Single-cell characterization of step-wise acquisition of carboplatin resistance in ovarian cancer.
NPJ systems biology and applications
2022; 8 (1): 20
The molecular underpinnings of acquired resistance to carboplatin are poorly understood and often inconsistent between in vitro modeling studies. After sequential treatment cycles, multiple isogenic clones reached similar levels of resistance, but significant transcriptional heterogeneity. Gene-expression based virtual synchronization of 26,772 single cells from 2 treatment steps and 4 resistant clones was used to evaluate the activity of Hallmark gene sets in proliferative (P) and quiescent (Q) phases. Two behaviors were associated with resistance: (1) broad repression in the P phase observed in all clones in early resistant steps and (2) prevalent induction in Q phase observed in the late treatment step of one clone. Furthermore, the induction of IFNalpha response in P phase or Wnt-signaling in Q phase were observed in distinct resistant clones. These observations suggest a model of resistance hysteresis, where functional alterations of the P and Q phase states affect the dynamics of the successive transitions between drug exposure and recovery, and prompts for a precise monitoring of single-cell states to develop more effective schedules for, or combination of, chemotherapy treatments.
View details for DOI 10.1038/s41540-022-00230-z
View details for PubMedID 35715421
Vitamin A and association with asparaginase-associated pancreatitis in children with acute lymphocytic leukemia.
LIPPINCOTT WILLIAMS & WILKINS. 2022
View details for Web of Science ID 000863680300025
Impact of acute lymphoblastic leukemia induction therapy: findings from metabolomics on non-fasted plasma samples from a biorepository.
Metabolomics : Official journal of the Metabolomic Society
2021; 17 (7): 64
INTRODUCTION: Acute lymphoblastic leukemia (ALL) is among the most common cancers in children. With improvements in combination chemotherapy regimens, the overall survival has increased to over 90%. However, the current challenge is to mitigate adverse events resulting from the complex therapy. Several chemotherapies intercept cancer metabolism, but little is known about their collective role in altering host metabolism.OBJECTIVES: We profiled the metabolomic changes in plasma of ALL patients initial- and post- induction therapy.METHODS: We exploited a biorepository of non-fasted plasma samples derived from the Dana Farber Cancer Institute ALL Consortium; these samples were obtained from 50 ALL patients initial- and post-induction therapy. Plasma metabolites and complex lipids were analyzed by high resolution tandem mass spectrometry and differential mobility tandem mass spectrometry. Data were analyzed using a covariate-adjusted regression model with multiplicity adjustment. Pathway enrichment analysis and co-expression network analysis were performed to identify unique clusters of molecules.RESULTS: More than 1200 metabolites and complex lipids were identified in the total of global metabolomics and lipidomics platforms. Over 20% of those molecules were significantly altered. In the pathway enrichment analysis, lipids, particularly phosphatidylethanolamines (PEs), were identified. Network analysis indicated that the bioactive fatty acids, docosahexaenoic acid (DHA)-containing (22:6) triacylglycerols (TAGs), were decreased in the post-induction therapy.CONCLUSION: Metabolomic profiling in ALL patients revealed a large number of alterations following induction chemotherapy. In particular, lipid metabolism was substantially altered. The changes in metabolites and complex lipids following induction therapy could provide insight into the adverse events experienced by ALL patients.
View details for DOI 10.1007/s11306-021-01814-2
View details for PubMedID 34175981
The role of asparagine synthetase on nutrient metabolism in pancreatic disease.
Pancreatology : official journal of the International Association of Pancreatology (IAP) ... [et al.]
The pancreas avidly takes up and synthesizes the amino acid asparagine (Asn), in part, to maintain an active translational machinery that requires incorporation of the amino acid. The de novo synthesis of Asn in the pancreas occurs through the enzyme asparagine synthetase (ASNS). The pancreas has the highest expression of ASNS of any organ, and it can further upregulate ASNS expression in the setting of amino acid depletion. ASNS expression is driven by an intricate feedback network within the integrated stress response (ISR), which includes the amino acid response (AAR) and the unfolded protein response (UPR). Asparaginase is a cancer chemotherapeutic drug that depletes plasma Asn. However, asparaginase-associated pancreatitis (AAP) is a major medical problem and could be related to pancreatic Asn depletion. In this review, we will provide an overview of ASNS and then describe its role in pancreatic health and in the exocrine disorders of pancreatitis and pancreatic cancer. We will offer the overarching perspective that a high abundance of ASNS expression is hardwired in the exocrine pancreas to buffer the high demands of Asn for pancreatic digestive enzyme protein synthesis, that perturbations in the ability to express or upregulate ASNS could tip the balance towards pancreatitis, and that pancreatic cancers exploit ASNS to gain a metabolic survival advantage.
