Biomarkers of NAFLD progression an omics approach to an epidemic

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1 Biomarkers of NAFLD progression an omics approach to an epidemic D. Lee Gorden 1,2, David S. Myers 3, Pavlina T. Ivanova 3, Eoin Fahy 4, Mano R. Maurya 4, Shakti Gupta 4, Jun Min 4, Nathanael J. Spann 5, Jeffrey G. McDonald 6, Samuel L. Kelly 7, Jingjing Duan 7, M. Cameron Sullards 7, Thomas J. Leiker 8, Robert M. Barkley 8, Oswald Quehenberger 9,10, Aaron M. Armando 10, Stephen B. Milne 3, Thomas P. Mathews 3, Michelle D. Armstrong 3, Chijun Li 11, Willie V. Melvin 1, Ronald H. Clements 1, M. Kay Washington 12, Alisha M. Mendonsa 2, Joseph L. Witztum 9, Ziqiang Guan 11, Christopher K. Glass 5, Robert C. Murphy 8, Edward A. Dennis 10,13, Alfred H. Merrill Jr. 7, David W. Russell 6, Shankar Subramaniam 4,13*, H. Alex Brown 3,14* 1 Department of Surgery, Vanderbilt University Medical Center, Nashville, TN, USA. 2 Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, TN, USA. 3 Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN, USA. 4 Department of Bioengineering, School of Engineering, University of California, San Diego, La Jolla, CA, USA. 5 Department of Cellular and Molecular Medicine and Department of Medicine, University of California, San Diego, La Jolla, CA, USA. 6 Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA. 7 Schools of Biology, Chemistry, and Biochemistry, and the Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA. 8 Department of Pharmacology, University of Colorado at Denver, Aurora, CO, USA. 9 Department of Medicine, School of Medicine, University of California, San Diego, La Jolla, CA, USA. 10 Department of Pharmacology, School of Medicine, University of California, San Diego, La Jolla, CA, USA. 11 Department of Biochemistry, Duke University Medical Center, Durham, NC, USA. 12 Departments of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA. 13 Department of Chemistry & Biochemistry, School of Medicine, University of California, San Diego, La Jolla, CA, USA. 14 Department of Biochemistry and the Vanderbilt Institute of Chemical Biology, Vanderbilt University Medical Center, Nashville, TN, USA. *To whom correspondence should be addressed: alex.brown@vanderbilt.edu; shankar@ucsd.edu Running Title: In search for NASH biomarkers

2 SUPPLEMENTARY MATERIALS Supplementary Figures Fig. S1. Plasma analytes participating in LDA-based discrimination between steatosis and NASH in Figure 5. Fig. S2. Lipid related genes by Ensembl ID. Fig. S3. Liver citric acid cycle and glycolysis pathways analytes with P<0.05 across histological categories. Fig. S4. Transcripts for collagen genes (COL1A1, COL1A2, COL3A1, COL4A4) consistently showed upregulation with disease progression. Fig. S5. Transcripts for interleukin IL1 (A), transforming growth factor beta 1 (TGF 1) (B), chemokine (C-C motif) ligand 2 (CCL2) (C), chemokine (C-X-C motif) ligand 1 (CXCL1) (D) and matrix metalloproteinase 9 (MMP9) (E) consistently showed upregulation with disease progression. MMP14 (F) also showed substantial upregulation between cirrhosis and other disease stages. Fig. S6. Comparison of log2 (fold-expression) levels between progressive disease states (columns: steatosis/normal; NASH/steatosis; cirrhosis/nash) for matrix metalloproteinase (MMP) related genes curated from the MMP module in WikiPathways. Fig. S7. LDA2 on plasma lipid data to classify NASH vs. steatosis samples. Supplementary Tables Table S1. Average lipid concentrations by class.

