Local, intestinal biomarkers for early detection of colorectal cancer Master’s degree project in drug discovery and development

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Martina_Andersson_Supplementary

Local, intestinal biomarkers for early detection of colorectal cancer Master’s degree project in drug discovery and development

30 HP, Spring 2021

Uppsala University, Department of Pharmacy Martina Andersson

Supervisors: Alexandra Teleki & Maria Karlgren

S1. A list with search words used to find relevant information together with hits and date of the search.

S2. Summary information of the most important mutations during early stages of CRC.

S3. Table with some of the most used cell models to investigate CRC.

S4. Short information of some mouse models that is used to investigate CRC.

S5. Literature used for biomarker selection that is relevant in early stages of colorectal cancer (CRC)

S6. Significant upreglated biomarkers that has been reported in the literature. The biomarkers have a fold change over 1,5. All information found is gathered here.

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S1. Search Conducted

Search conducted with number results

Search done for mutations Nr. Results Date

Mutations early crc 911 2021-02-05

Colorectal cancer mutation early 3185 2021-02-05

Search done for cell models

((("colorectal cancer") NOT (review)) AND (biomarker)) AND (early) AND (protein) AND (cell model) 171 2021-02-03

colorectal cancer AND (early-stage) model cell 229 2021-02-03

("colorectal cancer" OR "colon cancer") cell model* ("early-stage" or "early detection") 334 2021-02-03 ("colorectal cancer" OR "colon cancer") cell model* ("early-stage" or "early detection") AND (biomarker) 137 2021-02-03

(colorectal cancer) AND (biomarkers) AND ("in vitro") AND (early) 190 2021-02-03

colorectal neoplasms ("cell line" OR "cell model*") early "in vitro" 305 2021-02-04 (((colorectal neoplasms[MeSH Major Topic]) AND (early[Title/Abstract])) AND (in vitro[Title/Abstract])) AND ("cell line"[Text

Word] OR "cell model"[Text Word]) 215 2021-02-04

((mutation) AND ("colorectal adenocarcinoma")) AND (early or "stage I") 47 2021-02-07

Search conducted with PubMed; biomarkers

(colorectal adenocarcinoma[MeSH]) AND ("stage I") 292 2021-02-06

colorectal cancer biomarker early proteomics in vitro 16 2021-02-14

colorectal cancer biomarker proteomic cell line early 36 2021-02-18

colorectal cancer proteomics 2009 2021-02-26

quantitativ proteomic sw480 28 2021-03-03

shotgun proteomic colorectal cancer 50 2021-03-03

Search done for mouse models

mouse model adenoma colorectal early 132 2021-02-22

mouse model colorectal cancer early 170 2021-02-25

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S2. Mutations

Mutations most relevant in early stages of CRC

Mutation Comments Reference

APC

Early driver genes being mutated in both adenomas and carcinomas. APC is followed by mutations in other genes including KRAS, TP53, PIK3CA and BRAF. Loss of APC does not nessecary lead to invasive cancer. APC leads to a hyperactivation of the WNT signalling pathway. APC has many functions that affect the progress to cancer cells, such as poliferation, migration, and chromosome instability. Considered an early detection marker because nearly 100% of individuals with the mutation will develop colon cancer in the future.

1; 2; 3; 4; 5; 6;

7 KRAS

Classified as early driver genes being mutated in both adenomas and carcinomas. More than 50% of patients with adenocarcinoma of the colon carry a mutant allele of KRAS genes. KRAS has been identified in colon cancers, adenomas and tumor-associated tissues, but also normal appearing mucosa. But presence of KRAS does have different results throuhout the literature. Some does state that it is important during early stages of CRC, but there are other data stating that it does not appear in early stage. The reason for the different reports are unclear, but there might be due to population difference.

1; 3; 5; 7; 8; 9;

10 TP53

Classified as early driver genes being mutated in both adenomas and carcinomas. The other path of sporadic CRC are hypermutated and show microsatellite instability (MSI) and it is often associated with wild-type TP53. The defects of tumor suppressor genes are pivor point of colorectal tumorigenesis. The TP53 gene plays an important function in either cell proliferation or trigger senescene and apoptotis.

1; 4; 6

7. Srivastava S, Verma M, Henson DE. Biomarkers for early detection of colon cancer. Clin Cancer Res. 2001 May;7(5):1118-26. PMID: 11350874.

8. Igder S, Mohammadiasl J, Mokarram P. Altered miR-21, miRNA-148a Expression in Relation to KRAS Mutation Status as Indicator of Adenoma-Carcinoma Transitional Pattern in Colorectal Adenoma and Carcinoma Lesions. Biochem Genet. 2019 Dec;57(6):767-780. doi: 10.1007/s10528-019-09918-0. Epub 2019 Apr 17. PMID: 30997628.

9. Nash GM, Gimbel M, Cohen AM, Zeng ZS, Ndubuisi MI, Nathanson DR, Ott J, Barany F, Paty PB. KRAS mutation and microsatellite instability: two genetic markers of early tumor development that influence the prognosis of colorectal cancer. Ann Surg Oncol. 2010 Feb;17(2):416-24. doi: 10.1245/s10434-009-0713-0. Epub 2009 Oct 8. PMID: 19813061; PMCID: PMC4380015.

10. Watson R, Liu TC, Ruzinova MB. High frequency of KRAS mutation in early onset colorectal adenocarcinoma: implications for pathogenesis. Hum Pathol. 2016 Oct;56:163-70. doi: 10.1016/j.humpath.2016.06.010. Epub 2016 Jun 23.

PMID: 27346571.

1. Wolff RK, Hoffman MD, Wolff EC, Herrick JS, Sakoda LC, Samowitz WS, Slattery ML. Mutation analysis of adenomas and carcinomas of the colon: Early and late drivers. Genes Chromosomes Cancer. 2018 Jul;57(7):366-376. doi:

10.1002/gcc.22539. Epub 2018 Apr 30. PMID: 29575536; PMCID: PMC5951744.

2. Sakai E, Fukuyo M, Matsusaka K, Ohata K, Doi N, Takane K, Matsuhashi N, Fukushima J, Nakajima A, Kaneda A. TP53 mutation at early stage of colorectal cancer progression from two types of laterally spreading tumors. Cancer Sci. 2016 Jun;107(6):820-7. doi: 10.1111/cas.12930. Epub 2016 Apr 27. PMID: 26991699; PMCID: PMC4968595.

3. Hadac JN, Leystra AA, Paul Olson TJ, Maher ME, Payne SN, Yueh AE, Schwartz AR, Albrecht DM, Clipson L, Pasch CA, Matkowskyj KA, Halberg RB, Deming DA. Colon Tumors with the Simultaneous Induction of Driver Mutations in APC, KRAS, and PIK3CA Still Progress through the Adenoma-to-carcinoma Sequence. Cancer Prev Res (Phila). 2015 Oct;8(10):952-61. doi: 10.1158/1940-6207.CAPR-15-0003. Epub 2015 Aug 14.

PMID: 26276752; PMCID: PMC4596777.

4. Müller MF, Ibrahim AE, Arends MJ. Molecular pathological classification of colorectal cancer. Virchows Arch. 2016 Aug;469(2):125-34. doi: 10.1007/s00428-016-1956-3. Epub 2016 Jun 20. PMID: 27325016; PMCID:

PMC4978761.

5. Gausachs M, Borras E, Chang K, Gonzalez S, Azuara D, Delgado Amador A, Lopez-Doriga A, San Lucas FA, Sanjuan X, Paules MJ, Taggart MW, Davies GE, Ehli EA, Fowler J, Moreno V, Pineda M, You YN, Lynch PM, Lazaro C, Navin NE, Scheet PA, Hawk ET, Capella G, Vilar E. Mutational Heterogeneity in APC and KRAS Arises at the Crypt Level and Leads to Polyclonality in Early Colorectal Tumorigenesis. Clin Cancer Res. 2017 Oct 1;23(19):5936-5947. doi:

10.1158/1078-0432.CCR-17-0821. Epub 2017 Jun 23. PMID: 28645942; PMCID: PMC5626604.

6. Intarajak T, Udomchaiprasertkul W, Bunyoo C, Yimnoon J, Soonklang K, Wiriyaukaradecha K, Lamlertthon W, Sricharunrat T, Chaiwiriyawong W, Siriphongpreeda B, Sutheeworapong S, Kusonmano K, Kittichotirat W, Thammarongtham

C, Jenjaroenpun P, Wongsurawat T, Nookaew I, Auewarakul C, Cheevadhanarak S. Genetic Aberration Analysis in Thai Colorectal Adenoma and Early-Stage Adenocarcinoma Patients by Whole-Exome Sequencing. Cancers (Basel). 2019 Jul

12;11(7):977. doi: 10.3390/cancers11070977. PMID: 31336886; PMCID: PMC6679221.

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S3. Cell models

Information about cell models (https://web.expasy.org and https://www.lgcstandards-atcc.org)

Sadanandam

class Name Molecular

phenotype Mutant gene Zygosity Gene sequence Protein sequence Disease Ethnicity Gender Age Morphology Tissue Culture properties

APC heterozygous c.4287_4296delAACCATGCCA p.Q1429fs*41

APC heterozygous c.790C>T p.Q264*

KRAS heterozygous c.35G>C p.G12A

TP53 homozygous c.476C>A p.A159D

APC homozygous c.4348C>T p.R1450*

BRAF heterozygous c.1799T>A p.V600E

PIK3R1 homozygous c.1_2175del2175 p.0?

