Identification and Validation of PLOD2 as an Adverse Prognostic Biomarker for Oral Squamous Cell Carcinoma

Background: Procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2 (PLOD2), a key enzyme that catalyzes the hydroxylation of lysine, plays a crucial role in the progression of several solid tumors. However, its spatial expression profile and prognostic significance in oral squamous cell carcinoma (OSCC) have not been revealed. Materials: Mass spectrometry was used to explore amino acid perturbations between OSCC tumor tissues and paired normal tissues of 28 patients. Then, PLOD2 mRNA and protein levels were assessed using several public databases and 18 pairs of OSCC patients’ tissues. Additionally, PLOD2 spatial expression profiles were investigated in 100 OSCC patients by immunohistochemistry and its diagnostic and prognostic values were also evaluated. Lastly, gene set enrichment analysis (GSEA) was used to investigate the potential functions of PLOD2 in OSCC. Results: Lysine was significantly elevated in OSCC tissues and could effectively distinguish tumor from normal tissues (AUC = 0.859, p = 0.0035). PLOD2 mRNA and protein levels were highly increased in tumor tissues of head and neck squamous cell carcinoma (HNSCC) (p < 0.001) and OSCC compared with those in nontumor tissues (p < 0.001). Histopathologically, PLOD2 was ubiquitously expressed in tumor cells (TCs) and fibroblast-like cells (FLCs) of OSCC patients but absent in tumor-infiltrating lymphocytes (TILs). Patients with highly expressed PLOD2 in TCs (PLOD2TCs) and FLCs (PLOD2FLCs) showed poor differentiation, a worse pattern of invasion (WPOI) and more lymph node metastasis (LNM), contributing to higher postoperative metastasis risk and poor survival time. However, PLOD2FLCs rather than PLOD2TCs was an independent risk factor for survival outcomes in OSCC patients. Molecularly, GSEA demonstrated highly expressed PLOD2 was mainly enriched in epithelial–mesenchymal transformation (EMT), TGF-beta signaling and hypoxia pathway, which are associated with poor clinical outcomes of OSCC patients. Conclusions: PLOD2 was a poor prognostic biomarker for OSCC patients and may affect the metastasis of OSCC through EMT pathway. These findings might shed novel sights for future research in PLOD2 targeted OSCC therapy.

Designing Dynamic Systems For Advancing Aesthetic Spatial Engagement In Sound Art

<p>This thesis documents three years of extensive research into the field of sonic spatial expression and is the culmination of years of fascination about all of the ways music is made. In particular, it focuses on the way sounds move through space. This research stems from artistic practice and a desire to deeply explore spatial aesthetics in sound art. A potential for further development of tools designed for aesthetic engagement with spatial attributes of music is identified. It is proposed that with new tools designed for the manipulation of spatial attributes, new spatial aesthetics might emerge. In exploring this proposition, a number of contributions to the field of spatial sound art are presented. The main approach taken is to apply new technologies to the design of spatialisation performance interfaces. It is hoped that in designing novel interfaces that specifically engage with spatial parameters, new ways for aesthetically engaging with space will be afforded for composers and performers. The tools designed all aim to exhibit a high level of intuitiveness in their control systems, allowing non- expert users access to these spatially expressive tools. Additionally, the new tools aim to provide high levels of expressivity so that advanced composers who are looking for new ways to use space expressively may also use them. This thesis focuses on the design, development, implementation, analysis, and artistic use of new spatial interfaces. The design methodology implemented for all of the interfaces includes both testing and analysis phases that involve the composition and performance of new musical works. The development of the interfaces is closely coupled with the development of the new musical works, with each design phase applied to a new work and each new work or spatial idea exploring the new aesthetics afforded by the tools. The assessment of these new tools takes various forms: they are assessed by critical evaluation of the new works created, by user study evaluations from other composers who utilise the tools, and, where appropriate, by quantifiable methods of evaluation that are adopted to assess specific spatialisation tools. The new musical interfaces presented, described, and evaluated in this document were conceived of as musical instruments, each affording new approaches to spatial expression. This document also details an extensive collection of new musical works that feature the interfaces. It concludes by suggesting future directions for this research body and the spatialisation interface design field.</p>

