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Protein Phase Transitions in Health and Disease

About

Our lab aims at understanding how protein sequences can become toxic upon mutation.

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.

The concept of protein aggregation has mainly been associated to the formation of insoluble amyloid fibrils, best known for their implication 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, especially across bacteria and fungi. Recently, it has become clear that proteins can assemble also into a more dynamic and reversible state through a process of liquid de-mixing.

Liquid condensates are frequently formed by proteins containing intrinsically disordered regions.The self-assembly of these protein regions results in a distinct liquid phase and it’s key to the formation of many membrane-less organelles, hence contributing to the organisation of the intracellular space. However, also for proteins undergoing liquid de-mixing, the balance between function and dysfunction is far from clear. It is also unknown if, in vivo, liquid de-mixed states are precursors of insoluble amyloid-like states, and to which extent proteins are structured once in the liquid state.

How we do it

In order to understand how mutations affect these delicate equilibria and to elucidate when and why a sequence becomes toxic for the cell, our lab integrates experimental and computational approaches in different model systems. Recently, we developed a Deep Mutational Scanning (DMS) strategy that allows to quantify the toxicity of thousands of mutations in a disordered protein sequence . The idea behind this type of approach is that by portraying the full landscape of the effects of mutations in a specific protein domain we can reach a more systematic and comprehensive understanding of the determinants of toxicity. Besides developing high-throughput methods to measure the toxicity of thousands of mutations in parallel, we are also interested in developing similar strategies to measure in vivo the effect of mutations on the physical state the proteins acquire upon mutation (diffuse, liquid de-mixed, insoluble) and on their ability to nucleate amyloid fibrils. Overall, we aim at generating exhaustive datasets that will give insights into the specific conformations and mechanisms leading to toxicity.

We focus on classical amyloids, such as the amyloid-beta peptide, the main component of the plaques found in Alzheimer’s disease patients, but also on functional yeast prions and on a less characterised part of the human proteome: prion-like domains. Just like most disordered protein regions, prion-like domains are particularly difficult to study in vitro. In this perspective, in vivo 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.
Average effect of mutations on nucleation, visualised on the cross-section of an amyloid-beta fibril (PDB:5KK3)

Staff

Benedetta Bolognesi
Junior Group Leader
+34 934 035094 (Lab)
bbolognesiibecbarcelona.eu

Projects

INTERNATIONAL GRANTSFINANCERPI
MUTANOMICS · Determining in vivo protein structures and understanding genetic interactions using deep mutagenesis (2021-2025)European Commission / Proyectos I+DBenedetta Bolognesi

NATIONAL GRANTSFINANCERPI
Poly-STOP · Developing modulators of protein aggregation in polyglutamine diseases by deep mutational scanning (2021-2022)BIST · Barcelona Institute of Science and TechnologyBenedetta Bolognesi
DeepAmyloids · Massively parallel mutagenesis to understand, predict and prevent amyloid nucleation in neurodegenerative diseases (2021-2024)Obra Social La CaixaBenedetta Bolognesi

FINISHED PROJECTSFINANCERPI
PRIOMUT · Escaneado exhaustivo de mutaciones en un dominio priónico para entender la toxicidad inducida por proteínas (2019-2021)MICIU / Retos investigación: Proyectos I+DBenedetta Bolognesi

Publications

Equipment

  • Thermo MaxQ 8000

Collaborations

  • Ben Lehner
    CRG, Barcelona
  • Sofia Giorgetti
    University of Pavia, Italy
  • Xavier Salvatella
    IRB Barcelona
  • Priyanka Narayan
    NIDDK-NIH, Washington D.C
  • Broder Schmidt
    University of Stanford

News

The “la Caixa” Foundation will fund a large and innovative research project co-led by IBEC Junior Group Leader Benedetta Bolognesi and by ICREA research professor Ben Lehner at CRG, which aims to gain a better understanding of the genetic causes leading to neurodegenerative diseases. Researchers will combine deep mutagenesis and machine learning techniques to produce a “map of dementia” as a method to predict whether a person is more susceptible to suffer these diseases. 

Benedetta Bolognesi and Ben Lehner win competitive funding to join forces against neurodegenerative diseases 

The “la Caixa” Foundation will fund a large and innovative research project co-led by IBEC Junior Group Leader Benedetta Bolognesi and by ICREA research professor Ben Lehner at CRG, which aims to gain a better understanding of the genetic causes leading to neurodegenerative diseases. Researchers will combine deep mutagenesis and machine learning techniques to produce a “map of dementia” as a method to predict whether a person is more susceptible to suffer these diseases. 

IBEC researchers receive two “Ignite Seed Grants” to combine their skills with other BIST members to seek scientific answers to health challenges. Benedetta Bolognesi will study, with the IRB, Huntington’s disease and other neurodegenerative pathologies without treatment. On the other hand, Juan Manuel Fernández-Costa and researchers at ICFO will develop muscles-on-a-chip and biomagnetism sensors to accelerate the design of new treatments for muscular dystrophy.

