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High burden of clonal hematopoiesis in first responders exposed to the World Trade Center disaster

Abstract

The terrorist attacks on the World Trade Center (WTC) created an unprecedented environmental exposure to aerosolized dust, gases and potential carcinogens. Clonal hematopoiesis (CH) is defined as the acquisition of somatic mutations in blood cells and is associated with smoking and exposure to genotoxic stimuli. Here we show that deep targeted sequencing of blood samples identified a significantly higher proportion of WTC-exposed first responders with CH (10%; 48 out of 481) when compared with non-WTC-exposed firefighters (6.7%; 17 out of 255; odds ratio, 3.14; 95% confidence interval, 1.64–6.03; P = 0.0006) after controlling for age, sex and race/ethnicity. The frequency of somatic mutations in WTC-exposed first responders showed an age-related increase and predominantly affected DNMT3A, TET2 and other CH-associated genes. Exposure of lymphoblastoid cells to WTC particulate matter led to dysregulation of DNA replication at common fragile sites in vitro. Moreover, mice treated with WTC particulate matter developed an increased burden of mutations in hematopoietic stem and progenitor cell compartments. In summary, the high burden of CH in WTC-exposed first responders provides a rationale for enhanced screening and preventative efforts in this population.

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Fig. 1: Prevalence and characteristics of somatic mutations seen in WTC-exposed first responders.
Fig. 2: Characteristics of somatic mutations seen in WTC-exposed first responders.

Data availability

All sequencing data for first responders and controls have been deposited to the European Variation Archive Project under accession no. PRJEB49193 (https://www.ebi.ac.uk/eva/).

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Acknowledgements

The work was supported by National Institutes of Health grants U01OH011933 (A.V.), U01OH012271 (A.V., R.Z.-O.), U01OH11300 (A.N.), F30DK127699 (A.J.S.), R01HL119326 (A.N.), R00HL136870 (A.M.) and T32GM007347 (A.J.S), NIOSH contracts 200-2011-39383, 200-2011-39378 and 200-2017-93326 (R.Z.-O.), the Jane and Myles Dempsey Fund (A.V.), Leukemia Lymphoma Society (A.V., M.R.S), the Evans MDS Foundation (A.V., M.R.S.), the Valvano Foundation (A.V.), the Adventure Alle Fund (M.R.S.), the Biff Ruttenberg Foundation (M.R.S.), the Beverly and George Rawlings Directorship (M.R.S.), the Ann Melly Scholarship (AJS) and a gift from the Leinbach family (A.V.). The dataset(s) used for the analyses described were obtained from Vanderbilt University Medical Center’s BioVU which is supported by numerous sources: institutional funding, private agencies and federal grants. These include the NIH funded Shared Instrumentation Grant S10RR025141, S10OD025092 and S10OD017985; and CTSA grants UL1TR002243, UL1TR000445 and UL1RR024975. Genomic data are also supported by investigator-led projects that include U01HG004798, R01NS032830, RC2GM092618, P50GM115305, U01HG006378, U19HL065962, R01HD074711; and additional funding sources listed at https://victr.vumc.org/biovu-funding/.

Author information

Authors and Affiliations

Authors

Contributions

A.V., D.J.P., M.R.S., A.M., A.N. and R.Z.-O. designed the study and experiments and wrote the manuscript. S.J., O.G., D.G.G., A.B.-G., A.J.S., J.C., S.S., S.G.-M., G.S.C., S.A., T.D.B., A.S., C.A.B., S.S.S., T.P.S., V.T., H.G., J.G., S.H.H., M.R.S., A.V., M.B., G.N. and M.D.W. contributed samples, performed experiments and analyzed data. O.L., L.G., B.L.E., U.S. and B.W. analyzed and interpreted data. K.P., R.B., J.L. and F.F. performed bioinformatics analysis.

Corresponding authors

Correspondence to Anna Nolan, Advaitha Madireddy, Michael R. Savona, David J. Prezant or Amit Verma.

