The Whole Blood Transcriptomic Analysis in Sickle Cell Disease Reveals RUNX3 as a Potential Marker for Vaso-Occlusive Crises
Abstract
1. Introduction
2. Results
2.1. Characteristics of Participants
2.2. Determination of the Differentially-Expressed Genes
2.3. Potential Genetic Marker for Vaso-Occlusive Crisis
2.4. Validation of RUNX3 Through qRT-PCR and ELISA
3. Discussion
3.1. Molecular Mechanisms of RUNX3 in VOC Pathophysiology
- (1)
- Immune System Regulation: Based on our GO term enrichment analysis (Figure 2), RUNX3 down-regulation significantly impacts immune system processes, particularly through: (a) T-Cell Development and Function: RUNX3′s role in CD8+ T cell development aligns with our finding of down-regulated T cell receptor binding pathways.This is supported by previous studies showing RUNX3′s critical function in T-cell lineage specification [30]. The significant down-regulation of IL7R (12.76-fold) and CD3E (11.28-fold) in our study further supports this immune dysregulation pathway
- (2)
- Inflammatory Response: Our findings showed significant alterations in inflammatory pathways, specifically: (a) Cytokine Regulation: RUNX3 down-regulation correlates with altered inflammatory mediator expression. This is evidenced by the substantial down-regulation of CCL5 (9.24-fold) in our VOC samples. Previous studies have shown RUNX3′s protective role against inflammatory response through regulation of the JAK2/STAT3 pathway [33].
- (3)
- Cellular Response Mechanisms: The GO term enrichment analysis revealed: (a) Signal Transduction: Up-regulation of cellular localization and signal transduction regulation pathways. These changes suggest adaptive responses to the inflammatory and hypoxic environment during VOC. The diagram below illustrates the implications of RUNX3 gene downregulation on various molecular pathways and biological processes, as suggested by our g:Profiler results.
3.2. Integration with VOC Pathophysiology
- (a)
- Immune System Disruption: Impaired T-cell development and function, evidenced by down-regulation of key T-cell markers (IL7R, CD3E). Altered MHC protein complex binding, affecting immune response regulation
- (b)
- Inflammatory Cascade: Disrupted cytokine production and signaling. Altered inflammatory mediator expression (CCL5 down-regulation).
- (c)
- Cellular Stress Response: Enhanced cellular localization and signal transduction
3.3. Molecular Mechanisms Based on GO Term Enrichment Analysis
3.4. Timeline Limitations
3.5. Functional Confirmation Needs
4. Materials and Methods
4.1. Study Population
4.2. Sample Collection
4.3. RNA Extraction and Gene Expression Analysis
4.4. Quantitative Real-Time Polymerase Chain Reaction
4.5. Enzyme-Linked Immunosorbent Assay
4.6. Statistical Analysis
4.7. Gene Ontology (GO) Term Enrichment Analysis
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Parameters | Steady-State | VOC | p-Values | |
---|---|---|---|---|
