Tim-3 mediates T cell trogocytosis to limit antitumor immunity

T cell immunoglobulin mucin domain-containing protein 3 (Tim-3) negatively regulates innate and adaptive immunity in cancer. To identify the mechanisms of Tim-3 in cancer immunity, we evaluated the effects of Tim-3 blockade in human and mouse melanoma. Here, we show that human programmed cell death 1-positive (PD-1+) Tim-3+CD8+ tumor-infiltrating lymphocytes (TILs) upregulate phosphatidylserine (PS), a receptor for Tim-3, and acquire cell surface myeloid markers from antigen-presenting cells (APCs) through transfer of membrane fragments called trogocytosis. Tim-3 blockade acted on Tim-3+ APCs in a PS-dependent fashion to disrupt the trogocytosis of activated tumor antigen-specific CD8+ T cells and PD-1+Tim-3+ CD8+ TILs isolated from patients with melanoma. Tim-3 and PD-1 blockades cooperated to disrupt trogocytosis of CD8+ TILs in 2 melanoma mouse models, decreasing tumor burden and prolonging survival. Deleting Tim-3 in dendritic cells but not in CD8+ T cells impeded the trogocytosis of CD8+ TILs in vivo. Trogocytosed CD8+ T cells presented tumor peptide-major histocompatibility complexes and became the target of fratricide T cell killing, which was reversed by Tim-3 blockade. Our findings have uncovered a mechanism Tim-3 uses to limit antitumor immunity.

TIM-3+ T regulatory cells alter the lymphoid compartment in cold and Hot solid tumor Model

There is a progressive TIM-3+ T reg increase in solid tumors as the tumor progress. W have found that knocking out the ability of T reg to induce TIM-3 lead to delayed progression of tumors in the TIM-3 conditional knockout mice upon both hot (MC38) and cold (B16F10) syngeneic tumor challenges. We are employing our conditional T reg specific TIM-3 Knockout mouse to study if presence or absence of TIM-3 on T reg cells within these tumor models. Preliminary data has shown that our conditional Tim3 knockout T reg cells are found at a much lower frequency, and have an altered suppressive phenotype within the microenvironment of these tumors. We are currently investigating the other changes in the different subsets of lymphoid compartment in tumors. These data suggest that altering the expression of TIM-3+ on T reg has the potential to act as an effective target to alter tumor microenvironment.

Targeting TIM-3+ T reg may therefore be attractive model to study, along with other combination immunotherapy to increase the success in immunotherapy on patients who develop resistance to primary immunotherapy.

Mechanism of Tim-3 regulation of CD8+ T cell function

Tim-3 or transmembrane immunoglobulin and mucin domain-3 is a type I membrane protein expressed by various immune cell types, and has been shown to have a co-stimulatory role in T cells through the PI3K pathway. Tim-3 comprises extracellular, transmembrane and intracellular domains, the latter of which contains five tyrosine residues. We and others have shown that these tyrosines participate in TCR-mediated signaling pathways. Using LCMV infection, we also found that Tim-3 expression influences the formation of short-lived effector and memory precursor CD8+ T cells. We hypothesize that Tim-3 signaling through the tyrosine residues in its cytoplasmic domain modulates CD8+ T cell activation and differentiation. To test this hypothesis, we have used LCMV-specific TCR transgenic (P14) mice crossed to truncated version of Tim-3 and CD8+ conditional deletion of Tim-3. CD8+ T cell activation and memory were analyzed by flow cytometry after infection with LCMV Armstrong to induce an acute infection. The effects of Tim-3 on CD8+ T cells were found to be most prominent at the effector stage of infection and RNA sequencing has shown that loss of Tim-3 signaling promotes acquisition of a memory-like phenotype. Transcription factors T-bet and Blimp-1 were found to be lower in Tim-3 KO CD8+ T cells, while Tcf-1 maintained at higher levels in the absence of Tim-3 signaling. Cytokine production by effector CD8+ T cells was also found to be lower when Tim-3 was absent. Thus, we conclude that Tim-3 signaling via its cytoplasmic tyrosine residues plays a role in CD8+ T cells in an acute infection. These results may lead to a better understanding of CD8+ T cell activation and memory development in different settings.

