1
|
Okoh AK, Fugar S, Dodoo S, Selevany M, Al-Obaidi N, Ozturk E, Singh S, Tayal R, Lee LY, Russo MJ, Camacho M. Derivation and validation of the bridge to transplantation with left ventricular assist device score for 1 year mortality after heart transplantation. The BTT-LVAD score. Int J Artif Organs 2022; 45:470-477. [PMID: 35365063 PMCID: PMC10024971 DOI: 10.1177/03913988221082690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND To derive and validate a risk score that accurately predicts 1-year mortality after heart transplantation (HT) in patients bridged to transplant (BTT) with a left ventricular assist device (LVAD). METHODS The UNOS database was queried to identify patients BTT with an LVAD between 2008 and 2018. Patients with ⩾1-year follow up were randomly divided into derivation (70%) and validation (30%) cohorts. The primary endpoint was 1-year mortality. A simple additive risk score was developed based on the odds of 1-year mortality after HT. Risk groups were created, and survival was estimated and compared. RESULTS A total of 7759 patients were randomly assigned to derivation (n = 5431) and validation (n = 2328) cohorts. One-year post-transplant mortality was 9.8% (n = 760). A 33-point scoring was created from six recipient variables and two donor variables. Risk groups were classified as low (0-5), intermediate (6-10), and high (>10). In the validation cohort, the predicted 1-year mortality was significantly higher in the high-risk group than the intermediate and low-risk groups, 14.7% versus 9% versus 6.1% respectively (log-rank test: p < 0.0001). CONCLUSION The BTT-LVAD Score can serve as a clinical decision tool to guide therapeutic decisions in advanced heart failure patients.
Collapse
Affiliation(s)
- Alexis K Okoh
- Division of Cardiology, Emory Clinical Cardiovascular Research Institute, Emory University School of Medicine, Atlanta, GA, USA
| | - Setri Fugar
- Division of Cardiology, Rush University Medical Center, Chicago, IL, USA
| | - Sheriff Dodoo
- Department of Medicine, Piedmont Newnan Hospital, Newnan, GA, USA
| | - Mariam Selevany
- Cardiovascular Research Unit, RWJBarnabas Health, Newark Beth Israel Medical Center, Newark, NJ, USA
| | - Nawar Al-Obaidi
- Cardiovascular Research Unit, RWJBarnabas Health, Newark Beth Israel Medical Center, Newark, NJ, USA
| | - Ebru Ozturk
- Division of Biostatistics, Hacettepe University School of Medicine, Ankara, Turkey
| | - Swaiman Singh
- Cardiovascular Research Unit, RWJBarnabas Health, Newark Beth Israel Medical Center, Newark, NJ, USA
| | - Rajiv Tayal
- Cardiovascular Research Unit, RWJBarnabas Health, Newark Beth Israel Medical Center, Newark, NJ, USA
| | - Leonard Y Lee
- Division of Cardiothoracic Surgery, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Mark J Russo
- Division of Cardiothoracic Surgery, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Margarita Camacho
- Cardiovascular Research Unit, RWJBarnabas Health, Newark Beth Israel Medical Center, Newark, NJ, USA
- Division of Cardiothoracic Surgery, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| |
Collapse
|
2
|
Carter MS, Zhang X, Huang H, Bouvier JT, Francisco BS, Vetting MW, Al-Obaidi N, Bonanno JB, Ghosh A, Zallot RG, Andersen HM, Almo SC, Gerlt JA. Functional assignment of multiple catabolic pathways for D-apiose. Nat Chem Biol 2018; 14:696-705. [PMID: 29867142 DOI: 10.1038/s41589-018-0067-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 03/29/2018] [Indexed: 11/09/2022]
Abstract
Colocation of the genes encoding ABC, TRAP, and TCT transport systems and catabolic pathways for the transported ligand provides a strategy for discovering novel microbial enzymes and pathways. We screened solute-binding proteins (SBPs) for ABC transport systems and identified three that bind D-apiose, a branched pentose in the cell walls of higher plants. Guided by sequence similarity networks (SSNs) and genome neighborhood networks (GNNs), the identities of the SBPs enabled the discovery of four catabolic pathways for D-apiose with eleven previously unknown reactions. The new enzymes include D-apionate oxidoisomerase, which catalyzes hydroxymethyl group migration, as well as 3-oxo-isoapionate-4-phosphate decarboxylase and 3-oxo-isoapionate-4-phosphate transcarboxylase/hydrolase, which are RuBisCO-like proteins (RLPs). The web tools for generating SSNs and GNNs are publicly accessible ( http://efi.igb.illinois.edu/efi-est/ ), so similar 'genomic enzymology' strategies for discovering novel pathways can be used by the community.
