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Gupta S, Wang L, Slifker MJ, Cai KQ, Maclean KN, Wasek B, Bottiglieri T, Kruger WD. Analysis of differential neonatal lethality in cystathionine β-synthase deficient mouse models using metabolic profiling. FASEB J 2021; 35:e21629. [PMID: 33949005 DOI: 10.1096/fj.202100302r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/06/2021] [Accepted: 04/13/2021] [Indexed: 12/14/2022]
Abstract
Cystathionine beta-synthase (CBS) is a key enzyme of the trans-sulfuration pathway that converts homocysteine to cystathionine. Loss of CBS activity due to mutation results in CBS deficiency, an inborn error of metabolism characterized by extreme elevation of plasma total homocysteine (tHcy). C57BL6 mice containing either a homozygous null mutation in the cystathionine β-synthase (Cbs-/- ) gene or an inactive human CBS protein (Tg-G307S Cbs-/- ) are born in mendelian numbers, but the vast majority die between 18 and 21 days of age due to liver failure. However, adult Cbs null mice that express a hypomorphic allele of human CBS as a transgene (Tg-I278T Cbs-/- ) show almost no neonatal lethality despite having serum tHcy levels similar to mice with no CBS activity. Here, we characterize liver and serum metabolites in neonatal Cbs+/- , Tg-G307S Cbs-/- , and Tg-I278T Cbs-/- mice at 6, 10, and 17 days of age to understand this difference. In serum, we observe similar elevations in tHcy in both Tg-G307S Cbs-/- and Tg-I278T Cbs-/- compared to control animals, but methionine is much more severely elevated in Tg-G307S Cbs-/- mice. Large scale metabolomic analysis of liver tissue confirms that both methionine and methionine-sulfoxide are significantly more elevated in Tg-G307S Cbs-/- animals, along with significant differences in several other metabolites including hexoses, amino acids, other amines, lipids, and carboxylic acids. Our data are consistent with a model that the neonatal lethality observed in CBS-null mice is driven by excess methionine resulting in increased stress on a variety of related pathways including the urea cycle, TCA cycle, gluconeogenesis, and phosphatidylcholine biosynthesis.
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Affiliation(s)
- Sapna Gupta
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Liqun Wang
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Michael J Slifker
- Biostatistics and Bioinformatics Facility, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Kathy Q Cai
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Kenneth N Maclean
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Brandi Wasek
- Center of Metabolomics, Institute of Metabolic Disease, Baylor Scott & White Research Institute, Dallas, TX, USA
| | - Teodoro Bottiglieri
- Center of Metabolomics, Institute of Metabolic Disease, Baylor Scott & White Research Institute, Dallas, TX, USA
| | - Warren D Kruger
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA, USA
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2
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Mysore K, Sun L, Roethele JB, Li P, Igiede J, Misenti JK, Duman-Scheel M. A conserved female-specific larval requirement for MtnB function facilitates sex separation in multiple species of disease vector mosquitoes. Parasit Vectors 2021; 14:338. [PMID: 34174948 PMCID: PMC8234664 DOI: 10.1186/s13071-021-04844-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/11/2021] [Indexed: 11/28/2022] Open
Abstract
Background Clusters of sex-specific loci are predicted to shape the boundaries of the M/m sex-determination locus of the dengue vector mosquito Aedes aegypti, but the identities of these genes are not known. Identification and characterization of these loci could promote a better understanding of mosquito sex chromosome evolution and lead to the elucidation of new strategies for male mosquito sex separation, a requirement for several emerging mosquito population control strategies that are dependent on the mass rearing and release of male mosquitoes. This investigation revealed that the methylthioribulose-1-phosphate dehydratase (MtnB) gene, which resides adjacent to the M/m locus and encodes an evolutionarily conserved component of the methionine salvage pathway, is required for survival of female larvae. Results Larval consumption of Saccharomyces cerevisiae (yeast) strains engineered to express interfering RNA corresponding to MtnB resulted in target gene silencing and significant female death, yet had no impact on A. aegypti male survival or fitness. Integration of the yeast larvicides into mass culturing protocols permitted scaled production of fit adult male mosquitoes. Moreover, silencing MtnB orthologs in Aedes albopictus, Anopheles gambiae, and Culex quinquefasciatus revealed a conserved female-specific larval requirement for MtnB among different species of mosquitoes. Conclusions The results of this investigation, which may have important implications for the study of mosquito sex chromosome evolution, indicate that silencing MtnB can facilitate sex separation in multiple species of disease vector insects. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-021-04844-w.
