Parallel single-cell and bulk transcriptome analyses reveal key features of the gastric tumor microenvironment.

BACKGROUND: The tumor microenvironment (TME) has been shown to strongly influence treatment outcome for cancer patients in various indications and to influence the overall survival. However, the cells forming the TME in gastric cancer have not been extensively characterized. RESULTS: We combine bulk and single-cell RNA sequencing from tumors and matched normal tissue of 24 treatment-naïve GC patients to better understand which cell types and transcriptional programs are associated with malignant transformation of the stomach. Clustering 96,623 cells of non-epithelial origin reveals 81 well-defined TME cell types. We find that activated fibroblasts and endothelial cells are most prominently overrepresented in tumors. Intercellular network reconstruction and survival analysis of an independent cohort imply the importance of these cell types together with immunosuppressive myeloid cell subsets and regulatory T cells in establishing an immunosuppressive microenvironment that correlates with worsened prognosis and lack of response in anti-PD1-treated patients. In contrast, we find a subset of IFNγ activated T cells and HLA-II expressing macrophages that are linked to treatment response and increased overall survival. CONCLUSIONS: Our gastric cancer single-cell TME compendium together with the matched bulk transcriptome data provides a unique resource for the identification of new potential biomarkers for patient stratification. This study helps further to elucidate the mechanism of gastric cancer and provides insights for therapy.

IL3RA-Targeting Antibody-Drug Conjugate BAY-943 with a Kinesin Spindle Protein Inhibitor Payload Shows Efficacy in Preclinical Models of Hematologic Malignancies.

IL3RA (CD123) is the alpha subunit of the interleukin 3 (IL-3) receptor, which regulates the proliferation, survival, and differentiation of hematopoietic cells. IL3RA is frequently expressed in acute myeloid leukemia (AML) and classical Hodgkin lymphoma (HL), presenting an opportunity to treat AML and HL with an IL3RA-directed antibody-drug conjugate (ADC). Here, we describe BAY-943 (IL3RA-ADC), a novel IL3RA-targeting ADC consisting of a humanized anti-IL3RA antibody conjugated to a potent proprietary kinesin spindle protein inhibitor (KSPi). In vitro, IL3RA-ADC showed potent and selective antiproliferative efficacy in a panel of IL3RA-expressing AML and HL cell lines. In vivo, IL3RA-ADC improved survival and reduced tumor burden in IL3RA-positive human AML cell line-derived (MOLM-13 and MV-4-11) as well as in patient-derived xenograft (PDX) models (AM7577 and AML11655) in mice. Furthermore, IL3RA-ADC induced complete tumor remission in 12 out of 13 mice in an IL3RA-positive HL cell line-derived xenograft model (HDLM-2). IL3RA-ADC was well-tolerated and showed no signs of thrombocytopenia, neutropenia, or liver toxicity in rats, or in cynomolgus monkeys when dosed up to 20 mg/kg. Overall, the preclinical results support the further development of BAY-943 as an innovative approach for the treatment of IL3RA-positive hematologic malignancies.

Publisher Correction: Global characterization of T cells in non-small-cell lung cancer by single-cell sequencing.

In the version of this article originally published, the P statistic described in Fig. 3d was incorrect. It was described as "P < 22 × 10-16". It should have been "P < 2.2 × 10-16". Also, the "CD8+ Treg" label in Fig. 4f was incorrect. It should have been "CD4+ Treg". The errors have been corrected in the HTML and PDF versions of this article.

Global characterization of T cells in non-small-cell lung cancer by single-cell sequencing.

