Hirschsprung Home

Hirschsprung Disease

Inheritance

Testing and Counseling

Research and Bibliography

Johns Hopkins Research Study

Get Involved

Down syndrome

Helpful links

RESEARCH UPDATE

Our work is currently focused in 3 areas:

·        DNA “CHIP” STUDIES

Our lab has been one the earliest groups to adopt and use the new DNA “chip” technology for disease gene discovery.  These chips contain between one-half to one million sites in the human genome sequence whose genetic status can be interrogated by applying an individual’s own DNA to the chip.  Remember that the DNA code is complementary so that each part of the human genetic code identifies and ‘hybridizes’ onto the appropriate location on the chip and that person’s genetic status can be read by a laser scanner. This technology allows us to search for human disease genes, including Hirschsprung disease (HSCR) genes, broadly and without prior knowledge.  Thus, we can search for an association, an increase in the frequency of a DNA variant in patients as compared to those free of disease, between HSCR and sites in a region anywhere in the genome.  The power of this method comes from this generality.

Very simply, the idea is to find benign DNA variations (polymorphisms) that are present both in individuals with and without disease.  If enough polymorphisms and enough individuals with disease are analyzed, we may identify a small segment of the genome that is found more frequently in individuals with disease than those without disease.  This helps us to narrow in on that region as “suspicious”, in that it might contain a Hirschsprung gene. 

The first stage in our experiments focused on families where only one family member was affected with short-segment HSCR.  We analyzed 220 isolated short segment HSCR trios (affected child and 2 parents), and are currently following up on an interesting result pointing to chromosome 7 as a possibly containing a gene involved in causing Hirschsprung disease in some cases.

·        DNA SEQUENCING STUDY

Another ongoing project in the lab is a comprehensive DNA sequencing study of both coding and non-coding regions of the RET gene in a large number of patients in collaboration with the National Institutes of Health. RET is the main gene implicated in Hirschsprung disease and our studies suggests that all HSCR patients have at least one variant in RET and possible additional variants elsewhere.  Sequencing involves going letter-by-letter through the entire sequence of the gene, which is thousands of letters long!  There is a correct “spelling” of the gene, and a mutation is simply a misspelling that prevents the gene from working correctly.  680 individuals were included in this project, which includes 237 individuals with Hirschsprung and their family members. We will catalog all the different types and locations of mutations and variations in the RET gene which will help us better understand the gene and how a mutation in it could cause disease.  It will also improve interpretation of genetic testing results.  So far, we have found very high genetic variability overall, showing many novel and rare variants, some of which seem to interact with each other to define severe forms of Hirschsprung. Family groups have proven to be very useful, as they have allowed us to identify some gene deletions (literally, some letters are absent from the gene) that would have been missed otherwise. Our ongoing analysis is shedding light on such questions as the contribution of RET to HSCR, the parental origin of mutations, and the role of rare and common mutations. This is the most comprehensive study of the RET gene undertaken to date. 

·        ANIMAL MODELS

Studies of model organisms, primarily mouse and fish, have been pivotal to our understanding of the nature of Hirschsprung disease (HSCR) and the impact of mutations that contribute to disease susceptibility. We use animal models in a number of complementary ways. First, they allow us to uncover new genes important in the formation of the enteric nervous system, which may harbor mutations contributing to HSCR. Second, we use them to determine the relevance and severity of mutations identified within patients. Third, we use them to establish the potential for co-operation between mutations where more than one mutation has been identified within a patient. Fourth, animal models have allowed us to discover mutations that lie outside of genes, within control switches that direct when, where and how much a gene should be turned on, a particularly significant advance. Our ongoing animal work is not only pivotal to a better understanding of HSCR susceptibility but more broadly to disease susceptibility in general.

The zebrafish, a popular model organism

BIBLIOGRAPHY

The following is a list of publications from our laboratory about the genetics of Hirschsprung disease:

Badner JA, CHAKRAVARTI A:  Waardenburg syndrome and Hirschsprung disease: Evidence for pleiotropic effects of a single dominant gene.  American Journal of Medical Genetics 35:100-104, 1990.

