Long non-coding RNA PAX8-AS1 polymorphisms increase the risk of childhood acute lymphoblastic leukemia

Penalized Bayesian forward continuation ratio model with application to high-dimensional data with discrete survival outcomes

While time-to-event data are often continuous, there are several instances where discrete survival data, which are inherently ordinal, may be available or are more appropriate or useful. Several discrete survival models exist, but the forward continuation ratio model with a complementary log-log link has a survival interpretation and is closely related to the Cox proportional hazards model, despite being an ordinal model. This model has previously been implemented in the high-dimensional setting using the ordinal generalized monotone incremental forward stagewise algorithm. Here, we propose a Bayesian penalized forward continuation ratio model with a complementary log-log link and explore different priors to perform variable selection and regularization. Through simulations, we show that our Bayesian model outperformed the existing frequentist method in terms of variable selection performance, and that a 10% prior inclusion probability performed better than 1% or 50%. We also illustrate our model on a publicly available acute myeloid leukemia dataset to identify genomic features associated with discrete survival. We identified nine features that map to ten unique genes, five of which have been previously associated with leukemia in the literature. In conclusion, our proposed Bayesian model is flexible, allows simultaneous variable selection and uncertainty quantification, and performed well in simulation studies and application to real data.

Association of LncRNA-PAX8-AS1 and LAIR-2 polymorphisms along with their expression with clinical and subclinical hypothyroidism

The genetic and epigenetic architecture of clinical and subclinical hypothyroidism remains unclear. We investigated the impact of long noncoding RNA (LncRNA)-PAX8-AS1 and LAIR-2 genetic variants on the susceptibility to clinical and subclinical hypothyroidism, their influence on LncRNA-PAX8-AS1 and LAIR-2 expression and their potential as hypothyroid biomarkers. Hundred clinical hypothyroid patients, 110 subclinical hypothyroid patients, and 95 healthy controls were enrolled. Gene expression analysis and genotyping were performed by qPCR. LAIR-2 protein, a proinflammatory mediator, was tested by ELISA. Serum LncRNA-PAX8-AS1 was downregulated, whereas LAIR-2 mRNA and protein levels were upregulated in clinical and subclinical hypothyroid patients compared to healthy controls. LncRNA-PAX8-AS1 rs4848320 and rs1110839 were associated with increased risk of clinical hypothyroidism. Interestingly, both SNPs were associated with differential expression of serum LncRNA-PAX8-AS1 among clinical hypothyroid patients. LAIR-2 rs2287828 was associated with elevated risk of both clinical and subclinical hypothyroidism. Harboring the rs2287828 T allele augmented the LAIR-2 mRNA expression among clinical hypothyroid patients, while elevated both LAIR-2 mRNA and protein levels in subclinical hypothyroid patients. The rs4848320-rs1110839-rs2287828 TTT, CTT, and CGT haplotypes were associated with increased hypothyroid risk. Surprisingly, serum LncRNA-PAX8-AS1 and LAIR-2 mRNA expression demonstrated superior diagnostic accuracy for clinical hypothyroidism and turned out as independent predictors in the multivariate analysis. Conclusively, LncRNA-PAX8-AS1 and LAIR-2 genetic variants are novel genetic biomarkers of hypothyroidism that could alter the LncRNA-PAX8-AS1 and LAIR-2 expression. LncRNA-PAX8-AS1 and LAIR-2 expression profiles have the potential as effective diagnostic and prognostic indicators of hypothyroidism.

LncRNA-PAX8-AS1 Silencing Decreases Cell Viability, Enhances Apoptosis, and Suppresses Doxorubicin Resistance in Myeloid Leukemia via the miR-378g/ERBB2 Axis

Objective

Considering the role of lncRNAs reported as regulators in acute myeloid leukemia (AML) progression, the current research aims to investigate the role of PAX8-AS1 in chemo-resistant AML.

Methods

Human AML cells HL60 and human doxorubicin (ADM)-resistant AML cells (HL60/ADM cells) were used to establish in vitro models of chemo-sensitive AML and refractory/recurrent AML, respectively. CCK-8 assay and flow cytometry were used to determine cell resistance to ADM, viability, and apoptosis. PAX8-AS1, miR-378g, and ERBB2 expressions in the models and/or AML patients were quantified via qRT-PCR or Western blot. The miRNA/mRNA axis targeted by PAX8-AS1 was analyzed using Starbase, TargetScan, or GEO and validated through a dual-luciferase reporter assay. The expressions of Bcl-2, Bax, and C Caspase-3 in cells were quantitated by Western blot.

