CiliOPD: a ciliopathy-associated COPD endotype

Respiratory Research

Table 1 List of the main commonly deregulated cilia/ciliopathy-associated genes (n = 24) in COPD patients

Genes Ids	Uniprot Id	Gene name	Gene expression (Log2 fold change vs non-COPD)				Ref	HPA^a	SC^b
Whole lung			GSE47460	GSE57148	GSE76925	GSE103174			%	P
BBS7	Q8IWZ6	Bardet-Biedl syndrome 7 protein		0.21	− 0.29	− 0.06		MCC	+	All
BBS9	Q3SYG4	Bardet-Biedl syndrome 9 protein	− 0.01	0.13	0.04		[6]	MCC	+ +	MCC
CALM3	P0DP25	Calmodulin-3	0.02	0.11	0.03			MCC	+ + +	All
CEP78	Q5JTW2	Centrosomal protein of 78 kDa		0.10	0.10	− 0.05		NDC	+ +	MCC
DZIP1	Q86YF9	DAZ-interacting protein ½	0.02	0.22	0.11			MCC	+ +	MCC
GLI2	P10070	GLI family zinc finger protein 2	0.04	0.20	0.20		[17, 18]	All	+	All
NEK6	Q9HC98	Never in mitosis A-related kinase 6	0.05	0.40	0.09	0.08	[19]	EC	+	All
NUBP2	Q9Y5Y2	Nucleotide-binding protein 2	− 0.01	− 0.56	0.09			All	+ +	All
PDE6D	O43924	Retinal rod rhodopsin-sensitive cGMP 3′,5′-cyclic phosphodiesterase subunit delta	0.01	− 0.17	0.03			All	+	All
PRPF4	O43172	U4/U6 small nuclear ribonucleoprotein Prp4		0.15	0.03	0.04		All	+	All
PRPF8	Q6P2Q9	Pre-mRNA-processing-splicing factor 8	− 0.01	0.34	0.02			All	+ +	All
PTPDC1	A2A3K4	Protein tyrosine phosphatase domain-containing protein 1	− 0.02	0.12	0.04			NDC	+	All
TMEM138	Q9NPI0	Transmembrane protein 138	0.02	− 0.18	0.06			MCC	+ +	MCC
WDPCP	095876	WD repeat-containing and planar cell polarity effector protein fritz homolog	− 0.02	0.21		− 0.09	[20]	EC	+ +	MCC

Genes Ids	Uniprot Id	Gene name	Gene expression (Log2 fold change vs non-COPD)			Ref	HPA^a	SC^b
Small airway epithelial cells (SAEC)			GSE11784	GSE37147	GSE56341			%	P
ADAM15	Q13444	Disintegrin and metalloproteinase domain-containing protein 15		0.04	0.07	[21, 24]	MCC	+	All
ADCY6	O43306	Adenylate cyclase type 6		0.02	0.02		MCC	+	EC
ANKMY2	Q8IV38	Ankyrin repeat and MYND domain-containing protein 2	0.35	− 0.01			ND	+	All
ARMC4	Q5T2S8	Armadillo repeat-containing protein 4		− 0.02	− 0.02		MCC	+ + +	MCC
BBS4	Q96RK4	Bardet-Biedl syndrome 4 protein		− 0.03	− 0.03		EC	+ +	MCC
DCDC2	Q9UHG0	Doublecortin domain-containing protein 2		− 0.03	− 0.05	[22, 23]	All	+ +	MCC
EFCAB2	Q5VUJ9	Dynein regulatory complex protein 8		− 0.03	− 0.05		MCC	+ + +	MCC
PROM2	Q8N271	Prominin-2	0.55	0.04	0.06		EC	+ +	EC
TTC23	Q5W5X9	Tetratricopeptide repeat protein 23		− 0.02	− 0.04		All	+	All
WDR34	Q96EX3	Cytoplasmic dynein 2 intermediate chain 2	0.40	0.01		[6]	EC	+ + +	MCC

^aHPA, Human Protein Atlas protein localization (cell population)
^bSC, Single cell transcriptomic signature: % (percentage of cell expressing the transcript of interest; + , low (< 25%); + + , intermediate (25–50%); + + + , high (> 50%)) and P (principal cell population expressing the transcript of interest); MCC multiciliated cells, NDC non-differentiated cells, EC epithelial cells, All, epithelial and non-epithelial cells; ND not detected

ISSN: 1465-993X