Aberrant promoter hypermethylation inhibits RGMA expression and contributes to tumor progression in breast cancer

Epigenetic modification and tumor immunity: Unraveling the interplay with the tumor microenvironment and its therapeutic vulnerability and implications

In the ever-evolving arena of molecular biology, epigenetic modifications stand out as crucial determinants in the orchestration of cellular identity, function, and fate. This review analyzes the close relationship between epigenetics and tumor immunity, emphasizing the intricate interplay with the tumor microenvironment (TME). Rooted in the knowledge that the incidence of cancer correlates strongly with the biological and genetic age, we highlight DNA methylation as a cornerstone of the "epigenetic aging" process with close ties to tumorigenesis. The TME, with its diverse cellular and acellular constituents, is an active participant in tumor biology, further complicated by epigenetic alterations. These modifications, from DNA methylation to histone changes, not only shape the TME but are reciprocally influenced by it, reinforcing a cycle that propels malignancy. Through this exploration, we underline the importance of understanding this mutual relationship, as it holds significant implications for tumor growth, heterogeneity, and therapeutic resistance. Ultimately, this review illuminates the potential of harnessing epigenetic insights for innovative cancer therapeutic strategies, pointing towards a promising avenue for future cancer management.

Kaempferol targets Src to exert its chemopreventive effects on mammary tumorigenesis via regulation of the PI3K/AKT pathway

BACKGROUND

Breast cancer (BC) is a prevalent malignancy that poses significant risks to the health of women worldwide. The incidence and mortality rates of BC continue to be high, despite improvements in diagnosis and treatment, indicating a need for novel prevention strategies. Kaempferol (KAM) is a common dietary flavonoid with known antitumour properties, but its role in the chemoprevention of BC and the underlying mechanisms largely unexplored.

PURPOSE

This study aimed to evaluate the chemopreventive effects of KAM on carcinogen-induced BC in vivo and in vitro and to elucidate the underlying molecular mechanisms.

METHODS

In this study, we used an N-methyl-N-nitrosourea (NMU)-induced rat model of BC and 17β-oestradiol (E2)-treated MCF-10A cells to evaluate the chemopreventive effects of KAM on mammary tumorigenesis. The antioxidant capacity of KAM was assessed by measuring oxidative damage marker levels and antioxidant enzyme expression. Flow cytometry and Hoechst 33258 staining were utilized to analyse cell cycle distribution and apoptosis. The core target of KAM was identified by network pharmacology and validated by molecular docking, MD simulation, CESTA, and BLI. KEGG enrichment analysis, molecular biology tests and the application of specific protein inhibitors were conducted to elucidate the molecular mechanisms modulated by KAM.

RESULTS

In vivo, KAM inhibited the progression of mammary tumours and delayed pathological changes in the morphological structure of mammary gland cells to varying degrees. In vitro, KAM reduced cell viability, migration, and anchorage-independent growth while triggering cell cycle arrest and apoptosis in E2-treated MCF-10A cells. Furthermore, KAM increased cellular antioxidant capacity and attenuated E2-induced oxidative stress. Mechanistically, KAM directly interacted with Src and inhibited its phosphorylation, thus leading to PI3K/AKT pathway inhibition. Notably, the inhibition of E2-induced cell migration and anchorage-independent growth in vitro by Src- or PI3K/AKT pathway-specific inhibitors was not further enhanced when the cells were cultured with KAM.

CONCLUSION

In summary, KAM targets the Src-mediated PI3K/AKT pathway to reduce oxidative stress and facilitate apoptosis and cell cycle arrest, thereby inhibiting mammary tumorigenesis. Our study is the first to identify Src kinase as a direct target of KAM in mammary tumorigenesis. These findings give significant perspectives on the potential application of KAM in BC chemoprevention.

Therapeutic Targets for Gastric Cancer: Mendelian Randomization and Colocalization Analysis

BACKGROUND

Gastric cancer (GC) is one of the most prevalent malignancies in the world. Most patients are diagnosed at advanced stages of the disease, primarily attributable to the insidious nature of early symptoms and the infrequent occurrence of routine screening. Further biomarkers are still needed for more comprehensive analysis, targeted prognostication, and effective treatment strategies. Plasma proteins are promising biomarkers and potential drug targets in GC. This study aims to identify potential therapeutic targets for GC by conducting a comprehensive proteome-wide Mendelian randomization (MR) and colocalization analyses.

