Das Immunpeptidom vom klarzelligen Nierenzellkarzinom: Identifizierung und Charakterisierung von T-Zell-Epitopen für immuntherapeutische Ansätze

Current therapy of ccRCC is commonly constrained by low response rates and frequent resistance against administered drugs. In recent years, drug discovery is focusing on the positive modulation of the immune system. The lately approved checkpoint ab nivolumab for treatment of ccRCC is the first drug in the upcoming era of immunotherapy. Being an immunogenic tumor entity, specific immunotherapies have the potential to increase the anti-cancer response with lower side effects. To identify suitable targets for a specific immunotherapy a comprehensive analysis on the HLA ligandome of 58 ccRCC samples and corresponding adjacent benign tissues was conducted by LC-MS/MS and compared to an additional in-house database of benign immunopeptidomes. TUMAPs were selected according to several evaluations focusing on tumor exclusivity, quantitative expression and HLA restriction as well as the biological role of the source antigens. Overall, 26 peptides from six HLA alleles were selected and screened for their immunogenicity in CD8+ T cell priming experiments, with 19 peptides exhibiting immune recognition. This set of peptides can be considered for future specific immunotherapeutic approaches. HLA-C as well as HLA-E and HLA-G molecules possess important roles in both the innate and adaptive immunity with different immunomodulatory functions. However, the uncovering of the peptide motifs received insufficient attention until recent data from in vitro binding experiments for HLA-C allotypes. For this purpose, the characterization of the binding specificities of the most frequent HLA-C allotypes as well as HLA-E and HLA-G were accomplished by LC-MS/MS-based identification of naturally processed and presented HLA ligands from monoallelic C1R transfectants. HLA-C allotypes display anchors in the B or C pocket (position 2 or 3 within the peptide) and a less variable anchor in pocket F (C-terminal position within the peptide). Overall, 20,156 HLA-C ligands were identified. For HLA-E the previously reported small ligand repertoire could be confirmed with five identified ligands, whereas a large ligand repertoire for HLA-G (2258 ligands) could be unveiled with anchor positions 3 and 9 and an auxiliary anchor at position 1. The data was utilized to establish SYFPEITHI matrices for epitope prediction and for peptide assignment to the correct HLA. Especially for HLA-G the number of HLA ligands could be tremendously increased from three prior known HLA ligands within the IEDB database to more than 2000 HLA ligands.Die gegenwärtige Therapie vom klarzelligem Nierenzellkarzinom ist, sowohl durch eine niedrige Ansprechrate als auch durch die häufig auftretenden Resistenzen gegenüber der angewandten Medikation begrenzt. Dies ist ein Grund weshalb der Fokus immer weiter in Richtung Modulation des Immunsystems gesetzt wird. Der kürzlich für ccRCC zugelassene Checkpoint-Inhibitor-Antikörper Nivolumab ist das erste Medikament der bevorstehenden Ära der Immuntherapie. Spezifische Immuntherapien haben aufgrund der Immunogenität von ccRCC das Potential höherer Anspruchsraten als auch geringerer Nebenwirkungen. Um geeignete Angriffsziele für eine spezifische Immuntherapie zu identifizieren wurde eine umfangreiche Analyse des HLA Ligandoms von 58 ccRCC Proben und entsprechendem benachbarten Normalgewebe mittels LC-MS/MS durchgeführt und zusätzlich mit einer internen Immunpeptidom-Datenbank von diversen gesunden Organen verglichen. TUMAPs wurden durch Anwendung unterschiedlicher Auswertungen ausgewählt, die sowohl deren Tumorexklusivität, quantitative Expression und HLA-Restriktion als auch die Funktion des Quellantigens berücksichtigten. Insgesamt wurden 26 Peptide von sechs HLA-Allotypen ausgewählt und auf deren Immunogenität in CD8+ T Zell-Priming-Experimenten überprüft. 19 von 26 Peptiden konnten im Komplex mit HLA durch CD8+ T Zellen gesunder Spender erkannt werden. Dieses Set an Peptiden kann für zukünftige spezifische immuntherapeutische Ansätze in Betracht gezogen werden. HLA-C- als auch HLA-E- und HLA-G-Moleküle nehmen sowohl in der angeborenen als auch in der adaptiven Immunität diverse immunmodulatorische Funktionen ein. Nichtsdestotrotz wurden viele HLA-C-Bindemotive erst kürzlich über in vitro Bindungsexperimenten angegangen. Aus diesem Grund wurden die Bindungsspezifitäten der häufigsten HLA-C-Allotypen als auch die Bindungsspezifitäten von HLA-E und HLA-G charakterisiert. Hierfür wurden natürlich prozessierte und präsentierte HLA-Liganden aus monoallelischen C1R-Transfektanten mittels LC-MS/MS identifiziert. HLA-C-Allotypen zeigen Ankerpositionen in der B- oder C-Tasche (Interaktion mit Position 2 bzw. 3 im Peptid) und einen wenig variablen Anker in der F-Tasche (Interaktion mit C-terminaler Position im Peptid). Insgesamt wurden 20.156 HLA-C-Liganden identifiziert. Für HLA-E wurde das bekannte kleine Ligandenrepertoire (5 identifizierte Liganden) bestätigt, wohingegen das breite Repertoire von HLA-G (2258 Liganden) aufgedeckt werden konnte. Position 3 und der C-Terminus des Liganden bilden hierbei die Ankerpositionen und Position 1 einen Hilfsanker. Die Daten wurden verwendet um SYFPEITHI-Matrizen für die Epitopvorhersage als auch für die Peptidzuordnung zum entsprechenden HLA Molekül zu etablieren. Insbesondere für HLA-G konnte die Anzahl der HLA Liganden massiv von bisher drei bekannten Liganden IEDB Datenbank) auf über 2000 Liganden gesteigert werden