Ethics declarations

Competing interests

A.V. has received research funding from Prelude, BMS, GSK, Incyte, Medpacto, Curis and Eli Lilly, is a scientific advisor for Stelexis, Novartis, Acceleron and Celgene, receives honoraria from Stelexis and Janssen and holds equity in Stelexis and Throws Exception. B.L.E. has received research funding from Celgene, Deerfield, Novartis and Calico and consulting fees from GRAIL. He is a member of the scientific advisory board and shareholder for Neomorph Therapeutics, TenSixteen Bio, Skyhawk Therapeutics and Exo Therapeutics. M.R.S has acted as a scientific advisor for Abbvie, BMS, CTI, Geron, Karyopharm, Novartis, Ryvu, Sierra Oncology, Taiho, Takeda, TG Therapeutics; has received research funding from ALX Oncology, Astex, Incyte, Takeda, TG Therapeutics; and has equity positions in Karyopharm, Ryvu.

Peer review

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Nature Medicine thanks Duane Hassane Daniel Link, Catherine Metayer, Stanton Gerson and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Michael Basson was the primary editor on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.

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Extended data

Extended Data Fig. 1 Characteristics of somatic mutations seen in non-WTC-exposed first responder controls.

a: Frequency of genes found to be mutated are shown in non-WTC-exposed first responder controls. b: Numbers of specific types of non-synonymous mutations are shown. c: Numbers of exact nucleotide change for mutations are shown.

Extended Data Fig. 2 Mutational signatures for changes seen in WTC-exposed first responders.

a: Relative weight and underlying mechanisms of different mutation signatures inferred from the mutational spectra are shown. b:The 96 trinucleotide mutational spectra of somatic mutations seen in WTC exposed first responders. X-axis is showing the 96 combination of nucleotide changes, and their relative weights inferred by deconstructSigs is shown on the Y-axis.

Extended Data Fig. 3 WTC particulate matter (WTC PM) exposure induces DNA damage by promoting faster progression of cells through S-phase.

(a) Schematic of treatment regime. (b) Percentage of cells with H2AX foci in wildtype (WT) Untreated (blue bar), WT + Aphidicolin (grey bar), WT + WTC PM (green bar) and WT + 5uM Olaparib (orange bar) and 10uM Olaparib (yellow bar). Approximately 500 cells examined over three independent experiments. Statistical significance was assessed using a two-tailed t-test where ****p < .0001. (c) Percentage of cells with EdU incorporation in wildtype (WT) Untreated (blue bar), WT + Aphidicolin (grey bar), WT + WTC PM (green bar) and WT + 5uM Olaparib (orange bar) and 10uM Olaparib (yellow bar). Approximately 250 cells examined over three independent experiments. Statistical significance was assessed using a two-tailed t-test. (d) Spatiotemporal pattern of DNA replication. Percentage of cells with EdU incorporation patterns characteristic of early (blue bar), mid (red bar) and late (green bar) s-phase. Error bars represent mean ± s.d. from data collected where n = ~250 cells examined over three independent experiments. Statistical significance was assessed using a two-tailed t-test. (e) Schematic representation of the various stages of single molecule analysis of replicated DNA (SMARD). Cells are pulsed with nucleoside analogs (IdU-green; CIdU-red) and embedded in agarose plugs. The cells are first lysed; proteins are digested by proteinase K and then subjected to restriction digestion. The restriction digested DNA is resolved by pulse field gel electrophoresis. The slice containing the FRA16D locus is identified by PCR analysis. The agarose from the identified slice is melted and the DNA is stretched onto silanized glass slides. Biotinylated FISH probes are used for identification of the fragment and immunostaining is utilized to visualize the IdU tract in red, the CIdU tract in green and the FISH probes in blue. The resulting molecules are arranged to yield recognizable replication patterns (from the left): initiating molecules, terminating molecules, replication forks progressing in the 3’ to 5’ and 5’ to 3’ direction which are easily interpreted by the IdU incorporation histograms.

Extended Data Fig. 4 WTC PM exposure perturbs DNA replication at common fragile site FRA16D.