IBEC researchers win two “BIST Ignite Seed Grants”

IBEC researchers receive two “Ignite Seed Grants” to combine their skills with other BIST members to seek scientific answers to health challenges. Benedetta Bolognesi will study, with the IRB, Huntington’s disease and other neurodegenerative pathologies without treatment. On the other hand, Juan Manuel Fernández-Costa and researchers at ICFO will develop muscles-on-a-chip and biomagnetism sensors to accelerate the design of new treatments for muscular dystrophy.

Benedetta Bolognesi, junior group leader at IBEC, appears in different media for a recent study published in the eLife magazine. In the study they show the first map with all the possible mutations in the amyloid beta peptide and tested how they influence its aggregation into plaques, a pathological hallmark of Alzheimer’s disease.

One more step towards early detection of Alzheimer’s

Benedetta Bolognesi, junior group leader at IBEC, appears in different media for a recent study published in the eLife magazine. In the study they show the first map with all the possible mutations in the amyloid beta peptide and tested how they influence its aggregation into plaques, a pathological hallmark of Alzheimer’s disease.

A study published in the journal eLife made all the possible mutations in the amyloid beta peptide and tested how they influence its aggregation into plaques, a pathological hallmark of Alzheimer’s disease.

First comprehensive map of amyloid plaque mutations opens new avenues for early detection of Alzheimer’s disease

A study published in the journal eLife made all the possible mutations in the amyloid beta peptide and tested how they influence its aggregation into plaques, a pathological hallmark of Alzheimer’s disease.

The Mayor of Barcelona, Ada Colau, visited IBEC facilities last Friday to learn, by our Director and a group of researchers, how bioengineering can help find solutions to health problems such as COVID19, cancer, or degenerative diseases. When in early 2020, more than 200 scientists gathered in La Pedrera in Barcelona to discuss the present and future of bioengineering, no one imagined that the world would experience the first pandemic of the 21st century and that science would take on more importance than ever.

IBEC receives a visit from the Mayor of Barcelona interested in our research against Covid19

The Mayor of Barcelona, Ada Colau, visited IBEC facilities last Friday to learn, by our Director and a group of researchers, how bioengineering can help find solutions to health problems such as COVID19, cancer, or degenerative diseases. When in early 2020, more than 200 scientists gathered in La Pedrera in Barcelona to discuss the present and future of bioengineering, no one imagined that the world would experience the first pandemic of the 21st century and that science would take on more importance than ever.

Researchers from IBEC and CRG in Barcelona use a technique called high-throughput mutagenesis to study Amyotrophic Lateral Sclerosis (ALS), with unexpected results. Results showed that aggregation of TDP-43 is not harmful but actually protects cells, changing our understanding of ALS and opening the door to radically new therapeutic approaches. Amyotrophic lateral sclerosis (ALS) is a devastating and incurable nervous system disease that affects nerve cells in the brain and spinal cord, causing loss of muscle control and normally death within a few years of diagnosis. In ALS, like in other neurodegenerative diseases, specific protein aggregates have long been recognized as the pathological hallmarks, but it is not clear whether they represent the actual cause of the disease. Indeed, alleviating aggregation has repeatedly failed as a therapeutic strategy when trying to treat neurodegenerative diseases such as Alzheimer’s disease.

Researchers perform thousands of mutations to understand amyotrophic lateral sclerosis

Researchers from IBEC and CRG in Barcelona use a technique called high-throughput mutagenesis to study Amyotrophic Lateral Sclerosis (ALS), with unexpected results. Results showed that aggregation of TDP-43 is not harmful but actually protects cells, changing our understanding of ALS and opening the door to radically new therapeutic approaches. Amyotrophic lateral sclerosis (ALS) is a devastating and incurable nervous system disease that affects nerve cells in the brain and spinal cord, causing loss of muscle control and normally death within a few years of diagnosis. In ALS, like in other neurodegenerative diseases, specific protein aggregates have long been recognized as the pathological hallmarks, but it is not clear whether they represent the actual cause of the disease. Indeed, alleviating aggregation has repeatedly failed as a therapeutic strategy when trying to treat neurodegenerative diseases such as Alzheimer’s disease.

Jobs

Application Deadline: 24/10/2021Ref: PD-BB The Protein phase Transitions in Health and Disease group at the Institute for Bioengineering of Catalonia (IBEC) is looking for two Postdoctoral Researchers to develop deep mutagenesis projects in the context of amyloid forming proteins. The contract will be within the framework of a larger project funded by La Caixa.

2 Postdoctoral researchers at the Protein Phase Transitions in Health and Disease Research Group

Application Deadline: 24/10/2021Ref: PD-BB The Protein phase Transitions in Health and Disease group at the Institute for Bioengineering of Catalonia (IBEC) is looking for two Postdoctoral Researchers to develop deep mutagenesis projects in the context of amyloid forming proteins. The contract will be within the framework of a larger project funded by La Caixa.