METHODS

Plasma proteins were obtained from the UK Biobank Pharma Proteomics Project (UKB-PPP), including Genome-Wide Association Study(GWAS)data of 1463 plasma proteins. Genetic associations with cancer were derived from the European Bioinformatics Institute (EBI) database, including 1029 patients and 475,087 controls (dataset: ebi-a-gcst90018849). MR analysis was conducted to assess the association between plasma proteins and the risk of developing cancer. Additionally, colocalization analysis was employed to investigate whether the identified proteins and gastric cancer exhibited shared incidental variants. Finally, using the extensive Finnish database in the R9 version, the potential harmful effects of target proteins on the treatment of gastric cancer were explored through the whole phenomenon association study (PheWAS).

RESULT

The results showed that 15 proteins may be associated with the risk of gastric cancer, and one protein is expected to become a therapeutic target for gastric cancer. There was a positive genetic association between plasma levels of 11 proteins and increased GC risk, while 4 proteins exhibited an inverse association with GC risk (P < 0.05). Colocalization analysis revealed that PPCDC and GC exhibited shared genetic loci among the 15 proteins examined, indicating that PPCDC may serve as potential direct target for intervention in GC. Further phenotype wide association studies showed that PPCDC (P < 0.05) could be associated with certain potential side effects.

CONCLUSION

Our research examined the causal relationship between plasma proteins and gastric cancer, shedding light on potential therapeutic targets. These findings have significant implications for the development of early diagnostic markers and targeted therapies for GC, potentially improving patient outcomes and survival rates. Future studies should validate these findings in diverse populations and explore the clinical applications of these targets.

Heterogeneous Clustering of Multiomics Data for Breast Cancer Subgroup Classification and Detection

The rapid growth of diverse -omics datasets has made multiomics data integration crucial in cancer research. This study adapts the expectation-maximization routine for the joint latent variable modeling of multiomics patient profiles. By combining this approach with traditional biological feature selection methods, this study optimizes latent distribution, enabling efficient patient clustering from well-studied cancer types with reduced computational expense. The proposed optimization subroutines enhance survival analysis and improve runtime performance. This article presents a framework for distinguishing cancer subtypes and identifying potential biomarkers for breast cancer. Key insights into individual subtype expression and function were obtained through differentially expressed gene analysis and pathway enrichment for BRCA patients. The analysis compared 302 tumor samples to 113 normal samples across 60,660 genes. The highly upregulated gene COL10A1, promoting breast cancer progression and poor prognosis, and the consistently downregulated gene CDG300LG, linked to brain metastatic cancer, were identified. Pathway enrichment analysis revealed similarities in cellular matrix organization pathways across subtypes, with notable differences in functions like cell proliferation regulation and endocytosis by host cells. GO Semantic Similarity analysis quantified gene relationships in each subtype, identifying potential biomarkers like MATN2, similar to COL10A1. These insights suggest deeper relationships within clusters and highlight personalized treatment potential based on subtypes.

Expression, DNA methylation pattern and transcription factor EPB41L3 in gastric cancer: a study of 262 cases

PURPOSE

DNA methylation prominently inactivates tumor suppressor genes and facilitates oncogenesis. Previously, we delineated a chromosome 18 deletion encompassing the erythrocyte membrane protein band 4.1-like 3 (EPB41L3) gene, a progenitor for the tumor suppressor that is differentially expressed in adenocarcinoma of the lung-1 (DAL-1) in gastric cancer (GC).

METHODS

Our current investigation aimed to elucidate EPB41L3 expression and methylation in GC, identify regulatory transcription factors, and identify affected downstream pathways. Immunohistochemistry demonstrated that DAL-1 expression is markedly reduced in GC tissues, with its downregulation serving as an independent prognostic marker.

