Slide 1: RNA-seq data package
DATA REPORT RNA-seq data package Based on data published in Møllerhøj et al., 1 Example: RNA-seq data report. All data belong to Gubra.
Slide 2: Principal component analysis
Principal component analysis Sample variation within and between study groups 10 DIO-NASH Vehicle 8w Lanifibranor 8w DIO-NASH Vehicle 12w Semaglutide 8w 0 PC2 (16%) Semaglutide 12w -10 Lanifibranor 12w Lean-Chow Vehicle 12w -20 -30 -20 -10 0 10 20 PC1 (64%) Principal component analysis based on the
Slide 3: Differential gene expression analysis
Differential gene expression analysis Number of differentially expressed genes 10000 Number of regulated genes 7733 7907 8000 7190 6000 4000 3318 2000 1783 0 Number of differentially expressed genes for each study group compared to the corresponding DIO-NASH Vehicle at significance level padj < 0.05
Slide 4: Gene regulation overlaps
Gene regulation overlaps Overview of shared regulations Week 8 Week 12 Lanifibranor 8w Lean-Chow Vehicle 12w Semaglutide 8w 2616 Lanifibranor 12w Semaglutide 12w 525 3620 5171 2019 1299 972 110 176 3139 Number of differentially expressed genes regulated by either one or more study groups when compar
Slide 5: MASH: Genes of interest
MASH: Genes of interest Selected genes associated with NASH biology CD163 antigen CD68 antigen Collagen, type I, alpha 1 Collagen, type I, alpha 2 (Cd163) (Cd68) (Col1a1) (Col1a2) ### 40 12.5 6 20 10.0 30 # 4 20 *** ### ### 7.5 ### *** ### 10 *** *** ### 5.0 *** *** ### 2 10 2.5 ### ### 0 0 0 0.0 3-
Slide 6: Gubra curated gene panels
Gubra curated gene panels Regulation of disease-related genes Bile acid metabolism ECM organization ER stress Log2 Fold Change >3 Semaglutide 8w Lanifibranor 8w Lean-Chow Vehicle 12w 0 Semaglutide 12w Lanifibranor 12w <-3 Glucose metabolism Hepatocellular cell death Inflammation Semaglutide 8w Lanif
Slide 7: Unbiased pathway analysis
Unbiased pathway analysis Top-level pathways Semaglutide 8w Lanifibranor 8w Lean-Chow Vehicle 12w Semaglutide 12w Lanifibranor 12w Hemostasis Extracellular matrix organization Immune System Signal Transduction Metabolism Developmental Biology Metabolism of RNA Gene expression (Transcription) Cell-Ce
Slide 8: Unbiased pathway analysis
Unbiased pathway analysis Extracellular matrix organization sub-pathways Semaglutide 8w Lanifibranor 8w Lean-Chow Vehicle 12w Semaglutide 12w Lanifibranor 12w Collagen formation Degradation of the extracellular matrix Integrin cell surface interactions ECM proteoglycans Non-integrin membrane-ECM int
Slide 9: Gene expression data in GubraView
Gene expression data in GubraView We believe that the best way to fully exploit the potential of an RNA-seq dataset is to to enable our customers to explore and raise questions to the data. For this purpose, we have developed a panel of interactive functionalities in GubraView. An instructional vide
Slide 10: Appendix
Appendix 10 Example: RNA-seq data report. All data belong to Gubra.