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Affiliation(s)
- Keshava Mysore
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Raclin-Carmichael Hall, 1234 Notre Dame Ave., South Bend, IN, 46617, USA.,University of Notre Dame Eck Institute for Global Health, Notre Dame, IN, USA
| | - Longhua Sun
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Raclin-Carmichael Hall, 1234 Notre Dame Ave., South Bend, IN, 46617, USA.,University of Notre Dame Eck Institute for Global Health, Notre Dame, IN, USA
| | - Joseph B Roethele
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Raclin-Carmichael Hall, 1234 Notre Dame Ave., South Bend, IN, 46617, USA.,University of Notre Dame Eck Institute for Global Health, Notre Dame, IN, USA
| | - Ping Li
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Raclin-Carmichael Hall, 1234 Notre Dame Ave., South Bend, IN, 46617, USA.,University of Notre Dame Eck Institute for Global Health, Notre Dame, IN, USA
| | - Jessica Igiede
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Raclin-Carmichael Hall, 1234 Notre Dame Ave., South Bend, IN, 46617, USA.,University of Notre Dame Eck Institute for Global Health, Notre Dame, IN, USA
| | - Joi K Misenti
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Raclin-Carmichael Hall, 1234 Notre Dame Ave., South Bend, IN, 46617, USA.,University of Notre Dame Eck Institute for Global Health, Notre Dame, IN, USA
| | - Molly Duman-Scheel
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Raclin-Carmichael Hall, 1234 Notre Dame Ave., South Bend, IN, 46617, USA. .,University of Notre Dame Eck Institute for Global Health, Notre Dame, IN, USA.
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Lee N, Spears ME, Carlisle AE, Kim D. Endogenous toxic metabolites and implications in cancer therapy. Oncogene 2020; 39:5709-5720. [PMID: 32709924 PMCID: PMC7452860 DOI: 10.1038/s41388-020-01395-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 06/16/2020] [Accepted: 07/15/2020] [Indexed: 12/19/2022]
Abstract
It is well recognized that many metabolic enzymes play essential roles in cancer cells in producing building blocks such as nucleotides, which are required in greater amounts due to their increased proliferation. On the other hand, the significance of enzymes in preventing the accumulation of their substrates is less recognized. Here, we outline the evidence and underlying mechanisms for how many metabolites normally produced in cells are highly toxic, such as metabolites containing reactive groups (e.g., methylglyoxal, 4-hydroxynonenal, and glutaconyl-CoA), or metabolites that act as competitive analogs against other metabolites (e.g., deoxyuridine triphosphate and l-2-hydroxyglutarate). Thus, if a metabolic pathway contains a toxic intermediate, then we may be able to induce accumulation and poison a cancer cell by targeting the downstream enzyme. Furthermore, this poisoning may be cancer cell selective if this pathway is overactive in a cancer cell relative to a nontransformed cell. We describe this concept as illustrated in selenocysteine metabolism and other pathways and discuss future directions in exploiting toxic metabolites to kill cancer cells.
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Affiliation(s)
- Namgyu Lee
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Meghan E Spears
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Anne E Carlisle
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Dohoon Kim
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA.
