| Literature DB >> 32316437 |
Muzammil H Syed1, Abdelrahman Zamzam1, Jason Valencia1, Hamzah Khan1, Shubha Jain1, Krishna K Singh2, Rawand Abdin3, Mohammad Qadura4,5.
Abstract
Chronic limb-threatening ischemia (CLTI) results in devastating complications such as lower-limb amputations. In this study, a genome-wide plasma microRNAs (miRNA) sequencing was performed to identify miRNA(s) associated with CLTI. Blood samples were collected from early stage CLTI patients (ABI < 0.9) and non-PAD controls (ABI ≥ 0.9) for 3 experiments: discovery phase (n = 23), confirmatory phase (n = 52) and validation phase (n = 20). In the discovery phase, next generation sequencing (NGS) was used to identify miRNA circulating in the plasma CLTI (n = 13) patients, compared to non-PAD controls (n = 10). Two down-regulated miRNAs (miRNA-6843-3p and miRNA-6766-5p) and three upregulated miRNAs (miRNA-1827, miRNA-320 and miRNA-98-3p) were identified (≥2-fold change). In the confirmatory phase, these 5 deregulated miRNAs were further investigated in non-PAD (n = 21) and CTLI (n = 31) patients using qRT-PCR. Only miRNA-1827 was found to be significantly upregulated (≥3-fold, p-value < 0. 001) in the CLTI group. Lastly, to minimize the influence of confounding factors, miRNA-1827 plasma levels were validated in a third cohort of CLTI patients (n = 10) matched to non-PAD controls (n = 10). Our analysis demonstrated that miRNA-1827 expression was increased in the CLTI cohort (≥2-folds, p-value < 0.001). In summary, circulating miRNA-1827 is significantly elevated in patients with CLTI.Entities:
Keywords: chronic limb threatening ischemia; microRNA; next generation sequencing; quantitative polymerase chain reaction
Year: 2020 PMID: 32316437 PMCID: PMC7235988 DOI: 10.3390/diagnostics10040230
Source DB: PubMed Journal: Diagnostics (Basel) ISSN: 2075-4418
General demographics of the study subjects in the discovery, confirmation and validation experiments.
| Discovery Group ( | Confirmation Group ( | Validation Group ( | |||||||
|---|---|---|---|---|---|---|---|---|---|
| non-PAD ( | CLTI ( | non-PAD ( | CLTI ( | non-PAD ( | CLTI ( | ||||
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| |||||||||
| Age | 62.4(6.2) | 70.3(8.6) | 0.02 | 55.7(15.3) | 71.0(7.7) | <0.001 | 77.9(5.6) | 78.6(6.4) | 0.733 |
| ABI | 1.0 (0.1) | 0.4 (0.1) | <0.001 | 1.1 (0.1) | 0.4 (0.1) | <0.001 | 1.1 (0.1) | 0.5 (0.1) | <0.001 |
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| |||||||||
| Sex (male) | 5 (50) | 9 (69) | 0.417 | 8 (40) | 18 (58) | 0.258 | 9 (90) | 8 (80) | 1.00 |
| Hypertension | 5 (50) | 10 (77) | 0.221 | 3 (15) | 26 (84) | <0.001 | 8 (80) | 9 (90) | 1.00 |
| Hypercholesterolemia | 5 (50) | 12 (92) | 0.052 | 6 (30) | 26 (84) | <0.001 | 5 (50) | 9 (90) | 0.141 |
| Diabetes | 0 (0) | 1 (8) | 1.00 | 2 (10) | 14 (45) | 0.012 | 3 (30) | 2 (20) | 1.00 |
| Smoking History | 6 (60) | 12 (92) | 0.127 | 10 (50) | 25 (81) | 0.031 | 5 (50) | 8 (80) | 0.350 |
| Coronary artery disease | 0 (0) | 8 (62) | 0.003 | 1 (5) | 18 (58) | <0.001 | 3 (30) | 7 (70) | 0.179 |
| Stroke | 0 (0) | 0 (0) | NA | 1 (5) | 6 (19) | 0.229 | 0 (0) | 3 (30) | 0.211 |