TP53 homozygous c.712_725delTGTAACAGTTCCTG p.C238fs*21

APC homozygous c.4012C>T p.Gln1338Ter

KRAS homozygous c.35G>T p.Gly12Val

TP53 heterozygous c.818G>A p.Arg273His

TP53 heterozygous c.925C>T p.Pro309Ser

APC heterozygous c.2180G>T p.Arg727Met

APC heterozygous c.2979G>T p.Lys993Asn

APC heterozygous c.4248delC p.Ile1417Leufs*2

APC heterozygous c.6496C>T p.Arg2166Ter

B2M heterozygous c.68-1G>T Note=Splice acceptor mutation

B2M heterozygous c.90C>A p.Tyr30Ter

BRCA2 heterozygous c.3599_3600delGT (3827delGT) p.Cys1200Terfs BRCA2 heterozygous c.5350_5351delAA p.Asn1784Hisfs*7

KRAS heterozygous c.38G>A p.Gly13Asp

PIK3CA heterozygous c.1633G>A p.Glu545Lys PIK3CA heterozygous c.1645G>A p.Asp549Asn

TP53 heterozygous c.722C>T p.Ser241Phe

TP53 heterozygous c.1101-2A>C Note=Splice acceptor mutation

APC heterozygous c.1873C>T p.Q625*

APC heterozygous c.4348C>T p.R1450*

KRAS heterozygous c.34G>A p.G12S

TP53 heterozygous c.524G>A p.R175H

SMAD4 homozygous c.988G>T p.E330*

CTNNB1 heterozygous c.98C>A p.S33Y

EGFR heterozygous c.2155G>A p.G719S

FBXW7 heterozygous c.2001delG p.S668fs*39

ACVR2A heterozygous c.1310delA p.Lys437Argfs*5

BRAF heterozygous c.1799T>A p.Val600Glu

PIK3CA heterozygous c.3140A>G p.His1047Arg TGFBR2 heterozygous c.383delA p.Lys128Serfs*35 TGFBR2 heterozygous c.1355T>C p.Leu452Pro

KRAS c.35G>A) p.Gly12Asp

TP53 c.743G>A p.Arg248Gln

APC homozygous c.4012C>T p.Gln1338Ter

KRAS homozygous c.35G>T p.Gly12Val

TP53 heterozygous c.818G>A p.Arg273His

TP53 heterozygous c.925C>T p.Pro309Ser

APC homozygous c.4099C>T p.Gln1367Ter

CTNNB1 heterozygous c.734G>C p.Gly245Ala

SMAD4 homozygous c.1051G>C p.Asp351His

TP53 homozygous c.610G>T p.Glu204Ter

ACVR2A homozygous c.1310delA p.Lys437Argfs5 BRCA2 heterozygous c.8021dupA,c.8021_8022insA p.Ile2675Aspfs6

Colon, derived from metastatic site: lymph node

adherent

73 epithelial colon adherent

SW1417 MSS

Dukes' type C, grade III, colorectal

adenocarcinoma

caucasian female 53

SW1116 MSS

Dukes' type A, grade III, colorectal

adenocarcinoma

caucasian male

epithelial colon adherent

In fl am m at or y

HCT15 MSI Dukes' type C, Colon

adenocarcinoma male epithelial

T ran si t am p li fyi n g

SW48 MSI

Dukes' type C, grade IV colorectal

adenocarcinoma

caucasian female 82 epithelial

SW620 MSS Dukes' type C, Colon

adenocarcinoma caucasian male 51 epithelial

colon adherent

LS123 MSS

Dukes' type B, colorectal adenocarcinoma

caucasian female 65 epithelial colon adherent

colon adherent

epithelial colon adherent

CL-40 MSI Colon adenocarcinoma.

TNM stage 3 female N/A epithelial

RKO MSI carcionoma

colon adherent

epithelial colon

SW480 MSS

Dukes' type B, colorectal adenocarcinoma

caucasian male 50 epithelial colon

adherent

HCT116 MSI Colon carcinoma male 48 epithelial colon adherent

St em

adherent

Caco-2 MSS colorectal

adenocarcinoma caucasian male 72

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S3. Cell models

CDKN2A heterozygous c.68dupG,c.68_69insG p.Arg24Serfs20,p.G23fs CDKN2A heterozygous c.220delG p.Asp74fs21

CDKN2A heterozygous c.97delG p.Glu33Argfs20 EP300 heterozygous c.4408delA p.Met1470Cysfs22 EP300 heterozygous c.5099delA p.Asn1700Thrfs*9

KRAS heterozygous c.38G>A p.Gly13Asp

PIK3CA heterozygous c.3140A>G p.His1047Arg TGFBR2 homozygous c.383delA) p.Lys128Serfs*35

APC heterozygous c.2557G>T p.E853*

APC heterozygous c.4666_4667insA p.T1556fs*3

BRAF heterozygous c.1799T>A p.V600E

TP53 homozygous c.818G>A p.R273H

PIK3CA homozygous c.1345C>A p.P449T

SMAD4 homozygous c.931C>T p.Q311*

E n te roc yt e

HT115 MSS TP53 Heterozygous c.637C>T p.Arg213Ter Colon carcinoma epithelial colon

G ob le t

HT29 MSS Colorectal

adenocarcinoma caucasian female

HCT116 MSI Colon carcinoma male 48 epithelial colon adherent

St em

44 epithelial colon adherent

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S4. Mouse models

Some mouse models used to investigare CRC

Mouse model Comments Reference

APC

^-/+

Mice model for early disease biomarker discovery. Epigeneomic profiling of adenomas from APC min/+ mice has also been useful in identification of early biomarkers. Short lived for rapid studies. Tumors is mostly located in small rather than large intestine. APC mice rarely develops metastases.This is the classic mouse model where it is heterozygot for APC (homozygot is lethal in embryonic state). Develop about 30 small intestinal polyps and these only occasionally progress to invasive adenocarcinoma. No incidence of metastasis has been reported.

1; 2; 3; 4; 5

Apc

^+/Δ716

Cdx2

^+/−

Increased adenomas in the colon, reduced amount of polyps in the small intestine. 6

Apc1309/+ More colonic polyps than APC-/+ mice 4

APC

^15lox/+

Model with extended lifespan and that developed adenomas and adenocarcinomas in large intestine. Might be good to study the genetic alterations associated with the adenoma-carcinoma sequence

in the mouse. 3

Apc

^Min/+

; Smad3

^−/−

Reduced lifespan of 2 months due to rapid tumor development in the distal colon with mixed histology but no metastases 6

Catnb

^+/lox(ex3)

Krt1-19-Cre Early tumor development. Large amount of tumors, microadenomas in the colon. Short lifespan. 7

Fabpl-Cre; Apc

^15lox/þ

Extended lifespan compared with most APC-mutant models and does have a significant number of adenomas and adenocarcinomas in the large intestine. It is useful to study the genetic alterations associated with the adenoma-carcinoma sequence. These mice are highly predisposed to colon tumor development in gut epithelial cells. Whereas APC15lox/+ control littermates do not exhibit colonic aberrations. This model to be representative to early stages.

6; 8; 9

Long living APCmin/+ mice Some adenomas progress to adenocarcinomas 6

Tgfb1

^−/−

Rag2

^−/−

Rapid formation of adenomas and adenocarcinomas 6

7. Stastna M, Janeckova L, Hrckulak D, Kriz V, Korinek V. Human Colorectal Cancer from the Perspective of Mouse Models. Genes (Basel). 2019 Oct 11;10(10):788. doi: 10.3390/genes10100788. PMID: 31614493; PMCID: PMC6826908.

8. Robanus-Maandag EC, Koelink PJ, Breukel C, Salvatori DC, Jagmohan-Changur SC, Bosch CA, Verspaget HW, Devilee P, Fodde R, Smits R. A new conditional Apc-mutant mouse model for colorectal cancer. Carcinogenesis. 2010 May;31(5):946-52. doi:

9. Fijneman RJ, de Wit M, Pourghiasian M, Piersma SR, Pham TV, Warmoes MO, Lavaei M, Piso C, Smit F, Delis-van Diemen PM, van Turenhout ST, Terhaar sive Droste JS, Mulder CJ, Blankenstein MA, Robanus-Maandag EC, Smits R, Fodde R, van Hinsbergh VW, Meijer GA, Jimenez CR. Proximal fluid proteome profiling of mouse colon tumors reveals biomarkers for early diagnosis of human colorectal cancer. Clin Cancer Res. 2012 May 1;18(9):2613-24. doi: 10.1158/1078-0432.CCR-11-1937. Epub 2012 Feb 20.

6. Bürtin F, Mullins CS, Linnebacher M. Mouse models of colorectal cancer: Past, present and future perspectives. World J Gastroenterol. 2020 Apr 7;26(13):1394-1426. doi: 10.3748/wjg.v26.i13.1394. PMID: 32308343; PMCID: PMC7152519.

5. Evans JP, Sutton PA, Winiarski BK, Fenwick SW, Malik HZ, Vimalachandran D, Tweedle EM, Costello E, Palmer DH, Park BK, Kitteringham NR. From mice to men: Murine models of colorectal cancer for use in translational research. Crit Rev Oncol Hematol.

2016 Feb;98:94-105. doi: 10.1016/j.critrevonc.2015.10.009. Epub 2015 Nov 1. PMID: 26558688.

1. McIntyre RE, Buczacki SJ, Arends MJ, Adams DJ. Mouse models of colorectal cancer as preclinical models. Bioessays. 2015 Aug;37(8):909-20. doi: 10.1002/bies.201500032. Epub 2015 Jun 26. PMID: 26115037; PMCID: PMC4755199.

2. Clark CR, Starr TK. Mouse models for the discovery of colorectal cancer driver genes. World J Gastroenterol. 2016 Jan 14;22(2):815-22. doi: 10.3748/wjg.v22.i2.815. PMID: 26811627; PMCID: PMC4716079.

3. Karim BO, Huso DL. Mouse models for colorectal cancer. Am J Cancer Res. 2013 Jun 20;3(3):240-50. PMID: 23841024; PMCID: PMC3696531.

4. McCart AE, Vickaryous NK, Silver A. Apc mice: models, modifiers and mutants. Pathol Res Pract. 2008;204(7):479-90. doi: 10.1016/j.prp.2008.03.004. Epub 2008 Jun 5. PMID: 18538487.

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S4. Mouse models

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S5. Literature for biomarkers

Literature used to investigate biomarkers relevant in early stages of CRC

Author, year (reference) Aim Methods Samples in study Nr.

Proteins How the data was used

Zhang et al, 2014 (1)

Proteogenomic

characterization of human CRC.

LC-MS/MS

Ninety-five specimens from 90 patients. Normal colon epithelium biopsies from 30 subjects. Samples were taken both from ascending and descending colon, giving a total of 60 samples. These samples were averaged giving 30 normal colon tissues data.

7526

In the supplementary file, only tissue samples obtained from patients with stage I-II CRC were kept. All data from normal tissue samples were kept. This resulted in 50 CRC tissue samples and 30 Normal tissue samples. Mean values and 2-sided Ttest were performed using Windows ® Excel. Fold change were calculated for mean CRC/Normal tissue. Proteins with p<0.05 and fold change >1,5 were investigated if they were plasma membrane bound according to UniProt. Resulted in 255 proteins.

