Impact of NSD1 Alternative Transcripts in Actin Filament Formation and Cellular Division Pathways in Fibroblasts
Abstract
:1. Introduction
2. Materials and Methods
2.1. Patients
2.2. Cell Culture
2.3. Analysis of NSD1 Sequence
2.4. siRNA Transfection
2.5. Indirect Immunofluorescence
2.6. Gene Expression Profiling
2.7. Quantitative Real-Time RT–PCR
2.8. Western Blotting
2.9. Bioinformatic Analysis
3. Results
3.1. Effect of Anti-NSD1 siRNAs on NSD1 Isoform Expression
3.2. NSD1 Protein Isoform AT3 Exhibits Distinct Subcellular Localization with Respect to the Long Canonical Isoform in Fibroblasts
3.3. NSD1 AT2 and NSD1 AT3 Isoforms May Mediate Transcriptomic Effects on BCL2, KRAS and p53 Signaling Pathways
3.4. Gene Set Enrichment Analysis to Perform an Unbiased Biological Interpretation of the Data
3.5. NSD1 Is Involved in the Cytoskeleton Actin Stress Fiber (SFs) Organization Pathway
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Probe Set ID | Gene Symbol | Gene Name | Seq. Name | Log2 Fold Change | p-Value | p-Value Adjusted |
---|---|---|---|---|---|---|
A_33_P3389286 | SFN | stratifin | NM_006142 | 5.2 | 1.61 × 10−1 | 0.002 |
A_33_P3321205 | BEGAIN | brain-enriched guanylate kinase-associated | NM_001159531 | 1 | 0.002 | 0.011 |
A_33_P3363898 | TUBG1 | tubulin, γ 1 | NM_001070 | −0.29 | 0.011 | 0.03 |
A_32_P377880 | GDNF | glial cell derived neurotrophic factor | NM_001190468 | −0.4 | 0.009 | 0.025 |
A_23_P80694 | ACTR8 | ARP8 actin-related protein 8 homolog | NM_022899 | −0.5 | 0.003 | 0.014 |
A_23_P377376 | ACTR2 | ARP2 actin-related protein 2 homolog | NM_001005386 | −0.5 | 0.003 | 0.013 |
A_33_P3330283 | SP1 | Sp1 transcription factor | NM_138473 | −0.6 | 0.022 | 0.049 |
A_24_P726336 | PHACTR2 | phosphatase and actin regulator 2 | NM_001100164 | −0.6 | 0.018 | 0.043 |
A_33_P3363674 | NFYC | Nuclear transcription factor Y | NM_001142590 | −0.7 | 0.0019 | 0.010 |
A_33_P3260016 | NEDD1 | neural precursor cell expressed, developmentally down-regulated 1 | NM_152905 | −0.7 | 0.003 | 0.014 |
A_24_P251969 | FGF1 | fibroblast growth factor 1 | NM_000800 | −0.8 | 1.13 × 10−2 | 0.029 |
A_23_P153256 | FGF3 | fibroblast growth factor 3 | NM_005247 | −0.8 | 8.64 × 10−6 | 0.035 |
A_23_P123193 | ACTR3B | ARP3 actin-related protein 3 homolog B | NM_020445 | −0.9 | 2.3 × 10−2 | 0.002 |
A_23_P162596 | ACTR6 | ARP6 actin-related protein 6 homolog | NM_022496 | −1 | 0.006 | 0.019 |
A_23_P311201 | ACTR3 | ARP3 actin-related protein 3 homolog | NM_005721 | −1.1 | 6.2 × 10−2 | 0.031 |
A_23_P208961 | KRAS | Kirsten rat sarcoma viral oncogene homolog (KRAS) | NM_004985 | −1.1 | 8.00 × 10−6 | 0.039 |
A_33_P3363799 | NCAM1 | neural cell adhesion molecule 1 | NM_001242607 | −3.1 | 0.011 | 0.030 |
A_22_P00001924 | DDB1 | damage-specific DNA binding protein 1 | NM_001923 | −3.9 | 7.04 × 10−2 | 0.029 |
Probe Set ID | Gene Symbol | Gene Name | Seq. Name | Log2 Fold Change | p-Value | p-Value Adjusted |