Results

The highly expressed PAX8-AS1 was observed in AML patients and HL60 cells, which was more evident in refractory/recurrent AML patients and HL60/ADM cells. Compared with that in ADM-treated parental HL60 cells, the viability of ADM-treated HL60/ADM cells remained strong. PAX8-AS1 overexpression increased viability and Bcl-2 expression, while diminishing apoptosis, Bax, and C Caspase-3 expressions in HL60 cells. However, the abovementioned aspects were oppositely impacted by PAX8-AS1 silencing in HL60/ADM cells. PAX8-AS1 directly targeted miR-378g, whose expression pattern is opposite to that of PAX8-AS1 in AML. MiR-378g upregulation abrogated the effects of PAX8-AS1 overexpression on HL60 cells. MiR-378g downregulation offset PAX8-AS1 silencing-induced effects on HL60/ADM cells. Moreover, ERBB2 was recognized as the target of miR-378g, with a higher expression in HL60/ADM cells than in HL60 cells.

Conclusion

PAX8-AS1 silencing decreases cell viability, enhances apoptosis, and suppresses ADM resistance in AML via regulating the miR-378g/ERBB2 axis.

Association between PAX8AS1 (rs4848320 C > T, rs1110839 G > T, and rs6726151 T > G) and MEG3 (rs7158663) gene polymorphisms and non-Hodgkin lymphoma risk

Long non-coding RNA (lncRNA) PAX8 antisense RNA 1 (PAX8AS1) and Maternal-expressed gene 3 (MEG3) contribute to the pathogenesis of various malignancies including non-Hodgkin lymphoma (NHL). In this study, we aimed to examine the possible association of polymorphisms of PAX8 and MEG3 and the risk NHL. A total of 175 patients and 175 healthy subjects were genotyped by PCR-RFLP and Tetra-Arms PCR assays. Results demonstrated rs4848320 C > T and rs6726151 T > G of PAX8AS1 and rs7158663 of MEG3 play a potential role in the susceptibility of NHL and PAX8AS1 rs1110839 T > G variant was associated with decreased risk of NHL. Haplotype analysis of rs1110839, rs4848320, and rs6726151 demonstrated GCG haplotype is associated with increased risk of lymphoma and TTG, TTT, and GTT haplotypes are related to decreased lymphoma susceptibility.

Linear and Circular Long Non-Coding RNAs in Acute Lymphoblastic Leukemia: From Pathogenesis to Classification and Treatment

The coding regions account for only a small part of the human genome, and the remaining vast majority of the regions generate large amounts of non-coding RNAs. Although non-coding RNAs do not code for any protein, they are suggested to work as either tumor suppressers or oncogenes through modulating the expression of genes and functions of proteins at transcriptional, posttranscriptional and post-translational levels. Acute Lymphoblastic Leukemia (ALL) originates from malignant transformed B/T-precursor-stage lymphoid progenitors in the bone marrow (BM). The pathogenesis of ALL is closely associated with aberrant genetic alterations that block lymphoid differentiation and drive abnormal cell proliferation as well as survival. While treatment of pediatric ALL represents a major success story in chemotherapy-based elimination of a malignancy, adult ALL remains a devastating disease with relatively poor prognosis. Thus, novel aspects in the pathogenesis and progression of ALL, especially in the adult population, need to be further explored. Accumulating evidence indicated that genetic changes alone are rarely sufficient for development of ALL. Recent advances in cytogenic and sequencing technologies revealed epigenetic alterations including that of non-coding RNAs as cooperating events in ALL etiology and progression. While the role of micro RNAs in ALL has been extensively reviewed, less attention, relatively, has been paid to other non-coding RNAs. Herein, we review the involvement of linear and circular long non-coding RNAs in the etiology, maintenance, and progression of ALL, highlighting the contribution of these non-coding RNAs in ALL classification and diagnosis, risk stratification as well as treatment.

MAGI2-AS3 restrains proliferation, glycolysis, and triggers apoptosis in acute lymphoblastic leukemia via regulating miR-452-5p/FOXN3 pathway

OBJECTIVES

MAGI2-AS3 is a cancer suppressor gene of multiple malignancies. Acute lymphoblastic leukemia (ALL) is an important type of leukemia that especially occurs in children. Our work evaluated the modulation of MAGI2-AS3 in ALL.

MATERIALS AND METHODS

qPCR and Western blotting were adopted for detection of target molecular expression. Growth and apoptosis were determined by CCK8 assay and Annexin V/PI staining. Glycolysis was detected by commercial kits. The direct binding between miR-452-5p and MAGI2-AS3 or FOXN3 was assessed by luciferase reporter assay. Tumor growth was measured in nude mice in vivo.