Global mammal conservation: past trends, current challenges and optimal strategies for intervention

The conservation of the world's mammals has been one of the main goals for international agencies and NGOs in the past decades, as well as a core challenge for conservation scientists. Nonetheless, several mammal species went extinct in the past century and many others declined seriously in recent decades (a total of 76 species disappeared after 1500). Today 25% of mammal species are threatened with extinction, and the necessity of a globally coordinated conservation strategy has been proclaimed. At a global scale, factors such as habitat loss and direct kill, are the key drivers of mammal species decline and extinction. The current biodiversity crisis, and in particular the current decline of mammals, needs operational tools to be tackled. Such tools include both on-the-ground implementation of conservation actions and a well framed conservation decision making process. Yet, a poor integration of macroecological studies and conservation planning studies has characterised past strategies for global species conservation. The scope of this PhD thesis is to advance the knowledge on global mammal conservation, by integrating existing data and by combining multi-disciplinary methodologies to provide innovative approaches to conservation decision making. The objectives of this thesis are: (i) to characterise global patterns in the distribution of suitable habitat for mammals; (ii) to describe patterns and processes characterising the recent decline of mammal species; (iii) to provide insights into the characterisation of internal sources of mammal species extinction risk and to use them in conservation planning; (iv) to address the methodological challenges that affect the quantification of threats to biodiversity. (i) A key aspect determining the effectiveness of mammal species conservation is the knowledge of species distribution. However, large-scale and fine-resolution information on mammal distribution has often been lacking. We filled this gap by developing habitat suitability models for over 90% of existing terrestrial mammal species, based on their habitat preferences with a 300m pixel base. Based on the developed models, we conducted a global, fine-resolution analysis of patterns of species richness. We found that the richness of mammal species estimated by the overlap of their suitable habitat is on average one-third less than the one estimated by the overlap of their geographic ranges. Differences in the proportion of suitable habitat within mammal geographic ranges were correlated to species IUCN Red List category, with threatened species having smaller values than non-threatened ones. Assessing temporal changes in species' extinction risks is necessary for measuring conservation success or failure at large spatial and taxonomical scales. Yet such a knowledge is limited even in well-studied group, such as mammals. We addressed this gap by consulting past literature sources, and assigning retrospective Red List categories to the world’s carnivores and ungulates (n=550) for the past 40 years. We found that 23% of species moved one or more categories closer to extinction, with Southeast Asia showing the steepest declines (where the figure is 45%). We described a declining trend in mammal conservation status that was already underway 40 years ago, and has now accelerated, uncovering alarming future scenarios of global species losses. This declining trend is the ultimate result of geopolitical events, international regulations, shifting cultural values and natural resource exploitation. Studying trends in global species decline can help conservationists to recognize which conservation policies and strategies are (or are not) contributing to biodiversity protection. (iii) With one fourth of the world's mammals threatened with extinction and limited budget to save them, adopting an efficient conservation strategy is crucial. Previous approaches to setting global conservation priorities have assumed all species to have equal conservation value, or have focused on species with high extinction risk, species that may be hard to save. We propose a novel approach and focus on threatened species having the greatest recovery opportunity, using a new conservation benefit metric. We discover that 65-87% of all threatened and potentially recoverable mammal species are overlooked by existing prioritization approaches. Our innovative metric has the potential to integrate with every