Machine learning-enhanced T cell neoepitope discovery for immunotherapy design

Immune responses mediated by T cells are aimed at specific peptides, designated T cell epitopes, that are recognized when bound to human leukocyte antigen (HLA) molecules. The HLA genes are remarkably polymorphic in the human population allowing a broad and fine-tuned capacity to bind a wide array of peptide sequences. Polymorphisms might generate neoepitopes by impacting the HLA-peptide interaction and potentially alter the level and type of generated T cell responses. Multiple algorithms and tools based on machine learning (ML) have been implemented and are able to predict HLA-peptide binding affinity with considerable accuracy. Challenges in this field include the availability of adequate epitope datasets for training and benchmarking and the development of fully integrated pipelines going from next-generation sequencing to neoepitope prediction and quality analysis metrics. Effectively predicting neoepitopes from in silico data is a demanding task that has been facilitated by ML and will be of great value for the future of personalized immunotherapies against cancer and other diseases.The author(s) disclosed receipt of the following financial support for the research, authorship, and/or publication of this article: This research received funding from Fundação para a Ciência e a Tecnologia (FCT) contract IF/00474/2014; PhD scholarship SFRH/BD/132797/2017.info:eu-repo/semantics/publishedVersio

The neglected contribution of streptomycin to the tuberculosis drug resistance problem

Funding Information: Funding: This research was funded by NORTE-01-0145-FEDER-000039, NORTE-01-0145-FEDER-000013, and NORTE-01-0145-FEDER-00002, supported by Norte Portugal Regional Operational Program (NORTE 2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF). It was also funded through the Foundation for Science and Technology (FCT)—project FCT IF/00474/2014, UIDB/50026/2020, and UIDP/50026/2020. DR was funded by FCT Ph.D. scholarships (grant number SFRH/BD/135422/2017). DR was partially funded by the PGCD—Graduate Program Science for Development. MS is supported by FCT through the Estimulo ao Emprego Científico. Publisher Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland.The airborne pathogen Mycobacterium tuberculosis is responsible for a present major public health problem worsened by the emergence of drug resistance. M. tuberculosis has acquired and developed streptomycin (STR) resistance mechanisms that have been maintained and transmitted in the population over the last decades. Indeed, STR resistant mutations are frequently identified across the main M. tuberculosis lineages that cause tuberculosis outbreaks worldwide. The spread of STR resistance is likely related to the low impact of the most frequent underlying mutations on the fitness of the bacteria. The withdrawal of STR from the first-line treatment of tuberculosis potentially lowered the importance of studying STR resistance. However, the prevalence of STR resistance remains very high, could be underestimated by current genotypic methods, and was found in outbreaks of multi-drug (MDR) and extensively drug (XDR) strains in different geographic regions. Therefore, the contribution of STR resistance to the problem of tuberculosis drug resistance should not be neglected. Here, we review the impact of STR resistance and detail well-known and novel candidate STR resistance mechanisms, genes, and mutations. In addition, we aim to provide insights into the possible role of STR resistance in the development of multi-drug resistant tuberculosis.publishersversionpublishe

Assessing textile antiviral properties

Apresentação efetuada no MicroSummit 2022, no Porto, Portugal, 202

Investigação ao serviço da sociedade

[Excerto] A família Coronoviridae inclui uma panóplia de vírus compostos por envelope e RNA de cadeia simples que infetam aves e mamíferos (Payne, 2017). Existem pelo menos sete coronavírus humanos (HCoV), nomeadamente o HCoV-229E, o HCoV-OC43, o HCoV-NL63, o HCoV-HKU1, o coronavírus da síndrome respiratória aguda severa (SARS-CoV), o coronavírus da síndrome respiratória do Médio Oriente (MERS-CoV) e o mais recente coronavírus da síndrome respiratória aguda severa (SARS-CoV-2). Ao contrário dos SARS-CoV, MERS-CoV e SARS-CoV-2, os HCoV “comuns” geralmente causam doença pouco severa das vias respiratórias superiores e contribuem de forma sazonal para 15% a 30% dos casos de “gripe comum” em adultos (Liu, Liang, & Fung, 2020; Woo, Lau, Yip, Huang, & Yuen, 2009). A primeira epidemia severa causada por coronavírus remonta a novembro de 2002, com a transmissão entre pessoas do vírus SARS-CoV. Os sintomas de SARS incluem febre, mal-estar, dor de cabeça, diarreia, entre outros, não havendo um quadro de sintomas específico que permita per se o diagnóstico da doença. A origem do surto de SARS terá, presumivelmente, sido a infeção de pessoas a partir de morcegos num mercado com animais vivos em Guangdong, na China (Zhong et al., 2003). Este coronavírus altamente contagioso, e causador de elevada taxa de mortalidade (9.6%), infetou entre 2002 e 2003 mais de 8000 pessoas, matou mais de 700 e propagou-se a pelo menos 26 países (J. T. Wang & Chang, 2004). Constrangeu períodos de quarentena e de restrições a viagens que conduziram a perdas económicas estimadas num total de 40 mil milhões de dólares, correspondentes a prejuízos na ordem dos 2,6% do PIB na China, 1,05% em Hong Kong e 0,15% no Canadá (Website, 2020). O período de maior verosimilhança de uma pessoa infetada transmitir SARS-CoV foi descrito na segunda semana de doença, aquando do pico de cargas virais no hospedeiro e no qual os sintomas eram regularmente evidentes (Petersen et al., 2020). Esta característica do vírus pode ter ajudado na implementação de práticas adequadas de proteção, tento o notável esforço realizado permitido o controlo total desta epidemia no final de maio de 2003. Desde então, a transmissão entre pessoas do SARS-CoV parece ter parado, com exceção de casos esporádicos resultantes de acidentes laboratoriais (Lim et al., 2004). [...

