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Biology subjects

Lewis, A. M.

Publications and source records attributed to Lewis, A. M..

7 recordsLinked to original sources

An ancient polymorphism in myosin I a/b determines the left-right asymmetry of Japanese snails

Left-right (LR) asymmetry is a fundamental feature of animal development, yet progress in understanding its establishment has been limited by the fact that almost all animals exhibit invariant chirality. Snails are the exception because some wild-living species show abundant chiral variation, yet the existing knowledge is from snails in which the chirality mutation is rare and causes pathology. Here, we show that a chiral polymorphism in Japanese Euhadra snails is due to functional variation in an unconventional myosin I a/b, an isoform not previously implicated in LR specification in any animal. Both the sinistral and dextral gene variants are ancient, impart minimal transcriptional differences in the single-cell embryo and are not pathological. Phylogenetic and structural modelling suggests that dominant-acting amino acid substitutions in the myosin actin-binding domain and/or motor-level junction were enabled by relaxed selection. These results broaden the known molecular repertoire underlying LR asymmetry, suggest key mutations and positions that should be explored in other model animals, and highlight snails as a powerful model for understanding the origins of animal LR asymmetry.

evolutionary biology↗

Ecological determinants of disease and immunity in myelodysplastic syndromes

Myelodysplastic syndromes (MDS) are clonal hematopoietic malignancies characterized by ineffective hematopoiesis, dysplastic morphology, and risk of progression to acute myeloid leukemia. While genomic alterations intrinsic to malignant MDS disease-initiating cells have been well-characterized, molecular assessment of the bone marrow in situ has been limited. Here we present single cell spatial assessment of gene expression, T cell receptors, as well as MDS-defining mutations and RNA isoforms within fixed, decalcified human bone marrow core biopsies (41 MDS, 15 controls) paired with single cell immunogenomic analysis of bone marrow aspirates (35 MDS, 6 controls). Bone marrow spatial analyses of >7.47x106 cells identified hematopoietic and non-hematopoietic populations not readily captured in dissociated tissue. We developed computational methods to compare ecological niche structures, revealing enriched hematopoietic niches and reorganization of T cell immunity in MDS patient bone marrow. In situ genotyping of mutant cells revealed increased TGF{beta} expression in malignant megakaryocytes suppressing local T cell cytotoxicity. By contrast, TGF{beta} signaling was disrupted in mutant cells due to aberrant splicing of multiple TGF{beta} signaling components. This study provides a spatially resolved landscape of human MDS bone marrow and uncovers mechanisms by which malignant cells simultaneously promote intrinsic clonal persistence while rewiring the microenvironment for immune escape.

cancer biology↗

Biochemical Regulation of Brain Kynurenic Acid Synthesis and Inhibition in Rats is Sensitive to the Time of Day

Neurochemical imbalances, including elevations of the tryptophan metabolite kynurenic acid (KYNA), an endogenous antagonist of glutamatergic and cholinergic receptors, are linked to cognitive and sleep disturbances in psychiatric and neurocognitive disorders. Therapeutic strategies to reduce brain KYNA by inhibiting kynurenine aminotransferase II (KAT II) are under investigation. However, few studies consider time as a biological variable, despite recent evidence that the time of day can affect brain metabolism and drug effectiveness. Therefore, we explore the hypothesis that KYNA formation and synthesis inhibition change throughout the day. Using rats of both sexes, we measured basal KYNA levels and the effects of kynurenine (100 mg/kg, i.p.), to stimulate de novo KYNA, and/or PF-04859989 (KAT II inhibitor, 30 mg/kg, s.c.), at the beginning of light or dark phases. Microdialysis was used to assess extracellular KYNA in the dorsal hippocampus, and ex vivo assays evaluated KAT enzyme activity in separate animals. Additionally, we examined KYNA levels and the effect of PF-04859989 during acute sleep deprivation in male rats. Regardless of phase, PF-04859989 reduced basal KYNA levels in male but not female rats, yet it reduced kynurenine-stimulated KYNA synthesis in both sexes, demonstrating a context-specific action in female rats. Importantly, we observed a novel effect of phase in males, as kynurenine-induced KYNA synthesis and its inhibition by PF-04859989 were greater during the dark phase than during the light phase. Ex vivo, male KAT II activity was higher, and PF-04859989 was more effective, in the dark than in the light phase, suggesting that properties of the KAT II enzyme itself fluctuate with time of day. Finally, sleep deprivation increased extracellular KYNA levels in the light phase, and PF-04859989 fully ameliorated this increase. Overall, our findings highlight the need to consider time-dependent factors when developing therapies impacting KYNA synthesis. Lay SummaryChanges in brain neurochemistry, including elevations in the tryptophan metabolite kynurenic acid (KYNA), are common in brain disorders that present with sleep disturbances and cognitive deficits as symptoms. KYNA interferes with neurotransmission critical for cognition and sleep, so therapeutic strategies to reduce brain KYNA are being pursued. As recent literature has highlighted the impact of time on brain metabolism and drug efficacy, we, for the first time, explored the hypothesis that KYNA formation and synthesis inhibition change throughout the day. We measured extracellular KYNA levels in the brains of male and female rats and stimulated KYNA synthesis with physiological challenges (exogenous kynurenine, the KYNA bioprecursor, or acute sleep deprivation) and/or inhibited KYNA synthesis pharmacologically (PF-04859989, an inhibitor of the KYNA-synthesizing enzyme kynurenine aminotransferase II (KAT II)). KYNA formation, KAT II enzyme activity, and the effectiveness of PF-04859989 varied throughout the day, highlighting time as a key factor modulating KYNA brain metabolism. PF-04859989 reduced KYNA levels under most conditions. Our findings suggest that the timing of KYNA-targeted treatments should be carefully considered in therapeutic strategies to improve cognition and sleep in brain disorders.

