Biology subjects

Zha, G.

Publications and source records attributed to Zha, G..

3 recordsLinked to original sources

bioRxiv2024

Deep Generative Optimization of mRNA Codon Sequences for Enhanced Protein Production and Therapeutic Efficacy

Messenger RNA (mRNA) therapeutics show immense promise, but their efficacy is limited by suboptimal protein expression. Here, we present RiboDecode, a deep learning framework that generates mRNA codon sequences for enhanced mRNA translation. RiboDecode introduces several advances, including direct learning from large-scale ribosome profiling data and generative exploration of a large sequence space. In silico analysis demonstrates RiboDecode s robust predictive accuracy for unseen genes and cellular environments. In vitro experiments showed substantial improvements in protein expression, significantly outperforming past methods. In addition, RiboDecode enables mRNA design with consideration of cellular context and demonstrates robust performance across different mRNA formats, including m1{Psi}-modified and circular mRNAs, an important feature for mRNA therapeutics. In vivo mouse studies showed that optimized influenza hemagglutinin mRNAs induce ten times stronger neutralizing antibody responses against influenza virus compared to the unoptimized sequence. In an optic nerve crush model, optimized nerve growth factor mRNAs achieve equivalent neuroprotection of retinal ganglion cells at one-fifth the dose of the unoptimized sequence. Collectively, RiboDecode represents a paradigm shift from rule-based to a data-driven, context-aware approach for mRNA therapeutic applications, enabling the development of more potent and dose-efficient treatments.

bioinformatics↗

bioRxiv2024

SIRT5-mediated GLS and GDH desuccinylation attenuates autophagy in MAC-T cells induced by ammonia

Our previous research revealed that NH3 regulated autophagy dependent on SIRT5 in MAC-T cells. Interestingly, SIRT5 reduced the content of NH3 and glutamate by inhibiting GLS activity, ADP/ATP value also declined. In this study, SIRT5 interacted with endogenous GLS and GDH, and had no effect on endogenous GLS and GDH expression. SIRT5 declined significantly the succinylation levels of GLS and GDH, and further reduced the enzymatic activity of GLS and GDH. SIRT5 declined the glutamine metabolism, which attenuated ammonia release in MAC-T cells, accompanying with cellular autophagy decline, reducing the formation of autophagosome. Deletion of SIRT5 increased the content of NH3 and glutamate, as well as promotes autophagy, which could be alleviated by SIRT5 overexpression. SIRT5 KO was associated with increased succinylation and activity of GLS and GDH, as well as autophagy response in MAC-T cells. Furthermore, SIRT5 promoted the maintenance of mitochondria homeostasis. Mechanistically, SIRT5 modulated the succinylation levels and enzymatic activities of GLS and GDH in mitochondria and promoted the maintenance of mitochondria homeostasis, further attenuating ammonia-stimulated autophagy in MAC-T cells. HighlightsO_LISIRT5 catalyzed lysine desuccinylation of GLS and GDH. C_LIO_LIGLS and GDH enzymatic activity were enhanced by lysine succinylation. C_LIO_LIGLS and GDH were required for SIRT5 to regulate ammonia-induced cellular autophagy. C_LIO_LISIRT5 promoted the maintenance of mitochondrial homeostasis C_LI

physiology↗

bioRxiv2020

Selective germline genome edited pigs and their long immune tolerance in Non Human Primates

Organ transplantation is the only curative treatment for patients with terminal organ failure, however, there is a worldwide organ shortage. Genetically modified pig organs and tissues have become an attractive and practical alternative solution for the severe organ shortage, which has been made possible by significant progress in xenotransplantation in recent years. The past several decades witnessed an expanding list of genetically engineered pigs due to technology advancements, however, the necessary combination of genetic modifications in pig for human organ xenotransplantation has not been determined. In the current study, we created a selective germline genome edited pig (SGGEP). The first triple xenoantigens (GGTA, B4GAL, and CAMH) knockout somatic cells were generated to serve as a prototype cells and then human proteins were expressed in the xenoantigen knockout cells, which include human complement system negative regulatory proteins (CD46, CD55, and CD59); human coagulation system negative regulatory proteins thrombomodulin (THBD); tissue factor pathway inhibitor (TFPI); CD39; macrophage negative regulatory proteins (human CD47); and natural killer cell negative regulatory human HLA-E. After the successful establishment of SGGEP by the nuclear tranfer, we engrafted SGGEP skin to NHP, up to 25 days graft survival without immunosuppressive drugs was observed. Because a pig skin graft does not impact the success of a subsequent allograft or autograft or vice versa, thus our SGGEP could have a great potential for clinical value to save severe and large area burn patients and the other human organ failure. Therefore, this combination of specific gene modifications is a major milestone and provides proof of concept to initiate investigator-initiated clinical trials (IITs) in severe burn patients with defined processes and governance measures in place and the other clinical application.

synthetic biology↗