A5051248838- DNA Repair Mechanisms
- CRISPR and Genetic Engineering
- Cancer-related Molecular Pathways
- Cell death mechanisms and regulation
- PARP inhibition in cancer therapy
- Mitochondrial Function and Pathology
- Cellular transport and secretion
- Ubiquitin and proteasome pathways
- Microtubule and mitosis dynamics
- Protein Kinase Regulation and GTPase Signaling
- Enzyme Structure and Function
- Advanced biosensing and bioanalysis techniques
- RNA Interference and Gene Delivery
- Advanced Proteomics Techniques and Applications
- Protein Degradation and Inhibitors
- Gene Regulatory Network Analysis
- Glioma Diagnosis and Treatment
- Genomics and Chromatin Dynamics
- Chromatin Remodeling and Cancer
- Photosynthetic Processes and Mechanisms
- Glycosylation and Glycoproteins Research
- Glutathione Transferases and Polymorphisms
- Redox biology and oxidative stress
- Cell Image Analysis Techniques
- Chromosomal and Genetic Variations
Massachusetts Institute of Technology
2019-2024
University Medical Center Groningen
2023-2024
Leiden University
2023-2024
University of Groningen
2023-2024
Leiden University Medical Center
2021-2024
The Netherlands Cancer Institute
2012-2017
During apoptosis, the mitochondrial outer membrane is permeabilized, leading to release of cytochrome c that activates downstream caspases. Mitochondrial permeabilization (MOMP) has historically been thought occur synchronously and completely throughout a cell, rapid caspase activation apoptosis. Using new imaging approach, we demonstrate MOMP not an all-or-nothing event. Rather, find minority mitochondria can undergo in stress-regulated manner, phenomenon term "minority MOMP." Crucially,...
Abstract Protein phosphorylation is one of the most widespread post-translational modifications in biology 1,2 . With advances mass-spectrometry-based phosphoproteomics, 90,000 sites serine and threonine have so far been identified, several thousand associated with human diseases biological processes 3,4 For vast majority events, it not yet known which more than 300 protein serine/threonine (Ser/Thr) kinases encoded genome are responsible 3 Here we used synthetic peptide libraries to profile...
Abstract DNA double-strand breaks (DSB) are repaired by multiple distinct pathways, with outcomes ranging from error-free repair to mutagenesis and genomic loss. DSB-repair pathway cross-talk compensation is incompletely understood, despite its importance for stability, oncogenesis, genome editing using CRISPR/Cas9. To address this, we constructed validated three fluorescent Cas9-based reporters, named DSB-Spectrum, that simultaneously quantify the contribution of pathways at a DSB....
Joint DNA molecules are natural byproducts of replication and repair. Persistent joint give rise to ultrafine bridges (UFBs) in mitosis, compromising sister chromatid separation. The translocase PICH (ERCC6L) has a central role UFB resolution. A genome-wide loss-of-function screen is performed identify the genetic context dependency. In addition genes involved condensation, centromere stability, DNA-damage repair, we FIGNL1-interacting regulator recombination mitosis (FIRRM), formerly known...
Inactivating mutations in the BRCA1 and BRCA2 genes impair DNA double-strand break (DSB) repair by homologous recombination (HR), leading to chromosomal instability cancer. Importantly, BRCA1/2 deficiency also causes therapeutically targetable vulnerabilities. Here, we identify dependency on end resection factor EXO1 as a key vulnerability of BRCA1-deficient cells. generates poly(ADP-ribose)-decorated lesions during S phase that associate with unresolved DSBs genomic but not wild-type or...
The novel anticancer drug ABT-737 is a Bcl-2 Homology 3 (BH3)-mimetic that induces apoptosis by inhibiting pro-survival proteins. binds with equal affinity to Bcl-2, Bcl-xL and Bcl-w in vitro expected overrule resistance mediated these proteins measure. We have profiled specificity for all six proteins, p53 wild-type or p53-mutant human T-leukemic cells. Bcl-B was untargeted, like Bfl-1 Mcl-1, accord their low vitro. However, proved better target than Bcl-w. This reflected differential...
During the repair of interstrand crosslinks (ICLs) a DNA double-strand break (DSB) is generated. The Fanconi anemia (FA) core complex, which recruited to ICLs, promotes high-fidelity this DSB by homologous recombination (HR). However, whether FA complex also HR at ICL-independent DSBs, for example induced ionizing irradiation or nucleases, remains controversial. Here, we identified members FANCL and Ube2T as HR-promoting factors in CRISPR/Cas9-based screen. Using isogenic cell line models,...
