Profile-Rafael Contreras

Rafael Contreras-Galindo, Ph.D.

Techniques Used

Cytogenetics, next generation sequencing (Illumina, Pac Bio) and bioinformatics analysis, molecular biology techniques, PCRs (inverse, touchdown, RFLPs, RACEs, real-time qPCRs), Reverse Transcriptase activity, immuno-electron microscopy, western blotting, FISH, immunofluorescence and IPs, cell culture, viral replication and infectivity assays with reporter genes, flow cytometry, phylogenetic studies of viral populations, recombination assays, nucleic assay sequence-based amplification (NASBA)

Research Description

Human Centromere Sequences in Cancer and Genetic Disorders

The centromere is the functional unit responsible for faithful segregation of chromosomes, and its structure is made of centromeric proteins that bind to the underlying centromeric DNA sequence. During cell division, the microtubules bind to centromeric structures and pull chromosomes apart. Failure to reliably partition chromosomes to daughter cells results in chromosome instability (CIN) and aneuploidy, a hallmark of late-stage cancers and many genetic defects. Despite the well-known function of centromeres in cell division, little is known about the role of human centromere DNA in centromere formation and function. Decoding the centromere sequence has been challenging mainly due to the difficulty of assembling repetitive sequences with current technology; as such, a functional map of the human centromere remains one of the last frontiers of genomics. In view of the necessity for proper centromeric function in maintaining genomic stability, disordered centromere genetic function could play a crucial role in CIN and aneuploidy, although this issue has not been well-examined. We have recently devised rapid, PCR-based methods that can be used to study the structure, function, and sequence evolution of specific centromere sequences in cells of interest, and can now unambiguously study the centromeres of virtually all human chromosomes. Our preliminary studies suggest that the centromere landscape varies among modern humans and is severely mutated in certain cancer cells. The degree of mutation is more prevalent in the pericentromeric domains, areas of the genome that have been heavily invaded by retroelements during human evolution. We are exploring the effect of centromere mutations on cell and genome biology in health and disease. We study the role of centromere DNA on centromere function, genome instability and aneuploidy.  This work also holds the potential to lead to new therapeutic targets for centromere stability in cancer and other diseases.

Human Endogenous Retroviruses

Eight percent of the human genome is composed of endogenous retroviruses that are remnants of viruses that infected germ-line cells millions of years ago. Over the years these viruses accumulated mutations that inactivate their ability to replicate. Only one family of these viruses, termed HERV-K (HML-2), is able to produce viral-like particles and debate exists whether these particles are infectious. Our preliminary observations suggest that HERV-K viruses produced in the some cell lines are infectious. We have also recently observed and reported that these viruses are found in the plasma of people with certain cancers and HIV infection, however studies of the viral RNA genome revealed clues from viral replication only in patients with lymphoma and HIV infection. My project is intended to study the replication and pathogenesis of these viruses in modern humans.

Publications

1: Contreras-Galindo R, Kaplan MH, Dube D, Gonzalez-Hernandez MJ, Chan S, Meng F, Dai M, Omenn GS, Gitlin SD, Markovitz DM. Human Endogenous Retrovirus Type K (HERV-K) Particles Package and Transmit HERV-K-Related Sequences. J Virol. 2015 Jul;89(14):7187-201. doi: 10.1128/JVI.00544-15. Epub 2015 Apr 29. PubMed PMID: 25926654; PubMed Central PMCID: PMC4473553.

2: Zahn J, Kaplan MH, Fischer S, Dai M, Meng F, Saha AK, Cervantes P, Chan SM, Dube D, Omenn GS, Markovitz DM, Contreras-Galindo R. Expansion of a novel endogenous retrovirus throughout the pericentromeres of modern humans. Genome Biol. 2015 Apr 12;16:74. doi: 10.1186/s13059-015-0641-1. PubMed PMID: 25886262; PubMed Central PMCID: PMC4425911.

3: Dube D, Contreras-Galindo R, He S, King SR, Gonzalez-Hernandez MJ, Gitlin SD, Kaplan MH, Markovitz DM. Genomic flexibility of human endogenous retrovirus type K. J Virol. 2014 Sep 1;88(17):9673-82. doi: 10.1128/JVI.01147-14. Epub 2014 Jun 11. PubMed PMID: 24920813; PubMed Central PMCID: PMC4136327.

4: Gonzalez-Hernandez MJ, Cavalcoli JD, Sartor MA, Contreras-Galindo R, Meng F, Dai M, Dube D, Saha AK, Gitlin SD, Omenn GS, Kaplan MH, Markovitz DM. Regulation of the human endogenous retrovirus K (HML-2) transcriptome by the HIV-1 Tat protein. J Virol. 2014 Aug;88(16):8924-35. doi: 10.1128/JVI.00556-14. Epub 2014 May 28. PubMed PMID: 24872592; PubMed Central PMCID: PMC4136263.

