Article Figures & Data
Figures
- Figure 1.
Heatmap of top-ranked 20 miRNAs from postmenopausal samples. The heatmap provided insight into the data structure for each miRNA and sample. We used red and green colors for defining low and high expression values. Blue, cases; yellow, controls. The clustering methods partitioned the dataset into three clusters, identified on the left of the figure. Each miRNA is listed on the right.
- Figure 2.
Breast cancer disease-specific survival by miRNA expression. Kaplan–Meier analysis for the association between (A) miR145-3p and (B) miR145-5p expression levels with survival of patients with breast cancer (based on the METABRIC dataset). For each miRNA, we compared the third of patients with the highest expression levels of the corresponded miRNA (red) to the third of patients with the lowest expression (blue). The miRNA name and P value are indicated in the title.
- Figure 3.
In vitro effects of miR145-5p and miR145-3p. A, miR145-5p does not affect breast cancer cell proliferation. Proliferation assay was performed in MDA-MB-231 cells upon miR145-5p exogenous expression. Cells were collected and manually counted at the indicated time points. B, miR145-5p inhibits breast cancer cell migration. Transwell migration assay was performed in MDA-MB-231 and MDA-MB-468 cells upon miR145-5p exogenous expression. C, miR145-3p impinges breast cancer cell proliferation. Proliferation assay was performed in MDA-MB-231 cells upon miR145-3p exogenous expression. Cells were collected and manually counted at the indicated time points after transfection. D, miR145-3p impinges breast cancer cell colony formation ability. Clonogenic assay was performed in MDA-MB-231 cells upon miR145-3p exogenous expression. E, miR145-3p does not affect breast cancer cell migration. Transwell migration assay was performed in MDA-MB-231 cells upon miR145-3p exogenous expression. B, C, and E, histogram bars represent mean ± standard deviation of at least three independent replicates.
Tables
- Table 1.
Descriptive characteristics of the 133 postmenopausal women candidate to become breast cancer and 133 control women: baseline values
Cases Controls Median difference (IC 95%) t Student P value Age, y; median (SD) 57 (5.95) 56 (5.89) −0.5:2.5 0.85 Age at menarche, y; median (interquartile range) 13 (12–14) 13 (12–14) −0.36:0.36 0.93 IGF1; median (interquartile range) 115 (95.5–155) 111 (92.2–137.5) −6.2:14.2 0.16 TTS; median (interquartile range) 0.28 (0.21–0.36) 0.26 (0.2–0.32) −0.02:0.06 0.21 BMI, kg/m2; median (interquartile range) 25.6 (23.3–28.3) 25.7 (23.6–28.4) −1.13:0.78 0.42 Fasting glucose; median (interquartile range) 84 (78–91) 85 (78–90) −7.8:5.8 0.24 Alcohol intake, g/d; median (interquartile range) 4.8 (0–24) 3.4 (0–18) −2.3:5.1 0.75 Age at first birth; median (SD) 26 (4.6) 25 (3.6) −0.09:2.1 0.09 Full-term pregnancies; median (SD) 2 (1) 2 (1) −0.28:0.28 0.92 Smoking; % of smoker/ex smoker/not smoker 19/12/69 16/12/72 — 0.7a Abbreviations: IGFI, insulin growth factor 1; TTS, total testosterone.
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↵aχ2 P value.
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- Table 2.
List of the top 20-ranked miRNAs according to FDR values for miRNAs differentially expressed between women candidate to become breast cancer and healthy controls within the ORDET cohort
miRNA Log FCa P valuesb FDRc Downregulated miRNAs hsa-miR125a-5p −0.634 0.0021 0.400 hsa-miR141 −0.158 0.0023 0.400 hsa-miR582-5p −0.496 0.0028 0.400 hsa-miR138 −0.199 0.0034 0.400 hsa-miR199a-5p −0.581 0.0039 0.400 hsa-miR181c* −0.321 0.0041 0.400 hsa-miR28-3p −0.631 0.0042 0.400 hsa-miR224 −0.629 0.0047 0.400 hsa-miR145-3p −0.261 0.0053 0.408 hsa-miR223 −0.484 0.0079 0.503 hsa-miR145-5p −0.506 0.0083 0.503 hsa-miR539 −0.364 0.0098 0.504 hsa-miR99b −0.483 0.0112 0.504 hsa-miR199b-5p −0.314 0.0117 0.504 hsa-miR920 −0.147 0.0118 0.504 Upregulated miRNAs hsa-miR892b 0.460 0.0001 0.102 hsa-miR1288 0.304 0.0045 0.400 hsa-miR520a-3p 0.402 0.0061 0.430 hsa-miR542-5p 0.381 0.0102 0.504 hsa-miR122* 0.393 0.0118 0.504 NOTE: Downregulated and upregulated miRNAs in candidates to become breast cancer cases versus controls.
