HNF1B-driven three-dimensional chromatin structure for molecular classification in pancreatic cancers.

Pancreatic cancer is a highly aggressive tumor, and early diagnosis and treatment significantly improves the clinical benefit for patients. However, currently there is a lack of effective methods to accurately detect this disease. In our study, we develop a liquid biopsy signature of EV miRNAs based on associated radiomics features of patients’ tumors in order to provide new insights for the early diagnosis of pancreatic cancer.A total of eight datasets enrolled in this study, featuring clinical and imaging data from different benign pancreatic lesions and malignant pancreatic cancers as well as small RNAseq data from cargo of plasma extracellular vesicles of tumor patients. Radiomics Feature Extraction and different features analysis performed by limma packages. Feature selection was performed by Boruta algorithms and radiomics related signature model was build and validated by lasso regression algorithms. Radiomic signature related to low abundance EV miRNAs was analyzed by weighted gene co-expression network analysis. The diagnosis ability of above miRNA are validated by ten machine-learning algorithms. The shared target of candidate miRNAs were predicted and clustered followed by subsequently probing for predicting survival benefit of the patient, drug sensitivity of tumor cells and functional differences.A total of 88 significant radiologic features demonstrate differences between benign lesion and pancreatic cancer. Three radiomics factor related signature related a plasma EV-miRNAs triplet possessing high accuracy in diagnosis cancer from benign lesions. Moreover, clustering miRNA and there predicted molecular signaling partners in tumor tissue identified tow molecular subtypes of pancreatic cancer. Cluster stratification separates low risk tumors in terms of severely prolonged overall survival time of patients, higher sensitivity to immune therapies. We also propose the potential of purposing selected targeted drugs to specifically targeting the molecular activation markers in high-risk tumor cluster.Our three radiogenomics related blood plasma extracellular vesicle microRNA signature is a useful liquid biopsy tool for early diagnosis and molecular subtyping of pancreatic cancer, which might treatment decision making.The identification of a low-abundance microRNA signature in plasma-derived extracellular vesicles offers significant translational potential for the early diagnosis and subtyping of pancreatic cancer, particularly across diverse ethnic populations. This discovery could lead to the development of non-invasive liquid biopsies that improve early detection rates, a critical need for a cancer with notoriously poor prognosis due to late diagnosis. By incorporating this microRNA signature into clinical practice, oncologists may be able to detect pancreatic cancer at earlier, more treatable stages, enhancing patient survival rates. Additionally, the subtyping capability of this signature could guide personalized treatment strategies, allowing for more targeted therapies based on specific cancer subtypes. This could ultimately reduce the need for invasive diagnostic procedures and optimize treatment efficacy, reducing adverse effects and improving outcomes. The integration of radiogenomics and liquid biopsy technologies promises to be a powerful tool in the future of cancer medicine, particularly in underserved populations.

