Comparative studies of two generations of NanoString nCounter System

Yu, Lianbo; Bhayana, Sagar; Jacob, Naduparambil K.; Fadda, Paolo

doi:10.1371/journal.pone.0225505

Cited by 7 publications

(6 citation statements)

References 9 publications

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“…Our methods could be applied successfully on long-term archived fecal sample sets, originally collected for testing fecal blood, to stratify patients and could be used for microbiome-based early biomarker discovery for gut health (Rounge et al 2018 ). Of note, this is the first time that direct hybridization with n-counter flex DX platform was applied to microbiome studies and although second generation of platform already exists, both produced equivalent signals and signal deviations (Yu et al 2019 ). Finally, it is important to underline that using two different n-counter flex machines, we obtained similar results ( p > 0.05) showing both, reproducibility and robustness of the n-counter technology.…”

Section: Resultsmentioning

confidence: 99%

Dysbiosis in intestinal microbiome linked to fecal blood determined by direct hybridization

Cafiero

Pisconti

et al. 2020

3 Biotech

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The important physiological and pathophysiological roles of intestinal human microbiome (HMB) in human health have been emerging, owing to the access to molecular biology techniques. Herein we evaluated, for the first time, the intestinal HMB through direct hybridization approach using n-counter flex DX technology which bypasses the amplification procedure currently applied by other technologies to study the human microbiome. To this purpose, a clinical study was carried out on fecal samples, recruiting both healthy volunteers (N-FOB) and subjects positive for occult blood (P-FOB). A relevant custom panel of 79 16S rRNA target gene was engineered and 32 of them displayed a variation between the two clusters of subjects. Our findings revealed that bacteria belonging to Proteobacteria have higher distribution in P-FOB describing dysbiosis. Similarly, Bacteroidetes and Firmicutes phylum display high distribution in P-FOB. Of interest, the presence of Clostridium difficile that belongs to Firmicutes phylum displayed about 70% of low presence in N-FOB compared to P-FOB subjects. Only one bacterium belonging to the Actinobacteria phylum, the Bifidobacterium bifidum, was present.

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Section: Resultsmentioning

confidence: 99%

Dysbiosis in intestinal microbiome linked to fecal blood determined by direct hybridization

Cafiero

Pisconti

et al. 2020

3 Biotech

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“…Subsequently, the nCounter FLEX instrument quantified the gene expression levels by scanning 490 fields of view. 57 The raw gene expression data underwent quality checks, followed by normalization and log2 transformation using the Advanced Analysis module (v2.0) of NanoString nSolver software (v4.0). 58 Normalization was conducted using the geNorm algorithm based on the stable housekeeping genes.…”

Section: Methodsmentioning

confidence: 99%

GATA6 identifies an immune-enriched phenotype linked to favorable outcomes in patients with pancreatic cancer undergoing upfront surgery

van Eijck,

Real,

Malats

et al. 2024

Cell Reports Medicine

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“…RNA samples of 200 ng/5-7 uL were hybridized to target probes for 17 hours at 65°C. RNA expression levels were measured using the nCounter ® FLEX Instrument ( 31 ). The counting of the genes was done by scanning 490 Fields Of Views (FOV).…”

Section: Methodsmentioning

confidence: 99%

Spatial genomics reveals a high number and specific location of B cells in the pancreatic ductal adenocarcinoma microenvironment of long-term survivors

et al. 2023

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Background and aimOnly 10% of pancreatic ductal adenocarcinoma (PDAC) patients survive longer than five years. Factors underlining long-term survivorship in PDAC are not well understood. Therefore, we aimed to identify the key players in the tumor immune microenvironment (TIME) associated with long-term survivorship in PDAC patients.MethodsThe immune-related gene expression profiles of resected PDAC tumors of patients who survived and remained recurrence-free of disease for ≥36 months (long-term survivors, n=10) were compared to patients who had survived ≤6 months (short-term survivors, n=10) due to tumor recurrence. Validation was performed by the spatial protein expression profile of immune cells using the GeoMx™ Digital Spatial Profiler. An independent cohort of samples consisting of 12 long-term survivors and 10 short-term survivors, was used for additional validation. The independent validation was performed by combining qualitative immunohistochemistry and quantitative protein expression profiling.ResultsB cells were found to be significantly increased in the TIME of long-term survivors by gene expression profiling (p=0.018). The high tumor infiltration of B cells was confirmed by spatial protein profiling in the discovery and the validation cohorts (p=0.002 and p=0.01, respectively). The higher number of infiltrated B cells was found mainly in the stromal compartments of PDAC samples and was exclusively found within tumor cells in long-term survivors.ConclusionThis is the first comprehensive study that connects the immune landscape of gene expression profiles and protein spatial infiltration with the survivorship of PDAC patients. We found a higher number and a specific location of B cells in TIME of long-term survivors which emphasizes the importance of B cells and B cell-based therapy for future personalized immunotherapy in PDAC patients.

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Comparative studies of two generations of NanoString nCounter System

Cited by 7 publications

References 9 publications

Dysbiosis in intestinal microbiome linked to fecal blood determined by direct hybridization

Dysbiosis in intestinal microbiome linked to fecal blood determined by direct hybridization

GATA6 identifies an immune-enriched phenotype linked to favorable outcomes in patients with pancreatic cancer undergoing upfront surgery

Spatial genomics reveals a high number and specific location of B cells in the pancreatic ductal adenocarcinoma microenvironment of long-term survivors

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