Semi-quantitative RT-PCR method to estimate full-length mRNA levels of the multidrug resistance gene

Experimental validation of in silico target predictions on synergistic protein targets

Two relatively recent trends have become apparent in current early stage drug discovery settings: firstly, a revival of phenotypic screening strategies and secondly, the increasing acceptance that some drugs work by modulating multiple targets in parallel (‘multi-target drugs’).

QTL underlying resistance to two HG types of Heterodera glycines found in soybean cultivar 'L-10'

BACKGROUND

Resistance of soybean (Glycine max L. Merr.) cultivars to populations of cyst nematode (SCN; Heterodera glycines I.) was complicated by the diversity of HG Types (biotypes), the multigenic nature of resistance and the temperature dependence of resistance to biotypes. The objective here was to identify QTL for broad-spectrum resistance to SCN and examine the transcript abundances of some genes within the QTL.

RESULTS

A Total of 140 F(5) derived F(7) recombinant inbred lines (RILs) were advanced by single-seed-descent from a cross between 'L-10' (a soybean cultivar broadly resistant to SCN) and 'Heinong 37' (a SCN susceptible cultivar). Associated QTL were identified by WinQTL2.1. QTL Qscn3-1 on linkage group (LG) E, Qscn3-2 on LG G, Qscn3-3 on LG J and Qscn14-1 on LG O were associated with SCN resistance in both year data (2007 and 2008). Qscn14-2 on LG O was identified to be associated with SCN resistance in 2007. Qscn14-3 on LG D2 was identified to be associated with SCN resistance in 2008. Qscn14-4 on LG J was identified to be associated with SCN resistance in 2008. The Qscn3-2 on LG G was linked to Satt309 (less than 4 cM), and explained 19.7% and 23.4% of the phenotypic variation in 2007 and 2008 respectively. Qscn3-3 was less than 5 cM from Satt244 on LG J, and explained 19.3% and 17.95% of the phenotypic variations in 2007 and 2008 respectively. Qscn14-4 could explain 12.6% of the phenotypic variation for the SCN race 14 resistance in 2008 and was located in the same region as Qscn3-3. The total phenotypic variation explained by Qscn3-2 and Qscn3-3 together was 39.0% and 41.3% in 2007 and 2008, respectively. Further, the flanking markers Satt275, Satt309, Sat_350 and Satt244 were used for the selection of resistant lines to SCN race 3, and the accuracy of selection was about 73% in this RIL population. Four genes in the predicted resistance gene cluster of LG J (chromosome 16) were successfully cloned by RT-PCR. The transcript encoded by the gene Glyma16g30760.1 was abundant in the SCN resistant cultivar 'L-10' but absent in susceptible cultivar 'Heinong 37'. Further, the abundance was higher in root than in leaf for 'L-10'. Therefore, the gene was a strong candidate to underlie part of the resistance to SCN.

CONCLUSIONS

Satt275, Satt309, Sat_305 and Satt244, which were tightly linked to the major QTL for resistance to SCN on LG G and J, would be candidates for marker-assisted selection of lines resistant to the SCN race 3. Among the six RLK genes, Glyma16g30760.1 was found to accumulate transcripts in the SCN resistance cultivar 'L-10' but not in 'Heinong 37'. The transcript abundance was higher in root than in leaf for L-10.

A novel MDR1 GT1292-3TG (Cys431Leu) genetic variation and its effect on P-glycoprotein biologic functions

P-glycoprotein (P-gp) is a membrane-bound transporter protein that is encoded by the human multidrug resistance gene MDR1 (ABCB1). P-gp recognizes a wide range of xenobiotics, is pivotal in mediating cancer drug resistance, and plays an important role in limiting drug penetration across the blood-brain barrier. MDR1 genetic variation can lead to changes in P-gp function and may have implications on drug pharmacokinetics. We have identified a novel MDR1 (GT1292-3TG) (Cys431Leu) genetic variation through systematic profiling of subjects with leukemia. The cellular and transport function of this variation was investigated with recombinant human embryonic kidney cells expressing MDR1. Compared with the wild type, MDR1 (GT1292-3TG) recombinant cells exhibited a lower drug resistance phenotype for a panel of chemotherapeutic agents. When compared with wild type, MDR1 (GT1292-3TG) recombinant cells exposed exhibited a 75% decrease in IC₅₀ for doxorubicin (162.6 ± 17.4 to 37.9 ± 2.6 nM) and a 50% decrease in IC(50) for paclitaxel (155.7 ± 27.5 to 87.7 ± 9.2 nM), vinblastine (128.0 ± 15.9 to 65.9 ± 5.1 nM), and vincristine (593.7 ± 61.8 to 307.3 ± 17.0 nM). The effects of the Cys431Leu variation, due to MDR1 (GT1292-3TG) nucleotide transition, on P-gp-dependent intracellular substrate accumulation appeared to be substrate dependent where doxorubicin, vinblastine, and paclitaxel exhibit an increased accumulation (p < 0.05), while verapamil and Hoechst33342 exhibit a decreased intracellular concentration compared with wild type (p < 0.05). Collectively, these data suggest MDR1 (GT1292-3TG) variation of P-gp may reduce drug resistance and that subjects with this genotype undergoing chemotherapy with drugs that are transported by P-gp could potentially be more responsive to therapy than those with MDR1 wild-type genotype.