HABIT - a webserver for interactive T cell neoepitope discovery

bioRxiv - the Preprint Server for Biology.Neoepitopes generated by amino acid variants specifically found in pathogens or cancer cells are gaining momentum in immunotherapy development. HABIT (HLA Binding InTelligence) is a web platform designed to generate and analyse machine learning-based T cell epitope predictions for improved neoepitope discovery. Availability and Implementation: HABIT is available at http://habit.evobiomed.com . Peptide-HLA binding predictions by NetMHCpan 4.0 and NetMHCIIpan 3.1 were implemented in a web application for interactive data exploration using shiny package powered by RStudio.info:eu-repo/semantics/publishedVersio

Evolutionary genetics of Mycobacterium tuberculosis and HIV-1: “The Tortoise and the Hare”

The already enormous burden caused by Mycobacterium tuberculosis and Human Immunodeficiency Virus type 1 (HIV-1) alone is aggravated by co-infection. Despite obvious differences in the rate of evolution comparing these two human pathogens, genetic diversity plays an important role in the success of both. The extreme evolutionary dynamics of HIV-1 is in the basis of a robust capacity to evade immune responses, to generate drug-resistance and to diversify the populationlevel reservoir of M group viral subtypes. Compared to HIV-1 and other retroviruses, M. tuberculosis generates minute levels of genetic diversity within the host. However, emerging whole-genome sequencing data show that the M. tuberculosis complex contains at least nine human-adapted phylogenetic lineages. This level of genetic diversity results in differences in M. tuberculosis interactions with the host immune system, virulence and drug resistance propensity. In co-infected individuals, HIV-1 and M. tuberculosis are likely to co-colonize host cells. However, the evolutionary impact of the interaction between the host, the slowly evolving M. tuberculosis bacteria and the HIV-1 viral “mutant cloud” is poorly understood. These evolutionary dynamics, at the cellular niche of monocytes/macrophages, are also discussed and proposed as a relevant future research topic in the context of single-cell sequencing.This work has been funded by National funds, through the Foundation for Science and Technology (FCT)—project UIDB/50026/2020 and UIDP/50026/2020; by the projects NORTE-01- 0145-FEDER-000013 and NORTE-01-0145-FEDER-000023, supported by Norte Portugal Regional Operational Programme (NORTE 2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF) and by Gilead Génese PGG/009/2017. ASP, CM, and PMMA were funded by FCT PhD scholarships PD/BD/127827/2016, SFRH/BD/132797/2017 and PDE/BDE/113599/2015, respectively

The evolution of the HIV-1 protease folding stability

Financiado para publicación en acceso aberto: Universidade de Vigo/CISUGThe evolution of structural proteins is generally constrained by the folding stability. However, little is known about the particular capacity of viral proteins to accommodate mutations that can potentially affect the protein stability and, in general, the evolution of the protein stability over time. As an illustrative model case, here, we investigated the evolution of the stability of the human immunodeficiency virus (HIV-1) protease (PR), which is a common HIV-1 drug target, under diverse evolutionary scenarios that include (1) intra-host virus evolution in a cohort of seventy-five patients sampled over time, (2) intra-host virus evolution sampled before and after specific PR-based treatments, and (3) inter-host evolution considering extant and ancestral (reconstructed) PR sequences from diverse HIV-1 subtypes. We also investigated the specific influence of currently known HIV-1 PR resistance mutations on the PR folding stability. We found that the HIV-1 PR stability fluctuated over time within a constant and wide range in any studied evolutionary scenario, accommodating multiple mutations that partially affected the stability while maintaining activity. We did not identify relationships between change of PR stability and diverse clinical parameters such as viral load, CD4+ T-cell counts, and a surrogate of time from infection. Counterintuitively, we predicted that nearly half of the studied HIV-1 PR resistance mutations do not significantly decrease stability, which, together with compensatory mutations, would allow the protein to adapt without requiring dramatic stability changes. We conclude that the HIV-1 PR presents a wide structural plasticity to acquire molecular adaptations without affecting the overall evolution of stability.Ministerio de Economía y Competitividad | Ref. RYC-2015-18241Xunta de Galicia | Ref. ED431F 2018/08Xunta de Galicia | Ref. ED481A-2020/19

Mycobacterium tuberculosis Complex Exhibits Lineage-Specific Variations Affecting Protein Ductility and Epitope Recognition

