Biology subjects

Phelps, R.

Publications and source records attributed to Phelps, R..

3 recordsLinked to original sources

bioRxiv2023

H2A.Z chaperones converge on histone H4 acetylation for melanoma cell proliferation

High levels of H2A.Z promote melanoma cell proliferation and correlate with poor prognosis. However, the role of the two distinct H2A.Z histone chaperone complexes, SRCAP and P400-TIP60, in melanoma remains unclear. Here, we show that individual depletion of SRCAP, P400, and VPS72 (YL1) not only results in loss of H2A.Z deposition into chromatin, but also a striking reduction of H4 acetylation in melanoma cells. This loss of H4 acetylation is found at the promoters of cell cycle genes directly bound by H2A.Z and its chaperones, suggesting a highly coordinated regulation between H2A.Z deposition and H4 acetylation to promote their expression. Knockdown of each of the three subunits downregulates E2F1 and its targets, resulting in a cell cycle arrest akin to H2A.Z depletion. However, unlike H2A.Z deficiency, loss of the shared H2A.Z chaperone subunit YL1 induces apoptosis. Furthermore, YL1 is overexpressed in melanoma tissues, and its upregulation is associated with poor patient outcome. Together, these findings provide a rationale for future targeting of H2A.Z chaperones as an epigenetic strategy for melanoma treatment.

cancer biology↗

bioRxiv2023

The influence of marker number and sequencing depth on the ability to identify mismatch repair deficient tumours.

1.Analysis of somatic mutation patterns is widely used to infer exposure to exogenous and endogenous mutagenic influences. This raises the question of the amount of sequence data required to detect factors of interest. A common use of mutation pattern analysis is the identification of increased microsatellite instability to uncover mismatch repair (MMR) defects in tumours and normal tissues. Here we explore the effects of sequencing depth and the number of loci analysed on the ability to detect MMR deficiency using artificial neural networks and publicly available amplicon sequencing data from colorectal tumours on 24 short quasi monomorphic microsatellites (up to 12 bp in length, PMID 31471937) split in a training (99 samples) and a test set (95 samples). We show that, at a sequencing depth of 200, pairs mononucleotide repeats can achieve discrimination between MMR proficient and deficient colorectal tumours similar to that obtained with the full 24 marker panel, with accuracies above 97% and ROC AUCs in excess of 99% in the test set. Our results indicate that for short monomorphic microsatellites considering the length distribution of the different alleles at each locus, representing these distributions as two-dimensional structures and including convolutional layers in the network can facilitate discrimination between MMR deficient and proficient tumour material. They also indicate that, despite the limitations imposed by amplification, sequencing accuracy and the limited divergence time between the sequences from one locus, high depth sequencing can be used to identify MMR deficiency from a limited number of loci. However, they also suggest that, for a fixed total number of reads per sample, increasing sensitivity by increasing the number of targets is more efficient than by increasing per target sequencing depth. These results are of interest for screening large numbers of samples and for assessing the impact MMR deficiency in different areas of the genome.

genetics↗

bioRxiv2019

Complex Autoinflammatory Syndrome Unveils Fundamental Principles of JAK1 Transcriptional and Biochemical Function

Autoinflammatory disease can result from monogenic errors of immunity. We describe herein the first example of a patient with early-onset widespread autoinflammation resulting from a mosaic, heterozygous, gain-of-function mutation (S703I) in JAK1, encoding a kinase essential for signaling downstream of over twenty-five cytokines. By first-of-its-kind custom single-cell RNA sequencing, we examine mosaicism with single cell resolution. We uncover that JAK1 transcription is predominantly restricted to a single allele across different immune cells, introducing the concept of a mutational \"transcriptotype\" that differs from the genotype. Functionally, the S703I mutation not only increased JAK1 kinase activity, but also resulted in transactivation of partnering JAKs, independently of its catalytic domain. Further, S703I JAK1 was not solely hypermorphic for cytokine signaling, but neomorphic as well, as it enabled downstream signaling cascades not canonically mediated by JAK1. Given these results, the patient was treated with tofacitinib, a JAK inhibitor, which led to rapid resolution of her clinical disease. Together, these findings represent an unprecedented degree of personalized medicine with the concurrent discovery of fundamental biological principles.

immunology↗