Supplementary materials Comprehensive Biological Evaluation of Biomaterials Used in Spinal and Orthopedic Surgery

Piotr Komorowski 1,2,*, Małgorzata Siatkowska 1, Marta Kamińska 2, Witold Jakubowski 2, Marta Walczyńska 2,3, Magdalena Walkowiak‐Przybyło 2, Witold Szymański 2, Katarzyna Piersa 1, Patryk Wielowski 1, Paulina Sokołowska 1,4, Kamila Białkowska 1,5, Krzysztof Makowski 6, Marcin Elgalal 1,7, Agnieszka Kierzkowska 8, Lechosław Ciupik 8 and Bogdan Walkowiak 1,2,6

1 Molecular and Nanostructural Biophysics Laboratory, “Bionanopark” Ldt., Dubois 114/116,93‐465 Lodz, Poland; [email protected] (M.S.); [email protected] (K.P.); [email protected] (P.W.); [email protected] (P.S.); [email protected] (K.B.); [email protected] (M.E.); [email protected] (B.W.) 2 Division of Biophysics, Institute of Materials Science, Lodz University of Technology, Stefanowskiego 1/15, 90‐924 Lodz, Poland; [email protected] (M.K.); [email protected] (W.J.); [email protected] (M.W.); magdalena.walkowiak‐[email protected] (M.W.‐P.); [email protected] (W.S.) 3 Department of Medical Imaging Technique, Medical University of Lodz, Lindleya 8, 90‐419 Lodz, Poland 4 Department of Pharmacology and Toxicology, Medical University of Lodz, Zeligowskiego St. 7/9, 90‐752 Lodz, Poland 5 Department of General Biophysics, University of Lodz, Pomorska 141/143, 90, 90‐236 Lodz, Poland 6 Industrial Biotechnology Laboratory, “Bionanopark” Ldt., Dubois 114/116, 93‐465 Lodz, Poland; [email protected] 7 Department of Diagnostic Imaging, Radiation and Isotope Therapy, Medical University of Lodz, Pomorska 251, 92‐215 Lodz, Poland 8 “LfC” Ltd., Kozuchowska 41, 65‐364 Zielona Gora, Poland; [email protected] (A.K.); [email protected] (L.C.) * Correspondence: [email protected]

Results. Table S1 contains the whole list of with highly specifically and specifically altered expression, indication of up and down regulation, the corresponding /transcript name and a short description of protein/transcript function. Protein function was collected and compiled from https://www.ncbi.nlm.nih.gov/ and https://www.uniprot.org/ batabases. Metabolic pathways were collected and compiled from https://reactome.org/ and https://www.genecards.org/ databases.

Table S2. List of differentially expressed identified with LC‐MS/MS. Protein function collected and compiled from https://www.uniprot.org/ database. Metabolic pathways were collected and compiled from https://reactome.org/ and https://www.genecards.org/ databases.

Table S1. List of genes with highly specifically and specifically altered expression. Up (↑) and down (↓) regulation is indicated. Protein/Transcript function collected and compiled from https://www.ncbi.nlm.nih.gov/ and https://www.uniprot.org/ databases. Metabolic pathways were collected and compiled from https://reactome.org/ and https://www.genecards.org/ databases.

