Splicing factor SNRPA associated with microvascular invasion promotes hepatocellular carcinoma metastasis through activating NOTCH1/Snail pathway and is mediated by circSEC62/miR-625-5p axis

The novel tRNA-derived fragment, tiRNA-Met, inhibits the malignant progression of triple-negative breast cancer by regulating RANBP3L via a targeted interaction with SNRPA

BACKGROUND

tRNA-derived fragments (tRFs) have emerged as significant noncoding RNAs in cancer biology; however, their roles and mechanisms in triple-negative breast cancer (TNBC) remain inadequately characterized.

METHODS

tRF and tiRNA sequencing, real-time quantitative polymerase chain reaction (RT-qPCR), fluorescence in situ hybridization (FISH), and subcellular fractionation were used to explore the expression and characteristic of tiRNA-Met in TNBC. The biological functions of tiRNA-Met were assessed using CCK-8 assays, colony formation assays, and Transwell assays in vitro, alongside mouse xenograft models in vivo. RNA pull-down, mass spectrum, RNA immunoprecipitation (RIP), western blot, ubiquitination assays, RNA sequencing, actinomycin D assays, immunofluorescence, immunohistochemical staining, and rescue experiments were performed to explore the regulatory mechanisms of tiRNA-Met in TNBC.

RESULTS

tiRNA-Met was an uncharacterized tRF that originated from mitochondrial tRNAMet-CAT and was primarily localized in the cytoplasm. Its expression was significantly downregulated in TNBC tumor tissues compared with adjacent normal tissues. Overexpression of tiRNA-Met markedly inhibited the proliferation, migration, and invasion of TNBC cells; whereas, its reduced expression elicited opposite effects. In addition, tiRNA-Met overexpression suppressed TNBC cell growth in vivo. Mechanistically, tiRNA-Met directly interacted with the RNA recognition motif 2 (RRM2) domain of small nuclear ribonucleoprotein A (SNRPA), promoting SNRPA protein degradation via the ubiquitin/proteasome pathway. This interaction enhanced the stability of Ran-binding protein 3-like (RANBP3L) mRNA, resulting in increased RANBP3L expression and subsequent inhibition of the mTORC1/RPS6 signaling pathway.

CONCLUSIONS

Our study identified tiRNA-Met as a novel anti-oncogenic tRF and elucidated its mechanism for inhibiting the malignancy of TNBC. tiRNA-Met directly bound to SNRPA, promoting its degradation and stabilizing RANBP3L mRNA, ultimately leading to the inhibition of the mTORC1 signaling pathway. These findings position tiRNA-Met as a promising candidate for diagnostic and therapeutic applications in TNBC.

LncRNA CASC19 promotes the growth and glycolysis of colorectal cancer cells and tumor metastasis in mice

It has been reported that lncRNA CASC19 is abnormally highly expressed in colorectal cancer (CRC) progression, suggesting that it may regulate the occurrence and metastasis of CRC, but its specific mechanism is still unclear. To further explore the effect of CASC19 on CRC, we overexpressed or knocked down CASC19 in HR4838 cells. The results of Transwell invasion assay and cell clonogenic assay showed that CASC19 promoted cell invasion and proliferation. Flow cytometry results showed that CASC19 inhibited cell apoptosis. In addition, by detecting glucose uptake, lactate content and ATP production, it was found that CASC19 promoted glycolysis, while CASC19 silencing had the opposite effect. Interestingly, small nuclear ribonucleoprotein polypeptide A (SNRPA) is an RNA binding protein of CASC19. Overexpression of SNRPA promoted tumor cell invasion, proliferation, glycolysis, and inhibits apoptosis, while SNRPA silencing has the opposite effect. Moreover, SNRPA overexpression reversed the inhibitory effect of CASC19-sh on invasion, proliferation and glycolysis of HR4838 cells and the promoting effect on apoptosis, which was mediated by activating the Wnt/β-catenin pathway. In the subcutaneous transplantation tumor model of BALB/c nude mice, we observed that the tumor growth of CASC19 knockdown mice was slower, and the tumor weight and volume were smaller, which was related to the low expression of CASC19 and SNRPA. In conclusion, our results showed that CASC19 promoted the growth and glycolysis of CRC cells and tumor metastasis in mice by upregulating SNRPA, which may provide a new molecular marker for the diagnosis and treatment of CRC.

