Scholars@Duke
Linfeng Huang

Linfeng Huang

Associate Professor of Biology at Duke Kunshan University
DKU Faculty
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Selected Publications

H3K27me3-mediated epigenetic regulation in pluripotency maintenance and lineage differentiation.

Journal Article Cell insight · August 2024 Cell fate determination is an intricate process which is orchestrated by multiple regulatory layers including signal pathways, transcriptional factors, epigenetic modifications, and metabolic rewiring. Among the sophisticated epigenetic modulations, the re ... Full text Cite

Liver cancer cells as the model for developing liver-targeted RNAi therapeutics.

Journal Article Biochemical and biophysical research communications · February 2023 RNAi is a sequence-specific gene regulation mechanism that involves small interfering RNAs (siRNAs). RNAi therapeutic has become a new class of precision medicine and has shown great potential in treating liver-associated diseases, especially metabolic dis ... Full text Cite

Single-cell quantification and dose-response of cytosolic siRNA delivery.

Journal Article Nature communications · February 2023 Endosomal escape and subsequent cytosolic delivery of small interfering RNA (siRNA) therapeutics is believed to be highly inefficient. Since it has not been possible to quantify cytosolic amounts of delivered siRNA at therapeutic doses, determining deliver ... Full text Cite

Plakoglobin and High-Mobility Group Box 1 Mediate Intestinal Epithelial Cell Apoptosis Induced by Clostridioides difficile TcdB.

Journal Article mBio · October 2022 Clostridioides difficile infection (CDI) is the leading cause of antibiotic-associated intestinal disease, resulting in severe diarrhea and fatal pseudomembranous colitis. TcdB, one of the essential virulence factors secreted by this bacterium, induces hos ... Full text Cite

Bacterial Transcription Factors Bind to Coding Regions and Regulate Internal Cryptic Promoters.

Journal Article mBio · October 2022 Transcription factors (TFs) regulate transcription by binding to the specific sequences at the promoter region. However, the mechanisms and functions of TFs binding within the coding sequences (CDS) remain largely elusive in prokaryotes. To this end, we co ... Full text Cite

Spontaneous quorum-sensing hierarchy reprogramming in Pseudomonas aeruginosa laboratory strain PAO1.

Journal Article AMB Express · January 2022 Pseudomonas aeruginosa strain PAO1 has been commonly used in the laboratory, with frequent genome variations reported. Quorum sensing (QS), a cell-cell communication system, plays important role in controlling a variety of virulence factors. However, the e ... Full text Cite

Profiling MicroRNAs with Associated Spatial Dynamics in Acute Tissue Slices.

Journal Article ACS nano · March 2021 MicroRNAs (miRNAs) are suggested to play important roles in the pathogenesis and progress of human diseases with heterogeneous regulation in different types of cells. However, limited technique is available for profiling miRNAs with both expression and spa ... Full text Cite

Combined inhibition of RNA polymerase I and mTORC1/2 synergize to combat oral squamous cell carcinoma.

Journal Article Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie · January 2021 Oral squamous cell carcinoma (OSCC) is the major cause of morbidity and mortality in head and neck cancer patients worldwide. This malignant disease is challenging to treat because of the lack of effective curative strategies and the high incidence of recu ... Full text Cite

High-Efficiency Cellular Reprogramming by Nanoscale Puncturing.

Journal Article Nano letters · July 2020 Induced pluripotent stem cells (iPSCs) bear great potential for disease modeling, drug discovery, and regenerative medicine; however, the wide adoption of iPSC for clinically relevant applications has been hindered by the extremely low reprogramming effici ... Full text Cite

Tombusvirus p19 Captures RNase III-Cleaved Double-Stranded RNAs Formed by Overlapping Sense and Antisense Transcripts in Escherichia coli.

Journal Article mBio · June 2020 Antisense transcription is widespread in bacteria. By base pairing with overlapping sense RNAs, antisense RNAs (asRNA) can form double-stranded RNAs (dsRNA), which are cleaved by RNase III, a dsRNA endoribonuclease. The ectopic expression of plant Tombu ... Full text Cite

High-throughput intracellular biopsy of microRNAs for dissecting the temporal dynamics of cellular heterogeneity.

Journal Article Science advances · June 2020 The capability to analyze small RNAs responsible for post-transcriptional regulation of genes expression is essential for characterizing cellular phenotypes. Here, we describe an intracellular biopsy technique (inCell-Biopsy) for fast, multiplexed, and hig ... Full text Cite

Lipid-based Vehicles for siRNA Delivery in Biomedical Field.