Gene Name Up/Down Protein/Transcript Sample Protein/Transcript Function Expected Metabolic Pathways () Regulation Name Highly Specifically Altered Expression A scaffold protein that is a component of the PIKfyve protein kinase AISI VAC14 complex which is responsible for the synthesis of phosphatidylinositol 3,5– Metabolism of lipids, Phospholipid ↑ VAC14 Homolog 316L bisphosphate, one of the seven phosphoinositides important for proper metabolism, PIP Metabolosm (synthesis) functioning of cellular membranes Pro‐MCH is proteolytically processed in the brain and in peripherial organs generating multiply protein products. Main neuropeptides are melanin‐ PMCH Pro‐MCH concentrating hormone (MCH), neuropeptide‐glutamic acid‐isoleucine Signal transduction (NEI), and neuropeptide‐glycine‐glutamic acid (NGE) that play diverse physiological functions, including energy homeostasis. A seven‐transmembrane protein that belongs to the family 1 of G‐protein G‐protein coupled coupled receptors, probably acting as a receptor for adrenomedullin ‐ a GPR182 Sympathetic nerve pathway receptor 182 vasodilator peptide hormone expressed by all tissues, widely distributed in the cardiovascular system. Cytochrome b‐c1 A component of ubiquinol‐cytochrome C reductase dimer complex. As a complex UQCRFS1 respiratory chain, this complex generates energy essential for ATP Metabolism, respiratory electron transport mitochondrial synthesis in mitochondria. subunit Rieske ↑ Members of sorting nexin family are important during progression and PEEK completion of mitosis. In case of any deficiencies in the expression of those Protein sorting nexin‐ proteins, the cytokinesis are inhibited and as a result the cell cannot finish Metabolism, respiratory electron transport SNX18 18, containing phox the division. SNX18 protein was also identified as a positive regulator of Autophagy domain autophagosome formation, that during macroautophagy fuses with . Expendable cytoplasmic constituents are then degraded and recycled within the autolysosome. GDNF (glial cell line‐derived neurotrophic factor family) that constitute GDNF family glycosylphosphatidylinositol (GPI)‐linked cell surface receptor for GDNF GFRA2 Metabolism, respiratory electron transport receptor alpha‐2 and NTN. Other important function of GDNF receptor alpha‐2 is activation of RET tyrosine kinase receptor. Uncharacterized LOC1027234 LOC102723429 No further knowledge is available. 29 situated on short arm of 16th Plays an important role in signal transduction pathway. It phosphorylates a threonine and a tyrosine residue in p38 MAP kinase during different kinds Immune system, MAO kinase activation and Dual specificity of cellular stress or in response to inflammatory cytokines. Changed Interleukin‐1 family signalling MAP2K6 mitogen‐activated activity of this class of proteins may result in higher activity of NF‐κB—a Cellular response system, oxidative stress protein kinase 6 transcription factor regulating balance between cell survival and cell death. induced senescence Dysregulation of its function may result in activation of genes involved in , regulation of transcription cancerous processes. This gene is upregulated in different kinds of cancer. RNA gene belonging lnc‐DYDC1‐ This gene was found to be overexpressed in patients suffered from one of Gene expression, regulation of RUNX1 to the long non‐ 4 subtype of acute lymphoblastic leukaemia expression and activity coding RNA class A_22_P0001 Not annotated No further knowledge is available. 7766 RNA Gene belonging lnc‐ to the long This gene expression was found to be characteristic for one of molecular Gene expression, regulation of RUNX1 ZC3H12D‐2 non‐coding RNA subtype of breast cancer (subtype HER2 + HR+) expression and activity class A_22_P0002 Not annotated No further knowledge is available. 2299 Uncharacterized gene LOC1019288 situated on short arm No further knowledge is available. 94 of 11th chromosome putative Signal transduction dehydrogenase/reduc DHRS4L1 Plays an oxidoreductase function but no further knowledge is available. Retinoic Acid biosynthesis pathway tase SDR family Signalling by Retinoic Acid (RA) member 4‐like 1 Pentaspan membrane glycoprotein. It has five transmembrane segments. It is mainly expressed in epithelial cells. It binds cholesterol and plays a pivotal role in organization of membrane microdomains, such as Prominin 2 membrane protrusions essential in diverse biological processes like cell PROM2 a member of migration and adhesion, wound healing or sensing external environment. prominin family It inhibits caveolae formation due to inhibition of CDC42 (involved in the organization of the actin cytoskeleton and endocytosis). Together with overexpression of prominin‐2, larger number of membrane protrusions was observed as well as changes in PM organization. Participate in assembly of translocase membrane complex responsible for passing of proteins into mitochondrial compartments. Large part of Translocase of outer proteins needed for proper mitochondria function is encoded by nucleus of TOMM20L ↓ mitochondrial the cell thus those proteins must be transported through mitochondrial membrane 20 like membrane to the intermembrane space. Mitochondrial membrane is impermeable for molecules larger than 5 kDa, thus proper functioning of TOM complex is crucial for mitochondria. RNA gene, belonging XLOC_l2_00 to the long non‐ No further knowledge is available. 8203 coding RNA class. Belongs to the group of scaffold proteins mediating the activation of JNK C‐Jun‐N‐terminal signaling pathway that controls different cellular processes like kinase‐interacting proliferation or apoptosis.

