Mass Cytometry, Imaging Mass Cytometry, and Multiplexed Ion Beam Imaging Use in a Clinical Setting

Systemic and local immunosuppression in glioblastoma and its prognostic significance

The effectiveness of tumor therapy, especially immunotherapy and oncolytic virotherapy, critically depends on the activity of the host immune cells. However, various local and systemic mechanisms of immunosuppression operate in cancer patients. Tumor-associated immunosuppression involves deregulation of many components of immunity, including a decrease in the number of T lymphocytes (lymphopenia), an increase in the levels or ratios of circulating and tumor-infiltrating immunosuppressive subsets [e.g., macrophages, microglia, myeloid-derived suppressor cells (MDSCs), and regulatory T cells (Tregs)], as well as defective functions of subsets of antigen-presenting, helper and effector immune cell due to altered expression of various soluble and membrane proteins (receptors, costimulatory molecules, and cytokines). In this review, we specifically focus on data from patients with glioblastoma/glioma before standard chemoradiotherapy. We discuss glioblastoma-related immunosuppression at baseline and the prognostic significance of different subsets of circulating and tumor-infiltrating immune cells (lymphocytes, CD4+ and CD8+ T cells, Tregs, natural killer (NK) cells, neutrophils, macrophages, MDSCs, and dendritic cells), including neutrophil-to-lymphocyte ratio (NLR), focus on the immune landscape and prognostic significance of isocitrate dehydrogenase (IDH)-mutant gliomas, proneural, classical and mesenchymal molecular subtypes, and highlight the features of immune surveillance in the brain. All attempts to identify a reliable prognostic immune marker in glioblastoma tissue have led to contradictory results, which can be explained, among other things, by the unprecedented level of spatial heterogeneity of the immune infiltrate and the significant phenotypic diversity and (dys)functional states of immune subpopulations. High NLR is one of the most repeatedly confirmed independent prognostic factors for shorter overall survival in patients with glioblastoma and carcinoma, and its combination with other markers of the immune response or systemic inflammation significantly improves the accuracy of prediction; however, more prospective studies are needed to confirm the prognostic/predictive power of NLR. We call for the inclusion of dynamic assessment of NLR and other blood inflammatory markers (e.g., absolute/total lymphocyte count, platelet-to-lymphocyte ratio, lymphocyte-to-monocyte ratio, systemic immune-inflammation index, and systemic immune response index) in all neuro-oncology studies for rigorous evaluation and comparison of their individual and combinatorial prognostic/predictive significance and relative superiority.

Strategies for studying immune and non-immune human and canine mammary gland cancer tumour infiltrate

The tumour microenvironment (TME) is usually defined as a cell environment associated with tumours or cancerous stem cells where conditions are established affecting tumour development and progression through malignant cell interaction with non-malignant cells. The TME is made up of endothelial, immune and non-immune cells, extracellular matrix (ECM) components and signalling molecules acting specifically on tumour and non-tumour cells. Breast cancer (BC) is the commonest malignant neoplasm worldwide and the main cause of mortality in women globally; advances regarding BC study and understanding it are relevant for acquiring novel, personalised therapeutic tools. Studying canine mammary gland tumours (CMGT) is one of the most relevant options for understanding BC using animal models as they share common epidemiological, clinical, pathological, biological, environmental, genetic and molecular characteristics with human BC. In-depth, detailed investigation regarding knowledge of human BC-related TME and in its canine model is considered extremely relevant for understanding changes in TME composition during tumour development. This review addresses important aspects concerned with different methods used for studying BC- and CMGT-related TME that are important for developing new and more effective therapeutic strategies for attacking a tumour during specific evolutionary stages.

Bone marrow haematopoiesis in patients with COVID-19

AIMS

Severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) infection broadly affects organ homeostasis, including the haematopoietic system. Autopsy studies are a crucial tool for investigation of organ-specific pathologies. Here we perform an in-depth analysis of the impact of severe coronavirus disease 2019 (COVID-19) on bone marrow haematopoiesis in correlation with clinical and laboratory parameters.

