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Research: Long-read single-cell RNA sequencing enables the study of cancer subclone-specific genotypes and phenotypes in chronic lymphocytic leukemia
- Gage S. Black,
- Xiaomeng Huang,
- Yi Qiao,
- Philip Moos,
- Deepa Sampath,
- Deborah M. Stephens,
- Jennifer A. Woyach,
- and Gabor T. Marth
Genome Res. April 2025 35: 686-697; Published in Advance February 18, 2025, doi:10.1101/gr.279049.124
..., Columbus, Ohio 43210, USA ↵6 These authors contributed equally to this work. Corresponding author: gmarth@genetics.utah.eduAbstractBruton tyrosine kinase (BTK) inhibitors are effective for the treatment of chronic lymphocytic leukemia (CLL) due to BTK's role in B cell survival and proliferation. Treatment...
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Research: Integrating short-read and long-read single-cell RNA sequencing for comprehensive transcriptome profiling in mouse retina
- Meng Wang,
- Yumei Li,
- Jun Wang,
- Soo Hwan Oh,
- Yexuan Cao,
- and Rui Chen
Genome Res. April 2025 35: 740-754; Published in Advance March 6, 2025, doi:10.1101/gr.279167.124
...-specific exons, transcript isoforms, and splicing regulators (Murphy et al. 2016; Ciampi et al. 2022). A comprehensive understanding of the expressed transcript isoforms, coupled with insights into retina cell type–specific splicing events as well as the expression patterns of transcript isoforms at the single-cell...
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Method: A Bayesian framework for inferring dynamic intercellular interactions from time-series single-cell data
- Cameron Park,
- Shouvik Mani,
- Nicolas Beltran-Velez,
- Katie Maurer,
- Teddy Huang,
- Shuqiang Li,
- Satyen Gohil,
- Kenneth J. Livak,
- David A. Knowles,
- Catherine J. Wu,
- and Elham Azizi
Genome Res. September 2024 34: 1384-1396; Published in Advance September 5, 2024, doi:10.1101/gr.279126.124
...successful in integrating time-series single-cell data sets (Lönnberg et al. 2017), and in identifying key cell states with distinct temporal dynamics shaping response to immunotherapy in human leukemia (Bachireddy et al. 2021). By utilizing GPs, which encode temporal dependencies between all pairs of time...
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Method: A Bayesian framework to study tumor subclone–specific expression by combining bulk DNA and single-cell RNA sequencing data
- Yi Qiao,
- Xiaomeng Huang,
- Philip J. Moos,
- Jonathan M. Ahmann,
- Anthony D. Pomicter,
- Michael W. Deininger,
- John C. Byrd,
- Jennifer A. Woyach,
- Deborah M. Stephens,
- and Gabor T. Marth
Genome Res. January 2024 34: 94-105; Published in Advance January 9, 2024, doi:10.1101/gr.278234.123
...of cells are already known. We acquired bulk DNA sequencing and single-cell RNA sequencing (10x Genomics Chromium 5′ capture protocol) data from three chronic lymphocytic leukemia patients (Supplemental Fig. 4A). The bulk DNA sequencing data are from isolated B cells and B cells (as germline control...
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Method: Single-cell methylation sequencing data reveal succinct metastatic migration histories and tumor progression models
- Yuelin Liu,
- Xuan Cindy Li,
- Farid Rashidi Mehrabadi,
- Alejandro A. Schäffer,
- Drew Pratt,
- David R. Crawford,
- Salem Malikić,
- Erin K. Molloy,
- Vishaka Gopalan,
- Stephen M. Mount,
- Eytan Ruppin,
- Kenneth D. Aldape,
- and S. Cenk Sahinalp
Genome Res. July 2023 33: 1089-1100; Published in Advance June 14, 2023, doi:10.1101/gr.277608.122
...modalities, which is a critical asset especially in the single-cell context.Recent studies have leveraged CpG methylation in single cells sampled from colorectal cancer (CRC) (Bian et al. 2018), chronic lymphocitic leukemia (CLL) (Gaiti et al. 2019), glioblastoma (GBM), and IDH-mutant glioma (Chaligne et al...
