Transfer learning in a biomaterial fibrosis model identifies in vivo senescence heterogeneity and contributions to vascularization and matrix production across species and diverse pathologies

Cellular senescence is a state of permanent growth arrest that plays an important role in wound healing, tissue fibrosis, and tumor suppression. Despite senescent cells' (SnCs) pathological role and therapeutic interest, their phenotype in vivo remains poorly defined. Here, we developed an in vivo-derived senescence signature (SenSig) using a foreign body response-driven fibrosis model in a p16-CreERT2;Ai14 reporter mouse. We identified pericytes and "cartilage-like" fibroblasts as senescent and defined cell type-specific senescence-associated secretory phenotypes (SASPs). Transfer learning and senescence scoring identified these two SnC populations along with endothelial and epithelial SnCs in new and publicly available murine and human data single-cell RNA sequencing (scRNAseq) datasets from diverse pathologies. Signaling analysis uncovered crosstalk between SnCs and myeloid cells via an IL34-CSF1R-TGFβR signaling axis, contributing to tissue balance of vascularization and matrix production. Overall, our study provides a senescence signature and a computational approach that may be broadly applied to identify SnC transcriptional profiles and SASP factors in wound healing, aging, and other pathologies.

CD8+ T cell-intrinsic IL-6 signaling promotes resistance to anti-PD-L1 immunotherapy

Although immune checkpoint inhibitors (ICIs) are established as effective cancer therapies, overcoming therapeutic resistance remains a critical challenge. Here we identify interleukin 6 (IL-6) as a correlate of poor response to atezolizumab (anti-PD-L1) in large clinical trials of advanced kidney, breast, and bladder cancers. In pre-clinical models, combined blockade of PD-L1 and the IL-6 receptor (IL6R) causes synergistic regression of large established tumors and substantially improves anti-tumor CD8⁺ cytotoxic T lymphocyte (CTL) responses compared with anti-PD-L1 alone. Circulating CTLs from cancer patients with high plasma IL-6 display a repressed functional profile based on single-cell RNA sequencing, and IL-6-STAT3 signaling inhibits classical cytotoxic differentiation of CTLs in vitro. In tumor-bearing mice, CTL-specific IL6R deficiency is sufficient to improve anti-PD-L1 activity. Thus, based on both clinical and experimental evidence, agents targeting IL-6 signaling are plausible partners for combination with ICIs in cancer patients.

Spatial Positioning and Matrix Programs of Cancer-Associated Fibroblasts Promote T-cell Exclusion in Human Lung Tumors

It is currently accepted that cancer-associated fibroblasts (CAF) participate in T-cell exclusion from tumor nests. To unbiasedly test this, we used single-cell RNA sequencing coupled with multiplex imaging on a large cohort of lung tumors. We identified four main CAF populations, two of which are associated with T-cell exclusion: (i) MYH11+αSMA+ CAF, which are present in early-stage tumors and form a single cell layer lining cancer aggregates, and (ii) FAP+αSMA+ CAF, which appear in more advanced tumors and organize in patches within the stroma or in multiple layers around tumor nests. Both populations orchestrate a particular structural tissue organization through dense and aligned fiber deposition compared with T cell-permissive CAF. Yet they produce distinct matrix molecules, including collagen IV (MYH11+αSMA+ CAF) and collagen XI/XII (FAP+αSMA+ CAF). Hereby, we uncovered unique molecular programs of CAF driving T-cell marginalization, whose targeting should increase immunotherapy efficacy in patients bearing T cell-excluded tumors.

SIGNIFICANCE

The cellular and molecular programs driving T-cell marginalization in solid tumors remain unclear. Here, we describe two CAF populations associated with T-cell exclusion in human lung tumors. We demonstrate the importance of pairing molecular and spatial analysis of the tumor microenvironment, a prerequisite to developing new strategies targeting T cell-excluding CAF. See related commentary by Sherman, p. 2501. This article is highlighted in the In This Issue feature, p. 2483.

