Proteome Analysis of Human Perilymph using an Intraoperative Sampling Method
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1 Supporting Information Article Title Proteome Analysis of Human Perilymph using an Intraoperative Sampling Method Authors Heike A. Schmitt 1,3, Andreas Pich 2, Anke Schröder 2, Verena Scheper 1,3, Giorgio Lilli 1,3, Günter Reuter 1,3, Thomas Lenarz 1,3 Author Affiliations 1 Department of Otolaryngology, Hannover Medical School, Carl-Neuberg-Str. 1, Hannover, Germany 2 Core Facility Proteomics, Hannover Medical School, Hannover, Carl-Neuberg-Str. 1, Hannover, Germany 3 Cluster of Excellence of the German Research Foundation (DFG; Deutsche Forschungsgemeinschaft ) Hearing4all Table of Contents Figure S1: Protein intensity data of vestibular schwannoma perilymph samples depicted in a multi-scatter-plot by Pearson Table S1: Table of protein distribution in perilymph, cerebrospinal fluid and serum samples; XLSX Table S2: Table with Gene Ontology Annotation of perilymph specific proteins (Cellular Components) Table S3: Table of protein distribution in perilymph samples in different patient groups (children, adults and vestibular schwannoma); XLSX Table S4: Table of children-specific perilymph proteins unique identified in samples of two children
2 Figure S1 Figure S1: Protein intensity data of vestibular schwannoma perilymph samples depicted in a multi-scatter-plot by Pearson Compared was the protein distribution analyzed by label free quantification (LFQ) within the vestibular schwannoma group (n = 4) for measurement of the linear correlation between two variables. Each point shows the quantitative value of a detected protein by mass spectrometry in two samples of the vestibular schwannoma group. This diagram shows only a slight heterogeneity of the samples.
3 Table S2: Table with Gene Ontology Annotation of perilymph specific proteins (Cellular Components) Function Gene Name Count of protein extracellular exosome ADH5 AGA FAH LEG1 NID1 IVL CTSV MUC5B SULT2B1 EIF3B NAMPT PRELP NANS PPP2R4 PSMA2 TAGLN2 GPRC5B CAP1 MFAP4 RNASE4 GAA NAGK TTN SUMO3 BLVRA PTPRF ARF1 EVPL AKR1A1 THBS4 MNDA PTPRS TPM3 CSTB PGM1 HIST1H1B HSPA4 CKAP4 RPS9 DSG2 SORD ITGAM MFI2 BPI S100P IDH1 PYGB RAB10 FTL RARRES1 PRDX5 PSMB3 LAMB1 PLP2 COL6A3 LXN SNED1 GBA DNASE1 GRHPR CRYM DBI CDH11 ATP5B PRSS8 PSMD3 PSMD1 MYL12A CKMT1B PCBP1 GLUL HNRNPM ACLY HPRT1 CAND1 SERBP1 LAMC1 RPLP2 ANPEP NID2 CDC42 RPS18 RAB21 BPIFB2 LRP2 ANXA4 CALML3 SDCBP P4HB PEBP4 PDCD6IP MYH9 Number of proteins detected within the genome GO frequency within the dataset (%) (159 proteins) GO frequency within the genome (%) P- Value on E- 100
4 cytosol cell-cell adherens junction extracellular space extracellular matrix CMPK1 VSIG4 DNPH1 IL1RN ACAT2 C16orf89 NBN COPB2 PSMB3 PSMA2 MYH9 RPL6 RPS18 ITSN1 IDE ADH5 FTL GRHPR HMGCS1 FN3K GLUL PRDX5 ARF1 TPM3 TPM1 CDC42 ADH1B IDH1 CMPK1 BLVRA JAK1 CKM ACLY C16orf89 AKR1A1 FAH SDCBP CA3 NANS PDCD6IP SULT2B1 NAGK PSMD1 RPS9 HPRT1 PSMD3 BCAP31 MYL12A PGM1 EIF3B RPLP2 RPL29 TGFBR2 HSPA4 TTN NAMPT FBXO7 SORD CENPF SERBP1 RPL6 RPL29 IDH1 EVPL PKP3 SDCBP S100P PCBP1 TAGLN2 RAB10 MYH9 TRIM29 COL6A3 TCN1 SCGB2A1 ANPEP LEFTY1 LAMC1 THBS4 LAMB1 AKR1A1 CTSV SORD CEACAM16 SDCBP KRT87P PRELP AGA PRDX5 KRT33A MMP8 MUC5B IDE SERPINB2 PRSS8 IL1RN ITGAM CSTB GPRC5B LEG1 P4HB MFAP4 THBS4 HNRNPM LAMB1 COL2A on E on E on E on E- 20
