Advances in synthetic biology for engineering stem cell

CAI Bingyu; TAN Xiangtian; LI Wei

doi:10.12211/2096-8280.2023-101

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Advances in synthetic biology for engineering stem cell

Invited Review | 更新时间：2025-03-19

- Advances in synthetic biology for engineering stem cell
- Synthetic Biology Journal Vol. 5, Issue 4, Pages: 782-794(2024)
- 作者机构：
  
  1.中国科学院动物研究所，干细胞与生殖生物学国家重点实验室，北京 100101
  2.中国科学院大学，北京 100049
  3.中国科学院干细胞与再生医学创新研究院，北京 100101
  4.北京干细胞与再生医学研究院，北京 100101
- 作者简介：
- 基金信息：
- DOI：10.12211/2096-8280.2023-101
  CLC： Q81
- Received：01 December 2023，
  
  Revised：2024-03-12，
  
  Published：31 August 2024
- 稿件说明：
移动端阅览
蔡冰玉，谭象天，李伟. 合成生物学在干细胞工程化改造中的研究进展［J］. 合成生物学， 2024， 5（4）： 782-794

CAI Bingyu， TAN Xiangtian， LI Wei. Advances in synthetic biology for engineering stem cell［J］. Synthetic Biology Journal， 2024， 5（4）： 782-794
蔡冰玉，谭象天，李伟. 合成生物学在干细胞工程化改造中的研究进展［J］. 合成生物学， 2024， 5（4）： 782-794 DOI： 10.12211/2096-8280.2023-101.

CAI Bingyu， TAN Xiangtian， LI Wei. Advances in synthetic biology for engineering stem cell［J］. Synthetic Biology Journal， 2024， 5（4）： 782-794 DOI： 10.12211/2096-8280.2023-101.

摘要

多能干细胞具备自我更新能力和多向分化潜能，其分化衍生的细胞及类器官在再生医学中具有巨大的应用潜力。但是干细胞临床转化仍然存在许多挑战。合成生物学“自上而下”的设计理念，结合基因编辑以及合成受体在内的强大工具库，能够赋予细胞新的功能，实现干细胞工程化改造。在此，本文总结了多能干细胞的临床应用和干细胞临床转化面临的主要挑战（干细胞分化衍生物的致瘤性、异质性、免疫原性），以及合成生物学在干细胞工程化改造中的应用（精确控制细胞命运、调控细胞通信、优化类器官结构功能、监测并清除致瘤细胞）。这些合成生物学工具为干细胞工程化改造提供了新的策略和平台，有望解决干细胞临床应用现存的诸多挑战，推动再生医学的进一步发展，实现“器官再生”这一核心目标。

Abstract

Pluripotent stem cells are characterized by self-renewal and multi-differentiation potential

which can be used to reverse structurally dysfunctional tissues and organs back to a structurally and functionally intact state of health through repair

replacement

in-situ

regeneration of new cells

tissues

and even organs. Cells or multicellular systems derived from pluripotent stem cell differentiation

especially organoids

have great potential for application in regenerative medicine. However

the clinical application of stem cell-related therapies is still in its infancy

and the current challenges to th

e clinical translation of stem cells include the tumorigenicity

heterogeneity

and immunogenicity of stem cell derivatives. Synthetic biology

with its “top-down” design concept and powerful toolkit including synthetic receptors and gene circuits

allows for the rational assembly of standardized modules. With the rapid development of gene editing technology and the deepening of cell biology research

the engineering object of synthetic biology has shifted from lower model organisms such as

Escherichia coli

Saccharomyces cerevisiae

to mammalian cells. On the one hand

“top-down” design strategies can engineer stem cells by giving them new functions

and on the other hand

the acquisition of new phenotypes by stem cells can test known gene functions and improve understanding of cell biology. Therefore

the application of these synthetic biology tools to stem cell engineering provides new strategies and platforms for relevant cell therapies or organ transplantation. It offers potential advantages in precise control of cell fate

regulation of cell communication

optimization of organoid structure and function

and monitoring and elimination of tumorigenic cells. These synthetic biology tools have provided new strategies and platforms for the engineering and reprogramming of stem cells

offering the potential to address current challenges in the clinical application of stem cells. They are expected to drive further advancements in regenerative medicine and ultimately achieve the core goal of regenerative medicine

which is organ regeneration.

