Comprehensive single-cell transcriptome analysis reveals heterogeneity in endometrioid adenocarcinoma tissues.

Single cell transcriptome analysis of a cancer tissue can provide objective assessment of subtype population or the activation of each of various microenvironment component cells. In this study, we applied our newly developed technique of single cell analysis to the myometrial infiltration side (M-side) and the endometrial side (E-side) of a human endometrioid adenocarcinoma with squamous differentiation tissues. We also analyzed spherogenic cultures derived from the same tissue to identify putative regulators of stemness in vivo. Cancer cells in the E-side were highly malignant compared with those in the M-side. Many cells on the E-side were positive for spheroid-specific tumorigenesis-related markers including SOX2. In addition, there were higher numbers of epithelial-to-mesenchymal transition (EMT) cells in the E-side compared with the M-side. This study identified a site containing cells with high malignant potential such as EMT and cancer stem-like cells in cancer tissues. Finally, we demonstrate that established endometrioid adenocarcinoma subtype classifiers were variably expressed across individual cells within a tumor. Thus, such intratumoral heterogeneity may be related to prognostic implications.

Coordinated changes in DNA methylation in antigen-specific memory CD4 T cells.

Memory CD4(+) T cells are central regulators of both humoral and cellular immune responses. T cell differentiation results in specific changes in chromatin structure and DNA methylation of cytokine genes. Although the methylation status of a limited number of gene loci in T cells has been examined, the genome-wide DNA methylation status of memory CD4(+) T cells remains unexplored. To further elucidate the molecular signature of memory T cells, we conducted methylome and transcriptome analyses of memory CD4(+) T cells generated using T cells from TCR-transgenic mice. The resulting genome-wide DNA methylation profile revealed 1144 differentially methylated regions (DMRs) across the murine genome during the process of T cell differentiation, 552 of which were associated with gene loci. Interestingly, the majority of these DMRs were located in introns. These DMRs included genes such as CXCR6, Tbox21, Chsy1, and Cish, which are associated with cytokine production, homing to bone marrow, and immune responses. Methylation changes in memory T cells exposed to specific Ag appeared to regulate enhancer activity rather than promoter activity of immunologically relevant genes. In addition, methylation profiles differed between memory T cell subsets, demonstrating a link between T cell methylation status and T cell differentiation. By comparing DMRs between naive and Ag-specific memory T cells, this study provides new insights into the functional status of memory T cells.

Naïve CD4+ T cells of Peyer's patches produce more IL-6 than those of spleen in response to antigenic stimulation.

Peyer's patches (PPs) are potential sites where specific mucosal immune responses and oral tolerance are induced. The unique features of these immune responses are thought to occur in micromilieu and are largely affected by antigen-presenting cells (APCs) such as dendritic cells. In this study, we investigated the cytokine profiles induced by the activation of CD4(+) T cells of PPs. PP cells from TCR transgenic mice secreted greater amounts of IL-5 and IL-6 than spleen cells after antigenic stimulation. IL-5 was mainly produced by PP non-T cells, whereas IL-6 was secreted by PP CD4(+) cells. PPs contained two major populations including naïve and memory/activated CD4(+) cells; both populations secreted IL-6 upon activation. We also found that CD4(+)/CD62L(hi) naïve cells from PPs secreted a greater amount of IL-6 after stimulation than those from the spleen. Furthermore, subtraction and qPCR analyses revealed that PP CD4(+)/CD62L(hi) cells express a greater amount of transcripts of GA-binding protein ß subunit 1 than those of the spleen. These results suggest that naïve T cells as well as non-T cells and activated/memory T cells from PPs are distinct from their splenic counterparts and thus cause unique immune responses the in intestine.

Molecular mimics can induce a nonautoaggressive repertoire that preempts induction of autoimmunity.

