Proteomics for Pancreatic Cancer: History
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Subjects: Biology

Pancreatic cancer is a devastating disease that has a grim prognosis, highlighting the need for improved screening, diagnosis, and treatment strategies. The sole biomarker for pancreatic ductal adenocarcinoma (PDAC) authorized by the U.S. Food and Drug Administration is CA 19-9, which proves to be the most beneficial in tracking treatment response rather than in early detection.

  • pancreatic cancer
  • proteomics
  • biomarker

1. Introduction

Pancreatic ductal adenocarcinoma (PDA) is an invasive tumor with similar incidence and mortality rates. The incidence of PDA has increased worldwide in recent decades and is expected to continually rise [1,2,3,4,5], already being listed as the seventh leading cause of mortality by cancer worldwide [6].
By 2040, a 61.7% increase is expected in the total number of global cases [7]. The main difference between PDA and other cancers lies in the genomic heterogeneity of the tumors, which points to patient-specific tumoral genomic signatures [8]. This may explain the obstacles that prevent the identification of patient phenotypes predictive of better or worse prognosis. For instance, based on transcriptome analysis, the International Cancer Genome Consortium currently divides PDA into three molecular subtypes: progenitor, squamous, and aberrantly differentiated endocrine/exocrine types [9]. However, the decision from a multidisciplinary team, e.g., whether a specific patient with resectable disease would benefit from surgery, continues to be based on clinical information, laboratory tests, and imaging. In recent years, proteomics has emerged as a powerful tool for advancing our understanding of pancreatic cancer biology and identifying potential biomarkers and therapeutic targets [10].
Radical resection is the only potentially curative treatment for PDA [11]. Nonetheless, even after curative resection, up to 80% of patients experience disease relapse, resulting in a 5-year survival rate of only 20–30% [12]. Pancreaticoduodenectomy is associated with high morbidity (up to 60%) and an acceptable mortality rate below 5%, which strongly impacts both the patient’s quality of life and health costs [13]. Several studies and clinical trials have attempted to identify new biomarkers to improve therapies and formulate new healthcare policies. Major hurdles have been revealed in the diversity of disease phenotypes and in the costs of implementing new methodologies [14].