关键词

Keywords

references

JACOBSON L O , SIMMONS E L , MARKS E K , et al . Recovery from radiation injury [J ] . Science , 1951 , 113 ( 2940 ): 510 - 511 .

TILL J E , MCCULLOCH E A . A direct measurement of the radiation sensitivity of normal mouse bone marrow cells [J ] . Radiation Research , 1961 , 14 : 213 - 222 .

EVANS M J , KAUFMAN M H . Establishment in culture of pluripotential cells from mouse embryos [J ] . Nature , 1981 , 292 ( 5819 ): 154 - 156 .

THOMSON J A , ITSKOVITZ-ELDOR J , SHAPIRO S S , et al . Embryonic stem cell lines derived from human blastocysts [J ] . Science , 1998 , 282 ( 5391 ): 1145 - 1147 .

TAKAHASHI K , TANABE K , OHNUKI M , et al . Induction of pluripotent stem cells from adult human fibroblasts by defined factors [J ] . Cell , 2007 , 131 ( 5 ): 861 - 872 .

GUAN J Y , WANG G , WANG J L , et al . Chemical reprogramming of human somatic cells to pluripotent stem cells [J ] . Nature , 2022 , 605 ( 7909 ): 325 - 331 .

SCHWARTZ S D , REGILLO C D , LAM B L , et al . Human embryonic stem cell-derived retinal pigment epithelium in patients with age-related macular degeneration and Stargardt’s macular dystrophy: follow-up of two open-label phase 1/2 studies [J ] . Lancet , 2015 , 385 ( 9967 ): 509 - 516 .

KAMAO H , MANDAI M , OKAMOTO S , et al . Characterization of human induced pluripotent stem cell-derived retinal pigment epithelium cell sheets aiming for clinical application [J ] . Stem Cell Reports , 2014 , 2 ( 2 ): 205 - 218 .

PAGLIUCA F W , MILLMAN J R , GÜRTLER M , et al . Generation of functional human pancreatic β cells in vitro [J ] . Cell , 2014 , 159 ( 2 ): 428 - 439 .

SATO T , VRIES R G , SNIPPERT H J , et al . Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche [J ] . Nature , 2009 , 459 ( 7244 ): 262 - 265 .

SPENCE J R , MAYHEW C N , RANKIN S A , et al . Directed differentiation of human pluripotent stem cells into intestinal tissue in vitro [J ] . Nature , 2011 , 470 ( 7332 ): 105 - 109 .

MCCRACKEN K W , CATÁ E M , CRAWFORD C M , et al . Modelling human development and disease in pluripotent stem-cell-derived gastric organoids [J ] . Nature , 2014 , 516 ( 7531 ): 400 - 404 .

MONZEL A S , SMITS L M , HEMMER K , et al . Derivation of human midbrain-specific organoids from neuroepithelial stem cells [J ] . Stem Cell Reports , 2017 , 8 ( 5 ): 1144 - 1154 .

MUGURUMA K , NISHIYAMA A , KAWAKAMI H , et al . Self-organization of polarized cerebellar tissue in 3D culture of human pluripotent stem cells [J ] . Cell Reports , 2015 , 10 ( 4 ): 537 - 550 .

DYE B R , HILL D R , FERGUSON M A , et al . In vitro generation of human pluripotent stem cell derived lung organoids [J ] . eLife , 2015 , 4 : e05098 .

CAMP J G , SEKINE K , GERBER T , et al . Multilineage communication regulates human liver bud development from pluripotency [J ] . Nature , 2017 , 546 ( 7659 ): 533 - 538 .

TAKEBE T , SEKINE K , ENOMURA M , et al . Vascularized and functional human liver from an iPSC-derived organ bud transplant [J ] . Nature , 2013 , 499 ( 7459 ): 481 - 484 .

TAKASATO M , ER P X , BECROFT M , et al . Directing human embryonic stem cell differentiation towards a renal lineage generates a self-organizing kidney [J ] . Nature Cell Biology , 2014 , 16 ( 1 ): 118 - 126 .

TAKEBE T , ENOMURA M , YOSHIZAWA E , et al . Vascularized and complex organ buds from diverse tissues via mesenchymal cell-driven condensation [J ] . Cell Stem Cell , 2015 , 16 ( 5 ): 556 - 565 .

KOIKE H , IWASAWA K , OUCHI R , et al . Modelling human hepato-biliary-pancreatic organogenesis from the foregut-midgut boundary [J ] . Nature , 2019 , 574 ( 7776 ): 112 - 116 .

