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Differential expression of E-cadherin, N-cadherin and beta-catenin in proximal and distal segments of the rat nephron.

BACKGROUND: The classical cadherins such as E- and N-cadherin are Ca2+-dependent cell adhesion molecules that play important roles in the development and maintenance of renal epithelial polarity. Recent studies have shown that a variety of cadherins are present in the kidney and are differentially expressed in various segments of the nephron. However, the interpretation of these findings has been complicated by the fact that the various studies focused on different panels of cadherins and utilized different species. Moreover, since only a few of the previous studies focused on the rat, information regarding the expression and localization of renal cadherins in this important species is lacking. In the present study, we have employed dual immunofluorescent labeling procedures that utilized specific antibodies against either E- or N-cadherin, along with antibodies that target markers for specific nephron segments, to characterize the patterns of cadherin expression in frozen sections of adult rat kidney. RESULTS: The results showed that N-cadherin is the predominant cadherin in the proximal tubule, but is essentially absent in other nephron segments. By contrast, E-cadherin is abundant in the distal tubule, collecting duct and most medullary segments, but is present only at very low levels in the proximal tubule. Additional results revealed different patterns of N-cadherin labeling along various segments of the proximal tubule. The S1 and S2 segments exhibit a fine threadlike pattern of labeling at the apical cell surface, whereas the S3 segment show intense labeling at the lateral cell-cell contacts. CONCLUSIONS: These results indicate that E- and N-cadherin are differentially expressed in the proximal and distal tubules of rat kidney and they raise the possibility that differences in cadherin expression and localization may contribute to the differences in the susceptibility of various nephron segments to renal pathology or nephrotoxic injury.

Animals↗

Differential expression of porins OmpP2A and OmpP2B of Haemophilus ducreyi.

Haemophilus ducreyi is a strict human pathogen and the causative agent of the sexually transmitted disease chancroid. The genome of the human-passaged strain of H. ducreyi (35000HP) contains two homologous genes whose protein products have estimated molecular masses of 46 and 43 kDa. A comparative analysis of the deduced amino acid sequences revealed that these proteins share 27 to 33% identity to the outer membrane protein P2 (OmpP2), a major porin of Haemophilus influenzae. Therefore, these proteins have been designated OmpP2A and OmpP2B, respectively. The detection of ompP2A and ompP2B transcripts by reverse transcriptase PCR indicated that these genes were independently transcribed in H. ducreyi 35000HP. Western blot analysis of outer membrane proteins isolated from a geographically diverse collection of H. ducreyi clinical isolates revealed that OmpP2A and OmpP2B were differentially expressed among these strains. Although PCR analysis suggested that ompP2A and ompP2B were conserved among the strains tested, the differential expression observed was due to nucleotide additions and partial gene deletions. Purified OmpP2A and OmpP2B were isolated under nondenaturing conditions, and subsequent analysis demonstrated that these two proteins exhibited porin activity. OmpP2A and OmpP2B are the first porins described for H. ducreyi.

Amino Acid Sequence↗

Segmental message stabilization as a mechanism for differential expression from the Zymomonas mobilis gap operon.

In Zymomonas mobilis, three- to fourfold more glyceraldehyde-3-phosphate dehydrogenase protein than phosphoglycerate kinase is needed for glycolysis because of differences in catalytic efficiency. Consistent with this requirement, higher levels of glyceraldehyde-3-phosphate dehydrogenase were observed with two-dimensional polyacrylamide gel electrophoresis. The genes encoding these enzymes (gap and pgk, respectively) form a bicistronic operon, and some form of regulation is required to provide this differential expression. Two transcripts were observed in Northern RNA analyses with segments of gap as a probe: a more abundant 1.2-kb transcript that contained gap alone and a 2.7-kb transcript that contained both genes. Based on the relative amounts of these transcripts, the coding regions for glyceraldehyde-3-phosphate dehydrogenase were calculated to be fivefold more abundant than those for phosphoglycerate kinase. Assuming equal translational efficiency, this is sufficient to provide the observed differences in expression. Operon fusions with lacZ provided no evidence for intercistronic terminators or attenuation mechanisms. Both gap operon messages were very stable, with half-lives of approximately 16 min (1.2-kb transcript) and 7 min (2.7-kb transcript). Transcript mapping and turnover studies indicated that the shorter gap message was a stable degradation product of the full-length message. Thus differential expression of gap and pgk results primarily from increased translation of the more stable 5' segment of the transcript containing gap. The slow turnover of the messages encoding glyceraldehyde-3-phosphate dehydrogenase and phosphoglycerate kinase is proposed as a major feature contributing to the high level of expression of these essential enzymes.

Base Sequence↗

Differentially expressed genes in the Trypanosoma brucei life cycle identified by RNA fingerprinting.

