Gene knockdown by structure defined single-stem loop small non-coding RNAs with programmable regulatory activities.

Gene regulation by trans-acting small RNAs (sRNAs) has considerable advantages over other gene regulation strategies. However, synthetic sRNAs mainly take natural sRNAs (MicC or SgrS) as backbones and comprise three functional elements folding into two or more stem-loop structures: an mRNA base pairing region, an Hfq-binding structure, and a rho-independent terminator. Due to limited numbers of natural sRNAs and complicated backbone structures, synthetic sRNAs suffer from low activity programmability and poor structural modularity. Moreover, natural sRNA backbone sequences may increase the possibility of unwanted recombination. Here, we present a bottom-up approach for creating structure defined single-stem loop small non-coding RNAs (ssl-sRNAs), which contain a standardized scaffold of a 7 bp-stem-4 nt-loop-polyU-tail and a 24 nt basing pairing region covering the first eight codons. Particularly, ssl-sRNA requires no independent Hfq-binding structure, as the polyU tail fulfills the roles of binding Hfq. A thermodynamic-based scoring model and a web server sslRNAD (http://www.kangzlab.cn/) were developed for automated design of ssl-sRNAs with well-defined structures and programmable activities. ssl-sRNAs displayed weak polar effects when regulating polycistronic mRNAs. The ssl-sRNA designed by sslRNAD showed regulatory activities in both Escherichia coli and Bacillus subtilis. A streamlined workflow was developed for the construction of customized ssl-sRNA and ssl-sRNA libraries. As examples, the E. coli cell morphology was easily modified and new target genes of ergothioneine biosynthesis were quickly identified with ssl-sRNAs. ssl-sRNA and its designer sslRNAD enable researchers to rapidly design sRNAs for knocking down target genes.

Development of Novel CD47-Specific ADCs Possessing High Potency Against Non-Small Cell Lung Cancer in vitro and in vivo.

Targeted therapies hold promise for efficiently and accurately delivering cytotoxic drugs directly to tumor tissue to exert anticancer effects. CD47 is a membrane protein expressed in a variety of malignant tumors and hematopoietic cells, which plays a key role in immune escape and tumor progression. Although CD47 immunocheckpoint therapy has been developed in recent years, many patients cannot benefit from it because of its low efficiency. To strengthen and extend the therapeutic efficacy of anti-CD47 monoclonal antibody (mAb), we used the newly developed 7DC2 and 7DC4 mAbs as the targeting payload adaptor and VCMMAE as the toxin payload to construct novel CD47-specific immunotoxin (7DC-VCMMAE) by engineering cysteine residues. These CD47-specific ADCs have the better cell penetration, excellent DAR, similar payload distribution and good antigen-binding affinity. In vitro, 7DC-VCMMAE treatment induced death of non-small cell lung cancer (NSCLC) cell lines 95D and SPC-A1, but not A549 that express low levels of CD47 on the cell membrane. This finding suggests that 7DC-VCMMAE may possess greater therapeutic effect on NSCLC tumors expressing a high level of CD47 antigen; however, 7DC-VCMMAE treatment also promoted phagocytosis of A549 cells by macrophages. In vivo, 7DC-VCMMAE treatment had remarkable antitumor effects in a NSCLC cell line-derived xenograft (CDX) mouse model based on nonobese diabetic/severe combined immunodeficient (NOD/SCID). In summary, this study combined VCMMAE with anti-CD47 mAbs, emphasizing a novel and promising immunotherapy method for direct killing of NSCLC, which provides a valuable new way to meet the needs of the cancer therapy field.

Cigarette smoking promotes keratinocyte malignancy via generation of cancer stem-like cells.

Objectives: Cigarette smoking is involved in the pathogenesis of head and neck squamous cell carcinoma (HNSCC). However, the underlying molecular mechanisms of cigarette smoking-induced HNSCC carcinogenesis are unclear and may involve cancer stem-like cell generation. We examined the effects of cigarette smoke condensate (CSC) on the formation of cancer stem-like cells, which are rich in octamer-binding transcription factor (OCT)-4, inhibitor of differentiation 1 (ID1), nuclear factor (NF)-κB, and B lymphoma Mo-MLV insertion region 1 homolog (BMI-1). Materials and Methods: We used in vitro, in vivo, and archival human HNSCC tissue analysis to evaluate the effects of CSC on cancer stem-like cell formation. Results: We found that CSC regulated OCT-4 expression, which subsequently regulated ID1 and NF-κB, at the promoter, mRNA, and protein levels in vitro. Furthermore, OCT-4 knockdown with siRNA reduced ID1 expression. ID1 and NF-κB synergistically increased the expression of BMI-1 and stimulated keratinocyte sphere generation. In vivo, ID1 and NF-κB acted together to generate malignant xenograft tumors, which were aggressive locally and systemically metastatic. Clinical data confirmed that ID1- and NF-κB-positive patients had poor clinical outcomes and 5-year disease-free survival. Conclusion: Our data suggest that smoking cigarettes promoted cancer stem-like cell generation in the head and neck area via the OCT-4/ID1/NF-κB/BMI-1 signaling pathway.

Construction of Synthetic Promoters by Assembling the Sigma Factor Binding -35 and -10 Boxes.

