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1.
Mol Cell ; 82(11): 1992-2005.e9, 2022 06 02.
Article in English | MEDLINE | ID: mdl-35417664

ABSTRACT

Phospholipase A2, group VII (PLA2G7) is widely recognized as a secreted, lipoprotein-associated PLA2 in plasma that converts phospholipid platelet-activating factor (PAF) to a biologically inactive product Lyso-PAF during inflammatory response. We report that intracellular PLA2G7 is selectively important for cell proliferation and tumor growth potential of melanoma cells expressing mutant NRAS, but not cells expressing BRAF V600E. Mechanistically, PLA2G7 signals through its product Lyso-PAF to contribute to RAF1 activation by mutant NRAS, which is bypassed by BRAF V600E. Intracellular Lyso-PAF promotes p21-activated kinase 2 (PAK2) activation by binding to its catalytic domain and altering ATP kinetics, while PAK2 significantly contributes to S338-phosphorylation of RAF1 in addition to PAK1. Furthermore, the PLA2G7-PAK2 axis is also required for full activation of RAF1 in cells stimulated by epidermal growth factor (EGF) or cancer cells expressing mutant KRAS. Thus, PLA2G7 and Lyso-PAF exhibit intracellular signaling functions as key elements of RAS-RAF1 signaling.


Subject(s)
Phospholipids , Proto-Oncogene Proteins B-raf , Phospholipases A2 , Platelet Activating Factor/analogs & derivatives , Platelet Activating Factor/metabolism
2.
Mol Cell ; 81(18): 3833-3847.e11, 2021 09 16.
Article in English | MEDLINE | ID: mdl-34289383

ABSTRACT

Mutant isocitrate dehydrogenase (IDH) 1 and 2 play a pathogenic role in cancers, including acute myeloid leukemia (AML), by producing oncometabolite 2-hydroxyglutarate (2-HG). We recently reported that tyrosine phosphorylation activates IDH1 R132H mutant in AML cells. Here, we show that mutant IDH2 (mIDH2) R140Q commonly has K413 acetylation, which negatively regulates mIDH2 activity in human AML cells by attenuating dimerization and blocking binding of substrate (α-ketoglutarate) and cofactor (NADPH). Mechanistically, K413 acetylation of mitochondrial mIDH2 is achieved through a series of hierarchical phosphorylation events mediated by tyrosine kinase FLT3, which phosphorylates mIDH2 to recruit upstream mitochondrial acetyltransferase ACAT1 and simultaneously activates ACAT1 and inhibits upstream mitochondrial deacetylase SIRT3 through tyrosine phosphorylation. Moreover, we found that the intrinsic enzyme activity of mIDH2 is much higher than mIDH1, thus the inhibitory K413 acetylation optimizes leukemogenic ability of mIDH2 in AML cells by both producing sufficient 2-HG for transformation and avoiding cytotoxic accumulation of intracellular 2-HG.


Subject(s)
Isocitrate Dehydrogenase/genetics , Leukemia, Myeloid, Acute/metabolism , Acetyl-CoA C-Acetyltransferase/metabolism , Acetylation , Animals , Antineoplastic Agents/pharmacology , Female , Humans , Isocitrate Dehydrogenase/metabolism , Ketoglutaric Acids/metabolism , Leukemia, Myeloid, Acute/genetics , Lysine/genetics , Lysine/metabolism , Male , Mice , Mice, Inbred NOD , Mutation/genetics , NADP/metabolism , Nuclear Proteins/metabolism , Phosphorylation , Polymorphism, Single Nucleotide/genetics , Primary Cell Culture , Protein Binding , Protein Processing, Post-Translational , Protein-Tyrosine Kinases/metabolism
3.
Mol Cell ; 76(6): 857-871.e9, 2019 12 19.
Article in English | MEDLINE | ID: mdl-31586547

ABSTRACT

The oxidative pentose phosphate pathway (oxiPPP) contributes to cell metabolism through not only the production of metabolic intermediates and reductive NADPH but also inhibition of LKB1-AMPK signaling by ribulose-5-phosphate (Ru-5-P), the product of the third oxiPPP enzyme 6-phosphogluconate dehydrogenase (6PGD). However, we found that knockdown of glucose-6-phosphate dehydrogenase (G6PD), the first oxiPPP enzyme, did not affect AMPK activation despite decreased Ru-5-P and subsequent LKB1 activation, due to enhanced activity of PP2A, the upstream phosphatase of AMPK. In contrast, knockdown of 6PGD or 6-phosphogluconolactonase (PGLS), the second oxiPPP enzyme, reduced PP2A activity. Mechanistically, knockdown of G6PD or PGLS decreased or increased 6-phosphogluconolactone level, respectively, which enhanced the inhibitory phosphorylation of PP2A by Src. Furthermore, γ-6-phosphogluconolactone, an oxiPPP byproduct with unknown function generated through intramolecular rearrangement of δ-6-phosphogluconolactone, the only substrate of PGLS, bound to Src and enhanced PP2A recruitment. Together, oxiPPP regulates AMPK homeostasis by balancing the opposing LKB1 and PP2A.