Supported by R01 AI138504-01A1

PIK3IP1/TrIP Immune Regulation on CD8+ T Cells Restricts Anti-Tumor Immunity

The signaling pathways involving phosphoinositide-3-kinases (PI3Ks) are highly conserved and tightly regulated to influence the activation, proliferation, and survival of all cell types. Our lab has recently shown protein TrIP (Transmembrane Inhibitor of PI3K, Pik3ip1) has a distinctly high expression on T cells and is capable of downregulating PI3K signaling in these cells, acting as a negative regulator of T cell immune responses. These studies revealed that CD4+ T cells lacking TrIP expression exhibit a more Th1 inflammatory phenotype compared to WT T cells, both in vivo and in vitro. These data have led us to propose that TrIP restricts the inflammatory activity of T cells more generally, including CD8+ T cells, and that targeting/knockout of this regulator may promote anti-tumor immunity.

Using a conditional TrIP knockout mouse model developed in our lab, we have performed syngeneic tumor challenges in CD8+ T cell-specific TrIP knockout mice (TrIPfl/flE8icre) which show that TrIP knockout mice are resistant to growth of syngeneic tumors. In addition to this increased resistance, tumors harvested from our knockout mice contain twice as many infiltrating T cells compared to their WT counterparts. Of those, CD8+ T cells appeared to be the main drivers of this increased T cell infiltration as their frequency was double that of the CD4+ population. In addition, these TrIP KO CD8+ T cells have a significantly more inflammatory phenotype detailed through RNAseq analysis.

In conclusion, TrIP plays a significant role in the antitumor immune activity of CD8+ T cells. The TrIP KO mice are resistant to tumor challenge and display an increase in TIL T cell infiltrate. These data describes TrIP as an interesting potential target for immunotherapy.

Supported by grants from the NIH 5R01GM136148-02 and 5T32CA082084-20

Tim-3 deletion on Treg increases virus-specific T cell response and reduces viral burden in chronic LCMV infection

Tim-3, a surface protein, is upregulated on Treg during chronic viral infections. During HCV infection in humans there is an increase in frequency of Tim-3+ Treg, which have increased proliferation, survival, and expression of immunosuppressive cytokines like IL-10. Similarly, it’s been recently reported that there is an increase in Tim-3+ Treg in people with HIV (PWH). However, the role of regulatory T cells (Treg) during chronic viral infection has not been fully defined. We hypothesize that Tim-3 promotes an effector phenotype on Treg during chronic viral infection, which limits the virus-specific T cell response and impairs viral clearance. Using an inducible Treg-specific Tim-3 loss-of-function (Tim-3 Treg KO) model, we found a significant decrease in morbidity during LCMV chronic infection. Tim-3 Treg KO mice mounted a higher virus-specific T cell response and had lower viral burden in blood, liver, and kidney at 30dpi. Lack of Tim-3 expression on Treg limited their ability to upregulate IL-10, TGFb, CD39, PD-1, CD25, CTLA-4 and CD44. Similarly, in PWH Tim-3+ Treg have increased expression of IL-10 compared to HIV(−). In addition, Tim-3+ Treg from PWH show significant upregulation of Ki67+, CD73+, Gzmb+ and TGFb+ compared to their Tim-3− Treg counterpart. Our findings demonstrate that modulation of a surface protein in Treg can lead to a reduction in viral burden and enhance LCMV-specific T cell response. We found that Tim-3+ Treg have an increased suppressive phenotype, compared with Tim-3− Treg in PWH, regardless of viral suppression. Elucidation of the mechanism of Tim-3 function in Treg may provide insights into the biology of chronic infections and for developing novel potential strategies to achieve HIV remission off ART.

Supported by grants from NIH (T32GM008208, R01AI138504, U01AI131285)

639 PIK3IP1/TrIP immune regulation on CD8+ T cells restricts anti-tumor immunity

Background

The signaling pathways involving phosphoinositide-3-kinases (PI3Ks) are highly conserved and tightly regulated to influence the activation, proliferation, and survival of all cell types. PI3K signaling plays a major role in T cell responses to antigen due to its position directly downstream of T cell receptor (TCR)/CD28 ligation.1 2 Our lab has recently shown that the cell surface protein TrIP (Transmembrane Inhibitor of PI3K, gene name: Pik3ip1) has a distinctly high expression on T cells and is capable of downregulating PI3K signaling in CD4+ T cells, acting as a negative regulator of T cell immune responses.3 4 These studies revealed that CD4+ T cells lacking TrIP expression exhibit a more Th1 inflammatory phenotype compared to WT T cells, both in vivo and in vitro.3 These data have led us to propose that TrIP restricts the inflammatory activity of T cells more generally, including CD8+ T cells, and that targeting/knockout of this negative regulator may promote anti-tumor immunity.