3 Table S2. Lipid metabolites with correlation coefficient r such that r >0.4 against transcripts for collagen genes when all normal, steatotic, and NASH patients are considered. Table S3. Single nucleotide polymorphisms with P<0.001 for steatosis vs.nash, assessed using PLINK. Table S4. Single nucleotide polymorphisms with P< for normal vs. cirrhosis, assessed using PLINK.

4 A B C D E F G H

5 I J K L M N O P

6 Q R S T Figure S1. Plasma analytes participating in LDA-based discrimination between steatosis and NASH in Figure 5. (A) PC(32:0), (B) PC(36:0e), (C) PC(36:1e), (D) PC(36:2e), (E) PE(36:3), (F) PI(32:1), (G) LPI(18:0), (H) LPI(20:4), (I) CE(22:6), (J) FA(20:2), (K) dolichol- 20, (L) 24,25- epoxycholesterol, (M) C14DH Cer, (N) C26:1DH HexCer, (O) C24:1DH deoxycer, (P) C26DH deoxycer, (Q) sphingosine, (R) F16BP, (S) phosphoglyceric acid- PGA, (T) adenosine monophosphate- AMP.

7 Figure S2. Lipid related genes by Ensembl ID.

8 A B C D E F Figure S3. Liver citric acid cycle and glycolysis pathways analytes with P<0.05 across histological categories. (A) Malate, (B) succinate, (C) citrate, (D) glutamate, (E) F16BP, (F) 6-phosphogluconate (6PG).

9 Figure S4. Transcripts for collagen genes (COL1A1, COL1A2, COL3A1, COL4A4) consistently showed upregulation with disease progression.

10 Figure S5: Transcripts for interleukin IL1β (A), transforming growth factor beta 1 (TGFβ1) (B), chemokine (C-C motif) ligand 2 (CCL2) (C), chemokine (C-X-C motif) ligand 1 (CXCL1) (D) and matrix metalloproteinase 9 (MMP9) (E) consistently showed upregulation with disease progression. MMP14 (F) also showed substantial upregulation between cirrhosis and other disease stages.

11 Figure S6. Comparison of log2 (fold-expression) levels between progressive disease states (columns: steatosis/normal; NASH/steatosis; cirrhosis/nash) for matrix metalloproteinase (MMP) related genes curated from the MMP module in WikiPathways. Differential expression of several MMP genes is present in the transition between steatosis and NASH, though the transcripts most upregulated in the transition to cirrhosis differs somewhat and includes several tissue inhibitor of metalloproteinease genes (TIMPs). When more than one transcript for a gene was detected, the one with the highest average abundance was used. Color key: values shaded red correspond to >1.5-fold differences, blue for <0.67-fold, and gray for transcripts not detected in the array. All genes had P<0.05 by ANOVA analysis except MMP1, MMP8, MMP15, MMP17, MMP21, and TCF20.

12 Figure S7. LDA2 on plasma lipid data to classify NASH vs. steatosis samples. Linear discriminant analysis is applied on top 30 plasma lipids (ANOVA-based) and then 20 lipids contributing most to the linear discriminant are identified (see Methods). Another LDA is applied on these 20 lipids. Good separation is achieved (see also Supplementary data file 5).

