- About
- Staff
- Projects
- Publications
- Equipment
- Collaborations
- News
- Jobs
About
Our lab aims at understanding how genetic changes between individuals can or cannot result in disease by quantifying the impact mutations have on protein aggregation and toxicity.
We are particularly interested in amino acid sequences that can adopt different conformations and undergo a process of self-assembly which results in distinct physical states.
Protein self-assembly
The aggregation of proteins into insoluble amyloid fibrils is a key process in the pathogenesis of a number of neurodegenerative conditions, such as Parkinson’s disease or Amyotrophic Lateral Sclerosis. However, examples of functional amyloid are also widespread in nature, especially across bacteria and fungi. Our work aims at systematically deciphering the sequence-dependencies of the process of aggregation in both functional and pathological contexts.
Proteins can also self-assemble into a more dynamic and reversible state through a process of condensation which is thought to contribute to the organization of the intracellular space. However, also for proteins that undergo liquid-demixing to form biomolecular condensates, the balance between function and dysfunction is far from clear. It is also unknown if and how condensates are precursors of insoluble amyloid-like states, and to which extent proteins are structured once in the liquid state.
Quantifying the impact of mutations at scale
In order to understand how mutations affect these delicate equilibria and to elucidate when and why a sequence starts aggregating or becomes toxic for the cell, our lab integrates experimental and computational approaches in different model systems. Recently, we have developed different Multiplexed Assays of Variant Effects (MAVEs) to quantify the toxicity and aggregation propensity of hundreds of thousands of protein sequences in vivo. By capturing the full landscape of the effects of mutations in a specific protein sequence we can guide clinicians to better diagnose and treat human disease, but we also reach a comprehensive mechanistic understanding of the process of amyloid formation and protein-induced toxicity. This translates in the possibility of rationally developing better targeted therapeutics, as well as in a set of fundamental principles that can guide protein design in bioengineering.
Developing novel strategies to report on protein conformation
In collaboration with the Lehner lab we also develop combinatorial mutagenesis approaches to study the interactions between mutations. We then use such genetic interactions to report on the conformation different proteins adopt as they start aggregating. Overall, we aim at generating exhaustive datasets that will give mechanistic insights on the process of protein aggregation, while also reporting on specific conformations and mechanisms leading to cellular toxicity. The massive amount of data we generate is used to train new models of protein aggregation. Our strategy is also amenable to tackle many intrinsically disordered proteins, which are particularly difficult to study in vitro. In this perspective, in vivo selection approaches such as the ones we develop can provide a unique opportunity to investigate these sequences in a systematic way.

Map of the effect of mutations on toxicity of the TDP-43 Prion-like Domain.

