Category Archives: 研究發表

楊進木教授研究團隊發表研究成果於Front. Immunol.

連結網址：https://www.frontiersin.org/articles/10.3389/fimmu.2022.1080897/full

Abstract

Background: Drug repurposing is a fast and effective way to develop drugs for

an emerging disease such as COVID-19. The main challenges of effective drug

repurposing are the discoveries of the right therapeutic targets and the right

drugs for combating the disease.

Methods: Here, we present a systematic repurposing approach, combining

Homopharma and hierarchal systems biology networks (HiSBiN), to predict 327

therapeutic targets and 21,233 drug-target interactions of 1,592 FDA drugs for

COVID-19. Among these multi-target drugs, eight candidates (along with

pimozide and valsartan) were tested and methotrexate was identified to

affect 14 therapeutic targets suppressing SARS-CoV-2 entry, viral replication, and COVID-19 pathologies. Through the use of in vitro (EC50 = 0.4 mM) and in

vivo models, we show that methotrexate is able to inhibit COVID-19 via

multiple mechanisms.

Results: Our in vitro studies illustrate that methotrexate can suppress SARSCoV-

2 entry and replication by targeting furin and DHFR of the host,

respectively. Additionally, methotrexate inhibits all four SARS-CoV-2 variants

of concern. In a Syrian hamster model for COVID-19, methotrexate reduced

virus replication, inflammation in the infected lungs. By analysis of

transcriptomic analysis of collected samples from hamster lung, we

uncovered that neutrophil infiltration and the pathways of innate immune

response, adaptive immune response and thrombosis are modulated in the

treated animals.

Conclusions: We demonstrate that this systematic repurposing approach is

potentially useful to identify pharmaceutical targets, multi-target drugs and

regulated pathways for a complex disease. Our findings indicate that

methotrexate is established as a promising drug against SARS-CoV-2 variants

and can be used to treat lung damage and inflammation in COVID-19,

warranting future evaluation in clinical trials.

張晉源助理教授研究團隊發表研究成果於Communications Chemistry

連結網址：https://www.nature.com/articles/s42004-022-00765-6

Abstract

A grand challenge in terpene synthase (TS) enzymology is the ability to predict function from protein sequence. Given the limited number of characterized bacterial TSs and significant sequence diversities between them and their eukaryotic counterparts, this is currently impossible. To contribute towards understanding the sequence-structure-function relationships of type II bacterial TSs, we determined the structure of the terpentedienyl diphosphate synthase Tpn2 from Kitasatospora sp. CB02891 by X-ray crystallography and made structureguided mutants to probe its mechanism. Substitution of a glycine into a basic residue changed the product preference from the clerodane skeleton to a syn-labdane skeleton, resulting in the first syn-labdane identified from a bacterial TS. Understanding how a single residue can dictate the cyclization pattern in Tpn2, along with detailed bioinformatics analysis of bacterial type II TSs, sets the stage for the investigation of the functional scope of bacterial type II TSs and the discovery of novel bacterial terpenoids.

李明家副教授研究團隊發表研究成果於ACS Macro Lett

連結網址：https://pubmed.ncbi.nlm.nih.gov/36326692/

Abstract

This paper presents a facile method for fabricating a thin-film sample with a high asymmetry value of induced circularly polarized luminescence (iCPL) (|glum| = 2.0 × 10-3). The method involves mixing stereoregular poly(methyl methacrylate) (PMMA) and chiral chromophore (2,2,2-trifluoro-1-(9-anthryl)ethanol (TFAE)) to form a complex with a dynamic helical conformation of poly(methyl methacrylate) (PMMA) associated with TFAE via hydrogen bonding. This dynamic helical conformation can be stabilized by the stereocomplexation of a pair of stereoregular PMMA, where the TFAE is sandwiched between a double-helix isotactic PMMA and single-helix syndiotactic PMMA, resulting in a preferential one-handed helical conformation with a high value of iCPL from self-assembly.

蘇昱誠助理教授研究團隊發表研究成果於Bioconjug Chem.

