| Literature DB >> 25561975 |
Theo F J Kraus1, Andrea Greiner1, Virginie Guibourt1, Kristina Lisec1, Hans A Kretzschmar1.
Abstract
BACKGROUND: Recent research indicates that long non-coding RNAs (lncRNA) represent a new family of RNAs that is of fundamental importance for controlling transcription and translation. Thereby, there is increasing evidence that lncRNAs are also important in tumourigenesis. Thereby valid expression profiling using quantitative PCR requires suitable, stably expressed normalisers to achieve reliable and reproducible data. However, no systematic analysis of suitable references in lncRNA studies in human glioma has been performed yet.Entities:
Keywords: Glioma; Profiling.; References; lncRNA; long non-coding RNA; qPCR
Year: 2015 PMID: 25561975 PMCID: PMC4280393 DOI: 10.7150/jca.10867
Source DB: PubMed Journal: J Cancer ISSN: 1837-9664 Impact factor: 4.207
Tumour sample collection. Listed are all tumour samples used in this study including patient age at surgery, sex, tumour entity according to WHO-Grade, localisation and molecular genetic features of tumours. MGMT status: 0: not methylated; 1: methylated; 2: partially methylated; 9: not analysed due to low amount of tissue; IDH1-mutation: 0: wt; 1: R132H, 2: R132G; 3: R132C; 9: not analysed due to low amount of tissue; LOH1p/19q: 0: no; 1: 1p; 2: 19q; 3: 1p19q; 4: loss of some markers of 1p; 5: loss of some markers of 19q; 6: loss of some markers of 1p/19q; 9: not analysed due to low amount of tissue.
| Sample | Age at surgery [y] | Sex | Tumor Entity | WHO-Grade | Localisation of tumor | MGMT status | IDH1-mutation | LOH1p/19q |
|---|---|---|---|---|---|---|---|---|
| AII_1 | 34 | f | Diffuse astrocytoma | II | frontal left | 1 | 3 | 0 |
| AII_2 | 34 | m | Diffuse astrocytoma | II | fronto-temporal right | 1 | 1 | 2 |
| AII_3 | 34 | m | Diffuse astrocytoma | II | intraparenchymatous | 0 | 9 | 0 |
| AII_4 | 39 | f | Diffuse astrocytoma | II | frontal right | 2 | 2 | 0 |
| AII_5 | 28 | f | Diffuse astrocytoma | II | precentral right | 1 | 9 | 2 |
| AIII_1 | 21 | f | Anaplastic astrocytoma | III | frontal right | 1 | 1 | 0 |
| AIII_2 | 50 | f | Anaplastic astrocytoma | III | frontal right | 0 | 0 | 0 |
| AIII_3 | 25 | m | Anaplastic astrocytoma | III | intraparenchymatous | 1 | 2 | 0 |
| AIII_4 | 40 | m | Anaplastic astrocytoma | III | temporal left | 1 | 1 | 0 |
| AIII_5 | 39 | m | Anaplastic astrocytoma | III | temporoparietal left | 1 | 0 | 0 |
| GBM_1 | 49 | f | Glioblastoma | IV | frontal right | 1 | 1 | 5 |
| GBM_2 | 45 | f | Glioblastoma | IV | frontal right | 0 | 0 | 5 |
| GBM_3 | 41 | m | Glioblastoma | IV | frontal left | 1 | 1 | 9 |
| GBM_4 | 43 | m | Glioblastoma | IV | temporal right | 2 | 0 | 6 |
| GBM_5 | 54 | m | Glioblastoma | IV | intraparenchymatous | 1 | 0 | 9 |
| GBM_6 | 50 | m | Glioblastoma | IV | temporoparietal left | 0 | 0 | 2 |
| GBM_7 | 44 | m | Glioblastoma | IV | frontal left | 1 | 1 | 9 |
| GBM_8 | 46 | m | Glioblastoma | IV | temporal right | 0 | 0 | 9 |
| GBM_9 | 61 | m | Glioblastoma | IV | parietal left | 0 | 0 | 0 |
| GBM_10 | 55 | f | Glioblastoma | IV | bifrontal | 1 | 1 | 9 |
| GBM_11 | 45 | m | Glioblastoma | IV | frontal left | 1 | 0 | 2 |
| GBM_12 | 72 | f | Glioblastoma | IV | temporal | 1 | 0 | 0 |
| GBM_13 | 73 | m | Glioblastoma | IV | temporal left | 1 | 0 | 5 |
| GBM_14 | 67 | m | Glioblastoma | IV | occipital right | 0 | 0 | 0 |
| GBM_15 | 34 | f | Glioblastoma | IV | frontal left | 1 | 0 | 2 |
Control sample collection. Listed are all control samples used in this study including age of patients, sex, post-mortem intervals (PMI), investigated brain region and cause of death.
| Sample | Age [y] | Sex | PMI [h] | Region | Cause of death |
|---|---|---|---|---|---|
| WM_1 | 63 | m | 18 | Occipital white matter | Cardiac arrest |
| WM_2 | 75 | m | 27 | Occipital white matter | Cardiac arrest |
| WM_3 | 77 | f | 20 | Occipital white matter | Cardiac arrest |
| WM_4 | 53 | m | 22 | Occipital white matter | Cardiac arrest |
| WM_5 | 55 | f | 14 | Occipital white matter | Cardiac arrest |
Stably expressed lncRNAs in single glioma entities. We identified 24 suitable normalisers in diffuse astrocytoma (WHO-Grade II), 22 suitable normalisers in anaplastic astrocytoma (WHO-grade III) and 12 suitable normalisers in glioblastoma (WHO-Grade IV). All lncRNAs are arranged according to their stability values. Stability values are calculated using the NormFinder algorithm.
