Journal: Pharmaceuticals

Article Title: Silkworm Cocoon—Derived Carbon Dots for Post-Trauma Hemostasis and Tissue Repair

doi: 10.3390/ph18050603

Figure Lengend Snippet: In vitro biocompatibility and cytotoxicity assessment of SC-CDs. Hemolysis ( A ) ( n = 3) and cytotoxicity of SC-CDs on L929 cells ( B ) ( n = 6).

Article Snippet: L929 cells (catalog number: SCSP-5039; ATCC No.: CCL-1TM) were purchased from the Chinese Academy of Sciences Stem Cell Bank.

Techniques: In Vitro

Journal: Pharmaceuticals

Article Title: Silkworm Cocoon—Derived Carbon Dots for Post-Trauma Hemostasis and Tissue Repair

doi: 10.3390/ph18050603

Figure Lengend Snippet: In vitro activity of silkworm cocoon-derived carbon dots (SC-CDs). Coagulation activity (coagulation parameters ( A ), platelet aggregation ( B ), and platelet activation ( C – G )) (n = 3). L929 cell migration ( H ) and migration rate ( I ) (n = 6). * p < 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001, ns: p > 0.05.

Article Snippet: L929 cells (catalog number: SCSP-5039; ATCC No.: CCL-1TM) were purchased from the Chinese Academy of Sciences Stem Cell Bank.

Techniques: In Vitro, Activity Assay, Derivative Assay, Coagulation, Activation Assay, Migration

Journal: Immunity

Article Title: A RIPK1-specific PROTAC degrader achieves potent antitumor activity by enhancing immunogenic cell death.

doi: 10.1016/j.immuni.2024.04.025

Figure Lengend Snippet: Figure 1. Development of selective RIPK1-PROTAC degraders (A) Schematic representation of RIPK1-PROTACs. (B) HT1080Ripk1-HiBiT cells were treated with the indicated PROTACs for 24 h. HiBiT measurements are shown. RLU, relative light unit. (C) Western blot analysis evaluating RIPK1 degradation. Cells were incubated with the indicated concentrations of R1-ICR-5 for 6 h. (D) Micro-confocal images of the indicated endogenous proteins in cells treated with the indicated PROTACs for 20 h. Scale bars: 100 mm (HT1080/HT29) and 50 mm (EMT6/L929). (E) Quantification of relative endogenous RIPK1 levels from (D).