Subject(s)
AMP-Activated Protein Kinases/metabolism , Gluconates/metabolism , Neoplasms/enzymology , Protein Phosphatase 2/metabolism , A549 Cells , AMP-Activated Protein Kinase Kinases , Animals , Cell Proliferation , Enzyme Activation , Glucosephosphate Dehydrogenase/genetics , Glucosephosphate Dehydrogenase/metabolism , HEK293 Cells , HT29 Cells , Humans , K562 Cells , MCF-7 Cells , Mice, Nude , Neoplasms/genetics , Neoplasms/pathology , PC-3 Cells , Pentose Phosphate Pathway , Protein Binding , Protein Phosphatase 2/genetics , Protein Serine-Threonine Kinases/metabolism , Reactive Oxygen Species/metabolism , Ribulosephosphates/metabolism , Signal Transduction , Superoxide Dismutase/genetics , Superoxide Dismutase/metabolism , Tumor Burden , src-Family Kinases/metabolism
4.
Am J Hum Genet ; 110(5): 846-862, 2023 05 04.
Article in English | MEDLINE | ID: mdl-37086723

ABSTRACT

Craniosynostosis (CS) is the most common congenital cranial anomaly. Several Mendelian forms of syndromic CS are well described, but a genetic etiology remains elusive in a substantial fraction of probands. Analysis of exome sequence data from 526 proband-parent trios with syndromic CS identified a marked excess (observed 98, expected 33, p = 4.83 × 10-20) of damaging de novo variants (DNVs) in genes highly intolerant to loss-of-function variation (probability of LoF intolerance > 0.9). 30 probands harbored damaging DNVs in 21 genes that were not previously implicated in CS but are involved in chromatin modification and remodeling (4.7-fold enrichment, p = 1.1 × 10-11). 17 genes had multiple damaging DNVs, and 13 genes (CDK13, NFIX, ADNP, KMT5B, SON, ARID1B, CASK, CHD7, MED13L, PSMD12, POLR2A, CHD3, and SETBP1) surpassed thresholds for genome-wide significance. A recurrent gain-of-function DNV in the retinoic acid receptor alpha (RARA; c.865G>A [p.Gly289Arg]) was identified in two probands with similar CS phenotypes. CS risk genes overlap with those identified for autism and other neurodevelopmental disorders, are highly expressed in cranial neural crest cells, and converge in networks that regulate chromatin modification, gene transcription, and osteoblast differentiation. Our results identify several CS loci and have major implications for genetic testing and counseling.


Subject(s)
Craniosynostoses , Tretinoin , Humans , Mutation , Craniosynostoses/genetics , Gene Expression Regulation , Chromatin , Genetic Predisposition to Disease
5.
Bioessays ; : e2400184, 2024 Oct 03.
Article in English | MEDLINE | ID: mdl-39361252

ABSTRACT

The LIM domain kinases (LIMKs) are important actin cytoskeleton regulators. These proteins, LIMK1 and LIMK2, are nodes downstream of Rho GTPases and are the key enzymes that phosphorylate cofilin/actin depolymerization factors to regulate filament severing. They therefore perform an essential role in cascades that control actin depolymerization. Signaling of the LIMKs is carefully regulated by numerous inter- and intra-molecular mechanisms. In this review, we discuss recent findings that improve the understanding of LIM domain kinase regulation mechanisms. We also provide an up-to-date review of the role of the LIM domain kinases, their architectural features, how activity is impacted by other proteins, and the implications of these findings for human health and disease.

