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Jan 8, 2025 | 
nature.com | Robert R. Stickels |Zaki Abou-Mrad |Viviane Tabar |Brooke E. Howitt |Leif S. Ludwig |Ronan Chaligné | +1 more
AbstractSingle-cell genomics technologies have accelerated our understanding of cell-state heterogeneity in diverse contexts. Although single-cell RNA sequencing identifies rare populations that express specific marker transcript combinations, traditional flow sorting requires cell surface markers with high-fidelity antibodies, limiting our ability to interrogate these populations.
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Dec 8, 2024 | 00622-0?rss=yes&sz=64)
cell.com | Jiaying Toh |Andrea J. Reitsma |Tetsuya Tajima |Sheren F. Younes |Chimere Ezeiruaku |Kayla Jenkins | +24 more
IntroductionEpstein-Barr virus (EBV) is a broadly disseminated gamma-1 herpesvirus estimated to infect 90%–95% of adults globally.1,2 EBV infection is mostly asymptomatic, with the virus proceeding through a complex life cycle including a productive lytic phase but ultimately establishing a latent infection in a subset of memory B cells.3 In this manner, EBV persists for the lifetime of the host, though periodic reactivation of EBV drives further lytic replication and viral transmission.
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May 29, 2024 | 
nature.com | Jacob W. Freimer |Salvador Casaní-Galdón |Maya M. Arce |Bence Daniel |Katalin Sandor |Ralf Schmidt | +3 more
AbstractCis-regulatory elements (CREs) interact with trans regulators to orchestrate gene expression, but how transcriptional regulation is coordinated in multi-gene loci has not been experimentally defined. We sought to characterize the CREs controlling dynamic expression of the adjacent costimulatory genes CD28, CTLA4 and ICOS, encoding regulators of T cell-mediated immunity.
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May 9, 2024 | 
nature.com | Arjun Nanda |Megan S. Ostrowski |Leanne C Sayles |Ansuman T. Satpathy |E. Alejandro Sweet-Cordero |Hani Goodarzi | +1 more
AbstractConcurrent readout of sequence and base modifications from long unamplified DNA templates by Pacific Biosciences of California (PacBio) single-molecule sequencing requires large amounts of input material. Here we adapt Tn5 transposition to introduce hairpin oligonucleotides and fragment (tagment) limiting quantities of DNA for generating PacBio-compatible circular molecules.
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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 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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May 10, 2023 | 
nature.com | Daniel Haensel |Bence Daniel |Tania Fabo |Jeremy Bjelajac |Nancy Li |Ansuman T. Satpathy | +2 more
AbstractCancer immunotherapies have revolutionized treatment but have shown limited success as single-agent therapies highlighting the need to understand the origin, assembly, and dynamics of heterogeneous tumor immune niches. Here, we use single-cell and imaging-based spatial analysis to elucidate three microenvironmental neighborhoods surrounding the heterogeneous basal cell carcinoma tumor epithelia.
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Apr 12, 2023 | 
nature.com | Joshua Weinstock |Bala Bharathi Burugula |Mesbah Uddin |Bence Daniel |Shaneice Mitchell |Cecelia Laurie | +41 more
AbstractMutations in a diverse set of driver genes increase the fitness of haematopoietic stem cells (HSCs), leading to clonal haematopoiesis1. These lesions are precursors for blood cancers2,3,4,5,6, but the basis of their fitness advantage remains largely unknown, partly owing to a paucity of large cohorts in which the clonal expansion rate has been assessed by longitudinal sampling.
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Mar 8, 2023 | 
nature.com | Won-Ju Kim |Caleb A Lareau |Elena Sotillo |Yajie Yin |Alexander Dunn |Ansuman T. Satpathy | +2 more
AbstractAlthough chimeric antigen receptor (CAR) T cells have altered the treatment landscape for B cell malignancies, the risk of on-target, off-tumour toxicity has hampered their development for solid tumours because most target antigens are shared with normal cells1,2. Researchers have attempted to apply Boolean-logic gating to CAR T cells to prevent toxicity3,4,5; however, a truly safe and effective logic-gated CAR has remained elusive6.
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Feb 15, 2023 | 
nature.com | Caleb A Lareau |Vincent Liu |Samantha D. Praktiknjo |Pauline Kautz |Katalin Sandor |Karin Pelka | +3 more
Authors and AffiliationsDepartment of Pathology, Stanford University, Stanford, CA, USACaleb A. Lareau, Vincent Liu, Katalin Sandor, Yajie Yin, Jacob C. Gutierrez & Ansuman T. SatpathyParker Institute for Cancer Immunotherapy, San Francisco, CA, USACaleb A. Lareau & Ansuman T. SatpathyBroad Institute of MIT and Harvard, Cambridge, MA, USAChristoph Muus & Vijay G.