Collapse
Affiliation(s)
- Michael S Carter
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Xinshuai Zhang
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Hua Huang
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jason T Bouvier
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Brian San Francisco
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Matthew W Vetting
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Nawar Al-Obaidi
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jeffrey B Bonanno
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Agnidipta Ghosh
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Rémi G Zallot
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Harvey M Andersen
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Steven C Almo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - John A Gerlt
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA. .,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| |
Collapse
|
3
|
Huang H, Carter MS, Vetting MW, Al-Obaidi N, Patskovsky Y, Almo SC, Gerlt JA. Correction to “A General Strategy for the Discovery of Metabolic Pathways: d-Threitol, l-Threitol, and Erythritol Utilization in Mycobacterium smegmatis”. J Am Chem Soc 2016; 138:4267. [DOI: 10.1021/jacs.6b01906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
4
|
Huang H, Carter MS, Vetting MW, Al-Obaidi N, Patskovsky Y, Almo SC, Gerlt JA. A General Strategy for the Discovery of Metabolic Pathways: d-Threitol, l-Threitol, and Erythritol Utilization in Mycobacterium smegmatis. J Am Chem Soc 2015; 137:14570-3. [PMID: 26560079 DOI: 10.1021/jacs.5b08968] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We describe a general integrated bioinformatic and experimental strategy to discover the in vitro enzymatic activities and in vivo functions (metabolic pathways) of uncharacterized enzymes discovered in microbial genome projects using the ligand specificities of the solute binding proteins (SBPs) for ABC transporters. Using differential scanning fluorimetry, we determined that the SBP for an ABC transporter encoded by the genome of Mycobacterium smegmatis is stabilized by d-threitol. Using sequence similarity networks and genome neighborhood networks to guide selection of target proteins for pathway enzymes, we applied both in vitro and in vivo experimental approaches to discover novel pathways for catabolism of d-threitol, l-threitol, and erythritol.
Collapse
Affiliation(s)
| | | | - Matthew W Vetting
- Department of Biochemistry, Albert Einstein College of Medicine , Bronx, New York 10461, United States
| | - Nawar Al-Obaidi
- Department of Biochemistry, Albert Einstein College of Medicine , Bronx, New York 10461, United States
| | - Yury Patskovsky
- Department of Biochemistry, Albert Einstein College of Medicine , Bronx, New York 10461, United States
| | - Steven C Almo
- Department of Biochemistry, Albert Einstein College of Medicine , Bronx, New York 10461, United States
| | | |
Collapse
|
5
|
Wichelecki DJ, Vetting MW, Chou L, Al-Obaidi N, Bouvier JT, Almo SC, Gerlt JA. ATP-binding Cassette (ABC) Transport System Solute-binding Protein-guided Identification of Novel d-Altritol and Galactitol Catabolic Pathways in Agrobacterium tumefaciens C58. J Biol Chem 2015; 290:28963-76. [PMID: 26472925 DOI: 10.1074/jbc.m115.686857] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Indexed: 01/27/2023] Open
Abstract
Innovations in the discovery of the functions of uncharacterized proteins/enzymes have become increasingly important as advances in sequencing technology flood protein databases with an exponentially growing number of open reading frames. This study documents one such innovation developed by the Enzyme Function Initiative (EFI; U54GM093342), the use of solute-binding proteins for transport systems to identify novel metabolic pathways. In a previous study, this strategy was applied to the tripartite ATP-independent periplasmic transporters. Here, we apply this strategy to the ATP-binding cassette transporters and report the discovery of novel catabolic pathways for d-altritol and galactitol in Agrobacterium tumefaciens C58. These efforts resulted in the description of three novel enzymatic reactions as follows: 1) oxidation of d-altritol to d-tagatose via a dehydrogenase in Pfam family PF00107, a previously unknown reaction; 2) phosphorylation of d-tagatose to d-tagatose 6-phosphate via a kinase in Pfam family PF00294, a previously orphan EC number; and 3) epimerization of d-tagatose 6-phosphate C-4 to d-fructose 6-phosphate via a member of Pfam family PF08013, another previously unknown reaction. The epimerization reaction catalyzed by a member of PF08013 is especially noteworthy, because the functions of members of PF08013 have been unknown. These discoveries were assisted by the following two synergistic bioinformatics web tools made available by the Enzyme Function Initiative: the EFI-Enzyme Similarity Tool and the EFI-Genome Neighborhood Tool.
Collapse
Affiliation(s)
- Daniel J Wichelecki
- From the Departments of Biochemistry and Chemistry and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 and
| | - Matthew W Vetting
- the Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Liyushang Chou
- From the Departments of Biochemistry and Chemistry and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 and
| | - Nawar Al-Obaidi
- the Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Jason T Bouvier
- From the Departments of Biochemistry and Chemistry and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 and
| | - Steven C Almo
- the Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461
| | - John A Gerlt
- From the Departments of Biochemistry and Chemistry and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 and
| |
Collapse
|
6
|
Vetting MW, Al-Obaidi N, Zhao S, San Francisco B, Kim J, Wichelecki DJ, Bouvier JT, Solbiati JO, Vu H, Zhang X, Rodionov DA, Love JD, Hillerich BS, Seidel RD, Quinn RJ, Osterman AL, Cronan JE, Jacobson MP, Gerlt JA, Almo SC. Experimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes. Biochemistry 2015; 54:909-31. [PMID: 25540822 PMCID: PMC4310620 DOI: 10.1021/bi501388y] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
![]()
The
rate at which genome sequencing data is accruing demands enhanced
methods for functional annotation and metabolism discovery. Solute
binding proteins (SBPs) facilitate the transport of the first reactant
in a metabolic pathway, thereby constraining the regions of chemical
space and the chemistries that must be considered for pathway reconstruction.