連結網址：https://pubmed.ncbi.nlm.nih.gov/36320124/

Abstract

Sensitive quantification of methoxy poly(ethylene glycol) (mPEG)-conjugated therapeutics for pharmacokinetic determination is critical for mPEGylated drug development. However, sensitive measurement of low-molecular-weight (lmw) mPEG compounds remains challenging due to epitope competition between backbone-specific anti-PEG antibodies. Here, we engineered a high-affinity methoxy-specific anti-mPEG antibody for sensitive quantification of free mPEG molecules and mPEGylated therapeutics. The affinity-enhanced h15-2Y antibody variant shows a 10.3-fold increase in mPEG-binding activity compared to parental h15-2b. h15-2Y-based sandwich ELISA can effectively quantify lmw mPEG5K and high-molecular-weight (hmw) mPEG20K at concentrations as low as 3.4 and 5.1 ng mL-1, respectively. Moreover, lmw mPEG compounds (560, 750, 1000, and 2000 Da) can be efficiently quantified via h15-2Y-based competitive ELISA with detection limits at nanomolar levels. This study provides a promising approach for application in the quantitative analysis of the various sizes of mPEG molecules to accelerate the timeline of mPEG-conjugated drug development.

趙瑞益教授研究團隊發表研究成果於 Biochemical Pharmacology

連結網址：https://www.sciencedirect.com/science/article/pii/S0006295222003835

Abstract

Abstract

Colorectal cancer (CRC) is a leading cause and mortality worldwide. Aurora A and haspin kinases act pivotal roles in mitotic progression. However, the blockage of Aurora A and Haspin for CRC therapy is still unclear. Here we show that the Haspin and p-H3T3 protein levels were highly expressed in CRC tumor tissues of clinical patients. Overexpression of Haspin increased the protein levels of p-H3T3 and survivin in human CRC cells; conversely, the protein levels of p-H3T3 and survivin were decreased by the Haspin gene knockdown. Moreover, the gene knockdown of Aurora A induced abnormal chromosome segregation, mitotic catastrophe, and cell growth inhibition. Combined targeted by co-treatment of CHR6494, a Haspin inhibitor, and MLN8237, an Aurora A inhibitor, enhanced apoptosis and CRC tumor inhibition. MLN8237 and CHR6494 induced abnormal chromosome segregation and mitotic catastrophe. Meanwhile, MLN8237 and CHR6494 inhibited survivin protein levels but conversely induced p53 protein expression. Ectopic survivin expression by transfection with a survivin-expressed vector resisted the cell death in the MLN8237- and CHR6494-treated cells. In contrast, the existence of functional p53 increased the apoptotic levels by treatment with MLN8237 and CHR6494. Co-treatment of CHR6494 and MLN8237 enhanced the blockage of human CRC xenograft tumors in nude mice. Taken together, co-inhibition of Aurora A and Haspin enhances survivin inhibition, p53 pathway induction, mitotic catastrophe, apoptosis and tumor inhibition that may provide a potential strategy for CRC therapy.

陳亭妏副教授研究團隊發表研究成果於 Bioinformatics

連結網址：https://academic.oup.com/bioinformatics/article/38/18/4286/6649618

Abstract

Motivation: Microbiota analyses have important implications for health and science. These analyses make use of 16S/18S rRNA gene sequencing to identify taxa and predict species diversity. However, most available tools for analyzing microbiota data require adept programming skills and in-depth statistical knowledge for proper implementation. While long-read amplicon sequencing can lead to more accurate taxa predictions and is quickly becoming more common, practitioners have no easily accessible tools with which to perform their analyses.

Results: We present MOCHI, a GUI tool for microbiota amplicon sequencing analysis. MOCHI preprocesses sequences, assigns taxonomy, identifies different abundant species and predicts species diversity and function. It takes either taxonomic count table or FASTQ of partial 16S/18S rRNA or full-length 16S rRNA gene as input. It performs analyses in real time and visualizes data in both tabular and graphical formats.

Availability and implementation: MOCHI can be installed to run locally or accessed as a web tool at https://mochi.life.nctu.edu.tw

柯泰名助理教授研究團隊發表研究成果於 Clin Transl Med.

