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Prevalent de novo somatic mutations in superantigen genes of mouse mammary tumor viruses in the genome of C57BL/6J mice and its potential implication in the immune system.

Lee YK, Chiu S, Chew A, Greenhalgh DG, Cho K - BMC Immunol. (2011)

Bottom Line: Similarly, 69 unique SAg sequences (58 translated sequences) were cloned from the cDNAs of 18 different tissues.Examination of putative TCR Vβ specificity suggested that some of the SAg isoforms identified in this study have Vβ specificities different from the reference SAgs of Mtv-8, Mtv-9, or Mtv-17.The pool of diverse SAg isoforms, generated by de novo somatic mutation, may play a role in the shaping of the peripheral T cell repertoire including the autoimmune T cell population.

View Article: PubMed Central - HTML - PubMed

Affiliation: Shriners Hospitals for Children Northern California and Department of Surgery, University of California-Davis, Sacramento, CA 95817, USA.

ABSTRACT

Background: Superantigens (SAgs) of mouse mammary tumor viruses (MMTVs) play a crucial role in T cell selection in the thymus in a T cell receptor (TCR) Vβ-specific manner and SAgs presented by B cells activate T cells in the periphery. The peripheral T cell repertoire is dynamically shaped by the steady induction of T cell tolerance against self antigens throughout the lifespan. We hypothesize that de novo somatic mutation of endogenous MMTV SAgs contributes to the modulation of the peripheral T cell repertoire.

Results: SAg coding sequences were cloned from the genomic DNAs and/or cDNAs of various tissues of female C57BL/6J mice. A total of 68 unique SAg sequences (54 translated sequences) were identified from the genomic DNAs of liver, lungs, and bone marrow, which are presumed to harbor only three endogenous MMTV loci (Mtv-8, Mtv-9, and Mtv-17). Similarly, 69 unique SAg sequences (58 translated sequences) were cloned from the cDNAs of 18 different tissues. Examination of putative TCR Vβ specificity suggested that some of the SAg isoforms identified in this study have Vβ specificities different from the reference SAgs of Mtv-8, Mtv-9, or Mtv-17.

Conclusion: The pool of diverse SAg isoforms, generated by de novo somatic mutation, may play a role in the shaping of the peripheral T cell repertoire including the autoimmune T cell population.

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Related in: MedlinePlus

MMTV SAg isoforms isolated from the cDNA from 18 different tissues of normal C57BL/6J mice. A. Phylogenetic tree (nucleotide sequence) of MMTV SAg isoforms. Eighteen sets of unique MMTV SAg isoforms, which were isolated from 18 different tissues of normal C57BL/6J mice, were analyzed for their phylogenetic relatedness. A number of branching units of SAg isoforms were formed in the phylogenetic tree. Unique SAg isoforms that were found in more than one tissue type are indicated using various shapes and shades. Four reference SAg sequences from Mtv-8, Mtv-9, Mtv-17, and Mtv-30 were included for this analysis. B. Phylogenetic tree (putative amino acid sequence) of SAg isoforms. Eighteen sets of unique SAg isoforms were phylogenetically evaluated and a phylogenetic tree with a number of unique branching units was formed. Unique SAg isoforms that were found in more than one tissue type are indicated using various shapes and shades. Four reference SAg sequences from Mtv-8, Mtv-9, Mtv-17, and Mtv-30 were included for this analysis. black circle (identical to Mtv-17); gray triangle (identical to Mtv-9); black diamond (identical to Mtv-8); gray circle, black triangle, gray box, and black box (identical sequences among different tissue types). cLu (lung cDNA), cOv (ovary cDNA), cUt (uterus cDNA), cTh (thymus cDNA), cSG (salivary gland cDNA), cILN (inguinal lymph node cDNA), cSI (small intestine cDNA), cMLN (mesenteric lymph node cDNA), cALN (axillary lymph node cDNA), cKd (kidney cDNA), cSk (skin cDNA), cSt (stomach cDNA), cSp (spleen cDNA), cAG (adrenal gland cDNA), cBM (bone marrow cDNA), cBr (brain cDNA), cLi (liver cDNA), cCn (colon cDNA), N (normal tissue)
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Figure 2: MMTV SAg isoforms isolated from the cDNA from 18 different tissues of normal C57BL/6J mice. A. Phylogenetic tree (nucleotide sequence) of MMTV SAg isoforms. Eighteen sets of unique MMTV SAg isoforms, which were isolated from 18 different tissues of normal C57BL/6J mice, were analyzed for their phylogenetic relatedness. A number of branching units of SAg isoforms were formed in the phylogenetic tree. Unique SAg isoforms that were found in more than one tissue type are indicated using various shapes and shades. Four reference SAg sequences from Mtv-8, Mtv-9, Mtv-17, and Mtv-30 were included for this analysis. B. Phylogenetic tree (putative amino acid sequence) of SAg isoforms. Eighteen sets of unique SAg isoforms were phylogenetically evaluated and a phylogenetic tree with a number of unique branching units was formed. Unique SAg isoforms that were found in more than one tissue type are indicated using various shapes and shades. Four reference SAg sequences from Mtv-8, Mtv-9, Mtv-17, and Mtv-30 were included for this analysis. black circle (identical to Mtv-17); gray triangle (identical to Mtv-9); black diamond (identical to Mtv-8); gray circle, black triangle, gray box, and black box (identical sequences among different tissue types). cLu (lung cDNA), cOv (ovary cDNA), cUt (uterus cDNA), cTh (thymus cDNA), cSG (salivary gland cDNA), cILN (inguinal lymph node cDNA), cSI (small intestine cDNA), cMLN (mesenteric lymph node cDNA), cALN (axillary lymph node cDNA), cKd (kidney cDNA), cSk (skin cDNA), cSt (stomach cDNA), cSp (spleen cDNA), cAG (adrenal gland cDNA), cBM (bone marrow cDNA), cBr (brain cDNA), cLi (liver cDNA), cCn (colon cDNA), N (normal tissue)

