Novel Mutation Hotspots within Non-Coding Regulatory Regions of the Chronic Lymphocytic Leukemia Genome

Abstract

Mutations in non-coding DNA regions are increasingly recognized as cancer drivers. These mutations can modify gene expression in cis or by inducing high-order chormatin structure modifications with long-range effects. Previous analysis reported the detection of recurrent and functional noncoding DNA mutations in the chronic lymphocytic leukemia (CLL) genome, such as those in the 3′ untranslated region of NOTCH1 and in the PAX5 super-enhancer. In this report, we used whole genome sequencing data produced by the International Cancer Genome Consortium in order to analyze regions with previously reported regulatory activity. This approach enabled the identification of numerous recurrently mutated regions that were frequently positioned in the proximity of genes involved in immune and oncogenic pathways. By correlating these mutations with expression of their nearest genes, we detected significant transcriptional changes in genes such as PHF2 and S1PR2. More research is needed to clarify the function of these mutations in CLL, particularly those found in intergenic regions. A major part of mutations in the cancer genome occur in non-coding DNA regions, and their function is still beginning to be understood 1. Non-coding DNA comprises approximately 98% of the human genome, but recent research has proven that most of these regions are either part of regulatory motifs or actively transcribed to RNA 2,3. These mutations can induce functional genomic changes by altering the binding of transcription factors or by inducing high-order chromatin structural modifications 2,4. For example, mutations in 5′ and 3′ untranslated regions (UTRs) may disturb RNA structural conformation, modify microRNA binding sites or disrupt polyadenylation signals 2. In a similar fashion, mutations affecting non-protein coding genes such as microRNA and long intergenic RNA genes (lincRNAs) are known cancer driver events 2,5. Different studies have evidenced that the expression of genes such as BRCA1, CDH10, CCND1, MALAT1, PAX5, RB1, SDHD, TERT, TOX3, and TAL1 is influenced by non-coding DNA mutations in regulatory regions of the cancer genome 1,6,7. The Pancancer Analysis of Whole Genomes (PCAWG) project has revealed the existence of common and tumor-specific recurrently mutated functional elements near known cancer drivers 7. Some of these driver mutations can induce long-range changes in genome organization and trigger abnormal expression of distant oncogenes and tumor suppressors 8. Furthermore, the sequence distribution of these driver mutations is not random. Hornshøj et al. (2018) identified a significant enrichment in conserved CCCT-binding factor (CTCF) binding sites among recurrently mutated non-coding DNA regions with cancer specificity 6. Similarly, Line et al. (2019) identified 21 recurrently altered CTCF-rich insulator regions in the cancer genome, and elegantly demonstrated that some of these mutations drive tumor proliferation 9. Chronic Lymphocytic Leukemia (CLL) is among the most frequent lymphoproliferative disorders, and it is cha...

Chronic lymphocytic leukemia patients withIGHtranslocations are characterized by a distinct genetic landscape with prognostic implications

“…In this work, we have reported mutations in coding and non‐coding regions of BCL2 and IGLL5 and, specifically, we identified a novel recurrent 5′UTR mutation in BCL2 . Although this mutation has not been previously described, proximal mutations have been detected in other CLL and NHL studies 8,34,44 . Moreover, the vast majority of BCL2 mutations reported in Puente et al were detected in cases harboring IGH/BCL2 translocations, 8 which is consistent with our results (Supplementary Figure S3).…”

“…The Agilent SureSelect QXT Target Enrichment system for Illumina Multiplexed Sequencing (Agilent Technologies, Santa Clara, CA) was used to produce libraries of exonic regions from 54 genes CLL‐related as well as from BCL2 , IGLL5 and NOTCH1 UTR regions (Supplementary Methods). Genes included in the custom‐designed panel 31,32 are involved in CLL pathogenesis and the UTR regions were considered due to the previous identification of IGLL5 , BCL2 and NOTCH1 UTRs somatic mutations in CLL 8,33,34 (Supplementary Table S2). Paired‐end sequencing (151‐bp reads) was run on the Illumina NextSeq instrument (Illumina, San Diego, CA).…”

Pluripotent Stem Cell-Based Cell Therapy—Promise and Challenges

“…Synonymous mutations could change DNA structure and functions, especially splicing, and potentially could alter encoded proteins. Second, mutations in intergenic regions may be pathogenic (Mosquera Orgueira et al, 2020). Non-coding regions occupy 98% of genome and were called ''junk'' DNA.…”

How Chaotic Is Genome Chaos?

“…Many B cell tumors also showed evidence of ectopic AID-induced somatic hypermutation [ 156 , 157 , 158 , 159 ]. Many of the hypermutated regions do not encode proteins but include altered regulatory sites that stimulate expression of putative oncogenic loci in DLBCL tumors [ 160 , 161 ]. It was known from work on immunoglobulin SHM that AID activity was targeted specifically to V region exons in the producing cells by special “diversity activation” (DIVAC) enhancer elements at each IG locus [ 162 ].…”