Expression of ZNF695 Transcript Variants in Childhood B-Cell Acute Lymphoblastic Leukemia

ZNF695, A Potential Prognostic Biomarker, Correlates with Im mune Infiltrates in Cervical Squamous Cell Carcinoma and Endoce rvical Adenocarcinoma: Bioinformatic Analysis and Experimental Verification

BACKGROUND

The role of Zinc Finger Protein 695 (ZNF695) is unclear in cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC).

OBJECTIVE

The objective of this study was to conduct a comprehensive analysis and experimental validation of ZNF695 in CESC.

METHODS

The study investigated the expression of ZNF695 in both pan-cancer and CESC, utilizing data from The Cancer Genome Atlas (TCGA) database to assess its diagnostic value. The present study investigated the association between ZNF695 expression levels and clinical characteristics, as well as prognosis, in patients with CESC. The study explored potential regulatory networks involving ZNF695, including its association with immune infiltration, immune score, stemness index based on mRNA expression (mRNAsi), and drug sensitivity in CESC. We explored the expression of ZNF695 in CESC single cells. ZNF695 expression was validated using GSE29570.

RESULTS

ZNF695 was found to be aberrantly expressed in pan-cancer and CESC. There was a significant correlation observed between an elevated level of ZNF695 expression in patients with CESC and histological grade (p = 0.017). Furthermore, a strong association was found between high ZNF695 expression in CESC patients and poorer overall survival (OS) (HR: 1.87; 95% CI: 1.17-3.00; p = 0.009), Progression-free Survival (PFS) (HR: 1.86; 95% CI: 1.16-2.98; p = 0.010), and Disease-specific Survival (DSS) (HR: 1.98; 95% CI: 1.15-3.42; p = 0.014). The expression of ZNF695 in CESC patients (p = 0.006) was identified as an independent prognostic determinant. ZNF695 was associated with steroid hormone biosynthesis, oxidative phosphorylation, and so on. ZNF695 expression correlated with immune infiltration, immune score, and mRNAsi in CESC. ZNF695 expression significantly and negatively correlated with AICA ribonucleotide, BIX02189, QL-XI-92, STF-62247, and SNX-2112 in CESC. ZNF695 gene was upregulated in CESC tissues and cell lines. ZNF695 was significantly upregulated in the CESC cell lines.

CONCLUSION

ZNF695 may be a potential prognostic biomarker and immunotherapeutic target for CESC patients.

Circular RNA DLGAP4 alleviates sevoflurane-induced neurotoxicity by regulating miR-9-5p/Sirt1/BDNF pathway

BACKGROUND

Sevoflurane is a widely used anesthetic in infants. However, long and repeated exposure to this drug can cause developmental neurotoxicity. This study aimed to investigate the role and mechanism of circular RNA DLGAP4 (circDLGAP4) in sevoflurane-induced neurotoxicity.

METHODS

Neonatal mice and mouse hippocampal neuronal cell line HT22 were used to construct sevoflurane-induced nerve injury models. The role of circDLGAP4 in sevoflurane-induced neurotoxicity was evaluated by gain-and/or loss-of-function methods. Pathological alterations in hippocampus were analyzed by hematoxylin-eosin and Tunel staining. Cell injury was assessed by cell viability and apoptosis, which was detected by CCK-8 and flow cytometry. The expression of circDLGAP4 and miR-9-5p was determined by real-time PCR. Sirt1 and BDNF levels were measured by Western blot. Productions of TNF-α and IL-6 were examined by ELISA. Dual-luciferase reporter assay and/or RNA pull-down assay were used to confirm the direct binding among circDLGAP4, miR-9-5p, and Sirt1. Rescue experiments were used to further verify the mechanism of circDLGAP4.

RESULTS

CircDLGAP4 expression was decreased by sevoflurane both in vivo and in vitro. Overexpression of circDLGAP4 elevated cell viability, reduced apoptosis and levels of TNF-α and IL-6, while circDLGAP4 knockdown showed the opposite effects in sevoflurane-induced HT22 cells. Mechanically, circDLGAP4 functioned via directly binding to and regulating miR-9-5p, followed by targeting the Sirt1/BDNF pathway. Additionally, circDLGAP4 upregulation relieved sevoflurane-induced nerve injury, reduced levels of TNF-α, IL-6 and miR-9-5p, but increased the expression of Sirt1 and BDNF in hippocampus.