The advent of whole-genome sequencing has provided an unprecedented detail about the evolution and genetic significance of species-specific variations across the whole Mycobacterium tuberculosis Complex. However, little attention has been focused on understanding the functional roles of these variations in the protein coding sequences. In this work, we compare the coding sequences from 74 sequenced mycobacterial species including M. africanum, M. bovis, M. canettii, M. caprae, M. orygis, and M. tuberculosis. Results show that albeit protein variations affect all functional classes, those proteins involved in lipid and intermediary metabolism and respiration have accumulated mutations during evolution. To understand the impact of these mutations on protein functionality, we explored their implications on protein ductility/disorder, a yet unexplored feature of mycobacterial pro-teomes. In agreement with previous studies, we found that a Gly71Ile substitution in the PhoPR virulence system severely affects the ductility of its nearby region in M. africanum and animal-adapted species. In the same line of evidence, the SmtB transcriptional regulator shows amino acid variations specific to the Beijing lineage, which affects the flexibility of the N-terminal trans-activation domain. Furthermore, despite the fact that MTBC epitopes are evolutionary hyperconserved, we identify strain-and lineag-especific amino acid mutations affecting previously known T-cell epitopes such as EsxH and FbpA (Ag85A). Interestingly, in silico studies reveal that these variations result in differential interaction of epitopes with the main HLA haplogroups.Gobierno de Aragón (DGA-GC B18 and B25), the Spanish Ministry of Science and Competitiveness (BIO2014-52580P, CSIC13-4E-2490), Instituto de Salud Carlos III (PI12/01970) and the European Commission Horizon 2020 (H2020-PHC-643381). Some of these grants were partially financed by the EU FEDER Program. This work was also supported by Fundação para a Ciência e Tecnologia, Portugal (IF/00474/2014) and cofunded by Programa Operacional Regional do Norte (ON.2—O Novo Norte), Quadro de Referência Estratégico Nacional (QREN), through the Fundo Europeu de Desenvolvimento Regional (FEDER)info:eu-repo/semantics/publishedVersio

Nationwide study of drug resistance mutations in HIV-1 infected individuals under antiretroviral therapy in Brazil

The success of antiretroviral treatment (ART) is threatened by the emergence of drug resistance mutations (DRM). Since Brazil presents the largest number of people living with HIV (PLWH) in South America we aimed at understanding the dynamics of DRM in this country. We analyzed a total of 20,226 HIV-1 sequences collected from PLWH undergoing ART between 2008–2017. Results show a mild decline of DRM over the years but an increase of the K65R reverse transcriptase mutation from 2.23% to 12.11%. This increase gradually occurred following alterations in the ART regimens replacing zidovudine (AZT) with tenofovir (TDF). PLWH harboring the K65R had significantly higher viral loads than those without this mutation (p p < 0.001) association of K65R with subtype C (11.26%) when compared with subtype B (9.27%). Nonetheless, evidence for K65R transmission in Brazil was found both for C and B subtypes. Additionally, artificial neural network-based immunoinformatic predictions suggest that K65R could enhance viral recognition by HLA-B27 that has relatively low prevalence in the Brazilian population. Overall, the results suggest that tenofovir-based regimens need to be carefully monitored particularly in settings with subtype C and specific HLA profiles.This work has been funded by Portuguese National funds, through the Foundation for Science and Technology (FCT) (project UIDB/50026/2020 and UIDP/50026/2020; by the projects NORTE-01-0145-FEDER-000013 and NORTE-01-0145-FEDER-000023, supported by Norte Portugal Regional Operational Programme (NORTE 2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF) and by Gilead Génese PGG/009/2017. ASP and PMMA were funded by FCT PhD scholarships PD/BD/127827/2016, and PDE/BDE/113599/2015, respectively

Analysis of a Local HIV-1 Epidemic in Portugal Highlights Established Transmission of non-B and -G Subtypes

The existing data supports Portugal as the Western Europe country with highest HIV-1 subtype diversity. However, detailed phylogenetic studies of Portuguese HIV-1 epidemics are still scarce. Thus, our main goal was to analyze the phylodynamics of a local HIV-1 infection in the Portuguese region of Minho. Molecular epidemiological analysis was applied to data from 289 HIV-1 infected individuals followed in the reference Hospital of the province of Minho, Portugal, in which isolated viruses had been sequenced between 2000 and 2012. Viruses of the G (29.1%) and B (27.0%) subtypes were the most frequent, followed by recombinant forms (17.6%), C (14.5%), F1 (7.3%) and A1 (4.2%) subtypes. Multinomial logistic regression revealed that the odds of being infected with A1 and F1 subtype increased over the years when compared with B, G, C or recombinant viruses. As expected, polyphyletic patterns suggesting multiple and old introductions of subtypes B and G were found. However, transmission clusters of non-B and -G viruses among native individuals were also found with the dates of the most recent common ancestor estimated to the early 2000s. Our study supports that the HIV-1 subtype diversity in the Portuguese region of Minho is high and has been increasing in a manner that is apparently driven by factors other than immigration and international travel. Infections with A1 and F1 viruses in the region of Minho are becoming established and were mainly found in sexually transmitted clusters, reinforcing the need for more efficacious control measures targeting this infection route