Omics-Driven Biomarkers of Psoriasis: Recent Insights, Current Challenges, and Future Prospects

Figures & data

Figure 1 The workflow of biomarker discovery.

Table 1 Transcriptomic Signatures of Psoriasis

Gene Name	Method	Platform	Status	Tissue Type	Ref
AKR1B10, AKR1B15	Microarray	Affymetrix	Over-expressed	Psoriatic plaque	^Citation18
S100A7A, DEFB4, SERPINB4, PI3	Microarray	Affymetrix	Over-expressed	psoriatic plaque	^Citation19
THRSP, ELOVL3, WIF1, BTC, CCL27	Microarray	Affymetrix	Under-expressed	psoriatic plaque	^Citation19
S100A12A, S100A7A, LCE3E, DEFB4A, IL19	RNA-seq	AB 5500xl	Over-expressed	Lesional psoriasis	^Citation20
K16, DEFB5, IL19, IL8, CCL20, CXCL1	Microarray	Affymetrix	Under-expressed	Lesional psoriatic skin	^Citation16
SERPINB3, CD24, S100A12, KRT6A, SERPINB1, IL1F9, CD36, S100A8,	Microarray	Affymetrix	Over-expressed	Lesional psoriasis	^Citation21
CRIP1, CLDN8, FHL1, ASPN, LAMB4, EFEMP1, PCDH21, ITM2A, ADRB2, ID4, CCL27, FAM13A, TGFBI, POSTN	Microarray	Affymetrix	Under-expressed	Lesional psoriasis	^Citation21
S100A12, KLK7, SCCA2, SPRR2A, SPRR1B, TGM1, TGM3, PI3, DEFB2, S100A7, HBP17	Microarray	Affymetrix	Over-expressed	Chronic psoriasis vulgaris	^Citation15
IRF9, NMI, SUB1	qRT-PCR, ELISA	-	Under-expressed	Lesional psoriasis	^Citation32
S100A12, CCL22, IL1RN, TNPO1, CCL2, VEGFA, ICAM1, IL15, CXCL5, ACCP, TNF TNFRSF1B	Microarray	Affymetrix	Over-expressed	Psoriasis vulgaris skin and serum	^Citation22
TCN1, SPRR2C, OASL, BACH2, TMPRSS11D, ATP12A, LCN2, RHCG, KYNU,	Microarray	Affymetrix	Over-expressed	Lesional psoriasis	^Citation30
CLDN8, P2RX1, MERTK, ISG15, TMPSS11E, STAT1	Microarray	Affymetrix	Under-expressed	Lesional psoriasis	^Citation30
S100A8, S100A9, S100A12, PLK1, IRF7	RNA-seq	Illumina Hiseq X10	Under-expressed	PBMC of pustular psoriasis	^Citation29
CIITA and NKTR	RNA-seq	Illumina Hiseq X10	Over-expressed	PBMC of pustular psoriasis	^Citation29
SCYA19, SCYA21, SDF1, CXCL16, MIP4, TRIM22, STAT1	Microarray	Affymetrix	Over-expressed	Psoriasis vulgaris skin	^Citation23
SCYA27, SCYA14	Microarray	Affymetrix	Under-expressed	Psoriasis vulgaris skin	^Citation23

Abbreviations: RNA-seq, RNA-sequencing; PBMC, peripheral blood mononuclear cell.