Mentions: The identification of a number of MMTV SAg isoforms at the genomic level led us to investigate whether such a variability of SAg isoforms is present at the expression/transcription level and whether their mutation rates and profiles are associated with differences in tissue type. The SAg sequences were PCR cloned from cDNAs prepared from 18 different tissues from normal C57BL/6J mice (bone marrow, liver, lungs, kidney, salivary gland, adrenal gland, ovary, uterus, spleen, thymus, mesenteric lymph node, axillary lymph node, inguinal lymph node, small intestine, colon, brain, skin, and stomach) and subjected to alignment analyses to identify unique SAg coding sequences within each tissue. Subsequently, phylogenetic analyses of the SAg sequences from all 18 tissues (95 sequences in total) were performed to examine the distribution and similarities of the SAg cDNA isoforms (Figure 2A). Six SAg cDNA sequences were shared by more than one tissue type and a total of 69 unique SAg isoforms were identified from this study. The total number of unique SAg cDNA coding sequences (69) was similar to the number of unique genomic SAg coding sequences (68). However, a direct comparison of the number of unique SAg isoforms between these two groups (genomic vs. cDNA) may not be feasible since the cloning process was not normalized. Phylogenetic evaluation of the SAg cDNA isoforms with the same references used for the analysis of genomic SAg sequences revealed a unique tree pattern with a number of branching units that was substantially different from the genomic SAg tree (Figure 1A). A smaller number of SAg cDNA isoforms were present in the branching unit with the Mtv-8 SAg reference compared to the genomic SAg tree. In contrast, the branching unit with the Mtv-9 SAg reference had a larger number of SAg cDNA isoforms than the Mtv-9 branching unit in the genomic SAg tree. Similar to the genomic SAg tree, a few unique branching units, which are distant from the reference SAgs (Mtv-8, Mtv-9, Mtv-17, and Mtv-30), were formed in the SAg cDNA tree. One interesting finding is that none of the SAg cDNA isoforms isolated from the bone marrow were present in the branching units formed with the reference SAg of Mtv-8 or Mtv-17. The branching pattern of the SAg tree using in silico translated amino acid sequences resembled its nucleotide (cDNA) sequence tree (Figure 2B). Fifty eight unique SAg isoforms (translated amino acids) were identified in different tissues and a number of SAg cDNA isoforms share amino acid sequences that are identical to the reference Mtv-8, -9 and -17 SAgs. The unique branching pattern of the SAg cDNA isoforms (Figure 2) compared to the pattern from the genomic SAg isoforms (Figure 1) indicate that the expression of certain SAg isoforms is tissue type specific in conjunction with a range of internal as well as external stress signals. No significant differences in mutation rates were observed between the hypervariable and non-hypervariable regions of the SAgs at both the genomic DNA and cDNA levels.


