Biology subjects

Phillips, M. J.

Publications and source records attributed to Phillips, M. J..

5 recordsLinked to original sources

bioRxiv2026

Combination epigenetic-targeted therapy increases the immunogenicity of poorly immunogenic sarcomas

Immunotherapy approaches have shown limited efficacy in pediatric sarcomas, partly because these tumors have low mutation burden and few neoantigens. We sought to increase the immunogenicity of low mutation sarcomas by inducing expression of epigenetically silenced genes using the hypomethylating agent decitabine and histone deacetylase inhibitor entinostat. Using a mutated Kras-driven murine sarcoma model KP Sarc, sequential treatment with decitabine and entinostat significantly increased expression of silenced genes, including cancer testis antigens, and enhanced antigen presentation, including MHC I expression, compared with either agent alone. Vaccination with irradiated, epigenetically treated KP Sarc cells in a GM-CSF-secreting whole-cell vaccine induced T cell immunity against a matched tumor challenge. The anti-tumor response was directed toward epigenetically upregulated antigens, was T cell dependent, was further potentiated by immune checkpoint inhibition, and conferred immunologic memory. We showed that epigenetically regulated antigens can be shared between tumors providing protective immunity against both epigenetically treated KP Sarc and a second murine sarcoma M-3-9M. Treatment of human sarcoma lines with decitabine and entinostat induced similar gene expression changes, including shared antigen targets, and increased MHC I expression. These findings demonstrate that epigenetically upregulated antigens can serve as effective tumor-specific targets and broaden immunotherapy strategies for low-mutation sarcomas.

immunology↗

bioRxiv2021

Human pluripotent stem cell-derived photoreceptors switch from cell autonomous axon extension to non-cell autonomous process pulling during synaptic marker redistribution.

Photoreceptors (PRs) are the primary visual sensory cells, and their loss leads to blindness that is currently incurable. Cell replacement therapy holds promise as a therapeutic approach to restore vision to those who have lost PRs through damage or disease. While PR transplant research is ongoing in animal models, success is hindered by our limited understanding of PR axon growth during development and regeneration. Using a human pluripotent stem cell (hPSC) reporter line that labels PRs (WA09 CRX+/tdTomato), we generated retinal organoids in order to study mechanisms of PR process extension. We found that the earliest born PRs exhibit autonomous axon extension from dynamic terminals that appear similar to projection neuron growth cones. However, as hPSC-derived PRs age from 40 to 80 days of differentiation, they lose dynamic terminals in 2D plated cultures and within 3D retinal organoids, which does not correlate with cell birth date. Using a rod-specific hPSC reporter line (WA09 NRL+/eGFP), we further determined that rod PRs never form motile growth cones. Interestingly, PRs without motile terminals are still capable of extending axons, but neurites are generated from process stretching via their attachment to motile non-PR cells, which underlies the observed differences in PR neurite lengths on different substrata. While immobile PR terminals express actin, it is less polymerized and less organized than actin present in motile terminals. However, immobile PRs do localize synaptic proteins to their terminals, suggesting a normal developmental progression. These findings help inform the development of PR transplant therapies to treat blinding diseases and provide a platform to test treatments that restore autonomous PR axon extension. Significance StatementLoss of photoreceptors (PRs) in the retina through damage or disease causes irreversible vision loss and blindness. One treatment approach is to replace lost cells with transplanted human stem cell-derived PRs, but this requires PR axons to integrate into the host retina to restore the required neural connections. For this strategy to succeed, we need to understand how PRs extend processes to their targets during development in situ, and whether dissociated human stem cell (hPSC)-derived PRs behave in a similar fashion. In this paper, we show that hPSC-PRs have only a short window during which they are capable of autonomous axon extension, which has implications for PR transplant efforts and for our basic understanding of human retinal development.

neuroscience↗

bioRxiv2021

Using 3D geometric morphometrics to aid taxonomic and ecological understanding of a recent speciation event within a small Australian marsupial (genus Antechinus)

