Multiplex Immunohistochemistry Analysis of Melanoma Tumor-Infiltrating Lymphocytes

Tumor-infiltrating lymphocytes (TILs) are an important prognostic indicator in melanoma and play a key role in the patient's response to immune checkpoint blockade. However, until recently, it was not possible to combine multi-parameter markers to define the TILs and their histological context. Multiplex immunohistochemistry (mIHC) is a new technology which addresses this issue and enables simultaneous detection of melanoma and multiple immune subsets in formalin fixed paraffin embedded tissue. Following antigen retrieval, melanoma tissue sections are stained by OPAL on an autostainer, including serial rounds of epitope labelling with monoclonal antibodies followed by tyramide signal amplification (TSA). The stained tissue sections are then imaged on the Vectra instrument, and digital images are processed by analysis software (inForm and HALO) to derive tissue segmentation and immune subset densities within the tumor and tumor stroma. Spatial relationships between immune cells and tumor cells are then analyzed using a novel R algorithm. Taken together, multiplex IHC describes the histological context of the immune system in melanoma. The data is objective and allows for characterization of individual melanomas as T cell inflamed (hot), immune excluded, or no immune cells (cold).

Immune molecular profiling of a multiresistant primary prostate cancer with a neuroendocrine-like phenotype: a case report

Background

Understanding the drivers of recurrence in aggressive prostate cancer requires detailed molecular and genomic understanding in order to aid therapeutic interventions. We provide here a case report of histological, transcriptional, proteomic, immunological, and genomic features in a longitudinal study of multiple biopsies from diagnosis, through treatment, and subsequent recurrence.

Case presentation

Here we present a case study of a male in 70 s with high-grade clinically-localised acinar adenocarcinoma treated with definitive hormone therapy and radiotherapy. The patient progressed rapidly with rising PSA and succumbed without metastasis 52 months after diagnosis. We identified the expression of canonical histological markers of neuroendocrine PC (NEPC) including synaptophysin, neuron-specific enolase and thyroid transcription factor 1, as well as intact AR expression, in the recurrent disease only. The resistant disease was also marked by an extremely low immune infiltrate, extensive genomic chromosomal aberrations, and overactivity in molecular hallmarks of NEPC disease including Aurora kinase and E2F, as well as novel alterations in the cMYB pathway. We also observed that responses to both primary treatments (high dose-rate brachytherapy and androgen deprivation therapies) were consistent with known optimal responses—ruling out treatment inefficacy as a factor in relapse.

Conclusions

These data provide novel insights into a case of locally recurrent aggressive prostate cancer harbouring NEPC pathology, in the absence of detected metastasis.

High-dimensional analyses reveal a distinct role of T-cell subsets in the immune microenvironment of gastric cancer

Objectives

To facilitate disease prognosis and improve precise immunotherapy of gastric cancer (GC) patients, a comprehensive study integrating immune cellular and molecular analyses on tumor tissues and peripheral blood was performed.

Methods

The association of GC patients' outcomes and the immune context of their tumors was explored using multiplex immunohistochemistry (mIHC) and transcriptome profiling. Potential immune dysfunction mechanism/s in the tumors on the systemic level was further examined using mass cytometry (CyTOF) in complementary peripheral blood from selected patients. GC cohorts with mIHC and gene expression profiling data were also used as validation cohorts.

Results

Increased CD4⁺FOXP3⁺ T-cell density in the GC tumor correlated with prolonged survival. Interestingly, CD4⁺FOXP3⁺ T cells had a close interaction with CD8⁺ T cells rather than tumor cells. High densities of CD4⁺FOXP3⁺ T cells and CD8⁺ T cells (High-High) independently predicted prolonged patient survival. Furthermore, the interferon-gamma (IFN-γ) gene signature and PDL1 expression were up-regulated in this group. Importantly, a subgroup of genomically stable (GS) tumors and tumors with chromosomal instability (CIN) within this High-High group also had excellent survival. The High-High GS/CIN tumors were coupled with increased frequencies of Tbet⁺CD4⁺ T cells and central memory CD4⁺ T cells in the peripheral blood.

Conclusion

These novel findings identify the combination of CD8⁺ T cells and FOXP3⁺CD4⁺ T cells as a significant prognostic marker for GC patients, which also could potentially be targeted and applied in the combination therapy with immune checkpoint blockades in precision medicine.

