Long noncoding RNA LINC01234 promotes hepatocellular carcinoma progression through orchestrating aspartate metabolic reprogramming

IGF2BP1/AIFM2 axis regulates ferroptosis and glycolysis to drive hepatocellular carcinoma progression

BACKGROUND

Hepatocellular carcinoma (HCC) is aggressive liver tumor that is the third leading cause of cancer death. Ferroptosis and glycolysis play key roles in HCC progression. Apoptosis-inducing factor mitochondria-associated 2 (AIFM2) in involved in regulating ferroptosis and glycolysis in cancers, but its role in HCC remains unclear. This research explored the function of AIFM2 in HCC.

METHODS

AIFM2 expression in HCC tissues was evaluated using the UALCAN and GEPIA databases, as well as RT-qPCR. Kaplan-Meier survival analysis analyzed the correlation between AIFM2 and the prognosis of HCC patients. EdU and transwell assays were utilized to examine HCC cell proliferation, migration, and invasion. Ferroptosis markers were analyzed by measuring iron levels, ROS production (DCFH-DA assay), and oxidative stress indicators (SOD, MDA, and GSH). Glycolytic activity was assessed through glucose uptake, lactate production, and ATP levels. m6A modification on AIFM2 mRNA was confirmed by MeRIP assay, and mRNA stability was evaluated with Actinomycin D treatment. Tumor growth and metastasis were studied in xenograft and lung metastasis models.

RESULTS

UALCAN analysis showed that AIFM2 was significantly upregulated in HCC tissues, which correlated with poor survival rates of HCC patients. IGF2BP1 was also highly expressed in HCC tissues and positively correlated with AIFM2 levels in HCC tissues. Functionally, AIFM2 knockdown suppressed glycolysis and enhanced ferroptosis, while its overexpression had opposite effects. IGF2BP1 was found to stabilize AIFM2 mRNA via m6A modification, promoting AIFM2 expression. IGF2BP1 knockdown reduced glycolysis, proliferation, and invasion while promoting ferroptosis, while AIFM2 overexpression could reverse this effect. In vivo, IGF2BP1 or AIFM2 silencing significantly suppressed tumor growth and metastasis.

CONCLUSION

IGF2BP1 stabilized AIFM2 mRNA to regulate ferroptosis and glycolysis and promoted HCC progression.

A review of molecular interplay between inflammation and cancer: The role of lncRNAs in pathogenesis and therapeutic potential

The inflammatory microenvironment (IME) has been demonstrated to facilitate the initiation and progression of tumors throughout the inflammatory process. Simultaneously, cancer can initiate or intensify the inflammatory response, thereby promoting tumor progression. This review examines the dual role of long non-coding RNAs (lncRNAs) in the interplay between inflammation and cancer. LncRNA modulate inflammation-induced cancer by influencing the activation of signaling pathways (NF-κB, Wnt/β-catenin, mTOR, etc), microRNA (miRNA) sponging, protein interactions, interactions with immune cells, and encoding short peptides. In contrast, lncRNAs also impact cancer-induced inflammatory processes by regulating cytokine expression, mediating tumor-derived extracellular vesicles (EVs), modulating intracellular reactive oxygen species (ROS) levels, and facilitating metabolic reprogramming. Furthermore, the therapeutic potential of lncRNA and the challenges of clinical translation were explicitly discussed as well. Overall, this review aims to provide a comprehensive and systematic resource for future researchers investigating the impact of lncRNAs on inflammation and cancer.

ZNF384 and m6A methylation promote the progression of hepatocellular carcinoma by regulating the interaction between LINC00342 and DAPK1

Hepatocellular carcinoma (HCC) is a malignant tumor with high morbidity and mortality. Many lncRNAs play important regulatory roles in the pathogenesis of HCC, but the mechanism of action of LINC00342 in the progression of HCC remains unclear. In this study, we assessed 24 pairs of HCC tissues and adjacent normal tissues as well as HCC cells and a nude mouse model of HCC. Gene and protein expression was evaluated by flow cytometry, CCK-8, RIP, colony formation assay, and TUNEL staining. This study revealed that LINC00342 was highly expressed in HCC tissues and cells. LINC00342 knockdown significantly inhibited the proliferation and migration of HCC cells, promoted apoptosis, inhibited tumor growth in vivo, and increased the sensitivity of HCC cells to cisplatin. The opposite effect was observed in LINC00342-overexpressing cells. Mechanistically, ZNF384 and m6A methylation can promote the transcription and stability of LINC00342, and LINC00342 can bind to DAPK1, which inhibits Cyt C release and the activation of caspase family proteins to accelerate HCC progression. Our study indicated that the inhibition of LINC00342 expression may represent a new breakthrough for HCC treatment.

Identifying Genes Associated with the Anticancer Activity of a Fluorinated Chalcone in Triple-Negative Breast Cancer Cells Using Bioinformatics Tools

Fluorinated chalcones are molecules reported to possess potent anticancer properties against triple-negative breast cancer (TNBC) cells. However, their molecular mechanisms have not yet been fully explored. Using bioinformatics tools, we analyzed the transcriptomes of MDA-MB-231 cells treated with either a novel fluorinated chalcone (compound 3) or a control in order to identify differentially expressed (DE) genes associated with its anticancer activity and determine the biological processes in which these genes are involved. A fluorinated chalcone was synthesized using the Claisen-Schmidt method. The transcriptome of MDA-MB-231 cells was then analyzed on an Illumina NextSeq500, and DE genes with significant changes in expression were identified using the DESeq2 v1.38.0 bioinformatics tool under the strict detection criteria of |log2FC| ≥  2 and adjusted p < 0.05. We identified 504 DE genes, which were enriched in terms related to "regulation of cell death", "cation transport", "response to topologically incorrect proteins", and "response to unfolded proteins". Surprisingly, these genes were involved in "the HSF1-dependent transactivation pathway" and "the attenuation phase pathway". This bioinformatics-based study suggests that the tested fluorinated chalcone could influence HSF-1 silencing in addition to promoting the up-regulation of several genes involved in stress-induced apoptosis. Therefore, the tested compound could have enormous potential as a novel approach for TNBC treatment.

Low-intensity pulsed ultrasound affects proliferation and migration of human hepatocellular carcinoma cells

PURPOSE

Low-intensity pulsed ultrasound (LIPUS) is an effective ancillary treatment modality for various malignancies. However, the mechanisms underlying the role of LIPUS in cancer treatment have not been fully elucidated. We investigated the effects and underlying mechanism of LIPUS on the proliferation, apoptosis, migration, and invasion of hepatocellular carcinoma (HCC) cells.

METHODS

The HCC cell lines SMMC7721 and HCCLM3 were exposed to 1 MHz LIPUS at intensities of 0.5, 1.0, 1.5 W/cm2 for 60 s. Cell morphology, viability, apoptosis, colony formation, migration, and invasion were assessed. Intracellular reactive oxygen species (ROS) levels and mitochondrial membrane potential were evaluated using a ROS assay kit and a JC-1 staining kit. Western blotting was performed to quantify changes in matrix metallopeptidases and epithelial-mesenchymal transition-related proteins. Orthotopic Hep3B-Luc tumor-bearing mice were treated with LIPUS at 1.5 W/cm2 or 0 W/cm2 and growth trend was measured.

RESULTS

The results showed that different intensities of ultrasound affected cellular activity, inhibited cell proliferation and cloning, facilitated intracellular cytoskeletal protein reorganization, and induced cell apoptosis, particularly at the intensity of 1.5 W/cm2, through the ROS/mitochondria pathway. LIPUS enhanced SMCC7721 and HCCLM3 cell migration and invasion in a dose-dependent manner by regulating matrix metallopeptidases and epithelial-mesenchymal transition-related proteins. In vivo experiments confirmed the inhibitory effect of LIPUS at 1.5 W/cm2 on tumor growth.

CONCLUSIONS

Although LIPUS induced cell apoptosis and inhibited cell proliferation, it also promoted the invasion and metastasis of HCC cells under certain conditions, which was related to the regulation of matrix metallopeptidases and epithelial-mesenchymal transition-related proteins.

Long non-coding RNA LINC01532 sustains redox homeostasis and accelerates lenvatinib resistance in hepatocellular carcinoma

INTRODUCTION

Lenvatinib is the first-line therapy of hepatocellular carcinoma (HCC) and the high frequency of lenvatinib resistance hinders the improvement of HCC treatment. Since NADPH plays vital roles in antioxidant defense and reductive biosynthesis, cancer cells exert NADPH metabolic adaptation to support their malignant activities, including drug resistance. However, the underlying mechanisms need to be further studied.

OBJECTIVES

This study aims to delineate the latent mechanism by which HCC cells modulate NADPH metabolic adaptation and lenvatinib resistance.

METHODS

Using high-throughput screening, we screened LINC01532 as a critical regulator in NADPH metabolic adaptation. The function of LINC01532 in drug resistance of HCC cells was analyzed by in vitro and in vivo model. NADPH assay, malondialdehyde (MDA) assay, and glutathione (GSH) detection assay were carried out to explore the role of LINC01532 in NADPH metabolism. Furthermore, RNA-binding protein immunoprecipitation, RNA pull-down assay, co-immunoprecipitation, and chromatin immunoprecipitation experiments were utilized to uncover the underlying mechanisms.

