Browsing by Author "Liu, Lizhong"

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    Dissecting the dynamics of signaling events in the BMP, WNT, and NODAL cascade during self-organized fate patterning in human gastruloids
    (Public Library of Science, 2019) Chhabra, Sapna; Liu, Lizhong; Goh, Ryan; Kong, Xiangyu; Warmflash, Aryeh; Bioengineering; Biosciences
    microfiber mesh function to maintain scaffold cellularity under serum-free conditions as well as aid the deposition of GAGs. This supports the hypothesis that scaffolds with constituents more closely resembling native ECM components may be beneficial for cartilage regeneration.
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    Nodal is a short-range morphogen with activity that spreads through a relay mechanism in human gastruloids
    (Springer Nature, 2022) Liu, Lizhong; Nemashkalo, Anastasiia; Rezende, Luisa; Jung, Ji Yoon; Chhabra, Sapna; Guerra, M. Cecilia; Heemskerk, Idse; Warmflash, Aryeh; Bioengineering; Biosciences
    Morphogens are signaling molecules that convey positional information and dictate cell fates during development. Although ectopic expression in model organisms suggests that morphogen gradients form through diffusion, little is known about how morphogen gradients are created and interpreted during mammalian embryogenesis due to the combined difficulties of measuring endogenous morphogen levels and observing development in utero. Here we take advantage of a human gastruloid model to visualize endogenous Nodal protein in living cells, during specification of germ layers. We show that Nodal is extremely short range so that Nodal protein is limited to the immediate neighborhood of source cells. Nodal activity spreads through a relay mechanism in which Nodal production induces neighboring cells to transcribe Nodal. We further show that the Nodal inhibitor Lefty, while biochemically capable of long-range diffusion, also acts locally to control the timing of Nodal spread and therefore of mesoderm differentiation during patterning. Our study establishes a paradigm for tissue patterning by an activator-inhibitor pair.
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    Rapid changes in morphogen concentration control self-organized patterning in human embryonic stem cells
    (eLife Sciences Publications, Ltd, 2019) Heemskerk, Idse; Burt, Kari; Miller, Matthew; Chhabra, Sapna; Guerra, M.Cecilia; Liu, Lizhong; Warmflash, Aryeh; Bioengineering; Biosciences
    During embryonic development, diffusible signaling molecules called morphogens are thought to determine cell fates in a concentration-dependent way. Yet, in mammalian embryos, concentrations change rapidly compared to the time for making cell fate decisions. Here, we use human embryonic stem cells (hESCs) to address how changing morphogen levels influence differentiation, focusing on how BMP4 and Nodal signaling govern the cell-fate decisions associated with gastrulation. We show that BMP4 response is concentration dependent, but that expression of many Nodal targets depends on rate of concentration change. Moreover, in a self-organized stem cell model for human gastrulation, expression of these genes follows rapid changes in endogenous Nodal signaling. Our study shows a striking contrast between the specific ways ligand dynamics are interpreted by two closely related signaling pathways, highlighting both the subtlety and importance of morphogen dynamics for understanding mammalian embryogenesis and designing optimized protocols for directed stem cell differentiation.
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    Self-organized signaling in stem cell models of embryos
    (Elsevier, 2021) Liu, Lizhong; Warmflash, Aryeh; Bioengineering; Biosciences
    Mammalian embryonic development is a complex process driven by self-organization. Understanding how a fertilized egg develops into an embryo composed of more than 200 cell types in precise spatial patterns remains one of the fundamental challenges in biology. Pluripotent stem cells have been used as in vitro models for investigating mammalian development, and represent promising building blocks for regenerative therapies. Recently, sophisticated stem cell-based models that recapitulate early embryonic fate patterning and morphogenesis have been developed. In this article, we review recent advances in stem cell models of embryos in particular focusing on signaling activities underpinning cell fate decisions in space and time.
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    Single C-to-T substitution using engineered APOBEC3G-nCas9 base editors with minimum genome- and transcriptome-wide off-target effects
    (American Association for the Advancement of Science, 2020) Lee, Sangsin; Ding, Ning; Sun, Yidi; Yuan, Tanglong; Li, Jing; Yuan, Qichen; Liu, Lizhong; Yang, Jie; Wang, Qian; Kolomeisky, Anatoly B.; Hilton, Isaac B.; Zuo, Erwei; Gao, Xue; Center for Theoretical and Biological Physics
    Cytosine base editors (CBEs) enable efficient cytidine-to-thymidine (C-to-T) substitutions at targeted loci without double-stranded breaks. However, current CBEs edit all Cs within their activity windows, generating undesired bystander mutations. In the most challenging circumstance, when a bystander C is adjacent to the targeted C, existing base editors fail to discriminate them and edit both Cs. To improve the precision of CBE, we identified and engineered the human APOBEC3G (A3G) deaminase; when fused to the Cas9 nickase, the resulting A3G-BEs exhibit selective editing of the second C in the 5′-CC-3′ motif in human cells. Our A3G-BEs could install a single disease-associated C-to-T substitution with high precision. The percentage of perfectly modified alleles is more than 6000-fold for disease correction and more than 600-fold for disease modeling compared with BE4max. On the basis of the two-cell embryo injection method and RNA sequencing analysis, our A3G-BEs showed minimum genome- and transcriptome-wide off-target effects, achieving high targeting fidelity.