Purpose: To develop a statistical method of combining multimodal MRI (mMRI) of adult glial brain tumours to generate tissue heterogeneity maps that indicate tumour grade and infiltration margins.
Materials And Methods: We performed a retrospective analysis of mMRI from patients with histological diagnosis of glioma (n = 25). H Magnetic Resonance Spectroscopic Imaging (MRSI) was used to label regions of "pure" low- or high-grade tumour across image types. Normal brain and oedema characteristics were defined from healthy controls (n = 10) and brain metastasis patients (n = 10) respectively. Probability density distributions (PDD) for each tissue type were extracted from intensity normalised proton density and T-weighted images, and p and q diffusion maps. Superpixel segmentation and Bayesian inference was used to produce whole-brain tissue-type maps.
Results: Total lesion volumes derived automatically from tissue-type maps correlated with those from manual delineation (p < 0.001, r = 0.87). Large high-grade volumes were determined in all grade III & IV (n = 16) tumours, in grade II gemistocytic rich astrocytomas (n = 3) and one astrocytoma with a histological diagnosis of grade II. For patients with known outcome (n = 20), patients with survival time < 2 years (3 grade II, 2 grade III and 10 grade IV) had a high-grade volume significantly greater than zero (Wilcoxon signed rank p < 0.0001) and also significantly greater high grade volume than the 5 grade II patients with survival >2 years (Mann Witney p = 0.0001). Regions classified from mMRI as oedema had non-tumour-like H MRS characteristics.
Conclusions: H MRSI can label tumour tissue types to enable development of a mMRI tissue type mapping algorithm, with potential to aid management of patients with glial tumours.
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http://dx.doi.org/10.1016/j.nicl.2018.101648 | DOI Listing |
NMR Biomed
February 2025
MR Methodology, Department for Diagnostic and Interventional Neuroradiology, University of Bern, Bern, Switzerland.
The purpose of this study was to produce metabolite-specific T and concentration maps in a clinically compatible time frame. A multi-TE 2D MR spectroscopic imaging (MRSI) experiment (multi-echo single-shot MRSI [MESS-MRSI]) deployed truncated and partially sampled multi-echo trains from single scans and was combined with simultaneous multiparametric model fitting. It was tested in vivo for the brain in five healthy subjects.
View Article and Find Full Text PDFNat Genet
January 2025
Calico Life Sciences LLC, South San Francisco, CA, USA.
Sequence-based machine-learning models trained on genomics data improve genetic variant interpretation by providing functional predictions describing their impact on the cis-regulatory code. However, current tools do not predict RNA-seq expression profiles because of modeling challenges. Here, we introduce Borzoi, a model that learns to predict cell-type-specific and tissue-specific RNA-seq coverage from DNA sequence.
View Article and Find Full Text PDFHuman endocrine cell differentiation and islet morphogenesis play critical roles in determining islet cell mass and function, but the events and timeline of these processes are incompletely defined. To better understand early human islet cell development and maturation, we collected 115 pediatric pancreata and mapped morphological and spatiotemporal changes from birth through the first ten years of life. Using quantitative analyses and a combination of complementary tissue imaging approaches, including confocal microscopy and whole-slide imaging, we developed an integrated model for endocrine cell formation and islet architecture, including endocrine cell type heterogeneity and abundance, endocrine cell proliferation, and islet vascularization and innervation.
View Article and Find Full Text PDFAging (Albany NY)
December 2024
CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institute for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
The ability to accurately quantify biological age could help monitor and control healthy aging. Epigenetic clocks have emerged as promising tools for estimating biological age, yet they have been developed from heterogeneous bulk tissues, and are thus composites of two aging processes, one reflecting the change of cell-type composition with age and another reflecting the aging of individual cell-types. There is thus a need to dissect and quantify these two components of epigenetic clocks, and to develop epigenetic clocks that can yield biological age estimates at cell-type resolution.
View Article and Find Full Text PDFJ Immunother Cancer
January 2025
National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University, Xi'an, Shaanxi, China
Background: Clear cell renal cell carcinoma (ccRCC) is the most common histologic type of RCC. However, the spatial and functional heterogeneity of immunosuppressive cells and the mechanisms by which their interactions promote immunosuppression in the ccRCC have not been thoroughly investigated.
Methods: To further investigate the cellular and regional heterogeneity of ccRCC, we analyzed single-cell and spatial transcriptome RNA sequencing data from four patients, which were obtained from samples from multiple regions, including the tumor core, tumor-normal interface, and distal normal tissue.
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