13 Average lipid concentrations by class. C: Cirrhosis, H: Steatohepatitis, S: Steatosis, N: Normal Source Lipid Class Subclass Average Units SEM Phenotype Liver CE Cholesteryl esters pmol/mg C Liver CE Cholesteryl esters pmol/mg H Liver CE Cholesteryl esters pmol/mg N Liver CE Cholesteryl esters pmol/mg S Liver CL Cardiolipins pmol/mg 7.20 C Liver CL Cardiolipins pmol/mg 8.43 H Liver CL Cardiolipins pmol/mg 8.06 N Liver CL Cardiolipins pmol/mg S Liver DG 1,2 DGs pmol/mg C Liver DG 1,2 DGs pmol/mg H Liver DG 1,2 DGs pmol/mg N Liver DG 1,2 DGs pmol/mg S Liver EM Eicosanoids 5.82 pmol/mg 0.98 C Liver EM Eicosanoids 6.08 pmol/mg 1.13 H Liver EM Eicosanoids 7.22 pmol/mg 0.99 N Liver EM Eicosanoids 6.32 pmol/mg 1.70 S Liver EM Fatty acids pmol/mg C Liver EM Fatty acids pmol/mg H Liver EM Fatty acids pmol/mg N Liver EM Fatty acids pmol/mg S Liver GP acyl PA pmol/mg C Liver GP acyl PA pmol/mg H Liver GP acyl PA pmol/mg N Liver GP acyl PA pmol/mg S Liver GP acyl PE pmol/mg C Liver GP acyl PE pmol/mg H Liver GP acyl PE pmol/mg N Liver GP acyl PE pmol/mg S Liver GP acyl PG pmol/mg 3.37 C Liver GP acyl PG pmol/mg 4.81 H Liver GP acyl PG pmol/mg 4.45 N Liver GP acyl PG pmol/mg 6.87 S Liver GP acyl PS pmol/mg C Liver GP acyl PS pmol/mg H Liver GP acyl PS pmol/mg N Liver GP acyl PS pmol/mg S Liver GP acyl PC pmol/mg C Liver GP acyl PC pmol/mg H Liver GP acyl PC pmol/mg N Liver GP acyl PC pmol/mg S Liver GP alkyl PE pmol/mg C Liver GP alkyl PE pmol/mg H Liver GP alkyl PE pmol/mg N Liver GP alkyl PE pmol/mg S Liver GP alkyl PC pmol/mg C Liver GP alkyl PC pmol/mg H Liver GP alkyl PC pmol/mg N Liver GP alkyl PC pmol/mg S Liver GP BMP pmol/mg C Liver GP BMP pmol/mg H Liver GP BMP pmol/mg N Liver GP BMP pmol/mg S Liver GP Lyso PC pmol/mg C Liver GP Lyso PC pmol/mg 9.16 H Liver GP Lyso PC pmol/mg N Liver GP Lyso PC pmol/mg S Liver GP Lyso PE pmol/mg C Liver GP Lyso PE pmol/mg H

