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Article: Simultaneous and rapid colorimetric detection of distinct miRNAs using Split-LAMP.

Chua, Yi Jing / Sim, Steven Poh Chuen / Shridharan, Medha / Seow, Yiqi

Frontiers in bioengineering and biotechnology

2023 Volume 11, Page(s) 1271297

Abstract: Introduction: ...

Abstract	Introduction:
Language	English
Publishing date	2023-11-02
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2719493-0
ISSN	2296-4185
ISSN	2296-4185
DOI	10.3389/fbioe.2023.1271297
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Article ; Online: Generalizable anchor aptamer strategy for loading nucleic acid therapeutics on exosomes.

Han, Gang / Zhang, Yao / Zhong, Li / Wang, Biaobiao / Qiu, Shuai / Song, Jun / Lin, Caorui / Zou, Fangdi / Wu, Jingqiao / Yu, Huanan / Liang, Chao / Wen, Ke / Seow, Yiqi / Yin, HaiFang

EMBO molecular medicine

2024 Volume 16, Issue 4, Page(s) 1027–1045

Abstract: Clinical deployment of oligonucleotides requires delivery technologies that improve stability, target tissue accumulation and cellular internalization. Exosomes show potential as ideal delivery vehicles. However, an affordable generalizable system for ... ...

Abstract	Clinical deployment of oligonucleotides requires delivery technologies that improve stability, target tissue accumulation and cellular internalization. Exosomes show potential as ideal delivery vehicles. However, an affordable generalizable system for efficient loading of oligonucleotides on exosomes remain lacking. Here, we identified an Exosomal Anchor DNA Aptamer (EAA) via SELEX against exosomes immobilized with our proprietary CP05 peptides. EAA shows high binding affinity to different exosomes and enables efficient loading of nucleic acid drugs on exosomes. Serum stability of thrombin inhibitor NU172 was prolonged by exosome-loading, resulting in increased blood flow after injury in vivo. Importantly, Duchenne Muscular Dystrophy PMO can be readily loaded on exosomes via EAA (EXO
MeSH term(s)	Animals ; Mice ; Dystrophin/genetics ; Mice, Inbred mdx ; Exosomes/metabolism ; Morpholinos/metabolism ; Morpholinos/pharmacology ; Morpholinos/therapeutic use ; Muscular Dystrophy, Duchenne/drug therapy ; Muscular Dystrophy, Duchenne/genetics ; Oligonucleotides/metabolism ; Oligonucleotides/therapeutic use
Chemical Substances	Dystrophin ; Morpholinos ; Oligonucleotides
Language	English
Publishing date	2024-03-06
Publishing country	England
Document type	Journal Article
ZDB-ID	2467145-9
ISSN	1757-4684 ; 1757-4676
ISSN (online)	1757-4684
ISSN	1757-4676
DOI	10.1038/s44321-024-00049-7
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Zs.A 6784: Show issues

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Article ; Online: Complete remission of tumors in mice with neoantigen-painted exosomes and anti-PD-1 therapy.

Zhang, Yang / Zuo, Bingfeng / Yu, Zezhen / Zhao, Kangjie / Zhang, Yali / He, Kai / Seow, Yiqi / Yin, HaiFang

Molecular therapy : the journal of the American Society of Gene Therapy

2023 Volume 31, Issue 12, Page(s) 3579–3593

Abstract: Neoantigen-based cancer vaccines are emerging as promising tumor therapies, but enhancement of immunogenicity can further improve therapeutic outcomes. Here, we demonstrate that anchoring different peptide neoantigens on subcutaneously administered serum ...

Abstract	Neoantigen-based cancer vaccines are emerging as promising tumor therapies, but enhancement of immunogenicity can further improve therapeutic outcomes. Here, we demonstrate that anchoring different peptide neoantigens on subcutaneously administered serum exosomes promote lymph node homing and dendritic cell uptake, resulting in significantly enhanced antigenicity in vitro and in vivo. Exosomes anchoring of melanoma peptide neoantigens augmented the magnitude and breadth of T cell response in vitro and in vivo, to a greater extent with CD8
MeSH term(s)	Humans ; Animals ; Mice ; Melanoma ; Antigens, Neoplasm ; Exosomes/metabolism ; Peptides ; Immunotherapy/methods ; Colonic Neoplasms/therapy ; Colonic Neoplasms/drug therapy ; Cancer Vaccines
Chemical Substances	Antigens, Neoplasm ; Peptides ; Cancer Vaccines
Language	English
Publishing date	2023-11-03
Publishing country	United States
Document type	Journal Article
ZDB-ID	2010592-7
ISSN	1525-0024 ; 1525-0016
ISSN (online)	1525-0024
ISSN	1525-0016
DOI	10.1016/j.ymthe.2023.10.021
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Zs.A 5640: Show issues

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Article: Sub genomic analysis of SARS-CoV-2 using short read amplicon-based sequencing.

