Biology subjects

Bergink, S.

Publications and source records attributed to Bergink, S..

8 recordsLinked to original sources

bioRxiv2022

The FIGNL1-interacting protein C1orf112 is synthetic lethal with PICH and mediates RAD51 retention on chromatin.

Joint DNA molecules are natural by-products of DNA replication and repair. Persistent joint molecules give rise to ultrafine DNA bridges (UFBs) in mitosis, which compromise sister chromatid separation. The DNA translocase PICH (ERCC6L) plays a central role in UFB resolution. A genome-wide loss-of-function screen was performed to identify the genetic contexts in which cells become dependent on PICH. In addition to genes involved in DNA condensation, centromere stability and DNA damage repair, we identified the uncharacterized protein C1orf112. We find that C1orf112 interacts with and stabilizes the AAA+ ATPase FIGNL1. Inactivation of either C1orf112 or FIGNL1 resulted in UFB formation, prolonged retention of RAD51 on chromatin, impaired replication fork dynamics, and consequently impaired genome maintenance. Combined, our data reveal that inactivation of C1orf112 and FIGNL1 dysregulates RAD51 dynamics at replication forks, resulting in DNA replication defects, and a dependency on PICH to preserve cell viability.

cancer biology↗

bioRxiv2022

Glioblastoma is associated with extensive accelerated brain ageing

Progressive neurocognitive dysfunction is the leading cause of a reduced quality of life in patients with primary brain tumours. Understanding the mechanisms underlying cognitive impairments that occur in response to a brain tumour and its treatment is essential to improve patients quality of life. Here, we show that normal-appearing non-tumour brain regions of patients with glioblastoma display hallmarks of accelerated ageing and share multiple features with Alzheimers disease patients. Integrated transcriptomic and tissue analysis shows that normal-appearing brain tissue from glioblastoma patients has a significant overlap with brain tissue from Alzheimers disease patients, revealing shared mitochondrial and neuronal dysfunction, and proteostasis deregulation. Overall, the brain of glioblastoma patients undergoes Alzheimers disease-like accelerated ageing, providing novel or repurposed therapeutic targets for managing brain cancer-related side effects.

neuroscience↗

bioRxiv2022

In vivo suppression of polyglutamine aggregation via co-condensation of the molecular chaperone DNAJB6

Amyloidogenic protein aggregation is a hallmark of several human neurodegenerative conditions, including Alzheimers, Parkinsons, and Huntingtons disease (HD). Mutations and/or environmental stresses trigger conformational transition of specific proteins to amyloids, conferring them with gain of toxic function, which eventually leads to cell death in distinct brain areas. Cumulative data indicate that modulation of specific molecular chaperones can alleviate many of the pathological features of protein aggregation diseases. We previously showed that the Hsp70 co-chaperone DNAJB6 is among the strongest suppressors of amyloid aggregation, and that moderate DNAJB6 overexpression significantly extents lifespan of a mouse model of aggressive HD pathology. DNAJB6 alone delays amyloidogenic aggregation in vitro by several orders of magnitude at substoichiometric ratios, but its activity in cells is less efficient, albeit still markedly superior to most known anti-amyloidogenic agents. This suggests that downstream PQC factors are necessary for full DNAJB6-mediated suppression of aggregation in vivo, which might have to be co-stimulated in therapeutic strategies targeting DNAJB6 action. We explored here the PQC pathways required for optimal DNAJB6 inhibition of polyglutamine (polyQ) aggregation, focusing on the two main cellular proteolytic machineries: proteasomes and macroautophagy. Unexpectedly, DNAJB6 activity was largely insensitive to chemical blockage of either degradative pathway. Instead, live cell imaging unveiled a co-condensation mechanism of DNAJB6 with mobile polyQ assemblies. DNAJB6 was not required for polyQ condensation, but its expression increased the percentage of cells with mobile condensates by a factor of 3, suggesting that DNAJB6 prevents polyQ condensates to convert from the soluble to the solid state. This in turn, may keep the polyQ peptides competent for (regulated) degradation and accessible to factors allowing its extraction from the condensed state.

