Dataset Information

Quantitative Proteomic Analysis of Optimal Cutting Temperature (OCT) Embedded Core-Needle Biopsy of Lung Cancer.

ABSTRACT: With recent advances in understanding the genomic underpinnings and oncogenic drivers of pathogenesis in different subtypes, it is increasingly clear that proper pretreatment diagnostics are essential for the choice of appropriate treatment options for non-small cell lung cancer (NSCLC). Tumor tissue preservation in optimal cutting temperature (OCT) compound is commonly used in the surgical suite. However, proteins recovered from OCT-embedded specimens pose a challenge for LC-MS/MS experiments, due to the large amounts of polymers present in OCT. Here we present a simple workflow for whole proteome analysis of OCT-embedded NSCLC tissue samples, which involves a simple trichloroacetic acid precipitation step. Comparisons of protein recovery between frozen versus OCT-embedded tissue showed excellent consistency with more than 9200 proteins identified. Using an isobaric labeling strategy, we quantified more than 5400 proteins in tumor versus normal OCT-embedded core needle biopsy samples. Gene ontology analysis indicated that a number of proliferative as well as squamous cell carcinoma (SqCC) marker proteins were overexpressed in the tumor, consistent with the patient's pathology based diagnosis of "poorly differentiated SqCC". Among the most downregulated proteins in the tumor sample, we noted a number of proteins with potential immunomodulatory functions. Finally, interrogation of the aberrantly expressed proteins using a candidate approach and cross-referencing with publicly available databases led to the identification of potential druggable targets in DNA replication and DNA damage repair pathways. We conclude that our approach allows LC-MS/MS proteomic analyses on OCT-embedded lung cancer specimens, opening the way to bring powerful proteomics into the clinic. Graphical Abstract ?.

SUBMITTER: Zhao X

PROVIDER: S-EPMC5693617 | biostudies-literature | 2017 Oct

REPOSITORIES: biostudies-literature

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Quantitative Proteomic Analysis of Optimal Cutting Temperature (OCT) Embedded Core-Needle Biopsy of Lung Cancer.

Zhao Xiaozheng X Huffman Kenneth E KE Fujimoto Junya J Canales Jamie Rodriguez JR Girard Luc L Nie Guangjun G Heymach John V JV Wistuba Igacio I II Minna John D JD Yu Yonghao Y

Journal of the American Society for Mass Spectrometry 20170727 10

With recent advances in understanding the genomic underpinnings and oncogenic drivers of pathogenesis in different subtypes, it is increasingly clear that proper pretreatment diagnostics are essential for the choice of appropriate treatment options for non-small cell lung cancer (NSCLC). Tumor tissue preservation in optimal cutting temperature (OCT) compound is commonly used in the surgical suite. However, proteins recovered from OCT-embedded specimens pose a challenge for LC-MS/MS experiments, ...[more]

PMID: 28752479

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Project description:Accurate pathologic diagnosis and molecular classification of breast mass biopsy tissue is important for determining individualized therapy for (neo)adjuvant systemic therapies for invasive breast cancer. The CassiII rotational core biopsy system is a novel biopsy technique with a guide needle and a "stick-freeze" technology. The comprehensive assessments including the concordance rates of diagnosis and biomarker status between CassiII and core needle biopsy were evaluated in this study. Estrogen receptor (ER), progesterone receptor (PgR), human epidermal growth factor receptor 2 (HER2), and Ki67 were analyzed through immunohistochemistry. In total, 655 patients with breast cancer who underwent surgery after biopsy at Sir Run Run Shaw Hospital between January 2019 to December 2021 were evaluated. The concordance rates (CRs) of malignant surgical specimens with CassiII needle biopsy was significantly high compared with core needle biopsy. Moreover, CassiII needle biopsy had about 20% improvement in sensitivity and about 5% improvement in positive predictive value compared to Core needle biopsy. The characteristics including age and tumor size were identified the risk factors for pathological inconsistencies with core needle biopsies. However, CassiII needle biopsy was associated with tumor diameter only. The CRs of ER, PgR, HER2, and Ki67 using Cassi needle were 98.08% (kappa, 0.941; p<.001), 90.77% (kappa, 0.812; p<.001), 69.62% (kappa, 0.482; p<.001), and 86.92% (kappa, 0.552; p<.001), respectively. Post-biopsy complications with CassiII needle biopsy were also collected. The complications of CassiII needle biopsy including chest stuffiness, pain and subcutaneous ecchymosis are not rare. The underlying mechanism of subcutaneous congestion or hematoma after CassiII needle biopsy might be the larger needle diameter and the effect of temperature on coagulation function. In summary, CassiII needle biopsy is age-independent and has a better accuracy than CNB for distinguishing carcinoma in situ and invasive carcinoma.

Project description:ObjectiveTo evaluate the feasibility and diagnostic performance of ultrasound (US)-guided fine-needle aspiration cytology and core-needle biopsy (US-FNAC/CNB) for the diagnosis of laryngo-hypopharyngeal masses.Materials and methodsThis was a single-center prospective case series. From January 2018 to June 2019, we initially enrolled 40 patients with highly suspicious laryngo-hypopharyngeal masses on laryngoscopic examinations. Of these, 28 patients with the mass involving or abutting the pre-epiglottic, paraglottic, pyriform sinus, and/or subglottic regions were finally included. These patients underwent US examinations with/without subsequent US-FNAC/CNB under local anesthesia for evaluation of the laryngo-hypopharyngeal mass.ResultsOf the 28 patients who underwent US examinations, a laryngo-hypopharyngeal mass was identified in 26 patients (92.9%). US-FNAC/CNB was performed successfully in 25 of these patients (96.2%), while the procedure failed to target the mass in 1 patient (3.8%). The performance of US caused minor subclinical hematoma in 2 patients (7.7%), but no major complications occurred. US-FNAC/CNB yielded conclusive results in 24 (96.0%) out of the 25 patients with a successful procedure, including 23 patients with squamous cell carcinoma (SCC) and 1 patient with a benign mass. In one patient with atypical cells in US-FNAC, additional direct laryngoscopic biopsy (DLB) was required to confirm SCC. Among the 26 patients who received US-FNAC/CNB, the time from first visit to pathological diagnosis was 7.8 days. For 24 patients finally diagnosed with SCC, the time from first visit to the initiation of treatment was 25.2 days. The mean costs associated with US-FNAC/CNB was $272 under the Korean National Health Insurance Service System.ConclusionUS-FNAC/CNB for a laryngo-hypopharyngeal mass is technically feasible in selected patients, providing good diagnostic performance. This technique could be used as a first-line diagnostic modality by adopting appropriate indications to avoid general anesthesia and DLB-related complications.

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Dataset Information

Quantitative Proteomic Analysis of Optimal Cutting Temperature (OCT) Embedded Core-Needle Biopsy of Lung Cancer.

Publications

Quantitative Proteomic Analysis of Optimal Cutting Temperature (OCT) Embedded Core-Needle Biopsy of Lung Cancer.

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