Journal Article Current pharmaceutical biotechnology · January 2020 BackgroundGenetic drugs have aroused much attention in the past twenty years. RNA interference (RNAi) offers novel insights into discovering potential gene functions and therapies targeting genetic diseases. Small interference RNA (siRNA), typical ... Full text Cite

Self-assembled Lipid Nanoparticles for Ratiometric Codelivery of Cisplatin and siRNA Targeting XPF to Combat Drug Resistance in Lung Cancer.

Journal Article Chemistry, an Asian journal · May 2019 DNA damage repair through the nucleotide excision repair (NER) pathway is one of the major reasons for the decreased antitumor efficacy of platinum-based anticancer drugs that have been widely applied in the clinic. Inhibiting the intrinsic NER function ma ... Full text Cite

Autophagy inhibitor Vacuolin-1 interferes with lipid-based small interference RNA delivery.

Journal Article Biochemical and biophysical research communications · March 2019 Autophagy and endocytosis are important pathways regulating macromolecule recycling and regeneration. Small molecule inhibitors are utilized to modulate these pathways and to treat autophagy-related diseases. Vacuolin-1 is a small molecule that can potentl ... Full text Cite

Tumor-secreted extracellular vesicles promote the activation of cancer-associated fibroblasts via the transfer of microRNA-125b.

Journal Article Journal of extracellular vesicles · January 2019 Tumour cells release large quantities of extracellular vesicles (EVs) to mediate their interactions with other cells in the tumour microenvironment. To identify host cells that naturally take up EVs from tumour cells, we created breast cancer cell lines se ... Full text Cite

RNA interference technology

Chapter · January 1, 2019 RNA interference (RNAi) is the biological process of mRNA degradation induced by complementary sequences double-stranded (ds) small interfering RNAs (siRNA) and suppression of target gene expression. Exogenous siRNAs (perfectly paired dsRNAs of ~21-25 nt i ... Full text Cite

Milligram scale production of potent recombinant small interfering RNAs in Escherichia coli.

Journal Article Biotechnology and bioengineering · September 2018 Small interfering RNAs (siRNAs) are invaluable research tools for studying gene functions in mammalian cells. siRNAs are mainly produced by chemical synthesis or by enzymatic digestion of double-stranded RNA (dsRNA) produced in vitro. Recently, bacterial c ... Full text Cite

Regeneration of cortical tissue from brain injury by implantation of defined molecular gradient of semaphorin 3A.

Journal Article Biomaterials · March 2018 Despite great efforts in the exploration of therapeutic strategies for treating brain injuries, it is still challenging to regenerate neural tissues and to restore the lost function within an injured brain. In this report, we employed a tissue engineering ... Full text Cite

Production of highly potent recombinant siRNAs in Escherichia coli.

Journal Article Nature protocols · December 2013 We recently invented a method to produce highly potent siRNAs in Escherichia coli, based on the serendipitous discovery that ectopic expression of p19, a plant viral siRNA-binding protein, stabilizes otherwise unstable bacterial siRNAs, which we named pro- ... Full text Cite

Efficient and specific gene knockdown by small interfering RNAs produced in bacteria.

Journal Article Nature biotechnology · April 2013 Synthetic small interfering RNAs (siRNAs) are an indispensable tool to investigate gene function in eukaryotic cells and may be used for therapeutic purposes to knock down genes implicated in disease. Thus far, most synthetic siRNAs have been produced by c ... Full text Cite

H3K27me3-mediated epigenetic regulation in pluripotency maintenance and lineage differentiation.

Journal Article Cell insight · August 2024 Cell fate determination is an intricate process which is orchestrated by multiple regulatory layers including signal pathways, transcriptional factors, epigenetic modifications, and metabolic rewiring. Among the sophisticated epigenetic modulations, the re ... Full text Cite

Liver cancer cells as the model for developing liver-targeted RNAi therapeutics.

Journal Article Biochemical and biophysical research communications · February 2023 RNAi is a sequence-specific gene regulation mechanism that involves small interfering RNAs (siRNAs). RNAi therapeutic has become a new class of precision medicine and has shown great potential in treating liver-associated diseases, especially metabolic dis ... Full text Cite

Single-cell quantification and dose-response of cytosolic siRNA delivery.

Journal Article Nature communications · February 2023 Endosomal escape and subsequent cytosolic delivery of small interfering RNA (siRNA) therapeutics is believed to be highly inefficient. Since it has not been possible to quantify cytosolic amounts of delivered siRNA at therapeutic doses, determining deliver ... Full text Cite

Plakoglobin and High-Mobility Group Box 1 Mediate Intestinal Epithelial Cell Apoptosis Induced by Clostridioides difficile TcdB.

Journal Article mBio · October 2022 Clostridioides difficile infection (CDI) is the leading cause of antibiotic-associated intestinal disease, resulting in severe diarrhea and fatal pseudomembranous colitis. TcdB, one of the essential virulence factors secreted by this bacterium, induces hos ... Full text Cite

Bacterial Transcription Factors Bind to Coding Regions and Regulate Internal Cryptic Promoters.