cell biology↗

bioRxiv2021

Preserving protein homeostasis prevents motor impairment in DNA Damage Response-compromised C. elegans

To maintain genome integrity, cells rely on a complex system of DNA repair pathways and cell cycle checkpoints, together referred to as the DNA damage response (DDR). Impairments in DDR pathways are linked to cancer, but also to a wide range of degenerative processes, frequently including progressive neuropathy and accelerated aging. How defects in mechanistically distinct DDR pathways can drive similar degenerative phenotypes is not understood. Here we show that defects in various DDR components are linked to a loss of protein homeostasis in Caenorhabditis elegans. Prolonged silencing of atm-1, brc-1 or ung-1, central components in respectively checkpoint signaling, double strand break repair and base excision repair enhances the global aggregation of proteins occurring in adult animals, and accelerates polyglutamine protein aggregation in a model for neurodegenerative diseases. Overexpression of the molecular chaperone HSP-16.2 prevents enhanced protein aggregation in atm-1, brc-1 or ung-1-compromised animals. Strikingly, rebalancing protein homeostasis with HSP-16.2 almost completely rescues age-associated impaired motor function in these animals as well. This reveals that the consequences of a loss of atm-1, brc-1 or ung-1 converge on an impaired protein homeostasis to cause degeneration. These findings indicate that a loss of protein homeostasis is a crucial downstream consequence of DNA repair defects, and thereby provide an attractive novel framework for understanding the broad link between DDR defects and degenerative processes.

genetics↗

bioRxiv2021

The molecular chaperone DNAJB6 provides surveillance of FG-Nups and is required for interphase nuclear pore complex biogenesis

Biogenesis of nuclear pore complexes (NPCs) includes the formation of the permeability barrier composed of phenylalanine-glycine-rich nucleoporins (FG-Nups) that regulate the selective passage/crossing of biomolecules. The FG-Nups are intrinsically disordered and prone to liquid-liquid phase separate1,2 and aggregate when isolated3. It has remained largely unclear how FG-Nups are protected from making inappropriate interactions during NPC biogenesis. We found that DNAJB6, a molecular chaperone of the heat shock protein network, formed foci next to NPCs. The number of these foci decreases upon removal of proteins involved in the early steps of interphase NPC biogenesis. Reversely, when this process is stalled in the last steps, the number of DNAJB6-containing foci increases and they could be identified as herniations at the nuclear envelope (NE). Immunoelectron tomography showed that DNAJB6 localizes inside the lumen of the herniations arising at NPC biogenesis intermediates. Interestingly, loss of DNAJB6 results in annulate lamellae, which are structures containing partly assembled NPCs associated with disturbances in NPC biogenesis. We find that DNAJB6 binds to FG-Nups and can prevent the aggregation of the FG-region of several FG-Nups in cells and in vitro. Together, our data show that DNAJB6 provides quality control during NPC biogenesis and is the first molecular chaperone that is involved in the surveillance of native intrinsically disordered proteins, including FG-Nups.

molecular biology↗

bioRxiv2021

Targeting DNA topoisomerases or checkpoint kinases results in an overload of chaperone systems, triggering aggregation of a metastable subproteome

A loss of the checkpoint kinase ATM leads to impairments in the DNA damage response, and in humans causes cerebellar neurodegeneration, and a high risk to cancer. A loss of ATM is also associated with increased protein aggregation. The relevance and characteristics of this aggregation are still incompletely understood. Moreover, it is unclear to what extent other genotoxic conditions can trigger protein aggregation as well. Here, we show that targeting ATM, but also ATR or DNA topoisomerases result in a similar, widespread aggregation of a metastable, disease-associated subfraction of the proteome. Aggregation-prone model substrates, including Huntingtin exon1 containing an expanded polyglutamine repeat, aggregate faster under these conditions. This increased aggregation results from an overload of chaperone systems, which lowers the cell-intrinsic threshold for proteins to aggregate. In line with this, we find that inhibition of the HSP70 chaperone system further exacerbates the increased protein aggregation. Moreover, we identify the molecular chaperone HSPB5 as a potent suppressor of it. Our findings reveal that various genotoxic conditions trigger widespread protein aggregation in a manner that is highly reminiscent of the aggregation occurring in situations of proteotoxic stress and in proteinopathies.