RESULTS

MAGI2-AS3 was down-regulated in ALL. Enforced expression of MAGI2-AS3 inhibited growth and glycolysis while promoting apoptosis of ALL cells. Moreover, MAGI2-AS3 up-regulated FOXN3 via sponging miR-452-5p. FOXN3 depletion abrogated MAGI2-AS3-mediated anti-cancer action. More importantly, MAGI2-AS3 repressed ALL cell growth in nude mice through regulation of miR-452-5p/FOXN3.

CONCLUSION

MAGI2-AS3 inhibits ALL development via modulating miR-452-5p/FOXN3.

DNA methylation at a nutritionally sensitive region of the PAX8 gene is associated with thyroid volume and function in Gambian children

PAX8 is a key thyroid transcription factor implicated in thyroid gland differentiation and function, and PAX8 gene methylation is reported to be sensitive to the periconceptional environment. Using a novel recall-by-epigenotype study in Gambian children, we found that PAX8 hypomethylation at age 2 years is associated with a 21% increase in thyroid volume and an increase in free thyroxine (T4) at 5 to 8 years, the latter equivalent to 8.4% of the normal range. Free T4 was associated with a decrease in DXA-derived body fat and bone mineral density. Furthermore, offspring PAX8 methylation was associated with periconceptional maternal nutrition, and methylation variability was influenced by genotype, suggesting that sensitivity to environmental exposures may be under partial genetic control. Together, our results demonstrate a possible link between early environment, PAX8 gene methylation and thyroid gland development and function, with potential implications for early embryonic programming of thyroid-related health and disease.

Ferroptosis-Related Long Non-Coding RNA signature predicts the prognosis of Head and neck squamous cell carcinoma

Background: Head and neck squamous cell carcinoma (HNSCC) are head and neck cancers. On the other hand, ferroptosis is a novel iron-dependent and ROS reliant type of cell death observed various disease conditions.

Method: We constructed a prognostic multilncRNA signature based on ferroptosis-related differentially expressed lncRNAs in HNSCC.

Results: We identified 25 differently expressed lncRNAs associated with prognosis of HNSCC. Kaplan-Meier analyses revealed the high-risk lncRNAs signature associated with poor prognosis of HNSCC. Moreover, the AUC of the lncRNAs signature was 0.782, underscoring their utility in prediction HNSCC prognosis. Indeed, our risk assessment model was superior to traditional clinicopathological features in predicting HNSCC prognosis. GSEA revealed the immune and tumor-related pathways in the low risk group individuals. Moreover, TCGA revealed T cell functions including cytolytic activity, HLA, regulation of inflammationp, co-stimulation, co-inhibition and coordination of type II INF response were significantly different between the low-risk and high-risk groups. Immune checkpoints such as PDCD-1 (PD-1), CTLA4 and LAG3, were also expressed differently between the two risk groups.

Conclusion: A novel ferroptosis-related lncRNAs signature impacts on the prognosis of HNSCC.

Diagnostic value of candidate noncoding RNAs in leukocytes of patients with gestational diabetes mellitus

Noncoding RNAs (ncRNAs) are involved in the pathological processes of various diseases. The aim of the present study was to verify the expression levels and the diagnostic value of two candidate ncRNAs in the blood leukocytes of patients with gestational diabetes mellitus (GDM) compared to healthy controls. The long ncRNA paired box 8 antisense 1 (Pax8-AS1) and the microRNA miR-4646 were selected, which were identified to be associated with GDM by bioinformatics analysis of a dataset from the Gene Expression Omnibus GEO database. By using reverse transcription-quantitative PCR, the expression levels of Pax8-AS1 and miR-4646 were analysed in leukocytes of patients with GDM (n=35) and normal pregnant females (n=35). The results indicated a significant decrease in the expression levels of both Pax8-AS1 and miR-4646 in patients with GDM as compared with those in the healthy controls. In the second trimester, a strong negative correlation between Pax8-AS1/miR-4646 and 2-h glucose levels was detected in patients with GDM. Receiver operating characteristic curve analysis indicated that the levels of Pax8-AS1 and miR-4646 in the second trimester of pregnancy had a significant diagnostic value with high selectivity and specificity for GDM (area under the curve values, 0.902 and 0.891, respectively; P<0.001). Overall, the present study suggested that Pax8-AS1 and miR-4646 may serve as promising diagnostic biomarkers for GDM.