2. Proteomics as a Biomarker Source for Pancreatic Cancer

Pancreatic cancer is a devastating disease that arises in the pancreas. It is one of the most lethal types of cancer, as it is often diagnosed at a late or advanced stage, resulting in outcomes with a poor prognosis [129]. As a result, there is a need for new diagnostic tools for early detection and prognosis of this cancer. Recent advances in proteomic analysis have led to the identification of numerous biomarkers for the diagnosis, early detection, prognosis, and classification of pancreatic cancer, providing valuable insights into the disease. To provide an answer to these challenges, a range of proteomic studies have been carried out to detect specific proteins and extracellular vesicles (EVs) that are differentially expressed in pancreatic cancer.
For instance, Jia et al. (2020) [130] employed iTRAQ-based analysis to identify differential serum proteins (RAD50, TGF-β1, and APAF1) that serve as diagnostic markers of pancreatic ductal adenocarcinoma. Meanwhile, Wu et al. (2021), also utilizing iTRAQ and mass spectrometry, identified three proteins (PROZ, TNFRSF6B, and TNFRSF6B) that, when combined, could provide an AUC of 0.932 for early-stage pancreatic cancer detection [131].
As previously stated, several studies have focused on the proteomic analysis of extracellular vesicles produced by cancerous versus healthy pancreatic organoids. EVs are small vesicles secreted by cells that contain proteins, nucleic acids, and other molecules that can be used as biomarkers. These particles have been identified as being implicated in cellular transformation in several cancer types, with pancreatic cancer not being an exception. In fact, several researchers have pointed out that EVs contribute to the initialization of malignant cell transformation [132,133].
One study found that the proteomic analysis of EVs could distinguish cancerous from healthy pancreatic organoids with high sensitivity and specificity, with tumor-promoting candidates, LAMA5, SDCBP, and TENA consistently upregulated in PDAC-derived EVs [134].
In a study published in 2021, the researchers used iTRAQ-based analysis of plasma-derived exosoma-identified ALG-2 interacting protein X (ALIX) as a novel biomarker for the diagnosis and classification of pancreatic cancer. The researchers reported an AUC of 0.91, with a 90.6% sensitivity and an 83.9% specificity for this marker when combined with CA 19-9 [135]. This protein had already been described as a regulator of both epidermal growth factor receptor (EGFR) activity and programmed death-ligand 1 (PD-L1 or CD 274) surface marker, indicating its involvement or regulatory capability in tumor-mediated immunosuppression [136,137], with its use as a biomarker being pointed out in other tumors, such as oral squamous cell carcinoma [138] or colorectal carcinoma, among others [137].
It has also been discovered that circulating cancer-associated EVs, derived from the serum of PDAC patients, could be used as early detection and recurrence biomarkers for pancreatic cancer [139]. In this study, two novel biomarkers were identified, G protein-coupled receptor class C group 5 member C (GPRC5C) and epidermal growth factor receptor pathway substrate 8 (EPS8), that enabled the discrimination between healthy controls and early-stage PDAC, with AUC values of 0.946 when combined with each other. One study conducted by Chen et al. (2023) used iTRAQ-based analysis to identify differential plasma proteins, which could serve as diagnostic markers for pancreatic ductal adenocarcinoma. This study found that three proteins, when combined with CA19-9, AAT, RAB2B, and IGFBP2, resulted in an AUC of 0.90, indicating a high diagnostic accuracy [140].
Although several articles have identified pancreatic cancer biomarkers, the presented results do not always lead to clear identification of the biomarkers, in part due to the molecular complexity of the disease. In some situations, instead of a specific biomarker, several authors have investigated protein patterns. In a recent study, Son et al., using reaction monitoring–mass spectrometry, identified 24 proteins that could classify patient outcomes in four risk subgroups, thus providing clinicians with new tools to identify high-risk patients who could benefit from more aggressive treatment [141]. On a similar note, Kafita et al., performing proteogenomic analyses of pancreatic cancer subtypes, identified subtype-specific protein expression patterns and genetic alterations, including alterations in pathways related to cell cycle regulation, DNA damage repair, and immune response. The researchers also identified potential therapeutic targets, including several protein kinases and immune checkpoint molecules. These researchers have also identified potential therapeutic targets that could have important implications for the development of personalized treatments for pancreatic cancer patients. Of the two types of pancreatic tumors that the authors identified through machine learning, namely subtype-1 and subtype-2, a comparison was made regarding the expression levels of various proteins between the two disease subtypes. The discovery revealed that subtype-1 tumors displayed significantly elevated expression levels of multiple proteins, such as mTOR, E-Cadherin, and Raf-pS338, in contrast to subtype-2 tumors, which manifested significantly increased expression levels of proteins, including Stathmin, Mre11, and MAP2K1 [142]. Silwal-Pandit et al., using LC-MS, highlighted the importance of the extracellular matrix in pancreatic cancer progression, suggesting that extracellular matrix proteins could serve as potential prognostic biomarkers for pancreatic cancer patients. Further analysis found that an elevated expression of several proteins network involved in epithelial–mesenchymal transition and glycolytic activities, low oxidative phosphorylation, E2F, and DNA repair pathway activities [84].