Cancer immunotherapies have shown sustained clinical responses in treating non-small-cell lung cancer1-3, but efficacy varies and depends in part on the amount and properties of tumor infiltrating lymphocytes4-6. To depict the baseline landscape of the composition, lineage and functional states of tumor infiltrating lymphocytes, here we performed deep single-cell RNA sequencing for 12,346 T cells from 14 treatment-naïve non-small-cell lung cancer patients. Combined expression and T cell antigen receptor based lineage tracking revealed a significant proportion of inter-tissue effector T cells with a highly migratory nature. As well as tumor-infiltrating CD8+ T cells undergoing exhaustion, we observed two clusters of cells exhibiting states preceding exhaustion, and a high ratio of "pre-exhausted" to exhausted T cells was associated with better prognosis of lung adenocarcinoma. Additionally, we observed further heterogeneity within the tumor regulatory T cells (Tregs), characterized by the bimodal distribution of TNFRSF9, an activation marker for antigen-specific Tregs. The gene signature of those activated tumor Tregs, which included IL1R2, correlated with poor prognosis in lung adenocarcinoma. Our study provides a new approach for patient stratification and will help further understand the functional states and dynamics of T cells in lung cancer.

Immunity to intracellular Salmonella depends on surface-associated antigens.

Invasive Salmonella infection is an important health problem that is worsening because of rising antimicrobial resistance and changing Salmonella serovar spectrum. Novel vaccines with broad serovar coverage are needed, but suitable protective antigens remain largely unknown. Here, we tested 37 broadly conserved Salmonella antigens in a mouse typhoid fever model, and identified antigen candidates that conferred partial protection against lethal disease. Antigen properties such as high in vivo abundance or immunodominance in convalescent individuals were not required for protectivity, but all promising antigen candidates were associated with the Salmonella surface. Surprisingly, this was not due to superior immunogenicity of surface antigens compared to internal antigens as had been suggested by previous studies and novel findings for CD4 T cell responses to model antigens. Confocal microscopy of infected tissues revealed that many live Salmonella resided alone in infected host macrophages with no damaged Salmonella releasing internal antigens in their vicinity. In the absence of accessible internal antigens, detection of these infected cells might require CD4 T cell recognition of Salmonella surface-associated antigens that could be processed and presented even from intact Salmonella. In conclusion, our findings might pave the way for development of an efficacious Salmonella vaccine with broad serovar coverage, and suggest a similar crucial role of surface antigens for immunity to both extracellular and intracellular pathogens.

Mast cells in endometriosis: guilty or innocent bystanders?

Endometriosis (EMS) is a chronic, estrogen-dependent inflammatory disease characterized by growth of endometrial tissue outside the uterine cavity. Symptoms in EMS patients include severe pelvic pain, dysmenorrhea, dyspareunia and infertility. To date, medical therapies are mostly based on hormonal suppressive drugs that induce a hypoestrogenic state. Although being effective regarding the reduction of endometriotic tissue masses and pelvic pain, this treatment is accompanied by severe side effects. Since EMS is associated with chronic inflammation, novel therapeutic strategies also focus on immune modulating drugs. However, little is known about how and to what extent immune cell subsets contribute to the network of locally produced cytokines, chemokines and other mitogenic factors that modulate the growth of ectopic endometrial implants and the inflammation associated with them. Mast cells (MCs) are known to be key players of the immune system, especially during allergic reactions. However, in recent years MCs have been identified to exhibit a far broader range of functions and to be involved in host defense and wound healing responses. Here, recent reports that imply an involvement of MCs in EMS has been reviewed, while the value of novel mouse models for clarifying their contribution to the pathology of this condition has been discussed.

Mast cells in health and disease: from basic science to clinical application 4-5 July 2008, Stuttgart, Germany.