Methods

Using a conditional TrIP knockout mouse model developed in our lab, we have performed syngeneic tumor challenges in CD8+ T cell-specific TrIP knockout mice (TrIPfl/flE8icre). We have also characterized the tumor immune infiltrate of these mice to understand the impact of T cell-specific TrIP deficiency on the immune landscape.

Results

Our data thus far show that CD8+ T cell-specific TrIP knockout mice (TrIPfl/flE8icre) are resistant to growth of syngeneic tumors. In addition to increased tumor resistance, we have also found that tumors harvested from our TrIPfl/flE8icre knockout mice contain twice as many infiltrating T cells compared to their WT counterparts. We also found that CD8+ T cells appeared to be the main drivers of this increased T cell infiltration, as their frequency was double that of the CD4+ population in tumors transplanted into TrIP KO mice.

Conclusions

We describe data demonstrating that TrIP, a relatively novel PI3K inhibitor, plays a significant role in the antitumor immune activity of CD8+ T cells. Our that CD8+ T cell-specific TrIP knockout mice are resistant to tumor challenge and show more robust tumor CD8+ T cell infiltrate. With these data, we are excited to propose TrIP as a potential future immunotherapeutic target worthy of continued investigation.

References

Okkenhaug K, Turner M, Gold MR. PI3K signaling in B cell and T cell biology. Front Immunol 2014;5:557. doi:10.3389/fimmu.2014.00557

Kane LP, Weiss A. The PI-3 kinase/Akt pathway and T cell activation: pleiotropic pathways downstream of PIP3. Immunol Rev 2003;192:7–20. doi:10.1034/j.1600-065X.2003.00008.x

Uche UU, Piccirillo AR, Kataoka S, et al. PIK3IP1/TrIP restricts activation of T cells through inhibition of PI3K/Akt. J Exp Med 2018;215:3165–3179. doi:10.1084/jem.20172018

DeFrances MC, Debelius DR, Cheng J, Kane LP. Inhibition of T-cell activation by PIK3IP1. Eur J Immunol 2012;42:2754–2759. doi:10.1002/eji.201141653

692 Tim-3 expression drives phenotypic and functional changes in Treg in secondary lymphoid organs and the tumor microenvironment, effecting tumor burden

Background

Regulatory T cells (T reg) are critical mediators of self-tolerance but can also limit effective anti-tumor immunity. We and others previously reported that 40–60% percent of T reg-infiltrating head and neck cancer (HNC) and other tumors highly express Tim-3, compared with about 5% in lymphoid organs, it therefore gets imperative to characterize if Tim-3 is driving any T reg specific function in tumor microenvironment and under homeostasis.

Methods

Using a conditional TIM-3 inducible and knockout mouse model developed in our lab, we have performed syngeneic tumor challenges in T reg-specific Tim-3 transgenic and knockout mice (FoxP3ERT2CreSFS-Tim-3 and FoxP3ERT2Cre-FLEX4). We have also characterized the tumor immune infiltrate of these mice to understand the impact of T reg specific Tim-3induction and deficiency on the immune landscape.

Results

Tim-3 induction on T reg leads to rapid growth associated with higher progression of CD8 compartment towards exhaustion, while TIm-3 knockout in T reg specific manner leads top overall decline in T reg compartment in tumors associated with lower exhaustion in the CD8 compartment and decrease in tumor burden,

Conclusions

Tumor-infiltrating Tim-3+ Treg have enhanced suppressive function and display a more effector-like phenotype. Using a novel mouse model with cell type-specific Tim-3 expression, we show here that expression of Tim-3 by Treg is sufficient to drive Treg to a more effector-like phenotype, and increases suppressive activity, effector T cell exhaustion and tumor growth. We also show that inducible deletion of Tim-3 specifically from Treg enhances anti-tumor immunity and decrease in tumor burden along with a decrease in tumor associated Treg compartment. These findings may help to reconcile previous reports that some Tim-3 antibodies enhance T cell responses in vivo, while expression of Tim-3 has a cell-intrinsic ability to enhance TCR signaling and T cell activation. A major role of Tim-3 was found to be mediated through IL-10 and IL-10 R pathway in both Treg and CD8 compartment. Thus, we propose that Tim-3 regulates anti-tumor immunity at least in part through enhancement of Treg function. To our knowledge, this is the first example in which expression of a single co-stimulatory molecule is sufficient to drive differentiation of Treg in this manner.

