Analysis of Glaucoma Associated Genes in Response to Inflammation, an Examination of a Public Data Set Derived from Peripheral Blood from Patients with Hepatitis C

Figures & data

Table 1 Glaucoma Biomarker Gene Catalogue

Biomarker Gene	Literature Reference	Change in Expression (↑↓)/Seq. Variant (*)/Autoantibody Target (#)	Cell/Tissue Type
ABC1	Golubnitschaja & Flammer 2007^Citation70	↑	Blood, aqueous humor
AIF	Tezel et al, 2012^Citation40	↑, #	Retina
ANP	Nath et al, 2017^Citation71	↑	Leukocytes
ANX1	Tezel et al, 2012^Citation40	#	Serum
AP2TF	Golubnitschaja & Flammer, 2007^Citation70	↑	Leukocytes
ATOH7	Bhattacharya et al, 2013^Citation72	*	Review
BDNF	Ghaffariyeh et al, 2011^Citation73	↓	Serum
BIRC6	Tezel et al, 2012^Citation40	#	Serum
CALD1	Beutgen et al, 2019^Citation33	↓	Serum
CAT	Nath et al, 2017^Citation71	↓	Plasma
CAV1	Bhattacharya et al, 2013^Citation72	*	Review
CAV2	Bhattacharya et al, 2013^Citation72	*	Review
CBP	Tezel et al, 2012^Citation40	↑, #	Serum
CD23	Golubnitschaja & Flammer, 2007^Citation70	↑	Leukocytes
CDKN2BAS	Bhattacharya et al, 2013^Citation72	*	Blood
CDR1	Schmelter et al, 2017^Citation74	*	Blood
CDR2	Schmelter et al, 2017^Citation74	*	Blood
CDR3	Schmelter et al, 2017^Citation74	*	Blood
CYP46A1	Fourgeux et al, 2009^Citation75	*	Blood
DHC1	Tezel et al, 2012^Citation40	#	Serum
EFNA1	Tezel et al, 2012^Citation40	↑,#	Serum
ENO1	Beutgen et al, 2019^Citation33	#	Serum
EPO	Sun et al, 2020^Citation76	↑	Aqueous humor
ET1	Nath et al, 2017^Citation71	↑	Plasma
GAS7	Bhattacharya et al, 2013^Citation72	*	Review
GPX	Nath et al, 2017^Citation71	↓	Aqueous humor, Serum
HSPA1B	Beutgen et al, 2019^Citation33	#	Serum
HSPD1	Beutgen et al, 2019^Citation33	#	Serum
HTT	Tezel et al, 2012^Citation40	#	Serum
IL2	Nath et al, 2017^Citation71	↑	Blood
ITK	Golubnitschaja & Flammer, 2007^Citation70	↑	Leukocytes
LOX1	Bhattacharya et al, 2013^Citation72	*	Review
MDA	Nath et al, 2017^Citation71	↑	Plasma
MMP9	Golubnitschaja & Flammer, 2007^Citation70	↑	Leukocytes
MT1MMP	Golubnitschaja & Flammer, 2007^Citation70	↑	Leukocytes
NCAM1	Tezel et al, 2012^Citation40	#	Serum
NFRKB	Tezel et al, 2012^Citation40	#	Serum
NLRP2	Tezel et al, 2012^Citation40	#	Serum
P53	Golubnitschaja & Flammer, 2007^Citation70	↑	Leukocytes
PGAM1	Beutgen et al, 2019^Citation33	↑, #	Serum
SIX1	Bhattacharya et al, 2013^Citation72	*	Review
SOD	Nath et al, 2017^Citation71	↓	Aqueous humor, Serum
TAC	Nath et al, 2017^Citation71	↓	Serum
TIGR	Golubnitschaja & Flammer, 2007^Citation70	–	Leukocytes
TMCO1	Bhattacharya et al, 2013^Citation72	*	n/a
VDAC2	Beutgen et al, 2019^Citation33	#	Serum
VEGFA	Sun et al, 2020^Citation76	↑	Aqueous humor
VIM	Beutgen et al, 2019^Citation33	#	Serum
XAPC7	Golubnitschaja & Flammer, 2007^Citation70	↑	Leukocytes
XPGC	Golubnitschaja & Flammer, 2007^Citation70	↓	Leukocytes

Notes: Two reviews and 9 original research articles were used to identify potential glaucoma biomarkers. Column two indicates the reference for each gene identified in a study of human glaucoma patients. Column three indicates additional information from the study as follows: upregulated with glaucoma (↑), downregulated with glaucoma (↓), presence of a sequence variant (*), targeted by autoantibodies (#). Column four indicates the type of sample collected for each study or if the reference was from a review article. Please note that the majority of these samples were not collected from eye tissue.