A novel human multidrug resistance gene MDR1 variant G571A (G191R) modulates cancer drug resistance and efflux transport

The human multidrug resistance gene MDR1 encodes a membrane-bound transporter P-glycoprotein (Pgp) that confers the drug resistance of cancer cells by mediating an ATP-dependent drug efflux transport. We and others have reported a number of functionally significant MDR1 variants, including G1199A and G1199T, that modulate cancer drug resistance and intracellular levels of antivirals. In this report, we describe a novel G571A variant of MDR1 detected in 6.4% of leukemia patients. Because this nucleotide modification gives rise to an amino acid change from Gly to Arg at the 191 amino acid position of Pgp, we have developed and characterized the functional affect of the G571A variant in stable, recombinant cells. Using six chemotherapeutic drugs, doxorubicin HCl, daunorubicin HCl, vinblastine sulfate, vincristine sulfate, taxanes (paclitaxel), and epipodophyllotoxin (etoposide, VP-16), we found that the MDR1(571A) variant selectively reduced the degree of Pgp-mediated resistance in drug-dependent manner. Although there was a minimal effect on doxorubicin and daunorubicin, the MDR1-dependent resistance on vinblastine, vincristine, paclitaxel, and etoposide was reduced by approximately 5-fold. The increased drug sensitivity in MDR1(571A), compared with MDR1(wt), paralleled the intracellular drug levels. These data suggest that individuals with this novel MDR1 variant, the 571A genotype, may be more sensitive to the specific anticancer drugs that are Pgp substrates.

A novel MDR1 G1199T variant alters drug resistance and efflux transport activity of P-glycoprotein in recombinant Hek cells

The human multidrug resistance gene MDR1 encodes the protein product P-glycoprotein (P-gp). P-gp is an integral membrane protein which mediates ATP-dependent substrate efflux. We recently discovered a novel G --> T variant at 1199 nucleotide position of MDR1 which exhibits a 2.3% allelic frequency in leukemia patients. The functional effects of this MDR1-G1199T variant were evaluated with recombinant HEK cells that stably express the wild-type, G1199A, or G1199T variant of the MDR1 protein, P-gp, at comparable levels. A panel of cytotoxic P-gp substrates comprising doxorubicin, vinblastine, vincristine, paclitaxel, or topotecan (a poor P-gp substrate) was used to evaluate the functional impact of G1199 variations. Compared to MDR1(wt), MDR1(G1199A) exhibited an increased resistance to doxorubicin, paclitaxel, vinblastine, and vincristine. In contrast, MDR1(G1199T) reduced resistance to (1/4) that of MDR1(wt) for all drugs except topotecan. Expression of MDR1 exhibits some degree of resistance to topotecan, but 1199 variation has no impact. These data were consistent with the variation in intracellular doxorubicin concentrations measured in MDR1 recombinant cells. Our results suggest that patients with the novel MDR1-G1199T variant may exhibit a lower degree of MDR1 dependent chemoresistance, and those with the G1199A polymorphism may exhibit a higher degree of resistance, compared with MDR1 wild-type patients.