Slide 11: Bile acid metabolism - 1/2
Bile acid metabolism Bile acid metabolism - 1/2 ATP-binding cassette, ATP-binding cassette, Cytochrome P450, family a DIO-NASH Vehicle 8w sub-family B (MDR/TAP), sub-family B (MDR/TAP), 7, subfamily a, memb. memb. polypeptid. a Semaglutide 8w (Abcb11) (Abcb4) (Cyp7a1) Lanifibranor 8w ### 60 ### a 20
Slide 12: Bile acid metabolism - 2/2
Bile acid metabolism Bile acid metabolism - 2/2 Solute carrier family 22 Solute carrier family 27 a DIO-NASH Vehicle 8w Solute carrier family (organic anion (fatty acid 51, beta subunit a Semaglutide 8w transporte. transporter),. (Slc51b) (Slc22a7) (Slc27a5) Lanifibranor 8w 20 ### ### a 600 ** 2 15
Slide 13: ECM organization - 1/4
ECM organization ECM organization - 1/4 a DIO-NASH Vehicle 8w Collagen, type I, alpha 1 Collagen, type I, alpha 2 Collagen, type V, alpha 1 (Col1a1) (Col1a2) (Col5a1) a Semaglutide 8w 12.5 4 Lanifibranor 8w a 20 10.0 3 7.5 ###### a DIO-NASH Vehicle 12w ### ### 2 *** *** 10 *** *** ### 5.0 *** *** ##
Slide 14: ECM organization - 2/4
ECM organization ECM organization - 2/4 a DIO-NASH Vehicle 8w Cathepsin K Fibulin 5 Laminin gamma 3 Semaglutide 8w (Ctsk) (Fbln5) (Lamc3) a a Lanifibranor 8w 6 2.5 2.0 2 a DIO-NASH Vehicle 12w 4 1.5 ## ** *** *** ### ### Lean-Chow Vehicle 12w 2 *** 1.0 1 a ### ### 0.5 0 0.0 0 a Semaglutide 12w a Lan
Slide 15: ECM organization - 3/4
ECM organization ECM organization - 3/4 a DIO-NASH Vehicle 8w Lysyl oxidase-like 4 Matrix metallopeptidase 2 Matrix metallopeptidase 9 Semaglutide 8w (Loxl4) (Mmp2) (Mmp9) a a Lanifibranor 8w 0.5 7.5 0.6 0.4 a DIO-NASH Vehicle 12w 0.3 ## 5.0 0.4 0.2 ** 2.5 *** ### 0.2 ** *** a Lean-Chow Vehicle 12w
Slide 16: ECM organization - 4/4
ECM organization ECM organization - 4/4 Tissue inhibitor of Tissue inhibitor of a DIO-NASH Vehicle 8w Versican metalloproteinase 1 metalloproteinase 2 (Vcan) (Timp1) (Timp2) a Semaglutide 8w 16 Lanifibranor 8w 0.15 6 a 12 # a DIO-NASH Vehicle 12w 0.10 4 8 *** ### * *** *** ## ### Lean-Chow Vehicle 1
Slide 17: ER stress
ER stress ER stress Activating transcription Activating transcription a DIO-NASH Vehicle 8w X-box binding protein 1 factor 4 factor 6 Semaglutide 8w (Xbp1) (Atf4) (Atf6) a a Lanifibranor 8w * ### 50 *** ### 16 75 40 ### 12 a DIO-NASH Vehicle 12w 50 *** ### 30 8 20 a Lean-Chow Vehicle 12w 25 10 4 0 0
Slide 18: Glucose metabolism - 1/3
Glucose metabolism Glucose metabolism - 1/3 a DIO-NASH Vehicle 8w Forkhead box O1 Glycogen synthase 2 Insulin receptor (Foxo1) (Gys2) (Insr) a Semaglutide 8w 10.0 160 * ### ### ### Lanifibranor 8w 15 a 7.5 120 * 10 ** ** a DIO-NASH Vehicle 12w 5.0 80 2.5 5 a Lean-Chow Vehicle 12w 40 0.0 0 0 a Semagl
Slide 19: Glucose metabolism - 2/3
Glucose metabolism Glucose metabolism - 2/3 a DIO-NASH Vehicle 8w Ketohexokinase Protein kinase C, iota Protein kinase C, zeta a Semaglutide 8w (Khk) (Prkci) (Prkcz) a Lanifibranor 8w 600 5 ### *** 3 # DIO-NASH Vehicle 12w 400 4 a 3 2 200 *** 2 a Lean-Chow Vehicle 12w ### 1 1 0 0 0 a Semaglutide 12w
Slide 20: Glucose metabolism - 3/3
Glucose metabolism Glucose metabolism - 3/3 Solute carrier family 2 Sterol regulatory a DIO-NASH Vehicle 8w (facilitated glucose element binding trans. transcription fa. a Semaglutide 8w (Slc2a4) (Srebf1) Lanifibranor 8w a level(RPKM) 6 Expression 150 DIO-NASH Vehicle 12w 4 # a 100 2 # 50 a Lean-Cho