To determine the role that competition plays in a molecular mimic's capacity to induce autoimmunity, we studied the ability of naïve encephalitogenic T cells to expand in response to agonist altered peptide ligands (APLs), some capable of stimulating both self-directed and exclusively APL-specific T cells. Our results show that although the APLs capable of stimulating exclusively APL-specific T cells are able to expand encephalitogenic T cells in vitro, the encephalitogenic repertoire is effectively outcompeted in vivo when the APL is used as the priming immunogen. Competition as a mechanism was supported by: (i) the demonstration of a population of exclusively APL-specific T cells, (ii) an experiment in which an encephalitogenic T cell population was successfully outcompeted by adoptively transferred naïve T cells, and (iii) demonstrating that the elimination of competing T cells bestowed an APL with the ability to expand naïve encephalitogenic T cells in vivo. In total, these experiments support the existence of a reasonably broad T cell repertoire responsive to a molecular mimic (e.g., a microbial agent), of which the exclusively mimic-specific component tends to focus the immune response on the invading pathogen, whereas the rare cross-reactive, potentially autoreactive T cells are often preempted from becoming involved.

High-resolution analysis of the 5'-end transcriptome using a next generation DNA sequencer.

Massively parallel, tag-based sequencing systems, such as the SOLiD system, hold the promise of revolutionizing the study of whole genome gene expression due to the number of data points that can be generated in a simple and cost-effective manner. We describe the development of a 5'-end transcriptome workflow for the SOLiD system and demonstrate the advantages in sensitivity and dynamic range offered by this tag-based application over traditional approaches for the study of whole genome gene expression. 5'-end transcriptome analysis was used to study whole genome gene expression within a colon cancer cell line, HT-29, treated with the DNA methyltransferase inhibitor, 5-aza-2'-deoxycytidine (5Aza). More than 20 million 25-base 5'-end tags were obtained from untreated and 5Aza-treated cells and matched to sequences within the human genome. Seventy three percent of the mapped unique tags were associated with RefSeq cDNA sequences, corresponding to approximately 14,000 different protein-coding genes in this single cell type. The level of expression of these genes ranged from 0.02 to 4,704 transcripts per cell. The sensitivity of a single sequence run of the SOLiD platform was 100-1,000 fold greater than that observed from 5'end SAGE data generated from the analysis of 70,000 tags obtained by Sanger sequencing. The high-resolution 5'end gene expression profiling presented in this study will not only provide novel insight into the transcriptional machinery but should also serve as a basis for a better understanding of cell biology.

Complete refolding of bovine beta-lactoglobulin requires disulfide bond formation under strict conditions.

beta-Lactoglobulin (beta-LG) denatured with 6 M guanidine hydrochloride (GdnHCl) containing a reducing agent and subsequently dialysed against phosphate-buffered saline (PBS) resulted in incomplete refolding of this protein despite the fact that the biological activity for retinol-binding was recovered to almost the same degree as that of the native molecule [Hattori, M., Ametani, A., Katakura, Y., Shimizu, M., Kaminogawa, S. J., Biol. Chem. 268 (1993) 22414-22419]. The enzyme probe method, evaluation of hydrophilicity values, in-gel mobility on SDS-PAGE, and evaluation of disulfide bonds with the Ellman method showed exposure of the hydrophobic region(s) and incorrect disulfide bond formation in such dialyzed beta-LG molecules. We reveal in this present work that complete refolding could be attained by diluting denatured beta-LG with PBS containing a reducing agent, before slow reoxidation of the sulfhydryl groups upon dialysis for gradient removal of the reducing agent in 6 steps. Complete renaturation was confirmed by analyzing the retinol-binding activity, CD spectra, intrinsic fluorescence, binding ability of monoclonal antibodies (mAbs), and SDS-PAGE. Step-by-step disulfide bond formation was considered to be critical for the complete refolding of denatured beta-LG. Our method can contribute to establish a procedure for complete refolding of useful recombinant proteins in vitro without such biological aids as chaperones.