6.
J Biol Chem ; 299(9): 105098, 2023 09.
Article in English | MEDLINE | ID: mdl-37507023

ABSTRACT

RasGAP (p120RasGAP), the founding member of the GTPase-activating protein (GAP) family, is one of only nine human proteins to contain two SH2 domains and is essential for proper vascular development. Despite its importance, its interactions with key binding partners remains unclear. In this study we provide a detailed viewpoint of RasGAP recruitment to various binding partners and assess their impact on RasGAP activity. We reveal the RasGAP SH2 domains generate distinct binding interactions with three well-known doubly phosphorylated binding partners: p190RhoGAP, Dok1, and EphB4. Affinity measurements demonstrate a 100-fold weakened affinity for RasGAP-EphB4 binding compared to RasGAP-p190RhoGAP or RasGAP-Dok1 binding, possibly driven by single versus dual SH2 domain engagement with a dominant N-terminal SH2 interaction. Small-angle X-ray scattering reveals conformational differences between RasGAP-EphB4 binding and RasGAP-p190RhoGAP binding. Importantly, these interactions do not impact catalytic activity, implying RasGAP utilizes its SH2 domains to achieve diverse spatial-temporal regulation of Ras signaling in a previously unrecognized fashion.


Subject(s)
Receptor Protein-Tyrosine Kinases , p120 GTPase Activating Protein , Humans , GTPase-Activating Proteins/metabolism , p120 GTPase Activating Protein/chemistry , Phosphorylation , ras GTPase-Activating Proteins/chemistry , ras GTPase-Activating Proteins/metabolism , Receptor Protein-Tyrosine Kinases/metabolism , Signal Transduction , src Homology Domains , Calorimetry , Peptides/metabolism , Models, Molecular , Protein Structure, Tertiary , Scattering, Small Angle
7.
Mol Cell ; 62(3): 397-408, 2016 05 05.
Article in English | MEDLINE | ID: mdl-27153537

ABSTRACT

Cofilin/actin-depolymerizing factor (ADF) proteins are critical nodes that relay signals from protein kinase cascades to the actin cytoskeleton, in particular through site-specific phosphorylation at residue Ser3. This is important for regulation of the roles of cofilin in severing and stabilizing actin filaments. Consequently, cofilin/ADF Ser3 phosphorylation is tightly controlled as an almost exclusive substrate for LIM kinases. Here we determine the LIMK1:cofilin-1 co-crystal structure. We find an interface that is distinct from canonical kinase-substrate interactions. We validate this previously unobserved mechanism for high-fidelity kinase-substrate recognition by in vitro kinase assays, examination of cofilin phosphorylation in mammalian cells, and functional analysis in S. cerevisiae. The interface is conserved across all LIM kinases. Remarkably, we also observe both pre- and postphosphotransfer states in the same crystal lattice. This study therefore provides a molecular understanding of how kinase-substrate recognition acts as a gatekeeper to regulate actin cytoskeletal dynamics.


Subject(s)
Cofilin 1/metabolism , Lim Kinases/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae/enzymology , Binding Sites , Catalytic Domain , Cofilin 1/chemistry , Cofilin 1/genetics , Crystallography, X-Ray , HEK293 Cells , Humans , Lim Kinases/chemistry , Lim Kinases/genetics , Models, Molecular , Mutation , Phosphorylation , Protein Binding , Protein Conformation , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae Proteins/chemistry , Saccharomyces cerevisiae Proteins/genetics , Serine , Structure-Activity Relationship , Substrate Specificity , Transfection
8.
Mol Cell ; 64(5): 859-874, 2016 12 01.
Article in English | MEDLINE | ID: mdl-27867011

ABSTRACT

Mitochondrial acetyl-CoA acetyltransferase 1 (ACAT1) regulates pyruvate dehydrogenase complex (PDC) by acetylating pyruvate dehydrogenase (PDH) and PDH phosphatase. How ACAT1 is "hijacked" to contribute to the Warburg effect in human cancer remains unclear. We found that active, tetrameric ACAT1 is commonly upregulated in cells stimulated by EGF and in diverse human cancer cells, where ACAT1 tetramers, but not monomers, are phosphorylated and stabilized by enhanced Y407 phosphorylation. Moreover, we identified arecoline hydrobromide (AH) as a covalent ACAT1 inhibitor that binds to and disrupts only ACAT1 tetramers. The resultant AH-bound ACAT1 monomers cannot reform tetramers. Inhibition of tetrameric ACAT1 by abolishing Y407 phosphorylation or AH treatment results in decreased ACAT1 activity, leading to increased PDC flux and oxidative phosphorylation with attenuated cancer cell proliferation and tumor growth. These findings provide a mechanistic understanding of how oncogenic events signal through distinct acetyltransferases to regulate cancer metabolism and suggest ACAT1 as an anti-cancer target.