In July 2008, the fifth and last meeting of the Mast Cells and Chronic Inflammatory Diseases (MCCID) network was hosted by Axel Lorentz and Stephan Bischoff at the University of Hohenheim, in the Aula of the Chateau Hohenheim, Stuttgart. The MCCID initiative is a Marie Curie early stage research training (EST)-sponsored multi-partner project that fosters collaboration between fundamental research, clinics and industry. At the same time, this meeting was the founding meeting of the new European Mast Cell Research Network (EMCRN) initiated by SC Bischoff, U Blank, F Levi-Schaffer, M Mauer and G Nielsson (steering committee), in co-operation with P Valent from the European Competence Network on Mastocytosis (ECNM). A mixture of scientists from pharma, biotech and academic institutions attended the meeting, presenting recent data from the field with a special focus on novel therapeutic strategies and possible interactions between industry and research. The aim of this report is to briefly describe some of the most intriguing of these new findings and to discuss how they can be relevant for making use of mast cells as therapeutic targets.

siRNA stabilization prolongs gene knockdown in primary T lymphocytes.

RNA interference (RNAi)-mediated knockdown of target gene expression represents a powerful approach for functional genomics and therapeutic applications. However, for T lymphocytes, central regulators of immunity and immunopathologies, the application of RNAi has been limited due to the lack of efficient small interfering RNA (siRNA) delivery protocols, and an inherent inefficiency of the RNAi machinery itself. Here, we use nucleofection, an optimized electroporation approach, to deliver siRNA into primary T lymphocytes with high efficiency and negligible impairment of cell function. We identify siRNA stability within the cells as the critical parameter for efficient RNAi in primary T cells. While generally short-lived and immediately lost upon T-cell activation when conventional siRNA is used, target gene knockdown becomes insensitive to cell activation and can persist for up to 2 wk in non-dividing cells with siRNA stabilized by chemical modifications. Targeting CD4 and the transcription factor GATA-3, we show that the use of stabilized siRNA is imperative for functional gene analysis during T lymphocyte activation and differentiation in vitro as well as in vivo.

Functional analysis of effector and regulatory T cells in a parasitic nematode infection.

Parasitic nematodes typically modulate T-cell reactivity, primarily during the chronic phase of infection. We analyzed the role of CD4-positive (CD4+) T effector (T(eff)) cells and regulatory T (T(reg)) cells derived from mice chronically infected with the intestinal nematode Heligmosomoides polygyrus. Different CD4+ T-cell subsets were transferred into naïve recipients that were subsequently infected with H. polygyrus. Adoptive transfer of conventional T(eff) cells conferred protection and led to a significant decrease in the worm burdens of H. polygyrus-infected recipients. Roughly 0.2% of the CD4+ T cells were H. polygyrus specific based on expression of CD154, and cells producing interleukin 4 (IL-4) and IL-13 were highly enriched within the CD154+ population. In contrast, adoptive transfer of T(reg) cells, characterized by the markers CD25 and CD103 and the transcription factor Foxp3, had no effect on the worm burdens of recipients. Further analysis showed that soon after infection, the number of Foxp3+ T(reg) cells temporarily increased in the inflamed tissue while effector/memory-like CD103+ Foxp+ T(reg) cells systemically increased in the draining lymph nodes and spleen. In addition, T(reg) cells represented a potential source of IL-10 and reduced the expression of IL-4. Finally, under in vitro conditions, T(reg) cells from infected mice were more potent suppressors than cells derived from naïve mice. In conclusion, our data indicate that small numbers of T(eff) cells have the ability to promote host protective immune responses, even in the presence of T(reg) cells.

Identification and isolation of murine antigen-reactive T cells according to CD154 expression.

T helper (Th) cells are central regulators of adaptive immune responses. However, the detection of the small number of Th cells specific for a particular antigen or pathogen is still a major challenge. CD154 was recently introduced as a marker for antigen-specific Th cells. To date, this technology was not applicable for mice - arguably the most important immunological model system. CD154 is difficult to detect due to its rapid removal from the cell surface upon binding to CD40 during antigen-specific activation by APC. We present an efficient strategy to block the degradation of murine CD154 by combined use of antibodies against CD40 and CD154. This strategy makes CD154 easily accessible for surface staining, which allows isolation and expansion of rare antigen specific T cells. Importantly, CD154 identified all specific T cells in strongly Th1- or Th2-polarized immune responses against pathogens like Salmonella typhimurium and Heligmosomoides polygyrus, independent of their potential to produce cytokines. We demonstrate that CD154 can in fact be used as a reliable marker for antigen-specific CD4 T cells in mice, offering a unique option to analyze, isolate and rapidly expand the entire pool of Th-cells generated during a physiological T cell response in vivo.