molecular biology↗

bioRxiv2020

DNAJB chaperones inhibit aggregation of destabilised proteins via a C-terminal region distinct from that used to prevent amyloid formation

Disturbances to protein homeostasis (proteostasis) can lead to protein aggregation and inclusion formation, processes associated with a variety of neurodegenerative disorders. DNAJBs are molecular chaperones previously identified as potent suppressors of disease-related protein aggregation. In this work, we over-expressed a destabilised isoform of firefly luciferase (R188Q/R261Q Fluc; FlucDM) in cells to assess the capacity of DNAJBs to inhibit inclusion formation. Co-expression of all DNAJBs tested significantly inhibited the intracellular aggregation of FlucDM. Moreover, we show that DNAJBs suppress aggregation by supporting the Hsp70-dependent degradation of FlucDM via the proteasome. The serine-rich stretch in DNAJB6 and DNAJB8, essential for preventing fibrillar aggregation, is not involved in the suppression of FlucDM inclusion formation. Conversely, deletion of the C-terminal TTK-LKS region in DNAJB8, a region not required to suppress polyQ aggregation, abolished its ability to inhibit inclusion formation by FlucDM. Thus, our data suggest that DNAJB6 and DNAJB8 possess two distinct domains involved in the inhibition of protein aggregation, one responsible for binding to {beta}-hairpins that form during amyloid formation and another that mediates the degradation of destabilised client proteins via the proteasome. Summary statementSpecialised DNAJB molecular chaperones are potent suppressors of protein aggregation and interact with different types of client proteins via distinct C-terminal regions

cell biology↗

bioRxiv2020

Insulin-like growth factor 2 (IGF2) protects against Huntington's disease through the extracellular disposal of protein aggregates

Impaired neuronal proteostasis is a salient feature of many neurodegenerative diseases, highlighting alterations in the function of the endoplasmic reticulum (ER). We previously reported that targeting the transcription factor XBP1, a key mediator of the ER stress response, delays disease progression and reduces protein aggregation in various models of neurodegeneration. To identify disease-modifier genes that may explain the neuroprotective effects of XBP1 deficiency, we performed gene expression profiling of brain cortex and striatum of these animals and uncovered insulin-like growth factor 2 (Igf2) as the major upregulated gene. Here we studied the impact of IGF2 signaling on protein aggregation in models of Huntingtons disease (HD) as proof-of-concept. Cell culture studies revealed that IGF2 treatment decreases the load of intracellular aggregates of mutant huntingtin and a polyglutamine peptide. These results were validated using induced pluripotent stem cells (iPSC)-derived medium spiny neurons from HD patients. The reduction in the levels of mutant huntingtin was associated with a decrease in the half-life of the intracellular protein. The decrease in the levels of abnormal protein aggregation triggered by IGF2 were independent of the activity of autophagy and the proteasome pathways, the two main routes for mutant huntingtin clearance. Conversely, IGF2 signaling enhanced the secretion of soluble mutant huntingtin species through exosomes and microvesicles involving changes in actin dynamics. Administration of IGF2 into the brain of HD mice using gene therapy led to a significant decrease in the levels of mutant huntingtin in three different animal models. Moreover, analysis of human post-mortem brain tissue, and blood samples from HD patients showed a reduction of IGF2 level. This study identifies IGF2 as a relevant factor deregulated in HD, operating as a disease modifier that buffers the accumulation of abnormal protein aggregates. One sentence summaryIGF2 reduces the load of intracellular protein aggregates through the extracellular disposal of the mutant protein.

neuroscience↗