AUTHOR CONTRIBUTIONS R.C.W. designed and performed all scRNAseq experiments, analyzed the scRNAseq data, performed the RNAscope in-situ hybridization assays, performed and analyzed the CITE-seq and FACS experiments, analyzed the immunofluorescence data, performed the eQTL analyses, assisted with mouse colony breeding, drafted the manuscript, and led the study. D.W. assisted with the design of the scRNAseq experiments and performed scRNAseq capture and library preparation for all samples. D.T.P. performed scRNAseq capture and helped obtain human coronary samples. J.C. assisted with the scRNAseq capture, library preparation and sequencing. T.N. performed qPCR experiments, analyzed the qPCR data and performed TCF21 ChIPseq. M.P., C.L.M., B.L. and S.B.M. performed the eQTL analyses. R.K. performed the immunohistochemistry experiments and bred the mouse colonies. M.N. performed and analyzed immunohistochemistry experiments. K.Z., M.A. and R.C. assisted with network analysis. T.K.K., R.F. and Y.J.W. prepared the human tissue samples. M.D.T. and J.C.W. provided critical expert guidance on the manuscript. J.B.K. helped plan the mouse in situ histology studies, managed the mouse colonies, performed the TCF21 over-expression experiment and performed the quantitative immunohistochemistry analysis of lesion characteristics. T.Q. conceived and supervised the study. All authors discussed the results and contributed critical review to the manuscript.

Introduction Smooth muscle cells (SMC) play a critical role in atherosclerosis. The Aryl hydrocarbon receptor (AHR) is an environment-sensing transcription factor that contributes to vascular development, and has been implicated in coronary artery disease (CAD) risk. We hypothesized that AHR can affect atherosclerosis by regulating phenotypic modulation of SMC. MethodsWe combined RNA-Seq, ChIP-Seq, ATAC-Seq and in-vitro assays in human coronary artery SMC (HCASMC), with single-cell RNA-Seq (scRNA-Seq), histology, and RNAscope in an SMC-specific lineage-tracing Ahr knockout mouse model of atherosclerosis to better understand the role of AHR in vascular disease.Results Genomic studies coupled with functional assays in cultured HCASMC revealed that AHR modulates HCASMC phenotype and suppresses ossification in these cells. Lineage tracing and activity tracing studies in the mouse aortic sinus showed that the Ahr pathway is active in modulated SMC in the atherosclerotic lesion cap. Furthermore, scRNA-Seq studies of the SMC-specific Ahr knockout mice showed a significant increase in the proportion of modulated SMC expressing chondrocyte markers such as Col2a1 and Alpl, which localized to the lesion neointima. These cells, which we term "chondromyocytes" (CMC), were also identified in the neointima of human coronary arteries. In histological analyses, these changes manifested as larger lesion size, increased lineage-traced SMC participation in the lesion, decreased lineage-traced SMC in the lesion cap, and increased alkaline phosphatase activity in lesions in the Ahr knockout compared to wild-type mice. We propose that AHR is likely protective based on these data and inference from human genetic analyses. ConclusionOverall, we conclude that AHR promotes maintenance of lesion cap integrity and diminishes the disease related SMC-to-CMC transition in atherosclerotic tissues.

To elucidate the fundamental mechanisms and subsequent evolutionary aspects of plant cold acclimation, we examined the effect of cold acclimation on freezing tolerance in Klebsormidium flaccidum, a green alga belonging to Charophyceae, a sister group of land plants. Freezing tolerance of K. flaccidum was significantly enhanced by cold treatment: survival increased from 15% at -10°C when grown at 18°C to 55 and 85% after exposure at 2°C for 2 and 7 d, respectively. Accompanying the development of freezing tolerance, soluble sugars (glucose and sucrose), a putative glycoside and amino acids, including g-aminobutyric acid (GABA), accumulated to high levels in the alga, suggesting that these solutes play a crucial role in the cold acclimation of K. flaccidum. Interestingly, the application of abscisic acid (ABA) did not change the freezing tolerance of the alga. We also observed changes in cell structure, including increased numbers and sizes of starch grains in chloroplasts, chloroplast enlargement, vacuole size reduction and cytoplasmic volume increase. These results suggest that K. flaccidum responds well to cold treatment and develops freezing tolerance in a process comparable to that of land plants.

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Bryophyte species growing in areas in which temperatures fall below zero in winter are likely to have tolerance to freezing stress. It is well established in higher plants that freezing tolerance is acquired by exposure to non-freezing low temperatures, accompanied by expression of various genes and increases in levels of the stress hormone abscisic acid (ABA). However, little is known about the physiological changes induced by cold acclimation in non-vascular plants such as bryophytes. We examined the effects of low temperatures on protonema cells of the moss Physcomitrella patens (Hedw.) Bruch and Schimp. The freezing tolerance of protonema cells was clearly increased by incubation at low temperatures ranging from 10 degrees C to 0 degrees C, with maximum tolerance achieved by incubation at 0 degrees C for several days. The enhancement of freezing tolerance by low temperatures occurred in both light and dark conditions and was accompanied by accumulation of several transcripts for late-embryogenesis-abundant (LEA) proteins and boiling-soluble proteins. By de-acclimation, low-temperature-induced expression of these transcripts and proteins, as well as the freezing tolerance, was reduced. Interestingly, endogenous levels of ABA in tissues or that secreted into the culture medium were not specifically increased by low-temperature treatment. Furthermore, removal of ABA from the medium by addition of activated charcoal did not affect low-temperature-induced freezing tolerance of the protonema cells. Our results provide evidence that bryophytes have an ABA-independent cold-signaling pathway leading to expression of stress-related genes and resultant acquisition of freezing tolerance.

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