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Precise tumor immune rewiring via synthetic CRISPRa circuits gated by concurrent gain/loss of transcription factors

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  • Yafeng Wang

    (Model Animal Research Center at Medical School of Nanjing University
    The Affiliated Drum Tower Hospital of Nanjing University Medical School)

  • Guiquan Zhang

    (Model Animal Research Center at Medical School of Nanjing University)

  • Qingzhou Meng

    (Affiliated Cancer Hospital & Institute of Guangzhou Medical University)

  • Shisheng Huang

    (ShanghaiTech University)

  • Panpan Guo

    (The Affiliated Drum Tower Hospital of Nanjing University Medical School)

  • Qibin Leng

    (Affiliated Cancer Hospital & Institute of Guangzhou Medical University)

  • Lingyun Sun

    (The Affiliated Drum Tower Hospital of Nanjing University Medical School)

  • Geng Liu

    (Model Animal Research Center at Medical School of Nanjing University
    Medical School of Nanjing University)

  • Xingxu Huang

    (ShanghaiTech University
    Zhejiang Laboratory)

  • Jianghuai Liu

    (Model Animal Research Center at Medical School of Nanjing University
    Medical School of Nanjing University)

Abstract

Reinvigoration of antitumor immunity has recently become the central theme for the development of cancer therapies. Nevertheless, the precise delivery of immunotherapeutic activities to the tumors remains challenging. Here, we explore a synthetic gene circuit-based strategy for specific tumor identification, and for subsequently engaging immune activation. By design, these circuits are assembled from two interactive modules, i.e., an oncogenic TF-driven CRISPRa effector, and a corresponding p53-inducible off-switch (NOT gate), which jointly execute an AND-NOT logic for accurate tumor targeting. In particular, two forms of the NOT gate are developed, via the use of an inhibitory sgRNA or an anti-CRISPR protein, with the second form showing a superior performance in gating CRISPRa by p53 loss. Functionally, the optimized AND-NOT logic circuit can empower a highly specific and effective tumor recognition/immune rewiring axis, leading to therapeutic effects in vivo. Taken together, our work presents an adaptable strategy for the development of precisely delivered immunotherapy.

Suggested Citation

  • Yafeng Wang & Guiquan Zhang & Qingzhou Meng & Shisheng Huang & Panpan Guo & Qibin Leng & Lingyun Sun & Geng Liu & Xingxu Huang & Jianghuai Liu, 2022. "Precise tumor immune rewiring via synthetic CRISPRa circuits gated by concurrent gain/loss of transcription factors," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
  • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-29120-y
    DOI: 10.1038/s41467-022-29120-y
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    References listed on IDEAS

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    1. Simon Ausländer & David Ausländer & Marius Müller & Markus Wieland & Martin Fussenegger, 2012. "Programmable single-cell mammalian biocomputers," Nature, Nature, vol. 487(7405), pages 123-127, July.
    2. Muneaki Nakamura & Prashanth Srinivasan & Michael Chavez & Matthew A. Carter & Antonia A. Dominguez & Marie La Russa & Matthew B. Lau & Timothy R. Abbott & Xiaoshu Xu & Dehua Zhao & Yuchen Gao & Natha, 2019. "Anti-CRISPR-mediated control of gene editing and synthetic circuits in eukaryotic cells," Nature Communications, Nature, vol. 10(1), pages 1-11, December.
    3. Silvana Konermann & Mark D. Brigham & Alexandro E. Trevino & Julia Joung & Omar O. Abudayyeh & Clea Barcena & Patrick D. Hsu & Naomi Habib & Jonathan S. Gootenberg & Hiroshi Nishimasu & Osamu Nureki &, 2015. "Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex," Nature, Nature, vol. 517(7536), pages 583-588, January.
    4. Ming-Ru Wu & Lior Nissim & Doron Stupp & Erez Pery & Adina Binder-Nissim & Karen Weisinger & Casper Enghuus & Sebastian R. Palacios & Melissa Humphrey & Zhizhuo Zhang & Eva Maria Novoa & Manolis Kelli, 2019. "A high-throughput screening and computation platform for identifying synthetic promoters with enhanced cell-state specificity (SPECS)," Nature Communications, Nature, vol. 10(1), pages 1-10, December.
    5. Yuchen Liu & Yayue Zeng & Li Liu & Chengle Zhuang & Xing Fu & Weiren Huang & Zhiming Cai, 2014. "Synthesizing AND gate genetic circuits based on CRISPR-Cas9 for identification of bladder cancer cells," Nature Communications, Nature, vol. 5(1), pages 1-7, December.
    6. Jovan Mircetic & Antje Dietrich & Maciej Paszkowski-Rogacz & Mechthild Krause & Frank Buchholz, 2017. "Development of a genetic sensor that eliminates p53 deficient cells," Nature Communications, Nature, vol. 8(1), pages 1-11, December.
    7. Huiya Huang & Yiqi Liu & Weixi Liao & Yubing Cao & Qiang Liu & Yakun Guo & Yinying Lu & Zhen Xie, 2019. "Oncolytic adenovirus programmed by synthetic gene circuit for cancer immunotherapy," Nature Communications, Nature, vol. 10(1), pages 1-15, December.
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