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Identification and Functional Studies of Fusion Genes in Soft Tissue Tumors

Arbajian, Elsa (2012) MOBT19 20112
Degree Projects in Molecular Biology
Abstract
ABSTRACT

Soft tissue tumor-associated gene fusions are currently being used as diagnostic genetic markers and seem promising as potential prognostic markers. In the present study, a new fusion gene was discovered in one case of a specific subtype of soft tissue sarcoma displaying a t(6;16) translocation. Using fluorescence in situ hybridization (FISH), the FUS gene in 16p11 was shown to be rearranged. SNP array analysis provided a candidate partner gene in chromosome 6. This was confirmed by RT-PCR analysis which revealed an in-frame fusion transcript and by FISH analysis which showed co-localization of the two genes. In one case of another soft tissue tumor subtype, displaying a t(7;8;14) translocation, a novel fusion gene involving... (More)
ABSTRACT

Soft tissue tumor-associated gene fusions are currently being used as diagnostic genetic markers and seem promising as potential prognostic markers. In the present study, a new fusion gene was discovered in one case of a specific subtype of soft tissue sarcoma displaying a t(6;16) translocation. Using fluorescence in situ hybridization (FISH), the FUS gene in 16p11 was shown to be rearranged. SNP array analysis provided a candidate partner gene in chromosome 6. This was confirmed by RT-PCR analysis which revealed an in-frame fusion transcript and by FISH analysis which showed co-localization of the two genes. In one case of another soft tissue tumor subtype, displaying a t(7;8;14) translocation, a novel fusion gene involving NCOA2 in 8q13 was found. The latter gene has previously been shown to fuse with the AHRR gene in cases of this tumor subtype with the t(5;8) translocation. FISH analysis revealed that NCOA2 was rearranged in the present case as well, and a candidate partner gene in chromosome 7 was identified. RT-PCR analysis amplified an in-frame fusion transcript. New tumor-associated fusion chimeras are constantly being described in soft tissue tumors. However, little is known about the involvement of these chimeras in tumorigenesis. Therefore, we are setting up an inducible gene expression system - Lenti-X Tet-On 3G - to be able to study the effect of gene fusions on the cellular level.

Popular science summary:

Fusion Genes in Soft Tissue Tumors


Soft tissue tumor-associated gene fusions can help differentiate between different tumor subtypes and are thus currently being used as potent diagnostic markers. Therefore, characterizing these fusion genes could lead to a better understanding of the development of soft tissue tumors.

Soft tissue tumors arise in tissues of mesenchymal origin such as muscle, fat and connective tissue. They are a large, heterogeneous group of tumors that comprises a very large number of subtypes, many of which are dificult to differentiate from each other. Thus new objective markers are needed to overcome the problem of incorrect diagnosis and prognosis and to get a better understanding of tumor development.

Fusion genes are hybrid genes that arise from fusion of parts of two genes, one from each breakpoint, upon translocation of pieces of different chromosomes. The genes involved are usually transcription factor encoding and thus, the resulting hybrid gene encodes an aberrant transcriptional factor that deregulates gene expression in the target cells. Alone or in combination with other genetic events, this is believed to trigger transformation of permissive cells

In the following study we describe the finding of two new fusion genes, each in a specific soft tissue tumor subtype using different molecular genetic techniques. The first one was discovered in one case of a specific subtype of soft tissue sarcoma displaying a translocation between chromosomes 6 and 16. Using fluorescence in situ hybridization (FISH), the FUS gene in chromosome 16 was shown to be involved in the fusion. SNP array analysis provided a candidate partner gene in chromosome 6. This was confirmed by RT-PCR analysis and by FISH analysis. The second fusion, was discovered in one case of another soft tissue tumor subtype. FISH analysis revealed that NCOA2 was involved, and a candidate partner gene in chromosome 7 was identified. RT-PCR analysis confirmed these results.

In order to learn more about the roles and effects of soft tissue tumor associated fusion genes in permissive cells, functional studies can be performed. One possibility would be to use an inducible gene expression system such as the Lenti-X™ Tet-On® 3G Inducible Expression System where the effect of specific fusion genes can be studied by cloning them into target cells where their expression can be turned on or off. In our study, we also describe the setting up of such a system to be used for functional studies of a wide array of gene fusions and thus, as previously mentioned, gain a better understanding of the events and processes behind tumor development.


