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1.
Proc Natl Acad Sci U S A ; 121(31): e2400935121, 2024 Jul 30.
Article in English | MEDLINE | ID: mdl-39047034

ABSTRACT

The tumor suppressor von Hippel-Lindau, pVHL, is a multifaceted protein. One function is to dock to the hypoxia-inducible transcription factor (HIF) and recruit a larger protein complex that destabilizes HIF via ubiquitination, preventing angiogenesis and tumor development. pVHL also binds to the tumor suppressor p53 to activate specific p53 target genes. The oncogene Mdm2 impairs the formation of the p53-pVHL complex and activation of downstream genes by conjugating nedd8 to pVHL. While Mdm2 can impact p53 and pVHL, how pVHL may impact Mdm2 is unclear. Like p53 somatic mutations, point mutations are evident in pVHL that are common in renal clear cell carcinomas (RCC). In patients with RCC, Mdm2 levels are elevated, and we examined whether there was a relationship between Mdm2 and pVHL. TCGA and DepMap analysis revealed that mdm2 gene expression was elevated in RCC with vhl point mutations or copy number loss. In pVHL reconstituted or deleted isogenetically match RCC or MEF cell lines, Mdm2 was decreased in the presence of pVHL. Furthermore, through analysis using genetic and pharmacological approaches, we show that pVHL represses Mdm2 gene expression by blocking the MAPK-Ets signaling pathway and blocks Akt-mediated phosphorylation and stabilization of Mdm2. Mdm2 inhibition results in an increase in the p53-p21 pathway to impede cell growth. This finding shows how pVHL can indirectly impact the function of Mdm2 by regulating signaling pathways to restrict cell growth.


Subject(s)
Carcinoma, Renal Cell , Kidney Neoplasms , Proto-Oncogene Proteins c-mdm2 , Signal Transduction , Tumor Suppressor Protein p53 , Von Hippel-Lindau Tumor Suppressor Protein , Proto-Oncogene Proteins c-mdm2/metabolism , Proto-Oncogene Proteins c-mdm2/genetics , Humans , Von Hippel-Lindau Tumor Suppressor Protein/metabolism , Von Hippel-Lindau Tumor Suppressor Protein/genetics , Carcinoma, Renal Cell/metabolism , Carcinoma, Renal Cell/genetics , Carcinoma, Renal Cell/pathology , Tumor Suppressor Protein p53/metabolism , Tumor Suppressor Protein p53/genetics , Kidney Neoplasms/genetics , Kidney Neoplasms/metabolism , Kidney Neoplasms/pathology , Cell Line, Tumor , Gene Expression Regulation, Neoplastic
2.
Dalton Trans ; 53(9): 4278-4290, 2024 Feb 27.
Article in English | MEDLINE | ID: mdl-38345091

ABSTRACT

Oxyfluorides come in many different structures and are highly adaptable in composition, not least because of their mixed-anionic nature. Slight changes, unless specifically looked for, can easily go unnoticed. In this paper, we present two oxyfluorides, K3Mo2O5.6F3.4 and K3V2O3.3F5.7, synthesized under high-pressure/high-temperature conditions, and demonstrate the importance of careful analysis of composition, oxidation state and O/F anion distribution for an accurate description of oxyfluorides. Their crystal structures were determined by single-crystal X-ray diffraction and the transition metal cation valences analyzed by X-ray photoelectron spectroscopy (XPS). The O/F anion ratio was calculated using the principle of charge neutrality and the local distribution within the crystallographic framework was studied using bond valence (BV) and charge distribution (CHARDI) calculations. Madelung Part of Lattice Energy (MAPLE) calculations and magnetic measurements provide insight into phase stability and corroborate the mixed-valent nature of the compounds.