SPAG9 protein 4 It was shown that overexpression of SPAG9 gene is present in different Developmental biology, Myogenesis ↑ (other name: sperm kinds of cancer including lung, ovarian, breast and gastric cancer. The

associated antigen 9) protein product probably influence tumor growth and development however up to now, its exact role in this process is still obscure. A fusion protein that contains sequences identical with proline rich 5, renal Signal transduction by Rho GTPases PRR5‐ PRR5‐ARHGAP8 (PRR5) and Rho GTPase activating protein 8 (ARHGAP8) genes’ products. Gene expression, ARHGAP8 readthrough Resulting protein participates in signal transduction but its exact role is still Constitutive signaling in diseases unknown. ELI It is associated with neurodegeneration and may participate in host Stimulator of response to infections. It was shown that this protein may influence SCRG1 chondrogenesis 1 mesenchymal stem cells differentiation during bone regeneration by interacting with bone marrow stromal cell antigen 1 It release the from proteins designated to be transported to Ubiquitin specific USP14 proteasome. It regulates the function of proteasome and have a pivotal role Metabolism of proteins, Deubiquitinination ↓ peptidase 14 in the development of human carcinoma. The protein participate in acrosin binding—a major proteolytic of POM121 and ZP3 mammalian spermatozoa, present in acrosome. This protein functions as a POMZP3 fusion protein positive regulator of , thus influencing the process of fertilization. RNA gene affiliated lnc‐ Immune system costimulation by CD28 family ↑ with long non‐coding Tumor Necrosis Factor Superfamily Member TNFRSF14‐2 and TNFs bind their physiological receptors RNA class A_22_P0000 Not annotated No further knowledge is available. ELI‐ 1871 EBT Uncharacterized gene ↓ LOC1005070 situated on a long No further knowledge is available. 53 arm of 4th chromosome Specifically Altered Expression Transport of small molecules Iron uptake and

It is responsible for heme metabolism. It cleaves the heme ring to form transport HMOX1 Heme oxygenase 1 ↑ biliverdin, that is subsequently converted to bilirubin. Immune system interleukin 4 and 13 signalling