Specificity within protein kinase signaling cascades is determined by direct and indirect interactions between kinases their substrates. While the impact of localization recruitment on kinase–substrate targeting can be readily assessed, evaluating relative importance phosphorylation site remains challenging. In this study, we examine STE20 family serine–threonine to investigate basic mechanisms substrate targeting. We used peptide arrays define specificity for majority categorized them into...
Human NimA-related kinases (Neks) have multiple mitotic and non-mitotic functions, but few substrates are known. We systematically determined the phosphorylation-site motifs for entire Nek kinase family, except Nek11. While all strongly select hydrophobic residues in −3 position, family separates into four distinct groups based on specificity a serine versus threonine phospho-acceptor, preference basic or acidic other positions. Unlike Nek1-Nek9, Nek10 is dual-specificity that efficiently...
Overexpression of Cyclin E1 perturbs DNA replication, resulting in lesions and genomic instability. Consequently, E1-overexpressing cancer cells increasingly rely on repair, including RAD52-mediated break-induced replication during interphase. We show that not all induced by overexpression are resolved While upon S phase, a significant fraction these is transmitted into mitosis. triggers mitotic synthesis (MiDAS) RAD52-dependent fashion. Chemical or genetic inactivation MiDAS enhances...
ABSTRACT Protein phosphorylation is one of the most widespread post-translational modifications in biology. With advent mass spectrometry-based phosphoproteomics, more than 200,000 sites serine and threonine have been reported, which several thousand associated with human diseases biological processes. For vast majority events, it not yet known 300 protein Ser/Thr kinases encoded genome responsible. Here, we utilize synthetic peptide libraries to profile substrate sequence specificity nearly...
Abstract The majority of proteins in mammalian cells are modified by covalent attachment an acetyl-group to the N-terminus (Nt-acetylation). Paradoxically, Nt-acetylation has been suggested inhibit as well promote substrate degradation. Contrasting these findings, proteome-wide stability measurements failed detect any correlation between status and protein stability. Accordingly, analysis datasets, we found that predicted positively correlates with case GFP, but this does not hold for entire...
Homologous Recombination (HR) is a high-fidelity repair mechanism of DNA Double-Strand Breaks (DSBs), which are induced by irradiation, genotoxic chemicals or physiological damaging processes. DSBs also generated as intermediates during the interstrand crosslinks (ICLs). In this context, Fanconi anemia (FA) core complex, effectively recruited to ICLs, promotes HR-mediated DSB-repair. However, whether FA complex HR at ICL-independent remains controversial. Here, we identified members FANCL...
Abstract Repair of DNA double strand breaks (DSBs) occurs through multiple distinct repair pathways including canonical and microhomology-mediated/Pol Q-dependent end joining (c-NHEJ alt-NHEJ), homologous recombination (HR), single annealing (SSA). Exactly how a particular DSB dictates which pathway is selected for repair, the extent to different cross-talk with each other incompletely understood, but appears be influenced by specific type ends, resection, cell state stage cycle, chromatin...
Abstract Human NimA-related kinases (Neks) have multiple mitotic and non-mitotic functions, but few substrates are known. We systematically determined the phosphorylation-site motifs for entire Nek kinase family, except Nek11. While all strongly select hydrophobic residues in −3 position, family separates into four distinct groups based on specificity a serine versus threonine phospho-acceptor, preference basic or acidic other positions. Unlike Nek1-Nek9, Nek10 is dual-specificity that...
Deficiency for the repair of DNA double-strand breaks (DSBs) via homologous recombination (HR) leads to chromosomal instability and diseases such as cancer. Yet, defective HR also results in vulnerabilities that can be exploited targeted therapy. Here, we identify a vulnerability show BRCA1-deficient cells are dependent on long-range end-resection factor EXO1 survival. loss replication-induced lesions decorated by poly(ADP-ribose)-chains. In lack both BRCA1 EXO1, this is accompanied...
(Molecular Cell 57, 860–872; March 5, 2015) In the above article, authors inadvertently presented long exposure of caspase-3 input instead caspase-7 (Figure 2D). The is now shown. apologize for any confusion that this may have caused. Limited Mitochondrial Permeabilization Causes DNA Damage and Genomic Instability in Absence DeathIchim et al.Molecular CellFebruary 19, 2015In BriefDuring apoptosis, mitochondrial outer membrane permeabilization (MOMP) widespread, leading to rapid cell death....
ABSTRACT In response to genotoxic stress, multiple kinase signalling cascades are activated, many of them directed towards the tumour suppressor p53 which coordinates DNA damage (DDR). Defects in DDR pathways lead an accumulation mutations that can promote tumorigenesis. Emerging evidence implicates members NimA-related (NEK) family (NEK1, NEK10 and NEK11) DDR. Here, we describe a function for regulation transcriptional activity through tyrosine phosphorylation. loss increases cellular...