The neutrophil protein CD177 is a novel PDPN receptor that regulates human cancer-associated fibroblast physiology

The cancer-associated fibroblast (CAF) marker podoplanin (PDPN) is generally correlated with poor clinical outcomes in cancer patients and thus represents a promising therapeutic target. Despite its biomedical relevance, basic aspects of PDPN biology such as its cellular functions and cell surface ligands remain poorly uncharacterized, thus challenging drug development. Here, we utilize a high throughput platform to elucidate the PDPN cell surface interactome, and uncover the neutrophil protein CD177 as a new binding partner. Quantitative proteomics analysis of the CAF phosphoproteome reveals a role for PDPN in cell signaling, growth and actomyosin contractility, among other processes. Moreover, cellular assays demonstrate that CD177 is a functional antagonist, recapitulating the phenotype observed in PDPN-deficient CAFs. In sum, starting from the unbiased elucidation of the PDPN co-receptome, our work provides insights into PDPN functions and reveals the PDPN/CD177 axis as a possible modulator of fibroblast physiology in the tumor microenvironment.

Homeostatic functions of monocytes and interstitial lung macrophages are regulated via collagen domain-binding receptor LAIR1

Myeloid cells encounter stromal cells and their matrix determinants on a continual basis during their residence in any given organ. Here, we examined the impact of the collagen receptor LAIR1 on myeloid cell homeostasis and function. LAIR1 was highly expressed in the myeloid lineage and enriched in non-classical monocytes. Proteomic definition of the LAIR1 interactome identified stromal factor Colec12 as a high-affinity LAIR1 ligand. Proteomic profiling of LAIR1 signaling triggered by Collagen1 and Colec12 highlighted pathways associated with survival, proliferation, and differentiation. Lair1^-/- mice had reduced frequencies of Ly6C^- monocytes, which were associated with altered proliferation and apoptosis of non-classical monocytes from bone marrow and altered heterogeneity of interstitial macrophages in lung. Myeloid-specific LAIR1 deficiency promoted metastatic growth in a melanoma model and LAIR1 expression associated with improved clinical outcomes in human metastatic melanoma. Thus, monocytes and macrophages rely on LAIR1 sensing of stromal determinants for fitness and function, with relevance in homeostasis and disease.

Abstract PO084: Patterns of T cell clonal expansion in cancer patients associate with response to immunotherapy

Upon encountering their cognate antigens, T cells can undergo clonal expansion to produce multiple copies of a cell with a shared T cell receptor (TCR). Despite the fundamental role of clonal expansion in cancer immunity, little is known about its relationship with T cell subpopulations or antitumor responses in cancer patients. Here we have performed single-cell RNA sequencing (scRNA-seq) and deep analysis of TCR clonotypes (scTCR-seq) in cancer patients across several indications, assessing the profiles of TCRs in the various populations of T cells in tumors, normal adjacent tissue (NAT), and peripheral blood. We found that, although most clonotypes were represented by a single cell, the remaining clonal lineages showed expansion in either NAT or tumor exclusively, or dual-residence with expansion in both compartments. In a subset of patients, we find clear evidence of clonotypic expansion of T effector- and effector memory-like cells not only within the tumor but also in NAT. Importantly, expanded clonotypes found in the tumor and NAT can also typically be detected in peripheral blood, suggesting a continuously replenishment from sites outside of the tumor with fresh, non-exhausted replacement cells. Our data further suggests a continued activity of the cancer immunity cycle in these patients, the acceleration of which may be associated with clinical response.