View details for DOI 10.1016/j.pan.2020.08.002
View details for PubMedID 32800652
APTO-253 Stabilizes G-quadruplex DNA, Inhibits MYC Expression, and Induces DNA Damage in Acute Myeloid Leukemia Cells
MOLECULAR CANCER THERAPEUTICS
2018; 17 (6): 1177–86
APTO-253 is a phase I clinical stage small molecule that selectively induces CDKN1A (p21), promotes G0-G1 cell-cycle arrest, and triggers apoptosis in acute myeloid leukemia (AML) cells without producing myelosuppression in various animal species and humans. Differential gene expression analysis identified a pharmacodynamic effect on MYC expression, as well as induction of DNA repair and stress response pathways. APTO-253 was found to elicit a concentration- and time-dependent reduction in MYC mRNA expression and protein levels. Gene ontogeny and structural informatic analyses suggested a mechanism involving G-quadruplex (G4) stabilization. Intracellular pharmacokinetic studies in AML cells revealed that APTO-253 is converted intracellularly from a monomer to a ferrous complex [Fe(253)3]. FRET assays demonstrated that both monomeric APTO-253 and Fe(253)3 stabilize G4 structures from telomeres, MYC, and KIT promoters but do not bind to non-G4 double-stranded DNA. Although APTO-253 exerts a host of mechanistic sequelae, the effect of APTO-253 on MYC expression and its downstream target genes, on cell-cycle arrest, DNA damage, and stress responses can be explained by the action of Fe(253)3 and APTO-253 on G-quadruplex DNA motifs. Mol Cancer Ther; 17(6); 1177-86. ©2018 AACR.
View details for DOI 10.1158/1535-7163.MCT-17-1209
View details for Web of Science ID 000433932800004
View details for PubMedID 29626127
APTO-253 Is a New Addition to the Repertoire of Drugs that Can Exploit DNA BRCA1/2 Deficiency
MOLECULAR CANCER THERAPEUTICS
2018; 17 (6): 1167–76
APTO-253 is a small molecule with antiproliferative activity against cell lines derived from a wide range of human malignancies. We sought to determine the mechanisms of action and basis for resistance to APTO-253 so as to identify synthetic lethal interactions that can guide combination studies. The cellular pharmacology of APTO-253 was analyzed in Raji lymphoma cells and a subline selected for resistance (Raji/253R). Using LC/MS/ESI analysis, APTO-253 was found to convert intracellularly to a complex containing one molecule of iron and three molecules of APTO-253 [Fe(253)3]. The intracellular content of Fe(253)3 exceeded that of the native drug by approximately 18-fold, and Fe(253)3 appears to be the most active form. Treatment of cells with APTO-253 caused DNA damage, which led us to ask whether cells deficient in homologous recombination (i.e., loss of BRCA1/2 function) were hypersensitive to this drug. It was found that loss of either BRCA1 or BRCA2 function in multiple isogenic paired cell lines resulted in hypersensitivity to APTO-253 of a magnitude similar to the effects of PARP inhibitors, olaparib. Raji cells selected for 16-fold acquired resistance had 16-fold reduced accumulation of Fe(253)3 RNA-seq analysis revealed that overexpression of the ABCG2 drug efflux pump is a key mechanism of resistance. ABCG2-overexpressed HEK-293 cells were resistant to APTO-253, and inhibition of ABCG2 reversed resistance to APTO-253 in Raji/253R. APTO-253 joins the limited repertoire of drugs that can exploit defects in homologous recombination and is of particular interest because it does not produce myelosuppression. Mol Cancer Ther; 17(6); 1167-76. ©2018 AACR.
