Photo of Lucia Carbone, Ph.D.

Lucia Carbone Ph.D.

    • Assistant Professor of Medicine, Division of Cardiovascular Medicine School of Medicine
    • Assistant Professor of Molecular and Medical Genetics School of Medicine
    • Assistant Professor of Medical Informatics and Clinical Epidemiology School of Medicine

How do genomes change during evolution? To what extent are mechanisms responsible for evolutionary changes also relevant to human disease? Much is understood about fine-scale genomic changes (e.g. point mutations), but the mechanisms of large-scale chromosomal rearrangements (inversion, translocation, fission and fusion) are still unknown. Large-scale chromosome changes are key events in speciation and cancer; therefore it is critical to define how they occur, and their impact on genome architecture. Dr. Carbone's research has focused on chromosome evolution, particularly centromere repositioning and chromosomal rearrangements, and has recently highlighted a deep similarity between the sources of chromosome instability in species evolution and cancer. To learn about the causes of chromosomal rearrangements, she has studied chromosome evolution in gibbons, a family of primate species closely related to the great apes (human, chimpanzee, gorilla and orangutan). During the evolution of the gibbon species, there has been an exceptionally high frequency of chromosomal rearrangements, which is not explained by current models of chromosome evolution. Dr. Carbone's research has uncovered evidence that this phenomenon may have been driven by a defect in epigenetic controls. Epigenetic modifications are not reflected in the DNA sequence, but may nevertheless be heritable. Transposable Elements (TEs) often have deleterious effects on the integrity of the genome and cytosine methylation is a key epigenetic modification used by vertebrates to repress their activity. The study of chromosomal breakpoints in gibbon species revealed that TEs at the breakpoints are undermethylated when compared to their homologous human sequences. The significance of this observation is highlighted by the occurrence of a similar phenomenon in cancer cells. Cancer cell genomes are both globally hypomethylated and heavily rearranged, but no direct correlation between the two phenomena has yet been experimentally validated. One of the goals of the Carbone lab is to explore a mode of chromosome evolution in which the impairment of epigenetic repression of transposable elements causes a higher frequency of chromosomal rearrangements. The long-term strategy will be to use insights gleaned from species comparisons to understand the mechanism of chromosomal rearrangement in cancer, in combination with studies on cancer patients. The research in Carbone lab will benefit from innovative technologies, as massively parallel sequencing, and will contribute to the development of new tools for data production and analysis.