Citation Format: Shravan Madireddi, Thomas D. Wu, Patricia E. de Almeida, Romain Banchereau, Ying-Jiun J. Chen, Avantika S. Chitre, Hina Iftikhar, William E. O'Gorman, Amelia Au-Yeung, Chikara Takahashi, Leonard D. Goldstein, Chungkee Poon, Shilpa Keerthivasan, Sanjeev Mariathasan, Meghna Das Thakur, Mahrukh A. Huseni, Marcus Ballinger, Ivette Estay, Patrick Caplazi, Zora Modrusan, Lélia Delamarre, Ira Mellman, Richard Bourgon, Jane L. Grogan. Patterns of T cell clonal expansion in cancer patients associate with response to immunotherapy [abstract]. In: Abstracts: AACR Virtual Special Conference: Tumor Immunology and Immunotherapy; 2020 Oct 19-20. Philadelphia (PA): AACR; Cancer Immunol Res 2021;9(2 Suppl):Abstract nr PO084.

Abstract 2000: Systemic and tumor associated IL-8 correlates with resistance to PD-L1 blockade

Elevated plasma interleukin-8 (IL-8) is a poor prognostic factor for many cancers. However, the association of IL-8 with clinical outcomes to checkpoint inhibition has not been comprehensively evaluated in randomized studies. Moreover, the source of IL-8 and the underlying biology that influences resistance to immune checkpoint inhibitors remain unknown. Here we analyzed circulating IL-8 protein in plasma, and IL8 gene expression in peripheral blood mononuclear cells (PBMC) and tumors of patients treated with atezolizumab (anti-PD-L1 mAb), from multiple randomized trials in metastatic urothelial carcinoma (mUC) and metastatic renal cell carcinoma (mRCC). High levels of IL-8 in plasma, PBMCs and tumors, were associated with decreased efficacy in mUC and mRCC patients treated with atezolizumab, even in tumors that were classically CD8+ T cell inflamed. mUC patients treated with atezolizumab, but not with chemotherapy, who experienced an on-treatment decrease in plasma IL-8, exhibited improved overall survival. IL-8 is primarily expressed in circulating and intratumoral myeloid cells, and high IL8 expression was associated with the downregulation of the antigen presentation machinery in myeloid cells. A better understanding of IL-8-mediated myeloid inflammation in curtailing responses to checkpoint inhibitors is essential for developing new therapies for patients.

Citation Format: Kobe Yuen, Lifen Liu, Congfen Li, Deepali Rishipathak, Patrick Williams, Edward Kadel, Hartmut Koeppen, Shravan Madireddi, Shilpa Keerthivasan, Ying-Jun Chen, Zora Modrusen, Romain Banchereau, Ning Leng, Priti Hegde, Mahrukh Huseni, Sanjeev Mariathasan. Systemic and tumor associated IL-8 correlates with resistance to PD-L1 blockade [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2000.

High systemic and tumor-associated IL-8 correlates with reduced clinical benefit of PD-L1 blockade

Although elevated plasma interleukin-8 (pIL-8) has been associated with poor outcome to immune checkpoint blockade ¹, this has not been comprehensively evaluated in large randomized studies. Here we analyzed circulating pIL-8 and IL8 gene expression in peripheral blood mononuclear cells and tumors of patients treated with atezolizumab (anti-PD-L1 monoclonal antibody) from multiple randomized trials representing 1,445 patients with metastatic urothelial carcinoma (mUC) and metastatic renal cell carcinoma. High levels of IL-8 in plasma, peripheral blood mononuclear cells and tumors were associated with decreased efficacy of atezolizumab in patients with mUC and metastatic renal cell carcinoma, even in tumors that were classically CD8⁺ T cell inflamed. Low baseline pIL-8 in patients with mUC was associated with increased response to atezolizumab and chemotherapy. Patients with mUC who experienced on-treatment decreases in pIL-8 exhibited improved overall survival when treated with atezolizumab but not with chemotherapy. Single-cell RNA sequencing of the immune compartment showed that IL8 is primarily expressed in circulating and intratumoral myeloid cells and that high IL8 expression is associated with downregulation of the antigen-presentation machinery. Therapies that can reverse the impacts of IL-8-mediated myeloid inflammation will be essential for improving outcomes of patients treated with immune checkpoint inhibitors.

