A5022533121- Single-cell and spatial transcriptomics
- Immune cells in cancer
- Cancer Immunotherapy and Biomarkers
- Immunotherapy and Immune Responses
- Cancer Genomics and Diagnostics
- Cell Image Analysis Techniques
- CAR-T cell therapy research
- Radiomics and Machine Learning in Medical Imaging
- Advanced Biosensing Techniques and Applications
- Molecular Biology Techniques and Applications
- Nanoplatforms for cancer theranostics
- Cutaneous Melanoma Detection and Management
- Pancreatic and Hepatic Oncology Research
- vaccines and immunoinformatics approaches
- Atherosclerosis and Cardiovascular Diseases
- Bladder and Urothelial Cancer Treatments
- interferon and immune responses
- 3D Printing in Biomedical Research
- Advanced Proteomics Techniques and Applications
- Systemic Lupus Erythematosus Research
- Cancer Research and Treatments
- T-cell and B-cell Immunology
- Cancer Cells and Metastasis
- Gene expression and cancer classification
- Melanoma and MAPK Pathways
Akoya Biosciences (United States)
2022-2024
Head and neck squamous cell carcinomas (HNSCCs) are the seventh most common cancer represent a global health burden. Immune checkpoint inhibitors (ICIs) have shown promise in treating recurrent/metastatic disease with durable benefit ∼30% of patients. Current biomarkers for HNSCC limited their dynamic ability to capture tumor microenvironment (TME) features an increasing need deeper tissue characterization. Therefore, new needed accurately stratify patients predict responses therapy. Here,...
Abstract Background Recurrent/metastatic head and neck squamous cell carcinoma (R/M HNSCC) generally has a poor prognosis for patients with limited treatment options. While incorporating immune checkpoint inhibitors (ICIs) now become the standard of care, efficacy is variable, only subset responding. The complexity tumor microenvironment (TME) role tertiary lymphoid structures (TLS) have emerged as critical determinants immunotherapeutic response. Methods In this study, we analyzed two...
Single-cell spatial analysis of proteins is rapidly becoming increasingly important in revealing biological insights. Here, we present a protocol for automated high-plex multi-slide immunofluorescence staining and imaging human head neck cancer formalin-fixed paraffin-embedded (FFPE) sections using PhenoCycler-Fusion 2.0 technology. We describe steps preparing FFPE tissues, with panel immunophenotyping markers, Flow Cell assembly. then detail procedures setting up run, post-run removal,...
Abstract Spatial phenotyping is poised to revolutionize cancer research and treatment. Technologies like CO-Detection by indEXing (CODEX), which enable the detection of dozens protein biomarkers in situ, have already transformed immuno-oncology are expected play formative roles future research. To further support implementation CODEX research, we present a comprehensive 100 antibody panel that aimed at in-depth identification immune cell lineages, activation states, checkpoints, tissue...
Abstract Background The journey from discovering predictive spatial biomarkers (known as signatures) for immunotherapy responses to their clinical application necessitates a cohesive approach bridging ultrahigh-plex discovery experiments with high-throughput translational studies. This study focuses on integrating Akoya Biosciences multiplexed imaging technologies advanced data analysis techniques comprehensive phenotyping across the discovery-to-clinical continuum. Methods Human...
Abstract Background: Immune evasion is a key cancer hallmark, and one of the primary mechanisms PD-1/PD-L1 checkpoint axis. While immunotherapies that target these interactions have reshaped treatment, variable efficacy in patients not fully understood. Due to weak correlation between expression measured by single-plex assays observed clinical outcomes, there need understand protein at cellular subcellular level. Proximity Ligation Assays, detecting spatial ligand-receptor targets, provide...
Abstract The most well-described mechanism of immune evasion in PDAC is exclusion cells by a desmoplastic stroma, but such not uniform. Through single-nucleus RNA-seq and whole-transcriptome digital spatial profiling patient tumors, we previously reported marked heterogeneity the composition PDAC. Here, developed novel multi-omics workflow integrating single cell proteomics (96-plex, Akoya Phenocycler®-Fusion) transcriptomics (990-plex, Nanostring CosMx) primary tumors to systematically...
Abstract Background: Cutaneous squamous cell carcinoma (cSCC), arising from proliferation of malignant epidermal keratinocytes, is the second most common non-melanoma skin cancer. cSCC accounts for 75% all cancer related deaths excluding melanoma, and metastatic immunotherapy-resistant cases pose an emerging global threat. Tumor development a gradual process characterized by high mutational burden immunosuppressive tumor immune microenvironment (TiME); therefore, identifying underlying...
Abstract Background: Pancreatic cancer has a 5-year survival of only 12%. This is due to the lack effective treatments and virtually no early detection methods. To compound this already poor prognosis, African Americans face 20% higher incidence worse mortality compared non-African American patients. With substantial portion data tools employed for studying pancreatic failing adequately represent demographic we aim gain more insight into differences associated with outcomes cancer. achieve...
Abstract Background Targeted immune checkpoint inhibitors (ICI) with anti-PD-1/PD-L1 therapy offer durable treatment of mucosal head and neck squamous cell cancer (HNSCC), in both human papillomavirus-positive (HPV+) negative (HPV-) patients. However, currently available biomarker signatures for targeted ICI therapies have limited predictive value. Our recent ultrahigh-plex profiling HNSCC tissue 100+ hallmarks tumor immunobiology uncovered distinct spatial domains that serve as defining...