Integration of single-cell transcriptomics and bulk transcriptomics to explore prognostic and immunotherapeutic characteristics of nucleotide metabolism in lung adenocarcinoma

Background

Lung adenocarcinoma (LUAD) is a highly aggressive tumor with one of the highest morbidity and mortality rates in the world. Nucleotide metabolic processes are critical for cancer development, progression, and alteration of the tumor microenvironment. However, the effect of nucleotide metabolism on LUAD remains to be thoroughly investigated.

Methods

Transcriptomic and clinical data of LUAD were downloaded and organized from TCGA and GEO databases. Genes related to nucleotide metabolism were downloaded from the Msigdb database. Genes associated with LUAD prognosis were identified using univariate COX analysis, and a prognostic risk model was constructed using the machine learning combination of Lasso + Stepcox. The model's predictive validity was evaluated using KM survival and timeROC curves. Based on the prognostic model, LUAD patients were classified into different nucleotide metabolism subtypes, and the differences between patients of different subtypes were explored in terms of genomic mutations, functional enrichment, tumor immune characteristics, and immunotherapy responses. Finally, the key gene SNRPA was screened, and a series of in vitro experiments were performed on LUAD cell lines to explore the role of SNRPA in LUAD.

Result

LUAD patients could be accurately categorized into subtypes based on the nucleotide metabolism-related prognostic risk score (NMBRS). There were significant differences in prognosis between patients of different subtypes, and the NMBRS showed high accuracy in predicting the prognosis of LUAD patients. In addition, patients of different subtypes showed significant differences in genomic mutation and functional enrichment and exhibited different anti-tumor immune profiles. Importantly, NMBRS can be used to predict the responsiveness of LUAD patients to immunotherapy. The results of in vitro cellular experiments indicate that SNRPA plays an important role in the development and progression of lung adenocarcinoma.

Conclusion

This study comprehensively reveals the prognostic value and clinical application of nucleotide metabolism in LUAD. A prognostic signature constructed based on genes related to nucleotide metabolism accurately predicted the prognosis of LUAD patients, and this signature can be used as a guide for LUAD immunotherapy.

m6A-Modified SNRPA Controls Alternative Splicing of ERCC1 Exon 8 to Induce Cisplatin Resistance in Lung Adenocarcinoma

Alternative splicing (AS) generates protein diversity and is exploited by cancer cells to drive tumor progression and resistance to many cancer therapies, including chemotherapy. SNRPA is first identified as a spliceosome-related gene that potentially modulates resistance to platinum chemotherapy. Both the knockout or the knockdown of SNRPA via CRISPR/Cas9 and shRNA techniques can reverse the resistance of cisplatin-resistant lung adenocarcinoma (LUAD) cells to cisplatin. SNRPA overexpression enhanced the resistance of cisplatin-sensitive LUAD cells. Gene Ontology (GO) analysis reveals that SNRPA is associated with DNA damage repair. Depletion of SNRPA induced ERCC1 exon 8 skipping and reduced ERCC1-XPF complex formation, whereas SNRPA overexpression exerted the opposite effect. siRNAs targeting isoforms containing ERCC1 exon 8 [ERCC1-E8 (+)] reversed SNRPA-enhanced cisplatin resistance and DNA damage repair. Furthermore, the IGF2BP protein, an m6A reader, and the ELAVL1 protein, an RNA stabilizer recruited by IGF2BP1, are found to bind to the SNRPA mRNA. ELAVL1 promoted cisplatin resistance, DNA repair and ERCC1-E8 (+) expression in an SNRPA-dependent manner. In a mouse xenograft model, SNRPA-KO CRISPR enhanced the sensitivity of LUAD cells to cisplatin. Overall, this study illuminates the role of SNRPA in platinum-based drug resistance, thereby providing a novel avenue to potentially enhance chemosensitivity and improve the prognosis of patients with LUAD.