Subject(s)
Acetyl-CoA C-Acetyltransferase/metabolism , Mitochondria/enzymology , Pyruvate Dehydrogenase Complex/metabolism , Acetyl-CoA C-Acetyltransferase/genetics , Animals , Cell Line, Tumor , Cell Proliferation , Epidermal Growth Factor/metabolism , Gene Expression Regulation, Enzymologic , Gene Expression Regulation, Neoplastic , Humans , Mice , Mice, Nude , NIH 3T3 Cells , Neoplasms/enzymology , Neoplasms/pathology , Oligopeptides/genetics , Oligopeptides/metabolism , Phosphorylation , Protein-Tyrosine Kinases/metabolism , Receptor, Fibroblast Growth Factor, Type 1/genetics , Receptor, Fibroblast Growth Factor, Type 1/metabolism
9.
Hum Genet ; 142(1): 21-32, 2023 Jan.
Article in English | MEDLINE | ID: mdl-35997807

ABSTRACT

Lambdoid craniosynostosis (CS) is a congenital anomaly resulting from premature fusion of the cranial suture between the parietal and occipital bones. Predominantly sporadic, it is the rarest form of CS and its genetic etiology is largely unexplored. Exome sequencing of 25 kindreds, including 18 parent-offspring trios with sporadic lambdoid CS, revealed a marked excess of damaging (predominantly missense) de novo mutations that account for ~ 40% of sporadic cases. These mutations clustered in the BMP signaling cascade (P = 1.6 × 10-7), including mutations in genes encoding BMP receptors (ACVRL1 and ACVR2A), transcription factors (SOX11, FOXO1) and a transcriptional co-repressor (IFRD1), none of which have been implicated in other forms of CS. These missense mutations are at residues critical for substrate or target sequence recognition and many are inferred to cause genetic gain-of-function. Additionally, mutations in transcription factor NFIX were implicated in syndromic craniosynostosis affecting diverse sutures. Single cell RNA sequencing analysis of the mouse lambdoid suture identified enrichment of mutations in osteoblast precursors (P = 1.6 × 10-6), implicating perturbations in the balance between proliferation and differentiation of osteoprogenitor cells in lambdoid CS. The results contribute to the growing knowledge of the genetics of CS, have implications for genetic counseling, and further elucidate the molecular etiology of premature suture fusion.


Subject(s)
Craniosynostoses , Mice , Animals , Craniosynostoses/genetics , Craniosynostoses/metabolism , Mutation , Signal Transduction/genetics , Transcription Factors/genetics , Cell Differentiation , NFI Transcription Factors/genetics , NFI Transcription Factors/metabolism
10.
Blood ; 138(14): 1225-1236, 2021 10 07.
Article in English | MEDLINE | ID: mdl-34115827

ABSTRACT

Cutaneous T-cell lymphomas (CTCLs) are a clinically heterogeneous collection of lymphomas of the skin-homing T cell. To identify molecular drivers of disease phenotypes, we assembled representative samples of CTCLs from patients with diverse disease subtypes and stages. Via DNA/RNA-sequencing, immunophenotyping, and ex vivo functional assays, we identified the landscape of putative driver genes, elucidated genetic relationships between CTCLs across disease stages, and inferred molecular subtypes in patients with stage-matched leukemic disease. Collectively, our analysis identified 86 putative driver genes, including 19 genes not previously implicated in this disease. Two mutations have never been described in any cancer. Functionally, multiple mutations augment T-cell receptor-dependent proliferation, highlighting the importance of this pathway in lymphomagenesis. To identify putative genetic causes of disease heterogeneity, we examined the distribution of driver genes across clinical cohorts. There are broad similarities across disease stages. Many driver genes are shared by mycosis fungoides (MF) and Sezary syndrome (SS). However, there are significantly more structural variants in leukemic disease, leading to highly recurrent deletions of putative tumor suppressors that are uncommon in early-stage skin-centered MF. For example, TP53 is deleted in 7% and 87% of MF and SS, respectively. In both human and mouse samples, PD1 mutations drive aggressive behavior. PD1 wild-type lymphomas show features of T-cell exhaustion. PD1 deletions are sufficient to reverse the exhaustion phenotype, promote a FOXM1-driven transcriptional signature, and predict significantly worse survival. Collectively, our findings clarify CTCL genetics and provide novel insights into pathways that drive diverse disease phenotypes.


