scholarly journals NanoString technology distinguishes anti‐TIF‐1γ + from anti‐Mi‐2 + dermatomyositis patients

2021 ◽  
Vol 31 (3) ◽  
Author(s):  
Corinna Preusse ◽  
Pascale Eede ◽  
Lucie Heinzeling ◽  
Kiara Freitag ◽  
Randi Koll ◽  
...  
Keyword(s):  
Nanostring Technology

scholarly journals Nanostring technology on Fibrous Dysplasia bone biopsies. A pilot study suggesting different histology-related molecular profiles

Bone Reports ◽  
2022 ◽  
Vol 16 ◽  
pp. 101156
Author(s):  
Agnese Persichetti ◽  
Edoardo Milanetti ◽  
Biagio Palmisano ◽  
Annamaria di Filippo ◽  
Emanuela Spica ◽  
...  
Keyword(s):  
Pilot Study ◽  
Fibrous Dysplasia ◽  
Bone Biopsies ◽  
Molecular Profiles ◽  
Nanostring Technology

Sarcoma Subgrouping by Detection of Fusion Transcripts Using NanoString nCounter Technology

2018 ◽  
Vol 22 (3) ◽  
pp. 205-213 ◽  
Author(s):  
Javal Sheth ◽  
Anthony Arnoldo ◽  
Yunan Zhong ◽  
Paula Marrano ◽  
Carlos Pereira ◽  
...  
Keyword(s):  
Rt Pcr ◽  
Fusion Transcripts ◽  
Pediatric Sarcoma ◽  
Formalin Fixed Paraffin ◽  
Pediatric Sarcomas ◽  
Formalin Fixed Paraffin Embedded ◽  
Ffpe Tissues ◽  
Nanostring Technology ◽  
Future Work ◽  
Formalin Fixed

Background NanoString technology is an innovative barcode-based system that requires less tissue than traditional techniques and can test for multiple fusion transcripts in a single reaction. The objective of this study was to determine the utility of NanoString technology in the detection of sarcoma-specific fusion transcripts in pediatric sarcomas. Design Probe pairs for the most common pediatric sarcoma fusion transcripts were designed for the assay. The NanoString assay was used to test 22 specific fusion transcripts in 45 sarcoma samples that had exhibited one of these fusion genes previously by reverse transcription polymerase chain reaction (RT-PCR). A mixture of frozen (n = 18), formalin-fixed, paraffin-embedded (FFPE) tissue (n = 23), and rapid extract template (n = 4) were used for testing. Results Each of the 22 transcripts tested was detected in at least one of the 45 tumor samples. The results of the NanoString assay were 100% concordant with the previous RT-PCR results for the tumor samples, and the technique was successful using both FFPE and rapid extract method. Conclusion Multiplexed interrogation for sarcoma-specific fusion transcripts using NanoString technology is a reliable approach for molecular diagnosis of pediatric sarcomas and works well with FFPE tissues. Future work will involve validating additional sarcoma fusion transcripts as well as determining the optimal workflow for diagnostic purposes.

Benefits of platinum-based chemotherapy (Pt-chemo) in pancreatic adenocarcinoma (PC) associated with BRCA mutations:  A translational case series.

2012 ◽  
Vol 30 (15_suppl) ◽  
pp. 4058-4058 ◽  
Author(s):  
Olusola Olusesan Faluyi ◽  
Ben Tran ◽  
Zaheer Kanji ◽  
Sara Moore ◽  
George Zogopoulos ◽  
...  
Keyword(s):  
Gene Expression ◽  
Survival Data ◽  
Case Reports ◽  
Locally Advanced ◽  
Case Series ◽  
Brca Mutations ◽  
Platinum Based Chemotherapy ◽  
Gene Expression Studies ◽  
Nanostring Technology ◽  
Clinical Records

