KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit anti-mouse β-Actin antibody | Cell Signaling Technology | Cat#4967; RRID: AB_330288 |
| Mouse anti-mouse AGXT antibody | Santa Cruz Biotechnology | Cat# SC-517388 |
| Rabbit anti-mouse CYP7B1 antibody | Proteintech | CAT# 24889–1-AP RRID: AB_2879780 |
| Mouse anti-mouse B-ACTIN antibody | Cell Signaling Technology | CAT#3700 RRID: AB_2242334 |
| Rat anti-Galectin 3 antibody | Thermo Fisher Scientific | Cat#13-5301-81; RRID: AB_837112 |
| CCL5 (RANTES) Recombinant Polyclonal Antibody | ThermoFisher Scientific | Cat# 710001, RRID: AB_2532515 |
| 800CW Donkey anti-mouse IRDye | LI-COR Biosciences | Cat# 926–32212; RRID: AB_621847 |
| 680RD Donkey anti-rabbit IRDye | LI-COR Biosciences | Cat# 926–68073; RRID: AB_10954442 |
| 800CW Donkey anti-rabbit IRDye | LI-COR Biotechnology | CAT# 926–32213 RRID: AB_621848 |
| 680RD Donkey anti-mouse IRDye | LI-COR Biotechnology | CAT# 926–68072 RRID: AB_10953628 |
| Goat anti-Rat IgG (H+L) Secondary Antibody, HRP | ThermoFisher Scientific | Cat# 31470, RRID: AB_228356 |
| Alexa Fluor 647 donkey anti-rat | Jackson ImmunoResearch Laboratories | Cat# 712-605-153; RRID: AB_2340694 |
| Alexa Fluor 594 donkey anti-rabbit | Jackson ImmunoResearch Laboratories | Cat#711-585-152, RRID: AB_2340621 |
| Bacterial and Virus Strains | ||
| Stable Competent E. coli | New England Biolabs | Cat # C3040H |
| AAV-TBG-GFP | This paper | N/A |
| AAV-TBG-AGXT | This paper | N/A |
| Biological Samples | ||
| Serum from patients with or without sCAD | This paper | N/A |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Polyethylenimine | Sigma-Aldrich | Cat# 408727 |
| Dihydroethidium | Sigma-Aldrich | Cat# D7008 |
| MitoTEMPO | Sigma-Aldrich | Cat# SML0737 |
| Sodium oxalate | Sigma-Aldrich | Cat# 223433 |
| Oil red O | Sigma-Aldrich | Cat# O0625 |
| Sodium azide | Sigma-Aldrich | CAT#S2002 |
| Proteinase K | Sigma-Aldrich | CAT# 1245680500 |
| Trans-4-Hydroxy-L-proline | ACROS Organics | CAT#121785000 |
| UltraPure™ Phenol:Chloroform:Isoamyl Alcohol | ThermoFisher Scientific | CAT#15593–031 |
| Poloxamer 188 | Sigma-Aldrich | Cat# P5556 |
| Harris hematoxylin | ThermoFisher Scientific | Cat# 842 |
| Eosin Y | ThermoFisher Scientific | Cat# 832 |
| Clarifier Bluing reagent | ThermoFisher Scientific | Cat# 7401 |
| Bluing reagent | ThermoFisher Scientific | Cat# 7301 |
| MitoSOX Red | ThermoFisher Scientific | Cat# M36008 |
| Hoechst | ThermoFisher Scientific | Cat# H3570 |
| Trizol reagent | ThermoFisher Scientific | Cat# 5596026 |
| Canonical amino acid mix unlabeled standard | Cambridge Isotopes Laboratory | Cat# MSK-CAA-US-1 |
| Canonical amino acid mix | Cambridge Isotopes Laboratory | Cat# MSK-CAA-1 |
| O.C.T. Compound | Tissue-Tek | Cat# 4583 |
| iQ SYBR Green Supermix | Bio-Rad | Cat# 1708880 |
| Critical Commercial Assays | ||
| Wako Cholesterol E | FUJIFILM medical system | Cat# 999–02601 |
| RNeasy Maxi kit | QIAGEN | Cat# 75162 |
| EndoFree Plasmid Maxi Kit | QIAGEN | Cat# 12362 |
| Oxalate assay kit | Abcam | Cat# ab196990 |
| Mouse CCL2/JE/MCP-1 Quantikine ELISA Kit | R&D Systems | Cat# MJE00B |
| Mouse/Rat CCL5/RANTES Quantikine ELISA Kit | R&D Systems | Cat# MMR00 |
| Glucose test strips | Contour Next | Cat# NDC: 0193-7308-50 |
| Seahorse XFp Cell Mito Stress Test Kit | Agilent Technologies | Cat# 103010–100 |
| Gibson assembly kit | New England Biolabs | Cat# E5510 |
| NEBNext Ultra II Directional RNA Library Prep Kit for Illumina | New England Biolabs | CAT# E7760L |
| Poly(A) mRNA Magnetic Isolation Module | New England Biolabs | Cat# E7490L |
| NEBNext Multiplex Oligos for Illumina Unique dual | New England Biolabs | Cat# E6440L |
| Protease inhibitor | Thermo Fisher Scientific | Cat# A32965 |
| Phosphatase inhibitor | Roche Diagnostics | Cat# 04906845001 |
| SuperScript™ III First-Strand Synthesis System | ThermoFisher Scientific | Cat# 18080051 |
| CCK8 assay kit | Sigma-Aldrich | Cat# 96992 |
| SignalStain® DAB Substrate Kit | Cell Signaling Techonology | CAT#8059 |