Acknowledgements

We acknoledge Dr. Robert L. Ferris and Dr. Greg M. Delgoffe for their inputs and guidance with human and metabolism associated experiments.

The costimulatory activity of Tim-3 requires Akt and MAPK signaling and its recruitment to the immune synapse

Expression of the transmembrane protein Tim-3 is increased on dysregulated T cells undergoing chronic activation, including during chronic infection and in solid tumors. Thus, Tim-3 is generally thought of as an inhibitory protein. We and others previously reported that under some circumstances, Tim-3 exerts paradoxical costimulatory activity in T cells (and other cells), including enhancement of the phosphorylation of ribosomal S6 protein. Here, we examined the upstream signaling pathways that control Tim-3-mediated increases in phosphorylated S6 in T cells. We also defined the localization of Tim-3 relative to the T cell immune synapse and its effects on downstream signaling. Recruitment of Tim-3 to the immune synapse was mediated exclusively by the transmembrane domain, replacement of which impaired the ability of Tim-3 to costimulate T cell receptor (TCR)-dependent S6 phosphorylation. Furthermore, enforced localization of the Tim-3 cytoplasmic domain to the immune synapse in a chimeric antigen receptor still enabled T cell activation. Together, our findings are consistent with a model whereby Tim-3 enhances TCR-proximal signaling under acute conditions.

Expression of Tim-3 drives Treg to an effector-like state with enhanced suppressive activity and altered response to tumor

Regulatory T cells (T reg) are mediators effective anti-tumor immunity. We and others previously reported that 40–60% percent of T reg-infiltrating head and neck cancer (HNC) and other tumors highly express Tim-3, compared with about 5% in lymphoid organs. Tumor-infiltrating Tim-3+ T reg also have enhanced suppressive function. Using a novel mouse model with cell type-specific inducible Tim-3 expression, we show here that expression of Tim-3 by T reg is sufficient to drive Treg to a more effector-like phenotype, resulting in enhanced suppressive activity and increased tumor growth. TIM-3 +T reg also seem to be metabolically altered driven by active signaling in ERK and m-TOR pathway. We further see that T reg specific deletion of TIM-3 leads to decrease in T reg frequency in tumor infiltrating lymphocytes and delay in tumor progression. These findings suggest to a possibility of using Tim-3 as a target to alter the tumor progression and clearance highliting a qualitatively different role for TIM-3 in T reg cells. Thus, we propose that Tim-3 regulates anti-tumor immunity at least in part through enhancement of T reg function. To our knowledge, this is the first example in which expression of a single co-stimulatory molecule is sufficient to drive differentiation of T reg and alter immune response in this manner.

Enhanced suppressive phenotype of Tim-3+ Treg during chronic infection

T cell (or transmembrane) immunoglobulin and mucin-domain containing protein-3 (Tim-3) is a cell-surface protein expressed during T cell exhaustion, a process that leads to a progressive loss of effector function due to chronic T cell receptor (TCR) stimulation. In humans, Tim-3 expression has also been found to be increased on Treg isolated from tumors and during chronic viral infection. However, the role of Tim-3 on Treg during chronic viral infection remains largely unknown. Our main hypothesis is that Tim-3 expression on Treg will increase their proliferation and suppressive capacity during LCMV infection. To test this, we infected C57/BL6 mice for 30 days with LCMV clone-13, a well-established model for chronic infection. We found that at 16 days post-infection there is an increase in the frequency and number of Tim-3+Foxp3+ Treg in the spleen. By flow cytometry we found that Tim3+ Treg have increased expression of CD44, Ki67, Helios, ICOS, KLRG-1, CD39 and CD25, compared with Tim-3− Treg. Therefore, our data suggest that Tim-3+ Treg have a phenotype associated with higher activation, proliferation and suppression during chronic infection. Understanding the contributions of Tim-3 to Treg activation and function may provide new insights into the role of Tim-3 during disease progression and response to therapy.