Subject(s)
Lymphoma, T-Cell, Cutaneous/genetics , Transcriptome , Animals , Cells, Cultured , Forkhead Box Protein M1/genetics , Gene Expression Regulation, Neoplastic , Genes, Tumor Suppressor , Humans , Mice , Mutation , Oncogenes , Tumor Suppressor Protein p53/genetics
11.
Mol Cell ; 57(1): 191-201, 2015 Jan 08.
Article in English | MEDLINE | ID: mdl-25544564

ABSTRACT

The receptor tyrosine kinase KIT plays an important role in development of germ cells, hematopoietic cells, and interstitial pacemaker cells. Oncogenic KIT mutations play an important "driver" role in gastrointestinal stromal tumors, acute myeloid leukemias, and melanoma, among other cancers. Here we describe the crystal structure of a recurring somatic oncogenic mutation located in the C-terminal Ig-like domain (D5) of the ectodomain, rendering KIT tyrosine kinase activity constitutively activated. The structural analysis, together with biochemical and biophysical experiments and detailed analyses of the activities of a variety of oncogenic KIT mutations, reveals that the strength of homotypic contacts and the cooperativity in the action of D4D5 regions determines whether KIT is normally regulated or constitutively activated in cancers. We propose that cooperative interactions mediated by multiple weak homotypic contacts between receptor molecules are responsible for regulating normal ligand-dependent or oncogenic RTK activation via a "zipper-like" mechanism for receptor activation.


Subject(s)
Neoplasms/chemistry , Proto-Oncogene Proteins c-kit/chemistry , Animals , Baculoviridae/genetics , Binding Sites , Crystallography, X-Ray , Enzyme Activation , Humans , Ligands , Mice , Models, Molecular , Mutation , NIH 3T3 Cells , Neoplasms/enzymology , Neoplasms/genetics , Neoplasms/pathology , Protein Binding , Protein Folding , Protein Interaction Domains and Motifs , Protein Multimerization , Protein Structure, Secondary , Proto-Oncogene Proteins c-kit/genetics , Proto-Oncogene Proteins c-kit/metabolism , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Sf9 Cells , Spodoptera
12.
Mol Cell ; 59(3): 345-358, 2015 Aug 06.
Article in English | MEDLINE | ID: mdl-26145173

ABSTRACT

Many human cancers share similar metabolic alterations, including the Warburg effect. However, it remains unclear whether oncogene-specific metabolic alterations are required for tumor development. Here we demonstrate a "synthetic lethal" interaction between oncogenic BRAF V600E and a ketogenic enzyme 3-hydroxy-3-methylglutaryl-CoA lyase (HMGCL). HMGCL expression is upregulated in BRAF V600E-expressing human primary melanoma and hairy cell leukemia cells. Suppression of HMGCL specifically attenuates proliferation and tumor growth potential of human melanoma cells expressing BRAF V600E. Mechanistically, active BRAF upregulates HMGCL through an octamer transcription factor Oct-1, leading to increased intracellular levels of HMGCL product, acetoacetate, which selectively enhances binding of BRAF V600E but not BRAF wild-type to MEK1 in V600E-positive cancer cells to promote activation of MEK-ERK signaling. These findings reveal a mutation-specific mechanism by which oncogenic BRAF V600E "rewires" metabolic and cell signaling networks and signals through the Oct-1-HMGCL-acetoacetate axis to selectively promote BRAF V600E-dependent tumor development.


Subject(s)
Leukemia, Hairy Cell/metabolism , MAP Kinase Kinase 1/metabolism , Melanoma/metabolism , Octamer Transcription Factor-1/metabolism , Oxo-Acid-Lyases/metabolism , Proto-Oncogene Proteins B-raf/metabolism , Signal Transduction , Acetoacetates/metabolism , Cell Line, Tumor , Gene Expression Regulation, Neoplastic , Humans , Mutation , Proto-Oncogene Proteins B-raf/genetics , Up-Regulation
13.
Cell Mol Life Sci ; 79(12): 598, 2022 Nov 19.
Article in English | MEDLINE | ID: mdl-36401658

ABSTRACT

Signaling from the Rho family small GTPases controls a wide range of signaling outcomes. Key among the downstream effectors for many of the Rho GTPases are the p21-activated kinases, or PAK group. The PAK family comprises two types, the type I PAKs (PAK1, 2 and 3) and the type II PAKs (PAK4, 5 and 6), which have distinct structures and mechanisms of regulation. In this review, we discuss signal transduction from Rho GTPases with a focus on the type II PAKs. We discuss the role of PAKs in signal transduction pathways and selectivity of Rho GTPases for PAK family members. We consider the less well studied of the Rho GTPases and their PAK-related signaling. We then discuss the molecular basis for kinase domain recognition of substrates and for regulation of signaling. We conclude with a discussion of the role of PAKs in cross talk between Rho family small GTPases and the roles of PAKs in disease.


