Your browser doesn't support javascript.
loading
Show: 20 | 50 | 100
Results 1 - 20 de 65
Filter
1.
Nat Chem ; 16(5): 709-716, 2024 May.
Article in English | MEDLINE | ID: mdl-38528106

ABSTRACT

Hydrogen evolution is an important fuel-generating reaction that has been subject to mechanistic debate about the roles of monometallic and bimetallic pathways. The molecular iridium catalysts in this study undergo photoelectrochemical dihydrogen (H2) evolution via a bimolecular mechanism, providing an opportunity to understand the factors that promote bimetallic H-H coupling. Covalently tethered diiridium catalysts evolve H2 from neutral water faster than monometallic catalysts, even at lower overpotential. The unexpected origin of this improvement is non-covalent supramolecular self-assembly into nanoscale aggregates that efficiently harvest light and form H-H bonds. Monometallic catalysts containing long-chain alkane substituents leverage the self-assembly to evolve H2 from neutral water at low overpotential and with rates close to the expected maximum for this light-driven water splitting reaction. Design parameters for holding multiple catalytic sites in close proximity and tuning catalyst microenvironments emerge from this work.

2.
Proc Natl Acad Sci U S A ; 120(46): e2214334120, 2023 Nov 14.
Article in English | MEDLINE | ID: mdl-37931104

ABSTRACT

Civil infrastructure will be essential to face the interlinked existential threats of climate change and rising resource demands while ensuring a livable Anthropocene for all. However, conventional infrastructure planning largely neglects the contributions and maintenance of Earth's ecological life support systems, which provide irreplaceable services supporting human well-being. The stability and performance of these services depend on biodiversity, but conventional infrastructure practices, narrowly focused on controlling natural capital, have inadvertently degraded biodiversity while perpetuating social inequities. Here, we envision a new infrastructure paradigm wherein biodiversity and ecosystem services are a central objective of civil engineering. In particular, we reimagine infrastructure practice such that 1) ecosystem integrity and species conservation are explicit objectives from the outset of project planning; 2) infrastructure practices integrate biodiversity into diverse project portfolios along a spectrum from conventional to nature-based solutions and natural habitats; 3) ecosystem functions reinforce and enhance the performance and lifespan of infrastructure assets; and 4) civil engineering promotes environmental justice by counteracting legacies of social inequity in infrastructure development and nature conservation. This vision calls for a fundamental rethinking of the standards, practices, and mission of infrastructure development agencies and a broadening of scope for conservation science. We critically examine the legal and professional precedents for this paradigm shift, as well as the moral and economic imperatives for manifesting equitable infrastructure planning that mainstreams biodiversity and nature's benefits to people. Finally, we set an applied research agenda for supporting this vision and highlight financial, professional, and policy pathways for achieving it.


Subject(s)
Biodiversity , Ecosystem , Humans , Climate Change , Conservation of Natural Resources
3.
Expert Rev Proteomics ; 20(11): 251-266, 2023.
Article in English | MEDLINE | ID: mdl-37787106

ABSTRACT

INTRODUCTION: Continuous advances in mass spectrometry (MS) technologies have enabled deeper and more reproducible proteome characterization and a better understanding of biological systems when integrated with other 'omics data. Bioinformatic resources meeting the analysis requirements of increasingly complex MS-based proteomic data and associated multi-omic data are critically needed. These requirements included availability of software that would span diverse types of analyses, scalability for large-scale, compute-intensive applications, and mechanisms to ease adoption of the software. AREAS COVERED: The Galaxy ecosystem meets these requirements by offering a multitude of open-source tools for MS-based proteomics analyses and applications, all in an adaptable, scalable, and accessible computing environment. A thriving global community maintains these software and associated training resources to empower researcher-driven analyses. EXPERT OPINION: The community-supported Galaxy ecosystem remains a crucial contributor to basic biological and clinical studies using MS-based proteomics. In addition to the current status of Galaxy-based resources, we describe ongoing developments for meeting emerging challenges in MS-based proteomic informatics. We hope this review will catalyze increased use of Galaxy by researchers employing MS-based proteomics and inspire software developers to join the community and implement new tools, workflows, and associated training content that will add further value to this already rich ecosystem.


