MMP2-Targeting and Redox-Responsive PEGylated Chlorin e6 Nanoparticles for Cancer Near-Infrared Imaging and Photodynamic Therapy

A unique matrix metalloproteinase 2-targeted photosensitizer delivery platform was developed in this study for tumor-targeting imaging and photodynamic therapy. The model photosensitizer therapeutic agent chlorin e6 (Ce6) was first covalently conjugated with matrix metalloproteinase 2-cleavable polypeptide and then modified with polyethylene glycol via a redox-responsive cleavable disulfide linker. The resultant matrix metalloproteinase 2-cleavable polypeptide modified PEGylated Ce6 (PEG-SS-Ce6-MMP2) nanoparticles, which formed via self-assembly, were observed to be monodisperse and significantly stable in aqueous solution. In addition, owing to their cellular redox-responsiveness at the cleavable disulfide linker, the PEG-SS-Ce6-MMP2 nanoparticles were able to release Ce6 rapidly. Despite displaying enhanced intracellular internalization, the synthesized PEG-SS-Ce6-MMP2 nanoparticles did not compromise their phototoxic effects toward A549 cancer cells when compared with free Ce6 and PEGylated Ce6 nanoparticles. <i>In vivo</i> experiments further revealed that, in contrast with the free Ce6 or with the PEGylated Ce6 nanoparticles, the PEG-SS-Ce6-MMP2 nanoparticles showed a remarkable increase in tumor-targeting ability and a significantly improved photodynamic therapeutic efficiency in A549 tumor-bearing mice. These results suggest that the PEG-SS-Ce6-MMP2 nanoparticles hold great potential for tumor-targeting imaging and photodynamic therapy

Additional file 1: of Modeling central metabolism and energy biosynthesis across microbial life

Supplemental figures and figure descriptions. In addition, descriptions for each supplemental data tabs in “Additional file 2” are included at the end of the document. (DOCX 17183 kb

Additional file 2: of Modeling central metabolism and energy biosynthesis across microbial life

Supplemental data table associated with this study. There are twelve data tabs included in this table. Description for each data tab is at the end of “Additional file 1” document. (XLSX 2418 kb

Microbial life tree (16S OTU98.5)

Phylogenetic tree (nwk format) used to show pathway conservation analysis on central metabolis

16S alignment file

Sequence alignment file that has been used to generate the initial master tree. Based on this master tree, the microbial life tree that was used in this study (16S OTU98.5) was generated using a distance-based clustering algorithm

sj-xlsx-2-cix-10.1177_11769351221139491 – Supplemental material for TULIP: An RNA-seq-based Primary Tumor Type Prediction Tool Using Convolutional Neural Networks

Supplemental material, sj-xlsx-2-cix-10.1177_11769351221139491 for TULIP: An RNA-seq-based Primary Tumor Type Prediction Tool Using Convolutional Neural Networks by Sara Jones, Matthew Beyers, Maulik Shukla, Fangfang Xia, Thomas Brettin, Rick Stevens, M Ryan Weil and Satishkumar Ranganathan Ganakammal in Cancer Informatics</p

sj-docx-1-cix-10.1177_11769351221139491 – Supplemental material for TULIP: An RNA-seq-based Primary Tumor Type Prediction Tool Using Convolutional Neural Networks

Supplemental material, sj-docx-1-cix-10.1177_11769351221139491 for TULIP: An RNA-seq-based Primary Tumor Type Prediction Tool Using Convolutional Neural Networks by Sara Jones, Matthew Beyers, Maulik Shukla, Fangfang Xia, Thomas Brettin, Rick Stevens, M Ryan Weil and Satishkumar Ranganathan Ganakammal in Cancer Informatics</p

Schematic of prediction framework for promiscuous replacers.

<p>(1) Gene similarity trees are built around each gene in <i>E</i>. <i>coli</i>, including any distantly related gene in the RAST database. (2) A matrix is formed which links genes with their primary functions and also potential promiscuous functions. A gene (in this example, <i>eco1</i>) will take a potential secondary ‘promiscuous’ function in the matrix if its similarity tree includes any genes annotated with different functions (e.g., in this example, <i>shi4</i>, which encodes function fn4). (3) Cases in which a gene’s predicted promiscuous function is identical to the function of another gene in <i>E</i>. <i>coli</i> constitute predicted ‘direct’ target-replacer gene pairs (via PROPER). We also predict ‘indirect’ target-replacer pairs where a replacer bypasses the target’s function (via GEM-PROPER). (4) Promiscuous activity of a ‘replacer’ gene can be confirmed for target-replacer pairs in which the target is conditionally essential on a minimal medium, via the multicopy suppression assay.</p

Proposed novel pathway for promiscuous production of pyridoxal 5’-phosphate.

<p>GEM-PROPER was used to predict the indirect target-replacer pair, <i>∆pdxB/thiG</i>, which we then confirmed with experiments. The predicted secondary function of <i>thiG</i> is pyridoxal 5’-phosphate synthase (P5PS), which would bypass the known 6-enzymatic-step pathway for production of p5p in <i>E</i>. <i>coli</i>. (a) The two alternative pathways, along with known promiscuous pathways in <i>E</i>. <i>coli</i> for producing p5p after <i>pdxB</i> knockout (as reported in Kim: [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004705#pcbi.1004705.ref008" target="_blank">8</a>]). Abbreviations are: ru5p-D = D-Ribulose 5-phosphate; gln-L = L-glutamine; g3p = Glyceraldehyde 3-phosphate; glu-L = L-glutamate; Pi = Phosphate. (b) Structural alignment of a homology model of <i>thiG</i> (for <i>E</i>. <i>coli</i>, based on crystal structure of <i>thiG</i> from <i>B</i>. <i>subtilis</i>) with a crystal structure of <i>B</i>. <i>subtilis pdxS</i>, the gene that (in complex with another gene, <i>pdxT</i>) performs the P5PS function in <i>B</i>. <i>subtilis</i>. The proteins share the TIM barrel fold. (c) Close-up of the structural alignment in (b), focused on the active site of <i>pdxS</i> and the residues of <i>thiG</i> that we propose perform the <i>pdxS</i> function. The location of the close-up is shown with a box in (b).</p

Inactivating the <i>thiG</i> proposed secondary active site removes its ability to replace <i>pdxB</i>.

<p>Four strains (<i>ΔpdxB/empty</i> [- control], <i>ΔpdxB/pdxB</i> [+ control], <i>ΔpdxB/thiG</i>, <i>ΔpdxB/thiGmut</i>) were grown for 96 hours in deep-well microplates, in which a checkerboard matrix of varied IPTG (inducer) and NH₄Cl (nitrogen source) concentration in M9 glucose were assessed. Values shown are representative OD₆₀₀ readings at 96 hours post-inoculation. Additional OD₆₀₀ data are provided in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004705#pcbi.1004705.s017" target="_blank">S5 Table</a>. Box plots of OD₆₀₀ values at ~3% NH₄Cl (across IPTG concentrations) are shown in lower panel, along with the results of Ranksum tests of OD₆₀₀ values between relevant strain pairs.</p