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Inform eber probe

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The INFORM EBER probe is a laboratory equipment product designed for in situ hybridization analysis. It is used to detect the presence of Epstein-Barr virus-encoded small RNA (EBER) in tissue samples.

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Close spelling variants of this product

EBER probe (8 citations) INFORM EBER (2 citations)

36 protocols using inform eber probe

1

EBV Status Determination by ISH

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EBV status was determined by Epstein-Barr virus-encoded Early RNA (EBER) in situ hybridization (ISH) on the samples, brushes or TMA. Ventana BenchMark automated staining instruments (Ventana Medical systems, Tuscon, AZ, USA) were used for ISH of the samples or TMA using an EBV-specific probe (INFORM EBER PROBE; Ventana Medical systems) and ISH iVIEW Blue detection kit (Ventana Medical systems, Inc.) for staining using the manufacturer’s instructions in Innsbruck, Utrecht, Hong Kong, Stanford and London. Shenzhen used an EBER Probe (Zhongshan Jinquaiao Biotechnology Co.; Beijing, China) and an autostainer (Ventana Medical Systems, Inc.) to perform ISH. Singapore used a BONDTM Ready-to-use ISH EBER probe and a Leica Bond-Max autostainer (all Leica Biosystems, Wetzlar, Germany) for this purpose. In situ hybridization of xenografts and cell pellets was done using an EBV-specific probe (INFORM EBER PROBE; Ventana Medical systems) and ISH iVIEW Blue detection kit (Ventana Medical systems, Inc.) using the manufacturer’s instructions.
Lechner M., Schartinger V.H., Steele C.D., Nei W.L., Ooft M.L., Schreiber L.M., Pipinikas C.P., Chung G.T., Chan Y.Y., Wu F., To K.F., Tsang C.M., Pearce W., Morelli D., Philpott M., Masterson L., Nibhani R., Wells G., Bell C.G., Koller J., Delecluse S., Yip Y.L., Liu J., Forde C.T., Forster M.D., Jay A., Dudás J., Krapp A., Wan S., Uprimny C., Sprung S., Haybaeck J., Fenton T.R., Chester K., Thirlwell C., Royle G., Marafioti T., Gupta R., Indrasari S.R., Herdini C., Slim M.A., Indrawati I., Sutton L., Fles R., Tan B., Yeong J., Jain A., Han S., Wang H., Loke K.S., He W., Xu R., Jin H., Cheng Z., Howard D., Hwang P.H., Le Q.T., Tay J.K., West R.B., Tsao S.W., Meyer T., Riechelmann H., Oppermann U., Delecluse H.J., Willems S.M., Chua M.L., Busson P., Lo K.W., Wollmann G., Pillay N., Vanhaesebroeck B, & Lund V.J. (2021). Somatostatin receptor 2 expression in nasopharyngeal cancer is induced by Epstein Barr virus infection: impact on prognosis, imaging and therapy. Nature Communications, 12, 117.
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2

EBER-ISH Staining Procedure for Detection

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Biopsy specimens were fixed in formalin, dehydrated, embedded in paraffin, and sectioned with routine methods. The INFORM EBER probe (Ventana Medical Systems, Tucson, AZ, USA) was used for EBER‐ISH. Slides were stained on an automated stainer (Benchmark XT; Ventana Medical Systems), and for visualization the ISH iView Blue Detection Kit (Ventana Medical Systems) with alkaline phosphatase and NBT/BCIP substrate was used, with Nuclear Fast Red (Ventana Medical Systems) for contrast. Specimens in which nuclear expression of EBER was observed in 20% or more of the malignant cells were considered EBER‐positive.15
Okamoto A., Yanada M., Miura H., Inaguma Y., Tokuda M., Morishima S., Kanie T., Yamamoto Y., Mizuta S., Akatsuka Y., Yoshikawa T., Mizoguchi Y., Nakamura S., Okamoto M, & Emi N. (2015). Prognostic significance of Epstein–Barr virus DNA detection in pretreatment serum in diffuse large B‐cell lymphoma. Cancer Science, 106(11), 1576-1581.
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3