Subject(s)
Proteomics , Humans , Computational Biology/methods , Mass Spectrometry/methods , Proteomics/methods , Software
4.
Metabolites ; 13(10)2023 Oct 18.
Article in English | MEDLINE | ID: mdl-37887414

ABSTRACT

Hypoglycemia occurs frequently in people with type 1 and type 2 diabetes. Hypoglycemia activates the counter-regulatory response. Besides peripheral glucose sensors located in the pancreas, mouth, gastrointestinal tract, portal vein, and carotid body, many brain regions also contain glucose-sensing neurons that detect this fall in glucose. The autonomic nervous system innervates the heart, and during hypoglycemia, can cause many changes. Clinical and animal studies have revealed changes in electrocardiograms during hypoglycemia. Cardiac repolarization defects (QTc prolongation) occur during moderate levels of hypoglycemia. When hypoglycemia is severe, it can be fatal. Cardiac arrhythmias are thought to be the major mediator of sudden death due to severe hypoglycemia. Both the sympathetic and parasympathetic nervous systems of the brain have been implicated in regulating these arrhythmias. Besides cardiac arrhythmias, hypoglycemia can have profound changes in the heart and most of these changes are exacerbated in the setting of diabetes. A better understanding of how the brain regulates cardiac changes during hypoglycemia will allow for better therapeutic intervention to prevent cardiovascular death associated with hypoglycemia in people with diabetes. The aim of this paper is to provide a narrative review of what is known in the field regarding how the brain regulates the heart during hypoglycemia.

5.
Chemistry ; 29(29): e202300486, 2023 May 22.
Article in English | MEDLINE | ID: mdl-36892530

ABSTRACT

The photoreactivity of d0 metal dioxo complexes in activating C-H bonds has been recently studied.[1-3] We have previously reported that MoO2 Cl2 (bpy-t Bu) is an effective platform for light initiated C-H activation with unique product selectivity for the overall functionalization.[1] Herein we expand on these studies and report the synthesis and photoreactivity of several new Mo(VI) dioxo complexes with the general formula MoO2 (X)2 (NN); where X=F- , Cl- , Br- , CH3 - , PhO- , t BuO- and NN=2,2'-bipyridine (bpy) or 4,4'-tert-butyl-2,2'bipyridine (bpy-t Bu). Among these compounds, MoO2 Cl2 (bpy-t Bu) and MoO2 Br2 (bpy-t Bu) are able to participate in bimolecular photoreactivity with several substrates containing C-H bonds of various types such as allyls, benzyls, aldehydes (RCHO) and alkanes. MoO2 (CH3 )2 bpy and MoO2 (PhO)2 bpy do not participate in bimolecular photoreactions and instead they undergo photodecompositions. Computational studies indicate that the nature of the HOMO and LUMO is critical in supporting photoreactivity, with access to an LMCT (bpy→Mo) being necessary for tractable hydrocarbon functionalization.

6.
J Am Chem Soc ; 144(44): 20472-20483, 2022 11 09.
Article in English | MEDLINE | ID: mdl-36305785

ABSTRACT

MoO2Cl2(bpy-tBu) (1) is shown to be a potent one-electron oxidant upon irradiation with 365 nm light in various solvents, while being a weak two-electron oxidant in the dark. Complex 1 is characterized to activate various types of C-H bonds photochemically, including allylic and benzylic positions as well as alkanes and aldehydes. In all of these oxidations, 1 ultimately forms a bimetallic Mo(V)/Mo(V) species with a µ-oxo ligand (2). Depending on the substrate, the major organic product is identified as either an oxygenated or a C-C coupled (homodimerized) compound along with a minor chlorinated species. The product selectivity is proposed to be dependent upon the relative values between the bond dissociation enthalpy (BDE) of a potentially new C-OH bond within the product versus the BDE of a Mo-OH motif within a Mo(V)O(OH) intermediate. Based on this, we can estimate the BDE for Mo-OH to be 83-93 kcal/mol. Mechanistic studies suggest that the C-H activation occurs via a net hydrogen atom transfer (HAT) from 1* occurring either asynchronously or via a stepwise electron-proton transfer (ET-PT) process. Complex 2 is further demonstrated to reform dioxo 1 in the presence of chemical oxidants.


