Biomedical subjects

Rebecca A Ihrie

Publications and source records attributed to Rebecca A Ihrie.

8 recordsLinked to original sources

PubMed2023

GBMdeconvoluteR accurately infers proportions of neoplastic and immune cell populations from bulk glioblastoma transcriptomics data.

BACKGROUND: Characterizing and quantifying cell types within glioblastoma (GBM) tumors at scale will facilitate a better understanding of the association between the cellular landscape and tumor phenotypes or clinical correlates. We aimed to develop a tool that deconvolutes immune and neoplastic cells within the GBM tumor microenvironment from bulk RNA sequencing data. METHODS: We developed an IDH wild-type (IDHwt) GBM-specific single immune cell reference consisting of B cells, T-cells, NK-cells, microglia, tumor associated macrophages, monocytes, mast and DC cells. We used this alongside an existing neoplastic single cell-type reference for astrocyte-like, oligodendrocyte- and neuronal progenitor-like and mesenchymal GBM cancer cells to create both marker and gene signature matrix-based deconvolution tools. We applied single-cell resolution imaging mass cytometry (IMC) to ten IDHwt GBM samples, five paired primary and recurrent tumors, to determine which deconvolution approach performed best. RESULTS: Marker-based deconvolution using GBM-tissue specific markers was most accurate for both immune cells and cancer cells, so we packaged this approach as GBMdeconvoluteR. We applied GBMdeconvoluteR to bulk GBM RNAseq data from The Cancer Genome Atlas and recapitulated recent findings from multi-omics single cell studies with regards associations between mesenchymal GBM cancer cells and both lymphoid and myeloid cells. Furthermore, we expanded upon this to show that these associations are stronger in patients with worse prognosis. CONCLUSIONS: GBMdeconvoluteR accurately quantifies immune and neoplastic cell proportions in IDHwt GBM bulk RNA sequencing data and is accessible here: https://gbmdeconvoluter.leeds.ac.uk.

Humans↗

PubMed2006

The requirement for perp in postnatal viability and epithelial integrity reflects an intrinsic role in stratified epithelia.

Mice lacking the desmosome protein Perp exhibit blistering in their stratified epithelia and display postnatal lethality. However, it is unclear if these phenotypes are strictly related to Perp function in stratified epithelia, as Perp expression is not restricted to these tissues during embryogenesis, and certain desmosomal blistering diseases such as pemphigus vulgaris and pemphigus foliaceus have non-cell-intrinsic bases. Furthermore, we show here that Perp is expressed in the heart, raising the possibility that defects in heart function could account for lethality in the Perp-deficient mice. To determine conclusively if Perp function in stratified epithelia is crucial for postnatal survival and epithelial adhesion, we specifically ablated Perp in stratified epithelia by breeding conditional Perp knockout mice to keratin 5 (K5)-Cre transgenic mice. We found that the majority of mice lacking Perp in stratified epithelia die within 10 days after birth, accompanied by blistering and hyperproliferation in the epithelia, similar to the constitutive Perp null mice. Together, these findings indicate that Perp's requirement for both viability and epithelial integrity reflects a role in the stratified epithelial compartment.

Animals↗

PubMed2005

Mice lacking the p53/p63 target gene Perp are resistant to papilloma development.

Perp is a target of the p53 tumor suppressor involved in the DNA damage-induced apoptosis pathway. In addition, Perp is a target of the p53-related transcription factor p63 during skin development, where it participates in cell-cell adhesion mediated through desmosomes. Here we test the role of Perp in tumorigenesis in a two-step skin carcinogenesis model system. We find that mice lacking Perp in the skin are resistant to papilloma development, displaying fewer and smaller papillomas than wild-type mice. Proliferation levels, apoptotic indices and differentiation patterns are similar in the skin of treated Perp-deficient and wild-type mice. Instead, impaired adhesion through aberrant desmosome assembly may explain the diminished tumor development in the absence of Perp. These studies indicate that in certain contexts, Perp is required for efficient carcinogenesis and suggest a role for intact cell-cell adhesion in supporting tumor development in these settings.

9,10-Dimethyl-1,2-benzanthracene↗

PubMed2005

A new Perp in the lineup: linking p63 and desmosomal adhesion.

The process of stratified epithelial development depends upon a transcriptional program directed by the p53-related transcription factor p63. p63 is required for the commitment of the ectoderm to stratification and for the completion of terminal differentiation in stratified epithelia, and mutations in p63 have been identified in multiple developmental disorders affecting ectoderm-derived tissues. Recent work from our laboratory has determined that the p53 target gene Perp is required for the integrity of the stratified epithelia specified by p63, and that expression of Perp in these structures depends on the presence of p63. In these tissues, Perp is a critical component of the desmosome, a cell-cell adhesion complex whose constituents are frequently mutated in human diseases affecting the skin and hair. Perp's position downstream of p63 and p53, as well as its essential role in normal desmosome function, suggest that it, like other adhesion proteins, may be a target for mutation in human blistering diseases or cancer.

