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Nawale, G. N., Bahadorikhalili, S., Sengupta, P., Kadekar, S., Chatterjee, S. & Varghese, O. P. (2019). 4 '-Guanidinium-modified siRNA: a molecular tool to control RNAi activity through RISC priming and selective antisense strand loading. Chemical Communications, 55(62), 9112-9115
Open this publication in new window or tab >>4 '-Guanidinium-modified siRNA: a molecular tool to control RNAi activity through RISC priming and selective antisense strand loading
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2019 (English)In: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, Vol. 55, no 62, p. 9112-9115Article in journal (Refereed) Published
Abstract [en]

We designed novel 4 '-C-guanidinocarbohydrazidomethyl-5-methyl uridine (GMU) modified small interfering RNA (siRNA) and evaluated its biophysical and biochemical properties. Incorporation of GMU units significantly increased the thermodynamic stability as well as the enzymatic stability against nucleases in human serum. A gene silencing experiment indicated that GMU modfied siRNA (siRNA6) resulted in approximate to 4.9-fold more efficient knockdown than unmodified siRNA.

Place, publisher, year, edition, pages
ROYAL SOC CHEMISTRY, 2019
National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Identifiers
urn:nbn:se:uu:diva-392130 (URN)10.1039/c9cc04141a (DOI)000477960000008 ()31298670 (PubMedID)
Available from: 2019-09-03 Created: 2019-09-03 Last updated: 2019-09-03Bibliographically approved
Paidikondala, M., Rangasami, V. K., Nawale, G. N., Casalini, T., Perale, G., Kadekar, S., . . . Varghese, O. P. (2019). An Unexpected Role of Hyaluronic Acid in Trafficking siRNA Across the Cellular Barrier: The First Biomimetic, Anionic, Non-Viral Transfection Method. Angewandte Chemie International Edition, 58(9), 2815-2819
Open this publication in new window or tab >>An Unexpected Role of Hyaluronic Acid in Trafficking siRNA Across the Cellular Barrier: The First Biomimetic, Anionic, Non-Viral Transfection Method
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2019 (English)In: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 58, no 9, p. 2815-2819Article in journal (Refereed) Published
Abstract [en]

Circulating nucleic acids, such as short interfering RNA (siRNA), regulate many biological processes; however, the mechanism by which these molecules enter the cell is poorly understood. The role of extracellular-matrix-derived polymers in binding siRNAs and trafficking them across the plasma membrane is reported. Thermal melting, dynamic light scattering, scanning electron microscopy, and computational analysis indicate that hyaluronic acid can stabilize siRNA via hydrogen bonding and Van der Waals interactions. This stabilization facilitated HA size- and concentration-dependent gene silencing in a CD44-positive human osteosarcoma cell line (MG-63) and in human mesenchymal stromal cells (hMSCs). This native HA-based siRNA transfection represents the first report on an anionic, non-viral delivery method that resulted in approximately 60% gene knockdown in both cell types tested, which correlated with a reduction in translation levels.

Place, publisher, year, edition, pages
WILEY-V C H VERLAG GMBH, 2019
Keywords
nanoparticles, extracellular matrix, hyaluronic acid, RNAi, transfection
National Category
Cell and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-379591 (URN)10.1002/anie.201900099 (DOI)000459807200045 ()30644615 (PubMedID)
Funder
Swedish Foundation for Strategic Research , SBE13-0028
Available from: 2019-03-18 Created: 2019-03-18 Last updated: 2019-03-18Bibliographically approved
Paidikondala, M., Wang, S., Hilborn, J., Larsson, S. & Varghese, O. P. (2019). Impact of Hydrogel Cross-Linking Chemistry on the in Vitro and in VivoBioactivity of Recombinant Human Bone Morphogenetic Protein-2. ACS Applied Bio Materials
Open this publication in new window or tab >>Impact of Hydrogel Cross-Linking Chemistry on the in Vitro and in VivoBioactivity of Recombinant Human Bone Morphogenetic Protein-2
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2019 (English)In: ACS Applied Bio Materials, ISSN 2576-6422Article in journal, Editorial material (Refereed) Published
Abstract [en]

