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Updated: May 7, 2026
Glycomics-Guided Glycoproteomics Facilitates Comprehensive Profiling of the Glycoproteome in Complex Tumor Microenvironments
Published on: February 7, 2025
Integrative genomic and functional profiling of the pancreatic cancer genome
A Hunter Shain1, Keyan Salari, Craig P Giacomini
1Departments of Pathology, Stanford University School of Medicine, 269 Campus Drive, CCSR-3245A, Stanford, CA 94305-5176, USA. pollack1@stanford.edu.
Background:
Pancreatic cancer is a deadly disease with a five-year survival of less than 5%. A better understanding of the underlying biology may suggest novel therapeutic targets. Recent surveys of the pancreatic cancer genome have uncovered numerous new alterations; yet systematic functional characterization of candidate cancer genes has lagged behind. To address this challenge, here we have devised a highly-parallel RNA interference-based functional screen to evaluate many genomically-nominated candidate pancreatic cancer genes simultaneously.
Results:
For 185 candidate pancreatic cancer genes, selected from recurrently altered genomic loci, we performed a pooled shRNA library screen of cell growth/viability across 10 different cell lines. Knockdown-associated effects on cell growth were assessed by enrichment or depletion of shRNA hairpins, by hybridization to barcode microarrays. A novel analytical approach (COrrelated Phenotypes for On-Target Effects; COPOTE) was used to discern probable on-target knockdown, based on identifying different shRNAs targeting the same gene and displaying concordant phenotypes across cell lines. Knockdown data were integrated with genomic architecture and gene-expression profiles, and selected findings validated using individual shRNAs and/or independent siRNAs. The pooled shRNA library design delivered reproducible data. In all, COPOTE analysis identified 52 probable on-target gene-knockdowns. Knockdown of known oncogenes (KRAS, MYC, SMURF1 and CCNE1) and a tumor suppressor (CDKN2A) showed the expected contrasting effects on cell growth. In addition, the screen corroborated purported roles of PLEKHG2 and MED29 as 19q13 amplicon drivers. Most notably, the analysis also revealed novel possible oncogenic functions of nucleoporin NUP153 (ostensibly by modulating TGFβ signaling) and Kruppel-like transcription factor KLF5 in pancreatic cancer.
Conclusions:
By integrating physical and functional genomic data, we were able to simultaneously evaluate many candidate pancreatic cancer genes. Our findings uncover new facets of pancreatic cancer biology, with possible therapeutic implications. More broadly, our study provides a general strategy for the efficient characterization of candidate genes emerging from cancer genome studies.
Insights
This study screened 185 candidate pancreatic cancer genes using RNA interference, identifying 52 likely on-target effects. Novel oncogenic roles for NUP153 and KLF5 were uncovered, offering new therapeutic targets for pancreatic cancer.
Area of Science:
- Genomics
- Cancer Biology
- Functional Genomics
Background:
- Pancreatic cancer has a low survival rate, necessitating the identification of novel therapeutic targets.
- Genomic studies have identified numerous alterations, but functional characterization of candidate genes is lacking.
- A high-throughput RNA interference screen was developed to evaluate multiple candidate pancreatic cancer genes simultaneously.
Purpose of the Study:
- To systematically evaluate the function of 185 genomically-nominated candidate pancreatic cancer genes.
- To identify novel genes involved in pancreatic cancer development and progression.
- To develop a robust method for functional genomic screening of cancer genes.
Main Methods:
- A pooled shRNA library screen was performed across 10 pancreatic cancer cell lines to assess cell growth and viability.
- Knockdown effects were measured by shRNA hairpin enrichment or depletion using barcode microarrays.
- A novel analytical approach, COrrelated Phenotypes for On-Target Effects (COPOTE), was employed to identify reliable on-target gene knockdowns.
Main Results:
- The screen identified 52 probable on-target gene knockdowns out of 185 candidates evaluated.
- Known oncogenes (KRAS, MYC) and a tumor suppressor (CDKN2A) showed expected effects, validating the screen's reliability.
- Novel potential oncogenic roles were identified for NUP153, potentially via TGFβ signaling, and KLF5 in pancreatic cancer.
Conclusions:
- Integrating physical and functional genomic data enables simultaneous evaluation of numerous candidate cancer genes.
- The study reveals new aspects of pancreatic cancer biology with potential therapeutic implications.
- A general strategy for efficient characterization of candidate genes from cancer genomics studies was established.
