Particulate matter less than 10 μm (PM₁₀) activates cancer related genes in lung epithelial cells

Figures & data

Table 1. qRT-PCR primer information.

Gene	Accession No.	Product length	Sequence (F: Forward/R: Reverse)
CERS6-AS1	NR_045786.1, NR_045787.1	198	F: CGGCTGTGGAGGTAATCTTATT R: AGGTCCATGAAAGTTTGGCT
CYP1A1	NM_000499.5, NM_001319217.2, NM_001319216.2	80	F: GGATGAGAACGCCAATGTCC R: TGTCAAACCCAGCTCCAAAG
LINC01816	NR_024444.1	92	F: TTCTCTAAACTGCCGCGATG R: GGCTGGAGGGACAGAGTTC
CHI3L2	NM_001025197.1, NM_001025199.2, NM_004000.3	83	F: AGGGCCAAGCTCCTACTAC R: CCATGACCACCTTCTCTGATG
BPIFA2	NM_001319164.2, NM_080574.4	101	F: ACAAGTTCGTGAATAGCGTG R: CAGGGAGTGGATGAAGATGC
C1orf189	NM_001010979.3	95	F: AGAAGAAACCCGTATGCCAC R: GCAGCTTGACGGACCATTAG
CYP1B1	NM_000104.3	130	F: CGGCCACTATCACTGACATC R: ACGACCTGATCCAATTCTGC
CRTAC1	NM_001206528.2, NM_018058.7	116	F: GGACTTTGAGATCGTCGTGG R: CGTAGTAGGGTGAGCTGCG
CDIPT-AS1	NR_015396.1, NR_024370.1	97	F: TCAAGCTGCACCCTCCTTG R: CAAAGCCTCCTCCATGAGTTC
MEFV	NM_000243.3, NM_001198536.2	83	F: AGATCCAACTCCTCCACCAG R: TTCCATTTCTGAACGCAGGG
WFIKKN1	NM_053284.3	137	F: AGATGTATGGCAACGTGGTG R: CACAGAGAGTGGGAAGTCAG
PDE3A	NM_000921.4, NM_001244683.1	115	F: TGAAACAGAGTGCCTGAGAG R: CATGACAAGAGGTTCGGGAG
HIF3A	NM_022462.4, NM_152794.4, NM_152795.4, NM_152796.2	103	F: GGAGAGTATCGTCTGTGTCC R: CTGAATGGGTCTGCGAGAG
RGPD2	NM_001078170.2	118	F: AGGTAGTGAGAGAGAGAGCC R: CTTGGGTATGGAGGTTTCTTG
UPP2	NM_001135098.1, NM_173355.4	133	F: GGAATAGGGATTGCACCAGG R: CAGACAGTTCTTTGTCCAGTTC
TNFSF4	NM_001297562.2, NM_003326.5	125	F: GGTATCACATCGGTATCCTCG R: CTGAGTTGTTCTGCACCTTC
SCUBE2	NM_001170690.2, NM_001330199.2, NM_001367977.2, NM_020974.3	119	F: GAGGTGACAGAGAGCAACAC R: GTATCCTTACAGGTGCGGTC
USH2A	NM_007123.5, NM_206933.3	149	F: TCAGTTGGTTGTGTGACCAG R: GGAGAGGGTCCATTCAGTTC
SPIN2A	NM_019003.4	111	F: CAGGAGGAGTTGTAGATGGC R: ACACAGAGGGTTTGGTTTCC
CSNK1G2-AS1	NR_033400.1	99	F: TCCAGATTATGCAAACGGAGG R: TGTGATGGATTTGATGCAGATG

Figure 1. Venn diagram: the number of selected genes (Left: upregulated genes, Right: down regulated genes).

Table 2. Top 10 upregulated genes based on NGS results.

