FOXD1 regulates cell division in clear cell renal cell carcinoma

Multi-omic profiling of breast tumor microenvironment uncovers a role of mitochondrial calcium gatekeepers

In this study, we aimed to elucidate the role of mitochondrial calcium uptake 1/2 (MiCU1/2) in breast cancer (BRCA) by employing a comprehensive multi-omics approach. Unlike previous research, we utilized a novel web application tailored for whole tumor tissue, single-cell, and spatial transcriptomics analysis to investigate the association between MiCU1/2 and the tumor immune microenvironment (TIME). Our gene set enrichment analysis (GSEA) provided insights into the primary biological effects of MiCU1/2, while our CRISPR-based drug screening repository identified potential effective drugs. Our study revealed that high MiCU1/2 expression serves as an independent diagnostic biomarker, correlating with advanced clinical status and indicating poorer recurrence-free survival (RFS) rates in BRCA patients. Additionally, spatial transcriptome analysis highlighted the heightened expression of MiCU1/2 in tumors and its relevance in surrounding immune cells. Furthermore, using the CIBERSORT algorithm, we discovered a positive correlation between MiCU1/2 levels and macrophage infiltration, underscoring their potential impact on immune infiltration. We also identified expression patterns of immune-related genes associated with responses against various immune cell types, including CXCL, MIF, GDF, SPP1, and IL16. Finally, our pharmacogenomic screening identified potential small molecule drugs capable of effectively targeting breast cancer cells with elevated MiCU1/2 expression. Overall, our study establishes MiCU1/2 as a promising novel biomarker for BRCA diagnosis and prognostic prediction, as well as a potential therapeutic target, highlighting the importance of exploring these pathways to advance patient care and outcomes in BRCA treatment.

SUMOylation of RALY promotes vasculogenic mimicry in glioma cells via the FOXD1/DKK1 pathway

Human malignant gliomas are the most common and aggressive primary malignant tumors of the human central nervous system. Vasculogenic mimicry (VM), which refers to the formation of a tumor blood supply system independently of endothelial cells, contributes to the malignant progression of glioma. Therefore, VM is considered a potential target for glioma therapy. Accumulated evidence indicates that alterations in SUMOylation, a reversible post-translational modification, are involved in tumorigenesis and progression. In the present study, we found that UBA2 and RALY were upregulated in glioma tissues and cell lines. Downregulation of UBA2 and RALY inhibited the migration, invasion, and VM of glioma cells. RALY can be SUMOylated by conjugation with SUMO1, which is facilitated by the overexpression of UBA2. The SUMOylation of RALY increases its stability, which in turn increases its expression as well as its promoting effect on FOXD1 mRNA. The overexpression of FOXD1 promotes DKK1 transcription by activating its promoter, thereby promoting glioma cell migration, invasion, and VM. Remarkably, the combined knockdown of UBA2, RALY, and FOXD1 resulted in the smallest tumor volumes and the longest survivals of nude mice in vivo. UBA2/RALY/FOXD1/DKK1 axis may play crucial roles in regulating VM in glioma, which may contribute to the development of potential strategies for the treatment of gliomas.

Dissecting multifunctional roles of forkhead box transcription factor D1 in cancers

As a member of the forkhead box (FOX) family of transcription factors (TF), FOXD1 has recently been implicated as a crucial regulator in a variety of human cancers. Accumulating evidence has established dysregulated and aberrant FOXD1 signaling as a prominent feature in cancer development and progression. However, there is a lack of systematic review on this topic. Here, we summarized the present understanding of FOXD1 functions in cancer biology and reviewed the downstream targets and upstream regulatory mechanisms of FOXD1 as well as the related signaling pathways within the context of current reports. We highlighted the functional features of FOXD1 in cancers to identify the future research consideration of this multifunctional transcription factor and potential therapeutic strategies targeting its oncogenic activity.

FOXD1 expression-based prognostic model for uveal melanoma

FOXD1, a new member of the FOX transcription factor family, serves as a mediator and biomarker for cell reprogramming. But its contribution to prognosis of uveal melanoma (UVM) is unclear. This study demonstrated that FOXD1 might promote tumor growth and invasion, because FOXD1 expression was negatively correlated with overall survival, progression-free survival, and disease-specific survival in UVM patients. This conjecture was verified in cell culture with human uveal melanoma cell line (MUM2B) as model cells. Additionally, the biological mechanisms of FOXD1 based on FOXD1-related genomic spectrum, molecular pathways, tumor microenvironment, and drug treatment sensitivity were examined using The Cancer Genome Atlas (TCGA) database, aiming to reasonably explain why FOXD1 leads to poor prognosis of UVM. On these bases, a novel tumor prognostic model was established using the FOXD1-related immunomodulators TMEM173, TNFRSF4, TNFSF13, and ULBP1, which will enable the stratification of disease seriousness and clinical treatment for patients.