3.
PLoS One ; 18(11): e0291267, 2023.
Article in English | MEDLINE | ID: mdl-37939088

ABSTRACT

The chemical modification of RNA bases represents a ubiquitous activity that spans all domains of life. Pseudouridylation is the most common RNA modification and is observed within tRNA, rRNA, ncRNA and mRNAs. Pseudouridine synthase or 'PUS' enzymes include those that rely on guide RNA molecules and others that function as 'stand-alone' enzymes. Among the latter, several have been shown to modify mRNA transcripts. Although recent studies have defined the structural requirements for RNA to act as a PUS target, the mechanisms by which PUS1 recognizes these target sequences in mRNA are not well understood. Here we describe the crystal structure of yeast PUS1 bound to an RNA target that we identified as being a hot spot for PUS1-interaction within a model mRNA at 2.4 Å resolution. The enzyme recognizes and binds both strands in a helical RNA duplex, and thus guides the RNA containing the target uridine to the active site for subsequent modification of the transcript. The study also allows us to show the divergence of related PUS1 enzymes and their corresponding RNA target specificities, and to speculate on the basis by which PUS1 binds and modifies mRNA or tRNA substrates.


Subject(s)
Intramolecular Transferases , Saccharomyces cerevisiae , Saccharomyces cerevisiae/metabolism , RNA, Messenger/metabolism , RNA/metabolism , Intramolecular Transferases/genetics , Intramolecular Transferases/metabolism , RNA, Transfer/metabolism , Pseudouridine/metabolism
4.
ACS Pharmacol Transl Sci ; 6(11): 1692-1702, 2023 Nov 10.
Article in English | MEDLINE | ID: mdl-37974627

ABSTRACT

The N7-methyl guanosine cap structure is an essential 5' end modification of eukaryotic mRNA. It plays a critical role in many aspects of the life cycle of mRNA, including nuclear export, stability, and translation. Equipping synthetic transcripts with a 5' cap is paramount to the development of effective mRNA vaccines and therapeutics. Here, we report a simple and flexible workflow to selectively isolate and analyze structural features of the 5' end of an mRNA by means of DNA probe-directed enrichment with site-specific single-strand endoribonucleases. Specifically, we showed that the RNA cleavage by site-specific RNases can be effectively steered by a complementary DNA probe to recognition sites downstream of the probe-hybridized region, utilizing a flexible range of DNA probe designs. We applied this approach using human RNase 4 to isolate well-defined cleavage products from the 5' end of diverse uridylated and N1-methylpseudouridylated mRNA 5' end transcript sequences. hRNase 4 increases the precision of the RNA cleavage, reducing product heterogeneity while providing comparable estimates of capped products and their intermediaries relative to the widely used RNase H. Collectively, we demonstrated that this workflow ensures well-defined and predictable 5' end cleavage products suitable for analysis and relative quantitation of synthetic mRNA 5' cap structures by UHPLC-MS/MS.

5.
Nucleic Acids Res ; 50(18): e106, 2022 10 14.
Article in English | MEDLINE | ID: mdl-35871301

ABSTRACT

With the rapid growth of synthetic messenger RNA (mRNA)-based therapeutics and vaccines, the development of analytical tools for characterization of long, complex RNAs has become essential. Tandem liquid chromatography-mass spectrometry (LC-MS/MS) permits direct assessment of the mRNA primary sequence and modifications thereof without conversion to cDNA or amplification. It relies upon digestion of mRNA with site-specific endoribonucleases to generate pools of short oligonucleotides that are then amenable to MS-based sequence analysis. Here, we showed that the uridine-specific human endoribonuclease hRNase 4 improves mRNA sequence coverage, in comparison with the benchmark enzyme RNase T1, by producing a larger population of uniquely mappable cleavage products. We deployed hRNase 4 to characterize mRNAs fully substituted with 1-methylpseudouridine (m1Ψ) or 5-methoxyuridine (mo5U), as well as mRNAs selectively depleted of uridine-two key strategies to reduce synthetic mRNA immunogenicity. Lastly, we demonstrated that hRNase 4 enables direct assessment of the 5' cap incorporation into in vitro transcribed mRNA. Collectively, this study highlights the power of hRNase 4 to interrogate mRNA sequence, identity, and modifications by LC-MS/MS.