Limited clonality in autoimmunity: drivers and regulators.

The available T cell repertoire directed against self is appreciable owing to the escape of many clones from negative selection, largely because many determinants on self proteins are cryptic and not presented adequately. In addition, the degeneracy of T cell receptor specificity permits each lymphocyte a broad recognitive potential. Within the available self-reactive repertoire are T cells with high affinity, and these can compete favorably with other T cells with the same specificity. We have studied a "driver clone" and its two specific regulators in the B10.PL model of experimental autoimmune encephalomyelitis and found that each of these repertoires is highly limited. There is a single major clonal family comprising the aggressive driver population, which is public and of high affinity, and just one other minor public clonotype. The receptors of this Vbeta8.2/Jbeta2.7 driver are presented to a CD4 regulator and a CD8 suppressor, each of limited clonality, the latter killing the driver clone by apoptosis, completing a feedback control loop. This tightly regulated group of three cell types furnishes an excellent example of the immune homunculus.

Vaccination with an immunodominant peptide of bovine type II collagen induces an anti-TCR response, and modulates the onset and severity of collagen-induced arthritis.

T cell responses directed toward TCR-derived peptides have been shown to be an important regulatory mechanism of protection against autoimmunity. Here, we show that a naturally induced TCR-directed immune response can delay the onset of collagen-induced arthritis (CIA), an animal model of autoimmune rheumatoid arthritis in humans. DBA/1 mice were pretreated with an immunodominant peptide, p245-270, from bovine type II collagen (bCII) and were subsequently immunized with whole bCII for the induction of arthritis. The results showed that preactivation of p245-270-reactive cells delayed the onset and reduced the severity of CIA, compared with animals in the control group. Interestingly, the serum antibody response to bCII and the bCII-specific cytokine were not affected under these conditions. This result indicates that the observed protection was neither directly due to a lower antibody response nor due to the immune deviation of the anti-bCII T cell response. Furthermore, immunization with p245-270, but not bCII, induced a strong response to the B5 peptide, an immunodominant region of the TCR V(beta)8.2 (amino acids 76-101) that binds very strongly to I-A(q). These data suggest that at a critical phase in the loss of self-tolerance, an effective anti-TCR response, induced naturally, can regulate the pathogenic autoimmune response and thus may provide protection against autoimmunity.

Amino acid residue substitution at T-cell determinant-flanking sites in beta-lactoglobulin modulates antigen presentation to T cells through subtle conformational change.

We compared T-cell responses to regions in residues 21-40 of A and B variants of bovine milk beta-lactoglobulin (beta-LG) that vary by two different amino acid residues at 64 and 118. Results showed that T cells from C57/BL6 and C3H/HeN mice immunized with peptide 21-40 or BALB/c mice immunized with peptide 21-32 or 25-40 responded more vigorously to beta-LG B than to beta-LG A. This difference in response to 25-40 in BALB/c mice was not observed when beta-LGs B and A were denatured, suggesting that the conformation difference affects display of the determinant 25-40. Reactivity of anti-beta-LG monoclonal antibodies and molecular modeling using molecular dynamics calculations revealed subtle differences in the three-dimensional structure of these two variants. Furthermore, substitution of two amino acid residues at sites distant from the T-cell determinant induced differential determinant display on antigen-presenting cells, possibly due to subtle conformational changes in beta-LG.

Antigen feeding increases frequency and antigen-specific proliferation ability of intraepithelial CD4+ T cells in alphabeta T cell receptor transgenic mice.

To study how intestinal intraepithelial lymphocytes (IEL) are affected by orally ingested antigen, the phenotypes and responses of the IEL in mice expressing a transgenic T cell receptor alphabeta (TCR alphabeta) specific for ovalbumin (OVA) were analyzed after feeding OVA. In the OVA-fed mice, the abundance of alphabeta-IEL as a proportion of the total IEL population increased and the frequency of CD4+ cells increased within the TCR alphabeta+ IEL population. CD4(+) IEL from OVA-fed transgenic mice proliferated in vitro more markedly in response to antigen stimulation than IEL from mice fed the control diet. These results indicate that antigen-specific proliferation of CD4+ IEL was amplified as a result of oral administration of antigen.