Percentage of substitutions and insertions increasing or decreasing amyloid formation of the Amyloid-Beta peptide, visualized on the cross-section of ex-vivo fibrils (7Q4M).
Staff
Projects
NATIONAL GRANTS | FINANCER | PI |
---|---|---|
AMYNDEL · Deciphering the consequences of different types of genetic variation in amyloid forming sequences by deep mutagenesis ( 2022-2025) | MICIU · Generación Conocimiento: Proyectos I+D | Benedetta Bolognesi |
DeepAmyloids · Massively parallel mutagenesis to understand, predict and prevent amyloid nucleation in neurodegenerative diseases (2021-2024) | Obra Social La Caixa | Benedetta Bolognesi |
FINISHED PROJECTS | FINANCER | PI |
---|---|---|
Poly-STOP · Developing modulators of protein aggregation in polyglutamine diseases by deep mutational scanning (2021-2022) | BIST · Barcelona Institute of Science and Technology | Benedetta Bolognesi |
PRIOMUT · Escaneado exhaustivo de mutaciones en un dominio priónico para entender la toxicidad inducida por proteínas (2019-2021) | MICIU / Retos investigación: Proyectos I+D | Benedetta Bolognesi |
Publications
Claussnitzer, Melina, Parikh, Victoria N, Wagner, Alex H, Arbesfeld, Jeremy A, Bult, Carol J, Firth, Helen V, Muffley, Lara A, Ba, Alex N Nguyen, Riehle, Kevin, Roth, Frederick P, Tabet, Daniel, Bolognesi, Benedetta, Glazer, Andrew M, Rubin, Alan F, (2024). Minimum information and guidelines for reporting a multiplexed assay of variant effect Genome Biology 25, 100
Multiplexed assays of variant effect (MAVEs) have emerged as a powerful approach for interrogating thousands of genetic variants in a single experiment. The flexibility and widespread adoption of these techniques across diverse disciplines have led to a heterogeneous mix of data formats and descriptions, which complicates the downstream use of the resulting datasets. To address these issues and promote reproducibility and reuse of MAVE data, we define a set of minimum information standards for MAVE data and metadata and outline a controlled vocabulary aligned with established biomedical ontologies for describing these experimental designs.
JTD Keywords: Deep mutational scanning, Dms, Genetic variants, Genomics, Mave, Multiplexed assays of variant effect, Standards
Fowler, DM, Adams, DJ, Gloyn, AL, Hahn, WC, Marks, DS, Muffley, LA, Neal, JT, Roth, FP, Rubin, AF, Starita, LM, Hurles, ME, Ahituv, N, Bahcal, OG, Baldridge, D, Berg, JS, Berger, AH, Bianchi, AH, Bolognesi, B, Boutros, M, Brenner, S, Brush, MH, Bryant, V, Bult, CJ, Bulyk, M, Call, M, Carter, H, Claussnitzer, M, Chen, F, Cline, MS, Cuperus, JT, Dawood, M, De Jong, HN, Dias, M, Dunn, M, Engreitz, J, Farh, K, Febbo, PG, Fields, S, Findlay, GM, Firth, H, Fraser, JS, Frazer, J, Frontini, M, Romero, IG, Glazer, AM, Guler, M, Hartmann-Petersen, R, Houlston, R, Huang, KL, Hutter, CM, Jagannathan, S, James, RG, Kampmann, M, Karchin, R, Kinney, JB, Komor, AC, Kosuri, S, Lehner, B, Lindorff-Larsen, K, Lombard, Z, MacArthur, DG, Martin, M, McDermott, U, McNulty, SM, Ba, ANN, O'Donnell-Luria, A, O'Roak, BJ, Parikh, VN, Parts, L, Pazin, MJ, Pesaran, T, Petrovski, S, Queitsch, C, Root, DE, Shendure, J, Spurdle, AB, Taylor, KL, Turnbull, C, Villen, J, Vissers, LELM, Wagner, AH, Wakefield, MJ, Weile, J, Xiao, J, (2023). An Atlas of Variant Effects to understand the genome at nucleotide resolution Genome Biology 24, 147
Sequencing has revealed hundreds of millions of human genetic variants, and continued efforts will only add to this variant avalanche. Insufficient information exists to interpret the effects of most variants, limiting opportunities for precision medicine and comprehension of genome function. A solution lies in experimental assessment of the functional effect of variants, which can reveal their biological and clinical impact. However, variant effect assays have generally been undertaken reactively for individual variants only after and, in most cases long after, their first observation. Now, multiplexed assays of variant effect can characterise massive numbers of variants simultaneously, yielding variant effect maps that reveal the function of every possible single nucleotide change in a gene or regulatory element. Generating maps for every protein encoding gene and regulatory element in the human genome would create an 'Atlas' of variant effect maps and transform our understanding of genetics and usher in a new era of nucleotide-resolution functional knowledge of the genome. An Atlas would reveal the fundamental biology of the human genome, inform human evolution, empower the development and use of therapeutics and maximize the utility of genomics for diagnosing and treating disease. The Atlas of Variant Effects Alliance is an international collaborative group comprising hundreds of researchers, technologists and clinicians dedicated to realising an Atlas of Variant Effects to help deliver on the promise of genomics.
