KaryoTap-based scDNA seq assessment of aneuploidy induction by hydroquinone in hematopoietic stem cells
- 1NYU School of Medicine
Abstract
Monosomy 7 is a frequent cytogenetic alteration associated with poor outcomes in myelodysplastic syndrome and acute myeloid leukemia. The benzene metabolite hydroquinone (HQ) has been reported to induce chromosome 7 loss in cultured hematopoietic cells, suggesting a mechanism linking benzene exposure to these diseases. However, these findings were largely based on FISH analysis of selected chromosomes in relatively small numbers of cells. Here, we tested whether HQ increases aneuploidy in primary human CD34+ hematopoietic stem and progenitor cells (HSPCs) using KaryoTap, a single-cell DNA sequencing approach that measures copy number across all 22 autosomes, together with interphase FISH. We first identified 20 uM as the highest HQ concentration tested that preserved sufficient viable cells for single-cell analysis. We then examined cord blood and adult mobilized CD34+ cells, including the MPS1 inhibitor reversine as a positive control in the cord blood experiment. Reversine increased whole-chromosome gains and losses, including those of chromosome 7. HQ did not produce a reproducible increase in aneuploidy across three donors and two sources of CD34+ cells, including two concentrations and two timepoints in the adult donor. A modest increase in chromosome 7 loss in one cord blood donor was not reproduced in the other donors. In the other cord blood donor, the estimated upper bound on the HQ-associated increase was approximately 1.4 percentage points. HSPCs also showed a greater increase in chromosome losses than epithelial cells or melanocytes following the same reversine exposure. These findings do not support a substantial, reproducible increase in whole-chromosome aneuploidy after HQ exposure under the conditions tested. They are consistent with a model in which benzene exposure favors the expansion of pre-existing monosomy 7 clones, although this possibility requires direct testing.
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BibTeX
@misc{trifas2026karyotapbased,
title = {{KaryoTap-based scDNA seq assessment of aneuploidy induction by hydroquinone in hematopoietic stem cells}},
author = {M. Trifas and S. Aronson and F. Alfieri and M. Kogenaru and R. Kim and T. Davoli},
howpublished = {bioRxiv},
year = {2026},
month = nov,
doi = {10.64898/2026.11.02.763824},
url = {https://www.biorxiv.org/content/10.64898/2026.11.02.763824v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - KaryoTap-based scDNA seq assessment of aneuploidy induction by hydroquinone in hematopoietic stem cells
AU - M. Trifas
AU - S. Aronson
AU - F. Alfieri
AU - M. Kogenaru
AU - R. Kim
AU - T. Davoli
PY - 2026
DA - 2026/11/02
PB - bioRxiv
DO - 10.64898/2026.11.02.763824
UR - https://www.biorxiv.org/content/10.64898/2026.11.02.763824v1
AB - Monosomy 7 is a frequent cytogenetic alteration associated with poor outcomes in myelodysplastic syndrome and acute myeloid leukemia. The benzene metabolite hydroquinone (HQ) has been reported to induce chromosome 7 loss in cultured hematopoietic cells, suggesting a mechanism linking benzene exposure to these diseases. However, these findings were largely based on FISH analysis of selected chromosomes in relatively small numbers of cells. Here, we tested whether HQ increases aneuploidy in primary human CD34+ hematopoietic stem and progenitor cells (HSPCs) using KaryoTap, a single-cell DNA sequencing approach that measures copy number across all 22 autosomes, together with interphase FISH. We first identified 20 uM as the highest HQ concentration tested that preserved sufficient viable cells for single-cell analysis. We then examined cord blood and adult mobilized CD34+ cells, including the MPS1 inhibitor reversine as a positive control in the cord blood experiment. Reversine increased whole-chromosome gains and losses, including those of chromosome 7. HQ did not produce a reproducible increase in aneuploidy across three donors and two sources of CD34+ cells, including two concentrations and two timepoints in the adult donor. A modest increase in chromosome 7 loss in one cord blood donor was not reproduced in the other donors. In the other cord blood donor, the estimated upper bound on the HQ-associated increase was approximately 1.4 percentage points. HSPCs also showed a greater increase in chromosome losses than epithelial cells or melanocytes following the same reversine exposure. These findings do not support a substantial, reproducible increase in whole-chromosome aneuploidy after HQ exposure under the conditions tested. They are consistent with a model in which benzene exposure favors the expansion of pre-existing monosomy 7 clones, although this possibility requires direct testing.
ER -