Subject(s)
Endoribonucleases/chemistry , RNA, Messenger/chemistry , Sequence Analysis, RNA/methods , Tandem Mass Spectrometry , Chromatography, Liquid/methods , DNA, Complementary , Humans , Oligonucleotides/analysis , RNA, Messenger/genetics , Ribonuclease T1/metabolism , Tandem Mass Spectrometry/methods
6.
RNA ; 28(6): 878-894, 2022 06.
Article in English | MEDLINE | ID: mdl-35351812

ABSTRACT

Quality control of mRNA represents an important regulatory mechanism for gene expression in eukaryotes. One component of this quality control is the nuclear retention and decay of misprocessed RNAs. Previously, we demonstrated that mature mRNAs containing a 5' splice site (5'SS) motif, which is typically found in misprocessed RNAs such as intronic polyadenylated (IPA) transcripts, are nuclear retained and degraded. Using high-throughput sequencing of cellular fractions, we now demonstrate that IPA transcripts require the zinc finger protein ZFC3H1 for their nuclear retention and degradation. Using reporter mRNAs, we demonstrate that ZFC3H1 promotes the nuclear retention of mRNAs with intact 5'SS motifs by sequestering them into nuclear speckles. Furthermore, we find that U1-70K, a component of the spliceosomal U1 snRNP, is also required for the nuclear retention of these reporter mRNAs and likely functions in the same pathway as ZFC3H1. Finally, we show that the disassembly of nuclear speckles impairs the nuclear retention of reporter mRNAs with 5'SS motifs. Our results highlight a splicing independent role of U1 snRNP and indicate that it works in conjunction with ZFC3H1 in preventing the nuclear export of misprocessed mRNAs by sequestering them into nuclear speckles.


Subject(s)
RNA Splice Sites , Ribonucleoprotein, U1 Small Nuclear , Nuclear Speckles , RNA Splice Sites/genetics , RNA Splicing , RNA, Messenger/genetics , RNA, Messenger/metabolism , RNA, Small Nuclear/genetics , RNA, Small Nuclear/metabolism , Ribonucleoprotein, U1 Small Nuclear/genetics , Ribonucleoprotein, U1 Small Nuclear/metabolism , Spliceosomes/genetics , Spliceosomes/metabolism
7.
Dermatol Ther (Heidelb) ; 12(4): 911-920, 2022 Apr.
Article in English | MEDLINE | ID: mdl-35279805

ABSTRACT

INTRODUCTION: The lifetime incidence of nail psoriasis in patients with psoriasis is 80-90%, with 23-27% of patients having nail psoriasis at any given time. Nail psoriasis is even more prevalent in patients with comorbid psoriatic arthritis. Complete psoriasis clearance, an achievable therapeutic goal, should ideally include the resolution of nail psoriasis. Here, we assessed simultaneous skin and nail clearance in patients with psoriasis across five head-to-head trials comparing ixekizumab with other biologics. METHODS: Data were assessed in patients with moderate-to-severe psoriasis (with or without psoriatic arthritis) with nail psoriasis at baseline from the IXORA-R, IXORA-S, UNCOVER-2, UNCOVER-3, and SPIRIT-H2H trials. Ixekizumab patients received IXEQ2W to week 12 and IXEQ4W beyond week 12. PASI 100 depicted complete skin clearance, and PGA-F 0 (IXORA-R) or NAPSI 0 (all other trials) depicted complete nail clearance. Treatment comparisons were evaluated using the Cochran-Mantel-Haenszel test. Non-responder imputation was used for missing data. RESULTS: Ixekizumab achieved significantly greater simultaneous skin and nail complete clearance than etanercept (UNCOVER-2: p < 0.001 and UNCOVER-3: p < 0.001) at week 12, demonstrating an efficacious and rapid response. Across all five head-to-head trials, ixekizumab achieved a high rate of simultaneous skin and nail clearance (range: 28.6-45.9% of patients) by week 24 that was maintained up to week 52 (range: 40.5-51.4% of patients). Ixekizumab achieved numerically greater simultaneous complete clearance than guselkumab at week 24 (p = 0.079), but statistically significant greater simultaneous clearance compared to ustekinumab (p < 0.001) and adalimumab (p = 0.006) at week 24 and week 52 (p < 0.001 and p = 0.007, respectively). CONCLUSION: In five head-to-head trials, ixekizumab-treated patients had higher rates of simultaneous complete skin and nail clearance compared to etanercept, guselkumab, ustekinumab, and adalimumab, thereby reinforcing ixekizumab's ability to achieve high levels of efficacy in multiple domains of psoriatic disease. TRIAL REGISTRATION: NCT01474512, NCT01597245, NCT01646177, NCT03573323, NCT02561806, and NCT03151551.