MicroRNAs as the critical regulators of Forkhead box protein family during gynecological and breast tumor progression and metastasis

Gynecological and breast tumors are one of the main causes of cancer-related mortalities among women. Despite recent advances in diagnostic and therapeutic methods, tumor relapse is observed in a high percentage of these patients due to the treatment failure. Late diagnosis in advanced tumor stages is one of the main reasons for the treatment failure and recurrence in these tumors. Therefore, it is necessary to assess the molecular mechanisms involved in progression of these tumors to introduce the efficient early diagnostic markers. Fokhead Box (FOX) is a family of transcription factors with a key role in regulation of a wide variety of cellular mechanisms. Deregulation of FOX proteins has been observed in different cancers. MicroRNAs (miRNAs) as a group of non-coding RNAs have important roles in post-transcriptional regulation of the genes involved in cellular mechanisms. They are also the non-invasive diagnostic markers due to their high stability in body fluids. Considering the importance of FOX proteins in the progression of breast and gynecological tumors, we investigated the role of miRNAs in regulation of the FOX proteins in these tumors. MicroRNAs were mainly involved in progression of these tumors through FOXM, FOXP, and FOXO. The present review paves the way to suggest a non-invasive diagnostic panel marker based on the miRNAs/FOX axis in breast and gynecological cancers.

FOXD1 is associated with poor outcome and maintains tumor-promoting enhancer-gene programs in basal-like breast cancer

Breast cancer biology varies markedly among patients. Basal-like breast cancer is one of the most challenging subtypes to treat because it lacks effective therapeutic targets. Despite numerous studies on potential targetable molecules in this subtype, few targets have shown promise. However, the present study revealed that FOXD1, a transcription factor that functions in both normal development and malignancy, is associated with poor prognosis in basal-like breast cancer. We analyzed publicly available RNA sequencing data and conducted FOXD1-knockdown experiments, finding that FOXD1 maintains gene expression programs that contribute to tumor progression. We first conducted survival analysis of patients grouped via a Gaussian mixture model based on gene expression in basal-like tumors, finding that FOXD1 is a prognostic factor specific to this subtype. Then, our RNA sequencing and chromatin immunoprecipitation sequencing experiments using the basal-like breast cancer cell lines BT549 and Hs578T with FOXD1 knockdown revealed that FOXD1 regulates enhancer-gene programs related to tumor progression. These findings suggest that FOXD1 plays an important role in basal-like breast cancer progression and may represent a promising therapeutic target.

BMSC-Derived Exosomes Carrying lncRNA-ZFAS1 Alleviate Pulmonary Ischemia/Reperfusion Injury by UPF1-Mediated mRNA Decay of FOXD1

Bone marrow-derived mesenchymal stem cells (BMSCs) exert protective effects against pulmonary ischemia/reperfusion (I/R) injury; however, the potential mechanism involved in their protective ability remains unclear. Thus, this study aimed to explore the function and underlying mechanism of BMSC-derived exosomal lncRNA-ZFAS1 in pulmonary I/R injury. Pulmonary I/R injury models were established in mice and hypoxia/reoxygenation (H/R)-exposed primary mouse lung microvascular endothelial cells (LMECs). Exosomes were extracted from BMSCs. Target molecule expression was assessed by qRT-PCR and Western blotting. Pathological changes in the lungs, pulmonary edema, apoptosis, pro-inflammatory cytokine levels, SOD, MPO activities, and MDA level were measured. The proliferation, apoptosis, and migration of LMECs were detected by CCK-8, EdU staining, flow cytometry, and scratch assay. Dual-luciferase reporter assay, RNA pull-down, RIP, and ChIP assays were performed to validate the molecular interaction. In the mouse model of pulmonary I/R injury, BMSC-Exos treatment relieved lung pathological injury, reduced lung W/D weight ratio, and restrained apoptosis and inflammation, whereas exosomal ZFAS1 silencing abolished these beneficial effects. In addition, the proliferation, migration inhibition, apoptosis, and inflammation in H/R-exposed LMECs were repressed by BMSC-derived exosomal ZFAS1. Mechanistically, ZFAS1 contributed to FOXD1 mRNA decay via interaction with UPF1, thereby leading to Gal-3 inactivation. Furthermore, FOXD1 depletion strengthened the weakened protective effect of ZFAS1-silenced BMSC-Exos on pulmonary I/R injury. ZFAS1 delivered by BMSC-Exos results in FOXD1 mRNA decay and subsequent Gal-3 inactivation via direct interaction with UPF1, thereby attenuating pulmonary I/R injury.

Targets for Renal Carcinoma Growth Control Identified by Screening FOXD1 Cell Proliferation Pathways

Simple Summary

FOXD1 regulates the proliferation of clear cell renal cell carcinoma (ccRCC) cells, and ccRCC cells in which FOXD1 has been inactivated do not form tumors efficiently in an animal model. Reproducing growth inhibition in tumor cells by inhibiting FOXD1 pathways presents a possible therapeutic approach for ccRCC and other cancers. We have established an analysis strategy to identify FOXD1-regulated target pathways that may be therapeutically tractable, and compounds that modulate these pathways were selected for testing. Targets in three pathways were identified: FOXM1, PME1, and TMEM167A, which were inhibited by compounds FDI-6, AMZ-30, and silibinin, respectively. The effects of these compounds on the growth of tumor cells from patients cultured in a novel 3D tumor-replica culture environment revealed that FDI-6 and silibinin had strong growth inhibitory effects. This investigation informs new therapeutic targets to control ccRCC tumor growth, and provides a strategy to compare the responsiveness of individual patient tumor replicas to growth-inhibitory compounds.

