Matteo Pellegrini, Ph.D. 

Matteo Pellegrini, Ph.D., develops computational approaches to interpret genomic data collected from cell and tissue samples using high-throughput sequencing technologies. High throughput technologies use specialized machines to collect millions of data points in parallel and enable researchers to conduct whole genome sequencing, the mapping of an organisms’ unique genetic code. Pellegrini is developing tools to interpret and analyze these data to extract key insights into how the body is functioning. He hopes these insights will help doctors advise their patients to avoid health risks to which they are genetically predisposed and enable the early diagnosis of diseases like cancer.

Pellegrini’s lab analyzes human tissue samples to collect data on methylation, a biochemical process that occurs naturally in DNA. They also study RNA sequences in a sample to determine the amount of gene expression in a certain cell or tissue type. RNA serves an important purpose inside cells; it carries genetic messages from DNA. These messages direct cells to make the proteins that play many critical roles in the body. By collecting and comparing the data for different types of cells including stem cells, the lab can determine how these cell types normally function and identify how changes in the normal levels of gene activity or methylation can be viewed as a sign, or biomarker, of disease or predisposition to disease. The team is currently exploring biomarkers for normal and abnormal aging of tissues, for pregnancies that are more likely to have complications, as well as for the predisposition to obesity-related diseases. Widespread recognition and testing of these biomarkers would enable clinicians to predict their individual patients’ health outcomes, and to provide tailored advice to ameliorate these health risks. 

Pellegrini aims to apply these same methods to improve the diagnosis and treatment of cancer. His lab is working to establish methods to diagnose cancer from blood tests that can detect traces of the cancer’s DNA in patients' blood. Measuring the methylation of cancer DNA can shed light on the cancer’s epigenetic state and indicate which treatments might be most effective. These tests, called liquid biopsies, could be used to help find cancer at an early stage, before a lump or mass is big enough to be detected, and to closely monitor a given treatment’s efficacy. Pellegrini is also interested in analyzing blood samples on a cellular level to gain insights into a how a patient’s immune system is functioning and to detect inflammation.

In addition to researching human disease, Pellegrini collaborates with researchers from UCLA, UC Berkeley and UC San Diego to map the genomes of less studied organisms such as oak trees and the green alga Chromochloris zofingiensis. They hope this work will inform the development of novel biofuels and plant-based medicines, and help researchers predict how certain organisms will respond to climate change. 

Pellegrini earned a doctorate in physics from Stanford University and completed post-doctoral training in bioinformatics at UCLA.