We describe high-throughput protein production and differential scanning
fluorimetry platforms, which enabled the screening of 158 SBPs against
a 189 component library specifically tailored for this class of proteins.
Like all screening efforts, this approach is limited by the practical
constraints imposed by construction of the library, i.e., we can study
only those metabolites that are known to exist and which can be made
in sufficient quantities for experimentation. To move beyond these
inherent limitations, we illustrate the promise of crystallographic-
and mass spectrometric-based approaches for the unbiased use of entire
metabolomes as screening libraries. Together, our approaches identified
40 new SBP ligands, generated experiment-based annotations for 2084
SBPs in 71 isofunctional clusters, and defined numerous metabolic
pathways, including novel catabolic pathways for the utilization of
ethanolamine as sole nitrogen source and the use of d-Ala-d-Ala as sole carbon source. These efforts begin to define an
integrated strategy for realizing the full value of amassing genome
sequence data.
Collapse
Affiliation(s)
- Matthew W Vetting
- Department of Biochemistry, Albert Einstein College of Medicine , Bronx, New York 10461, United States
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
7
|
Wichelecki DJ, Vendiola JAF, Jones AM, Al-Obaidi N, Almo SC, Gerlt JA. Investigating the physiological roles of low-efficiency D-mannonate and D-gluconate dehydratases in the enolase superfamily: pathways for the catabolism of L-gulonate and L-idonate. Biochemistry 2014; 53:5692-9. [PMID: 25145794 PMCID: PMC4159206 DOI: 10.1021/bi500837w] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The
sequence/function space in the d-mannonate dehydratase
subgroup (ManD) of the enolase superfamily was investigated to determine
how enzymatic function diverges as sequence identity decreases [Wichelecki,
D. J., et al. (2014) Biochemistry53, 2722–2731]. That study revealed that members of the ManD
subgroup vary in substrate specificity and catalytic efficiency: high-efficiency
(kcat/KM =
103–104 M–1 s–1) for dehydration of d-mannonate, low-efficiency (kcat/KM = 10–102 M–1 s–1) for dehydration
of d-mannonate and/or d-gluconate, and no activity.
Characterization of high-efficiency members revealed that these are
ManDs in the d-glucuronate catabolic pathway {analogues of
UxuA [Wichelecki, D. J., et al. (2014) Biochemistry 53, 4087–4089]}. However, the genomes of organisms that encode
low-efficiency members of the ManDs subgroup encode UxuAs; therefore,
these must have divergent physiological functions. In this study,
we investigated the physiological functions of three low-efficiency
members of the ManD subgroup and identified a novel physiologically
relevant pathway for l-gulonate catabolism in Chromohalobacter
salexigens DSM3043 as well as cryptic pathways for l-gulonate catabolism in Escherichia coli CFT073
and l-idonate catabolism in Salmonella enterica subsp. enterica serovar Enteritidis str. P125109. However, we could not identify physiological roles
for the low-efficiency members of the ManD subgroup, allowing the
suggestion that these pathways may be either evolutionary relics or
the starting points for new metabolic potential.
Collapse
Affiliation(s)
- Daniel J Wichelecki
- Departments of Biochemistry and Chemistry and Institute for Genomic Biology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | | | | | | | | | | |
Collapse
|
8
|
Wichelecki DJ, Graff DC, Al-Obaidi N, Almo SC, Gerlt JA. Identification of the in vivo function of the high-efficiency D-mannonate dehydratase in Caulobacter crescentus NA1000 from the enolase superfamily. Biochemistry 2014; 53:4087-9. [PMID: 24947666 PMCID: PMC4082379 DOI: 10.1021/bi500683x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
The d-mannonate dehydratase
(ManD) subgroup of the enolase
superfamily contains members with varying catalytic activities (high-efficiency,
low-efficiency, or no activity) that dehydrate d-mannonate
and/or d-gluconate to 2-keto-3-deoxy-d-gluconate
[Wichelecki, D. J., et al. (2014) Biochemistry53, 2722–2731]. Despite extensive in vitro characterization, the in vivo physiological role
of a ManD has yet to be established. In this study, we report the in vivo functional characterization of a high-efficiency
ManD from Caulobacter crescentus NA1000 (UniProt
entry B8GZZ7) by in vivo discovery of its essential
role in d-glucuronate metabolism. This in vivo functional annotation may be extended to ∼50 additional proteins.
Collapse
Affiliation(s)
- Daniel J Wichelecki
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | | | | | | | | |
Collapse
|