially comparable with single-cell RNA sequencing (scRNA-seq) data, an increasingly pressing challenge since the necessity of multimodal experiments integration. For this reason, this study wants to improve the concept of the Gene Activity Matrix (GAM), which links the accessibility data to the genes, by proposing an improved version of the Genomic-Annotated Gene Activity Matrix (GAGAM) concept. Specifically, this paper presents GAGAM v1.2, a new and better version of GAGAM v1.0. GAGAM aims to label the peaks and link them to the genes through functional annotation of the whole genome. Using genes as features in scATAC-seq datasets makes different datasets comparable and allows linking gene accessibility and expression. This link is crucial for gene regulation understanding and fundamental for the increasing impact of multi-omics data. Results confirm that our method performs better than the previous GAMs and shows a preliminary comparison with scRNA-seq data.

New Insights Into the Epigenetic Regulation of Inflammatory Bowel Disease

Inflammatory bowel disease (IBD) is a chronic inflammatory disease of the colonic mucosa. Environmental factors, genetics, intestinal microbiota, and the immune system are all involved in the pathophysiology of IBD. Lately, accumulating evidence has shown that abnormal epigenetic changes in DNA methylation, histone markers, and non-coding RNA expression greatly contribute to the development of the entire disease. Epigenetics regulates many functions, such as maintaining the homeostasis of the intestinal epithelium and regulating the immune system of the immune cells. In the present study, we systematically summarized the latest advances in epigenetic modification of IBD and how epigenetics reveals new mechanisms of IBD. Our present review provided new insights into the pathophysiology of IBD. Moreover, exploring the patterns of DNA methylation and histone modification through epigenetics can not only be used as biomarkers of IBD but also as a new target for therapeutic intervention in IBD patients.

Mechanism and Therapeutic Opportunities of Histone Modifications in Chronic Liver Disease

Chronic liver disease (CLD) represents a global health problem, accounting for the heavy burden of disability and increased health care utilization. Epigenome alterations play an important role in the occurrence and progression of CLD. Histone modifications, which include acetylation, methylation, and phosphorylation, represent an essential part of epigenetic modifications that affect the transcriptional activity of genes. Different from genetic mutations, histone modifications are plastic and reversible. They can be modulated pharmacologically without changing the DNA sequence. Thus, there might be chances to establish interventional solutions by targeting histone modifications to reverse CLD. Here we summarized the roles of histone modifications in the context of alcoholic liver disease (ALD), metabolic associated fatty liver disease (MAFLD), viral hepatitis, autoimmune liver disease, drug-induced liver injury (DILI), and liver fibrosis or cirrhosis. The potential targets of histone modifications for translation into therapeutics were also investigated. In prospect, high efficacy and low toxicity drugs that are selectively targeting histone modifications are required to completely reverse CLD and prevent the development of liver cirrhosis and malignancy.

Epigenetic Alterations in Podocytes in Diabetic Nephropathy

Recently, epigenetic alterations have been shown to be involved in the pathogenesis of diabetes and its complications. Kidney podocytes, which are glomerular epithelial cells, are important cells that form a slit membrane—a barrier for proteinuria. Podocytes are terminally differentiated cells without cell division or replenishment abilities. Therefore, podocyte damage is suggested to be one of the key factors determining renal prognosis. Recent studies, including ours, suggest that epigenetic changes in podocytes are associated with chronic kidney disease, including diabetic nephropathy. Furthermore, the association between DNA damage repair and epigenetic changes in diabetic podocytes has been demonstrated. Detection of podocyte DNA damage and epigenetic changes using human samples, such as kidney biopsy and urine-derived cells, may be a promising strategy for estimating kidney damage and renal prognoses in patients with diabetes. Targeting epigenetic podocyte changes and associated DNA damage may become a novel therapeutic strategy for preventing progression to end-stage renal disease (ESRD) and provide a possible prognostic marker in diabetic nephropathy. This review summarizes recent advances regarding epigenetic changes, especially DNA methylation, in podocytes in diabetic nephropathy and addresses detection of these alterations in human samples. Additionally, we focused on DNA damage, which is increased under high-glucose conditions and associated with the generation of epigenetic changes in podocytes. Furthermore, epigenetic memory in diabetes is discussed. Understanding the role of epigenetic changes in podocytes in diabetic nephropathy may be of great importance considering the increasing diabetic nephropathy patient population in an aging society.