Research Scientist,
Columbia Genome Center, Associate Head, DNA Sequencing and Chemical Biology

Tel: (212) 851-5165
Fax: (212) 851-5215
Email: jjr4@columbia.edu

Sub-Group Members

Irina Morozova
Minchen Chien (Ming Chien)
Dave Weir

Key Words

• Cancer
• DNA Sequencing
• Gene Identification
• Herpesvirus
• Infectious Disease
• Legionella
• Mutation Detection
• Positional Cloning
• Association
• Aplysia

James Russo, Ph.D.

High throughput DNA sequencing has become an essential component of gene discovery, and the gold standard for identifying mutations that are responsible for the development of diseases. In our laboratory, we utilize DNA sequencing for both of these goals. Projects in the laboratory fall within four major areas: (1) whole genome sequencing; (2) disease gene discovery utilizing the positional candidate strategy; (3) identification of polymorphisms and mutations that directly cause diseases or increase the likelihood of developing disease phenotypes (association studies); and (4) designing biological applications of new sequencing and mutation analysis approaches developed by our colleagues in Dr. Jingyue Ju's laboratory. Examples from our work that typify each of these paradigms are presented. Investigators in our laboratory work closely with collaborators in a large number of basic science and clinical laboratories to translate these ideas into practical consequences. Moreover, many of these projects require cooperation among many specialties (neurobiology, genetics and epidemiology, molecular biology, chemical engineering, organic and photochemistry, and bioinformatics, to name a few).

Whole genome sequencing. Propelled by the Human Genome Initiative, sequencing of whole genomes has become commonplace. A number of years ago, in collaboration with Drs. Roy Bohenzky, Yuan Chang and Patrick S. Moore in the Department of Pathology, our laboratory obtained the 140 kb sequence of human herpesvirus 8, the causative agent of Kaposi sarcoma, the most common malignancy in AIDS patients. More recently, we completely sequenced the >3 million base genome of Legionella pneumophila. This bacterium is responsible for Legionnaires' disease and other pneumonia-like symptoms. It is found in most standing water supplies (water towers, plumbing systems, whirlpool baths, swimming pools), where it is part of biofilms and can survive within protozoa. When aerosols containing these bacteria are inhaled, they can enter lung macrophages. Rather than destroying these invaders, the macrophages serve as a pool for their replication. While many of the genes responsible for their pathogenicity are known from genetic analyses, having the complete genome sequence should aid greatly in identifying candidate genes to target with antibiotics and vaccines. Our approach to obtaining the complete sequence was a combined whole-genome, BAC-based shotgun approach. Further information on the Legionella genome project, along with tools for sequence retrieval and analysis, is available at http://legionella.cu-genome.org/. This project was a collaboration with Dr. Howard Shuman's laboratory in the Department of Microbiology, and members of the physical mapping and informatics groups of the Human Genome Center. We and our collaborators, including Dr. Sergey Kalachikov in the CGC, are involved in comparative genomics (looking for differences in potential virulence genes between pathogenic and non-pathogenic strains and species of Legionella by PCR/sequencing and computational approaches) and functional genomics (knocking out genes of interest in Legionella to determine their role in the organism's life cycle; utilizing Legionella gene microarrays for tracking changes in expression patterns during infection and following treatment with drugs). In the future, we expect to participate in projects to sequence other bacterial genomes (we have done some initial work and applied for funding to sequence non-pathogenic and pathogenic (in insect larvae) strains of Bacillus sphaericus), as well as eukaryotic genomes, in the latter case abetted by the newer sequencing approaches (pyrosequencing and SBE) beginning to come on line.

