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Mapping the topography of spatial gene expression with interpretable deep learning.
Nat Methods
January 2025
Department of Computer Science, Princeton University, Princeton, NJ, USA.
Spatially resolved transcriptomics technologies provide high-throughput measurements of gene expression in a tissue slice, but the sparsity of these data complicates analysis of spatial gene expression patterns. We address this issue by deriving a topographic map of a tissue slice-analogous to a map of elevation in a landscape-using a quantity called the isodepth. Contours of constant isodepths enclose domains with distinct cell type composition, while gradients of the isodepth indicate spatial directions of maximum change in expression.
View Article and Find Full Text PDFGenetic structure and divergence of marginal populations of black poplar (Populus nigra L.) in Poland.
Sci Rep
January 2025
Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, Kórnik, 62-035, Poland.
Genetic diversity is crucial to secure the survival and sustainability of ecosystems. Given anthropogenic pressure, as well as the projected alterations connected with the level and circulation of water, riparian forests are of particular concern. In this paper, we assessed the genetic variation of black poplar - one of the keystone tree species of riverine forests.
View Article and Find Full Text PDFRepeatome landscapes and cytogenetics of hortensias provide a framework to trace Hydrangea evolution and domestication.
Ann Bot
January 2025
Graduate School of Human Development and Environment, Kobe University, Nada-ku, Kobe, 657-8501, Japan.
Background And Aims: Ornamental hortensias are bred from a reservoir of over 200 species in the genus Hydrangea s.l. (Hydrangeaceae), and are valued in gardens, households and landscapes across the globe.
View Article and Find Full Text PDFIntegrating RNA-seq and scRNA-seq to explore the prognostic features and immune landscape of exosome-related genes in breast cancer metastasis.
Ann Med
December 2025
Department of Neurosurgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, PR China.
Objective: This study aims to explore the role of exosome-related genes in breast cancer (BRCA) metastasis by integrating RNA-seq and single-cell RNA-seq (scRNA-seq) data from BRCA samples and to develop a reliable prognostic model.
Methods: Initially, a comprehensive analysis was conducted on exosome-related genes from the BRCA cohort in The Cancer Genome Atlas (TCGA) database. Three prognostic genes (JUP, CAPZA1 and ARVCF) were identified through univariate Cox regression and Lasso-Cox regression analyses, and a metastasis-related risk score model was established based on these genes.
Assessing spatial sequencing and imaging approaches to capture the molecular and pathological heterogeneity of archived cancer tissues.
J Pathol
January 2025
The Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia.
Spatial transcriptomics (ST) offers enormous potential to decipher the biological and pathological heterogeneity in precious archival cancer tissues. Traditionally, these tissues have rarely been used and only examined at a low throughput, most commonly by histopathological staining. ST adds thousands of times as many molecular features to histopathological images, but critical technical issues and limitations require more assessment of how ST performs on fixed archival tissues.
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