Publicação
Metabolomic consequences of TDP-43 aggregation by FT-ICR mass spectrometry : insights from yeast and human
| Resumo: | Amyotrophic Lateral Sclerosis (ALS) is a progressive neurodegenerative disease broadly characterized by the presence of cytoplasmic TDP-43 inclusions. Although most cases have a sporadic origin, a minority are linked to genetic variants, among which are expansions in C9ORF72. ALS remains incurable, and current research is focused on finding robust molecular signatures to characterize disease mechanisms. In light of this, we investigated the metabolic alterations associated with TDP-43 aggregation in a controlled system and in human serum, using untargeted metabolomics with Fourier Transform Ion Cyclotron Resonance mass spectrometry (FT-ICR MS). In the Saccharomyces cerevisiae model, we introduced a plasmid encoding TDP-43, and its expression was confirmed by fluorescence microscopy. Different genetic backgrounds were used to evaluate how TDP-43 aggregation influenced the yeast metabolome. Besides the reference strain, we used strains with gene deletions linked to cellular processes disrupted in ALS, namely, cytoskeleton regulation (CAP1), vesicle trafficking (GLO3), and proteostasis (HSP82). Across strains, protein expression was mainly associated with dysregulation of carbohydrate and lipid metabolism. In addition, we profiled the serum metabolome of ALS patients to identify metabolic signatures specifically associated with the disease. In an attempt to standardize our workflow, we used NIST standard reference material (SRM 1950) as a control group. The differences between the groups were mainly reflected in the dysregulation of lipid metabolism. Furthermore, we compared the patients with and without the C9ORF72 mutation to identify possible metabolic differences between the groups, although no conclusive results were achieved. Finally, a metabolite level comparison between yeast and serum was performed to assess whether there were consistent alterations between the two organisms. Glycerophospholipids, prenol lipids, and fatty acyls were among the metabolites consistently identified in both analyses. Overall, this work established an integrative untargeted metabolomics workflow between yeast and human serum, though further interpretation remains limited by pathway mapping and lipid annotation ambiguity. |
|---|---|
| Autores principais: | Jorge,Ana Carolina Ferreira dos Santos |
| Assunto: | FT-ICR MS Untargeted Metabolomics TDP-43 aggregation Saccharomyces cerevisiae Amyotrophic Lateral Sclerosis |
| Ano: | 2026 |
| País: | Portugal |
| Tipo de documento: | dissertação de mestrado |
| Tipo de acesso: | acesso embargado |
| Instituição associada: | Universidade de Lisboa |
| Idioma: | inglês |
| Origem: | Repositório da Universidade de Lisboa |
| _version_ | 1869346082481242112 |
|---|---|
| author | Jorge,Ana Carolina Ferreira dos Santos |
| author_facet | Jorge,Ana Carolina Ferreira dos Santos |
| author_role | author |
| contributor_name_str_mv | Cordeiro,Carlos Alberto Alves Silva,Marta Sousa Faculty of Sciences Department of Chemistry and Biochemistry Repositório Científico de Acesso Aberto da ULisboa |
| country_str | PT |
| creators_json_txt | [{\"Person.name\":\"Jorge,Ana Carolina Ferreira dos Santos\"}] |
| datacite.contributors.contributor.contributorName.fl_str_mv | Cordeiro,Carlos Alberto Alves Silva,Marta Sousa Faculty of Sciences Department of Chemistry and Biochemistry Repositório Científico de Acesso Aberto da ULisboa |
| datacite.creators.creator.creatorName.fl_str_mv | Jorge,Ana Carolina Ferreira dos Santos |
| datacite.date.Accepted.fl_str_mv | 2026-01-01T00:00:00Z |
| datacite.date.available.fl_str_mv | 2026-06-03T17:30:01Z |
| datacite.date.embargoed.fl_str_mv | 2026-06-03T17:30:01Z |
| datacite.rights.fl_str_mv | http://purl.org/coar/access_right/c_f1cf |
| datacite.subjects.subject.fl_str_mv | FT-ICR MS Untargeted Metabolomics TDP-43 aggregation Saccharomyces cerevisiae Amyotrophic Lateral Sclerosis |
| datacite.titles.title.fl_str_mv | Metabolomic consequences of TDP-43 aggregation by FT-ICR mass spectrometry : insights from yeast and human |
| dc.contributor.none.fl_str_mv | Cordeiro,Carlos Alberto Alves Silva,Marta Sousa Faculty of Sciences Department of Chemistry and Biochemistry Repositório Científico de Acesso Aberto da ULisboa |
