LncRNAs: Novel therapeutic targets to treat Multiple Myeloma with RNA-based therapies

Multiple Myeloma (MM) is a hematologic neoplasm caused by the clonal proliferation of aberrant plasma cells in the bone marrow (BM). Hyperdiploidy and IGH translocations are the primary genetic events in MM, each affecting approximately 50% of patients. However, there are cases where the translocati...

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Detalhes bibliográficos
Autor: Amundarain, A. (Ane)|||/items/00686d5c-9be0-4e9d-b3ad-60b266e8cc94
Formato: tesis doctoral
Fecha de publicación:2023
País:España
Recursos:Universidad de Navarra
Repositorio:Dadun. Depósito Académico Digital de la Universidad de Navarra
Idioma:inglés
OAI Identifier:oai:dadun.unav.edu:10171/67866
Acesso em linha:https://hdl.handle.net/10171/67866
Access Level:acceso abierto
Palavra-chave:Materias Investigacion::Ciencias de la Salud::Oncología
LncRNAs
Multiple Myeloma
RNA-based therapies
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oai_identifier_str oai:dadun.unav.edu:10171/67866
network_acronym_str ES
network_name_str España
repository_id_str
dc.title.none.fl_str_mv LncRNAs: Novel therapeutic targets to treat Multiple Myeloma with RNA-based therapies
title LncRNAs: Novel therapeutic targets to treat Multiple Myeloma with RNA-based therapies
spellingShingle LncRNAs: Novel therapeutic targets to treat Multiple Myeloma with RNA-based therapies
Amundarain, A. (Ane)|||/items/00686d5c-9be0-4e9d-b3ad-60b266e8cc94
Materias Investigacion::Ciencias de la Salud::Oncología
LncRNAs
Multiple Myeloma
RNA-based therapies
title_short LncRNAs: Novel therapeutic targets to treat Multiple Myeloma with RNA-based therapies
title_full LncRNAs: Novel therapeutic targets to treat Multiple Myeloma with RNA-based therapies
title_fullStr LncRNAs: Novel therapeutic targets to treat Multiple Myeloma with RNA-based therapies
title_full_unstemmed LncRNAs: Novel therapeutic targets to treat Multiple Myeloma with RNA-based therapies
title_sort LncRNAs: Novel therapeutic targets to treat Multiple Myeloma with RNA-based therapies
dc.creator.none.fl_str_mv Amundarain, A. (Ane)|||/items/00686d5c-9be0-4e9d-b3ad-60b266e8cc94
author Amundarain, A. (Ane)|||/items/00686d5c-9be0-4e9d-b3ad-60b266e8cc94
author_facet Amundarain, A. (Ane)|||/items/00686d5c-9be0-4e9d-b3ad-60b266e8cc94
author_role author
dc.contributor.none.fl_str_mv Prosper-Cardoso, F. (Felipe)
Aguirre-Ena, X. (Xabier)
Dadun. Depósito Académico Digital Universidad de Navarra
dc.subject.none.fl_str_mv Materias Investigacion::Ciencias de la Salud::Oncología
LncRNAs
Multiple Myeloma
RNA-based therapies
topic Materias Investigacion::Ciencias de la Salud::Oncología
LncRNAs
Multiple Myeloma
RNA-based therapies
description Multiple Myeloma (MM) is a hematologic neoplasm caused by the clonal proliferation of aberrant plasma cells in the bone marrow (BM). Hyperdiploidy and IGH translocations are the primary genetic events in MM, each affecting approximately 50% of patients. However, there are cases where the translocation partner of IGH is still unknown. Moreover, beyond genetics, epigenomic and transcriptomic studies have uncovered the extensive chromatin activation of regulatory elements in MM, from where thousands of long non-coding RNAs (lncRNAs) are expressed. We hypothesize that these lncRNAs could be involved in translocations occurring in MM. Furthermore, the inhibition of one of these lncRNA, named SMILO, triggers MM cell death, suggesting the potential of lncRNAs as novel therapeutic targets in MM. To unravel the contribution of lncRNAs to translocations in MM, we identified fusion transcripts (FTs) from strand specific RNA-seq data in samples from different B cell subpopulations and MM patient samples. After a stringent computational filtering, we detected FTs in all studied subpopulations, implying that FTs present in healthy samples may be contributing to physiological processes. Nevertheless, FTs present in healthy samples were filtered to detect MM-specific FTs. As hypothesized, the 30% of MM-specific