Identification of novel therapeutic targets for diabetic neuropathy through integrated proteomics and transcriptomics approaches

Table 1 Result summary of Mendelian randomization and sensitivity analysis on the associations between plasma proteins and diabetic neuropathy

Protein	Method	nSNP	Beta	SE	P value	FDR	OR (95%CI)	MR-Egger	Q
								P value	P value IVW
MICB	Weighted median	25	-0.339	0.036	0.000	0.000	0.71 (0.66-0.76)	0.062	0.000
	MR Egger	25	-0.189	0.121	0.132	0.902	0.83 (0.65-1.05)
	Inverse variance weighted	25	-0.371	0.082	0.000	0.002	0.69 (0.59-0.81)
NOTUM	Weighted median	6	-0.526	0.198	0.008	0.473	0.59 (0.40-0.87)	0.126	0.365
	MR Egger	6	-0.067	0.321	0.845	0.993	0.94 (0.50-1.75)
	Inverse variance weighted	6	-0.611	0.161	0.000	0.024	0.54 (0.40-0.74)
WARS	Inverse variance weighted	7	0.445	0.108	0.000	0.008	1.56 (1.26-1.93)	0.781	0.512
	MR Egger	7	0.493	0.198	0.055	0.766	1.64 (1.11-2.42)
	Weighted median	7	0.457	0.123	0.000	0.031	1.58 (1.24-2.01)
HSPA1B	Wald ratio	1	-4.552	0.501	0.000	0.000	0.01 (0.00-0.03)
BTN3A1	Wald ratio	1	-2.852	0.695	0.000	0.009	0.06 (0.01-0.23)
PSMB9	Wald ratio	1	-3.272	0.854	0.000	0.022	0.04 (0.01-0.20)
SCGN	Inverse variance weighted	2	-1.415	0.375	0.000	0.026	0.24 (0.12-0.51)
CSNK2B	Wald ratio	1	1.470	0.888	0.000	0.000	4.35 (3.59-5.10)
BRD2	Wald ratio	1	0.623	0.564	0.000	0.000	1.86 (1.38-2.34)

OR: Odds ratio; CI: Confidence interval; nSNP: Number of single nucleotide polymorphisms; SNP: Single nucleotide polymorphisms; FDR: False discovery rate; MR: Mendelian randomization; IVW: Inverse variance-weighted.

Table 2 Mendelian randomization analysis of associations of plasma proteins with diabetic neuropathy in replicated stage (decode vs genome-wide association studies catalog)

Outcome	Exposure	Method	nSNP	Beta	SE	P value
GCST90129436	HSPA1B	Wald ratio	1	-0.997	1.117	0.372
GCST90129436	PSMB9	Wald ratio	1	1.346	1.542	0.383
GCST90129436	BTN3A1	Wald ratio	1	1.374	1.412	0.331
GCST90129436	SCGN	Inverse variance weighted	2	1.446	0.628	0.021
GCST90129436	NOTUM	Inverse variance weighted	4	-0.056	0.353	0.874
GCST90129436	MICB	Inverse variance weighted	22	-0.188	0.016	0.038
GCST90129436	WARS	Inverse variance weighted	6	-0.033	0.256	0.897
GCST90129436	BRD2	Wald ratio	1	3.393	1.267	0.007
GCST90129436	CSNK2B	Wald ratio	1	-5.066	1.980	0.010

nSNP: Number of single nucleotide polymorphisms; SNP: Single nucleotide polymorphisms.

Table 3 Mendelian randomization analysis of associations of plasma proteins with diabetic neuropathy in replicated stage (United Kingdom biobank pharma proteomics project vs genome-wide association studies Finngen)

Outcome	Exposure	Method	nSNP	Beta	SE	P value
DN	HSPA1B	Inverse variance weighted	2	3.696	2.072	0.074
DN	SCGN	Wald ratio	1	-0.938	0.346	0.007
DN	MICB	Inverse variance weighted	29	-0.187	0.001	0.008
DN	WARS	Inverse variance weighted	3	0.482	0.168	0.004
DN	BRD2	(-)	-	-	-	-
DN	CSNK2B	(-)	-	-	-	-
DN	PSMB9	(-)	-	-	-	-
DN	BTN3A1	(-)	-	-	-	-
DN	NOTUM	(-)	-	-	-	-

(-) represents that there is no match in the dataset. nSNP: Number of single nucleotide polymorphisms; SNP: Single nucleotide polymorphisms; DN: Diabetic neuropathy.

Table 4 Mendelian randomization analysis of associations of plasma proteins with diabetic neuropathy in replicated stage (United Kingdom biobank pharma proteomics project vs genome-wide association studies catalog)

Outcome	Exposure	Method	nSNP	β	SE	P value
GCST90129436	HSPA1B	Inverse variance weighted	3	-	0.61	0.320
				0.60	0
				6
GCST90129436	SCGN	Wald ratio	1	1.322	0.627	0.035
GCST90129436	MICB	Inverse variance weighted	27	-0.132	0.062	0.035
GCST90129436	WARS	Inverse variance weighted	2	-0.211	0.215	0.326
GCST90129436	BRD2	(-)	-	-	-	-
GCST90129436	CSNK2B	(-)	-	-	-	-
GCST90129436	PSMB9	(-)	-	-	-	-
GCST90129436	BTN3A1	(-)	-	-	-	-
GCST90129436	NOTUM	(-)	-	-	-	-

(-) represents that there is no match in the dataset. nSNP: Number of SNP; SNP: Single nucleotide polymorphisms.

Table 5 Summary of key target protein integration results

Proteins (genes)	Direction for DN risk of protein	Direction for DN risk of gene	Passed SMR analysis	Passed coloc analysis
Tier 1
BTN3A1	(-)	(-)	Yes	Yes
MICB	(-)	(-)	Yes	Yes
Tier 2
PSMB9	(-)	(-)	No	Yes
HSPA1B	(-)	(-)	No	Yes
SCGN	(-)	X	X	Yes
Tier 3
CSNK2B	(+)	(+)	No	No
BRD2	(+)	(+)	No	No
WARS	(+)	X	X	No
NOTUM	(-)	X	X	No

(+) represents that the beta value is positive; (-) represents that the beta value is negative. X represents the loss in the analysis due to data issues, where the relevant gene was not found. “Yes” indicates that the analysis has passed, while “No” indicates that it has not passed. DN: Diabetic neuropathy; SMR: Summary-data-based MR.

Table 6 Binding energy for Tier 1 target proteins with their drugs

Target	Drug	Binding energy (kcal/mol)
MICB	Cyclosporin A	-11.64
MICB	Valproic acid	-4.27
BTN3A1	Cyclosporin A	-10.39
BTN3A1	Valproic acid	-4.14