Research at the PPMF

As one of the goals of the Philippine Genome Center, the Protein, Proteomics and Metabolomics Facility (PPMF) aims to provide opportunities to our scientists, collaborators, and partners in their utilization of state-of-the-art technologies for relevant research. The PPMF is highly involved in protein characterization and OMICS-related research for health, agriculture, and biomaterials.

We invite you to partner and collaborate with us for your research. You may email us for inquiries with the subject “COLLAB: [topic/field]”

Ongoing Projects

1. Proteomic Analysis of Philippine SARS-CoV2 Patient Plasma by Artificial Intelligence and High-Resolution Mass Spectrometry (eASIA-Collaboration: MiByo Technology)

Despite the constant threat of COVID-19 globally, the pandemic has also provided an opportunity for the scientific community to collaborate to understand this disease and to develop vaccines and therapeutics at an unprecedented rate. Through OMICS technologies, the MiByo project aims to analyze the proteomic character of SARS-CoV-2 patient plasma from the Philippines in order to determine potential biomarkers that may be relevant for the prediction of disease severity and progression. Biomarker identification will employ two parallel methods: artificial intelligence (AI) and ultra-high-performance liquid chromatography and mass spectrometry (UHPLC-MS) systems. The AI technology will perform efficient analysis of the complex datasets from 2D gel electrophoresis profiles acquired from patients of a wide range of disease severities and phenotypic characters. A parallel analysis will be conducted using the UHPLC-MS system to validate the AI predictions. Data from this project may contribute to generating a wider database of patient samples from collaborating partners in Thailand and Japan. Through the identification of potential protein markers for disease severity and progression, improved test kits may be used for earlier detection, better disease assessment, and more effective treatment strategies.

2. Screening for Metabolomic Biomarkers of Diabetic Nephropathy in Filipino adult Type 2 Diabetes Mellitus Patients

Diabetes mellitus is one of the most prevalent diseases in the Philippines. Diabetes usually progresses to a form of diabetic or chronic kidney disease (DKD) or diabetic nephropathy (DN), which comprise a range of renal diseases arising from poorly controlled diabetes. DN or DKD is usually characterized by glomerular damage found in end-stage renal disease (ESRD), it is estimated that 5-40 % of diabetes patients will ultimately develop DN. The metabolomic analysis investigates a large number of small molecule metabolites from bodily fluids and tissues, with quantitative detection in a single step. Metabolomics through high-resolution mass spectrometry can give valuable data for translational and clinical research. This project aims to identify potential biomarkers present in type 2 diabetes mellitus (T2DM) Filipino patients during the different stages of DN using untargeted metabolomics analysis. The metabolic biomarkers that will be discovered would serve as a potential therapeutic target for the disease. This comparative analysis between healthy and sick patients may help give an insight into the pathogenesis of certain diseases, monitoring of therapies, as well as aid in prognosis, and early diagnosis.

Approved Projects

1. The Clinical Utility of HRMS Analysis in the Prognostication of Hereditary Breast Cancer in Filipino Patients

According to the Philippine Statistics Authority, three out of 100 Filipino women are said to be diagnosed with breast cancer in their lifetime. Despite its high prevalence, local prognosis methods for cancer are limited. Standard or conventional methods (e.g. immunohistochemistry staining, fluorescence in-situ hybridization) for characterizing breast cancer tissues are prone to considerable inter-observer variability and bias. Technological advancements have paved the way for the accurate quantification of breast cancer biomarkers, such as enzyme-linked immunosorbent assays (ELISA) and mass spectrometry (MS). ELISA kits are highly specific and reliable colorimetric techniques; however, these are costly, limited, and designed for quantifying single protein targets per run. In contrast, MS analysis is regarded as the gold standard for target protein analysis, and it allows more sensitive and efficient quantification of relevant protein biomarkers in a single run. The use of both high-resolution MS analysis, and commercially available ELISA kits for biomarker quantification would allow unbiased assessment of their accuracy and reliability for this purpose. Thus, this project aims to quantify and characterize breast cancer biomarkers using standard (IHC) and alternative (ELISA and MS) detection methods to aid the prognostication of hereditary breast cancer in Filipino patients. A proteome-based approach for characterizing the different breast cancer disease stages would allow oncologists to utilize molecular diagnostics for personalized treatment strategies. More importantly, defined biomarker levels for breast cancer staging would allow the development of point-of-care detection technologies for prognostication.

Collaborative Projects

1. Functionalization of bacterial cellulose with ultrasonication-induced silk fibroin β-sheet crystals

Bacterial cellulose (BC) is known to be more crystalline than plant cellulose but is limited by its design of repeating β-1,6 glycosidic-linked glucose molecules. Silk fibroin (SF), a silk-derived protein, is known to be highly biocompatible due to the inherent reactivity of its encoded amino acid sequence. In this study, we synthesized a BC-SF biocomposite where the BC was functionalized with beta-sheet SF, and succeedingly induced to form crystals by ultrasonication. SF was extracted from raw silk and dissolved using conventional methods. BC-SF biocomposites were synthesized by incubating SF with (BC) hydrogels followed by ultrasonication treatment. The formed beta-sheet crystals were analyzed using circular dichroism (CD) spectropolarimetry, Thioflavin T (ThT) assays, differential scanning calorimetry-thermogravimetric analysis (DSC-TGA), and infrared spectroscopy (FT-IR). Collected data revealed increased beta-sheet through increased ThT fluorescence values upon ultrasonication treatment of extracted SF. This was further supported by CD secondary structure analysis and peaks present in infrared spectra. Thermal analysis data suggest that the protein aggregates are silk II-dominant structures that were induced from their silk I structure via ultrasonication. This study was successful in proving the increase in beta-sheet content induced by tuning ultrasonication parameters. This method also proved to be a facile and reliable way to strengthen the polymer without compromising the crystalline structure of microbial cellulose, which is most suitable for biomedical applications.

2. Urine Metabolomic Characterization Among Children with Different Tuberculosis Status

Tuberculosis (TB) remains a significant cause of morbidity and mortality among children, with around one million developing the disease, and more than half of those are under five years old. Progress has been observed, but a lack of routine reporting in the age groups results in insufficient data to guide intervention and determine treatment outcomes. In this study, urine metabolomic outputs will be profiled using Liquid chromatography-mass spectroscopy to determine the metabolic profile of  four TB status in children; a) active TB infection, b) latent TB infection, c) healthy contacts, d) and converters to active TB. This non-invasive characterization to distinguish different TB pathologic status through urine metabolomic profiles should view altered cellular and or metabolic pathways that may aid in improving the diagnosis of children with TB, allow the early provision of anti-TB therapy, and monitor the effects of these employed therapies.