8.
J Biol Chem ; 298(4): 101751, 2022 04.
Article in English | MEDLINE | ID: mdl-35189146

ABSTRACT

The phosphorylated RNA polymerase II CTD interacting factor 1 (PCIF1) is a methyltransferase that adds a methyl group to the N6-position of 2'O-methyladenosine (Am), generating N6, 2'O-dimethyladenosine (m6Am) when Am is the cap-proximal nucleotide. In addition, PCIF1 has ancillary methylation activities on internal adenosines (both A and Am), although with much lower catalytic efficiency relative to that of its preferred cap substrate. The PCIF1 preference for 2'O-methylated Am over unmodified A nucleosides is due mainly to increased binding affinity for Am. Importantly, it was recently reported that PCIF1 can methylate viral RNA. Although some viral RNA can be translated in the absence of a cap, it is unclear what roles PCIF1 modifications may play in the functionality of viral RNAs. Here we show, using in vitro assays of binding and methyltransfer, that PCIF1 binds an uncapped 5'-Am oligonucleotide with approximately the same affinity as that of a cap analog (KM = 0.4 versus 0.3 µM). In addition, PCIF1 methylates the uncapped 5'-Am with activity decreased by only fivefold to sixfold compared with its preferred capped substrate. We finally discuss the relationship between PCIF1-catalyzed RNA methylation, shown here to have broader substrate specificity than previously appreciated, and that of the RNA demethylase fat mass and obesity-associated protein (FTO), which demonstrates PCIF1-opposing activities on capped RNAs.


Subject(s)
Adaptor Proteins, Signal Transducing , Nuclear Proteins , RNA Caps , Adaptor Proteins, Signal Transducing/metabolism , Adenosine/metabolism , Humans , Methyltransferases/genetics , Methyltransferases/metabolism , Nuclear Proteins/metabolism , Protein Binding , RNA Caps/genetics , RNA Caps/metabolism , RNA, Viral/metabolism
9.
Protein Expr Purif ; 190: 105987, 2022 02.
Article in English | MEDLINE | ID: mdl-34637916

ABSTRACT

Combinations of ribonucleases (RNases) are commonly used to digest RNA into oligoribonucleotide fragments prior to liquid chromatography-mass spectrometry (LC-MS) analysis. The distribution of the RNase target sequences or nucleobase sites within an RNA molecule is critical for achieving a high mapping coverage. Cusativin and MC1 are nucleotide-specific endoribonucleases encoded in the cucumber and bitter melon genomes, respectively. Their high specificity for cytidine (Cusativin) and uridine (MC1) make them ideal molecular biology tools for RNA modification mapping. However, heterogenous recombinant expression of either enzyme has been challenging because of their high toxicity to expression hosts and the requirement of posttranslational modifications. Here, we present two highly efficient and time-saving protocols that overcome these hurdles and enhance the expression and purification of these RNases. We first purified MC1 and Cusativin from bacteria by expressing and shuttling both enzymes to the periplasm as MBP-fusion proteins in T7 Express lysY/IqE. coli strain at low temperature. The RNases were enriched using amylose affinity chromatography, followed by a subsequent purification via a C-terminal 6xHIS tag. This fast, two-step purification allows for the purification of highly active recombinant RNases significantly surpassing yields reported in previous studies. In addition, we expressed and purified a Cusativin-CBD fusion enzyme in P. pastoris using chitin magnetic beads. Both Cusativin variants exhibited a similar sequence preference, suggesting that neither posttranslational modifications nor the epitope-tags have a substantial effect on the sequence specificity of the enzyme.


