Identification of RPS14 as the 5q- syndrome gene by RNA interference screen

Identification of RPS14 as the 5q- syndrome gene by RNA interference screen

| Benjamin L. Ebert, Jennifer Pretz, Jocelyn Bosco, Cindy Y. Chang, Pablo Tamayo, Naomi Galili, Azra Raza, David Root, Eyal Attar, Steven R. Ellis, Todd R. Golub
The supplementary materials provide detailed information on the identification of RPS14 as the gene associated with 5q- syndrome through an RNA interference screen. Key findings include: 1. **CD71/GlyA Expression**: Flow cytometry analysis shows that the percentage of immature erythroid precursor cells expressing CD71+/GlyA- decreases over time during in vitro erythroid differentiation, while the percentage of CD71+/GlyA+ cells increases. 2. **Screen of the Common Deleted Region**: A screen was conducted to identify genes that block terminal erythroid differentiation in the common deleted region of 5q- syndrome. Multiple shRNAs targeting each gene were used, and the ratio of mature (CD71+/GlyA+) to immature (CD71+/GlyA-) cells was determined. RPS14 was found to significantly alter the megakaryocytic/erythroid ratio. 3. **Enrichment Analysis**: Enrichment analysis using a Kolmogorov-Smirnov score showed that RPS14 is the only gene with a statistically significant enrichment score, indicating that it significantly alters the megakaryocytic/erythroid ratio. 4. **Combination of shRNAs**: Combinations of shRNAs targeting RPS14 and other 5q genes did not show an additive effect over the knock-down of RPS14 alone, as evaluated by flow cytometry for glycophorin A and CD41. 5. **Confirmation of Peak Identities**: Polysome profiles confirmed the identities of ribosomal subunit peaks using agarose gel electrophoresis. 6. **Relative Expression in Patients**: RNA from patients with and without 5q- syndrome was analyzed, showing that RPS14 expression was decreased in patients with 5q deletions compared to those without. 7. **Apoptosis and Pre-rRNA Processing**: Apoptosis was evaluated in TF-1 cells expressing RPS14 shRNAs or treated with apoptosis-inducing agents. Pre-rRNA processing was also assessed, showing that RPS14 shRNA did not affect the 30S/18SE ratio but increased it without apoptosis. 8. **Overexpression of RPS14**: Overexpression of RPS14 in CD34+ cells from patients with 5q- syndrome induced an erythroid gene expression program, as demonstrated by gene expression profiling and Gene Set Enrichment Analysis (GSEA). These supplementary materials provide comprehensive evidence supporting the role of RPS14 in 5q- syndrome and its impact on erythroid differentiation and megakaryocytic/erythroid ratio.The supplementary materials provide detailed information on the identification of RPS14 as the gene associated with 5q- syndrome through an RNA interference screen. Key findings include: 1. **CD71/GlyA Expression**: Flow cytometry analysis shows that the percentage of immature erythroid precursor cells expressing CD71+/GlyA- decreases over time during in vitro erythroid differentiation, while the percentage of CD71+/GlyA+ cells increases. 2. **Screen of the Common Deleted Region**: A screen was conducted to identify genes that block terminal erythroid differentiation in the common deleted region of 5q- syndrome. Multiple shRNAs targeting each gene were used, and the ratio of mature (CD71+/GlyA+) to immature (CD71+/GlyA-) cells was determined. RPS14 was found to significantly alter the megakaryocytic/erythroid ratio. 3. **Enrichment Analysis**: Enrichment analysis using a Kolmogorov-Smirnov score showed that RPS14 is the only gene with a statistically significant enrichment score, indicating that it significantly alters the megakaryocytic/erythroid ratio. 4. **Combination of shRNAs**: Combinations of shRNAs targeting RPS14 and other 5q genes did not show an additive effect over the knock-down of RPS14 alone, as evaluated by flow cytometry for glycophorin A and CD41. 5. **Confirmation of Peak Identities**: Polysome profiles confirmed the identities of ribosomal subunit peaks using agarose gel electrophoresis. 6. **Relative Expression in Patients**: RNA from patients with and without 5q- syndrome was analyzed, showing that RPS14 expression was decreased in patients with 5q deletions compared to those without. 7. **Apoptosis and Pre-rRNA Processing**: Apoptosis was evaluated in TF-1 cells expressing RPS14 shRNAs or treated with apoptosis-inducing agents. Pre-rRNA processing was also assessed, showing that RPS14 shRNA did not affect the 30S/18SE ratio but increased it without apoptosis. 8. **Overexpression of RPS14**: Overexpression of RPS14 in CD34+ cells from patients with 5q- syndrome induced an erythroid gene expression program, as demonstrated by gene expression profiling and Gene Set Enrichment Analysis (GSEA). These supplementary materials provide comprehensive evidence supporting the role of RPS14 in 5q- syndrome and its impact on erythroid differentiation and megakaryocytic/erythroid ratio.
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