Subject(s)
Hydrogen , Protons , Hydrogen/chemistry , Molybdenum/chemistry , Oxidation-Reduction , Oxidants/chemistry
7.
Structure ; 30(9): 1269-1284.e6, 2022 09 01.
Article in English | MEDLINE | ID: mdl-35716664

ABSTRACT

RING-between-RING (RBR) E3 ligases mediate ubiquitin transfer through an obligate E3-ubiquitin thioester intermediate prior to substrate ubiquitination. Although RBRs share a conserved catalytic module, substrate recruitment mechanisms remain enigmatic, and the relevant domains have yet to be identified for any member of the class. Here we characterize the interaction between the auto-inhibited RBR, HHARI (AriH1), and its target protein, 4EHP, using a combination of XL-MS, HDX-MS, NMR, and biochemical studies. The results show that (1) a di-aromatic surface on the catalytic HHARI Rcat domain forms a binding platform for substrates and (2) a phosphomimetic mutation on the auto-inhibitory Ariadne domain of HHARI promotes release and reorientation of Rcat for transthiolation and substrate modification. The findings identify a direct binding interaction between a RING-between-RING ligase and its substrate and suggest a general model for RBR substrate recognition.


Subject(s)
Cullin Proteins , Ubiquitin , Catalytic Domain , Cullin Proteins/metabolism , Ubiquitin/metabolism , Ubiquitin-Protein Ligases/chemistry , Ubiquitination
8.
Inorg Chem ; 61(18): 6742-6749, 2022 May 09.
Article in English | MEDLINE | ID: mdl-35471920

ABSTRACT

Iron nitride (Fe3N) and iron carbide (Fe3C) nanoparticles can be prepared via sol-gel synthesis. While sol-gel methods are simple, it can be difficult to control the crystalline composition, i.e., to achieve a Rietveld-pure product. In a previous in situ synchrotron study of the sol-gel synthesis of Fe3N/Fe3C, we showed that the reaction proceeds as follows: Fe3O4 → FeOx → Fe3N → Fe3C. There was considerable overlap between the different phases, but we were unable to ascertain whether this was due to the experimental setup (side-on heating of a quartz capillary which could lead to thermal gradients) or whether individual particle reactions proceed at different rates. In this paper, we use in situ wide- and small-angle X-ray scattering (wide-angle X-ray scattering (WAXS) and small-angle X-ray scattering (SAXS)) to demonstrate that the overlapping phases are indeed due to variable reaction rates. While the initial oxide nanoparticles have a small range of diameters, the size range expands considerably and very rapidly during the oxide-nitride transition. This has implications for the isolation of Rietveld-pure Fe3N, and in an extensive laboratory study, we were indeed unable to isolate phase-pure Fe3N. However, we made the surprising discovery that Rietveld-pure Fe3C nanoparticles can be produced at 500 °C with a sufficient furnace dwell time. This is considerably lower than the previous reports of the sol-gel synthesis of Fe3C nanoparticles.

