Functional consequences of PRPF39 on distant genes and cisplatin sensitivity

Prognostic implications of alternative splicing events and key splicing factors in head and neck squamous cell carcinoma

The incidence of head and neck squamous cell carcinoma (HNSCC) remains high, accompanied by low 5-year survival rates. Identifying prognostic factors is essential for advancing personalized treatment approaches. Increasing evidence implicates aberrant alternative splicing (AS) plays a key role in tumor progression. Utilizing data from TCGA and TCGA SpliceSeq, prognosis-associated AS events were identified through Cox regression analysis. A prognostic risk model was developed via multivariate Cox and LASSO regression, with validation conducted using Kaplan-Meier survival analysis and ROC curve analysis. The correlation between splicing factors (SFs) and prognosis-associated AS events was analyzed using Pearson's method, followed by the construction of an SF-AS regulatory network. Key splicing factors (KSFs) were identified using Cytoscape software. Expression of KSFs in HNSCC was confirmed by quantitative PCR and Western blotting. SiRNA-mediated knockdown in HNSCC cell lines (HONE1, HN4, SAS) demonstrated effects on cell proliferation, invasion, and migration, as assessed by CCK8, colony formation, Transwell, and wound healing assays. Tumor growth was further evaluated in a subcutaneous tumor model in vivo. A total of 2347 survival-related AS events were identified, of which eleven were used to construct the prognostic model. Patients in the low-risk group exhibited significantly improved outcomes (P = 0e + 00), underscoring the model's predictive accuracy. Notably, DDX39B and PRPF39 emerged as key splicing factors, exhibiting high expression in HNSCC and correlating with poor prognosis, positioning them as potential biomarkers and therapeutic targets.

Circular RNAs in hepatocellular carcinoma: Recent advances

Circular RNAs (circRNAs) have covalently closed loop structures at both ends, exhibiting characteristics dissimilar to those of linear RNAs. Emerging evidence suggests that aberrantly expressed circRNAs play crucial roles in hepatocellular carcinoma (HCC) by affecting the proliferation, apoptosis and invasive capacity of HCC cells. Certain circRNAs may be used as biomarkers to diagnose and predict the prognosis of HCC. Therefore, circRNAs are expected to become novel biomarkers and therapeutic targets for HCC. Herein, we briefly review the characteristics and biological functions of circRNAs, focusing on their roles in HCC to provide new insights for the early diagnosis and targeted therapy of HCC.

Cytotoxic capability and the associated proteomic profile of cell-free coelomic fluid extracts from the edible sea cucumber Holothuria tubulosa on HepG2 liver cancer cells

Hepatocellular carcinoma (HCC) is an aggressive cancer histotype and one of the most common types of cancer worldwide. The identification of compounds that might intervene to restrain neoplastic cell growth appears imperative due to its elevated overall mortality. The marine environment represents a reservoir rich in bioactive compounds in terms of primary and secondary metabolites produced by aquatic animals, mainly invertebrates. In the present study, we determined whether the water-soluble cell-free extract of the coelomic fluid (CFE) of the edible sea cucumber Holothuria tubulosa could play an anti-HCC role in vitro by analyzing the viability and locomotory behavior, cell cycle distribution, apoptosis and autophagy modulation, mitochondrial function and cell redox state of HepG2 HCC cells. We showed that CFE causes an early block in the cell cycle at the G2/M phase, which is coupled to oxidative stress promotion, autophagosome depletion and mitochondrial dysfunction ultimately leading to apoptotic death. We also performed a proteomic analysis of CFE identifying a number of proteins that are seemingly responsible for anti-cancer effects. In conclusion, H. tubulosa's CFE merits further investigation to develop novel promising anti-HCC prevention and/or treatment agents and also beneficial supplements for formulation of functional foods and food packaging material.

Pan-drug and drug-specific mechanisms of 5-FU, irinotecan (CPT-11), oxaliplatin, and cisplatin identified by comparison of transcriptomic and cytokine responses of colorectal cancer cells

Colorectal cancer (CRC) caused over 900,000 deaths worldwide in 2020. A majority of late-stage CRC patients are treated with 5-fluorouracil (5-FU) combined with either irinotecan (CPT-11), oxaliplatin, or both. Despite their widespread use, the mechanisms of efficacy and toxicity of these drugs remain incompletely understood. While previous work has investigated cellular responses to these agents individually, we directly compare the transcriptomic and cytokine profiles of HCT116 wild-type and p53-/- colorectal cancer cells treated with these drugs and report pan-drug, drug-specific, drug class-specific, p53-independent, and p53-dependent signatures. We observed downregulation of histone genes by 5-FU (that significantly correlates with improved survival in CRC patients) and upregulation of FOS and ATF3 by oxaliplatin (which may contribute to peripheral neuropathy). BTG2 was identified as a top gene upregulated by all four drugs, suggesting its critical role in the cellular response to chemotherapy in CRC. Soluble TRAILR2 (death receptor 5; DR5) is a decoy receptor for TRAIL, an apoptosis-inducing cytokine. TRAILR2 was down-regulated by oxaliplatin and 5-FU, was not affected by CPT-11, and was increased by cisplatin. There was an increase in IL-8 by oxaliplatin and increase in ferritin by cisplatin which may contribute to cancer cell survival. Novel drug-specific mechanisms of efficacy or toxicity identified in these signatures may be targeted with combination therapies or development of new targeted therapies. Together, the findings here contribute to our understanding of the molecular bases of efficacy and toxicity of chemotherapeutic agents often used for treatment of GI cancer such as CRC.