Protein localization AISI An cytosolic enzyme participating in pentose phosphate pathway, and Glucose‐6‐phosphate 316L G6PD responsible for NADPH production. Proper level of NADPH, an electron Metabolism, pentose phosphate pathway dehydrogenase donor is important during oxidative response of the cell snRNA, U6atac small Belongs to Lsm class of snRNA. snRNA function as a ribozymes during RNU6ATAC nuclear alternative splicing in the nucleus Interferon induced A protein that inhibits expression of viral mRNA thus inhibiting initiation protein with of translation and replication during viral infection. This antiviral activity is Immune system, interferon alpha/beta IFIT1 tetratricopeptide characteristic against several types of viruses, including human papilloma signalling and antiviral signalling repeats 1 and hepatitis C viruses. Small nucleolar RNA, Participates in pseudouridylation of rRNA, a process that influence SNORA48 ↓ H/ACA box 48 ribosome functionality. Is associated with specified proteins and functions as a ribonucleoproteins Small nucleolar RNA, that have enzymatic activity towards rRNA, thus are crucial for such SNORA2B H/ACA box 2B processes like protein synthesis, mRNA splicing or maintaining genome integrity It is acting as a receptor for brain injury‐derived neurotrophic peptide Transmembrane (BINP). The role of BINP is to support of neuron survival and protection of TMEM158 protein 158 hippocampal neurons in primary cultures from glutamate‐induced cell death. A protein that is a part of a large complex SNF/SWI and regulates the Signal transduction, activation of certain genes by rearrangement of chromatin structure. This Developmental biology, nervous system Transcription SMARCA4 protein can play its function due to helicase and ATPase activity. What is development activator BRG1 more it can bind to BRCA1 and also influence the expression of Gene expression by RUNX1 tumorigenic protein CD44 Chromatin organization A protein belonging to the MMP family involved in various physiological processes ‐ e.g., tissue remodelling, embryonic development or in pathological conditions like arthritis and metastasis. It participates in Extracellular matrix organization, collagen ↑ Matrix PEEK MMP14 collagen degradation, and also in skeletal connective tissue modelling. It degradation, activation of matrix metallopeptidase 14 was established that this protein activates MMP2 protein and together they metalloproteinases are involved in formation of fibrovascular tissues. According to literature the activity of MMP2 is related to tumour invasion. It was shown that this protein plays a neuroprotective role and suppress Alzheimer Disease‐related neurotoxicity in vivo. It demonstrates an Humanin‐like 2 antiapoptotic activity of humanin in vitro—it inhibits the executive phase of MTRNR2L2 a peptide of 24 amino apoptosis by interaction with Bax protein (an apoptosis‐inducing protein) acids preventing its translocation from cytosol to mitochondria and thus ‐ suppressing cytochrome C release. RNA gene affiliated Differential expression (down‐regulation) of this long non‐coding RNA lnc‐MINA‐3 with long non‐coding was found in patients suffered from cirrhosis that ultimately can lead to Chromatin organization RNA class hepatocellular carcinoma development. RNA gene affiliated lnc‐RNF13‐2 with long non‐coding No further knowledge is available. Innate immune system RNA class Is present in and has a transferase activity that transfer sulfo group to glucosamine residue in heparan. Also plays role in Heparan sulfate– anticoagulant heparan sulfate biosynthesis and conversion. HS3ST1 glucosamine 3– Heparan sulfate is a linear polysaccharide that exhibit multiple biologic Metabolism, glycosaminoglycan metabolism sulfotransferase 1 activities. It may bind with variety of protein ligands and form a proteoglycan (HSPG) that participates in regulating various biological processes, e.g., angiogenesis, blood coagulation, metastasis. Metabolism of proteins, glycosylation ADAM A protein belonging to the ADAMTS family, having in its structure Extracellular matrix organisation metallopeptidase metalloproteinase domain, disintegrin‐like domain, and thrombospondin‐ ADAMTS1 Degradation, collagen synthesis and with thrombospondin type motif. Exhibit antiangiogenic activity, expressed during process of modification, type 1 motif 1 inflammation; is also involved in development of cancer cachexia. Disease (Peters‐plus syndrome) A part of membrane‐bound cytokine receptor complex. Acts as a signal transducer for IL6, LIF, OSM, CNTF, IL11, CTF1 and BSF3. Binding a Interleukin 6 signal IL6ST substrate causes homodimerization of IL6SST which in turn activate Janus Immune system interleukin 6 and 12 signalling transducer kinase, that phosphorylates tyrosine residues on Il6ST and finally activates STAT3 (transcription activator). It contains C (UGAUGA) and D (CUGA) box sequence motifs that are SNORD12C Small nucleolar RNA, highly conserved. The main function of snRNAs from box C/D family is to

