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Article: Proteomic and phosphoproteomic profiling in heart failure with preserved ejection fraction (HFpEF).

Valero-Muñoz, María / Saw, Eng Leng / Hekman, Ryan M / Blum, Benjamin C / Hourani, Zaynab / Granzier, Henk / Emili, Andrew / Sam, Flora

Frontiers in cardiovascular medicine

2022 Volume 9, Page(s) 966968

Abstract: Although the prevalence of heart failure with preserved ejection fraction (HFpEF) is increasing, evidence-based therapies for HFpEF remain limited, likely due to an incomplete understanding of this disease. This study sought to identify the cardiac- ... ...

Abstract	Although the prevalence of heart failure with preserved ejection fraction (HFpEF) is increasing, evidence-based therapies for HFpEF remain limited, likely due to an incomplete understanding of this disease. This study sought to identify the cardiac-specific features of protein and phosphoprotein changes in a murine model of HFpEF using mass spectrometry. HFpEF mice demonstrated moderate hypertension, left ventricle (LV) hypertrophy, lung congestion and diastolic dysfunction. Proteomics analysis of the LV tissue showed that 897 proteins were differentially expressed between HFpEF and Sham mice. We observed abundant changes in sarcomeric proteins, mitochondrial-related proteins, and NAD-dependent protein deacetylase sirtuin-3 (SIRT3). Upregulated pathways by GSEA analysis were related to immune modulation and muscle contraction, while downregulated pathways were predominantly related to mitochondrial metabolism. Western blot analysis validated SIRT3 downregulated cardiac expression in HFpEF vs. Sham (0.8 ± 0.0 vs. 1.0 ± 0.0;
Language	English
Publishing date	2022-08-25
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2781496-8
ISSN	2297-055X
ISSN	2297-055X
DOI	10.3389/fcvm.2022.966968
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Dengue Virus Infection of

Gold, Alexander S / Feitosa-Suntheimer, Fabiana / Araujo, Ricardo V / Hekman, Ryan M / Asad, Sultan / Londono-Renteria, Berlin / Emili, Andrew / Colpitts, Tonya M

International journal of molecular sciences

2020 Volume 21, Issue 18

Abstract: Dengue is the most burdensome vector-borne viral disease in the world. Dengue virus (DENV), the etiological cause of dengue, is transmitted primarily by ... ...

Abstract	Dengue is the most burdensome vector-borne viral disease in the world. Dengue virus (DENV), the etiological cause of dengue, is transmitted primarily by the
MeSH term(s)	Aedes/metabolism ; Aedes/virology ; Animals ; Cells, Cultured ; Dengue/transmission ; Dengue/virology ; Dengue Virus ; Extracellular Vesicles/metabolism ; Female ; Humans ; Insect Proteins/metabolism ; Mosquito Vectors/metabolism ; Mosquito Vectors/virology
Chemical Substances	Insect Proteins
Language	English
Publishing date	2020-09-10
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms21186609
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Article ; Online: Use of neomycin as a structured amino-containing side chain motif for phenanthroline-based G-quadruplex ligands and telomerase inhibitors.

Singh, Mandeep / Wang, Siwen / Joo, Hyun / Ye, Zhihan / Christison, Krege M / Hekman, Ryan / Vierra, Craig / Xue, Liang

Chemical biology & drug design

2020 Volume 96, Issue 5, Page(s) 1292–1304

Abstract: In this paper, we report the synthesis of a phenanthroline and neomycin conjugate (7). Compound 7 binds to a human telomeric G-quadruplex (G1) with a higher affinity compared with its parent compounds (phenanthroline and neomycin), which is determined by ...

