Elevated expression of RNA methyltransferase BCDIN3D predicts poor prognosis in breast cancer

ChemRAP uncovers specific mRNA translation regulation via RNA 5' phospho-methylation

5'-end modifications play key roles in determining RNA fates. Phospho-methylation is a noncanonical cap occurring on either 5'-PPP or 5'-P ends. We used ChemRAP, in which affinity purification of cellular proteins with chemically synthesized modified RNAs is coupled to quantitative proteomics, to identify 5'-Pme "readers". We show that 5'-Pme is directly recognized by EPRS, the central subunit of the multisynthetase complex (MSC), through its linker domain, which has previously been involved in key noncanonical EPRS and MSC functions. We further determine that the 5'-Pme writer BCDIN3D regulates the binding of EPRS to specific mRNAs, either at coding regions rich in MSC codons, or around start codons. In the case of LRPPRC (leucine-rich pentatricopeptide repeat containing), a nuclear-encoded mitochondrial protein associated with the French Canadian Leigh syndrome, BCDIN3D deficiency abolishes binding of EPRS around its mRNA start codon, increases its translation but ultimately results in LRPPRC mislocalization. Overall, our results suggest that BCDIN3D may regulate the translation of specific mRNA via RNA-5'-Pme.

If the 5' cap fits (wear it) - Non-canonical RNA capping

RNA capping is a prominent RNA modification that influences RNA stability, metabolism, and function. While it was long limited to the study of the most abundant eukaryotic canonical m7G cap, the field recently went through a large paradigm shift with the discovery of non-canonical RNA capping in bacteria and ultimately all domains of life. The repertoire of non-canonical caps has expanded to encompass metabolite caps, including NAD, FAD, CoA, UDP-Glucose, and ADP-ribose, alongside alarmone dinucleoside polyphosphate caps, and methylated phosphate cap-like structures. This review offers an introduction into the field, presenting a summary of the current knowledge about non-canonical RNA caps. We highlight the often still enigmatic biological roles of the caps together with their processing enzymes, focusing on the most recent discoveries. Furthermore, we present the methods used for the detection and analysis of these non-canonical RNA caps and thus provide an introduction into this dynamic new field.

Associations of breast cancer related exposures and gene expression profiles in normal breast tissue-The Norwegian Women and Cancer normal breast tissue study

BACKGROUND

Normal breast tissue is utilized in tissue-based studies of breast carcinogenesis. While gene expression in breast tumor tissue is well explored, our knowledge of transcriptomic signatures in normal breast tissue is still incomplete. The aim of this study was to investigate variability of gene expression in a large sample of normal breast tissue biopsies, according to breast cancer related exposures (obesity, smoking, alcohol, hormone therapy, and parity).

METHODS

We analyzed gene expression profiles from 311 normal breast tissue biopsies from cancer-free, post-menopausal women, using Illumina bead chip arrays. Principal component analysis and K-means clustering was used for initial analysis of the dataset. The association of exposures and covariates with gene expression was determined using linear models for microarrays.

RESULTS

Heterogeneity of the breast tissue and cell composition had the strongest influence on gene expression profiles. After adjusting for cell composition, obesity, smoking, and alcohol showed the highest numbers of associated genes and pathways, whereas hormone therapy and parity were associated with negligible gene expression differences.

CONCLUSION

Our results provide insight into associations between major exposures and gene expression profiles and provide an informative baseline for improved understanding of exposure-related molecular events in normal breast tissue of cancer-free, post-menopausal women.

BCDIN3D RNA methyltransferase stimulates Aldolase C expression and glycolysis through let-7 microRNA in breast cancer cells

Type II diabetes (T2D) and specific cancers share many risk factors, however, the molecular mechanisms underlying these connections are often not well-understood. BCDIN3D is an RNA modifying enzyme that methylates specific precursor microRNAs and tRNA^His. In addition to breast cancer, BCDIN3D may also be linked to metabolism, as its gene locus is associated with obesity and T2D. In order to uncover metabolic pathways regulated by BCDIN3D in cancer, we performed an unbiased analysis of the metabolome, transcriptome, and proteome of breast cancer cells depleted for BCDIN3D. Intersection of these analyses showed that BCDIN3D-depleted cells have increased levels of Fructose 1,6 Bisphosphate (F1,6-BP), the last six-carbon glycolytic intermediate accompanied by reduced glycolytic capacity. We further show that elevated F1,6-BP is due to downregulation of Aldolase C (ALDOC), an enzyme that cleaves F1,6-BP mainly in the brain, but whose high expression/amplification is associated with poor prognosis in breast cancer. BCDIN3D regulates ALDOC through a non-canonical mechanism involving the crucial let-7 microRNA family and its target site on the 3'UTR of ALDOC. Overall, our results reveal an important connection between BCDIN3D, let-7 and glycolysis that may be relevant to breast cancer, obesity, and T2D.