neuroscience↗

Segmental duplications and their variation in a complete human genome

Despite their importance in disease and evolution, highly identical segmental duplications (SDs) have been among the last regions of the human reference genome (GRCh38) to be finished. Based on a complete telomere-to-telomere human genome (T2T-CHM13), we present the first comprehensive view of human SD organization. SDs account for nearly one-third of the additional sequence increasing the genome-wide estimate from 5.4% to 7.0% (218 Mbp). An analysis of 266 human genomes shows that 91% of the new T2T-CHM13 SD sequence (68.3 Mbp) better represents human copy number. We find that SDs show increased single-nucleotide variation diversity when compared to unique regions; we characterize methylation signatures that correlate with duplicate gene transcription and predict 182 novel protein-coding gene candidates. We find that 63% (35.11/55.7 Mbp) of acrocentric chromosomes consist of SDs distinct from rDNA and satellite sequences. Acrocentric SDs are 1.75-fold longer (p=0.00034) than other SDs, are frequently shared with autosomal pericentromeric regions, and are heteromorphic among human chromosomes. Comparing long-read assemblies from other human (n=12) and nonhuman primate (n=5) genomes, we use the T2T-CHM13 genome to systematically reconstruct the evolution and structural haplotype diversity of biomedically relevant (LPA, SMN) and duplicated genes (TBC1D3, SRGAP2C, ARHGAP11B) important in the expansion of the human frontal cortex. The analysis reveals unprecedented patterns of structural heterozygosity and massive evolutionary differences in SD organization between humans and their closest living relatives.

genomics↗

The structure, function, and evolution of a complete human chromosome 8

The complete assembly of each human chromosome is essential for understanding human biology and evolution. Using complementary long-read sequencing technologies, we complete the first linear assembly of a human autosome, chromosome 8. Our assembly resolves the sequence of five previously long-standing gaps, including a 2.08 Mbp centromeric -satellite array, a 644 kbp defensin copy number polymorphism important for disease risk, and an 863 kbp variable number tandem repeat at chromosome 8q21.2 that can function as a neocentromere. We show that the centromeric -satellite array is generally methylated except for a 73 kbp hypomethylated region of diverse higher-order -satellite enriched with CENP-A nucleosomes, consistent with the location of the kinetochore. Using a dual long-read sequencing approach, we complete the assembly of the orthologous chromosome 8 centromeric regions in chimpanzee, orangutan, and macaque for the first time to reconstruct its evolutionary history. Comparative and phylogenetic analyses show that the higher-order -satellite structure evolved specifically in the great ape ancestor, and the centromeric region evolved with a layered symmetry, with more ancient higher-order repeats located at the periphery adjacent to monomeric -satellites. We estimate that the mutation rate of centromeric satellite DNA is accelerated at least 2.2-fold, and this acceleration extends beyond the higher-order -satellite into the flanking sequence.

genomics↗

Telomere length and chromosomal instability for predicting individual radiosensitivity and risk via machine learning

The ability to predict a cancer patients response to radiotherapy and risk of developing adverse late health effects would greatly improve personalized treatment regimens and individual outcomes. Telomeres represent a compelling biomarker of individual radiosensitivity and risk, as exposure can result in dysfunctional telomere pathologies that coincidentally overlap with many radiation-induced late effects, ranging from degenerative conditions like fibrosis and cardiovascular disease to proliferative pathologies like cancer. Here, telomere length was longitudinally assessed in a cohort of fifteen prostate cancer patients undergoing Intensity Modulated Radiation Therapy (IMRT) utilizing Telomere Fluorescence in situ Hybridization (Telo-FISH). To evaluate genome instability and enhance predictions for individual patient risk of secondary malignancy, chromosome aberrations were also assessed utilizing directional Genomic Hybridization (dGH) for high-resolution inversion detection. We present the first implementation of individual telomere length data in a machine learning model, XGBoost, trained on pre-radiotherapy (baseline) and in vitro exposed (4 Gy {gamma}-rays) telomere length measures, to predict post-radiotherapy telomeric outcomes, which together with chromosomal instability provide insight into individual radiosensitivity and risk for radiation-induced late effects.

bioinformatics↗

A Chemical Biology Toolbox for the Study of Protein Methyltransferases and Epigenetic Signaling

Protein methyltransferases (PMTs) comprise a major class of epigenetic regulatory enzymes with therapeutic relevance. Here we present a collection of chemical probes and associated reagents and data to elucidate the function of human and murine PMTs in cellular studies. Our collection provides inhibitors and antagonists that together modulate most of the key regulatory methylation marks on histones H3 and H4, providing an important resource for modulating cellular epigenomes. We describe a comprehensive and comparative characterization of the probe collection with respect to their potency, selectivity, and mode of inhibition. We demonstrate the utility of this collection in CD4+ T cell differentiation assays revealing the remarkable potential of individual probes to alter multiple T cell subpopulations with important implications for T cell-mediated processes such as inflammation and immuno-oncology. In particular, we demonstrate a role for DOT1L in limiting Th1 cell differentiation and maintaining lineage integrity.

biochemistry↗