| dc.creator.none.fl_str_mv | Jorge,Ana Carolina Ferreira dos Santos |
| dc.date.Accepted.fl_str_mv | 2026-01-01T00:00:00Z |
| dc.date.available.fl_str_mv | 2026-06-03T17:30:01Z |
| dc.date.embargoed.fl_str_mv | 2026-06-03T17:30:01Z |
| dc.format.none.fl_str_mv | application/pdf |
| dc.identifier.none.fl_str_mv | http://hdl.handle.net/10400.5/118931 |
| dc.language.none.fl_str_mv | eng |
| dc.rights.none.fl_str_mv | http://purl.org/coar/access_right/c_f1cf |
| dc.subject.none.fl_str_mv | FT-ICR MS Untargeted Metabolomics TDP-43 aggregation Saccharomyces cerevisiae Amyotrophic Lateral Sclerosis |
| dc.title.fl_str_mv | Metabolomic consequences of TDP-43 aggregation by FT-ICR mass spectrometry : insights from yeast and human |
| dc.type.none.fl_str_mv | http://purl.org/coar/resource_type/c_bdcc |
| description | Amyotrophic Lateral Sclerosis (ALS) is a progressive neurodegenerative disease broadly characterized by the presence of cytoplasmic TDP-43 inclusions. Although most cases have a sporadic origin, a minority are linked to genetic variants, among which are expansions in C9ORF72. ALS remains incurable, and current research is focused on finding robust molecular signatures to characterize disease mechanisms. In light of this, we investigated the metabolic alterations associated with TDP-43 aggregation in a controlled system and in human serum, using untargeted metabolomics with Fourier Transform Ion Cyclotron Resonance mass spectrometry (FT-ICR MS). In the Saccharomyces cerevisiae model, we introduced a plasmid encoding TDP-43, and its expression was confirmed by fluorescence microscopy. Different genetic backgrounds were used to evaluate how TDP-43 aggregation influenced the yeast metabolome. Besides the reference strain, we used strains with gene deletions linked to cellular processes disrupted in ALS, namely, cytoskeleton regulation (CAP1), vesicle trafficking (GLO3), and proteostasis (HSP82). Across strains, protein expression was mainly associated with dysregulation of carbohydrate and lipid metabolism. In addition, we profiled the serum metabolome of ALS patients to identify metabolic signatures specifically associated with the disease. In an attempt to standardize our workflow, we used NIST standard reference material (SRM 1950) as a control group. The differences between the groups were mainly reflected in the dysregulation of lipid metabolism. Furthermore, we compared the patients with and without the C9ORF72 mutation to identify possible metabolic differences between the groups, although no conclusive results were achieved. Finally, a metabolite level comparison between yeast and serum was performed to assess whether there were consistent alterations between the two organisms. Glycerophospholipids, prenol lipids, and fatty acyls were among the metabolites consistently identified in both analyses. Overall, this work established an integrative untargeted metabolomics workflow between yeast and human serum, though further interpretation remains limited by pathway mapping and lipid annotation ambiguity. |
| dirty | 0 |
| eu_rights_str_mv | embargoedAccess |
| format | masterThesis |
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| identifier.url.fl_str_mv | http://hdl.handle.net/10400.5/118931 |
| inst_facet_str | urn:organizationAcronym:ul{{{_:::_}}}Universidade de Lisboa |
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| institution | Universidade de Lisboa |
| instname_str | Universidade de Lisboa |
| language | eng |
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| organization_str_mv | urn:organizationAcronym:ul |
| person_str_mv | Jorge,Ana Carolina Ferreira dos Santos |
| publishDate | 2026 |
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| reponame_str | Repositório da Universidade de Lisboa |