Publications

  • "Sequencing thousands of single-cell genomes with combinatorial indexing." Nature Methods  In: , Vol. 14, No. 3, 28.02.2017, p. 302-308.
  • "Endogenous retroviruses : With us and against us." Frontiers in Chemistry In: , Vol. 5, No. APR, 23, 2017.
  • "IFPA meeting 2016 workshop report I : Genomic communication, bioinformatics, trophoblast biology and transport systems." Placenta In: , 12.12.2016.
  • "Investigating somatic aneuploidy in the brain : why we need a new model." Chromosoma  In: , 16.09.2016, p. 1-14.
  • "Genomewide ancestry and divergence patterns from low-coverage sequencing data reveal a complex history of admixture in wild baboons." Molecular Ecology  In: , Vol. 25, No. 14, 01.07.2016, p. 3469-3483.
  • "Transcriptomic and epigenomic characterization of the developing bat wing." Nature Genetics  In: , Vol. 48, No. 5, 01.05.2016, p. 528-536.
  • "The flow of the gibbon LAVA element is facilitated by the LINE-1 retrotransposition machinery." Genome Biology and Evolution In: , Vol. 8, No. 10, 2016, p. 3209-3225.
  • "Whole-genome characterization in pedigreed non-human primates using genotyping-by-sequencing (GBS) and imputation." BMC Genomics  In: , Vol. 17, No. 1, 676, 2016.
  • "Mammalian pre-implantation chromosomal instability : Species comparison, evolutionary considerations, and pathological correlations." Systems Biology in Reproductive Medicine In: , Vol. 61, No. 6, 02.11.2015, p. 321-335.
  • "Response to Hron et al." Genome Biology In: , Vol. 16, No. 1, 165, 18.08.2015.
  • "Ring chromosomes, breakpoint clusters, and neocentromeres in sarcomas." Genes Chromosomes and Cancer  In: , Vol. 54, No. 3, 01.03.2015, p. 156-167.
  • "Examining phylogenetic relationships among gibbon genera using whole genome sequence data using an approximate bayesian computation approach." Genetics In: , Vol. 200, No. 1, 01.01.2015, p. 295-308.
  • "Gibbon genome and the fast karyotype evolution of small apes." Nature In: , Vol. 513, No. 7517, 11.09.2014, p. 195-201.
  • "Inference of Transposable Element Ancestry." PLoS Genetics In: , Vol. 10, No. 8, e1004482, 14.08.2014.
  • "Genomic organization and evolution of double minutes/homogeneously staining regions with MYC amplification in human cancer." Nucleic Acids Research  In: , Vol. 42, No. 14, 2014, p. 9131-9145.
  • "Conserved syntenic clusters of protein coding genes are missing in birds." Genome Biology In: , Vol. 15, No. 12, 2014, p. 565.
  • "Metabolic consequences of incorrect insulin administration techniques in aging subjects with diabetes." Diabetes Technology and Therapeutics In: , Vol. 15, No. SUPPL.1, 01.06.2013.
  • "Incomplete Lineage Sorting Is Common in Extant Gibbon Genera." PLoS One  In: , Vol. 8, No. 1, e53682, 18.01.2013.
  • "A comprehensive molecular cytogenetic analysis of chromosome rearrangements in gibbons." Genome Research  In: , Vol. 22, No. 12, 12.2012, p. 2520-2528.
  • "An alu-based phylogeny of gibbons (hylobatidae)." Molecular Biology and Evolution In: , Vol. 29, No. 11, 11.2012, p. 3441-3450.
  • "Centromere remodeling in Hoolock leuconedys (Hylobatidae) by a new transposable element unique to the gibbons." Genome Biology and Evolution In: , Vol. 4, No. 7, 2012, p. 648-658.
  • "Long-range massively parallel mate pair sequencing detects distinct mutations and similar patterns of structural mutability in two breast cancer cell lines." Cancer genetics  In: , Vol. 204, No. 8, 08.2011, p. 447-457.
  • "Patterns of genetic variation within and between gibbon species." Molecular Biology and Evolution In: , Vol. 28, No. 8, 08.2011, p. 2211-2218.
  • "Metabolic consequences of incorrect insulin administration techniques in aging subjects with diabetes." Acta Diabetologica  In: , Vol. 48, No. 2, 06.2011, p. 121-125.
  • "Isolation of specific clones from nonarrayed BAC libraries through homologous recombination." Journal of Biomedicine and Biotechnology In: , Vol. 2011, 560124, 2011.
  • "A small, variable, and irregular killer cell Ig-like receptor locus accompanies the absence of MHC-C and MHC-G in gibbons." Journal of Immunology  In: , Vol. 184, No. 3, 01.02.2010, p. 1379-1391.
  • "Genomics through the lens of next-generation sequencing." Genome Biology In: , Vol. 11, No. 6, 2010, p. 306.
  • "Evolutionary breakpoints in the gibbon suggest association between cytosine methylation and karyotype evolution." PLoS Genetics In: , Vol. 5, No. 6, e1000538, 06.2009.
  • "A chromosomal inversion unique to the northern white-cheeked gibbon." PLoS One In: , Vol. 4, No. 3, e4999, 25.03.2009.
  • "A satellite-like sequence, representing a "clone gap" in the human genome, was likely involved in the seeding of a novel centromere in macaque." Chromosoma  In: , Vol. 118, No. 2, 2009, p. 269-277.

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