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Characterization of Gene Expression Phenotype in Amyotrophic Lateral Sclerosis Monocytes

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Characterization of Gene Expression Phenotype in Amyotrophic Lateral Sclerosis Monocytes Supplementary Online Content Zhao W, Beers DR, Hooten KG, et al. Characterization of Gene Expression Phenotype in Amyotrophic Lateral Sclerosis Monocytes. JAMA Neurol. Published online April 24, 2017. doi:10.1001/jamaneurol.2017.0357. eFigure 1. Principle Component Analysis (PAC) Indicates That Positive Selection Failed to Distinguish ALS and Control Monocyte Samples While Negative Selected ALS Monocytes Were Distinguishable From Control Monocytes. eFigure 2. Venn Diagram of Differentially Expressed Genes (DEGs) in Monocytes From ALS Slow and Fast Patients eFigure 3. IL-8 Protein Levels in Sera of ALS Patients and Healthy Controls. eTable 1. DEGs of Monocytes Isolated From Total ALS Patients (vs Control) eTable 2. Disease Progression of ALS Patients for RNA-seq Study Based on a Cutoff of 1.5 AALS Points/Month or a Cutoff of 1.0 ALS FRS Points/Month eTable 3. 65 DEGs Solely Found in Monocytes From Slowly Progressing ALS Patients (vs Control) eTable 4. 237 DEGs Solely Found in Monocytes From Rapidly Progressing ALS Patients (vs Control) eTable 5. 43 DEGs Expressed in Monocytes of Both Slow and Fast Groups (vs Control) This supplementary material has been provided by the authors to give readers additional information about their work. © 2017 American Medical Association. All rights reserved. Downloaded From: https://jamanetwork.com/ on 09/27/2021 eFigure 1. Principle component analysis (PAC) indicates that positive selection failed to distinguish ALS and control monocyte samples while negative selected ALS monocytes were distinguishable from control monocytes. Monocytes by CD14+ monocytes by negative selection positive selection ALS monocytes by negative selection Control monocytes by negative selection ALS CD14+ monocytes by positive selection Control CD14+ monocytes by positive selection PAC represents the distribution of RNA expression data (FPKM) from positively selected CD14+ monocytes and Pan monocytes by negative selection. RNA expression data from positively selected CD14+ monocytes clustered together with no variation observed between ALS and control samples (purple circle). Significant differences were observed between ALS pan monocyte samples and controls (red circle). © 2017 American Medical Association. All rights reserved. Downloaded From: https://jamanetwork.com/ on 09/27/2021 eFigure 2. Venn diagram of differentially expressed genes (DEGs) in