JTD Keywords: functional genomics, genome interpretation, global alliance, multiplexed assay of variant effect, saturation mutagenesis, Functional genomics, Genome interpretation, Global alliance, Multiplexed assay of variant effect, Saturation mutagenesis, Variant effect
Seuma, M, Lehner, B, Bolognesi, B, (2022). An atlas of amyloid aggregation: the impact of substitutions, insertions, deletions and truncations on amyloid beta fibril nucleation Nature Communications 13, 7084
Multiplexed assays of variant effects (MAVEs) guide clinical variant interpretation and reveal disease mechanisms. To date, MAVEs have focussed on a single mutation type-amino acid (AA) substitutions-despite the diversity of coding variants that cause disease. Here we use Deep Indel Mutagenesis (DIM) to generate a comprehensive atlas of diverse variant effects for a disease protein, the amyloid beta (Aβ) peptide that aggregates in Alzheimer's disease (AD) and is mutated in familial AD (fAD). The atlas identifies known fAD mutations and reveals that many variants beyond substitutions accelerate Aβ aggregation and are likely to be pathogenic. Truncations, substitutions, insertions, single- and internal multi-AA deletions differ in their propensity to enhance or impair aggregation, but likely pathogenic variants from all classes are highly enriched in the polar N-terminal region of Aβ. This comparative atlas highlights the importance of including diverse mutation types in MAVEs and provides important mechanistic insights into amyloid nucleation.© 2022. The Author(s).
JTD Keywords: amyloid-beta(1-42), determinants, disease, mutants, protein, secondary nucleation, Atomic-resolution structure
Seuma, M, Bolognesi, B, (2022). Understanding and evolving prions by yeast multiplexed assays Current Opinion In Genetics & Development 75, 101941
Yeast genetics made it possible to derive the first fundamental insights into prion composition, conformation, and propagation. Fast-forward 30 years and the same model organism is now proving an extremely powerful tool to comprehensively explore the impact of mutations in prion sequences on their function, toxicity, and physical properties. Here, we provide an overview of novel multiplexed strategies where deep mutagenesis is combined to a range of tailored selection assays in yeast, which are particularly amenable for investigating prions and prion-like sequences. By mimicking evolution in a flask, these multiplexed approaches are revealing mechanistic insights on the consequences of prion self-assembly, while also reporting on the structure prion sequences adopt in vivo.Copyright © 2022 Elsevier Ltd. All rights reserved.
JTD Keywords: aggregation, appearance, domains, inheritance, mutations, nucleation, physical basis, propagation, protein, Phase-separation
Marte, L, Boronat, S, Barrios, R, Barcons-Simon, A, Bolognesi, B, Cabrera, M, Ayté, J, Hidalgo, E, (2022). Expression of Huntingtin and TDP-43 Derivatives in Fission Yeast Can Cause Both Beneficial and Toxic Effects International Journal Of Molecular Sciences 23, 3950
Many neurodegenerative disorders display protein aggregation as a hallmark, Huntingtin and TDP-43 aggregates being characteristic of Huntington disease and amyotrophic lateral sclerosis, respectively. However, whether these aggregates cause the diseases, are secondary by-products, or even have protective effects, is a matter of debate. Mutations in both human proteins can modulate the structure, number and type of aggregates, as well as their toxicity. To study the role of protein aggregates in cellular fitness, we have expressed in a highly tractable unicellular model different variants of Huntingtin and TDP-43. They each display specific patterns of aggregation and toxicity, even though in both cases proteins have to be very highly expressed to affect cell fitness. The aggregation properties of Huntingtin, but not of TDP-43, are affected by chaperones such as Hsp104 and the Hsp40 couple Mas5, suggesting that the TDP-43, but not Huntingtin, derivatives have intrinsic aggregation propensity. Importantly, expression of the aggregating form of Huntingtin causes a significant extension of fission yeast lifespan, probably as a consequence of kidnapping chaperones required for maintaining stress responses off. Our study demonstrates that in general these prion-like proteins do not cause toxicity under normal conditions, and in fact they can protect cells through indirect mechanisms which up-regulate cellular defense pathways. © 2022 by the authors. Licensee MDPI, Basel, Switzerland.
JTD Keywords: aggregation, antioxidant, degradation, features, fission yeast, gene, huntingtin, neurodegenerative diseases, pap1, polyglutamine toxicity, protein aggregation, proteins, stress, tdp-43, Amyotrophic-lateral-sclerosis, Chaperone, Chemistry, Dna binding protein, Dna-binding proteins, Fission yeast, Genetics, Human, Humans, Huntingtin, Metabolism, Molecular chaperones, Neurodegenerative diseases, Prion, Prions, Protein aggregate, Protein aggregates, Protein aggregation, Schizosaccharomyces, Tdp-43