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4
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Abstract
Multiple factors involving the methionine salvage pathway (MSP) and polyamine biosynthesis have been found to be involved in cancer cell proliferation, migration, invasion and metastasis. This review summarizes the relationships of the MSP enzyme acireductone dioxygenase (ARD), the ADI1 gene encoding ARD and other gene products (ADI1GP) with carcinomas and carcinogenesis. ARD exhibits structural and functional differences depending upon the metal bound in the active site. In the penultimate step of the MSP, the Fe2+ bound form of ARD catalyzes the on-pathway oxidation of acireductone leading to methionine, whereas Ni2+ bound ARD catalyzes an off-pathway reaction producing methylthiopropionate and carbon monoxide, a biological signaling molecule and anti-apoptotic. The relationship between ADI1GP, MSP and polyamine synthesis are discussed, along with possible role(s) of metal in modulating the cellular behavior of ADI1GP and its interactions with other cellular components.
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5
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The methionine salvage pathway-involving ADI1 inhibits hepatoma growth by epigenetically altering genes expression via elevating S-adenosylmethionine. Cell Death Dis 2019; 10:240. [PMID: 30858354 PMCID: PMC6411897 DOI: 10.1038/s41419-019-1486-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 02/18/2019] [Accepted: 02/25/2019] [Indexed: 02/06/2023]
Abstract
The 5′-methylthioadenosine (MTA) cycle-participating human acireductone dioxygenase 1 (ADI1) has been implicated as a tumor suppressor in prostate cancer, yet its role remains unclear in hepatocellular carcinoma (HCC). Here, we demonstrated a significant reduction of ADI1, either in protein or mRNA level, in HCC tissues. Additionally, higher ADI1 levels were associated with favorable postoperative recurrence-free survival in HCC patients. By altering ADI1 expression in HCC cells, a negative correlation between ADI1 and cell proliferation was observed. Cell-based and xenograft experiments were performed by using cells overexpressing ADI1 mutants carrying mutations at the metal-binding sites (E94A and H133A, respectively), which selectively disrupted differential catalytic steps, resulting in staying or leaving the MTA cycle. The results showed that the growth suppression effect was mediated by accelerating the MTA cycle. A cDNA microarray analysis followed by verification experiments identified that caveolin-1 (CAV1), a growth-promoting protein in HCC, was markedly decreased upon ADI1 overexpression. Suppression of CAV1 expression was mediated by an increase of S-adenosylmethionine (SAMe) level. The methylation status of CAV1 promoter was significantly altered upon ADI1 overexpression. Finally, a genome-wide methylation analysis revealed that ADI1 overexpression altered promoter methylation profiles in a set of cancer-related genes, including CAV1 and genes encoding antisense non-coding RNAs, long non-coding RNAs, and microRNAs, resulting in significant changes of their expression levels. In conclusion, ADI1 expression promoted MTA cycle to increase SAMe levels, which altered genome-wide promoter methylation profiles, resulting in altered gene expression and HCC growth suppression.
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6
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Dcona MM, Morris BL, Ellis KC, Grossman SR. CtBP- an emerging oncogene and novel small molecule drug target: Advances in the understanding of its oncogenic action and identification of therapeutic inhibitors. Cancer Biol Ther 2017; 18:379-391. [PMID: 28532298 PMCID: PMC5536941 DOI: 10.1080/15384047.2017.1323586] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
C-terminal Binding Proteins (CtBP) 1 and 2 are oncogenic transcriptional co-regulators overexpressed in many cancer types, with their expression level correlating to worse prognostic outcomes and aggressive tumor features. CtBP negatively regulates the expression of many tumor suppressor genes, while coactivating genes that promote proliferation, epithelial-mesenchymal transition, and cancer stem cell self-renewal activity. In light of this evidence, the development of novel inhibitors that mitigate CtBP function may provide clinically actionable therapeutic tools. This review article focuses on the progress made in understanding CtBP structure, role in tumor progression, and discovery and development of CtBP inhibitors that target CtBP's dehydrogenase activity and other functions, with a focus on the theory and rationale behind the designs of current inhibitors. We provide insight into the future development and use of rational combination therapy that may further augment the efficacy of CtBP inhibitors, specifically addressing metastasis and cancer stem cell populations within tumors.
