scholarly journals Proteomic analysis identifies deregulated metabolic and oxidative-associated proteins in Italian intrahepatic cholangiocarcinoma patients

BMC Cancer ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Giuliana Cavalloni ◽  
Caterina Peraldo-Neia ◽  
Annamaria Massa ◽  
Carlo Bergamini ◽  
Alessandro Trentini ◽  
...  
Keyword(s):  
Intrahepatic Cholangiocarcinoma ◽  
Cell Structure ◽  
Duct Cell ◽  
Molecular Classification ◽  
Antioxidant Systems ◽  
2D Electrophoresis ◽  
Proteomic Data ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Associated Proteins

Abstract Background Cholangiocarcinoma (CCA) is an aggressive disease with poor prognosis. A molecular classification based on mutational, methylation and transcriptomic features could allow identifying tailored therapies to improve CCA patient outcome. Proteomic remains partially unexplored; here, we analyzed the proteomic profile of five intrahepatic cholangiocarcinoma (ICC) derived from Italian patients undergone surgery and one normal bile duct cell line. Methods Proteome profile was investigated by using 2D electrophoresis followed by Mass Spectrometry (MS). To validate proteomic data, the expression of four overexpressed proteins (CAT, SOD, PRDX6, DBI/ACBP) was evaluated by immunohistochemistry in an independent cohort of formalin fixed, paraffin-embedded (FFPE) ICC tissues. We also compared proteomic data with those obtained by transcriptomic profile evaluated by microarray analysis of the same tissues. Results We identified 19 differentially expressed protein spots, which were further characterized by MS; 13 of them were up- and 6 were down-regulated in ICC. These proteins are mainly involved in redox processes (CAT, SODM, PRDX2, PRDX6), in metabolism (ACBP, ACY1, UCRI, FTCD, HCMS2), and cell structure and organization (TUB2, ACTB). CAT is overexpressed in 86% of patients, PRDX6 in 73%, SODM in 100%, and DBI/ACBP in 81% compared to normal adjacent tissues. A concordance of 50% between proteomic and transcriptomic data was observed. Conclusions This study pointed out that the impairment of the metabolic and antioxidant systems, with a subsequent accumulation of free radicals, might be a key step in CCA development and progression.

scholarly journals Intrahepatic Cholangiocarcinoma: Genomic Heterogeneity Between Eastern and Western Patients

2020 ◽  
pp. 557-569 ◽  
Author(s):  
Jingyu Cao ◽  
Jing Hu ◽  
Siqin Liu ◽  
Funda Meric-Bernstam ◽  
Reham Abdel-Wahab ◽  
...  
Keyword(s):  
Dna Repair ◽  
Intrahepatic Cholangiocarcinoma ◽  
Checkpoint Inhibitors ◽  
Asian Population ◽  
Asian Patients ◽  
Formalin Fixed Paraffin ◽  
Mutation Burden ◽  
Formalin Fixed Paraffin Embedded ◽  
Comprehensive Genomic Profiling ◽  
Ngs Data

PURPOSE Intrahepatic cholangiocarcinoma (IHCCA), a global health problem, is increasing in incidence and has differing etiologies worldwide. Next-generation sequencing (NGS) is rapidly being incorporated into the clinical management of biliary cancers. IHCCA is enriched with actionable mutations, and there are several promising targeted therapies under development. NGS data from Asia, where IHCCA is most prevalent, are limited. METHODS Comprehensive genomic profiling of formalin-fixed paraffin-embedded tumor tissue from 164 Asian and 283 Western patients with IHCCA was performed using NGS. We measured the distribution of DNA repair genetic aberrations (GAs) in IHCCA, along with actionable mutations. Also, we evaluated the association between DNA repair GAs and tumor mutation burden (TMB). Based on the TMB status, patients were distinguished into 3 levels: low (< 6 mut/Mb), intermediate (6-10 mut/Mb), and high (TMB-H; ≥ 10 mut/Mb). RESULTS Seventy-two percent of Asian patients had ≥ 1 actionable GA, with a significantly higher frequency in KMT2C , BRCA1/2, and DDR2 compared with Western patients ( P = .02, .003, and .003, respectively); 60.9% of Western patients had ≥ 1 actionable GA and higher frequency of CDKN2A/B and IDH1/2 GAs ( P = .0004 and < .001, respectively). GAs in nuclear factor kappa B pathway regulators and DNA repair genes occurred more frequently in Asian patients ( P = .006 and .001, respectively). There was a higher frequency of TMB-H in Asian compared with the Western cohort (12.2% v 5.9%; P = .07). CONCLUSION A higher burden of DNA repair mutations and frequency of patients with TMB-H in the Asian IHCCA cohort compared with the Western patients suggests a potential role for DNA repair and immune checkpoint inhibitors in the Asian population. Future clinical trials should account for this genetic heterogeneity.