Abstract	In this paper, we report the synthesis of a phenanthroline and neomycin conjugate (7). Compound 7 binds to a human telomeric G-quadruplex (G1) with a higher affinity compared with its parent compounds (phenanthroline and neomycin), which is determined by several biophysical studies. Compound 7 shows good selectivity for G-quadruplex (G4) DNA over duplex DNA. The binding of 7 with G1 is predominantly enthalpy-driven, and the binding stoichiometry of 7 with G1 is one for the tight-binding event as determined by ESI mass spectrometry. A plausible binding mode is a synergistic effect of end-stacking and groove interactions, as indicated by docking studies. Compound 7 can inhibit human telomerase activity at low micromolar concentrations, which is more potent than previously reported 5-substituted phenanthroline derivatives.
MeSH term(s)	Anti-Bacterial Agents/pharmacology ; Enzyme Inhibitors/pharmacology ; G-Quadruplexes ; Humans ; Ligands ; Molecular Dynamics Simulation ; Neomycin/pharmacology ; Phenanthrolines/metabolism ; Telomerase/antagonists & inhibitors ; Thermodynamics
Chemical Substances	Anti-Bacterial Agents ; Enzyme Inhibitors ; Ligands ; Phenanthrolines ; Telomerase (EC 2.7.7.49) ; Neomycin (I16QD7X297)
Language	English
Publishing date	2020-07-26
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2216600-2
ISSN	1747-0285 ; 1747-0277
ISSN (online)	1747-0285
ISSN	1747-0277
DOI	10.1111/cbdd.13741
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Article ; Online: Correction: Recombinant Lloviu virus as a tool to study viral replication and host responses.

Hume, Adam J / Heiden, Baylee / Olejnik, Judith / Suder, Ellen L / Ross, Stephen / Scoon, Whitney A / Bullitt, Esther / Ericsson, Maria / White, Mitchell R / Turcinovic, Jacquelyn / Thao, Tran T N / Hekman, Ryan M / Kaserman, Joseph E / Huang, Jessie / Alysandratos, Konstantinos-Dionysios / Toth, Gabor E / Jakab, Ferenc / Kotton, Darrell N / Wilson, Andrew A /

Emili, Andrew / Thiel, Volker / Connor, John H / Kemenesi, Gabor / Cifuentes, Daniel / Mühlberger, Elke

PLoS pathogens

2022 Volume 18, Issue 6, Page(s) e1010659

Abstract: This corrects the article DOI: 10.1371/journal.ppat.1010268.]. ...

Abstract	[This corrects the article DOI: 10.1371/journal.ppat.1010268.].
Language	English
Publishing date	2022-06-24
Publishing country	United States
Document type	Published Erratum
ZDB-ID	2205412-1
ISSN	1553-7374 ; 1553-7374
ISSN (online)	1553-7374
ISSN	1553-7374
DOI	10.1371/journal.ppat.1010659
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Article ; Online: Egg Case Protein 3: A Constituent of Black Widow Spider Tubuliform Silk.

Shanafelt, Mikayla / Larracas, Camille / Dyrness, Simmone / Hekman, Ryan / La Mattina-Hawkins, Coby / Rabara, Taylor / Wu, Wilson / Vierra, Craig A

Molecules (Basel, Switzerland)

2021 Volume 26, Issue 16

Abstract: Spider silk has outstanding mechanical properties, rivaling some of the best materials on the planet. Biochemical analyses of tubuliform silk have led to the identification of TuSp1, egg case protein 1, and egg case protein 2. TuSp1 belongs to the ... ...

Abstract	Spider silk has outstanding mechanical properties, rivaling some of the best materials on the planet. Biochemical analyses of tubuliform silk have led to the identification of TuSp1, egg case protein 1, and egg case protein 2. TuSp1 belongs to the spidroin superfamily, containing a non-repetitive
MeSH term(s)	Amino Acid Sequence ; Animal Structures/metabolism ; Animals ; Black Widow Spider/chemistry ; Egg Proteins/chemistry ; Egg Proteins/genetics ; Egg Proteins/metabolism ; Female ; Fibroins/chemistry ; Gene Expression Regulation ; Ovum/metabolism ; Ovum/ultrastructure ; Proteomics ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; Tandem Mass Spectrometry
Chemical Substances	Egg Proteins ; RNA, Messenger ; Fibroins (9007-76-5)
Language	English
Publishing date	2021-08-22
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules26165088
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Article ; Online: Recombinant Lloviu virus as a tool to study viral replication and host responses.

Emili, Andrew / Thiel, Volker / Connor, John H / Kemenesi, Gabor / Cifuentes, Daniel / Mühlberger, Elke

PLoS pathogens

2022 Volume 18, Issue 2, Page(s) e1010268

Abstract: Next generation sequencing has revealed the presence of numerous RNA viruses in animal reservoir hosts, including many closely related to known human pathogens. Despite their zoonotic potential, most of these viruses remain understudied due to not yet ... ...