- Table 3.
Cancer predicted pathways targeted by the three clusters identified by the cluster analysis
miRNA cluster Most significant predicted pathways Cluster 1 Wnt signaling pathway miR145-5p miR199a-5p miR542-5p miR892b miR1288 Steroid biosynthesis Glycosylphosphatidylinositol(GPI)-anchor biosynthesis Hedgehog signaling pathway Adherens junction Transcriptional misregulation in cancer Pathways in cancer TGFβ signaling pathway MAPK signaling pathway Cell cycle Cluster 2 MAPK signaling pathway miR28-3p miR122* miR138 miR141 miR145-3p miR181c* miR520-3p miR539 miR920 ErbB signaling pathway mTOR signaling pathway Insulin signaling pathway PI3K-Akt signaling pathway Transcriptional misregulation in cancer Chemokine signaling pathway Cluster 3 MAPK signaling pathway miR99b miR582-5p miR199b-5p Transcriptional misregulation in cancer Pathways in cancer - Table 4.
miR145-3p modulation in breast cancer cases and in a variety of breast cancer tissues and peritumoral tissues by different databases
miR145-3p ORDET Biagioni et al. (7) CGAN Farazi et al. (33) Enerly et al. (34) Tumor 133 (cases) 63 694 168 101 Peritumor — 59 83 — — Normal 133 (controls) — — 11 — Platform Agilent Agilent Illumina Solexa Agilent Subsets case vs. control T vs. PT Lum A-B vs. basal — Basal vs. Lum A mut p53 vs. wt p53 ER-p53 mut vs. ER-p53 wt proliferative samples Modulation Down Down Down — Down Abbreviations: basal, basal breast cancer; DCIS, ductal carcinoma in situ; ER, estrogen receptor; IDC, invasive ductal carcinoma; lum, luminal breast cancer; mut p53, mutated p53; PT, peritumoral tissue; T, tumor tissue; wt, wild-type.
- Table 5.
miR145-5p modulation in breast cancer cases and in a variety of breast cancer tissues and peritumoral tissues by different databases
miR145-5p ORDET Biagioni et al. (7) CGAN Farazi et al. (33) Enerly et al. (34) Tumor 133 (cases) 63 694 168 101 Peritumor — 59 83 — — Normal 133 (controls) — — 11 — Platform Agilent Agilent Illumina Solexa Agilent Subsets Case vs. control T vs. PT Lum. B vs. Basal DCIS vs. normal; Basal vs, Lum A; IDC HER2+ ER− vs. normal mut p53 vs. wt p53; ER-p53 mut vs. ER-p53 wt proliferative samples Modulation Down Down Down Down Down Abbreviations: basal, basal breast cancer; DCIS, ductal carcinoma in situ; ER, estrogen receptor; IDC, invasive ductal carcinoma; lum, luminal breast cancer; mut p53, mutated p53; PT, peritumoral tissue; T, tumor tissue; wt, wild-type.
- Table 6.