Disease gene discovery. Sequencing support provided by our laboratory was a major part of several gene discovery projects initiated by the Genome Center in collaboration with Dr. Riccardo Dalla-Favera of the Department of Pathology. Dr. Dalla-Favera's group is interested in cancers that involve various stage lymphocytes. These include lymphomas, leukemias, and multiple myelomas. Our approach was to use the positional cloning strategy. Once a locus has been delineated by deletion mapping or loss of heterozygosity analysis (in the case of putative tumor suppressor genes) or by the chance occurrence of a translocation breakpoint, and a physical map has been developed for the region, sequencing plays many important roles. Low-pass sequencing (2- to 3-fold coverage) of the area is accomplished following shotgun cloning of a tiling path of large clones (PACs, BACs or cosmids) within the region into plasmid sequencing vectors. At this level of coverage, the likelihood of having substantial sequence of most exons and all genes is quite high. Identification of genes is then possible by using various prediction algorithms, as well as from searches of the public EST databases,. Other approaches for determining candidate genes include cDNA selection or exon trapping with the regional clones as templates. The products of these reactions of course need to be sequenced not only to confirm that they represent true coding sequences, but in an attempt to ascertain their function. Sequencing of 3' and 5' RACE products is used to obtain full-length genes and to discover differentially spliced or polyadenylated gene variants. Candidate genes are prioritized based on their expression in lymphocytes, and available information on known homologues, after which mutation analysis is carried out by direct sequencing of cDNA's or exons in normal and tumor tissue. In addition to the cancer gene projects, this approach was also brought to bear in the Genome Center on several projects involving loci potentially involved in complex diseases, such as diabetes, obesity and neuropsychiatric disorders, though more commonly these are being pursued using association-based approaches (see below).

Another approach to discovery of tumor suppressor genes is to use subtractive methods in different pre-cancer stages. In one such project, Dr. Ramon Parson, another member of the Pathology Department, has used representational difference analysis (RDA) to identify potential new tumor suppressors in breast cancer. By sequencing many members of these RDA libraries, it should be possible to identify deleted regions of chromosomes that may harbor such tumor suppressors. With its collection of capillary based automated sequencers, our laboratory is in an excellent postion to rapidly sequence such RDA, SAGE, cDNA and other libraries.

Of particular interest has been the recent explosion of interest in miRNA's that are expected to play a role in developmental and pathogenic processes, via mainly post-transcriptional regulatory pathways (destruction of mRNA's or inhibition of translation). In collaboration with Dr. Thomas Tuschl at Rockefeller University, our group has been heavily involved in sequencing libraries of miRNA's obtained from numerous vertebrate (human, mouse, zebrafish) tissues and cell lines, including examples encoded by herpesviruses during their infectious process.

The sea slug Aplysia californica has been utilized by Dr. Eric Kandel at Columbia as an ideal model system for understanding the molecular basis of learning and memory formation, revolutionary work that resulted in his being awarded the 2000 Nobel Prize in Physiology or Medicine. Our group (Dr. Ju), Dr. Kandel and Dr. Leonid Moroz at the University of Florida, have been involved in preparing and sequencing neuron-specific and even subneuron-specific EST, SAGE tag and full-length cDNA libraries. We are currently following up these efforts with studies aimed at following expression patterns (using newly developed Aplysia microarrays) during facilitation and inhibition of memory formation, including the establishment of when particular mRNA's become translation-competent in their movement from soma to synapse. In addition, we have teamed with Drs. Bruce Birren and Eric Lander at the Broad Institute who have begun to sequence the Aplysia genome.

Identification of polymorphisms and mutations by direct sequencing.

The first category includes the mutation analyses that are part of the disease gene discovery projects described above. As an additional example, we participated in a project with Dr. Timothy Bestor from the Department of Genetics and Development. He and his colleagues were interested in the rare ICF syndrome which presents with immunodeficiency, centromere instability and facial abnormalities. We provided evidence that dominant mutations in a DNA methyltransferase gene (DNMT3B) were responsible for this disease state. This was the first time that methylation defects were clearly shown to be involved in a genetic disease.

In the second category of polymorphisms that may predispose toward disease in combination with other genes and environmental factors, the lab has considered such diseases as asthma, schizophrenia, diabetes, ALS, depression and suicide, Alzheimer’s disease, response to development of aneurysms and surgical procedures, and in separate projects, such genes as Rb1 (retinoblastoma) and ATM (ataxia telangiectasia). Many of the above association studies, spearheaded by leading investigators in various clinical departments and centers at Columbia University Medical Center, take advantage of haplotype analysis and linkage disequilibrium determination in subpopulations. The goal is to eventually provide critical information that can be brought to bear on patient care, and inform disease prediction, diagnosis, prognosis and treatment options.

Methods development. Drs. Jingyue Ju and Jim Russo, as head and associate head of the Sequencing and Chemical Biology section of the Genome Center, and their teams, work very closely with each other to develop new methods and then test them on biological problems. These methods include improved sequencing and alternative mutation analysis technologies that take advantage of time of flight mass spectroscopy, fluorescence energy transfer, sequencing by synthesis, or modified surface chemistries. The goal is to produce high throughput diagnostic tools for the assessment of major categories of simple and complex diseases. Supported by NHGRI, goals include bringing the cost of sequencing whole genomes to 1% and eventually 0.01% of current costs.

