Abstract IA04: The immune cell microenvironment of classical Hodgkin lymphoma by single-cell analysis

AbstractColorectal cancer (CRC) has one of the highest cancer incidences and mortality rates. In stage III, postoperative chemotherapy benefits <20% of patients, while more than 50% will develop distant metastases. Biomarkers for identification of patients at increased risk of disease recurrence following adjuvant chemotherapy are currently lacking. In this study, we assessed immune signatures in the tumor and tumor microenvironment (TME) using an in situ multiplexed immunofluorescence imaging and single-cell analysis technology (Cell DIVETM) and evaluated their correlations with patient outcomes. Tissue microarrays (TMAs) with up to three 1 mm diameter cores per patient were prepared from 117 stage III CRC patients treated with adjuvant fluoropyrimidine/oxaliplatin (FOLFOX) chemotherapy. Single sections underwent multiplexed immunofluorescence staining for immune cell markers (CD45, CD3, CD4, CD8, FOXP3, PD1) and tumor/cell segmentation markers (DAPI, pan-cytokeratin, AE1, NaKATPase, and S6). We used annotations and a probabilistic classification algorithm to build statistical models of immune cell types. Images were also qualitatively assessed independently by a Pathologist as ‘high’, ‘moderate’ or ‘low’, for stromal and total immune cell content. Excellent agreement was found between manual assessment and total automated scores (p < 0.0001). Moreover, compared to single markers, a multi-marker classification of regulatory T cells (Tregs: CD3+/CD4+FOXP3+/PD1−) was significantly associated with disease-free survival (DFS) and overall survival (OS) (p = 0.049 and 0.032) of FOLFOX-treated patients. Our results also showed that PD1− Tregs rather than PD1+ Tregs were associated with improved survival. These findings were supported by results from an independent FOLFOX-treated cohort of 191 stage III CRC patients, where higher PD1− Tregs were associated with an increase overall survival (p = 0.015) for CD3+/CD4+/FOXP3+/PD1−. Overall, compared to single markers, multi-marker classification provided more accurate quantitation of immune cell types with stronger correlations with outcomes.

Download Full-text

High dimensional single cell analysis reveals unexpected immune cell types, and loss of motility of alveolar macrophages regulated by PPARγ in chronic obstructive pulmonary disease

10.1055/s-0039-1678319 ◽

2019 ◽

Author(s):

W Fujii ◽

K Baßler ◽

T Kapellos ◽

AC Aschenbrenner ◽

K Händler ◽

...

Keyword(s):

Chronic Obstructive Pulmonary Disease ◽

Single Cell ◽

Alveolar Macrophages ◽

Immune Cell ◽

Single Cell Analysis ◽

Cell Types ◽

High Dimensional ◽

Chronic Obstructive ◽

Cell Analysis ◽

Obstructive Pulmonary Disease

Download Full-text

Deciphering Tumor Heterogeneity in Hepatocellular Carcinoma (HCC)—Multi-Omic and Singulomic Approaches

Seminars in Liver Disease ◽

10.1055/s-0040-1722261 ◽

2021 ◽

Author(s):

Renumathy Dhanasekaran

Keyword(s):

Single Cell ◽

Tumor Heterogeneity ◽

Immune Cell ◽

Single Cell Analysis ◽

Sampling Strategies ◽

Cell Analysis ◽

Single Cell Sequencing ◽

Sequencing Technologies ◽

Hepatocellular Carcinomas ◽

Generation Sequencing

AbstractTumor heterogeneity, a key hallmark of hepatocellular carcinomas (HCCs), poses a significant challenge to developing effective therapies or predicting clinical outcomes in HCC. Recent advances in next-generation sequencing-based multi-omic and single cell analysis technologies have enabled us to develop high-resolution atlases of tumors and pull back the curtain on tumor heterogeneity. By combining multiregion targeting sampling strategies with deep sequencing of the genome, transcriptome, epigenome, and proteome, several studies have revealed novel mechanistic insights into tumor initiation and progression in HCC. Advances in multiparametric immune cell profiling have facilitated a deeper dive into the biological complexity of HCC, which is crucial in this era of immunotherapy. Moreover, studies using liquid biopsy have demonstrated their potential to circumvent the need for tissue sampling to investigate heterogeneity. In this review, we discuss how multi-omic and single-cell sequencing technologies have advanced our understanding of tumor heterogeneity in HCC.

Download Full-text

Stratification of Chemotherapy-Treated Stage III Colorectal Cancer Patients Using Multiplexed Imaging and Single Cell Analysis of T Cell Populations

10.1101/2021.02.24.432210 ◽

2021 ◽

Author(s):

Xanthi Stachtea ◽

Maurice B. Loughrey ◽

Manuela Salvucci ◽

Andreas U. Lindner ◽

Sanghee Cho ◽

...

Keyword(s):

Colorectal Cancer ◽

Single Cell ◽

Immune Cells ◽

Immune Cell ◽

Single Cell Analysis ◽

Cell Segmentation ◽

Stage Iii ◽

Support Vector ◽

Cell Analysis ◽

Cell Markers

AbstractColorectal cancer (CRC) has one of the highest cancer incidences and mortality rates. In stage III, postoperative chemotherapy benefits <20% of patients, while more than 50% will develop distant metastases. Predictive biomarkers for identification of patients with increased risk for disease recurrence are currently lacking, with progress in biomarker discovery hindered by the disease’s inherent heterogeneity. The immune profile of colorectal tumors has previously been found to have prognostic value. The aims of this study were to evaluate immune signatures in the tumor microenvironment (TME) using an in situ multiplexed immunofluorescence imaging and single cell analysis technology (Cell DIVE™). Tissue microarrays (TMAs) with up to three 1mm diameter cores per patient were prepared from 117 stage III CRC patients treated with adjuvant fluoropyrimidine/oxaliplatin chemotherapy. Single sections underwent multilplexed immunofluorescence with Cy3- and Cy5-conjugated antibodies for immune cell markers (CD45, CD3, CD4, CD8, FOXP3, PD1) and cell segmentation markers (DAPI, pan-cytokeratin, AE1, NaKATPase and S6). We applied a probabilistic multi-class, multi-label classification algorithm based on multi-parametric models to build statistical models of protein expression to classify immune cells. Expert annotations of immune cell markers were made on a range of images, and Support Vector Machines (SVM) were used to derive a statistical model for cell classification. Images were also manually scored independently by a Pathologist as ‘high’, ‘moderate’ or ‘low’, for stromal and total immune cell content. Excellent agreement was found between manual and total automated scores (p<0.0001). Higher levels of multi-marker classified regulatory T cells (CD3+CD4+FOXP3+PD1-) were significantly associated with disease-free survival (DFS) and overall-survival (OS) (p=0.049 and 0.032), compared to FOXP3 alone. Our results also showed that PD1- Tregs rather than PD1+ Tregs were associated with improved survival. Overall, compared to single markers, multi-marker classification provided more accurate quantitation of immune cells with greater potential for predicting patient outcomes.

Download Full-text