Abstract	Next generation sequencing has revealed the presence of numerous RNA viruses in animal reservoir hosts, including many closely related to known human pathogens. Despite their zoonotic potential, most of these viruses remain understudied due to not yet being cultured. While reverse genetic systems can facilitate virus rescue, this is often hindered by missing viral genome ends. A prime example is Lloviu virus (LLOV), an uncultured filovirus that is closely related to the highly pathogenic Ebola virus. Using minigenome systems, we complemented the missing LLOV genomic ends and identified cis-acting elements required for LLOV replication that were lacking in the published sequence. We leveraged these data to generate recombinant full-length LLOV clones and rescue infectious virus. Similar to other filoviruses, recombinant LLOV (rLLOV) forms filamentous virions and induces the formation of characteristic inclusions in the cytoplasm of the infected cells, as shown by electron microscopy. Known target cells of Ebola virus, including macrophages and hepatocytes, are permissive to rLLOV infection, suggesting that humans could be potential hosts. However, inflammatory responses in human macrophages, a hallmark of Ebola virus disease, are not induced by rLLOV. Additional tropism testing identified pneumocytes as capable of robust rLLOV and Ebola virus infection. We also used rLLOV to test antivirals targeting multiple facets of the replication cycle. Rescue of uncultured viruses of pathogenic concern represents a valuable tool in our arsenal for pandemic preparedness.
MeSH term(s)	Animals ; Cell Line ; Chlorocebus aethiops ; Ebolavirus/genetics ; Filoviridae/genetics ; Filoviridae Infections/virology ; Genetic Complementation Test ; Genome, Viral ; Hemorrhagic Fever, Ebola/virology ; Host Microbial Interactions ; Humans ; Inclusion Bodies/virology ; Induced Pluripotent Stem Cells/virology ; Macrophages/virology ; RNA, Viral ; Reverse Genetics ; Vero Cells ; Virion/genetics ; Virus Replication
Chemical Substances	RNA, Viral
Language	English
Publishing date	2022-02-04
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2205412-1
ISSN	1553-7374 ; 1553-7374
ISSN (online)	1553-7374
ISSN	1553-7374
DOI	10.1371/journal.ppat.1010268
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Article ; Online: Pilot Study Showing Feasibility of Phosphoproteomic Profiling of Pathway-Level Molecular Alterations in Barrett's Esophagus.

Moore, Jarrod / Hekman, Ryan / Blum, Benjamin C / Lawton, Matthew / Lehoux, Sylvain / Stachler, Matthew / Pleskow, Douglas / Sawhney, Mandeep S / Cummings, Richard D / Emili, Andrew / Qureshi, Alia

Genes

2022 Volume 13, Issue 7

Abstract: 1) Background: Barrett's esophagus is a major risk factor for esophageal adenocarcinoma. In this pilot study, we employed precision mass spectrometry to map global (phospho)protein perturbations in Barrett's esophagus lesions and adjacent normal tissue ... ...

Abstract	(1) Background: Barrett's esophagus is a major risk factor for esophageal adenocarcinoma. In this pilot study, we employed precision mass spectrometry to map global (phospho)protein perturbations in Barrett's esophagus lesions and adjacent normal tissue to glean insights into disease progression. (2) Methods: Biopsies were collected from two small but independent cohorts. Comparative analyses were performed between Barrett's esophagus samples and adjacent matched (normal) tissues from patients with known pathology, while specimens from healthy patients served as additional controls. (3) Results: We identified and quantified 6810 proteins and 6395 phosphosites in the discovery cohort, revealing hundreds of statistically significant differences in protein abundances and phosphorylation states. We identified a robust proteomic signature that accurately classified the disease status of samples from the independent patient cohorts. Pathway-level analysis of the phosphoproteomic profiles revealed the dysregulation of specific cellular processes, including DNA repair, in Barrett's esophagus relative to paired controls. Comparative analysis with previously published transcriptomic profiles provided independent evidence in support of these preliminary findings. (4) Conclusions: This pilot study establishes the feasibility of using unbiased quantitative phosphoproteomics to identify molecular perturbations associated with disease progression in Barrett's esophagus to define potentially clinically actionable targets warranting further assessment.
MeSH term(s)	Barrett Esophagus/genetics ; Barrett Esophagus/metabolism ; Barrett Esophagus/pathology ; Disease Progression ; Feasibility Studies ; Humans ; Pilot Projects ; Proteomics
Language	English
Publishing date	2022-07-07
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2527218-4
ISSN	2073-4425 ; 2073-4425
ISSN (online)	2073-4425
ISSN	2073-4425
DOI	10.3390/genes13071215
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Article ; Online: A Cluster Randomized Trial of Primary Care Practice Redesign to Integrate Behavioral Health for Those Who Need It Most: Patients With Multiple Chronic Conditions.

