Identification of Aberrantly Expressed Long Non-Coding RNAs and Nearby Targeted Genes in Male Osteoporosis

Figures & data

Table 1 Patients Characteristics in RNA Sequencing

	Case 1	Case 2	Case 3	Control 1	Control 2
Age (years)	60	82	68	71	69
BMI(Kg/M^2)	31.8	16.73	22.5	22.7	30.5
BMD-T (femoral neck)	−4.2	−4	−2.5	0.5	−0.3
BMD-T (total lumbar vertebrae, L1-4)	−3.0	−4.4	−3.0	−0.6	1.0
BMD-T (total hip)	−3.8	−3.5	−2.3	0.4	0.7
History of smoking	No	No	No	No	No
History of Alcohol	No	No	No	No	No
History of coffee or carbonated drinks	No	No	No	No	No
Family history of matrilineal family	No	No	No	No	No
Lack of physical activity	No	No	No	No	No
Bone metabolism-related diseases	No	No	No	No	No
Bone metabolism-related drugs	No	No	No	No	No

Abbreviations: BMI, body mass index; BMD, bone mineral density.

Table 2 Top 10 Up- and Down-Regulated DEGs in Male Osteoporosis

Gene	Log2 (Fold-Change)	Log2 (Fold_Change) Normalized	P-value	Regulation
HBB	38.273358104	37.8935156174	<0.001	up
DAAM2	4.049243519	3.669401032	<0.001	up
KRT1	2.88216351	2.502321023	<0.001	up
IL18R1	2.716745816	2.336903329	<0.001	up
HLA-C	2.151771966	1.77192948	<0.001	up
IFIT1	2.132595751	1.752753264	<0.001	up
PFKFB2	1.940854019	1.561011533	<0.001	up
SIPA1L2	1.929315008	1.549472521	<0.001	up
WLS	1.717446143	1.337603657	<0.001	up
IL1R2	1.470397971	1.090555485	<0.001	up
HLA-DRB5	−3.99524647	−4.375088957	<0.001	down
FOLR3	−2.983447932	−3.363290418	<0.001	down
TMTC1	−2.97323309	−3.353075577	<0.001	down
PSMG4	−2.693022247	−3.072864733	<0.001	down
HBG1	−1.616140812	−1.995983298	<0.001	down
LTF	−1.424026283	−1.803868769	<0.001	down
HBA2	−1.177883217	−1.557725703	<0.001	down
HBA1	−1.128790938	−1.508633424	<0.001	down
RPS26	−1.080222198	−1.460064685	<0.001	down
GM2A	−1.033452527	−1.413295014	<0.001	down

Table 3 Top 10 Up- and Down-Regulated DElncRNAs in Male Osteoporosis

LncRNA	Log2 (Fold-Change)	Log2 (Fold-Change) Normalized	P-value	Regulation
LOC105372801	0.96622827	0.586385784	<0.001	up
LOC101927627	2.285128177	1.90528569	1.32E-10	up
HCG27	1.024098323	0.644255837	2.66E-07	up
TMX2-CTNND1	21.64147797	21.26163548	5.55E-06	up
LOC100129931	0.798952481	0.419109995	2.14E-05	up
LOC284454	1.281770969	0.901928482	2.88E-05	up
LOC643072	1.419376435	1.039533948	4.27E-05	up
LOC105371816	0.965234582	0.585392095	6.21E-05	up
LOC105377730	1.776493958	1.396651472	8.72E-05	up
LOC105376569	1.588230215	1.208387728	0.0001675	up
KCNQ1OT1	−0.323016511	−0.702858997	<0.001	down
NEAT1	−0.54808287	−0.927925356	<0.001	down
MALAT1	−0.116697115	−0.496539601	<0.001	down
LOC105370807	−3.663913842	−4.043756329	<0.001	down
LOC105374981	−0.187292593	−0.56713508	2.68E-12	down
LOC105374162	−0.135681661	−0.515524148	9.99E-12	down
LOC105377885	−0.786844269	−1.166686756	1.65E-09	down
LOC105376781	−0.138693678	−0.518536164	1.33E-08	down
LOC105376332	−1.392317423	−1.772159909	4.61E-07	down
LOC105377872	−0.788495895	−1.168338381	1.00E-06	down

Figure 1 The heat-maps of top 50 up- and down-regulated DEGs and DElncRNAs in male osteoporosis. (A) the heat-map of top 50 up- and down-regulated DEGs in male osteoporosis. Row and column were used to represent DEGs and samples, respectively. The color scale was used to represent the expression levels of DEGs. (B) the heat-maps of top 50 up- and down-regulated DElncRNAs in male osteoporosis compared to normal control. Row and column were used to represent DElncRNAs and samples, respectively. The color scale was used to represent the expression levels of DElncRNAs.

Figure 2 The male osteoporosis-specific PPI network. The PPI network was consisted of 101 nodes and 105 edges. Ellipses (nodes) were the proteins encoded by DEGs and ellipses with black border represented the proteins encoded by DEGs which belonged to the top 10 up- and down-regulated DEGs in male osteoporosis. Red and blue colors were used to represent up- and down-regulation in male osteoporosis, respectively.

Figure 3 The DElncRNAs-nearby targeted DEGs interaction network in male osteoporosis. The DElncRNAs-nearby targeted DEGs interaction network was consisted of 278 nodes and 168 edges. Ellipses and rhombuses were used to represent the DEGs and DElncRNAs in male osteoporosis, respectively. Red and blue colors were used to represent up- and down-regulation in male osteoporosis, respectively.

Figure 4 Functional annotation of all DEGs in male osteoporosis. (A) top 15 most significantly enriched biological process; (B) top 15 most significantly enriched cellular components; (C) top 15 most significantly enriched molecular functions; (D) top 15 most significantly enriched KEGG pathways. The x-axis shows -log FDR and y-axis shows the terms of GO/KEGG terms.

Figure 5 Pathway of osteoclast differentiation that enriched in DEGs in male osteoporosis. The red and green rectangles were represented the particles which regulated by the up- and down-regulated DEGs in male osteoporosis, respectively.

Figure 6 Functional annotations of nearby targeted DEGs of DElncRNAs in male osteoporosis. (A) top 15 most significantly enriched biological process; (B) top 15 most significantly enriched cellular components; (C) top 15 most significantly enriched molecular functions. The x-axis shows -log FDR and y-axis shows the terms of GO/KEGG terms.

Figure 7 The DElncRNAs-nearby targeted DEGs interaction network in male osteoporosis. The DElncRNAs-nearby targeted DEGs interaction network was consisted of 26 nodes and 22 edges. Ellipses and rhombuses were used to represent the DEGs and DElncRNAs in male osteoporosis, respectively. Ellipses with black or blue border represented the DEGs which belonged to the top 10 up- and down-regulated DEGs in male osteoporosis compared to normal control. Red and blue colors were used to represent up- and down-regulation in male osteoporosis, respectively.

Figure 8 QRT-PCR verification results. The X-axis was indicated different samples and the Y-axis was indicated the relative level of CCR2 mRNA (A) and LINC02009 lncRNA (B) for qRT-PCR results.