RESULTS

High-throughput bisulfite sequencing of 70 GC patient tissue pairs revealed that higher methylation of non-CpGs in the EPB41L3 promoter was correlated with more malignant tumor progression and higher-grade tissue classification. Such hypermethylation was shown to diminish DAL-1 expression, thus contributing to the malignancy of GC phenotypes. The DNA methyltransferase inhibitor 5-aza-2'-deoxycytidine (5-aza-CdR) was found to partially restore DAL-1 expression. Moreover, direct binding of the transcription factor CDC5L to the upstream region of the EPB41L3 promoter was identified via chromosome immunoprecipitation (ChIP)-qPCR and luciferase reporter assays. Immunohistochemistry confirmed the positive correlation between CDC5L and DAL-1 protein levels. Subsequent RNA-seq analysis revealed that DAL-1 significantly influences the extracellular matrix and space-related pathways. GC cell RNA-seq post-5-Aza-CdR treatment and single-cell RNA-seq data of GC tissues confirmed the upregulation of AREG and COL17A1, pivotal tumor suppressors, in response to EPB41L3 demethylation or overexpression in GC epithelial cells.

CONCLUSION

In conclusion, this study elucidates the association between non-CpG methylation of EPB41L3 and GC progression and identifies the key transcription factors and downstream molecules involved. These findings enhance our understanding of the role of EPB41L3 in gastric cancer and provide a solid theoretical foundation for future research and potential clinical applications.

NNBGWO-BRCA marker: Neural Network and binary grey wolf optimization based Breast cancer biomarker discovery framework using multi-omics dataset

BACKGROUND AND OBJECTIVE

Breast cancer is a multifaceted condition characterized by diverse features and a substantial mortality rate, underscoring the imperative for timely detection and intervention. The utilization of multi-omics data has gained significant traction in recent years to identify biomarkers and classify subtypes in breast cancer. This kind of research idea from part to whole will also be an inevitable trend in future life science research. Deep learning can integrate and analyze multi-omics data to predict cancer subtypes, which can further drive targeted therapies. However, there are few articles leveraging the nature of deep learning for feature selection. Therefore, this paper proposes a Neural Network and Binary grey Wolf Optimization based BReast CAncer bioMarker (NNBGWO-BRCAMarker) discovery framework using multi-omics data to obtain a series of biomarkers for precise classification of breast cancer subtypes.

METHODS

NNBGWO-BRCAMarker consists of two phases: in the first phase, relevant genes are selected using the weights obtained from a trained feedforward neural network; in the second phase, the binary grey wolf optimization algorithm is leveraged to further screen the selected genes, resulting in a set of potential breast cancer biomarkers.

RESULTS

The SVM classifier with RBF kernel achieved a classification accuracy of 0.9242 ± 0.03 when trained using the 80 biomarkers identified by NNBGWO-BRCAMarker, as evidenced by the experimental results. We conducted a comprehensive gene set analysis, prognostic analysis, and druggability analysis, unveiling 25 druggable genes, 16 enriched pathways strongly linked to specific subtypes of breast cancer, and 8 genes linked to prognostic outcomes.

CONCLUSIONS

The proposed framework successfully identified 80 biomarkers from the multi-omics data, enabling accurate classification of breast cancer subtypes. This discovery may offer novel insights for clinicians to pursue in further studies.

Unravelling the molecular landscape of endometrial cancer subtypes: insights from multiomics analysis

BACKGROUND

Endometrial cancer (EC) as one of the most common gynecologic malignancies is increasing in incidence during the past 10 years. Genome-Wide Association Studies (GWAS) extended to metabolic and protein phenotypes inspired us to employ multiomics methods to analyze the causal relationships of plasma metabolites and proteins with EC to advance our understanding of EC biology and pave the way for more targeted approaches to its diagnosis and treatment by comparing the molecular profiles of different EC subtypes.

METHODS

Two-sample mendelian randomization (MR) was performed to investigate the effects of plasma metabolites and proteins on risks of different subtypes of EC (endometrioid and nonendometrioid). Pathway analysis, transcriptomic analysis, and network analysis were further employed to illustrate gene-protein-metabolites interactions underlying the pathogenesis of distinct EC histological types.

RESULTS

The authors identified 66 causal relationships between plasma metabolites and endometrioid EC, and 132 causal relationships between plasma proteins and endometrioid EC. Additionally, 40 causal relationships between plasma metabolites and nonendometrioid EC, and 125 causal relationships between plasma proteins and nonendometrioid EC were observed. Substantial differences were observed between endometrioid and nonendometrioid histological types of EC at both the metabolite and protein levels. The authors identified seven overlapping proteins (RGMA, NRXN2, EVA1C, SLC14A1, SLC6A14, SCUBE1, FGF8) in endometrioid subtype and six overlapping proteins (IL32, GRB7, L1CAM, CCL25, GGT2, PSG5) in nonendometrioid subtype and conducted network analysis of above proteins and metabolites to identify coregulated nodes.