Selected Publications

Zhang, P., Zhang, J., Sheng, H., Russo, J.J., Osborne, B., Buetow, K. (2006) Gene functional similarity search tool (GFSST). BMC Bioinformatics 7:135.

Chen, P.Y., Manninga, H., Slanchev, K., Chien, M., Russo, J.J., Ju, J., Sheridan, R., John, B., Marks, D.S., Gaidatzis, D., Sander, C., Zavolan, M., Tuschl, T. (2005) The developmental miRNA profiles of zebrafish as determined by small RNA cloning. Genes Dev. 19:1288-1293.

Pfeffer, S., Sewer, A., Lagos-Quintana, M., Sheridan, R., Sander, C., Grasser, F.A., van Dyk, L.F., Ho, C.K., Shuman, S., Chien, M., Russo, J.J., Ju, J., Randall, G., Lindenbach, B.D., Rice, C.M., Simon, V., Ho, D.D., Zavolan, M., Tuschl, T. (2005) Identification of microRNAs of the herpesvirus family. Nature Methods 2:269-276.

Jakob, J., Nagase, S., Gazdar, A., Chien, M., Morozova, I., Russo, J.J., Nandula, S.V., Murty, V.V.V.S., Li, C.-M., Tycko, B., Parsons, R. (2005) Two somatic biallelic lesions within and near SMAD4 in a human breast cancer cell line. Genes Chrom Cancer 42:372-383.

Chien, M., Morozova, I., Shi, S., Sheng, H., Chen, J., Gomez, S.M., Asamani, G., Hill, K., Nuara, J., Feder, M., Rineer, J., Greenberg, J.J., Steshenko, V., Park, S.H., Zhao, B., Teplitskaya, E., Edwards, J.R., Pampou, S., Georghiou, A., Chou, I.-C., Iannuccilli, W., Ulz, M.E., Kim, D.H., Geringer-Sameth, A., Goldsberry, C., Morozov, P., Fischer, S.G., Segal, G., Qu, X., Rzhetsky, A., Zhang, P., Cayanis, E., De Jong, P.J., Ju, J., Kalachikov, S., Shuman, H.A., Russo, J.J. (2004) The genomic sequence of the accidental pathogen Legionella pneumophila. Science 305:1966-1968.

Pfeffer, S., Zavolan, M., Grasser, F.A., Chien, M., Russo, J.J., Ju, J., John, B., Enright, A.J., Marks, D., Sander, C. and Tuschl, T. (2004) Identification of virus-encoded microRNAs. Science 304:734-736.

Morozova, I., Qu, X., Shi, S., Asamani, G., Greenberg, J., Shuman, H.A. and Russo, J.J. (2004) Comparative sequence analysis of the icm/dot genes in Legionella. Plasmid 51:127-147

Kim, S., Shi, S., Bonome, T., Ulz, M.E., Edwards, J.R., Fodstad, H., Russo, J.J. and Ju, J. (2003) Multiplex genotyping of the human ?2-adrenergic receptor gene using solid-phase capturable dideoxynucleotides and mass spectrometry. Anal Biochem 316:251-258.

Qu, X., Morozova, I., Chien, M., Kalachikov, S., Segal, G., Chen, J., Park, H., Georghiou, A., Asamani, G., Feder, M., Rineer, J., Greenberg, J.J., Goldsberry, C., Rzhetsky, A., Fischer, S.G., DeJong, P., Zhang, P., Cayanis, E., Shuman, H.A. and Russo, J.J. (2002) The Legionella pneumophila sequencing project. in “Legionella” ASM Press (Washington, D.C.), pp. 97-104.

Tong, A.K., Li, Z., Jones, G.S., Russo, J.J. and Ju, J. Combinatorial fluorescence energy transfer tags for multiplex biological assays (2001) Nature Biotechnology 19: 756-759.

Hatzivassiliou, G., Miller, I., Takizawa, J., Palanisamy, N., Rao, P.H., Iida, S., Tagawa, S., Taniwaki, M., Russo, J., Neri, A., Cattoretti, G., Clynes, R., Mendelsohn, C., Chaganti, R.S. and Dalla-Favera, R. (2001) IRTA-1 and IRTA-2, novel Immunoglobulin Superfamily Receptors expressed in B cells and involved in chromosome 1q21 abnormalities in B cell malignancy. Immunity 14: 277-289.

