Browsing Over 138 Presentations
28P - Simultaneous unbiased and absolute quantification of a 500 protein panel in pancreatic cancer plasma using HRM mass spectrometry (ID 192)
- H. Yu
- H. Yu
- J. Vowinckel
- C. Escher
- D. Heinzmann
- N. Dupuis
Abstract
Background
Recent studies have demonstrated of utility of quantifying circulating proteins for early disease detection, prediction of therapeutic response, and treatment monitoring. Although the utility is clear, standardization of measurement methods for a large number of proteins from plasma remains challenging. Here, plasma proteins are detected using hyper-reaction monitoring (HRM) mass spectrometry in samples from normal and pancreatic cancer subjects. The data is acquired and analyzed simultaneously with unbiased label-free quantification of all proteins and absolute quantification of proteins from a > 500-protein panel constructed from stable-isotope standard (SIS) peptides.
Methods
Plasma samples from subjects with Stage IV pancreatic cancer (PC, n = 6) and age matched healthy donors (n = 15) were prepared for mass spectrometry. Prior to analysis, a panel of SIS peptides, covering 582 plasma proteins, was spiked into each sample. All samples were acquired using nano-flow liquid chromatography with separation over a one-hour gradient coupled online to a Thermo Scientific Q Exactive HF mass spectrometer. Protein data was extracted using Spectronaut (Biognosys) and statistical analysis was conducted to identify disease associated biomarker candidates.
Results
Analysis of the PQ500 panel enabled absolute quantification of 282 proteins across all samples. Univariate statistical testing identified 29 candidate proteins (27 up- and 2 down-regulated; q-value > 0.05 and fold change > 1.5). Key dysregulated proteins include CRP, SAA1, and C9. With unbiased, label-free quantification, 414 proteins were quantified, with 87 significantly regulated. In addition to the acute phase protein candidates identified in the PQ500 panel, 12 adhesion related protein candidates were identified (e.g. TLN1, MYH9, TPM4), 9 of which were decreased in PC. Notably, membrane associated ICAM1 and VCAM1, both potential therapeutic targets, were increased in PC.
Conclusions
Combining PQ500 with unbiased label-free quantification enables comprehensive characterization of the plasma proteome, while at the same time providing absolute quantification for a large subset of well annotated, clinically relevant proteins.
Legal entity responsible for the study
Biognosys AG, Schlieren, Switzerland.
Funding
Biognosys AG, Schlieren, Switzerland.
Disclosure
H. Yu, J. Vowinckel, C. Escher, D. Heinzmann, N. Dupuis: Employee: Biognosys AG.
31P - Comprehensive genomic profiling of Chinese esophageal squamous cell carcinoma patients (ID 141)
- Y. Ji
- Y. Ji
- Y. Wu
- W. Fu
- L. Liu
- Z. Tian
- S. Wen
- K. Zhang
- M. Yao
- A. Liu
- Y. Zhou
Abstract
Background
Esophageal squamous cell carcinoma (ESCC) is the most important pathological type of esophageal cancer with high incidence and limited efficient therapies in China and worldwide. Understanding of ESCC genomic features is advantageous for exploring clinical therapeutic strategies.
Methods
Deep sequencing targeting 450 cancer genes was performed on FFPE and matched blood samples collected from 90 Chinese ESCC patients(pts) with a median age of 60 years old. Genomic alterations (GAs) including single nucleotide variations, short and long indel, gene rearrangements and copy number variations were analyzed. Tumor mutation burden (TMB) was assessed in all samples by standard NGS algorithms. The expression of PD-L1 in 44 samples was evaluated by IHC (28-8 Ab).
Results
The most commonly found GAs were mutations in TP53 (94.4%), FGF3 (43.3%), CCND1 (43.3%), FGF4 (42.2%), FGF19 (42.2 %), CDKN2A (36.7%), NOTCH1 (25.6%), PIK3CA (22.2%), and ERBB2 amp(2.2%).Compared with TCGA data, the frequency of TP53 and ERBB2 amp mutations was similar, while the frequency of NOTCH1 mutations was significantly higher (25.6% vs 11%) and the frequency of EGFR amp was lower (5.6% vs 19%) in Chinese cohort. In addition, 4 of 90 samples harbored germline mutations (SDHA, RAD51C, PALB2 and BCL2L11). Among these GAs, 73.3% mutations were in cell cycle (62.2%) and PI3K/AKT (42.2%) pathway. In Chinese ESCC pts, the median TMB was 7.0 muts/Mb, and some pts showed high TMB (33.3%pts≥10 muts/Mb,11.1%pts≥20 muts/Mb). 15.6% pts (TMB≥10 muts/Mb) harbored chromosome 11q13 (FGF3/4/19 and CCND1) amp, which may be related to immunotherapy hyper-progression. Based on the IHC analysis, 10 of 44 Chinese pts showed positive (TPS≥1%) PD-L1 expression, and 7 of them also showed high TMB (≥10 muts /Mb). However, no correlation was found between high TMB and PD-L1 expression.
Conclusions
In this study, we found that the frequencies of GAs, such as EGFR and NOTCH1 alterations, were different between Chinese and western ESCC pts. Compared to Western ESCC pts, the positivity of PD-L1 expression was similar, while TMB was higher in Chinese ESCC pts. These findings suggested potential therapeutic targets for targeted and immunotherapies of Chinese ESCC pts.
Legal entity responsible for the study
OrigiMed.
Funding
Has not received any funding.
