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Small tRNA-derived RNAs are increased and more abundant than microRNAs in chronic hepatitis B and C.

Selitsky SR, Baran-Gale J, Honda M, Yamane D, Masaki T, Fannin EE, Guerra B, Shirasaki T, Shimakami T, Kaneko S, Lanford RE, Lemon SM, Sethupathy P - Sci Rep (2015)

Bottom Line: In contrast, in matched cancer tissue, 5' tRH abundance was reduced, and relative abundance of individual 5' tRHs was altered.In hepatitis B-associated HCC, 5' tRH abundance correlated with expression of the tRNA-cleaving ribonuclease, angiogenin.These results demonstrate that tRHs are the most abundant small RNAs in chronically infected liver and that their abundance is altered in liver cancer.

View Article: PubMed Central - PubMed

Affiliation: 1] Bioinformatics and Computational Biology Curriculum, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America [2] Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America [3] Departments of Medicine and Microbiology &Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America [4] Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America.

ABSTRACT
Persistent infections with hepatitis B virus (HBV) or hepatitis C virus (HCV) account for the majority of cases of hepatic cirrhosis and hepatocellular carcinoma (HCC) worldwide. Small, non-coding RNAs play important roles in virus-host interactions. We used high throughput sequencing to conduct an unbiased profiling of small (14-40 nts) RNAs in liver from Japanese subjects with advanced hepatitis B or C and hepatocellular carcinoma (HCC). Small RNAs derived from tRNAs, specifically 30-35 nucleotide-long 5' tRNA-halves (5' tRHs), were abundant in non-malignant liver and significantly increased in humans and chimpanzees with chronic viral hepatitis. 5' tRH abundance exceeded microRNA abundance in most infected non-cancerous tissues. In contrast, in matched cancer tissue, 5' tRH abundance was reduced, and relative abundance of individual 5' tRHs was altered. In hepatitis B-associated HCC, 5' tRH abundance correlated with expression of the tRNA-cleaving ribonuclease, angiogenin. These results demonstrate that tRHs are the most abundant small RNAs in chronically infected liver and that their abundance is altered in liver cancer.

No MeSH data available.


Related in: MedlinePlus

Angiogenin expression in viral hepatitis and hepatocellular carcinoma.(a) Normalized ANG mRNA levels from previously generated liver microarray data14 from uninfected subjects (n = 6), non-malignant (n = 7) and liver cancer (n = 8) tissue from HBV-infected subjects, and non-malignant (n = 11) and cancer tissue (n = 15) from HCV-infected subjects. **P < 0.01; ***P < 0.005, calculated by Mann-Whitney U-test. (b) Scatter plot of the levels of 5′ tRHs (RT-qPCR, -dCT normalized to RNU48) and ANG mRNA (microarray). 5′ tRHGly (“Gly[C/G]CC”): uninfected subjects (n = 7), non-cancer (n = 7) and cancer (n = 8) liver tissue from chronic hepatitis B subjects, and non-cancer (n = 11) and cancer (n = 15) liver tissue from chronic hepatitis C subjects; 5′ tRHVal: uninfected subjects (n = 6), non-cancer (n = 7) and cancer (n = 8) liver tissue from chronic hepatitis B subjects, and non-cancer (n = 11) and cancer (n = 15) liver tissue of chronic hepatitis C subjects. (c) Scatter plot of the levels of 5′ tRHs (RT-qPCR, -dCT normalized to RNU48) and ANG protein expression (normalized to β-actin) determined by immunoblot analysis. (d) Immunohistochemistry staining for ANG in formalin-fixed non-tumor (NT) and tumor tissue (T) from HBV-infected subject #10. (Right) Magnified view of non-tumor (NT). (e) ANG staining in adjacent tumor nodules (T1 and T2) and in non-tumor (NT) tissue from HCV-infected subject #7.
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f3: Angiogenin expression in viral hepatitis and hepatocellular carcinoma.(a) Normalized ANG mRNA levels from previously generated liver microarray data14 from uninfected subjects (n = 6), non-malignant (n = 7) and liver cancer (n = 8) tissue from HBV-infected subjects, and non-malignant (n = 11) and cancer tissue (n = 15) from HCV-infected subjects. **P < 0.01; ***P < 0.005, calculated by Mann-Whitney U-test. (b) Scatter plot of the levels of 5′ tRHs (RT-qPCR, -dCT normalized to RNU48) and ANG mRNA (microarray). 5′ tRHGly (“Gly[C/G]CC”): uninfected subjects (n = 7), non-cancer (n = 7) and cancer (n = 8) liver tissue from chronic hepatitis B subjects, and non-cancer (n = 11) and cancer (n = 15) liver tissue from chronic hepatitis C subjects; 5′ tRHVal: uninfected subjects (n = 6), non-cancer (n = 7) and cancer (n = 8) liver tissue from chronic hepatitis B subjects, and non-cancer (n = 11) and cancer (n = 15) liver tissue of chronic hepatitis C subjects. (c) Scatter plot of the levels of 5′ tRHs (RT-qPCR, -dCT normalized to RNU48) and ANG protein expression (normalized to β-actin) determined by immunoblot analysis. (d) Immunohistochemistry staining for ANG in formalin-fixed non-tumor (NT) and tumor tissue (T) from HBV-infected subject #10. (Right) Magnified view of non-tumor (NT). (e) ANG staining in adjacent tumor nodules (T1 and T2) and in non-tumor (NT) tissue from HCV-infected subject #7.

