Bioinformatic Identification of Potential RNA Alterations on the Atrial Fibrillation Remodeling from Human Pulmonary Veins
Abstract
:1. Introduction
2. Results
2.1. General Overview of Analysis Results
2.2. Differential Expression Genes (DEGs) in PV and LV
2.3. Co-Expression Network Analysis on DEGs
3. Discussion
3.1. The Priority of PV among Cardiac Regions on AF Remodeling
3.2. The Possible Basis of the Electrical Remodeling in PV in AF
3.3. Possible Classifying Post-Acquired Disturbances in AF by the Network Analysis
3.4. Limitations
4. Materials and Methods
4.1. RNA Extractions from Donated Hearts and Right Atrial Appendage Collections
4.2. RNA-Seq and Data Processing on the Samples
4.3. Differential Expression Gene (DEG) Analysis
4.4. Clustering and Heatmap Visualization
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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NO. | AF/SR | Age | Sex | Strain | Tabaco | Alcohol | HD | HT | DM | Cancer | Samples |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | SR | 52 | M | Caucasian | Yes | Yes | No | No | No | No | SAN, LA, LAA, RA, LV, RV, PV |
2 | SR | 46 | M | Filipino | Yes | Yes | No | medication | medication | No | SAN, LA, LAA, RA, LV, RV, PV |
3 | SR | 23 | F | Caucasian | Yes | No | No | No | No | No | SAN, LA, LAA, RA, LV, RV, PV |
4 | SR | 50 | M | Japanese | Yes | Yes | MR, TR | medication | No | No | RAA |
5 | SR | 50 | M | Japanese | Yes | Yes | MR | No | No | No | RAA |
6 | AF | 58 | M | Caucasian | Yes | Yes | CAD, AF | No | No | No | SAN, LA, LAA, RA, LV, RV, PV |
7 | AF | 54 | M | Caucasian | Yes | Yes | AF | No | No | No | SAN, LA, LAA, RA, LV, RV, PV |
8 | AF | 58 | F | Caucasian | Yes | Yes | AF | medication | No | No | SAN, LA, LAA, RA, LV, RV, PV |
9 | AF | 59 | M | Japanese | Yes | Yes | MR, TR, AF | medication | No | No | RAA |
10 | AF | 70 | F | Japanese | No | Yes | MR, HCH AF | medication | No | No | RAA |
Descriptions | Gene Symbols |
---|---|
cation channel activity | GRIA2, ATP5F1D, ATP6V0C, KCNH2, NALF2, LRRC38, CACNA1E, PKD2, SCN2B, KCNIP2, GRIN2C |
ion channel activity | GRIA2, GABRR1, ATP5F1D, ATP6V0C, KCNH2, NALF2, LRRC38, CACNA1E, PKD2, SCN2B, KCNIP2, GRIN2C |
channel activity | GRIA2, GABRR1, ATP5F1D, ATP6V0C, KCNH2, NALF2, LRRC38, CACNA1E, PKD2, SCN2B, KCNIP2, GRIN2C |
passive transmembrane transporter activity | GRIA2, GABRR1, ATP5F1D, ATP6V0C, KCNH2, NALF2, LRRC38, CACNA1E, PKD2, SCN2B, KCNIP2, GRIN2C |
gated channel activity | GRIA2, GABRR1, KCNH2, NALF2, LRRC38, CACNA1E, PKD2, SCN2B, KCNIP2, GRIN2C |
voltage-gated cation channel activity | KCNH2, LRRC38, CACNA1E, PKD2, KCNIP2, GRIN2C |
voltage-gated ion channel activity | KCNH2, LRRC38, CACNA1E, PKD2, SCN2B, KCNIP2, GRIN2C |
voltage-gated channel activity | KCNH2, LRRC38, CACNA1E, PKD2, SCN2B, KCNIP2, GRIN2C |