9.
Cureus ; 14(2): e21954, 2022 Feb.
Article in English | MEDLINE | ID: mdl-35282502

ABSTRACT

Background & Aim Skin cancer is the most common cancer around the world. Regional differences have been reported affecting the demographics and the prevalence of non-melanoma skin cancers; furthermore, non-melanoma skin cancers are believed to be underreported. In this study, we aim to identify and highlight any possible significant characteristics of skin cancer in our rural center in Scotland's Highlands. Methods This is a retrospective study analyzing and reporting cancerous skin lesions excision rates among all skin lesions excised and their characteristics in our rural center for one year. Clinical and histopathological data for patients attending our services for suspicious skin lesions excision were collected. Data included the patient's age, gender, lesion's diagnosis, site, size, color, borders, resection edges, recurrence, and complications. A database was created creating two cohorts: cancer and non-cancerous lesions groups, both cohorts' data was compared using student T-tests and Z-tests. P-values were considered statistically significant if < 0.5, Overall data was analyzed revealing trends and end results. Results From December 2019 to December 2020, 96 patients underwent skin lesions excision, 30% were cancerous. Basal cell carcinoma was the most common malignant growth standing for 76.7% of all malignant lesions excised. Squamous cell carcinoma and melanoma were found in 20% and 3.3% of patients with malignant lesions, respectively. Out of the total, 76% of cancerous lesions were in males. The most common site was head and neck (58.8%). High-risk lesions were the ones on the head and neck (P= 0.00988), in the elderly over 74.5 years (P= 0.000037), and males (P= 0.001). Conclusion Basal cell carcinoma was the most common malignant lesion. Elderly men with lesions on the head and neck had higher risks for cancer. Further clarification may be required with larger multi-center studies involving general practitioners, which might help identify regional variations.

10.
ACS Omega ; 6(40): 25860-25875, 2021 Oct 12.
Article in English | MEDLINE | ID: mdl-34660949

ABSTRACT

Information of the chemical, mechanical, and electrical properties of materials can be obtained using force volume mapping (FVM), a measurement mode of scanning probe microscopy (SPM). Protocols have been developed with FVM for a broad range of materials, including polymers, organic films, inorganic materials, and biological samples. Multiple force measurements are acquired with the FVM mode within a defined 3D volume of the sample to map interactions (i.e., chemical, electrical, or physical) between the probe and the sample. Forces of adhesion, elasticity, stiffness, deformation, chemical binding interactions, viscoelasticity, and electrical properties have all been mapped at the nanoscale with FVM. Subsequently, force maps can be correlated with features of topographic images for identifying certain chemical groups presented at a sample interface. The SPM tip can be coated to investigate-specific reactions; for example, biological interactions can be probed when the tip is coated with biomolecules such as for recognition of ligand-receptor pairs or antigen-antibody interactions. This review highlights the versatility and diverse measurement protocols that have emerged for studies applying FVM for the analysis of material properties at the nanoscale.

11.
Inorg Chem ; 60(10): 7062-7069, 2021 May 17.
Article in English | MEDLINE | ID: mdl-33944556

ABSTRACT

The sol-gel synthesis of iron carbide (Fe3C) nanoparticles proceeds through multiple intermediate crystalline phases, including iron oxide (FeOx) and iron nitride (Fe3N). The control of particle size is challenging, and most methods produce polydisperse Fe3C nanoparticles of 20-100 nm in diameter. Given the wide range of applications of Fe3C nanoparticles, it is essential that we understand the evolution of the system during the synthesis. Here, we report an in situ synchrotron total scattering study of the formation of Fe3C from gelatin and iron nitrate sol-gel precursors. A pair distribution function analysis reveals a dramatic increase in local ordering between 300 and 350 °C, indicating rapid nucleation and growth of iron oxide nanoparticles. The oxide intermediate remains stable until the emergence of Fe3N at 600 °C. Structural refinement of the high-temperature data revealed local distortion of the NFe6 octahedra, resulting in a change in the twist angle suggestive of a carbonitride intermediate. This work demonstrates the importance of intermediate phases in controlling the particle size of a sol-gel product. It is also, to the best of our knowledge, the first example of in situ total scattering analysis of a sol-gel system.