METHODS AND RESULTS

Twenty-eight autopsy cases and five controls from two academic centres were included in the study. We performed a comprehensive analysis of bone marrow pathology and microenvironment features with clinical and laboratory parameters and assessed SARS-CoV-2 infection of the bone marrow by quantitative polymerase chain reaction (qPCR) analysis. In COVID-19 patients, bone marrow specimens showed a left-shifted myelopoiesis (19 of 28, 64%), increased myeloid-erythroid ratio (eight of 28, 28%), increased megakaryopoiesis (six of 28, 21%) and lymphocytosis (four of 28, 14%). Strikingly, a high proportion of COVID-19 specimens showed erythrophagocytosis (15 of 28, 54%) and the presence of siderophages (11 of 15, 73%) compared to control cases (none of five, 0%). Clinically, erythrophagocytosis correlated with lower haemoglobin levels and was more frequently observed in patients from the second wave. Analysis of the immune environment showed a strong increase in CD68+ macrophages (16 of 28, 57%) and a borderline lymphocytosis (five of 28, 18%). The stromal microenvironment showed oedema (two of 28, 7%) and severe capillary congestion (one of 28, 4%) in isolated cases. No stromal fibrosis or microvascular thrombosis was found. While all cases had confirmed positive testing of SARS-CoV-2 in the respiratory system, SARS-CoV-2 was not detected in the bone marrow by high-sensitivity PCR, suggesting that SARS-CoV-2 does not commonly replicate in the haematopoietic microenvironment.

CONCLUSIONS

SARS-CoV-2 infection indirectly impacts the haematological compartment and the bone marrow immune environment. Erythrophagocytosis is frequent and associated with lower haemoglobin levels in patients with severe COVID-19.

Selective oxidative protection leads to tissue topological changes orchestrated by macrophage during ulcerative colitis

Ulcerative colitis is a chronic inflammatory bowel disorder with cellular heterogeneity. To understand the composition and spatial changes of the ulcerative colitis ecosystem, here we use imaging mass cytometry and single-cell RNA sequencing to depict the single-cell landscape of the human colon ecosystem. We find tissue topological changes featured with macrophage disappearance reaction in the ulcerative colitis region, occurring only for tissue-resident macrophages. Reactive oxygen species levels are higher in the ulcerative colitis region, but reactive oxygen species scavenging enzyme SOD2 is barely detected in resident macrophages, resulting in distinct reactive oxygen species vulnerability for inflammatory macrophages and resident macrophages. Inflammatory macrophages replace resident macrophages and cause a spatial shift of TNF production during ulcerative colitis via a cytokine production network formed with T and B cells. Our study suggests components of a mechanism for the observed macrophage disappearance reaction of resident macrophages, providing mechanistic hints for macrophage disappearance reaction in other inflammation or infection situations.

A 31-plex panel for high-dimensional single-cell analysis of murine preclinical models of solid tumors by imaging mass cytometry

Currently, the study of resistance mechanisms and disease progression in cancer relies on the capacity to analyze tumors as a complex ecosystem of healthy and malignant cells. Therefore, one of the current challenges is to decipher the intra-tumor heterogeneity and especially the spatial distribution and interactions of the different cellular actors within the tumor. Preclinical mouse models are widely used to extend our understanding of the tumor microenvironment (TME). Such models are becoming more sophisticated and allow investigating questions that cannot be addressed in clinical studies. Indeed, besides studying the tumor cell interactions within their environment, mouse models allow evaluating the efficacy of new drugs and delivery approaches, treatment posology, and toxicity. Spatially resolved analyses of the intra-tumor heterogeneity require global approaches to identify and localize a large number of different cell types. For this purpose, imaging mass cytometry (IMC) is a major asset in the field of human immuno-oncology. However, the paucity of validated IMC panels to study TME in pre-clinical mouse models remains a critical obstacle to translational or basic research in oncology. Here, we validated a panel of 31 markers for studying at the single-cell level the TME and the immune landscape for discovering/characterizing cells with complex phenotypes and the interactions shaping the tumor ecosystem in mouse models.

Macrophage GSK3β-deficiency inhibits the progression of hepatocellular carcinoma and enhances the sensitivity of anti-PD1 immunotherapy

BACKGROUND

Glycogen synthase kinase 3β (GSK3β) was originally discovered to regulate glycogen synthesis and show a relationship to tumors. However, the biological functions of GSK3β in tumor-associated macrophages (TAMs) in cancers including hepatocellular carcinoma (HCC) remain unclear.