FTs occurred with lncRNAs (lncFTs), and interestingly, an important percentage of MM-specific FTs were transcription readthroughs (RT) between adjacent genes, therefore leading to the identification of novel RNA transcript classes with unknown functional and prognostic potential in this disease. Finally, the contribution of lncFTs to the prognosis of MM patients was assessed by multivariate survival studies performed in the CoMMpass dataset including 599 MM patient samples, demonstrating that the combination of the presence of certain lncFTs with classical genomic high-risk markers can improve the prognostic stratification of MM patients. On the other hand, we propose the generation of aptamer-siRNA chimeras as RNA-based therapies that will enable the targeted silencing of oncogenic coding and non-coding genes, including lncRNAs and FTs, specifically in the pathological plasma cells of MM. The silencing is achieved with therapeutic siRNA molecules which are delivered specifically to pathological plasma cells by MM-specific RNA aptamers. To identify the MM-specific aptamers we applied a Cell-SELEX approach, where a random RNA aptamer library is subjected to iterative binding rounds with MM cell lines to enrich sequences able to bind target cells specifically. After 10 selection rounds, we identified 10 enriched aptamer clusters, from which aptamer 1 (APT1), aptamer 1 (APT3) and aptamer 1 (APT9) were selected for validation studies. Flow cytometry and confocal microscopy studies showed that all aptamers bind preferentially and internalize into MM cell lines, besides, APT3 and APT9 were minimally toxic to MM cell lines up to 5 M, suggesting they could be used as siRNAs carriers for targeted delivery without inherent toxic effects. Likewise, we identified effective siRNAs able to inhibit both SMILO lncRNA and RRM1 coding gene with known oncogenic effects in MM, so they were selected for chimera generation with the APT3 to obtain the therapeutic silencing of these genes in the MM cell. In conclusion, this doctoral thesis aimed at elucidating the involvement and the prognostic significance of lncRNAs in fusion transcripts occurring in MM, as well as to develop RNA-based therapeutic approaches that will enable the targeted silencing of these novel transcript classes together with coding genes in a cell-specific fashion.
publishDate 2023
dc.date.none.fl_str_mv 2023
2023-11-16
2023
2023-11-16
2023
2023-11-16
2023
2023-05-29
dc.type.none.fl_str_mv doctoral thesis
http://purl.org/coar/resource_type/c_db06
dc.type.openaire.fl_str_mv info:eu-repo/semantics/doctoralThesis
format doctoralThesis
dc.identifier.none.fl_str_mv https://hdl.handle.net/10171/67866
url https://hdl.handle.net/10171/67866
dc.language.none.fl_str_mv Inglés
eng
language_invalid_str_mv Inglés
language eng
dc.rights.none.fl_str_mv open access
http://purl.org/coar/access_right/c_abf2
dc.rights.openaire.fl_str_mv info:eu-repo/semantics/openAccess
rights_invalid_str_mv open access
http://purl.org/coar/access_right/c_abf2
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Universidad de Navarra
publisher.none.fl_str_mv Universidad de Navarra
dc.source.none.fl_str_mv reponame:Dadun. Depósito Académico Digital de la Universidad de Navarra
instname:Universidad de Navarra
instname_str Universidad de Navarra
reponame_str Dadun. Depósito Académico Digital de la Universidad de Navarra
collection Dadun. Depósito Académico Digital de la Universidad de Navarra
repository.name.fl_str_mv
repository.mail.fl_str_mv