Table 2 (VL-) Log2 Fold-Changes in Poly I:C-Responsive Glaucoma Biomarker Genes

Gene Symbol	Protein	Cell Population	FDR	Avg VL- Log2 FC
GPX1	Glutathione peroxidase 1	PBMC	3.54E-17	−2.32
GAS7	Growth arrest-specific protein 7	PBMC	6.53E-21	−2.08
MMP9	Matrix metalloproteinase-9	PBMC	9.35E-04	−1.66
ABCA1	Phospholipid-transporting ATPase ABCA1	PBMC	1.45E-03	−1.34
GPX4	Phospholipid hydroperoxide glutathione peroxidase	PBMC	1.61E-12	−1.17
GPX3	Glutathione peroxidase 3	PBMC	2.79E-13	−1.08
GPX4	Phospholipid hydroperoxide glutathione peroxidase	PBMC	8.93E-13	−1.05
GAS7	Growth arrest-specific protein 7	Macrophage	1.77E-05	−0.74
CAT	Catalase	PBMC	2.49E-11	−0.66
CAT	Catalase	PBMC	2.05E-07	−0.54
NCAM1	Neural cell adhesion molecule 1	PBMC	4.14E-08	0.48
NFKAPPAB1	Nuclear factor NF-kappa-B p105 subunit	PBMC	7.18E-11	0.55
ITK	Tyrosine-protein kinase ITK/TSK	PBMC	1.69E-06	0.76
HSPA1B	Heat shock 70 kDa protein 1B	PBMC	5.71E-07	0.78
HSPD1	60 kDa heat shock protein, mitochondrial	PBMC	1.57E-09	0.88
EDN1	Endothelin-1	PBMC	3.10E-10	1.13
HSPA1B	Heat shock 70 kDa protein 1B	Macrophage	6.21E-10	1.29

Notes: List of genes identified as having a significant (<0.05) P-value in the (VL-) and (VL+) groups. Criteria for selection included being present on the list of genes from Table 1 and having a P-value < 0.05.

Abbreviation: PBMC, peripheral blood mononuclear cells.

Table 3 Comparison of the Fold-Changes from the (VL-) and (VL+) Groups

Gene Symbol	Protein	Cell Population	Avg VL- Log2 FC	Avg VL+ Log2 FC	Δ Log2 FC	P-value
EDN1	Endothelin-1	PBMC	1.13	1.98	−0.86	0.0009
CAT	Catalase	PBMC	−0.66	−1.3	0.64	0.001
ABCA1	Phospholipid-transporting ATPase ABCA1	PBMC	−1.34	−0.5	−0.85	0.0276
CAT	Catalase	PBMC	−0.54	−0.85	0.31	0.0307
NCAM1	Neural cell adhesion molecule 1	PBMC	0.48	0.79	−0.31	0.0329
GPX1	Glutathione peroxidase 1	PBMC	−2.32	−2	−0.32	0.0377

Notes: List of genes identified as having a significant difference in expression between the (VL-) and (VL+) groups. Criteria for selection included being present on the list of genes from Table 1 and having a P-value < 0.05.

Abbreviations: FC, fold change; PBMC, peripheral blood mononuclear cells.

Figure 1 Regions of the eye expressing glaucoma biomarker genes found to be responsive to Poly(I:C) challenge in peripheral blood samples. Regions of the eye are listed along with the encoded proteins likely to affect them from the differentially expressed genes identified in Table 2. Differentially expressed genes were detected using microarray analysis of PBMCs taken from human blood samples of patients infected with HCV and then challenged with poly(I:C). Red indicates decreased PBMC gene expression compared to baseline in response to poly(I:C) challenge, while green indicates increased expression compared to baseline. Please note that the expression levels were not found in the regions indicated in the figure and do not represent them. That is beyond the scope of the current study. The regional classifications demonstrate areas where glaucoma-related immune response genes/proteins may be investigated in future studies.

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