Purpose
The Molecular Biology Laboratories host one of the leading genomic platforms in Romania and an outstanding biological resource center, currently possessing a retrospective collection of biospecimens such as tumor and normal tissues obtained after curative surgery, from over 2000 patients, mainly with digestive tumors. The laboratories are actively involved in the development of antitumor therapies through identification of molecular markers for diagnosis and prognosis, as well as therapeutic targets. As a key result, we will deliver a personalized medicine approach by translating the scientific results into clinical practice.
Currently, our main focus is the analysis of tissue samples through histological methods, and molecular biology methods such as real-time PCR, microarray, flow-cytometry, and high-throughput technologies (Next Generation Sequencing, protein sequencing) for the identification of new biomarkers involved in early diagnosis, progression and metastasis of gastro-intestinal cancers that have the potential to become new targets for personalized therapy.
The main research themes addressed in the laboratory and financed by grants are:
- Evaluation of the molecular mechanisms involved in pancreatic ductal adenocarcinoma (PDA) by multi-omic approach: transcription profiles of PDAC through RNAseq; relationship between metastases and their corresponding PDAC primary tumor, as well as the evaluation of the prognostic role of genomic changes (mutations and changes in gene expression levels).
- Identification of circulating biomarkers of hepatocellular carcinoma (HCC) for detection and evaluation of disease aggressiveness in patients at risk.
- Investigation of immune responses in HCC and the impact of microRNA expression on key immune pathways by performing scRNA-Seq and miRNA-Seq of tumor-infiltrating lymphocytes (TILs) from primary and metastatic HCC tissue.
- Validation of specific miRNA signatures in ovarian cancer, highlighting potential targets for personalized treatment anddefining ovarian cancer subtypes, based on their miRNA profile.
- Identification of biomarkers and potential therapy targets in gastric cancer subtypes, response and resistance biomarkers to standard therapy, as well as vascular stroma particularities and the role on immune checkpoints in gastric cancer subtypes.
LABORATORY OF SEQUENCING AND FRAGMENT ANALYSIS
Our laboratory focuses on identifying biomarkers for early diagnosis, monitoring the progression of cancer, screening, and personalized anti-cancer therapy (to achieve the general objectives of translational medicine in oncology).
It is equipped for Sanger sequencing experiments allowing for the identification of SNPs involved in different pathologies, as well as equipment for high-throughput next generation sequencing, such as The PGM Ion Torrent Sequencing, a reliable sequencing platform that combines simple sample preparation and data analysis solutions with scalable chip output, for ultimate project flexibility.
Furthermore, the NextSeq Series delivers the power of high-throughput sequencing with the speed, simplicity, and affordability of a desktop NGS (next-generation sequencing) system. The fast, integrated, sample-to-results workflow enables many sequencing applications—including transcriptomes, exomes, and targeted panels—in a single run.
With this systems, we can perform a variety of targeted gene sequencing applications, such as variant detection in cancer and genetic disorders.
Infrastructure
- NextSeq 500 Sequencing System (Illumina)
- PGM Ion Torrent™ Sequencing System (Life Technologies)
- DNA Sanger Sequencer- Capillary electrophoresis system for nucleic acids (DNA) sequencing (Beckman Coulter)
- Hybex Microsample Incubator (SciGene)
LABORATORY OF NUCLEIC ACID EXTRACTION
This laboratory is essential since total nucleic acid extraction (total RNA and genomic DNA) is one of the most important steps in molecular biology. This procedure marks a starting point in any molecular scientific experiment and is routinely used in many fields of the biological and medical sciences. It therefore offers an opportunity for genomic DNA and total RNA isolation and analysis since it contains all necessary equipment.
Infrastructure
- Maxwell 16 MDx (Promega)
- DNA 120 SpeedVac Concentrator (Thermo Scientific)
- Microcentrifuge (Eppendorf)
- Circulating Water Bath (ThermoFisher Scientific)
- MiniSpin Microcentrifuge (Eppendorf)
- Block Heaters (Thermo Scientific)
LABORATORY OF PCR AND MICROARRAY
The laboratory facilities allow us to perform a variety of targeted gene applications, such as detection of gene expression in cancer and genetic disorders.
- Microarray is an important tool for gene expression profiling that can simultaneously evaluate the expression of thousands of genes.
- Real-Time PCR Systems offer the flexibility to meet a range of research needs, from basic research and diagnostics to human identification testing.
Infrastructure
- DNA Microarray Scanner (Agilent Technologies)
- 2100 Bioanalyzer System (Agilent Technologies)
- Tape Station 2200 (Agilent Technologies)
- NanoDrop (Thermo Scientific)
- IKA MS 3 Vortexer (Agilent Technologies)
- UV Transilluminator 2000 (Bio-Rad)
LABORATORY OF PROTEOMICS
This laboratory focuses on the analysis of proteins and peptides by flow cytometry and protein sequencing. Protein analysis can show response patterns characteristic for various cellular states. Flow cytometric techniques permit investigators to look at intracellular proteins in several different cell populations simultaneously. The BD FACSCalibur™ platform offers a unique modular approach to flow cytometry and allows users to perform both cell analysis and cell sorting in an innovative single bench-top system. Protein sequencing refers to methods for determining proteins primary structure. The amino acids of proteins can be used in bioinformatic analyses to predict protein structure and possible conformational 3D structures.
Infrastructure
- Luminex 200 Xmap Array System (Luminex)
- Protein sequencer system with accessories and dedicated software (Shimadzu Scientific Instruments)
- Multicolor Flow Cytometer – FACSCalibur™ Systems (BD Biosciences)
- Tali Image Based Cytometer (Invitrogen)
LABORATORY OF BIOLOGICAL SAMPLES PROCESSING
This Laboratory is dedicated to processing various types of biological samples (peripheral blood, tissue) that were collected under signed consent from patients that undergo surgeries on various oncological pathologies (colon cancer, gastric cancer, rectal cancer, pancreatic cancer, liver cancer, liver metastasis, and other types of cancer)in our institute.
The biological material is collected after obtaining written informed consent, in compliance with international ethical standards and specific European Union legislations (Regulation (EU) 2016/679 on the protection of natural persons with regard to the processing of personal data and on the free movement of such data (General Data Protection Regulation) “, Declaration of Helsinki with regards to ethical principles in medical research that involves human subjects -1964, Parliament and European Council laws regarding the manipulation and protection of personal data).
Infrastructure
- Analytical Balance (Sartorius)
- Heraeus Megafuge 8 (ThermoFisher Scientific)
- Hettich® EBA 20 centrifuge (Sigma-Aldrich)
- Mini-spin centrifuge (Eppendorf)
- Thermoblock (FALC)
- PMR-30 rocking shaker (Grant-Bio)
- Refrigerator (Thermo Scientific)
LABORATORY OF BIOBANKING
Members
INNOVATIVE RESEARCH OF EUROPEAN LEVEL
CENTER OF EXCELLENCE IN TRANSLATIONAL MEDICINE
The strategic goal is to create research cores with advanced technological facilities in the form of research platforms by associating preclinical research laboratories and clinical research centers within the Fundeni Clinical Institute in a unique entity.
The newly created structure provides logistical support for biomedical research through the coordination of studies, quality management, data monitoring, dissemination of good clinical practice, database management and data analysis. Infrastructure is also dedicated to the production of vectors for gene and cellular therapy, as well as for the acquisition of new agents with therapeutic potential in digestive affection.