View details for DOI 10.1158/1535-7163.MCT-17-0834
View details for Web of Science ID 000433932800003
View details for PubMedID 29626126
Copper transporters and chaperones CTR1, CTR2, ATOX1, and CCS as determinants of cisplatin sensitivity
2016; 8 (9): 951–62
The development of resistance to cisplatin (cDDP) is commonly accompanied by reduced drug uptake or increased efflux. Previous studies in yeast and murine embryonic fibroblasts have reported that the copper (Cu) transporters and chaperones participate in the uptake, efflux, and intracellular distribution of cDDP. However, there is conflicting data from studies in human cells. We used CRISPR-Cas9 genome editing to individually knock out the human copper transporters CTR1 and CTR2 and the copper chaperones ATOX1 and CCS. Isogenic knockout cell lines were generated in both human HEK-293T and ovarian carcinoma OVCAR8 cells. All knockout cell lines had slowed growth compared to parental cells, small changes in basal Cu levels, and varying sensitivities to Cu depending on the gene targeted. However, all of the knockouts demonstrated only modest 2 to 5-fold changes in cDDP sensitivity that did not differ from the range of sensitivities of 10 wild type clones grown from the same parental cell population. We conclude that, under basal conditions, loss of CTR1, CTR2, ATOX1, or CCS does not produce a change in cisplatin sensitivity that exceeds the variance found within the parental population, suggesting that they are not essential to the mechanism by which cDDP enters these cell lines and is transported to the nucleus.
View details for DOI 10.1039/c6mt00076b
View details for Web of Science ID 000384311300016
View details for PubMedID 27157188
View details for PubMedCentralID PMC5025354
The copper transporter 1 (CTR1) is required to maintain the stability of copper transporter 2 (CTR2)
2015; 7 (11): 1477–87
Mammalian cells have two influx Cu transporters that form trimers in membranes. CTR1 is the high affinity transporter that resides largely in the plasma membrane, and CTR2 is the low affinity transporter that is primarily associated with vesicular structures inside the cell. The major differences between CTR1 and CTR2 are that CTR1 contains a HIS/MET-rich domain N-terminal of the METS that participate in the first two stacked rings that form the pore, and a longer C-terminal tail that includes a Cu binding HIS-CYS-HIS (HCH) motif right at the end. It has been reported that CTR1 and CTR2 are physically associated with each other in the cell. We used the CRISPR-Cas9 technology to knock out either CTR1 or CTR2 in fully malignant HEK293T and OVCAR8 human ovarian cancer cells to investigate the interaction of CTR1 and CTR2. We report here that the level of CTR2 protein is markedly decreased in CTR1 knockout clones while the CTR2 transcript level remains unchanged. CTR2 was found to be highly ubiquitinated in the CTR1 knock out cells, and inhibition of the proteasome prevented the degradation of CTR2 when CTR1 was not present while inhibition of autophagy had no effect. Re-expression of CTR1 rescued CTR2 from degradation in the CTR1 knockout cells. We conclude that CTR1 is essential to maintain the stability of CTR2 and that in the absence of CTR1 CTR2 is degraded by the proteasome. This reinforces the concept that the functions of CTR1 and CTR2 are inter-dependent within the Cu homeostasis system.
View details for DOI 10.1039/c5mt00131e
View details for Web of Science ID 000364822500002
View details for PubMedID 26205368
View details for PubMedCentralID PMC4635045
Molecular modulation of the copper and cisplatin transport function of CTR1 and its interaction with IRS-4
2014; 90 (4): 379–87
The copper influx transporter CTR1 is also a major influx transporter for cisplatin (cDDP) in tumor cells. It influences the cytotoxicity of cDDP both in vivo and in vitro. Whereas Cu triggers internalization of CTR1 from the plasma membrane, cDDP does not. To investigate the mechanisms of these effects, myc-tagged forms of wild type hCTR1 and variants in which Y103 was converted to alanine, C189 was converted to serine, or the K178/K179 dilysine motif was converted to alanines were re-expressed in mouse embryo cells in which both alleles of CTR1 had been knocked out and also in HEK293T cells. The Y103A mutation and to a lesser extent the C189S mutation reduced internalization of CTR1 induced by Cu while the K178A/K179A had little effect. Both Y103 and C189 were required for Cu and cDDP transport whereas the K178/K179 motif was not. While Y103 lies in an YXXM motif that, when phosphorylated, is a potential docking site for phosphatidylinositol 3-kinase and other proteins involved in endocytosis, Western blot analysis of immunoprecipitated myc-CTR1, and proteomic analysis of peptides derived from CTR1, failed to identify any basal or Cu-induced phosphorylation. However, proteomic analysis did identify an interaction of CTR1 with IRS-4 and this was confirmed by co-immunoprecipitation from HEK cells expressing either FLAG-CTR1 or myc-CTR1. The interaction was greater in the Y103A-expressing cells. We conclude that Y103 is required for the internalization of hCTR1 in response to Cu, that this occurs by a mechanism other than phosphorylation and that mutation of Y103 modulates the interaction with IRS-4.