(a) Locus map of the Region 1(R1)-PmeI and Region 2(R2)-SbfI segments, of CFS-FRA16D. The FISH probes that identify the segment are labeled in blue. (b-d) Top; Locus map of PmeI digested R1 segment. Bottom; Aligned photomicrograph images of labeled DNA molecules from the WILDTYPE (WT) lymphoblastoid cell line treated with 0.2 µM Aphidicolin for 20 h (B); or treated with 200 µg/ml WTC PM for 20 h (C); or treated with 5 µM olaparib for 20 h (D). (e) Percentage of molecules with replication initiation sites in Region 1 of CFS-FRA16D in wildtype (WT) Untreated (blue bar), WT + Aphidicolin (grey bar), WT + WTC-PM (green bar) and WT + olaparib (orange bar). Error bars represent mean ± s.d. from data collected where n = 40 molecules analyzed over three independent experiments. Statistical significance was assessed using a two-tailed t-test. Note: Aphidicolin, WTC PM and olaparib are present during IdU pulse. (f) Replication fork speed during the IdU pulse of SMARD (first 4 hours of pulsing) in Region 1 of CFS-FRA16D in wildtype (WT) Untreated (blue bar), WT + Aphidicolin (grey bar), WT + WTC PM (green bar) and WT + olaparib (orange bar). Error bars represent mean ± s.d. from data collected where n = ~200 DNA molecules analyzed from three independent experiments. Statistical significance was assessed using a two-tailed t-test where *p = 0.0439, **p = 0.0052. Note: Aphidicolin, WTC PM and olaparib are present during IdU pulse. (g-i) Top; Locus map of SbfI digested R2 segment. Bottom; Aligned photomicrograph images of labeled DNA molecules from the WILDTYPE (GM03798) lymphoblastoid cell line treated with 0.2 µM Aphidicolin for 20 h (G); or treated with 200 µg/ml WTC PM for 20 h (H); or treated with 5 µM olaparib for 20 h (I). The yellow arrows indicate the sites along the molecules where the IdU transitioned to CldU. White rectangles indicate representative sites of replication fork pausing. The molecules are arranged in the following order: molecules with initiation events, molecules with 3’ to 5’ progressing forks, molecules with 5’ to 3’ progressing forks and molecules with termination events. (j) Percentage of molecules with replication initiation sites in Region 2 of CFS-FRA16D in wildtype (WT) Untreated (blue bar), WT + Aphidicolin (grey bar), WT + WTC PM (green bar) and WT + olaparib (orange bar). Error bars represent mean ± s.d. from data collected where n = 40 molecules analyzed over three independent experiments. Statistical significance was assessed using a two-tailed t-test where *p = 0.0311. Note: Aphidicolin, WTC-PM and Olaparib are present during IdU pulse. (k) Replication fork speed during the IdU pulse of SMARD (first 4 hours of pulsing) in Region 2 of CFS-FRA16D in wildtype (WT) Untreated (blue bar), WT + Aphidicolin (grey bar), WT + WTC PM (green bar) and WT + Olaparib (orange bar). Error bars represent mean ± s.d. from data collected where n = ~200 DNA molecules analyzed from three independent experiments. Statistical significance was assessed using a two-tailed t-test where **p = 0.0016 Note: Aphidicolin, WTC PM and olaparib are present during IdU pulse.

Extended Data Fig. 5 WTC PM exposure perturbs DNA replication at common fragile site FRA6E.

(a): Locus map of a 375 kb region in the CFS-FRA6E obtained by PmeI digestion. The region includes the fragility core of CFS-FRA6E (pink line – 162 kb). The FISH probes that identify the segment are labeled in blue. (b-d): Top; Locus map of the PmeI digested FRA6E segment. Bottom; Aligned photomicrograph images of labeled DNA molecules from the WILDTYPE (GM03798) lymphoblastoid cell line treated with 0.2 µM Aphidicolin for 20 h (D); or treated with 200 µg/ml WTC PM for 20 h (E); or treated with 5 µM Olaparib for 20 h (F). (e): Percentage of molecules with replication initiation sites in CFS-FRA6E in wildtype (WT) Untreated (blue bar), WT + Aphidicolin (grey bar), WT + WTC PM (green bar) and WT + olaparib (orange bar). Error bars represent mean ± s.d. from data collected where n = 40 molecules analyzed over three independent experiments. Note: Aphidicolin, WTC-PM and Olaparib are present during IdU pulse. (f): Replication fork speed during the IdU pulse of SMARD (first 4 hours of pulsing) CFS-FRA6E in wildtype (WT) Untreated (blue bar), WT + Aphidicolin (grey bar), WT + WTC PM (green bar) and WT + Olaparib (orange bar). Error bars represent mean ± s.d. from data collected where n = ~200 DNA molecules analyzed from three independent experiments. Statistical significance was assessed using a two-tailed t-test where **p = 0.0035, ****p < 0.0001. Note: Aphidicolin, WTC PM and olaparib are present during IdU pulse.