CONCLUSIONS

Our studies found that circDLGAP4 relieved sevoflurane-induced neurotoxicity by sponging miR-9-5p to regulate Sirt1/BDNF pathway.

Long Non-Coding RNA Signatures in Lymphopoiesis and Lymphoid Malignancies

Lymphoid cells play a critical role in the immune system, which includes three subgroups of T, B, and NK cells. Recognition of the complexity of the human genetics transcriptome in lymphopoiesis has revolutionized our understanding of the regulatory potential of RNA in normal lymphopoiesis and lymphoid malignancies. Long non-coding RNAs (lncRNAs) are a class of RNA molecules greater than 200 nucleotides in length. LncRNAs have recently attracted much attention due to their critical roles in various biological processes, including gene regulation, chromatin organization, and cell cycle control. LncRNAs can also be used for cell differentiation and cell fate, as their expression patterns are often specific to particular cell types or developmental stages. Additionally, lncRNAs have been implicated in lymphoid differentiation, such as regulating T-cell and B-cell development, and their expression has been linked to immune-associated diseases such as leukemia and lymphoma. In addition, lncRNAs have been investigated as potential biomarkers for diagnosis, prognosis, and therapeutic response to disease management. In this review, we provide an overview of the current knowledge about the regulatory role of lncRNAs in physiopathology processes during normal lymphopoiesis and lymphoid leukemia.

Low Expression of BRCA1 as a Potential Relapse Predictor in B-Cell Acute Lymphoblastic Leukemia

B-cell acute lymphoblastic leukemia (B-ALL) is the most common childhood hematological malignancy worldwide. Treatment outcomes have improved dramatically in recent years; despite this, relapse is still a problem, and the potential molecular explanation for this remains an important field of study. We performed microarray and single-cell RNA-Seq data mining, and we selected significant data with a P -value<0.05. We validated BRCA1 gene expression by means of quantitative (reverse transcription-polymerase chain reaction.) We performed statistical analysis and considered a P -value<0.05 significant. We identified the overexpression of breast cancer 1, early onset (BRCA1; P -value=2.52 -134 ), by means of microarray analysis. Moreover, the normal distribution of BRCA1 expression in healthy bone marrow. In addition, we confirmed the increases in BRCA1 expression using real-time (reverse transcription-polymerase chain reaction and determined that it was significantly reduced in patients with relapse ( P -values=0.026). Finally, we identified that the expression of the BRCA1 gene could predict early relapse ( P -values=0.01). We determined that low expression of BRCA1 was associated with B-cell acute lymphoblastic leukemia relapse and could be a potential molecular prognostic marker.

A radiation resistance related index for biochemical recurrence and tumor immune environment in prostate cancer patients

PURPOSE

To establish and verify a novel radiation resistance related index for predicting biochemical recurrence and tumor immune environment in prostate cancer (PCa) patients.

MATERIALS AND METHODS

The transcriptome information of PCa were obtained from GEO and TCGA portal. We identified radiation resistance related genes (RRGs) between radioresistant and radiosensitive PCa cells. We conducted multivariate Cox analysis to construct a novel radiation resistance related index for predicting biochemical recurrence (BCR)-free survival (BCRFS). Internal and external validations were conducted. Preliminary experimental verifications were performed.

RESULTS

We identified 194 differentially expressed RRGs and three radiation resistance related molecular clusters for PCa. Moreover, we established a novel radiation resistance related index and succeeded in conducting internal and external validations. High-risk populations meant significantly worse BCRFS in training, testing and validating cohort. The area under receiver operating characteristic curve were 0.809, 0.698, and 0.712 in training, testing, and validating cohort. The immune microenvironment was significantly different between high and low-risk score patients. Preliminary experiment identified and validated three potential biomarkers related to radiation resistance (ZNF695, TM4SF19, CCDC3) of PCa.

CONCLUSIONS

This study successfully established and verified a novel radiation resistance related index, which had an excellent performance in predicting BCR and tumor immune microenvironment in patients with PCa.

