| 1. |
- Rivas-Carrillo, Salvador Daniel
(författare)
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The revolutionary partnership of computation and biology
- 2023
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The organization of living beings is complex. Science uses modeling in order to gain a deeper understanding, and to be able to manipulate the processes of living organisms. To this purpose, I used and developed computational tools to investigate and model different relevant biological phenomena. In paper I, I utilized whole-genome data from wild and domesticated European rabbit (Oryctolagus cuniculus sp.) populations to identify segregating insertions of endogenous retroviruses and compare their variation along the host phylogeny and domestication history. The results from this study highlight the importance of genomic modeling beyond reference organisms and reference individuals, and provide deep insights regarding strategies for variant analyses in host population comparative genomics. In paper IV, I studied the process of exaptation of foreign genetic elements at broad-scale by observing the presence and characteristics of retroviral env gene, syncytin, across vertebrates. I searched a library of more than 150 chromosome-length assemblies covering 17 taxonomical orders for syncytin homologs, where I identified and syntenically aligned over 300 loci insertions, including not previously known insertions. Additionally, three-dimensional structures of the recovered sequences were predicted using AlphaFold2. Phylogenomics analyses suggest a complex dynamic of multiple retroviral insertions at different time points with sequence conservation specific to clades that share a similar histo-physiological placental type.In paper II, I expanded the scope to encompass translational medicine by developing an unsupervised machine learning methodology for detecting anomalies in biomedical signals, MindReader, which I applied primarily to electroencephalogram. In paper III, I developed a hidden Markov model implementation that includes a hypothesis generator for stream time-domain signals, which is used as a dependency for paper II. The work in this thesis substantiates that a combination of biological knowledge, cutting-edge technology, and robust algorithmic design constitute the primordial factors for scientific advancement.
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| 2. |
- Vihinen, Mauno
(författare)
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How to Define Pathogenicity, Health, and Disease?
- 2017
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Ingår i: Human Mutation. - : Hindawi Limited. - 1059-7794. ; 38:2, s. 129-136
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Tidskriftsartikel (refereegranskat)abstract
- Scientific and clinical communities produce ever increasing amounts of data and details about health and disease. Our ability to understand and utilize this information is limited because of imprecise language and lack of well-defined concepts. This problem involves also the principal concepts of health, disease, and pathogenicity. Here, a systematic model is presented for pathogenicity, as well as for health and disease. It has three components: extent, modulation, and severity, which jointly define the continuum of pathogenicity. The model is population based, and once implemented, it can be used for numerous purposes such as diagnosis, patient stratification, prognosis, finding phenotype–genotype correlations, or explaining adverse drug reactions. The new model has several benefits including health economy by allowing evidence-based personalized/precision medicine.
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| 3. |
- Estupinan, HY, et al.
(författare)
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BTK gatekeeper residue variation combined with cysteine 481 substitution causes super-resistance to irreversible inhibitors acalabrutinib, ibrutinib and zanubrutinib
- 2021
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Ingår i: Leukemia. - : Springer Science and Business Media LLC. - 1476-5551 .- 0887-6924. ; 35:85, s. 1317-1329
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Tidskriftsartikel (refereegranskat)abstract
- Irreversible inhibitors of Bruton tyrosine kinase (BTK), pioneered by ibrutinib, have become breakthrough drugs in the treatment of leukemias and lymphomas. Resistance variants (mutations) occur, but in contrast to those identified for many other tyrosine kinase inhibitors, they affect less frequently the “gatekeeper” residue in the catalytic domain. In this study we carried out variation scanning by creating 11 substitutions at the gatekeeper amino acid, threonine 474 (T474). These variants were subsequently combined with replacement of the cysteine 481 residue to which irreversible inhibitors, such as ibrutinib, acalabrutinib and zanubrutinib, bind. We found that certain double mutants, such as threonine 474 to isoleucine (T474I) or methionine (T474M) combined with catalytically active cysteine 481 to serine (C481S), are insensitive to ≥16-fold the pharmacological serum concentration, and therefore defined as super-resistant to irreversible inhibitors. Conversely, reversible inhibitors showed a variable pattern, from resistance to no resistance, collectively demonstrating the structural constraints for different classes of inhibitors, which may affect their clinical application.
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| 4. |
- Carraro, Marco, et al.