Badner JA, Sieber W, Garver KL, CHAKRAVARTI A:  A genetic study of Hirschsprung disease.  American Journal of Human Genetics 46:568-580, 1990.

Angrist M, Kaufmann E, Slaugenhaupt SA, Matise TC, Puffenberger EG, Washington SS, Lipson A, Cass DT, Reyna T, Weeks DE, Sieber W, CHAKRAVARTI A:  A gene for Hirschsprung disease (megacolon) in the pericentromeric region of human chromosome 10.  Nature Genetics 4:351-356, 1993.

Puffenberger EG, Kauffman ER, Bolk S, Matise TC, Washington SS, Angrist M, Weissenbach J, Garver KL, Mascari M, Ladda R, Slaugenhaupt SA, CHAKRAVARTI A:  Identity-by-descent and association mapping of a recessive gene for Hirschsprung disease on human chromosome 13q22.  Human Molecular Genetics 3:1217-1225, 1994.

Puffenberger EG, Hosoda K, Washington SS, Nakao K, deWit D, Yanagisawa M, CHAKRAVARTI A: A missense mutation of the Endothelin-B Receptor Gene in Multigenic Hirschsprung's Disease. Cell 79:1257-1266, 1994.

Angrist A, Bolk S, Thiel B, Puffenberger EG, Hofstra RM, Buys HCM, CHAKRAVARTI A:  Mutation analysis of the RET receptor tyrosine kinase in Hirschsprung disease.  Human Molecular Genetics 4:821-830, 1995.

CHAKRAVARTI A:   Endothelin receptor-mediated signaling in Hirschsprung disease.  Human Molecular Genetics 5:303-307, 1996.

Bolk S, Angrist M, Schwartz S, Silvestri JM, Weese-Mayer DE, CHAKRAVARTI A: Congenital central hypoventilation syndrome:  mutation analysis of the receptor tyrosine kinase RET.  American Journal of Medical Genetics 63:603-609, 1996.

Hofstra RMW, Osinga J, Tan-Sindhunata G, Wu y, Kamsteeg EJ, Stulp RP, van Ravenswaaji-Arts C, Majoor-Krakauer D, Angrist M, CHAKRAVARTI A, Meijers C, Buys CHM: A homozygous mutation in the human endothelin-3 gene associated with a combined Waardenburg type 2 and Hirschsprung phenotype.  Nature Genetics 12:445-447, 1996.

Bolk S, Xie J, Angrist M, Silvestri JM, Weese-Mayer DE, Yanagisawa M, CHAKRAVARTI A: Endothelin-3 (EDN3) mutation in a patient with Congenital Central Hypoventilation Syndrome.  Nature Genetics 13:395-396, 1996.

Angrist M, Bolk S, Halushka M, Lapchak P, and CHAKRAVARTI A: Germline mutations in glial cell line-derived neurotrophic factor (GDNF) and RET in a Hirschsprung disease patient. Nature Genetics 14: 341-344, 1996.

Angrist M, Jing S, Bolk St, Bentley K, Nallasamy S, Halushka M, Fox G, CHAKRAVARTI A:  Human GFRA1:  Cloning, mapping, genomic structure and evaluation as a candidate gene for Hirschsprung disease susceptibility.  Genomics 48: 354-362, 1998.  PDF

Angrist M, Bolk S, Bentley K, Nallasamy S, Halushka M, CHAKRAVARTI A:  Genomic structure of the gene for the SH2 and pleckstrin homology domain-containing protein GRB10  and evaluation of its role in Hirschsprung disease.  Oncogene 17:3065-3070, 1998.  PDF

Southard-Smith E, Angrist M, Ellison J, Agarwala R, Baxevanis A, CHAKRAVARTI A, Pavan W: Mouse-human comparative analyses of SOX10. Genome Research  9: 215-225, 1999.  PDF

Bolk S, Pelet A, Hofstra R, Angrist M, Salomon R, Croaker D, Buys C, Lyonnet S, CHAKRAVARTI A:  Multigenic inheritance of Hirschsprung disease: requirements of a new 9q31 locus and RET for phenotypic expression.  Proceedings of the National Academy of Science (USA) 97:268-273, 2000.  PDF

