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1 month ago | 
nature.com | Michael Scherer |Indranil Singh |Martina Braun |Pedro Sanchez |Pedro Sánchez |Dominik Lindenhofer | +13 more
AbstractCurrent approaches used to track stem cell clones through differentiation require genetic engineering1,2 or rely on sparse somatic DNA variants3,4, which limits their wide application. Here we discover that DNA methylation of a subset of CpG sites reflects cellular differentiation, whereas another subset undergoes stochastic epimutations and can serve as digital barcodes of clonal identity.
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Apr 23, 2024 | 
nature.com | Katherine Mueller |Andy Chen |Yingshi Chen |Bence Daniel |Jose Arias-Umana |Alice Wang | +10 more
Correction to: Nature https://doi.org/10.1038/s41586-024-07300-8 Published online 10 April 2024In the version of the article initially published, in the black violin plots in Fig. 5a, a dashed line was used to represent the mean and dotted lines for quartiles. This has now been corrected to a solid line for the mean and dashed lines for the quartiles in the HTML and PDF versions of the article.
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Apr 22, 2024 | 
elifesciences.org | Kévin Nuno |Armon Azizi |Thomas Koehnke |Caleb A Lareau
Editor's evaluation The authors show convincingly that most relapses in AML occur without changes in driver mutations. By using ATAC-seq in matched diagnosis and relapsed samples, they show that epigeneticc mechanisms drive relapse in a large proportion of cases. These findings are of translational importance and are based on rigorous analysis of large set of primary samples.
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Apr 10, 2024 | 
nature.com | Katherine Mueller |Andy Chen |Yingshi Chen |Bence Daniel |Jose Arias-Umana |Alice Wang | +10 more
AbstractA major limitation of chimeric antigen receptor (CAR) T cell therapies is the poor persistence of these cells in vivo1. The expression of memory-associated genes in CAR T cells is linked to their long-term persistence in patients and clinical efficacy2,3,4,5,6, suggesting that memory programs may underpin durable CAR T cell function. Here we show that the transcription factor FOXO1 is responsible for promoting memory and restraining exhaustion in human CAR T cells.
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Mar 25, 2024 | 
protocols.io | Tsion Abay |Robert R. Stickels |Caleb A Lareau
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Feb 5, 2024 | 
nature.com | Lisa Butterfield |Caleb A Lareau |Alexander Marson
Correction to: Nature Medicine https://doi.org/10.1038/s41591-022-01986-x, published online 20 September 2022. In the version of the article initially published, the first name of Deena M. Maurer appeared incorrectly as Denna. This has now been corrected in the HTML and PDF versions of the article. About this articleBucktrout, S.L., Banovich, N.E., Butterfield, L.H. et al. Publisher Correction: Advancing T cell–based cancer therapy with single-cell technologies. Nat Med (2024).
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Nov 8, 2023 | 
nature.com | Caleb A Lareau |Yajie Yin |Katie Maurer |Katalin Sandor |Bence Daniel |Jose Sanz Peña | +20 more
AbstractCell therapies have yielded durable clinical benefits for patients with cancer, but the risks associated with the development of therapies from manipulated human cells are understudied. For example, we lack a comprehensive understanding of the mechanisms of toxicities observed in patients receiving T cell therapies, including recent reports of encephalitis caused by reactivation of human herpesvirus 6 (HHV-6)1.
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Oct 10, 2023 | 
biorxiv.org | Kévin Nuno |Armon Azizi |Caleb A Lareau |Thomas Koehnke
AbstractRelapse of acute myeloid leukemia (AML) is highly aggressive and often treatment refractory. We analyzed previously published AML relapse cohorts and found that 40% of relapses occur without changes in driver mutations, suggesting that non-genetic mechanisms drive relapse in a large proportion of cases. We therefore characterized epigenetic patterns of AML relapse using 26 matched diagnosis-relapse samples with ATAC-seq.
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Oct 3, 2023 | 00980-7&sz=64)
cell.com | Nora Schmidt |Alexander Gabel |Sebastian Zieliński |Caleb A Lareau
Highlights•SND1 is required for nascent SARS-CoV-2 RNA synthesis early during infection•SND1 directly interacts with NSP9 and both proteins bind negative-sense viral RNA•NSP9 is covalently linked to viral RNA at initiation sites, indicating protein priming•SND1 modulates the covalent linkage of NSP9 to positive- and negative-sense viral RNASummaryRegulation of viral RNA biogenesis is fundamental to productive SARS-CoV-2 infection.
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Aug 31, 2023 | 
nature.com | Caleb A Lareau |Leif S. Ludwig |Christoph Muus |Gad Getz |fei chen |Jason D. Buenrostro | +3 more
Correction to: Nature Biotechnology https://doi.org/10.1038/s41587-020-0645-6. Published online 12 August 2020. In the version of this article initially published, due to a coding error, cell clonotypes and allele frequencies were permuted, impacting the visualization of panels in Fig. 6i, j, k, and o. Corrected panels appear as Fig. 1 below, and the software and documentation listed in the Code availability section have been updated.