連結網址：https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9547115/

Summary

Ankylosing spondylitis (AS) is a chronic rheumatic disease that causes disability and severe impairment in the quality of life, especially in females. However, almost nothing is known about how large heterogenous circulating immune cells are involved in developing AS. Here we used droplet-based single-cell sequencing for multi-omic profiling of PBMCs obtained from female patients and sex-matched healthy individuals and performed multimodal single-cell analyses including single-cell-level unbiased transcriptome, surface protein expression, pseudotemporal trajectory analysis, cell-cell interaction analysis, and T-cell receptor repertoire. By applying multiple filtering strategies, we selected common single-cell blood features across the patients to reveal a unique T-cell state wherein GIMAP7 was up-regulated and NFKBIA was down-regulated. Furthermore, we identified a panel of cell-surface markers and dominant T-cell clonotypes on this unique T-cell subset (NFKBIA- GIMAP7+). We identified a unique VEGI signalling pathway between the T-cells and NK cells that uncovered potential triggers for developing exclusive T-cell states in female patients with AS. This finding could be valuable for developing innovative therapies that selectively target the aberrant immune response in female patients with AS.

陳亭妏助理教授研究團隊發表研究成果於 Journal of Infection

連結網址：https://www.sciencedirect.com/science/article/pii/S0163445322005175?via%3Dihub

Summary

Objectives: RNA therapeutics is an emerging field that widens the range of treatable targets and would improve disease outcome through bypassing the antibiotic bactericidal targets to kill Mycobacterium tuberculosis (M.tb).
Methods: We screened for microRNA with immune-regulatory functions against M.tb by next generation sequencing of peripheral blood mononuclear cells, followed by validation in an independent cohort.
Results: Twenty three differentially expressed microRNAs were identified between 12 active pulmonary TB patients and 4 healthy subjects, and 35 microRNAs before and after 6-month anti-TB therapy. Enriched predicted target pathways included proteoglycan, HIF-1 signaling, longevity-regulating, central carbon metabolism, and autophagy. We validated miR-431–3p down-regulation and miR-1303 up-regulation
accompanied with corresponding changes in their predicted target genes in an independent validation cohort of 46 active TB patients, 30 latent TB infection subjects, and 24 non-infected healthy subjects. In vitro experiments of transfections with miR-431–3p mimic/miR-1303 short interfering RNA in THP-1 cells under ESAT-6 stimuli showed that miR-431–3p and miR-1303 were capable to augment and suppress autophagy/apoptosis/phagocytosis of macrophage via targeting MDR1/MMP16/RIPOR2 and ATG5, respectively.
Conclusions: This study provides a proof of concept for microRNA-based host-directed immunotherapy for active TB disease. The combined miR-431–3p over-expression and miR-1303 knock-down revealed new vulnerabilities of treatment-refractory TB disease.

謝仁俊教授研究團隊發表研究成果於Hum Brain Mapp

連結網址：https://pubmed.ncbi.nlm.nih.gov/36005832/

Abstract

Abstract: Numerous studies have reported that long-term musical training can affect brain functionality and induce structural alterations in the brain. Singing is a form of vocal musical expression with an unparalleled capacity for communicating emotion; however, there has been relatively little research on neuroplasticity at the network level in vocalists (i.e., noninstrumental musicians). Our objective in this study was to elucidate changes in the neural network architecture following long-term training in the musical arts. We employed a framework based on graph theory to depict the connectivity and efficiency of structural networks in the brain, based on diffusion-weighted images obtained from 35 vocalists, 27 pianists, and 33 nonmusicians. Our results revealed that musical training (both voice and piano) could enhance connectivity among emotion-related regions of the brain, such as the amygdala. We also discovered that voice training reshaped the architecture of experience-dependent networks, such as those involved in vocal motor control, sensory feedback, and language processing. It appears that vocal-related changes in areas such as the insula, paracentral lobule, supramarginal gyrus, and putamen are associated with functional segregation, multisensory integration, and enhanced network interconnectivity. These results suggest that long-term musical training can strengthen or prune white matter connectivity networks in an experience-dependent manner.