Koh, Lian Chye Winston / Seow, Yiqi / Kong, Kiat Whye / Lau, Ming Li Lalita / Kumar, Shoban Krishna / Yan, Gabriel / Lee, Chun Kiat / Yan, Benedict / Tambyah, Paul Anantharajah / Hoon, Shawn

Frontiers in genetics

2023 Volume 14, Page(s) 1086865

Abstract: The novel coronavirus disease 2019 (COVID-19) pandemic poses a serious public health risk. In this report, we present a modified sequencing workflow using short tiling (280bp) amplicons library preparation method paired with Illumina's iSeq100 desktop ... ...

Abstract	The novel coronavirus disease 2019 (COVID-19) pandemic poses a serious public health risk. In this report, we present a modified sequencing workflow using short tiling (280bp) amplicons library preparation method paired with Illumina's iSeq100 desktop sequencer. We demonstrated the utility of our workflow in identifying gapped reads that capture characteristics of subgenomic RNA junctions within our patient cohort. These analytical and library preparation approaches allow a versatile, small footprint and decentralized deployment that can facilitate comprehensive genetics characterizations during outbreaks. Based on the sequencing data, Taqman assays were designed to accurately capture the quantity of subgenomic ORF5 and ORF7a RNA from patient samples and demonstrated utility in tracking subgenomic titres in patient samples when combined with a standard COVID-19 qRT-PCR assay.
Language	English
Publishing date	2023-02-24
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2606823-0
ISSN	1664-8021
ISSN	1664-8021
DOI	10.3389/fgene.2023.1086865
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Article ; Online: Cardio-respiratory and phenotypic rescue of dystrophin/utrophin-deficient mice by combination therapy.

Lin, Caorui / Han, Gang / Jia, Lulu / Zhao, Yiwen / Song, Jun / Ran, Ning / Yokota, Toshifumi / Seow, Yiqi / Yin, HaiFang

EMBO reports

2022 Volume 23, Issue 6, Page(s) e53955

Abstract: Duchenne muscular dystrophy (DMD) is a systemic progressive muscular disease caused by frame-disrupting mutations in the DMD gene. Although exon-skipping antisense oligonucleotides (AOs) are clinically approved and can correct DMD, insufficient muscle ... ...

Abstract	Duchenne muscular dystrophy (DMD) is a systemic progressive muscular disease caused by frame-disrupting mutations in the DMD gene. Although exon-skipping antisense oligonucleotides (AOs) are clinically approved and can correct DMD, insufficient muscle delivery limits efficacy. If AO activity can be enhanced by safe dietary supplements, clinical trials for efficacy can be undertaken rapidly to benefit patients. We showed previously that intravenous glycine enhanced phosphorodiamidate morpholino oligomer (PMO) delivery to peripheral muscles in mdx mice. Here, we demonstrate that the combination of oral glycine and metformin with intravenous PMO enhances PMO activity, dystrophin restoration, extends lifespan, and improves body-wide function and phenotypic rescue of dystrophin /utrophin double knock-out (DKO) mice without any overt adverse effects. The DKO mice treated with the combination without altering the approved administration protocol of PMO show improved cardio-respiratory and behavioral functions. Metformin and glycine individually are ineffective in DMD patients, but the combination of PMO with clinically-approved oral glycine and metformin might improve the efficacy of the treatment also in DMD patients. Our data suggest that this combination therapy might be an attractive therapy for DMD and potentially other muscle diseases requiring systemic treatment with AOs.
MeSH term(s)	Animals ; Dystrophin/genetics ; Genetic Therapy/methods ; Glycine/therapeutic use ; Humans ; Metformin/therapeutic use ; Mice ; Mice, Inbred mdx ; Morpholinos/genetics ; Morpholinos/therapeutic use ; Muscle, Skeletal ; Utrophin/genetics
Chemical Substances	Dystrophin ; Morpholinos ; Utrophin ; Metformin (9100L32L2N) ; Glycine (TE7660XO1C)
Language	English
Publishing date	2022-04-08
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2020896-0
ISSN	1469-3178 ; 1469-221X
ISSN (online)	1469-3178
ISSN	1469-221X
DOI	10.15252/embr.202153955
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Zs.A 5433: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
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Article: Towards a Rapid-Turnaround Low-Depth Unbiased Metagenomics Sequencing Workflow on the Illumina Platforms.