5 focal adhesion nucleoplasm cytoplasm plasma COL6A3 MYH9 ZP2 ATP5B CKAP4 PRELP RPS18 NID1 NID2 LAMC1 FHL1 ZNF185 RAB10 RPS9 CAP1 RPS18 CDC42 ARF1 RPL6 MYH9 JAK1 PDCD6IP P4HB RAB21 RPLP2 LMNB1 EIF3B NAMPT HMGCS1 SET PCBP1 UCHL1 HNRNPM TRIM29 IDE PPP2R4 MDH2 RPS9 SUMO3 RPS18 NBN CENPF PSMA2 PSMB3 PSMD3 NOL9 PSMD1 ACLY CAND1 YME1L1 APRT HPRT1 PDCD6IP S100P PRDX5 NANS CMPK1 GLUL HMGCS1 EVPL CENPF CAND1 FHL1 IDE SERPINB2 UCHL1 IVL SULT2B1 ACAT2 PPP2R4 CSTB CRYM SDCBP APRT CDC42 RPL8 RPS9 TRIM29 ZNF185 PGM1 SET HIP1R YBX3 FBXO7 PYGB IDH1 PSMD3 EIF3B JAK1 ACLY PCBP1 SDR9C7 MYH9 SERBP1 GRHPR AFP PSMB3 ANXA4 TLR3 CKAP4 PTPRF SDCBP ZNF185 CDH11 IL1RN PLP1 DSG2 PKP3 LRP2 FHL on E on E on E on E- 15
6 nucleus peroxisomal matrix extracellular region basement TGFBR2 PRSS8 MDH2 ITGAM SERPINB2 HMGCS1 PLP2 ACLY SLC9C1 RAB10 ANXA4 ITSN1 IFITM2 ZP2 CDC42 GYPC PTPRS ARF1 ATP5B MYH9 CD207 FHL1 DNPH1 PRDX5 PPP2R4 NBN ANXA4 SDCBP GPRC5B YBX3 S100P DNASE1 IDE PTMS GLUL FBXO7 PURA CENPF HMGCS1 PSMD3 MYH9 SUMO3 ACAT2 ATP5B RPL6 CAND1 SET RPS18 RPS9 JAK1 PSMA2 PSMB3 CMPK1 LDB1 PSMD1 IDE PRDX5 IDH1 CRYM GRHPR TCN1 RNASE4 LAMC1 CTSV SERPINB2 THBS4 MMP8 P4HB ZP2 GPHA2 NID1 COL6A3 MFAP4 KLK10 PRSS8 NID2 DNASE1 COL2A1 TTN LAMB1 PRELP NID2 THBS4 LAMB1 LAMC1 NID1 PSMD1 CAND1 CKAP4 RPS9 CDC42 PSMD3 PCBP1 SERBP1 GAA ACLY RPS18 RPL6 TLR3 PDCD6IP LMNB1 RPL29 ATP5B YME1L1 BCAP31 PLP2 SDCBP on E on E on E on E on E- 08
7 proteasome complex lysosomal lumen cell surface nucleolus laminin-1 complex laminin-10 complex lysosomal muscle thin filament tropomyosin stress fiber cytosolic large ribosomal subunit integral component of plasma mitochondrion endoplasmic reticulum C16orf89 RPLP2 HNRNPM GYPC FTL SORD NOL9 MYH9 SORCS1 PYGB PSMD1 PSMA2 PSMD3 PSMB3 PRELP GBA GAA CTSV ANXA4 ATP5B ITGAM TLR3 GPRC5B IDE DSG2 MFI2 ACAT2 GPRC5B RPS9 CSTB NBN RPL8 NOL9 SDR9C7 4 4 on E on E on E on E- 06 LAMB1 LAMC1 2 2 on E- LAMB1 LAMC1 2 2 on E- TLR3 GAA LRP2 5 5 on E- GBA ANPEP TPM1 TPM3 2 2 on E- TPM1 TPM3 MYH9 RPL29 RPL6 RPLP2 HNRNPM TLR3 BPI BCAP31 MFI2 ANPEP PTPRF PTPRS GYPC ACAT2 YME1L1 PSMB3 IDE FBXO7 CKMT1B ATP5B MDH2 PRDX5 ELOVL4 BCAP31 THBS4 CKAP4 PLP2 SET P4HB ZP2 AGA 3 3 on E- 3 3 on E- 9 9 on E- 9 9 on E- 9 9 on E- Perilymph specific proteins were classified according to the Gene Ontology Annotation.
8 Table S4: Children-specific perilymph proteins unique identified in samples of two children Protein name Uniprot ID Identified in PL sample of patients with disease Actin-related protein 2/3 complex subunit 3 C9JZD1 CMV Actin-related protein 3 F5H3P5 CMV Annexin B4DDF9 CMV Glucose-6-phosphate 1-dehydrogenase E7EM57 CMV Glycogenin 1, isoform CRA_e G5E9W8 CMV Ig kappa chain V-II region FR P01615 CMV Myeloid cell nuclear differentiation antigen P41218 CMV Myosin light polypeptide 6 F8VPF3 CMV Proteasome subunit beta type-2 P49721 CMV Alpha-fetoprotein P02771 LVA CD9 antigen A6NNI4 LVA Deoxyribonuclease-1 P24855 LVA Glia-derived nexin (Isoform 2) P LVA Glycoprotein hormone alpha-2 Q96T91 LVA G-protein coupled receptor family C group 5 member B Q9NZH0 LVA HCG Q9Y628 LVA Interferon-induced trans protein 2 Q01629 LVA Kunitz-type protease inhibitor 1 H3BTQ8 LVA Left-right determination factor 1 O75610 LVA Lysosomal alpha-glucosidase P10253 LVA Melanotransferrin P08582 LVA Mesothelin H3BUX1 LVA Nidogen-2 (Isoform 2) Q LVA Syntenin-1 (Isoform 3) O060-3 LVA TGF-beta receptor type-2 P37173 LVA Versican core protein D6RGZ6 LVA Vesicular integral- protein VIP36 D6RIU4 LVA von Willebrand factor P04275 LVA V-set and immunoglobulin domain-containing protein 4 (Isoform 2) Q9Y279-2 Most of the children-specific proteins were identified in two children. Identified solely in the perilymph of a child suffering from cytomegalovirus (CMV) were 9 proteins. Further 20 proteins were identified in the two perilymph samples of a child (bilateral CI) suffering from large vestibular aqueduct (LVA). LVA
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