Hsa‑circRNA‑G004213 promotes cisplatin sensitivity by regulating miR‑513b‑5p/PRPF39 in liver cancer

In recent years, increasing evidence has confirmed that exosomal circular RNAs (circRNAs) serve a crucial role in the prognostic prediction and diagnosis of liver cancer (LC). The present study compared the expression patterns of exosomal circRNAs during transarterial chemoembolization (TACE). CircRNA sequencing analysis identified 390 differentially expressed circRNAs between the prior TACE and following the first TACE operation groups and 489 differentially expressed circRNAs between the prior to TACE and following the second TACE operation groups. Gene Ontology analysis of the differentially expressed circRNAs demonstrated that they were associated with fatty acid metabolism, receptor binding and membrane protein complexes. Kyoto Encyclopedia of Genes and Genomes pathway analysis predicted that protein digestion and absorption pathways were activated following TACE. A novel gene was screened out; hsa‑circRNA‑G004213 (circ‑G004213) was significantly upregulated following TACE (fold change >10, P < 0.01). Further analysis found circ‑G004213 significantly increased the cisplatin sensitivity of HepG2 cells and positively associated with the prognosis of tumor‑bearing mice. Based on the potential downstream miRNAs and mRNAs, the circRNA‑miRNA‑mRNA network was constructed. It was demonstrated that circ‑G004213 regulated cisplatin resistance via the miR‑513b‑5p/PRPF39 axis. Finally, the present study confirmed that circ‑G004213 was positively associated with the prognosis of patients with LC following TACE. Therefore, circ‑G004213 may be used as an indicator for predicting the efficacy of TACE.

Identification of cancer-related potential biomarkers based on lncRNA-pseudogene-mRNA competitive networks

Accumulating evidence indicates that mRNAs and noncoding RNAs act as competitive endogenous RNAs (ceRNAs) and play a key role in tumorigenesis. However, the complex competitive relationship among genes remains unknown. In the present study, the long noncoding RNAs (lncRNAs), pseudogenes and mRNAs that compete with common microRNAs are defined as lncRNA-pseudogene-mRNA competitive triples. We find that some candidate ceRNAs, modules and triples are associated with cancers and can significantly divide patients into high-risk and low-risk groups; thus, they may serve as potential cancer biomarkers. In sum, the present study systematically analyzes the association between competitive triples and cancer, which provides a reference for a deeper understanding of cancer progression.

Regulation of protein-coding gene and long noncoding RNA pairs in liver of conventional and germ-free mice following oral PBDE exposure

Gut microbiome communicates with the host liver to modify hepatic xenobiotic biotransformation and nutrient homeostasis. Polybrominated diphenyl ethers (PBDEs) are persistent environmental contaminants that are detected in fatty food, household dust, and human breast milk at worrisome levels. Recently, long noncoding RNAs (lncRNAs) have been recognized as novel biomarkers for toxicological responses and may regulate the transcriptional/translational output of protein-coding genes (PCGs). However, very little is known regarding to what extent the interactions between PBDEs and gut microbiome modulate hepatic lncRNAs and PCGs, and what critical signaling pathways are impacted at the transcriptomic scale. In this study, we performed RNA-Seq in livers of nine-week-old male conventional (CV) and germ-free (GF) mice orally exposed to the most prevalent PBDE congeners BDE-47 and BDE-99 (100 μmol/kg once daily for 4-days; vehicle: corn oil, 10 ml/kg), and unveiled key molecular pathways and PCG-lncRNA pairs targeted by PBDE-gut microbiome interactions. Lack of gut microbiome profoundly altered the PBDE-mediated transcriptomic response in liver, with the most prominent effect observed in BDE-99-exposed GF mice. The top pathways up-regulated by PBDEs were related to xenobiotic metabolism, whereas the top pathways down-regulated by PBDEs were in lipid metabolism and protein synthesis in both enterotypes. Genomic annotation of the differentially regulated lncRNAs revealed that majority of these lncRNAs overlapped with introns and 3'-UTRs of PCGs. Lack of gut microbiome profoundly increased the percentage of PBDE-regulated lncRNAs mapped to the 3'-UTRs of PCGs, suggesting the potential involvement of lncRNAs in increasing the translational efficiency of PCGs by preventing miRNA-3'-UTR binding, as a compensatory mechanism following toxic exposure to PBDEs. Pathway analysis of PCGs paired with lncRNAs revealed that in CV mice, BDE-47 regulated nucleic acid and retinol metabolism, as well as circadian rhythm; whereas BDE-99 regulated fatty acid metabolism. In GF mice, BDE-47 differentially regulated 19 lncRNA-PCG pairs that were associated with glutathione conjugation and transcriptional regulation. In contrast, BDE-99 up-regulated the xenobiotic-metabolizing Cyp3a genes, but down-regulated the fatty acid-metabolizing Cyp4 genes. Taken together, the present study reveals common and unique lncRNAs and PCG targets of PBDEs in mouse liver, and is among the first to show that lack of gut microbiome sensitizes the liver to toxic exposure of BDE-99 but not BDE-47. Therefore, lncRNAs may serve as specific biomarkers that differentiate various PBDE congeners as well as environmental chemical-mediated dysbiosis. Coordinate regulation of PCG-lncRNA pairs may serve as a more efficient molecular mechanism to combat against xenobiotic insult, and especially during dysbiosis-induced increase in the internal dose of toxicants.