Peripheral T cell expansion predicts tumour infiltration and clinical response

Despite the resounding clinical success in cancer treatment of antibodies that block the interaction of PD1 with its ligand PDL1¹, the mechanisms involved remain unknown. A major limitation to understanding the origin and fate of T cells in tumour immunity is the lack of quantitative information on the distribution of individual clonotypes of T cells in patients with cancer. Here, by performing deep single-cell sequencing of RNA and T cell receptors in patients with different types of cancer, we survey the profiles of various populations of T cells and T cell receptors in tumours, normal adjacent tissue, and peripheral blood. We find clear evidence of clonotypic expansion of effector-like T cells not only within the tumour but also in normal adjacent tissue. Patients with gene signatures of such clonotypic expansion respond best to anti-PDL1 therapy. Notably, expanded clonotypes found in the tumour and normal adjacent tissue can also typically be detected in peripheral blood, which suggests a convenient approach to patient identification. Analyses of our data together with several external datasets suggest that intratumoural T cells, especially in responsive patients, are replenished with fresh, non-exhausted replacement cells from sites outside the tumour, suggesting continued activity of the cancer immunity cycle in these patients, the acceleration of which may be associated with clinical response.

Distinct Mesenchymal Cell Populations Generate the Essential Intestinal BMP Signaling Gradient

Intestinal stem cells (ISCs) are confined to crypt bottoms and their progeny differentiate near crypt-villus junctions. Wnt and bone morphogenic protein (BMP) gradients drive this polarity, and colorectal cancer fundamentally reflects disruption of this homeostatic signaling. However, sub-epithelial sources of crucial agonists and antagonists that organize this BMP gradient remain obscure. Here, we couple whole-mount high-resolution microscopy with ensemble and single-cell RNA sequencing (RNA-seq) to identify three distinct PDGFRA⁺ mesenchymal cell types. PDGFRA(hi) telocytes are especially abundant at the villus base and provide a BMP reservoir, and we identified a CD81⁺ PDGFRA(lo) population present just below crypts that secretes the BMP antagonist Gremlin1. These cells, referred to as trophocytes, are sufficient to expand ISCs in vitro without additional trophic support and contribute to ISC maintenance in vivo. This study reveals intestinal mesenchymal structure at fine anatomic, molecular, and functional detail and the cellular basis for a signaling gradient necessary for tissue self-renewal.

Single-Cell RNA Sequencing Reveals Stromal Evolution into LRRC15+ Myofibroblasts as a Determinant of Patient Response to Cancer Immunotherapy

With only a fraction of patients responding to cancer immunotherapy, a better understanding of the entire tumor microenvironment is needed. Using single-cell transcriptomics, we chart the fibroblastic landscape during pancreatic ductal adenocarcinoma (PDAC) progression in animal models. We identify a population of carcinoma-associated fibroblasts (CAF) that are programmed by TGFβ and express the leucine-rich repeat containing 15 (LRRC15) protein. These LRRC15⁺ CAFs surround tumor islets and are absent from normal pancreatic tissue. The presence of LRRC15⁺ CAFs in human patients was confirmed in >80,000 single cells from 22 patients with PDAC as well as by using IHC on samples from 70 patients. Furthermore, immunotherapy clinical trials comprising more than 600 patients across six cancer types revealed elevated levels of the LRRC15⁺ CAF signature correlated with poor response to anti-PD-L1 therapy. This work has important implications for targeting nonimmune elements of the tumor microenvironment to boost responses of patients with cancer to immune checkpoint blockade therapy. SIGNIFICANCE: This study describes the single-cell landscape of CAFs in pancreatic cancer during in vivo tumor evolution. A TGFβ-driven, LRRC15⁺ CAF lineage is associated with poor outcome in immunotherapy trial data comprising multiple solid-tumor entities and represents a target for combinatorial therapy.This article is highlighted in the In This Issue feature, p. 161.