Cell Adhesion↗

PubMed2005

Perp is a p63-regulated gene essential for epithelial integrity.

p63 is a master regulator of stratified epithelial development that is both necessary and sufficient for specifying this multifaceted program. We show here that Perp, a tetraspan membrane protein originally identified as an apoptosis-associated target of the p53 tumor suppressor, is the first direct target of p63 clearly involved in mediating this developmental program in vivo. During embryogenesis, Perp is expressed in an epithelial pattern, and its expression depends on p63. Perp-/- mice die postnatally, with dramatic blistering in stratified epithelia symptomatic of compromised adhesion. Perp localizes specifically to desmosomes, adhesion junctions important for tissue integrity, and numerous structural defects in desmosomes are observed in Perp-deficient skin, suggesting a role for Perp in promoting the stable assembly of desmosomal adhesive complexes. These findings demonstrate that Perp is a key effector in the p63 developmental program, playing an essential role in an adhesion subprogram central to epithelial integrity and homeostasis.

Animals↗

PubMed2004

Developmental context determines latency of MYC-induced tumorigenesis.

One of the enigmas in tumor biology is that different types of cancers are prevalent in different age groups. One possible explanation is that the ability of a specific oncogene to cause tumorigenesis in a particular cell type depends on epigenetic parameters such as the developmental context. To address this hypothesis, we have used the tetracycline regulatory system to generate transgenic mice in which the expression of a c-MYC human transgene can be conditionally regulated in murine hepatocytes. MYC's ability to induce tumorigenesis was dependent upon developmental context. In embryonic and neonatal mice, MYC overexpression in the liver induced marked cell proliferation and immediate onset of neoplasia. In contrast, in adult mice MYC overexpression induced cell growth and DNA replication without mitotic cell division, and mice succumbed to neoplasia only after a prolonged latency. In adult hepatocytes, MYC activation failed to induce cell division, which was at least in part mediated through the activation of p53. Surprisingly, apoptosis is not a barrier to MYC inducing tumorigenesis. The ability of oncogenes to induce tumorigenesis may be generally restrained by developmentally specific mechanisms. Adult somatic cells have evolved mechanisms to prevent individual oncogenes from initiating cellular growth, DNA replication, and mitotic cellular division alone, thereby preventing any single genetic event from inducing tumorigenesis.

Alleles↗

PubMed2004

Perp-etrating p53-dependent apoptosis.

The induction of apoptosis is a fundamental mechanism by which the p53 transcriptional activator protein suppresses tumor development. Recently, the roles of several p53 target genes in mediating the p53 apoptotic response have been queried through loss-of-function analysis with knockout mouse models. These studies have demonstrated that the p53 targets Noxa, Puma, and Perp play cell type-specific roles in p53-mediated apoptosis. Perp, a tetraspan protein localizing to the plasma membrane, rather than to mitochondria, is a novel type of p53 effector that may stimulate apoptosis through a different mechanism from the BH3-containing proteins Noxa, Puma, and Bax.

Animals↗

PubMed2003

Perp is a mediator of p53-dependent apoptosis in diverse cell types.

The induction of apoptosis by the p53 protein is critical for its activity as a tumor suppressor. Although it is clear that p53 induces apoptosis at least in part by direct transcriptional activation of target genes, the set of p53 target genes that mediate p53 function in apoptosis in vivo remains to be well defined. The Perp (p53 apoptosis effector related to PMP-22) gene is highly expressed in cells undergoing p53-dependent apoptosis as compared to cells undergoing p53-dependent G1 arrest. Perp is a direct p53 target, and its overexpression is sufficient to induce cell death in fibroblasts, implicating it as an important component of p53 apoptotic function. Here, through the generation of Perp-deficient mice, we analyze the role of Perp in the p53 apoptosis pathway in multiple primary cell types by comparing the cell death responses of Perp null cells to those of wild-type and p53 null cells. These experiments demonstrate the involvement of Perp in p53-mediated cell death in thymocytes and neurons but not in E1A-expressing MEFs, indicating a cell type-specific role for Perp in the p53 cell death pathway. In addition, we show that Perp is not required for proliferation-associated functions of p53. Thus, Perp selectively mediates the p53 apoptotic response, and the requirement for Perp is dictated by cellular context.

Animals↗