Autoreactive T cells can be protected from tolerance induction through competition by flanking determinants for access to class II MHC.

It is not clear why the N-terminal autoantigenic determinant of myelin basic protein (MBP), Ac1-9, is dominant in the B1O.PL (H-2(u)) mouse, given its weak I-A(u)-MHC binding affinity. Similarly, how do high-affinity T cells specific for this determinant avoid negative selection? Because the MBP:1-9 sequence is embryonically expressed uniquely in the context of Golli-MBP, determinants were sought within the contiguous N-terminal "Golli" region that could out-compete MBP:1-9 for MHC binding, and thereby prevent negative selection of the public response to Ac1-9, shown here to be comprised of a V beta 8.2J beta 2.7 and a V beta 8.2J beta 2.4 expansion. Specifically, we demonstrate that Ac1-9 itself can be an effective inducer of central tolerance induction; however, in the context of Golli-MBP, Ac1-9 is flanked by determinants which prevent its display to autoreactive T cells. Our data support competitive capture as a means of protecting high-affinity, autoreactive T cells from central tolerance induction.

Cytokine responses of human intestinal epithelial-like Caco-2 cells to the nonpathogenic bacterium Bacillus subtilis (natto).

Intestinal epithelial cells produce cytokines in response to pathogenic bacteria. However, cellular responses of these cells to nonpathogenic strains, such as Bacillus subtilis, are yet to be determined. In this study, we investigate whether epithelial-like human colon carcinoma Caco-2 cells produce cytokines in response to B. subtilis or B. subtilis (natto). The latter strain is utilized for manufacturing the fermented soy food "natto". Live cells of nonpathogenic B. subtilis JCM 1465(T), B. subtilis (natto) and E. coli JCM 1649(T), as well as pathogenic S. enteritidis JCM 1652 and P. aeruginosa JCM 5516 strains, induced secretion of interleukin-6 (IL-6) and/or IL-8, but not IL-7, IL-15 or tumor necrosis factor alpha (TNF-alpha). Transepithelial electrical resistance (TER) of Caco-2 cell monolayers cultured with E. coli, S. enteritidis or P. aeruginosa decreased more rapidly than that of cells cultured with B. subtilis or B. subtilis (natto). The amounts of cytokine induced by B. subtilis (natto) cells were strain-dependent. Moreover, B. subtilis (natto) cells subjected to hydrochloric acid treatment, but not autoclaving, induced a higher secretion of IL-6 and IL-8 than intact cells. Tyrosine kinase inhibitors, including AG126 and genistein, suppressed cytokine secretion. Our results suggest that the nonpathogenic B. subtilis (natto) bacterium induces cytokine responses in intestinal epithelial cells via activation of an intracellular signaling pathway, such as that of nuclear factor-kappa B (NF-kappaB).

Interleukin 12 and CD86 Regulate Th1 and Th2 Development Induced by a Range of Antigen Doses Presented by Peyer's Patch and Spleen Cells.

In this study, we demonstrate the role of interleukin 12 (IL-12), CD80 and CD86 in T helper type 1 (Th1) and Th2 differentiation induced through antigen presentation by Peyer's patch (PP) and spleen (SPL) cells with various doses of antigen. IL-12 was found to be critical for the induction of Th1-type cytokine producing cells, while antigen-dose dependent patterns of differentiation into Th2-type cytokine producing cells were not altered by the blockade of IL-12. Further, the difference in the pattern of Th2-type cytokine producing cell differentiation induced by PP and SPL cells depending on the antigen dosage were preserved in the absence of IL-12. When the function of CD86 was blocked by specific antibody, the induction of Th1-type cytokine producing cells was kept at high levels through every antigen dose, and the difference between PP and SPL cells was abrogated. With regard to Th2 induction, CD86 enhanced the differentiation of Th2-type cytokine producing cells but it was not essential in the case of antigen presentation by SPL cells. These results suggest that antigen-dose dependent changes in Th2 cell induction are regulated by additional factors which cannot induce antigen-dose dependent changes in Th1 cell differentiation by themselves.