Hao et al, 2017 (2)

To conduct a comprehensive proteomic analysis of paired tumor and adjacent tissues.

LC-MS/MS Paired samples of 22 CRC and 22 adjacent normal tissue.

Samples were from patients with different stages of CRC. 12380

In the supplementary file, only tissue samples obtained from patients with stage I-II CRC were kept. Mean; 2-sided paired Ttest and fold changes were calculated in Windows ® Excel. Proteins with p<0.05 and fold change >1,5 were investigated if they were plasma membrane bound. Resulting in 78 proteins.

Sethi et al, 2015 (3) Investigate total membrane- enriched proteome.

Triton X-114 phase partioning; SDS-PAGE;

LC-MS/MS

Eight pairs of CRC tissues and their corresponding adjacent

non-tumorigenic colon tissue. 948

In the supplementary, data from patients in stage I-II were kept and mean values were calculated. Paired T-test <0,05 and Fold change over 1,5. This resulted in 10 proteins that were stated as plasma membrane localized in UniProt.

Uzozie et al, 2014 (4) Explore the proteome of precancerous lesions.

iTRAQ 8plex. OFFGEL electrophoresis. LC MS/MS. q<0.02;

Paired samples of 30 colorectal adenomas with their respectively normal mucosa, taken from the same colon segment more than 2 cm from the lesion. In the result some were removed because of biased result and 21 tissue paired samples remained. They also conducted research with cell lines SW480, SW620, HT29, Caco2, CX1 and HCEC.

4325

Here proteins with a fold change over 1,5 were chosen from the result section. The proteins selected was those that were plasma membrane bound. Some proteins that was unclear was removed. This resulted in 35 proteins. Some of these were also found to be expressed similar in cell lines vs HCEC.

Saleem et al, 2019 (6) Identify proteins associated with advancement of CRC.

iTRAQ labeling; HPLC- ESI MS/MS; western blotting. P-value <0.05

12 tissue samples of non-cancer, normal (NC), non-cancer non-adenomatous polyp (NAP), colon cancer, non-metastatic (CC NM) and colon cancer metastatic (CC M)

2777

In the supplementary fold change were calculated from the log2 values stated, and only those over 1,5 was kept. Only values for non- adenomatous polyps and non- metastasis cancer were chosen. Leaving the result for metastases out. Unique peptides were set to be over 2. Mascot score was set to be over 22 as stated in the publication.

Resulting in 50 proteins. Mena fold change for non-adenoma polyps and non- metastasis cancer was used

Zhang et al, 2017 (7)

Evaluate new strategies for proteomic profiling changes in colorectal cancer.

Laser capture

microdissection: Stable isotopic labeling coupled with L linear ion trap Fourier transform ion cyclotron resonance mass spectrometry; western blotting.

20 CRC patients; 3 patients with stage III CRC, 1 patient with stage I and the rest were stage II. Paired normal mucosa samples was also used.

798 Proteins showed to be upregulated by >2 were listed in supplementary file. Some proteins were not used due to difficulty to identify correct protein. These were investigated if they were plasma membrane bound according to UniProt, resulting in 17 proteins.

1. Zhang, B., Wang, J., Wang, X. et al. Proteogenomic characterization of human colon and rectal cancer. Nature 513, 382–387 (2014). https://doi-org.ezproxy.its.uu.se/10.1038/nature13438

2. Hao, JJ., Zhi, X., Wang, Y. et al. Comprehensive Proteomic Characterization of the Human Colorectal Carcinoma Reveals Signature Proteins and Perturbed Pathways. Sci Rep 7, 42436 (2017). https://doi-org.ezproxy.its.uu.se/10.1038/srep42436

6. Saleem, S., Tariq, S., Aleem, I. et al. Proteomics analysis of colon cancer progression. Clin Proteom 16, 44 (2019). https://doi.org/10.1186/s12014-019-9264-y

7. Zhang, Y., Liu, Y., Ye, Y. et al. Quantitative proteome analysis of colorectal cancer-related differential proteins. J Cancer Res Clin Oncol 143, 233–241 (2017). https://doi-org.ezproxy.its.uu.se/10.1007/s00432-016-2274-5

3. Sethi MK, Thaysen-Andersen M, Kim H, Park CK, Baker MS, Packer NH, Paik YK, Hancock WS, Fanayan S. Quantitative proteomic analysis of paired colorectal cancer and non-tumorigenic tissues reveals signature proteins and perturbed pathways involved in CRC progression and metastasis. J Proteomics. 2015 Aug 3;126:54-67. doi: 10.1016/j.jprot.2015.05.037. Epub 2015 Jun 6. PMID: 26054784.

4. Uzozie A, Nanni P, Staiano T, Grossmann J, Barkow-Oesterreicher S, Shay JW, Tiwari A, Buffoli F, Laczko E, Marra G. Sorbitol dehydrogenase overexpression and other aspects of dysregulated protein expression in human precancerous colorectal neoplasms: a quantitative proteomics study. Mol Cell Proteomics. 2014 May;13(5):1198-218. doi: 10.1074/mcp.M113.035105. Epub 2014 Feb 24. PMID: 24567419; PMCID: PMC4014279.

5. Besson D, Pavageau AH, Valo I, Bourreau A, Bélanger A, Eymerit-Morin C, Moulière A, Chassevent A, Boisdron-Celle M, Morel A, Solassol J, Campone M, Gamelin E, Barré B, Coqueret O, Guette C. A quantitative proteomic approach of the different stages of colorectal cancer establishes OLFM4 as a new nonmetastatic tumor marker. Mol Cell Proteomics. 2011 Dec;10(12):M111.009712. doi: 10.1074/mcp.M111.009712. Epub 2011 Oct 10. PMID: 21986994; PMCID: PMC3237075.

Using supplementary of fold change for adenoma, stage I-IV. Mean fold change for stage I and II was calculated and those with fold change over 1,5 that were plasma membrane localized according to UniProt was kept. This resulted in 11 proteins. P- value in the supplementary was below 0,05.

Besson et al, 2011 (5)

Identify candidate biomarker of the early stages of colorectal cancer, focus on secreted proteins.

TRAQ labeling. OFFGEL fraction. MALDI

MS/MS. western blot

Paired samples of 28 tissue samples of tumor and their respectively normal colonic tissue taken at least 10 cm from the tumor at the distal edge of the resection.

10452

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S6. Upregulated biomarkers

Protein name Gene Un ip rot ac es sion

n r.

Exos

om e p rot ein

Ap ical /B as ol at er al rat io P- val ue

Fou

nd in th e p roxi

m al col on of IB D m ou se m od el

Fou

nd in th e d ist al col on of IB D m ou se m od el Fou

nd in C ac o- 2 ce ll IB D ce ll m od el SW480 SW620 H CT 116/

NC M 460

fol d ch an ge

H CT 116/

NC M 460 p- val ue

Zh an g et al . F ol d ch an ge Zh an g et al . P -val ue

H ao et al fol d ch an ge

H ao et al . P -val ue

An im al m od el (fol d ch an ge ) An im al m od el (P -val ue )

Fol d ch an ge p- val ue

q- val ue

Sp ec ifi c i nf or m at ion of ti ss ue sam pl es

Fe m al e/M al e Age (Y )

Multidrug resistance-associated protein 1 ABCC1 P33527 ✓ 0,952 4,74E-03 ✓ ✓ 4,53 8,33E-04

ATP-binding cassette sub-family D member 3 ABCD3 P28288 0,428 7,84E-06 0,727 3,39E-05 1,62 1,76E-02

Abl interactor 1 ABI1 Q8IZP0 ✓ ✓ ✓ 3,22 2,80E-43 1,31 1,36E-01

Apoptotic chromatin condensation inducer 1 ACIN1 Q9UKV3 3,40 5,84E-16 8,26 5,31E-04

Low molecular weight phosphotyrosine protein phosphatase ACP1 P24666 ✓ ✓ ✓ ✓ 0,857 4,12E-03 1,28 4,04E-03

Long-chain-fatty-acid--CoA ligase 1 ACSL1 P33121 0,110 1,83E-08 1,40 2,98E-03 0,662 5,95E-01

Acyl-CoA synthetase long chain family member 4 ACSL4 O60488 ✓ ✓ ✓ 0,237 3,44E-07 1,95 1,11E-15 3,93 6,08E-04

Actin like 6A ACTL6A O96019 3,67 4,61E-15 1,58 2,26E-03

Adhesion G protein-coupled receptor E5 ADGRE5 P48960 1,75 1,07E-03

Alcohol dehydrogenase 1B (class I), beta polypeptide ADH1B P00325 0,125 9,05E-25 0,186 1,08E-08

Adhesion regulating molecule 1 ADRM1 Q16186 0,623 1,13E-03 1,73 2,68E-05 2,36 2,82E-06

Afadin AFDN P55196 ✓ ✓ 4,06 3,28E-03

Adenosylhomocysteinase like 1 AHCYL1 O43865 ✓ ✓ ✓ 3,55 6,69E-17 0,659 4,78E-03

AHNAK nucleoprotein 2 AHNAK2 Q8IVF2 0,606 5,57E-55 1,61 7,19E-05 0,148 7,11E-02

Allograft inflammatory factor 1 AIF1 P55008 ✓ ✓ 0,641 1,35E-05 1,70 9,68E-02

Aldehyde dehydrogenase 3 family member A1 ALDH3A1 P30838 0,694 7,74E-08 1,17 4,71E-01

Alpha-methylacyl-CoA racemase AMACR Q9UHK6 1,88 2,60E-05 4,01 7,27E-03

Ankyrin 1 ANK1 P16157 2,48 8,19E-15 0,446 3,07E-01

Ankyrin 3 ANK3 Q12955 2,35 2,88E-17 0,452 7,64E-03

Annexin A3 ANXA3 P12429 ✓ 1,19 4,36E-05 ✓ ✓ 2,80 5,44E-11 2,06 1,30E-19 2,37 9,00E-06

Annexin A4 ANXA4 P09525 ✓ 0,668 2,94E-25 ✓ ✓ 1,00 9,49E-01 1,35 9,68E-05

Amine oxidase, copper containing 3 AOC3 Q16853 ✓ 0,239 5,21E-19 0,234 9,11E-09

Apolipoprotein B-100 APOB P04114 ✓ 0,897 1,09E-02 ✓ 2,40 4,92E-08 0,364 9,39E-02

Apolipoprotein B receptor APOBR Q0VD83 0,218 9,85E-22 1,21 5,66E-01

Apolipoprotein E APOE P02649 ✓ 0,958 1,13E-03 ✓ ✓ 1,13 3,37E-01 0,780 4,92E-01

ADP-ribosylation factor 4 ARF4 P18085 ✓ 1,05 1,22E-01 ✓ ✓ 0,702 6,51E-11 1,30 2,08E-03

