Page 195 - Haematologica Vol. 110 - January 2025

LETTER TO THE EDITOR
Increased frequency of clonal hematopoiesis of indeterminate potential in Bloom syndrome probands and carriers
Bloom syndrome (BSyn, OMIM #210900) is a rare autosomal recessive disorder characterized by growth restriction, sun sensitivity, insulin resistance, mild immune deficiency, and increased risk of early-onset malignancy.1 BSyn cases are caused by homozygous or compound heterozygous pathogenic variants (PV) in BLM, with over 547 different PV identified in ClinVar.2 The Bloom Syndrome Registry (BSR) recently reported that 53% of participants had developed cancer, with hema- tologic malignancies being the most common cancer risk.3 While several studies have shown no association of carriers having increased risk,4,5 recent studies have identified in- creased risk of cancers in BLM PV carriers such as colorectal cancer,6 breast cancer7 and mesothelioma.8
Clonal hematopoiesis of indeterminate potential (CHIP) is characterized by somatic mutations in leukemia-related genes detected in individuals without apparent hematologic malignancy.9 CHIP is associated with an annual increased risk of leukemia ranging from 0.5% to 1.0%.9 Increased age and presence of germline variants in DNA repair and telomere maintenance genes are associated with increased prevalence of CHIP.10
The latter suggests that germline PV can create a “permissive” environment for clonal evolution,11 leading to clonal selection in hematopoietic cells. In a longitudinal study spanning 14 years with 4,596 participants who developed blood malig- nancies, 18 genes were found to predispose individuals to clonal hematopoiesis. Notably, BLM was one of these genes.12 Therefore, we hypothesized that one or two germline BLM PV may heighten CHIP risk in a dose-dependent fashion with one germline PV associated with mildly elevated malignancy risk while two germline PV are associated with increased malig- nancy risk at an early age. Using exome sequencing of BSyn patients and BLM carriers, we found that both BSyn probands and BLM carriers exhibited an increased frequency of CHIP compared to sex- and age-matched controls. This study sheds new light on the interplay between genetic predispositions and somatic variation and highlights the need for additional studies to further evaluate the mechanisms and potential clinical implications for patients with one or two BLM PV. All study participants provided informed consent under a protocol for the BSR approved by the Weill Cornell Medical College Institutional Review Board, and a material transfer agreement was obtained. We performed exome sequencing with the Nextera DNA Flex Pre-Enrichment Library Prep and the Roche NimbleGen exome capture kit following stan- dard protocols. Libraries were indexed, multiplexed and sequenced on a 2x150 Illumina NovaSeq S1 flowcell at the
UCLA Technology Center for Genomics and Bioinformatics. Age- and sex-matched control trios were obtained from the publicly available dbGAP study phs000178.v11.p8.c1, submitted by the Center for Mendelian Genomics (CMG) - The Broad Institute Joint Center for Mendelian Genomics - The Broad Institute Joint Center for Mendelian Genomics. Control trios harbored undiagnosed disease without cancer phenotypes and samples were processed with the Illumina Nextera Ex- ome Kit and sequenced on an Illumina HiSeq. The following public datasets were used: SRA ID SRS2136666, SRS2813808, SRS2136486, SRS2140039, SRS2140061, SRS2136721, SRS2203482, SRS2202906, SRS2202907, SRS2130875, SRS2136628, SRS2130876, SRS2197363, SRS2197826, SRS2197795, SRS2140305, SRS2137393, SRS2137389, SRS2200570, SRS2200550, SRS2200596, SRS2195820, SRS2195786, SRS2195798, SRS2200588, SRS2200627, SRS2200615, SRS2205811, SRS2195821, SRS2195834, SRS2136679, SRS2136619, SRS2136617, SRS2136629, SRS2136659, SRS2136613, SRS2203316, SRS2202950, SRS2202953, SRS2203490, SRS2203471, SRS2203336, SRS2200551, SRS2200573, SRS2200609, SRS2200624, SRS2200562, SRS2200610, SRS2200576, SRS2200561, SRS2288808, SRS2288810, SRS2288816, SRS2200626, SRS2200613, SRS2288805, SRS2200605
All FASTQ files underwent unified quality control, mapping and variant-calling based on GATK best-practices pipeline13 (Online Supplementary Figure S1A, B). Variant calls were filtered to maintain read depth (DP)>10 over the alternate allele. Variants were initially filtered for DP and analyzed for coverage across regions of interest. Subsequent filtering for genotype quality (GQ) and a quality score of “PASS” were included (Online Supplementary Figure S1B).
Variant allele frequencies (VAF), representing the percent- age of sequencing reads matching a specific DNA variant, were used as a surrogate measure of allele proportion. A VAF<0.3 indicated acquired somatic variants, while VAF≥0.3 indicated likely germline or de novo variants.14 CHIP is fur- ther defined as a somatic mutation in peripheral blood leukocytes with a VAF>0.02.15
We performed exome sequencing on 29 peripheral blood DNA samples obtained from the BSR. The cohort consist- ed of ten BSyn probands and their biological parents who are obligate carriers of PV in BLM (Table 1). Among the ten BSyn probands, there were equal numbers of males and females, ranging from 10 months to 36 years of age at time of sample collection. Five of the BSyn probands had a history post-collection of at least one type of cancer
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