CircIQCH Contributes to the Progression of Breast Cancer by Elevating NFIB Through Decoying miR-139-5p

Circular RNAs (circRNAs) are implicated in the progression of breast cancer (BC). However, the explorations on circRNA IQ motif containing H (circIQCH) in BC progression remain limited. Functional experiments were conducted using in vitro and murine xenograft model assays, respectively. Dual-luciferase reporter assay and RIP assay detected the associations among circIQCH, miR-139-5p, and nuclear factor IB (NFIB). CircIQCH was upregulated in BC, and the silencing of circIQCH repressed BC cell growth, metastasis, and autophagy, arrested cell cycle, promoted cell apoptosis in vitro, and blocked tumor growth in vivo. CircIQCH positively modulated NFIB expression by sponging miR-139-5p. Moreover, the deletion of miR-139-5p abated the action of circIQCH deficiency on BC cell malignant behaviors. Overexpression of miR-139-5p repressed the malignant characteristics of BC cells, while these impacts were abolished by elevating NFIB. Collectively, CircIQCH functioned as an oncogene in BC through upregulating NFIB expression by sponging miR-139-5p.

cNEK6 induces gemcitabine resistance by promoting glycolysis in pancreatic ductal adenocarcinoma via the SNRPA/PPA2c/mTORC1 axis

Resistance to gemcitabine in pancreatic ductal adenocarcinoma (PDAC) leads to ineffective chemotherapy and, consequently, delayed treatment, thereby contributing to poor prognosis. Glycolysis is an important intrinsic reason for gemcitabine resistance as it competitively inhibits gemcitabine activity by promoting deoxycytidine triphosphate accumulation in PDAC. However, biomarkers are lacking to determine which patients can benefit significantly from glycolysis inhibition under the treatment of gemcitabine activity, and a comprehensive understanding of the molecular mechanisms that promote glycolysis in PDAC will contribute to the development of a strategy to sensitize gemcitabine chemotherapy. In this study, we aimed to identify a biomarker that can robustly indicate the intrinsic resistance of PDAC to gemcitabine and guide chemotherapy sensitization strategies. After establishing gemcitabine-resistant cell lines in our laboratory and collecting pancreatic cancer and adjacent normal tissues from gemcitabine-treated patients, we observed that circRNA hsa_circ_0008383 (namely cNEK6) was highly expressed in the peripheral blood and tumor tissues of patients and xenografts with gemcitabine-resistant PDAC. cNEK6 enhanced resistance to gemcitabine by promoting glycolysis in PDAC. Specifically, cNEK6 prevented K48 ubiquitination of small ribonucleoprotein peptide A from the BTRC, a ubiquitin E3 ligase; thus, the accumulated SNRPA stopped PP2Ac translation by binding to its G-quadruplexes in 5' UTR of mRNA. mTORC1 pathway was aberrantly phosphorylated and activated owing to the absence of PP2Ac. The expression level of cNEK6 in the peripheral blood and tumor tissues correlated significantly and positively with the activation of the mTORC1 pathway and degree of glycolysis. Hence, the therapeutic effect of gemcitabine is limited in patients with high cNEK6 levels, and in combination with the mTORC1 inhibitor, rapamycin, can enhance sensitivity to gemcitabine chemotherapy.

Non-coding RNAs in hepatocellular carcinoma metastasis: Remarkable indicators and potential oncogenic mechanism

Non-coding RNAs (ncRNAs), as key regulators involving in intercellular biological processes, are more prominent in many malignancies, especially for hepatocellular carcinoma (HCC). Herein, we conduct a comprehensive review to summarize diverse ncRNAs roles in HCC metastatic mechanism. We focus on four signaling pathways that predominate in HCC metastatic process, including Wnt/β-catenin, HIF-1α, IL-6, and TGF-β pathways. MicroRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) employed different mechanisms to participate in the regulation of the key genes in these pathways, typical as interaction with DNA to control transcription, with RNA to control translation, and with protein to control stability. Therefore, ncRNAs may become potential biomarkers and therapeutic targets for HCC metastasis.