Background: Pancreatic Cancer remains a dismal disease with the worst survival outcomes of any solid organ malignancy. The most common form is Pancreatic Ductal Adenocarcinoma (PDAC) which has a 5-year survival of only 5% and a median survival in the region of 6 months after diagnosis. The majority of patients present with metastatic or locally advanced disease that is unsuitable for surgical resection. The only potential curative treatment is surgery, yet only around 15 – 20% of patients undergo surgical resection. Of these, half of patients develop disease recurrence at 1 year, and only around 20% survive 5 years after surgery. These figures demonstrate that current treatment strategies are inadequate and better therapies and treatment selection tools are urgently needed. Recent large-scale next generation sequencing studies of pancreatic cancer have revealed a small set of consistent mutations found in most pancreatic cancer genomes, and beyond that a low prevalence of targetable mutations for current therapies. Transcriptomic analysis has revealed molecular subtypes with significant differences in gene expression and molecular pathways. This may explain the failure of conventional clinical trial designs to show any meaningful survival benefit, except in small and undefined patient sub-groups. With the development of next generation sequencing technology, genomic sequencing and analysis can be performed in a clinically meaningful turnaround time. This can identify therapeutic targets in individual patients and personalise treatment selection. Incorporating pre-clinical discovery and molecularly guided therapy into clinical trial design has the potential to significantly improve outcomes in this lethal malignancy. Aims: The aims of this PhD thesis are: 1. examine the clinical and pathological features of molecular subtypes of PDAC to identify novel biomarkers to select patients for surgical resection; 2. investigate therapeutic opportunities targeting DNA damage response machinery; and 3. develop clinical strategies to translate these findings into personalised clinical trials. Results: Early recurrence after surgery, particularly liver metastases, and metastatic presentation were strongly associated with gene expression sets that define the squamous subtype of PDAC (P < 0.001). Lung recurrence, localised disease and long-term survival were associated with the classical pancreatic subtype and an anti-tumour immune response (P < 0.001). Patients with tumours of the body and tail of pancreas had significantly worse survival than those with pancreatic head tumours (12.1 versus 22.0 months; P = 0.001). Location in the body and tail was associated with the squamous subtype of PDAC. Body and tail PDACs are enriched for gene programmes involved in tumour invasion and epithelial-to-mesenchymal transition, as well as features of poor antitumour immune response. In three independent PDAC cohorts (total participants = 1184) the relationship between aberrant expression of pro-metastatic proteins S100A2 and S100A4 and survival was assessed. High expression of either S100A2 or S100A4 were independent poor prognostic factors in a training cohort of 518 participants and two independent validation cohorts (Glasgow, n = 198; German, n = 468). A preoperative nomogram incorporating S100A2 and S100A4 expression predicted survival as well as nomograms derived using post-operative clinicopathological variables. DNA damage response (DDR) deficient cell lines and xenograft models were highly sensitive to Cisplatin and PARP inhibitors. A novel transcriptional signature of replication stress was generated and associated with the squamous subtype in both cell lines and bulk tumour samples. This signature predicted differential responses to cell cycle inhibitors of ATR, WEE1, CHK1, CDK4/6 and PLK4. Response to these inhibitors were independent of DDR status, but strongly associated with replication stress. These findings were used to inform the design of a phase Ib / II clinical trial targeting DDR deficiency and Replication Stress using PARP and ATR inhibitors in PDAC. A tissue acquisition protocol using endoscopic ultrasound guided biopsies for next generation sequencing was designed and allowed multi-omic characterisation of PDAC. This has been implemented within the PRECISION-Panc master protocol to allow molecular profiling of all patients, irrespective of disease stage, and facilitate precision medicine trials in PDAC. Conclusions: Significant phenotypic differences exist between molecular subtypes of PDAC and these differences informed the design of novel selection tools for surgical resection. Proof of concept data demonstrates DDR deficiency and increased Replication Stress to be attractive targets in PDAC. Therapeutic vulnerabilities extend beyond platinum chemotherapy and can be targeted with novel small molecule inhibitors, with independent biomarkers that predict response to agents targeting either DDR or replication stress. This has led to the design and development of personalised medicine trials via the PRECISION-Panc platform targeting DDR and Replication stress that will open in early 2019.

Highlights from Recent Cancer Literature

Rational molecular subtyping of pancreatic cancer based on genome, transcriptome, proteomics and metabolomics data, in combination with systematic biological analysis, have greatly enriched the traditional histopathological typing methods based on morphology. The introduction of molecular subtyping reflects the progress in deep understanding of the essence of tumorigenesis of pancreatic cancer, providing a necessary foundation for the development of molecular targeted therapy and implementation of precision medicine. Therefore, molecular subtyping of pancreatic cancer has broad application prospects. The current article reviews the current research status and recent progress of molecular subtyping of pancreatic cancer, and discusses the clinical significance of different subtyping methods. Key words: Pancreatic neoplasms; Pancreatic can-cer; Molecular subtypes; Molecular targeted therapy; Progress

Integrated chromosomal instability and tumor microbiome redefined prognosis-related subtypes of pancreatic cancer