3. Proteomics Signatures Associated with Treatment Response

As previously noted, pancreatic cancer is an extremely aggressive form of cancer with a grim prognosis. According to the American Cancer Society, the five-year survival rate for pancreatic cancer is only about 11% [159,160]. The limited treatment options for pancreatic cancer often include surgery, radiation therapy, and chemotherapy, but the outcomes of these treatments are generally unsatisfactory due to the aggressive nature of the disease [161]. As a result, there is an urgent need to identify new therapeutic targets and biomarkers for pancreatic cancer treatment.
Omics, which encompasses proteomics, has emerged as a powerful tool, for analyzing the global protein expression patterns of cancer cells. Proteomics can identify proteins that are differentially expressed between cancer and normal cells, and between different stages of pancreatic cancer, before, during, and after treatment, which can lead to the identification of new therapeutic targets and enable personalized cancer treatment. By applying these methodologies, the patient prognosis can be provided and help guide treatment decisions and predict drug-associated adverse events [162,163,164].
In the precision medicine or holistic medicine approaches, proteomic signatures or proteomic profiling have been researched in the context of pancreatic cancer treatment response and the patient’s overall outcome. For example, a study by Peng et al. identified a plasma proteomic signature associated with the response to chemotherapy in pancreatic cancer patients (vitamin-K dependent protein Z, sex hormone-binding globulin, von Willebrand factor, and CA 19-9). The authors suggested that this proteomic signature could be used to distinguish good responders from limited responders for stage III and stage IV patients with an AUC of 0.83 and 0.87, respectively [165]. One other study, conducted in tumor and adjacent pancreas tissue samples by Sahni et al., identified a group of 19 proteins (e.g., GRP78, CADM1, PGES2, and RUXF with AUC ≥ 0.92) that were significantly upregulated in poor-responders, enabling the prediction of chemo-resistant tumor phenotype [166]. Also, Le Large et al. [167], in a study conducted on gemcitabine-sensitive and gemcitabine-resistant cell lines, identified two proteins microtubule-associated protein 2 (MAP2) and anti-ankyrin-3 (ANK3), highly upregulated and phosphorylated in cell resistant cells. Kim et al., also working with cell lines, identified a panel of 107 proteins in which expression levels changed between oxaliplatin-resistant and sensitive cells. In this study, a stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative proteomics analysis strategy, myristoylated alanine-rich C-kinase substrate (MARCKS) and WLS (Wnt/β-catenin signaling), was demonstrated to be involved in oxaliplatin resistance in pancreatic cancer cells [168]. Similarly, Chiu et al. also pointed out in a review paper, the use of MARCKS in the metastasis and treatment resistance of solid tumors [169]. In the case of the WLS, several studies have pointed in the direction of developing small-molecular compounds targeting the WLS pathway in disease treatment, as reviewed by Liu et al. [170]. In addition, Lin et al., in a study on the evaluation of gemcitabine resistance metabolomic profile, observed that many differentially expressed proteins quantified in mutant gemcitabine-resistant cells, revealing that these cells modulate several pathways to adapt to gemcitabine-induced stress. These authors also postulate that the therapeutic effectiveness could be increased by targeting the gemcitabine metabolic pathways with the introduction of treatment combinations, which would increase gemcitabine efficacy [171]. Gemcitabine, being one of the main chemotherapy drugs used to treat pancreatic cancer, has led other researchers to evaluate the resistance and sensitivity to this drug. For instance, Kim et al. [172], identified 13 epithelial to mesenchymal transition-related proteins which were closely associated with drug resistance and differentially expressed. In a more recent study, Amrutkar et al. [173] identified multifunctional cell types found in endocrine and exocrine pancreatic tissue, known as pancreatic stellate cells, that are quiescent and regulate extracellular matrix production and, from these cells, identified diverse protein expression profiles that could be associated with gemcitabine-resistance.
However, despite the very interesting results obtained by Le Large et al. [167], Kim et al. [168], and others, with cell lines, it is important to keep in mind that the complexity of an in vivo system is very different from an in vitro system. In fact, as demonstrated by Coleman et al. [174], some proteins expression can be lost in cell lines, e.g., 63 proteins were exclusively expressed in patient tissue samples, and 324 proteins were identified as specific to the cell line, which, in this case, most probably are proteins associated with cell survival in culture.
In summary, these studies underscore the promising potential of proteomic signatures in forecasting treatment responses and patient outcomes in pancreatic cancer. Proteomic analyses have yielded invaluable insights into the molecular mechanisms driving the onset, progression, and treatment responses of this lethal disease, thanks to an understanding of these mechanisms. This has led to the creation of new tools for prognosis and prediction based on proteomic signatures, offering hope to enhance clinical care for patients with pancreatic cancer.

This entry is adapted from the peer-reviewed paper 10.3390/proteomes11030024

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