ADP ribosylation factor 6 ARF6 P62330 ✓ 0,827 5,87E-10 ✓ ✓ 0,664 1,56E-07 0,893 2,98E-01

Rho guanine nucleotide exchange factor 1 ARHGEF1 Q92888 ✓ ✓ 0,892 2,71E-02 2,18 4,75E-05

Rho guanine nucleotide exchange factor 2 ARHGEF2 Q92974 1,55 1,19E-05 3,60 4,13E-05

ADP ribosylation factor like GTPase 8A ARL8A Q96BM9 ✓ 0,751 6,98E-06 2,02 2,91E-12 0,903 3,86E-01

Aspartate beta-hydroxylase ASPH Q12797 3,70 2,16E-21 2,01 1,48E-04

ATPase family, AAA domain containing 3B ATAD3B Q5T9A4 4,61 5,24E-25 2,16 1,24E-06

ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 2 ATP2A2 P16615 3,42 6,45E-06 ✓ 15,2 1,64E-39 1,29 2,74E-03

ATPase plasma membrane Ca2+ transporting 1 ATP2B1 P20020 ✓ 1,13 4,32E-08 ✓ ✓ 4,37 1,22E-21 0,531 2,56E-04

ATPase plasma membrane Ca2+ transporting 2 ATP2B2 Q01814 1,42 4,09E-04 0,529 2,59E-04

ATPase plasma membrane Ca2+ transporting 4 ATP2B4 P23634 0,807 3,45E-04 ✓ ✓ 2,82 1,70E-11 0,337 1,63E-03

ATP synthase F1 subunit alpha ATP5A1 P25705 ✓ 6,46 2,26E-36 ✓ ✓ 30,0 1,88E-43 0,769 2,25E-03

(10)

S6. Upregulated biomarkers

ATPase H+ transporting V1 subunit E1 ATP6V1E1 P36543 ✓ 0,723 3,17E-08 ✓ 3,44 3,73E-21 1,07 3,79E-01

Ataxin 10 ATXN10 Q9UBB4 ✓ ✓ 2,16 4,11E-04 4,26 6,20E-40 2,06 1,84E-03

B cell receptor associated protein 31 BCAP31 P51572 1,31 2,17E-08 1,08 3,26E-01 1,77 4,43E-05

B-cell receptor-associated protein 31 BCAP31 P51572 1,31 2,17E-08 1,08 3,26E-01 1,77 4,43E-05

Biglycan BGN P21810 ✓ 2,48 1,03E-17 0,650 3,15E-02

Complement C1q binding protein C1QBP Q07021 1,20 3,06E-05 ✓ ✓ 1,36 4,23E-08 1,66 3,28E-04

Complement C4-A C4A P0C0L4 ✓ 2,04 1,61E-09 0,673 1,05E-01

Complement C4-B C4B P0C0L5 ✓ ✓ ✓ 2,01 5,50E-10 0,672 1,10E-01

C4b-binding protein alpha chain C4BPA P04003 2,10 1,87E-07 1,31 6,87E-01

Complement C5 C5 P01031 ✓ 1,75 2,72E-08 1,31 7,46E-01

Complement C6 C6 P13671 ✓ 2,23 1,01E-11 3,03 4,74E-01

Complement C7 C7 P10643 ✓ 1,45 4,64E-03 1,10 9,21E-01

Complement C8 alpha chain C8A P07357 ✓ 2,08 1,29E-13 1,25 7,97E-01

Complement C8 beta chain C8B P07358 ✓ 2,30 7,14E-14 1,41 6,63E-01

Complement C8 gamma chain C8G P07360 ✓ 1,96 4,07E-07 0,798 6,03E-01

Complement component C9 C9 P02748 ✓ 1,67 6,42E-05 0,898 8,18E-01

Carbonic anhydrase 2 CA2 P00918 ✓ 0,112 2,07E-47 0,350 2,38E-07

Caveolin 1 CAV1 Q03135 1,10 3,38E-01 0,293 8,45E-05

Caveolae associated protein 1 CAVIN1 Q6NZI2 0,279 4,05E-04

Coiled-coil and C2 domain containing 1A CC2D1A Q6P1N0 ✓ 0,595 1,96E-07 2,93 3,71E-03

Girdin CCDC88A Q3V6T2 1,50 6,42E-01

Chaperonin containing TCP1 subunit 3 CCT3 P49368 ✓ 0,730 5,73E-06 ✓ ✓ 2,89 2,69E-11 23,9 1,61E-22 1,46 2,25E-05

B-lymphocyte antigen CD19 CD19 P15391 ✓ 2,74 4,41E-01

CD46 molecule CD46 P15529 ✓ ✓ ✓ 3,33 4,94E-16 5,50 3,42E-03

CD47 molecule CD47 Q08722 1,32 1,95E-13 ✓ ✓ 3,10 2,38E-44 0,959 5,71E-01

CD55 molecule (Cromer blood group) CD55 P08174 ✓ ✓ 2,08 1,10E-07 0,564 2,60E-01

Cell division control protein 42 homolog CDC42 P60953 ✓ 0,751 2,75E-05 ✓ ✓ 1,89 9,85E-23 1,03 6,57E-01

CDV3 homolog CDV3 Q9UKY7 0,795 1,12E-01 1000 7,45E-02

Carcinoembryonic antigen related cell adhesion molecule 1 CEACAM1 P13688 ✓ ✓ ✓ ✓ ✓ 0,773 2,06E-02 1,57 1,00E-02

Carcinoembryonic antigen-related cell adhesion molecule 3 CEACAM3 P40198

Carcinoembryonic antigen-related cell adhesion molecule 5 CEACAM5 P06731 ✓ ✓ 0,916 5,22E-01 3,41 2,16E-05

Carcinoembryonic antigen related cell adhesion molecule 8 CEACAM8 P31997 3,18 2,23E-21 1,80 1,73E-04

Complement factor B CFB P00751 ✓ ✓ 1,81 3,68E-08 0,578 6,36E-02

Complement factor I CFI P05156 ✓ 1,42 5,66E-03 0,409 1,41E-03

Charged multivesicular body protein 3 CHMP3 Q9Y3E7 ✓ 3,23 2,04E-46 0,906 5,18E-01

Charged multivesicular body protein 4a CHMP4A Q9BY43 0,473 2,95E-13 1,27 3,38E-01

Charged multivesicular body protein 4B CHMP4B Q9H444 ✓ 0,673 5,33E-05 ✓ ✓ 0,562 2,27E-12 1,30 1,69E-02

Cytoskeleton-associated protein 5 CKAP5 Q14008 0,921 1,92E-01 ✓ ✓ 1,53 1,82E-06 3,39 2,98E-05

Cytoplasmic linker associated protein 2 CLASP2 O75122 1,67 3,32E-07 2,49 1,07E-01

Chloride intracellular channel protein 1 CLIC1 O00299 ✓ 0,705 6,39E-13 ✓ ✓ 1,08 2,18E-02 1,44 2,03E-05

Clathrin interactor 1 CLINT1 Q14677 3,25 8,55E-20 1,57 1,67E-02

CLPTM1, transmembrane protein CLPTM1 O96005 0,467 1,87E-03 1,01 9,08E-01 1,81 4,10E-04

Clathrin light chain A CLTA P09496 ✓ 2,76 4,66E-16 1,26 1,20E-01

Clathrin heavy chain like 1 CLTCL1 P53675 57,9 1,49E-57 1,09 6,40E-02

cGMP-gated cation channel alpha-1 CNGA1 P29973 0,154 1,12E-01

2',3'-cyclic-nucleotide 3'-phosphodiesterase CNP P09543 ✓ 0,955 4,46E-03 ✓ ✓ 1,59 9,63E-06 0,727 3,18E-03

Cannabinoid receptor interacting protein 1 CNRIP1 Q96F85 0,323 9,36E-05

Collagen type VI alpha 1 chain COL6A1 P12109 ✓ ✓ ↑ N/A 0,881 5,95E-02 0,505 2,91E-04

Collagen type VI alpha 3 chain COL6A3 P12111 ✓ ✓ 0,855 2,39E-03 0,543 5,56E-04

Coatomer subunit alpha COPA P53621 1,27 1,06E-13 √ √ 0,954 2,03E-01 1,26 1,64E-02

Coronin-1A CORO1A P31146 ✓ 1,19 4,30E-03 1,15 3,76E-01

Carboxypeptidase D CPD O75976 0,826 6,99E-26 2,50 4,43E-16 2,06 5,35E-03

Copine 1 CPNE1 Q99829 ✓ 1,56 1,14E-48 ✓ ✓ ✓ ✓ 0,461 3,49E-07 1,42 1,17E-04 2,16 8,32E-06

Complement receptor type 2 CR2 P20023 ✓ 1,35 2,63E-02 0,215 9,05E-02

(11)

S6. Upregulated biomarkers

Adapter molecule crk CRK P46108 ✓ ✓ ✓ 2,84 9,24E-06 0,485 6,17E-20 0,903 4,16E-01

Crk-like protein CRKL P46109 ✓ ✓ 0,698 1,89E-07 1,61 2,24E-03

Crystallin alpha B CRYAB P02511 ✓ 0,658 2,68E-03 ✓ 0,290 8,29E-16 0,133 3,18E-06

Cold shock domain containing E1 CSDE1 O75534 1,00 8,79E-01 ✓ 7,60 2,23E-62 2,38 6,12E-06

Catenin alpha 2 CTNNA2 P26232 0,474 1,46E-10 ✓ ✓ 0,726 6,07E-09 1,38 9,88E-04

Catenin beta 1 CTNNB1 P35222 0,888 9,94E-11 ✓ ✓ 0,745 2,50E-08 1,56 6,00E-04

Catenin delta 1 CTNND1 O60716 0,876 1,85E-09 ✓ ✓ 28,2 8,50E-34 1,37 2,10E-02

Cathepsin G CTSG P08311 ✓ ✓ 1,44 2,26E-02 1,05 7,81E-01

Cathepsin Z CTSZ Q9UBR2 ✓ ✓ 0,370 3,20E-30 0,741 1,96E-02

Src substrate cortactin CTTN Q14247 1,91 6,07E-10 ✓ ✓ 1,17 7,12E-02 6,48 1,61E-04