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Affiliation(s)
- M Michael Dcona
- a Department of Internal Medicine , Virginia Commonwealth University , Richmond , VA , USA
| | - Benjamin L Morris
- b Department of Human and Molecular Genetics , Virginia Commonwealth University , Richmond , VA , USA
| | - Keith C Ellis
- c Department of Medicinal Chemistry , Virginia Commonwealth University , Richmond , VA , USA.,d Institute for Structural Biology , Drug Discovery and Development, Virginia Commonwealth University , Richmond , VA , USA.,e VCU Massey Cancer Center , Virginia Commonwealth University , Richmond , VA , USA
| | - Steven R Grossman
- a Department of Internal Medicine , Virginia Commonwealth University , Richmond , VA , USA.,b Department of Human and Molecular Genetics , Virginia Commonwealth University , Richmond , VA , USA.,d Institute for Structural Biology , Drug Discovery and Development, Virginia Commonwealth University , Richmond , VA , USA.,e VCU Massey Cancer Center , Virginia Commonwealth University , Richmond , VA , USA
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7
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Patel J, Baranwal S, Love IM, Patel NJ, Grossman SR, Patel BB. Inhibition of C-terminal binding protein attenuates transcription factor 4 signaling to selectively target colon cancer stem cells. Cell Cycle 2015; 13:3506-18. [PMID: 25483087 DOI: 10.4161/15384101.2014.958407] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Selective targeting of cancer stem cells (CSCs), implicated in tumor relapse, holds great promise in the treatment of colorectal cancer. Overexpression of C-terminal binding protein (CtBP), an NADH dependent transcriptional regulator, is often observed in colon cancer. Of note, TCF-4 signaling is also up-regulated in colonic CSCs. We hypothesized that CtBP, whose dehydrogenase activity is amenable to pharmacological inhibition by 4-methylthio-2-oxobutyric acid (MTOB), positively regulates TCF-4 signaling, leading to CSC growth and self-renewal. CSCs demonstrated significant upregulation of CtBP1 and CtBP2 levels (mRNA and protein) and activity partly due to increased NADH/NAD ratio, as well as increased TCF/LEF transcriptional activity, compared to respective controls. Depletion of CtBP2 inhibited, while its overexpression enhanced, CSC growth (1° spheroids) and self-renewal (2°/3° spheroids). Similarly, MTOB caused a robust inhibition of spheroid growth and self-renewal in a dose dependent manner. MTOB displayed significantly greater selectivity for growth inhibition in the spheroids, at least in part through induction of apoptosis, compared to monolayer controls. Moreover, MTOB inhibited basal as well as induced (by GSK-3β inhibitor) TCF/LEF activity while suppressing mRNA and protein levels of several β-catenin target genes (CD44, Snail, C-MYC and LGR5). Lastly, CtBP physically interacted with TCF-4, and this interaction was significantly inhibited in the presence of MTOB. The above findings point to a novel role of CtBPs in the promotion of CSC growth and self-renewal through direct regulation of TCF/LEF transcription. Moreover, small molecular inhibition of its function can selectively target CSCs, presenting a novel approach for treatment of colorectal cancer focused on targeting of CSCs.