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER NaveniFlex MR Bethyl Laboratories Cat#NF.MR.100 CellTiter-GLO Promega Cat#G9681 RNeasy RNA extraction kit Qiagen Cat#74106 QuantiTec Reverse Transcription kit Qiagen Cat#205314 Pierce BCA protein assay kit Thermo Fisher Scientific Cat#23227 Deposited data Bulk RNA-seq (Sham Vs RT-treated EO771 cells) Sequence read archive ID: PRJNA1094427 Mass spectrometry: Human and mouse whole proteome analysis PRIDE ID: PXD043560 TCGA Pan-cancer analyses cBioPortal N/A SCAN-B TNBC patient data GEO Database GEO: GSE96058 GSEA analyses (hallmark gene set collection) The Molecular Signatures Database (MSigDB) N/A Raw western blots and image from this paper Mendeley https://doi.org/10.17632/822syk52yw.1 Experimental models: Cell lines HEK293T ATCC Cat#CRL-3216 HT1080 ATCC Cat#CCL-121 U937 ATCC Cat#CRL-3253 HT29 ATCC Cat#HTB-38 MDA-MB-231 ATCC Cat#CRM-HTB-26 MDA-MB-361 ATCC Cat#HTB-27 MDA-MB-468 ATCC Cat#HTB-132 HaCaT ATCC discontinued LLC ATCC CatCL-101 L929 ATCC Cat#CRL-6364 THP-1 ATCC Cat#TIB-202 EMT6 ATCC Cat#CRL-2755 Lim1215 Laboratory of Prof. Chris Marshall N/A A431 ATCC Cat#CRL-1555 F3II Laboratory of Prof. Daniel Alonso N/A D2A1 Laboratory of Prof. Clare Isacke N/A Kym-1 Laboratory of Prof. John Silke N/A Immortalized MDFs Charles River (Cells generated in house) N/A MCA-205 Sigma Aldrich Cat#SCC-173 EO771 CH3 Biosystems Cat#94A001 MC38 Kerafast Cat#ENH204-FP Wildtype BMDMs and Lung fibroblasts (C57BL/6) Charles River (Cells generated in house) N/A Spata2-/- BMDMs (C57BL/6) Laboratory of Prof. Mads Gyrd-Hansen’s N/A Trif-/- BMDMs (C57BL/6) (Ticam1-/-) Laboratory of Prof. Manolis Pasparakis N/A Zbp1-/- BMDMs (C57BL/6) Laboratory of Prof. Manolis Pasparakis N/A Trif-/-Zbp1-/- BMDMs and LFs (C57BL/6) (Ticam1-/-Zbp1-/-) Laboratory of Prof. Manolis Pasparakis N/A L929 Tradd-/- This Manuscript N/A L929 Tradd-/- reconstituted with TRADDWT This Manuscript N/A L929 Tradd-/- reconstituted with TRADD DD-only This Manuscript N/A L929 Tradd-/- reconstituted with TRADD Y16A/F18A This Manuscript N/A (Continued on next page) e5 Immunity 57, 1–19.e1–e15, July 9, 2024

Techniques: Western Blot, Incubation

Journal: Immunity

Article Title: A RIPK1-specific PROTAC degrader achieves potent antitumor activity by enhancing immunogenic cell death.

doi: 10.1016/j.immuni.2024.04.025

Figure Lengend Snippet: Figure 2. Acute degradation of RIPK1 deregulates TNFR1 and TLR3 signaling (A) Schematic representation depicting RIPK1’s regulation of TNFR1 and TLR3/4-induced signaling and cell death. (B) Relative mRNA expression of NF-kB target genes in BMDMs pretreated with DMSO or R1-ICR-5 for 4 h, followed by indicated TNF treatment. (C) Relative Tnf mRNA expression in BMDMs treated for 4 h with the indicated conditions. MK2i refers to an MK2 inhibitor. (D) Western blot analysis of TNFR1 signaling complex-I. Cells were treated with DMSO or R1-ICR-5 (overnight). (E) L929 cells were treated as in (D) before anti-GST-TUBE pull-down to isolate the ubiquitylated proteome. * Indicates nonspecific signal. (F) Western blot analysis of BMDMs pretreated with DMSO or R1-ICR-5 for 4 h, followed by TNF exposure for the indicated time points. (G) Relative mRNA expression of NF-kB or IFN target genes. BMDMs were pretreated with DMSO or R1-ICR-5 for 4 h, followed by stimulation with poly(I:C). Data show mean ± SD and are representative of (C and E) two, (B and G) three, (F) four, or (D) five independent biological repeats. p values were calculated using (B) two-way ANOVA (Sidak’s multiple comparison test) or (C and G) one-way ANOVA (Bonferroni’s multiple comparison test).

