Sotillo, E. et al. Convergence of acquired mutations and alternative splicing of CD19 enables resistance to CART-19 immunotherapy. Cancer Discov. 5, 1282–1295 (2015).
CAS PubMed PubMed Central Article Google Scholar
Orlando, E. J. et al. Genetic mechanisms of target antigen loss in CAR19 therapy of acute lymphoblastic leukemia. Nat. Med. 24, 1504–1506 (2018).
CAS PubMed Article Google Scholar
Zhao, Y. et al. Tumor-intrinsic and -extrinsic determinants of response to blinatumomab in adults with B-ALL. Blood 137, 471–484 (2021).
Sanson, K. R. et al. Optimized libraries for CRISPR–Cas9 genetic screens with multiple modalities. Nat. Commun. 9, 5416 (2018).
CAS PubMed PubMed Central Article Google Scholar
Bradbury, L. E., Kansas, G. S., Levy, S., Evans, R. L. & Tedder, T. F. The CD19/CD21 signal transducing complex of human B lymphocytes includes the target of antiproliferative antibody-1 and Leu-13 molecules. J. Immunol. 149, 2841–2850 (1992).
Shoham, T. et al. The tetraspanin CD81 regulates the expression of CD19 during B cell development in a postendoplasmic reticulum compartment. J. Immunol. 171, 4062–4072 (2003).
CAS PubMed Article Google Scholar
David, V., Hochstenbach, F., Rajagopalan, S. & Brenner, M. B. Interaction with newly synthesized and retained proteins in the endoplasmic reticulum suggests a chaperone function for human integral membrane protein IP90 (calnexin). J. Biol. Chem. 268, 9585–9592 (1993).
CAS PubMed Article Google Scholar
Lang, S. et al. Different effects of Sec61alpha, Sec62 and Sec63 depletion on transport of polypeptides into the endoplasmic reticulum of mammalian cells. J. Cell Sci. 125, 1958–1969 (2012).
CAS PubMed PubMed Central Google Scholar
Kozmik, Z., Wang, S., Dorfler, P., Adams, B. & Busslinger, M. The promoter of the CD19 gene is a target for the B-cell-specific transcription factor BSAP. Mol. Cell Biol. 12, 2662–2672 (1992).
CAS PubMed PubMed Central Google Scholar
Cortés-López, M. et al. High-throughput mutagenesis identifies mutations and RNA-binding proteins controlling CD19 splicing and CART-19 therapy resistance. Preprint at bioRxiv https://doi.org/2021.2010.2008.463671 (2021).
Weintraub, A. S. et al. YY1 Is a structural regulator of enhancer–promoter loops. Cell 171, 1573–1588.e1528 (2017).
CAS PubMed PubMed Central Article Google Scholar
Bailey, S. D. et al. ZNF143 provides sequence specificity to secure chromatin interactions at gene promoters. Nat. Commun. 2, 6186 (2015).
Myslinski, E., Krol, A. & Carbon, P. ZNF76 and ZNF143 are two human homologs of the transcriptional activator Staf. J. Biol. Chem. 273, 21998–22006 (1998).
CAS PubMed Article Google Scholar
Consortium, E. P. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57–74 (2012).
Zhou, Q. et al. ZNF143 mediates CTCF-bound promoter–enhancer loops required for murine hematopoietic stem and progenitor cell function. Nat. Commun. 12, 43 (2021).
CAS PubMed PubMed Central Article Google Scholar
Witkowski, M.T. et al. Extensive remodeling of the immune microenvironment in B cell acute lymphoblastic leukemia. Cancer Cell 37, 867–882 (2020).
Wessels, H. H. et al. Massively parallel Cas13 screens reveal principles for guide RNA design. Nat. Biotechnol. 38, 722–727 (2020).
CAS PubMed PubMed Central Article Google Scholar
Yang, Q., Gilmartin, G. M. & Doublie, S. Structural basis of UGUA recognition by the Nudix protein CFI(m)25 and implications for a regulatory role in mRNA 3′ processing. Proc. Natl Acad. Sci. USA 107, 10062–10067 (2010).
CAS PubMed PubMed Central Article Google Scholar
Bentley, D. L. Coupling mRNA processing with transcription in time and space. Nat. Rev. Genet. 15, 163–175 (2014).
CAS PubMed PubMed Central Article Google Scholar
Brumbaugh, J. et al. Nudt21 controls cell fate by connecting alternative polyadenylation to chromatin signaling. Cell 172, 629–631 (2018).