RESULTS

High expression of LINC01532 predicted poorer prognosis in HCC patients. LINC01532 stimulated NADPH production and blunted lenvatinib-induced cell death, leading to drug resistance. Mechanistically, LINC01532 bound to hnRNPK and promoted CDK2-mediated phosphorylation of hnRNPK, which facilitated G6PD pre-mRNA splicing, resulting in high expression of G6PD and upregulated NADPH synthesis. The elevated NADPH cleared reactive oxygen species (ROS), supported biomass synthesis, and epigenetically modulated gene expression. Inhibition of LINC01532 significantly enhanced lenvatinib sensitivity of HCC cells. The m6A modification induced by mTORC1 promoted the expression of LINC01532 in HCC cells.

CONCLUSION

Collectively, our findings demonstrate that LINC01532 confers lenvatinib resistance of HCC cells by modulating NADPH metabolic adaptation. LINC01532 might be a prognostic or therapeutic target for HCC.

The Mechanism of TRIM21 Inhibiting the Invasion and Migration of ccRCC by Stabilizing ASS1

Clear cell renal cell carcinoma (ccRCC) is characterized by its aggressive invasion and metastasis, presenting significant clinical challenges. Gaining insights into the molecular mechanisms underlying its progression is crucial for the development of effective therapeutic strategies. Addressing a critical knowledge gap in understanding ccRCC tumorigenesis, this study aims to elucidate the expression patterns of TRIM21 in ccRCC, unravel its impact on ccRCC patient prognosis, and investigate the regulatory role of TRIM21 in ASS1 expression and urea cycle dysregulation within the context of ccRCC. The results demonstrate that TRIM21 is downregulated in ccRCC, and low expression of TRIM21 predicts an unfavorable prognosis for ccRCC patients. Furthermore, the upregulation of TRIM21 can inhibit the migration and invasion of ccRCC cells by regulating the ubiquitination modification of ASS1. This not only expands the functional role of TRIM21 in ccRCC tumorigenesis but also demonstrates its ability to reverse urea cycle dysregulation through stabilizing ASS1 expression. Specifically, abnormal downregulation of TRIM21 in ccRCC reduces K63 ubiquitination modification of ASS1, leading to decreased stability of the ASS1 protein, aggravated urea cycle dysregulation, and facilitated migration and invasion of ccRCC cells. Additionally, reduction in ASS1 reverses the depressed migration and invasion caused by overexpression of TRIM21 in ccRCC cells. In summary, our findings contribute to a deeper understanding of the functional role played by TRIM21 in ccRCC progression, pinpoint a unique and novel regulatory mechanism involving ectopic downregulation-mediated ASS1 ubiquitination modification and urea cycle dysfunction during ccRCC progression, and provide fresh insights for further investigation into the pathogenesis and metabolic reprogramming associated with ccRCC.

Noncoding RNA, friend or foe for nephrolithiasis?

Nephrolithiasis is one of the most common diseases in urology, characterized by notable incidence and recurrence rates, leading to significant morbidity and financial burden. Despite its prevalence, the precise mechanisms underlying stone formation remain incompletely understood, thus hindering significant advancements in kidney stone management over the past three decades. Investigating the pivotal biological molecules that govern stone formation has consistently been a challenging and high-priority task. A significant portion of mammalian genomes are transcribed into noncoding RNAs (ncRNAs), which have the ability to modulate gene expression and disease progression. They are thus emerging as a novel target class for diagnostics and pharmaceutical exploration. In recent years, the role of ncRNAs in stone formation has attracted burgeoning attention. They have been found to influence stone formation by regulating ion transportation, oxidative stress injury, inflammation, osteoblastic transformation, autophagy, and pyroptosis. These findings contributes new perspectives on the pathogenesis of nephrolithiasis. To enhance our understanding of the diagnostic and therapeutic potential of nephrolithiasis-associated ncRNAs, we summarized the expression profiles, biological functions, and clinical significance of these ncRNAs in the current review.

LncRNA-HMG incites colorectal cancer cells to chemoresistance via repressing p53-mediated ferroptosis

Upon chemotherapy, excessive reactive oxygen species (ROS) often lead to the production of massive lipid peroxides in cancer cells and induce cell death, namely ferroptosis. The elimination of ROS is pivotal for tumor cells to escape from ferroptosis and acquire drug resistance. Nevertheless, the precise functions of long non-coding RNAs (lncRNAs) in ROS metabolism and tumor drug-resistance remain elusive. In this study, we identify LncRNA-HMG as a chemoresistance-related lncRNA in colorectal cancer (CRC) by high-throughput screening. Abnormally high expression of LncRNA-HMG predicts poorer prognosis in CRC patients. Concurrently, we found that LncRNA-HMG protects CRC cells from ferroptosis upon chemotherapy, thus enhancing drug resistance of CRC cells. LncRNA-HMG binds to p53 and facilitates MDM2-mediated degradation of p53. Decreased p53 induces upregulation of SLC7A11 and VKORC1L1, which contribute to increase the supply of reducing agents and eliminate excessive ROS. Consequently, CRC cells escape from ferroptosis and acquire chemoresistance. Importantly, inhibition of LncRNA-HMG by anti-sense oligo (ASO) dramatically sensitizes CRC cells to chemotherapy in patient-derived xenograft (PDX) model. LncRNA-HMG is also a transcriptional target of β-catenin/TCF and activated Wnt signals trigger the marked upregulation of LncRNA-HMG. Collectively, these findings demonstrate that LncRNA-HMG promotes CRC chemoresistance and might be a prognostic or therapeutic target for CRC.

Inhibiting lncRNA NEAT1 Increases Glioblastoma Response to TMZ by Reducing Connexin 43 Expression

OBJECTIVES

Glioblastoma multiforme (GBM) is considered the most assailant subtype of gliomas, presenting a formidable obstacle because of its inherent resistance to temozolomide (TMZ). This study aimed to characterize the function of lncRNA NEAT1 in facilitating the advancement of gliomas.

METHODS

The expression level of NEAT1 in glioma tissues and cells was detected by qRT-PCR. RNA interference experiment, cell proliferation assay, FITC/PI detection assay, immunoblotting, bioinformatics prediction, a double luciferase reporter gene assay, RNA immunoprecipitation (RIP) assay, SLDT assay and correlation analysis of clinical samples were performed to explore the regulatory effects of NEAT1, miR-454-3p and Cx43 and their role in malignant progression of GBM. The role of NEAT1 in vivo was investigated by an intracranial tumor formation experiment in mice.

RESULTS

The results showed that recurring gliomas displayed elevated levels of NEAT1 compared to primary gliomas. The suppression of NEAT1 led to a restoration of sensitivity in GBM cells to TMZ. NEAT1 functioned as a competitive endogenous RNA against miR-454-3p. Connexin 43 was identified as a miR-454-3p target. NEAT1 was found to regulate gap junctional intercellular communication by modulating Connexin 43, thereby impacting the response of GBM cells to TMZ chemotherapy. Downregulation of NEAT1 resulted in enhanced chemosensitivity to TMZ and extended the survival of mice.

CONCLUSIONS

Overall, these results indicated that the NEAT1/miR-454-3p/Connexin 43 pathway influences GBM cell response to TMZ and could offer a potential new strategy for treating GBM.

FOXM1 Upregulates O-GlcNAcylation Level Via The Hexosamine Biosynthesis Pathway to Promote Angiogenesis in Hepatocellular Carcinoma

Hepatocellular carcinoma (HCC) presents significant challenges in treatment and prognosis because of its aggressive nature and high metastatic potential. This study aims to investigate the role of the hexosamine biosynthesis pathway (HBP) and its association with HCC progression and prognosis. We identified SPP1 and FOXM1 as hub genes within the HBP pathway, showing their correlation with poor prognosis and late-stage progression. In addition, the analysis uncovered the complex participation of the HBP pathway in nutrients and oxygen reactions, PI3K-AKT signaling, AMPK activation, and angiogenesis regulation. The disruption of these pathways is pivotal in influencing the growth and progression of HCC. Targeting the HBP presents a promising therapeutic approach to modulate the tumor microenvironment, thereby enhancing the efficacy of immunotherapy. In addition, FOXM1 was identified as the HBP pathway regulator, influencing cellular O-GlcNAcylation level and VEGF secretion, thereby promoting angiogenesis in HCC. Inhibition of O-GlcNAcylation significantly hindered angiogenesis, which is suggested as a potential avenue for therapeutic intervention. Our research demonstrates the practicality of using the HBP-related gene as a prognostic marker in liver cancer patients and suggests targeting FOXM1 as a novel avenue for personalized therapy.