View details for DOI 10.1016/j.bcp.2014.06.019
View details for Web of Science ID 000339460200006
View details for PubMedID 24967972
View details for PubMedCentralID PMC4343213
Characterization of a monoclonal antibody capable of reliably quantifying expression of Human Copper Transporter 1 (hCTR1)
JOURNAL OF TRACE ELEMENTS IN MEDICINE AND BIOLOGY
2014; 28 (2): 151–59
Human copper transporter 1 (hCTR1) is the high-affinity copper influx transporter in mammalian cells that also mediates the influx of cisplatin. Loss of hCTR1 expression has been implicated in the development of resistance to this cancer chemotherapeutic agent. It has turned out to be very difficult to develop antibodies to hCTR1 and polyclonal antibodies produced by different laboratories have yielded conflicting results. We have characterized a newly-available rabbit monoclonal antibody that reacts with an epitope on the N-terminal end of hCTR1 that now permits rigorous identification and quantification of hCTR1 using Western blot analysis. Postnuclear membrane (PNM) preparations made from cells engineered to express high levels of myc-tagged hCTR1, and cells in which the expression of hCTR1 was knocked down, were used to characterize the antibody. The identity of the bands detected was confirmed by immunoprecipitation, surface biotinylation and deglycosylation of myc-tagged hCTR1. Despite the specificity expected of a monoclonal antibody, the anti-hCTR1 detected a variety of bands in whole cell lysates (WCL), which made it difficult to quantify hCTR1. This problem was overcome by isolating post-nuclear membranes and using these for further analysis. Three bands were identified using this antibody in PNM preparations that migrated at 28, 33-35 and 62-64kDa. Multiple lines of evidence presented here suggest that the 33-35 and 62-64kDa bands are hCTR1 whereas the 28kDa band is a cross-reacting protein of unknown identify. The 33-35kDa band is consistent with the expected MW of the glycosylated hCTR1 monomer. This analysis now permits rigorous identification and quantification of hCTR1.
View details for DOI 10.1016/j.jtemb.2013.12.003
View details for Web of Science ID 000335706000008
View details for PubMedID 24447817
View details for PubMedCentralID PMC3989404
Copper influx transporter 1 is required for FGF, PDGF and EGF-induced MAPK signaling
2012; 84 (8): 1007–13
Copper transporter 1 (CTR1) is the major copper (Cu) influx transporter in mammalian cells. We report here that CTR1 is required for the activation of signaling to the MAPK pathway by the ligands of three major receptor tyrosine kinases (RTK) including FGF, PDGF and EGF. Induction of Erk1/2 phosphorylation was compared in isogenic wild type CTR1(+/+) and CTR1(-/-) cells. Whereas all three ligands increased pErk1/2 in the CTR1(+/+) cells, they failed to do this in CTR1(-/-) cells. While FGF did not enhance the phosphorylation of AKT in the CTR1(+/+) cells, both PDGF and EGF increased pAKT in the CTR1(+/+) but not CTR1(-/-) cells. The deficit in Erk1/2 phosphorylation in the CTR1(-/-) cells was rescued by adding Cu to the medium, and it was induced in CTR1(+/+) cells by treatment with a Cu chelator. Intracellular Cu availability was reduced in the CTR1(-/-) cells as reflected by increased expression of the Cu chaperone CCS. The failure of RTK-induced signaling to both Erk1/2 and AKT suggested the presence of a Cu-dependent step upstream of Ras. The Cu-dependent enzyme SOD1 is responsible for generating the hydrogen peroxide in response to RTK activation that serves to inhibit phosphatases that normally limit RTK signaling. SOD1 activity was reduced by a factor of 17-fold in the CTR1(-/-) cells, and addition of hydrogen peroxide restored signaling. We conclude that Cu acquired from CTR1 is required for signaling in pathways regulated by RTKs that play major roles in development and cancer.