CONCLUSIONS

Our findings observed substantial differences between endometrioid and nonendometrioid EC at the metabolite and protein levels, providing novel insights into gene-protein-metabolites interactions that could influence future EC treatments.

Targeted demethylation of the CDO1 promoter based on CRISPR system inhibits the malignant potential of breast cancer cells

BACKGROUND

Cysteine dioxygenase 1 (CDO1) is frequently methylated, and its expression is decreased in many human cancers including breast cancer (BC). However, the functional and mechanistic aspects of CDO1 inactivation in BC are poorly understood, and the diagnostic significance of serum CDO1 methylation remains unclear.

METHODS

We performed bioinformatics analysis of publicly available databases and employed MassARRAY EpiTYPER methylation sequencing technology to identify differentially methylated sites in the CDO1 promoter of BC tissues compared to normal adjacent tissues (NATs). Subsequently, we developed a MethyLight assay using specific primers and probes for these CpG sites to detect the percentage of methylated reference (PMR) of the CDO1 promoter. Furthermore, both LentiCRISPR/dCas9-Tet1CD-based CDO1-targeted demethylation system and CDO1 overexpression strategy were utilized to detect the function and underlying mechanism of CDO1 in BC. Finally, the early diagnostic value of CDO1 as a methylation biomarker in BC serum was evaluated.

RESULTS

CDO1 promoter was hypermethylated in BC tissues, which was related to poor prognosis (p < .05). The CRISPR/dCas9-based targeted demethylation system significantly reduced the PMR of CDO1 promotor and increased CDO1 expression in BC cells. Consequently, this leads to suppression of cell proliferation, migration and invasion. Additionally, we found that CDO1 exerted a tumour suppressor effect by inhibiting the cell cycle, promoting cell apoptosis and ferroptosis. Furthermore, we employed the MethyLight to detect CDO1 PMR in BC serum, and we discovered that serum CDO1 methylation was an effective non-invasive biomarker for early diagnosis of BC.

CONCLUSIONS

CDO1 is hypermethylated and acts as a tumour suppressor gene in BC. Epigenetic editing of abnormal CDO1 methylation could have a crucial role in the clinical treatment and prognosis of BC. Additionally, serum CDO1 methylation holds promise as a valuable biomarker for the early diagnosis and management of BC.

Aptamers against cancer drug resistance: Small fighters switching tactics in the face of defeat

Discovering novel cancer therapies has attracted extreme interest in the last decade. In this regard, multidrug resistance (MDR) to chemotherapies is the primary challenge in cancer treatment. Cancerous cells are growingly become resistant to existing chemotherapeutics by employing diverse mechanisms, highlighting the significance of discovering approaches to overcome MDR. One promising strategy is utilizing aptamers as unique tools to target elements or signalings incorporated in resistance mechanisms or develop active targeted drug delivery systems or chimeras enabling the precise delivery of novel agents to inhibit the conventionally undruggable resistance elements. Further, due to their advantages over their proteinaceous counterparts, particularly antibodies, including improved targeting action, enhanced thermal stability, easier production, and superior tumor penetration, aptamers are emerging and have frequently been considered for developing cancer therapeutics. Here, we highlighted significant chemoresistance pathways and thoroughly discussed using aptamers as prospective tools to surmount cancer MDR.

A Phase 1B open-label study of gedatolisib (PF-05212384) in combination with other anti-tumour agents for patients with advanced solid tumours and triple-negative breast cancer

BACKGROUND

This Phase 1b study (B2151002) evaluated the PI3K/mTOR inhibitor gedatolisib (PF-05212384) in combination with other anti-tumour agents in advanced solid tumours.

METHODS

Patients with various malignancies were administered gedatolisib (90‒310 mg intravenously every week [QW]) plus docetaxel (arm A) or cisplatin (arm B) (each 75 mg/m2 intravenously Q3W) or dacomitinib (30 or 45 mg/day orally). The safety and tolerability of combination therapies were assessed during dose escalation; objective response (OR) and safety were assessed during dose expansion.