Designing strategies to deliver functional proteins at physiologically relevant concentrations using chemically cross-linked biocompatible hydrogels is a major field of research. However, the impact of cross-linking chemistry on the encapsulated protein bioactivity is rarely studied. Here we examine the two well-known cross-linking reactions namely; hydrazone cross-linking chemistry and thiol-Michael addition reaction to form hyaluronic acid (HA) hydrogels. As a therapeutic protein, we employed recombinant human bone morphogenetic protein-2 (rhBMP-2) for this study. Incubation of rhBMP-2 with HA functionalized with a thiol diminished phosphorylation of Smad 1/5/8, a signal transducer for osteogenic differntiation, whereas an aldehyde functionalized HA had no effect. This indicates that thiol functionalized polymers indeed has an impact on protein function. To validate this result in an in vivo setting we performed BMP-2 induced bone formation in a rat ectopic model. These experiments revealed that the hydrazone-cross-linked HA-hydrogel induced significantly higher bone formation (18.90 ± 4.25 mm3) as compared to the HA-thiol-Michael hydrogels (1.25 ± 0.52 mm3) after 8 weeks as determined by micro-computed tomography. The histological examination of the neo-bone indicated that hydrazone-hydrogels promoted a better quality of bone formation with improved mineralization and collagen formation as compared to the thiol-Michael hydrogels. We believe such a direct comparison of two cross-linking chemistries will provide new insight for developing biomaterials for protein delivery for in vivo applications.

Keywords
bone tissue engineering; cross-linking chemistry; drug delivery; hyaluronic acid; regenerative medicine
National Category
Polymer Chemistry
Identifiers
urn:nbn:se:uu:diva-382321 (URN)10.1021/acsabm.9b00060 (DOI)
Available from: 2019-04-24 Created: 2019-04-24 Last updated: 2019-04-24
Paidikondala, M., Kadekar, S. & Varghese, O. P. (2019). Innovative strategy for 3D transfection of primary human stem cells with BMP-2 expressing plasmid DNA: A clinically translatable strategy for ex vivogene therapy. International Journal of Molecular Sciences, 20(1), Article ID 56.
Open this publication in new window or tab >>Innovative strategy for 3D transfection of primary human stem cells with BMP-2 expressing plasmid DNA: A clinically translatable strategy for ex vivogene therapy
2019 (English)In: International Journal of Molecular Sciences, ISSN 1422-0067, E-ISSN 1422-0067, Vol. 20, no 1, article id 56Article in journal (Refereed) Published
Abstract [en]

Ex vivo gene therapy offers enormous potential for cell-based therapies, however, cumbersome in vitro cell culture conditions have limited its use in clinical practice. We have optimized an innovative strategy for the transient transfection of bone morphogenetic protein-2 (BMP-2) expressing plasmids in suspended human stem cells within 5-min that enables efficient loading of the transfected cells into a 3D hydrogel system. Such a short incubation time for lipid-based DNA nanoparticles (lipoplexes) reduces cytotoxicity and at the same time reduces the processing time for cells to be transplanted. The encapsulated human mesenchymal stromal/stem cells (hMSCs) transfected with BMP-2 plasmid demonstrated high expression of an osteogenic transcription factor, namely RUNX2, but not the chondrogenic factor (SOX9), within the first three days. This activation was also reflected in the 7-day and 21-day experiment, which clearly indicated the induction of osteogenesis but not chondrogenesis. We believe our transient transfection method demonstrated in primary MSCs can be adapted for other therapeutic genes for different cell-based therapeutic applications.

