All Publications


  • Systematic discovery of recombinases for efficient integration of large DNA sequences into the human genome. Nature biotechnology Durrant, M. G., Fanton, A., Tycko, J., Hinks, M., Chandrasekaran, S. S., Perry, N. T., Schaepe, J., Du, P. P., Lotfy, P., Bassik, M. C., Bintu, L., Bhatt, A. S., Hsu, P. D. 2022

    Abstract

    Large serine recombinases (LSRs) are DNA integrases that facilitate the site-specific integration of mobile genetic elements into bacterial genomes. Only a few LSRs, such as Bxb1 and PhiC31, have been characterized to date, with limited efficiency as tools for DNA integration in human cells. In this study, we developed a computational approach to identify thousands of LSRs and their DNA attachment sites, expanding known LSR diversity by >100-fold and enabling the prediction of their insertion site specificities. We tested their recombination activity in human cells, classifying them as landing pad, genome-targeting or multi-targeting LSRs. Overall, we achieved up to seven-fold higher recombination than Bxb1 and genome integration efficiencies of 40-75% with cargo sizes over 7kb. We also demonstrate virus-free, direct integration of plasmid or amplicon libraries for improved functional genomics applications. This systematic discovery of recombinases directly from microbial sequencing data provides a resource of over 60 LSRs experimentally characterized in human cells for large-payload genome insertion without exposed DNA double-stranded breaks.

    View details for DOI 10.1038/s41587-022-01494-w

    View details for PubMedID 36217031

  • In vivo CRISPR screens reveal the landscape of immune evasion pathways across cancer. Nature immunology Dubrot, J., Du, P. P., Lane-Reticker, S. K., Kessler, E. A., Muscato, A. J., Mehta, A., Freeman, S. S., Allen, P. M., Olander, K. E., Ockerman, K. M., Wolfe, C. H., Wiesmann, F., Knudsen, N. H., Tsao, H., Iracheta-Vellve, A., Schneider, E. M., Rivera-Rosario, A. N., Kohnle, I. C., Pope, H. W., Ayer, A., Mishra, G., Zimmer, M. D., Kim, S. Y., Mahapatra, A., Ebrahimi-Nik, H., Frederick, D. T., Boland, G. M., Haining, W. N., Root, D. E., Doench, J. G., Hacohen, N., Yates, K. B., Manguso, R. T. 2022

    Abstract

    The immune system can eliminate tumors, but checkpoints enable immune escape. Here, we identify immune evasion mechanisms using genome-scale in vivo CRISPR screens across cancer models treated with immune checkpoint blockade (ICB). We identify immune evasion genes and important immune inhibitory checkpoints conserved across cancers, including the non-classical major histocompatibility complex class I (MHC class I) molecule Qa-1b/HLA-E. Surprisingly, loss of tumor interferon-gamma (IFNgamma) signaling sensitizes many models to immunity. The immune inhibitory effects of tumor IFN sensing are mediated through two mechanisms. First, tumor upregulation of classical MHC class I inhibits natural killer cells. Second, IFN-induced expression of Qa-1b inhibits CD8+ T cells via the NKG2A/CD94 receptor, which is induced by ICB. Finally, we show that strong IFN signatures are associated with poor response to ICB in individuals with renal cell carcinoma or melanoma. This study reveals that IFN-mediated upregulation of classical and non-classical MHC class I inhibitory checkpoints can facilitate immune escape.

