From patterns to patients: Advances in clinical machine learning for cancer diagnosis, prognosis, and treatment

K Swanson, E Wu, A Zhang, AA Alizadeh, J Zou - Cell, 2023 - cell.com
Machine learning (ML) is increasingly used in clinical oncology to diagnose cancers, predict
patient outcomes, and inform treatment planning. Here, we review recent applications of ML …

Spatial mapping of cellular senescence: emerging challenges and opportunities

AU Gurkar, AA Gerencser, AL Mora, AC Nelson… - Nature aging, 2023 - nature.com
Cellular senescence is a well-established driver of aging and age-related diseases. There
are many challenges to mapping senescent cells in tissues such as the absence of specific …

[HTML][HTML] Fumarate induces vesicular release of mtDNA to drive innate immunity

V Zecchini, V Paupe, I Herranz-Montoya, J Janssen… - Nature, 2023 - nature.com
Mutations in fumarate hydratase (FH) cause hereditary leiomyomatosis and renal cell
carcinoma. Loss of FH in the kidney elicits several oncogenic signalling cascades through …

Single-cell multi-ome and immune profiles of the Inspiration4 crew reveal conserved, cell-type, and sex-specific responses to spaceflight

JK Kim, BT Tierney, EG Overbey, E Dantas… - Nature …, 2024 - nature.com
Spaceflight induces an immune response in astronauts. To better characterize this effect, we
generated single-cell, multi-ome, cell-free RNA (cfRNA), biochemical, and hematology data …

Spatial mapping of the total transcriptome by in situ polyadenylation

DW McKellar, M Mantri, MM Hinchman… - Nature …, 2023 - nature.com
Spatial transcriptomics reveals the spatial context of gene expression, but current methods
are limited to assaying polyadenylated (A-tailed) RNA transcripts. Here we demonstrate that …

Distinct longevity mechanisms across and within species and their association with aging

A Tyshkovskiy, S Ma, AV Shindyapina, S Tikhonov… - Cell, 2023 - cell.com
Lifespan varies within and across species, but the general principles of its control remain
unclear. Here, we conducted multi-tissue RNA-seq analyses across 41 mammalian species …

[HTML][HTML] Lymphatics act as a signaling hub to regulate intestinal stem cell activity

RE Niec, T Chu, M Schernthanner, S Gur-Cohen… - Cell stem cell, 2022 - cell.com
Barrier epithelia depend upon resident stem cells for homeostasis, defense, and repair.
Epithelial stem cells of small and large intestines (ISCs) respond to their local …

Spatial transcriptomics stratifies psoriatic disease severity by emergent cellular ecosystems

RL Castillo, I Sidhu, I Dolgalev, T Chu, A Prystupa… - Science …, 2023 - science.org
Whereas the cellular and molecular features of human inflammatory skin diseases are well
characterized, their tissue context and systemic impact remain poorly understood. We thus …

BCL2 Inhibition Reveals a Dendritic Cell–Specific Immune Checkpoint That Controls Tumor Immunosurveillance

L Zhao, P Liu, M Mao, S Zhang, C Bigenwald… - Cancer discovery, 2023 - AACR
We developed a phenotypic screening platform for the functional exploration of dendritic
cells (DC). Here, we report a genome-wide CRISPR screen that revealed BCL2 as an …

Performance of tumour microenvironment deconvolution methods in breast cancer using single-cell simulated bulk mixtures

KA Tran, V Addala, RL Johnston, D Lovell… - Nature …, 2023 - nature.com
Cells within the tumour microenvironment (TME) can impact tumour development and
influence treatment response. Computational approaches have been developed to …