Journal Article mBio · October 2022 Transcription factors (TFs) regulate transcription by binding to the specific sequences at the promoter region. However, the mechanisms and functions of TFs binding within the coding sequences (CDS) remain largely elusive in prokaryotes. To this end, we co ... Full text Cite

Spontaneous quorum-sensing hierarchy reprogramming in Pseudomonas aeruginosa laboratory strain PAO1.

Journal Article AMB Express · January 2022 Pseudomonas aeruginosa strain PAO1 has been commonly used in the laboratory, with frequent genome variations reported. Quorum sensing (QS), a cell-cell communication system, plays important role in controlling a variety of virulence factors. However, the e ... Full text Cite

Profiling MicroRNAs with Associated Spatial Dynamics in Acute Tissue Slices.

Journal Article ACS nano · March 2021 MicroRNAs (miRNAs) are suggested to play important roles in the pathogenesis and progress of human diseases with heterogeneous regulation in different types of cells. However, limited technique is available for profiling miRNAs with both expression and spa ... Full text Cite

Combined inhibition of RNA polymerase I and mTORC1/2 synergize to combat oral squamous cell carcinoma.

Journal Article Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie · January 2021 Oral squamous cell carcinoma (OSCC) is the major cause of morbidity and mortality in head and neck cancer patients worldwide. This malignant disease is challenging to treat because of the lack of effective curative strategies and the high incidence of recu ... Full text Cite

High-Efficiency Cellular Reprogramming by Nanoscale Puncturing.

Journal Article Nano letters · July 2020 Induced pluripotent stem cells (iPSCs) bear great potential for disease modeling, drug discovery, and regenerative medicine; however, the wide adoption of iPSC for clinically relevant applications has been hindered by the extremely low reprogramming effici ... Full text Cite

Tombusvirus p19 Captures RNase III-Cleaved Double-Stranded RNAs Formed by Overlapping Sense and Antisense Transcripts in Escherichia coli.

Journal Article mBio · June 2020 Antisense transcription is widespread in bacteria. By base pairing with overlapping sense RNAs, antisense RNAs (asRNA) can form double-stranded RNAs (dsRNA), which are cleaved by RNase III, a dsRNA endoribonuclease. The ectopic expression of plant Tombu ... Full text Cite

High-throughput intracellular biopsy of microRNAs for dissecting the temporal dynamics of cellular heterogeneity.

Journal Article Science advances · June 2020 The capability to analyze small RNAs responsible for post-transcriptional regulation of genes expression is essential for characterizing cellular phenotypes. Here, we describe an intracellular biopsy technique (inCell-Biopsy) for fast, multiplexed, and hig ... Full text Cite

Lipid-based Vehicles for siRNA Delivery in Biomedical Field.

Journal Article Current pharmaceutical biotechnology · January 2020 BackgroundGenetic drugs have aroused much attention in the past twenty years. RNA interference (RNAi) offers novel insights into discovering potential gene functions and therapies targeting genetic diseases. Small interference RNA (siRNA), typical ... Full text Cite

Self-assembled Lipid Nanoparticles for Ratiometric Codelivery of Cisplatin and siRNA Targeting XPF to Combat Drug Resistance in Lung Cancer.

Journal Article Chemistry, an Asian journal · May 2019 DNA damage repair through the nucleotide excision repair (NER) pathway is one of the major reasons for the decreased antitumor efficacy of platinum-based anticancer drugs that have been widely applied in the clinic. Inhibiting the intrinsic NER function ma ... Full text Cite

Autophagy inhibitor Vacuolin-1 interferes with lipid-based small interference RNA delivery.

Journal Article Biochemical and biophysical research communications · March 2019 Autophagy and endocytosis are important pathways regulating macromolecule recycling and regeneration. Small molecule inhibitors are utilized to modulate these pathways and to treat autophagy-related diseases. Vacuolin-1 is a small molecule that can potentl ... Full text Cite

Tumor-secreted extracellular vesicles promote the activation of cancer-associated fibroblasts via the transfer of microRNA-125b.

Journal Article Journal of extracellular vesicles · January 2019 Tumour cells release large quantities of extracellular vesicles (EVs) to mediate their interactions with other cells in the tumour microenvironment. To identify host cells that naturally take up EVs from tumour cells, we created breast cancer cell lines se ... Full text Cite

RNA interference technology

Chapter · January 1, 2019 RNA interference (RNAi) is the biological process of mRNA degradation induced by complementary sequences double-stranded (ds) small interfering RNAs (siRNA) and suppression of target gene expression. Exogenous siRNAs (perfectly paired dsRNAs of ~21-25 nt i ... Full text Cite

Milligram scale production of potent recombinant small interfering RNAs in Escherichia coli.

