FXR1 expression domain in Wilms tumor

PRMT5-mediated arginine methylation of FXR1 is essential for RNA binding in cancer cells

Emerging evidence indicates that arginine methylation promotes the stability of arginine-glycine-rich (RGG) motif-containing RNA-binding proteins (RBPs) and regulates gene expression. Here, we report that post-translational modification of FXR1 enhances the binding with mRNAs and is involved in cancer cell growth and proliferation. Independent point mutations in arginine residues of FXR1's nuclear export signal (R386 and R388) and RGG (R453, R455 and R459) domains prevent it from binding to RNAs that form G-quadruplex (G4) RNA structures. Disruption of G4-RNA structures by lithium chloride failed to bind with FXR1, indicating its preference for G4-RNA structure containing mRNAs. Furthermore, loss-of-function of PRMT5 inhibited FXR1 methylation both in vivo and in vitro, affecting FXR1 protein stability, inhibiting RNA-binding activity and cancer cell growth and proliferation. Finally, the enhanced crosslinking and immunoprecipitation (eCLIP) analyses reveal that FXR1 binds with the G4-enriched mRNA targets such as AHNAK, MAP1B, AHNAK2, HUWE1, DYNC1H1 and UBR4 and controls its mRNA expression in cancer cells. Our findings suggest that PRMT5-mediated FXR1 methylation is required for RNA/G4-RNA binding, which promotes gene expression in cancer cells. Thus, FXR1's structural characteristics and affinity for RNAs preferentially G4 regions provide new insights into the molecular mechanism of FXR1 in oral cancer cells.

Comprehensive bioinformatics analysis of FXR1 across pan-cancer: Unraveling its diagnostic, prognostic, and immunological significance

Fragile X-related protein 1 (FXR1) is an RNA-binding protein that belongs to the fragile X-related (FXR) family. Studies have shown that FXR1 plays an important role in cancer cell proliferation, invasion and migration and is differentially expressed in cancers. This study aimed to gain a comprehensive and systematic understanding of the analysis of FXR1's role in cancers. This would lead to a better understanding of how it contributes to the development and progression of various malignancies. this study conducted through The Cancer Genome Atlas (TCGA), GTEx, cBioPortal, TISIDB, GEPIA2 and HPA databases to investigated FXR1's role in cancers. For data analysis, various software platforms and web platforms were used, such as R, Cytoscape, hiplot plateform. A significant difference in FXR1 expression was observed across molecular and immune subtypes and across types of cancer. FXR1 expression correlates with disease-specific survival (DSS), and overall survival (OS) in several cancer pathways, further in progression-free interval (PFI) in most cancers. Additionally, FXR1 showed a correlation with genetic markers of immunomodulators in different cancer types. Our study provides insights into the role of FXR1 in promoting, inhibiting, and treating diverse cancers. FXR1 has the potential to serve as a diagnostic and prognostic biomarker for cancer, with therapeutic value in immune-based, targeted, or cytotoxic treatments. Further clinical validation and exploration of FXR1 in cancer treatment is necessary.

Exploiting embryonic niche conditions to grow Wilms tumor blastema in culture

Introduction

Wilms Tumor (WT), or nephroblastoma, is the most common pediatric kidney cancer. Most WTs display a “favorable” triphasic histology, in which the tumor is comprised of blastemal, stromal, and epithelial cell types. Blastemal predominance after neoadjuvant chemotherapy or diffuse anaplasia (“unfavorable” histology; 5-8%) portend a worse prognosis. Blastema likely provide the putative cancer stem cells (CSCs), which retain molecular and histologic features characteristic of nephron progenitor cells (NPCs), within WTs. NPCs arise in the metanephric mesenchyme (MM) and populate the cap mesenchyme (CM) in the developing kidney. WT blastemal cells, like NPCs, similarly express markers, SIX2 and CITED1. Tumor xenotransplantation is currently the only dependable method to propagate tumor tissue for research or therapeutic screening, since efforts to culture tumors in vitro as monolayers have invariably failed. Therefore, a critical need exists to propagate WT stem cells rapidly and efficiently for high-throughput, real-time drug screening.