Cullin-1 CUL1 Q13616 ✓ ✓ 1,68 3,81E-07 2,16 8,59E-05

Cullin 3 CUL3 Q13618 ✓ 1,11 1,69E-01 1,32 1,13E-03

Cytochrome b-245 heavy chain CYBB P04839 ✓ ✓ 1,20 4,65E-02 1,93 2,27E-03

Drebrin 1 DBN1 Q16643 1,02 5,52E-01 ✓ ✓ 3,37 9,58E-10 4,02 5,02E-25 1,56 5,98E-03

Drebrin like DBNL Q9UJU6 ✓ ✓ ✓ 0,969 5,56E-01 1,74 1,91E-06

Dynactin subunit 3 DCTN3 O75935 2,33 4,00E-20 0,770 7,01E-02

DExD-box helicase 50 DDX50 Q9BQ39 0,462 4,52E-05 1,29 1,68E-03 5,11 1,25E-07

DNA fragmentation factor subunit alpha DFFA O00273 2,82 2,08E-16 3,06 1,77E-02

Diablo IAP-binding mitochondrial protein DIABLO Q9NR28 0,407 1,04E-02 2,97 9,51E-20 1,31 5,13E-02

Discs large MAGUK scaffold protein 1 DLG1 Q12959 ✓ 0,678 2,79E-19 ✓ ✓ 3,97 5,27E-19 1,81 3,67E-03

Dystrophin DMD P11532 1,44 5,42E-03 0,0634 4,59E-04

Dedicator of cytokinesis 8 DOCK8 Q8NF50 2,11 3,00E-06 2,74 2,17E-02

Dipeptidase 1 DPEP1 P16444 ✓ 3,24 1,35E-13 14,14 4,84E-03

Dihydropyrimidinase-related protein 2 DPYSL2 Q16555 ✓ 2,15 2,47E-04 ✓ ✓ 10,7 2,05E-07 3,21 1,63E-26 0,653 1,09E-04

Desmocollin 2 DSC2 Q02487 ✓ 3,51 1,38E-23 1,33 2,33E-01

Desmoplakin DSP P15924 ✓ ✓ ✓ 3,51 5,35E-40 1,26 1,67E-01

Desmoplakin DSP P15924 ✓ √ √ 3,51 5,35E-40 1,26 1,67E-01

Dual specificity protein phosphatase 3 DUSP3 P51452 ✓ 1,69 4,33E-06 0,620 3,65E-02

Dysferlin DYSF O75923 ✓ 1,57 5,99E-06 0,725 2,70E-01

Calcium release activated channel regulator 2A EFCAB4B Q9BSW2 7,40 4,22E-68 1000 3,29E-01

Elastase, neutrophil expressed ELANE P08246 ✓ ✓ 11,8 1,19E-42 3,77 1,22E-02

EMILIN-1 EMILIN1 Q9Y6C2 ✓ ✓ 0,652 2,71E-14 0,644 7,36E-04

Alpha-enolase ENO1 P06733 ✓ 1,05 6,21E-01 ✓ ✓ 2,15 1,93E-08 2,92 6,06E-29 1,34 3,45E-05

Ectonucleoside triphosphate diphosphohydrolase 1 ENTPD1 P49961 ✓ ✓ 2,89 1,83E-25 0,959 8,38E-01

Erythrocyte membrane protein band 4.1 EPB41 P11171 ✓ ✓ 0,383 1,86E-05 2,10 2,64E-10 0,569 1,28E-01

Erythrocyte membrane protein band 4.1 like 2 EPB41L2 O43491 ✓ ✓ ✓ 3,62 5,56E-23 1,89 1,02E-03

EPH receptor B3 EPHB3 P54753 1,72 2,40E-05 11,0 3,65E-03

Bifunctional glutamate/proline--tRNA ligase EPRS1 P07814 0,299 1,13E-45 1,82 3,70E-05

Epidermal growth factor receptor substrate 15 EPS15 P42566 0,964 7,07E-01 1,39 1,54E-01

Epidermal growth factor receptor pathway substrate 15 like 1 EPS15L1 Q9UBC2 3,19 2,04E-18 1,69 4,76E-03

EWS RNA binding protein 1 EWSR1 Q01844 0,815 2,98E-10 0,857 4,83E-03 1,85 4,11E-07

Exocyst complex component 4 EXOC4 Q96A65 0,519 3,20E-04 ✓ ✓ 1,39 1,06E-03 1,63 1,28E-02

Exocyst complex component 7 EXOC7 Q9UPT5 ✓ ✓ 0,963 9,20E-01

Ezrin EZR P15311 ✓ 1,22 3,98E-20 ✓ ✓ 8,09 5,41E-14 1,46 2,75E-14 1,19 3,32E-02

Family with sequence similarity 120A FAM120A Q9NZB2 0,490 2,55E-11 0,976 6,70E-01 1,74 1,80E-04

FERM, ARH/RhoGEF and pleckstrin domain protein 1 FARP1 Q9Y4F1 ✓ ✓ 0,423 1,58E-03 1,61 1,51E-05 1,57 1,50E-01

Fatty acid synthase FASN P49327 ✓ 0,680 3,10E-70 ✓ ✓ 2,67 4,19E-15 1,62 1,09E-06 2,01 5,36E-05

Low affinity immunoglobulin gamma Fc region receptor III-A FCGR3A P08637 ✓ 5,34 6,52E-04

Fermitin family member 2 FERMT2 Q96AC1 0,629 3,86E-12 ✓ ✓ ↑ N/A 5,64 3,36E-29 0,263 1,76E-03

Fibrinogen alpha chain FGA P02671 ✓ ✓ ✓ 99,4 1,94E-82 1,07 8,65E-01

Fibrinogen beta chain FGB P02675 ✓ ✓ ✓ 14,9 4,80E-45 1,05 8,89E-01

Fibrinogen gamma chain FGG P02679 ✓ ✓ ✓ 1,90 2,62E-10 0,947 8,24E-01

Filamin-C FLNC Q14315 1,80 1,06E-36 ✓ 1,90 1,17E-12 0,306 2,49E-03

(12)

S6. Upregulated biomarkers

Fibronectin 1 FN1 P02751 ✓ 1,52 7,82E-04 ✓ ✓ 2,85 2,19E-27 1,40 1,45E-01

Formin-binding protein 1-like FNBP1L Q5T0N5 ✓ ✓ 5,88 6,50E-05

Fascin FSCN1 Q16658 ✓ 1,52 1,29E-14 ✓ ✓ ✓ ✓ 217 8,39E-08 1,52 3,22E-05 1,76 2,49E-03

Glyceraldehyde-3-phosphate dehydrogenase GAPDH P04406 ✓ 1,24 3,29E-04 ✓ ✓ 2,22 7,59E-07 40,6 1,73E-28 1,08 1,01E-01

Guanylate-binding protein 1 GBP1 P32455 ✓ 2,04 6,68E-07 2,39 2,58E-03

Gamma-glutamyltransferase 5 GGT5 P36269 ✓ 4,05 1,61E-37 0,639 5,87E-02

Golgi apparatus protein 1 GLG1 Q92896 ✓ 0,657 5,95E-31 1,23 1,38E-03 1,50 1,84E-03

G protein subunit alpha i1 GNAI1 P63096 ✓ 0,856 2,97E-05 ✓ ✓ ✓ 4,01 4,16E-06 2,14 2,36E-11 0,691 8,65E-05

Guanine nucleotide-binding protein G(i) subunit alpha-2 GNAI2 P04899 ✓ 0,721 1,97E-11 ✓ ✓ ✓ 2,47 1,12E-27 0,858 6,77E-02

Glucose-6-phosphate isomerase GPI P06744 ✓ 1,09 1,92E-06 ✓ ✓ 53,6 2,12E-28 1,20 5,78E-03

Glycoprotein nmb GPNMB Q14956 1,24 7,82E-10 0,277 8,84E-17 0,487 2,90E-03

G protein-coupled receptor class C group 5 member A GPRC5A Q8NFJ5 ✓ 1,96 8,71E-06 ✓ ✓ 1,70 4,40E-06 5,66 2,66E-05

Beta-adrenergic receptor kinase 1 GRK2 P25098 ✓ 2,28 7,90E-04

Glutathione S-transferase pi 1 GSTP1 P09211 ✓ 0,636 3,22E-05 ✓ ✓ 0,355 1,98E-32 1,39 8,71E-05

Vigilin HDLBP Q00341 0,747 2,88E-30 7,34 7,74E-35 1,81 8,68E-05

HLA class II histocompatibility antigen, DQ alpha 1 chain HLA-DQA1 P01909 ✓ 4,21 6,11E-31 0,391 4,90E-02

Major histocompatibility complex, class II, DR beta 1 HLA-DRB1 P01911 0,616 2,11E-05 0,959 7,25E-01

Minor histocompatibility antigen H13 HM13 Q8TCT9 2,77 4,24E-04 ✓ ✓ 6,10 6,78E-45 1,38 2,73E-03

High mobility group protein B1 HMGB1 P09429 ✓ ✓ 0,937 3,61E-01 1,54 6,41E-04

Rho GTPase-activating protein 45 HMHA1 Q92619 10,2 4,06E-49 1,37 3,83E-01

Heterogeneous nuclear ribonucleoprotein F HNRNPF P52597 ✓ ✓ ✓ 1,02 6,65E-01 1,65 4,05E-07

3-hydroxyacyl-CoA dehydrogenase type-2 HSD17B10 Q99714 1,30 4,55E-06 0,418 5,02E-09 8,52 2,45E-26 1,45 1,24E-03

Heat shock protein 90 alpha family class A member 1 HSP90AA1 P07900 ✓ 1,13 1,84E-04 ✓ ✓ 3,71 1,94E-04 1,22 9,59E-07 1,34 2,52E-05

Heat shock protein 90 alpha family class B member 1 HSP90AB1 P08238 ✓ 1,15 1,06E-01 ✓ ✓ 2,74 1,47E-09 1,28 9,59E-07 1,48 1,11E-06