Badia, M, Bolognesi, B, (2021). Assembling the right type of switch: Protein condensation to signal cell death Current Opinion In Cell Biology 69, 55-61
© 2020 Elsevier Ltd Protein phase transitions are particularly amenable for cell signalling as these highly cooperative processes allow cells to make binary decisions in response to relatively small intracellular changes. The different processes of condensate formation and the distinct material properties of the resulting condensates provide a dictionary to modulate a range of decisions on cell fate. We argue that, on the one hand, the reversibility of liquid demixing offers a chance to arrest cell growth under specific circumstances. On the other hand, the transition to amyloids is better suited for terminal decisions such as those leading to apoptosis and necrosis. Here, we review recent examples of both scenarios, highlighting how mutations in signalling proteins affect the formation of biomolecular condensates with drastic effects on cell survival.
JTD Keywords: amyloid, cell death, deep mutagenesis, llps, rna-binding proteins, Amyloid, Cell death, Deep mutagenesis, Llps, Phase transition, Proteins, Rna-binding proteins, Signal transduction
Seuma, M, Faure, AJ, Badia, M, Lehner, B, Bolognesi, B, (2021). The genetic landscape for amyloid beta fibril nucleation accurately discriminates familial Alzheimer's disease mutations Elife 10, e63364
Plaques of the amyloid beta (A beta) peptide are a pathological hallmark of Alzheimer's disease (AD), the most common form of dementia. Mutations in A beta also cause familial forms of AD (fAD). Here, we use deep mutational scanning to quantify the effects of >14,000 mutations on the aggregation of A beta. The resulting genetic landscape reveals mechanistic insights into fibril nucleation, including the importance of charge and gatekeeper residues in the disordered region outside of the amyloid core in preventing nucleation. Strikingly, unlike computational predictors and previous measurements, the empirical nucleation scores accurately identify all known dominant fAD mutations in A beta, genetically validating that the mechanism of nucleation in a cell-based assay is likely to be very similar to the mechanism that causes the human disease. These results provide the first comprehensive atlas of how mutations alter the formation of any amyloid fibril and a resource for the interpretation of genetic variation in A beta.
JTD Keywords: aggregation, kinetics, oligomers, onset, rates, state, Aggregation, Alzheimer disease, Alzheimer's, Amyloid, Amyloid beta-peptides, Computational biology, Deep mutagenesis, Dna mutational analysis, Genetics, Genomics, High-throughput nucleotide sequencing, Kinetics, Mutation, Nucleation, Oligomers, Onset, Plasmids, Precursor protein, Rates, S. cerevisiae, Saccharomyces cerevisiae, State, Systems biology
Bolognesi, Benedetta, Faure, Andre J., Seuma, Mireia, Schmiedel, Jörrn M., Tartaglia, Gian Gaetano, Lehner, Ben, (2019). The mutational landscape of a prion-like domain Nature Communications 10, (1), 4162
Insoluble protein aggregates are the hallmarks of many neurodegenerative diseases. For example, aggregates of TDP-43 occur in nearly all cases of amyotrophic lateral sclerosis (ALS). However, whether aggregates cause cellular toxicity is still not clear, even in simpler cellular systems. We reasoned that deep mutagenesis might be a powerful approach to disentangle the relationship between aggregation and toxicity. We generated >50,000 mutations in the prion-like domain (PRD) of TDP-43 and quantified their toxicity in yeast cells. Surprisingly, mutations that increase hydrophobicity and aggregation strongly decrease toxicity. In contrast, toxic variants promote the formation of dynamic liquid-like condensates. Mutations have their strongest effects in a hotspot that genetic interactions reveal to be structured in vivo, illustrating how mutagenesis can probe the in vivo structures of unstructured proteins. Our results show that aggregation of TDP-43 is not harmful but protects cells, most likely by titrating the protein away from a toxic liquid-like phase.
JTD Keywords: Computational biology and bioinformatics, Genomics, Mechanisms of disease, Neurodegeneration, Systems biology
Bolognesi, Benedetta, Lehner, Ben, (2018). Reaching the limit eLife 7, e39804
How many copies of a protein can be made before it becomes toxic to the cell?
JTD Keywords: Protein burden, Overexpression, Glycolysis
Equipment
- Thermo MaxQ 8000
Collaborations
- Priyanka Narayan
NIH-NIDDK - Xavier Salvatella
IRB, Barcelona - Fran Supek
IRB, Barcelona - Ben Lehner
CRG, Barcelona - Luke McAlary /Justin Yerbury
University of Wollongong, Australia
News

