
Bio
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.
Publications
- Mapping human haematopoietic stem cells from haemogenic endothelium to birthPublished in Nature on Wednesday, April 13, 2022
- The cardiomyocyte disrupts pyrimidine biosynthesis in non-myocytes to regulate heart repairPublished in Journal of Clinical Investigation on Tuesday, November 23, 2021
- Development of allogeneic HSC-engineered iNKT cells for off-the-shelf cancer immunotherapyPublished in Cell on Tuesday, November 16, 2021
- Targeting monoamine oxidase A-regulated tumor-associated macrophage polarization for cancer immunotherapyPublished in Nature Communications on Thursday, June 10, 2021
- Metabolic reprogramming and epigenetic changes of vital organs in SARS-CoV-2 induced systemic toxicityPublished in JCI Insight on Monday, December 7, 2020
- Endocardially Derived Macrophages Are Essential for Valvular RemodelingPublished in Developmental Cell on Thursday, February 21, 2019
- Topological Arrangement of Cardiac Fibroblasts Regulates Cellular PlasticityPublished in Circulation Research on Tuesday, April 24, 2018
- Glucose inhibits cardiac muscle maturation through nucleotide biosynthesisPublished in eLife on Tuesday, December 12, 2017
- Sequencing of Cancer Cell Subpopulations Identifies Micrometastases in Bladder CancerPublished in Oncotarget on Friday, April 21, 2017
- Human Embryonic Stem Cells Do Not Change Their X Inactivation Status during DifferentiationPublished in Cell Reports on Thursday, December 15, 2016
- Cardiac Fibroblasts Adopt Osteogenic Fates and Can Be Targeted to Attenuate Pathological Heart CalcificationPublished in Cell Stem Cell on Thursday, November 17, 2016
- Biased Expression of the FOXP3Δ3 Isoform in Aggressive Bladder Cancer Mediates Differentiation and Cisplatin Chemotherapy ResistancePublished in Clinical Cancer Research on Monday, November 7, 2016
- CRISPR/Cas9-mediated correction of the sickle mutation in human hematopoietic stem/progenitor cells Published in Molecular Therapy on Friday, July 29, 2016
- A Designed Inhibitor of p53 Aggregation Rescues p53 Tumor Suppression in Ovarian CarcinomasPublished in Cancer Cell on Monday, January 11, 2016
- Molecular Profiling of Premalignant Lesions in Lung Squamous Cell Carcinomas Identifies Mechanisms Involved in Stepwise CarcinogenesisPublished in Cancer Prevention Research on Tuesday, March 11, 2014
- SRA- and SET-domain-containing proteins link RNA polymerase V occupancy to DNA methylationPublished in Nature on Wednesday, January 22, 2014
- Estrogen and progesterone together expand murine endometrial epithelial progenitor cellsPublished in Stem Cells on Sunday, March 24, 2013
- Stage-Specific Roles for Tet1 and Tet2 in DNA Demethylation in Primordial Germ CellsPublished in Cell Stem Cell on Thursday, February 14, 2013
- The ontogeny of cKIT+ human primordial germ cells proves to be a resource for human germ line reprogramming, imprint erasure and in vitro differentiationPublished in Nature Cell Biology on Sunday, December 16, 2012
- Scl Represses Cardiomyogenesis in Prospective Hemogenic Endothelium and EndocardiumPublished in Cell on Thursday, August 2, 2012
- Novel Stem/Progenitor Cell Population from Murine Tracheal Submucosal Gland Ducts with Multipotent Regenerative PotentialPublished in Stem Cells on Friday, June 24, 2011
- Global phosphoproteomics reveals crosstalk between Bcr-Abl and negative feedback mechanisms controlling Src signalingPublished in Science Signaling on Tuesday, March 29, 2011
- Molecular analyses of human induced pluripotent stem cells and embryonic stem cellsPublished in Cell Stem Cell on Friday, August 6, 2010
- Relationship between nucleosome positioning and DNA methylationPublished in Nature on Sunday, May 30, 2010
- Induced Pluripotent Stem Cells and Embryonic Stem Cells Are Distinguished by Gene Expression SignaturesPublished in Cell Stem Cell on Thursday, July 2, 2009
- Epigenetic reprogramming by adenovirus e1aPublished in Science on Friday, August 22, 2008
- Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterningPublished in Nature on Sunday, February 17, 2008
Honors & Affiliations
Affiliations
- UCLA Jonsson Comprehensive Cancer Center
- UCLA California Nanosystems Institute
- UCLA Institute for Quantitative and Computational Biosciences
- UCLA Institute for Genomics and Proteomics
Funding
Pellegrini’s research is supported by the National Institutes of Health, the National Science Foundation and the United States Department of Energy.