strategy that aims to maximize the likelihood of conservation success. (iv) Anthropogenic threats drive species to extinction and are the focus of extinction risk analysis and conservation planning. However, the effects that multiple threats quantification methods have on threat measurement remain untested. We addressed this gap by quantifying the magnitude of human footprint for 901 Southeast Asian mammals according to several methods. We demonstrate that adopting different threat quantification techniques causes significant disagreement in threat measurements. We found that biases were non-linear and dependent on distal factors, such as the proportion of suitable habitat within species' range and species' habitat specialism. Threatened species were best predicted when measuring their proportion of range exposed to high levels of human footprint (a proxy of threat extent). Improving techniques to quantify biodiversity threats will enhance the effectiveness of extinction risk analyses and conservation decisions. Based on the outcomes of the presented PhD research, we propose that three main factors influence the global extinction risk of mammal species: human threats, species biology and conservation actions. The role of these factors in determining species decline or recovery, has been explored both theoretically and analytically. However, our understanding of how they interact to determine a species' final condition of endangerment is still limited. A key research challenge in the next future would be the exploration of such an interaction. In this thesis, we set a basis for the realization of such an analysis and the next step will be the investigation of the combinatory effects of all the mentioned factors. The urgency to properly address the current biodiversity crisis calls for a more coordinative effort in defining shared global strategies for intervention. Having a global coordination of conservation plan has a great potential to be more cost-effective than having several scattered plans, without contrasting the need for local scale practical interventions. We believe that increasing the biological inputs in conservation planning, through the consideration of species' biological characteristics, represents a promising field of future research expansion where expertise from multiple backgrounds can be integrated to define innovative strategies to address global scale extinction risk. The research findings presented in this thesis will contribute to improve future mammal conservation by: guiding the definition of more biologically-informed conservation strategies, improving our ability to analyze evidence of conservation success, providing general guidelines to address methodological uncertainty in conservation

Spanish validation of the Shorter Version of the Workplace Incivility Scale: An employment status invariant measure

Workplace Incivility (WI) occurs worldwide and has negative consequences on individuals and organizations. Valid and comprehensive instruments have been used, specifically in English speaking countries, to measure sucadverse process at work, but it is not available a validated instrument for research carried out in Spanish speaking countries. In this study we aim to test the psychometric properties of the Matthews and Ritter’s four-item Workplace Incivility Scale (2016) with Spanish workers (N = 407) from different sectors. Participants’ mean age was 38.73 (SD = 10.45) years old and the percentage of female employees was 59.2%. Confirmatory factor analysis using AMOS 19.0 was carried out, presenting a good fit. The internal consistency, convergent and concurrent validity of the scale were examined. Results show good scale reliability and expected high correlations with social undermining. Moreover, the scale related to propensity to leave a job, job satisfaction, and psychological well-being in the expected way. After configural invariance across groups was established, testing for metric invariance and scalar invariance was performed. Considering Δχ2 and ΔCFI tests for two nested models, the 4-item scale was invariant when the employment status is considered (permanent vs. temporal, full-time vs. part-time, and supervisor vs. non-supervisors). Overall, our findings showed good psychometric properties of the shorter version of the WIS in Spain. Theoretical and practical implications of this study are discussed.Ministerio de Economía y Competitividad de España PSI2015-64894-PFundação para a Ciência e a Tecnologia (FCT) Portugal SFRH/BPD/121748/201