Disclosure
M. Yao, A. Liu, Y. Zhou: Employee: OrigiMed. All other authors have declared no conflicts of interest.
32P - Clinical correlation between different CKIT exon mutations and clinical outcome imatinib mesylate treatment in gastrointestinal stromal tumor (GIST) patients (ID 71)
- G. Zakaria
- G. Zakaria
- N. Allahloubi
- A. Bahnasy
- O. Khorshid
Abstract
Background
The clinical behavior of GISTs is highly variable. This study aims at detection of different histo-pathological tumor features and correlation with different clinical aspects after treatment with imatinib, based on C-KIT exon mutation status.
Methods
This is a retrospective study that included all cases diagnosed as GIST who presented to NCI from 2005 to 2017, The following data were collected from the patient’s files: age, gender, tumor site, size, mitotic rate, histological grade, capsular rupture, risk stratification by Joensuu criteria, treatment setting, date of start and end of treatment, dose and toxicity. KIT mutation was assessed on tumor tissues of all patients; clinical correlation between different clinical aspects after treatment with imatinib, based on C-KIT exon mutation status, was done.
Results
Eighty-nine cases of GIST presented to NCI in the period September 2005 to January 2017. Median age at diagnosis was 48 years old with a median follow up of 22 months. More than 75% of the patients had positive C-KIT mutation, while it was negative in 24.7 % of the patients. C-kit positive mutations were significantly associated with tumors more than 5 cm, high mitosis, and with high tumor risk stratification by Joensuu criteria in more than fifty percent of the patients. Exon 9 mutations had poor ORR (55.6 %) compared to those with exon 11(67.6%) (P = 0.33), with the latter having PFS of 55 months compared 120 months for exon 9 mutations, (P = 0.002). No statistically difference in OS was observed with exon 9 (70 months) compared to exon 11 mutations (77 months) (P = 0.55).
Conclusions
C-kIT-positive mutation per-se is an independent poor risk factor, associated with more aggressive tumor features whereas response to imatinib was affected by exon mutations with exon 11 having a tendency for better ORR, compared to exon 9 mutation, with the latter having longer PFS compared with exon 11, with no statistically difference in OS with exon 9 compared to exon 11 mutations.
Legal entity responsible for the study
NCI.
Funding
Has not received any funding.
Disclosure
All authors have declared no conflicts of interest.
33P - Proteomic analysis of UKF-NB-4 cells reveals a stimulatory activity of MT-3 on cellular senescence and apoptosis (ID 88)
- M. Merlos Rodrigo
- M. Merlos Rodrigo
- H. Buchtelova
- V. Strmiska
- A. Jimenez Jimenez
- I. Casal
- V. Adam
- Z. Heger
Abstract
Background
Metallothioneins (MTs) family is a intracellular and cysteine-rich proteins with a high affinity to metals. MT-3 could play important neuromodulatory and neuroprotective roles. MT-3 has been also found up-regulated in a number of cancers. Neuroblastoma (Nbl) is a cancer is the most common extra-cranial solid tumour of childhood. The main aim was to provide novel insights into the molecular mechanisms of hMT-3 up-regulation and to elucidate the effects beneath the MT-3 up-regulation in Nbl cells.
Methods
To increase the expression of MT-3 Nbl (UKF-NB-4) cells were transiently transfected with a plasmid containing MT-3 gene (pcDNA3.1-GFP-hMT-3-TOPO). Separations of tryptic digests were carried out on an Easy-nLC 1000 nano system. MS analysis was performed using a Q-Exactive MS. The mass spectrum *.raw file was searched against the human SwissProt 57.15 database using MASCOT search engine (version 2.3, Matrix Science).
Results
The efficiency of transfection analysed through a fluorescence of GFP tag expressed at the C-terminus of MT-3 showed more 70% transfection efficiency for both constructed plasmids (mock and MT-3). From the total of common proteins in dataset (hMT-3 vs. mock), 176, 20 and 1244 proteins were quantitatively identified with up-regulation, down-regulation, and no significant differences between hMT-3 and mock treatments. Noteworthy, the bioinformatical analyses revealed the exclusive expression (induced by MT-3) and up-regulation proteins of a number of proteins affecting biological pathways related to mitotic cell cycle, cellular responses to stress, positive regulation of proteolysis, negative regulation of cell cycle and programmed cell death.
Conclusions
Our proteomic data shed some light on the proteins involved in inducing senescence and apoptosis in tested Nbl cells with up-regulated MT-3. Organisms with renewable tissues had to evolve mechanisms to prevent the development of cancer. Cellular senescence and apoptosis are among those mechanisms. Further experiments will be performed to functionally verify these data to provide novel insights into the Nbl biology. These might be useful to develop novel therapeutic protocols utilizing MT-3 as prognostic biomarker or therapeutic target.
Legal entity responsible for the study
Department of Chemistry and Biochemistry, Mendel University in Brno, Brno, CZ.
Funding
European Research Council (ERC) under the European Uniońs Horizon 2020 Research and Innovation Programme (grant agreement No. 759585).
Disclosure
All authors have declared no conflicts of interest.
Session DOI (ID 216)
Cancer evolution as a therapeutic target (ID 111)
- A. Bardelli
- A. Bardelli
Introduction (ID 11)
- R. Plummer
- R. Plummer
DNA polymerase Theta (POLθ) as an anticancer target (ID 12)
- G. Higgins
- G. Higgins
Targeting the WNT pathway for cancer therapy (ID 13)
- D. Tan
- D. Tan
Clinical development of oxidative phosphorylation (OXPHOS) inhibitors (ID 14)
- T. Yap
- T. Yap
HIF-2a (ID 15)
- E. Jonasch
- E. Jonasch