Methods

Previously, our lab developed niche conditions that support the propagation of murine NPCs in culture. Applying similar conditions to WTs, we assessed our ability to maintain key NPC "stemness" markers, SIX2, NCAM, and YAP1, and CSC marker ALDHI in cells from five distinct untreated patient tumors.

Results

Accordingly, our culture conditions maintained the expression of these markers in cultured WT cells through multiple passages of rapidly dividing cells.

Discussion

These findings suggest that our culture conditions sustain the WT blastemal population, as previously shown for normal NPCs. As a result, we have developed new WT cell lines and a multi-passage in vitro model for studying the blastemal lineage/CSCs in WTs. Furthermore, this system supports growth of heterogeneous WT cells, upon which potential drug therapies could be tested for efficacy and resistance.

Development and validation of a prognostic model based on a single-cell RNA-seq in Wilms tumor in children

To analyze the heterogeneity between different cell types in pediatric Wilms tumor (WT) tissue, and identify the differentially expressed genes (DEGs) of malignant tumor cells, thereby establishing a prognostic model. The single-cell sequencing data of pediatric WT tissues were downloaded from the public database. Data filtration and normalization, principal component analysis, and T-distributed stochastic neighbor embedding cluster analysis were performed using the Seurat package of R language. Cells were divided into different clusters, malignant tumor cells were extracted, and DEGs were obtained. Then, the pseudo-time trajectory analysis was performed. Prognostic biomarkers were determined by univariate and multivariate COX regression analyses and LASSO regression analysis. Kaplan-Meier survival analysis and receiver operator characteristic curve analysis were performed. Combined with the prognostic biomarkers and clinical characteristics, a nomogram was generated to predict WT prognosis. The prognostic power was validated in the external datasets. Cells in the WT tissue were divided into 10 clusters. Three prognostic biomarkers that affected the survival time of patients were screened from 215 DEGs in malignant tumor cells, and a nomogram was constructed using the three genes and clinical characteristics. The area under the curve (AUC) values of 3- and 5-year disease-free survival were 0.756 and 0.734, respectively. In the external validation dataset, the AUC value of this nomogram model was 0.826. Based on the single-cell RNA-seq, we recognized cell clusters in the WT tissue of children, identified prognostic biomarkers in malignant tumor cells, and established a comprehensive prognostic model. Our findings might provide new ideas and methods for the diagnosis and treatment of WT.

FXR1 facilitates axitinib resistance in clear cell renal cell carcinoma via regulating KEAP1/Nrf2 signaling pathway

Axitinib is emerging as a first-line combination treatment drug for metastatic renal cell carcinoma, but the acquired resistance significantly bothers the treatment efficacy. This article is to investigate the impact of fragile X mental retardation autosomal homolog 1 (FXR1) and its mechanistic involvement with Kelch-like epoxy chloropropan-associated protein 1 (KEAP1)/NF-E2-related factor 2 (Nrf2) pathway on cell resistance to axitinib in clear cell renal cell carcinoma (ccRCC). Establishment of axitinib resistance cells (786-O, Caki-1, 786-O/axitinib, or Caki-1/axitinib) was made, and the cells were then transfected with sh-FXR1, or co-transfected with sh-FXR1 and sh-KEAP1. The quantitative real-time PCR (qRT-PCR) and western blotting assays were employed to measure the expression of FXR1, KEAP1, Nrf2, LC3 II/I, Beclin 1, p62, MDR-1, and MRP-1. In addition, the binding between FXR1 and KEAP1 was verified by RNA-immunoprecipitation and RNA pull-down assays, and FXR1-dependent KEAP1 mRNA degradation was determined. Herein, FXR1 was demonstrated to be overexpressed in ccRCC cells, and showed higher expression in 786-O/axitinib and Caki-1/axitinib cells. Mechanistically, FXR1 enriched KEAP1 mRNA, and pulled downed by biotinylated KEAP1 probes. Results of RNA stability assay reveled that KEAP mRNA stability was suppressed by FXR1. Furthermore, knockdown of FXR1 promoted cell apoptosis and showed a restrained feature on cell resistance to axitinib. Of note, KEAP1 knockdown suppressed cell autophagy, oxidative stress, resistance to axitinib, and promoted apoptosis, despite FXR1 was downregulated in ccRCC cells. In conclusion, FXR1 played an encouraging role in ccRCC cell resistance to axitinib by modulating KEAP/Nrf2 pathway.