Putative heat shock protein HSP 90-beta 4 HSP90AB4P Q58FF6 1,59 2,32E-05

Heat shock 70 kDa protein 14 HSPA14 Q0VDF9 1,73 1,11E-11 8,64 1,80E-05

Heat shock 70 kDa protein 1A HSPA1A P0DMV8 ✓ 0,596 4,05E-31

Heat shock-related 70 kDa protein 2 HSPA2 P54652 ✓ 1,48 5,78E-12 1,78 5,27E-22 1,02 6,88E-01

Heat shock cognate 71 kDa protein HSPA8 P11142 ✓ 0,768 4,30E-13 ✓ ✓ 2,78 1,90E-32 1,26 2,11E-05

60 kDa heat shock protein, mitochondrial HSPD1 P10809 ✓ 1,22 4,72E-11 ✓ ✓ 1,29 4,60E-07 1,67 1,04E-05

Serine protease HTRA2, mitochondrial HTRA2 O43464 1,64 4,22E-07 1,30 2,73E-02

Insulin degrading enzyme IDE P14735 ✓ ✓ 0,977 7,31E-01 2,23 8,64E-06

Interferon-induced transmembrane protein 1 IFITM1 P13164 4,98 1,93E-38 2,87 1,86E-04

Interferon-induced transmembrane protein 3 IFITM3 Q01628 1,30 5,17E-14 ✓ ✓ ✓ 4,75 3,80E-40 2,86 1,95E-04

Cation-independent mannose-6-phosphate receptor IGF2R P11717 ✓ 1,31 5,75E-14 1,80 1,15E-06 2,30 5,81E-04

Immunoglobulin kappa variable 4-1 IGKV4-1 P01625 0,733 2,26E-03

Immunoglobulin lambda-like polypeptide 1 IGLL1 P15814 2,19 3,84E-06 0,330 2,98E-02

Immunoglobulin lambda-like polypeptide 5 IGLL5 B9A064 ✓ 5,18 5,22E-25 0,679 6,01E-03

Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1 INPP5D Q92835 ✓ ✓ 1,54 3,50E-04 8,59 4,76E-04

Insulin receptor substrate 2 IRS2 Q9Y4H2 12,0 2,11E-01

Integrin alpha-5 ITGA5 P08648 0,815 2,25E-06 ✓ ✓ ✓ 1,11 4,73E-01 0,310 1,16E-02

Integrin subunit alpha 6 ITGA6 P23229 0,663 7,22E-39 ✓ ✓ ✓ 0,608 1,68E-15 1,59 5,19E-03

Integrin alpha-M ITGAM P11215 ✓ ✓ 2,20 8,66E-09 3,12 4,50E-03

Integrin alpha-V ITGAV P06756 ✓ 1,16 2,02E-04 ✓ ✓ 0,393 3,09E-09 9,84 1,09E-69 1,29 7,56E-02

Integrin alpha-V ITGAV P06756 ✓ 1,16 2,02E-04 √ √ 0,393 3,09E-09 9,84 1,09E-69 1,29 7,56E-02

Integrin beta-2 ITGB2 P05107 ✓ ✓ ✓ 1,32 3,83E-03 2,25 1,03E-02

Integrin beta-4 ITGB4 P16144 0,870 2,10E-12 ✓ ✓ 21,8 1,29E-68 1,90 3,95E-03

Intelectin 1 ITLN1 Q8WWA0 ✓ ✓ 0,0732 3,37E-32 0,370 6,47E-04

Inositol 1,4,5-trisphosphate receptor type 2 ITPR2 Q14571 1,96 9,66E-11 2,79 7,26E-02

Inositol 1,4,5-trisphosphate receptor type 3 ITPR3 Q14573 1,22 2,90E-02 3,72 4,97E-04

Intersectin-2 ITSN2 Q9NZM3 ✓ 4,06 1,41E-03

Junctophilin-1 JPH1 Q9HDC5 1,56 7,34E-04 1000 9,63E-02

Lysine--tRNA ligase KARS Q15046 0,230 1,15E-13 ✓ ✓ ✓ 8,30 3,11E-26 1,85 9,36E-05

(13)

S6. Upregulated biomarkers

Potassium channel tetramerization domain containing 12 KCTD12 Q96CX2 0,695 3,79E-06 0,635 1,14E-04

KH domain-containing, RNA-binding, signal transduction-associated protein 1 KHDRBS1 Q07666 1,10 6,53E-02 1,87 2,35E-04

Kininogen 1 KNG1 P01042 ✓ ✓ ✓ 12,3 2,33E-65 0,522 1,27E-02

Kininogen-1 KNG1 P01042 ✓ ✓ ✓ 12,3 2,33E-65 0,522 1,27E-02

Importin subunit alpha-1 KPNA2 P52292 ✓ ✓ 3,41 1,63E-18 19,5 4,84E-05

Kinectin KTN1 Q86UP2 5,44 1,57E-28 1,32 4,58E-02

Ragulator complex protein LAMTOR2 LAMTOR2 Q9Y2Q5 1,07 1,71E-01 0,294 1,99E-06 1,47 3,12E-06 1,20 3,58E-01

Galectin 3 LGALS3 P17931 ✓ 1,04 6,49E-02 ✓ ✓ 0,675 6,92E-09 0,913 8,00E-02

LIM domain and actin-binding protein 1 LIMA1 Q9UHB6 ✓ ✓ 0,375 7,55E-10 0,449 6,95E-16 2,01 1,26E-02

LIM and senescent cell antigen-like-containing domain protein 1 LIMS1 P48059 0,973 5,74E-01 8,11 3,69E-62 0,631 6,58E-02

LIM zinc finger domain containing 2 LIMS2 Q7Z4I7 4,66 6,90E-40 0,158 7,87E-03

Lysophosphatidylcholine acyltransferase 1 LPCAT1 Q8NF37 3,52 3,40E-06 0,416 3,32E-06 1,65 5,46E-07 2,87 6,72E-03

Lipoma-preferred partner LPP Q93052 ✓ 1,28 9,29E-03 0,281 3,38E-03

Alpha-2-macroglobulin receptor-associated protein LRPAP1 P30533 0,702 8,46E-07 1,27 4,46E-02 6,23 1,35E-03

LRR binding FLII interacting protein 1 LRRFIP1 Q32MZ4 0,761 2,42E-02 3,27 8,45E-05

Lactotransferrin LTF P02788 ✓ ✓ ✓ 12,4 3,40E-38 3,90 4,43E-04

Lymphocyte antigen 75 LY75 O60449 ✓ ↓ N/A 2,66 7,70E-20 1,31 2,97E-01

Acyl-protein thioesterase 1 LYPLA1 O75608 ✓ ✓ ✓ 0,639 4,36E-13 1,47 4,16E-04

Cation-dependent mannose-6-phosphate receptor M6PR P20645 1,41 1,80E-01 ✓ 1,50 4,66E-06 1,19 1,82E-01

Microtubule-actin cross-linking factor 1, isoforms 1/2/3/5 MACF1 Q9UPN3 1,15 2,55E-01 2,77 1,61E-17 2,36 2,32E-04

Magnesium transporter 1 MAGT1 Q9H0U3 2,72 4,79E-02 0,719 1,10E-05 1,36 9,76E-03

Microtubule-associated protein 4 MAP4 P27816 0,523 2,14E-88 3,97 2,95E-07 13,5 4,09E-32 1,21 4,98E-01

Ensconsin MAP7 Q14244 3,46 4,24E-29 6,46 1,90E-03

Mitogen-activated protein kinase 3 MAPK3 P27361 1,93 5,81E-10 0,829 2,77E-02

Microtubule associated protein RP/EB family member 1 MAPRE1 Q15691 0,886 1,21E-01 ✓ ✓ 1,36 2,06E-09 1,66 8,37E-05

Microtubule-associated protein tau MAPT P10636 2,91 1,41E-23 0,806 8,62E-01

Malignant T-cell-amplified sequence 1 MCTS1 Q9ULC4 ✓ ✓ 7,33 1,64E-77 1,39 3,65E-02

LRP chaperone MESD MESD Q14696 0,650 2,31E-05 3,16 9,53E-07

Microsomal glutathione S-transferase 1 MGST1 P10620 0,378 5,30E-07 2,03 6,16E-15 1,29 7,24E-02

Macrophage migration inhibitory factor MIF P14174 ✓ 0,717 2,67E-10 ✓ ✓ 2,84 2,12E-05 0,418 1,06E-27 1,32 3,29E-02

Mitochondrial ribosomal protein L44 MRPL44 Q9H9J2 ✓ 0,787 1,09E-03 1,79 1,17E-03

Myotrophin MTPN P58546 ✓ ✓ 0,769 1,83E-05 1,08 4,07E-01

Mucin-5B MUC5B Q9HC84 ✓ 0,839 2,83E-01 0,746 2,18E-01

Interferon-induced GTP-binding protein Mx1 MX1 P20591 2,63 9,31E-07 28,2 1,65E-02

Interferon-induced GTP-binding protein Mx2 MX2 P20592 2,21 2,23E-07 14,5 1,10E-02

Myosin heavy chain 9 MYH9 P35579 ✓ 2,12 5,36E-169 ✓ ✓ 1,15 5,50E-04 1,35 5,16E-05

Myosin light chain kinase, smooth muscle MYLK Q15746 9,76 4,91E-35 0,173 3,06E-03

Myosin IB MYO1B O43795 ✓ ✓ ✓ 3,00 1,97E-08 1,87 9,07E-20 2,26 6,36E-04

Myosin VI MYO6 Q9UM54 ✓ ✓ ✓ 1,13 9,67E-02 2,09 7,33E-04

Myoferlin MYOF Q9NZM1 ✓ 1,40 8,73E-07 ✓ ✓ ✓ 4,43 3,75E-11 1,89 1,05E-12 1,73 1,58E-03

Neurobeachin-like protein 2 NBEAL2 Q6ZNJ1 0,495 6,51E-03 1,71 3,21E-08 6,77 2,66E-02

Neutral cholesterol ester hydrolase 1 NCEH1 Q6PIU2 ✓ 4,13 3,57E-20 2,20 9,95E-04

Neutrophil cytosol factor 1 NCF1 P14598 1,31 3,97E-02 3,67 4,00E-03

Neutrophil cytosol factor 2 NCF2 P19878 4,05 2,28E-35 3,98 5,43E-04

NCK associated protein 1 NCKAP1 Q9Y2A7 ✓ 0,969 1,06E-01 ✓ ✓ 0,810 1,30E-02 1,36 2,16E-02