Subject(s)
Endoribonucleases , Escherichia coli , Gene Expression , Ribonucleases , Endoribonucleases/biosynthesis , Endoribonucleases/chemistry , Endoribonucleases/genetics , Endoribonucleases/isolation & purification , Escherichia coli/genetics , Escherichia coli/metabolism , Recombinant Proteins/biosynthesis , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/isolation & purification , Ribonucleases/biosynthesis , Ribonucleases/chemistry , Ribonucleases/genetics , Ribonucleases/isolation & purification
10.
Nucleic Acids Res ; 48(20): 11645-11663, 2020 11 18.
Article in English | MEDLINE | ID: mdl-33091126

ABSTRACT

While splicing has been shown to enhance nuclear export, it has remained unclear whether mRNAs generated from intronless genes use specific machinery to promote their export. Here, we investigate the role of the major nuclear pore basket protein, TPR, in regulating mRNA and lncRNA nuclear export in human cells. By sequencing mRNA from the nucleus and cytosol of control and TPR-depleted cells, we provide evidence that TPR is required for the efficient nuclear export of mRNAs and lncRNAs that are generated from short transcripts that tend to have few introns, and we validate this with reporter constructs. Moreover, in TPR-depleted cells reporter mRNAs generated from short transcripts accumulate in nuclear speckles and are bound to Nxf1. These observations suggest that TPR acts downstream of Nxf1 recruitment and may allow mRNAs to leave nuclear speckles and properly dock with the nuclear pore. In summary, our study provides one of the first examples of a factor that is specifically required for the nuclear export of intronless and intron-poor mRNAs and lncRNAs.


Subject(s)
Cell Nucleus/metabolism , Nuclear Pore Complex Proteins/physiology , Proto-Oncogene Proteins/physiology , RNA, Long Noncoding/metabolism , RNA, Messenger/metabolism , Active Transport, Cell Nucleus , Cell Line , Cytoplasm/metabolism , Humans , Introns , Nucleotide Motifs , RNA Processing, Post-Transcriptional , RNA Stability , RNA, Messenger/chemistry
11.
Space Sci Rev ; 216(5): 100, 2020.
Article in English | MEDLINE | ID: mdl-32764836

ABSTRACT

TRAPPIST-1 is a fantastic nearby (∼39.14 light years) planetary system made of at least seven transiting terrestrial-size, terrestrial-mass planets all receiving a moderate amount of irradiation. To date, this is the most observationally favourable system of potentially habitable planets known to exist. Since the announcement of the discovery of the TRAPPIST-1 planetary system in 2016, a growing number of techniques and approaches have been used and proposed to characterize its true nature. Here we have compiled a state-of-the-art overview of all the observational and theoretical constraints that have been obtained so far using these techniques and approaches. The goal is to get a better understanding of whether or not TRAPPIST-1 planets can have atmospheres, and if so, what they are made of. For this, we surveyed the literature on TRAPPIST-1 about topics as broad as irradiation environment, planet formation and migration, orbital stability, effects of tides and Transit Timing Variations, transit observations, stellar contamination, density measurements, and numerical climate and escape models. Each of these topics adds a brick to our understanding of the likely-or on the contrary unlikely-atmospheres of the seven known planets of the system. We show that (i) Hubble Space Telescope transit observations, (ii) bulk density measurements comparison with H2-rich planets mass-radius relationships, (iii) atmospheric escape modelling, and (iv) gas accretion modelling altogether offer solid evidence against the presence of hydrogen-dominated-cloud-free and cloudy-atmospheres around TRAPPIST-1 planets. This means that the planets are likely to have either (i) a high molecular weight atmosphere or (ii) no atmosphere at all. There are several key challenges ahead to characterize the bulk composition(s) of the atmospheres (if present) of TRAPPIST-1 planets. The main one so far is characterizing and correcting for the effects of stellar contamination. Fortunately, a new wave of observations with the James Webb Space Telescope and near-infrared high-resolution ground-based spectrographs on existing very large and forthcoming extremely large telescopes will bring significant advances in the coming decade.

13.
Oncogene ; 39(29): 5228-5239, 2020 07.
Article in English | MEDLINE | ID: mdl-32555333

ABSTRACT

Mutations in the tumor suppressor TP53 are rare in renal cell carcinomas. p53 is a key factor for inducing antiangiogenic genes and RCC are highly vascularized, which suggests that p53 is inactive in these tumors. One regulator of p53 is the Mdm2 oncogene, which is correlated with high-grade, metastatic tumors. However, the sole activity of Mdm2 is not just to regulate p53, but it can also function independent of p53 to regulate the early stages of metastasis. Here, we report that the oncoprotein Mdm2 can bind directly to the tumor suppressor VHL, and conjugate nedd8 to VHL within a region that is important for the p53-VHL interaction. Nedd8 conjugated VHL is unable to bind to p53 thereby preventing the induction of antiangiogenic factors. These results highlight a previously unknown oncogenic function of Mdm2 during the progression of cancer to promote angiogenesis through the regulation of VHL. Thus, the Mdm2-VHL interaction represents a pathway that impacts tumor angiogenesis.


