Showing papers in "Cell in 2018"
TL;DR: A diagnostic tool based on a deep-learning framework for the screening of patients with common treatable blinding retinal diseases, which demonstrates performance comparable to that of human experts in classifying age-related macular degeneration and diabetic macular edema.
2,750 citations
TL;DR: This review categorizes lncRNA loci into those that regulate gene expression in cis versus those that perform functions in trans and proposes an experimental approach to dissect lncRNAs activity based on these classifications.
2,241 citations
Nationwide Children's Hospital1, University of North Carolina at Chapel Hill2, Henry Ford Health System3, University of Texas MD Anderson Cancer Center4, Broad Institute5, Walter Reed National Military Medical Center6, Buck Institute for Research on Aging7, New York University8, University of Pittsburgh9, Sage Bionetworks10, University of California, San Francisco11, Institute for Systems Biology12
TL;DR: These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale.
1,928 citations
Memorial Sloan Kettering Cancer Center1, Swiss Institute of Bioinformatics2, Harvard University3, Princeton University4, University of Texas at Dallas5, Washington University in St. Louis6, Institute for Systems Biology7, Bilkent University8, Van Andel Institute9, University of Pennsylvania10, University of Texas MD Anderson Cancer Center11, Mayo Clinic12, Columbia University Medical Center13, Fred Hutchinson Cancer Research Center14, University of California, San Francisco15, University of Michigan16, Peter MacCallum Cancer Centre17, Baylor College of Medicine18
TL;DR: This work charted the detailed landscape of pathway alterations in 33 cancer types, stratified into 64 subtypes, and identified patterns of co-occurrence and mutual exclusivity.
1,841 citations
TL;DR: This review considers how TFs are identified and functionally characterized, principally through the lens of a catalog of over 1,600 likely human TFs and binding motifs for two-thirds of them, highlighting the importance of continued effort to understand TF-mediated gene regulation.
1,833 citations
TL;DR: RNA sequencing of half a million single cells was used to create a detailed census of cell types in the mouse nervous system and mapped cell types spatially and derived a hierarchical, data-driven taxonomy.
1,735 citations
Washington University in St. Louis1, Johns Hopkins University2, Discovery Institute3, Genome Institute of Singapore4, University of Miami5, Broad Institute6, Harvard University7, University of Texas MD Anderson Cancer Center8, Memorial Sloan Kettering Cancer Center9, Cornell University10, University of Cambridge11, Catalan Institution for Research and Advanced Studies12, University of California, Santa Cruz13, Baylor College of Medicine14
TL;DR: This study reports a PanCancer and PanSoftware analysis spanning 9,423 tumor exomes (comprising all 33 of The Cancer Genome Atlas projects) and using 26 computational tools to catalog driver genes and mutations, identifying 299 driver genes with implications regarding their anatomical sites and cancer/cell types.
1,623 citations
TL;DR: Molecular similarities among histologically or anatomically related cancer types provide a basis for focused pan-cancer analyses, such as pan-gastrointestinal, Pan-gynecological, pan-kidney, and pan-squamous cancers, and those related by stemness features, which may inform strategies for future therapeutic development.
1,535 citations
Aix-Marseille University1, Cornell University2, Washington University in St. Louis3, Charité4, Pasteur Institute5, French Institute of Health and Medical Research6, Keio University7, University of California, San Francisco8, Laboratory of Molecular Biology9, VU University Amsterdam10, University of Oxford11, University of Amsterdam12
TL;DR: The advances in ILC biology over the past decade are distill the advances to refine the nomenclature of ILCs and highlight the importance of I LCs in tissue homeostasis, morphogenesis, metabolism, repair, and regeneration.
1,252 citations
TL;DR: This study developed Microwell-seq, a high-throughput and low-cost scRNA-seq platform using simple, inexpensive devices, and built a web-based "single-cell MCA analysis" pipeline that accurately defines cell types based on single-cell digital expression.
1,234 citations
TL;DR: A model is developed to show that the measured saturation concentrations of phase separation are inversely proportional to the product of the numbers of arginine and tyrosine residues, which suggests it is possible to predict phase-separation properties based on amino acid sequences.
TL;DR: A preprocessing pipeline, SEQC, and a Bayesian clustering and normalization method, Biscuit, are developed to address computational challenges inherent to single-cell data and support a model of continuous activation in T cells and do not comport with the macrophage polarization model in cancer.
