Experimental and bioinformatics comparison of gene expression between T cells from TIL of liver cancer and T cells from UniGene

Biaoru Li, Supriya Perabekam, Ge Liu, Mei Yin, Shiwen Song, Alan Larson

Research output: Contribution to journalArticle

10 Citations (Scopus)

Abstract

Background. The major difficulty of mapping parallel gene expression obtained from solid tumors is mainly due to contaminating cells. In this study, by applying a strategy of parallel gene expression at a cell-cluster or colony level, we have identified the gene expression pattern of T cells within tumor-infiltrating lymphocytes (TILs) obtained from two liver cancer patients. Methods. Here a new method was utilized to analyze the parallel gene expression. By using bioinformatics analysis, the data were also compared with T-cell gene expression present in UniGene. Results. Our results demonstrated that 18 genes in specimen A and 13 genes in specimen B were highly expressed after the removal of a nonspecific TIL cDNA library, by pairing gene hybridization; the genes were expressed in CD3+ cells from peripheral blood mononuclear cells (PBMC). By using BlastN search, 17 of the 18, and 12 of the 13 sequences were exhibited, respectively, in Homo sapiens, with a range of BlastN E values of 0 to 4 × 10-13. The LocusLink distribution in chromosomes obtained from both specimens was not significantly different; 17 of 19 putative genes (both specimen A and specimen B) were observed in the UniGene cluster in Homo sapiens, except for dihydropyrimidinase-related protein-3 and diacyglycerol kinase alpha. Interestingly, only 4 of 19 (21%) putative genes were displayed in the T-cell UniGene database (i.e., LD-78 in Hs. 73817, IL-8 in Hs. 624, TRAIL in Hs. 83429, and Fas ligand in Hs. 2007). Conclusions. By comparison with the reported data and UniGene, the parallel gene expression of T cells obtained from TIL can provide essential new insights into T-cell activity, T-cell extravasation into tumor tissues, and T-cell cytotoxicity against tumor cells.

Original languageEnglish (US)
Pages (from-to)275-282
Number of pages8
JournalJournal of Gastroenterology
Volume37
Issue number4
DOIs
StatePublished - May 21 2002

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Tumor-Infiltrating Lymphocytes
Liver Neoplasms
Computational Biology
T-Lymphocytes
Gene Expression
Genes
dihydropyrimidinase
Neoplasms
Fas Ligand Protein
Interleukin-8
Gene Library
Blood Cells
Phosphotransferases
Chromosomes
Databases

Keywords

  • Expressed sequence tag sequencing (EST)
  • High throughput screening (HTS)
  • Microarray
  • Subtractive cloning
  • T cell
  • Tumor infiltrating lymphocytes(TILs)

ASJC Scopus subject areas

  • Gastroenterology

Cite this

Experimental and bioinformatics comparison of gene expression between T cells from TIL of liver cancer and T cells from UniGene. / Li, Biaoru; Perabekam, Supriya; Liu, Ge; Yin, Mei; Song, Shiwen; Larson, Alan.

In: Journal of Gastroenterology, Vol. 37, No. 4, 21.05.2002, p. 275-282.

Research output: Contribution to journalArticle

Li, Biaoru ; Perabekam, Supriya ; Liu, Ge ; Yin, Mei ; Song, Shiwen ; Larson, Alan. / Experimental and bioinformatics comparison of gene expression between T cells from TIL of liver cancer and T cells from UniGene. In: Journal of Gastroenterology. 2002 ; Vol. 37, No. 4. pp. 275-282.
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abstract = "Background. The major difficulty of mapping parallel gene expression obtained from solid tumors is mainly due to contaminating cells. In this study, by applying a strategy of parallel gene expression at a cell-cluster or colony level, we have identified the gene expression pattern of T cells within tumor-infiltrating lymphocytes (TILs) obtained from two liver cancer patients. Methods. Here a new method was utilized to analyze the parallel gene expression. By using bioinformatics analysis, the data were also compared with T-cell gene expression present in UniGene. Results. Our results demonstrated that 18 genes in specimen A and 13 genes in specimen B were highly expressed after the removal of a nonspecific TIL cDNA library, by pairing gene hybridization; the genes were expressed in CD3+ cells from peripheral blood mononuclear cells (PBMC). By using BlastN search, 17 of the 18, and 12 of the 13 sequences were exhibited, respectively, in Homo sapiens, with a range of BlastN E values of 0 to 4 × 10-13. The LocusLink distribution in chromosomes obtained from both specimens was not significantly different; 17 of 19 putative genes (both specimen A and specimen B) were observed in the UniGene cluster in Homo sapiens, except for dihydropyrimidinase-related protein-3 and diacyglycerol kinase alpha. Interestingly, only 4 of 19 (21{\%}) putative genes were displayed in the T-cell UniGene database (i.e., LD-78 in Hs. 73817, IL-8 in Hs. 624, TRAIL in Hs. 83429, and Fas ligand in Hs. 2007). Conclusions. By comparison with the reported data and UniGene, the parallel gene expression of T cells obtained from TIL can provide essential new insights into T-cell activity, T-cell extravasation into tumor tissues, and T-cell cytotoxicity against tumor cells.",
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T1 - Experimental and bioinformatics comparison of gene expression between T cells from TIL of liver cancer and T cells from UniGene