The epitranscriptome landscape of small noncoding RNAs in stem cells

Stem cells (SCs) are unique cells that have an inherent ability to self‐renew or differentiate. Both fate decisions are strongly regulated at the molecular level via intricate signaling pathways. The regulation of signaling networks promoting self‐renewal or differentiation was thought to be largely governed by the action of transcription factors. However, small noncoding RNAs (ncRNAs), such as vault RNAs, and their post‐transcriptional modifications (the epitranscriptome) have emerged as additional regulatory layers with essential roles in SC fate decisions. RNA post‐transcriptional modifications often modulate RNA stability, splicing, processing, recognition, and translation. Furthermore, modifications on small ncRNAs allow for dual regulation of RNA activity, at both the level of biogenesis and RNA‐mediated actions. RNA post‐transcriptional modifications act through structural alterations and specialized RNA‐binding proteins (RBPs) called writers, readers, and erasers. It is through SC‐context RBPs that the epitranscriptome coordinates specific functional roles. Small ncRNA post‐transcriptional modifications are today exploited by different mechanisms to facilitate SC translational studies. One mechanism readily being studied is identifying how SC‐specific RBPs of small ncRNAs regulate fate decisions. Another common practice of using the epitranscriptome for regenerative applications is using naturally occurring post‐transcriptional modifications on synthetic RNA to generate induced pluripotent SCs. Here, we review exciting insights into how small ncRNA post‐transcriptional modifications control SC fate decisions in development and disease. We hope, by illustrating how essential the epitranscriptome and their associated proteome are in SCs, they would be considered as novel tools to propagate SCs for regenerative medicine.

MiR-195-3p inhibits cell proliferation in cervical cancer by targeting BCDIN3D

BACKGROUND

Cervical cancer (CC) is one of the most prevailing cancers among females. Accumulated studies concentrated on the regulatory role of micro RNA in cancers. This research is to explore the potential role of mir-195-3p in cervical cancer progression.

METHODS

Bioinformatics tools were used to investigate differential expression of mir-195-3p and BCDIN3D in cervical cancer. RNA expression patterns of both mir-195-3p and BCDIN3D were detected by RT-PCR in CC cell lines. The protein expression of BCDIN3D was measured by Western Blot. Hela and Siha cell lines were transfected with mir-195-3p inhibitors, mir-195-3p mimics and BCDIN3D si-RNA, si-NC. Luciferase reporter assays were adopted to confirm the binding. The interplays between mir-195-3p and BCDIN3D were explored in CC cell lines. CCK-8 assays checked how mir-195-3p regulated cell proliferation and Ki67 was examined by Western blot for its protein expressions as a biomarker for CC cell proliferation.

RESULTS

MiR-195-3p was downregulated while BCDIN3D was upregulated in cervical cancer cell lines. The binding was confirmed via Luciferase Assay. RT-PCR suggested that upregulation of mir-195-3p inhibited BCDIN3D and downregulation of BCDIN3D in return induced mir-195-3p. CCK-8 pointed out that overexpression of mir-195-3p inhibited the cell viability. Ki67 protein expression was inhibited by miR-195-3p mimics or silence of BCDIN3D.

CONCLUSION

The present research led us to a conclusion that mir-195-3p might inhibit cervical cancer cell proliferation and was reversely regulated by BCDIN3D. This suggests that miR-195-3p mimics/ BCDIN3D si-RNA might be used in the treatments of cervical cancer in the future after various animal assays and clinical trials.