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spelling LncRNAs: Novel therapeutic targets to treat Multiple Myeloma with RNA-based therapiesAmundarain, A. (Ane)|||/items/00686d5c-9be0-4e9d-b3ad-60b266e8cc94Materias Investigacion::Ciencias de la Salud::OncologíaLncRNAsMultiple MyelomaRNA-based therapiesMultiple Myeloma (MM) is a hematologic neoplasm caused by the clonal proliferation of aberrant plasma cells in the bone marrow (BM). Hyperdiploidy and IGH translocations are the primary genetic events in MM, each affecting approximately 50% of patients. However, there are cases where the translocation partner of IGH is still unknown. Moreover, beyond genetics, epigenomic and transcriptomic studies have uncovered the extensive chromatin activation of regulatory elements in MM, from where thousands of long non-coding RNAs (lncRNAs) are expressed. We hypothesize that these lncRNAs could be involved in translocations occurring in MM. Furthermore, the inhibition of one of these lncRNA, named SMILO, triggers MM cell death, suggesting the potential of lncRNAs as novel therapeutic targets in MM. To unravel the contribution of lncRNAs to translocations in MM, we identified fusion transcripts (FTs) from strand specific RNA-seq data in samples from different B cell subpopulations and MM patient samples. After a stringent computational filtering, we detected FTs in all studied subpopulations, implying that FTs present in healthy samples may be contributing to physiological processes. Nevertheless, FTs present in healthy samples were filtered to detect MM-specific FTs. As hypothesized, the 30% of MM-specific FTs occurred with lncRNAs (lncFTs), and interestingly, an important percentage of MM-specific FTs were transcription readthroughs (RT) between adjacent genes, therefore leading to the identification of novel RNA transcript classes with unknown functional and prognostic potential in this disease. Finally, the contribution of lncFTs to the prognosis of MM patients was assessed by multivariate survival studies performed in the CoMMpass dataset including 599 MM patient samples, demonstrating that the combination of the presence of certain lncFTs with classical genomic high-risk markers can improve the prognostic stratification of MM patients. On the other hand, we propose the generation of aptamer-siRNA chimeras as RNA-based therapies that will enable the targeted silencing of oncogenic coding and non-coding genes, including lncRNAs and FTs, specifically in the pathological plasma cells of MM. The silencing is achieved with therapeutic siRNA molecules which are delivered specifically to pathological plasma cells by MM-specific RNA aptamers. To identify the MM-specific aptamers we applied a Cell-SELEX approach, where a random RNA aptamer library is subjected to iterative binding rounds with MM cell lines to enrich sequences able to bind target cells specifically. After 10 selection rounds, we identified 10 enriched aptamer clusters, from which aptamer 1 (APT1), aptamer 1 (APT3) and aptamer 1 (APT9) were selected for validation studies. Flow cytometry and confocal microscopy studies showed that all aptamers bind preferentially and internalize into MM cell lines, besides, APT3 and APT9 were minimally toxic to MM cell lines up to 5 M, suggesting they could be used as siRNAs carriers for targeted delivery without inherent toxic effects. Likewise, we identified effective siRNAs able to inhibit both SMILO lncRNA and RRM1 coding gene with known oncogenic effects in MM, so they were selected for chimera generation with the APT3 to obtain the therapeutic silencing of these genes in the MM cell. In conclusion, this doctoral thesis aimed at elucidating the involvement and the prognostic significance of lncRNAs in fusion transcripts occurring in MM, as well as to develop RNA-based therapeutic approaches that will enable the targeted silencing of these novel transcript classes together with coding genes in a cell-specific fashion.Universidad de NavarraProsper-Cardoso, F. (Felipe)Aguirre-Ena, X. (Xabier)Dadun. Depósito Académico Digital Universidad de Navarra20232023-11-1620232023-11-1620232023-11-1620232023-05-29doctoral thesishttp://purl.org/coar/resource_type/c_db06info:eu-repo/semantics/doctoralThesisapplication/pdfhttps://hdl.handle.net/10171/67866reponame:Dadun. Depósito Académico Digital de la Universidad de Navarrainstname:Universidad de NavarraInglésengopen accesshttp://purl.org/coar/access_right/c_abf2info:eu-repo/semantics/openAccessoai:dadun.unav.edu:10171/678662026-06-21T12:47:57Z
score 15.301603

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