Gender [n (%)] | Male | 9 (90) | 9 (90) | 1 |
Female | 1 (10) | 1 (10) | ||
Age Mean in years ± SD | 33 ± 10.82 | 34.9 ± 9.3 | 0.68 | |
No. of VOC per year ± SD | 9.7 ± 6.16 | 8.3 ± 5.38 | 0.59 | |
No. of Hospital admissions per year Mean ± SD | 3.3 ± 1.83 | 3.7 ± 1.64 | 0.61 | |
White Blood Cell counts Mean in × 109/L ± SD | 5.4 ± 2.95 | 6.05 ± 3.91 | 0.68 | |
Red Blood Cell counts Mean in × 1012/L ± SD | 4.89 ± 0.94 | 4.07 ± 0.95 | 0.07 | |
Hemoglobin Mean in g/dL ± SD | 11.17 ± 1.14 | 10.48 ± 1.51 | 0.27 | |
Platelet Mean in × 109/L ± SD | 309.19 ± 205.84 | 201.2 ± 118.04 | 0.17 | |
Hemoglobin F Mean in % ± SD | 13.88 ± 8.3 | 18.26 ± 6.02 | 0.2 | |
Hemoglobin S Mean in % ± SD | 79.81± 7.97 | 76.25± 5.41 | 0.26 |
ID | Gene Symbol | Chromosome | Group | p-Values | Fold Change |
---|---|---|---|---|---|
SCD Patients in Steady-State Compared to Healthy Controls | |||||
TC1100010092.hg.1 | EIF4G2; SNORD97 | chr11 | Multiple_Complex | 1.31 × 10−10 | −16.33 |
TC0200007835.hg.1 | ACTR2 | chr2 | Multiple_Complex | 3.00 × 10−11 | −8.22 |
TC1500009865.hg.1 | ANP32A | chr15 | Multiple_Complex | 1.79 × 10−9 | −6.67 |
TC1700007383.hg.1 | RPL23A; SNORD4B; SNORD42B; SNORD42A | chr17 | Multiple_Complex | 1.93 × 10−11 | −6.6 |
TSUnmapped00000264.hg.1 | RPL7A | Coding | 2.88 × 10−12 | −6.47 | |
TC0700010538.hg.1 | HNRNPA2B1 | chr7 | Multiple_Complex | 3.42 × 10−12 | −6.07 |
TC0600007378.hg.1 | HIST1H4J | chr6 | Coding | 1.34 × 10−8 | −5.81 |
TC1500008312.hg.1 | IQGAP1 | chr15 | Multiple_Complex | 1.18 × 10−5 | −5.64 |
TC0800010667.hg.1 | PDE7A | chr8 | Multiple_Complex | 2.26 × 10−8 | −5.64 |
TC0600011227.hg.1 | HIST1H4K | chr6 | Coding | 1.66 × 19−8 | −5.6 |
SCD Patients in VOC Compared to Healthy Controls | |||||
TC0500007138.hg.1 | IL7R | chr5 | Multiple_Complex | 2.75 × 10−10 | −12.76 |
TC1100009200.hg.1 | CD3E | chr11 | Multiple_Complex | 2.61 × 10−12 | −11.28 |
TC1700012052.hg.1 | ACTG1 | chr17 | Multiple_Complex | 2.01 × 10−7 | −10.4 |
TC1200007758.hg.1 | HNRNPA1 | chr12 | Multiple_Complex | 6.70 × 10−10 | −9.75 |
TC0600011173.hg.1 | GUSBP2 | chr6 | Multiple_Complex | 2.47 × 10−7 | −9.28 |
TC1700010447.hg.1 | CCL5 | chr17 | Coding | 4.51 × 10−8 | −9.24 |
TC0500013430.hg.1 | GNB2L1; SNORD95; SNORD96A | chr5 | Multiple_Complex | 6.41 × 10−9 | −8.96 |
TC0100007676.hg.1 | LCK | chr1 | Multiple_Complex | 8.11 × 10−10 | −8.92 |
TC0400011548.hg.1 | LEF1 | chr4 | Multiple_Complex | 7.22 × 10−9 | −8.88 |
TC0600011517.hg.1 | HLA-DPA1 | chr6 | Multiple_Complex | 6.94 × 10−7 | −8.79 |
ID | Gene Symbol | Chromo-Some | p-Values | Fold Change | ||
---|---|---|---|---|---|---|
VOC vs. Steady-State | VOC vs. Healthy | Steady-State vs Healthy | ||||
TC0100017110.hg.1 | FCMR | chr1 | 2.75 × 10−7 | −10.98 | −9.24 | −1.98 |
TC0200008268.hg.1 | GNLY | chr2 | 1.76 × 10−5 | −7.37 | −8.92 | −1.48 |
TC1200010850.hg.1 | TESPA1 | chr12 | 2.22 × 10−5 | −6.3 | −8.72 | −1.48 |
TC1700010447.hg.1 | CCL5 | chr17 | 7.39 × 10−7 | −6.24 | −7.92 | −1.46 |