MIURA K , OKADA Y , AOI T , et al . Variation in the safety of induced pluripotent stem cell lines [J ] . Nature Biotechnology , 2009 , 27 ( 8 ): 743 - 745 .

The International Stem Cell Initiative . Screening ethnically diverse human embryonic stem cells identifies a chromosome 20 minimal amplicon conferring growth advantage [J ] . Nature Biotechnology , 2011 , 29 ( 12 ): 1132 - 1144 .

OSAFUNE K , CARON L , BOROWIAK M , et al . Marked differences in differentiation propensity among human embryonic stem cell lines [J ] . Nature Biotechnology , 2008 , 26 ( 3 ): 313 - 315 .

MACFARLAN T S , GIFFORD W D , DRISCOLL S , et al . Embryonic stem cell potency fluctuates with endogenous retrovirus activity [J ] . Nature , 2012 , 487 ( 7405 ): 57 - 63 .

ZHAO T B , ZHANG Z N , RONG Z L , et al . Immunogenicity of induced pluripotent stem cells [J ] . Nature , 2011 , 474 ( 7350 ): 212 - 215 .

DEUSE T , HU X M , AGBOR-ENOH S , et al . De novo mutations in mitochondrial DNA of iPSCs produce immunogenic neoepitopes in mice and humans [J ] . Nature Biotechnology , 2019 , 37 ( 10 ): 1137 - 1144 .

CAMP J G , BADSHA F , FLORIO M , et al . Human cerebral organoids recapitulate gene expression programs of fetal neocortex development [J ] . Proceedings of the National Academy of Sciences of the United States of America , 2015 , 112 ( 51 ): 15672 - 15677 .

BAXTER M , WITHEY S , HARRISON S , et al . Phenotypic and functional analyses show stem cell-derived hepatocyte-like cells better mimic fetal rather than adult hepatocytes [J ] . Journal of Hepatology , 2015 , 62 ( 3 ): 581 - 589 .

GORDON A , YOON S J , TRAN S S , et al . Long-term maturation of human cortical organoids matches key early postnatal transitions [J ] . Nature Neuroscience , 2021 , 24 ( 3 ): 331 - 342 .

KITADA T , DIANDRETH B , TEAGUE B , et al . Programming gene and engineered-cell therapies with synthetic biology [J ] . Science , 2018 , 359 ( 6376 ): eaad1067 .

TOLLE F , STÜCHELI P , FUSSENEGGER M . Genetic circuitry for personalized human cell therapy [J ] . Current Opinion in Biotechnology , 2019 , 59 : 31 - 38 .

MANSOURI M , FUSSENEGGER M . Therapeutic cell engineering: designing programmable synthetic genetic circuits in mammalian cells [J ] . Protein & Cell , 2022 , 13 ( 7 ): 476 - 489 .

KIM Y G , CHA J , CHANDRASEGARAN S . Hybrid restriction enzymes: zinc finger fusions to Fok Ⅰ cleavage domain [J ] . Proceedings of the National Academy of Sciences of the United States of America , 1996 , 93 ( 3 ): 1156 - 1160 .

CHRISTIAN M , CERMAK T , DOYLE E L , et al . Targeting DNA double-strand breaks with TAL effector nucleases [J ] . Genetics , 2010 , 186 ( 2 ): 757 - 761 .

CONG L , RAN F A , COX D , et al . Multiplex genome engineering using CRISPR/Cas systems [J ] . Science , 2013 , 339 ( 6121 ): 819 - 823 .

STRICKLETT P K , NELSON R D , KOHAN D E . Site-specific recombination using an epitope tagged bacteriophage P1 Cre recombinase [J ] . Gene , 1998 , 215 ( 2 ): 415 - 423 .

RAMÍREZ-SOLIS R , LIU P , BRADLEY A . Chromosome engineering in mice [J ] . Nature , 1995 , 378 ( 6558 ): 720 - 724 .

SU H , WANG X , BRADLEY A . Nested chromosomal deletions induced with retroviral vectors in mice [J ] . Nature Genetics , 2000 , 24 ( 1 ): 92 - 95 .

RIVENBARK A G , STOLZENBURG S , BELTRAN A S , et al . Epigenetic reprogramming of cancer cells via targeted DNA methylation [J ] . Epigenetics , 2012 , 7 ( 4 ): 350 - 360 .

