The deubiquitinase USP9X suppresses pancreatic ductal adenocarcinoma

Evaluating risks of insertional mutagenesis by DNA transposons in gene therapy

Investigational therapy can be successfully undertaken using viral- and nonviral-mediated ex vivo gene transfer. Indeed, recent clinical trials have established the potential for genetically modified T cells to improve and restore health. Recently, the Sleeping Beauty (SB) transposon/transposase system has been applied in clinical trials to stably insert a chimeric antigen receptor (CAR) to redirect T-cell specificity. We discuss the context in which the SB system can be harnessed for gene therapy and describe the human application of SB-modified CAR(+) T cells. We have focused on theoretical issues relating to insertional mutagenesis in the context of human genomes that are naturally subjected to remobilization of transposons and the experimental evidence over the last decade of employing SB transposons for defining genes that induce cancer. These findings are put into the context of the use of SB transposons in the treatment of human disease.

Genetically engineered mouse models of pancreatic adenocarcinoma

Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal types of human cancer for which there are no effective therapies. Deep sequencing of PDAC tumors has revealed the presence of a high number of mutations (>50) that affect at least a dozen key signaling pathways. This scenario highlights the urgent need to develop experimental models that faithfully reproduce the natural history of these human tumors in order to understand their biology and to design therapeutic approaches that might effectively interfere with their multiple mutated pathways. Over the last decade, several models, primarily based on the genetic activation of resident KRas oncogenes knocked-in within the endogenous KRas locus have been generated. These models faithfully reproduce the histological lesions that characterize human pancreatic tumors. Decoration of these models with additional mutations, primarily involving tumor suppressor loci known to be also mutated in human PDAC tumors, results in accelerated tumor progression and in the induction of invasive and metastatic malignancies. Mouse PDACs also display a desmoplastic stroma and inflammatory responses that closely resemble those observed in human patients. Interestingly, adult mice appear to be resistant to PDAC development unless the animals undergo pancreatic damage, mainly in the form of acute, chronic or even temporary pancreatitis. In this review, we describe the most representative models available to date and how their detailed characterization is allowing us to understand their cellular origin as well as the events involved in tumor progression. Moreover, their molecular dissection is starting to unveil novel therapeutic strategies that could be translated to the clinic in the very near future.

Deubiquitinase FAM/USP9X interacts with the E3 ubiquitin ligase SMURF1 protein and protects it from ligase activity-dependent self-degradation

Ubiquitination is an essential post-translational modification that mediates diverse cellular functions. SMAD-specific E3 ubiquitin protein ligase 1 (SMURF1) belongs to the Nedd4 family of HECT ubiquitin ligases that directly catalyzes ubiquitin conjugation onto diverse substrates. As a result, SMURF1 regulates a great variety of cellular physiologies including bone morphogenetic protein (BMP) signaling, cell migration, and planar cell polarity. Structurally, SMURF1 consists of a C2 domain, two WW domain repeats, and a catalytic HECT domain essential for its E3 ubiquitin ligase activity. This modular architecture allows for interactions with other proteins, which are either substrates or adaptors of SMURF1. Despite the increasing number of SMURF1 substrates identified, current knowledge regarding regulatory proteins and their modes of action on controlling SMURF1 activity is still limited. In this study, we employed quantitative mass spectrometry to analyze SMURF1-associated cellular complexes, and identified the deubiquitinase FAM/USP9X as a novel interacting protein for SMURF1. Through domain mapping study, we found the second WW domain of SMURF1 and the carboxyl terminus of USP9X critical for this interaction. SMURF1 is autoubiquitinated through its intrinsic HECT E3 ligase activity, and is degraded by the proteasome. USP9X association antagonizes this activity, resulting in deubiquitination and stabilization of SMURF1. In MDA-MB-231 breast cancer cells, SMURF1 expression is elevated and is required for cellular motility. USP9X stabilizes endogenous SMURF1 in MDA-MB-231 cells. Depletion of USP9X led to down-regulation of SMURF1 and significantly impaired cellular migration. Taken together, our data reveal USP9X as an important regulatory protein of SMURF1 and suggest that the association between deubiquitinase and E3 ligase may serve as a common strategy to control the cellular protein dynamics through modulating E3 ligase stability.