L’IBEC destaca en el BIST Forum amb 4 projectes BIST Ignite i un BIST Ignite Award
Avui s’ha celebrat el BIST Forum, un esdeveniment que reuneix la comunitat científica del BIST i que aquest any s’ha centrat en la iniciativa conjunta dels set centres CERCA per impulsar la medicina de precisió en l’envelliment saludable. Durant l’acte, s’han anunciat els nous projectes BIST IGNITE per fomentar la recerca multidisciplinària, amb la participació de l’IBEC en quatre dels cinc seleccionats. A més, un dels projectes amb participació de l’IBEC ha estat guardonat amb un BIST Ignite Award.

L’IBEC i el VHIR celebren una jornada de col·laboració per fomentar les sinergies
La 1a Jornada Col·laborativa Translacional entre el Vall d’Hebron Institut de Recerca (VHIR) i l’Institut de Bioenginyeria de Catalunya (IBEC), celebrada el 21 de novembre, ha estat una oportunitat per conèixer els projectes i les línies de recerca d’ambdues institucions i promoure la interacció entre els professionals.

Tres investigadors de l’IBEC seleccionats en la convocatòria Caixa Research 2024 per liderar projectes de recerca en salut
Els investigadors de l’IBEC Benedetta Bolognesi, Xavier Fernàndez Busquets i Xavier Trepat han estat seleccionats en la convocatòria CaixaResearch 2024 per liderar sengles projectes de recerca. Les ajudes rebudes suposen un suport econòmic perquè els científics duguin a terme la seva recerca en àrees clau com el càncer, la malària i l’esclerosi lateral amiotròfica.

BIST Forum, una trobada per posar en valor la recerca de frontera
El BIST Forum ha tractat de com la ciència d’excel·lència potencia el desenvolupament de la societat i el creixement econòmic. Hi han assistit el president de la Generalitat, l’alcalde de Barcelona, els responsables de les màximes institucions econòmiques i els rectors de les principals universitats. A l’acte s’han anunciat els nous projectes BIST IGNITE per la recerca multidisciplinària, dels quals tres compten amb la participació de l’IBEC.

