A novel 5-gene pancreatic adenocarcinoma classifier: Meta-analysis of transcriptome data – Clinical Genomics Research @BIDMC | Leaders in Pharmaceutical Business Intelligence (LPBI) Group

« Liquid Biopsy Chip detects an array of metastatic cancer cell markers in blood – R&D @Worcester Polytechnic Institute, Micro and Nanotechnology Lab

Funding Oncorus’s Immunotherapy Platform: Next-generation Oncolytic Herpes Simplex Virus (oHSV) for Brain Cancer, Glioblastoma Multiforme (GBM) »

A novel 5-gene pancreatic adenocarcinoma classifier: Meta-analysis of transcriptome data – Clinical Genomics Research @BIDMC

December 28, 2016 by 2012pharmaceutical

A novel 5-gene pancreatic adenocarcinoma classifier: Meta-analysis of transcriptome data – Clinical Genomics Research @BIDMC

Curator: Tilda Barliya, PhD

Analysis of Bhasin et al paper and Literature search

Table 1: 5-genes classifiers as biomarkers for PDAC:

Gene symbol	Gene name	Subcellular localization
ECT2	Epithelial cell transforming sequence 2 oncogene	Nucleus, cytoplasm
AHNAK2	AHNAKE nucleoprotein 2	Plasma membrane, cytoplasm
POSTN	Periostin, osteoblast specific factor	Extracellular space
TMPRSS4	Transmembrane protease, serine 4	Plasma membrane
SERPINB5	Serpin peptidase inhibitor, clade B (ovalbumin) member 5	Extracellular space

Introduction:

Bhasin et al, conducted a beautiful study using a powerful meta-analysis from different sources to identify the “important/classifier” genes associated with Pancreatic Cancer (PDAC).
The authors identified 5 genes that were considered as good classifiers (table 1).
It is important to note that the meta-analysis was performed on tissue and microdissection samples.
In their summary, the authors aim to validate these genes in blood/urine samples.
While these genes might be over expressed in tissue samples it may not be true to their existence in blood and careful examination and validation is required.
Liquid biopsies are emerging as the go-to use tools for disease detection, mostly aimed for early diagnosis.
Liquid biopsies are non-invasive biopsies of blood, urine (potentially saliva) and their “exotic” components, i.e miRNA, exosomes etc.
Since Liquid biopsies are non-invasive, they are painless and patients are more complied.
It is important to note that there is a gap between the expression of a gene or a protein in tissue section and their expression in the blood and may not necessarily correlate.
It will be very interesting to follow their research and future outcomes.

Additional References:

TMPRSS4: an emerging potential therapeutic target in cancer.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4453593/

The tumour trail left in blood

http://www.nature.com/nature/journal/v532/n7598/full/532269a.html

Aashir Awan, PhD, wrote on 12/28/2016

I was wondering if these same 5 genes were upregulated in the pancreatic ductal adenocarcinoma cell lines that are available out there. In doing cell biology work, there is always a dilemma whether cancer cell lines correctly re-capitulate in vivo tumors or not. Personally, I prefer primary cell lines to do analysis but this finding can be used to test primary vs cell line. In addition, I’ve attached the gene network for Ect2. If you look carefully, the two big proteins that jump out are RACGAP1 and KIF23. I think in designing therapies, combinatorial targets can yield the best outcomes. Drugs directed towards two or more targets would seem ideal in my opinion.

Gene Network for Ect2

Original Research

Oncotarget. 2016 Apr 26;7(17):23263-81. doi: 10.18632/oncotarget.8139.

Meta-analysis of transcriptome data identifies a novel 5-gene pancreatic adenocarcinoma classifier.

Bhasin MK¹, Ndebele K², Bucur O^2,³, Yee EU², Otu HH⁴, Plati J², Bullock A⁵, Gu X¹, Castan E¹, Zhang P¹, Najarian R², Muraru MS², Miksad R⁵, Khosravi-Far R², Libermann TA¹.