Prevalent de novo somatic mutations in superantigen genes of mouse mammary tumor viruses in the genome of C57BL/6J mice and its potential implication in the immune system.

Lee YK, Chiu S, Chew A, Greenhalgh DG, Cho K - BMC Immunol. (2011)

MMTV SAg isoforms isolated from the cDNA from 18 different tissues of normal C57BL/6J mice. A. Phylogenetic tree (nucleotide sequence) of MMTV SAg isoforms. Eighteen sets of unique MMTV SAg isoforms, which were isolated from 18 different tissues of normal C57BL/6J mice, were analyzed for their phylogenetic relatedness. A number of branching units of SAg isoforms were formed in the phylogenetic tree. Unique SAg isoforms that were found in more than one tissue type are indicated using various shapes and shades. Four reference SAg sequences from Mtv-8, Mtv-9, Mtv-17, and Mtv-30 were included for this analysis. B. Phylogenetic tree (putative amino acid sequence) of SAg isoforms. Eighteen sets of unique SAg isoforms were phylogenetically evaluated and a phylogenetic tree with a number of unique branching units was formed. Unique SAg isoforms that were found in more than one tissue type are indicated using various shapes and shades. Four reference SAg sequences from Mtv-8, Mtv-9, Mtv-17, and Mtv-30 were included for this analysis. black circle (identical to Mtv-17); gray triangle (identical to Mtv-9); black diamond (identical to Mtv-8); gray circle, black triangle, gray box, and black box (identical sequences among different tissue types). cLu (lung cDNA), cOv (ovary cDNA), cUt (uterus cDNA), cTh (thymus cDNA), cSG (salivary gland cDNA), cILN (inguinal lymph node cDNA), cSI (small intestine cDNA), cMLN (mesenteric lymph node cDNA), cALN (axillary lymph node cDNA), cKd (kidney cDNA), cSk (skin cDNA), cSt (stomach cDNA), cSp (spleen cDNA), cAG (adrenal gland cDNA), cBM (bone marrow cDNA), cBr (brain cDNA), cLi (liver cDNA), cCn (colon cDNA), N (normal tissue)
© Copyright Policy - open-access
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Figure 2: MMTV SAg isoforms isolated from the cDNA from 18 different tissues of normal C57BL/6J mice. A. Phylogenetic tree (nucleotide sequence) of MMTV SAg isoforms. Eighteen sets of unique MMTV SAg isoforms, which were isolated from 18 different tissues of normal C57BL/6J mice, were analyzed for their phylogenetic relatedness. A number of branching units of SAg isoforms were formed in the phylogenetic tree. Unique SAg isoforms that were found in more than one tissue type are indicated using various shapes and shades. Four reference SAg sequences from Mtv-8, Mtv-9, Mtv-17, and Mtv-30 were included for this analysis. B. Phylogenetic tree (putative amino acid sequence) of SAg isoforms. Eighteen sets of unique SAg isoforms were phylogenetically evaluated and a phylogenetic tree with a number of unique branching units was formed. Unique SAg isoforms that were found in more than one tissue type are indicated using various shapes and shades. Four reference SAg sequences from Mtv-8, Mtv-9, Mtv-17, and Mtv-30 were included for this analysis. black circle (identical to Mtv-17); gray triangle (identical to Mtv-9); black diamond (identical to Mtv-8); gray circle, black triangle, gray box, and black box (identical sequences among different tissue types). cLu (lung cDNA), cOv (ovary cDNA), cUt (uterus cDNA), cTh (thymus cDNA), cSG (salivary gland cDNA), cILN (inguinal lymph node cDNA), cSI (small intestine cDNA), cMLN (mesenteric lymph node cDNA), cALN (axillary lymph node cDNA), cKd (kidney cDNA), cSk (skin cDNA), cSt (stomach cDNA), cSp (spleen cDNA), cAG (adrenal gland cDNA), cBM (bone marrow cDNA), cBr (brain cDNA), cLi (liver cDNA), cCn (colon cDNA), N (normal tissue)
Mentions: The identification of a number of MMTV SAg isoforms at the genomic level led us to investigate whether such a variability of SAg isoforms is present at the expression/transcription level and whether their mutation rates and profiles are associated with differences in tissue type. The SAg sequences were PCR cloned from cDNAs prepared from 18 different tissues from normal C57BL/6J mice (bone marrow, liver, lungs, kidney, salivary gland, adrenal gland, ovary, uterus, spleen, thymus, mesenteric lymph node, axillary lymph node, inguinal lymph node, small intestine, colon, brain, skin, and stomach) and subjected to alignment analyses to identify unique SAg coding sequences within each tissue. Subsequently, phylogenetic analyses of the SAg sequences from all 18 tissues (95 sequences in total) were performed to examine the distribution and similarities of the SAg cDNA isoforms (Figure 2A). Six SAg cDNA sequences were shared by more than one tissue type and a total of 69 unique SAg isoforms were identified from this study. The total number of unique SAg cDNA coding sequences (69) was similar to the number of unique genomic SAg coding sequences (68). However, a direct comparison of the number of unique SAg isoforms between these two groups (genomic vs. cDNA) may not be feasible since the cloning process was not normalized. Phylogenetic evaluation of the SAg cDNA isoforms with the same references used for the analysis of genomic SAg sequences revealed a unique tree pattern with a number of branching units that was substantially different from the genomic SAg tree (Figure 1A). A smaller number of SAg cDNA isoforms were present in the branching unit with the Mtv-8 SAg reference compared to the genomic SAg tree. In contrast, the branching unit with the Mtv-9 SAg reference had a larger number of SAg cDNA isoforms than the Mtv-9 branching unit in the genomic SAg tree. Similar to the genomic SAg tree, a few unique branching units, which are distant from the reference SAgs (Mtv-8, Mtv-9, Mtv-17, and Mtv-30), were formed in the SAg cDNA tree. One interesting finding is that none of the SAg cDNA isoforms isolated from the bone marrow were present in the branching units formed with the reference SAg of Mtv-8 or Mtv-17. The branching pattern of the SAg tree using in silico translated amino acid sequences resembled its nucleotide (cDNA) sequence tree (Figure 2B). Fifty eight unique SAg isoforms (translated amino acids) were identified in different tissues and a number of SAg cDNA isoforms share amino acid sequences that are identical to the reference Mtv-8, -9 and -17 SAgs. The unique branching pattern of the SAg cDNA isoforms (Figure 2) compared to the pattern from the genomic SAg isoforms (Figure 1) indicate that the expression of certain SAg isoforms is tissue type specific in conjunction with a range of internal as well as external stress signals. No significant differences in mutation rates were observed between the hypervariable and non-hypervariable regions of the SAgs at both the genomic DNA and cDNA levels.

