Role of ZNF143 and Its Association with Gene Expression Patterns, Noncoding Mutations, and the Immune System in Human Breast Cancer

Abstract

The function of noncoding sequence variations at ZNF143 binding sites in breast cancer cells is currently not well understood. Distal elements and promoters, also known as cis-regulatory elements, control the expression of genes. They may be identified by functional genomic techniques and sequence conservation, and they frequently show cell- and tissue-type specificity. The creation, destruction, or modulation of TF binding and function may be influenced by genetic modifications at TF binding sites that affect the binding affinity. Therefore, noncoding mutations that affect the ZNF143 binding site may be able to alter the expression of some genes in breast cancer. In order to understand the relationship among ZNF143, gene expression patterns, and noncoding mutations, we adopted an integrative strategy in this study and paid close attention to putative immunological signaling pathways. The immune system-related pathways ErbB, HIF1a, NF-kB, FoxO, JAK-STAT, Wnt, Notch, cell cycle, PI3K–AKT, RAP1, calcium signaling, cell junctions and adhesion, actin cytoskeleton regulation, and cancer pathways are among those that may be significant, according to the overall analysis.

In‐silico and in‐vitro evidence suggest LINC01405 as a sponge for miR‐29b and miR‐497‐5p, and a potential regulator of Wnt, PI3K, and TGFB signaling pathways in breast carcinoma

“…Breast cancer is a multifaceted disease that requires further understanding of its underlying mechanisms. Current endeavors have been concentrated on exploring the molecular aspects participating in the onset and advancement of breast cancer 3,9,21 . Hundreds of molecular elements, such as proteins and RNAs, are involved in disease generation 22 .…”

“…GSE134359 (Long noncoding RNA landscape in breast cancer, 75 adjuvant tumors, and 12 Adjacent normal tissue), GSE29431 (Identifying breast cancer biomarkers in breast cancer, 54 tumors, and 12 normal tissue), GSE27562 (Expression data from human PBMCs, 57 tumors, and 37 control peripheral blood mononuclear cells (PBMCs), and GSE12777 (Analysis of 51 human breast cancer cell lines gene expression profiles). Next, the selected microarray datasets were subjected to a meta‐analysis to identify DEGs 3,9,18 . Before starting data processing, we annotated all genes and probe IDs as Entrez IDs to ensure consistency.…”

“…Next, the selected microarray datasets were subjected to a meta‐analysis to identify DEGs. 3 , 9 , 18 Before starting data processing, we annotated all genes and probe IDs as Entrez IDs to ensure consistency. In addition, we utilized the Sva package (version 3.40.0) in the R software to eliminate hidden batch effects and merge the four datasets.…”

“…LncRNAs play vital roles in the physiologic or pathologic status of cells, such as proliferation, development, and immunity 7 . They could adjust gene expression at the transcription, post‐transcription, and translation levels, as recent studies have implied their involvement in epigenetic regulation 8,9 . MicroRNAs are non‐coding, small RNAs with a length of 17 to 22 nucleotides that control the expression of genes.…”

“… 7 They could adjust gene expression at the transcription, post‐transcription, and translation levels, as recent studies have implied their involvement in epigenetic regulation. 8 , 9 MicroRNAs are non‐coding, small RNAs with a length of 17 to 22 nucleotides that control the expression of genes. They, impede translational progress by degrading mRNA through Watson and Crick base pairing between 3'‐UTR MREs and miRNA seed sequences.…”