Place, publisher, year, edition, pages
Basel, Switzerland: MDPI, 2019
Keywords
hydrogel; DNA; transfection; ex vivo; hyaluronic acid
National Category
Biomaterials Science
Identifiers
urn:nbn:se:uu:diva-369655 (URN)10.3390/ijms20010056 (DOI)000459747700056 ()30583610 (PubMedID)
Funder
EU, FP7, Seventh Framework Programme, FP7/2007-2013/607868Swedish Foundation for Strategic Research , SBE13-0028
Available from: 2018-12-14 Created: 2018-12-14 Last updated: 2019-03-18Bibliographically approved
Paidikondala, M., Nawale, G. N. & Varghese, O. P. (2019). Insights into siRNA Transfection in Suspension: Efficient Gene Silencing in Human Mesenchymal Stem Cells Encapsulated in Hyaluronic Acid Hydrogel. Biomacromolecules, 20(3), 1317-1324
Open this publication in new window or tab >>Insights into siRNA Transfection in Suspension: Efficient Gene Silencing in Human Mesenchymal Stem Cells Encapsulated in Hyaluronic Acid Hydrogel
2019 (English)In: Biomacromolecules, ISSN 1525-7797, E-ISSN 1526-4602, Vol. 20, no 3, p. 1317-1324Article in journal (Refereed) Published
Abstract [en]

Small interfering RNAs (siRNAs) are powerful toolsfor post-transcriptional gene silencing, which offers enormousopportunities for tissue engineering applications. However, poorserum stability, inefficient intracellular delivery, and inevitabletoxicity of transfection reagents are the key barriers for their clinicaltranslation. Thus, innovative strategies that allow safe and efficientintracellular delivery of the nucleic acid drugs at the desired site isurgently needed for a smooth clinical translation of therapeuticallyappealing siRNA-based technology. In this regard, we havedeveloped an innovative siRNA transfection protocol that employsa short incubation time of just 5 min. This allows easy transfection insuspension followed by transplantation of the cells in a hyaluronicacid (HA) hydrogel system. We also report here the unique ability ofsiRNA to bind HA that was quantified by siRNA release andrheological characterization of the HA-hydrogel. Such interactions also showed promising results to deliver functional siRNA insuspension transfection conditions within 30 min using native HA, although removal of excess HA by centrifugation seem to beessential. In the 2D experiments, suspension transfection of hMSCs with RNAiMAX resulted in ≈90% gene silencing (with orwithout removal of the excess reagent by centrifugation), while HA demonstrated a modest ≈40% gene silencing after removalof excess reagent after 30 min. Transplantation of such transfected cells in the HA-hydrogel system demonstrated an improvedknockdown (≈90% and ≈60% with RNAiMAX and HA respectively after 48 h), with lower cytotoxicity (up to 5-days) asdetermined by PrestoBlue assay. The gene silencing efficiency in the 2D and 3D conditions were also confirmed at the proteinlevels by Western blot analysis. We postulate this novel transfection method could be applied for in vivo applications as it allowsminimal manipulation of cells that are to be transplanted and reduce toxicity.

National Category
Polymer Chemistry
Identifiers
urn:nbn:se:uu:diva-379682 (URN)10.1021/acs.biomac.8b01712 (DOI)000461270500019 ()30642167 (PubMedID)
Funder
Swedish Foundation for Strategic Research , 2009-1035Swedish Foundation for Strategic Research , SBE13-0028EU, FP7, Seventh Framework Programme, FP7/2007-2013/607868
Available from: 2019-03-19 Created: 2019-03-19 Last updated: 2019-04-12Bibliographically approved
Han, Y., Qiu, Z., Nawale, G. N., Varghese, O. P., Hilborn, J., Tian, B. & Leifer, K. (2019). MicroRNA detection based on duplex-specific nuclease-assisted target recycling and gold nanoparticle/graphene oxide nanocomposite-mediated electrocatalytic amplification. Biosensors & bioelectronics, 127, 188-193
Open this publication in new window or tab >>MicroRNA detection based on duplex-specific nuclease-assisted target recycling and gold nanoparticle/graphene oxide nanocomposite-mediated electrocatalytic amplification
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2019 (English)In: Biosensors & bioelectronics, ISSN 0956-5663, E-ISSN 1873-4235, Vol. 127, p. 188-193Article in journal (Refereed) Published
Abstract [en]