Author information

Abstract

PURPOSE:

Pancreatic ductal adenocarcinoma (PDAC) is largely incurable due to late diagnosis. Superior early detection biomarkers are critical to improving PDAC survival and risk stratification.

EXPERIMENTAL DESIGN:

Optimized meta-analysis of PDAC transcriptome datasets identified and validated key PDAC biomarkers. PDAC-specific expression of a 5-gene biomarker panel was measured by qRT-PCR in microdissected patient-derived FFPE tissues. Cell-based assays assessed impact of two of these biomarkers, TMPRSS4 and ECT2, on PDAC cells.

RESULTS:

A 5-gene PDAC classifier (TMPRSS4, AHNAK2, POSTN, ECT2, SERPINB5) achieved on average 95% sensitivity and 89% specificity in discriminating PDAC from non-tumor samples in four training sets and similar performance (sensitivity = 94%, specificity = 89.6%) in five independent validation datasets. This classifier accurately discriminated PDAC from chronic pancreatitis (AUC = 0.83), other cancers (AUC = 0.89), and non-tumor from PDAC precursors (AUC = 0.92) in three independent datasets. Importantly, the classifier distinguished PanIN from healthy pancreas in the PDX1-Cre;LSL-KrasG12D PDAC mouse model. Discriminatory expression of the PDAC classifier genes was confirmed in microdissected FFPE samples of PDAC and matched surrounding non-tumor pancreas or pancreatitis. Notably, knock-down of TMPRSS4 and ECT2 reduced PDAC soft agar growth and cell viability and TMPRSS4 knockdown also blocked PDAC migration and invasion.

CONCLUSIONS:

This study identified and validated a highly accurate 5-gene PDAC classifier for discriminating PDAC and early precursor lesions from non-malignant tissue that may facilitate early diagnosis and risk stratification upon validation in prospective clinical trials. Cell-based experiments of two overexpressed proteins encoded by the panel, TMPRSS4 and ECT2, suggest a causal link to PDAC development and progression, confirming them as potential therapeutic targets.

KEYWORDS:

bioinformatics; biomarkers; meta-analysis; pancreatic cancer; transcriptome

PMID:: 26993610
PMCID:: PMC5029625
DOI:: 10.18632/oncotarget.8139

SOURCE

https://www.ncbi.nlm.nih.gov/pubmed/26993610

Oncotarget, Vol. 7, No. 17 – Referred as PDF, above

BIDMC Researchers Discover Early Indicators of Pancreatic Cancer

Markers may help doctors detect pancreatic cancer before it becomes deadly

Date: 3/28/2016
BIDMC Contact: Jennifer Kritz
Phone: 617-667-7301
Email: jkritz@bidmc.harvard.edu

In photo: First author Manoj Bhasin, PhD, and co-senior author Towia Libermann, PhD, Co-Director and Director of BIDMC’s Genomics, Proteomics, Bioinformatics and Systems Biology Center.

SOURCE

http://www.bidmc.org/News/PRLandingPage/2016/March/Libermann-Pancreatic-Cancer-Research-2016.aspx

BOSTON – Pancreatic cancer, the fourth leading cause of cancer death in the United States, is often diagnosed at a late stage, when curative treatment is no longer possible. A team led by investigators at Beth Israel Deaconess Medical Center (BIDMC) has now identified and validated an accurate 5-gene classifier for discriminating early pancreatic cancer from non-malignant tissue. Described online in the journal Oncotarget, the finding is a promising advance in the fight against this typically fatal disease.

“Pancreatic cancer is a devastating disease with a death rate close to the incidence rate,” said co-senior author Towia Libermann, PhD, Director of the Genomics, Proteomics, Bioinformatics and Systems Biology Center at BIDMC and Associate Professor of Medicine at Harvard Medical School (HMS). “Because more than 90 percent of pancreatic cancer cases are diagnosed at the metastatic stage, when there are only limited therapeutic options, earlier diagnosis is anticipated to have a major impact on extending life expectancy for patients. There has been a lack of reliable markers, early indicators and risk factors associated with pancreatic cancer, but this new way of differentiating between healthy and malignant tissue offers hope for earlier diagnosis and treatment.”