METHODS

The enrichment of GSK3β in tumor tissues was assessed by Gene Expression Omnibus (GEO) database. The in vitro and in vivo assays assisted in evaluating how GSK3β in TAMs affected HCC in terms of proliferation, invasion and migration. Immunofluorescence was used to assess GSK3β expression in TAMs in the anti-PD1 therapy non-responsive HCC group and the responsive group. Western blot and coimmunoprecipitation were performed to demonstrate the interaction between GSK3β and PD-L1. We carried out in vivo experiments in a C57BL/6 mouse model of HCC established through subcutaneous injection.

RESULTS

GEO single-cell RNA sequencing data suggested that GSK3β was highly enriched in TAMs of HCC. According to in vitro and in vivo experiments, reducing GSK3β in TAMs inhibits the cancer cell proliferation, invasion, and migration. The immunofluorescence and immunohistochemistry results confirmed that the GSK3β is significantly upregulated in TAMs of the anti-PD1 therapy non-responsive group in comparison with the responsive group. In vitro and in vivo experiments confirmed that reduced GSK3β in TAMs are capable of enhancing the sensitivity of anti-PD1 immunotherapy for HCC by decreasing PD-L1 ubiquitination. Mass spectrometry results suggested that high expression of CD14⁺GSK3β⁺ in the peripheral blood mononuclear cell (PBMC) can predict non-responsive to anti-PD1 treatment. Moreover, escitalopram is confirmed to act as GSK3β inhibitor that can increase the sensitivity of anti-PD1 immunotherapy for HCC.

CONCLUSIONS

This study revealed that macrophage GSK3β deficiency can inhibit the development of HCC by inhibiting the M2 phenotype and enhance the sensitivity of anti-PD1 immunotherapy for HCC by decreasing PD-L1 ubiquitination. The expression of CD14⁺GSK3β⁺ in PBMC can noninvasively predict anti-PD1 sensitivity in HCC patients, which provides novel strategies to predict anti-PD1 sensitivity, increase anti-PD1 therapeutic effect, and bring new hope for HCC patients.

Spatial multi-omics analyses of the tumor immune microenvironment

In the past decade, single-cell technologies have revealed the heterogeneity of the tumor-immune microenvironment at the genomic, transcriptomic, and proteomic levels and have furthered our understanding of the mechanisms of tumor development. Single-cell technologies have also been used to identify potential biomarkers. However, spatial information about the tumor-immune microenvironment such as cell locations and cell–cell interactomes is lost in these approaches. Recently, spatial multi-omics technologies have been used to study transcriptomes, proteomes, and metabolomes of tumor-immune microenvironments in several types of cancer, and the data obtained from these methods has been combined with immunohistochemistry and multiparameter analysis to yield markers of cancer progression. Here, we review numerous cutting-edge spatial ‘omics techniques, their application to study of the tumor-immune microenvironment, and remaining technical challenges.

Assessment of human milk in the era of precision health

PURPOSE OF REVIEW

Precision health provides an unprecedented opportunity to improve the assessment of infant nutrition and health outcomes. Breastfeeding is positively associated with infant health outcomes, yet only 58.3% of children born in 2017 were still breastfeeding at 6 months. There is an urgent need to examine the application of precision health tools that support the development of public health interventions focused on improving breastfeeding outcomes.

RECENT FINDINGS

In this review, we discussed the novel and highly sensitive techniques that can provide a vast amount of omics data and clinical information just by evaluating small volumes of milk samples, such as RNA sequencing, cytometry by time-of-flight, and human milk analyzer for clinical implementation. These advanced techniques can run multiple samples in a short period of time making them ideal for the routine clinical evaluation of milk samples.

SUMMARY

Precision health tools are increasingly used in clinical research studies focused on infant nutrition. The integration of routinely collected multiomics human milk data within the electronic health records has the potential to identify molecular biomarkers associated with infant health outcomes.

