Identification of Novel Mutations and Expressions of EPAS1 in Phaeochromocytomas and Paragangliomas
Abstract
:1. Introduction
2. Materials and Methods
2.1. Recruitments of Tissues and Sample Selection
2.2. Clinical Data of the Selected Cases
2.3. Extractions of DNA and RNA
2.4. High-Resolution Melt (HRM) Curve Analysis
2.5. Confirmation of Mutations by Sanger Sequencing
2.6. In Silico Analysis
2.7. Quantitative Real-Time PCR (qPCR) Analysis
2.8. Immunofluorescence
2.9. Statistical Analysis
3. Results
3.1. Identification of Novel EPAS1 Mutations in Phaeochromocytomas/Paragangliomas
3.2. EPAS1 DNA Number Variations in Phaeochromocytomas/Paragangliomas
3.3. EPAS1 mRNA Expressions in Phaeochromocytomas/Paragangliomas
3.4. EPAS1 Protein Expression in Phaeochromocytomas/Paragangliomas
3.5. Association of EPAS1 DNA Number Variation, mRNA Expression, Protein Expression and Mutations in Phaeochromocytomas
4. Discussion
5. Conclusions
Author Contributions
Funding
Conflicts of Interest
References
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Sample ID | Type | Change in DNA Sequence | Change in Protein Sequence | DNA Copy Number Change | mRNA Expression | Protein Expression | Effects on Protein Features | In Silico Prediction | ||
---|---|---|---|---|---|---|---|---|---|---|
Mutation Taster | PROVEAN | SIFT | ||||||||
P3 | PCC | c.1091A>T | p.Lys364Met | No change | High | High | Amino acids sequence change Protein structure (might be) affected Splice site changes | Diseases causing | Deleterious | Damaging |
P33 | PCC | c.1091A>T | p.Lys364Met | Amplification | High | High | Amino acids sequence change Protein structure (might be) affected Splice site changes | Diseases causing | Deleterious | Damaging |
P78 | PCC | c.1129A>T | P.Ser377Cys | Amplification | High | High | Amino acids sequence changed | Polymorphism | Neutral | Tolerated |
P81 | PCC | c.1091A>T | p.Lys364Met | Amplification | No Change | No Change | Amino acids sequence change Protein structure (might be) affected Splice site changes | Diseases causing | Deleterious | Damaging |
P93 | PCC | c.1129A>T | P.Ser377Cys | Amplification | High | High | Amino acids sequence changed | Polymorphism | Neutral | Tolerated |
P94 * | PCC | c.1091A>T | p.Lys364Met | Amplification | No Change | Low | Amino acids sequence change Protein structure (might be) affected Splice site changes | Diseases causing | Deleterious | Damaging |
P99 | PCC | c.1091A>T | p.Lys364Met | Amplification | High | High | Amino acids sequence change Protein structure (might be) affected Splice site changes | Diseases causing | Deleterious | Damaging |
P122 * | PGL | c.1091A>T | p.Lys364Met | Amplification | High | Low | Amino acids sequence change Protein structure (might be) affected Splice site changes | Diseases causing | Deleterious | Damaging |
Features | Number | Mutation Positive | Mutation Negative | p-Value |
---|---|---|---|---|
Total patients | 71 (100.00%) | 8 (11.26%) | 63 (88.74%) | - |
Gender | ||||
Male | 37 (52.11%) | 4 (10.81%) | 33 (89.19%) | 0.596 |
Female | 34 (47.89%) | 4 (11.76%) | 30 (88.24%) | |
Age | ||||
≤50 | 40 (56.34%) | 6 (15.00%) | 34 (85.00%) | 0.229 |
>50 | 31 (43.66%) | 2 (6.45%) | 29 (93.55%) | |
Race | ||||
Chinese | 56 (78.87%) | 8 (14.29%) | 48 (85.71%) | 0.134 |
Non-Chinese | 15 (21.13%) | - | 15 (100.00%) | |
Side | ||||
Unilateral | 63 (88.73%) | 7 (11.11%) | 56 (88.89%) | 0.636 |
Bilateral | 8 (11.27%) | 1 (12.50%) | 7 (87.50%) | |
Tumour location | ||||
Adrenal gland | 57 (80.28%) | 6 (10.53%) | 51 (89.47%) | 0.497 |