Molecular and Immunohistochemical Expression of LTA4H and FXR1 in Canine Oral Melanoma

Oral melanoma is a common canine tumor whose prognosis is considered ominous, but poorly predicted by histology alone. In the present study the gene and protein expression of Leukotriene A4 hydrolase (LTA4H) and Fragile-X-mental retardation-related protein1 (FXR1), both reported as related to metastatic potential in different tumors, were investigated in canine oral melanoma. The main aim of the study was to confirm and quantify the presence of LTA4H and FXR1 genes and protein in oral melanomas. A secondary aim was to investigate their association with histologic prognostic criteria (mitotic count, Ki-67 index). Formalin-fixed-paraffin-embedded canine oral melanomas (36) were collected and histopathological evaluation carried out. Immunolabelling for LTA4H and FXR1 and Ki-67 were performed. RT-PCR evaluated LTA4H and FXR1 gene expressions. Histologically, most tumors were epithelioid cell melanomas (19/36) and were amelanotic, mildly or moderately pigmented (5, 12 and 13/36 respectively), only 6 were highly pigmented. Mitotic count ranged 1-106, Ki-67 index ranged 4.5–52.3. Thirty-two (32/32) melanomas immunolabelled for LTA4H and 33/34 for FXR1. RT-PCR values ranged 0.76–5.11 ΔCt for LTA4H and 0.22–6.24 ΔCt for FXR1. Molecular and immunohistochemical expression of both LTA4H and FXR1 did not statically correlate with mitotic count or Ki-67 index. The present study demonstrates LTA4H and FXR1 gene and protein in canine oral melanoma, however their expression is apparently unrelated to histopathologic prognostic criteria. Although LTA4H and FXR1 seem unrelated to tumor behavior, their extensive expression in the present cohort of cases suggest that they may play a role in canine oral melanoma oncogenesis.

Changes in FXR1 expression after Chemotherapy for Rhabdomyosarcoma

BACKGROUND

Rhabdomyosarcoma (RMS) arises from abnormal muscle development. We reported previously that Fragile-X-Related 1 (FXR1), essential to normal myogenesis, was highly expressed in RMS relative to other embryonal tumors. This current study explored FXR1 expression across RMS disease characteristics and treatment response.

METHODS

RMS patients ≤18 years (1980-2019; n = 152) were categorized according to tumor histology, PAX/FOXO1 translocation, and vital status. FXR1 protein expression was compared before and after chemotherapy. Impact of FXR1 expression on relapse-free (RFS) and overall survival (OS) was analyzed.

RESULTS

FXR1 was most intensely expressed in the cytosol of undifferentiated rhabdomyoblasts. At diagnosis, FXR1 expression was ubiquitous and strong across all disease characteristics and foremost associated with worse RFS in translocation-positive patients (p = 0.0411). Among embryonal and translocation-negative RMS, survivors showed a significantly greater decrease in FXR1 expression after chemotherapy (p < 0.001) compared to decedents (p = 0.8). In contrast, alveolar and translocation-positive RMS specimens showed insignificant changes in FXR1 expression across therapy. As expected, alveolar histology, translocation presence, stage, and clinical group associated with worse survival.

CONCLUSIONS

FXR1 was expressed strongly across RMS specimens at diagnosis regardless of disease or patient characteristics, and particularly in undifferentiated cells. Reduction in FXR1 expression after chemotherapy associated with improved survival for embryonal and translocation-negative RMS patients.