Uncovering SIRT3 and SHMT2-dependent pathways as novel targets for apigenin in modulating colorectal cancer: In vitro and in vivo studies

Despite significant advances in the treatment of colorectal cancer (CRC), identification of novel targets and treatment options are imperative for improving its prognosis and survival rates. The mitochondrial SIRT3 and SHMT2 have key roles in metabolic reprogramming and cell proliferation. This study investigated the potential use of the natural product apigenin in CRC treatment employing both in vivo and in vitro models and explored the role of SIRT3 and SHMT2 in apigenin-induced CRC apoptosis. The role of SHMT2 in CRC patients' survival was verified using TCGA database. In vivo, apigenin treatment restored the normal colon appearance. On the molecular level, apigenin augmented the immunohistochemical expression of cleaved caspase-3 and attenuated SIRT3 and SHMT2 mRNA expression CRC patients with decreased SHMT2 expression had improved overall and disease-free survival rates. In vitro, apigenin reduced the cell viability in a time-dependent manner, induced G0/G1 cell cycle arrest, and increased the apoptotic cell population compared to the untreated control. Mechanistically, apigenin treatment mitigated the expression of SHMT2, SIRT3, and its upstream long intergenic noncoding RNA LINC01234 in CRC cells. Conclusively, apigenin induces caspase-3-dependent apoptosis in CRC through modulation of SIRT3-triggered mitochondrial pathway suggesting it as a promising therapeutic agent to improve patient outcomes.

Emerging roles of long noncoding RNAs in enzymes related intracellular metabolic pathways in cancer biology

Metabolic reprogramming plays critical roles in the development and progression of tumor by providing cancer cells with a sufficient supply of nutrients and other factors needed for fast-proliferating. Emerging evidence indicates that long noncoding RNAs (lncRNAs) are involved in the initiation of metastasis via regulating the metabolic reprogramming in various cancers. In this paper, we aim to summarize that lncRNAs could participate in intracellular nutrient metabolism including glucose, amino acid, lipid, and nucleotide, regardless of whether lncRNAs have tumor-promoting or tumor-suppressor function. Meanwhile, modulation of lncRNAs in glucose metabolic enzymes in glycolysis, pentose phosphate pathway and tricarboxylic acid cycle (TCA) in cancer is reviewed. We also discuss therapeutic strategies targeted at interfering with enzyme activity to decrease the utilization of glucoses, amino acid, nucleotide acid and lipid in tumor cells. This review focuses on our current understanding of lncRNAs participating in cancer cell metabolic reprogramming, paving the way for further investigation into the combination of such approaches with existing anti-cancer therapies.

Alterations in serum metabolic profiles of early-stage hepatocellular carcinoma patients after radiofrequency ablation therapy

OBJECTIVE

To investigate the alterations in serum metabolic profiles and early-stage hepatocellular carcinoma (HCC) patient characteristics after radiofrequency ablation (RFA) therapy. This evaluation aimed to assess treatment effectiveness and identify potential novel approaches and targets for HCC treatment and prognosis monitoring.

METHODS

Untargeted metabolomics technology was employed to analyze serum metabolic profiles in healthy volunteer controls (NCs) and early stage HCC patients before and after RFA therapy. Additionally, Human Metabolome Database and Kyoto Encyclopedia of Genes and Genomes database were used to identify the differential metabolites (DMs) and metabolic pathways. Cystoscape was utilized to construct DM gene networks. Amino acid analyses were performed to validate our findings.

RESULTS

We identified 11, 14, and six DMs between the NC and HCC groups, HCC patients before and after RFA therapy, and post-RFA HCC and NC groups, respectively. The expression levels of these DMs, particularly those of amino acids and lipids, significantly changed. Compared with the NC group, higher levels of L-tyrosine, aspartate, and 18-oxo-oleate were observed in HCC patients, which were significantly reduced in patients after RFA therapy. Meanwhile, HCC patients after RFA therapy had increased levels of L-arginine, phosphatidic acid (20:3), and lysophosphatidyl choline (LPC) (20:4) compared to those before therapy, while their levels before therapy were lower than those of NC. Moreover, most metabolites in the post-RFA and NC groups showed no significant changes in expression, except for L-tyrosine and LPC (16:0). These metabolites could potentially serve as characteristic factors of early-stage HCC patients after RFA therapy. Joint pathway analysis revealed striking changes, mainly in phenylalanine, tyrosine, and tryptophan biosynthesis; alanine, aspartate, and glutamate metabolism; and arginine and aminoacyl-tRNA biosynthesis. Bioinformatics analysis of publicly available data preliminarily identified 187 DM-related metabolic enzymes.

CONCLUSION

Our study proposed novel targets for early-stage HCC treatment, laying the groundwork for improving treatment efficacy and prognosis of early-stage HCC patients.

ANXA5: A Key Regulator of Immune Cell Infiltration in Hepatocellular Carcinoma

BACKGROUND Hepatocellular carcinoma (HCC) poses a significant threat to human life and is the most prevalent form of liver cancer. The intricate interplay between apoptosis, a common form of programmed cell death, and its role in immune regulation stands as a crucial mechanism influencing tumor metastasis. MATERIAL AND METHODS Utilizing HCC samples from the TCGA database and 61 anoikis-related genes (ARGs) sourced from GeneCards, we analyzed the relationship between ARGs and immune cell infiltration in HCC. Subsequently, we identified long non-coding RNAs (lncRNAs) associated with ARGs, using the least absolute shrinkage and selection operator (LASSO) regression analysis to construct a robust prognostic model. The predictive capabilities of the model were then validated through examination in a single-cell dataset. RESULTS Our constructed prognostic model, derived from lncRNAs linked to ARGs, comprised 11 significant lncRNAs: NRAV, MCM3AP-AS1, OTUD6B-AS1, AC026356.1, AC009133.1, DDX11-AS1, AC108463.2, MIR4435-2HG, WARS2-AS1, LINC01094, and HCG18. The risk score assigned to HCC samples demonstrated associations with immune indicators and the infiltration of immune cells. Further, we identified Annexin A5 (ANXA5) as the pivotal gene among ARGs, with it exerting a prominent role in regulating the lncRNA gene signature. Our validation in a single-cell database elucidated the involvement of ANXA5 in immune cell infiltration, specifically in the regulation of mononuclear cells. CONCLUSIONS This study delves into the intricate correlation between ARGs and immune cell infiltration in HCC, culminating in the development of a novel prognostic model reliant on 11 ARGs-associated lncRNAs. Furthermore, our findings highlight ANXA5 as a promising target for immune regulation in HCC, offering new perspectives for immune therapy in the context of HCC.

U3 snoRNA inter-regulates with DDX21 in the perichromosomal region to control mitosis

U3 snoRNA is essential for ribosome biogenesis during interphase. Upon mitotic onset, the nucleolus disassembles and U3 snoRNA relocates to the perichromosomal region (PR) to be considered as a chromosome passenger. Whether U3 controls mitosis remains unknown. Here, we demonstrate that U3 snoRNA is required for mitotic progression. We identified DDX21 as the predominant U3-binding protein during mitosis and confirmed that U3 snoRNA colocalizes with DDX21 in the PR. DDX21 knockdown induces mitotic catastrophe and similar mitotic defects caused by U3 snoRNA depletion. Interestingly, the uniform PR distribution of U3 snoRNA and DDX21 is interdependent. DDX21 functions in mitosis depending on its PR localization. Mechanistically, U3 snoRNA regulates DDX21 PR localization through maintaining its mobility. Moreover, Cy5-U3 snoRNA downsizes the fibrous condensates of His-DDX21 at proper molecular ratios in vitro. This work highlights the importance of the equilibrium between U3 snoRNA and DDX21 in PR formation and reveals the potential relationship between the PR assembly and mitotic regulation.

LINC00540 promotes sorafenib resistance and functions as a ceRNA for miR-4677-3p to regulate AKR1C2 in hepatocellular carcinoma

Sorafenib resistance is one of the main causes of poor prognosis in patients with advanced hepatocellular carcinoma (HCC). Long noncoding RNAs (lncRNAs) function as suppressors or oncogenic factors during tumor progression and drug resistance. Here, to identify therapeutic targets for HCC, the biological mechanisms of abnormally expressed lncRNAs were examined in sorafenib-resistant HCC cells. Specifically, we established sorafenib-resistant HCC cell lines (Huh7-S and SMMC7721-S), which displayed an epithelial-mesenchymal transition (EMT) phenotype. Transcriptome sequencing (RNA-Seq) was performed to established differential lncRNA expression profiles for sorafenib-resistant cells. Through this analysis, we identified LINC00540 as significantly up-regulated in sorafenib-resistant cells and a candidate lncRNA for further mechanistic investigation. Functionally, LINC00540 knockdown promoted sorafenib sensitivity and suppressed migration, invasion, EMT and the activation of PI3K/AKT signaling pathway in sorafenib-resistant HCC cells, whereas overexpression of LINC00540 resulted in the opposite effects in parental cells. LINC00540 functions as a competing endogenous RNA (ceRNA) by competitively binding to miR-4677-3p , thereby promoting AKR1C2 expression. This is the first study that demonstrates a role for LINC00540 in enhancing sorafenib resistance, migration and invasion of HCC cells through the LINC00540/miR-4677-3p/AKR1C2 axis, suggesting that LINC00540 may represent a potential therapeutic target and prognosis biomarker for HCC.

