|
Antibodies
|
| Actin |
Santa Cruz |
sc-1616 |
| ASC |
Cell Signaling |
67824S |
| CXCL8 |
Thermo Fisher |
M801 |
| Erk1/2 |
Cell Signaling |
4695 |
| MEK1/2 |
Cell Signaling |
4694 |
| NLRP3 |
Cell Signaling |
15101S |
| P65 |
Cell Signaling |
8242 |
| pErk1/2 |
Cell Signaling |
4370 |
| pMEK1/2 |
Cell Signaling |
3958 |
| pMLKL (S358) |
Abcam |
ab187091 |
| pP65 |
Cell Signaling |
3033 |
| pP90 |
Cell Signaling |
11989 |
| pPKC (S660, pan) |
Cell Signaling |
9371 |
| pSRF |
Cell Signaling |
4261 |
| RIPK3 |
Cell Signaling |
95702 |
| SRF |
Cell Signaling |
5147 |
| Alexa Fluor 700 anti-mouse CD11c |
Thermo Fisher |
56–0114-82 |
| APC anti-mouse CD163 |
Thermo Fisher |
17–1631-82 |
| Brilliant Violet 421 anti-mouse Ly-6G |
BioLegend |
127627 |
| Brilliant Violet 510 anti-mouse Ly-6C |
BioLegend |
128033 |
| Brilliant Violet 650 anti-mouse CD45 |
BioLegend |
103151 |
| Brilliant Violet 711 anti-mouse CD206 |
BioLegend |
141727 |
| Brilliant Violet 785 anti-mouse/human CD11b |
BioLegend |
101243 |
| FITC anti-mouse F4/80 |
Thermo Fisher |
11–4801-82 |
| PE anti-mouse CD103 |
Thermo Fisher |
12–1031-82 |
| PE/Cyanine7 anti-mouse CD80 |
BioLegend |
104734 |
| PerCP-eFluor 710 anti-mouse MHC Class II (I-A/I-E) |
Thermo Fisher |
46–5321-80 |
|
Biological Samples
|
|
|
| Human stage IV cancer samples |
This paper |
Institute for Precision Medicine and the Pitt Biospecimen Core |
|
Organisms/Strains
|
| C57BL/6J |
JAX |
000664 |
|
Chemicals, Peptides, and Recombinant Proteins
|
| 4-OHT |
Sigma |
H6278 |
| 5Z-7-Oxozeaenol |
Caymanchem |
253863–19-3 |
| Annexin V-Alexa Fluor-647 |
Thermo Fisher |
A23204 |
| B/B homodimerizer |
Clontech |
635059 |
| BAPTA-AM |
Tocris |
2787 |
| Bisindolylmaleimide I |
Caymanchem |
13298 |
| BMS345541 |
Caymanchem |
16667 |
| CAPE |
Calbiochem |
211200 |
| Cycloheximide |
Sigma |
C-7698 |
| Digitonin |
TCI America |
TCD0540 |
| Go6976 |
Caymanchem |
13310 |
| Go6983 |
Caymanchem |
13311 |
| ionomycin |
Calbiochem |
11932 |
| Lcl-161 |
Medchemexpress |
HY-15518 |
| Lipofectamine 2000 |
Invitrogen |
11668019 |
| Lipofectamine RNAiMAX |
Invitrogen |
13778075 |
| MG132 |
Caymanchem |
10012628 |
| mTNF |
Peprotech |
315–01A |
| PD 0325901 |
Caymanchem |
13034 |
| Phorbol 12-myristate 13-acetate |
Sigma |
79346 |
| Recombinant Mouse CXCL1/GRO alpha/KC/CINC-1 Protein |
Novusbio |
NBP2–35153 |
| Recombinant Mouse LIF Protein |
Novusbio |
NBP2–35147 |
| SytoxGreen |
Invitrogen |
S7020 |
| TNFR1-Fc |
ENZO |
ALX-522–013-C050 |
| TPCA-1 |
Caymanchem |
15115 |
| Trametinib |
Caymanchem |
16292 |
| YM-58483 |
Selleckchem |
YM-58483 |
| zVAD-fmk |
APExBIO |
A1902 |
|
Critical Commercial Assays
|
| CellTiter-Glo™ Luminescent Cell Viability Assay Kit |
Promega |
G7572 |
| Mouse CXCL1/KC DuoSet ELISA |
R&D systems |
DY453–05 |
| Mouse CXCL1/KC Quantikine ELISA Kit |
R&D systems |
MKC00B |
| Zombie NIR Fixable Viability Kit |
BioLegend |
423105 |
|