Generation and characterization of transgene-free human induced pluripotent stem cells and conversion to putative clinical-grade status

Introduction

The reprogramming of a patient’s somatic cells back into induced pluripotent stem cells (iPSCs) holds significant promise for future autologous cellular therapeutics. The continued presence of potentially oncogenic transgenic elements following reprogramming, however, represents a safety concern that should be addressed prior to clinical applications. The polycistronic stem cell cassette (STEMCCA), an excisable lentiviral reprogramming vector, provides, in our hands, the most consistent reprogramming approach that addresses this safety concern. Nevertheless, most viral integrations occur in genes, and exactly how the integration, epigenetic reprogramming, and excision of the STEMCCA reprogramming vector influences those genes and whether these cells still have clinical potential are not yet known.

Methods

In this study, we used both microarray and sensitive real-time PCR to investigate gene expression changes following both intron-based reprogramming and excision of the STEMCCA cassette during the generation of human iPSCs from adult human dermal fibroblasts. Integration site analysis was conducted using nonrestrictive linear amplification PCR. Transgene-free iPSCs were fully characterized via immunocytochemistry, karyotyping and teratoma formation, and current protocols were implemented for guided differentiation. We also utilized current good manufacturing practice guidelines and manufacturing facilities for conversion of our iPSCs into putative clinical grade conditions.

Results

We found that a STEMCCA-derived iPSC line that contains a single integration, found to be located in an intronic location in an actively transcribed gene, PRPF39, displays significantly increased expression when compared with post-excised stem cells. STEMCCA excision via Cre recombinase returned basal expression levels of PRPF39. These cells were also shown to have proper splicing patterns and PRPF39 gene sequences. We also fully characterized the post-excision iPSCs, differentiated them into multiple clinically relevant cell types (including oligodendrocytes, hepatocytes, and cardiomyocytes), and converted them to putative clinical-grade conditions using the same approach previously approved by the US Food and Drug Administration for the conversion of human embryonic stem cells from research-grade to clinical-grade status.

Conclusion

For the first time, these studies provide a proof-of-principle for the generation of fully characterized transgene-free human iPSCs and, in light of the limited availability of current good manufacturing practice cellular manufacturing facilities, highlight an attractive potential mechanism for converting research-grade cell lines into putatively clinical-grade biologics for personalized cellular therapeutics.

Genetic and epigenetic variants contributing to clofarabine cytotoxicity

2-chloro-2-fluoro-deoxy-9-D-arabinofuranosyladenine (Clofarabine), a purine nucleoside analog, is used in the treatment of hematologic malignancies and as induction therapy for stem cell transplantation. The discovery of pharmacogenomic markers associated with chemotherapeutic efficacy and toxicity would greatly benefit the utility of this drug. Our objective was to identify genetic and epigenetic variants associated with clofarabine toxicity using an unbiased, whole genome approach. To this end, we employed International HapMap lymphoblastoid cell lines (190 LCLs) of European (CEU) or African (YRI) ancestry with known genetic information to evaluate cellular sensitivity to clofarabine. We measured modified cytosine levels to ascertain the contribution of genetic and epigenetic factors influencing clofarabine-mediated cytotoxicity. Association studies revealed 182 single nucleotide polymorphisms (SNPs) and 143 modified cytosines associated with cytotoxicity in both populations at the threshold P ≤ 0.0001. Correlation between cytotoxicity and baseline gene expression revealed 234 genes at P ≤ 3.98 × 10(-6). Six genes were implicated as: (i) their expression was directly correlated to cytotoxicity, (ii) they had a targeting SNP associated with cytotoxicity, and (iii) they had local modified cytosines associated with gene expression and cytotoxicity. We identified a set of three SNPs and three CpG sites targeting these six genes explaining 43.1% of the observed variation in phenotype. siRNA knockdown of the top three genes (SETBP1, BAG3, KLHL6) in LCLs revealed altered susceptibility to clofarabine, confirming relevance. As clofarabine's toxicity profile includes acute kidney injury, we examined the effect of siRNA knockdown in HEK293 cells. siSETBP1 led to a significant change in HEK293 cell susceptibility to clofarabine.