Differential mRNA and long noncoding RNA expression profiles in pediatric B-cell acute lymphoblastic leukemia patients

BACKGROUND

Long non-coding RNAs (lncRNAs) are transcripts longer than 200 nucleotides (nt) that are involved in the pathogenesis and development of various cancers including B cell acute lymphoblastic leukemia (B-ALL). To determine the potential roles of lncRNAs involved in pathogenesis of B-ALL, we analyzed the expression profile of lncRNAs and mRNAs in B-ALL, respectively, and constructed lncRNAs/mRNAs interaction network.

METHODS

We performed RNA sequencing of 10 non-leukemic blood disease donors and 10 B-ALL patients for Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Interactions among mRNAs were predicted using the STRING database. Quantitative real time PCR (qRT-PCR) was performed to verify the RNA-seq data of lncRNAs and mRNAs. Potential functions of subtype-specific lncRNAs were determined by using coexpression-based analysis on distally (trans-pattern) located protein-coding genes.

RESULTS

A total of 1813 differentially expressed transcripts (DETs) and 2203 lncRNAs were identified. Moreover, 10 dysregulated lncRNAs and 10 mRNAs were randomly selected, and further assessed by RT-qPCR in vitro. Go and KEGG analysis demonstrated that the differentially expressed mRNAs were most closely associated with myeloid leukocyte activation and in transcriptional misregulation in cancer, respectively. In addition, co-expression analysis demonstrated that these lncRNAs, including MSTRG.27994.3, MSTRG.21740.1, ENST00000456341, MSTRG.14224.1 and MSTRG.20153.1, may mediate the pathogenesis and development of B-ALL via lncRNA-mRNA network interactions.

CONCLUSIONS

These results showed that several mRNAs and lncRNAs are aberrantly expressed in the bone marrow of B-ALL patients and play potential roles in B-ALL development, and be useful for diagnostic and/or prognostic purposes in pediatric B-ALL.

DATA AVAILABILITY

The datasets used during our study are available through HARVARD Dataverse Persistent ID doi: https://doi.org/10.7910/DVN/LK9T4Z .

Alternative splicing of BCL-X and implications for treating hematological malignancies

BCL-X is a member of the BCL-2 family. It regulates apoptosis and plays a critical role in hematological malignancies. It is well-known that >90% of human genes undergo alternative splicing. A total of 10 distinct splicing transcripts of the BCL-X gene have been identified, including transcript variants 1–9 and ABALON. Different transcripts from the same gene have different functions. The present review discusses the progress in understanding the different alternative splicing transcripts of BCL-X, including their characteristics, functions and expression patterns. The potential use of BCL-X in targeted therapies for hematological malignancies is also discussed.

LncRNAs serve as novel biomarkers for diagnosis and prognosis of childhood ALL

Background

Although some studies have demonstrated that lncRNAs are dysregulated in hematopoietic malignancies and may regulate the progression of leukemia, the detailed mechanism underlying tumorigenesis is still unclear. This study aimed to investigate lncRNAs that are differentially expressed in childhood B-cell acute lymphoblastic leukemia (B-ALL) and T-cell acute lymphoblastic leukemia (T-ALL) and their potential roles in the progression of childhood ALL.

Methods

Microarrays were used to detect differentially expressed lncRNAs and mRNAs. Several aberrantly expressed lncRNAs were validated by qRT-PCR. Leukemia-free survival was analyzed using the Kaplan–Meier method with a log-rank test. The co-expression correlations of lncRNAs and mRNAs were determined by Spearman’s correlation coefficient. CCK-8 assays and flow cytometry were performed to measure cell proliferation and apoptosis.

