RESUMEN
SUMMARY: Several outlier and subgroup identification statistics (OASIS) have been proposed to discover transcriptomic features with outliers or multiple modes in expression that are indicative of distinct biological processes or subgroups. Here, we borrow ideas from the OASIS methods in the bioinformatics and statistics literature to develop the 'most informative spacing test' (MIST) for unsupervised detection of such transcriptomic features. In an example application involving 14 cases of pediatric acute megakaryoblastic leukemia, MIST more robustly identified features that perfectly discriminate subjects according to gender or the presence of a prognostically relevant fusion-gene than did seven other OASIS methods in the analysis of RNA-seq exon expression, RNA-seq exon junction expression and micorarray exon expression data. MIST was also effective at identifying features related to gender or molecular subtype in an example application involving 157 adult cases of acute myeloid leukemia. AVAILABILITY: MIST will be freely available in the OASIS R package at http://www.stjuderesearch.org/site/depts/biostats CONTACT: stanley.pounds@stjude.org SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Asunto(s)
Análisis de Secuencia de ARN/métodos , Adulto , Biometría , Niño , Exones , Femenino , Expresión Génica , Humanos , Leucemia Mieloide Aguda/genética , Masculino , Modelos GenéticosRESUMEN
Despite extensive research efforts to characterize peripheral regulatory T (T(reg)) cells expressing transcription factor Foxp3, their subset complexity, phenotypic characteristics, TCR repertoire and Ag specificities remain ambiguous. In this study, we identify and define two subsets of peripheral T(reg) cells differing in Foxp3 expression level and TCR repertoires. T(reg) cells expressing a high level of Foxp3 and TCRs not used by naive CD4(+) T cells present a stable suppressor phenotype and dominate the peripheral T(reg) population in unmanipulated mice. The second T(reg) subset, expressing a lower level of Foxp3 and using TCRs shared with naive CD4(+) T cells constitutes a small fraction of all T(reg) cells in unmanipulated mice and enriches T(reg) population with the same Ag specificities as expressed by activated/effector T cells. This T(reg) subset undergoes extensive expansion during response to Ag when it becomes a major population of Ag-specific T(reg) cells. Thus, T(reg) cells expressing TCRs shared with naive CD4(+) T cells have a flexible phenotype and may down-regulate Foxp3 expression which may restore immune balance at the conclusion of immune response or convert these cells to effector T cells producing inflammatory cytokines.
Asunto(s)
Antígenos CD4/biosíntesis , Factores de Transcripción Forkhead/biosíntesis , Factores de Transcripción Forkhead/genética , Regulación de la Expresión Génica/inmunología , Receptores de Antígenos de Linfocitos T/biosíntesis , Receptores de Antígenos de Linfocitos T/genética , Subgrupos de Linfocitos T/inmunología , Linfocitos T Reguladores/inmunología , Traslado Adoptivo , Animales , Antígenos CD4/administración & dosificación , Diferenciación Celular/genética , Diferenciación Celular/inmunología , Células Cultivadas , Técnicas de Cocultivo , Regulación hacia Abajo/genética , Regulación hacia Abajo/inmunología , Factores de Transcripción Forkhead/antagonistas & inhibidores , Proteínas Fluorescentes Verdes/biosíntesis , Proteínas Fluorescentes Verdes/genética , Inmunidad Innata/genética , Inmunofenotipificación , Ratones , Ratones Endogámicos C57BL , Ratones Transgénicos , Modelos Inmunológicos , Receptores de Antígenos de Linfocitos T/fisiología , Fase de Descanso del Ciclo Celular/genética , Fase de Descanso del Ciclo Celular/inmunología , Subgrupos de Linfocitos T/metabolismo , Subgrupos de Linfocitos T/trasplante , Linfocitos T Reguladores/metabolismo , Linfocitos T Reguladores/trasplante , Timo/citología , Timo/inmunología , Timo/metabolismoRESUMEN
The presence of Foxp3(+) regulatory CD4(+) T cells in tumor lesions is considered one of the major causes of ineffective immune response in cancer. It is not clear whether intratumoral T(reg) cells represent T(reg) cells pre-existing in healthy mice, or arise from tumor-specific effector CD4(+) T cells and thus representing adaptive T(reg) cells. The generation of T(reg) population in tumors could be further complicated by recent evidence showing that both in humans and mice the peripheral population of T(reg) cells is heterogenous and consists of subsets which may differentially respond to tumor-derived antigens. We have studied T(reg) cells in cancer in experimental mice that express naturally selected, polyclonal repertoire of CD4(+) T cells and which preserve the heterogeneity of the T(reg) population. The majority of T(reg) cells present in healthy mice maintained a stable suppressor phenotype, expressed high level of Foxp3 and an exclusive set of TCRs not used by naive CD4(+) T cells. A small T(reg) subset, utilized TCRs shared with effector T cells and expressed a lower level of Foxp3. We show that response to tumor-derived antigens induced efficient clonal recruitment and expansion of antigen-specific effector and T(reg) cells. However, the population of T(reg) cells in tumors was dominated by cells expressing TCRs shared with effector CD4(+) T cells. In contrast, T(reg) cells expressing an exclusive set of TCRs, that dominate in healthy mice, accounted for only a small fraction of all T(reg) cells in tumor lesions. Our results suggest that the T(reg) repertoire in tumors is generated by conversion of effector CD4(+) T cells or expansion of a minor subset of T(reg) cells. In conclusion, successful cancer immunotherapy may depend on the ability to block upregulation of Foxp3 in effector CD4(+) T cells and/or selectively inhibiting the expansion of a minor T(reg) subset.