Biology subjects

Knudsen, M.

Publications and source records attributed to Knudsen, M..

4 recordsLinked to original sources

bioRxiv2023

Field cancerization impacts tumor development, T-cell exhaustion and clinical outcomes in bladder cancer

Bladder field cancerization may be associated with disease outcome in patients with bladder cancer. To investigate this, we analyzed biopsies from bladder urothelium and urine samples by genomics and proteomics analyses. Samples were procured from multiple timepoints from 134 patients with early stage bladder cancer and detailed long term follow-up. We measured the field cancerization in normal-appearing bladder biopsies and found that high levels were associated with high tumor mutational burden, high neoantigen load, and high tumor-associated CD8 T-cell exhaustion. Non-synonymous mutations in known bladder cancer driver genes such as KDM6A and TP53 were identified as early disease drivers in normal urothelium. High field cancerization was associated with worse outcome but not with response to BCG. The level of urinary tumor DNA (utDNA) reflected the bladder tumor burden and originated from both tumors and field cancerization. High utDNA levels after BCG were associated with worse clinical outcomes for the patients. Our results indicate that the level of field cancerization may affect clinical outcome, tumor development and immune responses. utDNA measurements have significant prognostic value and reflect the disease status of the bladder.

cancer biology↗

bioRxiv2022

Identifying genes and pathways linking astrocyte regional specificity to Alzheimer's disease susceptibility

Astrocytes have been shown to play a central role in Alzheimers Disease (AD). However, the genes and biological pathways underlying disease manifestation are unknown, and it is unclear whether regional molecular differences among astrocytes contribute to regional specificity of disease. Here, we began to address these challenges with integrated experimental and computational approaches. We constructed a human astrocyte-specific functional gene network using Bayesian integration of a large compendium of human functional genomics data, as well as regional astrocyte gene expression profiles we generated in the mouse. This network identifies likely region-specific astrocyte pathways that operate in healthy brains. We leveraged our findings to compile genome-wide astrocyte-associated disease-gene predictions, employing a novel network-guided differential expression analysis (NetDIFF). We also used this data to predict a list of astrocyte-expressed genes mediating region-specific human disease, using a network-guided shortest path method (NetPATH). Both the network and our results are publicly available using an interactive web interface at http://astrocyte.princeton.edu. Our experimental and computational studies propose a strategy for disease gene and pathway prediction that may be applied to a host of human neurological disorders.

systems biology↗

bioRxiv2022

Single nucleus and spatially resolved intra-tumor subtype heterogeneity in bladder cancer

Current transcriptomic classification systems for bladder cancer do not consider the level of intra-tumor subtype heterogeneity. Here we present an investigation of the extent and possible clinical impact of intra-tumor heterogeneity across early and more advanced disease stages of bladder cancer. We performed single nucleus RNA-sequencing of 48 bladder tumors and four of these tumors were additionally analyzed using spatial transcriptomics. Total bulk RNA-sequencing and spatial proteomics data were available from the same tumors for comparison, along with detailed clinical follow-up of the patients. We demonstrate that tumors display varying levels of intra-tumor subtype heterogeneity and show that a higher class 2a weight estimated from bulk RNA-sequencing data is associated with worse outcome in patients with molecular high-risk class 2a tumors. Our results indicate that discrete subtype assignments from bulk RNA-sequencing data may lack biological granularity and continuous class scores could improve clinical risk stratification of patients. HighlightsO_LISingle nucleus RNA-sequencing of tumors from 48 bladder cancer patients. C_LIO_LITumors display varying levels of intra-tumor subtype heterogeneity at single nucleus and bulk tumor level. C_LIO_LIThe level of subtype heterogeneity could be estimated from both single nucleus and bulk RNA-sequencing data with a high concordance between the two. C_LIO_LIHigh class 2a weight estimated from bulk RNA-sequencing data is associated with worse outcome in patients with molecular high-risk class 2a tumors. C_LI

cancer biology↗

bioRxiv2022

Improved Protocol for Single Nucleus RNA-sequencing of Frozen Human Bladder Tumor Biopsies

This paper provides a laboratory workflow for single-nucleus RNA-sequencing (snRNA-seq) including a protocol for gentle nuclei isolation from fresh frozen tumor biopsies, making it possible to analyze biobanked material. To develop this protocol, we used non-frozen and frozen human bladder tumors and cell lines. We tested different lysis buffers (IgePal and Nuclei EZ) and incubation times in combination with different approaches for tissue and cell dissection; sectioning, semi-automated dissociation, manual dissociation with pestles, and semi-automated dissociation combined with manual dissociation with pestles. Our results showed a combination of IgePal lysis buffer, tissue dissection by sectioning and short incubation time was the best conditions for gentle nuclei isolation applicable for snRNA-seq, and we found limited confounding transcriptomic changes based on the isolation procedure. This protocol makes it possible to analyze biobanked material from patients with well described clinical and histopathological information and known clinical outcomes with snRNA-seq.

cancer biology↗