Association of Mast Cell Burden and TIM-3 Expression with Recalcitrant Chronic Rhinosinusitis with Nasal Polyps

OBJECTIVES

Previous work showed that higher polyp mast cell load correlated with worse postoperative endoscopic appearance in patients with chronic rhinosinusitis with nasal polyps (CRSwNP). Polyp epithelial mast cells showed increased expression of T-cell/transmembrane immunoglobulin and mucin domain protein 3 (TIM-3), a receptor that promotes mast cell activation and cytokine production. In this study, CRSwNP patients were followed post-operatively to investigate whether mast cell burden or TIM-3 expression among mast cells can predict recalcitrant disease.

METHODS

Nasal polyp specimens were obtained via functional endoscopic sinus surgery (FESS) and separated into epithelial and stromal layers via enzymatic digestion. Mast cells and TIM-3-expressing mast cells were identified via flow cytometry. Mann-Whitney U tests and Cox proportional hazard models assessed whether mast cell burden and TIM-3 expression were associated with clinical outcomes, including earlier recurrence of polypoid edema and need for treatment with steroids.

RESULTS

Twenty-three patients with CRSwNP were studied and followed for 6 months after undergoing FESS. Higher mast cell levels were associated with earlier recurrence of polypoid edema: epithelial HR = 1.283 (P = .02), stromal HR = 1.103 (P = .02). Percent of mast cells expressing TIM-3 in epithelial or stromal layers was not significantly associated with earlier recurrence of polypoid edema. Mast cell burden and TIM-3+ expression were not significantly associated with need for future treatment with steroids post-FESS.

CONCLUSIONS

Mast cell load in polyp epithelium and stroma may predict a more refractory postoperative course for CRSwNP patients. The role of TIM-3 in the chronic inflammatory state seen in CRSwNP remains unclear.

Functionally significant metabolic differences between B and T lymphocyte lineages

Activation of B and T lymphocytes leads to major remodelling of the metabolic landscape of the cells enabling their post-activation functions. However, naive B and T lymphocytes also show metabolic differences, and the genesis, nature and functional significance of these differences are not yet well understood. Here we show that resting B-cells appeared to have lower energy demands than resting T-cells as they consumed lower levels of glucose and fatty acids and produced less ATP. Resting B-cells are more dependent on OXPHOS, while T-cells show more dependence on aerobic glycolysis. However, despite an apparently higher energy demand, T lineage cells showed lower rates of protein synthesis than equivalent B lineage stages. These metabolic differences between the two lineages were established early during lineage differentiation, and were functionally significant. Higher levels of protein synthesis in B-cells were associated with increased synthesis of MHC class II molecules and other proteins associated with antigen internalization, transport and presentation. The combination of higher energy demand and lower protein synthesis in T-cells was consistent with their higher ATP-dependent motility. Our data provide an integrated perspective of the metabolic differences and their functional implications between the B and T lymphocyte lineages.

Immune regulation by Tim-3

T-cell immunoglobulin and mucin domain 3 (Tim-3) is a transmembrane protein that in both mice and humans has been shown to possess various functions in a context-dependent manner. Thus, Tim-3 has been associated with both inhibitory and co-stimulatory function, depending in part on the specific cell type and immune response course. Though originally described on T cells, Tim-3 is now known to be expressed by both lymphoid and non-lymphoid cells within the immune system and even by non-immune cells. In addition, though widely thought of as a negative regulator of immunity, Tim-3 has been shown in more recent studies to have a positive function on both myeloid and lymphoid cells, including T cells. Tim-3 is often expressed at a high level on exhausted T cells in tumors and chronic infection and may engage in crosstalk with other so-called "checkpoint" molecules such as PD-1. Thus, Tim-3 has emerged as a possible therapeutic target, which is being actively explored both pre-clinically and clinically. However, recent research suggests a more complex in vivo role for this protein, compared with other targets in this area.