14 Liver GP Lyso PE pmol/mg N Liver GP Lyso PE pmol/mg S Liver GP Lyso PG pmol/mg 5.20 C Liver GP Lyso PG pmol/mg H Liver GP Lyso PG pmol/mg N Liver GP Lyso PG pmol/mg S Liver GP Lyso PI pmol/mg 2.75 C Liver GP Lyso PI pmol/mg 5.98 H Liver GP Lyso PI pmol/mg 5.64 N Liver GP Lyso PI pmol/mg S Liver PR CoQs pmol/mg C Liver PR CoQs pmol/mg H Liver PR CoQs pmol/mg N Liver PR CoQs pmol/mg S Liver PR Dolichols pmol/mg 8.30 C Liver PR Dolichols pmol/mg H Liver PR Dolichols pmol/mg N Liver PR Dolichols pmol/mg S Liver SP Ceramides pmol/mg 8.83 C Liver SP Ceramides pmol/mg 8.96 H Liver SP Ceramides pmol/mg N Liver SP Ceramides pmol/mg S Liver SP DeoxyCeramides 2.47 pmol/mg 0.33 C Liver SP DeoxyCeramides 4.45 pmol/mg 0.47 H Liver SP DeoxyCeramides 2.69 pmol/mg 0.26 N Liver SP DeoxyCeramides 3.98 pmol/mg 0.92 S Liver SP Dihydro ceramides 2.87 pmol/mg 0.33 C Liver SP Dihydro ceramides 3.43 pmol/mg 0.28 H Liver SP Dihydro ceramides 2.98 pmol/mg 0.37 N Liver SP Dihydro ceramides 2.69 pmol/mg 0.27 S Liver SP Dihydro DeoxyCeramides 0.70 pmol/mg 0.11 C Liver SP Dihydro DeoxyCeramides 2.48 pmol/mg 0.39 H Liver SP Dihydro DeoxyCeramides 1.58 pmol/mg 0.27 N Liver SP Dihydro DeoxyCeramides 1.62 pmol/mg 0.37 S Liver SP Dihydro hexosylceramides 0.61 pmol/mg 0.11 C Liver SP Dihydro hexosylceramides 0.62 pmol/mg 0.15 H Liver SP Dihydro hexosylceramides 0.71 pmol/mg 0.19 N Liver SP Dihydro hexosylceramides 0.40 pmol/mg 0.08 S Liver SP Dihydro sphingomyelins pmol/mg 5.57 C Liver SP Dihydro sphingomyelins pmol/mg 4.89 H Liver SP Dihydro sphingomyelins pmol/mg 8.39 N Liver SP Dihydro sphingomyelins pmol/mg 6.25 S Liver SP GalactosylCeramides 0.67 pmol/mg 0.07 C Liver SP GalactosylCeramides 0.64 pmol/mg 0.06 H Liver SP GalactosylCeramides 0.72 pmol/mg 0.06 N Liver SP GalactosylCeramides 0.77 pmol/mg 0.09 S Liver SP GlcucosylCeramides pmol/mg 1.84 C Liver SP GlcucosylCeramides pmol/mg 2.73 H Liver SP GlcucosylCeramides pmol/mg 1.66 N Liver SP GlcucosylCeramides pmol/mg 1.77 S Liver SP Hexosyl ceramides pmol/mg 1.85 C Liver SP Hexosyl ceramides pmol/mg 2.73 H Liver SP Hexosyl ceramides pmol/mg 1.71 N Liver SP Hexosyl ceramides pmol/mg 1.77 S Liver SP Long chain bases pmol/mg 2.38 C Liver SP Long chain bases pmol/mg 6.31 H Liver SP Long chain bases pmol/mg 3.26 N Liver SP Long chain bases pmol/mg 6.67 S Liver SP Sphingomyelins pmol/mg C Liver SP Sphingomyelins pmol/mg H Liver SP Sphingomyelins pmol/mg N Liver SP Sphingomyelins pmol/mg S

15 Liver ST Sterols nmol/mg C Liver ST Sterols nmol/mg H Liver ST Sterols nmol/mg 8.32 N Liver ST Sterols nmol/mg S Liver TG TGs pmol/mg C Liver TG TGs pmol/mg H Liver TG TGs pmol/mg N Liver TG TGs pmol/mg S Plasma CE Cholesteryl esters nmol/ml C Plasma CE Cholesteryl esters nmol/ml H Plasma CE Cholesteryl esters nmol/ml N Plasma CE Cholesteryl esters nmol/ml S Plasma DG 1,2 DGs nmol/ml 3.55 C Plasma DG 1,2 DGs nmol/ml H Plasma DG 1,2 DGs nmol/ml 9.32 N Plasma DG 1,2 DGs nmol/ml S Plasma EM Eicosanoids pmol/ml C Plasma EM Eicosanoids pmol/ml H Plasma EM Eicosanoids pmol/ml N Plasma EM Eicosanoids pmol/ml S Plasma EM Fatty acids pmol/ml C Plasma EM Fatty acids pmol/ml H Plasma EM Fatty acids pmol/ml N Plasma EM Fatty acids pmol/ml S Plasma GP acyl PA pmol/ml C Plasma GP acyl PA pmol/ml H Plasma GP acyl PA pmol/ml N Plasma GP acyl PA pmol/ml S Plasma GP acyl PE pmol/ml C Plasma GP acyl PE pmol/ml H Plasma GP acyl PE pmol/ml N Plasma GP acyl PE pmol/ml S Plasma GP acyl PC pmol/ml C Plasma GP acyl PC pmol/ml H Plasma GP acyl PC pmol/ml N Plasma GP acyl PC pmol/ml S Plasma GP alkyl PE pmol/ml C Plasma GP alkyl PE pmol/ml H Plasma GP alkyl PE pmol/ml N Plasma GP alkyl PE pmol/ml S Plasma GP alkyl PC pmol/ml C Plasma GP alkyl PC pmol/ml H Plasma GP alkyl PC pmol/ml N Plasma GP alkyl PC pmol/ml S Plasma GP Lyso PC pmol/ml C Plasma GP Lyso PC pmol/ml H Plasma GP Lyso PC pmol/ml N Plasma GP Lyso PC pmol/ml S Plasma GP Lyso PE pmol/ml C Plasma GP Lyso PE pmol/ml H Plasma GP Lyso PE pmol/ml N Plasma GP Lyso PE pmol/ml S Plasma GP Lyso PI pmol/ml C Plasma GP Lyso PI pmol/ml H Plasma GP Lyso PI pmol/ml N Plasma GP Lyso PI pmol/ml S Plasma PR CoQs pmol/ml C Plasma PR CoQs pmol/ml H Plasma PR CoQs pmol/ml N Plasma PR CoQs pmol/ml S Plasma PR Dolichols pmol/ml 2.13 C Plasma PR Dolichols pmol/ml 1.78 H