Accumulation of CD103+ CD8+ T cells in a cutaneous melanoma micrometastasis

Objective

The immune system can halt cancer progression by suppressing outgrowth of clinically occult micrometastases in a state of cancer-immune equilibrium. Cutaneous melanoma provides a unique opportunity to study the immune contexture of such lesions, as miniscule skin metastases are accessible to clinical inspection and diagnostic biopsy.

Methods

Here, we analysed by multiplex immunofluorescence microscopy samples from a melanoma patient presenting with an overt and an occult in-transit metastasis (ITM), the latter of which appeared as a small erythematous papule.

Results

Microarchitecture and immune composition in the two lesions were vastly different. CD4⁺ and CD8⁺ T cells accumulated around the margin of the overt SOX10⁺ Melan A⁺ ITM but were largely excluded from the tumor centre. By contrast, the occult micrometastasis contained only few SOX10⁺ Melan A^- melanoma cells which were scattered within a dense infiltrate of T cells, including a prominent population of CD103⁺ CD8⁺ T cells resembling tissue-resident memory T (T_RM) cells. Notably, almost every single melanoma cell in the micrometastasis was in close proximity to these T_RM-like cells.

Conclusion

Such results support the emerging concept that CD103⁺ CD8⁺ T_RM cells are key mediators of cancer surveillance and imply an important function of these cells in controlling clinically occult micrometastases in humans.

CD28 Superagonistic Activation of T Cells Induces a Tumor Cell-Like Metabolic Program

CD28 superagonist (CD28SA), a therapeutic immunomodulatory monoclonal antibody triggered rapid and exaggerated activation of CD4⁺ effector memory T cells (T_EMs) in humans with unwanted serious adverse effects. It is well known that distinct metabolic programs determine the fate and responses of immune cells. In this study, we show that human CD4⁺ T_EMs stimulated with CD28SA adopt a metabolic program similar to those of tumor cells with enhanced glucose utilization, lipid biosynthesis, and proliferation in hypoxic conditions. Identification of metabolic profiles underlying hyperactive T cell activation would provide a platform to test safety of immunostimulatory antibodies.

Cutting Edge: Human CD49e- NK Cells Are Tissue Resident in the Liver

Most knowledge on NK cells is based on studies of what are now known as conventional NK cells in the mouse spleen or human peripheral blood. However, recent studies in mice indicate the presence of tissue-resident NK cells in certain organs, such as the liver, that display different markers and transcription factor dependencies as compared with conventional NK cells. In this study, we provide evidence from cytometry by time-of-flight analysis and humanized mice indicating that human CD49e^- NK cells are tissue resident in the liver. Thus, these studies indicate that tissue-resident NK cells are evolutionarily conserved in humans and mice, providing a foundation to explore their role in human disease.

Human liver contains two populations of NK cells based on CD49e expression

Natural killer cells are a subset of innate immune lymphocytes that can kill transformed and infected cells, and produce cytokines that modulate the host immune response. Previous studies on human NK cells have primarily characterized NK cells isolated from peripheral blood. However, studies in mice from our lab and others indicate an additional tissue-resident NK (trNK) population that does not re-circulate in contrast to conventional NK (cNK). When the mouse liver was excised and flushed with saline, trNK cells were detected, indicating that the trNK cells reside in the liver sinusoidal space. Recent studies to identify trNK cells in the human liver have concentrated on the differential expression of CD56-dim/bright populations of NK cells and also CD49a, a marker we previously defined for mouse trNK cells in the liver. Herein we obtained samples from liver transplantation cadaveric donors. Matching donor venous blood and serial liver saline flushes were studied. Our preliminary data identifies a subset of putative liver-trNK cells based on lack of CD49e expression which appeared in the terminal liver flush aliquot and was not present in earlier liver flushes nor peripheral blood whereas CD49a expression was not discriminatory. Mass cytometry experiments with cytometry by time-of-flight instrument and a panel of 42 antibodies corroborated these findings. Interestingly, the liver-resident CD49e− cells have elevated EOMES but lower Tbet expression which contrasts the CD49a+ trNK cell populations in human and mouse liver. Finally, the putative trNK cells express different killer immunoglobulin-like receptor (KIR) repertoire than cNK cells thus, a unique population of trNK cells that reside in the sinusoidal space of the human liver.