Subject(s)
Angiogenesis Inhibitors/therapeutic use , Proto-Oncogene Proteins c-mdm2/metabolism , Von Hippel-Lindau Tumor Suppressor Protein/metabolism , Angiogenesis Inhibitors/pharmacology , Animals , Cell Line, Tumor , Humans , Mice , Transfection
14.
Cell Rep ; 31(8): 107693, 2020 05 26.
Article in English | MEDLINE | ID: mdl-32460013

ABSTRACT

The mammalian mRNA nuclear export process is thought to terminate at the cytoplasmic face of the nuclear pore complex through ribonucleoprotein remodeling. We conduct a stringent affinity-purification mass-spectrometry-based screen of the physical interactions of human RNA-binding E3 ubiquitin ligases. The resulting protein-interaction network reveals interactions between the RNA-binding E3 ubiquitin ligase MKRN2 and GLE1, a DEAD-box helicase activator implicated in mRNA export termination. We assess MKRN2 epistasis with GLE1 in a zebrafish model. Morpholino-mediated knockdown or CRISPR/Cas9-based knockout of MKRN2 partially rescue retinal developmental defects seen upon GLE1 depletion, consistent with a functional association between GLE1 and MKRN2. Using ribonomic approaches, we show that MKRN2 binds selectively to the 3' UTR of a diverse subset of mRNAs and that nuclear export of MKRN2-associated mRNAs is enhanced upon knockdown of MKRN2. Taken together, we suggest that MKRN2 interacts with GLE1 to selectively regulate mRNA nuclear export and retinal development.


Subject(s)
Mass Spectrometry/methods , RNA, Messenger/metabolism , RNA-Binding Proteins/metabolism , Retina/physiopathology , Ribonucleoproteins/metabolism , Zebrafish Proteins/metabolism , Animals , Humans , Zebrafish
15.
Nat Commun ; 10(1): 5649, 2019 12 11.
Article in English | MEDLINE | ID: mdl-31827082

ABSTRACT

Clonal hematopoiesis of indeterminate potential (CHIP) increases with age and is associated with increased risks of hematological malignancies. While TP53 mutations have been identified in CHIP, the molecular mechanisms by which mutant p53 promotes hematopoietic stem and progenitor cell (HSPC) expansion are largely unknown. Here we discover that mutant p53 confers a competitive advantage to HSPCs following transplantation and promotes HSPC expansion after radiation-induced stress. Mechanistically, mutant p53 interacts with EZH2 and enhances its association with the chromatin, thereby increasing the levels of H3K27me3 in genes regulating HSPC self-renewal and differentiation. Furthermore, genetic and pharmacological inhibition of EZH2 decreases the repopulating potential of p53 mutant HSPCs. Thus, we uncover an epigenetic mechanism by which mutant p53 drives clonal hematopoiesis. Our work will likely establish epigenetic regulator EZH2 as a novel therapeutic target for preventing CHIP progression and treating hematological malignancies with TP53 mutations.


Subject(s)
Epigenesis, Genetic , Hematologic Diseases/metabolism , Hematopoiesis , Tumor Suppressor Protein p53/genetics , Tumor Suppressor Protein p53/metabolism , Animals , Enhancer of Zeste Homolog 2 Protein/genetics , Enhancer of Zeste Homolog 2 Protein/metabolism , Female , Hematologic Diseases/genetics , Hematologic Diseases/physiopathology , Hematopoietic Stem Cells/cytology , Hematopoietic Stem Cells/metabolism , Histones/genetics , Histones/metabolism , Humans , Male , Methylation , Mice, Inbred C57BL , Mutation , Protein Binding
16.
Science ; 365(6453): 587-590, 2019 08 09.
Article in English | MEDLINE | ID: mdl-31395782

ABSTRACT

In 2017, western Canadian wildfires injected smoke into the stratosphere that was detectable by satellites for more than 8 months. The smoke plume rose from 12 to 23 kilometers within 2 months owing to solar heating of black carbon, extending the lifetime and latitudinal spread. Comparisons of model simulations to the rate of observed lofting indicate that 2% of the smoke mass was black carbon. The observed smoke lifetime in the stratosphere was 40% shorter than calculated with a standard model that does not consider photochemical loss of organic carbon. Photochemistry is represented by using an empirical ozone-organics reaction probability that matches the observed smoke decay. The observed rapid plume rise, latitudinal spread, and photochemical reactions provide new insights into potential global climate impacts from nuclear war.