monocytes from ALS slow (n=13) and fast patients (n=9). © 2017 American Medical Association. All rights reserved. Downloaded From: https://jamanetwork.com/ on 09/27/2021 eFigure 3. IL-8 protein levels in sera of ALS patients and healthy controls. A B IL-8 protein in serum 50 40 30 pg/ml 20 10 0 NC ALS IL-8 protein in serum 80 *# 60 pg/ml 40 20 0 NC ALS SLOW ALS FAST A: There was a trend for increased IL-8 protein in sera of all ALS patients (n=66) comparing with healthy controls (NC, n=32). B: The serum IL-8 levels were higher in rapidly progressing patients (ALS fast, n=36) than in slowly progressing ALS patients (n=30) or healthy controls (NC, n=32). * p<0.05 vs. NC; # p<0.05 vs. ALS slow. © 2017 American Medical Association. All rights reserved. Downloaded From: https://jamanetwork.com/ on 09/27/2021 eTable 1. DEGs of monocytes isolated from total ALS patients (vs. control) TransID Gen log2 p FDR TransID Gene log2 p F e Fold val Name Fold valu D Nam Chan ue Chan e R e ge ge NR_0460 ADI 1.367 0.0 0.16 NM_005304_chr FFAR3 1.533 0.00 0. 83_chr1 POR 02 19 1 1 1 4 NM_001 ADI 1.363 0.0 0.15 NM_001145776 FKBP5 3.97 0 0. 290629_ POR 02 _chr6 0 chr1 1 4 NM_001 ALC 1.847 0.0 0.16 NM_001160030 FLT1 1.858 0.00 0. 243283_ AM 02 _chr13 2 1 chr3 9 NM_001 AMZ 1.299 0.0 0.25 NM_006732_chr FOSB 2.351 0 0. 289054_ 2 05 19 0 chr17 1 NM_001 ARE 3.36 0 0.06 NM_001114171 FOSB 1.724 0.00 0. 657_chr4 G _chr19 1 1 4 NM_001 ARF 7.65 0 0.03 NM_005438_chr FOSL1 2.248 0 0. 242856_ IP2 11 0 chr11 2 NM_001 ARH 5.844 0.0 0.2 NM_015714_chr G0S2 1.789 0.00 0. 256025_ GAP 03 1 1 1 chr10 22 5 NM_212 ARL 1.058 0.0 0.13 NR_073568_chr GHRLOS 6.733 0.00 0. 460_chr7 4A 01 3 1 1 1 NM_001 ATF 1.117 0.0 0.13 NM_004951_chr GPR183 1.588 0 0. 030287_ 3 01 13 0 chr1 3 NM_017 BAI 7.053 0.0 0.16 NM_001001550 GRB10 2.316 0.00 0. 451_chr1 AP2 02 _chr7 4 2 7 1 NM_001 BAS 1.088 0.0 0.22 NM_001191013 GSTO2 5.387 0.00 0. 271606_ P1 04 _chr10 1 1 chr5 4 NR_0283 BRE 1.493 0.0 0.12 NM_001195422 GTPBP3 1.348 0.00 0. 08_chr2 -AS1 01 _chr19 3 2 1 NM_001 C6or 4.164 0.0 0.11 NM_001161587 GYS1 3.043 0.00 0. 287397_ f1 01 _chr19 4 2 chr6 2 NM_001 CAL 1.231 0.0 0.21 NM_004893_chr H2AFY 1.266 0 0. 199672_ U 04 5 0 chr7 7 NM_033 CCD 3.952 0.0 0.12 NM_001945_chr HBEGF 1.824 0 0. 626_chr C12 01 5 0 X 0 3 NM_005 CCI 1.377 0.0 0.15 NM_177551_chr HCAR2 1.056 0.00 0. 893_chr9 N 01 12 1 1 2 NM_020 CD2 1.941 0.0 0.15 NR_045406_chr HIF1A- 1.547 0.00 0. 404_chr1 48 01 14 AS2 5 2 © 2017 American Medical Association. All rights reserved. Downloaded From: https://jamanetwork.com/ on 09/27/2021 1 3 NM_001 CD8 1.411 0 0.07 NM_001199829 HORMA 5.805 0.00 0. 251901_ 3 _chr1 D1 4 2 chr6 1 NM_001 CD8 1.281 0.0 0.12 NR_038366_chr HOTAIR 1.749 0 0. 