12.
Chem Sci ; 11(25): 6442-6449, 2020 Mar 06.
Article in English | MEDLINE | ID: mdl-34094109

ABSTRACT

The photochemistry of metal hydride complexes is dominated by H2 evolution, limiting access to reductive transformations based on photochemical hydride transfer. In this article, the innate H2 evolution photochemistry of the iridium hydride complexes [Cp*Ir(bpy-OMe)H]+ (1, bpy-OMe = 4,4'-dimethoxy-2,2'-bipyridine) and [Cp*Ir(bpy)H]+ (2, bpy = 2,2'-bipyridine) is diverted towards photochemical hydrodechlorination. Net hydride transfer from 1 and 2 to dichloromethane produces chloromethane with high selectivity and exceptional photochemical quantum yield (Φ ≤ 1.3). Thermodynamic and kinetic mechanistic studies are consistent with a non-radical-chain reaction sequence initiated by "self-quenching" electron transfer between excited state and ground state hydride complexes, followed by proton-coupled electron transfer (PCET) hydrodechlorination that outcompetes H-H coupling. This unique photochemical mechanism provides a new hope for the development of light-driven hydride transfer reactions.

13.
Inorg Chem ; 58(21): 14853-14862, 2019 Nov 04.
Article in English | MEDLINE | ID: mdl-31617356

ABSTRACT

Materials with the apatite structure have a range of important applications in which their function is influenced by details of their local structure. Here, we describe an average and local structural study to probe the origins of high-temperature oxide ion mobility in La10(GeO4)6O3 and La8Bi2(GeO4)6O3 oxygen-excess materials, using the low-conductivity interstitial oxide-free La8Sr2(GeO4)6O2 as a benchmark. For La10 and La8Bi2, we locate the interstitial oxygen, Oint, responsible for conductivity by Rietveld refinement and relate the P63/m to P1̅ phase transitions on cooling to oxygen ordering. Local structural studies using neutron total scattering reveal that well-ordered GeO5 square pyramidal groups form in the structure at low temperature, but that Oint becomes significantly more disordered in the high-conductivity, high-temperature structures, with a transition to more trigonal-bipyramid-like average geometry. We relate the higher conductivity of Bi materials to the presence of several Oint sites of similar energy in the structure, which correlates with its less-distorted low-temperature average structure.

14.
Nat Commun ; 10(1): 3578, 2019 08 08.
Article in English | MEDLINE | ID: mdl-31395880

ABSTRACT

How genomic and transcriptomic alterations affect the functional proteome in lung cancer is not fully understood. Here, we integrate DNA copy number, somatic mutations, RNA-sequencing, and expression proteomics in a cohort of 108 squamous cell lung cancer (SCC) patients. We identify three proteomic subtypes, two of which (Inflamed, Redox) comprise 87% of tumors. The Inflamed subtype is enriched with neutrophils, B-cells, and monocytes and expresses more PD-1. Redox tumours are enriched for oxidation-reduction and glutathione pathways and harbor more NFE2L2/KEAP1 alterations and copy gain in the 3q2 locus. Proteomic subtypes are not associated with patient survival. However, B-cell-rich tertiary lymph node structures, more common in Inflamed, are associated with better survival. We identify metabolic vulnerabilities (TP63, PSAT1, and TFRC) in Redox. Our work provides a powerful resource for lung SCC biology and suggests therapeutic opportunities based on redox metabolism and immune cell infiltrates.


Subject(s)
Carcinoma, Squamous Cell/genetics , Gene Expression Regulation, Neoplastic , Lung Neoplasms/genetics , Proteogenomics , Aged , Carcinoma, Squamous Cell/pathology , DNA Copy Number Variations , Female , Humans , Lung , Lung Neoplasms/pathology , Male , Middle Aged , Mutation , Sequence Analysis, RNA
15.
Cell ; 177(4): 1035-1049.e19, 2019 05 02.
Article in English | MEDLINE | ID: mdl-31031003