Designing Dynamic Systems For Advancing Aesthetic Spatial Engagement In Sound Art

<p>This thesis documents three years of extensive research into the field of sonic spatial expression and is the culmination of years of fascination about all of the ways music is made. In particular, it focuses on the way sounds move through space. This research stems from artistic practice and a desire to deeply explore spatial aesthetics in sound art. A potential for further development of tools designed for aesthetic engagement with spatial attributes of music is identified. It is proposed that with new tools designed for the manipulation of spatial attributes, new spatial aesthetics might emerge. In exploring this proposition, a number of contributions to the field of spatial sound art are presented. The main approach taken is to apply new technologies to the design of spatialisation performance interfaces. It is hoped that in designing novel interfaces that specifically engage with spatial parameters, new ways for aesthetically engaging with space will be afforded for composers and performers. The tools designed all aim to exhibit a high level of intuitiveness in their control systems, allowing non- expert users access to these spatially expressive tools. Additionally, the new tools aim to provide high levels of expressivity so that advanced composers who are looking for new ways to use space expressively may also use them. This thesis focuses on the design, development, implementation, analysis, and artistic use of new spatial interfaces. The design methodology implemented for all of the interfaces includes both testing and analysis phases that involve the composition and performance of new musical works. The development of the interfaces is closely coupled with the development of the new musical works, with each design phase applied to a new work and each new work or spatial idea exploring the new aesthetics afforded by the tools. The assessment of these new tools takes various forms: they are assessed by critical evaluation of the new works created, by user study evaluations from other composers who utilise the tools, and, where appropriate, by quantifiable methods of evaluation that are adopted to assess specific spatialisation tools. The new musical interfaces presented, described, and evaluated in this document were conceived of as musical instruments, each affording new approaches to spatial expression. This document also details an extensive collection of new musical works that feature the interfaces. It concludes by suggesting future directions for this research body and the spatialisation interface design field.</p>

De-noising Spatial Expression Profiling Data Based on in situ Position and Image Information

Spatial expression profiling (SEP) technologies provide gene expression close to or even superior to single-cell resolution while retaining the physical locations of sequencing and often also providing matched pathology images. However, the expression data captured by SEP technologies suffer from high noise levels, including but not limited to drop-outs as in regular single-cell RNA-sequencing (scRNA-seq). The extra experimental steps for preserving the spatial locations of sequencing could result in even more severe noises, compared to regular scRNA-seq. Fortunately, such noises could be largely reduced by leveraging information from the physical locations of sequencing and the tissue and cellular organization reflected by corresponding pathology images. In this work, we demonstrated the extensive levels of noise in SEP data. We developed a mathematical model, named Sprod, to reduce such noises based on latent space and graph learning of matched location and imaging data. We comprehensively validated Sprod and demonstrated its advantages over prior methods for removing drop-outs in scRNA-seq data. We further showed that, after adequately de-noising by Sprod, differential expression analyses, pseudotime analyses, and cell-to-cell interaction inferences yield significantly more informative results in various biological application settings. In particular, with Sprod, we discovered 3-4 times more RNA transcripts that were actively transported in mouse hippocampus neurons. We also showed that the tumor cells at the tumor-stroma boundaries demonstrate differential transcriptomic features from the tumor cells in the central regions, caused by their interactions with the stroma/immune cells. Overall, we envision denoising by Sprod to become a key first step to empower SEP technologies for biomedical discoveries and innovations.