Drivers of change in the realised climatic niche of terrestrial mammals

The breadth of a species’ climatic niche is an important ecological trait that allows adaptation to climate change, but human activities often reduce realised niche breadth by impacting species distributions. Some life-history traits, such as dispersal ability and reproductive speed, allow species to cope with both human impact and climate change. But how do these traits interact with human pressure to determine niche change? Here we investigate the patterns and drivers of change in the realised climatic niche of 258 terrestrial mammal species. Our goal is to disentangle the impacts of human land use, climate change and life history. We quantified the past and present climatic niches of each species by considering past climatic conditions (Mid Holocene) within their pre-human impact distributions, and current climatic conditions within the current distributions. Depending on the difference between past and current niche, we defined four categories of change: ‘shrink’, ‘shift’, ‘stable’ and ‘expand’. We found over half of the species in our sample have undergone niche shrink, while only one in six retained a stable niche. Climate change and distribution change were the strongest correlates of species niche change, followed by biogeography, anthropogenic land use and life-history traits. Factors that increased the probability of niche shrink included: overall climatic instability, reduction in distribution range, historical land use, large body mass and long weaning age. Species with these characteristics might require interventions that facilitate natural dispersal or assisted colonisation to survive rapidly changing climates

Implications of exceeding the Paris Agreement for mammalian biodiversity

The Paris Agreement settled to limit global warming to 2 C and possibly 1.5 C from pre-industrial times. However, little is known about the implications of such climatic goals for biodiversity once species' adaptability to new climatic conditions is accounted for. Here, we projected the bioclimatic space loss for mammalian communities across terrestrial biomes, under four alternative emission scenarios to year 2050, and evaluated the risk for taxonomic, phylogenetic, and functional biodiversity in each biome. The high-emission scenario (largely overshooting Paris limits) will lead to an average 34% bioclimatic space loss across biomes, surpassing critical levels in half of them (31 out of 63), including six biomes with high biodiversity content. Overall, these biomes account for an area at risk which is 10 times larger compared to that identified under low-emission scenarios. Under intermediate-emission scenario the loss is reduced to 28%, but two biomes with high biodiversity content will still be at risk. Achieving the 1.5 C target would reduce the average bioclimatic space loss to 19%, with only eight biomes facing critical levels of loss, none of which hosts high biodiversity content. These results highlight the biological risk of climate inaction and the consequences of exceeding Paris Agreement's climatic goals

Be friendly, stay well: The effects of job resources on well-being in a discriminatory work environment

Many studies have focused on the negative effects of discrimination on workers’ well-being. However, discrimination does not affect just victims but also those people who witness discriminatory acts or who perceived they are working in a discriminatory work environment. Although perceiving a discriminatory work environment might be a stressor, the presence of job resources might counteract its negative effects, as suggested by the Job Demand-Resources model. The goal of this study is to test the effect of perceiving a discriminatory work environment on workers’ psychological well-being when job autonomy and co-workers and supervisor support act as mediator and moderators respectively. To test the moderated mediation model data were gathered with a sample of Italian 114 truckers. Results demonstrated that job autonomy partially mediates the relationship between perceiving a discriminatory work environment and workers’ well-being. Main interactional effects have been observed when co-workers support is introduced in the model as moderator, while no main interactional effects exist when supervisor support is introduced. Theoretical and practical implications are discussed.Fundação para a Ciência e a Tecnologia (Portugal) SFRH/BPD/121748/2016Ministerio de Economía y Competitividad de España PSI2015-64894-

Quantification of habitat fragmentation reveals extinction risk in terrestrial mammals