RESULTS

Of 110 patients enrolled, 107 received gedatolisib combination treatment. Seven of 70 (10.0%) evaluable patients had dose-limiting toxicities; the most common was grade 3 oral mucositis (n = 3). Based upon reprioritisation of the sponsor's portfolio, dose expansion focused on arm B, gedatolisib (180 mg QW) plus cisplatin in patients (N = 22) with triple-negative breast cancer (TNBC). OR (95% CI) was achieved in four of ten patients in first-line (overall response rate 40.0% [12.2-73.8%]) and four of 12 in second/third-line (33.3% [9.9-65.1%]) settings. One patient in each TNBC arm (10%, first-line; 8.3%, second/third-line) achieved a complete response.

CONCLUSIONS

Gedatolisib combination therapy showed an acceptable tolerability profile, with clinical activity at the recommended Phase 2 dose in patients with TNBC.

CLINICAL TRIAL

ClinicalTrial.gov: NCT01920061.

LncRNA RP11-551L14.4 suppresses breast cancer development by inhibiting the expression of miR-4472

Background

Previous studies have been reported that long non-coding RNA (lncRNA) can regulate the expression of genes which are involved in many important cellular processes The potential role of lncRNA RP11-551L14.4 in the development of breast cancer and the possible regulatory mechanisms was investigated.

Methods

Quantitative real-time polymerase chain reaction (qRT-PCR) was conducted to analyze RP11-551L14.4 expression in 36 paired breast cancer tissues and adjacent tissues. The expression of RP11-551L14.4 in multiple breast cancer cell lines was detected by qRT-PCR. Meanwhile, overexpression of RP11-551L14.4 models was established using lentivirus in BT474 and T47D breast cancer cells. Cell counting kit-8 (CCK-8), cell colony formation and cell cycle assays were performed to detect the effects of RP11-551L14.4 on the biological function of breast cancer cells. Besides, bioinformatics techniques, dual luciferase reporter gene assay and rescue experiments were used to investigate the potential mechanisms.

Results

RP11-551L14.4 expression was negatively associated with the advanced tumor stage. Breast cancer patients with low RP11-551L14.4 expression manifested a poorer prognosis. The results of qRT-PCR showed that RP11-551L14.4 expression in breast cancer tissues was significantly lower than in adjacent tissues. Meanwhile, overexpression of RP11-551L14.4 significantly decreased the cell proliferation and cell cycle. Bioinformatics technology showed that RP11-551L14.4 could complementarily bind to miR-4472. qRT-PCR results indicated that the expression levels of miR-4472 and RP11-551L14.4 in breast cancer were negatively correlated. Luciferase reporter gene assay showed that miR-4472 remarkably decreased the relative luciferase activity of the wild-type RP11-551L14.4 vector. miR-4472 is a direct target gene of RP11-551L14.4. miR-4472 levels were reduced, and repulsive guidance molecule A (RGMA) mRNA or protein levels were increased after overexpression of RP11-551L14.4 in the breast cancer cells. miR-4472 reversed the effects caused by RP11-551L14.4 in breast cancer cells.

Conclusion

RP11-551L14.4 expression was remarkably decreased in breast cancer tissues and cells. RP11-551L14.4 may inhibit the malignant progression of breast cancer by regulating miR-4472 expression.

Association between EPHA5 methylation status in peripheral blood leukocytes and the risk and prognosis of gastric cancer

Purpose

Altered DNA methylation, genetic alterations, and environmental factors are involved in tumorigenesis. As a tumor suppressor gene, abnormal EPHA5 methylation was found in gastric cancer (GC) tissues and was linked to the initiation, progression and prognosis of GC. In this study, the EPHA5 methylation level in peripheral blood leukocytes (PBLs) was detected to explore its relationship with GC risk and prognosis.

Methods

A total of 366 GC cases and 374 controls were selected as the subjects of this study to collect their environmental factors, and the EPHA5 methylation status was detected through the methylation-sensitive high-resolution melting method. Logistic regression analysis was utilized to evaluate the associations among EPHA5 methylation, environmental factors and GC risk. Meanwhile, the propensity score (PS) was used to adjust the imbalance of some independent variables.