4058 Background: The prognosis of PC is poor with limited response to standard chemotherapy. Prior randomized studies of cisplatin and gemcitabine in PC demonstrated no additional benefit over gemcitabine alone. Preclinical data and case reports suggest that BRCA mutant PC may have increased sensitivity to Pt-chemo. Our case series characterizes the benefits of Pt-chemo in germline BRCA mutant PC. Methods: Patients with PC and germline BRCA mutations were identified using the Ontario Pancreatic Cancer Study and Pharmacy databases. Review of clinical records provided demographic, treatment and survival data. Radiology review assessed responses to chemotherapy. RNA was extracted from tumor samples for gene expression studies using a panel of DNA repair genes and Nanostring technology. BRCA loss of heterozygosity (LOH) was also investigated. Results: We identified 14 PC patients with BRCA mutations (8 BRCA2, 6 BRCA1). 11 of these had metastatic disease of which 5 received Pt-chemo. Of the 5 treated with Pt-chemo, there were 3 partial responses (PR) and 2 complete responses (CR) using Recist criteria. For the remaining 6 not treated with Pt-chemo, there was 1 PR with gemcitabine. Additionally, two patients with locally advanced disease at diagnosis became resectable following Pt-chemo. Overall survival was superior for patients receiving Pt-chemo (33.0±25.6 vs 7.3±4.5 months; p=0.04). Gene expression and LOH results will be presented. Conclusions: Responses and survival associated with Pt-chemo observed in our case series of BRCA mutant PC adds to existing data supporting the use of Pt-chemo in this subgroup. Despite the low (2 to 5%) prevalence of BRCA mutations in PC, the benefits gained from personalizing treatment using Pt-chemo supports BRCA testing in selected patients.

Dynamic of molecular subtypes of high‐grade serous ovarian cancer in paired primary and relapsed biopsies.

2019 ◽  
Vol 37 (15_suppl) ◽  
pp. e17091-e17091
Author(s):  
Elena Ioana Braicu ◽  
Hagen Kulbe ◽  
Felix Dreher ◽  
Eliane T Taube ◽  
Frauke Ringel ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
Clinical Outcome ◽  
Molecular Subtypes ◽  
Molecular Subtype ◽  
High Grade ◽  
Serous Ovarian Cancer ◽  
Microarray Gene Expression ◽  
Tissue Samples ◽  
Paired Samples ◽  
Nanostring Technology

e17091 Background: Previously four molecular subtypes of high grade serous ovarian cancer (HGSOC) with distinct biological features and clinical outcome have been described: C1 (mesenchymal), C2 (immunoreactive), C4 (differentiated), and C5 (proliferative). Using Nanostring technique and a minimal signature of 39 classifier genes could reproduce the subtypes identified by microarray gene expression profiling (Leong HS et al. Australian Ovarian Cancer Study. J Pathol. 2015). Methods: We characterized paraffin embedded tissue samples from 279 HGSOC patients for molecular subtypes, utilizing the 39 classifier signature and 9 control genes by Nanostring nCounter Analysis System. From 16 patients paired primary and relapsed samples were available. Only chemonaive primary HGSOC patients were included in the study. FFPEs and clinical data were provided by TOC ( www.toc-network.de ). For each sample, probability scores for the four molecular subtypes (C1, C2, C4, and C5) were calculated. The highest calculated score determined the most likely subtype of the tumor. Results: Of all analyzed primary tumor samples, 88 (31.5%) were classified as C1, 83 (29.8%), 53 (19.0%) and 55 (19.7%) as subtypes C2, C4 and C5, respectively. Our results confirmed data by the AOCS study, which described the distribution of HGSOC with 40.2% (C1), 22.5% (C2), 20.1% (C4) and 17.2% (C5), respectively. Within the paired samples, for 12 of the 16 patients dynamic changes in the molecular subtypes between primary and relapse occurred, while in the remaining 4 patients the phenotype was stable. Conclusions: Molecular subtypes of HGSOC using Nanostring technology with a small panel of classifier genes can be confirmed. Furthermore, the data showed that a change of the established molecular subtype might occur during the evolution of the disease, and therefore translate in a different clinical outcome.

scholarly journals Global Analysis of the Zinc Homeostasis Network in Pseudomonas aeruginosa and Its Gene Expression Dynamics