Advisor: Fredrik Mertens
Master´s Degree Project 60 credits in Molecular Genetics and Biotechnology
Department of Biology, Lund University (Less)
Please use this url to cite or link to this publication:
author
Arbajian, Elsa
supervisor
organization
course
MOBT19 20112
year
type
H2 - Master's Degree (Two Years)
subject
language
English
id
3633151
date added to LUP
2013-04-12 11:51:31
date last changed
2013-04-12 11:51:31
@misc{3633151,
  abstract     = {ABSTRACT

Soft tissue tumor-associated gene fusions are currently being used as diagnostic genetic markers and seem promising as potential prognostic markers. In the present study, a new fusion gene was discovered in one case of a specific subtype of soft tissue sarcoma displaying a t(6;16) translocation. Using fluorescence in situ hybridization (FISH), the FUS gene in 16p11 was shown to be rearranged. SNP array analysis provided a candidate partner gene in chromosome 6. This was confirmed by RT-PCR analysis which revealed an in-frame fusion transcript and by FISH analysis which showed co-localization of the two genes. In one case of another soft tissue tumor subtype, displaying a t(7;8;14) translocation, a novel fusion gene involving NCOA2 in 8q13 was found. The latter gene has previously been shown to fuse with the AHRR gene in cases of this tumor subtype with the t(5;8) translocation. FISH analysis revealed that NCOA2 was rearranged in the present case as well, and a candidate partner gene in chromosome 7 was identified. RT-PCR analysis amplified an in-frame fusion transcript. New tumor-associated fusion chimeras are constantly being described in soft tissue tumors. However, little is known about the involvement of these chimeras in tumorigenesis. Therefore, we are setting up an inducible gene expression system - Lenti-X Tet-On 3G - to be able to study the effect of gene fusions on the cellular level.

Popular science summary:

Fusion Genes in Soft Tissue Tumors


Soft tissue tumor-associated gene fusions can help differentiate between different tumor subtypes and are thus currently being used as potent diagnostic markers. Therefore, characterizing these fusion genes could lead to a better understanding of the development of soft tissue tumors.
 
Soft tissue tumors arise in tissues of mesenchymal origin such as muscle, fat and connective tissue. They are a large, heterogeneous group of tumors that comprises a very large number of subtypes, many of which are dificult to differentiate from each other. Thus new objective markers are needed to overcome the problem of incorrect diagnosis and prognosis and to get a better understanding of tumor development.

Fusion genes are hybrid genes that arise from fusion of parts of two genes, one from each breakpoint, upon translocation of pieces of different chromosomes. The genes involved are usually transcription factor encoding and thus, the resulting hybrid gene encodes an aberrant transcriptional factor that deregulates gene expression in the target cells. Alone or in combination with other genetic events, this is believed to trigger transformation of permissive cells

In the following study we describe the finding of two new fusion genes, each in a specific soft tissue tumor subtype using different molecular genetic techniques. The first one was discovered in one case of a specific subtype of soft tissue sarcoma displaying a translocation between chromosomes 6 and 16. Using fluorescence in situ hybridization (FISH), the FUS gene in chromosome 16 was shown to be involved in the fusion. SNP array analysis provided a candidate partner gene in chromosome 6. This was confirmed by RT-PCR analysis and by FISH analysis. The second fusion, was discovered in one case of another soft tissue tumor subtype. FISH analysis revealed that NCOA2 was involved, and a candidate partner gene in chromosome 7 was identified. RT-PCR analysis confirmed these results.

In order to learn more about the roles and effects of soft tissue tumor associated fusion genes in permissive cells, functional studies can be performed. One possibility would be to use an inducible gene expression system such as the Lenti-X™ Tet-On® 3G Inducible Expression System where the effect of specific fusion genes can be studied by cloning them into target cells where their expression can be turned on or off. In our study, we also describe the setting up of such a system to be used for functional studies of a wide array of gene fusions and thus, as previously mentioned, gain a better understanding of the events and processes behind tumor development.


Advisor: Fredrik Mertens
Master´s Degree Project 60 credits in Molecular Genetics and Biotechnology
Department of Biology, Lund University},
  author       = {Arbajian, Elsa},
  language     = {eng},
  note         = {Student Paper},
  title        = {Identification and Functional Studies of Fusion Genes in Soft Tissue Tumors},
  year         = {2012},
}