ABSTRACT

We performed the first proteogenomic study on a prospectively collected colon cancer cohort. Comparative proteomic and phosphoproteomic analysis of paired tumor and normal adjacent tissues produced a catalog of colon cancer-associated proteins and phosphosites, including known and putative new biomarkers, drug targets, and cancer/testis antigens. Proteogenomic integration not only prioritized genomically inferred targets, such as copy-number drivers and mutation-derived neoantigens, but also yielded novel findings. Phosphoproteomics data associated Rb phosphorylation with increased proliferation and decreased apoptosis in colon cancer, which explains why this classical tumor suppressor is amplified in colon tumors and suggests a rationale for targeting Rb phosphorylation in colon cancer. Proteomics identified an association between decreased CD8 T cell infiltration and increased glycolysis in microsatellite instability-high (MSI-H) tumors, suggesting glycolysis as a potential target to overcome the resistance of MSI-H tumors to immune checkpoint blockade. Proteogenomics presents new avenues for biological discoveries and therapeutic development.


Subject(s)
Colonic Neoplasms/genetics , Colonic Neoplasms/therapy , Proteogenomics/methods , Apoptosis/genetics , Biomarkers, Tumor/genetics , Biomarkers, Tumor/metabolism , CD8-Positive T-Lymphocytes , Cell Proliferation/genetics , Colonic Neoplasms/metabolism , Genomics/methods , Glycolysis , Humans , Microsatellite Instability , Mutation , Phosphorylation , Prospective Studies , Proteomics/methods , Retinoblastoma Protein/genetics , Retinoblastoma Protein/metabolism
16.
J Virol ; 92(18)2018 09 15.
Article in English | MEDLINE | ID: mdl-29976678

ABSTRACT

Zika virus (ZIKV) glycoproteins are the primary target of the humoral immune response. In this study, we explored the capacity of these glycoproteins to tolerate insertion of linear epitope sequences and the potential of antibodies that bind these epitopes to inhibit infection. We first created a panel of ZIKV mutants with the FLAG epitope inserted in the premembrane (prM) and envelope (E) glycoprotein regions. The insertion locations were based on the results of our recent transposon insertional mutagenesis screen. Although FLAG insertions in prM greatly impaired viral fitness, this sequence was tolerated in numerous surface-exposed E protein sites. We observed that mutants bearing FLAG epitopes in E domains I and II and the E domain I-II hinge region were all neutralized by FLAG antibody; however, the neutralization sensitivity varied highly. We measured the antibody binding efficiency and found that this closely matched the pattern of neutralization sensitivity. We determined that E glycosylation did not affect antibody binding to a nearby epitope or its capacity to serve as a neutralization target. Although we could not generate infectious viruses with FLAG epitope insertions in a buried region of E protein domain III, we found that the V5 epitope could be inserted at this site without greatly impacting fitness. Furthermore, this virus was efficiently neutralized by V5 antibodies, highlighting that even buried epitopes can function as neutralization targets. Finally, we analyzed the timing of antibody neutralization activity during cell entry and found that all antibodies blocked a step after cell attachment.IMPORTANCE Zika virus (ZIKV) infections are associated with severe birth defects and neurological disease. The structure of the mature ZIKV particle reveals a virion surface covered by the envelope glycoprotein, which is the dominant target of the humoral immune response. It is unclear if all regions of the envelope protein surface or even buried epitopes can function as neutralization targets. To test this, we created a panel of ZIKV mutants with epitope insertions in different regions of the envelope protein. In characterizing these viruses, we found that the strength of antibody binding to an epitope is the major determinant of the neutralization potential of an antibody, that even a buried region of the envelope protein can be efficiently targeted, and that the sole potential envelope glycan does not impact nearby epitope antibody binding and neutralization. Furthermore, this work provides important insights into our understanding of how antibodies neutralize ZIKV.