Weese-Mayer DE, Bolk S, Silvestri JM, CHAKRAVARTI A: Idiopathic Congenital Central Hypoventilation Syndrome: Evaluation of Brain-Derived Neurotrophic Factor Genomic DNA Sequence Variation. American Journal of Medical  Genetics 107:306-310,  2002.  PDF

Bolk Gabriel S, Salomon R, Pelet A, Angrist M, Amiel J, Attie-Bitach T, Olson JM, Hofstra R, Buys C, Steffann J, Munnich A, Lyonnet S, CHAKRAVARTI A: Splitting a multigenic disease: segregation at three loci explains sibling recurrence risk in Hirschsprung disease. Nature Genetics  31:89-93, 2002.  PDF

Marshall DG, Meier-Ruge WA, CHAKRAVARTI A, Langer JC:  Chronic constipation due to Hirschsprung’s disease and desmosis coli in a single family. Pediatric Surgical International 18:110-114, 2002.  PDF

Carrasquillo MM, McCallion AS, Puffenberger EG, Kashuk CS, Nouri N, CHAKRAVARTI A:  Genome-wide association study and mouse model identify interaction between RET and EDNRB pathways in Hirschsprung disease.  Nature Genetics  32:237-244, 2002.  PDF

McCallion AS, Stames E, Conlon RA, CHAKRAVARTI A:  Phenotype variation in two-locus mouse models of Hirschsprung disease: Tissue-specific interaction between Ret and Ednrb. Proceedings of the National Academy of Science (USA)  100:1826-1831, 2003.  PDF

McCallion AS, Sproat-Emison EE, Kashuk CS, Bush RT, Kenton M, Carrasquillo MM, Jones KW, Kennedy GC, Portnoy M, Green E, CHAKRAVARTI A:  Genomic variation in multigenic traits: Hirschsprung disease. Cold Spring Harbor Symposium on Quantitative Biology LXVIII 373-381, 2003. 

Emison ES, McCallion AS, Kashuk CS, Bush RT, Grice E, Lin S, Portnoy ME, NISC Comparative Sequencing Program, Cutler DJ, GreenED, CHAKRAVARTI A:  A common, sex-dependent mutation in a putative RET enhancer underlies Hirschsprung disease susceptibility. Nature 434:857-863, 2005.  PDF

Kashuk CS, Stone EA, Grice EA, Portnoy ME, Green ED, Sidow A, CHAKRAVARTI A, McCallion A: Genotype : Phenotype correlation in Hirschsprung disease illuminated by comparative RET protein sequence analysis.  Proceedings of the National Academy of Science (USA) 102:8949-8954, 2005.  PDF

Amiel J et al. Hirschsprung disease: associated syndromes and genetics.  J Med Genet. 2007 Dec 5; [Epub ahead of print]. PDF

Grice EA, Rochelle ES, Green ED, Chakravarti A, McCallion AS.  Evaluation of the RET regulatory landscape reveals the biological relevance of a HSCR-implicated enhancer.  Hum Mol Genet. 2005 Dec 15;14(24):3837-45. PDF

Reviews:

CHAKRAVARTI A, Lyonnet S: Hirschsprung Disease.  Chapter 251 in The Metabolic and Molecular Bases of Inherited Disease  (8^th edn.)  Eds.  Scriver CR, Beaudet AL, Valle D, Sly WS, Childs B, Kinzler K, Vogelstein B. McGraw-Hill, New York, NY, pp. 6231 – 6255, 2001.

McCallion AS, CHAKRAVARTI A:  EDNRB/EDN3 and Hirschsprung disease type II.  Pigment Cell Research 14:161-169, 2001.

McCallion AS, CHAKRAVARTI A: RET, Hirschsprung disease and multiple endocrine neoplasia type 2. In, Inborn Errors of Development, Eds. Epstein C, Erickson R,and Wynshaw-Boris  A,  Oxford University Press, San Francisco, Chapter 36, pp 421-432,2004.

Back to top