DNA technology based bio-responsive nanomaterials have been widely studied as promising tools for biomedical applications. Gold nanoparticles (AuNPs) and graphene oxide (GO) sheets are representative zero- and two-dimensional nanomaterials that have long been combined with DNA technology for point-of-care diagnostics. Herein, a cascade amplification system based on duplex-specific nuclease (DSN)-assisted target recycling and electrocatalytic water-splitting is demonstrated for the detection of microRNA. Target microRNAs can form DNA: RNA heteroduplexes with DNA probes on the surface of AuNPs, which can be hydrolyzed by DSN. MicroRNAs are preserved during the reaction and released into the suspension for the digestion of multiple DNA probes. After the DSN-based reaction, AuNPs are collected and mixed with GO to form AuNP/GO nanocomposite on an electrode for the following electrocatalytic amplification. The utilization of AuNP/GO nanocomposite offers large surface area, exceptional affinity to water molecules, and facilitated mass diffusion for the water-splitting reaction. For let-7b detection, the proposed biosensor achieved a limit detection of 1.5 fM in 80 min with a linear detection range of approximately four orders of magnitude. Moreover, it has the capability of discriminating non-target microRNAs containing even single-nucleotide mismatches, thus holding considerable potential for clinical diagnostics.

Keywords
Gold nanoparticles, Graphene oxide, MicroRNA detection, Electrocatalytic amplification, Duplex-specific nuclease
National Category
Analytical Chemistry Physical Chemistry
Identifiers
urn:nbn:se:uu:diva-377203 (URN)10.1016/j.bios.2018.12.027 (DOI)000457508800026 ()30611105 (PubMedID)
Funder
Swedish Research Council, 2016-05259Knut and Alice Wallenberg FoundationEU, Horizon 2020, 713683
Available from: 2019-02-25 Created: 2019-02-25 Last updated: 2019-04-24Bibliographically approved
Bermejo-Velasco, D., Azémar, A., Oommen, O. P., Hilborn, J. & Varghese, O. P. (2019). Modulating thiol pKa promotes disulfide formation at physiological pH: An elegant strategy to design disulfide cross-linked hyaluronic acid hydrogels. Biomacromolecules, 20(3), 1412-1420
Open this publication in new window or tab >>Modulating thiol pKa promotes disulfide formation at physiological pH: An elegant strategy to design disulfide cross-linked hyaluronic acid hydrogels
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2019 (English)In: Biomacromolecules, ISSN 1525-7797, E-ISSN 1526-4602, Vol. 20, no 3, p. 1412-1420Article in journal (Refereed) Published
Abstract [en]