Gene	Gene ID	${\mathit{Log}}_2$ FC					Mean ${\mathit{Log}}_2$ FC
		A549	BEAS-2B	NCI-H292	NCI-H358	HCC-827
CERS6-AS1	100861402	0	9.264546	2.603576	0	10.203257	4.4142758
CYP1A1	1543	5.791131	3.5019065	1.6503337	6.4653176	3.6737695	4.21649166
LINC01816	100133985	3.9500154	5.243921	0.0919466	2.9002497	4.1104364	3.25931382
CHI3L2	1117	3.91904	2.95507	1.9908174	3.089704	0.895698	2.57006588
BPIFA2	140683	5.4528737	3.8683584	0	3.238818	0	2.51201002
C1orf189	388701	0.37685856	2.5400324	4.7506833	4.8246193	0	2.498438712
CYP1B1	1545	3.855276	1.835235	2.250385	2.410229	1.978739	2.4659728
CRTAC1	55118	3.0631703	1.6210691	1.0310698	4.11449	2.4237342	2.45070668
CDIPT-AS1	440356	3.34983	1.9172676	1.9774233	0.79256207	4.1486464	2.437145874
MEFV	4210	4.4437695	1.73431	2.517296	2.8876875	0.4871619	2.41404498

The order of genes was arranged in the order of the average value.

FC indicates fold change.

Table 3. Top 10 down regulated genes based on NGS results.

Gene	Gene ID	${\mathit{Log}}_2$ FC					Mean ${\mathit{Log}}_2$ FC
		A549	BEAS-2B	NCI-H292	NCI-H358	HCC-827
WFIKKN1	117166	−3.128075	−2.8599928	−3.6617926	−2.2506022	−3.4626412	−3.07262076
PDE3A	5139	−2.64282	−1.985941	−0.4189085	−4.52294343	−3.4321864	−2.600559866
HIF3A	64344	−3.7611496	−3.9656172	−2.2571223	−2.93798093	0	−2.584374006
RGPD2	400966	−1.5777714	−2.7655523	−3.7538457	−2.9762993	−1.7802739	−2.57074852
UPP2	151531	−3.2619754	−1.9713619	−3.5384872	−2.0089476	−1.7228113	−2.50071668
TNFSF4	7292	−3.4981155	−4.9354773	−0.1320266	−1.2461033	−2.4626412	−2.45487278
SCUBE2	57758	−0.171633	−0.9744007	−4.662819	−2.1895198	−4.0476036	−2.40919522
USH2A	7399	−5.76115	−2.13241034	−1.0210305	−1.7332882	−0.8928797	−2.308151748
SPIN2A	54466	−5.3965173	−1.3253762	−0.7835579	−2.50934	−1.3114252	−2.26524332
CSNK1G2-AS1	255193	−3.9562893	−1.0013619	−2.5952883	−2.539142	−1.1170058	−2.24181746

The order of genes was arranged in the order of the average value.

FC indicates fold change.

Table 4. Validation of the top 10 upregulated genes by qRT-PCR.

Gene	Fold change					Mean fold change
	A549	BEAS-2B	NCI-H292	NCI-H358	HCC-827
CERS6-AS1	0.69	NC	NC	NC	NC	0.69
CYP1A1	8.3	33.7	2.6	96.6	4.7	29.18
LINC01816	1.23	1.19	1.03	1.17	NC	1.155
CHI3L2	1.86	0.73	0.92	1.39	0.56	1.092
BPIFA2	1.77	7.53	3.45	3.49	NC	4.06
C1orf189	0.83	0.81	0.89	1.56	NC	1.0225
CYP1B1	5.98	1.53	2.75	5.89	1.92	3.614
CRTAC1	5.1	NC	NC	NC	NC	5.1
CDIPT-AS1	1.22	0.66	0.9	1.16	NC	0.985
MEFV	0.64	0.82	0.82	1.54	NC	0.955

NC indicates not calculated; As a result of PCR, RNA was not detected. When the mean fold change was calculated, this value was excluded.

Table 5. Validation of the top 10 down regulated genes by qRT-PCR.

Gene	Fold change					Mean fold change
	A549	BEAS-2B	NCI-H292	NCI-H358	HCC-827
WFIKKN1	0.58	0.4	0.57	1.45	0.36	0.672
PDE3A	0.42	NC	0.67	1.11	NC	0.733
HIF3A	NC	0.39	0.74	0.69	NC	0.607
RGPD2	2.67	2.38	NC	NC	NC	2.525
UPP2	0.4	0.27	0.97	0.73	NC	0.593
TNFSF4	1.14	NC	0.65	1.86	NC	1.217
SCUBE2	1.87	NC	0.61	NC	NC	1.24
USH2A	NC	NC	0.44	1.47	NC	0.955
SPIN2A	1.35	0.59	0.76	1.76	0.67	1.026
CSNK1G2-AS1	0.52	0.25	0.64	1.61	NC	0.755

NC indicates not calculated; As a result of PCR, RNA was not detected. When the mean fold change was calculated, this value was excluded.