Abstract Head and neck squamous cell carcinomas (HNSCC) are the seventh most common cancer represent a global health burden. Immune checkpoint inhibitors (ICIs) have shown promise in treating recurrent/metastatic cases, with durable benefit ∼30% of patients. Current biomarkers for head tumors limited their dynamic ability to capture tumor microenvironment (TME) features, an increasing need deeper tissue characterization. Therefore, new needed accurately stratify patients predict responses...
Abstract Immune checkpoint inhibitor (ICI) therapy has drastically improved the treatment strategies for mucosal head and neck squamous cell cancer (HNSCC). To increase response rates highly targeted ICI therapies, predictive prognostic biomarkers are being actively explored. Specifically, cytokine expression patterns in tumor microenvironment (TME) now recognized as key to understanding immune responsive resistant phenotypes. Cytokines play an essential role regulation of TME, specifically...
Abstract Introduction: The diverse tumor environment of high-grade glioma, which remains refractory to treatment, demands new innovative, multi-omic approaches characterize heterogeneity and expression profiles associated with progression therapeutic response. Approach: We have applied an integrated, approach using paired spatial in situ sequencing (Xenium) protein profiling (PhenoCycler® Fusion) glioma tissue identify distinct cellular phenotypes, activation states metabolic pathways at...
Abstract Single cell RNA-seq (scRNA-seq) performed on suspensions isolated from tumor biopsies provides substantial insights into the transcriptional state of cells in microenvironment (TME). Complementing this work with multi-omic Cellular Indexing Transcriptomes and Epitopes (CITE-seq), which adds barcoded antibodies to label surface cells, allows us additionally characterize proteins. While information gleaned these studies is dramatically expanding our understanding evolving immune...
Abstract Background: Cutaneous squamous cell carcinoma (cSCC) is the second most common skin cancer and represents a major global health burden. Approximately 50% of cSCC patients develop primary resistance 20% will secondary to immune checkpoint inhibitors (ICI). There are limited biomarkers that reflect tumor dynamics predictive response ICI therapy, therefore we need explore new can better understand microenvironment (TME). Methods: Our retrospective study profiled pre-treatment cutaneous...
Abstract Background: It has been well established that the tumor microenvironment (TME), which comprises cancer cells, stromal and surrounding extracellular matrix, plays a critical role in development, progression, control. The immunological components within tumors, known as immune (TiME), have also implicated recurrence, metastasis. Effective strategies for immunotherapies will require deep understanding of factors shape both TME TiME. Here, we describe spatial multiomics approach...
Abstract Background: Immune checkpoint inhibitors (ICI) have proven to be game-changing treatments for mucosal head and neck squamous cell cancer (HNSCC). Emerging successes with anti-PD-1/PD-L1 therapy led durable responses prolonged survival in both human papillomavirus-positive (HPV+) negative (HPV-) patients. There is now a need predictive biomarkers guide patient selection highly targeted ICI therapies as currently available diagnostic limited value. The tumor microenvironment (TME)...
Abstract Background: ~75% of diagnosed bladder tumors are non-muscle-invasive, requiring instillation M. bovis Bacillus Calmette-Guérin (BCG) with recurrence rates observed in ~50% patients. Treatments for BCG-resistant have lagged because few studies tried to understand the relationship between timing tumor and state immune system at time recurrence. Natural Killer (NK) cells very early responders cells. HLA-E, like PD-L1, is sensitive IFN-γ strongly inhibits NKG2A+ NK CD8 T commonly...
Abstract Autoimmune diseases like systemic lupus erythematosus (SLE) affect the health of multiple organ systems including central nervous system, skin, joints, and kidneys. The heterogeneity clinical profiles observed with SLE reflects a complex dysregulation cellular processes, metabolism, apoptotic clearance, inflammation. Diagnosis treatment is thus challenging, few new treatments have been approved over past 60 years. In this study, we aimed to characterize spatial immune metabolic at...
Abstract The Tumor microenvironment (TME) is critical in cancer development, progression, and control. Immunological components within tumors, known as the tumor immune (TIME), have been implicated progression. Effective strategies for immunotherapies will require a deep understanding of factors that shape TME TIME. Here, we describe spatial multiomics assay utilizing RNAscope™ ISH technology paired with high-plex whole-slide phenotyping PhenoCycler ®-Fusion platform. This two-step approach...
<h3>Background</h3> By integrating genomics, transcriptomics, proteomics, and metabolomics, researchers have gained unprecedented insights into the complex interplay between tumors immune system. This wealth of data has fueled discovery novel biomarkers for early cancer detection, prognostic stratification, prediction treatment response. Ultrahigh-plex multispectral immunohistochemistry enables ability to analyze a large set simultaneously while maintaining context tissue architecture....
<h3>Background</h3> Cutaneous squamous cell carcinoma (cSCC) is the second most common skin cancer, accounting for 75% of deaths due to excluding melanoma. Although prognoses are typically favorable, metastasis and resistance immune checkpoint inhibitors pose an emerging threat. There few biomarkers that can reliably aid in patient stratification, thus multiplex strategies required understand dynamics tumor regulation over course therapy. Here, we aim track microenvironment (TME) inhibitor...
<h3>Background</h3> The pathway from discovery to clinical adoption of predictive spatial biomarkers (spatial signatures) for immunotherapy response requires a solution that bridges ultrahigh-plex experiments with targeted high-throughput translational and studies. A critical step toward ensuring the successful transition is harmonizing technologies staining, imaging, data analysis. aim this study demonstrate how integration multiplexed imaging Akoya Biosciences® associated analysis methods...