---|---|---|---|---|---|---|
A_23_P77493 | TUBB3 | tubulin, β 3 class III | NM_006086 | 1 | 0.002 | 0.006 |
A_23_P102122 | ARPC2 | actin-related protein 2/3 complex, subunit 2, 34 kDa | NM_152862 | −0.2 | 0.007 | 0.010 |
A_23_P377376 | ACTR2 | ARP2 actin-related protein 2 | NM_001005386 | −0.4 | 7.9 × 10−3 | 0.004 |
A_24_P167473 | ARPC3 | actin-related protein 2/3 complex, subunit 3, 21 kDa | NM_001278556 | −0.5 | 0.002 | 0.006 |
A_33_P3416946 | ACTR10 | actin-related protein 10 homolog | NM_018477 | −0.7 | 0.013 | 0.014 |
A_24_P72479 | ARPC1A | actin-related protein 2/3 complex, subunit 1A, 41 kDa | NM_006409 | −0.8 | 0.005 | 0.009 |
A_23_P19291 | TUBB2A | tubulin, β 2A class IIa | NM_001069 | −0.8 | 0.002 | 0.006 |
A_33_P3338909 | ARPC5 | actin-related protein 2/3 complex, subunit 5, 16 kDa | NM_001270439 | −0.9 | 9.12 × 10−2 | 0.004 |
A_23_P60283 | PHACTR2 | phosphatase and actin regulator 2 | NM_014721 | −1 | 0.001 | 0.005 |
A_21_P0014389 | ACTR3 | ARP3 actin-related protein 3 homolog | NM_005721 | −1 | 1.96 × 10−3 | 0.003 |
A_23_P162596 | ACTR6 | ARP6 actin-related protein 6 homolog | NM_022496 | −1 | 5.24 × 10−2 | 0.002 |
A_23_P123193 | ACTR3B | ARP3 actin-related protein 3 homolog B | NM_005247 | −1.1 | 0.002 | 0.007 |
Probe Set ID | Gene Symbol | Gene Name | Seq. Name | Log2 Fold Change | p-Value | p-Value Adjusted |
---|---|---|---|---|---|---|
A_23_P344555 | NEDD9 | neural precursor cell expressed, developmentally down-regulated 9 | NM_006403 | −0.05 | 1.13 × 10−2 | 0.0013 |
A_33_P3270009 | NCOA1 | nuclear receptor coactivator 1 | NM_147223 | −0.4 | 8.13 × 10−1 | 0.01 |
A_32_P75902 | MEIOB | meiosis specific with OB domains | NM_152764 | −0.6 | 8.08 × 10−8 | 0.01 |
A_23_P76774 | GSC | goosecoid homeobox | NM_173849 | −1.1 | 1.92 × 10−2 | 0.002 |
A_33_P3302389 | FEM1A | fem−1 homolog a | NM_018708 | −1.3 | 2.22 × 10−10 | 1.74 × 10−6 |
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Conteduca, G.; Cangelosi, D.; Baldo, C.; Arado, A.; Testa, B.; Wagner, R.T.; Robertson, K.D.; Dequiedt, F.; Fitzsimmons, L.; Malacarne, M.; et al. Impact of NSD1 Alternative Transcripts in Actin Filament Formation and Cellular Division Pathways in Fibroblasts. Genes 2024, 15, 1117. https://doi.org/10.3390/genes15091117
Conteduca G, Cangelosi D, Baldo C, Arado A, Testa B, Wagner RT, Robertson KD, Dequiedt F, Fitzsimmons L, Malacarne M, et al. Impact of NSD1 Alternative Transcripts in Actin Filament Formation and Cellular Division Pathways in Fibroblasts. Genes. 2024; 15(9):1117. https://doi.org/10.3390/genes15091117
Chicago/Turabian StyleConteduca, Giuseppina, Davide Cangelosi, Chiara Baldo, Alessia Arado, Barbara Testa, Ryan T. Wagner, Keith D. Robertson, Franck Dequiedt, Lane Fitzsimmons, Michela Malacarne, and et al. 2024. "Impact of NSD1 Alternative Transcripts in Actin Filament Formation and Cellular Division Pathways in Fibroblasts" Genes 15, no. 9: 1117. https://doi.org/10.3390/genes15091117