miRNAs modulation in breast cancer tissues versus normal tissues in the 1,359 patients with breast cancer from the METABRIC study and in subtypes of breast cancer tissues versus normal tissues derived from the highly characterized subgroup of 81 participants
P value for all subtyped together P value for matched samples by subtype Expression in Caldas dataset (METABRIC) Direction of change N vs. T (81 vs. 1,278) Matched N vs. T (81) Normal-like (15) Her2 (5) Basal-like (15) Lum A (27) Lum B (19) KM P value Downregulated miRNAs hsa-miR125a-5p Expressed Upregulated in T <0.001 <0.001 0.814 0.110 0.724 <0.001 <0.001 0.791 hsa-miR141 Expressed Upregulated in T <0.001 <0.001 0.198 0.056 0.445 <0.001 <0.001 0.0637 hsa-miR582-5p Expressed Upregulated in T <0.001 <0.001 0.421 0.503 0.483 0.004 0.130 0.144 hsa-miR138 Not Expressed — — — — — — — — — hsa-miR199a-5p Expressed No difference 0.109 0.304 0.743 0.079 0.615 0.094 0.018 0.0043 hsa-miR181c* Expressed No difference 0.063 0.489 0.470 0.008 0.353 0.018 0.987 0.00857 hsa-miR28-3p Not Expressed — — — — — — — — — hsa-miR224 Expressed Downregulated in T <0.001 <0.001 <0.001 0.598 0.511 <0.001 <0.001 0.202 hsa-miR145-3p Expressed Downregulated in T <0.001 <0.001 <0.001 0.061 0.012 0.002 <0.001 0.00121 hsa-miR145-5p Expressed Downregulated in T <0.001 <0.001 0.005 0.007 <0.001 <0.001 <0.001 0.112 hsa-miR223 Expressed No difference 0.169 0.364 0.372 0.427 0.101 0.870 0.498 0.0086 hsa-miR539 Expressed Downregulated in T <0.001 0.081 0.263 0.570 0.974 0.747 0.008 0.0113 hsa-miR99b Expressed Downregulated in T 0.003 0.439 0.315 0.114 0.673 0.392 0.160 0.0197 hsa-miR199b-5p Expressed Downregulated in T <0.001 0.003 0.008 0.184 0.125 0.476 0.012 <0.001 hsa-miR920 Not expressed — — — — — — — — — Upregulated miRNAs hsa-miR892b Not expressed — — — — — — — — — hsa-miR1288 Not expressed — — — — — — — — — hsa-miR520a-3p Not expressed — — — — — — — — — hsa-miR542-5p Expressed No difference 0.122 0.249 0.565 0.256 0.060 0.095 0.103 0.0188 hsa-miR122* Not expressed — — — — — — — — — NOTE: For each miRNA, it is indicated whether it is expressed in the METABRIC dataset (column 2); for the expressed miRNAs, it is also indicated whether they are over- or underexpressed in the tumor tissue relative to normal samples (column 3), and corresponding P values for all samples together (column 4), only in matched tumor and normal samples from the same patient across all subtypes (column 5), and for each subtype alone (columns 6–10). The number of patients in each comparison is indicated in parentheses in the column heads. The last column contains P values for Kaplan–Meier analysis, comparing the difference in survival between the third of patients with the highest expression of the miRNA to the third of patients with lowest expression.
Abbreviations: N, normal tissue; T, tumoral tissue.
Supplementary Tables 1-18, Figure 1
Files in this Data Supplement:
- Data Supplement - Supplementary Table 1 - miR-125a-5p expression across different databases; Supplementary Table 2 - miR-99b expression across different databases; Supplementary Table 3 - miR-199a-5p expression across different databases; Supplementary Table 4 - miR-199b-5p expression across different databases; Supplementary Table 5 - miR-892b expression across different databases; Supplementary Table 6 - miR-141 expression across different databases; Supplementary Table 7 - miR-582-5p expression across different databases; Supplementary Table 8 - miR-138 expression across different databases; Supplementary Table 9 - miR-181c* expression across different databases; Supplementary Table 10 - miR-28-3p expression across different databases; Supplementary Table 11 - miR-1288 expression across different databases; Supplementary Table 12 - miR-224 expression across different databases; Supplementary Table 13 - miR-520a-3p expression across different databases; Supplementary Table 14 - miR-223 expression across different databases; Supplementary Table 15 - miR-539 expression across different databases; Supplementary Table 16 - miR-542-5p expression across different databases; Supplementary Table 17 - miR-122* expression across different databases; Supplementary Table 18 - miR-920 expression across different databases.
- Data Supplement - Supplementary Figure 1. qRT-PCR analysis of miR-145-5p expression in MDA-MB-231 cells used for proliferation assay.
- Data Supplement - Figure Legend Supplementary Material
Volume 23, Issue 11