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| Statin | 4 (40) | 13 (100) | 0.002 | 6 (30) | 24 (77) | 0.005 | 5 (50) | 9 (90) | 0.141 |
| ACEi/Arb | 3 (30) | 8 (62) | 0.214 | 3 (15) | 20 (65) | 0.001 | 7 (70) | 8 (80) | 1.00 |
| Beta Blocker | 1 (10) | 4 (31) | 0.339 | 1 (5) | 11 (36) | 0.017 | 3 (30) | 7 (70) | 0.179 |
| Insulin | 0 (0) | 0 (0) | NA | 0 (0) | 4 (13) | 0.145 | 0 (0) | 2 (20) | 0.474 |
ABI: Ankle bronchial index, ACEi/Arb: Angiotensin-converting enzyme (ACE) inhibitors. α the significance of the difference between CLTI and non-PAD groups. † Differences between groups were compared using Mann-Whitney test. ‡ Differences between groups were compared using chi-square test. Means and standard deviations were calculated for continuous variables; all numbers were rounded to one decimal place. Frequencies and percentages were calculated for categorical variables; all numbers were rounded up with zero decimal place. All p-values were rounded to three decimal places.
Figure 1Volcano plot representing the fold change and p-values for all miRNA identified via Next Generation Sequencing in CLTI patients (n = 13) relative to non-PAD controls (n = 10). All miRNA with at least 2-fold increase and p-value p < 0.05 are shown in the top left box (down regulated) and top right box (up regulated).
Figure 2Confirmation of Next Generation Sequencing. The plasma levels of upregulated miRNA in control non-PADs (n = 20) and CLTI patients (n = 31) were investigated via qRT-PCR. Compared with miRNA levels in control subjects, only miRNA-1827 showed a statistically significant increase in CLTI patients (3.2 folds, p-value < 0.001).
Figure 3Validation of miRNA-1827 in age-cardiovascular risk factors-matched non-PAD controls (n = 10) and CLTI (n = 10) patients. miRNA-1827 was validated in a new cohort of patients via qRT-PCR. Compared with miRNA levels in matched control, miRNA-1827 remained significantly increased in CLTI patients (2-folds, p-value < 0.001).
Top five gene ontologic terms populated by a CPDB over-representation analysis of the miRNA-1827.
| GO Term | Overlapping Gene IDs | |
|---|---|---|
| Positive regulation of transport | CASP8; HCAR2; AHSG; HCLS1; DAB2; PPID; BCL2 | 4.34 × 10−5 |
| Regulation of protein localization | CASP8; HCAR2; HCLS1; DAB2; LCP1; PPID; BCL2 | 4.80 × 10−5 |
| Regulation of transport | CASP8; THBS1; HCAR2; AHSG; HCLS1; DAB2; LCP1; PPID; BCL2 | 5.44 × 10−5 |
| Response to hormone | BTG2; CASP8; THBS1; AHSG; HCLS1; DAB2; BCL2 | 5.50 × 10−5 |
| Negative regulation of metabolic process | TNFSF13; BTG2; THBS1; HCAR2; AHSG; HCLS1; DAB2; PPID; GPRC5A; CTDSP2; BCL2 | 6.89 × 10−5 |
Top five biologic pathways populated by a CPDB over-representation analysis of miRNA-1827.
| Pathway | Protein Members | Source | |
|---|---|---|---|
| Hydroxycarboxylic acid-binding receptors | HCAR3; HCAR2 | Reactome | 6.07 × 10−6 |
| P53 signaling pathway— | BCL2; CASP8; THBS1 | KEGG | 0.0001 |
| Nanomaterial induced apoptosis | CASP8; BCL2 | Wikipathways | 0.0003 |
| Ceramide signaling pathway | CASP8; BCL2 | BioCarta | 0.0010 |
| Apoptosis—multiple species— | CASP8; BCL2 | KEGG | 0.0010 |