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Method: Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data
- Jean Fan,
- Hae-Ock Lee,
- Soohyun Lee,
- Da-eun Ryu,
- Semin Lee,
- Catherine Xue,
- Seok Jin Kim,
- Kihyun Kim,
- Nikolaos Barkas,
- Peter J. Park,
- Woong-Yang Park,
- and Peter V. Kharchenko
Genome Res. August 2018 28: 1217-1227; Published in Advance June 13, 2018, doi:10.1101/gr.228080.117
...associated with distinct genetic subclones. Single-cell RNA-sequencing (scRNA-seq) methods can provide detailed information on the transcriptional state of the cancer cells. However, integration with genotypic information at the single-cell level is necessary to establish correspondence between...
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Resource: Murine single-cell RNA-seq reveals cell-identity- and tissue-specific trajectories of aging
- Jacob C. Kimmel,
- Lolita Penland,
- Nimrod D. Rubinstein,
- David G. Hendrickson,
- David R. Kelley,
- and Adam Z. Rosenthal
Genome Res. December 2019 29: 2088-2103; Published in Advance November 21, 2019, doi:10.1101/gr.253880.119
...and environments on the trajectory of aging in individual cells remains unclear. Here, we performed single-cell RNA-seq on >50,000 individual cells across three tissues in young and old mice to allow for direct comparison of aging phenotypes across cell types. We found transcriptional features of aging common...
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Research: DNA methylation epitypes highlight underlying developmental and disease pathways in acute myeloid leukemia
- Brian Giacopelli,
- Min Wang,
- Ada Cleary,
- Yue-Zhong Wu,
- Anna Reister Schultz,
- Maximilian Schmutz,
- James S. Blachly,
- Ann-Kathrin Eisfeld,
- Bethany Mundy-Bosse,
- Sebastian Vosberg,
- Philipp A. Greif,
- Rainer Claus,
- Lars Bullinger,
- Ramiro Garzon,
- Kevin R. Coombes,
- Clara D. Bloomfield,
- Brian J. Druker,
- Jeffrey W. Tyner,
- John C. Byrd,
- and Christopher C. Oakes
Genome Res. May 2021 31: 747-761; Published in Advance March 11, 2021, doi:10.1101/gr.269233.120
...sequences, all cell types have distinct epigenetic patterns, thus patterns originating from normal counterparts must be accounted for when determining tumor cell–specific epigenetic changes. We have previously shown this to be important for deriving tumor-specific events in chronic lymphocytic leukemia (CLL...
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Research: Dynamics of broad H3K4me3 domains uncover an epigenetic switch between cell identity and cancer-related genes
- Mohamed Belhocine,
- Mathieu Simonin,
- José David Abad Flores,
- Agata Cieslak,
- Iris Manosalva,
- Lydie Pradel,
- Charlotte Smith,
- Eve-Lyne Mathieu,
- Guillaume Charbonnier,
- Joost H.A. Martens,
- Hendrik G. Stunnenberg,
- Muhammad Ahmad Maqbool,
- Aneta Mikulasova,
- Lisa J. Russell,
- Daniel Rico,
- Denis Puthier,
- Pierre Ferrier,
- Vahid Asnafi,
- and Salvatore Spicuglia
Genome Res. July 2022 32: 1328-1342; Published in Advance June 23, 2021, doi:10.1101/gr.266924.120
...chronic lymphocytic leukemia (CLL) lead to consistent results (Supplemental Fig. S8). Therefore, broad H3K4me3 domain–associated genes are more significantly deregulated in leukemia, independent of their relative expression level.View larger version: In this window In a new window Figure 4. Dynamic...
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Perspective: Challenges in identifying mRNA transcript starts and ends from long-read sequencing data
- Ezequiel Calvo-Roitberg,
- Rachel F. Daniels,
- and Athma A. Pai
Genome Res. November 2024 34: 1719-1734; doi:10.1101/gr.279559.124
...sequencing error, and robust computational pipelines. Although much focus has been placed on defining mRNA exon composition and structure with LRS data, less careful characterization has been done of the ability to assess the terminal ends of isoforms, specifically, transcription start and end sites...
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