Subject(s)
Smoke , Stratospheric Ozone/analysis , Wildfires , Canada
17.
Nat Methods ; 16(8): 737-742, 2019 08.
Article in English | MEDLINE | ID: mdl-31308550

ABSTRACT

Protein complexes are key macromolecular machines of the cell, but their description remains incomplete. We and others previously reported an experimental strategy for global characterization of native protein assemblies based on chromatographic fractionation of biological extracts coupled to precision mass spectrometry analysis (chromatographic fractionation-mass spectrometry, CF-MS), but the resulting data are challenging to process and interpret. Here, we describe EPIC (elution profile-based inference of complexes), a software toolkit for automated scoring of large-scale CF-MS data to define high-confidence multi-component macromolecules from diverse biological specimens. As a case study, we used EPIC to map the global interactome of Caenorhabditis elegans, defining 612 putative worm protein complexes linked to diverse biological processes. These included novel subunits and assemblies unique to nematodes that we validated using orthogonal methods. The open source EPIC software is freely available as a Jupyter notebook packaged in a Docker container (https://hub.docker.com/r/baderlab/bio-epic/).


Subject(s)
Caenorhabditis elegans Proteins/metabolism , Caenorhabditis elegans/metabolism , Multiprotein Complexes/isolation & purification , Multiprotein Complexes/metabolism , Protein Interaction Mapping , Proteome/analysis , Software , Animals , Caenorhabditis elegans Proteins/isolation & purification
18.
Am J Clin Oncol ; 42(3): 247-252, 2019 03.
Article in English | MEDLINE | ID: mdl-30724781

ABSTRACT

OBJECTIVES: The main objectives of this study were to prospectively evaluate the safety and efficacy of stereotactic body radiation therapy (SBRT) in the neoadjuvant setting for resectable or borderline resectable pancreatic cancer. MATERIALS AND METHODS: Eighteen patients were enrolled from November 2014 to June 2017. Following 3 cycles of chemotherapy, SBRT was delivered to the tumor and abutting vessel and a 3 mm planning target volume (PTV) margin to 33 Gy (6.6 Gy×5) with an optional elective PTV to 25 Gy (5 Gy×5) customized to the nodal space and mesenteric vessels. The primary endpoint is ≥grade 3 acute and late gastrointestinal toxicity. RESULTS: Fifteen patients had borderline resectable tumors due to arterial abutment (n=7) or superior mesenteric vein encasement (n=8); 3 patients had resectable tumors. There were no ≥grade 3 acute or late gastrointestinal events. Following SBRT, surgery was performed in 12 patients (67%) with 11 (92%) R0 resections. The median overall survival and progression-free survival was 21 months (95% CI: 18-29) and 11 months (95% CI: 8.4-16). Progression occurred in 83% (10/12) of resected patients (distant [n=4, 40%], local-only [n=4, 40%], and local and distant [n=2, 20%]). The cumulative incidence of local failure (LF) at 12 months from resection was 50% (95% CI: 20-80). All LF were outside to the PTV33. CONCLUSIONS: Neoadjuvant SBRT was well tolerated, however LFs were predominantly observed outside the PTV33 volume that would have been covered with conventional RT volumes. The durability of local control after SBRT in the neoadjuvant setting merits examination relative to chemoradiation before incorporation into routine practice.