scholarly journals Assessment of a High Sensitivity Method for Identification of IDH1 R132x Mutations in Tumors and Plasma of Intrahepatic Cholangiocarcinoma Patients

Cancers ◽  
2019 ◽  
Vol 11 (4) ◽  
pp. 454 ◽  
Author(s):  
Caterina Peraldo-Neia ◽  
Maria Scatolini ◽  
Enrico Grosso ◽  
Pasquale Lombardi ◽  
Roberto Filippi ◽  
...  
Keyword(s):  
Disease Progression ◽  
Intrahepatic Cholangiocarcinoma ◽  
Nested Pcr ◽  
Sanger Sequencing ◽  
High Efficiency ◽  
High Sensitivity ◽  
Circulating Free Dna ◽  
Formalin Fixed Paraffin ◽  
Ffpe Samples ◽  
Formalin Fixed Paraffin Embedded

Hotspot codon 132 mutations (R132xIDH1m) are frequent in intrahepatic cholangiocarcinoma (ICC), are druggable by anti-IDH1m agents, and could represent a marker of disease progression. Developing an assay to identify R132xIDH1m would provide a useful tool to select patients benefitting from targeted treatments. We tested a quantitative real-time allele-specific polymerase chain reaction (qPCR)-based method to detect the main R132xIDH1m in an Italian ICC series (n = 61) of formalin-fixed paraffin-embedded (FFPE) samples, and on circulating-free DNA samples. The outcomes were compared with nested PCR/Sanger sequencing. Reconstitution experiments of plasmids harboring the different R132xIDH1m mixed with wild-type (WT) DNA demonstrated that qPCR is able to detect at least 2% of all mutated allele. High efficiency was also observed on patient-derived mutated DNA mixed with WT DNA (up to 10% and 0.3 ng of mutated template); qPCR detected 16.4% of mutated samples (one R132G, three R132C and six R132L) while nested PCR/Sanger sequencing only 8.2% (four R132L and one R132G). In a single patient with an R132C-mutated tumor, qPCR was also performed on plasma samples collected at four time-points, observing an increase correlating with disease progression. In conclusion, we developed a qPCR assay which could represent a fast, inexpensive and sensitive tool both for detection of R132xIDH1m in ICC samples and monitoring disease progression from liquid biopsy.

scholarly journals A Stepwise Data Interpretation Process For Renal Amyloidosis Subtyping by LMD-MS

2021 ◽  
Author(s):  
Ming Ke ◽  
Xin Li ◽  
Lin Wang ◽  
Shuling Yue ◽  
Beibei Zhao
Keyword(s):  
Data Interpretation ◽  
Receiver Operating Curve ◽  
Renal Amyloidosis ◽  
Amyloid Protein ◽  
Proteomic Data ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Interpretation Process ◽  
Interpretation Method ◽  
Formalin Fixed

Abstract Backgrounds: Systemic amyloidosis is classified according to the deposited amyloid protein, which determines its best therapeutic scheme. The laser microdissection combined with mass spectrometry (LMD-MS) technique is a promising approach for precise subtyping of amyloidosis, however, is hampered by how to interpret the MS data.Objectives: The objective of the present study is to establish a complete data interpretation procedure for LMD-MS based amyloidosis subtyping.Methods: Formalin fixed paraffin-embedded specimens from patients with renal amyloidosis were analyzed by LMD-MS for proteome quantification. Forty-two specimens were used for training the data interpretation procedure, which was validated by another 50 validation specimens. Area under receiver operating curve (AUROC) analysis of amyloid accompanying proteins (APOE, APOA4 and SAMP) for discriminating amyloidosis from non-amyloid nephropathies was performed.Results: A stepwise data interpretation procedure that include or exclude the subtypes group by group was established, in which, involvement of non-immunoglobulin amyloid protein is determined by P-score, involvement of immunoglobulin light chain is determined by variable of λ-κ, and immunoglobulin heavy chain’s participation is judged by H-score. This data interpretation method achieved a 88% accuracy in 50 validation specimens. The amyloid accompanying proteins showed significant quantitative differences between amyloidosis specimens and non-amyloid nephropathies. Each of the single accompanying protein had a AUROC value more than 0.9 for diagnosis of amyloidosis from non-amyloid control, and the averaged value of spectral count of the three accompanying proteins showed the highest AUROC (0.966), indicating it might be an alternative indicator for amyloidosis diagnosis.Conclusions: The proteomic data interpretation procedure for amyloidosis subtyping based on LMD-MS was established successfully, which has high clinical application value.

scholarly journals Molecular Classification of Small B-Cell Lymphomas Using Digital Multiplexed Gene Expression Applicable to Formalin-Fixed Paraffin-Embedded Tissues

Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 5770-5770
Author(s):  
Min Xiao ◽  
Jianfeng Zhou ◽  
Wei Zhang
Keyword(s):  
B Cell ◽  
Cell Lymphoma ◽  
B Cell Lymphoma ◽  
Molecular Classification ◽  
Classification Model ◽  
B Cell Lymphomas ◽  
Formalin Fixed Paraffin ◽  
Mantle Cell ◽  
Formalin Fixed Paraffin Embedded

Background: Small B-cell lymphomas encompass a group of lymphoid neoplasms with high heterogeneity. However, the lack of relatively specific diagnostic markers for most of these diseases make their diagnosis challenging. Methods: Using NanoString platform, a random forest-based molecular classification model was trained on 203 malignant and 98 non-malignant formalin-fixed paraffin-embedded (FFPE) tissues. Candidate genes were selected from microarray gene expression data of 891 small B-cell lymphomas. All malignant biopsies were derived from individuals diagnosed as a well-defined small B-cell lymphoma entity, including 17 chronic lymphocytic leukemia/small lymphocytic B-cell lymphoma (CLL/SLL), 74 follicular lymphoma (FL), 34 classical mantle cell lymphoma (cMCL), 5 non-nodal mantle cell lymphoma (nnMCL), 56 mucosa-associated lymphoid tissue lymphoma (MALT), 3 splenic marginal zone lymphoma (SMZL), and 14 nodal marginal zone lymphoma (NMZL). A leave-one-out prediction (CLL/SLL, FL, MCL, MZL, and non-malignancy) was applied to test the accuracy of prediction of the model, and Gini Index of each gene was taken into consideration in simplifying the molecular assay applicable to routine test. Results: A total of 154 candidate genes were initially selected for training the molecular classification model. Genes were initially selected for training the molecular classification model. Thirty-two genes were specifically highly expressed in a single subgroup with Gini Index more than 0.001. The most important genes for classification were CCND1, ZBTB32, MME, BHLHE41, SOX11, and RGS13. The most distinguishable entity was CLL/SLL (ZBTB32, CLNK, and CD200), followed by cMCL/nnMCL (CCND1 and SOX11), and FL (MME, RGS13, and ELL3). Using the molecular classification model trained on the most specific 33 genes, the consistency of diagnosis were 97.5%. Conclusions: In conclusion, our molecular model robustly recognized different subtypes of small B-cell lymphomas in leukemic FFPE samples, which provides a novel approach to precise diagnosis and classification of small B-cell lymphomas. Figure Disclosures Zhou: Nanjing Iaso Biotherapeutics Co. Ltd.: Other: Chairman of Advisory Committee of Science and Medicine.

scholarly journals HGG-45. PROTEOMIC ANALYSIS OF PEDIATRIC DIFFUSE ASTROCYTOMAS YIELDS PATHWAYS ASSOCIATED WITH BOTH PROGRESSION-FREE AND OVERALL SURVIVAL

2020 ◽  
Vol 22 (Supplement_3) ◽  
pp. iii352-iii352
Author(s):  
Blake Sells ◽  
Jessica Fleming ◽  
Richard Graham ◽  
Joseph McElroy ◽  
Jahar Haque ◽  
...  
Keyword(s):  
Diffuse Astrocytoma ◽  
Primary Tumors ◽  
Proteomic Data ◽  
New Therapeutic Approaches ◽  
Formalin Fixed Paraffin ◽  
Risk Of Progression ◽  
Formalin Fixed Paraffin Embedded ◽  
Diffuse Gliomas ◽  
Grade Ii

Abstract Brain tumors are now responsible for more deaths each year than any other childhood cancer. Current studies aim to discover key molecular drivers that can explain prognosis and serve as targets for new therapeutic approaches, reducing morbidity. In this study, we performed LC-MS/MS proteomics on a cohort of 28 primary diffuse astrocytoma formalin-fixed paraffin embedded samples (WHO Grades II-IV) from patients at Nationwide Children’s Hospital with a median follow-up time of 2.3 (0.6–20.2) years. Ingenuity Pathway Analysis was used to analyze the proteomic data after using both age and grade as covariates and only including proteins with p-values less than 0.05. The upregulation of a well-known oncogenic pathway, the Protein Kinase A signaling pathway, was significantly associated with greater risk of progression and death (P=5.5E-07 and P=4.6E-04). Integrin signaling, a pathway commonly suppressed in cancer, was similarly downregulated in those with greater risk of progression and death (P=3.3E-04 and P=1.7E-07). A global upstream analysis of the proteomic data also predicted activation of the oncogene MYCN in those who performed poorly, supporting previous studies. When comparing grade II (n=10) to grade III (n=8) and IV (n=10) primary tumors, the pathway most upregulated in higher histopathological grades was EIF2 Signaling (P=4.9E-49). This pathway has previously been associated with resistance in adult glioblastoma. These pathways, and the proteins detected within, may provide novel means by which to better understand and treat pediatric diffuse gliomas. Ongoing studies are in progress to understand how these pathways drive aggressiveness and differ from adult astrocytomas.

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