Acetylation and deacetylation of histone in adipocyte differentiation and the potential significance in cancer

Deciphering the role of acetylation-related gene NAT10 in colon cancer progression and immune evasion: implications for overcoming drug resistance

BACKGROUND

Colon cancer (CC) is one of the most common and lethal cancers worldwide, with rising incidence rates in both developed and developing countries. Although advances in treatments such as surgery, chemotherapy, and targeted therapies have been made, prognosis for advanced colon cancer, particularly with metastasis, remains poor. Recent studies highlight the significant role of post-transcriptional modifications like acetylation in cancer biology, affecting processes like gene transcription, metabolism, and tumor progression.

METHODS

This study applied multi-omics analyses, including single-cell RNA sequencing (scRNA-seq), spatial transcriptomics, and Mendelian randomization. Data were obtained from public datasets like GSE132465, UCSC Xena, and GeneCards. We focused on acetylation-related genes, specifically NAT10 and GNE, using scoring methods, cell-cell interaction models, and survival analyses to investigate their role in colon cancer development, metastasis, and immune evasion.

RESULTS

This study identifies that NAT10 is highly expressed in epithelial cells of colorectal cancer (CC) and is closely associated with tumor progression and metastasis. Single-cell RNA sequencing analysis revealed that NAT10-positive epithelial cells exhibited strong interactions with myeloid cells and T cells, with significant differences in cell-cell communication (p < 0.05). Based-on-summary-data Mendelian randomization (SMR) analysis further supports a causal relationship between NAT10 and colorectal cancer. In the MR analysis, a significant positive correlation was observed between NAT10 and colorectal cancer risk using summary data from genome-wide association studies (GWAS) and expression quantitative trait loci (eQTL) studies (β_SMR = 0.004, p_SMR = 0.041, p_HEIDI = 0.737). These findings suggest that NAT10 may serve as a pathogenic factor in colorectal cancer development, providing additional genetic evidence that links this acetylation-related gene to colorectal cancer. Survival analysis further demonstrated that NAT10-positive epithelial cells are associated with poorer prognosis. In the TCGA dataset, patients with NAT10-positive epithelial cells exhibited a significantly shorter disease-free survival (DFS) (p = 0.012). Unlike GNE-positive cells, NAT10-positive epithelial cells exhibited immune escape characteristics, and TIDE analysis indicated that NAT10-positive epithelial cells were associated with a lower response to immune checkpoint blockade therapy (p = 1.3e-5), suggesting that they may impair the efficacy of immunotherapy by promoting immune evasion. In contrast, GNE was also significantly expressed in epithelial cells of colorectal cancer, but its role differs from that of NAT10. GNE-positive epithelial cells demonstrated strong communication with immune cells, particularly in interactions between myeloid cells and T cells through receptor-ligand pairs. Despite the important role of GNE-positive epithelial cells in the tumor microenvironment, their association with immune escape is weaker compared to NAT10. Survival analysis revealed that GNE-positive epithelial cells were associated with a better prognosis (p = 0.015). In the TCGA dataset, patients with GNE-positive epithelial cells displayed longer disease-free survival (DFS), contrary to the results from the SMR analysis.

CONCLUSIONS

Leveraging SMR and multi-omics analysis, this study highlights the significant role of acetylation-related genes, particularly NAT10, in colon cancer. The findings suggest that acetylation modifications in epithelial cells contribute to immune evasion and cancer progression. NAT10 could serve as a promising biomarker and therapeutic target for early diagnosis and targeted therapy, offering new avenues for improving colon cancer treatment and patient outcomes.

14-3-3ζ allows for adipogenesis by modulating chromatin accessibility during the early stages of adipocyte differentiation

OBJECTIVE

We previously established the scaffold protein 14-3-3ζ as a critical regulator of adipogenesis and adiposity, but whether 14-3-3ζ exerted its regulatory functions in mature adipocytes or in adipose progenitor cells (APCs) remained unclear.

METHODS

To decipher which cell type accounted for 14-3-3ζ-regulated adiposity, adipocyte- (Adipoq14-3-3ζKO) and APC-specific (Pdgfra14-3-3ζKO) 14-3-3ζ knockout mice were generated. To further understand how 14-3-3ζ regulates adipogenesis, Tandem Affinity Purification (TAP)-tagged 14-3-3ζ-expressing 3T3-L1 preadipocytes (TAP-3T3-L1) were generated with CRISPR-Cas9, and affinity proteomics was used to examine how the nuclear 14-3-3ζ interactome changes during the initial stages of adipogenesis. ATAC-seq was used to determine how 14-3-3ζ depletion modulates chromatin accessibility during differentiation.

