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Gene Commanding Height (GCH) hierarchy in the cancer nucleus and cancer-free resection margins from a surgically removed prostatic adenocarcinoma of a 65y old black man

ABSTRACT: We profiled the transcriptomes of the dominan nodule (Gleason score 4+5=9) and of the cancer free resection margins of a surgically removed prostate tumor from a 65y old black man. Normalized to the median of valid spots expression data where used to determine the Gene Commanding Height (GCH) Score for every coding and non-coding transcript adequately quantified in all four cancer and four normal tissue samples. The analysis proved that cancer and normal tissue have distinct gene hiearchies. The top three genes in the cancer region were: BAIAP2L1 (BAI1-associated protein 2-like 1 ), FAM71E1 (amily with sequence similarity 71, member E1 ) and MAP6D1 (MAP6 domain containing 1 ), while the top three genes in the cancer-free region were: TOR1A (torsin family 1, member A ), MRPS12 (mitochondrial ribosomal protein S12 ) and GTF2H1 (general transcription factor IIH, polypeptide 1).

ORGANISM(S): Homo sapiens

PROVIDER: GSE133906 | GEO | 2019/07/07

REPOSITORIES: GEO

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Gene Commanding Height (GCH) hierarchy in the cancer nucleus and cancer-free resection margins from a surgically removed prostatic adenocarcinoma of a 47y old white man

Project description:We profiled the transcriptomes of the cancer nucleus (Gleason score 4+5=9) and of the cancer free resection margins of a surgically removed prostate tumor from a 47y old white man. Normalized to the median of valid spots expression data where used to determine the Gene Commanding Height (GCH) Score for every coding and non-coding transcript adequately quantified in all four cancer and four normal tissue samples. The analysis proved that cancer and normal tissue have distinct gene hiearchies. The top three genes in the cancer region were: LOC145474 (uncharacterized long non-coding RNA), PRRG1 (proline rich Gla (G-carboxyglutamic acid) 1) and ASAP3 (ArfGAP with SH3 domain, ankyrin repeat and PH domain 3), while the top three genes in the cancer-free region were: SFR1 (SWI5-dependent recombination repair 1 ), EDF1 (endothelial differentiation-related factor 1) and RHOD (ras homolog family member D).

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Gene Commanding Height (GCH) hierarchy in the cancer nucleus and cancer-free resection margins from a surgically removed prostatic adenocarcinoma of a 47y old white man

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Hierarchal gene master regulators of one case of papillary thyroid cancer

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2017-06-03 | GSE99590 | GEO

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Validation of the Personalized Gene Therapy by stably transfection of PANK2 in the papillary (BCPAP) and anaplastic (8505C) thyroid cancer cell lines

Project description:An ideal cancer gene therapy would selectively destroy the cancer cells without affecting much the healthy tissue. This would be possible if and only if the cancer and normal cells of the tumor are governed by distinct gene master regulators (GMRs). Logic dictates that, while being strongly protected by the homeostatic mechanisms, expression of a GMR governs the phenotype by modulating major functional pathways through controlling the expression of the involved genes. We determined the GMRs of the standard papillary (BCPAP) and anaplastic (8505C) thyroid cancer cell lines. The hierarchy of the known biomarkers was established based on their gene commanding height (GCH), an original measure combining the expression control and coordination with expression of other genes. We found that the sets of the GMRs are largely different in the two thyroid cancer cell lines, indicatibg that each type of thyroid cancer needs a different gene-targeting therapy. In this experiment, we determined the transcriptomic effects of the stable transfection of PANK2 gene In the papillary (BCPAP) and anaplastic (8505C) thyroid cancer cell lines. PANK2 was selected because it has significantly different GCHs in the two cell lines: 44.64 in BCPAP and 3.61 in 8505C. The significantly more up- and down-regulated genes in the transfected BCPAP than in the transfected 8505C cells compared to their untransfected counterparts validated the theory and indicated the usefulness of our personalized gene therapy approach.

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Validation of the Personalized Gene Therapy by stably transfection of DDX19B in the papillary (BCPAP) and anaplastic (8505C) thyroid cancer cell lines

Project description:An ideal cancer gene therapy would selectively destroy the cancer cells without affecting much the healthy tissue. This would be possible if and only if the cancer and normal cells of the tumor are governed by distinct gene master regulators (GMRs). Logic dictates that, while being strongly protected by the homeostatic mechanisms, expression of a GMR governs the phenotype by modulating major functional pathways through controlling the expression of the involved genes. We determined the GMRs of the standard papillary (BCPAP) and anaplastic (8505C) thyroid cancer cell lines. The hierarchy of the known biomarkers was established based on their gene commanding height (GCH), an original measure combining the expression control and coordination with expression of other genes. We found that the sets of the GMRs are largely different in the two thyroid cancer cell lines, indicatibg that each type of thyroid cancer needs a different gene-targeting therapy. In this experiment, we determined the transcriptomic effects of the stable transfection of DDX19B gene In the papillary (BCPAP) and anaplastic (8505C) thyroid cancer cell lines. DDX19B was selected because it has significantly different GCHs in the two cell lines: 1.64 in BCPAP and 6.03 in 8505C. The significantly more up- and down-regulated genes in the transfected 8505C than in the transfected BCPAP cells compared to their untransfected counterparts validated the theory and indicated the usefulness of our personalized gene therapy approach.

2017-03-25 | GSE97028 | GEO

Validation of the Personalized Gene Therapy by stably transfection of UBALD1 in the papillary (BCPAP) and anaplastic (8505C) thyroid cancer cell lines

Project description:An ideal cancer gene therapy would selectively destroy the cancer cells without affecting much the healthy tissue. This would be possible if and only if the cancer and normal cells of the tumor are governed by distinct gene master regulators (GMRs). Logic dictates that, while being strongly protected by the homeostatic mechanisms, expression of a GMR governs the phenotype by modulating major functional pathways through controlling the expression of the involved genes. We determined the GMRs of the standard papillary (BCPAP) and anaplastic (8505C) thyroid cancer cell lines. The hierarchy of the known biomarkers was established based on their gene commanding height (GCH), an original measure combining the expression control and coordination with expression of other genes. We found that the sets of the GMRs are largely different in the two thyroid cancer cell lines, indicatibg that each type of thyroid cancer needs a different gene-targeting therapy. In this experiment, we determined the transcriptomic effects of the stable transfection of UBALD1 gene in the BCPAP and 8505C thyroid cancer cell lines. UBALD1 was selected because it has significantly different GCHs in the two cell lines: 10.31 in 8505C and 1.12 in BCPAP. The significantly more up- and down-regulated genes in the transfected 8505C cells than in the transfected BCPAP cells compared to their untransfected counterparts validated the theory and indicated the usefulness of our personalized gene therapy approach.

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