Antigen presentation by Peyer's patch cells can induce both Th1- and Th2-type responses depending on antigen dosage, but a different cytokine response pattern from that of spleen cells.

The Th1 and Th2 preference induced by cells from the Peyer's patch (PP) and spleen (SPL) with various doses of an antigen was examined. The same splenic T cell receptor-transgenic CD4+ T cells were first incubated with PP or SPL cells in the presence of various doses of an antigen, and the cytokine response was observed after secondary stimulation. A Th2-type pattern was only obtained for primary stimulation at 10 microM of the antigen with PP cells, whereas a Th1 pattern was induced at both higher and lower concentrations. SPL cells in the presence of 0.1 to 1 microM of the antigen induced the secretion of Th2-type cytokines. Ten and 100 microM of the antigen plus SPL cells did not induce the release of a large quantity of cytokines. PP cells induced a different cytokine pattern at the antigen concentration that induced a similar level of T cell proliferation with SPL cells. Our findings suggest that the antigen-dose dependent development of Th1/Th2 cells is differentially modulated by the antigen-presentation function of cells in PP and SPL.

Naive CD4+ T cells exhibit distinct expression patterns of cytokines and cell surface molecules on their primary responses to varying doses of antigen.

The amount of an Ag used for stimulation affects the type and magnitude of T cell responses. In this study we have investigated the primary response of naive CD4(+) T cells derived from OVA-specific TCR-transgenic mice (OVA23-3) upon stimulation with varying doses of the antigenic peptide, OVA(323-339). IL-4 expression was maximal with 50 nM Ag and decreased significantly with increasing doses. In contrast, IFN-gamma expression, which was also detected at 50 nM Ag, increased with increasing doses. The expression patterns of mRNA for the Th2-specific transcription factors GATA-3 and c-Maf were parallel to that of IL-4. These expression profiles were not altered by the addition of anti-IL-4 plus anti-IL-12 mAbs, suggesting that cytokine receptor signaling is not essential. Naive CD4(+) T cells stimulated with 5 nM Ag elicited IgM secretion from cocultured B cells, whereas those stimulated with 50 nM Ag or more elicited apoptosis of B cells. This may be because at lower doses of Ag (5 nM), naive CD4(+) T cells express CD40 ligand and OX40, whereas at higher doses (50 nM), they express Fas ligand. Clearly, the expression of each type of molecule depends on the Ag dose, and different molecules had different expression patterns. Thus, in the primary response, naive CD4(+) T cells can exhibit different functions depending on the dose of Ag.

Murine T cell lines can change CD25 expression patterns as well as proliferation and cell death patterns in response to interleukin 2.

T cell subpopulations were obtained from F12.5 and B245/270D T cell lines during long-term culture. Two altered F12.5 subpopulations proliferated more intensively than the original clone. These two subpopulations of F12.5 constantly expressed CD25 (interleukin 2 receptor alpha chain) at a high level and exogenously added interleukin 2 (IL-2) enhanced cell death for one of these subpopulations. However, the original clone expressed CD25 only after activation and IL-2 inhibited cell death of the original clone. On the other hand, the altered B245/270D subpopulation lost the antigen-specific proliferation ability. This altered cell line under the stimulation culture did not express CD25 even after activation, although the original line expressed CD25. However, the expression pattern of CD25on the altered cell line at resting state was induced similar to that of the original one. These results suggest that an expression pattern of CD25 can be changed during long-term cultures, accompanied with alteration in response to proliferation and cell death.