| Total Bile Acid Assays Kit | Cell Biolabs, INC | CAT#STA-631 |
| Cholesterol fluorometric assay kit | Cayman Chemical | CAT#10007640 |
| LabAssay™ Triglyceride kit | FUJIFILM medical system | CAT# 290–63701 |
| Deposited Data | ||
| RNA-sequencing | This paper | NCBI’s SRA (accession number: PRJNA671451) |
| Raw data | This paper | Mendeley Data (doi:10.17632/n8nkdgd258.1) |
| Experimental Models: Cell Lines | ||
| HEK293T | ATCC | CRL-3216; RRID: CVCL_0063 |
| L929 cells | ATCC | CRL-1; RRID: CVCL_0462 |
| Bone marrow derived-macrophages | This paper | N/A |
| Experimental Models: Organisms/Strains | ||
| Mouse: C57BL/6J | The Jackson Laboratory | JAX: 000664; RRID: IMSR_JAX:000664 |
| Mouse: Apoe−/− | The Jackson Laboratory | JAX: 002052; RRID: IMSR_JAX:002052 |
| Mouse: Agxt−/− | Rom et al., 2020 | N/A |
| Mouse: Agxt+/+/Apoe−/− | This paper | N/A |
| Mouse: Agxt−/−/Apoe−/− | This paper | N/A |
| Oligonucleotides | ||
| Guide-RNA targeting the mouse Agxt exon1: 5’-GGGTCCGGGGCCCTCCAACC-3’ | Integrated DNA Technologies | N/A |
| Primer sequences for Agxt genotyping: forward: 5’-ACACCTCCACTGTCCTGTCC-3’ | Integrated DNA Technologies | N/A |
| Primer sequences for Agxt genotyping: reverse: 5’-GGTCAGATCTGCCTGCTACC-3’ | Integrated DNA Technologies | N/A |
| Primer for Sanger sequencing: 5’-GCAGAGCTAGCTGGGAAATG-3’ | Integrated DNA Technologies | N/A |
| Primer sequences for Apoe genotyping: forward: 5′-GCCTAGCCGAGGGAGAGCCG-3′ | Integrated DNA Technologies | N/A |
| Primer sequences for Apoe genotyping: reverse 1: 5′-TGTGACTTGGGAGCTCTGCAGC-3′ | Integrated DNA Technologies | N/A |
| Primer sequences for Apoe genotyping: reverse 2: 5′-GCCGCCCCGACTGCATCT-3’ | Integrated DNA Technologies | N/A |
| Primer sequences for qPCR, see Table S2 | Integrated DNA Technologies | N/A |
| Recombinant DNA | ||
| pAdDeltaF6 | Jiandie Lin’s lab, University of Michigan; Guo et al., 2017 | N/A |
| pAAV2/8 | Jiandie Lin’s lab, University of Michigan; Guo et al., 2017 | N/A |
| pAAV-TBG-GFP | Jiandie Lin’s lab, University of Michigan; Guo et al., 2017 | N/A |
| pAAV-TBG-MCS | Jiandie Lin’s lab, University of Michigan; Guo et al., 2017 | N/A |
| AGXT Human Tagged ORF Clone | Origene | CAT# RG212899 |
| Software and Algorithms | ||
| ImageJ | National Institutes of Health | RRID:SCR_003070 https://imagej.nih.gov/ij/download.html |
| GraphPad Prism | GraphPad Software | Version 8.0 RRID:SCR_002798 https://www.graphpad.com/scientific-software/prism/ |
| R statistics | Hosted by Vienna, University of Economics and Business | http://www.R-project.org/. |
| RStudio | RStudio Team (2020). | http://www.rstudio.com/.RRID:SCR_000432 |
| IBM SPSS software | IBM Corporation | Version 23.0; RRID:SCR_019096 https://www.ibm.com/analytics/spss-statistics-software |
| FastQC | Babraham Bioinformatics | Version 0.11.8 RRID:SCR_014583 https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ |
| Trimmomatic | Bolger et al., 2014 | Version 0.35 RRID:SCR_011848 http://www.usadellab.org/cms/?page=trimmomatic |
| HISAT2 | Kim et al., 2015 | Version 2.1.0.13; RRID:SCR_015530 http://daehwankimlab.github.io/hisat2/download/ |
| HTSeq | Anders et al., 2015 | Version 0.6.0; RRID:SCR_005514 https://htseq.readthedocs.io/en/master/install.html |
| Analyst software | Applied Biosystems | Version 1.6.2; RRID:SCR_015785 https://sciex.com/products/software/analyst-software |
| LI-COR Image studio | LI-COR Biosciences | Version 2.1; RRID:SCR_015795 https://www.licor.com/bio/image-studio-lite/download |
| SPOT Basic software | SPOT imaging | RRID:SCR_014313 https://www.spotimaging.com/software/spot-basic/ |
| Other | ||
| Mouse standard diet | LabDiet | Cat# 5L0D |
| Mouse Western diet | Envigo | Cat# TD.88137 |
| Mouse Western diet supplemented with hydroxy-L-proline (HLP) | Envigo | CAT# TD.190842 |
| Dulbecco’s Modified Eagle Medium | Gibco | Cat# 11965092 |
| Iscove’s Modified Dulbecco’s Media | Gibco | Cat# 12440053 |
| Agilent Poroshell 120 EC-C18 column | Agilent Technologies | Cat# 699775–902 |
| Superose 6 Increase 10/300 GL columns | Sigma-Aldrich | CAT# GE29-0915-96 |