Carotid body | 14 (19.72%) | 2 (12.29%) | 12 (85.71%) | |
Tumour size | ||||
<50 mm | 33 (46.48%) | 1 (3.030%) | 32 (96.97%) | 0.044 |
≥50 mm | 38 (53.52%) | 7 (18.42%) | 31 (81.58%) | |
Tumour weight * | ||||
≤50 gm | 17 (45.95%) | - | 17 (100.00%) | 0.000 |
>50 gm | 20 (54.05%) | 3 (15.00%) | 17 (85.00%) | |
Tumour types | ||||
Non-metastasizing | 59 (83.10%) | 5 (8.47%) | 54 (91.53%) | 0.167 |
Metastasizing | 12 (16.90%) | 3 (25.00%) | 9 (75.00%) |
Features | Number | DNA Amplification | DNA Deletion | p-Value |
---|---|---|---|---|
Total patients | 71 (100.00%) | 8 (11.26%) | 63 (88.74%) | - |
Gender | ||||
Male | 37 (52.11%) | 28 (75.68%) | 9 (24.32%) | 0.347 |
Female | 34 (47.89%) | 28 (82.35%) | 6 (17.65%) | |
Age | ||||
≤50 | 40 (56.34%) | 30 (75.00%) | 10 (25.00%) | 0.271 |
>50 | 31 (43.66%) | 26 (83.87%) | 5 (16.13%) | |
Race | ||||
Chinese | 56 (78.87%) | 45 (80.36%) | 11 (19.64%) | 0.392 |
Non-Chinese | 15 (21.13%) | 11 (73.33%) | 4 (26.67%) | |
Side | ||||
Unilateral | 63 (88.73%) | 51 (80.95%) | 12 (19.05%) | 0.219 |
Bilateral | 8 (11.27%) | 5 (62.50%) | 3 (37.50%) | |
Tumour location | ||||
Adrenal gland | 57 (80.28%) | 48 (84.21%) | 9 (15.79%) | 0.037 |
Carotid body | 14 (19.72%) | 8 (57.14%) | 6 (15.79%) | |
Tumour size | ||||
<50 mm | 33 (46.48%) | 23 (69.70%) | 10 (30.30%) | 0.120 |
≥50 mm | 38 (53.52%) | 32 (84.21%) | 6 (15.79%) | |
Tumour weight * | ||||
≤50 gm | 17 (45.95%) | 14 (82.35%) | 3 (17.65%) | 0.857 |
>50 gm | 20 (54.05%) | 17 (85.00%) | 17 (15.00%) | |
Tumour types | ||||
Non-metastasizing | 59 (83.10%) | 47 (79.66%) | 12 (20.34%) | 0.852 |
Metastasizing | 12 (16.90%) | 9 (75.00%) | 3 (25.00%) |
Features | Number | High Expression | Low Expression | p-Value |
---|---|---|---|---|
Total patients | 45 (100.00%) | 24 (53.33%) | 21 (46.67%) | - |
Gender | ||||
Male | 25 (55.56%) | 14 (56.00%) | 11 (44.00%) | 0.460 |
Female | 20 (44.44%) | 10 (50.00%) | 6 (50.00%) | |
Age | ||||
≤50 | 28 (62.22%) | 16 (57.14%) | 12 (42.86%) | 0.363 |
>50 | 17 (37.78%) | 8 (47.06%) | 9 (52.94%) | |
Race | ||||
Chinese | 35 (77.78%) | 18 (51.43%) | 17 (48.57%) | 0.454 |
Non-Chinese | 10 (22.22%) | 6 (60.00%) | 4 (40.00%) | |
Side | ||||
Unilateral | 41 (91.11%) | 23 (56.10%) | 18 (43.90%) | 0.254 |
Bilateral | 4 (8.89%) | 1 (25.00%) | 3 (75.00%) | |
Tumour location | ||||
Adrenal gland | 37 (82.22%) | 24 (64.86%) | 13 (35.14%) | 0.001 |
Carotid body | 8 (17.78%) | - | 8 (100%) | |
Tumour size | ||||
<50 mm | 17 (37.78%) | 7 (41.2%) | 10 (58.8%) | 0.167 |
≥50 mm | 28 (62.22%) | 17 (60.71%) | 11 (39.29%) | |
Tumour weight * | ||||
≤50 gm | 6 (35.29%) | 3 (50.0%) | 3 (50.0%) | 0.627 |
>50 gm | 11 (64.71%) | 5 (45.45%) | 6 (54.55%) | |
Tumour types | ||||
Non-metastasizing | 36 (80.0%) | 22 (61.11%) | 14 (38.89%) | 0.057 |
Metastasizing | 9 (20.0%) | 2 (22.22%) | 7 (77.78%) |
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Islam, F.; Pillai, S.; Gopalan, V.; Lam, A.K.-Y. Identification of Novel Mutations and Expressions of EPAS1 in Phaeochromocytomas and Paragangliomas. Genes 2020, 11, 1254. https://doi.org/10.3390/genes11111254
Islam F, Pillai S, Gopalan V, Lam AK-Y. Identification of Novel Mutations and Expressions of EPAS1 in Phaeochromocytomas and Paragangliomas. Genes. 2020; 11(11):1254. https://doi.org/10.3390/genes11111254
Chicago/Turabian StyleIslam, Farhadul, Suja Pillai, Vinod Gopalan, and Alfred King-Yin Lam. 2020. "Identification of Novel Mutations and Expressions of EPAS1 in Phaeochromocytomas and Paragangliomas" Genes 11, no. 11: 1254. https://doi.org/10.3390/genes11111254