(författare)
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Performance of in silico tools for the evaluation of p16INK4a (CDKN2A) variants in CAGI
- 2017
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Ingår i: Human Mutation. - : Hindawi Limited. - 1059-7794 .- 1098-1004. ; 38:9, s. 1042-1050
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Tidskriftsartikel (refereegranskat)abstract
- Correct phenotypic interpretation of variants of unknown significance for cancer-associated genes is a diagnostic challenge as genetic screenings gain in popularity in the next-generation sequencing era. The Critical Assessment of Genome Interpretation (CAGI) experiment aims to test and define the state of the art of genotype-phenotype interpretation. Here, we present the assessment of the CAGI p16INK4a challenge. Participants were asked to predict the effect on cellular proliferation of 10 variants for the p16INK4a tumor suppressor, a cyclin-dependent kinase inhibitor encoded by the CDKN2A gene. Twenty-two pathogenicity predictors were assessed with a variety of accuracy measures for reliability in a medical context. Different assessment measures were combined in an overall ranking to provide more robust results. The R scripts used for assessment are publicly available from a GitHub repository for future use in similar assessment exercises. Despite a limited test-set size, our findings show a variety of results, with some methods performing significantly better. Methods combining different strategies frequently outperform simpler approaches. The best predictor, Yang&Zhou lab, uses a machine learning method combining an empirical energy function measuring protein stability with an evolutionary conservation term. The p16INK4a challenge highlights how subtle structural effects can neutralize otherwise deleterious variants.
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| 5. |
- Rasila, Tiina S., et al.
(författare)
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Mu transpososome activity-profiling yields hyperactive MuA variants for highly efficient genetic and genome engineering
- 2018
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Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 46:9, s. 4649-4661
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Tidskriftsartikel (refereegranskat)abstract
- The phage Mu DNA transposition system provides a versatile species non-specific tool for molecular biology, genetic engineering and genome modification applications. Mu transposition is catalyzed by MuA transposase, with DNA cleavage and integration reactions ultimately attaching the transposon DNA to target DNA. To improve the activity of the Mu DNA transposition machinery, we mutagenized MuA protein and screened for hyperactivity-causing substitutions using an in vivo assay. The individual activity-enhancing substitutions were mapped onto the MuA-DNA complex structure, containing a tetramer of MuA transposase, two Mu end segments and a target DNA. This analysis, combined with the varying effect of the mutations in different assays, implied that the mutations exert their effects in several ways, including optimizing protein-protein and protein-DNA contacts. Based on these insights, we engineered highly hyperactive versions of MuA, by combining several synergistically acting substitutions located in different subdomains of the protein. Purified hyperactive MuA variants are now ready for use as second-generation tools in a variety of Mu-based DNA transposition applications. These variants will also widen the scope of Mu-based gene transfer technologies toward medical applications such as human gene therapy. Moreover, the work provides a platform for further design of custom trans-posases.
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| 6. |
- Azevedo, Carla, et al.
(författare)
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Parkinsons disease and multiple system atrophy patient iPSC-derived oligodendrocytes exhibit alpha-synuclein-induced changes in maturation and immune reactive properties
- 2022
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 119:12
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Tidskriftsartikel (refereegranskat)abstract
- Limited evidence has shed light on how aSYN proteins affect the oligodendrocyte phenotype and pathogenesis in synucleinopathies that include Parkinsons disease (PD) and multiple system atrophy (MSA). Here, we investigated early transcriptomic changes within PD and MSA O4(+) oligodendrocyte lineage cells (OLCs) generated from patient-induced pluripotent stem cells (iPSCs). We found impaired maturation of PD and MSA O4(+) OLCs compared to controls. This phenotype was associated with changes in the human leukocyte antigen (HLA) genes, the immunoproteasome subunit PSMB9, and the complement component C4b for aSYN p.A53T and MSA O4(+) OLCs, but not in SNCA(trip) O4(+) OLCs despite high levels of aSYN assembly formation. Moreover, SNCA overexpression resulted in the development of O4(+) OLCs, whereas exogenous treatment with aSYN species led to significant toxicity. Notably, transcriptome profiling of genes encoding proteins forming Lewy bodies and glial cytoplasmic inclusions revealed clustering of PD aSYN p.A53T O4(+) OLCs with MSA O4(+) OLCs. Our work identifies early phenotypic and pathogenic changes within human PD and MSA O4(+) OLCs.
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| 7. |
- Yang, Yang, et al.
(författare)
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PON-Sol : Prediction of effects of amino acid substitutions on protein solubility
- 2016
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Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 32:13, s. 2032-2034
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Tidskriftsartikel (refereegranskat)abstract
- Motivation: Solubility is one of the fundamental protein properties. It is of great interest because of its relevance to protein expression. Reduced solubility and protein aggregation are also associated with many diseases. Results: We collected from literature the largest experimentally verified solubility affecting amino acid substitution (AAS) dataset and used it to train a predictor called PON-Sol. The predictor can distinguish both solubility decreasing and increasing variants from those not affecting solubility. PONSol has normalized correct prediction ratio of 0.491 on cross-validation and 0.432 for independent test set. The performance of the method was compared both to solubility and aggregation predictors and found to be superior. PON-Sol can be used for the prediction of effects of disease-related substitutions, effects on heterologous recombinant protein expression and enhanced crystallizability. One application is to investigate effects of all possible AASs in a protein to aid protein engineering.