Detection of EBV by ISH Staining

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According to the manufacturer’s instruction, EBV was detected by in-situ-hybridization (ISH) using the INFORM EBER probe (Ventana Medical Systems, Inc., Tucson, AZ, USA). The slides were stained using an automated stainer (Benchmark Ultra, Ventana Medical Systems, Inc., Tucson, AZ, USA). The visualization was by ISH iView Blue Detection kit (Ventana Medical Systems, Inc., Tucson, AZ, USA) with alkaline phosphatase 5-bromo-4-chloro-3-indolyl phosphate/nitro blue tetrazolium (BCIP NBT/) substrate. Nuclear Fast red (Ventana Medical Systems, Inc., Tucson, AZ, USA) was used as a contrast. Appropriate positive and negative controls were set up parallel to the section analyzed.
Uzoma I.C., Taiwo I.A., Granai M., Di Stefano G., Sorrentino E., Mannucci S., Durosinmi M.A., Lazzi S., Leoncini L, & Akinloye O. (2021). Distinct pattern of lymphoid neoplasms characterizations according to the WHO classification (2016) and prevalence of associated Epstein–Barr virus infection in Nigeria population. Infectious Agents and Cancer, 16, 36.
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4

Evaluating Tumor Molecular Markers

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EBV-encoded RNA (EBER) in situ hybridization (ISH) was performed using INFORM EBER Probe (Ventana, Tucson, AZ, USA) [14 (link)]. A tumor was considered to be EBER-positive if the signal was observed in 20% or more of the tumor cells. The results of EBER ISH were assessed by two independent specialists blinded to each other.
The microsatellite instable (MSI) status of the PDX models was evaluated by the expression of mismatch repair (MMR) proteins by immunohistochemical analysis. Monoclonal antibodies specific for MLH1, PMS2, MSH2, and MSH6 were obtained from GeneTech, Inc., Shanghai, China. As positive controls stromal cells were used. The loss of MMR protein expression was defined as the absence of nuclear staining in neoplastic epithelial cells. The IHC results were assessed by two independent specialists blinded to each other.
Chen Z., Huang W., Tian T., Zang W., Wang J., Liu Z., Li Z., Lai Y., Jiang Z., Gao J, & Shen L. (2018). Characterization and validation of potential therapeutic targets based on the molecular signature of patient-derived xenografts in gastric cancer. Journal of Hematology & Oncology, 11, 20.
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5

EBER and SLAMF8 expression analysis

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EBV‐encoded RNA (EBER) was detected via chromogenic in situ hybridisation using fluorescein‐labelled oligonucleotide probes (INFORM EBER Probe, Ventana, Cambridgeshire, England). EBER positivity was defined when >20% of the tumor cells were stained for EBER. The RNA scope 2.5 An HD reagent kit was used for the ISH assay (ACD, California, USA) according to the manufacturer’s instructions, with the murine SLAMF8 probe (catalogue #571981, ACD, California, USA) used as a target probe for hybridisation and the other two probes used as positive (catalogue #313911, ACD, California, USA) and negative control probes (catalogue #310043, ACD, California, USA). The average SLAMF8 density was calculated by FiJi ImageJ software using the manufacturer’s instructions.
Zhang Q., Cheng L., Qin Y., Kong L., Shi X., Hu J., Li L., Ding Z., Wang T., Shen J., Yang Y., Yu L., Liu B., Liu C, & Qian X. (2021). SLAMF8 expression predicts the efficacy of anti‐PD1 immunotherapy in gastrointestinal cancers. Clinical & Translational Immunology, 10(10), e1347.
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6