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| spelling | engenAmyotrophic Lateral Sclerosis (ALS) is a progressive neurodegenerative disease broadly characterized by the presence of cytoplasmic TDP-43 inclusions. Although most cases have a sporadic origin, a minority are linked to genetic variants, among which are expansions in C9ORF72. ALS remains incurable, and current research is focused on finding robust molecular signatures to characterize disease mechanisms. In light of this, we investigated the metabolic alterations associated with TDP-43 aggregation in a controlled system and in human serum, using untargeted metabolomics with Fourier Transform Ion Cyclotron Resonance mass spectrometry (FT-ICR MS). In the Saccharomyces cerevisiae model, we introduced a plasmid encoding TDP-43, and its expression was confirmed by fluorescence microscopy. Different genetic backgrounds were used to evaluate how TDP-43 aggregation influenced the yeast metabolome. Besides the reference strain, we used strains with gene deletions linked to cellular processes disrupted in ALS, namely, cytoskeleton regulation (CAP1), vesicle trafficking (GLO3), and proteostasis (HSP82). Across strains, protein expression was mainly associated with dysregulation of carbohydrate and lipid metabolism. In addition, we profiled the serum metabolome of ALS patients to identify metabolic signatures specifically associated with the disease. In an attempt to standardize our workflow, we used NIST standard reference material (SRM 1950) as a control group. The differences between the groups were mainly reflected in the dysregulation of lipid metabolism. Furthermore, we compared the patients with and without the C9ORF72 mutation to identify possible metabolic differences between the groups, although no conclusive results were achieved. Finally, a metabolite level comparison between yeast and serum was performed to assess whether there were consistent alterations between the two organisms. Glycerophospholipids, prenol lipids, and fatty acyls were among the metabolites consistently identified in both analyses. Overall, this work established an integrative untargeted metabolomics workflow between yeast and human serum, though further interpretation remains limited by pathway mapping and lipid annotation ambiguity.application/pdfenMetabolomic consequences of TDP-43 aggregation by FT-ICR mass spectrometry : insights from yeast and humanJorge,Ana Carolina Ferreira dos SantosCordeiro,Carlos Alberto AlvesSilva,Marta SousaFaculty of SciencesDepartment of Chemistry and BiochemistryHostingInstitutionOrganizationalRepositório Científico de Acesso Aberto da ULisboae-mailmailto:repositorio@ulisboa.ptrepositorio@ulisboa.pt2026-06-03T17:30:01Z20262026-01-01T00:00:00ZHandlehttp://hdl.handle.net/10400.5/118931http://purl.org/coar/access_right/c_f1cfembargoed accessFT-ICR MSUntargeted MetabolomicsTDP-43 aggregationSaccharomyces cerevisiaeAmyotrophic Lateral Sclerosis1706798 bytesliteraturehttp://purl.org/coar/resource_type/c_bdccmaster thesishttp://purl.org/coar/access_right/c_f1cfapplication/pdffulltexthttps://repositorio.ulisboa.pt/bitstreams/46178593-7e0b-4cd2-82cc-d86860e55683/download |
| spellingShingle | Metabolomic consequences of TDP-43 aggregation by FT-ICR mass spectrometry : insights from yeast and human Jorge,Ana Carolina Ferreira dos Santos FT-ICR MS Untargeted Metabolomics TDP-43 aggregation Saccharomyces cerevisiae Amyotrophic Lateral Sclerosis |
| status | SINGLETON |
| subject.fl_str_mv | FT-ICR MS Untargeted Metabolomics TDP-43 aggregation Saccharomyces cerevisiae Amyotrophic Lateral Sclerosis |
| title | Metabolomic consequences of TDP-43 aggregation by FT-ICR mass spectrometry : insights from yeast and human |
| title_full | Metabolomic consequences of TDP-43 aggregation by FT-ICR mass spectrometry : insights from yeast and human |
| title_fullStr | Metabolomic consequences of TDP-43 aggregation by FT-ICR mass spectrometry : insights from yeast and human |
| title_full_unstemmed | Metabolomic consequences of TDP-43 aggregation by FT-ICR mass spectrometry : insights from yeast and human |
| title_short | Metabolomic consequences of TDP-43 aggregation by FT-ICR mass spectrometry : insights from yeast and human |
| title_sort | Metabolomic consequences of TDP-43 aggregation by FT-ICR mass spectrometry : insights from yeast and human |
| topic | FT-ICR MS Untargeted Metabolomics TDP-43 aggregation Saccharomyces cerevisiae Amyotrophic Lateral Sclerosis |
| topic_facet | FT-ICR MS Untargeted Metabolomics TDP-43 aggregation Saccharomyces cerevisiae Amyotrophic Lateral Sclerosis |
| url | http://hdl.handle.net/10400.5/118931 |
| visible | 1 |