TC0600007657.hg.1 | HLA-DQA1 | chr6 | 3.97 × 10−5 | −6.1 | −6.5 | −1.41 |
TC1900011774.hg.1 | EMP3 | chr19 | 2.17 × 10−7 | −5.99 | −6 | −1.34 |
TC0500012470.hg.1 | CD74 | chr5 | 1.06 × 10−6 | −5.89 | −5.9 | −1.32 |
TC1200006738.hg.1 | KLRG1 | chr12 | 0.0001 | −5.72 | −5.83 | −1.19 |
TC1200012571.hg.1 | ITFG2 | chr12 | 8.44 × 10−9 | −5.52 | −5.82 | −1.15 |
TC2200008641.hg.1 | RAC2 | chr22 | 9.48 × 10−7 | −5.43 | −5.8 | −1.07 |
TC0200011075.hg.1 | PTMA | chr2 | 3.16 × 10−8 | −5.41 | −5.76 | −1.07 |
TC1000011904.hg.1 | ABLIM1 | chr10 | 5.35 × 10−7 | −5.22 | −5.69 | −1.06 |
TC1600006888.hg.1 | CIITA | chr16 | 1.76 × 10−7 | −5.21 | −5.69 | 1 |
TC1200012801.hg.1 | CS | chr12 | 2.63 × 10−6 | −5.19 | −5.34 | 1.01 |
TC1200012583.hg.1 | CD27 | chr12 | 2.89 × 10−5 | −5.14 | −4.99 | 1.03 |
TC1100013190.hg.1 | CFL1 | chr11 | 6.80 × 10−7 | −4.97 | −4.59 | 1.05 |
TC0600007650.hg.1 | HLA-DRA | chr6 | 7.56 × 10−6 | −4.96 | −4.53 | 1.1 |
TC1900007839.hg.1 | FXYD5 | chr19 | 2.52 × 10−8 | −4.95 | −4.53 | 1.12 |
TC1200010616.hg.1 | TUBA1B | chr12 | 1.20 × 10−7 | −4.8 | −4.36 | 1.14 |
TC0100007676.hg.1 | LCK | chr1 | 6.31 × 10−7 | −4.52 | −4.31 | 1.14 |
TC0300006993.hg.1 | CRTAP | chr3 | 2.83 × 10−6 | −4.4 | −4.27 | 1.15 |
TC1100007790.hg.1 | CD5 | chr11 | 8.94 × 10−8 | −4.39 | −4.18 | 1.16 |
TC1400006656.hg.1 | OXA1L | chr14 | 1.78 × 10−8 | −4.36 | −4.16 | 1.18 |
TC0100013339.hg.1 | RUNX3 | chr1 | 2.33 × 10−8 | −4.12 | −4.08 | 1.22 |
TC0100018246.hg.1 | LRRC8C | chr1 | 1.94 × 10−6 | −4.09 | −4.04 | 1.3 |
TC0800009819.hg.1 | DOK2 | chr8 | 3.24 × 10−6 | −4.07 | −4.03 | 1.32 |
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Taha, S.; Abdulwahab, H.; Aljishi, M.; Sultan, A.; Bakhiet, M.; Spicuglia, S.; Belhocine, M. The Whole Blood Transcriptomic Analysis in Sickle Cell Disease Reveals RUNX3 as a Potential Marker for Vaso-Occlusive Crises. Int. J. Mol. Sci. 2025, 26, 6338. https://doi.org/10.3390/ijms26136338
Taha S, Abdulwahab H, Aljishi M, Sultan A, Bakhiet M, Spicuglia S, Belhocine M. The Whole Blood Transcriptomic Analysis in Sickle Cell Disease Reveals RUNX3 as a Potential Marker for Vaso-Occlusive Crises. International Journal of Molecular Sciences. 2025; 26(13):6338. https://doi.org/10.3390/ijms26136338
Chicago/Turabian StyleTaha, Safa, Hawra Abdulwahab, Muna Aljishi, Ameera Sultan, Moiz Bakhiet, Salvatore Spicuglia, and Mohamed Belhocine. 2025. "The Whole Blood Transcriptomic Analysis in Sickle Cell Disease Reveals RUNX3 as a Potential Marker for Vaso-Occlusive Crises" International Journal of Molecular Sciences 26, no. 13: 6338. https://doi.org/10.3390/ijms26136338
APA StyleTaha, S., Abdulwahab, H., Aljishi, M., Sultan, A., Bakhiet, M., Spicuglia, S., & Belhocine, M. (2025). The Whole Blood Transcriptomic Analysis in Sickle Cell Disease Reveals RUNX3 as a Potential Marker for Vaso-Occlusive Crises. International Journal of Molecular Sciences, 26(13), 6338. https://doi.org/10.3390/ijms26136338