A Study to Investigate the Role of GULP/ CED 6 Gene in "Eat Me" Signaling in Cellular Efferocytosis and Immunosurveillance

In this report, investigations were done to study human GULP/ CED 6 genes role in presenting cancer cells to scavenger cells. CED 6 SiRNA was used to knock out the gene in Astrocytoma (HTB-12) cell lines to study its effects on expression of various "eat me" signals on these cells including Phosphatidyl serine (PtdSer) expression, nitric oxide (NO) signaling and Leukotrine B4 (LTB4) expression and Caspase 3 activation. Investigations were done by fluorescence microscopy techniques, ELISA assay and colorimetric assays using a standard microplate reader and spectrophotometer. Initial results showed all the above mentioned "eat me" signals were significantly decreased in CED 6 knock out cell lines. Therefore CED 6 gene must have a role in cancer cell clearance, pathway involved in the cross talk between CED 6 and other genes in this process is a matter of farther investigation.

Role of apoptosis-inducing factor (Aif) in the T cell lineage

Multiple checkpoints regulating finely balanced death-versus-survival decisions characterize both thymic development and peripheral homeostasis of T lymphocytes. While exploring the mechanisms of T cell death involved at various stages during the life of a T cell, we have observed and reported a variety of non-redundant roles for apoptosis inducing factor (Aif), a mitochondrial flavoprotein. Aif is ubiquitously expressed in all cell lineages and functions as an NADH oxidase in its mitochondrial location. It is released following the mitochondrial death signals, whereupon it translocates to the nucleus, binds to DNA and causes large-scale DNA fragmentation. During T cell development, Aif is important for developing thymocytes to navigate the double negative (DN)3 to DN4 transition (beta-selection), via its oxidoreductase property which protects the rapidly proliferating cells from death due to reactive oxygen species (ROS). In peripheral mature T cells, Aif deficiency leads to an increased susceptibility of T cell blasts to activation induced cell death (AICD), possibly mediated by its antioxidant function, and decreased sensitivity to neglect-induced death (NID). Thus, Aif seems to have pro-apoptotic and anti-apoptotic roles in the same lineage in different contexts and at different stages. Surprisingly, in the closely related B lymphocyte lineage, Aif deficiency does not result in any abnormality. These findings generate the possibility of specific T cell dysfunction in human disease caused by Aif deficiency, as well as in mitochondriopathies due to other causes. Also, these data raise questions regarding the basis of lineage-specific consequences of the dysfunction/deficiency of apparently ubiquitous molecules.

A role for apoptosis-inducing factor in T cell development

Apoptosis-inducing factor (Aif) is a mitochondrial flavoprotein that regulates cell metabolism and survival in many tissues. We report that aif-hypomorphic harlequin (Hq) mice show thymic hypocellularity and a cell-autonomous thymocyte developmental block associated with apoptosis at the β-selection stage, independent of T cell receptor β recombination. No abnormalities are observed in the B cell lineage. Transgenes encoding wild-type or DNA-binding-deficient mutant Aif rectify the thymic defect, but a transgene encoding oxidoreductase activity-deficient mutant Aif does not. The Hq thymic block is reversed in vivo by antioxidant treatment, and Hq T but not B lineage cells show enhanced oxidative stress. Thus, Aif, a ubiquitous protein, serves a lineage-specific nonredundant antiapoptotic role in the T cell lineage by regulating reactive oxygen species during thymic β-selection.

Apoptosis-inducing factor regulates death in peripheral T cells

Apoptosis-inducing factor (Aif) is a mitochondrial flavoprotein with multiple roles in apoptosis as well as in cellular respiration and redox regulation. The harlequin (Hq) mouse strain carries an aif locus modification causing reduced Aif expression. We demonstrate that activated CD4(+) and CD8(+) peripheral T cells from Hq mice show resistance to neglect-induced death (NID) triggered by growth factor withdrawal, but not to death induced by multiple agents that trigger DNA damage. Aif translocates to the nucleus in cells undergoing NID, and, in Hq T cell blasts, resistance to NID is associated with reduced cytosolic release of mitochondrial cytochrome c, implicating Aif in this event. In contrast, Hq T cell blasts express higher levels of CD95L, demonstrating increased susceptibility to activation-induced cell death (AICD) and apoptosis triggered by hydrogen peroxide. Superoxide scavenging protects from AICD in wild-type, but not Hq, T cell blasts, suggesting that Aif plays a crucial superoxide-scavenging role to regulate T cell AICD. Finally, the altered pattern of death susceptibility is reproduced by siRNA-mediated reduction of Aif expression in normal T cells. Thus, Aif serves nonredundant roles, both proapoptotic and antiapoptotic, in activated peripheral T cells.