Promoter is one of the key elements in regulating gene expression. Many natural or synthetic promoters have been modulated by their cis- or tans-regulatory elements to confer instant gene expression change in responding to designated stimuli. In addition, bacterial cells also engage different sigma factors to control the gene expression network at different growth phases or in response to the changing environment and external stresses. In this study, a set of promoters that assimilate the endogenous regulation of different sigma factors σ70 , σ38 , σ32 , and σ24 are synthesized. Promoters are designed to contain two or more kinds of interlocking sigma factor binding sites. The most competitive sigma factors will be automatically selected by the cell to take over the synthetic promoters during the cell growth course. Some of the synthetic promoters exhibit very strong strengths under different conditions, including stationary phase, low temperature, acidic pH, and high osmotic pressure. Comparing to the T7 promoter, synthetic promoter P21285 achieved higher yields of L-asparaginase and acid urease in Escherichia coli. The research not only expands the synthetic biology toolbox but also provide another strategy to design and construct synthetic promoters in prokaryotes.

Engineering of multiple modular pathways for high-yield production of 5-aminolevulinic acid in Escherichia coli.

5-aminolevulinic acid (ALA), an important precursor of tetrapyrroles, has various applications in medicine and agriculture fields. Several methods have been adopted to enhance ALA synthesis in our previous studies. In this study, systematic metabolic engineering strategies were implemented to further improve ALA production in Escherichia coli. Firstly, hemA and hemL with different strength of RBS from the artificially constructed mutation libraries were randomly assembled to balance metabolic flux. Then the expression of ALA dehydratase was rationally regulated by replacing promoter with fliCp to weaken ALA catabolism. Besides, the activity of glutamate-1-semialdehyde aminotransferase was increased through strengthening the native biosynthesis pathway of cofactor pyridoxal 5'-phosphate. Moreover, plasmid stability was improved by 21.4% by deleting recA and endA in the recombinant. Finally, stepwise improvements in ALA production were increased to 5.25 g/L with a pH two-stage strategy in a 3-L fermenter. This study proved the importance of metabolic balance in the pathway.

Combined α-programmed death-1 monoclonal antibody blockade and fractionated radiation therapy reduces tumor growth in mouse EL4 lymphoma.

The programmed death (PD) pathway is frequently present in the tumor microenvironment (TME) and suppresses tumor immunity by inhibiting the activity of tumor-infiltrating lymphocytes (TILs), particularly, CD8+ lymphocytes. PD immunotherapy involves stimulation of the immune response in the region surrounding the tumor but is insufficient to prevent tumor progression. Therefore, in this study, we examined the effects of combined PD immunotherapy with fractionated radiotherapy (RT) on antitumor immunity and tumor growth in lymphoma. The immune cell profiles of the TME, blood, and secondary lymphoid organs were determined 7 days after treatment. Four combination therapies were compared. The synergistic effects of αPD-1 mAb and fractionated RT on increased CD8+ lymphocytes in the TME, blood, and secondary lymphoid organs led to substantial tumor regression in mouse EL4 lymphoma, both locally and systemically. Fractionated RT for 4 days followed by αPD-1 mAb therapy was significantly superior to other schemes in terms of overall survival rates and curative rates in xenograft model mice. Our data indicated that substantial immune responses occurred following combination therapy with fractionated RT and αPD-1 mAb immunotherapy. Our findings provide important insights into the use of RT plus αPD-1 mAb as an efficacious combinatorial therapy.

Scarless assembly of unphosphorylated DNA fragments with a simplified DATEL method.

Efficient assembly of multiple DNA fragments is a pivotal technology for synthetic biology. A scarless and sequence-independent DNA assembly method (DATEL) using thermal exonucleases has been developed recently. Here, we present a simplified DATEL (sDATEL) for efficient assembly of unphosphorylated DNA fragments with low cost. The sDATEL method is only dependent on Taq DNA polymerase and Taq DNA ligase. After optimizing the committed parameters of the reaction system such as pH and the concentration of Mg2+ and NAD+, the assembly efficiency was increased by 32-fold. To further improve the assembly capacity, the number of thermal cycles was optimized, resulting in successful assembly 4 unphosphorylated DNA fragments with an accuracy of 75%. sDATEL could be a desirable method for routine manual and automated assembly.

5-Aminolevulinic acid production from inexpensive glucose by engineering the C4 pathway in Escherichia coli.

5-Aminolevulinic acid (ALA), the first committed intermediate for natural biosynthesis of tetrapyrrole compounds, has recently drawn intensive attention due to its broad potential applications. In this study, we describe the construction of recombinant Escherichia coli strains for ALA production from glucose via the C4 pathway. The hemA gene from Rhodobacter capsulatus was optimally overexpressed using a ribosome binding site engineering strategy, which enhanced ALA production substantially from 20 to 689 mg/L. Following optimization of biosynthesis pathways towards coenzyme A and precursor (glycine and succinyl-CoA), and downregulation of hemB expression, the production of ALA was further increased to 2.81 g/L in batch-fermentation.

N-terminal engineering of glutamyl-tRNA reductase with positive charge arginine to increase 5-aminolevulinic acid biosynthesis.

Five-Aminolevulinic acid (ALA), the universal precursor of all tetrapyrroles, has various applications in medicine and agriculture industries. Glutamyl-tRNA reductase (GluTR) as the first key enzyme of C5 pathway is feedback regulated by heme, and its N-terminus plays a critical role on its stability control. Here, the GluTR N-terminus was engineered by inserting different numbers of positively charged lysine and arginine residues. The results confirmed that insertion of lysine or arginine residues (especially one arginine residue) behind Thr2 significantly increased the stability of GluTR. By co-expression of the GluTR variant R1 and the glutamate-1-semialdehyde aminotransferase, ALA production was improved 1.76-fold to 1220 mg/L. The GluTR variant R1 constructed here could be used for engineering the C5 pathway to enhance ALA and other products.