Biology subjects

Jacobson, M. P.

Publications and source records attributed to Jacobson, M. P..

8 recordsLinked to original sources

bioRxiv2025

A structure-based tool to interpret the significance of kinase mutations in clinical next generation sequencing in cancer

IntroductionClinical workflows to analyze variants of unknown significance (VUSs) found in clinical next generation sequencing (NGS) are labor intensive, requiring manual analysis of published data for each variant. There is a strong need for tools and resources that provide a consistent way to analyze variants. With the explosion of clinical NGS data and the concurrent availability of protein structures through the Protein Data Bank and protein models through programs such as AlphaFold, there exists an unprecedented opportunity to use structural information to help standardize NGS analysis with the overall goal of advancing personalized cancer therapy. MethodsUsing the Catalogue of Somatic Mutations in Cancer (COSMIC), the largest curated database of clinical cancer mutations, we mapped thousands of missense mutations in the kinase and juxtamembrane (JM) domains of 48 receptor tyrosine kinases (RTKs) onto structurally aligned kinase structures, then clustered known activating mutations along with VUSs based on proximity in three-dimensional structure. Using cell-based models we illustrate that our resource can be used to identify activating mutations and provide insight into mechanisms of kinase activation and regulation. ResultsWe provide a database of structurally aligned and functionally annotated mutations that can be used as a tool to evaluate kinase VUSs based on their structural alignment with known activating mutations. The tool can be accessed through a user-friendly website in which one can input a kinase mutation of interest, and the system will output a list of structurally analogous mutations in other kinases, as well as their functional annotations. DiscussionWe expect our database to be an important addition to the current tools and resources used to analyze clinical NGS, with important clinical implications to guide recommendations for personalized cancer therapy.

cancer biology↗

bioRxiv2024

A role for pH dynamics regulating transcription factor DNA binding selectivity

Intracellular pH (pHi) dynamics regulates diverse cell processes such as proliferation, dysplasia, and differentiation, often mediated by the protonation state of a functionally critical histidine residue in endogenous pH sensing proteins. How pHi dynamics can directly regulate gene expression and whether transcription factors can function as pH sensors has received limited attention. We tested the prediction that transcription factors with a histidine in their DNA binding domain (DBD) that forms hydrogen bonds with nucleotides can have pH-regulated activity, which is relevant to more than 85 transcription factors in distinct families, including FOX, KLF, SOX and MITF/Myc. Focusing on FOX family transcription factors, we used unbiased SELEX-seq to identify pH-dependent DNA binding motif preferences, then confirm pH-regulated binding affinities for FOXC2, FOXM1, and FOXN1 to a canonical FkhP DNA motif that are 2.5 to 7.5 greater at pH 7.0 compared with pH 7.5. For FOXC2, we also find greater activity for an FkhP motif at lower pHi in cells and that pH-regulated binding and activity are dependent on a conserved histidine (His122) in the DBD. RNA-seq with FOXC2 also reveals pH-dependent differences in enriched promoter motifs. Our findings identify pH-regulated transcription factor-DNA binding selectivity with relevance to how pHi dynamics can regulate gene expression for myriad cell behaviours.

biochemistry↗

bioRxiv2022

Dissecting the effects of GTPase and kinase domain mutations on LRRK2 endosomal localization and activity

Parkinsons disease-causing LRRK2 mutations lead to varying degrees of Rab GTPase hyperphosphorylation. Puzzlingly, LRRK2 GTPase-inactivating mutations--which do not affect intrinsic kinase activity--lead to higher levels of cellular Rab phosphorylation than kinase-activating mutations. Here, we investigated whether mutation-dependent differences in LRRK2 cellular localization could explain this discrepancy. We discovered that blocking endosomal maturation leads to the rapid formation of mutant LRRK2+ endosomes on which LRRK2 phosphorylates substrate Rabs. LRRK2+ endosomes are maintained through positive feedback, which mutually reinforces membrane localization of LRRK2 and phosphorylated Rab substrates. Furthermore, across a panel of mutants, cells expressing GTPase-inactivating mutants formed strikingly more LRRK2+ endosomes than cells expressing kinase-activating mutants, resulting in higher total cellular levels of phosphorylated Rabs. Our study suggests that an increased probability of LRRK2 GTPase-inactivating mutants to be retained on intracellular membranes over the kinase-activating mutants leads to higher substrate phosphorylation.

systems biology↗

bioRxiv2021

Analogs of the Dopamine Metabolite 5,6-Dihydroxyindole Bind Directly to and Activate the Nuclear Receptor Nurr1 (NR4A2)

The nuclear receptor-related 1 protein, Nurr1, is a transcription factor critical for the development and maintenance of dopamine-producing neurons in the substantia nigra pars compacta, a cell population that progressively loses the ability to make dopamine and degenerates in Parkinsons disease. Recently, we demonstrated that Nurr1 binds directly to and is regulated by the endogenous dopamine metabolite 5,6-dihydroxyindole (DHI). Unfortunately, DHI is an unstable compound, and thus a poor tool for studying Nurr1 function. Here we report that 5-chloroindole, an unreactive analog of DHI, binds directly to the Nurr1 ligand binding domain with micromolar affinity and stimulates the activity of Nurr1, including the transcription of genes governing the synthesis and packaging of dopamine.

neuroscience↗

bioRxiv2020

Altered specificity of 15-LOX-1 in the biosynthesis of 7S,14S-diHDHA implicates 15-LOX-2 in biosynthesis of resolvin D5