5: Contreras-Galindo R, Kaplan MH, He S, Contreras-Galindo AC, Gonzalez-Hernandez MJ, Kappes F, Dube D, Chan SM, Robinson D, Meng F, Dai M, Gitlin SD, Chinnaiyan AM, Omenn GS, Markovitz DM. HIV infection reveals widespread expansion of novel centromeric human endogenous retroviruses. Genome Res. 2013 Sep;23(9):1505-13. doi: 10.1101/gr.144303.112. Epub 2013 May 8. PubMed PMID: 23657884; PubMed Central PMCID: PMC3759726.

6: Monde K, Contreras-Galindo R, Kaplan MH, Markovitz DM, Ono A. Human endogenous retrovirus K Gag coassembles with HIV-1 Gag and reduces the release efficiency and infectivity of HIV-1. J Virol. 2012 Oct;86(20):11194-208. Epub 2012 Aug 1. PubMed PMID: 22855497; PubMed Central PMCID: PMC3457174.

7: Gonzalez-Hernandez MJ, Swanson MD, Contreras-Galindo R, Cookinham S, King SR, Noel RJ Jr, Kaplan MH, Markovitz DM. Expression of human endogenous retrovirus type K (HML-2) is activated by the Tat protein of HIV-1. J Virol. 2012 Aug;86(15):7790-805. doi: 10.1128/JVI.07215-11. Epub 2012 May 16. PubMed PMID: 22593154; PubMed Central PMCID: PMC3421662.

8: Contreras-Galindo R, Kaplan MH, Contreras-Galindo AC, Gonzalez-Hernandez MJ, Ferlenghi I, Giusti F, Lorenzo E, Gitlin SD, Dosik MH, Yamamura Y, Markovitz DM. Characterization of human endogenous retroviral elements in the blood of HIV-1-infected individuals. J Virol. 2012 Jan;86(1):262-76. doi: 10.1128/JVI.00602-11. Epub 2011 Oct 26. PubMed PMID: 22031938; PubMed Central PMCID: PMC3255917.

9: Dai M, Thompson RC, Maher C, Contreras-Galindo R, Kaplan MH, Markovitz DM, Omenn G, Meng F. NGSQC: cross-platform quality analysis pipeline for deep sequencing data. BMC Genomics. 2010 Dec 2;11 Suppl 4:S7. doi: 10.1186/1471-2164-11-S4-S7. PubMed PMID: 21143816; PubMed Central PMCID: PMC3005923.

10: Contreras-Galindo R, Kaplan MH, Leissner P, Verjat T, Ferlenghi I, Bagnoli F, Giusti F, Dosik MH, Hayes DF, Gitlin SD, Markovitz DM. Human endogenous retrovirus K (HML-2) elements in the plasma of people with lymphoma and breast cancer. J Virol. 2008 Oct;82(19):9329-36. doi: 10.1128/JVI.00646-08. Epub 2008 Jul 16. PubMed PMID: 18632860; PubMed Central PMCID: PMC2546968.  

11: Contreras-Galindo R, Almodóvar-Camacho S, González-Ramírez S, Lorenzo E, Yamamura Y. Comparative longitudinal studies of HERV-K and HIV-1 RNA titers in HIV-1-infected patients receiving successful versus unsuccessful highly active antiretroviral therapy. AIDS Res Hum Retroviruses. 2007 Sep;23(9):1083-6. PubMed PMID: 17919102.

12: Contreras-Galindo R, López P, Vélez R, Yamamura Y. HIV-1 infection increases the expression of human endogenous retroviruses type K (HERV-K) in vitro. AIDS Res Hum Retroviruses. 2007 Jan;23(1):116-22. PubMed PMID: 17263641.

13: Contreras-Galindo R, Kaplan MH, Markovitz DM, Lorenzo E, Yamamura Y. Detection of HERV-K(HML-2) viral RNA in plasma of HIV type 1-infected individuals. AIDS Res Hum Retroviruses. 2006 Oct;22(10):979-84. PubMed PMID: 17067267.

14: Contreras-Galindo R, González M, Almodovar-Camacho S, González-Ramírez S, Lorenzo E, Yamamura Y. A new Real-Time-RT-PCR for quantitation of human endogenous retroviruses type K (HERV-K) RNA load in plasma samples: increased HERV-K RNA titers in HIV-1 patients with HAART non-suppressive regimens. J Virol Methods. 2006 Sep;136(1-2):51-7. Epub 2006 May 6. PubMed PMID: 16678919.