Loss of grand histone H3 lysine 27 trimethylation domains mediated transcriptional activation in esophageal squamous cell carcinoma

Enhancer demethylation-regulated gene score identified molecular subtypes, inspiring immunotherapy or CDK4/6 inhibitor therapy in oesophageal squamous cell carcinoma

BACKGROUND

The 5-year survival rate of oesophageal squamous cell carcinoma (ESCC) is approximately 20%. The prognosis and drug response exhibit substantial heterogeneity in ESCC, impeding progress in survival outcomes. Our goal is to identify a signature for tumour subtype classification, enabling precise clinical treatments.

METHODS

Utilising pre-treatment multi-omics data from an ESCC dataset (n = 310), an enhancer methylation-eRNA-target gene regulation network was constructed and validated by in vitro experiments. Four machine learning methods collectively identified core target genes, establishing an Enhancer Demethylation-Regulated Gene Score (EDRGS) model for classification. The molecular function of EDRGS subtyping was explored in scRNA-seq (n = 60) and bulk-seq (n = 310), and the EDRGS's potential to predict treatment response was assessed in datasets of various cancer types.

FINDINGS

EDRGS stratified ESCCs into EDRGS-high/low subtypes, with EDRGS-high signifying a less favourable prognosis in ESCC and nine additional cancer types. EDRGS-high exhibited an immune-hot but immune-suppressive phenotype with elevated immune checkpoint expression, increased T cell infiltration, and IFNγ signalling in ESCC, suggesting a better response to immunotherapy. Notably, EDRGS outperformed PD-L1 in predicting anti-PD-1/L1 therapy effectiveness in ESCC (n = 42), kidney renal clear cell carcinoma (KIRC, n = 181), and bladder urothelial carcinoma (BLCA, n = 348) cohorts. EDRGS-low showed a cell cycle-activated phenotype with higher CDK4 and/or CDK6 expression, demonstrating a superior response to the CDK4/6 inhibitor palbociclib, validated in ESCC (n = 26), melanoma (n = 18), prostate cancer (n = 15) cells, and PDX models derived from patients with pancreatic cancer (n = 30).

INTERPRETATION

Identification of EDRGS subtypes enlightens ESCC categorisation, offering clinical insights for patient management in immunotherapy (anti-PD-1/L1) and CDK4/6 inhibitor therapy across cancer types.

FUNDING

This study was supported by funding from the National Key R&D Program of China (2021YFC2501000, 2020YFA0803300), the National Natural Science Foundation of China (82030089, 82188102), the CAMS Innovation Fund for Medical Sciences (2021-I2M-1-018, 2022-I2M-2-001, 2021-I2M-1-067), the Fundamental Research Funds for the Central Universities (3332021091).

Fatty Acid Amide Hydrolase and Cannabinoid Receptor Type 1 Genes Regulation is Modulated by Social Isolation in Rats

Social isolation is a state of lack of social connections, involving the modulation of different molecular signalling cascades and associated with high risk of mental health issues. To investigate if and how gene expression is modulated by social experience at the central level, we analyzed the effects of 5 weeks of social isolation in rats focusing on endocannabinoid system genes transcription in key brain regions involved in emotional control. We observed selective reduction in mRNA levels for fatty acid amide hydrolase (Faah) and cannabinoid receptor type 1 (Cnr1) genes in the amygdala complex and of Cnr1 in the prefrontal cortex of socially isolated rats when compared to controls, and these changes appear to be partially driven by trimethylation of Lysine 27 and acetylation of Lysine 9 at Histone 3. The alterations of Cnr1 transcriptional regulation result also directly correlated with those of oxytocin receptor gene. We here suggest that to counteract the effects of SI, it is of relevance to restore the endocannabinoid system homeostasis via the use of environmental triggers able to revert those epigenetic mechanisms accounting for the alterations observed.

Histone 3 lysine 9 acetylation-specific reprogramming regulates esophageal squamous cell carcinoma progression and metastasis

Dysregulation of histone acetylation is widely implicated in tumorigenesis, yet its specific roles in the progression and metastasis of esophageal squamous cell carcinoma (ESCC) remain unclear. Here, we profiled the genome-wide landscapes of H3K9ac for paired adjacent normal (Nor), primary ESCC (EC) and metastatic lymph node (LNC) esophageal tissues from three ESCC patients. Compared to H3K27ac, we identified a distinct epigenetic reprogramming specific to H3K9ac in EC and LNC samples relative to Nor samples. This H3K9ac-related reprogramming contributed to the transcriptomic aberration of targeting genes, which were functionally associated with tumorigenesis and metastasis. Notably, genes with gained H3K9ac signals in both primary and metastatic lymph node samples (common-gained gene) were significantly enriched in oncogenes. Single-cell RNA-seq analysis further revealed that the corresponding top 15 common-gained genes preferred to be enriched in mesenchymal cells with high metastatic potential. Additionally, in vitro experiment demonstrated that the removal of H3K9ac from the common-gained gene MSI1 significantly downregulated its transcription, resulting in deficiencies in ESCC cell proliferation and migration. Together, our findings revealed the distinct characteristics of H3K9ac in esophageal squamous cell carcinogenesis and metastasis, and highlighted the potential therapeutic avenue for intervening ESCC through epigenetic modulation via H3K9ac.