Construction of a 14-lncRNA risk score system predicting survival of children with acute myelocytic leukemia

Acute myelocytic leukemia (AML) is a frequent type of acute leukemia. The present study was performed to build a risk score system for the prognostic prediction of AML. AML RNA-sequencing data from samples from 111 children were downloaded from The Cancer Genome Atlas database. Using the DEseq and edgeR packages, the differentially expressed long non-coding RNAs (DE-lncRNAs) between bad and good prognosis groups were identified. A survival package was used to screen prognosis-associated lncRNAs and clinical factors. The optimal lncRNA combination was selected using the penalized package, and the risk-score system was built and evaluated. After the lncRNA-mRNA expression correlation network was constructed, the potential pathways involving the key lncRNAs were enriched using Gene Set Enrichment Analysis. Among the 61 DE-lncRNAs, 48 lncRNAs were significantly associated with prognosis. Relapse was an independent prognostic factor. The optimal 14-lncRNA risk score system was constructed. After 730 differentially expressed mRNAs were identified between the good and bad prognosis groups divided using a prognostic index, the lncRNA-mRNA expression correlation network was constructed. Enrichment analysis showed that semaphorin-3C [SEMA3C; regulated by probable leucine-tRNA ligase, mitochondrial (LARS2-AS1)] and secreted frizzled-related protein 5 [SFRP5; mediated by WASH complex subunit 5 (WASHC5)-antisense RNA 1 (AS1)] were involved in axon guidance and the Wnt signaling pathway, respectively. A 14-lncRNA (including paired box protein Pax8-AS1 and MYB AS1) risk-score system might be effective in predicting the prognosis of AML. Axon guidance (involving SEMA3C and LARS2-AS1) and the Wnt signaling pathway (involving SFRP5 and WASHC5-AS1) might be two important pathways affecting the prognosis of AML.

Genetics of blood malignancies among Iranian population: an overview

BACKGROUND

Blood malignancies are among the leading causes of cancer related deaths in the world. Different environmental and genetic risk factors are involved in progression of blood malignancies. It has been shown that the lifestyle changes have affected the epidemiological patterns of these malignancies. Hematologic cancers are the 5th common cancer among Iranian population. It has been observed that there is a rising trend of blood malignancies incidences during the recent decades. Therefore, it is required to design novel diagnostic methods for the early detection of such malignancies in this population.

MAIN BODY

In present review we have summarized all of the significant genes which have been reported among Iranian patients with blood malignancies. The reported genes were categorized based on their cell and molecular functions to clarify the molecular biology and genetics of blood malignancies among Iranian patients.

CONCLUSION

It was observed that the epigenetic and immune response factors were the most frequent molecular processes associated with progression of blood malignancies among Iranian population. This review paves the way of introducing a population based panel of genetic markers for the early detection of blood malignancies in this population.

Polymorphism in lncRNA AC016683.6 and its interaction with smoking exposure on the susceptibility of lung cancer

Background

Long non-coding RNAs play pivotal roles in the carcinogenesis of multiple types of cancers. This study is firstly to evaluate influence of rs4848320 and rs1110839 polymorphisms in long non-coding RNA AC016683.6 on the susceptibility of lung cancer.

Methods

The present study was a hospital-based case–control study with 434 lung cancer patients and 593 cancer-free controls. Genotyping of the two SNPs detected by Taqman^® allelic discrimination method.

Results

There were no statistically significant associations between rs4848320 and rs1110839 polymorphisms in AC016683.6 and risk of lung cancer in overall population. However, in the smoking population, rs4848320 and rs1110839 polymorphisms significantly increased the risk of lung cancer in dominant and homozygous models (Rs4848320: P = 0.029; Rs1110839: P = 0.034), respectively. In male population, rs1110839 genetic variant was related to the risk of lung cancer in all genetic models (GG vs. TT: P = 0.008; Dominant model: P = 0.029; Recessive model: P = 0.027) rather than heterozygous model. The crossover analyses provided rs4848320 and rs1110839 risk genotypes carriers combined with smoking exposure 2.218-fold, 1.755-fold increased risk of lung cancer (Rs4848320: P = 0.005; Rs1110839: P = 0.017). Additionally, there were significantly positive multiplicative interaction of rs4848320 polymorphism with smoking status, with adjusted OR of 2.244 (1.162–4.334), but rs1110839 polymorphism did not exist.

Conclusions

Rs4848320 and rs1110839 polymorphisms may be associated with lung cancer susceptibility. Interaction of rs4848320 risk genotypes with smoking exposure may strengthen the risk effect on lung cancer.