De novo assembly and transcriptome analysis of Plasmodium gallinaceum identifies the Rh5 interacting protein (ripr), and reveals a lack of EBL and RH gene family diversification

Background

Malaria parasites that infect birds can have narrow or broad host-tropisms. These differences in host specificity make avian malaria a useful model for studying the evolution and transmission of parasite assemblages across geographic ranges. The molecular mechanisms involved in host-specificity and the biology of avian malaria parasites in general are important aspects of malaria pathogenesis that warrant further examination. Here, the transcriptome of the malaria parasite Plasmodium gallinaceum was characterized to investigate the biology and the conservation of genes across various malaria parasite species.

Methods

The P. gallinaceum transcriptome was annotated and KEGG pathway mapping was performed. The ripr gene and orthologous genes that play critical roles in the purine salvage pathway were identified and characterized using bioinformatics and phylogenetic methods.

Results

Analysis of the transcriptome sequence database identified essential genes of the purine salvage pathway in P. gallinaceum that shared high sequence similarity to Plasmodium falciparum when compared to other mammalian Plasmodium spp. However, based on the current sequence data, there was a lack of orthologous genes that belonged to the erythrocyte-binding-like (EBL) and reticulocyte-binding-like homologue (RH) family in P. gallinaceum. In addition, an orthologue of the Rh5 interacting protein (ripr) was identified.

Conclusions

These findings suggest that the pathways involved in parasite red blood cell invasion are significantly different in avian Plasmodium parasites, but critical metabolic pathways are conserved throughout divergent Plasmodium taxa.

Electronic supplementary material

The online version of this article (doi:10.1186/s12936-015-0814-0) contains supplementary material, which is available to authorized users.

Heme oxygenase-1 regulates dendritic cell function through modulation of p38 MAPK-CREB/ATF1 signaling

Dendritic cells (DCs) are critical for the initiation of immune responses including activation of CD8 T cells. Intracellular reactive oxygen species (ROS) levels influence DC maturation and function. Intracellular heme, a product of catabolism of heme-containing metalloproteins, is a key inducer of ROS. Intracellular heme levels are regulated by heme oxygenase-1 (HO-1), which catalyzes the degradation of heme. Heme oxygenase-1 has been implicated in regulating DC maturation; however, its role in other DC functions is unclear. Furthermore, the signaling pathways modulated by HO-1 in DCs are unknown. In this study, we demonstrate that inhibition of HO-1 activity in murine bone marrow-derived immature DCs (iDCs) resulted in DCs with raised intracellular ROS levels, a mature phenotype, impaired phagocytic and endocytic function, and increased capacity to stimulate antigen-specific CD8 T cells. Interestingly, our results reveal that the increased ROS levels following HO-1 inhibition did not underlie the changes in phenotype and functions observed in these iDCs. Importantly, we show that the p38 mitogen-activated protein kinase (p38 MAPK), cAMP-responsive element binding protein (CREB), and activating transcription factor 1 (ATF1) pathway is involved in the mediation of the phenotypic and functional changes arising from HO-1 inhibition. Furthermore, up-regulation of HO-1 activity rendered iDCs refractory to lipopolysaccharide-induced activation of p38 MAPK-CREB/ATF1 pathway and DC maturation. Finally, we demonstrate that treatment of iDC with the HO-1 substrate, heme, recapitulates the effects that result from HO-1 inhibition. Based on these results, we conclude that HO-1 regulates DC maturation and function by modulating the p38 MAPK-CREB/ATF1 signaling axis.

Nuclear factor-erythroid 2 (NF-E2) p45-related factor-2 (Nrf2) modulates dendritic cell immune function through regulation of p38 MAPK-cAMP-responsive element binding protein/activating transcription factor 1 signaling