Extended Data Fig. 6 Genomic alterations induced by exposure to WTC PM in vivo.

a: Mice were treated with WTC PM and used for bone marrow stem and progenitor FACS analysis. Representative control and WTC PM treated mice samples are shown. b: Hematopoietic Kit + , Sca1 + , Lineage –ve stem cells are shown for WTC PM treated and control mice (N = 4 individual mice per group, Means + /- SD, Two tailed TTest, P = 0.036). c: Numbers of high impact deletions are shown for WTC PM and control treated mice within stem cell compartments (N = 4 individual mice per group, Means + /- SD, Two tailed TTest, P = 0.007). d: Numbers of high impact indels are shown for WTC PM and control treated mice within stem cell compartments (N = 4 individual mice per group, Means + /- SD, Two tailed TTest, P = 0.046). e: Numbers of high impact non-synonymous SNPs are shown for WTC PM and control treated mice within stem cell compartments. N = 4 individual mice per group, Means + /- SD, Two tailed TTest, P = 0.03). f: Variant allele frequency (VAF) of high impact non-synonymous genomic changes in WTC PM treated stem cells. g: Circos plot showing magnitude of non-synonymous genomic changes in 4 WTC PM and 4 control mice.

Extended Data Fig. 7 Mice treated with WTC PM were analyzed for stem and progenitor alterations.

a: Mice were treated with WTC PM were sacrificed at 30 days after oropharyngeal exposure and used for bone marrow stem and progenitor FACS analysis. Representative sorting strategy for KSL stem cells is shown. b: Relative proportions of stem and progenitor populations are shown. Means + /- SD of 4 mice in each group.

Extended Data Fig. 8 Hematopoietic stem cells from mice treated with WTC PM show genomic instability.

a: Numbers of high, moderate, low and modifier impact SNPs are shown for WTC PM treated and control mice within stem cell compartments. Individual mice are shown. b: Numbers of high, moderate, low and modifier impact deletions are shown for WTC PM treated and control mice within stem cell compartments. Individual mice are shown. c: Numbers of high, moderate, low and modifier impact indels are shown for WTC PM treated and control mice within stem cell compartments. Individual mice are shown.

Extended Data Fig. 9 Murine mutational signatures similar to human mutational signatures associated with smoking and defective DNA repair.

a: De novo murine mutational signatures (Msig1 and Msig2) were created from high and moderate impact snps and show greater signature activities in the WTC-PM exposed mice. b: The murine signatures were compared to known human mutational signatures. Greater similarity was shown with higher intensity of color on the heatmap. Human signatures with most similarity to Msig1 were SBS45, SBS4, SBS94. Human signatures with most similarity to Msig2 were SBS5, SBS3, SBS40. c: Human signatures with most similarity to murine signatures were SBS 03, 04, 05, 40, 45 and 90.

Extended Data Table 1 Demographics of WTC-exposed and non-WTC-exposed first responders. (Smoking information was only available for 203 controls)

Supplementary information

Supplementary Information

Supplementary Table 1: Non-synonymous alterations seen in WTC-exposed first responders. Supplementary Table 2: Non-synonymous alterations seen in non-WTC-exposed firefighter controls responders. Supplementary Table 3: Blood counts in WTC-exposed first responders. Supplementary Table 4: Antibodies used for FACS analysis.

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Jasra, S., Giricz, O., Zeig-Owens, R. et al. High burden of clonal hematopoiesis in first responders exposed to the World Trade Center disaster. Nat Med 28, 468–471 (2022). https://doi.org/10.1038/s41591-022-01708-3

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