The investigators used a number of publicly available gene expression datasets for pancreatic cancer and developed a strategy to reanalyze these datasets together, applying rigorous statistical criteria to compare different datasets from different laboratories and different platforms with each other. The team then selected a subset of data for developing a panel for differentiating between pancreatic cancer and healthy pancreas tissue and thereafter applied this “Pancreatic Cancer Predictor” to the remaining datasets for independent validation to confirm the accuracy of the markers.

After demonstrating and independently validating that a 5-gene pancreatic cancer predictor discriminated between cancerous and healthy tissue, the researchers applied the predictor to datasets that also included benign lesions of the pancreas, including pancreatitis and early stage cancer. The predictor accurately differentiated pancreatic cancer, benign pancreatic lesions, early stage pancreatic cancer and healthy tissue. The predictor achieved on average 95 percent sensitivity and 89 percent specificity in discriminating pancreatic cancer from non-tumor samples in four training sets and similar performance (94 percent sensitivity, 90 percent specificity) in five independent validation datasets.

“Using innovative data normalization and gene selection approaches, we combined the statistical power of multiple genomic studies and masked their variability and batch effects to identify robust early diagnostic biomarkers of pancreatic cancer,” said first author Manoj Bhasin, PhD, Co-Director of BIDMC’s Genomics, Proteomics, Bioinformatics and Systems Biology Center and Assistant Professor of Medicine at HMS.

“The identification and initial validation of a highly accurate 5-gene pancreatic cancer biomarker panel that can discriminate late and early stages of pancreatic cancer from normal pancreas and benign pancreatic lesions could facilitate early diagnosis of pancreatic cancer,” said co-senior author Roya Khosravi-Far, PhD, Associate Professor of Pathology at BIDMC. “Our findings may open a window of opportunity for earlier diagnosis and, consequently, earlier intervention and more effective treatment of this deadly cancer, leading to higher survival rates.”

The first diagnostic application of the panel may be for analyses of fine needle biopsies routinely used for diagnosing pancreatic cancer and for determining the malignant potential of mostly benign pancreatic cysts that can sometimes be precursors of pancreatic cancer. In addition to providing a new tool for diagnoses, the research may also lead to new insights into how pancreatic cancer arises.

“Because these five genes are ‘turned on’ so early in the development of pancreatic cancer, they may play roles as drivers of this disease and may be exciting targets for therapies,” said Libermann. Most of the five genes—named TMPRSS4, AHNAK2, POSTN, ECT2 and SERPINB5—have been linked to migration, invasion, adhesion, and metastasis of pancreatic or other cancers.

The scientists next plan to evaluate the precise roles of the five genes and to validate the accuracy of their diagnostic assay in a prospective clinical study. “Moving forward, we will explore the potential to convert this tissue-based diagnostic into a noninvasive blood or urine test,” Libermann said.

“To further enhance the diagnostic power of this biomarker, we plan to expand it by including non-coding RNAs, proteins, metabolites and mutations associated with pancreatic cancer. This will result in development of the first of its kind biomarker that gauges pancreatic cancer alterations from multiple genomic angles for making highly accurate diagnoses,” added Bhasin. Such an inexpensive and simple test could help transform the landscape of pancreatic cancer and help prevent many of the estimated 330,000 deaths that it causes worldwide each year.

Study coauthors include BIDMC investigators Kenneth Ndebele, Octavian Bucur, Eric Yee, Jessica Plati, Andrea Bullock, Xuesong Gu, Eduardo Castan, Peng Zhang, Robert Najarian, Maria Muraru and Rebecca Miksad, and the University of Nebraska-Lincoln’s Hasan H. Otu. The work was supported by the National Institutes of Health, National Cancer Institute and Ben and Rose Cole Charitable Pria Foundation.

SOURCE

http://www.bidmc.org/News/PRLandingPage/2016/March/Libermann-Pancreatic-Cancer-Research-2016.aspx