View details for DOI 10.1016/j.bcp.2012.07.014
View details for Web of Science ID 000309307100004
View details for PubMedID 22842628
View details for PubMedCentralID PMC3464187
TRIM24 links a non-canonical histone signature to breast cancer
2010; 468 (7326): 927-U320
Recognition of modified histone species by distinct structural domains within 'reader' proteins plays a critical role in the regulation of gene expression. Readers that simultaneously recognize histones with multiple marks allow transduction of complex chromatin modification patterns into specific biological outcomes. Here we report that chromatin regulator tripartite motif-containing 24 (TRIM24) functions in humans as a reader of dual histone marks by means of tandem plant homeodomain (PHD) and bromodomain (Bromo) regions. The three-dimensional structure of the PHD-Bromo region of TRIM24 revealed a single functional unit for combinatorial recognition of unmodified H3K4 (that is, histone H3 unmodified at lysine 4, H3K4me0) and acetylated H3K23 (histone H3 acetylated at lysine 23, H3K23ac) within the same histone tail. TRIM24 binds chromatin and oestrogen receptor to activate oestrogen-dependent genes associated with cellular proliferation and tumour development. Aberrant expression of TRIM24 negatively correlates with survival of breast cancer patients. The PHD-Bromo of TRIM24 provides a structural rationale for chromatin activation through a non-canonical histone signature, establishing a new route by which chromatin readers may influence cancer pathogenesis.
View details for DOI 10.1038/nature09542
View details for Web of Science ID 000285344600039
View details for PubMedID 21164480
View details for PubMedCentralID PMC3058826
Targeting DNA Repair in Chronic Lymphocytic Leukemia Cells with a Novel Acyclic Nucleotide Analogue, GS-9219
CLINICAL CANCER RESEARCH
2009; 15 (11): 3760–69
GS-9219 is a cell-permeable prodrug of the acyclic nucleotide analogue 9-(2-phosphonylmethoxyethyl)guanine (PMEG); the incorporation of the active metabolite PMEG diphosphate (PMEGpp) into DNA results in DNA chain termination due to the lack of a 3'-hydroxyl moiety. We hypothesized that the incorporation of PMEGpp into DNA during repair resynthesis would result in the inhibition of DNA repair and the accumulation of DNA breaks in chronic lymphocytic leukemia (CLL) cells that would activate signaling pathways to cell death.To test this hypothesis, CLL cells were irradiated with UV light to stimulate nucleotide excision repair pathways, enabling the incorporation of PMEGpp into DNA. The combination effects of GS-9219 and DNA-damaging agents and the signaling mechanisms activated in response to DNA repair inhibition by GS-9219, as well as changes in CLL cell viability, were investigated.PMEGpp was incorporated into DNA in CLL cells when nucleotide excision repair was activated by UV. Following PMEGpp incorporation, DNA repair was inhibited, which led to the accumulation of DNA strand breaks. The presence of DNA strand breaks activated the phosphatidylinositol 3-kinase-like protein kinase family members ataxia-telangiectasia mutated and DNA-dependent protein kinase. P53 was phosphorylated and stabilized in response to the inhibition of DNA repair. P53 targeted proteins, Puma and Bax, were up-regulated and activated. The combination of GS-9219 and DNA-damaging agents resulted in more cell death than the sum of the single agents alone.GS-9219 inhibits DNA repair in CLL cells, an action that stimulates signaling pathways for apoptosis induction.
View details for DOI 10.1158/1078-0432.CCR-08-2848
View details for Web of Science ID 000266659000015
View details for PubMedID 19435836