C/D box 12C participate in process of RNA methylation. SNORD12C is predicted to play role during 2′ O‐ribose methylation of the ribosomal 28S RNA subunit. That is a non‐catalytic component of gamma secretase complex ↓ (endoprotease complex) responsible for cleavage of integral membrane Aph‐1 homolog A, proteins playing important role in Notch or Wnt signalling cascades. It APH1A gamma‐secretase Signal transduction by NOTCH1, 3, 4, participates also in APP (amyloid‐beta precursor protein) processing. It subunit was shown that APH‐1A gene polymorphism contribute to increased incidence of Alzheimer Disease. Small nucleolar RNA, snRNAs with H/ACA box were identified as factors participating in SNORA16A H/ACA box 16A, 134 pseudouridynylation of 18S and 28S rRNAs, influencing a ribosomal nucleotides long functional features. Small nucleolar RNA, ↑ SNORD105B 92 nucleotides long, Can acts as oncogene and is involved in development of gastric cancer. ELI C/D box 105B lnc‐RP1‐ Long non‐coding No further knowledge is available. Gene expression 177G6.2.1‐2 RNA TATA‐binding It belongs to a TET family of RNA‐binding proteins. It participates in the Gene expression regulation TAF15 ↓ protein‐associated process of gene transcription by polymerase II as a component of TFIID Diseases, infectious factor 2N complexes. Chromatin organization It was shown that downregulation of FOXD3‐AS1 in malignant glioma cells has an inhibitory effect on cell proliferation, migration and invasion. Upregulation of this RNA gene results in poorer prognosis and lower Non‐coding RNA: survival probability for glioma patients. It was stated that FOXD3‐AS1 has Developmental biology, transcriptional FOXD3‐AS1 FOXD3 antisense a tumorigenic property that may cause development of glioma. Another regulation of stem cells RNA 1 study demonstrated that this non‐coding RNA is highly expressed in breast cancer—and may serve as a prognostic biomarker for breast cancer patients. A_22_P0002 Not annotated No further knowledge is available. 0320 A protein present in mitochondria that catalyze the pyrophosphate hydrolysis to the inorganic phosphate. Impaired function of this hydrolase Inorganic can result in deregulation of mitochondrial membrane potential, affecting PPA2 Metabolism, phyrophosphate hydrolysis pyrophosphatase 2 proper function of whole mitochondrium. It is also essential for proper cell metabolism. Mutation in PPA2 gene is correlated with occurrence of mitochondrial diseases and cardiomyopathy. A protein that takes part in regulation of CDKN1A expression and other proteins involved in Wnt signal transduction pathways. In Wnt signaling NLE1 Notchless homolog 1 pathways signals are passed to the cell through cell surface receptors and are important for normal cell functioning, but also impaired activity of this pathway can contribute to cancer spreading. Metabolism of lipids estrogen, cholesterol synthesis Immune system, interleukin 3, 5 and GM‐CSF A mitochondrial inner‐membrane protein. It was demonstrated that this signaling protein plays a significant role in mitochondrial respiratory chain. Transmembrane Organelle biogenesis and maintenance TMEM65 ↑ Mutation in TMEM65 results in mitochondrial dysfunction and clinically is protein 65 Cell‐cell communication Nectin/Necl trans demonstrated by encephalomyopathy. This protein is also suspected for heterodimerization participating in maintaining mitochondrial DNA stability. Metabolism, complex I biogenesis and electron transport ELI‐ Transport of small molecules EBT A metalloprotease belonging to a /B subfamily, that catalyses proteolysis of C‐terminal amino acids. It plays a probable role in hyperacetylation and also is considered as a cancer related gene. Increased expression of CPA4 protein was found in cancer tissue derived from patients suffered from colorectal cancer. It was shown that the CPA4 ↓ Carboxypeptidase A4 presence of elevated level of this protein was corelated with poorer prognosis. In vivo studies confirmed tumorigenic function of this protein due to activation of STAT3 and ERK pathways (the first one act as a signal transducer and activator of transcription, the later ‐ is a mitogen activated protein kinase that regulates different cellular processes like autophagy, protein trafficking and integrity of genome). What is more, group of Sun et al. has observed that higher expression of CPA4 was a good prognostic parameter for prediction of hepatic metastasis, its progression and stage. A protein involved in activation of endothelial cells. It is localized in and may play role of transcription factor that regulates cardiac gene expression. It is also linked to the epithelial‐mesenchymal transition (EMT) during cancer development. It was shown that ANKRD1 is overexpressed in EGFR‐TKIs‐resistant non‐ Ankyrin repeat ANKRD1 small cell lung cancer (NSCLC; EGFR‐TKIs ‐ epidermal growth factor Metabolism, lipid metabolism domain 1 receptor tyrosine kinase inhibitors). ANKRD1 gene silencing caused decreased resistance of cancer cells towards therapeutic drugs—afatinib and osimertinib. Inhibition of ANKRD1 expression at mRNA or protein level can be a promising therapeutic target for EGFR‐mutant NSCLC patients.

