Multi-omics analysis to identify novel prognostic biomarker for brain cancer Ravi Bhushan1, Humaira Noor2, and Miya John3* 1 .Centre for Genetic Disorders, Institute of Science, Banaras Hindu University, India 2. University of Sydney, New South Wales, Australia 3.Gynaecological Cancer Research Group, Lowy Cancer Research Centre, Faculty of Medicine, University of New South Wales, Australia. *Correspondence to MJ: miya.john@unsw.edu.au
Abstract
Methods and Materials
Background: Low-grade gliomas (LGG) are infiltrative brain tumors (gliomas) comprising 15% of all brain cancers with poor overall survival rate. Rationale: There is a dearth of prognostic markers for gliomas that can aid in categorizing patients and assessing the effect of treatment in clinical trials. Methods: Correlation between PODNL1 expression and survival was analyzed in four independent transcriptomic datasets along with analysis of differential PODNL1 expression in IDH status. Correlation of PODNL1 mRNA expression with various clinical attributes and DNA methylation were analysed on the MEXPRESS portal. Gene and transcript variant expression of PODNL1 in normal human tissues was analysed on the GTEx portal while correlation of PODNL1 expression with various invasive gene signatures was analyzed on GEPIA2. Results: High PODNL1 expression was strongly correlated with poor survival in all datasets of LGG (HR>1, p<0.0001). PODNL1 expression was significantly (p<0.0001) much higher in case of wild type IDH as compared to mutant IDH along with poorer survival in both cases of IDH status. PODNL1 shows significantly higher expression in grade III and astrocytoma subtype. Across healthy human tissue samples profiled in the GTEx cohort, highest expression of PODNL1 gene and its transcripts were found in the tibial nerve, cultured fibroblasts and artery. PODNL1 expressions significantly correlate with an extracellular matrix gene signature for invasive phenotype.
Multi-omic data for PODNL1 and clinical data from 4 independent LGG cohorts downloaded from GlioVis and MEXPRESS portals
Correlation analysis between PODNL mRNA expression and survival
Analysis of PODNL mRNA expression in different histological subtype and grade
Analysis of PODNL total mRNA and transcript variant expression in various human tissues
Conclusion: PODNL1 is a novel and robust prognostic biomarker that is potentially involved in invasion and metastasis of LGG.
Correlation between PODNL1 promoter methylation and mRNA expression
Results PODNL1 is an unfavourable prognostic Biomarker in LGG
Fig.1. Correlation between PODNL1 expression and survival. Analysis of correlation between PODNL1 and survival in four independent transcriptomic datasets, A-C). The Cancer Genome Atlas (TCGA)-LGG, D-F). Chinese Glioma Genome Atlas (CGGA), G-I). REMBRADNT and J-L) GSE16011 reveals that PODNL1 expression is significantly related with poor survival. Data was downloaded from GlioVis portal.
Correlation between PODNL1 mRNA expression and survival is independent of IDH status in LGG Patient
PODNL1 is highly expressed in astrocytoma subtype and grade III of LGG
Fig.2. Correlation between PODNL1 expression and IDH status. Survival analysis for 2A,D) LGG (combined data for astrocytoma, oligodendroglioma and oligoastrocytoma, the two histological subtypes of LGG – 2B,E) astrocytoma and 2C,F) oligodendroglioma in IDH status idntifies that poorer survival due to increased expression of PODNL1 is independent of IDH status.
Fig.3. PODNL1 mRNA expression in different histological subtypes and grade of LGG. PODNL1 mRNA expression in different histological sub-type (astrocytoma and oligodendroglioma; Fig. 2A, C, E, G) and grade (grade II and III; Fig. 2B, D, F, H) shows higher expression in astrocytoma and grade III in four independent transcriptomic datasets i.e. TCGA, CGGA, REMBRADNT and GSE16011.
PODNL1 expression is significantly correlated with DNA methylation status and various clinical attributes
PODNL1 gene and its transcript variants expression across healthy human tissues A.
B.
Fig.5. PODNL1 and its transcripts expression in the healthy human tissues. PODNL1 total mRNA (A) and transcript variant (B) expression across human tissues profiled in the GTEx cohort. Across healthy human tissue samples profiled in GTEx cohorts, highest PODNL1 expression was found in the tribial nerve, cultured fibroblast and artery (Fig.6A). GTEx data reveals around thirteen transcripts of PODNL1 and all of them had higher expression in nerve cells (Fig.6B). Data analyzed on GTEx portal.
Conclusions PODNL1 is a novel and robust prognostic biomarker for LGG. PODNL1 is an unfavorable prognostic biomarker and is independent of IDH1/2 status. In light of these findings, the role of PODNL1 in LGG should be closely examined.
References Fig.5. Multi-omic data analysis of PODNL1. Correlation between DNA methylation status and various clinical data as well as the relationship between them was analysed on mexpress. Data was analyzed on MEXPRESS. For all the variants of PODNL1, mRNA expression was inversely proportional to the methylation status i.e. with increasing methylation, expression of PODNL1 was decreasing. Among various clinical attraibutes, mRNA expression of PODNL1 significantly correlates with family history (p value=0.022), histological subtype (p value=1.9e-7), IDH1 mutation (p value=4.6e-5), neoplasmic histologic grade (p value=2.0e-6), new tumor event after initial treatment (p value=0.032), person neoplasm cancer status (p value=0.035), primary therapy outcome success (p value=0.007), supratentorial localisation (p value=4.9e-4), and tumor location (p value=5.2e-7).
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Acknowledgement Indian Council of Medical Research (ICMR) is highly acknowledged