Mentions: Angiogenin (encoded by the gene ANG) is best known for its role in angiogenesis, but several studies suggest its RNase activity contributes to tRH biogenesis2021. Consistent with this, analysis of previous microarray data obtained from these tissues14 revealed that ANG mRNA was reduced in both HBV- and HCV-associated cancer compared to non-malignant tissue (P<0.01 and P<0.005, respectively) or uninfected liver (P<0.005 and P = 0.01) (Figure 3a). Analysis of data from The Cancer Genome Atlas (https://tcga-data.nci.nih.gov/tcga/) also indicates that ANG expression is reduced in HCC compared to non-malignant tissue, although the difference is significant only for HBV-associated cancer (HBV P<0.005, HCV P = 0.12) (Supplemental Figure 5). ANG mRNA abundance correlated strongly with 5′ tRH expression in the HBV-infected subjects we studied (5′ tRHGly: Spearman's rho = 0.67, P<0.01; 5′ tRHVal: rho = 0.74, P<0.005) (Figure 3b). Quantitative immunoblot analyses (Supplemental Figure 6) confirmed a correlation between ANG protein abundance and 5′ tRH expression in HBV-associated cancer (5′ tRHGly: rho = 0.83, P<0.005; 5′ tRHVal: rho = 0.87, P<0.005) (Figure 3c). ANG was expressed within the cytoplasm of hepatocytes (Figure 3d), and although its expression varied substantially in different tumors (Figure 3e), reductions in ANG expression likely explain the reduced tRH abundance we observed in most HBV-associated cancers. Unfortunately, however, the available tissue sections from these subjects were insufficient to power a formal analysis of the correlation between cytoplasmic versus nuclear expression of ANG and tRH abundance. ANG expression correlated poorly with tRH abundance in HCV-infected livers, suggesting that other factors determine tRH biogenesis.


Small tRNA-derived RNAs are increased and more abundant than microRNAs in chronic hepatitis B and C.

Selitsky SR, Baran-Gale J, Honda M, Yamane D, Masaki T, Fannin EE, Guerra B, Shirasaki T, Shimakami T, Kaneko S, Lanford RE, Lemon SM, Sethupathy P - Sci Rep (2015)

Angiogenin expression in viral hepatitis and hepatocellular carcinoma.(a) Normalized ANG mRNA levels from previously generated liver microarray data14 from uninfected subjects (n = 6), non-malignant (n = 7) and liver cancer (n = 8) tissue from HBV-infected subjects, and non-malignant (n = 11) and cancer tissue (n = 15) from HCV-infected subjects. **P < 0.01; ***P < 0.005, calculated by Mann-Whitney U-test. (b) Scatter plot of the levels of 5′ tRHs (RT-qPCR, -dCT normalized to RNU48) and ANG mRNA (microarray). 5′ tRHGly (“Gly[C/G]CC”): uninfected subjects (n = 7), non-cancer (n = 7) and cancer (n = 8) liver tissue from chronic hepatitis B subjects, and non-cancer (n = 11) and cancer (n = 15) liver tissue from chronic hepatitis C subjects; 5′ tRHVal: uninfected subjects (n = 6), non-cancer (n = 7) and cancer (n = 8) liver tissue from chronic hepatitis B subjects, and non-cancer (n = 11) and cancer (n = 15) liver tissue of chronic hepatitis C subjects. (c) Scatter plot of the levels of 5′ tRHs (RT-qPCR, -dCT normalized to RNU48) and ANG protein expression (normalized to β-actin) determined by immunoblot analysis. (d) Immunohistochemistry staining for ANG in formalin-fixed non-tumor (NT) and tumor tissue (T) from HBV-infected subject #10. (Right) Magnified view of non-tumor (NT). (e) ANG staining in adjacent tumor nodules (T1 and T2) and in non-tumor (NT) tissue from HCV-infected subject #7.
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Related In: Results  -  Collection

