NanoString Digital Molecular Profiling of Protein and microRNA in Rhabdomyosarcoma

Ahmed, Atif; Farooqi, Midhat S.; Habeebu, Sultan S.; Gonzalez, Elizabeth M.; Flatt, Terrie; Wilson, Ashley; Barr, Frederic G.

doi:10.3390/cancers14030522

Cited by 10 publications

(11 citation statements)

References 38 publications

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“…Utilization of the NanoString digital profiling technology in different prognostic groups of ERMS and spindle-cell sclerosing RMS (SRMS) patients revealed significant upregulation of either oncomiR or tumor suppressive miRNA ( 147 ). Of note, SRMS is biologically heterogeneous and like ERMS, it harbors a variety of genetic mutations that can result in different clinical outcomes.…”

Section: Oncomir Implicated In Rmsmentioning

confidence: 99%

“…This study revealed differential expression of miRNA between the different prognostic groups. For example, miR-612, miR-3144-3p, miR-548y, miR-302d-3p, miR-421, miR-548y and miR-548ar-5p were significantly overexpressed in tumors with adverse/poor prognosis compared to those with favorable prognosis ( 147 ). These may be interesting miRNA players in RMS development and progression, but their specific roles in RMS have not been determined.…”

Section: Oncomir Implicated In Rmsmentioning

confidence: 99%

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Non-coding RNA in rhabdomyosarcoma progression and metastasis

et al. 2022

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Rhabdomyosarcoma (RMS) is a soft tissue sarcoma of skeletal muscle differentiation, with a predominant occurrence in children and adolescents. One of the major challenges facing treatment success is the presence of metastatic disease at the time of diagnosis, commonly associated with the more aggressive fusion-positive subtype. Non-coding RNA (ncRNA) can regulate gene transcription and translation, and their dysregulation has been associated with cancer development and progression. MicroRNA (miRNA) are short non-coding nucleic acid sequences involved in the regulation of gene expression that act by targeting messenger RNA (mRNA), and their aberrant expression has been associated with both RMS initiation and progression. Other ncRNA including long non-coding RNA (lncRNA), circular RNA (circRNA) and ribosomal RNA (rRNA) have also been associated with RMS revealing important mechanistic roles in RMS biology, but these studies are still limited and require further investigation. In this review, we discuss the established roles of ncRNA in RMS differentiation, growth and progression, highlighting their potential use in RMS prognosis, as therapeutic agents or as targets of treatment.

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Section: Oncomir Implicated In Rmsmentioning

confidence: 99%

Section: Oncomir Implicated In Rmsmentioning

confidence: 99%

Non-coding RNA in rhabdomyosarcoma progression and metastasis

et al. 2022

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“…Characterization of the tumor microenvironment while maintaining spatial orientation has become an essential resource for the understanding of complex immune cell interactions and the assessment of biomarkers for prognosis and prediction of immunotherapy response. The Nanostring GeoMx DSP platform [19,20,25] allows for characterization of the tumor microenvironment through high-plex digital quantification of proteins and mRNA from FFPE tissues with spatial resolution [26]. The application of spatial technologies to large numbers of patient samples that are available in pathology archives as FFPE blocks potentially provides unparalleled insight into cell types, cell location, biomarkers, and the interactions that may underlie disease progression.…”

Section: Discussionmentioning

confidence: 99%

Feasibility Study Utilizing NanoString’s Digital Spatial Profiling (DSP) Technology for Characterizing the Immune Microenvironment in Barrett’s Esophagus FFPE Tissues

