Genome Med. 2023 May 10; 15(1):35
High level of complexity and global diversity of the 3q29 locus revealed by optical mapping and long-read sequencing
Yilmaz F, Gurusamy U, Mosley TJ, Hallast P, Kim K, Mostovoy Y, et al.
High sequence identity between segmental duplications (SDs) can facilitate copy number variants (CNVs) via non-allelic homologous recombination (NAHR). These CNVs are one of the fundamental causes of genomic disorders such as the 3q29 deletion syndrome (del3q29S). There are 21 protein-coding genes lost or gained as a result of such recurrent 1.6-Mbp deletions or duplications, respectively, in the 3q29 …
© 2023. The Author(s).
Cell Genom. 2023 May 10; 3(5):100291
Resolution of structural variation in diverse mouse genomes reveals chromatin remodeling due to transposable elements
Ferraj A, Audano PA, Balachandran P, Czechanski A, Flores JI, Radecki AA, et al.
Diverse inbred mouse strains are important biomedical research models, yet genome characterization of many strains is fundamentally lacking in comparison with humans. In particular, catalogs of structural variants (SVs) (variants ≥ 50 bp) are incomplete, limiting the discovery of causative alleles for phenotypic variation. Here, we resolve genome-wide SVs in 20…
© 2023 The Author(s).
Cell Genom. 2023 Apr 12; 3(4):100283
Genetic dissection of the pluripotent proteome through multi-omics data integration
Aydin S, Pham DT, Zhang T, Keele GR, Skelly DA, Paulo JA, et al.
Genetic background drives phenotypic variability in pluripotent stem cells (PSCs). Most studies to date have used transcript abundance as the primary molecular readout of cell state in PSCs. We performed a comprehensive proteogenomics analysis of 190 genetically diverse mouse embryonic stem cell (mESC) lines. The quantitative proteome is highly variable across lines, and we identified pluripotency-associated pathways …
© 2023 The Author(s).
Sci Immunol. 2023 Feb 24; 8(80):eadd5204
Immunosuppressive reprogramming of neutrophils by lung mesenchymal cells promotes breast cancer metastasis
Gong Z, Li Q, Shi J, Li P, Hua L, Shultz LD, et al.
Neutrophils, the most abundant innate immune cells, function as crucial regulators of the adaptive immune system in diverse pathological conditions, including metastatic cancer. However, it remains largely unknown whether their immunomodulatory functions are intrinsic or acquired within the pathological tissue environment. Here, using mouse models of metastatic breast cancer in the lungs, we show that, although neutrophils isolated from bone marrow (BM) or blood are…
Cell Host Microbe. 2023 Feb 8; 31(2):273-287.e5
Multi-'omics of gut microbiome-host interactions in short- and long-term myalgic encephalomyelitis/chronic fatigue syndrome patients
Xiong R, Gunter C, Fleming E, Vernon SD, Bateman L, Unutmaz D, et al.
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a complex, debilitating disorder manifesting as severe fatigue and post-exertional malaise. The etiology of ME/CFS remains elusive. Here, we present a deep metagenomic analysis of stool combined with plasma metabolomics and clinical phenotyping of two ME/CFS cohorts with short-term (<4 years, n = 75) or long-term disease (>10 years, n = 79)…
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