16 Plasma PR Dolichols pmol/ml 1.61 N Plasma PR Dolichols pmol/ml 2.06 S Plasma SP Ceramides pmol/ml C Plasma SP Ceramides pmol/ml H Plasma SP Ceramides pmol/ml N Plasma SP Ceramides pmol/ml S Plasma SP DeoxyCeramides pmol/ml 9.18 C Plasma SP DeoxyCeramides pmol/ml H Plasma SP DeoxyCeramides pmol/ml N Plasma SP DeoxyCeramides pmol/ml S Plasma SP Dihydro ceramides pmol/ml 4.74 C Plasma SP Dihydro ceramides pmol/ml 8.28 H Plasma SP Dihydro ceramides pmol/ml 4.92 N Plasma SP Dihydro ceramides pmol/ml 6.54 S Plasma SP Dihydro DeoxyCeramides pmol/ml 3.94 C Plasma SP Dihydro DeoxyCeramides pmol/ml H Plasma SP Dihydro DeoxyCeramides pmol/ml N Plasma SP Dihydro DeoxyCeramides pmol/ml 7.54 S Plasma SP Dihydro hexosylceramides pmol/ml 3.22 C Plasma SP Dihydro hexosylceramides pmol/ml 1.96 H Plasma SP Dihydro hexosylceramides pmol/ml 1.45 N Plasma SP Dihydro hexosylceramides pmol/ml 1.69 S Plasma SP Dihydro sphingomyelins pmol/ml C Plasma SP Dihydro sphingomyelins pmol/ml H Plasma SP Dihydro sphingomyelins pmol/ml N Plasma SP Dihydro sphingomyelins pmol/ml S Plasma SP GalactosylCeramides pmol/ml 8.66 C Plasma SP GalactosylCeramides pmol/ml H Plasma SP GalactosylCeramides pmol/ml N Plasma SP GalactosylCeramides pmol/ml S Plasma SP GlcucosylCeramides pmol/ml C Plasma SP GlcucosylCeramides pmol/ml H Plasma SP GlcucosylCeramides pmol/ml N Plasma SP GlcucosylCeramides pmol/ml S Plasma SP Hexosyl ceramides pmol/ml C Plasma SP Hexosyl ceramides pmol/ml H Plasma SP Hexosyl ceramides pmol/ml N Plasma SP Hexosyl ceramides pmol/ml S Plasma SP Long chain bases pmol/ml C Plasma SP Long chain bases pmol/ml H Plasma SP Long chain bases pmol/ml N Plasma SP Long chain bases pmol/ml S Plasma SP Sphingomyelins pmol/ml C Plasma SP Sphingomyelins pmol/ml H Plasma SP Sphingomyelins pmol/ml N Plasma SP Sphingomyelins pmol/ml S Plasma ST Sterols pmol/ml C Plasma ST Sterols pmol/ml H Plasma ST Sterols pmol/ml N Plasma ST Sterols pmol/ml S Plasma TG TGs nmol/ml C Plasma TG TGs nmol/ml H Plasma TG TGs nmol/ml N Plasma TG TGs nmol/ml S Urine CE Cholesteryl esters pmol/ml C Urine CE Cholesteryl esters pmol/ml H Urine CE Cholesteryl esters pmol/ml N Urine CE Cholesteryl esters pmol/ml S Urine DG 1,2 DGs pmol/ml 2.33 C Urine DG 1,2 DGs pmol/ml H Urine DG 1,2 DGs pmol/ml N Urine DG 1,2 DGs pmol/ml S