Koh, Winston Lian Chye / Poh, Si En / Lee, Chun Kiat / Chan, Tim Hon Man / Yan, Gabriel / Kong, Kiat Whye / Lau, Lalita / Lee, Wai Yip Thomas / Cheng, Clark / Hoon, Shawn / Seow, Yiqi

Bioengineering (Basel, Switzerland)

2023 Volume 10, Issue 5

Abstract: Unbiased metagenomic sequencing is conceptually well-suited for first-line diagnosis as all known and unknown infectious entities can be detected, but costs, turnaround time and human background reads in complex biofluids, such as plasma, hinder ... ...

Abstract	Unbiased metagenomic sequencing is conceptually well-suited for first-line diagnosis as all known and unknown infectious entities can be detected, but costs, turnaround time and human background reads in complex biofluids, such as plasma, hinder widespread deployment. Separate preparations of DNA and RNA also increases costs. In this study, we developed a rapid unbiased metagenomics next-generation sequencing (mNGS) workflow with a human background depletion method (HostEL) and a combined DNA/RNA library preparation kit (AmpRE) to address this issue. We enriched and detected bacterial and fungal standards spiked in plasma at physiological levels with low-depth sequencing (<1 million reads) for analytical validation. Clinical validation also showed 93% of plasma samples agreed with the clinical diagnostic test results when the diagnostic qPCR had a Ct < 33. The effect of different sequencing times was evaluated with the 19 h iSeq 100 paired end run, a more clinically palatable simulated iSeq 100 truncated run and the rapid 7 h MiniSeq platform. Our results demonstrate the ability to detect both DNA and RNA pathogens with low-depth sequencing and that iSeq 100 and MiniSeq platforms are compatible with unbiased low-depth metagenomics identification with the HostEL and AmpRE workflow.
Language	English
Publishing date	2023-04-25
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2746191-9
ISSN	2306-5354
ISSN	2306-5354
DOI	10.3390/bioengineering10050520
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Article ; Online: Smad‑binding decoy reduces extracellular matrix expression in human hypertrophic scar fibroblasts.

Fan, Chen / El Andaloussi, Samir / Lehto, Taavi / Kong, Kiat Whye / Seow, Yiqi

Molecular medicine reports

2020 Volume 22, Issue 6, Page(s) 4589–4600

Abstract: The exact mechanisms underlying hypertrophic scarring is yet to be fully understood. However, excessive collagen deposition by fibroblasts has been demonstrated to result in hypertrophic scar formation, and collagen synthesis in dermal fibroblasts is ... ...

Abstract	The exact mechanisms underlying hypertrophic scarring is yet to be fully understood. However, excessive collagen deposition by fibroblasts has been demonstrated to result in hypertrophic scar formation, and collagen synthesis in dermal fibroblasts is regulated by the transforming growth factor‑β1/Smad signaling pathway. In view of this, a Smad‑binding decoy was designed and its effects on hypertrophic scar‑derived human skin fibroblasts was evaluated. The results of the present study revealed that the Smad decoy attenuates the total amount of collagen, collagen I and Smad2/3 expression in scar fibroblasts. Data from RNA sequencing indicated that the Smad decoy induced more than 4‑fold change in 178 genes, primarily associated with to the extracellular matrix, compared with the untreated control. In addition, results from quantitative real‑time polymerase chain reaction further confirmed that the Smad decoy significantly attenuated the expression of extracellular matrix‑related genes, including COL1A1, COL1A2 and COL3A1. Furthermore, the Smad decoy reduced transforming growth factor‑β1‑induced collagen deposition in scar fibroblasts. Data generated from the present study provide evidence supporting the use of the Smad decoy as a potential hypertrophic scar treatment.
MeSH term(s)	Actins/metabolism ; Cells, Cultured ; Cicatrix, Hypertrophic/metabolism ; Collagen/metabolism ; Collagen Type I/metabolism ; Extracellular Matrix/metabolism ; Fibroblasts/metabolism ; Humans ; Primary Cell Culture ; Signal Transduction ; Skin/pathology ; Smad Proteins/metabolism ; Transforming Growth Factor beta1/metabolism
Chemical Substances	Actins ; Collagen Type I ; Smad Proteins ; Transforming Growth Factor beta1 ; Collagen (9007-34-5)
Language	English
Publishing date	2020-09-29
Publishing country	Greece
Document type	Journal Article
ZDB-ID	2469505-1
ISSN	1791-3004 ; 1791-2997
ISSN (online)	1791-3004
ISSN	1791-2997
DOI	10.3892/mmr.2020.11549
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Article ; Online: A fluid-supported 3D hydrogel bioprinting method.

Beh, Cyrus W / Yew, Dionis S / Chai, Ruth J / Chin, Sau Yin / Seow, Yiqi / Hoon, Shawn S

Biomaterials

2021 Volume 276, Page(s) 121034

Abstract: Hydrogels are used in many biomedical applications, including regenerative medicine and surgical training phantoms. However, the ability to shape these materials into complex anatomical structures using additive manufacturing is limited in part by their ... ...