Human correlates of provocative questions in pancreatic pathology

Studies of cell lines and of animal models of pancreatic cancer have raised a number of provocative questions about the nature and origins of human pancreatic cancer and have provided several leads into exciting new approaches for the treatment of this deadly cancer. In addition, clinicians with little or no contact with human pathology have challenged the way that pancreatic pathology is practiced, suggesting that "genetic signals" may be more accurate than today's multimodal approach to diagnoses. In this review, we consider 8 provocative issues in pancreas pathology, with an emphasis on "the evidence derived from man."

Genetically engineered mouse models of pancreatic cancer

Pancreatic ductal adenocarcinoma is the 10th most common cancer and the fourth leading cause of cancer-related death in the United States. Despite great effort, the prognosis for patients with this disease remains dismal with a 5-year survival rate of just 4% to 6%. Although several important advances have improved our understanding of the underlying biology of pancreatic cancer, this knowledge has not translated into novel therapeutic approaches and effective systemic or targeted therapies. Pancreatic cancer is one of the malignancies most difficult to treat, with remarkable intrinsic resistance to both standard and targeted chemotherapy as well as ionizing radiation. Surgical intervention remains the only potentially curative approach. However, most patients present with inoperable and/or metastatic disease and are therefore excluded from surgery. Accordingly, new therapeutic options are desperately needed. In vivo models to study innovative and alternative treatment approaches are of major importance. A variety of genetically engineered mouse models of pancreatic cancer have been developed over the last decade. However, these models display different characteristics, and not all of them are suited for preclinical studies. In this review, we aim to review the mouse models available, their experimental use, their clinical relevance and limitations, and future directions.

[New aspects of surgery for pancreatic cancer. Principles, results and evidence]

Ductal adenocarcinoma is the most frequent malignant tumor of the pancreas and total resection of the pancreatic tumor is still the only curative treatment option. Most tumors are located in the pancreatic head, therefore, pylorus-preserving pancreaticoduodenectomy (Whipple PPPD) is the oncological standard procedure. By concentrating pancreatic resections in specialized centers for pancreatic surgery perioperative mortality and morbidity has decreased in recent years. However, pancreatic resections remain complex and difficult operations and pancreatic anastomosis is particular challenging. To achieve complete resection (R0) resection and reconstruction of large venous vessels is often necessary. Resection of arterial vessels is rarely performed and usually does not lead to an R0 resection of the tumor. Currently adjuvant chemotherapy after total tumor resection is standard of care for all tumor stages but neoadjuvant regimes have recently been reported increasingly more often. Advances in translational research has led to a better understanding of tumor biology and new diagnostic options and therapies are expected in the near future.

Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes

Pancreatic cancer is a highly lethal malignancy with few effective therapies. We performed exome sequencing and copy number analysis to define genomic aberrations in a prospectively accrued clinical cohort (n = 142) of early (stage I and II) sporadic pancreatic ductal adenocarcinoma. Detailed analysis of 99 informative tumours identified substantial heterogeneity with 2,016 non-silent mutations and 1,628 copy-number variations. We define 16 significantly mutated genes, reaffirming known mutations (KRAS, TP53, CDKN2A, SMAD4, MLL3, TGFBR2, ARID1A and SF3B1), and uncover novel mutated genes including additional genes involved in chromatin modification (EPC1 and ARID2), DNA damage repair (ATM) and other mechanisms (ZIM2, MAP2K4, NALCN, SLC16A4 and MAGEA6). Integrative analysis with in vitro functional data and animal models provided supportive evidence for potential roles for these genetic aberrations in carcinogenesis. Pathway-based analysis of recurrently mutated genes recapitulated clustering in core signalling pathways in pancreatic ductal adenocarcinoma, and identified new mutated genes in each pathway. We also identified frequent and diverse somatic aberrations in genes described traditionally as embryonic regulators of axon guidance, particularly SLIT/ROBO signalling, which was also evident in murine Sleeping Beauty transposon-mediated somatic mutagenesis models of pancreatic cancer, providing further supportive evidence for the potential involvement of axon guidance genes in pancreatic carcinogenesis.