Abstract

Clinical association studies suggest that FOXD1 is a determinant of patient outcome in clear cell renal cell carcinoma (ccRCC), and laboratory investigations have defined a role for this transcription factor in controlling the growth of tumors through regulation of the G2/M cell cycle transition. We hypothesized that the identification of pathways downstream of FOXD1 may define candidates for pharmacological modulation to suppress the G2/M transition in ccRCC. We developed an analysis pipeline that utilizes RNA sequencing, transcription factor binding site analysis, and phenotype validation to identify candidate effectors downstream from FOXD1. Compounds that modulate candidate pathways were tested for their ability to cause growth delay at G2/M. Three targets were identified: FOXM1, PME1, and TMEM167A, which were targeted by compounds FDI-6, AMZ-30, and silibinin, respectively. A 3D ccRCC tumor replica model was used to investigate the effects of these compounds on the growth of primary cells from five patients. While silibinin reduced 3D growth in a subset of tumor replicas, FDI-6 reduced growth in all. This study identifies tractable pathways to target G2/M transition and inhibit ccRCC growth, demonstrates the applicability of these strategies across patient tumor replicas, and provides a platform for individualized patient testing of compounds that inhibit tumor growth.

The Expression and Survival Significance of FOXD1 in Lung Squamous Cell Carcinoma: A Meta-Analysis, Immunohistochemistry Validation, and Bioinformatics Analysis

Accumulating evidence demonstrated that FOXD1 dysregulation was correlated with a broad spectrum of malignancies. However, litter is known about the role of FOXD1 in the progression of lung squamous cell carcinoma (LUSC). We conducted the comprehensive bioinformatics analysis to investigate FOXD1 expression in LUSC from TCGA and GEO datasets, and validated the FOXD1 expression pattern in clinical samples using immunohistochemistry method. ESTIMATE and CIBERSORT algorithms were performed to assess the relationship of FOXD1 and tumor microenvironment and immune cell infiltration. Our study showed that FOXD1 expression was significantly upregulated in LUSC tissues in TCGA dataset, validated by GEO datasets and clinical samples. In TCGA dataset, Kaplan-Meier curves showed that high FOXD1 expression was significantly correlated with favorable prognosis in LUSC patients. Moreover, FOXD1 expression has an impact on immune score and the proportions of immune cell infiltration subgroups. Finally, we predicted FOXD1 may be involved in many immune-related biological functions and cancer-related signaling pathways. Taken together, FOXD1 was upregulated in LUSC tissues, and FOXD1 expression could be a potential prognostic marker. FOXD1 might be associated with tumor microenvironment and perhaps a potential target in the tumor immunotherapy.

Determination of Exosome Mitochondrial DNA as a Biomarker of Renal Cancer Aggressiveness

Simple Summary

Components of liquid biopsy are potential non-invasive biomarkers for monitoring renal cell carcinoma (RCC) status. The aim of our study was to examine mitochondrial genes (such as HV1 and CYB) included in exosomal fractions as promising and innovative biomarkers in RCC. We found that phase C containing different types of vesicles and phase F rich in exosomes with a high mitochondrial DNA (mtDNA) content could be considered as powerful biomarkers for susceptibility to RCC. Interestingly, mtDNA was a good genetic marker when aggressiveness was evaluated.

Abstract

Here, the role of non-invasive biomarkers in liquid biopsy was evaluated, mainly in exosomes and mitochondrial DNA (mtDNA) as promising, novel, and stable biomarkers for renal cell carcinoma (RCC). A total of 140 fractions (named from B to F) obtained by ultracentrifugations of whole blood samples from 28 individuals (13 patients and 15 controls) were included. Nanoparticle Tracking Analysis (NTA) was conducted to characterized exosomal fraction. Subsequently, an analysis of digital PCR (dPCR) using the QuantStudio™ 3D Digital PCR platform was performed and the quantification of mtDNA copy number by QuantStudioTM 12K Flex Real-Time PCR System (qPCR) was developed. Moreover, Next Generation Sequencing (NGS) analyses were included using MiSeq system (Illumina, San Diego, CA, USA). An F fraction, which contains all exosome data and all mitochondrial markers, was identified in dPCR and qPCR with statistically significant power (adjusted p values ≤ 0.03) when comparing cases and controls. Moreover, present analysis in mtDNA showed a relevant significance in RCC aggressiveness. To sum up, this is the first time a relation between exosomal mtDNA markers and clinical management of RCC is analyzed. We suggest a promising strategy for future liquid biopsy RCC analysis, although more analysis should be performed prior to application in routine clinical practice.