Biology subjects

Fortina, P.

Publications and source records attributed to Fortina, P..

5 recordsLinked to original sources

bioRxiv2022

Toll-like receptor 4 signaling in osteoblasts is required for load-induced bone formation in mice

During skeletal development, expression of nerve growth factor (NGF) leads to the survival of afferent sensory nerves that express neurotrophic tyrosine kinase receptor type 1 (TrkA), the high affinity receptor for NGF. In adulthood, NGF is expressed by mature osteoblasts following mechanical loading and signals through TrkA receptors in resident sensory nerves to support load-induced bone formation. However, the regulation of NGF in osteoblasts following loading is not well understood. In this study, we sought to determine whether osteoblastic expression of toll-like receptor 4 (TLR4), a key receptor in the NF-{kappa}B signaling pathway, is required to initiate NGF-TrkA signaling to support skeletal adaptation following mechanical loading. First, we observed that NF-{kappa}B inhibition reduces NGF expression induced by axial forelimb compression. Moreover, we observed that TLR4+ periosteal cells are increased after mechanical loading. Therefore, we generated a novel mouse model in which Tlr4 is selectively removed from the mature osteoblast lineage. Although Tlr4 conditional knockout mice have normal skeletal mass and strength in adulthood, the loss of TLR4 signaling results in significant reductions in periosteal lamellar bone formation following axial forelimb compression. Furthermore, we demonstrated that the upregulation of Ngf following application of fluid shear stress to calvarial osteoblasts is significantly reduced by NF-{kappa}B and TLR4 inhibitors. Finally, RNA sequencing demonstrated that the deficits in load-induced bone formation in CKO mice can be attributed to dysregulated inflammatory signaling. In total, our study reveals a novel role for TLR4 in skeletal adaptation to mechanical loading in bone, which may enable new therapeutic strategies for diseases of low bone mass and provide new targets for musculoskeletal pain relief.

cell biology↗

bioRxiv2021

Multimodal genomic markers predict immunotherapy response in the head and neck squamous cell carcinoma

Immune checkpoint blockade (ICB) therapy has had a major impact on the clinical management of head and neck squamous cell carcinoma (HNSCC). However, clinical responses to ICB are observed in only a fraction of patients. In the present paper, we used multimodal approaches to a) evaluate the utility of existing ICB biomarkers including tumor mutation burden (TMB), microsatellite instability (MSI), and a T-cell specific signature in predicting therapy response in HNSCC using TCGA cohort, and; b) identify a novel molecular signature to predict ICB therapy response using an ICB clinical trial of HNSCC. Our results confirm previous reports showing TMB efficacy as a biomarker and its outcome can be influenced by age, tumor sub-site, and smoking status; and that High-TMB and high-MSI tumors are associated with T-cell signature, and better survival probability in the HNSCC. We go on to demonstrate that High-TMB and high-MSI utilizes cell-cycle/cell proliferation processes for their molecular functionality; and identify a novel Cell Proliferation ICB-therapy Predicting (CPIP) signature capable of predicting ICB therapy response in HNSCC, retrospectively, where traditional biomarkers of ICB response were insufficient. In summary, the present study defines strategies and novel signatures that can be appropriately used for patient selection for ICB therapy that can improve the clinical outcomes of HNSCC patients.

genomics↗

bioRxiv2019

Epigenomic profiling of neuroblastoma cell lines

Understanding the aberrant transcriptional landscape of neuroblastoma is necessary to provide insight to the underlying influences of the initiation, progression and persistence of this developmental cancer. Here, we present chromatin immunoprecipitation sequencing (ChIP-Seq) data for the oncogenic transcription factors, MYCN and MYC, as well as regulatory histone marks H3K4me1, H3K4me3, H3K27Ac, and H3K27me3 in ten commonly used human neuroblastoma-derived cell line models. In addition, for all of the profiled cell lines we provide ATAC-Seq as a measure of open chromatin. We validate specificity of global MYCN occupancy in MYCN amplified cell lines and functional redundancy of MYC occupancy in MYCN non-amplified cell lines. Finally, we show with H3K27Ac ChIP-Seq that these cell lines retain expression of key neuroblastoma super-enhancers (SE). We anticipate this dataset, coupled with available transcriptomic profiling on the same cell lines, will enable the discovery of novel gene regulatory mechanisms in neuroblastoma.

bioinformatics↗

bioRxiv2019

iSeqQC: A Tool for Expression-Based Quality Control in RNA Sequencing

Quality Control in any high-throughput sequencing technology is a critical step, which if overlooked can compromise the data. A number of methods exist to identify biases during sequencing or alignment, yet not many tools exist to interpret biases due to outliers or batch effects. Hence, we developed iSeqQC, an expression-based QC tool that detects outliers either produced by batch effects due to laboratory conditions or due to dissimilarity within a phenotypic group. iSeqQC implements various statistical approaches including unsupervised clustering, agglomerative hierarchical clustering and correlation coefficients to provide insight into outliers. It can be utilized either through command-line (Github: https://github.com/gkumar09/iSeqQC) or web-interface (http://cancerwebpa.jefferson.edu/iSeqQC). iSeqQC is a fast, light-weight, expression-based QC tool that detects outliers by implementing various statistical approaches.

bioinformatics↗

bioRxiv2018

Miniaturized Permeability Assay for CRISPR-Mediated Genome-Wide Screens

The impermeability of the luminal endothelial cell monolayer is crucial for the normal performance of the vascular and lymphatic systems. A key to this function is the integrity of the monolayers intercellular junctions. The known repertoire of junction-regulating genes is incomplete. Current permeability assays are incompatible with high-throughput genome-wide screens that could identify these genes. To overcome these limitations, we designed a new permeability assay that consists of cell monolayers grown on [~]150 m microcarriers. Each microcarrier functions as a miniature individual assay of permeability (MAP). We demonstrate that false-positive results can be minimized, and that MAP sensitivity to thrombin-induced increase in monolayer permeability is similar to the sensitivity of the measurement of impedance. We validate the assay by showing that the expression of single guide RNAs (sgRNAs) that target genes encoding known thrombin signaling proteins blocks effectively thrombin-induced junction disassembly, and that MAPs carrying such cells can be separated effectively by a fluorescent probe from those that carry cells expressing non-targeting sgRNAs. These results indicate that MAPs are suitable for high-throughput experimentation and for genome-wide screens for genes that mediate the disruptive effect of thrombin on endothelial cell junctions.

cell biology↗