Relevance of gene mutations and methylation to the growth of pancreatic intraductal papillary mucinous neoplasms based on pyrosequencing

Variabilities in global DNA methylation and β-sheet richness establish spectroscopic landscapes among subtypes of pancreatic cancer

PURPOSE

Knowledge about pancreatic cancer (PC) biology has been growing rapidly in recent decades. Nevertheless, the survival of PC patients has not greatly improved. The development of a novel methodology suitable for deep investigation of the nature of PC tumors is of great importance. Molecular imaging techniques, such as Fourier transform infrared (FTIR) spectroscopy and Raman hyperspectral mapping (RHM) combined with advanced multivariate data analysis, were useful in studying the biochemical composition of PC tissue.

METHODS

Here, we evaluated the potential of molecular imaging in differentiating three groups of PC tumors, which originate from different precursor lesions. Specifically, we comprehensively investigated adenocarcinomas (ACs): conventional ductal AC, intraductal papillary mucinous carcinoma, and ampulla of Vater AC. FTIR microspectroscopy and RHM maps of 24 PC tissue slides were obtained, and comprehensive advanced statistical analyses, such as hierarchical clustering and nonnegative matrix factorization, were performed on a total of 211,355 Raman spectra. Additionally, we employed deep learning technology for the same task of PC subtyping to enable automation. The so-called convolutional neural network (CNN) was trained to recognize spectra specific to each PC group and then employed to generate CNN-prediction-based tissue maps. To identify the DNA methylation spectral markers, we used differently methylated, isolated DNA and compared the observed spectral differences with the results obtained from cellular nuclei regions of PC tissues.

RESULTS

The results showed significant differences among cancer tissues of the studied PC groups. The main findings are the varying content of β-sheet-rich proteins within the PC cells and alterations in the relative DNA methylation level. Our CNN model efficiently differentiated PC groups with 94% accuracy. The usage of CNN in the classification task did not require Raman spectral data preprocessing and eliminated the need for extensive knowledge of statistical methodologies.

CONCLUSIONS

Molecular spectroscopy combined with CNN technology is a powerful tool for PC detection and subtyping. The molecular fingerprint of DNA methylation and β-sheet cytoplasmic proteins established by our results is different for the main PC groups and allowed the subtyping of pancreatic tumors, which can improve patient management and increase their survival. Our observations are of key importance in understanding the variability of PC and allow translation of the methodology into clinical practice by utilizing liquid biopsy testing.

White Paper: Mimetics of Class 2 Tumor Suppressor Proteins as Novel Drug Candidates for Personalized Cancer Therapy

Simple Summary

A concept is presented for a new therapeutic approach, still in its early stages, which focuses on the phenotypic mimicry (“mimesis”) of proteins encoded by highly disease-relevant class 2 tumor suppressor genes that are silenced by DNA promoter methylation. Proteins derived from tumor suppressor genes are usually considered control systems of cells against oncogenic properties. Thus they represent the brakes in the “car-of-life.” Restoring this “brake function” in tumors by administering mimetic drugs may have a significant therapeutic effect. The proposed approach could thus open up a new, hitherto unexploited area of research for the development of anticancer drugs for difficult-to-treat cancers.

Abstract

The aim of our proposed concept is to find new target structures for combating cancers with unmet medical needs. This, unfortunately, still applies to the majority of the clinically most relevant tumor entities such as, for example, liver cancer, pancreatic cancer, and many others. Current target structures almost all belong to the class of oncogenic proteins caused by tumor-specific genetic alterations, such as activating mutations, gene fusions, or gene amplifications, often referred to as cancer “driver alterations” or just “drivers.” However, restoring the lost function of tumor suppressor genes (TSGs) could also be a valid approach to treating cancer. TSG-derived proteins are usually considered as control systems of cells against oncogenic properties; thus, they represent the brakes in the “car-of-life.” Restoring these tumor-defective brakes by gene therapy has not been successful so far, with a few exceptions. It can be assumed that most TSGs are not being inactivated by genetic alteration (class 1 TSGs) but rather by epigenetic silencing (class 2 TSGs or short “C2TSGs”). Reactivation of C2TSGs in cancer therapy is being addressed by the use of DNA demethylating agents and histone deacetylase inhibitors which act on the whole cancer cell genome. These epigenetic therapies have neither been particularly successful, probably because they are “shotgun” approaches that, although acting on C2TSGs, may also reactivate epigenetically silenced oncogenic sequences in the genome. Thus, new strategies are needed to exploit the therapeutic potential of C2TSGs, which have also been named DNA methylation cancer driver genes or “DNAme drivers” recently. Here we present a concept for a new translational and therapeutic approach that focuses on the phenotypic imitation (“mimesis”) of proteins encoded by highly disease-relevant C2TSGs/DNAme drivers. Molecular knowledge on C2TSGs is used in two complementary approaches having the translational concept of defining mimetic drugs in common: First, a concept is presented how truncated and/or genetically engineered C2TSG proteins, consisting solely of domains with defined tumor suppressive function can be developed as biologicals. Second, a method is described for identifying small molecules that can mimic the effect of the C2TSG protein lost in the cancer cell. Both approaches should open up a new, previously untapped discovery space for anticancer drugs.

Modern aspects of the management of pancreatic intraductal papillary mucinous neoplasms: a narrative review

Intraductal papillary mucinous neoplasms (IPMNs) account for approximately 35% of all cystic tumors in the pancreas and represent the largest subgroup. They are characterized by mucin production and intraductal papillary epithelium growth. IPMNs range from benign to malignant lesions. Biomarkers combined with 18F-Fluorodeoxyglucose-positron emission tomography (18FDG-PET) is the best diagnostic tool. The risk of malignant transformation for main-duct IPMNs is between 34-68% and for low-risk branch-duct (BD)-IPMNs it is 1.1%. Monitoring is crucial for determining the optimal time of surgical excision. Novel artificial intelligence combining clinical, tumor biomarkers, imaging and molecular genomics plays a determinant role in the evaluation of such lesions. The first diagnostic tool is multidetector helical computed tomography (MDHCT) or up-to-date magnetic resonance imaging (MRI). MRI detects malignancy by enhancing mural nodules ≥3 mm. Novel endosonographic interventional techniques have been added to the diagnostic armamentarium. Pancreatoscopy is feasible and effective but challenging for evaluating the diagnosis, invasiveness, and extent of IPMNs. Its findings may change the surgical approach. Pancreatic juice and duodenal fluid have been used recently for molecular biological analysis. The genes most frequently altered include Kirsten rat sarcoma viral proto-oncogene (KRAS), tumor protein p53 (TP53), cyclin-dependent kinase inhibitor 2A (CDKN2A), SMAD family member 4 (SMAD4), and guanine nucleotide-binding protein, alpha stimulating (GNAS). Despite the advances in diagnostic modalities, assessment of this premalignant lesion of pancreatic cancer, with its poor prognosis, is a challenging task. Pancreatectomy is the indicated approach for malignant or high-risk IPMNs with potent malignancy. Conservative management or enucleation for preserving the pancreas of low-risk BD-IPMNs is recommended, but long-term follow-up for recurrence is necessary. The management of IPMNs must be individualized based on preoperative high-risk stigmata and worrisome features.