Knockout of the longevity gene Klotho perturbs aging and Alzheimer's disease-linked brain microRNAs and tRNA fragments

Overexpression of the longevity gene Klotho prolongs lifespan, while its knockout shortens lifespan and impairs cognition via perturbation of myelination and synapse formation. However, comprehensive analysis of Klotho knockout effects on mammalian brain transcriptomics is lacking. Here, we report that Klotho knockout alters the levels of aging- and cognition related mRNAs, long non-coding RNAs, microRNAs and tRNA fragments. These include altered neuronal and glial regulators in murine models of aging and Alzheimer's disease and in human Alzheimer's disease post-mortem brains. We further demonstrate interaction of the knockout-elevated tRNA fragments with the spliceosome, possibly affecting RNA processing. Last, we present cell type-specific short RNA-seq datasets from FACS-sorted neurons and microglia of live human brain tissue demonstrating in-depth cell-type association of Klotho knockout-perturbed microRNAs. Together, our findings reveal multiple RNA transcripts in both neurons and glia from murine and human brain that are perturbed in Klotho deficiency and are aging- and neurodegeneration-related.

MiR-339-5p Inhibits Ferroptosis by Promoting Autophagic Degradation of FTH1 Through Targeting ATG7 in Liver Cancer Cells

Background

Liver cancer has a high incidence and mortality rate worldwide, and there is an urgent need to identify new therapeutic strategies and predictive targets to improve the clinical outcomes of advanced liver cancer. Ferroptosis holds promise as a novel strategy for cancer therapy. Epigenetic dysregulation is a hallmark of cancer, and noncoding RNAs are tightly involved in cell fate determination. Therefore, we aimed to identify a novel ferroptosis regulator from aberrantly expressed microRNAs that may serve as a novel biomarker and therapeutic target for liver cancer.

Methods

The expression signature and prognostic value of miR-339 was assessed using TCGA data set. The role of miR-339/ATG7/FTH1 axis in liver cancer cells were evaluated through growth curve, colony formation, 7-AAD staining. The role of miR-339 in regulation of ferroptosis was determined by immunofluorescence staining, flow cytometry, and Elisa kits.

Results

Here, we showed that miR-339 is aberrantly overexpressed in patients with liver cancer. In addition, miR-339 inhibition dramatically suppresses liver cancer progression. Furthermore, miR-339 silencing drives cell death and inhibits liver cancer progression, indicating that miR-339 may serve as a novel ferroptosis suppressor. Mechanistically, we demonstrated that miR-339 targets ATG7 to facilitate the autophagic degradation of FTH1 and prevent ferroptosis in liver cancer cells.

Conclusions

We provide important evidence that the miR-339 inhibition activates of the autophagy pathway to promote ferroptosis by degrading FTH1 in liver cancer cells. We found that miR-339 regulates the balance between ferroptosis and autophagy in liver cancer cells.

Spleen tyrosine kinase facilitates the progression of papillary thyroid cancer regulated by the hsa_circ_0006417/miR-377-3p axis