Although habitat fragmentation is often assumed to be a primary driver of extinction, global patterns of fragmentation and its relationship to extinction risk have not been consistently quantified for any major animal taxon. We developed high-resolution habitat fragmentation models and used phylogenetic comparative methods to quantify the effects of habitat fragmentation on the world's terrestrial mammals, including 4,018 species across 26 taxonomic Orders. Results demonstrate that species with more fragmentation are at greater risk of extinction, even after accounting for the effects of key macroecological predictors, such as body size and geographic range size. Species with higher fragmentation had smaller ranges and a lower proportion of high-suitability habitat within their range, andmost high-suitability habitat occurred outside of protected areas, further elevating extinction risk. Our models provide a quantitative evaluation of extinction risk assessments for species, allow for identification of emerging threats in species not classified as threatened, and provide maps of global hotspots of fragmentation for the world's terrestrial mammals. Quantification of habitat fragmentation will help guide threat assessment and strategic priorities for global mammal conservation

COMBINE: a coalesced mammal database of intrinsic and extrinsic traits

The use of species’ traits in macroecological analyses has gained popularity in the last decade, becoming an important tool to understand global biodiversity patterns. Currently, trait data can be found across a wide variety of data sets included in websites, articles, and books, each one with its own taxonomic classification, set of traits and data management methodology. Mammals, in particular, are among the most studied taxa, with large sources of trait information readily available. To facilitate the use of these data, we did an extensive review of published mammal trait data sources between 1999 and May 2020 and produced COMBINE: a COalesced Mammal dataBase of INtrinsic and Extrinsic traits. Our aim was to create a taxonomically integrated database of mammal traits that maximized trait number and coverage without compromising data quality. COMBINE contains information on 54 traits for 6,234 extant and recently extinct mammal species, including information on morphology, reproduction, diet, biogeography, life‐habit, phenology, behavior, home range and density. Additionally, we calculated other relevant traits such as habitat and altitudinal breadths for all species and dispersal for terrestrial non‐volant species. All data are compatible with the taxonomies of the IUCN Red List v. 2020‐2 and PHYLACINE v. 1.2. Missing data were adequately flagged and imputed for non‐biogeographical traits with 20% or more data available. We obtained full data sets for 21 traits such as female maturity, litter size, maximum longevity, trophic level, and dispersal, providing imputation performance statistics for all. This data set will be especially useful for those interested in including species’ traits in large‐scale ecological and conservation analyses. There are no copyright or proprietary restrictions; we request citation of this publication and all relevant underlying data sources (found in Data S1: trait_data_sources.csv), upon using these data

He vivido, lo confieso

Fil: Moreno de Di Marco, María del Rosario. Universidad Nacional de Cuyo. Facultad de Odontologí

Approaching the discriminatory work environment as stressor: The protective role of job satisfaction on health

Discrimination is a complex phenomenon with adverse consequences at personal and organizational levels. Past studies have demonstrated that workers who are victims of discrimination might show less job satisfaction, less organizational commitment and worse levels of health and productivity. Although most research has focused on the effects of discrimination on victims, less is known about the extent to which discrimination produces consequences on workers who perceive the existence of a discriminatory work environment. The goal of this article is to analyze the consequences of the perception of a discriminatory work environment on employees' health. The importance of this relationship is studied taking into account the mediating effect of job satisfaction. In order to reach this goal a cross-sectional study was carried out with a sample of 1633 Italian workers (male = 826, female = 764), employed in private and public sectors, and in different hierarchical positions. Results suggest that the perception of a discriminatory work environment is negatively associated with employees' health. This relationship is partially mediated by job satisfaction (R (2) = 0.17). This study demonstrates that perceiving a discriminatory work environment might have a negative impact on workers' health. A higher level of job satisfaction might buffer this effect. These findings have several practical implications. On the one hand, Human Resource Managers need to intervene in order to recognize and diminish implicit biases, creating a healthy and inclusive environment (e.g., through training, diversity policies, etc.). On the other hand, promoting job satisfaction (e.g., providing mechanisms of voice) might help workers to preserve their well-being, coping with the negative effects of a discriminatory work environment