Abstract 463: Integrated digital pathology and transcriptome analysis identifies molecular mediators of T cell exclusion in ovarian cancer

Background:

Close proximity between cytotoxic T lymphocytes and tumor cells is required for effective immunotherapy. Three tumor-immune (TI) phenotypes, infiltrated, excluded and desert, have been previously described based on the infiltration patterns of CD8+ T cells. However, no quantitative methods exist to define these phenotypes robustly in human solid tumors. Importantly, the molecular features and mechanisms determining these phenotypes are not well understood. Here we report a novel integrated approach to classify and functionally dissect TI phenotypes in human ovarian cancer.

Methods:

CD8 IHC and RNAseq analysis were performed on 370 ovarian tumors from the ICON7 phase III clinical trial, a front-line trial testing the addition of bevacizumab to chemotherapies. A digital image analysis algorithm was developed to quantify the quantity and spatial distribution of CD8+ T cells. Coupling digital pathology with transcriptome analysis, a random forest machine learning algorithm was applied to identify genes associated with these two metrics using a training set (n=155). A gene expression-based classifier was developed for classifying TI phenotypes and validated using testing sets from ICON7 trial and a vendor collection. Functional characterization of key mediators promoting T cell exclusion were carried out by integrating in situ, in vitro and ex vivo analyses on ovarian tumor tissues, cancer associated fibroblasts (CAFs) and ovarian cancer cell lines. Anti-tumor activity of TGFβ blockade in combination with anti-PD-L1 was evaluated in the mouse BrKras ovarian cancer model in FVB background.

Results:

Integrating digital pathology and machine learning on large ovarian tumor cohorts, we developed and validated a 157-gene molecular classifier. We show the TI phenotypes are of biological and clinical importance in ovarian cancer. Two hallmarks of T cell exclusion were identified: 1) loss of MHC I on tumor cells and 2) upregulation of TGFβ/stromal activities. We show that MHC I in ovarian cancer cells is likely regulated by epigenetic mechanisms and TGFβ is a key mediator of T cell exclusion. TGFβ reduced MHC I expression in ovarian cancer cells and induced extracellular matrix and immunosuppressive molecules in human primary fibroblasts. Finally, we demonstrated that combining anti-TGFβ and anti-PD-L1 in the BrKras mouse model improved the anti-tumor efficacy and survival.

Conclusion:

This study provided the first systematic and in-depth characterization of the molecular features and mechanisms underlying the tumor-immune phenotypes in human ovarian cancer. We illuminated a multi-faceted role of TGFβ in mediating crosstalk between tumor cells and CAFs to shape the tumor-immune contexture. Our findings support that targeting the TGFβ pathway represents a promising therapeutic strategy to overcome T cell exclusion and optimize response to cancer immunotherapy.

Citation Format: Melanie Desbois, Akshata Udyavar, Lisa Ryner, Cleopatra Kozlowski, Yinghui Guan, Milena Dürrbaum, Shan Lu, Jean-Philippe Fortin, Hartmut Koeppen, James Ziai, Ching-Wei Chang, Amy Lo, Shilpa Keerthivasan, Marie Plante, Richard Bourgon, Carlos Bais, Priti Hegde, Anneleen Daemen, Shannon Turley, Yulei Wang. Integrated digital pathology and transcriptome analysis identifies molecular mediators of T cell exclusion in ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 463.

FAP Delineates Heterogeneous and Functionally Divergent Stromal Cells in Immune-Excluded Breast Tumors