Subject(s)
p21-Activated Kinases , rho GTP-Binding Proteins , p21-Activated Kinases/genetics , p21-Activated Kinases/chemistry , p21-Activated Kinases/metabolism , rho GTP-Binding Proteins/metabolism , Signal Transduction
14.
PLoS Biol ; 17(3): e2006540, 2019 03.
Article in English | MEDLINE | ID: mdl-30897078

ABSTRACT

Specificity within protein kinase signaling cascades is determined by direct and indirect interactions between kinases and their substrates. While the impact of localization and recruitment on kinase-substrate targeting can be readily assessed, evaluating the relative importance of direct phosphorylation site interactions remains challenging. In this study, we examine the STE20 family of protein serine-threonine kinases to investigate basic mechanisms of substrate targeting. We used peptide arrays to define the phosphorylation site specificity for the majority of STE20 kinases and categorized them into four distinct groups. Using structure-guided mutagenesis, we identified key specificity-determining residues within the kinase catalytic cleft, including an unappreciated role for the kinase ß3-αC loop region in controlling specificity. Exchanging key residues between the STE20 kinases p21-activated kinase 4 (PAK4) and Mammalian sterile 20 kinase 4 (MST4) largely interconverted their phosphorylation site preferences. In cells, a reprogrammed PAK4 mutant, engineered to recognize MST substrates, failed to phosphorylate PAK4 substrates or to mediate remodeling of the actin cytoskeleton. In contrast, this mutant could rescue signaling through the Hippo pathway in cells lacking multiple MST kinases. These observations formally demonstrate the importance of catalytic site specificity for directing protein kinase signal transduction pathways. Our findings further suggest that phosphorylation site specificity is both necessary and sufficient to mediate distinct signaling outputs of STE20 kinases and imply broad applicability to other kinase signaling systems.


Subject(s)
Protein Serine-Threonine Kinases/metabolism , Signal Transduction/physiology , p21-Activated Kinases/metabolism , Catalysis , Cell Line , Humans , Mutagenesis/genetics , Mutagenesis/physiology , Phosphorylation/genetics , Phosphorylation/physiology , Protein Serine-Threonine Kinases/genetics , Signal Transduction/genetics , p21-Activated Kinases/genetics
15.
Mol Cell ; 53(1): 140-7, 2014 Jan 09.
Article in English | MEDLINE | ID: mdl-24374310

ABSTRACT

Eukaryotic protein kinases are generally classified as being either tyrosine or serine-threonine specific. Though not evident from inspection of their primary sequences, many serine-threonine kinases display a significant preference for serine or threonine as the phosphoacceptor residue. Here we show that a residue located in the kinase activation segment, which we term the "DFG+1" residue, acts as a major determinant for serine-threonine phosphorylation site specificity. Mutation of this residue was sufficient to switch the phosphorylation site preference for multiple kinases, including the serine-specific kinase PAK4 and the threonine-specific kinase MST4. Kinetic analysis of peptide substrate phosphorylation and crystal structures of PAK4-peptide complexes suggested that phosphoacceptor residue preference is not mediated by stronger binding of the favored substrate. Rather, favored kinase-phosphoacceptor combinations likely promote a conformation optimal for catalysis. Understanding the rules governing kinase phosphoacceptor preference allows kinases to be classified as serine or threonine specific based on their sequence.


Subject(s)
Peptides/chemistry , Protein Serine-Threonine Kinases/chemistry , p21-Activated Kinases/chemistry , Binding Sites , Crystallography, X-Ray , HEK293 Cells , Humans , Kinetics , Peptides/genetics , Peptides/metabolism , Phosphorylation , Protein Serine-Threonine Kinases/genetics , Protein Serine-Threonine Kinases/metabolism , Substrate Specificity/physiology , p21-Activated Kinases/genetics , p21-Activated Kinases/metabolism
16.
Mol Cell ; 53(4): 534-48, 2014 Feb 20.
Article in English | MEDLINE | ID: mdl-24486017

ABSTRACT

Mitochondrial pyruvate dehydrogenase complex (PDC) is crucial for glucose homeostasis in mammalian cells. The current understanding of PDC regulation involves inhibitory serine phosphorylation of pyruvate dehydrogenase (PDH) by PDH kinase (PDK), whereas dephosphorylation of PDH by PDH phosphatase (PDP) activates PDC. Here, we report that lysine acetylation of PDHA1 and PDP1 is common in epidermal growth factor (EGF)-stimulated cells and diverse human cancer cells. K321 acetylation inhibits PDHA1 by recruiting PDK1, and K202 acetylation inhibits PDP1 by dissociating its substrate PDHA1, both of which are important in promoting glycolysis in cancer cells and consequent tumor growth. Moreover, we identified mitochondrial ACAT1 and SIRT3 as the upstream acetyltransferase and deacetylase, respectively, of PDHA1 and PDP1, while knockdown of ACAT1 attenuates tumor growth. Furthermore, Y381 phosphorylation of PDP1 dissociates SIRT3 and recruits ACAT1 to PDC. Together, hierarchical, distinct posttranslational modifications act in concert to control molecular composition of PDC and contribute to the Warburg effect.