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Affiliation(s)
- Jagrut Patel
- a Hunter Holmes McGuire VA Medical Center ; Richmond , VA USA
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8
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Expression of MTAP inhibits tumor-related phenotypes in HT1080 cells via a mechanism unrelated to its enzymatic function. G3-GENES GENOMES GENETICS 2014; 5:35-44. [PMID: 25387827 PMCID: PMC4291467 DOI: 10.1534/g3.114.014555] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Methylthioadenosine Phosphorylase (MTAP) is a tumor suppressor gene that is frequently deleted in human cancers and encodes an enzyme responsible for the catabolism of the polyamine byproduct 5′deoxy-5′-methylthioadenosine (MTA). To elucidate the mechanism by which MTAP inhibits tumor formation, we have reintroduced MTAP into MTAP-deleted HT1080 fibrosarcoma cells. Expression of MTAP resulted in a variety of phenotypes, including decreased colony formation in soft-agar, decreased migration, decreased in vitro invasion, increased matrix metalloproteinase production, and reduced ability to form tumors in severe combined immunodeficiency mice. Microarray analysis showed that MTAP affected the expression of genes involved in a variety of processes, including cell adhesion, extracellular matrix interaction, and cell signaling. Treatment of MTAP-expressing cells with a potent inhibitor of MTAP’s enzymatic activity (MT-DADMe-ImmA) did not result in a MTAP− phenotype. This finding suggests that MTAP’s tumor suppressor function is not the same as its known enzymatic function. To confirm this, we introduced a catalytically inactive version of MTAP, D220A, into HT1080 cells and found that this mutant was fully capable of reversing the soft agar colony formation, migration, and matrix metalloproteinase phenotypes. Our results show that MTAP affects cellular phenotypes in HT1080 cells in a manner that is independent of its known enzymatic activity.
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9
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Structural and biochemical basis for the inhibition of cell death by APIP, a methionine salvage enzyme. Proc Natl Acad Sci U S A 2013; 111:E54-61. [PMID: 24367089 DOI: 10.1073/pnas.1308768111] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
APIP, Apaf-1 interacting protein, has been known to inhibit two main types of programmed cell death, apoptosis and pyroptosis, and was recently found to be associated with cancers and inflammatory diseases. Distinct from its inhibitory role in cell death, APIP was also shown to act as a 5-methylthioribulose-1-phosphate dehydratase, or MtnB, in the methionine salvage pathway. Here we report the structural and enzymatic characterization of human APIP as an MtnB enzyme with a Km of 9.32 μM and a Vmax of 1.39 μmol min(-1) mg(-1). The crystal structure was determined at 2.0-Å resolution, revealing an overall fold similar to members of the zinc-dependent class II aldolase family. APIP/MtnB exists as a tetramer in solution and exhibits an assembly with C4 symmetry in the crystal lattice. The pocket-shaped active site is located at the end of a long cleft between two adjacent subunits. We propose an enzymatic reaction mechanism involving Glu139* as a catalytic acid/base, as supported by enzymatic assay, substrate-docking study, and sequence conservation analysis. We explored the relationship between two distinct functions of APIP/MtnB, cell death inhibition, and methionine salvage, by measuring the ability of enzymatic mutants to inhibit cell death, and determined that APIP/MtnB functions as a cell death inhibitor independently of its MtnB enzyme activity for apoptosis induced by either hypoxia or etoposide, but dependently for caspase-1-induced pyroptosis. Our results establish the structural and biochemical groundwork for future mechanistic studies of the role of APIP/MtnB in modulating cell death and inflammation and in the development of related diseases.