Subject(s)
Antibodies, Neutralizing/immunology , Membrane Glycoproteins/immunology , Mutation , Viral Envelope Proteins/immunology , Zika Virus/genetics , Animals , Antibodies, Neutralizing/chemistry , Antibodies, Neutralizing/metabolism , Binding Sites, Antibody/genetics , Binding Sites, Antibody/immunology , Chlorocebus aethiops , Epitopes/chemistry , Epitopes/genetics , Epitopes/immunology , Glycosylation , Humans , Immunity, Humoral , Membrane Glycoproteins/genetics , Mutagenesis, Insertional , Neutralization Tests , Vero Cells , Zika Virus/chemistry , Zika Virus/immunology
17.
Mol Cell Proteomics ; 17(3): 422-430, 2018 03.
Article in English | MEDLINE | ID: mdl-29222161

ABSTRACT

Alternative splicing dramatically increases transcriptome complexity but its contribution to proteome diversity remains controversial. Exon-exon junction spanning peptides provide direct evidence for the translation of specific splice isoforms and are critical for delineating protein isoform complexity. Here we found that junction-spanning peptides are underrepresented in publicly available mass spectrometry-based shotgun proteomics data sets. Further analysis showed that evolutionarily conserved preferential nucleotide usage at exon boundaries increases the occurrence of lysine- and arginine-coding triplets at the end of exons. Because both lysine and arginine residues are cleavage sites of trypsin, the nearly exclusive use of trypsin as the protein digestion enzyme in shotgun proteomic analyses hinders the detection of junction-spanning peptides. To study the impact of enzyme selection on splice junction detectability, we performed in-silico digestion of the human proteome using six proteases. The six enzymes created a total of 161,125 detectable junctions, and only 1,029 were common across all enzyme digestions. Chymotrypsin digestion provided the largest number of detectable junctions. Our experimental results further showed that combination of a chymotrypsin-based human proteome analysis with a trypsin-based analysis increased detection of junction-spanning peptides by 37% over the trypsin-only analysis and identified over a thousand junctions that were undetectable in fully tryptic digests. Our study demonstrates that detection of proteome diversity resulted from alternative splicing is limited by trypsin cleavage specificity, and that complementary digestion schemes will be essential to comprehensively analyze the translation of alternative splicing isoforms.


Subject(s)
Alternative Splicing , Peptide Hydrolases/chemistry , Proteome , Cell Line, Tumor , Exons , Humans , Neoplasm Proteins/chemistry , Neoplasms/metabolism , Peptides/chemistry
18.
Cancer Res ; 77(21): e43-e46, 2017 11 01.
Article in English | MEDLINE | ID: mdl-29092937

ABSTRACT

Proteogenomics has emerged as a valuable approach in cancer research, which integrates genomic and transcriptomic data with mass spectrometry-based proteomics data to directly identify expressed, variant protein sequences that may have functional roles in cancer. This approach is computationally intensive, requiring integration of disparate software tools into sophisticated workflows, challenging its adoption by nonexpert, bench scientists. To address this need, we have developed an extensible, Galaxy-based resource aimed at providing more researchers access to, and training in, proteogenomic informatics. Our resource brings together software from several leading research groups to address two foundational aspects of proteogenomics: (i) generation of customized, annotated protein sequence databases from RNA-Seq data; and (ii) accurate matching of tandem mass spectrometry data to putative variants, followed by filtering to confirm their novelty. Directions for accessing software tools and workflows, along with instructional documentation, can be found at z.umn.edu/canresgithub. Cancer Res; 77(21); e43-46. ©2017 AACR.


Subject(s)
Computational Biology/methods , Genomics/methods , Neoplasms/genetics , Software , Genome, Human , Humans , Proteomics/methods , Tandem Mass Spectrometry , Transcriptome/genetics
19.
Gastroenterology ; 153(4): 1082-1095, 2017 10.
Article in English | MEDLINE | ID: mdl-28625833

