Combined transcriptomics and in-silico approach uncovers the role of prognostic biomarkers in hepatocellular carcinoma

Solanki, Rubi; Singh, Prithvi; Beg, Md Amjad; Dohare, Ravins; Verma, Amit Kumar; Ahmad, Farhan Jalees; Alankar, Bhavya; Athar, Fareeda; Kaur, Harleen

doi:10.1016/j.humgen.2023.201154

Cited by 4 publications

(4 citation statements)

References 97 publications

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“…mRNA HTseq and miRNA-seq count data of TCGA-LUAD were retrieved from the UCSC Xena browser ( https://xenabrowser.net/ ) 9 . Back-log-transformation and cross-checking of the mRNA-seq and miRNA-seq LUAD cohort samples with TCGA-GDC 10 data portal was performed as discussed previously 11 , 12 . Pre-processing (i.e., normalization and transformation) of mRNA-seq and miRNA-seq cohorts was performed as discussed previously 11 , 12 .…”

Section: Methodsmentioning

confidence: 99%

“…Back-log-transformation and cross-checking of the mRNA-seq and miRNA-seq LUAD cohort samples with TCGA-GDC 10 data portal was performed as discussed previously 11 , 12 . Pre-processing (i.e., normalization and transformation) of mRNA-seq and miRNA-seq cohorts was performed as discussed previously 11 , 12 . Batch correction of pre-processed values was performed as discussed previously 12 .…”

Section: Methodsmentioning

confidence: 99%

“…Pre-processing (i.e., normalization and transformation) of mRNA-seq and miRNA-seq cohorts was performed as discussed previously 11 , 12 . Batch correction of pre-processed values was performed as discussed previously 12 . Ensembl IDs to their corresponding HGNC symbol(s) mapping in the mRNA-seq cohort was performed as discussed previously 12 .…”

Section: Methodsmentioning

confidence: 99%

“…Batch correction of pre-processed values was performed as discussed previously 12 . Ensembl IDs to their corresponding HGNC symbol(s) mapping in the mRNA-seq cohort was performed as discussed previously 12 . Duplicate genes were handled as discussed previously 13 – 18 .…”

Section: Methodsmentioning

confidence: 99%

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Exploring the role of miR-200 family in regulating CX3CR1 and CXCR1 in lung adenocarcinoma tumor microenvironment: implications for therapeutic intervention

Sharma,

Singh,

Jha

et al. 2023

Sci Rep

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Lung adenocarcinoma (LUAD) is the most common malignant subtype of lung cancer (LC). miR-200 family is one of the prime miR regulators of epithelial-mesenchymal transition (EMT) and worst overall survival (OS) in LC patients. The study aimed to identify and validate the key differentially expressed immune-related genes (DEIRGs) regulated by miR-200 family which may serve for therapeutic aspects in LUAD tumor microenvironment (TME) by affecting cancer progression, invasion, and metastasis. The study identified differentially expressed miRNAs (DEMs) in LUAD, consisting of hsa-miR-200a-3p and hsa-miR-141-5p, respectively. Two highest-degree subnetwork motifs identified from 3-node miRNA FFL were: (i) miR-200a-3p-CX3CR1-SPIB and (ii) miR-141-5p-CXCR1-TBX21. TIMER analysis showed that the expression levels of CX3CR1 and CXCR1 were significantly positively correlated with infiltrating levels of M0-M2 macrophages and natural killer T (NKT) cells. The OS of LUAD patients was significantly affected by lower expression levels of hsa-miR-200a-3p, CX3CR1 and SPIB. These DEIRGs were validated using the human protein atlas (HPA) web server. Further, we validated the regulatory role of hsa-miR-200a-3p in an in-vitro indirect co-culture model using conditioned media from M0, M1 and M2 polarized macrophages (THP-1) and LUAD cell lines (A549 and H1299 cells). The results pointed out the essential role of hsa-miR-200a-3p regulated CX3CL1 and CX3CR1 expression in progression of LC TME. Thus, the study augments a comprehensive understanding and new strategies for LUAD treatment where miR-200 family regulated immune-related genes, especially chemokine receptors, which regulate the metastasis and invasion of LUAD, leading to the worst associated OS.

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