Papillary thyroid cancer (PTC) is a prevalent malignancy worldwide. Spleen tyrosine kinase (SYK) is a crucial enzyme that participates in various biological processes, including cancer progression. This study aims to uncover the biological function of SYK in PTC. SYK expression patterns in PTC were evaluated using quantitative real time polymerase chain reaction (qRT-PCR), immunohistochemistry (IHC), and western blot. Cell function assays were performed to assess the effects of SYK on PTC. Bioinformatics analysis was conducted to identify intriguing microRNA (miRNA) and circular RNA (circRNA). Dual-Luciferase Reporter or RNA immunoprecipitation assays were used to investigate the correlation among SYK, miR-377-3p, and hsa_circ_0006417. SYK was upregulated in PTC. Overexpression of SYK exhibited a positive correlation with tumor size, lymph node metastasis, and unfavorable disease-free survival. Functional assays revealed that SYK exerted tumorigenic effect on PTC cells through mTOR/4E-BP1 pathway. Mechanistically, hsa_circ_0006417 and miR-377-3p regulated SYK expression, offering modulating its tumor-promoting effects. Collectively, SYK acts as an oncogene in PTC through mTOR/4E-BP1 pathway, which is regulated by the hsa_circ_0006417/miR-377-3p axis, thereby providing a potential alternative for PTC treatment.

Identification of M2-like macrophage-related signature for predicting the prognosis, ecosystem and immunotherapy response in hepatocellular carcinoma

BACKGROUND

Hepatocellular carcinoma is one of the most common malignancies worldwide, representing a big health-care challenge globally. M2-like macrophages are significantly correlated with tumor progression, metastasis and treatment resistance.

METHODS

Integrative 10 machine learning algorithms were performed to developed a M2-like macrophage related prognostic signature (MRPS). Single-cell RNA-sequencing analysis was performed to dissect the ecosystem of HCC. Several approaches, including TIDE score, immunophenoscore, TMB score and tumor escape score were used to evaluate the predictive role of MRPS in immunology response.

RESULTS

The optimal MRPS constructed by the combination of stepCox + superPC algorithm served as an independent risk factor and showed stable and powerful performances in predicting the overall survival rate of HCC patients with 2-, 3-, and 4-year AUCs of 0. 763, 0.751, and 0.699 in TCGA cohort. HCC patients with low risk score possessed a more interaction of immunoactivated cells, including NK, CD8+ cytotoxic T, and activated B, and a less interaction of immunosuppressive cells, including Treg, CD4+ exhauster T, and M2-like macrophage. Low risk score indicated a higher PD1&CTLA4 immunophenoscore, higher TMB score, lower TIDE score and lower tumor escape score in HCC, suggesting a better immunotherapy response. The IC50 value of docetaxel, gemcitabine, crizotinib and Osimertinib in HCC with high risk score were lower versus that with low risk score. HCC patients with high risk score had a higher score of cancer-related hallmarks, including angiogenesis, DNA repair, EMT, glycolysis, and NOTCH signaling.

CONCLUSION

Our study proposed a novel MRPS for predicting the prognosis, ecosystem and immunotherapy response in HCC.

Heterogeneity characterization of hepatocellular carcinoma based on the sensitivity to 5-fluorouracil and development of a prognostic regression model

Background: 5-Fluorouracil (5-FU) is a widely used chemotherapeutic drug in clinical cancer treatment, including hepatocellular carcinoma (HCC). A correct understanding of the mechanisms leading to a low or lack of sensitivity of HCC to 5-FU-based treatment is a key element in the current personalized medical treatment. Methods: Weighted gene co-expression network analysis (WGCNA) was used to analyze the expression profiles of the cancer cell line from GDSC2 to identify 5-FU-related modules and hub genes. According to hub genes, HCC was classified and the machine learning model was developed by ConsensusClusterPlus and five different machine learning algorithms. Furthermore, we performed quantitative reverse transcription-polymerase chain reaction (qRT-PCR) analysis on the genes in our model. Results: A total of 19 modules of the cancer cell line were divided by WGCNA, and the most negative correlation with 5-FU was the midnight blue module, from which 45 hub genes were identified. HCC was divided into three subgroups (C1, C2, and C3) with significant overall survival (OS) differences. OS of C1 was the shortest, which was characterized by a high clinical grade and later T stage and stage. OS of C3 was the longest. OS of C2 was between the two subtypes, and its immune infiltration was the lowest. Five out of 45 hub genes, namely, TOMM40L, SNRPA, ILF3, CPSF6, and NUP205, were filtered to develop a risk regression model as an independent prognostic indicator for HCC. The qRT-PCR results showed that TOMM40L, SNRPA, ILF3, CPSF6, and NUP205 were remarkably highly expressed in hepatocellular carcinoma. Conclusion: The HCC classification based on the sensitivity to 5-FU was in line with the prognostic differences observed in HCC and most of the genomic variation, immune infiltration, and heterogeneity of pathological pathways. The regression model related to 5-FU sensitivity may be of significance in individualized prognostic monitoring of HCC.