RESULTS

We show a pivotal role for 14-3-3ζ in APC differentiation, whereby male and female Pdgfra14-3-3ζKO mice displayed impaired or potentiated weight gain, respectively, as well as fat mass. Proteomics revealed that regulators of chromatin remodeling, like DNA methyltransferase 1 (DNMT1) and histone deacetylase 1 (HDAC1), were significantly enriched in the nuclear 14-3-3ζ interactome and their activities were impacted upon 14-3-3ζ depletion. Enhancing DNMT activity with S-Adenosyl methionine rescued the differentiation of 14-3-3ζ-depleted 3T3-L1 cells. ATAC-seq revealed that 14-3-3ζ depletion impacted the accessibility of up to 1,244 chromatin regions corresponding in part to adipogenic genes, promoters, and enhancers during the initial stages of adipogenesis. Finally, 14-3-3ζ-regulated chromatin accessibility correlated with the expression of key adipogenic genes.

CONCLUSION

Our study establishes 14-3-3ζ as a crucial epigenetic regulator of adipogenesis and highlights the usefulness of deciphering the nuclear 14-3-3ζ interactome to identify novel pro-adipogenic factors and pathways.

Overview of the epigenetic/cytotoxic dual-target inhibitors for cancer therapy

Epigenetic dysregulation plays a pivotal role in the initiation and progression of various cancers, influencing critical processes such as tumor growth, invasion, migration, survival, apoptosis, and angiogenesis. Consequently, targeting epigenetic pathways has emerged as a promising strategy for anticancer drug discovery in recent years. However, the clinical efficacy of epigenetic inhibitors, such as HDAC inhibitors, has been limited, often accompanied by resistance. To overcome these challenges, innovative therapeutic approaches are required, including the combination of epigenetic inhibitors with cytotoxic agents or the design of dual-acting inhibitors that target both epigenetic and cytotoxic pathways. In this review, we provide a comprehensive overview of the structures, biological functions and inhibitors of epigenetic regulators (such as HDAC, LSD1, PARP, and BET) and cytotoxic targets (including tubulin and topoisomerase). Furthermore, we discuss recent advancement of combination therapies and dual-target inhibitors that target both epigenetic and cytotoxic pathways, with a particular focus on recent advances, including rational drug design, pharmacodynamics, pharmacokinetics, and clinical applications.

Epigenetics in autosomal dominant polycystic kidney disease

Autosomal dominant polycystic kidney disease (ADPKD) is the fourth leading cause of end-stage renal disease, contributing substantially to patient morbidity, mortality, and healthcare system strain. Emerging research highlights a pivotal role of epigenetics in ADPKD's pathophysiology, where mechanisms like DNA methylation, histone modifications, and non-coding RNA regulation significantly impact disease onset and progression. These epigenetic factors influence gene expression and regulate key processes involved in cyst formation and expansion, fibrosis, and inflammatory infiltration, thus accelerating ADPKD progression. Consequently, exploring epigenetic regulatory mechanisms presents a valuable pathway for developing novel therapeutic strategies and diagnostic biomarkers aimed at slowing or preventing ADPKD progression. This review systematically examines existing studies on epigenetic alterations-including DNA methylation, histone modification, and non-coding RNA regulation-in ADPKD patients, providing insights into gene expression changes and functions, and identifying potential drug targets for ADPKD treatment. CLINICAL SIGNIFICANCE: Autosomal dominant polycystic kidney disease (ADPKD) is the fourth leading cause of end-stage renal disease, causing significant morbidity, increasing patient mortality, and weakening the healthcare system. Further study on ADPKD has revealed that epigenetics plays an important role in the pathophysiological process of ADPKD. Epigenetics has a significant impact on the formation and progression of ADPKD through a variety of processes including DNA methylation, histone modification, and non-coding RNA. In addition to boosting cyst formation and proliferation, it induces cystic fibrosis and inflammatory cell infiltration, ultimately leading to a poor prognosis. This review summarizes the current understanding of the associated alterations in gene expression and function produced by epigenetic regulation in ADPKD, as well as potential treatment targets.