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10
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Mary C, Duek P, Salleron L, Tienz P, Bumann D, Bairoch A, Lane L. Functional identification of APIP as human mtnB, a key enzyme in the methionine salvage pathway. PLoS One 2012; 7:e52877. [PMID: 23285211 PMCID: PMC3532061 DOI: 10.1371/journal.pone.0052877] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Accepted: 11/22/2012] [Indexed: 02/08/2023] Open
Abstract
The methionine salvage pathway is widely distributed among some eubacteria, yeast, plants and animals and recycles the sulfur-containing metabolite 5-methylthioadenosine (MTA) to methionine. In eukaryotic cells, the methionine salvage pathway takes place in the cytosol and usually involves six enzymatic activities: MTA phosphorylase (MTAP, EC 2.4.2.28), 5′-methylthioribose-1-phosphate isomerase (mtnA, EC 5.3.1.23), 5′-methylthioribulose-1-phosphate dehydratase (mtnB, EC: 4.2.1.109), 2,3-dioxomethiopentane-1-phosphate enolase/phosphatase (mtnC, EC 3.1.3.77), aci-reductone dioxygenase (mtnD, EC 1.13.11.54) and 4-methylthio-2-oxo-butanoate (MTOB) transaminase (EC 2.6.1.-). The aim of this study was to complete the available information on the methionine salvage pathway in human by identifying the enzyme responsible for the dehydratase step. Using a bioinformatics approach, we propose that a protein called APIP could perform this role. The involvement of this protein in the methionine salvage pathway was investigated directly in HeLa cells by transient and stable short hairpin RNA interference. We show that APIP depletion specifically impaired the capacity of cells to grow in media where methionine is replaced by MTA. Using a Shigella mutant auxotroph for methionine, we confirm that the knockdown of APIP specifically affects the recycling of methionine. We also show that mutation of three potential phosphorylation sites does not affect APIP activity whereas mutation of the potential zinc binding site completely abrogates it. Finally, we show that the N-terminal region of APIP that is missing in the short isoform is required for activity. Together, these results confirm the involvement of APIP in the methionine salvage pathway, which plays a key role in many biological functions like cancer, apoptosis, microbial proliferation and inflammation.
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Affiliation(s)
- Camille Mary
- CALIPHO Group, SIB-Swiss Institute of Bioinformatics, University of Geneva, Geneva, Switzerland.
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11
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Linard B, Nguyen NH, Prosdocimi F, Poch O, Thompson JD. EvoluCode: Evolutionary Barcodes as a Unifying Framework for Multilevel Evolutionary Data. Evol Bioinform Online 2011; 8:61-77. [PMID: 22267905 PMCID: PMC3256995 DOI: 10.4137/ebo.s8814] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Evolutionary systems biology aims to uncover the general trends and principles governing the evolution of biological networks. An essential part of this process is the reconstruction and analysis of the evolutionary histories of these complex, dynamic networks. Unfortunately, the methodologies for representing and exploiting such complex evolutionary histories in large scale studies are currently limited. Here, we propose a new formalism, called EvoluCode (Evolutionary barCode), which allows the integration of different evolutionary parameters (eg, sequence conservation, orthology, synteny …) in a unifying format and facilitates the multilevel analysis and visualization of complex evolutionary histories at the genome scale. The advantages of the approach are demonstrated by constructing barcodes representing the evolution of the complete human proteome. Two large-scale studies are then described: (i) the mapping and visualization of the barcodes on the human chromosomes and (ii) automatic clustering of the barcodes to highlight protein subsets sharing similar evolutionary histories and their functional analysis. The methodologies developed here open the way to the efficient application of other data mining and knowledge extraction techniques in evolutionary systems biology studies. A database containing all EvoluCode data is available at: http://lbgi.igbmc.fr/barcodes.