Hsa_circ_0008500 inhibits apoptosis of adipose-derived stem cells under high glucose through hsa-miR-1273h-5p/ELK1 axis

Preliminary researches have confirmed that the number of apoptosis of adipose tissue-derived stem cells (ADSCs) in patients with diabetes is significantly increased, leading to a difficult healing wound. Increasing researches revealed that circular RNAs (circRNAs) can control apoptosis. However, it is still unclear whether and how circRNAs are critical for regulating ADSCs apoptosis. In this study, we utilized in vitro model in which ADSCs were cultivated with normal glucose (NG) (5.5 mM) or high glucose (HG) (25 mM) medium, respectively, and found that more apoptotic ADSCs were observed in HG medium comparing to ADSCs in NG medium. Furthermore, we found that hsa_circ_0008500 attenuated HG-mediated ADSCs apoptosis. In addition, Hsa_circ_0008500 could directly interact with hsa-miR-1273h-5p, acting as a miRNA sponge, which subsequently suppressed Ets-like protein-1(ELK1) expression, the downstream target of hsa-miR-1273h-5p. Thus, these results indicated that targeting the hsa_circ_0008500/hsa-miR-1273h-5p/ELK1 signaling pathway in ADSCs may be a potential target for repairing diabetic wounds.

Nanoparticles Mediated circROBO1 Silencing to Inhibit Hepatocellular Carcinoma Progression by Modulating miR-130a-5p/CCNT2 Axis

BACKGROUND

Circular RNAs (circRNAs) are becoming vital biomarkers and therapeutic targets for malignant tumors due to their high stability and specificity in tissues. However, biological functions of circRNAs in hepatocellular carcinoma (HCC) are still not well studied.

METHODS

Gene Expression Omnibus (GEO) database and qRT-PCR were used to evaluate expression of circROBO1 (hsa_circ_0066568) in HCC tissues and cell lines. CCK-8, colony formation, EdU staining, flow cytometry for cell cycle analysis, and xenograft model assays were performed to detect the circROBO1 function in vitro and in vivo. RNA pull-down, RNA immunoprecipitation (RIP), and Luciferase reporter assays were used to investigate the relationship among circROBO1, miR-130a-5p, and CCNT2. More importantly, we developed nanoparticles made from poly lactic-co-glycolic acid (PLGA) and polyethylene glycol (PEG) chains as the delivery system of si-circROBO1 and then applied them to HCC in vitro and in mice.

RESULTS

circROBO1 was obviously upregulated in HCC tissues and cell lines, and elevated circROBO1 was closely correlated with worse prognosis for HCC patients. Functionally, knocking down circROBO1 significantly suppressed HCC cells growth in vitro and in mice. Mechanistically, circROBO1 acted as a competing endogenous RNA to downregulate miR-130a-5p, leading to CCNT2 expression upregulation. Furthermore, miR-130a-5p mimic or CCNT2 knockdown reversed the role of circROBO1 overexpression on HCC cells, which demonstrated that circROBO1 promoted HCC development via miR-130a-5p/CCNT2 axis. In addition, we developed nanoparticles loaded with si-circROBO1, named as PLGA-PEG (si-circROBO1) NPs, which significantly prevented the proliferation of HCC cells, and did not exhibit apparent toxicity to major organs in vivo.

CONCLUSION

Our findings firstly demonstrate that circROBO1 overexpression promotes HCC progression by regulating miR-130a-5p/CCNT2 axis, which may serve as an effective nanotherapeutic target for HCC treatment.