Subject(s)
Acetyl-CoA C-Acetyltransferase/metabolism , Pyruvate Dehydrogenase (Lipoamide)-Phosphatase/metabolism , Pyruvate Dehydrogenase (Lipoamide)/metabolism , Sirtuin 3/metabolism , Tyrosine/chemistry , Animals , Cell Line, Tumor , Cell Proliferation , Gene Expression Regulation, Enzymologic , Gene Expression Regulation, Neoplastic , Glycolysis , Humans , Lysine/chemistry , Male , Mice , Mice, Nude , Mitochondria/metabolism , Neoplasm Transplantation , Neoplasms/metabolism , Phosphorylation
17.
Mol Cell ; 55(4): 552-65, 2014 Aug 21.
Article in English | MEDLINE | ID: mdl-25042803

ABSTRACT

Although the oxidative pentose phosphate pathway is important for tumor growth, how 6-phosphogluconate dehydrogenase (6PGD) in this pathway is upregulated in human cancers is unknown. We found that 6PGD is commonly activated in EGF-stimulated cells and human cancer cells by lysine acetylation. Acetylation at K76 and K294 of 6PGD promotes NADP(+) binding to 6PGD and formation of active 6PGD dimers, respectively. Moreover, we identified DLAT and ACAT2 as upstream acetyltransferases of K76 and K294, respectively, and HDAC4 as the deacetylase of both sites. Expressing acetyl-deficient mutants of 6PGD in cancer cells significantly attenuated cell proliferation and tumor growth. This is due in part to reduced levels of 6PGD products ribulose-5-phosphate and NADPH, which led to reduced RNA and lipid biosynthesis as well as elevated ROS. Furthermore, 6PGD activity is upregulated with increased lysine acetylation in primary leukemia cells from human patients, providing mechanistic insights into 6PGD upregulation in cancer cells.


Subject(s)
Acetyl-CoA C-Acetyltransferase/metabolism , Dihydrolipoyllysine-Residue Acetyltransferase/metabolism , Histone Deacetylases/metabolism , Leukemia/pathology , Lung Neoplasms/pathology , Lysine/metabolism , Phosphogluconate Dehydrogenase/metabolism , Acetylation , Animals , Cell Line, Tumor , Gene Expression Regulation, Neoplastic , Humans , Leukemia/metabolism , Lung Neoplasms/metabolism , Mice , NADP/metabolism , Neoplasms, Experimental , Protein Binding/physiology , Protein Multimerization
18.
Proc Natl Acad Sci U S A ; 116(30): 15116-15121, 2019 07 23.
Article in English | MEDLINE | ID: mdl-31292255

ABSTRACT

Craniosynostosis (CS) is a frequent congenital anomaly featuring the premature fusion of 1 or more sutures of the cranial vault. Syndromic cases, featuring additional congenital anomalies, make up 15% of CS. While many genes underlying syndromic CS have been identified, the cause of many syndromic cases remains unknown. We performed exome sequencing of 12 syndromic CS cases and their parents, in whom previous genetic evaluations were unrevealing. Damaging de novo or transmitted loss of function (LOF) mutations were found in 8 genes that are highly intolerant to LOF mutation (P = 4.0 × 10-8); additionally, a rare damaging mutation in SOX11, which has a lower level of intolerance, was identified. Four probands had rare damaging mutations (2 de novo) in TFAP2B, a transcription factor that orchestrates neural crest cell migration and differentiation; this mutation burden is highly significant (P = 8.2 × 10-12). Three probands had rare damaging mutations in GLI2, SOX11, or GPC4, which function in the Hedgehog, BMP, and Wnt signaling pathways; other genes in these pathways have previously been implicated in syndromic CS. Similarly, damaging de novo mutations were identified in genes encoding the chromatin modifier KAT6A, and CTNNA1, encoding catenin α-1. These findings establish TFAP2B as a CS gene, have implications for assessing risk to subsequent children in these families, and provide evidence implicating other genes in syndromic CS. This high yield indicates the value of performing exome sequencing of syndromic CS patients when sequencing of known disease loci is unrevealing.