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Affiliation(s)
- Benjamin Linard
- Laboratoire De Bioinformatique Et Génomique Intégratives, Institut de Génétique et de Biologie Moléculaire et Cellulaire CNRS/INSERM/UDS, Illkirch, France
| | - Ngoc Hoan Nguyen
- Laboratoire De Bioinformatique Et Génomique Intégratives, Institut de Génétique et de Biologie Moléculaire et Cellulaire CNRS/INSERM/UDS, Illkirch, France
| | | | - Olivier Poch
- Laboratoire De Bioinformatique Et Génomique Intégratives, Institut de Génétique et de Biologie Moléculaire et Cellulaire CNRS/INSERM/UDS, Illkirch, France
| | - Julie D. Thompson
- Laboratoire De Bioinformatique Et Génomique Intégratives, Institut de Génétique et de Biologie Moléculaire et Cellulaire CNRS/INSERM/UDS, Illkirch, France
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Straza MW, Paliwal S, Kovi RC, Rajeshkumar B, Trenh P, Parker D, Whalen GF, Lyle S, Schiffer CA, Grossman SR. Therapeutic targeting of C-terminal binding protein in human cancer. Cell Cycle 2010; 9:3740-50. [PMID: 20930544 DOI: 10.4161/cc.9.18.12936] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The CtBP transcriptional corepressors promote cancer cell survival and migration/invasion. CtBP senses cellular metabolism via a regulatory dehydrogenase domain, and is antagonized by p14/p19(ARF) tumor suppressors. The CtBP dehydrogenase substrate 4-methylthio-2-oxobutyric acid (MTOB) can act as a CtBP inhibitor at high concentrations, and is cytotoxic to cancer cells. MTOB induced apoptosis was p53-independent, correlated with the derepression of the proapoptotic CtBP repression target Bik, and was rescued by CtBP overexpression or Bik silencing. MTOB did not induce apoptosis in mouse embryonic fibroblasts (MEFs), but was increasingly cytotoxic to immortalized and transformed MEFs, suggesting that CtBP inhibition may provide a suitable therapeutic index for cancer therapy. In human colon cancer cell peritoneal xenografts, MTOB treatment decreased tumor burden and induced tumor cell apoptosis. To verify the potential utility of CtBP as a therapeutic target in human cancer, the expression of CtBP and its negative regulator ARF was studied in a series of resected human colon adenocarcinomas. CtBP and ARF levels were inversely-correlated, with elevated CtBP levels (compared with adjacent normal tissue) observed in greater than 60% of specimens, with ARF absent in nearly all specimens exhibiting elevated CtBP levels. Targeting CtBP may represent a useful therapeutic strategy in human malignancies.
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Affiliation(s)
- Michael W Straza
- Department of Cancer Biology, University of Massachusetts Medical School and UMass Memorial Cancer Center, Worcester, MA, USA
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13
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Na YJ, Farley J, Zeh A, del Carmen M, Penson R, Birrer MJ. Ovarian cancer: markers of response. Int J Gynecol Cancer 2010; 19 Suppl 2:S21-9. [PMID: 19955910 DOI: 10.1111/igc.0b013e3181c2aeb5] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
OBJECTIVES Despite improved knowledge regarding the etiology of ovarian cancer, as well as application of aggressive surgery and chemotherapy, there has been only a modest change in the mortality statistics over the last 30 years. Given these results and the evolution of targeted therapies, there is an increasing need for prognostic and predictive factors to stratify patients for individualized care. Many laboratories have also investigated the specific individual biomarkers correlating them with clinicopathologic characteristics. Unfortunately, the vast majorities of these biomarkers have not proved clinically valuable. In this article, we review published genomic signatures including data generated in our laboratory for their relevance. METHODS Multiple published expression profiling articles were selected for review and discussion. Genomic studies were separated from those with dichotomized survival data and unsupervised analysis to identify discreet subsets of tumors and studies that generated activated pathways. RESULTS The identification of prognostic and predictive individual biomarkers has been common. Few of these have been validated. Genomic profiles have been obtained that distinguish short- from long-term survivors. The relevance of these studies to the large number of patients within the extremes remains unclear. Unsupervised clustering studies of ovarian cancers have identified potential subsets of tumors that reflect different clinical behavior. These studies will require large numbers of independent samples for validation. Another approach has been to identify genes that correlate with patient survival as a continuous variable. These genes are then placed into biologic context using pathway analysis. These pathways provide potential therapeutic targets, and those patients whose tumors express these targets may be most effectively treated by using inhibitors specific for the pathway. CONCLUSIONS There is a major need for prognostic and predictive biomarkers for ovarian cancer. With the development of new genomic technologies, there is an opportunity to identify gene expression signatures that can be used to stratify patients according to their ultimate survival and response to chemotherapy. Large independent sets and robust statistical techniques will be required to fully exploit this approach.