Grain Dispersal Mechanism In Cereals Arose From a Genome Duplication Followed By Changes in Spatial Expression of Genes Involved In Pollen Development

One of the most critical events in the process of cereal domestication was the loss of the natural mode of grain dispersal. Grain dispersal in barley is controlled by two major genes, Btr1 and Btr2, which affect the thickness of cell walls around the disarticulation zone. The barley genome also encodes Btr1-like and Btr2-like genes, which have been shown to be the ancestral copies. While Btr and Btr-like genes are non-redundant, the biological function of Btr-like genes is unknown. We explored the potential biological role of the Btr-like genes by surveying their expression profile across 212 publicly available transcriptome datasets representing diverse organs, developmental stages and stress conditions. We found that Btr1-like and Btr2-like are expressed exclusively in immature anther samples throughout Prophase I of meiosis within the meiocyte. The similar and restricted expression profile of these two genes suggests they are involved in a common biological function. Further analysis revealed 141 genes co-expressed with Btr1-like and 122 genes co-expressed with Btr2-like, with 105 genes in common, supporting Btr-like genes involvement in a shared molecular pathway. We hypothesize that the Btr-like genes play a crucial role in pollen development by facilitating the formation of the callose wall around the meiocyte or in the secretion of callase by the tapetum. Our data suggest that Btr genes retained an ancestral function in cell wall modification and gained a new role in grain dispersal due to changes in their spatial expression becoming spike specific after gene-duplication.

Benchmarking Computational Integration Methods for Spatial Transcriptomics Data

The increasing popularity of spatial transcriptomics has allowed researchers to analyze transcriptome data in its tissue sample’s spatial context. Various methods have been developed for detecting SV (spatially variable) genes, with distinct spatial expression patterns. However, the accuracy of using such SV genes in clustering cell types has not been thoroughly studied. On the other hand, in single cell resolution sequencing data, clustering analysis is usually done on highly variable (HV) genes. Here we investigate if integrating SV genes and HV genes from spatial transcriptomics data can improve clustering performance beyond using SV genes alone. We evaluated six methods that integrate different features measured from the same samples including MOFA+, scVI, Seurat v4, CIMLR, SNF, and the straightforward concatenation approach. We applied these methods on 19 real datasets from three different spatial transcriptomics technologies (merFISH, SeqFISH+, and Visium) as well as 20 simulated datasets of varying spatial expression conditions. Our evaluations show that the performances of these integration methods are largely dependent on spatial transcriptomics platforms. Despite the variations among the results, in general MOFA+ and simple concatenation have good performances across different types of spatial transcriptomics platforms. This work shows that integrating quantitative and spatial marker genes in the spatial transcriptomics data can improve clustering. It also provides practical guides on the choices of computational methods to accomplish this goal.

Spatial and temporal expression of PORCN is highly dynamic in the developing mouse cochlea.

The mammalian organ of Corti is a highly specialized sensory organ of the cochlea with fine-grained pattern that is essential for auditory function. Previous studies show that the Wnt pathway regulates proliferation, promotes medial compartment formation in the cochlea, differentiation of the mechanosensory hair cells and axon guidance of Type II afferent neurons. WNT ligand expressions are highly dynamic throughout development but are insufficient to explain the roles of the Wnt pathway. We address a potential way for how WNTs specify the medial compartment by characterizing the expression of Porcupine (PORCN), an O-acyltransferase that palmitoylates WNT ligands for secretion. We show PORCN expression across embryonic ages (E)12.5 - E14.5, E16.5, and postnatal day (P)1. Our results showed enriched PORCN in the medial domains during early stages of development, indicating that WNTs have a stronger influence on patterning of the medial compartment. PORCN was rapidly downregulated after E14.5, following the onset of sensory cell differentiation; residual expression remained in some hair cells and supporting cells. On E14.5 and E16.5, we also examined the spatial expression of Gsk3β, an inhibitor of canonical Wnt signaling to determine its potential role in radial patterning of the cochlea. Gsk3β was broadly expressed across the radial axis of the epithelium; therefore, unlikely to control WNT-mediated medial specification. In conclusion, the spatial expression of PORCN enriches WNT secretion from the medial domains of the cochlea to influence the specification of cell fates in the medial sensory domain.