metal ion transmembrane transporter activity | SLC22A3, KCNH2, NALF2, LRRC38, CACNA1E, PKD2, SCN2B, KCNIP2, GRIN2C, SLC5A1 |
Unique Names/Ensembl IDs | Fold Changes (log2) in PV in AF | Expressional Changes in Extra-Cardiovascular Carcinoma |
---|---|---|
SAMMSON | 9.29 | GBM, HCC, MME |
FOXCUT | 8.41 | NCP, GAC, BLBC, ESCC, OSCC |
ENSG00000251320 | 5.99 | KIRC, LUSC, HNSC |
ENSG00000248927 | 4.16 | KIRC, PRAD |
ENSG00000237807 | 2.46 | BRCA, COAD, PRAD |
ENSG00000286429 | −4.73 | NA |
SCTR-AS1 | −3.60 | LUSC |
ENSG00000289474 | −9.35 | NA |
CHL1-AS2 | −3.41 | NA |
LINC02517 | −3.55 | NA |
ENSG00000237596 | −3.72 | NA |
ENSG00000289623 | −6.12 | NA |
ENSG00000287592 | −3.61 | NA |
ENSG00000254002 | −3.82 | NA |
LINC01405 | −6.77 | HNSC |
LINC01629 | −6.76 | NA |
Unique Name | Gene type | Degree |
---|---|---|
NRXN3 | protein_coding | 50 |
TPH1 | protein_coding | 47 |
RTN1 | protein_coding | 47 |
PLD5 | protein_coding | 45 |
PCDH10 | protein_coding | 45 |
TRIM36 | protein_coding | 44 |
C8orf34 | protein_coding | 44 |
ACAN | protein_coding | 43 |
ADAMTSL1 | protein_coding | 42 |
NT5DC3 | protein_coding | 41 |
CNTN1 | protein_coding | 40 |
MRAP2 | protein_coding | 39 |
GPR176 | protein_coding | 39 |
MYH10 | protein_coding | 37 |
ARPP21 | protein_coding | 36 |
CNTN4 | protein_coding | 35 |
GRIA2 | protein_coding | 35 |
HPSE2 | protein_coding | 35 |
RIMS1 | protein_coding | 34 |
CDH8 | protein_coding | 34 |
SUSD5 | protein_coding | 33 |
GABRR1 | protein_coding | 33 |
TMEM30B | protein_coding | 33 |
PCDH11Y | protein_coding | 33 |
C1orf87 | protein_coding | 32 |
CYTL1 | protein_coding | 32 |
CARTPT | protein_coding | 32 |
IL31RA | protein_coding | 32 |
PCDH11X | protein_coding | 32 |
SAMMSON | lncRNA | 32 |
ST6GAL2 | protein_coding | 31 |
DSC3 | protein_coding | 31 |
FOXCUT | lncRNA | 31 |
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Igarashi, W.; Takagi, D.; Okada, D.; Kobayashi, D.; Oka, M.; Io, T.; Ishii, K.; Ono, K.; Yamamoto, H.; Okamoto, Y. Bioinformatic Identification of Potential RNA Alterations on the Atrial Fibrillation Remodeling from Human Pulmonary Veins. Int. J. Mol. Sci. 2023, 24, 10501. https://doi.org/10.3390/ijms241310501
Igarashi W, Takagi D, Okada D, Kobayashi D, Oka M, Io T, Ishii K, Ono K, Yamamoto H, Okamoto Y. Bioinformatic Identification of Potential RNA Alterations on the Atrial Fibrillation Remodeling from Human Pulmonary Veins. International Journal of Molecular Sciences. 2023; 24(13):10501. https://doi.org/10.3390/ijms241310501
Chicago/Turabian StyleIgarashi, Wataru, Daichi Takagi, Daigo Okada, Daiki Kobayashi, Miho Oka, Toshiro Io, Kuniaki Ishii, Kyoichi Ono, Hiroshi Yamamoto, and Yosuke Okamoto. 2023. "Bioinformatic Identification of Potential RNA Alterations on the Atrial Fibrillation Remodeling from Human Pulmonary Veins" International Journal of Molecular Sciences 24, no. 13: 10501. https://doi.org/10.3390/ijms241310501