A5077463542- Single-cell and spatial transcriptomics
- Molecular Biology Techniques and Applications
- Advanced Biosensing Techniques and Applications
- Cancer Research and Treatments
- Cancer Genomics and Diagnostics
- Neuroinflammation and Neurodegeneration Mechanisms
- Bioinformatics and Genomic Networks
- Virus-based gene therapy research
- Advanced Proteomics Techniques and Applications
- Alzheimer's disease research and treatments
- Advanced Fluorescence Microscopy Techniques
- RNA modifications and cancer
- Cell Image Analysis Techniques
- Advanced biosensing and bioanalysis techniques
- Immunotherapy and Immune Responses
- Veterinary Oncology Research
- GABA and Rice Research
- Chemokine receptors and signaling
- Radiomics and Machine Learning in Medical Imaging
- Colorectal Cancer Treatments and Studies
- Extracellular vesicles in disease
- Gene expression and cancer classification
- Peroxisome Proliferator-Activated Receptors
- Immune cells in cancer
- Nanoplatforms for cancer theranostics
Bruker (Switzerland)
2024
Nanostring Technologies (United States)
2017-2024
Mapping cell types across a tissue is central concern of spatial biology, but type abundance difficult to extract from gene expression data. We introduce SpatialDecon, an algorithm for quantifying populations defined by single sequencing within the regions studies. SpatialDecon incorporates several advancements in deconvolution. propose harnessing log-normal regression and modelling background, outperforming classical least-squares methods. compile profile matrices 75 types. identify genes...
Abstract The Spatial Molecular Imaging platform (CosMx TM SMI, NanoString Technologies, Seattle, WA) utilizes high-plex in-situ imaging chemistry for both RNA and protein detection. This automated instrument provides 1000’s of plex, at high sensitivity (1 to 2 copies/cell), very low error rate (0.0092 false calls/cell) background (∼0.04 counts/cell). system generates three-dimensional super-resolution localization analytes ∼2 million cells per sample, four samples run. Cell segmentation is...
Abstract Background Late-onset Alzheimer’s disease (LOAD) is the most common form of dementia worldwide. To date, animal models have focused on rare familial mutations, due to a lack frank neuropathology from based genes. Recent multi-cohort studies postmortem human brain transcriptomes identified set 30 gene co-expression modules associated with LOAD, providing molecular catalog relevant endophenotypes. Results This resource enables precise gene-based alignment between new and signatures...
Emerging spatial profiling technology has enabled high-plex molecular in biological tissues, preserving the and morphological context of gene expression. Here, we describe expanding chemistry for Digital Spatial Profiling platform to quantify whole transcriptomes human mouse tissues using a wide range strategies sample types. We designed multiplexed situ hybridization probes targeting protein-coding genes transcriptomes, referred as or Whole Transcriptome Atlas (WTA). Human WTAs were...
Abstract Emerging spatial profiling technology has enabled high-plex molecular in biological tissues, preserving the and morphological context of gene expression. Here we describe expanding chemistry for Digital Spatial Profiling platform to quantify whole transcriptomes human mouse tissues using a wide range strategies sample types. We designed multiplexed situ hybridization probe pools targeting protein-coding genes transcriptomes, hereafter referred as or Whole Transcriptome Atlas (WTA)....
Abstract We introduce SpatialDecon, an algorithm for quantifying cell populations defined by single RNA sequencing within the regions of spatially-resolved gene expression studies. It obtains abundance estimates that are spatially-resolved, granular, and paired with highly multiplexed data. SpatialDecon incorporates several advancements in field deconvolution. propose based log-normal regression, attaining sometimes dramatic performance improvements over classical least-squares methods....
Abstract Cancer research across drug development, molecular biomarkers, and patient response depends on understanding biology that is dependent complex interactions between malignant, immune, stromal cells. To survive clearance mechanisms, a tumor can rely myriad of escape strategies, the microenvironment architected around current path escape. enable more comprehensive picture biology, we have developed CosMx™ Spatial Molecular Imager (SMI) technology to capture snapshot thousands RNA...
Patients with locally/regionally advanced melanoma were treated neoadjuvant combination immunotherapy high-dose interferon α-2b (HDI) and ipilimumab in a phase I clinical trial. Tumor specimens obtained prior to the initiation of therapy, at time surgery progression if available. In this study, gene expression profiles tumor (N = 27) investigated using NanoString nCounter® platform evaluate associations outcomes (pathologic response, radiologic relapse-free survival (RFS), overall (OS))...
Abstract Background The brain is complex and heterogeneous where cell function cell‐to‐cell communication are critical for rapid accurate performance. ability to explore protein‐driven activities at high resolution within spatial context of their immediate environment gain comprehensive pictures development, activity, aging, disease or dysfunction, inflammatory responses. Many existing approaches high‐plex single proteomics face issues around simplicity, speed, scalability, big data...
ABSTRACT Background Late-onset Alzheimer’s disease (LOAD) is the most common form of dementia worldwide. To date, animal models have focused on rare familial mutations, due to a lack frank neuropathology from based genes. Recent multi-cohort studies postmortem human brain transcriptomes identified set 30 gene co-expression modules associated with LOAD, providing molecular catalog relevant endophenotypes. Results This resource enables precise gene-based alignment between new and signatures...
Abstract The spatial interactions between the immune system and tumor cells greatly influence antitumoral immunity. Characterization of cell composition infiltration within niche informs prognosis, drug delivery efficiency, therapeutic efficacy. However, few methods exist to query large numbers biomarkers at subcellular resolution. CosMx™ Spatial Molecular Imager is first platform demonstrate simultaneous single-cell detection over 100 proteins on standard, biobanked, FFPE tissue samples....
