The advent of genomics in human health-care management has led to the introduction of a new powerful tool for diagnosis, allowing for genetic variants potentially associated to a disease phenotype to be identified using the genome sequence of a single patient. The development of improved technologies together with the cost reduction, made the whole genome sequencing (WGS) feasible for domestic animals as well. Cats are among the most common pets and share different diseases with humans, representing therefore a valuable biomedical model for studies focused on human disorders. The 99 Lives Cat Genome Sequencing Initiative was launched in 2015, with the main aim of collecting 99 whole genome cat sequences through the collaboration of different researchers and institutes worldwide. Up to date, almost 200 cats of different breeds and random bred cats have joined the project and have their whole genome sequences as part of the database. Some disease-causing variants have already been identified thanks to the sequencing data available from the database, while many others are currently under investigation. The present PhD project shows how WGS is suitable for different kinds of research, including the detection of disease-associated variants and genomic breed descriptive studies. The main part of the present PhD project has been focused on the investigation of the pathogenic pathways characterizing feline amyloidosis, a common disease in both the Abyssinian and Siamese breeds. The whole genome sequences of two affected Siamese and two affected Abyssinians were used to detect amyloidosis associated variants and were compared to the WGS data of the other cats present in the 99 Lives database for variants exclusion. Each breed was analyzed separately. At first, all the analyses were carried out referring to the version 6.2 of the cat genome assembly and using the WGS of 113 cats. Amyloidosis resulted to be a polygenic disease and variants underlying the affected phenotype were not shared between Abyssinian and Siamese cats, leading to the hypothesis of different mechanisms involved in the disease onset in the two breeds. With the advent of the version 9.0 of the Felis catus genome in November 2017, and the increased number of cats that joined the 99 Lives Project, the analysis was repeated using the new genome assembly and 195 cats as controls for variants filtering. Moreover, as in the first part of the work feline amyloidosis turned out to be a multifactorial complex disorder, the new genomic analyses were further integrated with both proteomic and miRNAomic approach in the Abyssinians. When the variants detection with the version 9.0 of the cat genome was repeated, most of the variants related to the affected cats mapped into intronic or intergenic regions, and the variants mapping within exonic regions did not match those found with version 6.2. However, through the multi-omics approach conducted in the Abyssinian breed, different miRNAs resulted to be differentially expressed between healthy and affected Abyssinians. In particular, almost all the downregulated miRNAs were already reported in the Alzheimer Disease (AD) literature, a disorder having many features in common with amyloidosis. Additionally, these miRNAs targeted proteins expressed exclusively in the affected cats and one gene resulted mutated in the binding site of one of the most significantly downregulated miRNA. Finally, the sequencing data of the 99 Lives Project were used to detect Copy Number Variants (CNVs) in 41 cats belonging to 14 different breeds. This genomic structure characterization, which represents the first study mapping CNVs in domestic cats, showed that individuals belonging to different breeds can cluster together based on their CNVs similarities. Overall, the present PhD project demonstrated how WGS data available through the 99 Lives Initiative represent an important source for genomic analyses in cats, providing useful data for research and bridging the gap between the new frontiers of genomics and cats health-care.

NEXT GENERATION GENOMIC AND PROTEOMIC ANALYSES IN FELINE AMYLOIDOSIS / F. Genova ; tutor: M. Longeri; co-tutor: L. Lyons; coordinatore: V. Grieco. - Milano : Università degli studi di Milano. DIPARTIMENTO DI MEDICINA VETERINARIA, 2020 Feb 05. ((32. ciclo, Anno Accademico 2019.

NEXT GENERATION GENOMIC AND PROTEOMIC ANALYSES IN FELINE AMYLOIDOSIS

GENOVA, FRANCESCA
2020-02-05

Abstract

The advent of genomics in human health-care management has led to the introduction of a new powerful tool for diagnosis, allowing for genetic variants potentially associated to a disease phenotype to be identified using the genome sequence of a single patient. The development of improved technologies together with the cost reduction, made the whole genome sequencing (WGS) feasible for domestic animals as well. Cats are among the most common pets and share different diseases with humans, representing therefore a valuable biomedical model for studies focused on human disorders. The 99 Lives Cat Genome Sequencing Initiative was launched in 2015, with the main aim of collecting 99 whole genome cat sequences through the collaboration of different researchers and institutes worldwide. Up to date, almost 200 cats of different breeds and random bred cats have joined the project and have their whole genome sequences as part of the database. Some disease-causing variants have already been identified thanks to the sequencing data available from the database, while many others are currently under investigation. The present PhD project shows how WGS is suitable for different kinds of research, including the detection of disease-associated variants and genomic breed descriptive studies. The main part of the present PhD project has been focused on the investigation of the pathogenic pathways characterizing feline amyloidosis, a common disease in both the Abyssinian and Siamese breeds. The whole genome sequences of two affected Siamese and two affected Abyssinians were used to detect amyloidosis associated variants and were compared to the WGS data of the other cats present in the 99 Lives database for variants exclusion. Each breed was analyzed separately. At first, all the analyses were carried out referring to the version 6.2 of the cat genome assembly and using the WGS of 113 cats. Amyloidosis resulted to be a polygenic disease and variants underlying the affected phenotype were not shared between Abyssinian and Siamese cats, leading to the hypothesis of different mechanisms involved in the disease onset in the two breeds. With the advent of the version 9.0 of the Felis catus genome in November 2017, and the increased number of cats that joined the 99 Lives Project, the analysis was repeated using the new genome assembly and 195 cats as controls for variants filtering. Moreover, as in the first part of the work feline amyloidosis turned out to be a multifactorial complex disorder, the new genomic analyses were further integrated with both proteomic and miRNAomic approach in the Abyssinians. When the variants detection with the version 9.0 of the cat genome was repeated, most of the variants related to the affected cats mapped into intronic or intergenic regions, and the variants mapping within exonic regions did not match those found with version 6.2. However, through the multi-omics approach conducted in the Abyssinian breed, different miRNAs resulted to be differentially expressed between healthy and affected Abyssinians. In particular, almost all the downregulated miRNAs were already reported in the Alzheimer Disease (AD) literature, a disorder having many features in common with amyloidosis. Additionally, these miRNAs targeted proteins expressed exclusively in the affected cats and one gene resulted mutated in the binding site of one of the most significantly downregulated miRNA. Finally, the sequencing data of the 99 Lives Project were used to detect Copy Number Variants (CNVs) in 41 cats belonging to 14 different breeds. This genomic structure characterization, which represents the first study mapping CNVs in domestic cats, showed that individuals belonging to different breeds can cluster together based on their CNVs similarities. Overall, the present PhD project demonstrated how WGS data available through the 99 Lives Initiative represent an important source for genomic analyses in cats, providing useful data for research and bridging the gap between the new frontiers of genomics and cats health-care.
LONGERI, MARIA LINA
GRIECO, VALERIA
Settore AGR/17 - Zootecnica Generale e Miglioramento Genetico
NEXT GENERATION GENOMIC AND PROTEOMIC ANALYSES IN FELINE AMYLOIDOSIS / F. Genova ; tutor: M. Longeri; co-tutor: L. Lyons; coordinatore: V. Grieco. - Milano : Università degli studi di Milano. DIPARTIMENTO DI MEDICINA VETERINARIA, 2020 Feb 05. ((32. ciclo, Anno Accademico 2019.
Doctoral Thesis
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Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/2434/709439
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