Results

After PS adjustment, EPHA5 Pm (positive methylation) was more likely to increase the GC risk than EPHA5 Nm (negative methylation) (OR^b = 1.827, 95% CI [1.202-2.777], P = 0.005). EPHA5 Pm had a more significant association with GC risk in the elderly (OR^a = 2.785, 95% CI [1.563-4.961], P = 0.001) and H. pylori-negative groups (OR^a = 2.758, 95% CI [1.369-5.555], P = 0.005). Moreover, the combined effects of EPHA5 Pm and H. pylori infection (OR_c ^a = 3.543, 95% CI [2.233-5.621], P < 0.001), consumption of alcohol (OR_c ^a = 2.893, 95% CI [1.844-4.539], P < 0.001), and salty food intake (OR_c ^a = 4.018, 95% CI [2.538-6.362], P < 0.001) on increasing the GC risk were observed. In addition, no convincing association was found between EPHA5 Pm and the GC prognosis.

Conclusions

EPHA5 methylation in PBLs and its combined effects with environmental risk factors are related to the GC risk.

Transfection with Plasmid-Encoding lncRNA-SLERCC nanoparticle-mediated delivery suppressed tumor progression in renal cell carcinoma

Background

The accumulating evidence confirms that long non-coding RNAs (lncRNAs) play a critical regulatory role in the progression of renal cell carcinoma (RCC). But, the application of lncRNAs in gene therapy remains scarce. Here, we investigated the efficacy of a delivery system by introducing the plasmid-encoding tumor suppressor lncRNA-SLERCC (SLERCC) in RCC cells.

Methods

We performed lncRNAs expression profiling in paired cancer and normal tissues through microarray and validated in our clinical data and TCGA dataset. The Plasmid-SLERCC@PDA@MUC12 nanoparticles (PSPM-NPs) were tested in vivo and in vitro, including cellular uptake, entry, CCK-8 assay, tumor growth inhibition, histological assessment, and safety evaluations. Furthermore, experiments with nude mice xenografts model were performed to evaluate the therapeutic effect of PSPM-NPs nanotherapeutic system specific to the SLERCC.

Results

We found that the expression of SLERCC was downregulated in RCC tissues, and exogenous upregulation of SLERCC could suppress metastasis of RCC cells. Furthermore, high expression DNMT3A was recruited at the SLERCC promoter, which induced aberrant hypermethylation, eventually leading to downregulation of SLERCC expression in RCC. Mechanistically, SLERCC could directly bind to UPF1 and exert tumor-suppressive effects through the Wnt/β-catenin signaling pathway, thereby inhibiting progression and metastasis in RCC. Subsequently, the PSPM-NPs nanotherapeutic system can effectively inhibit the growth of RCC metastases in vivo.

Conclusions

Our findings suggested that SLERCC is a promising therapeutic target and that plasmid-encapsulated nanomaterials targeting transmembrane metastasis markers may open a new avenue for the treatment in RCC.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13046-022-02467-2.

Perspective: cell death mechanisms and early diagnosis as precondition for disease modification in Parkinson's disease: are we on the right track?

INTRODUCTION

Current research paradigms on biomarkers for chronic neurodegenerative diseases, such as Parkinson's disease, focus on identification of reliable, easy-to-apply tools for diagnostic screening and progression assessment.

AREAS COVERED

This perspective discusses possible misconceptions of biomarker research in chronic neurodegeneration from a clinician's view based on a not systematic literature search. Multifactorial disease triggers, heterogeneity of symptom and their progression are main reasons for the still missing availability of biomarkers.

EXPERT OPINION

Onset of chronic neurodegenerative disease entities may probably result from a decompensated endogenous repair machinery in the central nervous system, for example the neogenin receptor associated repulsive guidance molecule pathway. Future clinical research is warranted on these repair structures and aim to identify markers for the imbalance between damage and repair, which hypothetically contributes to generation of disease. An assignment to a specific chronic neurodegenerative disease entity probably appears to be secondary. Decryption of probable molecular signals of an impaired repair potential will enable an earlier diagnosis, better monitoring of disease progress and of treatment response. This concept will hopefully provide better preconditions for prevention, cure or therapeutic beneficial disease modification. These unmet therapeutic needs may be achieved for example via antagonism of repulsive guidance molecule A.