Slide 21: Hepatocellular cell death - 1/2
Hepatocellular cell death Hepatocellular cell death - 1/2 a DIO-NASH Vehicle 8w Absent in melanoma 2 Caspase 1 Caspase 3 (Aim2) (Casp1) (Casp3) a Semaglutide 8w 6 ### Lanifibranor 8w ## a 1.0 10 *** ## 4 * ### a DIO-NASH Vehicle 12w ** ** * ### 0.5 ### 5 2 a Lean-Chow Vehicle 12w 0.0 0 0 a Semagluti
Slide 22: Hepatocellular cell death - 2/2
Hepatocellular cell death Hepatocellular cell death - 2/2 Receptor a DIO-NASH Vehicle 8w NLR family, pyrin domain NLR family, pyrin domain (TNFRSF)-interacting containing 1B containing 3 Semaglutide 8w (Nlrp1b) (Nlrp3) serine-threonine kin. a (Ripk1) Lanifibranor 8w 0.4 6 # a 0.75 * 0.3 # a DIO-NASH
Slide 23: Inflammation - 1/4
Inflammation Inflammation - 1/4 Adhesion G Amine oxidase, copper a DIO-NASH Vehicle 8w protein-coupled receptor CD14 antigen containing 3 Semaglutide 8w (Cd14) E1 (Aoc3) a (Adgre1) Lanifibranor 8w 10.0 a 0.08 7.5 20 0.06 a DIO-NASH Vehicle 12w *** ## # 5.0 0.04 Lean-Chow Vehicle 12w 2.5 ### 10 * ###
Slide 24: Inflammation - 2/4
Inflammation Inflammation - 2/4 a DIO-NASH Vehicle 8w CD163 antigen CD68 antigen CD86 antigen Semaglutide 8w (Cd163) (Cd68) (Cd86) a a Lanifibranor 8w ### 40 6 3 DIO-NASH Vehicle 12w 30 # ### a 4 20 *** ### 2 * ** *** ### ### a Lean-Chow Vehicle 12w 2 10 1 0 0 0 a Semaglutide 12w a Lanifibranor 12w
Slide 25: Inflammation - 3/4
Inflammation Inflammation - 3/4 Mitogen-activated a DIO-NASH Vehicle 8w Toll-like receptor 4 Tumor necrosis factor protein kinase 11 Semaglutide 8w (Tlr4) (Tnf) (Mapk11) a a Lanifibranor 8w 0.6 0.9 a DIO-NASH Vehicle 12w 1.0 0.5 ### 0.4 ** ** ### ## 0.6 ### a Lean-Chow Vehicle 12w 0.2 0.3 0.0 0.0 0.
Slide 26: Inflammation - 4/4
Inflammation Inflammation - 4/4 TNF receptor-associated TNF receptor-associated a DIO-NASH Vehicle 8w factor 2 factor 6 (Traf2) (Traf6) a Semaglutide 8w 4 4 ### Lanifibranor 8w ## ### a level(RPKM) Expression 3 *** ### 3 a DIO-NASH Vehicle 12w 2 2 1 1 a Lean-Chow Vehicle 12w 0 0 a Semaglutide 12w a
Slide 27: Lipid metabolism - 1/3
Lipid metabolism Lipid metabolism - 1/3 a DIO-NASH Vehicle 8w Apolipoprotein A-I Apolipoprotein A-V Apolipoprotein C-II Semaglutide 8w (Apoa1) (Apoa5) (Apoc2) a a Lanifibranor 8w ### 1000 2.0 # 7500 750 # 1.5 a DIO-NASH Vehicle 12w 5000 500 *** ### 1.0 Lean-Chow Vehicle 12w 2500 a 250 0.5 0 0 0.0 a
Slide 28: Lipid metabolism - 2/3
Lipid metabolism Lipid metabolism - 2/3 3-hydroxy-3-methylglutaryl 3-hydroxy-3-methylglutaryl a DIO-NASH Vehicle 8w Fatty acid synthase Coenzyme A reductase Coenzyme A synthase 1 Semaglutide 8w (Fasn) (Hmgcr) (Hmgcs1) a a Lanifibranor 8w *** ### 50 ### ### 150 DIO-NASH Vehicle 12w 200 40 a 30 100 **
Slide 29: Lipid metabolism - 3/3
Lipid metabolism Lipid metabolism - 3/3 Peroxisome proliferator Peroxisome proliferator a DIO-NASH Vehicle 8w Squalene epoxidase activated receptor gamma activator receptor delta (Sqle) (Pparg) (Ppard) a Semaglutide 8w ### 10.0 Lanifibranor 8w 30 1.5 ## a 7.5 ** DIO-NASH Vehicle 12w 20 ### *** ### #
Slide 30: Inflammation signaling
Inflammation signaling Inflammation signaling a DIO-NASH Vehicle 8w SMAD family member 2 SMAD family member 3 SMAD family member 4 (Smad2) (Smad3) (Smad4) a Semaglutide 8w 4 ### ### 5 15 # ### Lanifibranor 8w a level(RPKM) *** Expression 3 4 10 *** 3 a DIO-NASH Vehicle 12w 2 2 5 Lean-Chow Vehicle 12