Search for a novel biomarker for the brain cancer astrocytoma by using surface enhanced laser desorption/ionisation (SELDI) technique

The protein chip surface enhanced laser desorption/ionisation (SELDI) technique is a highly versatile analytical mass spectrometry system with considerable potential for detection, identification and quantitation of protein complex mixtures. Astrocytoma is a tumour of the astrocytes with a very poor prognosis. There is no effective biomarker system for detection of astrocytoma. The SELDI technique was used to study differential protein expression in astrocytoma cells in comparison to normal brain astrocytes. Several novel proteins were found to be expressed in the astrocytoma cells, not present in the astrocytes.

Identification of a mouse orthologue of the CED-6 gene of Caenorhabditis elegans

The rapid engulfment of apoptotic cells is a specialized innate immune response used by organisms to remove apoptotic cells. In mammals, several receptors that recognize apoptotic cells have been identified. Previous analysis of the engulfment gene ced-6 in Caenorhabditis elegans (C. elegans) has suggested that CED-6 is an adapter protein that participates in signal transduction pathway that mediates the specific recognition and engulfment of apoptotic cells. Here, we describe our isolation and partial characterization of a mouse cDNA, which is like an orthologue of C. elegans CED-6. PCR screening of mouse cDNA pool with primers designed from the C. elegans CED-6 cDNA sequence resulted in about 300 bp PCR product which was partially sequenced and then screened to a mouse full-length cDNA library. Thus in this study we report the identification of a novel C. elegans CED-6-like orthologue in mouse, which has probable apoptotic like function.

Differential recognition of the polypyrimidine-tract by the general splicing factor U2AF65 and the splicing repressor sex-lethal

The polypyrimidine-tract (Py-tract) adjacent to 3' splice sites is an essential splicing signal and is recognized by several proteins, including the general splicing factor U2AF65 and the highly specific splicing repressor Sex-lethal (SXL). They both contain ribonucleoprotein-consensus RNA-binding motifs. However, U2AF65 recognizes a wide variety of Py-tracts, whereas SXL recognizes specific Py-tracts such as the nonsex-specific Py-tract of the transformer pre-mRNA. It is not understood how these seemingly similar proteins differentially recognize the Py-tract. To define these interactions, we used chemical interference and protection assays, saturation mutagenesis, and RNAs containing modified nucleotides. We find that these proteins recognize distinct features of the RNA. First, although uracils within the Py-tract are protected from chemical modification by both of these proteins, modification of any one of seven uracils by hydrazine, or any of eight phosphates by ethylnitrosourea strongly interfered with the binding of SXL only. Second, the 2' hydroxyl groups or backbone conformation appeared important for the binding of SXL, but not U2AF65. Third, although any of the bases (cytosine >> adenine > guanine) could substitute for uracils for U2AF65 binding, only guanine partially substituted for certain uracils for SXL binding. The different dependence on individual contacts and nucleotide preference may provide a basis for the different RNA-binding specificities and thus functions of U2AF65 and SXL in 3' splice site choice.

Search for a novel killer toxin in yeast Pichia pastoris

Certain yeast strains secrete a protein toxin, which inhibits the growth of sensitive pathogens and yeasts. Studies have shown that production of the toxin is dependent on presence of linear, double-stranded DNA plasmids in the killer yeasts. In the yeast Pichia pastoris, two linear double-stranded DNA plasmids have been identified. In the present study, the search for toxin-producing capability in P. pastoris has been conducted. No killer activity could be detected when 14 different indicator strains were tested.

Identification of linear DNA plasmids of the yeast Pichia pastoris

Two DNA plasmids, approximately 11 and 8 kb in size, have been identified in a strain of the yeast Pichia pastoris (Northern Regional Research Laboratories No. Y4290). The plasmids are resistant to RNase A and lambda exonuclease, but are sensitive to digestion by DNase I, suggesting that they are linear and double-stranded DNA with 5'-protected ends. A restriction map has been constructed for the 11-kb plasmid, confirming that it is linear.