Advancements in understanding the role and mechanism of sirtuin family (SIRT1-7) in breast cancer management

Breast cancer (BC) is the most prevalent type of cancer in women worldwide and it is classified into a few distinct molecular subtypes based on the expression of growth factor and hormone receptors. Though significant progress has been achieved in the search for novel medications through traditional and advanced approaches, still we need more efficacious and reliable treatment options to treat different types and stages of BC. Sirtuins (SIRT1-7) a class III histone deacetylase play a major role in combating various cancers including BC. Studies reveal thateach sirtuin has a unique and well-balanced biology, indicating that it regulates a variety of biological processes that result in the initiation, progression,and metastasis of BC. SIRT also plays a major role in numerous vital biological functions, including apoptosis, axonal protection, transcriptional silencing, DNA recombination and repair, fat mobilization, and aging. As per the current demand, we wish to outline the structural insights into sirtuin's catalytic site, substantial variations among all SIRT types, and their mechanism in BC management. Additionally, this review will focus on the application of SIRT modulators along with their clinical significance, hurdles, and future perspective to develop successful SIRT-based drug candidates to conquer the BC problem.

HDAC8 Enhances the Function of HIF-2α by Deacetylating ETS1 to Decrease the Sensitivity of TKIs in ccRCC

Drug resistance after long-term use of Tyrosine kinase inhibitors (TKIs) has become an obstacle for prolonging the survival time of patients with clear cell renal cell carcinoma (ccRCC). Here, genome-wide CRISPR-based screening to reveal that HDAC8 is involved in decreasing the sensitivity of ccRCC cells to sunitinib is applied. Mechanically, HDAC8 deacetylated ETS1 at the K245 site to promote the interaction between ETS1 and HIF-2α and enhance the transcriptional activity of the ETS1/HIF-2α complex. However, the antitumor effect of inhibiting HDAC8 on sensitized TKI is not very satisfactory. Subsequently, inhibition of HDAC8 increased the expression of NEK1, and up-regulated NEK1 phosphorylated ETS1 at the T241 site to promote the interaction between ETS1 and HIF-2α by impeded acetylation at ETS1-K245 site is showed. Moreover, TKI treatment increased the expression of HDAC8 by inhibiting STAT3 phosphorylation in ccRCC cells is also found. These 2 findings highlight a potential mechanism of acquired resistance to TKIs and HDAC8 inhibitors in ccRCC. Finally, HDAC8-in-PROTACs to optimize the effects of HDAC8 inhibitors through degrading HDAC8 and overcoming the resistance of ccRCC to TKIs are synthesized. Collectively, the results revealed HDAC8 as a potential therapeutic candidate for resistance to ccRCC-targeted therapies.

14-3-3ζ regulates adipogenesis by modulating chromatin accessibility during the early stages of adipocyte differentiation

We previously established the scaffold protein 14-3-3ζ as a critical regulator of adipogenesis and adiposity, but the temporal specificity of its action during adipocyte differentiation remains unclear. To decipher if 14-3-3ζ exerts its regulatory functions on mature adipocytes or on adipose precursor cells (APCs), we generated Adipoq14-3-3ζKO and Pdgfra14-3-3ζKO mouse models. Our findings revealed a pivotal role for 14-3-3ζ in APC differentiation in a sex-dependent manner, whereby male and female Pdgfra14-3-3ζKO mice display impaired or potentiated weight gain, respectively, as well as fat mass. To better understand how 14-3-3ζ regulates the adipogenic transcriptional program in APCs, CRISPR-Cas9 was used to generate TAP-tagged 14-3-3ζ-expressing 3T3-L1 preadipocytes. Using these cells, we examined if the 14-3-3ζ nuclear interactome is enriched with adipogenic regulators during differentiation. Regulators of chromatin remodeling, such as DNMT1 and HDAC1, were enriched in the nuclear interactome of 14-3-3ζ, and their activities were impacted upon 14-3-3ζ depletion. The interactions between 14-3-3ζ and chromatin-modifying enzymes suggested that 14-3-3ζ may control chromatin remodeling during adipogenesis, and this was confirmed by ATAC-seq, which revealed that 14-3-3ζ depletion impacted the accessibility of up to 1,244 chromatin regions corresponding in part to adipogenic genes, promoters, and enhancers during the initial stages of adipogenesis. Moreover, 14-3-3ζ-dependent chromatin accessibility was found to directly correlate with the expression of key adipogenic genes. Altogether, our study establishes 14-3-3ζ as a crucial epigenetic regulator of adipogenesis and highlights the usefulness of deciphering the nuclear 14-3-3ζ interactome to identify novel pro-adipogenic factors and pathways.