Abstract	Hydrogels are used in many biomedical applications, including regenerative medicine and surgical training phantoms. However, the ability to shape these materials into complex anatomical structures using additive manufacturing is limited in part by their low mechanical stiffness. We developed a hydrogel 3D printer, that projects patterns directly onto a thin layer of fluid-supported hydrogel precursor, which serves as a floating, liquid projection screen. This approach avoids inadvertent adhesion that affects typical resin-based 3D printers, and enables fast, continuous printing. As a consequence, we can print smooth objects free of layering artifacts, at rates of 200 mm/h along the Z-axis. We demonstrate the versatility of our approach by printing various complex structures, including free-standing channel networks with 500 μm-thick walls, using hydrogels with a wide range of stiffness from 7 kPa to more than 4 MPa. Lastly, because the printer features a free surface, we combined it with an extruder to perform multi-material printing. We use this strategy to create centimeter-scale, cell-laden hydrogels containing channels, that help address the key nutrient supply problem in bioprinting.
Language	English
Publishing date	2021-07-21
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	603079-8
ISSN	1878-5905 ; 0142-9612
ISSN (online)	1878-5905
ISSN	0142-9612
DOI	10.1016/j.biomaterials.2021.121034
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Zs.B 2371: Show issues

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Article: Erratum: Fructose Promotes Uptake and Activity of Oligonucleotides with Different Chemistries in a Context-Dependent Manner in

Cao, Limin / Han, Gang / Lin, Caorui / Gu, Ben / Gao, Xianjun / Moulton, Hong M / Seow, Yiqi / Yin, HaiFang

Molecular therapy. Nucleic acids

2020 Volume 22, Page(s) 1040–1042

Abstract: This corrects the article DOI: 10.1038/mtna.2016.46.]. ...

Abstract	[This corrects the article DOI: 10.1038/mtna.2016.46.].
Language	English
Publishing date	2020-11-19
Publishing country	United States
Document type	Published Erratum
ZDB-ID	2662631-7
ISSN	2162-2531
ISSN	2162-2531
DOI	10.1016/j.omtn.2020.08.028
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Article ; Online: Universal immunotherapeutic strategy for hepatocellular carcinoma with exosome vaccines that engage adaptive and innate immune responses.

Zuo, Bingfeng / Zhang, Yang / Zhao, Kangjie / Wu, Li / Qi, Han / Yang, Rong / Gao, Xianjun / Geng, Mengyuan / Wu, Yingjie / Jing, Renwei / Zhou, Qibing / Seow, Yiqi / Yin, HaiFang

Journal of hematology & oncology

2022 Volume 15, Issue 1, Page(s) 46

Abstract: Background: Personalized immunotherapy utilizing cancer vaccines tailored to the tumors of individual patients holds promise for tumors with high genetic heterogeneity, potentially enabling eradication of the tumor in its entirety.: Methods: Here, we ...

Abstract	Background: Personalized immunotherapy utilizing cancer vaccines tailored to the tumors of individual patients holds promise for tumors with high genetic heterogeneity, potentially enabling eradication of the tumor in its entirety. Methods: Here, we demonstrate a general strategy for biological nanovaccines that trigger tailored tumor-specific immune responses for hepatocellular carcinoma (HCC). Dendritic cell (DC)-derived exosomes (DEX) are painted with a HCC-targeting peptide (P47-P), an α-fetoprotein epitope (AFP212-A2) and a functional domain of high mobility group nucleosome-binding protein 1 (N1ND-N), an immunoadjuvant for DC recruitment and activation, via an exosomal anchor peptide to form a "trigger" DEX vaccine (DEX Results: DEX Conclusions: These findings demonstrate the capacity of universal DEX vaccines to induce tumor-specific immune responses by triggering an immune response tailored to the tumors of each individual, thus presenting a generalizable approach for personalized immunotherapy of HCC, by extension of other tumors, without the need to identify tumor antigens.
MeSH term(s)	Animals ; Cancer Vaccines/therapeutic use ; Carcinoma, Hepatocellular ; Exosomes ; Humans ; Immunity, Innate ; Immunotherapy/methods ; Liver Neoplasms ; Mice ; Peptides ; alpha-Fetoproteins
Chemical Substances	Cancer Vaccines ; Peptides ; alpha-Fetoproteins
Language	English
Publishing date	2022-04-29
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2429631-4
ISSN	1756-8722 ; 1756-8722
ISSN (online)	1756-8722
ISSN	1756-8722
DOI	10.1186/s13045-022-01266-8
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