Multidrug Resistance Gene G1199A Polymorphism Alters Efflux Transport Activity of P-Glycoprotein

The significance of the human multidrug resistance gene (MDR1) G1199A polymorphism, resulting in a Ser400Asn modification in P-glycoprotein (P-gp), remains unclear. We have developed stable recombinant LLC-PK1 epithelial cells expressing either MDR1wt or MDR11199 to evaluate functional consequences of G1199A [N-(4-[2-(1,2,3,4-tetrahydro-6,7-dimethoxy-2-isoquinolinyl)ethyl]-phenyl)-9,10-dihydro-5-methoxy-9-oxo-4-acridine carboxamide]. P-gp activity observed in MDR1wt and MDR11199 cells was completely inhibited in the presence of the specific P-gp inhibitor GF120918. Comparable expression of mRNA and protein in the MDR1-expressed cells and correct localization of P-gp in the apical membrane of recombinant cells was verified. Mean intracellular rhodamine-123 (R123) accumulation, measured by flow cytometry, was approximately 4.75-fold higher in MDR11199 recombinant cells than MDR1wt cells. Cytotoxicity studies have shown that MDR1wt and MDR11199 cells exhibited similar resistance, as measured by EC50 values, to doxorubicin (155 +/- 68 versus 120 +/- 32 nM); however, MDR11199 cells were more resistant to vinblastine (1.41 +/- 0.51 versus 15.7 +/- 4.0 nM; p < 0.001) and vincristine (1.18 +/- 0.56 versus 3.41 +/- 1.47 nM; p < 0.05). The apparent transepithelial permeability ratios of R123 in MDR1wt and MDR11199 cells were 3.54 +/- 0.94 and 2.02 +/- 0.51 (p < 0.05), respectively. Therefore, the G1199A polymorphism alters the efflux and transepithelial permeability of a fluorescent substrate and sensitivity to select cytotoxic agents, which may influence drug disposition and therapeutic efficacy of some P-gp substrates.

Only truncated, not complete cytochrome p450 2D6 RNA transcript and no detectable enzyme activity are expressed in human lymphocytes

Genotyping of the highly polymorphic cytochrome p450 2D6 (CYP2D6) permits a gross classification of individual phenotype (viz. ultra-rapid, extensive, and poor metabolizers). It does not, however, provide a precise prediction of CYP2D6 activity, particularly in an individual possessing at least one functional CYP2D6 allele. It has been suggested that the level of mRNA expression or enzyme activity in lymphocytes, isolated from blood, could potentially provide a better quantitative estimate of in vivo hepatic enzymatic activity in human subjects. Although short sequences of CYP2D6 mRNA have been detected in human lymphocytes by reverse transcriptase-polymerase chain reaction (RT-PCR) that suggests the potential use of lymphocyte RNA as a readily accessible biomarker, it is not known whether a functional enzyme is expressed in human lymphocytes. In this study, human lymphocyte activity was assessed with a CYP2D6-specific, high-turnover probe substrate that is severalfold more sensitive than traditional markers of CYP2D6 (e.g., dextromethorphan). CYP2D6 catalytic activity could not be detected in homogenates of human lymphocytes, even at high protein concentrations and with supplementation of enzyme cofactors. Further RT-PCR analysis of lymphocytes collected from eight human donors revealed the presence of only a fragment, but not the complete transcript, of CYP2D6 mRNA. Northern blot RNA transcript analysis also failed to indicate the presence of the full-length transcript in lymphocytes. Collectively, these data indicate that human lymphocytes express neither the full-length CYP2D6 mRNA transcript nor functional enzyme activity. Therefore, the utility of lymphocytes as a functional biomarker for CYP2D6 enzyme activity is not clear at present.

Cloning and characterization of the rat multidrug resistance-associated protein 1

Multidrug resistance-associated protein 1 (MRP1) was originally shown to confer resistance of human tumor cells to a broad range of natural product anticancer drugs. MRP1 has also been shown to mediate efflux transport of glutathione and glucuronide conjugates of drugs and endogenous substrates. An ortholog of MRP1 in the mouse has been cloned and characterized. Significant functional differences between murine and human MRP1 have been noted. Since drug disposition and pharmacology studies often are conducted in rats, there is a need to clone and characterize the rat ortholog of MRP1. We isolated a rat MRP1 (rMRP1) cDNA from rat brain astrocytes, characterized its coding sequences, and verified the transport activity of the protein expressed in MRP1 cDNA-transfected Madin-Darby canine kidney (MDCK) cells. Our results showed that rMRP1 has a coding sequence of 4599 bp, which predicts a polypeptide of 1533 amino acids with an apparent molecular weight of 190 kd by Western immunoblot analysis. rMRP1-transfected MDCK cells are capable of efflux transport of a fluorescent MRP1 marker - calcein - that is inhibitable by known MRP1 inhibitors, indomethacin, and MK571. Sequence analysis indicates that rMRP1 is more closely related to mouse MRP1 than human MRP1.