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Affiliation(s)
- Young-Jeong Na
- Comprehensive Gynecologic Cancer Center, Bundang CHA General Hospital, School of Medicine, CHA University, Gyunggido, Korea
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Singh LR, Gupta S, Honig NH, Kraus JP, Kruger WD. Activation of mutant enzyme function in vivo by proteasome inhibitors and treatments that induce Hsp70. PLoS Genet 2010; 6:e1000807. [PMID: 20066033 PMCID: PMC2795852 DOI: 10.1371/journal.pgen.1000807] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2009] [Accepted: 12/09/2009] [Indexed: 01/30/2023] Open
Abstract
Missense mutant proteins, such as those produced in individuals with genetic diseases, are often misfolded and subject to processing by intracellular quality control systems. Previously, we have shown using a yeast system that enzymatic function could be restored to I278T cystathionine beta-synthase (CBS), a cause of homocystinuria, by treatments that affect the intracellular chaperone environment. Here, we extend these studies and show that it is possible to restore significant levels of enzyme activity to 17 of 18 (94%) disease causing missense mutations in human cystathionine beta-synthase (CBS) expressed in Saccharomyces cerevisiae by exposure to ethanol, proteasome inhibitors, or deletion of the Hsp26 small heat shock protein. All three of these treatments induce Hsp70, which is necessary but not sufficient for rescue. In addition to CBS, these same treatments can rescue disease-causing mutations in human p53 and the methylene tetrahydrofolate reductase gene. These findings do not appear restricted to S. cerevisiae, as proteasome inhibitors can restore significant CBS enzymatic activity to CBS alleles expressed in fibroblasts derived from homocystinuric patients and in a mouse model for homocystinuria that expresses human I278T CBS. These findings suggest that proteasome inhibitors and other Hsp70 inducing agents may be useful in the treatment of a variety of genetic diseases caused by missense mutations.
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Affiliation(s)
- Laishram R. Singh
- Cancer Genetics and Signaling Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania, United States of America
| | - Sapna Gupta
- Cancer Genetics and Signaling Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania, United States of America
| | - Nicholaas H. Honig
- Cancer Genetics and Signaling Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania, United States of America
| | - Jan P. Kraus
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Warren D. Kruger
- Cancer Genetics and Signaling Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania, United States of America
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15
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Albers E. Metabolic characteristics and importance of the universal methionine salvage pathway recycling methionine from 5â²-methylthioadenosine. IUBMB Life 2009; 61:1132-42. [DOI: 10.1002/iub.278] [Citation(s) in RCA: 144] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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16
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Abstract
Methionine adenosyltransferases (MATs) are the family of enzymes that synthesize the main biological methyl donor, S-adenosylmethionine. The high sequence conservation among catalytic subunits from bacteria and eukarya preserves key residues that control activity and oligomerization, which is reflected in the protein structure. However, structural differences among complexes with substrates and products have led to proposals of several reaction mechanisms. In parallel, folding studies begin to explain how the three intertwined domains of the catalytic subunit are produced, and to highlight the importance of certain intermediates in attaining the active final conformation. This review analyzes the available structural data and proposes a consensus interpretation that facilitates an understanding of the pathological problems derived from impairment of MAT function. In addition, new research opportunities directed toward clarification of aspects that remain obscure are also identified.
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Affiliation(s)
- G. D. Markham
- Institute for Cancer Research, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111 USA
| | - M. A. Pajares
- Instituto de Investigaciones Biomédicas “Alberto Sols” (CSIC-UAM), Arturo Duperier 4, 28029 Madrid, Spain
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17
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Pirkov I, Norbeck J, Gustafsson L, Albers E. A complete inventory of all enzymes in the eukaryotic methionine salvage pathway. FEBS J 2008; 275:4111-20. [DOI: 10.1111/j.1742-4658.2008.06552.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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18
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Affiliation(s)
- Vern L Schramm
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461.
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