Crystal structure of human cytoplasmic tRNAHis-specific 5'-monomethylphosphate capping enzyme

BCDIN3 domain containing RNA methyltransferase, BCDIN3D, monomethylates the 5′-monophosphate of cytoplasmic tRNA^His with a G₋₁:A₇₃ mispair at the top of an eight-nucleotide-long acceptor helix, using S-adenosyl-l-methionine (SAM) as a methyl group donor. In humans, BCDIN3D overexpression is associated with the tumorigenic phenotype and poor prognosis in breast cancer. Here, we present the crystal structure of human BCDIN3D complexed with S-adenosyl-l-homocysteine. BCDIN3D adopts a classical Rossmann-fold methyltransferase structure. A comparison of the structure with that of the closely related methylphosphate capping enzyme, MePCE, which monomethylates the 5′-γ-phosphate of 7SK RNA, revealed the important residues for monomethyl transfer from SAM onto the 5′-monophosphate of tRNA^His and for tRNA^His recognition by BCDIN3D. A structural model of tRNA^His docking onto BCDIN3D suggested the molecular mechanism underlying the different activities between BCDIN3D and MePCE. A loop in BCDIN3D is shorter, as compared to the corresponding region that forms an α-helix to recognize the 5′-end of RNA in MePCE, and the G₋₁:A₇₃ mispair in tRNA^His allows the N-terminal α-helix of BCDIN3D to wedge the G₋₁:A₇₃ mispair of tRNA^His. As a result, the 5′-monophosphate of G₋₁ of tRNA^His is deep in the catalytic pocket for 5′-phosphate methylation. Thus, BCDIN3D is a tRNA^His-specific 5′-monomethylphosphate capping enzyme that discriminates tRNA^His from other tRNA species, and the structural information presented in this study also provides the molecular basis for the development of drugs against breast cancers.

BCDIN3D regulates tRNAHis 3' fragment processing

5' ends are important for determining the fate of RNA molecules. BCDIN3D is an RNA phospho-methyltransferase that methylates the 5' monophosphate of specific RNAs. In order to gain new insights into the molecular function of BCDIN3D, we performed an unbiased analysis of its interacting RNAs by Thermostable Group II Intron Reverse Transcriptase coupled to next generation sequencing (TGIRT-seq). Our analyses showed that BCDIN3D interacts with full-length phospho-methylated tRNAHis and miR-4454. Interestingly, we found that miR-4454 is not synthesized from its annotated genomic locus, which is a primer-binding site for an endogenous retrovirus, but rather by Dicer cleavage of mature tRNAHis. Sequence analysis revealed that miR-4454 is identical to the 3' end of tRNAHis. Moreover, we were able to generate this 'miRNA' in vitro through incubation of mature tRNAHis with Dicer. As found previously for several pre-miRNAs, a 5'P-tRNAHis appears to be a better substrate for Dicer cleavage than a phospho-methylated tRNAHis. Moreover, tRNAHis 3'-fragment/'miR-4454' levels increase in cells depleted for BCDIN3D. Altogether, our results show that in addition to microRNAs, BCDIN3D regulates tRNAHis 3'-fragment processing without negatively affecting tRNAHis's canonical function of aminoacylation.

RNA methyltransferase BCDIN3D is crucial for female fertility and miRNA and mRNA profiles in Drosophila ovaries

RNA methyltransferases post-transcriptionally add methyl groups to RNAs, which can regulate their fates and functions. Human BCDIN3D (Bicoid interacting 3 domain containing RNA methyltransferase) has been reported to specifically methylate the 5′-monophosphates of pre-miR-145 and cytoplasmic tRNA^His. Methylation of the 5′-monophosphate of pre-miR-145 blocks its cleavage by the miRNA generating enzyme Dicer, preventing generation of miR-145. Elevated expression of BCDIN3D has been associated with poor prognosis in breast cancer. However, the biological functions of BCDIN3D and its orthologs remain unknown. Here we studied the biological and molecular functions of CG1239, a Drosophila ortholog of BCDIN3D. We found that ovary-specific knockdown of Drosophila BCDIN3D causes female sterility. High-throughput sequencing revealed that miRNA and mRNA profiles are dysregulated in BCDIN3D knockdown ovaries. Pathway analysis showed that many of the dysregulated genes are involved in metabolic processes, ribonucleoprotein complex regulation, and translational control. Our results reveal BCDIN3D’s biological role in female fertility and its molecular role in defining miRNA and mRNA profiles in ovaries.