Protein NDRG1 NDRG1 Q92597 ✓ ✓ ✓ 2,33 1,85E-12 1,06 6,70E-01

Neurofibromin 2 NF2 P35240 1,19 2,28E-02 4,35 4,02E-42 1000 1,66E-02

Ninein NIN Q8N4C6 2,23 4,50E-20 1,16 1,65E-01

Nucleoside diphosphate kinase A NME1 P15531 ✓ ✓ ✓ 4,90 7,03E-25 1,40 1,98E-04

N-myristoyltransferase 1 NMT1 P30419 1,53 5,08E-07 ✓ 2,03 1,53E-05 1,12 1,08E-01 3,67 2,46E-06

5'-nucleotidase ecto NT5E P21589 ✓ 1,23 9,75E-09 ✓ 2,38 1,49E-08 3,08 1,10E-21 0,462 4,78E-02

(14)

S6. Upregulated biomarkers

2'-5'-oligoadenylate synthase 3 OAS3 Q9Y6K5 ✓ 4,02 3,29E-14 10,57 1,34E-05

Obscurin OBSCN Q5VST9 5,78 2,42E-48 0,544 1,83E-01

UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit OGT O15294 ✓ 2,38 2,37E-17 3,96 5,85E-04

Olfactomedin-4 OLFM4 Q6UX06 ✓ 4,07 1,57E-10 5,83 6,84E-04

Oxysterol binding protein OSBP P22059 ✓ ✓ 0,704 1,81E-08 1,72 1,61E-04

Protein disulfide-isomerase P4HB P07237 ✓ 1,08 3,22E-03 ✓ ✓ 0,863 5,03E-04 1,45 6,70E-04

Serine/threonine-protein kinase PAK 1 PAK1 Q13153 ✓ ✓ 5,77 1,47E-25 1,76 1,02E-03

Serine/threonine-protein kinase PAK 2 PAK2 Q13177 ✓ ✓ 2,21 2,17E-14 2,02 2,85E-04

Protein mono-ADP-ribosyltransferase PARP14 PARP14 Q460N5 ✓ 3,00 1,69E-17 8,37 1,20E-02

28 kDa heat- and acid-stable phosphoprotein PDAP1 Q13442 ✓ ✓ 0,523 1,66E-07 10,1 2,06E-03

cAMP-specific 3',5'-cyclic phosphodiesterase 4D PDE4D Q08499 1,72 1,35E-04 0,125 1,75E-01

PDZ and LIM domain protein 4 PDLIM4 P50479 ✓ ✓ 1,14 2,82E-01 0,368 8,51E-02

Sister chromatid cohesion protein PDS5 homolog A PDS5A Q29RF7 1,55 1,88E-05 3,01 7,78E-06

Peroxisomal biogenesis factor 19 PEX19 P40855 0,793 8,28E-01

Phosphoglucomutase 5 PGM5 Q15124 0,305 2,21E-13 0,099 1,22E-04

Progesterone receptor membrane component 1 PGRMC1 O00264 ✓ ✓ 0,420 8,10E-07 0,694 1,65E-10 1,19 2,01E-03

Prohibitin PHB P35232 ✓ ✓ 0,893 1,87E-03 1,17 1,48E-02

Prohibitin-2 PHB2 Q99623 ✓ 9,24 3,38E-22 1,12 6,35E-02

Phosphatidylinositol glycan anchor biosynthesis class U PIGU Q9H490 1,71 3,95E-03

Phospholipase A2, membrane associated PLA2G2A P14555 ✓ 1,41 1,80E-02 1,48 6,62E-01

1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase delta-1 PLCD1 P51178 ✓ 1,85 5,41E-10 0,224 7,25E-04

Plasminogen PLG P00747 ✓ ✓ ✓ 1,89 4,90E-07 1,28 7,65E-01

Perilipin-2 PLIN2 Q99541 1,72 3,54E-06 1000 5,32E-02

Plexin-A4 PLXNA4 Q9HCM2 6,14 5,73E-33 0,776 5,73E-01

Pinin, desmosome associated protein PNN Q9H307 1,34 1,41E-03 4,95 1,67E-05

Periplakin PPL O60437 ✓ 0,471 3,75E-10 1,90 1,54E-06 4,27 5,69E-02

Serine/threonine-protein phosphatase PP1-alpha catalytic subunit PPP1CA P62136 ✓ 1,48 7,47E-09 ✓ ✓ 9,30 2,54E-19 1,29 1,16E-04

Serine/threonine-protein phosphatase PP1-beta catalytic subunit PPP1CB P62140 ✓ ✓ 2,43 8,40E-25 1,19 1,51E-03

Serine/threonine-protein phosphatase PP1-gamma catalytic subunit PPP1CC P36873 1,28 7,51E-08 ✓ ✓ 5,14 5,23E-64 1,25 2,75E-04

Protein phosphatase 1 regulatory subunit 12A PPP1R12A O14974 2,29 1,63E-04 8,55 8,18E-61 0,539 3,95E-01

Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform PPP3CA Q08209 ✓ ✓ 5,96 1,17E-55 1,08 4,34E-01

Serine/threonine-protein phosphatase 2B catalytic subunit beta isoform PPP3CB P16298 2,48 7,47E-15 0,902 3,82E-01

Serine/threonine-protein phosphatase 6 regulatory subunit 3 PPP6R3 Q5H9R7 3,31 2,66E-43 2,95 1,77E-02

cAMP-dependent protein kinase catalytic subunit alpha PRKACA P17612 ✓ ✓ ✓ 5,45 2,85E-42 0,600 1,39E-05

Protein kinase cAMP-activated catalytic subunit beta PRKACB P22694 ✓ 3,10 1,00E-41 0,567 1,89E-05

Protein C receptor PROCR Q9UNN8 ✓ 1,35 6,45E-05 ✓ 0,457 5,01E-20 0,973 8,13E-01

Myeloblastin PRTN3 P24158 ✓ ✓ 8,12 9,93E-31 2,35 3,21E-03

Prosaposin PSAP P07602 ✓ 0,854 1,50E-02 ✓ 0,384 1,98E-07 2,99 2,57E-07 1,09 6,95E-01

26S proteasome regulatory subunit 8 PSMC5 P62195 ✓ 1,08 3,16E-02 √ √ 2,75 5,39E-32 1,51 1,84E-04

Prostacyclin synthase PTGIS Q16647 ✓ 1,12 3,12E-01 0,112 1,33E-03

Inactive tyrosine-protein kinase 7 PTK7 Q13308 1,16 1,70E-05 ✓ ✓ 1,76 8,57E-05 1,92 7,90E-03

Tyrosine-protein phosphatase non-receptor type 6 PTPN6 P29350 ✓ ✓ ✓ 7,38 1,67E-27 0,955 7,91E-01

Paxillin PXN P49023 3,44 2,71E-05 1,89 2,60E-08 1,35 5,96E-01

RAB10, member RAS oncogene family RAB10 P61026 ✓ 0,951 5,06E-01 ✓ ✓ 0,488 4,63E-02 1,58 9,44E-10 1,19 1,58E-02

Ras-related protein Rab-11A RAB11A P62491 ✓ 4,36 3,06E-19 1,12 2,40E-02

Ras-related protein Rab-13 RAB13 P51153 ✓ 0,796 8,08E-04 ✓ ✓ 2,31 1,14E-13 1,22 3,46E-02

Ras-related protein Rab-15 RAB15 P59190 ✓ 0,966 9,88E-03 1,81 3,09E-18 1,08 3,17E-01

Ras-related protein Rab-18 RAB18 Q9NP72 1,06 3,62E-03 ✓ 5,55 2,83E-77 0,968 6,34E-01

RAB21, member RAS oncogene family RAB21 Q9UL25 ✓ 0,876 2,62E-04 ✓ ✓ 1,27 1,49E-03 1,28 1,14E-03

Ras-related protein Rab-27B RAB27B O00194 ✓ 1,67 5,17E-14 0,963 8,43E-01

Ras-related protein Rab-35 RAB35 Q15286 ✓ 0,769 5,72E-11 ✓ ✓ 3,32 1,40E-20 1,01 9,11E-01

Rab3 GTPase-activating protein non-catalytic subunit RAB3GAP2 Q9H2M9 1,82 3,91E-08 2,55 6,83E-03

(15)

S6. Upregulated biomarkers

Rab3 GTPase-activating protein non-catalytic subunit RAB3GAP2 Q9H2M9 1,82 3,91E-08 2,55 6,83E-03

Ras-related protein Rab-6A RAB6A P20340 ✓ ✓ ✓ 13,4 1,09E-35 1,24 1,28E-02

RAB7A, member RAS oncogene family RAB7A P51149 ✓ 0,837 2,52E-26 ✓ ✓ 0,984 6,61E-01 1,28 4,35E-04

Ras-related protein Rab-8B RAB8B Q92930 ✓ 0,966 9,29E-02 ✓ ✓ 1,53 5,39E-08 0,974 6,56E-01

Radixin RDX P35241 ✓ 1,05 7,47E-02 ✓ ✓ 7,83 4,85E-29 0,969 5,92E-01

Protein RER1 RER1 O15258 1,48 6,79E-07 0,959 6,32E-01 1,55 2,31E-03

Raftlin RFTN1 Q14699 ✓ 0,761 8,49E-18 1,82 2,05E-08 2,76 4,35E-03

E3 ubiquitin-protein ligase RNF114 RNF114 Q9Y508 2,34 1,88E-27 12,1 4,69E-03

60S ribosomal protein L36a-like RPL36AL Q969Q0 3,88 3,91E-17 2,67 5,85E-04

40S ribosomal protein S15a RPS15A P62244 ✓ 1,15 3,99E-12 √ √ 0,929 1,86E-02 1,41 3,21E-04

Ribosomal RNA processing 12 homolog RRP12 Q5JTH9 8,54 4,05E-51 4,42 3,02E-05

Reticulon-3 RTN3 O95197 0,991 4,39E-01 4,83 9,63E-45 1,08 4,13E-01

Protein S100-A12 S100A12 P80511 2,94 6,66E-20 4,25 2,32E-01

S100 calcium binding protein A6 S100A6 P06703 ✓ 1,47 2,62E-06 ✓ ✓ 0,806 1,71E-02 1,01 9,52E-01