Authorship Patterns in Cancer Genomics Publications Across Africa

PURPOSE

Authorship is a proxy indicator of research capacity. Understanding the research capacity is imperative for developing population-specific cancer control strategies. This is particularly apropos for African nations, where mortality from cancer is projected to surpass that from infectious disease and the populations are critically under-represented in cancer and genomics studies. Here, we present an analysis and discussion of the patterns of authorship in Africa as they pertain to cancer genomics research across African countries.

METHODS

PubMed metadata of relevant cancer genomics peer-reviewed publications on African populations, published between January 1, 1990, and December 31, 2019, were retrieved and analyzed for patterns of authorship affiliation using R packages, RISmed, and Pubmed.mineR.

RESULTS

The data showed that only 0.016% (n = 375) of cancer publications globally were on cancer genomics of African people. More than 50% of the first and last authors of these publications originated from the North African countries of Tunisia, Morocco, Egypt, and Algeria. South Africa (13.6% and 12.7%) and Nigeria (2.2% and 1.9%) were the Sub-Saharan African countries most represented by first and last authorship positions, respectively. The United States contributed 12.6% of first and last authored papers, and nearly 50% of all African countries had no contributing author for the publications we reviewed.

CONCLUSION

This study highlights and brings awareness to the paucity of cancer genomics research on African populations and by African authors and identifies a need for concerted efforts to encourage and enable more research in Africa, needed for achieving global equity in cancer outcomes.

A Review of Cancer Genetics and Genomics Studies in Africa

Cancer is the second leading cause of death globally and is projected to overtake infectious disease as the leading cause of mortality in Africa within the next two decades. Cancer is a group of genomic diseases that presents with intra- and inter-population unique phenotypes, with Black populations having the burden of morbidity and mortality for most types. At large, the prevention and treatment of cancers have been propelled by the understanding of the genetic make-up of the disease of mostly non-African populations. By the same token, there is a wide knowledge gap in understanding the underlying genetic causes of, and genomic alterations associated with, cancer among black Africans. Accordingly, we performed a review of the literature to survey existing studies on cancer genetics/genomics and curated findings pertaining to publications across multiple cancer types conducted on African populations. We used PubMed MeSH terms to retrieve the relevant publications from 1990 to December 2019. The metadata of these publications were extracted using R text mining packages: RISmed and Pubmed.mineR. The data showed that only 0.329% of cancer publications globally were on Africa, and only 0.016% were on cancer genetics/genomics from Africa. Although the most prevalent cancers in Africa are cancers of the breast, cervix, uterus, and prostate, publications representing breast, colorectal, liver, and blood cancers were the most frequent in our review. The most frequently reported cancer genes were BRCA1, BRCA2, and TP53. Next, the genes reported in the reviewed publications’ abstracts were extracted and annotated into three gene ontology classes. Genes in the cellular component class were mostly associated with cell part and organelle part, while those in biological process and molecular function classes were mainly associated with cell process, biological regulation, and binding, and catalytic activity, respectively. Overall, this review highlights the paucity of research on cancer genomics on African populations, identified gaps, and discussed the need for concerted efforts to encourage more research on cancer genomics in Africa.

Wilms Tumor in Sub-Saharan Africa: Molecular and Social Determinants of a Global Pediatric Health Disparity