Results

We revealed that many lncRNAs were abnormally expressed in B-ALL and T-ALL. LncRNA/mRNA co-expression and the gene locus network showed that dysregulated lncRNAs are involved in diverse cellular processes. We also assessed the diagnostic value of the differentially expressed lncRNAs and confirmed the optimal combination of TCONS_00026679, uc002ubt.1, ENST00000411904, and ENST00000547644 with an area under the curve of 0.9686 [95 % CI: 0.9369–1.000, P < 0.001], with 90.7 % sensitivity and 92.19 % specificity, at a cut-off point of -0.5700 to distinguish childhood B-ALL patients from T-ALL patients, implying that these specific lncRNAs may have potential to detect subsets of childhood ALL. Notably, we found that the 8-year leukemia-free survival of patients with high TCONS_00026679 (p = 0.0081), ENST00000522339 (p = 0.0484), ENST00000499583 (p = 0.0381), ENST00000457217 (p = 0.0464), and ENST00000451368 (p = 0.0298) expression levels was significantly higher than that of patients with low expression levels of these lncRNAs, while patients with high uc002ubt.1 (p = 0.0499) and ENST00000547644 (p = 0.0451) expression levels exhibited markedly shorter 8-year leukemia-free survival. In addition, some lncRNAs were found to play different roles in cell proliferation and apoptosis in T-ALL and B-ALL.

Conclusions

Dysregulated lncRNAs involved in different regulatory mechanisms underlying the progression of childhood T-ALL and B-ALL might serve as novel biomarkers to distinguish ALL subsets and indicate poor outcomes.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40364-021-00303-x.

LINC00221 suppresses the malignancy of children acute lymphoblastic leukemia

As the most common malignant disease in childhood, children acute lymphoblastic leukemia (ALL) is a heterogeneous disease caused by the accumulated genetic alterations. Long non-coding RNAs (lncRNAs) are reported as critical regulators in diseases. GEPIA database indicated that long intergenic non-protein coding RNA 221 (LINC00221) was conspicuously down-regulated in acute myeloid leukemia. However, its expression pattern in ALL has not been revealed. This work was carried out to study the role of LINC00221 in ALL cells. Quantitative real-time PCR (qRT-PCR) quantified LINC00221 expression in ALL cells. The function of LINC00221 in ALL was determined by ki-67 immunofluorescence staining, EdU, TUNEL, JC-1, and caspase-3/8/9 activity assays. RNA pull down and Ago2-RNA immunoprecipitation (RIP) assays investigated the interaction between miR-152-3p and LINC00221 or ATPase sarcoplasmic/endoplasmic reticulum Ca2⁺ transporting 2 (ATP2A2). Our study revealed the low expression of LINC00221 in ALL cells. Subsequently, LINC00221 was verified to bind with miR-152-3p. Moreover, functional assays pointed out that LINC00221 overexpression posed anti-proliferation and pro-apoptosis effects in ALL cells, and these effects could be separately reversed by miR-152-3p up-regulation. Afterward, LINC00221 was revealed to regulate ATP2A2 expression via sponging miR-152-3p. Additionally, ATP2A2 was verified to involve in regulating LINC00221-mediated ALL cell proliferation and apoptosis. In conclusion, LINC00221 suppressed ALL cell proliferation and boosted ALL cell apoptosis via sponging miR-152-3p to up-regulate ATP2A2.

Transcriptome Analysis Identifies LINC00152 as a Biomarker of Early Relapse and Mortality in Acute Lymphoblastic Leukemia

Evidence showing the role of long non-coding RNAs (lncRNAs) in leukemogenesis have emerged in the last decade. It has been proposed that these genes can be used as diagnosis and/or prognosis biomarkers in childhood acute lymphoblastic leukemia (ALL). To know if lncRNAs are associated with early relapse and early mortality, a microarray-based gene expression analysis in children with B-lineage ALL (B-ALL) was conducted. Cox regression analyses were performed. Hazard ratios (HR) and 95% confidence intervals (95% CI) were calculated. LINC00152 and LINC01013 were among the most differentially expressed genes in patients with early relapse and early mortality. For LINC00152 high expression, the risks of relapse and death were HR: 4.16 (95% CI: 1.46–11.86) and HR: 1.99 (95% CI: 0.66–6.02), respectively; for LINC01013 low expression, the risks of relapse and death were HR: 3.03 (95% CI: 1.14–8.05) and HR: 6.87 (95% CI: 1.50–31.48), respectively. These results were adjusted by NCI risk criteria and chemotherapy regimen. The lncRNA–mRNA co-expression analysis showed that LINC00152 potentially regulates genes involved in cell substrate adhesion and peptidyl–tyrosine autophosphorylation biological processes. The results of the present study point out that LINC00152 could be a potential biomarker of relapse in children with B-ALL.