Editors: Donna E. Hansel, MD, PhD, division head of pathology and laboratory medicine, MD Anderson Cancer Center, Houston; James Solomon, MD, PhD, assistant professor, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York; Erica Reinig, MD, assistant professor and medical director of molecular diagnostics, University of Wisconsin-Madison; Marcela Riveros Angel, MD, molecular genetic pathology fellow, Department of Pathology, Oregon Health and Science University, Portland; Maedeh Mohebnasab, MD, assistant professor of pathology, University of Pittsburgh; Alicia Dillard, MD, clinical pathology chief resident, New York-Presbyterian/Weill Cornell Medical Center; and Richard Wong, MD, PhD, assistant professor of pathology, University of California San Diego.
Use of telomere profiling to determine telomere lengths
July 2024—Telomeres are repetitive DNA sequences at the end of a chromosome that protect the chromosome from damage. They are maintained in equilibrium, as continual shortening at each round of DNA replication is counterbalanced by the de novo addition of telomere sequence repeats by telomerase. Failure to maintain the length distribution leads to short telomere syndromes that manifest as age-related degenerative diseases, such as pulmonary fibrosis, immunodeficiency, and bone marrow failure. In contrast, long telomeres can predispose people to cancer. Mutations that increase telomerase expression are one of the most common cancer-associated molecular findings. Telomere length distribution can be interrogated using such methods as Southern blotting, flow cytometry fluorescence in situ hybridization (flow-FISH), and quantitative fluorescence in situ hybridization (qFISH). However, some of these methods cannot distinguish which telomere comes from which chromosome. Moreover, they are cumbersome and not widely available or amenable for clinical use. The authors conducted a study in which they described telomere profiling, a reproducible, accurate, and accessible tool that measures the length of telomeres in the cell at near-nucleotide resolution. Telomere profiling is based on the physical enrichment and sequencing of telomeres using MinIon long-read sequencing (Oxford Nanopore Technologies). This method digests DNA and enriches telomeric ends via a biotin/streptavidin protocol (TeloTag). The enriched telomeric regions then undergo restriction enzyme digestion and are sequenced. Telomere profiling resulted in an approximately 3,400-fold increase in telomere reads when compared to whole genome sequencing. The overall process is amenable to multiplexing and can be incorporated into other sequencing workflows. The authors evaluated a number of algorithms for determining telomere length. Mapping sequencing reads to a reference genome was unreliable because subtelomere sequences vary in the population. To overcome this issue, the authors developed an algorithm (TeloNP) to define the telomere length on each telomere read. TeloNP defines the subtelomere boundary based on a discontinuity in telomere sequence content and measures length from that boundary to the TeloTag. Telomere profiling of blood from six test subjects produced results comparable to findings from Southern blotting and flow-FISH. The authors then examined chromosome end–specific lengths in 147 subjects. They found that chromosomes 17p, 20q, and 12p tended to be the shortest telomeres across the population, and 4q, 12q, and 3p tended to be the longest. To determine whether chromosome end–specific telomere lengths are present at birth, the authors performed telomere profiling on cord blood. They found that the same chromosome arms had the longest and shortest telomere lengths, a finding in line with previous work that suggested that differences in telomere lengths are established at birth. Being able to accurately measure chromosome end–specific telomere length has important implications for understanding human disease. Telomere length measurement may provide clinical insights about patients with idiopathic bone marrow failure, immunodeficiency, and pulmonary fibrosis–emphysema. Telomere profiling uses an accessible multifunctional sequencing platform that can be developed in research and clinical labs at manageable start-up costs, allowing broad access to accurate and reproducible telomere length determinations. This method hopefully will lower the barrier to adoption of more widespread telomere testing for clinical and research endeavors.
Karimian K, Groot A, Huso V, et al. Human telomere length is chromosome end-specific and conserved across individuals. Science. 2024;384(6695):533–539.
Correspondence: Dr. Carol W. Greider at cgreider@ucsc.edu
Link between an IKZF1 variant and leukemia risk in Hispanic and Latino children
Acute lymphoblastic leukemia is the most common malignancy in U.S. children. Within this cohort, patients of Hispanic or Latino ancestry have the greatest risk of leukemia (59.6 cases per 1 million people). This group has an approximately 1.3-fold increased incidence of B-cell acute lymphoblastic leukemia (B-ALL) when compared to non-Hispanic white children, and this difference rises to more than twofold in adolescents and young adults. Previous genomewide association studies (GWASs) have focused on the genetic predisposition of B-ALL and identified several single nucleotide polymorphisms (SNPs) associated with increased disease risk. These have included variants in close proximity to genes involved in B-cell development and hematopoiesis, such as IKZF1, ARID5B, CEBPE, and GATA3. Some of these high-risk alleles have occurred at a higher frequency in Hispanic and Latino populations than among people of predominantly European ancestry. The authors assessed ALL risk in the former group. They focused on a GWAS of childhood ALL in self-reported Hispanic and Latino people (1,878 cases and 8,441 controls) from the California Cancer Records Linkage Project. They identified 109 genomewide significant SNPs within the IKZF1 gene. This gene encodes a transcription factor associated with chromatin remodeling and is primarily expressed in hematopoietic and lymphopoietic cells. The three SNPs most associated with risk of ALL were located in the promoter region of IKZF1 or localized to the 3’ end of the gene, regions noted to be ALL risk loci in previous GWASs of population groups. Statistical fine-mapping identified additional variants in linkage disequilibrium with these high-risk SNPs. One of these variants, called rs1451367, overlapped a putative functional regulatory element of IKZF1 and may be an important contributor to the increased risk of acquiring ALL. This regulatory element is critical for chromatin accessibility in B cells and their precursors, with the greatest accessibility at the pro-B stage but minimal or no accessibility in other hematopoietic lineages. Therefore, these SNPs may influence ALL predisposition during early B-cell development. This finding is consistent with the observation that IKZF1 SNPs appear to confer risk for B-precursor ALL but not for T-cell ALL. To further interrogate this finding, the authors mined a large collection of chromatin data from 156 patients with B-precursor ALL and found that the rs1451367 variant significantly reduced chromatin accessibility. In vitro functional studies showed that this variant affected enhancer activity in REH cells, which resemble human pro-B cells, but did not impact other human cell lines, including HEK293T and HepG2 cells. The increased incidence of ALL in the Hispanic and Latino populations is a well-established cancer disparity that impacts children and young adolescents across the United States and Latin America. Additional research is warranted to better understand the biologic impact of the genetic variants that confer this disparity in the incidence of ALL and how that may affect other clinical endpoints.
De Smith AJ, Wahlster L, Jeon S, et al. A noncoding regulatory variant in IKZF1 increases acute lymphoblastic leukemia risk in Hispanic/Latino children. Cell Genom. 2024. doi:10.1016/j.xgen.2024.100526
Correspondence: Dr. Adam J. de Smith at desmith@usc.edu or Dr. Vijay G. Sankaran at sankaran@broadinstitute.org