LINC00629, a HOXB4-downregulated long noncoding RNA, inhibits glycolysis and ovarian cancer progression by destabilizing c-Myc

Ovarian cancer (OC) cells typically reprogram their metabolism to promote rapid proliferation. However, the role of long noncoding RNAs (lncRNAs) in the metabolic reprogramming of ovarian cancer, especially in glucose metabolic reprogramming, remains largely unknown. LINC00629 has been reported in our previous study to promote osteosarcoma progression. Upregulated LINC00629 was found to enhance the growth-suppressive effect of apigenin on oral squamous cell carcinoma. However, the precise function of LINC00629 in ovarian cancer development remains poorly understood. In this study, we found that LINC00629 was significantly downregulated in OC tissues and that low LINC00629 expression was associated with poor survival. Inhibition of LINC00629 was required for increased glycolysis activity and cell proliferation in ovarian cancer. In vivo, overexpression of LINC00629 dramatically inhibited tumor growth and lung metastasis. Mechanistically, LINC00629 interacted with and destabilized c-Myc, leading to its ubiquitination and proteasome degradation, further resulting in increased expression of downstream glycolysis-related genes and glucose metabolic reprogramming in OC. Interestingly, HOXB4 bound to the LINC00629 promoter and inhibited its transcription, indicating that LINC00629 is a transcriptional target of HOXB4. Collectively, these findings establish a direct role for LINC00629 in suppressing glucose metabolism, and HOXB4/LINC00629/c-Myc might serve as a potential biomarker and an effective therapeutic strategy for OC cancer treatment.

The roles and molecular mechanisms of non-coding RNA in cancer metabolic reprogramming

One of the key features of cancer is energy metabolic reprogramming which is tightly related to cancer proliferation, invasion, metastasis, and chemotherapy resistance. NcRNAs are a class of RNAs having no protein-coding potential and mainly include microRNAs, lncRNAs and circRNAs. Accumulated evidence has suggested that ncRNAs play an essential role in regulating cancer metabolic reprogramming, and the altered metabolic networks mediated by ncRNAs primarily drive carcinogenesis by regulating the expression of metabolic enzymes and transporter proteins. Importantly, accumulated research has revealed that dysregulated ncRNAs mediate metabolic reprogramming contributing to the generation of therapeutic tolerance. Elucidating the molecular mechanism of ncRNAs in cancer metabolic reprogramming can provide promising metabolism-related therapeutic targets for treatment as well as overcome therapeutic tolerance. In conclusion, this review updates the latest molecular mechanisms of ncRNAs related to cancer metabolic reprogramming.

CSTB accelerates the progression of hepatocellular carcinoma via the ERK/AKT/mTOR signaling pathway

Hepatocellular carcinoma (HCC) is a significant contributor to global cancer-related deaths, leading to high mortality rates. However, the pathogenesis of HCC remains unclear. In this research, by the bioinformatics data analysis, we found that elevated CSTB expression correlated with advanced disease and predicted diminished overall survival (OS) in HCC patients. We subsequently verified the oncogenic role of CSTB as well as the potential underlying mechanisms in HCC through a series of in vitro experiments, such as CCK-8 assays, cloning assays, flow cytometry, Transwell assays, and western blotting. Our findings illustrated that the silencing of CSTB effectively suppressed cellular proliferation by inducing cell cycle arrest in the G2 phase and impaired HCC cell invasion and migration by stimulating epithelial-mesenchymal transition (EMT). Additionally, we analyzed the pathways enriched in HCC using RNA sequencing and found that the ERK/AKT/mTOR signaling pathway was related to increased CSTB expression in HCC. Finally, we confirmed the tumorigenic role of CSTB via in vivo experiments. Thus, our findings revealed that silencing CSTB inhibited the HCC progression via the ERK/AKT/mTOR signaling pathway, highlighting new perspectives for investigating the mechanisms of HCC.

HCC-Related lncRNAs: Roles and Mechanisms

Hepatocellular carcinoma (HCC) presents a significant global health threat, particularly in regions endemic to hepatitis B and C viruses, and because of the ongoing pandemic of obesity causing metabolic-dysfunction-related fatty liver disease (MAFLD), a precursor to HCC. The molecular intricacies of HCC, genetic and epigenetic alterations, and dysregulated signaling pathways facilitate personalized treatment strategies based on molecular profiling. Epigenetic regulation, encompassing DNA methyltion, histone modifications, and noncoding RNAs, functions as a critical layer influencing HCC development. Long noncoding RNAs (lncRNAs) are spotlighted for their diverse roles in gene regulation and their potential as diagnostic and therapeutic tools in cancer. In this review, we explore the pivotal role of lncRNAs in HCC, including MAFLD and viral hepatitis, the most prevalent risk factors for hepatocarcinogenesis. The dysregulation of lncRNAs is implicated in HCC progression by modulating chromatin regulation and transcription, sponging miRNAs, and influencing structural functions. The ongoing studies on lncRNAs contribute to a deeper comprehension of HCC pathogenesis and offer promising routes for precision medicine, highlighting the utility of lncRNAs as early biomarkers, prognostic indicators, and therapeutic targets.

Everolimus Acts in Synergy with Vinorelbine to Suppress the Growth of Hepatocellular Carcinoma

Hepatocellular carcinoma (HCC) is a challenging cancer to treat, as traditional chemotherapies have shown limited effectiveness. The mammalian target of rapamycin/sirolimus (mTOR) and microtubules are prominent druggable targets for HCC. In this study, we demonstrated that co-targeting mTOR using mTOR inhibitors (everolimus and sirolimus) along with the microtubule inhibitor vinorelbine yielded results superior to those of the monotherapies in HCC PDX models. Our research showed that the vinorelbine arrests cells at the mitotic phase, induces apoptosis, and normalizes tumor blood vessels but upregulates survivin and activates the mTOR/p70S6K/4EBP1 pathway. The addition of the everolimus significantly improved the tumor response to the vinorelbine, leading to improved overall survival (OS) in most tested orthotopic HCC PDX models. The mechanistic investigation revealed that this marked antitumor effect was accompanied by the downregulations of mTOR targets (p-p70S6K, p-4EBP1, and p-S6K); several key cell-cycle regulators; and the antiapoptotic protein survivin. These effects did not compromise the normalization of the blood vessels observed in response to the vinorelbine in the vinorelbine-sensitive PDX models or to the everolimus in the everolimus-sensitive PDX models. The combination of the everolimus and vinorelbine (everolimus/vinorelbine) also promoted apoptosis with minimal toxicity. Given the cost-effectiveness and established effectiveness of everolimus, and especially sirolimus, this strategy warrants further investigation in early-phase clinical trials.

Comprehensive analysis of cuproptosis-related long non-coding RNAs in prognosis, immune microenvironment infiltration and chemotherapy response of hepatocellular carcinoma

The objective of this study is to explore the relationship between cuproptosis-related long noncoding RNAs (lncRNAs) in hepatocellular carcinoma (HCC). RNA-seq data, including lncRNAs and related clinical information of HCC patients, were downloaded from The Cancer Genome Atlas database. A signature composed 3 cuproptosis-related lncRNAs was constructed by LASSO analysis, and HCC patients were classified into high- and low-risk groups. Patients in the high-risk group had a poorer prognosis compared with the low-risk group. Univariate Cox and multivariate Cox regression analyses confirmed that the signature model was an independent risk factor compared to other clinical biomarkers. Furthermore, gene set enrichment analysis indicated that metabolism-related pathways were enriched in low-risk group, including drug metabolism, and fatty acid metabolism. Further research demonstrated that there were markedly differences in drug response between the high- and low-risk group. Immune related analysis showed that the most type of immune cells and immunological function in the high-risk group were different with the risk-group. Finally, TP53 mutation rate and the tumor mutational burden in the high-risk group were higher compared with the low-risk group. In conclusion, we constructed a prognostic signature based on the expression of cuproptosis-related lncRNAs to predict HCC patients' prognosis, drug response and immune microenvironment, and further research will be conducted to uncover the mechanisms.

LncRNA AGAP2-AS1 interacts with IGF2BP2 to promote bladder cancer progression via regulating LRG1 mRNA stability

BACKGROUND

The long non-coding RNA (lncRNA) AGAP2-AS1 was implicated in tumorigenesis, yet with unclear mechanism in the development of Bladder Cancer (BCa).

METHODS

We collected the clinicopathological features and tissue samples of 45 patients with BCa in Xiangya Hospital. Expressions of AGAP2-AS1 and LRG1 were detected by RT-qPCR in BCa tissues and normal tissues as well as in BCa cells. The roles of AGAP2-AS1 and LRG1 were investigated by CCK-8, colony formation assay, transwell assays and tube formation assay. The subcellular localization of AGAP2-AS1 was detected by Fluorescence in situ hybridization. Bioinformatics method, RNA immunoprecipitation, RNA pull-down assay and Actinomycin D test were used to predict and identify the relationships between AGAP2-AS1, LRG1 and IGF2BP2. Xenografted tumors were produced to explore the function of AGAP2-AS1 in BCa in vivo.