The disulfide bond plays a crucial role in protein biology and has been exploited by scientists to develop antibody-drug conjugates, sensors and for the immobilization other biomolecules to materials surfaces. In spite of its versatile use, the disulfide chemistry suffers from some inevitable limitations such as the need for basic conditions (pH > 8.5), strong oxidants and long reaction times. We demonstrate here that thiol-substrates containing electron-withdrawing groups at the β-position influence the deprotonation of the thiol group, which is the key reaction intermediate in the formation of disulfide bonds. Evaluation of reaction kinetics using small molecule substrate such as L-cysteine indicated disulfide formation at a 2.8-fold higher (k1 = 5.04 x 10-4 min-1) reaction rate as compared to the conventional thiol substrate, namely 3-mercaptopropionic acid (k1 = 1.80 x 10-4 min-1) at physiological pH (pH 7.4). Interestingly, the same effect could not be observed when N-acetyl-L-cysteine substrate (k1 = 0.51 x 10-4 min-1) was used. We further grafted such thiol-containing molecules (cysteine, N-acetyl-cysteine, and 3-mercaptopropionic acid) to a biopolymer namely hyaluronic acid (HA) and determined the pKa value of different thiol groups by spectrophotometric analysis. The electron-withdrawing group at the β-position reduced the pKa of the thiol group to 7.0 for HA-cysteine (HA-Cys); 7.4 for N-acetyl cysteine (HA-ActCys) and 8.1 for HA-thiol (HA-SH) derivatives respectively. These experiments further confirmed that the concentration of thiolate (R-S-) ions could be increased with the presence of electron-withdrawing groups, which could facilitate disulfide cross-linked hydrogel formation at physiological pH. Indeed, HA grafted with cysteine or N-acetyl groups formed hydrogels within 3.5 minutes or 10 hours, respectively at pH 7.4. After completion of crosslinking reaction both gels demonstrated a storage modulus G’ ≈3300–3500 Pa, indicating comparable levels of crosslinking. The HA-SH gel, on the other hand, did not form any gel at pH 7.4 even after 24 h. Finally, we demonstrated that the newly prepared hydrogels exhibited excellent hydrolytic stability but can be degraded by cell-directed processes (enzymatic and reductive degradation). We believe our study provides a valuable insight on the factors governing the disulfide formation and our results are useful to develop strategies that would facilitate generation of stable thiol functionalized biomolecules or promote fast thiol oxidation according to the biomedical needs.

National Category
Materials Chemistry
Research subject
Chemistry with specialization in Materials Chemistry
Identifiers
urn:nbn:se:uu:diva-375001 (URN)10.1021/acs.biomac.8b01830 (DOI)000461270500028 ()30726668 (PubMedID)
Funder
Swedish Foundation for Strategic Research , 139400127EU, FP7, Seventh Framework Programme, 607868Swedish Foundation for Strategic Research , 139400126
Available from: 2019-01-24 Created: 2019-01-24 Last updated: 2019-04-11Bibliographically approved
Kadekar, S., Nawale, G. N., Karlsson, K., Ålander, C., Podiyan, O. & Varghese, O. P. (2019). Synthetic design of asymmetric miRNA with engineered 3′-overhang to improve strand selection. Molecular Therapy - Nucleic Acids, 16, 597-604
Open this publication in new window or tab >>Synthetic design of asymmetric miRNA with engineered 3′-overhang to improve strand selection
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2019 (English)In: Molecular Therapy - Nucleic Acids, ISSN 2162-2531, E-ISSN 2162-2531, Vol. 16, p. 597-604Article in journal (Refereed) Published
Abstract [en]

We have developed a novel miRNA design that significantly improves strand selection within the RISC complex by engineering the 3′-end by adding extra nucleotides. Addition of seven nucleotides at the 3′-ends of the miR or miR* strand resulted in a thermodynamic asymmetry at either of the two-ends, which resulted in selective RISC recruitment as demonstrated by the stem-loop quantitative PCR experiment. Such selective recruitment was also corroborated at the protein level by Western blot analysis. In order to investigate the functional effect due to selective recruitment, we performed apoptosis and metastasis studies using human colon carcinoma cells (HCT116) and human osteosarcoma cells (MG63). These experiments indicated that the recruitment of miR strand is responsible for inducing apoptosis as well as to inhibit invasiveness of cancer cells. Recruitment of miR* strand, on the other hand, showed opposite effect. To the best of our knowledge, our strand engineering strategy is the first report of improved strand selection of desired miRNA strand by RISC without using any chemical modifications or mismatches. We believe such structural modifications of miR34a could mitigate some of the off-target effects of miRNA therapy and would also allow a better understanding of sequence-specific gene regulation. Such a design could also be adapted to other miRNA to enhance their therapeutic potential.