Deposited Data
|
| RNA seq data for PM damaged cells |
This study |
GEO: GSE166538
|
| Human kidney biopsies RNA-seq |
(Gong et al., 2017b) |
https://www.obvibase.com/#token/cHIuv8Hv4Cdb/r/hka6j0CQmzwp
|
| Mouse kidney biopsies microarray |
(Liu et al., 2014) |
GEO: GSE52004
|
| mRNA array data for B/B induced hMLKL1–181-2Fv-NIH 3T3 cells |
(Gong et al., 2017b) |
GEO: GSE85660
|
| Mouse kidney biopsies RNAseq |
(Liu et al., 2017) |
GEO: GSE98622
|
| Mouse kidney biopsies single nuclear RNAseq |
(Kirita et al., 2020) |
GEO: GSE139107
|
| TNF induced transcriptome change in NIH3T3 cells |
(Orozco et al., 2019) |
GEO: GSE134234
|
|
Experimental Models: Cell Lines
|
| RIPK3–2Fv-NIH3T3 |
(Yatim et al., 2015) |
N/A |
| RIPK3(ΔRHIM)-2Fv-NIH3T3 |
(Yatim et al., 2015) |
N/A |
| hMLKL1–140-2Fv-Venus-MEFMlkl−/−-CHMP4B-mCherry |
(Gong et al., 2017b) |
N/A |
| hMLKL1–181-2Fv-NIH3T3 |
(Gong et al., 2017b) |
N/A |
| hMLKL1–181-2Fv-LLC |
This study |
N/A |
| hMLKL1–181-2Fv-MEFMlkl-/-
|
This study |
N/A |
| L929Mlkl-/-
|
(Gong et al., 2017b) |
N/A |
| GSDMDNter-HBD*-NIH3T3 |
This study |
N/A |
| GSDMDNter-HBD*-LLC |
This study |
N/A |
| GCaMP3- hMLKL1–181-2Fv-NIH3T3 |
(Gong et al., 2017b) |
N/A |
| Raw264.7-ASC |
This study |
N/A |
| HT-29 Mlkl-/-
|
(Gong et al., 2017b) |
N/A |
|
Oligonucleotides
|
| siRNAs, sgRNAs and Primers were list in Table S2. |
|
|
|
Recombinant DNA
|
| NF-κB driven CFP |
Addgene |
118094 |
| hMLKL1–181-2Fv |
(Gong et al., 2017b) |
|
| GSDMDNter-HBD* |
This study |
|
| STIM1-CFP |
Addgene |
19755 |
| pSpCas9(BB)-2A-GFP (PX458) |
Addgene |
48138 |
| GFP-pcDNA3-PKCgamma-cys1Acys1B |
Addgene |
21190 |
| GFP-C2gamma |
Addgene |
21215 |
| PKC alpha DN |
Addgene |
21235 |
| PKC beta I DN |
Addgene |
16381 |
| PKC gamma DN |
Addgene |
21239 |
|
Software and Algorithms
|
| Gen5 |
BioTek |
https://www.biotek.com/products/software-robotics-software/gen5-microplate-reader-and-imager-software/
|
| FlowJo |
FlowJo LLC |
https://www.flowjo.com/
|
| NIS-Elements |
Nikon |
https://www.microscope.healthcare.nikon.com/products/software/nis-elements/nis-elements-advanced-research
|
| ImageJ |
NIH |
https://imagej.nih.gov/ij/
|
| Salmon-0.7.2 |
Academic, Kingsford Lab |
Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C. Salmon provides fast and bias-aware quantification of transcript expression. Nat Methods. 2017;14(4):417–419. doi:10.1038/nmeth.4197
https://salmon.readthedocs.io/en/latest/salmon.html
|
| Seurat-V4 |
Academic, Satija Lab |
https://satijalab.org/seurat/
|
| R-4.0.3 |
The R Foundation for Statistical Computing |
https://www.r-project.org/foundation/
|
| Matlab-2019B |
mathworks |
https://www.mathworks.com/
|
| Molecular-Signatures-Database/GSEA |
Broad/UCSC |
http://www.gsea-msigdb.org/gsea/msigdb/index.jsp#citing_msigdb
|
| GSEA Implemented in R as fgsea package |
Sergushichev lab |
https://bioconductor.org/packages/release/bioc/html/fgsea.html
|