Taxonomic distinction of species forms the foundation of biodiversity assessments and conservation priorities. However, traditional morphological and/or genetics-based taxonomic assessments frequently miss the opportunity of elaborating on the ecological and functional context of species diversification. Here, we used 3D geometric morphometrics of the cranium to improve taxonomic differentiation and add eco-morphological characterisation of a young cryptic divergence within the marsupial carnivorous genus Antechinus. Specifically, we used 168 museum specimens to characterise the recently proposed clades A. stuartii "south", A. stuartii "north" and A. subtropicus. Beyond slight differences attributable to overall size (and therefore not necessarily diagnostic), we also found clear allometry-independent shape variation. This allowed us to define new, easily measured diagnostic traits in the palate, which differentiate the three clades. Contrary to previous suggestions, we found no support for a latitudinal gradient as causing the differentiation between the clades. However, skull shape co-varied with temperature and precipitation seasonality, suggesting that the clades may be adapted to environmental variables that are likely to be impacted by climate change. Our study demonstrates the use of 3D geometric morphometrics to improve taxonomic diagnosis of cryptic mammalian species, while providing perspectives on the adaptive origins and potential future threats of mammalian diversity.

zoology↗

bioRxiv2020

Australian rodents reveal conserved Cranial Evolutionary Allometry across 10 million years of murid evolution

Among vertebrates, placental mammals are particularly variable in the covariance between their cranial shapes and body size (allometry), with the notable exception of rodents. Australian murid rodents present an opportunity to assess the cause of this anomaly because they radiated on an ecologically diverse continent unique for lacking other terrestrial placentals. Here we used 3D geometric morphometrics to quantify species-level and evolutionary allometries in 38 species (317 crania) from all Australian murid genera. We ask if ecological opportunity resulted in greater allometric diversity; conversely, we test if intrinsic constraints and/or stabilizing selection conserved allometry. To increase confidence in species-level allometric slopes, we introduce a new phylogeny-based method of bootstrapping and randomly resampling across the whole sample. We found exceedingly conserved allometry across the 10 million year split between Mus and the clade containing Australian murids. Cranial shapes followed craniofacial evolutionary allometry (CREA) patterns, with larger species having relatively longer snouts and smaller braincases. CREA is consistent with both intrinsic constraints and stabilizing selection hypotheses for conserved allometry. However, large-bodied frugivores evolved faster, while carnivorous specialists showed skull modifications known to conflict with masticatory efficiency. These results suggest a strong role of stabilizing selection on the masticatory apparatus of murid rodents.

evolutionary biology↗

bioRxiv2018

The soft explosive model of placental mammal evolution

Recent molecular dating estimates for placental mammals echo fossil inferences for an explosive interordinal diversification, but typically place this event some 10-20 million years earlier than the Paleocene fossils, among apparently more \"primitive\" mammal faunas. However, current models of molecular evolution do not adequately account for parallel rate changes, and result in dramatic divergence underestimates for large, long-lived mammals such as whales and hominids. Calibrating among these taxa shifts the rate model errors deeper in the tree, inflating interordinal divergence estimates. We employ simulations based on empirical rate variation, which show that this \"error-shift inflation\" can explain previous molecular dating overestimates relative to fossil inferences. Molecular dating accuracy is substantially improved in the simulations by focusing on calibrations for taxa that retain plesiomorphic life-history characteristics. Applying this strategy to the empirical data favours the soft explosive model of placental evolution, in line with traditional palaeontological interpretations - a few Cretaceous placental lineages give rise to a rapid interordinal diversification following the 66 Ma Cretaceous-Paleogene boundary mass extinction. Our soft explosive model for the diversification of placental mammals brings into agreement previously incongruous molecular, fossil, and ancestral life history estimates, and closely aligns with a growing consensus for a similar model for bird evolution. We show that recent criticism of the soft explosive model relies on ignoring both experimental controls and statistical confidence, as well as misrepresentation, and inconsistent interpretations of morphological phylogeny. More generally, we suggest that the evolutionary properties of adaptive radiations may leave current molecular dating methods susceptible to overestimating the timing of major diversification events.

evolutionary biology↗