Table S2. List of differentially expressed proteins identified with LC‐MS/MS. Protein function collected and compiled from https://www.uniprot.org/ database. Metabolic pathways were collected and compiled from https://reactome.org/ and https://www.genecards.org/ databases.

Number Protein Gene Isoelectric Spot Molecular of Sequence Expected Metabolic Name Full Protein Name Point Scores Protein Function (UniProt Database) No. Weight [kDa] Identified Coverage Pathways (Human) [pI] Peptides [%] Development, Chaperon mediated Tubulin alpha‐1B protein folding chain OS = Homo 1 TBA1B 50.1 4.8 474.3 10 27.9 Tubulin is the major constituent of Cytoskeleton sapiens GN = TUBA1B . It binds two moles of remodeling PE= 1 SV = 1 GTP, one at an exchangeable site on Ubiquitin‐Proteasomal the beta chain and one at a Pathway non‐exchangeable site on the alpha Cel cycle regulation Tubulin beta chain OS chain. Development 2 TBB5 = Homo sapiens GN = 49.6 4.6 920.7 19 37.6 Innate immune system TUBB PE = 1 SV = 2 Organelle biogenesis and maintenance Mitochondrial membrane ATP synthase (F1F0 ATP synthase or Complex V) produces ATP from ADP in the presence of a proton gradient across the membrane which is generated by electron transport complexes of the respiratory chain. F‐ Metabolosm, type ATPases consist of two structural respiratory electron ATP synthase subunit domains, F1—containing the transport beta, mitochondrial extramembraneous catalytic core, and Organelle biogenesis 3 ATPB OS = Homo sapiens 56.5 5.1 151.8 3 6.2 F0 ‐ containing the membrane proton and maintenance GN = ATP5B PE = 1 channel, linked together by a central Mitochondrial SV = 3 stalk and a peripheral stalk. During biogenesis, catalysis, ATP synthesis in the catalytic mitochondrial protein domain of F1 is coupled via a rotary import mechanism of the central stalk subunits to proton translocation. Subunits alpha and beta form the catalytic core in F1. Rotation of the central stalk against the surrounding alpha3beta3 subunits leads to hydrolysis of ATP in three separate catalytic sites on the beta subunits. May function as a chaperone that Metabolism of proteins, Protein disulfide‐ inhibits aggregation of misfolded Regulation of Insulin‐ isomerase A6 OS = proteins. Plays a role in platelet like Growth Factor PDIA6 48.1 4.8 114.6 3 9.3 Homo sapiens GN = aggregation and activation by agonists XBP1(S) activates PDIA6 PE = 1 SV = 1 such as convulxin, collagen and chaperone genes thrombin.