Bottom Line: Similarly, 69 unique SAg sequences (58 translated sequences) were cloned from the cDNAs of 18 different tissues.Examination of putative TCR Vβ specificity suggested that some of the SAg isoforms identified in this study have Vβ specificities different from the reference SAgs of Mtv-8, Mtv-9, or Mtv-17.The pool of diverse SAg isoforms, generated by de novo somatic mutation, may play a role in the shaping of the peripheral T cell repertoire including the autoimmune T cell population.

View Article: PubMed Central - HTML - PubMed

Affiliation: Shriners Hospitals for Children Northern California and Department of Surgery, University of California-Davis, Sacramento, CA 95817, USA.

ABSTRACT

Background: Superantigens (SAgs) of mouse mammary tumor viruses (MMTVs) play a crucial role in T cell selection in the thymus in a T cell receptor (TCR) Vβ-specific manner and SAgs presented by B cells activate T cells in the periphery. The peripheral T cell repertoire is dynamically shaped by the steady induction of T cell tolerance against self antigens throughout the lifespan. We hypothesize that de novo somatic mutation of endogenous MMTV SAgs contributes to the modulation of the peripheral T cell repertoire.

Results: SAg coding sequences were cloned from the genomic DNAs and/or cDNAs of various tissues of female C57BL/6J mice. A total of 68 unique SAg sequences (54 translated sequences) were identified from the genomic DNAs of liver, lungs, and bone marrow, which are presumed to harbor only three endogenous MMTV loci (Mtv-8, Mtv-9, and Mtv-17). Similarly, 69 unique SAg sequences (58 translated sequences) were cloned from the cDNAs of 18 different tissues. Examination of putative TCR Vβ specificity suggested that some of the SAg isoforms identified in this study have Vβ specificities different from the reference SAgs of Mtv-8, Mtv-9, or Mtv-17.

Conclusion: The pool of diverse SAg isoforms, generated by de novo somatic mutation, may play a role in the shaping of the peripheral T cell repertoire including the autoimmune T cell population.

Show MeSH
Related in: MedlinePlus