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER NaveniFlex MR Bethyl Laboratories Cat#NF.MR.100 CellTiter-GLO Promega Cat#G9681 RNeasy RNA extraction kit Qiagen Cat#74106 QuantiTec Reverse Transcription kit Qiagen Cat#205314 Pierce BCA protein assay kit Thermo Fisher Scientific Cat#23227 Deposited data Bulk RNA-seq (Sham Vs RT-treated EO771 cells) Sequence read archive ID: PRJNA1094427 Mass spectrometry: Human and mouse whole proteome analysis PRIDE ID: PXD043560 TCGA Pan-cancer analyses cBioPortal N/A SCAN-B TNBC patient data GEO Database GEO: GSE96058 GSEA analyses (hallmark gene set collection) The Molecular Signatures Database (MSigDB) N/A Raw western blots and image from this paper Mendeley https://doi.org/10.17632/822syk52yw.1 Experimental models: Cell lines HEK293T ATCC Cat#CRL-3216 HT1080 ATCC Cat#CCL-121 U937 ATCC Cat#CRL-3253 HT29 ATCC Cat#HTB-38 MDA-MB-231 ATCC Cat#CRM-HTB-26 MDA-MB-361 ATCC Cat#HTB-27 MDA-MB-468 ATCC Cat#HTB-132 HaCaT ATCC discontinued LLC ATCC CatCL-101 L929 ATCC Cat#CRL-6364 THP-1 ATCC Cat#TIB-202 EMT6 ATCC Cat#CRL-2755 Lim1215 Laboratory of Prof. Chris Marshall N/A A431 ATCC Cat#CRL-1555 F3II Laboratory of Prof. Daniel Alonso N/A D2A1 Laboratory of Prof. Clare Isacke N/A Kym-1 Laboratory of Prof. John Silke N/A Immortalized MDFs Charles River (Cells generated in house) N/A MCA-205 Sigma Aldrich Cat#SCC-173 EO771 CH3 Biosystems Cat#94A001 MC38 Kerafast Cat#ENH204-FP Wildtype BMDMs and Lung fibroblasts (C57BL/6) Charles River (Cells generated in house) N/A Spata2-/- BMDMs (C57BL/6) Laboratory of Prof. Mads Gyrd-Hansen’s N/A Trif-/- BMDMs (C57BL/6) (Ticam1-/-) Laboratory of Prof. Manolis Pasparakis N/A Zbp1-/- BMDMs (C57BL/6) Laboratory of Prof. Manolis Pasparakis N/A Trif-/-Zbp1-/- BMDMs and LFs (C57BL/6) (Ticam1-/-Zbp1-/-) Laboratory of Prof. Manolis Pasparakis N/A L929 Tradd-/- This Manuscript N/A L929 Tradd-/- reconstituted with TRADDWT This Manuscript N/A L929 Tradd-/- reconstituted with TRADD DD-only This Manuscript N/A L929 Tradd-/- reconstituted with TRADD Y16A/F18A This Manuscript N/A (Continued on next page) e5 Immunity 57, 1–19.e1–e15, July 9, 2024

Techniques: Expressing, Western Blot, Comparison

Journal: Immunity

Article Title: A RIPK1-specific PROTAC degrader achieves potent antitumor activity by enhancing immunogenic cell death.

doi: 10.1016/j.immuni.2024.04.025

Figure Lengend Snippet: Figure 3. RIPK1 degraders drive TNFR1-driven necroptosis, independent of TRIF and ZBP1 (A and B) Quantification of propidium-iodide-positive (PI+) cells, treated with the indicated conditions. Cells were pretreated with DMSO, R1-ICR-5, or RIPK2 degrader (A, 18 h; B, 5 h), before stimulation with the indicated conditions (A, 5 h; B, 7 h). (C) Western blot analysis monitoring RIPK3 and MLKL activation. Cells were pretreated for 18 h before exposure to TNF/Emricasan (TE) for the indicated time points. * Indicates nonspecific signal. (D and E) Quantification of PI+ cells. Cells were pretreated with DMSO, R1-ICR-3, or R1-ICR-5 for 4 h, followed by the indicated treatments (3 h). (F) Quantification of PI+ BMDMs. Cells were pretreated with DMSO or R1-ICR-5 for 4 h, followed by the indicated treatment. (G) Quantification of PI+ L929 cells. Cells were untreated or pretreated with R1-ICR-5 for 12 h, followed by treatment with the indicated agents. RIPK1 kinase inhibitors were added 30 min prior to TE (6.5 h).