| Diffuse Astrocytoma (WHO-Grade II) | Anaplastic Astrocytoma (WHO-Grade III) | Glioblastoma (WHO-Grade IV) | ||||||
|---|---|---|---|---|---|---|---|---|
| Gene name | Stability value | Standard error | Gene name | Stability value | Standard error | Gene name | Stability value | Standard error |
| Zfhx2as | 0.008 | 0.004 | SNHG4 | 0.005 | 0.004 | LUST | 0.016 | 0.005 |
| H19 | 0.010 | 0.004 | H19 ups. cons. 1, 2 | 0.006 | 0.004 | SNHG4 | 0.019 | 0.005 |
| EgoA | 0.010 | 0.004 | Dio3os (family) | 0.010 | 0.005 | EgoA | 0.034 | 0.007 |
| IGF2AS (family) | 0.010 | 0.004 | Hoxa11as | 0.011 | 0.005 | H19 ups. cons. 1, 2 | 0.035 | 0.008 |
| Hoxa11as | 0.012 | 0.005 | IGF2AS (family) | 0.013 | 0.005 | EGO B | 0.036 | 0.008 |
| SNHG4 | 0.013 | 0.005 | HOXA6as | 0.013 | 0.005 | Zfhx2as | 0.041 | 0.009 |
| ST7OT | 0.015 | 0.006 | H19 | 0.013 | 0.006 | ncR-uPAR | 0.045 | 0.009 |
| HOTAIRM1 | 0.015 | 0.006 | HAR1A | 0.013 | 0.006 | 21A | 0.048 | 0.010 |
| Nespas | 0.016 | 0.006 | H19 antisense | 0.014 | 0.006 | HOXA6as | 0.051 | 0.010 |
| 21A | 0.017 | 0.006 | LUST | 0.016 | 0.006 | GAS5-family | 0.065 | 0.013 |
| H19 antisense | 0.018 | 0.007 | Air | 0.017 | 0.007 | NDM29 | 0.067 | 0.013 |
| snaR | 0.018 | 0.007 | 21A | 0.019 | 0.007 | BC200 | 0.086 | 0.017 |
| Tsix | 0.019 | 0.007 | CAR Intergenic 10 | 0.020 | 0.008 | |||
| Dio3os (family) | 0.019 | 0.007 | ncR-uPAR | 0.024 | 0.009 | |||
| EGO B | 0.021 | 0.008 | GAS5-family | 0.025 | 0.009 | |||
| LUST | 0.025 | 0.009 | EgoA | 0.027 | 0.010 | |||
| HOXA6as | 0.025 | 0.009 | HOTAIRM1 | 0.029 | 0.011 | |||
| lincRNA-p21 | 0.026 | 0.009 | EGO B | 0.030 | 0.011 | |||
| GAS5-family | 0.027 | 0.010 | BC200 | 0.034 | 0.012 | |||
| H19 ups. cons. 1, 2 | 0.029 | 0.010 | Zfhx2as | 0.037 | 0.013 | |||
| ncR-uPAR | 0.029 | 0.010 | Tsix | 0.053 | 0.019 | |||
| NEAT1 (family) | 0.030 | 0.011 | NDM29 | 0.069 | 0.025 | |||
| BC200 | 0.042 | 0.015 | ||||||
| NDM29 | 0.045 | 0.016 | ||||||
Stably expressed lncRNAs suitable for studies in different human glioma entities. We identified 7 lncRNAs that are suitable for studies in multiple glioma entities. All lncRNAs are arranged according to their stability values. Intragroup and intergroup variations indicated were calculated using the NormFinder algorithm.
| Glioma | |||||||
|---|---|---|---|---|---|---|---|
| Gene name | Stability value | A II | A III | GBM | A II | A III | GBM |
| Zfhx2as | 0.014 | 0.000 | 0.001 | 0.001 | 0.000 | -0.006 | 0.005 |
| SNHG4 | 0.017 | 0.001 | 0.000 | 0.001 | -0.013 | 0.001 | 0.013 |
| HOXA6as | 0.018 | 0.001 | 0.000 | 0.004 | 0.002 | 0.005 | -0.007 |
| H19 ups. cons. 1, 2 | 0.019 | 0.000 | 0.000 | 0.002 | -0.017 | 0.004 | 0.013 |
| ncR-uPAR | 0.024 | 0.001 | 0.000 | 0.001 | -0.004 | 0.023 | -0.019 |
| 21A | 0.025 | 0.000 | 0.000 | 0.002 | 0.005 | -0.027 | 0.021 |
| BC200 | 0.029 | 0.001 | 0.001 | 0.007 | 0.027 | 0.000 | -0.027 |
Stably expressed lncRNAs suitable for studies in human gliomas and normal brain tissue. We identified 4 lncRNAs that show stable expression levels in all three glioma entities and in normal occipital white matter. These lncRNAs may be regarded as universal normalisers applicable in a broad range of lncRNA studies. All lncRNAs are arranged according to their stability values. Intragroup and intergroup variations indicated were calculated using the NormFinder algorithm.
| Glioma and white matter | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| A II | A III | GBM | WM | A II | A III | GBM | WM | ||
| HOXA6as | 0.019 | 0.001 | 0.000 | 0.003 | 0.001 | -0.002 | 0.003 | -0.004 | 0.002 |
| H19 ups. cons. 1, 2 | 0.024 | 0.000 | 0.000 | 0.002 | 0.001 | -0.025 | -0.002 | 0.012 | 0.014 |
| Zfhx2as | 0.030 | 0.000 | 0.002 | 0.001 | 0.000 | -0.015 | -0.020 | -0.003 | 0.038 |
| BC200 | 0.044 | 0.001 | 0.001 | 0.007 | 0.005 | 0.042 | 0.018 | -0.005 | -0.055 |