EBV-Encoded Small RNA Detection

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Chromogenic in situ hybridization with EBV-encoded small RNA (EBER) was performed to detect EBV infection using fluorescein-labeled oligonucleotide probes (INFORMEBER Probe; Ventana). Specimen in which EBER nuclear expression was observed in >20% of the tumor cells were considered EBER positive.
Ge S., Xia X., Ding C., Zhen B., Zhou Q., Feng J., Yuan J., Chen R., Li Y., Ge Z., Ji J., Zhang L., Wang J., Li Z., Lai Y., Hu Y., Li Y., Li Y., Gao J., Chen L., Xu J., Zhang C., Jung S.Y., Choi J.M., Jain A., Liu M., Song L., Liu W., Guo G., Gong T., Huang Y., Qiu Y., Huang W., Shi T., Zhu W., Wang Y., He F., Shen L, & Qin J. (2018). A proteomic landscape of diffuse-type gastric cancer. Nature Communications, 9, 1012.
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7

EBER In Situ Hybridization of Xenografts

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Pieces of C666-1 and C17 xenografts were fixed in 4% paraformaldehyde, paraffin-embedded and cut in 4 µM sections. EBER detection was performed by in situ hybridization using the INFORM EBER Probe (specific of the EBER1 RNA) and the i-VIEW Blue Detection Kit from Ventana-Roche (Ref 800–2842 and 800-092 respectively)(Tucson, AZ, USA).
Gressette M., Vérillaud B., Jimenez-Pailhès A.S., Lelièvre H., Lo K.W., Ferrand F.R., Gattolliat C.H., Jacquet-Bescond A., Kraus-Berthier L., Depil S, & Busson P. (2014). Treatment of Nasopharyngeal Carcinoma Cells with the Histone-Deacetylase Inhibitor Abexinostat: Cooperative Effects with Cis-platin and Radiotherapy on Patient-Derived Xenografts. PLoS ONE, 9(3), e91325.
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8

In Situ Detection of EBV-encoded RNAs

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In situ hybridization for detection of the EBV-encoded small RNAs (EBER) was performed using the INFORM EBER Probe (Ventana/ROCHE, Tucson, AZ, US). The technique was carried out in the BenchMark Ultra (Ventana/ROCHE) platform according to the manufacturer’s instructions, as previously described [20 (link)].
Lo Bello G., Akarca A.U., Ambrosio M.R., Agostinelli C., Molina-Kirsch H., Ramsay A., Rodriguez-Justo M., Pugh M., Zhao S., DeLisser M., Sabattini E., Dojcinov S., Pileri S.A., Natkunam Y., Leoncini L, & Marafioti T. (2018). Granulysin, a novel marker for extranodal NK/T cell lymphoma, nasal type. Virchows Archiv, 473(6), 749-757.
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9

EBER Detection via Chromogenic In-Situ Hybridization

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EBV-encoded RNA (EBER) was detected via chromogenic in-situ hybridization using fluorescein-labeled oligonucleotide probes (INFORM EBER Probe, Ventana). When >20% of the tumor cells showed staining for EBER, the case was defined as EBER positive.
Jin S., Xu B., Yu L., Fu Y., Wu H., Fan X., Wei J, & Liu B. (2017). The PD-1, PD-L1 expression and CD3+ T cell infiltration in relation to outcome in advanced gastric signet-ring cell carcinoma, representing a potential biomarker for immunotherapy. Oncotarget, 8(24), 38850-38862.
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10

In Situ Detection of EBV-encoded RNA

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EBV-encoded small RNA was analyzed through in situ hybridization of EBER genes 1 and 2 with an inform EBER probe (Ventana Medical Systems, Tucson, USA) according to the manufacturer’s protocol. The intended target is the early RNA transcripts of EBV accumulate in the nucleus of EBV-infected cells, as evaluated by a blue reaction that is localized to EBV-infected nuclei. Positive hybridization was defined as punctuate or diffuse signals in the nucleus of the tumor cells. An appropriate positive control was used in all cases.
Hu C., Lin L., Ye M., Liu Y., Huang Q., Yuan C., Sun J, & Sun H. (2024). Re-evaluating a historic cohort of sinonasal and skull base mucoepidermoid carcinoma: an institutional experience. Diagnostic Pathology, 19, 46.
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