| Literature DB >> 33608382 |
Bénédicte Burlet1,2, Selim Ramla1,3, Cyril Fournier1,2, Maria Jimena Abrey-Recalde1, Camille Sauter1, Marie-Lorraine Chrétien1,4, Cédric Rossi1,5, Yannis Duffourd1, Sylviane Ragot2, Céline Buriller6, Benjamin Tournier1,2,3, Caroline Chapusot3, Nathalie Nadal6, Jessica Racine4, Julien Guy4, François Bailly4, Laurent Martin1,3, Olivier Casasnovas1,5, Jean-Noël Bastie1,5, Denis Caillot1,5, Juliette Albuisson7, Cyril Broccardo8, Catherine Thieblemont9,10, Laurent Delva1, Marc Maynadié1,4,11, Romain Aucagne1,2, Mary B Callanan1,2.
Abstract
Diagnosis of B-cell chronic lymphocytic leukemia (B-CLL) is usually straightforward, involving clinical, immunophenotypic (Matutes score), and (immuno)genetic analyses (to refine patient prognosis for treatment). CLL cases with atypical presentation (e.g., Matutes ≤ 3) are also encountered, and for these diseases, biology and prognostic impact are less clear. Here we report the genomic characterization of a case of atypical B-CLL in a 70-yr-old male patient; B-CLL cells showed a Matutes score of 3, chromosomal translocation t(14;18)(q32;q21) (BCL2/IGH), mutated IGHV, deletion 17p, and mutations in BCL2, NOTCH1 (subclonal), and TP53 (subclonal). Quite strikingly, a novel PAX5 mutation that was predicted to be loss of function was also seen. Exome sequencing identified, in addition, a potentially actionable BRAF mutation, together with novel somatic mutations affecting the homeobox transcription factor NKX2-3, known to control B-lymphocyte development and homing, and the epigenetic regulator LRIF1, which is implicated in chromatin compaction and gene silencing. Neither NKX2-3 nor LRIF1 mutations, predicted to be loss of function, have previously been reported in B-CLL. Sequencing confirmed the presence of these mutations together with BCL2, NOTCH1, and BRAF mutations, with the t(14;18)(q32;q21) translocation, in the initial diagnostic sample obtained 12 yr prior. This is suggestive of a role for these novel mutations in B-CLL initiation and stable clonal evolution, including upon treatment withdrawal. This case extends the spectrum of atypical B-CLL with t(14;18)(q32;q21) and highlights the value of more global precision genomics for patient follow-up and treatment in these patients.Entities:
Keywords: hematological neoplasm
Year: 2021 PMID: 33608382 PMCID: PMC7903887 DOI: 10.1101/mcs.a005934
Source DB: PubMed Journal: Cold Spring Harb Mol Case Stud ISSN: 2373-2873
Variants of interest by exome sequencing in an atypical case of B-cell chronic lymphocytic leukemia (B-CLL) with t(14;18)(q32;q21)
| Gene | Chromo some | Exon | Accession ID | mRNA change | Predicted protein effect | Variant type | COSMIC | Sequenc ing depth | Ref depth | Alt depth | Variant allele frequency | GERP++ RS scorea | CADD phred scoreb | PolyPhen-2 HDIV scorec | SIFT scored | ExAC pLI scoree | Metadome tolerance scoref | ClinVar signifi canceg |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 18q21.33 | 2/3 | NM_000633.2 | c.17G > C | p.A6T | Missense | COSV61 374585 | 35 | 28 | 7 | 20.0% | 3.61 | 16.37 | 0.534 (possibly damaging) | 0.015 (damaging) | 0.2965 | 0.51 (intolerant) | / | |
| 7q34 | 11/18 | NM_004333.4 | c.1406G > C | p.G469A | Missense | COSV56 061424 | 34 | 24 | 10 | 29.4% | 5.62 | 27.50 | / | 0.000 (damaging) | 0.9968 (intolerant) | 0.48 (intolerant) | Pathogenic | |
| 1p13.3 | 2/4 | NM_018372.3 | c.793dupA | p.T265fs | Frameshift | N/A | 49 | 30 | 19 | 38.8% | / | / | / | / | 0.0906 (tolerant) | 0.63 (slightly intolerant) | / | |
| 10q24.2 | 2/2 | NM_145285.2 | c.547A > G | p.S183G | Missense | COSV10 0755073 | 61 | 33 | 28 | 45.9% | 5.45 | 27.10 | 0.217 (benign) | 0.159 (tolerated) | 0.9505 (intolerant) | 0.32 (intolerant) | / | |
| 9p13.2 | 5/10 | NM_016734.2 | c.570_582 delCAGCGC CGACACC | p.S191fs | Frameshift | N/A | 36 | 27 | 9 | 25.0% | / | / | / | / | 0.6463 | 0.37 (intolerant) | / |
See text for reference publications on pathogenicity prediction scores.
(COSMIC) Catalog Of Somatic Mutations In Cancer, (GERP++RS) Genomic Evolutionary Rate Profiling (GERP)—Rejected Substitutions (RS) score, (CADD) Combined Annotation Dependent Depletion, (PolyPhen-2) Polymorphism Phenotyping v2, (SIFT) Sorting Intolerant From Tolerant, (N/A) not applicable, (/) not determined.
aFrom −12.3 to 6.17. The higher the score, the more conserved the site.
b<20: variant is in the top 1% to 0.1% most damaging variations; <30: variant is in the top 0.1 to 0.01% most damaging variations.
cFrom 0 to 1. The higher the score, the higher the probability for the mutation to be damaging for the protein.
dPredicts whether an amino acid substitution affects protein function.
eDescribes the probability of a gene being loss of function intolerant. >0.9: extremely intolerant; <0.1: tolerant.
fThe MetaDome tolerance is based on the tolerance colors of the web server MetaDome (https://stuart.radboudumc.nl/metadome/).
ghttps://www.ncbi.nlm.nih.gov/clinvar/
Figure 1.(A) Integrated Genomic Viewer (IGV) display (at progression) and Sanger validation (at diagnosis [DIAG] and progression [PROG]) of the PAX5, NKX2-3, LRIF1, and BRAF mutations identified in the patient's blood. (B) Representation of PAX5, NKX2-3, LRIF1, and BRAF proteins with annotated domains and amino acids numbered underneath. Plots were generated (https://www.cbioportal.org/mutation_mapper) with recurrent mutations (green, missense; blue, truncating; red, other) identified in COSMIC (hematopoietic and lymphoid tissues). Mutations seen in the patient are shown beneath the protein map. (C) Gene expression of NKX2-3 and LRIF1 in hematopoietic populations isolated from cord blood, bone marrow, and peripheral blood of healthy donors (nBM, normal bone marrow; PB, peripheral blood). RNA-seq data (GSE51984 and GSE48846) were downloaded from the Gene Expression Omnibus (GEO).