Nrf2 is a redox-responsive transcription factor that has been implicated in the regulation of DC immune function. Loss of Nrf2 results in increased co-stimulatory molecule expression, enhanced T cell stimulatory capacity, and increased reactive oxygen species (ROS) levels in murine immature DCs (iDCs). It is unknown whether altered immune function of Nrf2-deficient DCs (Nrf2^−/− iDCs) is due to elevated ROS levels. Furthermore, it is unclear which intracellular signaling pathways are involved in Nrf2-mediated regulation of DC function. Using antioxidant vitamins to reset ROS levels in Nrf2^−/− iDCs, we show that elevated ROS is not responsible for the altered phenotype and function of these DCs. Pharmacological inhibitors were used to explore the role of key MAPKs in mediating the altered phenotype and function in Nrf2^−/− iDCs. We demonstrate that the increased co-stimulatory molecule expression (MHC II and CD86) and antigen-specific T cell activation capacity observed in Nrf2^−/− iDCs was reversed by inhibition of p38 MAPK but not JNK. Importantly, we provide evidence for increased phosphorylation of cAMP-responsive element binding protein (CREB) and activating transcription factor 1 (ATF1), transcription factors that are downstream of p38 MAPK. The increased phosphorylation of CREB/ATF1 in Nrf2^−/− iDCs was sensitive to p38 MAPK inhibition. We also show data to implicate heme oxygenase-1 as a potential molecular link between Nrf2 and CREB/ATF1. These results indicate that dysregulation of p38 MAPK-CREB/ATF1 signaling axis underlies the altered function and phenotype in Nrf2-deficient DCs. Our findings provide new insights into the mechanisms by which Nrf2 mediates regulation of DC function.

Dysregulation in p38 signalling contributes to altered phenotype and function in Nrf2 deficient dendritic cells (P5025)

Nrf2 is a redox sensitive transcription factor vital for the maintenance of cellular homeostasis. Dendritic cells (DCs) are potent APCs responsible for the initiation of an immune response. Our previous study highlights the role of Nrf2 in DC function (increased costimulatory receptors expression and T cell stimulatory capacity) and intracellular signaling (such as ROS, NFκB and MAPKs). The p38 MAPK pathway plays a pivotal role in the up regulation of costimulatory receptors (CD86 & MHC II). However, it is unclear how Nrf2 affects the integrity of this pathway. In the current study using bone marrow-derived immature DCs from Nrf2 deficient (KO) and wild type mice, we investigate the effect of Nrf2 on various signaling events in the p38 pathway and associated functional responses. Our results indicate that the loss of Nrf2 in DCs resulted in elevated basal p38 phosphorylation. Furthermore, an increase in basal phosphorylation of CREB and ATF-1 - downstream targets of p38, was also observed. This was coupled with increased IL-10 cytokine production at basal conditions and also upon exposure to LPS. Increased costimulatory receptor expression, antigen specific T cell activation propensity and LPS stimulated IL-10 production observed in the KO DCs can be reversed by pharmacological inhibition of p38. These results suggest that deficiency of Nrf2 in DCs leads to dysregulation of the p38 signaling pathway contributing to the altered phenotype and function of these DCs.

Loss of transcription factor nuclear factor-erythroid 2 (NF-E2) p45-related factor-2 (Nrf2) leads to dysregulation of immune functions, redox homeostasis, and intracellular signaling in dendritic cells

Dendritic cells (DCs) are critical mediators of immunity and immune tolerance by orchestrating multiple aspects of T cell activation and function. Immature DCs (iDCs) expressing low levels of co-stimulatory receptors are highly efficient at antigen capture but are poor activators of T cells. Maturation of DCs is associated with increased expression of co-stimulatory molecules. Co-stimulatory receptor gene expression is regulated by intracellular redox, NF-κB, and MAPK pathways and by histone deacetylase (HDAC) activity. The transcription factor, Nrf2, is important for maintaining intracellular glutathione (GSH) levels and redox homeostasis and has been implicated in modulating DC co-stimulatory receptor expression. It is unclear whether Nrf2 mediates this effect by GSH-dependent mechanisms and whether it influences DC signaling pathways. Using bone marrow-derived iDCs from Nrf2^+/+ and Nrf2^−/− mice, we demonstrate that Nrf2^−/− iDCs have lower basal GSH levels, enhanced co-stimulatory receptor expression, impaired phagocytic functions, and increased antigen-specific CD8 T cell stimulation capacity. Interestingly, lowering GSH levels in Nrf2^+/+ iDCs did not recapitulate the Nrf2^−/− iDC phenotype. Loss of Nrf2 resulted in elevated basal levels of reactive oxygen species but did not affect basal NF-κB activity or p38 MAPK phosphorylation. Using pharmacological inhibitors, we demonstrate that enhanced co-stimulatory receptor phenotype of Nrf2^−/− iDC does not require ERK activity but is dependent on HDAC activity, indicating a potential interaction between Nrf2 function and HDAC. These results suggest that Nrf2 activity is required to counter rises in intracellular reactive oxygen species and to regulate pathways that control DC co-stimulatory receptor expression.