Journal Article Biotechnology and bioengineering · September 2018 Small interfering RNAs (siRNAs) are invaluable research tools for studying gene functions in mammalian cells. siRNAs are mainly produced by chemical synthesis or by enzymatic digestion of double-stranded RNA (dsRNA) produced in vitro. Recently, bacterial c ... Full text Cite

Regeneration of cortical tissue from brain injury by implantation of defined molecular gradient of semaphorin 3A.

Journal Article Biomaterials · March 2018 Despite great efforts in the exploration of therapeutic strategies for treating brain injuries, it is still challenging to regenerate neural tissues and to restore the lost function within an injured brain. In this report, we employed a tissue engineering ... Full text Cite

Production of highly potent recombinant siRNAs in Escherichia coli.

Journal Article Nature protocols · December 2013 We recently invented a method to produce highly potent siRNAs in Escherichia coli, based on the serendipitous discovery that ectopic expression of p19, a plant viral siRNA-binding protein, stabilizes otherwise unstable bacterial siRNAs, which we named pro- ... Full text Cite

Efficient and specific gene knockdown by small interfering RNAs produced in bacteria.

Journal Article Nature biotechnology · April 2013 Synthetic small interfering RNAs (siRNAs) are an indispensable tool to investigate gene function in eukaryotic cells and may be used for therapeutic purposes to knock down genes implicated in disease. Thus far, most synthetic siRNAs have been produced by c ... Full text Cite

Nucleotide bias of DCL and AGO in plant anti-virus gene silencing.

Journal Article Protein & cell · September 2010 Plant Dicer-like (DCL) and Argonaute (AGO) are the key enzymes involved in anti-virus post-transcriptional gene silencing (AV-PTGS). Here we show that AV-PTGS exhibited nucleotide preference by calculating a relative AV-PTGS efficiency on processing viral ... Full text Cite

An atypical RNA polymerase involved in RNA silencing shares small subunits with RNA polymerase II.

Journal Article Nature structural & molecular biology · January 2009 Genetic evidence indicates that plant-specific homologs of DNA-dependent RNA polymerase (Pol) II large subunits form Pol IV and Pol V complexes involved in small interfering RNA production and RNA-directed DNA methylation. Here we describe evidence that Po ... Full text Cite

Analyses on mutation patterns, detection of population bottlenecks, and suggestion of deleterious-compensatory evolution among members of the genus Potyvirus.

Journal Article Archives of virology · August 2006 Viruses of the family Potyviridae exhibited a robust single-nucleotide polymorphism profile at the between-species level, conforming to the neutral theory rule. However, the ratios of nonsynonymous to synonymous mutations (Ka/Ks) were relatively greater be ... Full text Cite

Quantitative in situ assay of salicylic acid in tobacco leaves using a genetically modified biosensor strain of Acinetobacter sp. ADP1.

Journal Article The Plant journal : for cell and molecular biology · June 2006 Salicylic acid (SA) plays important roles in plants, most notably in the induction of systemic acquired resistance (SAR) against pathogens. A non-destructive in situ assay for SA would provide new insights into the functions of SA in SAR and other SA-regul ... Full text Cite

Within-population variation in hybridisation and transgene transfer between wild Brassica rapa and Brassica napus in the UK

Journal Article Annals of Applied Biology · April 1, 2006 Several studies in Europe and North America have shown that cultivated Brassica napus will readily hybridise with wild Brassica rapa but at widely different frequencies. To understand the implications of this phenomenon with regard to transgene flow, we ex ... Full text Cite

The complete genome sequence, organization and affinities of carrot red leaf virus.

Journal Article Archives of virology · September 2005 A sequence of 5723 nucleotides (GenBank accession number: AY695933) is reported for the RNA genome of an isolate of Carrot red leaf virus (CtRLV). The sequence is predicted to contain six large open reading frames and non coding sequences of 28 nucleotides ... Full text Cite

Chromosomally located gene fusions constructed in Acinetobacter sp. ADP1 for the detection of salicylate.

Journal Article Environmental microbiology · September 2005 Acinetobacter sp. ADP1 is a common soil-associated bacterium with high natural competency, allowing it to efficiently integrate foreign DNA fragments into its chromosome. This property was exploited to engineer salicylate-inducible luxCDABE and green fluor ... Full text Cite

Heterogeneity in codon usages of sobemovirus genes.

Journal Article Archives of virology · August 2005 When conventional phylogenetic trees were built using 14 genome sequences of 9 sobemoviruses, two main lineages were apparent: monocot-infecting viruses and dicot-infecting viruses. To investigate whether members of the genus Sobemovirus originated from mo ... Full text Cite