ABSTRACT

BACKGROUND AND AIMS: Proteomics holds promise for individualizing cancer treatment. We analyzed to what extent the proteomic landscape of human colorectal cancer (CRC) is maintained in established CRC cell lines and the utility of proteomics for predicting therapeutic responses. METHODS: Proteomic and transcriptomic analyses were performed on 44 CRC cell lines, compared against primary CRCs (n=95) and normal tissues (n=60), and integrated with genomic and drug sensitivity data. RESULTS: Cell lines mirrored the proteomic aberrations of primary tumors, in particular for intrinsic programs. Tumor relationships of protein expression with DNA copy number aberrations and signatures of post-transcriptional regulation were recapitulated in cell lines. The 5 proteomic subtypes previously identified in tumors were represented among cell lines. Nonetheless, systematic differences between cell line and tumor proteomes were apparent, attributable to stroma, extrinsic signaling, and growth conditions. Contribution of tumor stroma obscured signatures of DNA mismatch repair identified in cell lines with a hypermutation phenotype. Global proteomic data showed improved utility for predicting both known drug-target relationships and overall drug sensitivity as compared with genomic or transcriptomic measurements. Inhibition of targetable proteins associated with drug responses further identified corresponding synergistic or antagonistic drug combinations. Our data provide evidence for CRC proteomic subtype-specific drug responses. CONCLUSIONS: Proteomes of established CRC cell line are representative of primary tumors. Proteomic data tend to exhibit improved prediction of drug sensitivity as compared with genomic and transcriptomic profiles. Our integrative proteogenomic analysis highlights the potential of proteome profiling to inform personalized cancer medicine.


Subject(s)
Antineoplastic Agents/pharmacology , Biomarkers, Tumor/metabolism , Colorectal Neoplasms/drug therapy , Colorectal Neoplasms/metabolism , Neoplasm Proteins/metabolism , Precision Medicine , Proteome , Biomarkers, Tumor/genetics , Cell Line, Tumor , Chromatography, Liquid , Colorectal Neoplasms/genetics , Colorectal Neoplasms/pathology , Databases, Protein , Dose-Response Relationship, Drug , Drug Screening Assays, Antitumor , Gene Expression Profiling , Gene Expression Regulation, Neoplastic , Humans , Mutation , Neoplasm Proteins/genetics , Patient Selection , Polymorphism, Single Nucleotide , Proteomics/methods , Signal Transduction , Stromal Cells/metabolism , Tandem Mass Spectrometry , Transcriptome , Tumor Microenvironment
20.
J Am Chem Soc ; 139(24): 8222-8228, 2017 06 21.
Article in English | MEDLINE | ID: mdl-28535334

ABSTRACT

Despite the promise of utilizing metal-organic frameworks (MOFs) as highly tunable photocatalytic materials, systematic studies that interrogate the relationship between their catalytic performances and the amount of functionalized linkers are lacking. Aminated linkers are known to enhance the absorption of light and afford photocatalysis with MOFs under visible-light irradiation. However, the manner in which the photocatalytic performances are impacted by the amount of such linkers is poorly understood. Here, we assess the photocatalytic activity of MIL-125, a TiO2/1,4-benzenedicarboxylate (bdc) MOF for the oxidation of benzyl alcohol to benzaldehyde when increasing amounts of bdc-NH2 linkers (0%, 20%, 46%, 70%, and 100%) are incorporated in the framework. Analytical TEM allowed assessing the homogeneous localization of bdc-NH2 in these mixed-linker MOFs. Steady state reaction rates reveal two regimes of catalytic performances: a first linear regime up to ∼50% bdc-NH2 into the hybrid framework whereby increased amounts of bdc-NH2 yielded increased photocatalytic rates, followed by a plateau up to 100% bdc-NH2. This unexpected "saturation" of the catalytic activity above ∼50% bdc-NH2 content in the framework whatever the wavelength filters used demonstrates that amination of all linkers of the MOF is not required to obtain the maximum photocatalytic activity. This is rationalized on the basis of mixed-valence Ti3+/Ti4+ intermediate catalytic centers revealed by electron spin resonance (ESR) measurements and recent knowledge of lifetime excited states in MIL-125-type of solids.

SELECTION OF CITATIONS
SEARCH DETAIL
...