La investigadora Benedetta Bolognesi guardonada amb una prestigiosa beca europea ERC Consolidator Grant
La investigadora de l’Institut de Bioenginyeria de Catalunya ha estat guardonada amb una «ERC Consolidator Grant». Aquest prestigiós finançament europeu dona suport a científics en l’etapa de consolidació dels seus equips de recerca, permetent-los perseguir idees científiques innovadores. 2 milions d’euros durant 5 anys permetran a Bolognesi i el seu equip desenvolupar un nou mètode per identificar les mutacions que condueixen a la formació d’amiloides, agregats de proteïnes que causen multitud de malalties, incloent-hi l’Alzheimer o La investigadora de l’Institut de Bioenginyeria de Catalunya ha estat guardonada amb una «ERC Consolidator Grant». Aquest prestigiós finançament europeu dona suport a científics en l’etapa de consolidació dels seus equips de recerca, permetent-los perseguir idees científiques innovadores. 2 milions d’euros durant 5 anys permetran a Bolognesi i el seu equip desenvolupar un nou mètode per identificar les mutacions que condueixen a la formació d’amiloides, agregats de proteïnes que causen multitud de malalties, incloent-hi l’Alzheimer o el Parkinson.

Un nou atles revela quines mutacions estan darrere de la formació nociva d’amiloide
Investigadors de l’Institut de Bioenginyeria de Catalunya (IBEC) han elaborat l’atles més complet fins avui amb les mutacions genètiques que causen la formació de fibril·les d’amiloide BETA, una proteïna que està darrere de la … Read more

Ciència i Art: l’IBEC col·labora en una obra d’Antoni Muntadas a l’Ars Electronica 2022
Quan es considera extint un ésser viu? Aquesta és una de les qüestions fonamentals de l’obra d’art presentada a l’Ars Electronica 2022 per Antoni Muntadas, artista català establert als EUA … Read more

Postdoctoral researcher at the Protein Phase Transitions in Health and Disease Research group
Ref: Postdoctoral / Deadline: 24th August

Lab Technician at the Protein phase transitions in health and disease Research Group
Ref: Lab Technician / Deadline: 29th July 2022

Investigadors de l’IBEC i CRG reben finançament de la Fundació “la Caixa” per a lluitar contra la demència
La Fundació “la Caixa” finançarà un ampli i innovador projecte de recerca codirigit per Benedetta Bolognesi, Júnior Group Leader a l’IBEC, i pel professor de recerca ICREA Ben Lehner del CRG, l’objectiu del qual és conèixer millor les causes genètiques que condueixen a malalties neurodegeneratives. Els investigadors combinaran tècniques de “mutagenesis profunda” i aprenentatge automàtic per a produir un “mapa de la demència” com a mètode per a predir si una persona és més susceptible a patir aquestes malalties.
Jobs
Research Assistant at Protein Phase Transitions in Health and Disease Research Group
Ref: RA-BB //Deadline : 16/01/2025
Research Assistant at the Protein Phase Transitions in Health and Disease Research Group
RA-BB // Deadline: 16/09/2024
Predoctoral researcher at the Phase Transitions in Health and Disease Research Group
Ref: PHDR_BB // Deadline: 12/08/2024
Post-doctoral researcher in the Protein Phase Transitions in Health and Disease Research Group
Ref: PR_BB // Deadline 30/10/2024
Predoctoral researcher at the Phase Transitions in Health and Disease Research Group
BB_PR // Deadline: 25/07/2024
Research Assistant at the Protein Phase Transitions in Health and Disease Research Group (RA_BB)
Ref: RA_BB // Deadline: 26/01/2024
Senior Laboratory Technician at the Protein Phase Transitions in Health and Disease Research Group (SLT_BB)
Ref: SLT_BB // Deadline: 11/01/2024
Research Assistant at the Protein Phase Transitions in Health and Disease Research Group
Ref: RA_BB // Deadline: 04/08/2023
Research Assistant at the Protein Phase Transitions in Health and Disease Research Group
Ref : RA_BB // Deadline 28/04/2023
Postdoctoral researcher at the Protein Phase Transitions in Health and Disease Research group
Ref: Postdoctoral / Deadline: 24th August