Subject(s)
Craniosynostoses/genetics , Glypicans/genetics , Histone Acetyltransferases/genetics , Mutation , Nuclear Proteins/genetics , SOXC Transcription Factors/genetics , Transcription Factor AP-2/genetics , Zinc Finger Protein Gli2/genetics , alpha Catenin/genetics , Adolescent , Child , Child, Preschool , Craniosynostoses/diagnosis , Craniosynostoses/pathology , Exome , Female , Gene Expression , Humans , Male , Pedigree , Risk Assessment , Signal Transduction , Skull/abnormalities , Skull/growth & development , Skull/metabolism , Exome Sequencing
19.
Proc Natl Acad Sci U S A ; 116(45): 22730-22736, 2019 11 05.
Article in English | MEDLINE | ID: mdl-31624127

ABSTRACT

The prognosis of advanced/recurrent cervical cancer patients remains poor. We analyzed 54 fresh-frozen and 15 primary cervical cancer cell lines, along with matched-normal DNA, by whole-exome sequencing (WES), most of which harboring Human-Papillomavirus-type-16/18. We found recurrent somatic missense mutations in 22 genes (including PIK3CA, ERBB2, and GNAS) and a widespread APOBEC cytidine deaminase mutagenesis pattern (TCW motif) in both adenocarcinoma (ACC) and squamous cell carcinomas (SCCs). Somatic copy number variants (CNVs) identified 12 copy number gains and 40 losses, occurring more often than expected by chance, with the most frequent events in pathways similar to those found from analysis of single nucleotide variants (SNVs), including the ERBB2/PI3K/AKT/mTOR, apoptosis, chromatin remodeling, and cell cycle. To validate specific SNVs as targets, we took advantage of primary cervical tumor cell lines and xenografts to preclinically evaluate the activity of pan-HER (afatinib and neratinib) and PIK3CA (copanlisib) inhibitors, alone and in combination, against tumors harboring alterations in the ERBB2/PI3K/AKT/mTOR pathway (71%). Tumors harboring ERBB2 (5.8%) domain mutations were significantly more sensitive to single agents afatinib or neratinib when compared to wild-type tumors in preclinical in vitro and in vivo models (P = 0.001). In contrast, pan-HER and PIK3CA inhibitors demonstrated limited in vitro activity and were only transiently effective in controlling in vivo growth of PIK3CA-mutated cervical cancer xenografts. Importantly, combinations of copanlisib and neratinib were highly synergistic, inducing long-lasting regression of tumors harboring alterations in the ERBB2/PI3K/AKT/mTOR pathway. These findings define the genetic landscape of cervical cancer, suggesting that a large subset of cervical tumors might benefit from existing ERBB2/PIK3CA/AKT/mTOR-targeted drugs.


Subject(s)
Class I Phosphatidylinositol 3-Kinases/genetics , Exome Sequencing , Mutation , Receptor, ErbB-2/genetics , Uterine Cervical Neoplasms/genetics , Uterine Cervical Neoplasms/therapy , Animals , Cell Line, Tumor , Combined Modality Therapy , DNA Copy Number Variations , Female , Heterografts , Humans , Polymorphism, Single Nucleotide , Uterine Cervical Neoplasms/pathology
20.
J Biol Chem ; 295(31): 10511-10521, 2020 07 31.
Article in English | MEDLINE | ID: mdl-32540970

ABSTRACT

The Src homology 2 (SH2) domain has a highly conserved architecture that recognizes linear phosphotyrosine motifs and is present in a wide range of signaling pathways across different evolutionary taxa. A hallmark of SH2 domains is the arginine residue in the conserved FLVR motif that forms a direct salt bridge with bound phosphotyrosine. Here, we solve the X-ray crystal structures of the C-terminal SH2 domain of p120RasGAP (RASA1) in its apo and peptide-bound form. We find that the arginine residue in the FLVR motif does not directly contact pTyr1087 of a bound phosphopeptide derived from p190RhoGAP; rather, it makes an intramolecular salt bridge to an aspartic acid. Unexpectedly, coordination of phosphotyrosine is achieved by a modified binding pocket that appears early in evolution. Using isothermal titration calorimetry, we find that substitution of the FLVR arginine R377A does not cause a significant loss of phosphopeptide binding, but rather a tandem substitution of R398A (SH2 position ßD4) and K400A (SH2 position ßD6) is required to disrupt the binding. These results indicate a hitherto unrecognized diversity in SH2 domain interactions with phosphotyrosine and classify the C-terminal SH2 domain of p120RasGAP as "FLVR-unique."


Subject(s)
Evolution, Molecular , p120 GTPase Activating Protein/chemistry , Crystallography, X-Ray , Humans , p120 GTPase Activating Protein/genetics , p120 GTPase Activating Protein/metabolism , src Homology Domains
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