Cancer-associated fibroblasts (CAFs) are generally associated with poor clinical outcome. CAFs support tumor growth in a variety of ways and can suppress antitumor immunity and response to immunotherapy. However, a precise understanding of CAF contributions to tumor growth and therapeutic response is lacking. Discrepancies in this field of study may stem from heterogeneity in the composition and function of fibroblasts in the tumor microenvironment. Furthermore, it remains unclear whether CAFs directly interact with and suppress T cells. Here, mouse and human breast tumors were used to examine stromal cells expressing fibroblast activation protein (FAP), a surface marker for CAFs. Two discrete populations of FAP⁺ mesenchymal cells were identified on the basis of podoplanin (PDPN) expression: a FAP⁺PDPN⁺ population of CAFs and a FAP⁺PDPN^- population of cancer-associated pericytes (CAPs). Although both subsets expressed extracellular matrix molecules, the CAF transcriptome was enriched in genes associated with TGFβ signaling and fibrosis compared with CAPs. In addition, CAFs were enriched at the outer edge of the tumor, in close contact with T cells, whereas CAPs were localized around vessels. Finally, FAP⁺PDPN⁺ CAFs suppressed the proliferation of T cells in a nitric oxide-dependent manner, whereas FAP⁺PDPN^- pericytes were not immunosuppressive. Collectively, these findings demonstrate that breast tumors contain multiple populations of FAP-expressing stromal cells of dichotomous function, phenotype, and location.

β-Catenin promotes colitis and colon cancer through imprinting of proinflammatory properties in T cells

The density and type of lymphocytes that infiltrate colon tumors are predictive of the clinical outcome of colon cancer. High densities of T helper 17 (T(H)17) cells and inflammation predict poor outcome, whereas infiltration by T regulatory cells (Tregs) that naturally suppress inflammation is associated with longer patient survival. However, the role of Tregs in cancer remains controversial. We recently reported that Tregs in colon cancer patients can become proinflammatory and tumor-promoting. These properties were directly linked with their expression of RORγt (retinoic acid-related orphan receptor-γt), the signature transcription factor of T(H)17 cells. We report that Wnt/β-catenin signaling in T cells promotes expression of RORγt. Expression of β-catenin was elevated in T cells, including Tregs, of patients with colon cancer. Genetically engineered activation of β-catenin in mouse T cells resulted in enhanced chromatin accessibility in the proximity of T cell factor-1 (Tcf-1) binding sites genome-wide, induced expression of T(H)17 signature genes including RORγt, and promoted T(H)17-mediated inflammation. Strikingly, the mice had inflammation of small intestine and colon and developed lesions indistinguishable from colitis-induced cancer. Activation of β-catenin only in Tregs was sufficient to produce inflammation and initiate cancer. On the basis of these findings, we conclude that activation of Wnt/β-catenin signaling in effector T cells and/or Tregs is causatively linked with the imprinting of proinflammatory properties and the promotion of colon cancer.

NOTCH1 Can Initiate NF-κB Activation via Cytosolic Interactions with Components of the T Cell Signalosome

T cell stimulation requires the input and integration of external signals. Signaling through the T cell receptor (TCR) is known to induce formation of the membrane-tethered CBM complex, comprising CARMA1, BCL10, and MALT1, which is required for TCR-mediated NF-κB activation. TCR signaling has been shown to activate NOTCH proteins, transmembrane receptors also implicated in NF-κB activation. However, the link between TCR-mediated NOTCH signaling and early events leading to induction of NF-κB activity remains unclear. In this report, we demonstrate a novel cytosolic function for NOTCH1 and show that it is essential to CBM complex formation. Using a model of skin allograft rejection, we show in vivo that NOTCH1 acts in the same functional pathway as PKCθ, a T cell-specific kinase important for CBM assembly and classical NF-κB activation. We further demonstrate in vitro NOTCH1 associates physically with PKCθ and CARMA1 in the cytosol. Unexpectedly, when NOTCH1 expression was abrogated using RNAi approaches, interactions between CARMA1, BCL10, and MALT1 were lost. This failure in CBM assembly reduced inhibitor of kappa B alpha phosphorylation and diminished NF-κB–DNA binding. Finally, using a luciferase gene reporter assay, we show the intracellular domain of NOTCH1 can initiate robust NF-κB activity in stimulated T cells, even when NOTCH1 is excluded from the nucleus through modifications that restrict it to the cytoplasm or hold it tethered to the membrane. Collectively, these observations provide evidence that NOTCH1 may facilitate early events during T cell activation by nucleating the CBM complex and initiating NF-κB signaling.