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| 8. |
- Schaafsma, Gerard C. P., et al.
(författare)
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Genetic Variation in Bruton Tyrosine Kinase
- 2015
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Ingår i: Agammaglobulinemia. - Cham : Springer International Publishing. - 9783319227146 ; , s. 75-85
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Bokkapitel (refereegranskat)abstract
- X-linked agammaglobulinemia (XLA) is a hereditary immunodeficiency caused by variations in the gene encoding for Bruton's tyrosine kinase (BTK). Patients with XLA have decreased numbers of mature B cells, lack all immunoglobulin isotypes, and therefore have susceptibility to severe bacterial infections. XLA-causing variations are collected into BTKbase freely available at http://structure.bmc.lu.se/idbase/BTKbase/. Details of the variations are provided at DNA, RNA, and protein levels, using standardized systematic names and a plain English description. In addition, clinical details from the patients are provided when available. BTKbase contains variation entries for 1362 patients from 1198 unrelated families altogether for 742 unique molecular events. The localization of the variations on the gene and protein for BTK can be analyzed by clicking sequences on web pages. The distribution of the variations in the five structural domains is approximately according to the length of the domains, except for the TH and SH3 domains. The most frequently affected sites are CpG dinucleotides. The majority of the amino acid substitutions are structural affecting protein fold or stability. Detailed statistics is provided highlighting variation types, affected domains, exons and introns, as well as structural consequences.
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| 9. |
- Savchenko, Ekaterina, et al.
(författare)
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FGF family members differentially regulate maturation and proliferation of stem cell-derived astrocytes
- 2019
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 9:1
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Tidskriftsartikel (refereegranskat)abstract
- The glutamate transporter 1 (GLT1) is upregulated during astrocyte development and maturation in vivo and is vital for astrocyte function. Yet it is expressed at low levels by most cultured astrocytes. We previously showed that maturation of human and mouse stem cell-derived astrocytes - including functional glutamate uptake - could be enhanced by fibroblast growth factor (FGF)1 or FGF2. Here, we examined the specificity and mechanism of action of FGF2 and other FGF family members, as well as neurotrophic and differentiation factors, on mouse embryonic stem cell-derived astrocytes. We found that some FGFs - including FGF2, strongly increased GLT1 expression and enhanced astrocyte proliferation, while others (FGF16 and FGF18) mainly affected maturation. Interestingly, BMP4 increased astrocytic GFAP expression, and BMP4-treated astrocytes failed to promote the survival of motor neurons in vitro. Whole transcriptome analysis showed that FGF2 treatment regulated multiple genes linked to cell division, and that the mRNA encoding GLT1 was one of the most strongly upregulated of all astrocyte canonical markers. Since GLT1 is expressed at reduced levels in many neurodegenerative diseases, activation of this pathway is of potential therapeutic interest. Furthermore, treatment with FGFs provides a robust means for expansion of functionally mature stem cell-derived astrocytes for preclinical investigation.
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| 10. |
- Vihinen, Mauno
(författare)
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Establishment of an international database for genetic variants in esophageal cancer
- 2016
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Ingår i: Annals of the New York Academy of Sciences. - : Wiley. - 0077-8923. ; 1381:1, s. 45-49
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Tidskriftsartikel (refereegranskat)abstract
- The establishment of a database has been suggested in order to collect, organize, and distribute genetic information about esophageal cancer. The World Organization for Specialized Studies on Diseases of the Esophagus and the Human Variome Project will be in charge of a central database of information about esophageal cancer–related variations from publications, databases, and laboratories; in addition to genetic details, clinical parameters will also be included. The aim will be to get all the central players in research, clinical, and commercial laboratories to contribute. The database will follow established recommendations and guidelines. The database will require a team of dedicated curators with different backgrounds. Numerous layers of systematics will be applied to facilitate computational analyses. The data items will be extensively integrated with other information sources. The database will be distributed as open access to ensure exchange of the data with other databases. Variations will be reported in relation to reference sequences on three levels––DNA, RNA, and protein—whenever applicable. In the first phase, the database will concentrate on genetic variations including both somatic and germline variations for susceptibility genes. Additional types of information can be integrated at a later stage.
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