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f3: Angiogenin expression in viral hepatitis and hepatocellular carcinoma.(a) Normalized ANG mRNA levels from previously generated liver microarray data14 from uninfected subjects (n = 6), non-malignant (n = 7) and liver cancer (n = 8) tissue from HBV-infected subjects, and non-malignant (n = 11) and cancer tissue (n = 15) from HCV-infected subjects. **P < 0.01; ***P < 0.005, calculated by Mann-Whitney U-test. (b) Scatter plot of the levels of 5′ tRHs (RT-qPCR, -dCT normalized to RNU48) and ANG mRNA (microarray). 5′ tRHGly (“Gly[C/G]CC”): uninfected subjects (n = 7), non-cancer (n = 7) and cancer (n = 8) liver tissue from chronic hepatitis B subjects, and non-cancer (n = 11) and cancer (n = 15) liver tissue from chronic hepatitis C subjects; 5′ tRHVal: uninfected subjects (n = 6), non-cancer (n = 7) and cancer (n = 8) liver tissue from chronic hepatitis B subjects, and non-cancer (n = 11) and cancer (n = 15) liver tissue of chronic hepatitis C subjects. (c) Scatter plot of the levels of 5′ tRHs (RT-qPCR, -dCT normalized to RNU48) and ANG protein expression (normalized to β-actin) determined by immunoblot analysis. (d) Immunohistochemistry staining for ANG in formalin-fixed non-tumor (NT) and tumor tissue (T) from HBV-infected subject #10. (Right) Magnified view of non-tumor (NT). (e) ANG staining in adjacent tumor nodules (T1 and T2) and in non-tumor (NT) tissue from HCV-infected subject #7.
Mentions: Angiogenin (encoded by the gene ANG) is best known for its role in angiogenesis, but several studies suggest its RNase activity contributes to tRH biogenesis2021. Consistent with this, analysis of previous microarray data obtained from these tissues14 revealed that ANG mRNA was reduced in both HBV- and HCV-associated cancer compared to non-malignant tissue (P<0.01 and P<0.005, respectively) or uninfected liver (P<0.005 and P = 0.01) (Figure 3a). Analysis of data from The Cancer Genome Atlas (https://tcga-data.nci.nih.gov/tcga/) also indicates that ANG expression is reduced in HCC compared to non-malignant tissue, although the difference is significant only for HBV-associated cancer (HBV P<0.005, HCV P = 0.12) (Supplemental Figure 5). ANG mRNA abundance correlated strongly with 5′ tRH expression in the HBV-infected subjects we studied (5′ tRHGly: Spearman's rho = 0.67, P<0.01; 5′ tRHVal: rho = 0.74, P<0.005) (Figure 3b). Quantitative immunoblot analyses (Supplemental Figure 6) confirmed a correlation between ANG protein abundance and 5′ tRH expression in HBV-associated cancer (5′ tRHGly: rho = 0.83, P<0.005; 5′ tRHVal: rho = 0.87, P<0.005) (Figure 3c). ANG was expressed within the cytoplasm of hepatocytes (Figure 3d), and although its expression varied substantially in different tumors (Figure 3e), reductions in ANG expression likely explain the reduced tRH abundance we observed in most HBV-associated cancers. Unfortunately, however, the available tissue sections from these subjects were insufficient to power a formal analysis of the correlation between cytoplasmic versus nuclear expression of ANG and tRH abundance. ANG expression correlated poorly with tRH abundance in HCV-infected livers, suggesting that other factors determine tRH biogenesis.

Bottom Line: In contrast, in matched cancer tissue, 5' tRH abundance was reduced, and relative abundance of individual 5' tRHs was altered.In hepatitis B-associated HCC, 5' tRH abundance correlated with expression of the tRNA-cleaving ribonuclease, angiogenin.These results demonstrate that tRHs are the most abundant small RNAs in chronically infected liver and that their abundance is altered in liver cancer.

View Article: PubMed Central - PubMed

Affiliation: 1] Bioinformatics and Computational Biology Curriculum, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America [2] Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America [3] Departments of Medicine and Microbiology &Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America [4] Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America.

ABSTRACT
Persistent infections with hepatitis B virus (HBV) or hepatitis C virus (HCV) account for the majority of cases of hepatic cirrhosis and hepatocellular carcinoma (HCC) worldwide. Small, non-coding RNAs play important roles in virus-host interactions. We used high throughput sequencing to conduct an unbiased profiling of small (14-40 nts) RNAs in liver from Japanese subjects with advanced hepatitis B or C and hepatocellular carcinoma (HCC). Small RNAs derived from tRNAs, specifically 30-35 nucleotide-long 5' tRNA-halves (5' tRHs), were abundant in non-malignant liver and significantly increased in humans and chimpanzees with chronic viral hepatitis. 5' tRH abundance exceeded microRNA abundance in most infected non-cancerous tissues. In contrast, in matched cancer tissue, 5' tRH abundance was reduced, and relative abundance of individual 5' tRHs was altered. In hepatitis B-associated HCC, 5' tRH abundance correlated with expression of the tRNA-cleaving ribonuclease, angiogenin. These results demonstrate that tRHs are the most abundant small RNAs in chronically infected liver and that their abundance is altered in liver cancer.

No MeSH data available.


Related in: MedlinePlus