β-catenin promotes colitis and colon cancer through imprinting of pro-inflammatory properties in T-cells. (LYM3P.727)

The density and type of lymphocytes infiltrating colon tumors are predictive of the clinical outcome of colon cancer. High densities of TH17 cells and inflammation predict poor outcome, while infiltration by T regulatory cells (Tregs) that naturally suppress inflammation is associated with longer patient survival. However, the role of Tregs in cancer remains controversial. We previously reported that Tregs in colon cancer patients can become pro-inflammatory and tumor promoting. These properties were directly linked with their expression of RORγt, the signature transcription factor of TH17 cells. Here, we report that Wnt/β-catenin signaling in T-cells promotes expression of RORγt. Expression of β-catenin was elevated in T-cells, including Tregs, of patients with colon cancer. Genetically engineered activation of β-catenin in mouse T-cells resulted in enhanced chromatin accessibility in the proximity of Tcf-1 binding sites genome-wide, induced expression of TH17 signature genes including RORγt, and promoted TH17-mediated inflammation. Strikingly, the mice had inflammation of small-intestine and colon and developed lesions indistinguishable from colitis-induced cancer. Activation of β-catenin only in Tregs was sufficient to produce inflammation and initiate cancer. Based on these findings we conclude that activation of Wnt/β-catenin signaling in effector T-cells and/or Tregs is causatively linked with the imprinting of pro-inflammatory properties and promotion of colon cancer.

β-Catenin induces T-cell transformation by promoting genomic instability (HEM4P.237)

Deregulated activation of β-catenin has been correlated with genomic instability in cancer. During thymocyte development β-catenin activates transcription in partnership with Tcf-1, an essential T-cell specific DNA-binding protein. We previously reported that targeted activation of β-catenin in thymocytes (CAT mice) induces lymphomas that depend on recombination-activating-gene (RAG) and c-Myc activities. Here we show that these lymphomas have recurring Tcra/Myc translocations that resulted from illegitimate RAG-recombination events and resembled oncogenic translocations in ponies. We therefore used the CAT animal model to obtain mechanistic insights into the transformation process. Interestingly, ChIP-seq analysis uncovered a link between Tcf-1 and RAG2 showing that the two proteins shared binding sites marked by trimethylated histone-3 lysine-4 (H3K4me3) throughout the genome, including sites near the translocation. Pre-transformed CAT thymocytes had increased DNA damage at the translocating loci and showed altered repair of RAG induced DNA double strand breaks (DSBs). Importantly these cells were able to survive despite DNA damage as activated β-catenin promoted an anti-apoptosis gene expression profile. Thus, activated β-catenin promotes genomic instability that leads to T-cell lymphomas and this is associated with compromised DSB repair and increased survival of thymocytes with damaged DNA.

Generation of CD4CreER(T²) transgenic mice to study development of peripheral CD4-T-cells

After thymic emigration CD4-T-cells continue to differentiate into multiple effector and suppressor sublineages in peripheral lymphoid organs. In vivo analysis of peripheral CD4-T-cell differentiation has relied on animal models with targeted gene mutations. These are expressed either constitutively or conditionally after Cre mediated recombination. Available Cre transgenic strains to specifically target T-cells act at stages of thymocyte development that precede thymic selection. Tracing gene functions in CD4-T-cell development after thymic exit becomes complicated when the targeted gene is essential during thymic development. Other approaches to conditionally modify gene functions in peripheral T-cells involve infection of in vitro activated cells with Cre expressing lenti-, retro-, or adenoviruses, which precludes in vivo analyses. To study molecular mechanisms of peripheral CD4-T-cell differentiation in vivo and in vitro we generated transgenic mice expressing a tamoxifen inducible Cre recombinase (CreER(T2) ) under the control of the CD4 gene promoter. We show here that in CD4CreER(T2) mice Cre is inducibly and selectively activated in CD4-T-cells. Tamoxifen treatment both in vivo and in vitro results in efficient recombination of loci marked by LoxP sites. Moreover, this strain shows no abnormalities related to transgene insertion. Therefore it provides a valuable tool for studying gene function during differentiation of naïve peripheral CD4-T-cells into effector or suppressor sub-lineages.