KONERMANN S , BRIGHAM M D , TREVINO A , et al . Optical control of mammalian endogenous transcription and epigenetic states [J ] . Nature , 2013 , 500 ( 7463 ): 472 - 476 .

KEARNS N A , GENGA R M , ENUAMEH M S , et al . Cas9 effector-mediated regulation of transcription and differentiation in human pluripotent stem cells [J ] . Development , 2014 , 141 ( 1 ): 219 - 223 .

GILBERT L A , LARSON M H , MORSUT L , et al . CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes [J ] . Cell , 2013 , 154 ( 2 ): 442 - 451 .

KONERMANN S , BRIGHAM M D , TREVINO A E , et al . Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex [J ] . Nature , 2015 , 517 ( 7536 ): 583 - 588 .

LIU P , CHEN M , LIU Y X , et al . CRISPR-based chromatin remodeling of the endogenous Oct4 or Sox2 locus enables reprogramming to pluripotency [J ] . Cell Stem Cell , 2018 , 22 ( 2 ): 252 - 261 . e4.

CHAVEZ A , SCHEIMAN J , VORA S , et al . Highly efficient Cas9-mediated transcriptional programming [J ] . Nature Methods , 2015 , 12 ( 4 ): 326 - 328 .

LIU X S , WU H , KRZISCH M , et al . Rescue of fragile X syndrome neurons by DNA methylation editing of the FMR1 gene [J ] . Cell , 2018 , 172 ( 5 ): 979 - 992 . e6.

MANHAS J , EDELSTEIN H I , LEONARD J N , et al . The evolution of synthetic receptor systems [J ] . Nature Chemical Biology , 2022 , 18 ( 3 ): 244 - 255 .

BRENNER J , CHO J H , WONG W W . Synthetic biology: sensing with modular receptors [J ] . Nature Chemical Biology , 2017 , 13 ( 2 ): 131 - 132 .

LABANIEH L , MACKALL C L . CAR immune cells: design principles, resistance and the next generation [J ] . Nature , 2023 , 614 ( 7949 ): 635 - 648 .

CAPPELL K M , KOCHENDERFER J N . Long-term outcomes following CAR T cell therapy: what we know so far [J ] . Nature Reviews Clinical Oncology , 2023 , 20 ( 6 ): 359 - 371 .

ENGELOWSKI E , SCHNEIDER A , FRANKE M , et al . Synthetic cytokine receptors transmit biological signals using artificial ligands [J ] . Nature Communications , 2018 , 9 ( 1 ): 2034 .

ISHIZUKA S , LAI C Y , OTSU M , et al . Designing motif-engineered receptors to elucidate signaling molecules important for proliferation of hematopoietic stem cells [J ] . ACS Synthetic Biology , 2018 , 7 ( 7 ): 1709 - 1714 .

MOSSNER S , KUCHNER M , FAZEL MODARES N , et al . Synthetic interleukin 22 (IL-22) signaling reveals biological activity of homodimeric IL-10 receptor 2 and functional cross-talk with the IL-6 receptor gp130 [J ] . The Journal of Biological Chemistry , 2020 , 295 ( 35 ): 12378 - 12397 .

SCHELLER L , STRITTMATTER T , FUCHS D , et al . Generalized extracellular molecule sensor platform for programming cellular behavior [J ] . Nature Chemical Biology , 2018 , 14 ( 7 ): 723 - 729 .

KROEZE W K , SASSANO M F , HUANG X P , et al . PRESTO-Tango as an open-source resource for interrogation of the druggable human GPCRome [J ] . Nature Structural & Molecular Biology , 2015 , 22 ( 5 ): 362 - 369 .

KIPNISS N H , DINGAL P C D P , ABBOTT T R , et al . Engineering cell sensing and responses using a GPCR-coupled CRISPR-Cas system [J ] . Nature Communications , 2017 , 8 ( 1 ): 2212 .

MORSUT L , ROYBAL K T , XIONG X , et al . Engineering customized cell sensing and response behaviors using synthetic Notch receptors [J ] . Cell , 2016 , 164 ( 4 ): 780 - 791 .

ZHU I , LIU R , GARCIA J M , et al . Modular design of synthetic receptors for programmed gene regulation in cell therapies [J ] . Cell , 2022 , 185 ( 8 ): 1431 - 1443 . e16.

DARINGER N M , DUDEK R M , SCHWARZ K A , et al . Modular extracellular sensor architecture for engineering mammalian cell-based devices [J ] . ACS Synthetic Biology , 2014 , 3 ( 12 ): 892 - 902 .