Protein folding Signaling, signal transduction, Actin, cytoplasmic 1 Actins are highly conserved proteins Vesicle mediated OS = Homo sapiens that are involved in various types of 4 ACTB 41.7 5.2 594.3 13 32.3 transport, Clathrin‐ GN = ACTB PE = 1 SV cell motility and are ubiquitously mediated endocytosis = 1 expressed in all eukaryotic cells. Developmental biology Cell‐cell communication Disease oncogenic signaling Required for the assembly and/or stability of the 40S ribosomal subunit. Viral mRNA translation Required for the processing of the 20S Influenza viral RNA 5 95.7 2 7.1 rRNA‐precursor to mature 18S rRNA transcription and in a late step of the maturation of 40S replication ribosomal subunits. Also functions as rRNA processing in the 40S ribosomal protein a cell surface receptor for laminin. nucleous and cytosol SA OS = Homo RSSA 32.8 4.6 Plays a role in cell adhesion to the sapiens GN = RPSA basement membrane and in the PE = 1 SV = 4 consequent activation of signaling transduction pathways. May play a 6 101.9 2 7.1 role in cell fate determination and tissue morphogenesis. Acts as a PPP1R16B‐dependent substrate of PPP1CA Implicated in mitochondrial protein 60 kDa heat shock import and macromolecular assembly. protein, mitochondrial May facilitate the correct folding of 7 CH60 OS = Homo sapiens 61.0 5.6 322.9 7 12.4 imported proteins. May also prevent Gene expression GN = HSPD1 PE = 1 misfolding and promote the refolding Protein localization SV = 2 and proper assembly of unfolded polypeptides generated under stress conditions in the mitochondrial matrix. One of the major pre‐mRNA‐binding proteins. Binds tenaciously to poly(C) sequences. Likely to play a role in the nuclear metabolism of hnRNAs, particularly for pre‐mRNAs that contain cytidine‐rich sequences. Can also bind poly(C) single‐stranded DNA. Plays an important role in Heterogeneous p53/TP53 response to DNA damage,

nuclear acting at the level of both transcription RNA metabolism ribonucleoprotein K activation and repression. When HNRPK 50.9 5.3 117.5 3 6.5 Disease infectious OS = Homo sapiens sumoylated, acts as a transcriptional disease GN = HNRNPK PE = 1 coactivator of p53/TP53, playing a role Protein metabolism SV = 1 in p21/CDKN1A and 14‐3‐3 sigma/SFN induction (By similarity). As far as transcription repression is concerned, acts by interacting with long intergenic RNA p21 (lincRNA‐p21), a non‐coding RNA induced by p53/TP53. This interaction is necessary for the induction of apoptosis, but not cell cycle arrest Molecular chaperone that promotes the maturation, structural maintenance and proper regulation of specific target proteins involved for instance in cell cycle control and signal Chaperone mediated Heat shock protein transduction. Undergoes a functional autophagy HSP 90‐beta OS = cycle that is linked to its ATPase Signal transduction HS90B Homo sapiens GN = 83.2 4.8 677.2 14 20.7 activity. This cycle probably induces Cellular response to HSP90AB1 PE = 1 SV = 8 conformational changes in the client external stimuli heat 4 proteins, thereby causing their stress activation. Interacts dynamically with Metabolism oxidation various co‐chaperones that modulate its substrate recognition, ATPase cycle and chaperone function. Heat shock protein Molecular chaperone that promotes

HS90A HSP 90‐alpha OS = 84.6 4.8 598.8 15 22.1 the maturation, structural Cell cycle Homo sapiens GN = maintenance and proper regulation of HSP90AA1 PE = 1 SV specific target proteins involved for Chaperone mediated = 5 instance in cell cycle control and signal autophagy transduction. Undergoes a functional Disease, signaling in cycle that is linked to its ATPase cancer activity. This cycle probably induces Drug resistance conformational changes in the client Signal transduction proteins, thereby causing their Iinnate immune system activation. Interacts dynamically with Metabolism of NO various co‐chaperones that modulate Influenza infection its substrate recognition, ATPase cycle Gene expression, gene and chaperone function. Binds silencing bacterial lipopolysaccharide (LPS) et Interleukin 4 and 13 mediates LPS‐induced inflammatory signalling response, including TNF secretion by Organelle biogenesis monocytes. and maintenance Immune system Metabolism of proteins Molecular chaperone that functions in chaperon activate, the processing and transport of regulation of insuli‐like secreted proteins. When associated Endoplasmin OS = GF with CNPY3, required for proper 9 ENPL Homo sapiens GN = 92.4 4.6 535.9 14 15.7 Immune system folding of Toll‐like receptors (By HSP90B1 PE = 1 SV = 1 interleukin 4 and 13 similarity). Functions in endoplasmic signaling reticulum associated degradation Vesicle mediated (ERAD). Has ATPase activity. transport