Single-cell RNA-seq revolutionized single-cell biology, by providing a complete whole transcriptome view of individual cells. Regrettably, this was accomplished only for individual, tissue-dissociated High-plex spatial biology has begun to recover the x, y, and z-coordinates single-cells, but typically at expense far less than coverage. To solve problem, Bruker Spatial Biology commercial-grade panel (CosMx® Molecular Imager Whole Transcriptome Panel (WTx)), using 37,872 imaging barcodes,...
Abstract Harnessing the immune system to eliminate cancer and prevent its recurrence is proving be a powerful therapeutic approach that has achieved unprecedented successes in hematological malignancies some with high tumor burden. Next generation therapies improve clinical responses widen reach of immunotherapy are being designed at rapid pace, informative pre-clinical testing these approaches can greatly facilitated using competent animals spontaneous tumors. Pet dogs immunologically...
Abstract The advancement of spatially resolved, multiplex proteomic and transcriptomic technologies has revolutionized redefined the approaches to complex biological questions pertaining tissue heterogeneity, tumor microenvironments, cellular interactions, diversity, therapeutic response. While spatial transcriptomics traditionally led way in plex, multiple studies have demonstrated a poor correlation between RNA expression protein abundance, owing transcriptional translational regulation,...
Abstract Clinical specimens including formalin-fixed, paraffin embedded (FFPE) tumor sections preserve spatial and molecular information of cells their surrounding microenvironment. This valuable is loss with bulk RNA-seq, the most prevalent method for gene expression profiling archival FFPE samples. In contrast, NanoString GeoMx™ Digital Spatial Profiler (DSP) a high multiplexing assay that can profile thousands RNAs from user selectable regions interest (ROIs) in sections. Here we...
Abstract The power of spatial biology lies in the integration multiple scales information from subcellular to tissue scale. Until recently, analysis protein biomarkers tissues was limited a few markers at time using traditional IHC colorimetric or fluorescent readout. Here, we demonstrate ability NanoString’s CosMx™ Spatial Molecular Imager (SMI) platform quantify more than 70 proteins encompassing key targets immuno-oncology and tumor biology, localize analyze expression single cell level....
<h3>Background</h3> Pre-clinical testing of combination therapies including chemotherapy, radiation, targeted and immunotherapy to treat hematological solid malignancies can be greatly facilitated using immune competent animals with spontaneous tumors. Pet dogs are immunologically outbred, develop tumors such as hemangiosarcoma, astrocytoma, osteosarcoma, urothelial carcinoma, lymphoma melanoma that share remarkable clinical, biological genetic features their human counterparts. comparative...
Abstract The emerging field of spatial genomics represents a significant advance for biology. To drive new discoveries in and immuno-oncology, we introduce the GeoMx Cancer Transcriptome Atlas (CTA) Panel comprehensive analysis cancer pathways using Nanostring Digital Spatial Profiler (DSP). We demonstrate profiling 1600+ immuno-oncology targets tumor, microenvironment, immune compartments archival FFPE tissue sections, coupled to downstream Next Generation Sequencing (NGS) readout enable...
Clinical specimens including formalin-fixed, paraffin embedded (FFPE) tumor sections preserve spatial and molecular information of cells their surrounding microenvironment. This valuable is loss with bulk RNA-seq, the most prevalent method for gene expression profiling archival FFPE samples. In contrast, NanoString GeoMx™ Digital Spatial Profiler (DSP) a high multiplexing assay that can profile thousands RNAs from user selectable regions interest (ROIs) in sections. Here we introduce 1600+...
Abstract Detecting and analyzing large numbers of proteins using whole-slide imaging is critical for a comprehensive picture immune response to cancer. Many existing approaches high-plex proteomics face issues around simplicity, speed, scalability, big data analysis. Here, we present an integrated workflow from sample preparation through downstream analysis that addresses many key concerns high plex proteomics. The CosMx Spatial Molecular Imager (SMI) AtoMx Informatics Platform (SIP)...
Abstract Spatial distribution of T cells is key in understanding the escape tumors from immune surveillance via adaptive response, including interactions between and surrounding tumor microenvironment. are critical to response pathogens cancers, mediating an antigen-specific through both specificity diversity cell receptor (TCR) clonotypes. Many methods exist determine specific clonotypes overall TCR present bulk tissues or sorted populations; however, nearly all fail capture spatial...
Abstract Background: Combination therapy to treat hematological and solid malignancies including chemotherapy, radiation, targeted immunotherapy all hold huge potential for eliciting clinical responses. Informative pre-clinical testing of these approaches can be greatly facilitated using immune competent animals with spontaneous tumors. Pet dogs are immunologically outbred, develop tumors such as non Hodgkin’s lymphoma, glioblastoma, osteosarcoma, urothelial carcinoma melanoma that share...
<h3>Background</h3> The standard of care for early-stage HER2-positive (HER2+) breast cancer is neoadjuvant anti-HER2 therapy-based chemotherapy, with the preferred regimen being TCHP (docetaxel, carboplatin, trastuzumab, and pertuzumab). Approximately half such patients have a pathological complete response (pCR) this regimen. There compelling need to understand biology that underlies or failure respond. Such an understanding central development alternative therapeutic strategies. To end,...
<h3>Background</h3> The advancement of spatially resolved, multiplex proteomic and transcriptomic technologies has revolutionized redefined the approaches to complex biological questions pertaining tissue heterogeneity, tumor microenvironments, cellular interactions, diversity, therapeutic response. While spatial transcriptomics traditionally led way in plex, multiple studies have demonstrated a poor correlation between RNA expression protein abundance, owing transcriptional translational...