Migliazza, A., Bosch, F., Komatsu, H., Cayanis, E., Martinotti, S., Toniato, E., Guccione, E., Qu, X., Chien, M., Murty, V.V.V., Gaidano, G., Inghirami, G., Zhang, P., Fischer, S., Kalachikov, S.M., Russo, J., Edelman, I., Efstratiadis, A. and Dalla-Favera, R. (2001) Nucleotide sequence, transcription map and mutation analysis of the 13q14 chromosomal region deleted in B-cell chronic lymphocytic leukemia. Blood 97: 2098-2104.

Rzhetsky, A., T. Koike, S. Kalachikov, S.M. Gomez, M. Krauthammer, S.H. Kaplan, P. Kra, J.J. Russo and C. Friedman (2000) A Knowledge model for analysis and simulation of regulatory networks. Bioinformatics 16: 1120-1128.

Migliazza, A., Cayanis, E., Bosch-Albareda, F., Komatsu, H., Martinotti, S., Toniato, E., Kalachikov, S., Bonaldo, M.F., Jelenc, P., Ye, X., Rzhetsky, A., Qu, X., Chien, M., Inghirami, G., Gaidano, G., Vitolo, U., Saglio, G., Resegotti, L., Zhang, P., Soares, M.B., Russo, J., Fischer, S.G., Edelman, I.S., Efstratiadis, A. and Dalla-Favera, R. (2000) Molecular pathogenesis of B-cell chronic lymphocytic leukemia: analysis of 13q14 chromosomal deletions. Curr. Top. Microbiol. Immunol. 252: 275-284.

Xu, G-L., Bestor, T.H., Bourc'his, D., Hsieh, C-L., Tommerup, N., Bugge, M., Hulten, M., Qu, X., Russo, J.J. and Viegas-Péquignot, E. (1999) Chromosome instability and immunodeficiency syndrome caused by mutations in a DNA methyltransferase gene. Nature 402: 187-191.

Segal, G., Russo, J.J. and Shuman, H.A. (1999) Relationships between a new type IV secretion system and the icm/dot virulence system of Legionella pneumophila. Molec. Microbiol. 34: 799-809.

Zhang, P., Ye, X., Liao, L., Russo, J.J. and Fischer, S.G. (1999) Integrated Mapping Project (IMP): A Physical Mapping Software Tool Kit. Genomics 55: 78-87.

Qu, X., Hauptschein, R.S., Rzhetsky, A., Scotto, L., Chien, M., Ye, X., Frigeri, F., Rao, P.H., Pasqualucci, L., Gamberi, B., Zhang, P., Chaganti, R.S.K., Dalla-Favera, R. and Russo, J.J. (1998) Analysis of a 69 kb contiguous genomic sequence at a putative tumor suppressor gene locus on human chromosome 6q27. DNA Seq. 9: 189-204.

Hall, E.J., Schiff, P.B., Hanks, G.E., Brenner, D.J., Russo, J., Chen, J., Sawant, S.G. and Pandita, T.K. (1998) A preliminary report: frequency of A-T heterozygotes among prostate cancer patients with severe late responses to radiation therapy. Cancer J. Sci. Am. 4: 385-389.

Cayanis, E., Russo, J.J., Kalachikov, S., Ye, X., Park, S.H., Sunjevaric, I., de Fatima Bonaldo, M., Lawton, L., Venkatraj, V.S., Schon, E., Soares, M.B., Rothstein, R., Warburton, D., Edelman, I.S., Zhang, P., Efstratiadis, A. and Fischer, S.G. (1998) High resolution YAC-cosmid-STS map of human chromosome 13. Genomics 47: 26-43.

Rzhetsky, A., Kalachikov, S., Ye, X., Zhang, P. and Russo, J.J. (1998) Tools for visualization and integration of intermediate sequencing results in large disease gene discovery projects. Gene 208: 31-35.