DRUM: Inference of Disease-Associated m6A RNA Methylation Sites From a Multi-Layer Heterogeneous Network

Recent studies have revealed that the RNA N 6-methyladenosine (m6A) modification plays a critical role in a variety of biological processes and associated with multiple diseases including cancers. Till this day, transcriptome-wide m6A RNA methylation sites have been identified by high-throughput sequencing technique combined with computational methods, and the information is publicly available in a few bioinformatics databases; however, the association between individual m6A sites and various diseases are still largely unknown. There are yet computational approaches developed for investigating potential association between individual m6A sites and diseases, which represents a major challenge in the epitranscriptome analysis. Thus, to infer the disease-related m6A sites, we implemented a novel multi-layer heterogeneous network-based approach, which incorporates the associations among diseases, genes and m6A RNA methylation sites from gene expression, RNA methylation and disease similarities data with the Random Walk with Restart (RWR) algorithm. To evaluate the performance of the proposed approach, a ten-fold cross validation is performed, in which our approach achieved a reasonable good performance (overall AUC: 0.827, average AUC 0.867), higher than a hypergeometric test-based approach (overall AUC: 0.7333 and average AUC: 0.723) and a random predictor (overall AUC: 0.550 and average AUC: 0.486). Additionally, we show that a number of predicted cancer-associated m6A sites are supported by existing literatures, suggesting that the proposed approach can effectively uncover the underlying epitranscriptome circuits of disease mechanisms. An online database DRUM, which stands for disease-associated ribonucleic acid methylation, was built to support the query of disease-associated RNA m6A methylation sites, and is freely available at: www.xjtlu.edu.cn/biologicalsciences/drum.

Secreted Frizzled-Related Protein 2 Is Associated with Disease Progression and Poor Prognosis in Breast Cancer

Purpose

Secreted frizzled-related protein 2 (sFRP2) is a secreted protein associated with cancer drug resistance and metastasis. However, few studies have reported serum sFRP2 levels in breast cancer. We evaluated serum sFRP2 as a potential biomarker for breast cancer.

Methods

Serum sFRP2 concentrations were detected in 274 breast cancer patients along with 147 normal healthy controls by enzyme-linked immunosorbent assay (ELISA). Diagnostic significance was evaluated by area under the curve (AUC) analysis and the Youden index. Prognostic significance was determined by Kaplan-Meier survival method and univariate and multivariate Cox proportional hazard regression model analyses.

Results

Serum sFRP2 was elevated in breast cancer patients compared to normal healthy controls (P < 0.001). The sensitivity of sFRP2 in diagnosing breast cancer was 76.9% at a specificity of 76.6%. Elevated serum sFRP2 levels are associated with primary tumor size, TNM stage, and lymph node metastases. The Kaplan-Meier curves showed a significant association of serum sFRP2 with progression-free survival. The multivariate Cox analysis confirmed that high serum sFRP2 was an independent prognostic factor for poor prognosis (HR = 3.89, 95% CI = 1.95-7.68, P = 0.001).

Conclusions

In conclusion, serum sFRP2 may serve as a potential biomarker for breast cancer diagnosis and prognostic evaluation.

Effect of HMGN2 on proliferation and apoptosis of MCF-7 breast cancer cells

We investigated the effect of high mobility group protein N2 (HMGN2) on the proliferation and apoptosis of the human MCF-7 breast cancer cell line, and its effect on tumor growth in a subcutaneous heterotopic transplantation tumor model of breast cancer. The cell viability assay was used to verify the effect of the recombinant human HMGN2 on MCF-7 cell proliferation. The Transwell chamber assay was used to verify the effect of HMGN2 on MCF-7 cell migration. Flow cytometry and Hoechst staining were used to detect the effect of HMGN2 on MCF-7 cell apoptosis. MCF-7 was injected to establish a subcutaneous heterotopic transplantation tumor model of breast cancer in nude mice. The size, weight and volume of tumor in each group were compared after the administration of different concentrations of HMGN2 solution around the tumor tissue at day 1, 3, 5 and 7. The tumor tissue was removed and cut into sections, and the apoptotic cells in tumors of nude mice were detected by a TUNEL kit. The CCK-8 assay showed that HMGN2 at different concentrations inhibited the proliferation of the MCF-7 breast cancer cells, and the proliferation of MCF-7 cells were significantly inhibited when the concentration of HMGN2 reached 3 µg/ml (P<0.01). The Transwell chamber assay showed that 3 µg/ml of HMGN2 significantly decreased the migration capacity of MCF-7 cells (P<0.01). Flow cytometry and Hoechst staining showed that 3 µg/ml of HMGN2 significantly increased apoptosis of MCF-7 cells (P<0.01). After the nude mouse model of breast cancer was established, HMGN2 at different concentrations was injected around the tumor tissue at day 1, 3, 5 and 7. We demonstrated that the growth of breast cancer was significantly inhibited when the concentration of HMGN2 reached 15 µg/ml. TUNEL staining showed that the number of apoptotic cells in the 15 µg/ml dose group was significantly higher than that in the control group (P<0.01). Therefore, in vitro and in vivo experiments proved that recombinant human HMGN2 could significantly inhibit the proliferation and migration of breast cancer cells, which increased the apoptosis of breast cancer cells and exerted anti-breast cancer effects, which enriched our understanding of the biological roles of HMGN2.