RESULTS

AGAP2-AS1 and LRG1 were highly upregulated in BCa. AGAP2-AS1 positively correlated with T stage, grade and vascular invasion, but negatively correlated with the survival of patients. Overexpressions of AGAP2-AS1 promoted proliferation, migration, invasion, tumor angiogenesis in vitro and tumor growth, metastasis in vivo, knockdown of AGAP2-AS1 exhibited the opposite effects. AGAP2-AS1 localized mainly in the cytoplasm. AGAP2-AS1 directly bound to IGF2BP2 protein to enhance LRG1 mRNA stability. Inhibition of BCa progression by AGAP2-AS1 knockdown may be reversed by LRG1 overexpression.

CONCLUSION

AGAP2-AS1 can promote BCa progression and metastasis by recruiting IGF2BP2 to stabilize LRG1.

Long non‑coding RNAs, lipid metabolism and cancer (Review)

Cancer has emerged as the most common cause of death in China. The change in lipid metabolism has been confirmed to have a role in several tumor types, such as esophageal, gastric, colorectal and liver cancer. Cancer cells use lipid metabolism for energy and then rapidly proliferate, invade and migrate. The main pathway by which cancer cell lipid metabolism influences cancer progression is increased fatty acid synthesis. Long non-coding (lnc)RNAs are important ncRNAs that were indicated to have significant roles in the development of human tumors. They are considered potential tumor biomarkers. Increased lipid synthesis or uptake due to deregulation of lncRNAs contributes to rapid tumor growth. In the present review, current studies on the relationship between lncRNAs, lipid metabolism and the occurrence and development of tumors were collated and summarized, and their mechanism of action was discussed. The review is expected to provide a theoretical basis for tumor treatment and prognosis evaluation based on the effective regulation of lncRNAs and lipid metabolism.

Effects of Bacillus halophilus on growth, intestinal flora and metabolism of Larimichthys crocea

The incorporation of probiotics into the diet of large yellow croaker has been demonstrated by several studies to confer partial disease resistance. Bacillus halophilic isolated from the intestinal flora was used to study its effects on performance growth indicators, intestinal tissue structure, intestinal flora and the metabolism of Larimichthys crocea. A total of 180 fishes with an initial body weight of (164.00 ± 54.00) g were fed diets with three different concentrations of Bacillus halophilic: 0 cfu/mL (FC0, control group), 108 cfu/mL (FC8, treatment group), and 1012 cfu/mL (FC12, treatment group). The results showed that there were no significant differences in specific growth rate among all groups (P > 0.05). Compared to the FC0 group, the final body weight and Weight gain rate were significantly higher in FC8 and FC12 groups (P < 0.05). The Survival of the FC12 group significantly improved (P < 0.05). Compared to the FC0 group, crude protein content in muscle of the FC8 group significantly increased (P < 0.05), crude fat content significantly increased in the FC12 group (P < 0.05), crude protein content in whole fish experimental groups significantly increased (P < 0.05), and ash content significantly increased in the FC8 group (P < 0.05). In terms of antioxidant ability, the content of LZM in blood increased significantly in the FC8 group (P < 0.05), GSH content in liver of the FC12 group increased significantly (P < 0.05), while the content of MDA and AKP in blood and liver had no significant difference (P > 0.05). At the level of intestinal structure, there were no significant differences in villus height, crypt depth and goblet cell number between control group and treatment groups (P > 0.05). At the phylum level, Firmicutes was the dominant phylum, and the genus level, Lactobacillus and Bacteroides were the dominant bacteria in FC8 and FC12. A total of 1070 metabolites were identified, among which lipid metabolites accounted for 46.7%. Metabolites were involved in six main ways, mainly related to the metabolism of amino acids and lipids. The correlation analysis between microbes and metabolites showed that the intestinal flora of Larimichthys crocea could promote the synthesis of metabolites, among which Bacteroides and Megamonas could promote the synthesis of beneficial metabolites such as amino acids and vitamins. Through this study, we found that Bacillus halophilic can significantly improve growth, the antioxidant immunity ability and promote the expression of growth related metabolites, with the FC12 group being the better successful.

Downregulated Acetyl-CoA Acyltransferase 2 Promoted the Progression of Hepatocellular Carcinoma and Participated in the Formation of Immunosuppressive Microenvironment

Background

The aim of this study is to explore the role of acetyl-CoA acyltransferase 2 (ACAA2) in the progression of hepatocellular carcinoma (HCC).

Methods

Bulk RNA data and single-cell RNA data were acquired from The Cancer Genome Atlas and Gene Expression Omnibus. Both in vitro and in vivo studies were used to determine the effect of ACAA2 on the progression of HCC, and RNA sequencing analysis was performed to explore the mechanism.

Results

We found downregulation of ACAA2 was involved in the malignant progression of HCC. The patient with low ACAA2 level had an immunosuppressive microenvironment in the HCC and predicted to have a poor prognosis. Decreased ACAA2 facilitated HCC proliferation and metastasis by activating the nuclear factor-κB (NFκB) signaling pathway. And increased CXCL1 induced by NFκB signaling pathway might be responsible for low level of ACAA2 related immunosuppressive microenvironment. Furthermore, the expression of ACAA2 was also detected in immune cells. The expression of ACAA2 in CD4+TCF7+T, CD4+FOXP3+T, CD8+GZMK+T, and CD8+KLRD1+T cells was inversely correlated with the composition of CD8+PDCD1+T cells in HCC. This effect might be due to the CCL5-CCRs and HLA-E-KLRCs ligand-receptor networks.

Conclusion

In a conclusion, downregulated ACAA2 promoted the progression of hepatocellular carcinoma and might be participated in the formation of immunosuppressive microenvironment. ACAA2 could be served as a favorable indicator for the prognosis of HCC and an ideal biomarker for immunotherapy.

The role of noncoding RNAs in metabolic reprogramming of cancer cells

Metabolic reprogramming is a well-known feature of cancer that allows malignant cells to alter metabolic reactions and nutrient uptake, thereby promoting tumor growth and spread. It has been discovered that noncoding RNAs (ncRNAs), including microRNA (miRNA), long noncoding RNA (lncRNA), and circular RNA (circRNA), have a role in a variety of biological functions, control physiologic and developmental processes, and even influence disease. They have been recognized in numerous cancer types as tumor suppressors and oncogenic agents. The role of ncRNAs in the metabolic reprogramming of cancer cells has recently been noticed. We examine this subject, with an emphasis on the metabolism of glucose, lipids, and amino acids, and highlight the therapeutic use of targeting ncRNAs in cancer treatment.

Amino acid metabolism regulated by lncRNAs: the propellant behind cancer metabolic reprogramming

Metabolic reprogramming is one of the main characteristics of cancer cells and plays pivotal role in the proliferation and survival of cancer cells. Amino acid is one of the key nutrients for cancer cells and many studies have focused on the regulation of amino acid metabolism, including the genetic alteration, epigenetic modification, transcription, translation and post-translational modification of key enzymes in amino acid metabolism. Long non-coding RNAs (lncRNAs) are composed of a heterogeneous group of RNAs with transcripts of more than 200 nucleotides in length. LncRNAs can bind to biological molecules such as DNA, RNA and protein, regulating the transcription, translation and post-translational modification of target genes. Now, the functions of lncRNAs in cancer metabolism have aroused great research interest and significant progress has been made. This review focuses on how lncRNAs participate in the reprogramming of amino acid metabolism in cancer cells, especially glutamine, serine, arginine, aspartate, cysteine metabolism. This will help us to better understand the regulatory mechanism of cancer metabolic reprogramming and provide new ideas for the development of anti-cancer drugs. Video Abstract.

Activation of ACLY by SEC63 deploys metabolic reprogramming to facilitate hepatocellular carcinoma metastasis upon endoplasmic reticulum stress

BACKGROUND

Tumor cells display augmented capability to maintain endoplasmic reticulum (ER) homeostasis and hijack ER stress pathway for malignant phenotypes under microenvironmental stimuli. Metabolic reprogramming is a well-known hallmark for tumor cells to provide specific adaptive traits to the microenvironmental alterations. However, it's unknown how tumor cells orchestrate metabolic reprogramming and tumor progression in response to ER stress. Herein, we aimed to explore the pivotal roles of SEC63-mediated metabolic remodeling in hepatocellular carcinoma (HCC) cell metastasis after ER stress.

METHODS

The expression levels of SEC63 in HCC tissues and adjacent non-cancerous tissues were determined by immunohistochemistry and western blot. The regulatory roles of SEC63 in HCC metastasis were investigated both in vitro and in vivo by RNA-sequencing, metabolites detection, immunofluorescence, and transwell migration/invasion analyses. GST pull-down, immunoprecipitation/mass spectrometry and in vivo ubiquitination/phosphorylation assay were conducted to elucidate the underlying molecular mechanisms.