Wilms tumor (WT) is the most common renal malignancy of childhood. Global disparities in WT have been reported with the highest incidence and lowest overall survival occurring in sub-Saharan African nations. After a detailed search of PubMed, we reviewed available literature on WT in sub-Saharan Africa and summarized findings that explore biologic and social factors contributing to this alarming cancer health disparity. Access to care and treatment abandonment are the most frequently reported factors associated with decreased outcomes. Implementation of multidisciplinary teams, collaborative networks, and financial support has improved overall survival in some nations. However, treatment abandonment remains a challenge. In high-income countries globally, WT therapy now is risk-stratified according to biology and histology. To a significantly lesser extent, biologic features have been studied only recently in sub-Saharan African WT, yet unique molecular and genetic signatures, including congenital anomaly-associated syndromes and biomarkers associated with treatment-resistance and poor prognosis have been identified. Together, challenges with access to and delivery of health care in addition to adverse biologic features likely contribute to increased burden of disease in sub-Saharan African children having WT. Publications on biologic features of WT that inform treatment stratification and personalized therapy in resource-limited regions of sub-Saharan Africa have lagged in comparison to publications that discuss social determinants of health. Further efforts to understand both WT biology and social factors relevant to appropriate treatment delivery should be prioritized in order to reduce health disparities for children residing in resource-limited areas of sub-Saharan Africa battling this lethal childhood cancer.

Fragile X-related protein family: a double-edged sword in neurodevelopmental disorders and cancer

The fragile X-related (FXR) family proteins FMRP, FXR1, and FXR2 are RNA binding proteins that play a critical role in RNA metabolism, neuronal plasticity, and muscle development. These proteins share significant homology in their protein domains, which are functionally and structurally similar to each other. FXR family members are known to play an essential role in causing fragile X mental retardation syndrome (FXS), the most common genetic form of autism spectrum disorder. Recent advances in our understanding of this family of proteins have occurred in tandem with discoveries of great importance to neurological disorders and cancer biology via the identification of their novel RNA and protein targets. Herein, we review the FXR family of proteins as they pertain to FXS, other mental illnesses, and cancer. We emphasize recent findings and analyses that suggest contrasting functions of this protein family in FXS and tumorigenesis based on their expression patterns in human tissues. Finally, we discuss current gaps in our knowledge regarding the FXR protein family and their role in FXS and cancer and suggest future studies to facilitate bench to bedside translation of the findings.

Identification of a five-mRNA signature as a novel potential prognostic biomarker in pediatric Wilms tumor

Background

The aim of this study was to generate a prognostic model to predict survival outcome in pediatric Wilms tumor (WT).

Methods

The data including mRNA expression and clinical information of pediatric WT patients were downloaded from the Therapeutically Available Research to Generate Effective Treatments (TARGET) database. The differentially expressed genes were identified and a prognostic signature of pediatric WT was generated according to the results of univariate and multivariate Cox analysis. Receiver operating characteristic (ROC) curve was used to evaluate the five‐mRNA signature in pediatric Wilms tumor patients. Bootstrap test with 500 times was used to perform the internal validation.

Results

We identified 6,964 differentially expressed mRNAs associated with pediatric WT, including 3,190 downregulated mRNAs and 3,774 up‐regulated mRNAs. Univariate and multivariate Cox analysis identified five mRNAs (SPRY1, SPIN4, MAP7D3, C10orf71, and SPAG11A) to establish a predictive model. The risk score formula is as follows: Risk score = 0.3036*SPIN4 + 0.8576*MAP7D3 −0.1548*C10orf71 −0.7335*SPRY1 −0.2654*SPAG11A. The pediatric WT patients were divided into low‐risk group and high‐risk group based on the median risk score (value = 1.1503). The receiver operating characteristic (ROC) curve analysis revealed good performance of the 5‐mRNA prognostic model (the area under the curve [AUC] was 0.821). Bootstrap test (Bootstrap resampling times = 500) was used to perform the internal validation and revealed that the AUC was 0.822. REACTOME, KEGG, and BIOCARTA pathway analyses demonstrated that these survival‐related genes were mainly enriched in ErbB2 and ErbB3 signaling pathways, and calcium signaling pathway.

Conclusion

The five‐mRNA signature can predict the prognosis of patients with pediatric WT. It has significant implication in the understanding of therapeutic targets for pediatric WT patients. However, further study is needed to validate this five‐mRNA signature and uncover more novel diagnostic or prognostic mRNAs candidates in pediatric WT patients.