17 Urine EM Eicosanoids pmol/ml C Urine EM Eicosanoids pmol/ml H Urine EM Eicosanoids pmol/ml N Urine EM Eicosanoids pmol/ml S Urine PR CoQs pmol/ml C Urine PR CoQs pmol/ml H Urine PR CoQs pmol/ml N Urine PR CoQs pmol/ml S Urine PR Dolichols pmol/ml 6.36 C Urine PR Dolichols pmol/ml 7.12 H Urine PR Dolichols pmol/ml 5.31 N Urine PR Dolichols pmol/ml S Urine SP Ceramides pmol/ml C Urine SP Ceramides pmol/ml 5.58 H Urine SP Ceramides pmol/ml N Urine SP Ceramides pmol/ml S Urine SP Deoxyceramides 0.57 pmol/ml 0.06 C Urine SP Deoxyceramides 0.46 pmol/ml 0.04 H Urine SP Deoxyceramides 0.52 pmol/ml 0.05 N Urine SP Deoxyceramides 0.64 pmol/ml 0.15 S Urine SP Dihydro ceramides 4.03 pmol/ml 0.48 C Urine SP Dihydro ceramides 4.75 pmol/ml 0.71 H Urine SP Dihydro ceramides 5.62 pmol/ml 0.69 N Urine SP Dihydro ceramides pmol/ml S Urine SP Dihydro deoxyceramides 0.67 pmol/ml 0.06 C Urine SP Dihydro deoxyceramides 0.81 pmol/ml 0.07 H Urine SP Dihydro deoxyceramides 0.92 pmol/ml 0.07 N Urine SP Dihydro deoxyceramides 1.02 pmol/ml 0.18 S Urine SP Dihydro hexosylceramides 2.07 pmol/ml 0.35 C Urine SP Dihydro hexosylceramides 1.95 pmol/ml 0.33 H Urine SP Dihydro hexosylceramides 2.40 pmol/ml 0.36 N Urine SP Dihydro hexosylceramides 2.55 pmol/ml 0.43 S Urine SP Dihydro sphingomyelins pmol/ml 8.95 C Urine SP Dihydro sphingomyelins pmol/ml 4.98 H Urine SP Dihydro sphingomyelins pmol/ml 7.53 N Urine SP Dihydro sphingomyelins pmol/ml S Urine SP Galactosylceramides 4.19 pmol/ml 1.51 C Urine SP Galactosylceramides 3.93 pmol/ml 0.57 H Urine SP Galactosylceramides 2.95 pmol/ml 0.52 N Urine SP Galactosylceramides 5.50 pmol/ml 2.35 S Urine SP Glcucosylceramides 5.38 pmol/ml 2.77 C Urine SP Glcucosylceramides 1.86 pmol/ml 0.21 H Urine SP Glcucosylceramides 2.19 pmol/ml 0.41 N Urine SP Glcucosylceramides 2.53 pmol/ml 0.69 S Urine SP Hexosyl ceramides pmol/ml C Urine SP Hexosyl ceramides pmol/ml 2.38 H Urine SP Hexosyl ceramides pmol/ml 4.22 N Urine SP Hexosyl ceramides pmol/ml 8.26 S Urine SP Long chain bases pmol/ml 3.28 C Urine SP Long chain bases pmol/ml 8.39 H Urine SP Long chain bases pmol/ml 5.73 N Urine SP Long chain bases pmol/ml S Urine SP Sphingomyelins pmol/ml C Urine SP Sphingomyelins pmol/ml H Urine SP Sphingomyelins pmol/ml N Urine SP Sphingomyelins pmol/ml S Urine TG TGs pmol/ml 6.55 C Urine TG TGs pmol/ml H Urine TG TGs pmol/ml N Urine TG TGs pmol/ml S