RESULTS

We identified SEC63 as a new regulator of HCC cell metabolism. Upon ER stress, the phosphorylation of SEC63 at T537 by IRE1α pathway contributed to SEC63 activation. Then, the stability of ACLY was upregulated by SEC63 to increase the supply of acetyl-CoA and lipid biosynthesis, which are beneficial for improving ER capacity. Meanwhile, SEC63 also entered into nucleus for increasing nuclear acetyl-CoA production to upregulate unfolded protein response targets to improve ER homeostasis. Importantly, SEC63 coordinated with ACLY to epigenetically modulate expression of Snail1 in the nucleus. Consequently, SEC63 promoted HCC cell metastasis and these effects were reversed by ACLY inhibition. Clinically, SEC63 expression was significantly upregulated in HCC tissue specimens and was positively correlated with ACLY expression. Importantly, high expression of SEC63 predicted unfavorable prognosis of HCC patients.

CONCLUSIONS

Our findings revealed that SEC63-mediated metabolic reprogramming plays important roles in keeping ER homeostasis upon stimuli in HCC cells. Meanwhile, SEC63 coordinates with ACLY to upregulate the expression of Snail1, which further promotes HCC metastasis. Metastasis is crucial for helping cancer cells seek new settlements upon microenvironmental stimuli. Taken together, our findings highlight a cancer selective adaption to ER stress as well as reveal the potential roles of the IRE1α-SEC63-ACLY axis in HCC treatment.

A Statistical Approach to the Diagnosis and Prediction of HCC Using CK19 and Glypican 3 Biomarkers

Various statistical models predict the probability of developing hepatocellular carcinoma (HCC) in patients with cirrhosis, with GALAD being one of the most extensively studied scores. Biomarkers like alpha-fetoprotein (AFP), AFP-L3, and des-g-carboxyprothrombin (DCP) are widely used alone or in conjunction with ultrasound to screen for HCC. Our study aimed to compare the effectiveness of Cytokeratin 19 (CK19) and Glypican-3 (GPC3) as standalone biomarkers and in a statistical model to predict the likelihood of HCC. We conducted a monocentric prospective study involving 154 participants with previously diagnosed liver cirrhosis, divided into two groups: 95 patients with confirmed HCC based on clinical, biological, and imaging features and 59 patients without HCC. We measured the levels of AFP, AFP-L3, DCP, GPC3, and CK19 in both groups. We used univariate and multivariate statistical analyses to evaluate the ability of GPC3 and CK19 to predict the presence of HCC and incorporated them into a statistical model-the GALKA score-which was then compared to the GALAD score. AFP performed better than AFP-F3, DCP, GPC3, and CK19 in predicting the presence of HCC in our cohort. Additionally, GPC3 outperformed CK19. We used multivariate analysis to compute the GALKA score to predict the presence of HCC. Using these predictors, the following score was formulated: 0.005*AFP-L3 + 0.00069*AFP + 0.000066*GPC3 + 0.01*CK19 + 0.235*Serum Albumin-0.277. The optimal cutoff was >0.32 (AUROC = 0.98, sensitivity: 96.8%, specificity: 93%, positive predictive value-95.8%, negative predictive value-94.8%). The GALKA score had a similar predictive value to the GALAD score for the presence of HCC. In conclusion, AFP, AFP-L3, and DCP were the best biomarkers for predicting the likelihood of HCC. Our score performed well overall and was comparable to the GALAD score.

KIFC3 regulates progression of hepatocellular carcinoma via EMT and the AKT/mTOR pathway

INTRODUCTION

Hepatocellular carcinoma (HCC) is the fourth leading cause of cancer-related deaths worldwide. Despite an overall downward trend in cancer mortality, HCC-related mortality continues to increase. KIFC3 is involved in cell division and cancers. However, the role of KIFC3 in HCC has yet to be elucidated.

METHODS

A total of 36 cases of HCC tissues, 4 HCC cell lines, and TCGA databases were searched to explore the expression of KIFC3 in HCC. Subsequently, Western blot analysis, immunofluorescence, bioinformatic analysis, molecular docking, and Co-IP were performed to investigate the molecular mechanisms of KIFC3 in HCC.

RESULT

We found that the expression of KIFC3 was upregulated in HCC, and high KIFC3 expression was related to poor overall survival. In addition, the knockdown of KIFC3 inhibited the proliferation, migration, and invasion of HCC cells in vitro, and impeded the growth of HCC in vivo, while overexpression of KIFC3 in HCC cells revealed the opposite effect. Mechanistically, KIFC3 promotes the progression of HCC through the PI3K/AKT/mTOR signalling. And KIFC3 had slight effect on the protein expression of p-PI3K, p-AKT and p-mTOR in TRIP13-ablated or LY294002-treated HCC cells. The KIFC3 knockdown could further enhance the inhibitory effect of LY294002.

CONCLUSION

Our data revealed that KIFC3 is upregulated in HCC and may serve as a novel biomarker for predicting survival in HCC patients. Targeting KIFC3 may serve as a novel therapeutic strategy for HCC patients.

A prognostic risk model, tumor immune environment modulation, and drug prediction of ferroptosis and amino acid metabolism-related genes in hepatocellular carcinoma

The prognosis of hepatocellular carcinoma (HCC) is challenging due to its heterogeneity. Ferroptosis and amino acid metabolism have been shown to be closely related to HCC. We obtained HCC-related expression data from The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) databases. We then crossed differentially expressed genes (DEGs), amino acid metabolism genes, and ferroptosis-related genes (FRGs) to obtain amino acid metabolism-ferroptosis-related differentially expressed genes (AAM-FR DEGs). Moreover, we developed a prognostic model using Cox analysis, followed by a correlation analysis of risk scores with clinical characteristics. We also performed an immune microenvironment analysis and drug sensitivity analysis. Finally, the expression levels of model genes were verified by quantitative real-time polymerase chain reaction (qRT-PCR) and immunohistochemical assays. We found that the 18 AAM-FR DEGs were mainly enriched to the alpha-amino acid metabolic process and amino acid biosynthesis pathways. Cox analysis identified CBS, GPT2, SUV39H1, and TXNRD1 as prognostic biomarkers for the risk model construction. Our results showed that the risk scores differed between pathology stage, pathology T stage, and HBV, and the number of HCC patients in the two groups. In addition, the expression of PD-L1 and CTLA-4 was high in the high-risk group, and the half-maximal inhibitory concentration (IC50) of sorafenib also differed between the two groups. Finally, the experimental validation demonstrated that the expression of biomarkers was consistent with the study analysis. Therefore, in this study, we constructed and validated a prognostic model (CBS, GPT2, SUV39H1, and TXNRD1) related to ferroptosis and amino acid metabolism and examined their prognostic value for HCC.

Combining a machine-learning derived 4-lncRNA signature with AFP and TNM stages in predicting early recurrence of hepatocellular carcinoma

BACKGROUND

Near 70% of hepatocellular carcinoma (HCC) recurrence is early recurrence within 2-year post surgery. Long non-coding RNAs (lncRNAs) are intensively involved in HCC progression and serve as biomarkers for HCC prognosis. The aim of this study is to construct a lncRNA-based signature for predicting HCC early recurrence.

METHODS

Data of RNA expression and associated clinical information were accessed from The Cancer Genome Atlas Liver Hepatocellular Carcinoma (TCGA-LIHC) database. Recurrence associated differentially expressed lncRNAs (DELncs) were determined by three DEG methods and two survival analyses methods. DELncs involved in the signature were selected by three machine learning methods and multivariate Cox analysis. Additionally, the signature was validated in a cohort of HCC patients from an external source. In order to gain insight into the biological functions of this signature, gene sets enrichment analyses, immune infiltration analyses, as well as immune and drug therapy prediction analyses were conducted.

RESULTS

A 4-lncRNA signature consisting of AC108463.1, AF131217.1, CMB9-22P13.1, TMCC1-AS1 was constructed. Patients in the high-risk group showed significantly higher early recurrence rate compared to those in the low-risk group. Combination of the signature, AFP and TNM further improved the early HCC recurrence predictive performance. Several molecular pathways and gene sets associated with HCC pathogenesis are enriched in the high-risk group. Antitumor immune cells, such as activated B cell, type 1 T helper cell, natural killer cell and effective memory CD8 T cell are enriched in patients with low-risk HCCs. HCC patients in the low- and high-risk group had differential sensitivities to various antitumor drugs. Finally, predictive performance of this signature was validated in an external cohort of patients with HCC.

CONCLUSION

Combined with TNM and AFP, the 4-lncRNA signature presents excellent predictability of HCC early recurrence.

Prognosis and Personalized Treatment Prediction in Different Mutation-Signature Hepatocellular Carcinoma

Introduction

Mutation patterns have been extensively explored to decipher the etiologies of hepatocellular carcinoma (HCC). However, the study and potential clinical role of mutation patterns to stratify high-risk patients and optimize precision therapeutic strategies remain elusive in HCC.

Methods

Using exon-sequencing data in public (n=362) and in-house (n=30) cohorts, mutation signatures were extracted to decipher relationships with the etiology and prognosis in HCC. The proteomics (n=159) and cell-line transcriptome data (n=1019) were collected to screen the implication of sensitive drugs. A novel multi-step machine-learning framework was then performed to construct a classification predictor, including recognizing stable reversed gene pairs, establishing a robust prediction model, and validating the robustness of the predictor in five independent cohorts (n=900).