Kalachikov, S., Migliazza, A., Cayanis, E., Fracchiolla, N.S., Bonaldo, M.F., Lawton, L., Jelenc, P., Ye, X., Qu, X., Chien, M., Hauptschein, R., Gaidano, G., Vitolo, U., Saglio, G., Resegotti, L., Brodjansky, V., Yankovsky, N., Zhang, P., Soares, M.B., Russo, J., Edelman, I.S., Efstratiadis, A., Dalla-Favera, R. and Fischer, S.G. (1997) Cloning and gene mapping of the chromosome 13q14 region deleted in chronic lymphocytic leukemia. Genomics 42: 369-377.

Sarid, R., Sato, T., Bohenzky, R.A., Russo, J.J. and Chang, Y. (1997) Kaposiís sarcoma-associated herpesvirus encodes a functional bcl-2 homologue. Nat. Med. 3: 293-298.

Russo, J.J., Bohenzky, R.A., Chien, M.C., Chen, J., Yan, M., Maddalena, D., Parry, J.P., Peruzzi, D., Edelman, I.S., Chang, Y. and Moore, P.S. (1996) Nucleotide sequence of the Kaposi sarcoma-associated herpesvirus (HHV8). Proc. Natl. Acad. Sci. U.S.A. 93: 14862-14867.

Fischer, S.G., Cayanais, E., de Fatima Bonaldo, M., Bowcock, A.M., Deaven, L.L., Edelman, I.S., Gallardo, T., Kalachikov, S., Lawton, L., Longmire, J.L., Lovett, M., Osborne-Lawrence, S., Rothstein, R., Russo, J.J., Soares, M.B., Sunjevaric, I., Venkatraj, V.S., Warburton, D., Zhang, P. and Efstratiadis, A. (1996) A high-resolution annotated physical map of the human chromosome 13q12-13 region containing the breast cancer susceptibility locus BRCA2. Proc. Natl. Acad. Sci. U.S.A. 93: 690-694.

Brown, S., Russo, J., Chitayat, D. and Warburton, D. (1995) The 13q- syndrome: the molecular definition of a critical deletion region in band 13q32. Am. J. Hum. Genet. 57: 859-866.

Fischer, S.G., Cayanis, E., Russo, J.J., Sunjevaric, I., Boukhgalter, B., Zhang, P., Yu, M.T., Rothstein, R., Warburton, D., Edelman, I.S., and Efstratiadis, A. (1994) Assembly of ordered contigs of cosmids selected with YACs of human chromosome 13. Genomics 21: 525-537.

Warburton, D., Yu, M.T., Tantravahi, U., Lee, C., Cayanis, E., Russo, J. and Fischer, S.G. (1993) Regional localization of 32 NotI-HindIII fragments from a human chromosome 13 library by a somatic cell hybrid panel and in situ hybridization.. Genomics 16: 355-360.

Russo, J.J. and Sweadner, K.J. (1993) Na(+)-K(+)-ATPase subunit isoform pattern modification by mitogenic insulin concentration in 3T3-L1 preadipocytes. Am. J. Physiol. 264: C311-C316.

Petrukhin, K., Fischer, S.G., Pirastu, M., Tanzi, R.E., Chernov, I., Devoto, M. Brzustowicz, L.M., Cayanis, E., Vitale, E., Russo, J.J., Matseoane, D., Boukhgalter, B., Wasco, W., Figus, A.L., Loudianos, J., Cao, A., Sternlieb, I. Evgrafov, O., Parano, E., Pavone, L., Warburton, D., Ott, J., Penchaszadeh, G.K., Scheinberg, I.H. and Gilliam, T.C. (1993) Mapping, cloning and genetic characterization of the region containing the Wilsonís disease gene. Nat. Genet. 5: 338-343.

Russo, J.J., Manuli, M.A., Ismail-Beigi, F., Sweadner, K.J. and Edelman, I.S. (1990) Na(+)-K(+)-ATPase in adipocyte differentiation in culture. Am. J. Physiol. 259: C968-C977.

Russo, J.J., Merchant, J.L., Eager, P.R. and Barrnett, R.J. (1987) Characterization and use of polyclonal antibody to Na+,K+-ATPase: immunocytochemical localization in salt glands of the duck. Cell Biochem. Funct. 5: 1-15.

Russo, J.J. and Black, V.H. (1982) Hormone-dependent changes in peroxisomal enzyme activity in guinea pig adrenal. J. Biol. Chem. 257: 3883-3889.

Black, V.H. and Russo, J.J. (1980) Stereological analysis of the guinea pig adrenal: effects of dexamethasone and ACTH treatment with emphasis on the inner cortex. Am. J. Anat. 159: 85-120.

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