MALAGUTI M , PORTERO MIGUELES R , ANNOH J , et al . SyNPL: Synthetic Notch pluripotent cell lines to monitor and manipulate cell interactions in vitro and in vivo [J ] . Development , 2022 , 149 ( 12 ): dev200226 .

SAXENA P , BOJAR D , ZULEWSKI H , et al . Generation of glucose-sensitive insulin-secreting beta-like cells from human embryonic stem cells by incorporating a synthetic lineage-control network [J ] . Journal of Biotechnology , 2017 , 259 : 39 - 45 .

CAHAN P , LI H , MORRIS S A , et al . CellNet: network biology applied to stem cell engineering [J ] . Cell , 2014 , 158 ( 4 ): 903 - 915 .

TODA S , BLAUCH L R , TANG S K Y , et al . Programming self-organizing multicellular structures with synthetic cell-cell signaling [J ] . Science , 2018 , 361 ( 6398 ): 156 - 162 .

ZHANG S H , ZHAO H , LIU Z X , et al . Monitoring of cell-cell communication and contact history in mammals [J ] . Science , 2022 , 378 ( 6623 ): eabo5503 .

MA Y T , BUDDE M W , MAYALU M N , et al . Synthetic mammalian signaling circuits for robust cell population control [J ] . Cell , 2022 , 185 ( 6 ): 967 - 979 . e12.

CHAO G , WANNIER T M , GUTIERREZ C , et al . helixCAM: a platform for programmable cellular assembly in bacteria and human cells [J ] . Cell , 2022 , 185 ( 19 ): 3551 - 3567 . e39.

STEVENS A J , HARRIS A R , GERDTS J , et al . Programming multicellular assembly with synthetic cell adhesion molecules [J ] . Nature , 2023 , 614 ( 7946 ): 144 - 152 .

MIKI K , ENDO K , TAKAHASHI S , et al . Efficient detection and purification of cell populations using synthetic microRNA switches [J ] . Cell Stem Cell , 2015 , 16 ( 6 ): 699 - 711 .

JUILLERAT A , TKACH D , BUSSER B W , et al . Modulation of chimeric antigen receptor surface expression by a small molecule switch [J ] . BMC Biotechnology , 2019 , 19 ( 1 ): 44 .

ZAH E , LIN M Y , SILVA-BENEDICT A , et al . T cells expressing CD19/CD20 bispecific chimeric antigen receptors prevent antigen escape by malignant B cells [J ] . Cancer Immunology Research , 2016 , 4 ( 6 ): 498 - 508 .

FRY T J , SHAH N N , ORENTAS R J , et al . CD22-targeted CAR T cells induce remission in B-ALL that is naive or resistant to CD19-targeted CAR immunotherapy [J ] . Nature Medicine , 2018 , 24 ( 1 ): 20 - 28 .

STRATI P , BACHANOVA V , GOODMAN A , et al . Preliminary results of a phase Ⅰ trial of FT516, an off-the-shelf natural killer (NK) cell therapy derived from a clonal master induced pluripotent stem cell (iPSC) line expressing high-affinity, non-cleavable CD16 (hnCD16), in patients (pts) with relapsed/refractory (R/R) B-cell lymphoma (BCL) [J ] . Journal of Clinical Oncology , 2021 , 39 ( 15_suppl ): 7541 .

ITAKURA G , KAWABATA S , ANDO M , et al . Fail-safe system against potential tumorigenicity after transplantation of iPSC derivatives [J ] . Stem Cell Reports , 2017 , 8 ( 3 ): 673 - 684 .

KOJIMA K , MIYOSHI H , NAGOSHI N , et al . Selective ablation of tumorigenic cells following human induced pluripotent stem cell-derived neural stem/progenitor cell transplantation in spinal cord injury [J ] . Stem Cells Translational Medicine , 2019 , 8 ( 3 ): 260 - 270 .

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Related Institution

School of Life Science and Technology， ShanghaiTech University

Synthetic Biology and Biomedical Engineering Laboratory， Biomedical Synthetic Biology Research Center， Shanghai Key Laboratory of Regulatory Biology， Institute of Biomedical Sciences and School of Life Sciences， East China Normal University

CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety， CAS Center for Excellence in Nanoscience， National Center for Nanoscience and Technology of China

School of Nanoscience and Engineering， University of Chinese Academy of Sciences

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