Human BCDIN3D Is a Cytoplasmic tRNAHis-Specific 5'-Monophosphate Methyltransferase

Bicoid interacting 3 domain containing RNA methyltransferase (BCDIN3D) is a member of the Bin3 methyltransferase family and is evolutionary conserved from worm to human. BCDIN3D is overexpressed in breast cancer, which is associated with poor prognosis of breast cancers. However, the biological functions and properties of BCDIN3D have been enigmatic. Recent studies have revealed that human BCDIN3D monomethylates 5'-monophsosphate of cytoplasmic tRNA^Hisin vivo and in vitro. BCDIN3D recognizes the unique and exceptional structural features of cytoplasmic tRNA^His and discriminates tRNA^His from other cytoplasmic tRNA species. Thus, BCDIN3D is a tRNA^His-specific 5'-monophosphate methyltransferase. Methylation of the 5'-phosphate group of tRNA^His does not significantly affect tRNA^His aminoacylation by histidyl-tRNA synthetase in vitro nor the steady state level or stability of tRNA^Hisin vivo. Hence, methylation of the 5'-phosphate group of tRNA^His by BCDIN3D or tRNA^His itself may be involved in certain unknown biological processes, beyond protein synthesis. This review discusses recent reports on BCDIN3D and the possible association between 5'-phosphate monomethylation of tRNA^His and the tumorigenic phenotype of breast cancer.

RNA-modifying proteins as anticancer drug targets

All major biological macromolecules (DNA, RNA, proteins and lipids) undergo enzyme-catalysed covalent modifications that impact their structure, function and stability. A variety of covalent modifications of RNA have been identified and demonstrated to affect RNA stability and translation to proteins; these mechanisms of translational control have been termed epitranscriptomics. Emerging data suggest that some epitranscriptomic mechanisms are altered in human cancers as well as other human diseases. In this Review, we examine the current understanding of RNA modifications with a focus on mRNA methylation, highlight their possible roles in specific cancer indications and discuss the emerging potential of RNA-modifying proteins as therapeutic targets.

Human BCDIN3D monomethylates cytoplasmic histidine transfer RNA

Human RNA methyltransferase BCDIN3D is overexpressed in breast cancer cells, and is related to the tumorigenic phenotype and poor prognosis of breast cancer. Here, we show that cytoplasmic tRNAHis is the primary target of BCDIN3D in human cells. Recombinant human BCDIN3D, expressed in Escherichia coli, monomethylates the 5΄-monophosphate of cytoplasmic tRNAHis efficiently in vitro. In BCDN3D-knockout cells, established by CRISPR/Cas9 editing, the methyl moiety at the 5΄-monophosphate of cytoplasmic tRNAHis is lost, and the exogenous expression of BCDIN3D in the knockout cells restores the modification in cytoplasmic tRNAHis. BCIDN3D recognizes the 5΄-guanosine nucleoside at position -1 (G-1) and the eight-nucleotide acceptor helix with the G-1-A73 mis-pair at the top of the acceptor stem of cytoplasmic tRNAHis, which are exceptional structural features among cytoplasmic tRNA species. While the monomethylation of the 5΄-monophosphate of cytoplasmic tRNAHis affects neither the overall aminoacylation process in vitro nor the steady-state level of cytoplasmic tRNAHisin vivo, it protects the cytoplasmic tRNAHis transcript from degradation in vitro. Thus, BCDIN3D acts as a cytoplasmic tRNAHis-specific 5΄-methylphosphate capping enzyme. The present results also suggest the possible involvement of the monomethylation of the 5΄-monophosphate of cytoplasmic tRNAHis and/or cytoplasmic tRNAHis itself in the tumorigenesis of breast cancer cells.