Direct access to CD4+ T cells specific for defined antigens according to CD154 expression.

The direct assessment of T helper (T(H))-cell responses specific for antigens is essential to evaluate pathogenic and protective immunity. Presently, analysis and isolation of antigen-specific T(H) cells is restricted to cells that produce cytokines, or can be performed only with a rare selection of specific peptide major histocompatibility complex class II (MHC II) multimers. Here we report a new method that enables the assessment and isolation of T(H) cells specific for a defined antigen according to CD154 expression induced after stimulation in vitro. We show that antigen-induced CD154 expression is highly sensitive and specific for human and mouse antigen-specific T(H) cells. Moreover, the isolation of antigen-specific CD154(+) T(H) cells necessitates only surface staining with antibodies, thereby enabling the fast generation of antigen-specific T(H) cell lines. Our approach allows assessment of T(H) cells with a defined specificity for the combined quantitative and qualitative analysis of T(H)-cell immunity as well as for the isolation of specific T(H) cells for targeted cellular immunotherapies.

Sensitive visualization of peptide presentation in vitro and ex vivo.

BACKGROUND: The presentation of antigenic peptides to specific T cells is one of the key events for the induction of a T-cell-dependent immune response. The nature of the antigen-presenting cells which present distinct peptides has been difficult to analyze so far due to the low number of peptides presented in vivo by a single antigen-presenting cell. METHODS: We have used magnetofluorescent liposomes to identify and characterize antigen-presenting cells according to presentation of a hapten-labeled antigenic peptide in vitro and ex vivo. RESULTS: Magnetofluorescent liposomes allowed the identification and isolation of antigen-presenting cells according to the presentation of less than 100 peptides per cell, the physiological threshold for activation of specific T cells. Ex vivo, we could demonstrate peptide presentation by B lymphocytes and dendritic cells already 1 h after intravenous peptide injection; this rapidly declined to background level after 12-24 h. CONCLUSIONS: The sensitive visualization of peptide presentation allows the phenotypical and functional characterization of those antigen-presenting cells which present specific peptides at physiological relevant quantities. This technology will help to characterize the antigen-presenting cells (APC) which are responsible for the induction of distinct immune reactions in vivo, e.g., the generation of tolerance or immunity.

Visualization of peptide presentation following oral application of antigen in normal and Peyer's patches-deficient mice.

Orally applied antigens generate systemic unresponsiveness by induction of anergy and deletion of specific T cells at high antigen doses, and induction of regulatory T cells at low doses of antigen. These different immune reactions have been attributed to different types of antigen-presenting cells (APC) and/or different secondary lymphoid organs participating in the induction of the immune response. We used high-sensitivity immunofluorescence to directly identify for the first time the cells presenting orally applied antigen in vivo. At low peptide doses (<1 mg) peptide presentation was exclusively detected on dendritic cells (DC) of the Peyer's patches (PP) and mesenteric lymph nodes (mLN). At high doses (>1 mg) peptides were presented systemically and by all types of APC but presentation was still maximal on DC of the PP (up to 65%). Nevertheless, at limiting antigen doses T cell activation in the gut-associated lymphoid tissue occurs preferentially in the mLN but not in PP. PP-deficient mice have the same frequencies of peptide-presenting cells in mLN, peripheral lymph nodes and spleen and activation of naive T cells in vivo is not affected. Therefore, PP are not critical for antigen presentation as well as for T cell activation in response to orally applied soluble antigens.