Targeting epigenetic deregulations for the management of esophageal carcinoma: recent advances and emerging approaches

Ranking from seventh in incidence to sixth in mortality, esophageal carcinoma is considered a severe malignancy of food pipe. Later-stage diagnosis, drug resistance, and a high mortality rate contribute to its lethality. Esophageal squamous cell carcinoma and esophageal adenocarcinoma are the two main histological subtypes of esophageal carcinoma, with squamous cell carcinoma alone accounting for more than eighty percent of its cases. While genetic anomalies are well known in esophageal cancer, accountability of epigenetic deregulations is also being explored for the recent two decades. DNA methylation, histone modifications, and functional non-coding RNAs are the crucial epigenetic players involved in the modulation of different malignancies, including esophageal carcinoma. Targeting these epigenetic aberrations will provide new insights into the development of biomarker tools for risk stratification, early diagnosis, and effective therapeutic intervention. This review discusses different epigenetic alterations, emphasizing the most significant developments in esophageal cancer epigenetics and their potential implication for the detection, prognosis, and treatment of esophageal carcinoma. Further, the preclinical and clinical status of various epigenetic drugs has also been reviewed.

TBX18 knockdown sensitizes esophageal squamous cell carcinoma to radiotherapy by blocking the CHN1/RhoA axis

OBJECTIVE

Radioresistance is a challenge in the effective treatment of esophageal squamous cell carcinoma (ESCC). Herein, this research ascertained whether TBX18 reduced the radiosensitivity of ESCC.

METHODS

Bioinformatics analysis was utilized to retrieve differentially expressed genes. Then, the expression of corresponding candidate genes was tested using qRT-PCR in ESCC clinical specimens, and TBX18 was selected for subsequent experiments. The binding between TBX18 and CHN1 was evaluated by dual-luciferase reporter and ChIP assays, and the relationship between CHN1 and RhoA was identified by GST pull-down. Ectopic expression or knockdown experiments and radiation treatment were performed in cells and the nude mouse xenograft model to clarify the impacts of TBX18, CHN1, and RhoA on radiosensitivity in ESCC.

RESULTS

Bioinformatics analysis and qRT-PCR retrieved upregulated TBX18 in ESCC for the follow-up study. Additionally, TBX18 was positively correlated with CHN1 in ESCC clinical specimens. Mechanistically, TBX18 bound to the CHN1 promoter region to transcriptionally activate CHN1, thus elevating RhoA activity. Moreover, TBX18 knockdown reduced ESCC cell proliferation and migration while augmenting their apoptosis after radiation, which was negated by further overexpressing CHN1 or RhoA. CHN1 or RhoA knockdown diminished ESCC cell proliferation and migration, as well as enhanced cell apoptosis, subsequent to radiation. Likewise, TBX18 overexpression increased ESCC cell autophagy after radiation, which was partially reversed by knockdown of RhoA. The results of in vivo xenograft experiments in nude mice were concurrent with the in vitro results.

CONCLUSION

TBX18 knockdown lowered CHN1 transcription and thus reduced RhoA activity, which sensitized ESCC cells to radiotherapy.

Targeting Aberrant Histone Posttranscription Modification Machinery in Esophageal Squamous Cell Carcinoma: Current Findings and Challenges

Esophageal squamous cell carcinoma (ESCC) is an aggressive malignancy, but the survival rates of patients with ESCC have not improved as yet largely because the available targeted therapies are limited. Histone posttranscription modification (PTM) is a critical epigenetic regulation. Several deregulations in histone PTM machinery have been identified to promote malignant phenotypes of ESCC, providing druggable targets in treating ESCC. Hereby, we briefly describe current progress and challenges ahead in this field.

MAFB promotes the malignant phenotypes by IGFBP6 in esophageal squamous cell carcinomas

Esophageal squamous cell carcinoma (ESCC) is one of the most common malignant diseases in the world. Although the somatic alterations have been fully identified, there are still no targeted drugs at present. Our previous studies revealed that loss of grand H3K27me3 domains mediated transcriptional activation of a series of genes in ESCC. Among them, we focus on the investigation of MAFB, as its high expression is associated with a poor prognosis in ESCC. Functional assays show that knockdown of MAFB significantly suppresses cell growth, migration and invasion. Mechanistic investigation demonstrates that MAFB exerts its function by upregulating IGFBP6. Our findings suggest that MAFB may play a tumor-promoting role and may act as a potential therapeutic target for ESCC.

Integrated bioinformatics analysis reveals that EZH2-rich domains promote transcriptional repression in cervical cancer

Cervical cancer is the third female cancer most common worldwide. The carcinogenic process involves an alteration of the mechanisms associated with transcription. Several studies have reported an oncogenic role of the polycomb complex subunit, EZH2. However, the role of EZH2 in cervical cancer is unknown. Hence, the objective of this study was to determine the role of EZH2 in transcriptional regulation in cervical cancer. The EZH2 expression and the methylation status of its promoter were analyzed in The Cancer Genome Atlas. The EZH2 enrichment profile was analyzed using chromatin immunoprecipitation with massively parallel DNA sequencing data provided by ENCODE project. The chromatin compartments were identified in the 4D Nucleome Data Portal. The functional annotation was examined in Enrichr. We report that EZH2 expression is increased in cervical cancer which is associated with hypomethylation of its promoter. EZH2 is enriched at promoter and distal intergenic regions. We identified that EZH2 defines chromatin domains enriched with H3K27me3 within repressive compartments in the HeLa-S3 cell line. Additionally, high EZH2 expression is associated with the repression of the senescent phenotype in cervical cancer patients. Our results suggest the participation of EZH2 in the generation of domains with a silencer function in cervical cancer, which regulate the expression of genes associated with cellular senescence.