    View details for DOI 10.1038/s41590-022-01315-x

    View details for PubMedID 36151395

  • Pathogenic or benign? Nature biotechnology Du, P. P., Liu, K., Bassik, M. C., Hess, G. T. 2022

    View details for DOI 10.1038/s41587-022-01333-y

    View details for PubMedID 35578021

  • Checkpoint blockade-induced CD8+T cell differentiation in head and neck cancer responders JOURNAL FOR IMMUNOTHERAPY OF CANCER Zhou, L., Zeng, Z., Egloff, A., Zhang, F., Guo, F., Campbell, K. M., Du, P., Fu, J., Zolkind, P., Ma, X., Zhang, Z., Zhang, Y., Wang, X., Gu, S., Riley, R., Nakahori, Y., Keegan, J., Haddad, R., Schoenfeld, J. D., Griffith, O., Manguso, R. T., Lederer, J. A., Liu, X., Uppaluri, R. 2022; 10 (1)

    Abstract

    Immune checkpoint blockade (ICB) response in recurrent/metastatic head and neck squamous cell carcinoma (HNSCC) is limited to 15%-20% of patients and underpinnings of resistance remain undefined.Starting with an anti-PD1 sensitive murine HNSCC cell line, we generated an isogenic anti-PD1 resistant model. Mass cytometry was used to delineate tumor microenvironments of both sensitive parental murine oral carcinoma (MOC1) and resistant MOC1esc1 tumors. To examine heterogeneity and clonal dynamics of tumor infiltrating lymphocytes (TILs), we applied paired single-cell RNA and TCR sequencing in three HNSCC models.Anti-PD1 resistant MOC1esc1 line displayed a conserved cell intrinsic immune evasion signature. Immunoprofiling showed distinct baseline tumor microenvironments of MOC1 and MOC1esc1, as well as the remodeling of immune compartments on ICB in MOC1esc1 tumors. Single cell sequencing analysis identified several CD8 +TIL subsets including Tcf7 +Pd1- (naïve/memory-like), Tcf7 +Pd1+ (progenitor), and Tcf7-Pd1+ (differentiated effector). Mapping TCR shared fractions identified that successful anti-PD1 or anti-CTLA4 therapy-induced higher post-treatment T cell lineage transitions.These data highlight critical aspects of CD8 +TIL heterogeneity and differentiation and suggest facilitation of CD8 +TIL differentiation as a strategy to improve HNSCC ICB response.

    View details for DOI 10.1136/jitc-2021-004034

    View details for Web of Science ID 000745064500001

    View details for PubMedID 35058328

    View details for PubMedCentralID PMC8772459

  • Epigenetic silencing by SETDB1 suppresses tumour intrinsic immunogenicity NATURE Griffin, G. K., Wu, J., Iracheta-Vellve, A., Patti, J. C., Hsu, J., Davis, T., Dele-Oni, D., Du, P. P., Halawi, A. G., Ishizuka, J. J., Kim, S. Y., Klaeger, S., Knudsen, N. H., Miller, B. C., Nguyen, T. H., Olander, K. E., Papanastasiou, M., Rachimi, S., Robitschek, E. J., Schneider, E. M., Yeary, M. D., Zimmer, M. D., Jaffe, J. D., Carr, S. A., Doench, J. G., Haining, W., Yates, K. B., Manguso, R. T., Bernstein, B. E. 2021; 595 (7866): 309-+

    Abstract

    Epigenetic dysregulation is a defining feature of tumorigenesis that is implicated in immune escape1,2. Here, to identify factors that modulate the immune sensitivity of cancer cells, we performed in vivo CRISPR-Cas9 screens targeting 936 chromatin regulators in mouse tumour models treated with immune checkpoint blockade. We identified the H3K9 methyltransferase SETDB1 and other members of the HUSH and KAP1 complexes as mediators of immune escape3-5. We also found that amplification of SETDB1 (1q21.3) in human tumours is associated with immune exclusion and resistance to immune checkpoint blockade. SETDB1 represses broad domains, primarily within the open genome compartment. These domains are enriched for transposable elements (TEs) and immune clusters associated with segmental duplication events, a central mechanism of genome evolution6. SETDB1 loss derepresses latent TE-derived regulatory elements, immunostimulatory genes, and TE-encoded retroviral antigens in these regions, and triggers TE-specific cytotoxic T cell responses in vivo. Our study establishes SETDB1 as an epigenetic checkpoint that suppresses tumour-intrinsic immunogenicity, and thus represents a candidate target for immunotherapy.