040280_ 3 01 7 M1 0 chr6 4 NM_003 CH2 3.506 0.0 0.21 NM_001193322 IKBKE 1.088 0 0. 956_chr1 5H 04 _chr1 0 0 9 NM_000 CHR 3.191 0.0 0.12 NM_000572_chr IL10 1.859 0 0. 742_chr8 NA2 01 1 0 2 NM_001 CLI 1.024 0.0 0.24 NM_000576_chr IL1B 1.59 0 0. 287593_ C1 05 2 0 chr6 8 NM_001 COR 4.064 0.0 0.19 NM_000600_chr IL6 2.381 0.00 0. 276471_ O1C 03 7 1 1 chr12 4 NM_001 CXC 1.782 0 0.03 NM_000584_chr IL8 1.866 0 0. 511_chr4 L1 4 0 3 NM_002 CXC 1.792 0 0.04 NM_176786_chr IL9R 2.224 0.00 0. 089_chr4 L2 X 2 1 5 NM_002 CXC 1.375 0.0 0.19 NM_001199799 ILDR1 6.072 0.00 0. 090_chr4 L3 03 _chr3 5 2 4 NM_001 DIS 6.912 0.0 0.23 NM_001145000 ITGAV 1.451 0.00 0. 164541_ C1 05 _chr2 5 2 chr1 3 NM_004 DUS 1.224 0.0 0.24 NM_001287440 JADE1 1.043 0.00 0. 418_chr2 P2 05 _chr4 2 1 8 NM_001 EGR 1.848 0.0 0.21 NR_047655_chr KANSL3 2.271 0.00 0. 199881_ 3 04 2 1 1 chr8 1 NM_004 EGR 1.844 0.0 0.11 NM_001199866 KIF16B 1.01 0.00 0. 430_chr8 3 01 _chr20 2 1 7 NM_001 EGR 1.748 0.0 0.25 NM_181986_chr LILRA5 2.251 0 0. 199880_ 3 05 19 0 chr8 8 NM_183 EIF5 1.026 0 0.03 NR_047524_chr LINC011 8.096 0 0. 004_chr1 1 28 0 4 7 NM_001 EMP 1.227 0.0 0.18 NR_024409_chr LOC1001 4.838 0.00 0. 423_chr1 1 02 3 28164 2 1 2 8 NM_001 ERE 1.857 0 0.03 NM_012323_chr MAFF 1.977 0.00 0. 432_chr4 G 22 3 2 NM_001 ETF 2.078 0.0 0.19 NM_001161573 MAFF 1.917 0.00 0. 282185_ 1 03 _chr22 1 1 chr5 1 © 2017 American Medical Association. All rights reserved. Downloaded From: https://jamanetwork.com/ on 09/27/2021 NM_005 ETV 1.118 0 0.08 NM_182763_chr MCL1 1.053 0 0. 240_chr1 3 1 0 3 NM_001 EXO 1.08 0.0 0.14 NM_001278215 MIER1 1.16 0.00 0. 013839_ C7 01 _chr1 4 2 chr17 1 NM_001 FAM 2.268 0.0 0.12 NR_040073_chr MIR181A 1.833 0.00 0. 184942_ 219 01 1 1HG 1 1 chr9 A 1 NM_001 FAM 6.209 0.0 0.2 NM_170739_chr MRPL11 1.089 0.00 0. 252270_ 69A 03 11 2 1 chr1 6 NM_133 FCA 3.499 0 0.04 NM_005746_chr NAMPT 1.118 0 0. 273_chr1 R 7 0 9 3 NM_133 FCA 2.175 0 0.05 NM_001283018 NAPB 2.833 0 0. 278_chr1 R _chr20 0 9 6 NM_133 FCA 2.012 0 0.01 NM_001146276 NCEH1 1.19 0.00 0. 272_chr1 R _chr3 3 1 9 9 NM_133 FCA 1.45 0 0.02 NM_001282211 NDRG2 2.792 0.00 0. 279_chr1 R _chr14 5 2 9 4 eTable 1. DEGs of monocytes isolated from total ALS patients (vs. control) (continued 1) TransID Gene log2 p FDR TransID Gene log2 p F Name Fold val Name Fold v D Change ue Cha al R nge u e NM_006 NEBL 21.422 0 0 NM_152386 SGPP2 1.09 0 0. 393_chr1 _chr2 2 0 0 9 NM_006 NEDD9 1.862 0 0.08 NM_001206 SLC16 2.44 0 0. 403_chr6 951_chr17 A3 2 0 7 NM_001 NEK6 1.063 0.0 0.23 NM_001206 SLC16 1.49 0. 0. 166167_ 05 952_chr17 A3 0 1 chr9 0 2 1 NM_001 NEK6 1.061 0.0 0.24 NM_001286 SLC2A 3.83 0 0.
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