2021 ◽  
Vol 12 ◽  
Author(s):  
Verena Ducret ◽  
Melina Abdou ◽  
Catarina Goncalves Milho ◽  
Sara Leoni ◽  
Oriane Martin--Pelaud ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Bacterial Infections ◽  
Global Analysis ◽  
Opportunistic Pathogen ◽  
Zinc Homeostasis ◽  
Protein Levels ◽  
Its Gene ◽  
Zn Homeostasis ◽  
Gene Expression Dynamics ◽  
Nanostring Technology

Zinc is one of the most important trace elements for life and its deficiency, like its excess, can be fatal. In the bacterial opportunistic pathogen Pseudomonas aeruginosa, Zn homeostasis is not only required for survival, but also for virulence and antibiotic resistance. Thus, the bacterium possesses multiple Zn import/export/storage systems. In this work, we determine the expression dynamics of the entire P. aeruginosa Zn homeostasis network at both transcript and protein levels. Precisely, we followed the switch from a Zn-deficient environment, mimicking the initial immune strategy to counteract bacterial infections, to a Zn-rich environment, representing the phagocyte metal boost used to eliminate an engulfed pathogen. Thanks to the use of the NanoString technology, we timed the global silencing of Zn import systems and the orchestrated induction of Zn export systems. We show that the induction of Zn export systems is hierarchically organized as a function of their impact on Zn homeostasis. Moreover, we identify PA2807 as a novel Zn resistance component in P. aeruginosa and highlight new regulatory links among Zn-homeostasis systems. Altogether, this work unveils a sophisticated and adaptive homeostasis network, which complexity is key in determining a pathogen spread in the environment and during host-colonization.

scholarly journals Prognostication of Diffuse Large B-Cell Lymphoma By Lympho2Cx Assay and BCL2 and MYC Expression: Application in a Real Life Context of 154 Patients

Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 5308-5308
Author(s):  
Stefania Bettelli ◽  
Raffaella Marcheselli ◽  
Samantha Manfredini ◽  
Alessia Bari ◽  
Samantha Pozzi ◽  
...  
Keyword(s):  
Cell Lymphoma ◽  
Real Life ◽  
B Cell Lymphoma ◽  
Protein Overexpression ◽  
Large B Cell Lymphoma ◽  
Life Context ◽  
Bcl2 Protein ◽  
Nanostring Technology ◽  
Large B Cell

Abstract BACKGROUND: About one third of patients with diffuse large B-cell lymphoma (DLBCL) eventually die from their disease. Thus, it is extremely important to identify powerful and reliable predictive and prognostic markers. In real life patient management, the clinical relevance of the assessment of the Cell of Origin (COO), of MYC and BCL2 protein overexpression, is still not fully clarified. The aim of the study is to evaluate the predictive and prognostic value of COO with Lympho2Cx assay by Nanostring technology and BCL2 and MYC overexpression by immunohistochemistry (IHC), in a real-life context. METHODS: This is a retrospective multicenter study which recruited 154 DLBCL patients treated with R-containing regimen between June 2010 and December 2016 in Modena, Rome (Italy) and Haifa (Israel). All clinical data were recorded at diagnosis and during follow up, including response assessment and survival outcome. COO was determined on formalin-fixed paraffin-embedded diagnostic specimens either by IHC using a panel of antibodies which included CD10, BCL6, MUM1 (i.e. Hans algorithm), or at RNA level with Lymph2Cx assay by Nanostring technology. Expression of MYC and BCL2 was evaluated by IHC. Event free survival (EFS) is defined as the time from diagnosis to the time of last follow-up, or to one of the following events: any response other than complete remission (CR) at the end of therapy or death from any cause. It is assessed by Kaplan-Meier estimates and groups of risk are compared using the log rank test. RESULT: We have currently evaluated the data of 60% (95 out of the 154) of the patients enrolled in the study (Tab 1). After a median follow up of 49 months, EFS is 63% (95CI 51-72%). In univariate analysis, the variables with the greatest impact on the response and on EFS are absolute granulocyte count and BCL2 expression (MYC ongoing). Patients with low IPI showed better survival in comparison with patients with high IPI, but the difference is not statistically significant. By IHC non-GCB subtype was more common than GCB (56% vs. 44%); by Nanostring ABC, GCB and unclassified subtypes were 33%, 50% and 17%, respectively, and K statistics was 0,647, showing a substantial agreement between the results obtained by IHC and by Lympho2Cx assay. No statistically significant differences were observed in EFS among ABC, GCB and unclassified subtypes. However, BCL2 protein overexpression in ABC subtype is associated with shorter EFS. CONCLUSION: Early retrospective studies showed a survival advantage for GCB-type disease. Clinical trial data evaluating the impact of COO determined by GEP on prognosis have shown inconsistent results with 2 studies observing inferior survival of ABC subtype and 2 German studies showing no significant differences in PFS or OS among COO subtypes. Determination of COO by Lympho2Cx is attractive as it is relatively easy and rapid to perform and potentially applicable to clinical practice. However, these preliminary results do not support, at this point, its use as prognostic factor in clinical practice. The analysis of the remaining 59 patients will help to clarify the role Lympho2Cx assay in the context of real life. Table 1. Patients baseline characteristics. Disclosures Tadmor: ABBVIE: Consultancy; ROCHE: Research Funding; JNJ: Consultancy; NOVARTIS: Consultancy; PFIEZER: Consultancy.