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER NaveniFlex MR Bethyl Laboratories Cat#NF.MR.100 CellTiter-GLO Promega Cat#G9681 RNeasy RNA extraction kit Qiagen Cat#74106 QuantiTec Reverse Transcription kit Qiagen Cat#205314 Pierce BCA protein assay kit Thermo Fisher Scientific Cat#23227 Deposited data Bulk RNA-seq (Sham Vs RT-treated EO771 cells) Sequence read archive ID: PRJNA1094427 Mass spectrometry: Human and mouse whole proteome analysis PRIDE ID: PXD043560 TCGA Pan-cancer analyses cBioPortal N/A SCAN-B TNBC patient data GEO Database GEO: GSE96058 GSEA analyses (hallmark gene set collection) The Molecular Signatures Database (MSigDB) N/A Raw western blots and image from this paper Mendeley https://doi.org/10.17632/822syk52yw.1 Experimental models: Cell lines HEK293T ATCC Cat#CRL-3216 HT1080 ATCC Cat#CCL-121 U937 ATCC Cat#CRL-3253 HT29 ATCC Cat#HTB-38 MDA-MB-231 ATCC Cat#CRM-HTB-26 MDA-MB-361 ATCC Cat#HTB-27 MDA-MB-468 ATCC Cat#HTB-132 HaCaT ATCC discontinued LLC ATCC CatCL-101 L929 ATCC Cat#CRL-6364 THP-1 ATCC Cat#TIB-202 EMT6 ATCC Cat#CRL-2755 Lim1215 Laboratory of Prof. Chris Marshall N/A A431 ATCC Cat#CRL-1555 F3II Laboratory of Prof. Daniel Alonso N/A D2A1 Laboratory of Prof. Clare Isacke N/A Kym-1 Laboratory of Prof. John Silke N/A Immortalized MDFs Charles River (Cells generated in house) N/A MCA-205 Sigma Aldrich Cat#SCC-173 EO771 CH3 Biosystems Cat#94A001 MC38 Kerafast Cat#ENH204-FP Wildtype BMDMs and Lung fibroblasts (C57BL/6) Charles River (Cells generated in house) N/A Spata2-/- BMDMs (C57BL/6) Laboratory of Prof. Mads Gyrd-Hansen’s N/A Trif-/- BMDMs (C57BL/6) (Ticam1-/-) Laboratory of Prof. Manolis Pasparakis N/A Zbp1-/- BMDMs (C57BL/6) Laboratory of Prof. Manolis Pasparakis N/A Trif-/-Zbp1-/- BMDMs and LFs (C57BL/6) (Ticam1-/-Zbp1-/-) Laboratory of Prof. Manolis Pasparakis N/A L929 Tradd-/- This Manuscript N/A L929 Tradd-/- reconstituted with TRADDWT This Manuscript N/A L929 Tradd-/- reconstituted with TRADD DD-only This Manuscript N/A L929 Tradd-/- reconstituted with TRADD Y16A/F18A This Manuscript N/A (Continued on next page) e5 Immunity 57, 1–19.e1–e15, July 9, 2024

Techniques: Western Blot, Activation Assay

Journal: Polymers

Article Title: Responsive Polyesters with Alkene and Carboxylic Acid Side-Groups for Tissue Engineering Applications

doi: 10.3390/polym13101636

Figure Lengend Snippet: Optical microscopy images depicting the adhesion and morphology of L929 fibroblasts after 4 days in culture on the ( a ) TCPS control, ( b ) P(PTPAE‒ alt ‒AD), ( c ) PE‒Prop50, ( d ) PE‒Glyc50, ( e ) PE‒Prop80, and ( f ) PE‒Glyc80 films. Scale bar represents 50 μm and is the same in all images.

Article Snippet: The biocompatibility assessment was conducted using L929 fibroblast cells of passage 13 and lower (cat. No. ACC-2, DSMZ GmbH, Braunschweig, Germany).

Techniques: Microscopy, Control