Results

Two heterogeneous mutation signature clusters were identified, and a high-risk prognosis cluster was recognized for further analysis. Notably, mutation signature cluster 1 (MSC1) was featured by activated anti-tumor immune and metabolism dysfunctional states, higher genomic instability (high TMB, SNV neoantigen, indel neoantigens, and total neoantigens), and a dismal prognosis. Notably, MSC performed as an independent risk factor than clinical traits (eg, stage, vascular invasion). Additionally, afatinib and canertinib were recognized which might have potential therapeutic implications in MSC1, and the targets of these drugs presented a higher expression in both gene and protein levels in HCC.

Discussion

Our studies may provide a promising platform for improving prognosis and tailoring therapy in HCC.

CBX2-mediated suppression of SIAH2 triggers WNK1 accumulations to promote glycolysis in hepatocellular carcinoma

Previous studies have highlighted the poor prognosis of liver cancer, and treatment effects are overall limited. We aimed to confirm the biological roles of SIAH2 in liver cancer and provide potential therapeutic targets. Differential analysis was conducted based on public datasets and found that SIAH2 expressed lowly in HCC samples relative to normal tissues, which was demonstrated in tumor samples via immunohistochemistry (IHC). Besides, SIAH2 overexpression could significantly suppress HCC proliferation. SIAH2 deficiency induced cell proliferation, migration and self-renewal abilities in vitro and in vivo. Mechanistically, SIAH2 could interact with WNK1, and trigger the ubiquitination and degradation of WNK1 proteins. In addition, low SIAH2 depended on elevated WNK1 proteins to drive HCC malignant features, including proliferation, migration and stemness. Meanwhile, we further found that CBX2 could regulate SIAH2 expressions. CBX2 cooperated with EZH2 to mediate the H3K27me3 enrichment on the promoter region of SIAH2 to suppress its transcriptional levels. High CBX2/EZH2 levels in HCC correlated with poor prognosis of patients. Gene set enrichment analysis (GSEA) further implicated that WNK1 correlates tightly with glycolytic process in HCC samples. WNK1 overexpression was found to notably enhance glycolytic activity, whereas WNK1 deficiency could significantly suppress the HCC glycolysis activity. Lastly, the subcutaneous tumor model further demonstrated that targeting WNK1 was effective to inhibit the in vivo tumor growth of SIAH2^low HCC. Collectively, down-regulated SIAH2 expressions induced by CBX2/EZH2 could drive progression and glycolysis via accumulating WNK1 proteins, indicating that CBX2/SIAH2/WNK1 axis is a potential prognostic biomarker and therapeutic vulnerability for human HCC.

Patient-derived xenograft model in colorectal cancer basic and translational research

Colorectal cancer (CRC) is one of the most popular malignancies globally, with 930 000 deaths in 2020. The evaluation of CRC-related pathogenesis and the discovery of potential therapeutic targets will be meaningful and helpful for improving CRC treatment. With huge efforts made in past decades, the systematic treatment regimens have been applied to improve the prognosis of CRC patients. However, the sensitivity of CRC to chemotherapy and targeted therapy is different from person to person, which is an important cause of treatment failure. The emergence of patient-derived xenograft (PDX) models shows great potential to alleviate the straits. PDX models possess similar genetic and pathological characteristics as the features of primary tumors. Moreover, PDX has the ability to mimic the tumor microenvironment of the original tumor. Thus, the PDX model is an important tool to screen precise drugs for individualized treatment, seek predictive biomarkers for prognosis supervision, and evaluate the unknown mechanism in basic research. This paper reviews the recent advances in constructed methods and applications of the CRC PDX model, aiming to provide new knowledge for CRC basic research and therapeutics.

MARCKS is a New Prognostic Biomarker in Hepatocellular Carcinoma

Background

Hepatocellular carcinoma (HCC) is one of the most common type of cancers, but there is still a lack of known biomarkers for the effective diagnosis or prognosis of HCC. Myristoylated alanine-rich C-kinase substrate (MARCKS) is a substrate of protein kinase C, which was located in the cell plasma membrane. The purpose of our study was to evaluate the role of MARCKS in HCC.

Methods

The role of MARCKS in HCC was explored by bioinformatics and experiment.

Results

We demonstrated that MARCKS expression was significantly elevated in HCC datasets of TCGA. MARCKS was up-regulated in tumor sample in HCC. Functional enrichment indicated that MARCKS-related differentially expressed genes (DEGs) were mainly enriched in cell junction tissue, response to growth factors and cell population proliferation. Tumor and ECM-receptor interactions related pathways were enriched by the KEGG. MARCKS expression in HCC patients was higher in females, younger individuals, and those at worse clinical stages. Cox regression analysis showed that MARCKS expression was a risk factor for overall survival and disease-specific survival of patients.

Conclusion

MARCKS was up-regulated in HCC, may play a crucial role in HCCs, and has prognostic value for clinical outcomes.

Crosstalk between Methylation and ncRNAs in Breast Cancer: Therapeutic and Diagnostic Implications

Breast cancer, as a highly heterogeneous malignant tumor, is one of the primary causes of death among females worldwide. The etiology of breast cancer involves aberrant epigenetic mechanisms and abnormal expression of certain non-coding RNA (ncRNAs). DNA methylation, N6-methyladenosine(m6A), and histone methylation are widely explored epigenetic regulation types in breast cancer. ncRNAs are a group of unique RNA transcripts, mainly including microRNA (miRNAs), long non-coding RNA (lncRNAs), circular RNA (circRNAs), small interfering RNA (siRNAs), piwi-interacting RNA (piRNAs), etc. Different types of methylation and ncRNAs mutually regulate and interact to form intricate networks to mediate precisely breast cancer genesis. In this review, we elaborate on the crosstalk between major methylation modifications and ncRNAs and discuss the role of their interaction in promoting breast cancer oncogenesis. This review can provide novel insights into establishing a new diagnostic marker system on methylation patterns of ncRNAs and therapeutic perspectives of combining ncRNA oligonucleotides and phytochemical drugs for breast cancer therapy.

ESPL1 is Elevated in Hepatocellular Carcinoma and Predicts Prognosis

PURPOSE

The extra spindle pole bodies-like 1 (ESPL1) gene is associated with malignant biological behaviors in several tumors. Nevertheless, the correlation between hepatocellular carcinoma (HCC) and ESPL1 has not been determined. The present study analyzed the molecular function and prognostic value of ESPL1 in HCC.

PATIENTS AND METHODS

Samples from 121 HCCs and 119 adjacent normal tissue specimens were subjected to next-generation sequencing. Clinicopathological and genetic data of HCC patients in The Cancer Genome Atlas (TCGA) were also collected. ESPL1 expression was assessed in 20 pairs of HCC and normal liver specimens by qRT-PCR and immunohistochemistry (IHC). The prognostic value of ESPL1 expression was determined by Cox univariate and multivariate regression analyses. ESPL1-related co-expressed genes were evaluated by weighted gene co-expression network analysis (WGCNA). Processes and pathways involving ESPL1 in HCC were determined by Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. The prognostic values of hub genes were determined by joint effect survival analysis.

RESULTS

RNA-Seq, RT-qPCR and IHC showed that ESPL1 expression was significantly higher in HCC than in normal liver tissues. Increased ESPL1 expression, greater tumor size and advanced BCLC stage were independently prognostic of poorer overall survival; and increased ESPL1 and advanced BCLC stage were independently prognostic of poorer recurrence-free survival. WGCNA showed that the top 10 co-expressed genes associated with ESPL1 were GTSE1, KIF18B, BUB1B, GINS1, PRC1, KIF23, KIF18A, TOP2A, NEK2 and FANCD2. Enrichment analysis indicated that ESPL1 and its co-expressed genes might be involved in the cell cycle and cell division of HCC. Joint effect survival analysis showed that the mortality rate was approximately 3.37 times higher in HCC patients with high than low expression of ESPL1, GTSE1, BUB1B, PRC1, KIF23, and TOP2A.

CONCLUSION

ESPL1 might be associated with cell cycle and might be an effective prognostic indicator in patients with HCC.

Non-coding RNAs in hepatocellular carcinoma: Insights into regulatory mechanisms, clinical significance, and therapeutic potential

Hepatocellular carcinoma (HCC) is a complex and heterogeneous malignancy with high incidence and poor prognosis. In addition, owing to the lack of diagnostic and prognostic markers, current multimodal treatment options fail to achieve satisfactory outcomes. Tumor immune microenvironment (TIME), angiogenesis, epithelial-mesenchymal transition (EMT), invasion, metastasis, metabolism, and drug resistance are important factors influencing tumor development and therapy. The intercellular communication of these important processes is mediated by a variety of bioactive molecules to regulate pathophysiological processes in recipient cells. Among these bioactive molecules, non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), account for a large part of the human transcriptome, and their dysregulation affects the progression of HCC. The purpose of this review is to evaluate the potential regulatory mechanisms of ncRNAs in HCC, summarize novel biomarkers from somatic fluids (plasma/serum/urine), and explore the potential of some small-molecule modulators as drugs. Thus, through this review, we aim to contribute to a deeper understanding of the regulatory mechanisms, early diagnosis, prognosis, and precise treatment of HCC.