Table 2 Epigenomic Signatures of Psoriasis

Epigenetic Marker*	Marker Type	Expression Pattern	Tissue Type	Method	Reference
Promoter 2 of SHP-1	DMR	Hypomethylated	Lesional psoriatic skin	BS-PCR	^Citation97
ID4 promoter	DMR	Hypermethylated	Chronic psoriatic plaque	BS-Seq	^Citation48
p15 and p21	DMR	Hypomethylated	Chronic psoriatic plaque	BS-PCR	^Citation49
p16INK4a	DMR	Hypomethylated	Psoriatic skin	BS-PCR	^Citation98
FOXP3	DMR	Hypermethylated	Psoriatic whole blood	BS-HRM-PCR	^Citation50
OAS2	DMR	Hypomethylated	Psoriatic skin	BS- Pyrosequencing	^Citation52
S100A9, PTPN22	DMR	Hypomethylated	Psoriatic skin	Methylation Array	^Citation51
SELENBP1	DMR	Hypermethylated	Psoriatic skin	Methylation Array	^Citation51
PDCD5 and TIMP2	DMR	Hypermethylated	Psoriasis vulgaris skin	MeDIP-Seq	^Citation54
MGRN1	DMR	Hypermethylated	Psoriatic skin	BS-PCR	^Citation53
TP73-AS1, EMX2OS, PCOLCE-AS1	lncRNA	Over-expressed	Psoriatic skin	RNA-seq	^Citation42
PRINS	lncRNA	Over-expressed	Psoriatic skin	RT-PCR	^Citation34
LncRNA-AL162231.4	lncRNA	Under-expressed	Psoriatic skin	RNA-seq, Microarray	^Citation47
TRHDE-AS1, CYP4Z2P, HINT1	lncRNA	Over-expressed	Chronic plaque psoriasis skin	RNA-seq	^Citation43
MSX2P1/miR-6731-5p/S100A7	lncRNA-miRNA-mRNA complex	Over-expressed/Under-expressed/over-expressed	Leisonal psoriatic skin	Microarray, RT-PCR	^Citation46
miR-143, miR-223	miRNA	Under-expressed	Psoriatic patients’ PBMCs	Microarray, RT-PCR	^Citation38
miR-142-3p, miR-21, miR-378, miR-100, miR-31, miR-203-AS, miR-135b, miR-205	miRNA	Over-expressed	Psoriatic skin	RNA-seq, qRT-PCR, WB	^Citation35
miR-146b	miRNA	Over-expressed	Leisonal psoriatic PBMC	qRT-PCR, ISH	^Citation99
H4	Histone	Hypoacetylated	Psoriasis vulgaris PBMCs	RT-PCR	^Citation56
H3K27 and H3K4	Histone	methylated	Psoriatic PBMC	ELISA	^Citation55
miR-155-5p	miRNA	Over-expressed	Psoriatic skin	Microarray, RT-PCR	^Citation36
miR-203	miRNA	Over-expressed	Leisonal psoriatic skin	qRT-PCR, Western Blot	^Citation39
miR-125	miRNA	Under-expressed	Psoriatic skin	qRT-PCR	^Citation100
miR-99a, miR-197	miRNA	Under-expressed	Psoriatic skin	Microarray, ISH	^Citation37
miR-520	miRNA	Under-expressed	HaCaT cell line	qRT-PCR, WB	^Citation101

Note: *represents methylated DNA region, lncRNA, miRNA or histone modification.

Abbreviations: DMR, differentially methylated region; LncRNA, long-non-coding RNA; miRNA, micro RNA; BS-PCR, bisulfite-specific polymerase chain reaction; BS-Seq, bisulfite sequencing; BS-HRM-PCR, bisulfite high resolution melt polymerase chain reaction; BS-pyrosequencing, bisulfite pyrosequencing; MeDIP-Seq, methylated DNA immunoprecipitation sequencing; RT-PCR, reverse transcription polymerase chain reaction; RNA-seq, RNA sequencing; qRT-PCR, real time quantitative reverse transcription polymerase chain reaction; WB, Western blot; ISH, in situ hybridization; ELISA, enzyme-linked immunosorbent assay.