TL;DR: The study of immune cell transcriptomes from tumors demonstrates a strategy for identifying predictors, mechanisms, and targets for enhancing checkpoint immunotherapy by targeting novel combinations of factors in exhausted cells.
TL;DR: MAGIC as mentioned in this paper is a Markov affinity-based graph imputation of cells that shares information across similar cells, via data diffusion, to denoise the cell count matrix and fill in missing transcripts.
TL;DR: Features of brain organization are revealed, including a gene-expression module for synthesizing axonal and presynaptic components, patterns in the co-deployment of voltage-gated ion channels, functional distinctions among the cells of the vasculature and specialization of glutamatergic neurons across cortical regions.
Henry Ford Health System1, Harvard University2, Stanford University3, University of Hasselt4, University of Texas MD Anderson Cancer Center5, Nencki Institute of Experimental Biology6, École Polytechnique Fédérale de Lausanne7, Sage Bionetworks8, Université libre de Bruxelles9, Poznan University of Medical Sciences10, George Washington University11, Cold Spring Harbor Laboratory12, University of Kansas13, University of California, Santa Cruz14, University of North Carolina at Chapel Hill15, Van Andel Institute16
TL;DR: Novel stemness indices for assessing the degree of oncogenic dedifferentiation are provided and it is found that the dedifferentiated oncogenic phenotype was generally most prominent in metastatic tumors.
TL;DR: This study describes a representative collection of well-characterized BC organoids available for cancer research and drug development, as well as a strategy to assess in vitro drug response in a personalized fashion.
TL;DR: It is reported that diverse ADs form phase- separated condensates with the Mediator coactivator, suggesting that diverse TFs can interact with Mediator through the phase-separating capacity of their ADs and that formation of condensate with Mediation is involved in gene activation.
TL;DR: A cellular and molecular checkpoint for intratumoral cDC1 recruitment is revealed that is targeted by tumor-derived PGE2 for immune evasion and that could be exploited for cancer therapy.
TL;DR: The principles of immune normalization are highlighted and lessons learned are learned to guide better designs for future cancer immunotherapies.
TL;DR: The metagenomically characterized the murine and human mucosal-associated gastrointestinal microbiome and found it to only partially correlate with stool microbiome, indicating that empiric probiotics supplementation may be limited in universally and persistently impacting the gut mucosa.
TL;DR: The fidelity of multiplexed spatial cytometry demonstrated here allows for quantitative systemic characterization of tissue architecture in normal and clinically aberrant samples.
TL;DR: A resistance program expressed by malignant cells that is associated with T cell exclusion and immune evasion is identified, and this study provides a high-resolution landscape of ICI-resistant cell states, identifies clinically predictive signatures, and suggests new therapeutic strategies to overcome immunotherapy resistance.
TL;DR: This study provides in vivo evidence that mutant KRAS can be selectively targeted and reveals ARS-1620 as representing a new generation of KRASG12C-specific inhibitors with promising therapeutic potential.
TL;DR: Air-liquid interface method propagated patient-derived organoids (PDOs) from >100 human biopsies or mouse tumors in syngeneic immunocompetent hosts as tumor epithelia with native embedded immune cells to enable immuno-oncology investigations within the TME and facilitate personalized immunotherapy testing.
TL;DR: It is demonstrated that two cell-surface molecules, CD10 and GPR77, specifically define a CAF subset correlated with chemoresistance and poor survival in multiple cohorts of breast and lung cancer patients, and suggested that targeting the CD10+GPR77+ CAFs subset could be an effective therapeutic strategy against CSC-driven solid tumors.
TL;DR: NKG2A targeting with monalizumab is thus a novel checkpoint inhibitory mechanism promoting anti-tumor immunity by enhancing the activity of both T and NK cells, which may complement first-generation immunotherapies against cancer.
TL;DR: This work identifies an uncharacterized family of RNA-guided, RNA-targeting CRISPR systems that is classified as type VI-D, and presents CasRx as a programmable RNA-binding module for efficient targeting of cellular RNA, enabling a general platform for transcriptome engineering and future therapeutic development.
TL;DR: It is shown that access of Bacillus Calmette-Guérin to the bone marrow changes the transcriptional landscape of hematopoietic stem cells (HSCs) and multipotent progenitors (MPPs), leading to local cell expansion and enhanced myelopoiesis at the expense of lymphopoiedis.
TL;DR: The data showed that resistant genotypes were pre-existing and adaptively selected by NAC, while transcriptional profiles were acquired by reprogramming in response to chemotherapy in TNBC patients.