scholarly journals The mutational load and a T-cell inflamed tumor phenotype identify ovarian cancer patients rendering tumor-reactive T cells from PD-1+ tumor-infiltrating lymphocytes

2020 ◽  
Author(s):  
Diego Salas-Benito ◽  
Enrique Conde ◽  
Ibon Tamayo-Uria ◽  
Uxua Mancheño ◽  
Edurne Elizalde ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
T Cells ◽  
T Cell ◽  
Predictive Biomarkers ◽  
Tumor Infiltrating Lymphocytes ◽  
Ovarian Tumors ◽  
Autologous Tumor ◽  
Tumor Mutational Burden ◽  
Nanostring Technology ◽  
Infiltrating Lymphocytes

Abstract Background: Adoptive immunotherapy with tumor-infiltrating lymphocytes (TIL) may benefit from the use of selective markers, such as programmed cell death protein 1 (PD-1), for tumor-specific T-cell enrichment, as well as predictive biomarkers that help identify those patients capable of rendering tumor-reactive TIL products. We have investigated this in ovarian cancer (OC) patients as candidate for TIL therapy implementation. Methods: PD-1- and PD-1+ CD8 TILs were isolated from resected ovarian tumors and, after polyclonal expansion, TIL products were tested against autologous tumor cells. Reactivity was assessed by IFNg production (ELISPOT) and upregulation of CD137. Baseline tumor samples were examined using flow cytometry, multiplexed quantitative immunofluorescence, Nanostring technology, for gene expression profile (GEP) analyses, as well as a next generation sequencing gene panel, for tumor mutational burden (TMB) calculation, to identify those features that distinguished patients with tumor-reactive and non-tumor-reactive TIL products.Results: Tumor-reactive TILs were detected in half of patients and were exclusively present in cells derived from the PD-1+ fraction. Flow-cytometric studies revealed that fresh tumors from patients rendering tumor-reactive TILs presented a significantly higher frequency of CD137+ cells within the PD1+CD8+ subset. Multiplexed immunofluorescence supported this finding, which was particularly striking in intraepithelial CD8 TILs. Baseline GEP analysis showed that patients rendering tumor-reactive TILs exhibited a significantly higher T-cell inflamed signature. Despite no correlation between TMB and GEP, both parameters stratified tumors, with patients with higher TMB and/or T-cell inflamed signature score rendering tumor-reactive TILs. Conclusion: We have demonstrated that PD-1 identifies autologous-tumor specific CD8 T cells infiltrating ovarian tumors and have uncovered predictive factors that identify OC patients who are likely to render tumor-reactive cells from PD-1+ TILs. These findings have important implications for improving the efficacy of TIL therapy in OC.

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