AU - Li, Biaoru

AU - Perabekam, Supriya

AU - Liu, Ge

AU - Yin, Mei

AU - Song, Shiwen

AU - Larson, Alan

PY - 2002/5/21

Y1 - 2002/5/21

N2 - Background. The major difficulty of mapping parallel gene expression obtained from solid tumors is mainly due to contaminating cells. In this study, by applying a strategy of parallel gene expression at a cell-cluster or colony level, we have identified the gene expression pattern of T cells within tumor-infiltrating lymphocytes (TILs) obtained from two liver cancer patients. Methods. Here a new method was utilized to analyze the parallel gene expression. By using bioinformatics analysis, the data were also compared with T-cell gene expression present in UniGene. Results. Our results demonstrated that 18 genes in specimen A and 13 genes in specimen B were highly expressed after the removal of a nonspecific TIL cDNA library, by pairing gene hybridization; the genes were expressed in CD3+ cells from peripheral blood mononuclear cells (PBMC). By using BlastN search, 17 of the 18, and 12 of the 13 sequences were exhibited, respectively, in Homo sapiens, with a range of BlastN E values of 0 to 4 × 10-13. The LocusLink distribution in chromosomes obtained from both specimens was not significantly different; 17 of 19 putative genes (both specimen A and specimen B) were observed in the UniGene cluster in Homo sapiens, except for dihydropyrimidinase-related protein-3 and diacyglycerol kinase alpha. Interestingly, only 4 of 19 (21%) putative genes were displayed in the T-cell UniGene database (i.e., LD-78 in Hs. 73817, IL-8 in Hs. 624, TRAIL in Hs. 83429, and Fas ligand in Hs. 2007). Conclusions. By comparison with the reported data and UniGene, the parallel gene expression of T cells obtained from TIL can provide essential new insights into T-cell activity, T-cell extravasation into tumor tissues, and T-cell cytotoxicity against tumor cells.

AB - Background. The major difficulty of mapping parallel gene expression obtained from solid tumors is mainly due to contaminating cells. In this study, by applying a strategy of parallel gene expression at a cell-cluster or colony level, we have identified the gene expression pattern of T cells within tumor-infiltrating lymphocytes (TILs) obtained from two liver cancer patients. Methods. Here a new method was utilized to analyze the parallel gene expression. By using bioinformatics analysis, the data were also compared with T-cell gene expression present in UniGene. Results. Our results demonstrated that 18 genes in specimen A and 13 genes in specimen B were highly expressed after the removal of a nonspecific TIL cDNA library, by pairing gene hybridization; the genes were expressed in CD3+ cells from peripheral blood mononuclear cells (PBMC). By using BlastN search, 17 of the 18, and 12 of the 13 sequences were exhibited, respectively, in Homo sapiens, with a range of BlastN E values of 0 to 4 × 10-13. The LocusLink distribution in chromosomes obtained from both specimens was not significantly different; 17 of 19 putative genes (both specimen A and specimen B) were observed in the UniGene cluster in Homo sapiens, except for dihydropyrimidinase-related protein-3 and diacyglycerol kinase alpha. Interestingly, only 4 of 19 (21%) putative genes were displayed in the T-cell UniGene database (i.e., LD-78 in Hs. 73817, IL-8 in Hs. 624, TRAIL in Hs. 83429, and Fas ligand in Hs. 2007). Conclusions. By comparison with the reported data and UniGene, the parallel gene expression of T cells obtained from TIL can provide essential new insights into T-cell activity, T-cell extravasation into tumor tissues, and T-cell cytotoxicity against tumor cells.

KW - Expressed sequence tag sequencing (EST)

KW - High throughput screening (HTS)

KW - Microarray

KW - Subtractive cloning

KW - T cell

KW - Tumor infiltrating lymphocytes(TILs)

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