Pancreatic cancer (PC) is a highly aggressive malignancy in humans, where early diagnosis significantly improves patient outcomes. However, effective methods for accurate and early detection remain limited. In this multiethnic study involving human subjects, we developed a liquid biopsy signature based on extracellular vesicle (EV)-derived microRNAs (miRNAs) linked to radiomics features extracted from patients’ tumor imaging. We integrated eight datasets containing clinical records, imaging data of benign and malignant pancreatic lesions, and small RNA sequencing data from plasma-derived EVs of PC patients. Radiomics features were extracted and analyzed using the limma package, with feature selection conducted via the Boruta algorithm and model construction through Least Absolute Shrinkage and Selection Operator regression. Radiomics-related low-abundance EV miRNAs were identified via weighted gene co-expression network analysis and validated for diagnostic accuracy using 10 machine-learning algorithms. Three key EV miRNAs were found to robustly distinguish malignant from benign lesions. Subsequent molecular clustering of these miRNAs and their predicted targets identified two PC subtypes, with distinct survival profiles and therapeutic responses. Specifically, one cluster was associated with prolonged overall survival and higher predicted sensitivity to immunotherapy, while the other indicated high-risk tumors potentially amenable to targeted drug interventions. This radiogenomic EV miRNA signature in human plasma represents a promising non-invasive biomarker for early diagnosis and molecular subtyping of PC, with potential implications for precision treatment strategies.

Transcriptomic profiling classifies pancreatic ductal adenocarcinoma (PDAC) into several molecular subtypes with distinctive histological and clinical characteristics. However, little is known about the molecular mechanisms that define each subtype and their correlation with clinical outcome. Mutant KRAS is the most prominent driver in PDAC, present in over 90% of tumors, but the dependence of tumors on oncogenic KRAS signaling varies between subtypes. In particular, the squamous subtype is relatively independent of oncogenic KRAS signaling and typically displays much more aggressive clinical behavior versus the progenitor subtype. Here, we identified that yes-associated protein 1 (YAP1) activation is enriched in the squamous subtype and associated with poor prognosis. Activation of YAP1 in progenitor subtype cancer cells profoundly enhanced malignant phenotypes and transformed progenitor subtype cells into squamous subtype. Conversely, depletion of YAP1 specifically suppressed tumorigenicity of squamous subtype PDAC cells. Mechanistically, we uncovered a significant positive correlation between WNT5A expression and YAP1 activity in human PDAC and demonstrated that WNT5A overexpression led to YAP1 activation and recapitulated a YAP1-dependent but Kras-independent phenotype of tumor progression and maintenance. Thus, our study identifies YAP1 oncogene as a major driver of squamous subtype PDAC and uncovers the role of WNT5A in driving PDAC malignancy through activation of the YAP pathway.

Integrated genomic analysis of 456 pancreatic ductal adenocarcinomas identified 32 recurrently mutated genes that aggregate into 10 pathways: KRAS, TGF-β, WNT, NOTCH, ROBO/SLIT signalling, G1/S transition, SWI-SNF, chromatin modification, DNA repair and RNA processing. Expression analysis defined 4 subtypes: (1) squamous; (2) pancreatic progenitor; (3) immunogenic; and (4) aberrantly differentiated endocrine exocrine (ADEX) that correlate with histopathological characteristics. Squamous tumours are enriched for TP53 and KDM6A mutations, upregulation of the TP63∆N transcriptional network, hypermethylation of pancreatic endodermal cell-fate determining genes and have a poor prognosis. Pancreatic progenitor tumours preferentially express genes involved in early pancreatic development (FOXA2/3, PDX1 and MNX1). ADEX tumours displayed upregulation of genes that regulate networks involved in KRAS activation, exocrine (NR5A2 and RBPJL), and endocrine differentiation (NEUROD1 and NKX2-2). Immunogenic tumours contained upregulated immune networks including pathways involved in acquired immune suppression. These data infer differences in the molecular evolution of pancreatic cancer subtypes and identify opportunities for therapeutic development.

ASGE guideline on screening for pancreatic cancer in individuals with genetic susceptibility: summary and recommendations

Faculty Opinions recommendation of Genomic analyses identify molecular subtypes of pancreatic cancer.

Through molecular subtyping, therapeutic vulnerabilities can be exploited for developing personalized medicine. The real utility of molecular subtyping lies in the clinical translation for disease characterization. Proteomic methods with defined marker sets hold great promise for improving therapy outcomes by improving the speed of predictions for devising treatment strategies.See related article by Son et al., p. 3370.

Chronic Pancreatitis and Pancreatic Cancer: Prediction and Mechanism

Targeting KRAS Mutations

Reviewer #1 (Public review): Human multiethnic radiogenomics reveals low-abundancy microRNA signature in plasma-derived extracellular vesicles for early diagnosis and molecular subtyping of pancreatic cancer

Simulating Clinical Features of Pancreatic Cancer in a Mouse Model with Specific Genetic Alterations in Kras and p53