Protein S100-A8 S100A8 P05109 ✓ ✓ ✓ 5,09 2,16E-33 1,92 5,48E-05

Protein S100-A9 S100A9 P06702 ✓ ✓ ✓ 6,28 5,32E-22 1,86 2,68E-03

S100 calcium binding protein P S100P P25815 ✓ 1,77 1,62E-05 4,96 2,36E-02

Secretory carrier membrane protein 1 SCAMP1 O15126 0,809 2,13E-10 2,10 5,99E-04

Lysosome membrane protein 2 SCARB2 Q14108 ✓ 0,809 8,99E-06 ✓ ✓ 0,267 5,40E-05 2,79 1,27E-21 1,13 2,05E-01

Sec1 family domain-containing protein 1 SCFD1 Q8WVM8 3,49 3,75E-20 1,59 1,17E-02

Syntenin-1 SDCBP O00560 ✓ 0,632 1,60E-48 ✓ ✓ ✓ 0,333 2,49E-08 2,06 6,27E-08 3,12 1,05E-02

Selenide, water dikinase 1 SEPHS1 P49903 6,40 1,15E-75 1,68 1,42E-02

Septin-7 SEPT7 Q16181 ✓ ✓ ✓ 23,5 1,74E-39 0,913 2,98E-01

SERPINE1 mRNA binding protein 1 SERBP1 Q8NC51 ✓ 1,65 1,56E-12 23,6 1,20E-83 32,2 3,12E-04

SH3 domain-containing kinase-binding protein 1 SH3KBP1 Q96B97 ✓ 3,84 1,59E-24 2,76 1,23E-02

Sigma non-opioid intracellular receptor 1 SIGMAR1 Q99720 1,69 1,65E-03

Solute carrier family 12 member 1 SLC12A1 Q13621 ✓ 1,72 3,91E-03

Solute carrier family 12 member 2 SLC12A2 P55011 1,79 9,98E-14 ✓ ✓ 0,0924 1,61E-11 1,20 2,70E-02 3,27 3,45E-04

Solute carrier family 16 member 3 SLC16A3 O15427 0,764 3,39E-15 ✓ ✓ 2,80 4,71E-05

Solute carrier family 1 member 4 SLC1A4 P43007 ✓ ✓ ✓ 1,61 7,35E-03

Neutral amino acid transporter B(0) SLC1A5 Q15758 1,54 2,40E-08 ✓ ✓ 0,313 2,27E-08 1,69 8,40E-09 2,26 2,62E-06

Mitochondrial 2-oxoglutarate/malate carrier protein SLC25A11 Q02978 13,6 5,52E-63 0,890 2,10E-01

Phosphate carrier protein, mitochondrial SLC25A3 Q00325 ✓ 7,57 6,35E-08 7,71 1,50E-33 1,11 2,27E-01

ADP/ATP translocase 1 SLC25A4 P12235 1,68 1,51E-14 1,18 1,65E-03

Solute carrier family 25 member 5 SLC25A5 P05141 ✓ 1,11 1,66E-02 1,24 2,74E-04

Very long-chain acyl-CoA synthetase SLC27A2 O14975 ✓ 0,269 1,27E-06 2,84 2,43E-23 3,78 1,42E-02

Solute carrier family 27 member 4 SLC27A4 Q6P1M0 0,397 9,42E-18 2,13 3,00E-03

Solute carrier family 2, facilitated glucose transporter member 1 SLC2A1 P11166 ✓ 1,04 1,38E-02 ✓ ✓ ✓ 2,83 7,72E-17 1,52 4,60E-02

Solute carrier family 2 member 3 SLC2A3 P11169 ✓ ✓ ✓ ↑ N/A 1,71 1,44E-02

Solute carrier family 39 member 11 SLC39A11 Q8N1S5 1,07 4,54E-01 2,09 1,20E-03

Solute carrier family 3 member 2 SLC3A2 P08195 ✓ 1,29 8,14E-58 ✓ ✓ 1,49 1,18E-09 2,47 1,74E-05

Band 3 anion transport protein SLC4A1 P02730 ✓ 1,11 3,72E-01 0,839 4,90E-01

Sphingomyelin phosphodiesterase 4 SMPD4 Q9NXE4 1,88 1,00E-12 3,13 3,55E-03

Synaptosomal-associated protein 23 SNAP23 O00161 ✓ 0,886 9,22E-02 ✓ ✓ 0,386 2,90E-08 2,01 1,94E-11 1,38 2,14E-01

Sorting nexin 9 SNX9 Q9Y5X1 ✓ ✓ ✓ 10,7 6,79E-07 0,666 3,34E-07 1,66 1,30E-03

Sorbin and SH3 domain-containing protein 1 SORBS1 Q9BX66 ✓ 7,53 1,25E-29 0,160 3,06E-03

Sorbin and SH3 domain-containing protein 2 SORBS2 O94875 ✓ ✓ 2,86 2,47E-19 0,054 1,10E-02

(16)

S6. Upregulated biomarkers

Spectrin alpha chain, erythrocytic 1 SPTA1 P02549 1,38 1,40E-02 0,598 3,35E-01

Sorcin SRI P30626 ✓ 1,05 8,14E-06 ✓ ✓ 12,6 1,07E-20 0,989 9,22E-01

SRSF protein kinase 1 SRPK1 Q96SB4 ✓ 2,43 3,55E-14 4,13 2,57E-05

Signal transducer and activator of transcription 2 STAT2 P52630 ✓ 1,91 1,52E-09 5,61 3,34E-04

Signal transducer and activator of transcription 3 STAT3 P40763 ✓ ✓ 19,2 2,51E-62 1,17 9,18E-02

Staufen double-stranded RNA binding protein 1 STAU1 O95793 0,381 7,97E-15 6,71 1,78E-45 3,02 2,03E-04

Serine/threonine-protein kinase 26 STK26 Q9P289 ✓ ✓ 2,10 4,93E-04

Stomatin STOM P27105 ✓ 1,56 3,01E-07 ✓ 1,57 9,28E-10 0,935 5,70E-01

Stomatin-like protein 2, mitochondrial STOML2 Q9UJZ1 1,15 8,81E-04 1,60 3,23E-03

Syntaxin 4 STX4 Q12846 ✓ 0,902 9,09E-03 ✓ ✓ 0,262 7,45E-05 0,704 2,57E-04 1,04 6,85E-01

Syntaxin binding protein 5 STXBP5 Q5T5C0 1,60 1,03E-02

Supervillin SVIL O95425 ✓ 0,281 1,91E-02 1,97 2,58E-08 0,134 1,40E-01

Symplekin SYMPK Q92797 1,93 1,87E-09 5,21 4,45E-03

Synaptophysin like 1 SYPL1 Q16563 ✓ 0,914 2,36E-05 ✓ ✓ 0,612 2,62E-08 1,12 1,13E-01

Synaptotagmin-like protein 5 SYTL5 Q8TDW5 2,63 1,11E-29

Antigen peptide transporter 1 TAP1 Q03518 √ √ 1,75 1,92E-08 2,16 1,22E-04

Testin TES Q9UGI8 ✓ 13,7 1,37E-77 0,450 3,22E-02

Transferrin receptor TFRC P02786 ✓ 0,987 5,43E-03 ✓ ✓ 1,78 3,12E-10 3,53 2,83E-06

Transforming growth factor beta-1-induced transcript 1 protein TGFB1I1 O43294 6,40 2,78E-42 0,234 3,92E-03

Transforming growth factor beta induced TGFBI Q15582 ✓ 2,17 8,26E-17 1,59 3,31E-03

Protein-glutamine gamma-glutamyltransferase 2 TGM2 P21980 ✓ ✓ ✓ ✓ 1,63 9,25E-12 0,815 1,63E-01

Thrombospondin-1 THBS1 P07996 ✓ 5,14 6,03E-30 1,66 2,96E-01

Tight junction protein ZO-3 TJP3 O95049 0,339 1,53E-14 4,99 9,80E-03

Stimulator of interferon genes protein TMEM173 Q86WV6 1,71 2,54E-07 0,964 8,68E-01

Target of Myb protein 1 TOM1 O60784 ✓ 0,836 3,84E-05 5,38 2,50E-68 1,80 1,49E-02

TNF receptor-associated factor 2 TRAF2 Q12933 1,72 4,22E-10 2,06 2,22E-01

Tetraspanin 8 TSPAN8 P19075 ✓ 0,606 1,31E-07 1,49 6,90E-02

UBE2D3 UBE2D3 P61077 ✓ 4,81 1,99E-53 1,08 4,47E-01

Ubiquilin-1 UBQLN1 Q9UMX0 4,71 1,67E-26 3,21 2,76E-05

Ubiquilin-2 UBQLN2 Q9UHD9 2,44 1,29E-05 2,87 2,74E-12 1,59 6,84E-03

Small subunit processome component 20 homolog UTP20 O75691 2,22 3,06E-13 12,4 1,58E-03

Vesicle associated membrane protein 8 VAMP8 Q9BV40 ✓ ✓ 0,677 1,11E-03 1,91 6,30E-04

Vesicle-associated membrane protein-associated protein B/C VAPB O95292 ✓ ✓ 2,30 1,11E-13 1,47 1,98E-03

Vinculin VCL P18206 ✓ 1,09 7,12E-03 ✓ ✓ 2,37 7,80E-10 103,2 1,16E-64 0,535 4,18E-04

Voltage-dependent anion-selective channel protein 1 VDAC1 P21796 ✓ ✓ ✓ 1,13 6,00E-03 1,56 5,95E-05

Vacuolar protein sorting-associated protein 28 homolog VPS28 Q9UK41 ✓ ✓ ✓ 3,21 1,02E-33 1,21 2,99E-01

Vacuolar protein sorting-associated protein 4A VPS4A Q9UN37 ✓ ✓ ✓ 5,79 2,57E-08 1,35 1,99E-03 1,16 2,14E-02

Vitronectin VTN P04004 ✓ 1,25 3,54E-02 0,925 8,51E-01

WD repeat-containing protein 1 WDR1 O75083 ✓ 0,762 9,71E-21 ✓ ✓ 2,47 4,21E-27 0,917 1,70E-01

Synaptobrevin homolog YKT6 YKT6 O15498 1,12 2,55E-01 ✓ ✓ 1,90 5,70E-07 1,40 1,05E-02

14-3-3 protein eta YWHAH Q04917 ✓ ✓ ✓ 3,24 5,42E-07 0,923 1,58E-02 1,11 5,12E-02