The oxylipins, 7S,14S-diHDHA and 7S,17S-diHDHA (RvD5), have been found in macrophages exudates and are believed to function as specialized pro-resolving mediators (SPMs). Their biosynthesis is thought to proceed through sequential oxidations of docosahexaenoic acid (DHA) by lipoxygenase enzymes, specifically by h5-LOX first to 7S-HDHA, followed by h12-LOX to form 7S,14S-diHDHA or h15-LOX-1 to form 7S,17S-diHDHA (RvD5). In this work, we determined that oxidation of 7S-HpDHA to 7S,14S-diHDHA can be performed by either h12-LOX or h15-LOX-1, with similar kinetics. The oxidation at C14 of DHA by h12-LOX was expected, but the non-canonical reaction of h15-LOX-1 to make primarily 7S,14S-diHDHA was unexpected. Computer modeling suggests the alcohol on C7 of 7S-HDHA hydrogen bonds with the backbone carbonyl of I399, forcing the hydrogen abstraction from C12 to oxygenate on C14, and not C17. This result raised questions regarding synthesis of 7S,17S-diHDHA (RvD5). Strikingly, we find h15-LOX-2 oxygenates 7S-HDHA almost exclusively at C17, forming RvD5 with faster kinetics than h15-LOX-1. The presence of h15-LOX-2 in neutrophils and macrophages, suggests it may have a greater role in biosynthesizing SPMs than previously thought. We also determined that the reactions of h5-LOX with 14S-HpDHA and 17S-HpDHA are kinetically slow compared to DHA, suggesting these may be minor biosynthetic routes in-vivo. Additionally, we show that 7S,14S-diHDHA and RvD5 have anti-aggregation properties with platelets at low micro-molar potencies, which could directly regulate clot resolution.

biochemistry↗

bioRxiv2018

Conserved tau microtubule-binding repeat histidines confer pH-dependent tau-microtubule association

Tau, a member of the MAP2/tau family of microtubule-associated proteins, functions to stabilize and organize axonal microtubules in healthy neurons. In contrast, tau dissociates from microtubules and forms neurotoxic extracellular aggregates in neurodegenerative tauopathies. MAP2/tau family proteins are characterized by three to five conserved, intrinsically disordered repeat regions that mediate electrostatic interactions with the microtubule surface. We use molecular dynamics, microtubule-binding experiments and live cell microscopy to show that highly conserved histidine residues near the C terminus of each MT-binding repeat are pH sensors that can modulate tau-MT interaction strength within the physiological intracellular pH range. At lower pH, these histidines are positively charged and form cation-{pi} interactions with phenylalanine residues in a hydrophobic cleft between adjacent tubulin dimers. At higher pH, tau deprotonation decreases microtubule-binding both in vitro and in cells. However, electrostatic and hydrophobic characteristics of histidine are required for tau-MT-binding as substitution with constitutively positively charged, non-aromatic lysine or uncharged alanine greatly reduces or abolishes tau-MT binding. Consistent with these findings, tau-MT binding is reduced in a cancer cell model with increased intracellular pH but is rapidly rescued by decreasing pH to normal levels. Thus, these data add a new dimension to the intracellular regulation of tau activity and could be relevant in normal and pathological conditions.

cell biology↗

bioRxiv2018

Covalent Modification and Regulation of the Nuclear Receptor Nurr1 by a Dopamine Metabolite

Nurr1, a nuclear receptor essential for the development, maintenance, and survival of midbrain dopaminergic neurons, is a potential therapeutic target for Parkinsons disease, a neurological disorder characterized by the degeneration of these same neurons. Efforts to identify Nurr1 agonists have been hampered by the recognition that it lacks several classic regulatory elements of nuclear receptor function, including the canonical ligand-binding pocket. Here we report that the dopamine metabolite 5,6-dihydroxyindole (DHI) binds directly to and modulates the activity of Nurr1. Using biophysical assays and x-ray crystallography we show that DHI binds to the ligand binding domain within a non-canonical pocket, forming a covalent adduct with Cys566. In cultured cells and zebrafish, DHI stimulates Nurr1 activity, including the transcription of target genes underlying dopamine homeostasis. These findings suggest avenues for developing synthetic Nurr1 ligands to ameliorate the symptoms and progression of Parkinsons disease.

biophysics↗

bioRxiv2017

Prominent Features Of The Amino Acid Mutation Landscape In Cancer

Cancer can be viewed as a set of different diseases with distinctions based on tissue origin, driver mutations, and genetic signatures. Accordingly, each of these distinctions have been used to classify cancer subtypes and to reveal common features. Here, we present a different analysis of cancer based on amino acid mutation signatures. Non-negative Matrix Factorization and principal component analysis of 29 cancers revealed six amino acid mutation signatures, including four signatures that were dominated by either arginine to histidine (Arg>His) or glutamate to lysine (Glu>Lys) mutations. Sample-level analyses reveal that while some cancers are heterogeneous, others are largely dominated by one type of mutation. Using a non-overlapping set of samples from the COSMIC somatic mutation database, we validate five of six mutation signatures, including signatures with prominent arginine to histidine (Arg>His) or glutamate to lysine (Glu>Lys) mutations. This suggests that our classification of cancers based on amino acid mutation patterns may provide avenues of inquiry pertaining to specific protein mutations that may generate novel insights into cancer biology.

bioinformatics↗