Ain,

Frei,

Khoshiwal

et al. 2023

Preprint

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To date, characterization of the Barrett’s esophagus (BE) immune microenvironment in patients with known progression status to determine how the microenvironment may influence BE progression to esophageal adenocarcinoma (EAC) has been understudied, hindering both the biological understanding of progression and the development of novel diagnostics and therapies. Therefore, this study’s aim was to determine if highly multiplex interrogation of the immune microenvironment can be performed on endoscopic formalin-fixed, paraffin-embedded (FFPE) samples utilizing the Nanostring GeoMx digital spatial profiling (GeoMx DSP) platform. We performed spatial proteomic analysis of 49 proteins expressed in the microenvironment and epithelial cells of histologically identical FFPE endoscopic biopsies from patients with non-dysplastic BE (NDBE) who later progressed to high-grade dysplasia (HGD) or EAC (N=7) or from patients who after at least 5 years follow up did not (N=8). In addition, we performed RNA analysis of 1,812 cancer related transcripts on a series of three endoscopic mucosal resections containing regions of normal tissue, BE, dysplasia (DYS), and EAC. Our primary goal was to determine feasibility of this approach and begin to identify the types of specific immune cell populations that may mediate the progression of pre-neoplastic BE to EAC. Spatial proteomic and transcriptomic profiling with GeoMx DSP showed reasonable quality metrics and detected expected differences between epithelium and stroma. Several proteins were found to have increased expression within non-dysplastic BE biopsies from progressors compared to non-progressors, suggesting further studies on the BE microenvironment are warranted.SummaryNew biological insights into the stepwise development and progression of esophageal adenocarcinoma (EAC) from Barrett’s esophagus (BE) are imperative to develop tailored approaches for early detection and optimal clinical management of the disease. This study aimed to determine the feasibility to spatially profile stromal and immunologic properties that accompany malignant transformation of BE to EAC in formalin-fixed, paraffin-embedded (FFPE) tissues. NanoString’s Digital Spatial Profiling (DSP) technology can detect and quantify protein and RNA transcripts in a highly multiplexed manner with spatial resolution, within specific regions of interest on FFPE tissue. Here, we performed a pilot study using the Nanostring GeoMx DSP, for measurement of protein and ribonucleic acid (RNA) expression on a series of FFPE slides from endoscopic biopsies and endoscopic mucosal resections (EMR) of BE. We compare a small series of biopsies of non-dysplastic BE (NDBE) from patients who progressed to more advanced disease to patients with NBDE who did not progress and then perform RNA profiling on EMRs with a range of histologic diagnoses.

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“…The DSP assay (NanoString Technologies, Seattle, WA, USA) was performed as previously described [28]. Following tissue rehydration and antigen retrieval, the slide was stained with the 4 morphology markers and 57 quantifiable antibodies (all NanoString Technologies, Seattle, WA, USA).…”

Section: Digital Spatial Profiling (Dsp Nanostring)mentioning

confidence: 99%

Non-Canonical Activin A Signaling Stimulates Context-Dependent and Cellular-Specific Outcomes in CRC to Promote Tumor Cell Migration and Immune Tolerance

Wiley,

Bauer,

Mehrotra

et al. 2023

Cancers

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We have shown that activin A (activin), a TGF-β superfamily member, has pro-metastatic effects in colorectal cancer (CRC). In lung cancer, activin activates pro-metastatic pathways to enhance tumor cell survival and migration while augmenting CD4+ to CD8+ communications to promote cytotoxicity. Here, we hypothesized that activin exerts cell-specific effects in the tumor microenvironment (TME) of CRC to promote anti-tumoral activity of immune cells and the pro-metastatic behavior of tumor cells in a cell-specific and context-dependent manner. We generated an Smad4 epithelial cell specific knockout (Smad4−/−) which was crossed with TS4-Cre mice to identify SMAD-specific changes in CRC. We also performed IHC and digital spatial profiling (DSP) of tissue microarrays (TMAs) obtained from 1055 stage II and III CRC patients in the QUASAR 2 clinical trial. We transfected the CRC cells to reduce their activin production and injected them into mice with intermittent tumor measurements to determine how cancer-derived activin alters tumor growth in vivo. In vivo, Smad4−/− mice displayed elevated colonic activin and pAKT expression and increased mortality. IHC analysis of the TMA samples revealed increased activin was required for TGF-β-associated improved outcomes in CRC. DSP analysis identified that activin co-localization in the stroma was coupled with increases in T-cell exhaustion markers, activation markers of antigen presenting cells (APCs), and effectors of the PI3K/AKT pathway. Activin-stimulated PI3K-dependent CRC transwell migration, and the in vivo loss of activin lead to smaller CRC tumors. Taken together, activin is a targetable, highly context-dependent molecule with effects on CRC growth, migration, and TME immune plasticity.

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NanoString Digital Molecular Profiling of Protein and microRNA in Rhabdomyosarcoma

Cited by 10 publications

References 38 publications

Non-coding RNA in rhabdomyosarcoma progression and metastasis

Non-coding RNA in rhabdomyosarcoma progression and metastasis

Feasibility Study Utilizing NanoString’s Digital Spatial Profiling (DSP) Technology for Characterizing the Immune Microenvironment in Barrett’s Esophagus FFPE Tissues

Non-Canonical Activin A Signaling Stimulates Context-Dependent and Cellular-Specific Outcomes in CRC to Promote Tumor Cell Migration and Immune Tolerance

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