    View details for DOI 10.1038/s41586-021-03520-4

    View details for Web of Science ID 000647544800003

    View details for PubMedID 33953401

    View details for PubMedCentralID PMC9166167

  • In vivo screens using a selective CRISPR antigen removal lentiviral vector system reveal immune dependencies in renal cell carcinoma IMMUNITY Dubrot, J., Lane-Reticker, S., Kessler, E. A., Ayer, A., Mishra, G., Wolfe, C. H., Zimmer, M. D., Du, P. P., Mahapatra, A., Ockerman, K. M., Davis, T. R., Kohnle, I. C., Pope, H. W., Allen, P. M., Olander, K. E., Iracheta-Vellve, A., Doench, J. G., Haining, W., Yates, K. B., Manguso, R. T. 2021; 54 (3): 571-+

    Abstract

    CRISPR-Cas9 genome engineering has increased the pace of discovery for immunology and cancer biology, revealing potential therapeutic targets and providing insight into mechanisms underlying resistance to immunotherapy. However, endogenous immune recognition of Cas9 has limited the applicability of CRISPR technologies in vivo. Here, we characterized immune responses against Cas9 and other expressed CRISPR vector components that cause antigen-specific tumor rejection in several mouse cancer models. To avoid unwanted immune recognition, we designed a lentiviral vector system that allowed selective CRISPR antigen removal (SCAR) from tumor cells. The SCAR system reversed immune-mediated rejection of CRISPR-modified tumor cells in vivo and enabled high-throughput genetic screens in previously intractable models. A pooled in vivo screen using SCAR in a CRISPR-antigen-sensitive renal cell carcinoma revealed resistance pathways associated with autophagy and major histocompatibility complex class I (MHC class I) expression. Thus, SCAR presents a resource that enables CRISPR-based studies of tumor-immune interactions and prevents unwanted immune recognition of genetically engineered cells, with implications for clinical applications.

    View details for DOI 10.1016/j.immuni.2021.01.001

    View details for Web of Science ID 000627409300021

    View details for PubMedID 33497609

  • Loss of ADAR1 in tumours overcomes resistance to immune checkpoint blockade. Nature Ishizuka, J. J., Manguso, R. T., Cheruiyot, C. K., Bi, K. n., Panda, A. n., Iracheta-Vellve, A. n., Miller, B. C., Du, P. P., Yates, K. B., Dubrot, J. n., Buchumenski, I. n., Comstock, D. E., Brown, F. D., Ayer, A. n., Kohnle, I. C., Pope, H. W., Zimmer, M. D., Sen, D. R., Lane-Reticker, S. K., Robitschek, E. J., Griffin, G. K., Collins, N. B., Long, A. H., Doench, J. G., Kozono, D. n., Levanon, E. Y., Haining, W. N. 2019; 565 (7737): 43–48

    Abstract

    Most patients with cancer either do not respond to immune checkpoint blockade or develop resistance to it, often because of acquired mutations that impair antigen presentation. Here we show that loss of function of the RNA-editing enzyme ADAR1 in tumour cells profoundly sensitizes tumours to immunotherapy and overcomes resistance to checkpoint blockade. In the absence of ADAR1, A-to-I editing of interferon-inducible RNA species is reduced, leading to double-stranded RNA ligand sensing by PKR and MDA5; this results in growth inhibition and tumour inflammation, respectively. Loss of ADAR1 overcomes resistance to PD-1 checkpoint blockade caused by inactivation of antigen presentation by tumour cells. Thus, effective anti-tumour immunity is constrained by inhibitory checkpoints such as ADAR1 that limit the sensing of innate ligands. The induction of sufficient inflammation in tumours that are sensitized to interferon can bypass the therapeutic requirement for CD8+ T cell recognition of cancer cells and may provide a general strategy to overcome immunotherapy resistance.

    View details for DOI 10.1038/s41586-018-0768-9

    View details for PubMedID 30559380