GEN-MKT-18-7897-A
Apr 10, 2025 | Blogs, Life Science Research | 0 comments
Pancreatic cancer remains one of the most fatal types of cancer, and the rates of occurrences and mortalities continue to be on a global rise.1,2 Recent statistics have reported that the diagnosis of pancreatic cancer is the eighth most common type of cancer and accounts for the third highest number of cancer-related deaths. Incidence rates for pancreatic cancer for both genders are reported highest in North America, Europe, and Australia/New Zealand.1 Unfortunately, the survival rate for diagnosed pancreatic cancer patients is the poorest among all other types of cancer, with only 11% predicted to survive five years. While there are multiple subtypes of pancreatic cancer, the main subtype is pancreatic ductal adenocarcinoma (PDAC), which accounts for >90% of cases of malignant pancreatic neoplasms.2
At the Department of Biochemistry and Biomedicine Discovery Institute, Monash University in Victoria, Australia, under the supervision of Prof. Dr. Anthony Purcell, Mohammadreza (Reza) Dorvash specializes in antigen discovery for pancreatic cancer immunotherapy using mass spectrometry (LC-MS/MS). Reza utilizes state-of-the-art proteomics technologies to advance his investigation of pancreatic cancer immunopeptidome (T-cell targets) isolated from minimal input materials. His research focuses on immunopeptides derived from tumor-associated antigens and endogenous retroviruses, as well as studying the effects of perturbed signaling pathways on the immunoligandome of pancreatic cancer. In this video, Reza presents an overview of his current work.
The dismal prognosis of pancreatic cancer
If a patient is diagnosed in the earlier stages of the disease, they at least can profit from conventional chemoradiotherapy and surgical options for their pancreatic cancer. However, most patients with pancreatic cancer remain asymptomatic until the disease reaches an advanced stage.3 Unfortunately, conventional approaches are less effective against the disease after local advancement or distant metastasis to other tissues and organs. As a result, there has been significant effort towards immunotherapy options for this disease.
Optimizing immunopeptidomics methods for T cell tumor-antigen identification
Recent studies have demonstrated that T cells can be effective weapons against pancreatic cancer. Although the cancer of the pancreas is considered immunologically cold (whereby the T cells within pancreatic tumors are generally infrequent or incapable of eliciting anti-tumor immunity), a “calibrated T cell immunity” can still propagate towards eliminating cancer cells. These studies suggest that pancreatic cancer patients’ clinical outcomes can be improved by unveiling the complex immune biology of this disease.4
One of the goals of an immunopeptidomics study is to have a rational design for T-cell-based immunotherapy. Immunopeptides are peptide fragments derived from source antigens through specific machinery in the cell. They are presented on the cell surface to assist immune cells, like T cells, with immune surveillance. These peptides bind to a family of proteins called Major Histocompatibility Complexes (MHC), which has two classes, MHC Class I and MHC Class II. Each MHC class has unique characteristics, like length distribution and the type of motif accepted (in terms of arrangement of amino acids).
To study the immunopeptidome, Reza explains that they first need to co-immunoprecipitate the MHC-peptide complex, isolate and purify the peptides, and then characterize them using mass spectrometry. If certain characteristics typical to immunopeptides, such as the length distribution or sequence motif(s), are observed, the workflow would continue with target discovery.
Various peptide antigens constitute the repertoire of immunopeptides, such as tumor-associated antigens, mutated peptides (or neoantigens), post-translationally modified (PTM-) peptides, and endogenous retrovirus-derived peptides. A plethora of literature has harnessed a subset of these immunopeptides to target various tumors, including pancreatic cancer. Regardless of the type of peptides recovered, various immunotherapy approaches can be utilized. Reza explains,
“For example, there are potentially immunogenic peptides that are upregulated on the tumor cells but are not upregulated (or are not present) on healthy (pancreatic) tissue, or even healthy distant tissue (healthy skin, for instance) in a pancreatic cancer patient. So, suppose you can find an immunogenic peptide that is upregulated on the tumor cells, regardless of its flavor (or type). In that case, you have an effective immunotherapy approach or at least a step closer towards it.”
ZT Scan DIA advances immunopeptidomics via improved proteomic quantitative accuracy
To study the immunopeptidomic targets of PDAC, Reza uses the SCIEX ZenoTOF 7600+ system coupled to a Waters M-class liquid chromatography system to analyze pancreatic cancer cells. Using IonOpticks Aurora Elite nanoflow columns, Reza injected an on-column amount equivalent to 2.5 million cells of aliquot or peptides derived from 2.5 million Panc-1 cells in one run and then 25 million Panc-1 cells on-column in another run. Reza identified 12,000 peptides from this very low-yielding cancer type in a single run, which he exclaims “is just amazing”.
However, Reza continues to explain that the preeminent value of ZT Scan DIA is its quantitative accuracy and precision, with a tighter coefficient of variation (CV) compared to other methods. In his work, Reza presented data showcasing tighter CVs with sample loads of either 2.5 million or 25 million cells when using ZT Scan DIA compared to other DIA methods.
In addition, ZT Scan DIA identifies all the expected motifs of the present allotypes in Panc-1, which are HLA-A*02:01, -A*11:01, -B*38:01 and -C*12:03.
Furthermore, Reza presents data on targets he was able to recover. In the first example, he shows the results of a ZT Scan DIA spectral library match of PRAME, a well-recognized tumor-associated antigen in pancreatic cancer. As quoted by Reza,
“Here you are, seeing the ZT Scan DIA spectra. This beautiful, clean ZT Scan DIA spectra on the top versus the library spectra on the bottom, on the negative axis. And, well, seeing how DIA-NN [software] is performing well in isolating or extracting the signals across a very narrow peak and showing the co-elution of the fragments in this run for this peptide.”
Reza shares the mirror plot in the second example for another tumor-associated kinase called TTK, or Threonine and Tyrosine Kinase. Again, Reza shares the high quality of the ZT Scan DIA spectrum compared to its library fragments. Furthermore, ZT Scan DIA resolves interfering fragments, which, he explains, results from the very narrow 1 over M/Z isolation windows deployed by the acquisition method.
The potential for better outcomes
“Though the clinical efficacy of T cell therapy in PDAC is limited, it is a promising field of research with ongoing research exploring its effectiveness in various stages and combinations with other therapies.5 As we continue to optimize the technology to advance immunopeptidomics workflows, we hope to understand pancreatic cancer immunity further and improve the outcomes for these patients.”
Imagine having a tech expert at your fingertips to solve computer issues or a fitness trainer guiding you through workouts from the comfort of your home. In today’s fast-paced world, the ability to provide and receive service and support remotely is no longer a luxury but a necessity. Whether it’s troubleshooting a software issue, repairing a device, offering customer assistance, or enjoying the convenience of telehealth as a private individual, remote capabilities have revolutionized how businesses operate and how individuals get help
It is no secret that (bio)pharmaceutical research and development is complex, both scientific and regulatory processes. Here is an overview of just some of the ways SCIEX is working to support these challenges.
In a recent webinar, available on demand, scientists Luiza Chrojan and Ryan Hylands from Pharmaron, provided insights into the deployment of capillary gel electrophoresis (CGE) within cell and gene therapy. Luiza and Ryan shared purity data on plasmids used for adeno-associated virus (AAV) manufacturing and data on AAV genome integrity, viral protein (VP) purity and VP ratios using the BioPhase 8800 system.
Posted by
You must be logged in to post a comment.
Share this post with your network