18 Table S2. Lipid metabolites with correlation coefficient r such that r >0.4 against transcripts for collagen genes when all normal, steatotic, and NASH patients are considered. When more than one transcript for a gene was detected, the one with the lowest p-value across categories was used. P=0.05 is reached for r > 0.2. crosscorrelation: COL1A1 COL1A2 COL3A1 COL4A1 COL4A2 COL4A4 COL4A6 COL5A1 COL5A2 COL5A3 COL6A2 COL6A3 COL6A6 COL11A1 COL11A2 6k PGE ,15 dk-,dh- PGF1a dhk PGF2a HETE HETrE oxoETE oxoETE ,15-EET FA(20:3 N3) FA(22:1) FA(22:2) CL (74:7) Dolichol Dolichol Dolichol Dolichol Cholestanol CE(18:3) CE(18:2) CE(18:1) CE(20:4) CE(20:3) CE(20:1) CE(22:6) CE(22:5) TAG(48:3) TAG(50:5) TAG(50:4) TAG(56:1) TAG(58:2) TAG(58:1) TAG(60:3) C22 Cer C24 Cer C16DH HexCer C16DH Sphingomyelin C26:1 GalCer PA(36:4) PA(40:6) PC(36:4) PC(38:5e) PE(32:1) PE(36:4p) PE(40:6) PI(38:4) PS(40:6)

19 Table S3. Single nucleotide polymorphisms with P<0.001 for steatosis vs. NASH, assessed using PLINK. SNP Gene P-value Odds ratio Alleles [WT/ mutation] Mutation information rs PIK3C2B 1.26E [A/G] Synonymous_N1198N rs ZNF E [A/G] Missense_T301A rs KATNAL2 3.37E [A/C] Silent,Missense_C254F exm PEAR1 4.90E [A/G] Missense_R885H rs ZNF E [A/G] Missense_R387H rs EFHB 7.81E [A/C] Missense_G99V Missense_R777Q,Missense_R917 exm VARS2 9.35E [A/G] Q,Missense_R947Q

20 Table S4. Single nucleotide polymorphisms with P< for normal vs. cirrhosis, assessed using PLINK. SNP Gene P Odds Ratio Alleles Mutation rs PNPLA3 1.77E [C/G] Missense_I148M exm NUAK1 2.39E [C/G] Missense_P543R exm8127 AJAP1 2.68E [A/G] Missense_G263R rs ARHGAP E [A/G] Synonymous_R85R rs9482 ATF6 3.27E [A/G] Synonymous_S632S rs SAMM E [A/G] Missense_D110G

Biomarkers of NAFLD progression an omics approach to an epidemic

Biomarkers of NAFLD progression an omics approach to an epidemic D. Lee Gorden 1,2, David S. Myers 3, Pavlina T. Ivanova 3, Eoin Fahy 4, Mano R. Maurya 4, Shakti Gupta 4, Jun Min 4, Nathanael J. Spann