Table 3 Metabolomic Signatures of Psoriasis

Metabolite	Expression Pattern	Tissue Type	Method	Ref
Arachidonic acid, 12-HETE (hydroxyeicosatetraenoic acid)	Higher/higher	chronic plaque psoriasis skin	GC-MS	^Citation57
α-ketoglutaric acid, asparagine, glutamine, glucuronic acid	Higher/lower/lower/higher	Psoriatic patient serum	GC-TOF-MS	^Citation58
Threonine, ornithine, and methionine	Lower/lower/lower	Plasma from mild or severe psoriasis	LC-MS	^Citation59
Glucose, myo-inositol, taurine, choline	Higher/higher/lower/lower	Lesional psoriatic skin	MR spectroscopy	^Citation60
Homocysteine, ADMA, citrulline	Higher/higher/lower	chronic plaque psoriasis blood	HPLC–MS	^Citation61
Choline, glutamic acid, phenylalanine, lactic acid, urocanic acid, citrulline	Higher/higher/higher/lower/lower/lower	Lesional psoriatic skin	nano-DESI MS	^Citation62
Crotonic acid, azelaic acid, ethanolamine, and cholesterol	Lower/lower/ lower/lower	Psoriatic patients’ serum	GC-MS	^Citation63
citrate, alanine, methylsuccinate, trigonelline, carnitine, and hippurate	lower	Psoriatic patients’ urine	NMR	^Citation64
tetranor-12(S)-HETE,12(S)-HETE	Higher/lower	Psoriatic patients’ urine	HPLC–MS-MS	^Citation65

Abbreviations: GC-MS, gas chromatography mass spectrometry; GC-TOF-MS, gas chromatography time-of-flight mass spectrometry; LC-MS, liquid chromatography mass spectrometry; MR spectroscopy, magnetic resonance spectroscopy; HPLC-MS, high performance liquid chromatography mass spectrometry; nano-DESI MS, nanospray desorption electrospray ionization mass spectrometry; NMR, nuclear magnetic resonance.

Table 4 Glycomic Signatures of Psoriasis

Glycoprotein or Glycoform Name	Method	Specification	Lesion Type	Expression Pattern	Ref
Zinc-α2-glycoprotein, Cathepsin D	IHC, RT-PCR	Pathogenesis marker	Lesional psoriasis	Under-expressed	^Citation69
Corneodesmosin	IHC	Pathogenesis marker	Psoriasis Vulgaris skin	Over-expressed	^Citation70
CD134 and CD134L	IHC	Pathogenesis marker	Psoriasis Vulgaris skin	Over-expressed	^Citation71
MMP2, TIMP2	Western blot, Zymography	Pathogenesis marker	plaque psoriasis skin	Over-expressed	^Citation72
Chondroitin Sulfate	Phage display, ELISA	Therapeutic target	Psoriasis skin	Over-expressed	^Citation73
E-selectin, IL-8	ELISA	Activity marker	Lesional Psoriasis serum	Over-expressed	^Citation74
S100A8, S100A9	ELISA, IHC	Proliferation marker	Psoriasis Vulgaris serum	Over-expressed	^Citation75
CD163, LAMP2, MARCO	IHC, RT-PCR	Pathogenesis marker	Lesional Psoriasis skin	Over-expressed	^Citation76
Galectin-3	Western Blot, RT-PCR	Diagnostic marker	Psoriasis Vulgaris skin	Under-expressed	^Citation77
GlycA	nMRI, PET/CT	Inflammatory marker	Psoriasis	Under-expressed	^Citation79
Haptoglobin fucosylation	HPLC, Lectin array	Pathogenesis marker	psoriasis vulgaris plasma	Over-expressed	^Citation13
Endocan	ELISA	Risk assessment marker	psoriasis vulgaris serum	Over-expressed	^Citation81
VEGF	ELISA	Therapeutic target	Psoriatic serum	Over-expressed	^Citation82
CEACAM1, CEACAM6, CEA	Immunoblot	Pathogenesis marker	Psoriasis Vulgaris skin	Over-expressed	^Citation83
Podoplanin	RT-PCR, Western Blot	Pathogenesis marker	Lesional Psoriasis skin	Over-expressed	^Citation84

Abbreviations: ELISA, enzyme-linked immunosorbent assay; IHC, immunohistochemistry; RT-PCR, reverse transcriptase polymerase chain reaction; HPLC, high performance liquid chromatography; nMRI, nuclear magnetic resonance imaging; PET/CT, positron emission tomography – computed tomography.

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