Littenberg, Benjamin / Clifton, Jessica / Crocker, Abigail M / Baldwin, Laura-Mae / Bonnell, Levi N / Breshears, Ryan E / Callas, Peter / Chakravarti, Prama / Clark/Keefe, Kelly / Cohen, Deborah J / deGruy, Frank V / Eidt-Pearson, Lauren / Elder, William / Fox, Chester / Frisbie, Sylvie / Hekman, Katie / Hitt, Juvena / Jewiss, Jennifer / Kaelber, David C /

Kelley, Kairn Stetler / Kessler, Rodger / O'Rourke-Lavoie, Jennifer B / Leibowitz, George S / Macchi, C R / Martin, Matthew P / McGovern, Mark / Mollis, Brenda / Mullin, Daniel / Nagykaldi, Zsolt / Natkin, Lisa W / Pace, Wilson / Pinckney, Richard G / Pomeroy, Douglas / Reynolds, Paula / Rose, Gail L / Scholle, Sarah Hudson / Sieber, William J / Soucie, Jeni / Stancin, Terry / Stange, Kurt C / Stephens, Kari A / Teng, Kathryn / Waddell, Elizabeth Needham / van Eeghen, Constance

Annals of family medicine

2024 Volume 21, Issue 6, Page(s) 483–495

Abstract: Purpose: Patient outcomes can improve when primary care and behavioral health providers use a collaborative system of care, but integrating these services is difficult. We tested the effectiveness of a practice intervention for improving patient ... ...

Abstract	Purpose: Patient outcomes can improve when primary care and behavioral health providers use a collaborative system of care, but integrating these services is difficult. We tested the effectiveness of a practice intervention for improving patient outcomes by enhancing integrated behavioral health (IBH) activities. Methods: We conducted a pragmatic, cluster randomized controlled trial. The intervention combined practice redesign, quality improvement coaching, provider and staff education, and collaborative learning. At baseline and 2 years, staff at 42 primary care practices completed the Practice Integration Profile (PIP) as a measure of IBH. Adult patients with multiple chronic medical and behavioral conditions completed the Patient-Reported Outcomes Measurement Information System (PROMIS-29) survey. Primary outcomes were the change in 8 PROMIS-29 domain scores. Secondary outcomes included change in level of integration. Results: Intervention assignment had no effect on change in outcomes reported by 2,426 patients who completed both baseline and 2-year surveys. Practices assigned to the intervention improved PIP workflow scores but not PIP total scores. Baseline PIP total score was significantly associated with patient-reported function, independent of intervention. Active practices that completed intervention workbooks (n = 13) improved patient-reported outcomes and practice integration ( Conclusion: Intervention assignment had no effect on change in patient outcomes; however, we did observe improved patient outcomes among practices that entered the study with greater IBH. We also observed more improvement of integration and patient outcomes among active practices that completed the intervention compared to active practices that did not. Additional research is needed to understand how implementation efforts to enhance IBH can best reach patients.
MeSH term(s)	Adult ; Humans ; Multiple Chronic Conditions ; Primary Health Care
Language	English
Publishing date	2024-04-13
Publishing country	United States
Document type	Randomized Controlled Trial ; Journal Article
ZDB-ID	2171425-3
ISSN	1544-1717 ; 1544-1709
ISSN (online)	1544-1717
ISSN	1544-1709
DOI	10.1370/afm.3027
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Article ; Online: Structural Characterization of Black Widow Spider Dragline Silk Proteins CRP1 and CRP4.