Emerging frontiers in pancreatic cancer research: elaboration of key genes, cells and the extracellular milieu

PURPOSE OF REVIEW

We review recent literature with a view to forge an integrative understanding of the molecular, cellular and extracellular milieu of pancreatic cancer, and discuss them in the context of development of novel, personalized therapeutic options.

RECENT FINDINGS

Pancreatic tumorigenesis, examined using genetically engineered mouse models, appears to be driven by local inflammation, in concert with the 'big four' mutations involving oncogenic KRAS, SMAD4, CDKN2A, and TP53, through induction of epithelial-to-mesenchymal transition (EMT) and cancer stem cells, and accompanied by metastasis. High-throughput sequencing of pancreatic ductal adenocarcinoma as well as neuroendocrine tumors and rarer subtypes of cancers of the pancreas has revealed several novel mutations in genes like PALB2, guanine nucleotide-binding protein, alpha stimulating, death-domain-associated protein, α thalassemia/mental retardation syndrome X linked, switch/sucrose nonfermentable pathway related, and in genes in the ubiquitin-dependent pathways such as USP9X. Therapeutic targeting of the tumor-stroma axis by cytokines and immune response modulators and the role of autophagy in pancreatic cancer are some other salient themes explored in the recent publications.

SUMMARY

Recent publications shed new light on the mutational landscape of pancreatic cancer and further delineate the distinctive pancreatic cancer-stroma ecosystem as determined by the dynamic interplay of inflammation, hallmark mutations, EMT, and cancer stem cells.

Genetic disruption of USP9X sensitizes colorectal cancer cells to 5-fluorouracil

The X-linked deubiquitinase USP9X affects the stability and activity of numerous regulatory proteins that influence cell survival. Recent studies suggest that decreased USP9X expression can confer a selective advantage onto developing cancer cells and thereby promotes disease progression. To examine the effect of USP9X on the cellular responses to anticancer therapies, we derived cancer cell lines in which the USP9X locus was disrupted by homologous recombination. The resulting USP9X-deficient cancer cells exhibited increased activation of apoptotic pathways and markedly decreased clonogenic survival in response to 5-fluorouracil, a chemotherapeutic drug that is widely used for treatment of gastrointestinal malignancies. These unexpected results suggest that cancers with low USP9X expression might be specifically sensitized to some conventional therapeutic agents.

TAPDANCE: an automated tool to identify and annotate transposon insertion CISs and associations between CISs from next generation sequence data

Background

Next generation sequencing approaches applied to the analyses of transposon insertion junction fragments generated in high throughput forward genetic screens has created the need for clear informatics and statistical approaches to deal with the massive amount of data currently being generated. Previous approaches utilized to 1) map junction fragments within the genome and 2) identify Common Insertion Sites (CISs) within the genome are not practical due to the volume of data generated by current sequencing technologies. Previous approaches applied to this problem also required significant manual annotation.

Results

We describe Transposon Annotation Poisson Distribution Association Network Connectivity Environment (TAPDANCE) software, which automates the identification of CISs within transposon junction fragment insertion data. Starting with barcoded sequence data, the software identifies and trims sequences and maps putative genomic sequence to a reference genome using the bowtie short read mapper. Poisson distribution statistics are then applied to assess and rank genomic regions showing significant enrichment for transposon insertion. Novel methods of counting insertions are used to ensure that the results presented have the expected characteristics of informative CISs. A persistent mySQL database is generated and utilized to keep track of sequences, mappings and common insertion sites. Additionally, associations between phenotypes and CISs are also identified using Fisher’s exact test with multiple testing correction. In a case study using previously published data we show that the TAPDANCE software identifies CISs as previously described, prioritizes them based on p-value, allows holistic visualization of the data within genome browser software and identifies relationships present in the structure of the data.

Conclusions

The TAPDANCE process is fully automated, performs similarly to previous labor intensive approaches, provides consistent results at a wide range of sequence sampling depth, has the capability of handling extremely large datasets, enables meaningful comparison across datasets and enables large scale meta-analyses of junction fragment data. The TAPDANCE software will greatly enhance our ability to analyze these datasets in order to increase our understanding of the genetic basis of cancers.