Place, publisher, year, edition, pages
Elsevier, 2019
Keywords
RNA interference, miRNA, miR34a, strand selection, anticancer therapy
National Category
Polymer Chemistry
Identifiers
urn:nbn:se:uu:diva-382299 (URN)10.1016/j.omtn.2019.04.012 (DOI)000470250900053 ()31085353 (PubMedID)
Funder
Swedish Foundation for Strategic Research , SBE13-0028National initiative on Stem Cells for Regenerative Therapy, 2009-1035
Available from: 2019-04-24 Created: 2019-04-24 Last updated: 2019-06-26Bibliographically approved
Ferreira, S. A., Motwani, M. S., Faull, P. A., Seymour, A. J., Yu, T. T., Enayati, M., . . . Gentleman, E. (2018). Bi-directional cell-pericellular matrix interactions direct stem cell fate. Nature Communications, 9(1), Article ID 4049.
Open this publication in new window or tab >>Bi-directional cell-pericellular matrix interactions direct stem cell fate
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2018 (English)In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 9, no 1, article id 4049Article in journal (Refereed) Published
Abstract [en]

Modifiable hydrogels have revealed tremendous insight into how physical characteristics of cells' 3D environment drive stem cell lineage specification. However, in native tissues, cells do not passively receive signals from their niche. Instead they actively probe and modify their pericellular space to suit their needs, yet the dynamics of cells' reciprocal interactions with their pericellular environment when encapsulated within hydrogels remains relatively unexplored. Here, we show that human bone marrow stromal cells (hMSC) encapsulated within hyaluronic acid-based hydrogels modify their surroundings by synthesizing, secreting and arranging proteins pericellularly or by degrading the hydrogel. hMSC's interactions with this local environment have a role in regulating hMSC fate, with a secreted proteinaceous pericellular matrix associated with adipogenesis, and degradation with osteogenesis. Our observations suggest that hMSC participate in a bi-directional interplay between the properties of their 3D milieu and their own secreted pericellular matrix, and that this combination of interactions drives fate.

Place, publisher, year, edition, pages
Nature Publishing Group, 2018
National Category
Polymer Chemistry
Identifiers
urn:nbn:se:uu:diva-364894 (URN)10.1038/s41467-018-06183-4 (DOI)000446331900001 ()30282987 (PubMedID)
Funder
Wellcome trust, FC001999
Note

Correction in: NATURE COMMUNICATIONS, Volume: 9, Article Number: 5419, DOI: 10.1038/s41467-018-07843-1

Available from: 2018-11-06 Created: 2018-11-06 Last updated: 2019-01-17Bibliographically approved
Wang, S., Nawale, G. N., Kadekar, S., Oommen, O. P., Jena, N. K., Chakraborty, S., . . . Varghese, O. P. (2018). Saline Accelerates Oxime Reaction with Aldehyde and Keto Substrates at Physiological pH. Scientific Reports, 8, Article ID 2193.
Open this publication in new window or tab >>Saline Accelerates Oxime Reaction with Aldehyde and Keto Substrates at Physiological pH
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2018 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 2193Article in journal (Refereed) Published
Abstract [en]

We have discovered a simple and versatile reaction condition for oxime mediated bioconjugation reaction that could be adapted for both aldehyde and keto substrates. We found that saline accelerated the oxime kinetics in a concentration-dependent manner under physiological conditions. The reaction mechanism is validated by computational studies, and the versatility of the reaction is demonstrated by cell-surface labeling experiments. Saline offers an efficient and non-toxic catalytic option for performing the bioorthogonal-coupling reaction of biomolecules at the physiological pH. This saline mediated bioconjugation reaction represents the most biofriendly, mild and versatile approach for conjugating sensitive biomolecules and does not require any extensive purification step.

Place, publisher, year, edition, pages
NATURE PUBLISHING GROUP, 2018
National Category
Polymer Chemistry
Identifiers
urn:nbn:se:uu:diva-347090 (URN)10.1038/s41598-018-20735-0 (DOI)000423787500168 ()29391582 (PubMedID)
Funder
Swedish Foundation for Strategic Research
Available from: 2018-03-26 Created: 2018-03-26 Last updated: 2018-03-26Bibliographically approved
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Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0001-8872-9928

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