Notch signaling regulates mouse and human Th17 differentiation

Th17 cells are known to play a critical role in adaptive immune responses to several important extracellular pathogens. Additionally, Th17 cells are implicated in the pathogenesis of several autoimmune and inflammatory disorders as well as in cancer. Therefore, it is essential to understand the mechanisms that regulate Th17 differentiation. Notch signaling is known to be important at several stages of T cell development and differentiation. In this study, we report that Notch1 is activated in both mouse and human in vitro-polarized Th17 cells and that blockade of Notch signaling significantly downregulates the production of Th17-associated cytokines, suggesting an intrinsic requirement for Notch during Th17 differentiation in both species. We also present evidence, using promoter reporter assays, knockdown studies, as well as chromatin immunoprecipitation, that IL-17 and retinoic acid-related orphan receptor γt are direct transcriptional targets of Notch signaling in Th17 cells. Finally, in vivo inhibition of Notch signaling reduced IL-17 production and Th17-mediated disease progression in experimental autoimmune encephalomyelitis, a mouse model of multiple sclerosis. Thus, this study highlights the importance of Notch signaling in Th17 differentiation and indicates that selective targeted therapy against Notch may be an important tool to treat autoimmune disorders, including multiple sclerosis.

Notch signaling regulates human and mouse TH17 development. (139.13)

TH17 immune cells, a recently discovered subset of CD4+ T-helper cells, are known to play important role in pathogenesis of several autoimmune diseases, inflammatory disorders and cancers. Although Notch ligand DLL4 was shown to drive TH17 polarization, downstream pathways conducting those signals are unknown. We demonstrated that the Notch signaling pathway has an important role in TH17 polarization. We found that gamma secretase inhibitors (GSI) that inhibit Notch signaling blocked the in-vitro polarization of mouse or human naïve CD4+ T cells towards the TH17 pathway without affecting cell proliferation. Next, we showed that, among various Notch receptors, Notch-1 is upregulated in TH17 polarizing cells and that knocking down Notch-1 by siRNA inhibited TH17 polarization. We further discovered that, in addition to polarizing naïve T cells towards TH17 pathway, Notch-1 is important for maintenance of this phenotype. Furthermore, reporter luciferase assays and chromatin immunoprecipitation (ChIP) assays suggest that the IL-17 as well as RORC promoters are direct transcriptional targets of Notch-1. Finally, in-vivo administration of GSI inhibits TH17 mediated disease progression in mouse experimental autoimmune encephalomyelitis model of multiple sclerosis. Thus our data suggest a key role for Notch signaling, especially Notch-1, in TH17 polarization.

Transcriptional upregulation of human cathepsin L by VEGF in glioblastoma cells

The role of vascular endothelial growth factor (VEGF) on cathepsin L expression was investigated in human glioblastoma cells (U87MG). Our results demonstrate the transcriptional upregulation of cathepsin L expression by VEGF. Transient transfection of U87MG cells with VEGF expression vector significantly increased cathepsin L activity. These results were further corroborated by a parallel increase in the mRNA levels and promoter activity of cathepsin L by VEGF. By deletion analysis, we identified a 47 base pair VEGF response element (VRE) in human cathepsin L promoter. Site directed mutagenesis studies demonstrated that both SP-1 and AP-4 motifs present in this region contribute to VEGF responsiveness. These results prove for the first time that over-expression of VEGF in human glioblastoma cells induces cathepsin L expression at the transcriptional level. This mechanism could be involved in the enhanced tumorogenic potential of these cells.