Subject(s)
Antineoplastic Combined Chemotherapy Protocols/therapeutic use , Neoadjuvant Therapy/mortality , Neoplasm Recurrence, Local/pathology , Pancreatic Neoplasms/pathology , Radiosurgery/mortality , Aged , Aged, 80 and over , Combined Modality Therapy , Dose Fractionation, Radiation , Female , Follow-Up Studies , Humans , Male , Middle Aged , Neoplasm Recurrence, Local/mortality , Neoplasm Recurrence, Local/therapy , Pancreatic Neoplasms/mortality , Pancreatic Neoplasms/therapy , Prospective Studies , Survival Rate , Treatment Failure
19.
Sci Signal ; 11(524)2018 04 03.
Article in English | MEDLINE | ID: mdl-29615516

ABSTRACT

The transcription factors p53 and p73 are critical to the induction of apoptotic cell death, particularly in response to cell stress that activates c-Jun N-terminal kinase (JNK). Mutations in the DNA-binding domain of p53, which are commonly seen in cancers, result in conformational changes that enable p53 to interact with and inhibit p73, thereby suppressing apoptosis. In contrast, wild-type p53 reportedly does not interact with p73. We found that JNK-mediated phosphorylation of Thr81 in the proline-rich domain (PRD) of p53 enabled wild-type p53, as well as mutant p53, to form a complex with p73. Structural algorithms predicted that phosphorylation of Thr81 exposes the DNA-binding domain in p53 to enable its binding to p73. The dimerization of wild-type p53 with p73 facilitated the expression of apoptotic target genes [such as those encoding p53-up-regulated modulator of apoptosis (PUMA) and Bcl-2-associated X protein (BAX)] and, subsequently, the induction of apoptosis in response to JNK activation by cell stress in various cells. Thus, JNK phosphorylation of mutant and wild-type p53 promotes the formation of a p53/p73 complex that determines cell fate: apoptosis in the context of wild-type p53 or cell survival in the context of the mutant. These findings refine our current understanding of both the mechanistic links between p53 and p73 and the functional role for Thr81 phosphorylation.


Subject(s)
Apoptosis , JNK Mitogen-Activated Protein Kinases/metabolism , Tumor Protein p73/metabolism , Tumor Suppressor Protein p53/metabolism , Apoptosis Regulatory Proteins/genetics , Apoptosis Regulatory Proteins/metabolism , Binding Sites/genetics , Cell Line, Tumor , Cell Survival , Humans , JNK Mitogen-Activated Protein Kinases/chemistry , JNK Mitogen-Activated Protein Kinases/genetics , Models, Molecular , Mutation , Phosphorylation , Protein Binding , Protein Conformation , Signal Transduction , Tumor Protein p73/chemistry , Tumor Protein p73/genetics , Tumor Suppressor Protein p53/chemistry , Tumor Suppressor Protein p53/genetics
20.
Oncotarget ; 8(61): 104455-104466, 2017 Nov 28.
Article in English | MEDLINE | ID: mdl-29262653

ABSTRACT

Mouse double minute 2 (Mdm2) and MdmX dimerize in response to low levels of genotoxic stress to function in a ubiquitinating complex, which signals for destabilization of p53. Under growth conditions, Mdm2 functions as a neddylating ligase, but the importance and extent of MdmX involvement in this process are largely unknown. Here we show that when Mdm2 functions as a neddylating enzyme, MdmX is stabilized. Furthermore, we demonstrate that under growth conditions, MdmX enhances the neddylation activity of Mdm2 on p53 and is a substrate for neddylation itself. Importantly, MdmX knockdown in MCF-7 breast cancer cells resulted in diminished neddylated p53, suggesting that MdmX is important for Mdm2-mediated neddylation. Supporting this finding, the lack of MdmX in transient assays or in p53/MdmX-/- MEFs results in decreased or altered neddylation of p53 respectively; therefore, MdmX is a critical component of the Mdm2-mediated neddylating complex. c-Src is the upstream activator of this Mdm2-MdmX neddylating pathway and loss of Src signaling leads to the destabilization of MdmX that is dependent on the RING (Really Interesting New Gene) domain of MdmX. Treatment with a small molecule inhibitor of neddylation, MLN4924, results in the activation of Ataxia Telangiectasia Mutated (ATM). ATM phosphorylates Mdm2, converting Mdm2 to a ubiquitinating enzyme which leads to the destabilization of MdmX. These data show how distinct signaling pathways engage neddylating or ubiquitinating activities and impact the Mdm2-MdmX axis.

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