The Systematic Analyses of RING Finger Gene Signature for Predicting the Prognosis of Patients with Hepatocellular Carcinoma

RING finger (RNF) proteins are frequently dysregulated in human malignancies and are tightly associated with tumorigenesis. However, the expression profiles of RNF genes in hepatocellular carcinoma (HCC) and their relations with prognosis remain undetermined. Here, we aimed at constructing a prognostic model according to RNF genes for forecasting the outcomes of HCC patients using the data from The Cancer Genome Atlas (TCGA) program. We collected HCC datasets to validate the values of our model in predicting prognosis of HCC patients from International Cancer Genome Consortium (ICGC) platform. Then, functional experiments were carried out to explore the roles of the representative RNF in HCC progression. A total of 107 differentially expressed RNFs were obtained between TCGA-HCC tumor and normal tissues. After comprehensive evaluation, a prognostic signature composed of 11 RNFs (RNF220, RNF25, TRIM25, BMI1, RNF216P1, RNF115, RNF2, TRAIP, RNF157, RNF145, and RNF19B) was constructed based on TCGA cohort. Then, the Kaplan-Meier (KM) curves and the receiver operating characteristic curve (ROC) were employed to evaluate predictive power of the prognostic model in testing cohort (TCGA) and validation cohort (ICGC). The KM and ROC curves illustrated the good predictive power in testing and validation cohort. The areas under the ROC curve are 0.77 and 0.76 in these two cohorts, respectively. Among the prognostic signature genes, BMI1 was selected as a representative for functional study. We found that BMI1 protein level was significantly upregulated in HCC tissues. Moreover, the inhibitor of BMI1, PTC-209, displayed an excellent anti-HCC effect in vitro. Enrichment analysis of BMI1 downstream targets showed that BMI1 might be involved in tumor immunotherapy. Together, our overall analyses revealed that the 11-RNFs prognostic signature might provide us latent chances for evaluating HCC prognosis and developing novel HCC therapy.

Regulatory Roles of Noncoding RNAs in the Progression of Gastrointestinal Cancers and Health Disparities

Annually, more than a million individuals are diagnosed with gastrointestinal (GI) cancers worldwide. With the advancements in radio- and chemotherapy and surgery, the survival rates for GI cancer patients have improved in recent years. However, the prognosis for advanced-stage GI cancers remains poor. Site-specific GI cancers share a few common risk factors; however, they are largely distinct in their etiologies and descriptive epidemiologic profiles. A large number of mutations or copy number changes associated with carcinogenesis are commonly found in noncoding DNA regions, which transcribe several noncoding RNAs (ncRNAs) that are implicated to regulate cancer initiation, metastasis, and drug resistance. In this review, we summarize the regulatory functions of ncRNAs in GI cancer development, progression, chemoresistance, and health disparities. We also highlight the potential roles of ncRNAs as therapeutic targets and biomarkers, mainly focusing on their ethnicity-/race-specific prognostic value, and discuss the prospects of genome-wide association studies (GWAS) to investigate the contribution of ncRNAs in GI tumorigenesis.

Prognostic significance of long noncoding RNA HOTAIR in hepatocellular carcinoma: A protocol for systematic review and meta-analysis

BACKGROUND

Homeobox transcript antisense intergenic RNA (HOTAIR), a long noncoding RNA, has been reported to associate with the prognosis of patients with hepatocellular carcinoma (HCC) in several studies, however, the definite conclusion has not been obtained for conflicting results across different studies. The aim of this study is to determine the association of HOTAIR expression with overall survival, progression-free survival, and clinical features in HCC.

METHODS

PubMed, Cochrane Library, and Embase will be comprehensively searched to seek the relevant studies. The studies meeting the inclusion criteria will be included into this systematic review and meta-analysis. A combination of hazard ratio and 95% confidence interval is used to estimate the impact of HOTAIR expression on the overall survival and progression-free survival in HCC. The relationship between HOTAIR expression and clinical features of HCC is evaluated using the odds ratio and 95% confidence interval. The study quality is evaluated with the "risk of bias assessment" tool in Cochrane System Assessment Manual or Newcastle-Ottawa Scale. The subgroup analysis, publication bias, and sensitivity analysis are performed.

RESULTS

This study provides a strict and classic protocol for systematic review and meta-analysis to determine the prognostic significance of HOTAIR expression in HCC. The findings of this systematic review and meta-analysis may provide a novel diagnostic indicator and potential therapeutic target of HCC.

ETHICS AND DISSEMINATION

This study is only a protocol for systematic review and meta-analysis, and all data used in this study is acquired through published studies. Therefore, the ethical review is not needed for this study.

REGISTRATION NUMBER

INPLASY202230050.

LINC01234 Accelerates the Progression of Breast Cancer via the miR-525-5p/Cold Shock Domain-Containing E1 Axis

Backgrounds. Long noncoding RNAs (lncRNAs) are strongly associated with the development of breast cancer (BC). As yet, the function of LINC01234 in BC remains unknown. Methods. Using biological information, the potential lncRNA, miRNA, and target gene were predicted. LINC01234 and miR-525-5p expression in BC tissues was detected using quantitative real-time reverse transcription polymerase chain reaction. Fluorescence in situ hybridization was used to determine the distribution of LINC01234. Cell proliferation was analyzed using CCK-8 assay, colony formation, terminal deoxynucleotidyl transferase dUTP nick end labeling staining, and apoptosis evaluated using flow cytometry. Western blotting was used to evaluate protein expression. Dual-luciferase® reporter, RNA pull-down, and RNA immunoprecipitation assays were performed to analyze the binding relationships among LINC01234, miR-525-5p, and cold shock domain-containing E1 (CSDE1). Results. We screened out LINC01234, found to be significantly increased in BC tissues, associated with a poor prognosis, and positively correlated with tumor size of BC. Knockdown of LINC01234 suppressed BC cell growth and facilitated apoptosis. Dual-luciferase reporter®, RNA pull-down, and RNA immunoprecipitation assays confirmed that LINC01234 and CSDE1 directly interacted with miR-525-5p. Upregulation of miR-525-5p and suppression of CSDE1 inhibited BC cell growth and induced cell apoptosis. Conclusion. Upregulation of LINC01234 contributes to the development of BC through the miR-525-5p/CSDE1 axis. LINC01234 may be one of the potential diagnostic and treatment targets for BC.

Emerging roles and potential clinical applications of long non-coding RNAs in hepatocellular carcinoma

Hepatocellular carcinoma is one of the most common highly malignant tumors in humans, as well as the leading cause of cancer-related death worldwide. Growing evidence has indicated that lncRNAs are implicated in different molecular mechanisms, including interactions with DNA, RNA, or protein, so that to regulate the gene expression at epigenetic, transcriptional, or posttranscriptional level. Moreover, the mechanism of action of lncRNA is closely related to its subcellular localization. An increasing number of studies have certified that lncRNA plays a significant biological function in the occurrence and development of hepatocellular carcinoma, such as involving in cell proliferation, metastasis, apoptosis, ferroptosis, autophagy, and reprogramming of energy metabolism. As a result, lncRNA has great potential as a novel biomarker for diagnosis or therapeutics of hepatocellular carcinoma. In this review, we highlight the correlation between subcellular localization of lncRNA and its mechanism of action, discuss the biological roles of lncRNA and the latest research advances in hepatocellular carcinoma, and emphasize the potential of lncRNA as a therapeutic target for advanced patients of hepatocellular carcinoma.

HLA-DQB1-AS1 Promotes Cell Proliferation, Inhibits Apoptosis, and Binds with ZRANB2 Protein in Hepatocellular Carcinoma

Major histocompatibility complex, class II, DQ beta 1 antisense RNA 1 (HLA-DQB1-AS1) conferred the susceptibility to hepatocellular carcinoma. Sustaining cell growth and resisting apoptosis are two hallmarks of hepatocellular carcinoma. The present study explored the role of HLA-DQB1-AS1 in the proliferation and apoptosis of hepatocellular carcinoma cells and investigated its downstream pathway. Colony formation assay was performed to assess cell proliferation. Cell apoptosis was assessed with the TdT-mediated dUTP nick end labeling method. HLA-DQB1-AS1 deficiency exerts antiproliferative and proapoptotic effects on hepatocellular carcinoma cells. Moreover, based on bioinformatic analysis combined with the results of RNA immunoprecipitation assay, HLA-DQB1-AS1 was revealed to bind with zinc finger RANBP2-type containing 2 (ZRANB2) protein. ZRANB2 was upregulated in hepatocellular carcinoma at a clinical and cellular level. HLA-DQB1-AS1 caused no significant effects on ZRANB2 mRNA and protein expression. ZRANB2 knockdown suppressed cell proliferation and enhanced cell apoptosis of hepatocellular carcinoma. Moreover, ZRANB2 overexpression rescued the anticancer effect of silenced HLA-DQB1-AS1 in hepatocellular carcinoma cells. In conclusion, HLA-DQB1-AS1 promotes cell proliferation and inhibits apoptosis in hepatocellular carcinoma by the interaction with ZRANB2 protein.