Shanafelt, Mikayla / Rabara, Taylor / MacArt, Danielle / Williams, Caroline / Hekman, Ryan / Joo, Hyun / Tsai, Jerry / Vierra, Craig

Molecules (Basel, Switzerland)

2020 Volume 25, Issue 14

Abstract: Spider dragline silk represents a biomaterial with outstanding mechanical properties, possessing high-tensile strength and toughness. In black widows at least eight different proteins have been identified as constituents of dragline silk. These represent ...

Abstract	Spider dragline silk represents a biomaterial with outstanding mechanical properties, possessing high-tensile strength and toughness. In black widows at least eight different proteins have been identified as constituents of dragline silk. These represent major ampullate spidroins MaSp1, MaSp2, MaSp', and several low-molecular weight cysteine-rich protein (CRP) family members, including CRP1, CRP2, and CRP4. Molecular modeling predicts that CRPs contain a cystine slipknot motif, but experimental evidence to support this assertion remains to be reported. To advance scientific knowledge regarding CRP function, we recombinantly expressed and purified CRP1 and CRP4 from bacteria and investigated their secondary structure using circular dichroism (CD) under different chemical and physical conditions. We demonstrate by far-UV CD spectroscopy that these proteins contain similar secondary structure, having substantial amounts of random coil conformation, followed by lower levels of beta sheet, alpha helical and beta turn structures. CRPs are thermally and pH stable; however, treatment with reagents that disrupt disulfide bonds impact their structural conformations. Cross-linking mass spectrometry (XL-MS) data also support computational models of CRP1. Taken together, the chemical and thermal stability of CRPs, the cross-linking data, coupled with the structural sensitivity to reducing agents, are experimentally consistent with the supposition CRPs are cystine slipknot proteins.
MeSH term(s)	Amino Acid Sequence ; Animals ; Black Widow Spider/chemistry ; Hydrogen-Ion Concentration ; Insect Proteins/chemistry ; Insect Proteins/isolation & purification ; Models, Molecular ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Recombinant Proteins ; Silk/chemistry ; Tandem Mass Spectrometry
Chemical Substances	Insect Proteins ; Recombinant Proteins ; Silk
Language	English
Publishing date	2020-07-14
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules25143212
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Article ; Online: Dengue Virus Infection of Aedes aegypti Alters Extracellular Vesicle Protein Cargo to Enhance Virus Transmission

Alexander S. Gold / Fabiana Feitosa-Suntheimer / Ricardo V. Araujo / Ryan M. Hekman / Sultan Asad / Berlin Londono-Renteria / Andrew Emili / Tonya M. Colpitts

International Journal of Molecular Sciences, Vol 21, Iss 6609, p

2020 Volume 6609

Abstract: Dengue is the most burdensome vector-borne viral disease in the world. Dengue virus (DENV), the etiological cause of dengue, is transmitted primarily by the Aedes aegypti mosquito. Like any arbovirus, the transmission cycle of dengue involves the complex ...

Abstract	Dengue is the most burdensome vector-borne viral disease in the world. Dengue virus (DENV), the etiological cause of dengue, is transmitted primarily by the Aedes aegypti mosquito. Like any arbovirus, the transmission cycle of dengue involves the complex interactions of a multitude of human and mosquito factors. One point during this transmission cycle that is rich in these interactions is the biting event by the mosquito, upon which its saliva is injected into the host. A number of components in mosquito saliva have been shown to play a pivotal role in the transmission of dengue, however one such component that is not as well characterized is extracellular vesicles. Here, using high-performance liquid chromatography in tandem with mass spectrometry, we show that dengue infection altered the protein cargo of Aedes aegypti extracellular vesicles, resulting in the packaging of proteins with infection-enhancing ability. Our results support the presence of an infection-dependent pro-viral protein packaging strategy that uses the differential packaging of pro-viral proteins in extracellular vesicles of Ae. aegypti saliva to promote transmission. These studies represent the first investigation into the function of Ae. aegypti extracellular vesicle cargo during dengue infection.
Keywords	dengue virus ; Aedes aegypti ; extracellular vesicles ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	570
Language	English
Publishing date	2020-09-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
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