CAS PubMed Article Google Scholar
Sun, M. et al. NUDT21 regulates 3′-UTR length and microRNA-mediated gene silencing in hepatocellular carcinoma. Cancer Lett. 410, 158–168 (2017).
CAS PubMed Article Google Scholar
Nourse, J., Spada, S. & Danckwardt, S. Emerging roles of RNA 3′-end cleavage and polyadenylation in pathogenesis, diagnosis and therapy of human disorders. Biomolecules 10, 915 (2020).
CAS PubMed Central Article Google Scholar
Majzner, R. G. et al. Tuning the antigen density requirement for CAR T-cell activity. Cancer Discov. 10, 702–723 (2020).
CAS PubMed PubMed Central Article Google Scholar
Ramakrishna, S. et al. Modulation of target antigen density improves CAR T-cell functionality and persistence. Clin. Cancer Res. 25, 5329–5341 (2019).
CAS PubMed PubMed Central Article Google Scholar
Pillai, V. et al. CAR T-cell therapy is effective for CD19-dim B-lymphoblastic leukemia but is impacted by prior blinatumomab therapy. Blood Adv. 3, 3539–3549 (2019).
PubMed PubMed Central Article Google Scholar
Ma, C. et al. Leukemia-on-a-chip: dissecting the chemoresistance mechanisms in B cell acute lymphoblastic leukemia bone marrow niche. Sci. Adv. 6, eaba5536 (2020).
CAS PubMed PubMed Central Article Google Scholar
Eyquem, J. et al. Targeting a CAR to the TRAC locus with CRISPR/Cas9 enhances tumour rejection. Nature 543, 113–117 (2017).
CAS PubMed PubMed Central Article Google Scholar
Rabilloud, T. et al. Single-cell profiling identifies pre-existing CD19-negative subclones in a B-ALL patient with CD19-negative relapse after CAR-T therapy. Nat. Commun. 12, 865 (2021).
CAS PubMed PubMed Central Article Google Scholar
Wang, E. et al. Surface antigen-guided CRISPR screens identify regulators of myeloid leukemia differentiation. Cell Stem Cell 28, 718–731 (2021).
Ramkumar, P. et al. CRISPR-based screens uncover determinants of immunotherapy response in multiple myeloma. Blood Adv. 4, 2899–2911 (2020).
CAS PubMed PubMed Central Article Google Scholar
Li, S., Ilaria, R.L., Million, R.P., Daley, G.Q. & Van Etten, R.A. The P190, P210, and P230 forms of the BCR/ABL oncogene induce a similar chronic myeloid leukemia-like syndrome in mice but have different lymphoid leukemogenic activity. J. Exp. Med. 189, 1399–1412 (1999).
Shi, J. et al. Discovery of cancer drug targets by CRISPR–Cas9 screening of protein domains. Nat. Biotechnol. 33, 661–667 (2015).
CAS PubMed PubMed Central Article Google Scholar
Ran, F. A. et al. Genome engineering using the CRISPR–Cas9 system. Nat. Protoc. 8, 2281–2308 (2013).
CAS PubMed PubMed Central Article Google Scholar
Doench, J. G. et al. Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR–Cas9. Nat. Biotechnol. 34, 184–191 (2016).
CAS PubMed PubMed Central Article Google Scholar
Van Nostrand, E. L. et al. Robust, cost-effective profiling of RNA binding protein targets with single-end enhanced crosslinking and immunoprecipitation (seCLIP). Methods Mol. Biol. 1648, 177–200 (2017).
PubMed PubMed Central Article Google Scholar
Zawada, A. M. et al. Massive analysis of cDNA ends (MACE) and miRNA expression profiling identifies proatherogenic pathways in chronic kidney disease. Epigenetics 9, 161–172 (2014).
CAS PubMed Article Google Scholar
Kuleshov, M. V. et al. Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Res. 44, W90–97 (2016).
CAS PubMed PubMed Central Article Google Scholar
Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).
CAS PubMed Article Google Scholar
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).
PubMed PubMed Central Article Google Scholar
Lazaris, C., Kelly, S., Ntziachristos, P., Aifantis, I. & Tsirigos, A. HiC-bench: comprehensive and reproducible Hi-C data analysis designed for parameter exploration and benchmarking. BMC Genom. 18, 22 (2017).
Li, H.W. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. Preprint at https://doi.org/10.48550/arXiv.1303.3997 (2013).
Kloetgen, A. et al. Three-dimensional chromatin landscapes in T cell acute lymphoblastic leukemia. Nat. Genet. 52, 388–400 (2020).
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