Heterogeneous nuclear ribonucleoprotein K Metabolism of RNA 10 HNRPK 50.9 5.3 81.8 1 1.9 The same as for spot No. 7 OS = Homo sapiens Disease infectious GN = HNRNPK PE = 1 Metabolism of proteins SV = 1 Serum albumin, the main protein of plasma, has a good binding capacity Metabolism of proteins, for water, Ca2+ , Na+, K+, fatty acids, regulation of insulin‐ Serum albumin OS = hormones, bilirubin and drugs. Its like GF 11 ALBU Homo sapiens GN = 69.3 5.9 212.3 4 7.1 main function is the regulation of the Metabolism of ALB PE = 1 SV = 2 colloidal osmotic pressure of blood. porophyrins, bile acid Major transporter in plasma, and salt typically binds about 80% of all Transport of small plasma zinc. molecules Vesicle mediated transport Hemostasis, platelet activation, signaling and activation 60S acidic ribosomal protein P0 OS = Homo Ribosomal protein P0 is the functional Gene expression, 12 RLA0 34.3 5.6 103.5 3 14.2 sapiens GN = RPLP0 equivalent of E.coli protein L10, transcription PE = 1 SV = 1 Metabolism of proteins L‐lactate dehydrogenase B This protein is involved in step 1 of the Metabolism, respiratory 13 LDHB chain OS = Homo 36.6 5.7 161.2 3 10.5 subpathway that synthesizes and electron transport sapiens GN = LDHB (S)‐lactate from pyruvate, m.in.. PE = 1 SV = 2 Ubiquitin‐protein hydrolase involved both in the processing of ubiquitin precursors and of ubiquitinated proteins. This enzyme is a thiol Ubiquitin carboxyl‐ that recognizes and terminal hydrolase hydrolyzes a peptide bond at the Metabolism of proteins, 14 UCHL1 isozyme L1 OS = 24.8 5.2 58.8 1 4.5 C‐terminal glycine of ubiquitin. Also deubiquitination Homo sapiens GN = binds to free monoubiquitin and may UCHL1 PE = 1 SV = 2 prevent its degradation in . The homodimer may have ATP‐independent ubiquitin ligase activity

Table S3. Expected metabolic pathways assigned to results obtained on the base of transcriptome and proteome analyses. The frequency of the metabolic pathway representation is given in brackets.

Expected Metabolic Pathways

Metabolic Transcriptome Proteome Pathway Number 1 Autophagy (3) 2 Cell–cell communication (1) 3 Cellular response (1) Autophagy (1) 4 Developmental biology (3) Cell—cell communication (1) 5 Disease (4) Cellular response (1) 6 Gene expression (3) Developmental biology (3) 7 Immune system (4) Disease (3) 8 Metabolism (14) Gene expression (7) 9 Organelle maintenance (3) Immune system (6) 10 Protein localization (1) Metabolism (11) 11 Signal transduction (3) Organelle maintenance (1) 12 Transport of small molecules (1) Protein localization (1) 13 Chaperon mediated processes (5) Signal transduction (5) 14 Cell cycle regulation (2) Transport of small molecules (2) 15 Cytoskeletal reorganization (1)

16 Drug resistance (1) Extracellular matrix organization (1) 17 Haemostasis (1) Chromatin organization (3) 18 Vesicle mediated transport (3)

19 Protein folding (1) 20 RNA processing (1) 21 Viral translocation (1)