Molecular Genetics of Chronic Lymphocytic Leukaemia


Chronic lymphocytic leukaemia (CLL) is a B‐cell malignancy and the most prevalent leukaemia in the Western world, most prevalent in elderly individuals. The disease exhibits vast clinical heterogeneity, ranging from a benign disease for many decades, to one requiring immediate treatment. With the application of modern genomic technologies, we now have a detailed view of the genomic architecture of the CLL genome. This includes a detailed catalogue of the genes targeted by copy number changes and mutations in the disease, as well as their clinical impact. In addition, we have an expanding understanding of the epigenetic profile of the disease that gives fundamental insights into the original transforming cell, and the regulatory networks contributing to the disease. This information has considerable clinical implications, improving diagnosis, prognostication and helping to guide therapeutic interventions with greater accuracy.

Key Concepts

  • CLL is a disease with a very heterogeneous clinical outcome such that patients can exhibit an indolent or a progressive disease resistant to chemo‐immunotherapy.
  • This reflects considerable biological variability such that the mutational and epigenomic landscape differs between patients.
  • Only by understanding this biological variability can a patient's clinical heterogeneity be understood.
  • Immunogenetic analysis, through the study of immunoglobulin structure, has helped divide CLL patients into two prognostically relevant subgroups.
  • Chromosomal deletions and aneuploidy events, not fusion‐genes and chromosomal rearrangements define CLL, where their presence can aid in patient stratification.
  • The genome of CLL harbours a relatively low number of somatic lesions, but those that are identified target genes important in DNA damage response, cell cycle control, intracellular signalling, RNA processing and chromatin remodelling.
  • Epigenetic analysis of CLL provides important information regarding the cell from which the tumour arose, and also the regulatory mechanisms that are dysregulated.

Keywords: chronic lymphocytic leukaemia (CLL); haematology; cancer; immunoglobulin structure; somatic mutations; genomic lesions; mutational landscape; epigenetics; DNA methylation; chromatin re‐modelling

Figure 1. B‐cell development andCLLtransformation: Shows B‐cell development and maturation parallel to CLL transformation. B cells develop, undergo selection and differentiate into plasma cells or memory B cells. Key to this process is somatic hypermutation (SHM) and (if required) class switching. Naïve B cells, that have not undergone any SHM which then become CLL cells, possess 100% homology to the germline IGHV genes (unmutated CLL or U‐CLL). B cells that do undergo full SHM and/or class switching and become CLL cells will possess less than 98% homology to the germline IGHV genes (mutated CLL or M‐CLL). CLL pathogenesis can occur anywhere between these two points, producing a spectrum of CLL cells that will possess a greater/lower homology to the germline IGHV genes; this is why IGHV mutational status is a good indicator of cell of origin. IGHV mutational status in B cells also has a good concordance with methylation status of B cells. B cells that have undergone very limited SHM (or no SHM) are also typically hypermethylated; these usually correspond to U‐CLL cases and termed low programmed (LP). B cells that have experienced SHM are typically hypomethylated; these usually correspond to M‐CLL cases and termed high programmed (HP). As with IGHV mutational status, there is a spectrum of cells that will have varying degrees of methylation. This intermediate group are referred to as intermediate programmed (IP).
Figure 2. Snapshot of theCLL(epi)genome: (a) Chromosomal aberrations: A brief glimpse of the genomic regions where the main lesions occur. In CLL, chromosome 13 frequently has a deletion of the q arm; this deletion can vary in size but has a minimally deleted region (MDR) as portrayed in the figure. This region includes DLEU2 which also consists of the miRNA cluster 15a/16‐1, known for their roles in BCL2 suppression. The q arm of chromosome 11 is frequently deleted, affecting the ATM gene. Whilst not shown, the ATM gene can be fully lost or partially deleted, resulting in no protein production or defunct ATM protein production respectively. Of several common chromosome 17 deletions, the most biologically relevant aberration is that on the p arm, as depicted in the figure, where TP53 is affected. (b) Histone modifications and DNA methylation: A brief overview of epigenetic mechanisms taking place at the chromatin and/or the DNA level. Using ZAP70 as an example, Panel (i) shows the H3K4me3 histone marker, a well‐established marker of actively transcribed genes; the level of this modification is known to largely correlate with transcriptional activity. It is possible to have other histone modifications, including H3K36me3 (active gene), H3K27me3 (repressed gene) and acetylated H4 markers (also involved in active transcription) (as shown in the figure). Typically, H3 and H4 histones are modified due to their long tails; however, H2A and H2B are also capable of modification. Panel (ii) depicts methylation on a DNA level. Using ZAP70 again, it is possible to see CpG islands between exons 1 and 2. Zooming in on this structure shows the cytosine–guanine dinucleotides with methylated cytosine residues, typically associated with reduced transcriptional activity. C‐246 and C‐343 are known to be unmethylated in ZAP70 positive CLL patients. (c) miRNA miR‐150: An example of miRNA gene regulation. miR‐150 is a well‐known miRNA in CLL, being the most highly expressed miRNA in CLL patients. However, miRNA expression has great heterogeneity between patients and is associated with a range of clinical outcomes. miR‐150 was found to be down‐regulating expression of FOXP1 and GAB1, assisting B‐cell maturation and preventing uncontrolled proliferation. Studies found that patients with high levels of miR‐150 typically had a better OS, whereas the inverse situation did not. (d) NOTCH1 Mutation: Panel (i) depicts the most common NOTCH1 mutation found in CLL (P2514fs or ΔCT7544‐7545). This mutation is the deletion of 2 residues (cytosine and thymine), shifting the reading frame out by 2 base pairs. As a consequence, an altered peptide chain is created; 4 codons down from the site of the deletion is a stop codon. The mutation takes place in the PEST domain; as a result, the PEST domain is truncated due to the premature stop codon. Panel (ii) shows how this truncated version of the protein continues to signal, due to the inability to degrade the protein using ubiquitin (Ub), in comparison to a healthy variant of NOTCH1‐ICD in which the signal is diminished through PEST degradation. (e) SF3B1 Mutation: Panel (i) depicts one of the most common mutations observed in SF3B1‐mutated CLL patients (K700E). The altered amino acid results in the abnormal folding of the protein and thereby distorts the final tertiary structure. Panel (ii) shows the result of this substitution; altered SF3B1 conformation causes aberrant splicing, producing abnormal spliced variants.
Figure 3. Common mutations inCLL: (a) Captures a snapshot of the CLL mutational landscape from sample data obtained from the COSMIC database (data from: Genes mutated at a prevalence of less than 2% are excluded from the graph; in addition, mutant genes known to appear as false positives (e.g. PCLO) or mutations of genes known to not be driving CLL pathology (e.g. ILGL5 and KLHL6 which are both off‐target sites of SHM) have also been excluded. The key take‐home message from this graph is that four genes are mutated in relatively high frequencies (SF3B1, ATM, NOTCH1 and TP53), and there is a tail of genes mutated more rarely. (b) A summary of common mutations in CLL, derived from multiple cohorts and studies published in literature, and their corresponding prevalence range across published studies.


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Further Reading

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Makewita, Lara E, and Strefford, Jonathan C(Mar 2019) Molecular Genetics of Chronic Lymphocytic Leukaemia. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0028437]