The Role of Pathology-Based Methods in Qualitative and Quantitative Approaches to Cancer Immunotherapy

Simple Summary

Immunotherapy has become the filar of modern oncological treatment, and programmed death-ligand 1 expression is one of the primary immune markers assessed by pathologists. However, there are still some issues concerning the evaluation of the marker and limited information about the interaction between the tumour and associated immune cells. Recent studies have focused on cancer immunology to try to understand the complex tumour microenvironment, and multiplex imaging methods are more widely used for this purpose. The presented article aims to provide an overall review of a different multiplex in situ method using spectral imaging, supported by automated image-acquisition and software-assisted marker visualisation and interpretation. Multiplex imaging methods could improve the current understanding of complex tumour-microenvironment immunology and could probably help to better match patients to appropriate treatment regimens.

Abstract

Immune checkpoint inhibitors, including those concerning programmed cell death 1 (PD-1) and its ligand (PD-L1), have revolutionised the cancer therapy approach in the past decade. However, not all patients benefit from immunotherapy equally. The prediction of patient response to this type of therapy is mainly based on conventional immunohistochemistry, which is limited by intraobserver variability, semiquantitative assessment, or single-marker-per-slide evaluation. Multiplex imaging techniques and digital image analysis are powerful tools that could overcome some issues concerning tumour-microenvironment studies. This novel approach to biomarker assessment offers a better understanding of the complicated interactions between tumour cells and their environment. Multiplex labelling enables the detection of multiple markers simultaneously and the exploration of their spatial organisation. Evaluating a variety of immune cell phenotypes and differentiating their subpopulations is possible while preserving tissue histology in most cases. Multiplexing supported by digital pathology could allow pathologists to visualise and understand every cell in a single tissue slide and provide meaning in a complex tumour-microenvironment contexture. This review aims to provide an overview of the different multiplex imaging methods and their application in PD-L1 biomarker assessment. Moreover, we discuss digital imaging techniques, with a focus on slide scanners and software.

Current challenges in metastasis research and future innovation for clinical translation

While immense strides have been made in understanding tumor biology and in developing effective treatments that have substantially improved the prognosis of cancer patients, metastasis remains the major cause of cancer-related death. Improvements in the detection and treatment of primary tumors are contributing to a growing, detailed understanding of the dynamics of metastatic progression. Yet challenges remain in detecting metastatic dissemination prior to the establishment of overt metastases and in predicting which patients are at the highest risk of developing metastatic disease. Further improvements in understanding the mechanisms governing metastasis have great potential to inform the adaptation of existing therapies and the development of novel approaches to more effectively control metastatic disease. This article presents a forward-looking perspective on the challenges that remain in the treatment of metastasis, and the exciting emerging approaches that promise to transform the treatment of metastasis in cancer patients.

Recent progress in cytometric technologies and their applications in ecotoxicology and environmental risk assessment

Environmental toxicology focuses on identifying and predicting impact of potentially toxic anthropogenic chemicals on biosphere at various levels of biological organization. Presently there is a significant drive to gain deeper understanding of cellular and sub-cellular mechanisms of ecotoxicity. Most notable is increased focus on elucidation of cellular-response networks, interactomes, and greater implementation of cell-based biotests using high-throughput procedures, while at the same time decreasing the reliance on standard animal models used in ecotoxicity testing. This is aimed at discovery and interpretation of molecular pathways of ecotoxicity at large scale. In this regard, the applications of cytometry are perhaps one of the most fundamental prospective analytical tools for the next generation and high-throughput ecotoxicology research. The diversity of this modern technology spans flow, laser-scanning, imaging, and more recently, Raman as well as mass cytometry. The cornerstone advantages of cytometry include the possibility of multi-parameter measurements, gating and rapid analysis. Cytometry overcomes, thus, limitations of traditional bulk techniques such as spectrophotometry or gel-based techniques that average the results from pooled cell populations or small model organisms. Novel technologies such as cell imaging in flow, laser scanning cytometry, as well as mass cytometry provide innovative and tremendously powerful capabilities to analyze cells, tissues as well as to perform in situ analysis of small model organisms. In this review, we outline cytometry as a tremendously diverse field that is still vastly underutilized and often largely unknown in environmental sciences. The main motivation of this work is to highlight the potential and wide-reaching applications of cytometry in ecotoxicology, guide environmental scientists in the technological aspects as well as popularize its broader adoption in environmental risk assessment.