lncRNAs–mRNAs Co–Expression Network Underlying Childhood B–Cell Acute Lymphoblastic Leukaemia: A Pilot Study
Abstract
:Simple Summary
Abstract
1. Introduction
2. Results
2.1. The Landscape of B–ALL Transcriptome
2.2. Identification of Key lncRNAs in B–ALL through Unsupervised PCA–Based Feature Extraction (FE) Approach
2.3. lncRNA Signature as Diagnostic Candidate for B–ALL
2.4. Functional Analyses and Co–Expression Network
2.4.1. Signalling Pathways of Differentially Expressed mRNAs and lncRNAs
2.4.2. lncRNA–mRNA Co–Expression Network
2.4.3. Ex–Vivo Validation
2.4.4. KEGG Analysis of B–ALL Disease Associated Pathways
2.4.5. Prediction of lncRNA Functions
3. Discussion
4. Materials and Methods
4.1. Identification of Differentially Expressed mRNAs and lncRNAs in B–ALL
4.2. Gene Selection Using PCA–Based Unsupervised Feature Extraction (FE) Approach
4.3. In–Silico Validation
4.4. Ex Vivo Validation
4.5. Functional Enrichment Analysis and Guilt–By–Association Approach
4.6. Co–Expression Network Construction
4.7. Statistical Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Ensembl ID | LncRNA Symbol GhR37 p.13/GhR38 p.13 | Log2FC a | p Adjusted | Average Expression Healthy Subjects | Average Expression Tumour Samples | Expression Trend | References |
---|---|---|---|---|---|---|---|
ENSG00000236800 | RP11–534L6.2/AC068898.1 | −4.368 | 3.05 × 10−3 | 15.21 | 0.15 | Down–regulated | none |
ENSG00000198106 | SNX29P2/AC025279.1 | −4.203 | 8.97 × 10−8 | 149.57 | 6.56 | Down–regulated | none |
ENSG00000246528 | RP11–159H10.3/AC079089.1 | −4.182 | 2.01 × 10−3 | 18.54 | 0.32 | Down–regulated | none |
ENSG00000205056 | RP11–693J15.5/LINC02397 | −4.149 | 4.69 × 10−6 | 624.81 | 25.57 | Down–regulated | [34] |
ENSG00000245869 | RP11–158I9.5/AP004609.3 | −4.053 | 3.60 × 10−5 | 78.48 | 3.03 | Down–regulated | none |
ENSG00000251538 | RP11–166A12.1/LINC02201 | −3.989 | 9.89 × 10−3 | 11.20 | 0.14 | Down–regulated | [35] |
ENSG00000255864 | RP11–444D3.1/not annotated | −3.961 | 7.50 × 10−3 | 108.99 | 11.97 | Down–regulated | none |
ENSG00000247982 | LINC00926/LINC00926 | −3.918 | 2.21 × 10−7 | 4566.18 | 244.07 | Down–regulated | [12] |
ENSG00000237438 | CECR7/CECR7 | −3.691 | 6.59 × 10−6 | 105.06 | 6.23 | Down–regulated | [36,37] |
ENSG00000258810 | RP11–219E7.1/AL133371.2 | −3.399 | 6.77 × 10−4 | 37.33 | 2.64 | Down–regulated | none |
ENSG00000224875 | AC083949.1/EML4–AS1 | −3.369 | 1.21 × 10−5 | 50.18 | 4.33 | Down–regulated | none |
ENSG00000231105 | RP5–1071N3.1/ECE1–AS1 | −3.309 | 5.67 × 10−7 | 271.25 | 24.22 | Down–regulated | none |
ENSG00000224610 | RP11–265P11.1/AC108879.1 | −3.305 | 1.64 × 10−3 | 42.31 | 2.89 | Down–regulated | none |
ENSG00000253535 | RP11–624C23.1/AC120193.1 | −3.213 | 3.00 × 10−4 | 236.05 | 19.76 | Down–regulated | [8] |
ENSG00000261618 | RP11–79H23.3/LINC02605 | −3.13 | 2.16 × 10−3 | 38.87 | 3.35 | Down–regulated | [38,39] |
ENSG00000261114 | RP11–325K4.2/AC012181.1 | −3.112 | 1.40 × 10−8 | 142.67 | 14.54 | Down–regulated | none |
ENSG00000225331 | AP001055.6/LINC01678 | −3.054 | 5.02 × 10−3 | 27.10 | 2.35 | Down–regulated | none |
