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Mutational landscape of atherosclerotic plaques reveals large clonal cell populations
Lasse Bach Steffensen, Stephanie Kavan, Pia Søndergaard Jensen, Matilde Kvist Pedersen, Steffen Møller Bøttger, Martin Jakob Larsen, Maja Dembic, Otto Bergman, Ljubica Matic, Ulf Hedin, Lars van Brakel Andersen, Jes Sanddal Lindholt, Kim Christian Houlind, Lars Peter Riber, Mads Thomassen, Lars Melholt Rasmussen
Lasse Bach Steffensen, Stephanie Kavan, Pia Søndergaard Jensen, Matilde Kvist Pedersen, Steffen Møller Bøttger, Martin Jakob Larsen, Maja Dembic, Otto Bergman, Ljubica Matic, Ulf Hedin, Lars van Brakel Andersen, Jes Sanddal Lindholt, Kim Christian Houlind, Lars Peter Riber, Mads Thomassen, Lars Melholt Rasmussen
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Research Article Genetics Vascular biology

Mutational landscape of atherosclerotic plaques reveals large clonal cell populations

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Abstract

The notion of clonal cell populations in human atherosclerosis has been suggested but not demonstrated. Somatic mutations are used to define cellular clones in tumors. Here, we characterized the mutational landscape of human carotid plaques through whole-exome sequencing to explore the presence of clonal cell populations. Somatic mutations were identified in 12 of 13 investigated plaques, while no mutations were detected in 11 non-atherosclerotic arteries. Mutated clones often constituted over 10% of the sample cell population, with genes related to the contractile apparatus enriched for mutations. In carriers of clonal hematopoiesis of indeterminate potential (CHIP), hematopoietic clones had infiltrated the plaque tissue and constituted substantial fractions of the plaque cell population alongside locally expanded clones. Our findings establish somatic mutations as a common feature of human atherosclerosis and demonstrate the existence of mutated clones expanding locally, as well as CHIP clones invading from the circulation. While our data do not support plaque monoclonality, we observed a pattern suggesting the coexistence of multiple mutated clones of considerable size spanning different regions of plaques. Mutated clones are likely to be relevant to disease development, and somatic mutations will serve as a convenient tool to uncover novel pathological processes of atherosclerosis in future studies.

Authors

Lasse Bach Steffensen, Stephanie Kavan, Pia Søndergaard Jensen, Matilde Kvist Pedersen, Steffen Møller Bøttger, Martin Jakob Larsen, Maja Dembic, Otto Bergman, Ljubica Matic, Ulf Hedin, Lars van Brakel Andersen, Jes Sanddal Lindholt, Kim Christian Houlind, Lars Peter Riber, Mads Thomassen, Lars Melholt Rasmussen

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Figure 4

Contribution of clonal hematopoiesis of indeterminate potential (CHIP) clones to the carotid plaque cell population.

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Contribution of clonal hematopoiesis of indeterminate potential (CHIP) c...
(A) Six of the 13 plaque donors were CHIP carriers. The plot shows clonal cell frequencies of CHIP mutations detected in buffy coat (blood leukocytes) DNA. For each patient, the identity of the mutated gene with the highest clonal cell frequency is shown. Dot sizes indicate variant reads, and colors indicate the type of mutation. The dashed line shows the defined limit of detection. (B) CHIP clonal cell frequencies in buffy coats (yellow bars) and in subdivided plaque segments (gray bars). Clonal cell frequencies are represented by the proportion of colored area within yellow bars or gray subsamples (relative to the subsample bar area). Mutation type is indicated by dot color. (C and D) Validation of VAFs for a TET2 loss-of-function mutation, identified in patient 8, was conducted by comparing VAFs derived from ddPCR with those from whole-exome sequencing of both buffy coat and plaque samples from patient 8 (by linear regression analysis), as well as from samples of other patients (serving as negative controls).

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