ENSG00000235192 | AC009495.2/AC009495.3 | −2.865 | 8.94 × 10−3 | 26.86 | 2.88 | Down–regulated | [40] |
ENSG00000251364 | CTD–2516F10.2/AC107884.1 | −2.827 | 1.94 × 10−5 | 181.05 | 23.66 | Down–regulated | [41] |
ENSG00000229151 | RP11–348F1.3/AC233976.1 | −2.755 | 6.32 × 10−3 | 34.97 | 4.25 | Down–regulated | none |
ENSG00000228403 | RP11–563N6.6/AC035139.1 | −2.557 | 2.74 × 10−3 | 46.95 | 7.03 | Down–regulated | none |
ENSG00000269918 | AF131215.9/AF131215.6 | −2.533 | 1.97 × 10−3 | 46.61 | 7.17 | Down–regulated | none |
ENSG00000255310 | AF131215.2/AF131215.5 | −2.236 | 4.47 × 10−4 | 97.41 | 19.14 | Down–regulated | none |
ENSG00000267787 | RP11–35G9.5/AC027097.2 | −1.86 | 1.21 × 10−3 | 216.93 | 57.25 | Down–regulated | none |
ENSG00000226674 | TEX41/TEX41 | 5.218 | 4.88 × 10−7 | 2.44 | 170.21 | Up–regulated | [42,43,44] |
ENSG00000100181 | TPTEP1/TPTEP1 | 3.527 | 5.58 × 10−4 | 7.33 | 112.53 | Up–regulated | [45,46] |
ENSG00000269968 | RP5–940J5.9/AC006064.4 | 3.362 | 1.40 × 10−4 | 4.25 | 53.74 | Up–regulated | none |
ENSG00000259330 | LINC00984/INAFM2 | 2.279 | 1.87 × 10−4 | 26.76 | 131.75 | Up–regulated | [46,47] |
ENSG00000224597 | PTCHD3P1/SVIL–AS1 | 2.234 | 8.04 × 10−4 | 10.61 | 51.60 | Up–regulated | [10] |
ENSG00000255026 | RP11–326C3.2/AC136475.3 | 2.211 | 3.15 × 10−4 | 31.38 | 147.22 | Up–regulated | [48,49] |
Gene | Forward Primer | Reverse Primer |
---|---|---|
RPS18: | fw 5′-CGATGGGCGGCGGAAAATA-3′; | rev 5′-CTGCTTTCCTCAACACCACA-3′; |
TEX41: | fw 5′-TCATCTGTGAGGACCGTGAC-3′; | rev 5′-AGCACAGGAGAAGCTGAGTT-3′; |
RTN4: | fw 5′-TGCGTCAGACTGTTCCACAC-3′; | rev 5′-CAGTCTCCTCTGCTGCACAA-3′; |
UBASH3B: | fw 5′-GCTGGACGTGCTCCTCTC-3′; | rev 5′-AGTCACATGCTGCCTGAACA-3′; |
CHST15: | fw 5′-CACACCAGATCCATCAAGGAC-3′; | rev 5′-TCCAGGCATTATTATCCCACA-3′; |
RP11-534L6.2: | fw 5′-GGTGATGGTGATCAGGTGACT-3′; | rev 5′-TCGCTGCAGGGAGACTTC-3′; |
MUC16: | fw 5′-CACAGTGGATGTGGGAACCT-3′; | rev 5′-GGTGAAGTTGAGGGTGAACG; |
EML6: | fw 5′-GGGCAGGCAGAGGATTTC-3′; | rev 5′-TTTGGATCCGAAATTGACAGT-3′. |
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Affinito, O.; Pane, K.; Smaldone, G.; Orlandella, F.M.; Mirabelli, P.; Beneduce, G.; Parasole, R.; Ripaldi, M.; Salvatore, M.; Franzese, M. lncRNAs–mRNAs Co–Expression Network Underlying Childhood B–Cell Acute Lymphoblastic Leukaemia: A Pilot Study. Cancers 2020, 12, 2489. https://doi.org/10.3390/cancers12092489
Affinito O, Pane K, Smaldone G, Orlandella FM, Mirabelli P, Beneduce G, Parasole R, Ripaldi M, Salvatore M, Franzese M. lncRNAs–mRNAs Co–Expression Network Underlying Childhood B–Cell Acute Lymphoblastic Leukaemia: A Pilot Study. Cancers. 2020; 12(9):2489. https://doi.org/10.3390/cancers12092489
Chicago/Turabian StyleAffinito, Ornella, Katia Pane, Giovanni Smaldone, Francesca Maria Orlandella, Peppino Mirabelli, Giuliana Beneduce, Rosanna Parasole, Mimmo Ripaldi, Marco Salvatore, and Monica Franzese. 2020. "lncRNAs–mRNAs Co–Expression Network Underlying Childhood B–Cell Acute Lymphoblastic Leukaemia: A Pilot Study" Cancers 12, no. 9: 2489. https://doi.org/10.3390/cancers12092489