RNA fingerprinting by arbitrarily primed polymerase chain reaction (RAP-PCR) was used to identify genes that were differentially expressed during the life cycle of Trypanosoma brucei, as well as in response to heat shock. The standard RAP-PCR protocol was varied in two ways. First, the PCR reactions sometimes included a primer derived from the 5' mini-exon sequence, to ensure that most of the products contained the 5' end of mRNAs. Second, differentially amplified products were reamplified, isolated on single strand conformation polymorphism (SSCP) gels, cloned, and sequenced. Clones representing 32 different expressed sequence tags (ESTs) were obtained. Twenty-four ESTs were confirmed as differentially expressed by RT-PCR between different stages of the parasite cycle, or in response to temperature elevation. Nine clones had significant similarities to sequences already in the database. These transcripts included genes encoding cell surface proteins, metabolic enzymes, and heat shock proteins, either from trypanosomes or other organisms. Of particular interest, ESAG1 was shown to be heat-inducible in the procyclic stage. Most of the transcripts were unrelated to any other sequences in the database, and were deposited as new ESTs. The identification of stage-specific and heat shock-regulated transcripts will complement the growing T. brucei database. In addition, this experimental approach allows previous entries in the sequence database to be annotated with regulatory information.

Animals↗

Differential expression of the interleukin 2 receptor beta (p75) chain on human peripheral blood natural killer subsets.

The interleukin-2 receptor (IL-2R) is composed of at least two subunits, the IL-2R alpha (P55, CD25/Tac) and IL-2R beta (p70-75) chains. In the present study we have identified the quantitative expression of IL-2R beta on subsets of NK cells in peripheral blood using flow cytometry and a recently established mAb against IL-2R beta (TU27). We demonstrate that NK cells are not a homogeneous population but that phenotypic subsets exist, and that the levels of IL-2R beta expression correlate with these subsets. The levels of IL-2R beta expression on NK subsets are CD3- CD16- CD56bright NK cells (immature NK) greater than CD16+CD4- NK cells (mature NK) greater than CD16+CD57+ NK cells (more mature NK) in adult peripheral blood lymphocytes. The level of IL-2R beta expression on CD16+ NK cells in cord blood is significantly higher than that in adult PBL. These findings suggest that there may be a inverse relationship between IL-2R beta expression and the differentiation of NK cells. IL-2R beta, preferentially expressed on the NK cells, may play an important role in differentiation and maturation of NK cells.

Adult↗

Immature transformed rat islet beta-cells differentially express C-peptides derived from the genes coding for insulin I and II as well as a transfected human insulin gene.

Synthetic peptides representing unique sequences in rat proinsulin C-peptide I and II were used to generate highly specific antisera, which, when applied on sections of normal rat pancreas, confirm a homogeneous coexpression of the two C-peptides in all islet beta-cells. Insulin gene expression is induced in the transformed heterogeneous rat islet cell clone, NHI-6F, by transient in vivo passage. During this process a transfected human insulin gene is coactivated with the endogenous nonallelic rat insulin I and II genes. Newly established cultures from NHI-6F insulinomas having a high frequency of insulin-producing cells showed highly differential expression at the cellular level of the three proinsulin C-peptide immunoreactivities, as follows: C-peptide I greater than human C-peptide greater than C-peptide II. The fractions of cells expressing human C-peptide and C-peptide II decreased in time and were absent after more than 50 successive passages, while a C-peptide I-producing population was still present. Double-labeling experiments revealed a heterogeneous distribution of the three different C-peptides. Surprisingly, in the early passages a large fraction of cells would express only a single species of proinsulin-C-peptide immunoreactivity but still at high levels. However, rat C-peptide II and human C-peptide were often colocalized, even in later passages. In situ hybridization studies combined with the immunocytochemical data suggest that the differential expression occurs at the level of transcription.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗

Differential expression of the mammalian homologue of fasciclin II during olfactory development in vivo and in vitro.

Developing olfactory sensory neurons are guided to the glomeruli of the olfactory bulb by an increasingly stringent process that is influenced by expression of odorant receptors, cell adhesion molecules (CAMs), and other kinds of signaling cascades. A fundamental feature of the projection is the connecting of broad zones in the epithelium to broad zones in the bulb, also termed rhinotopy. One molecule that parallels and may aid neurons in establishing rhinotopy is the mammalian homologue of fasciclin II (OCAM/mamFas II; also known as RNCAM and NCAM-2), an immunoglobulin superfamily CAM that is differentially expressed in the developing and mature olfactory epithelium (OE): Axons elaborated by ventral and lateral epithelium express the protein at high levels, whereas dorsomedial axons express little or no OCAM/mamFas II. Our investigation has demonstrated that OCAM/mamFas II is detectable early in the development of the rat OE. mRNA is evident on RT-PCR and in situ hybridization by E12.5, and protein is apparent by immunohistochemistry by E13.5. By using a tissue culture system that separates ventral septal epithelium (OCAM/mamFas II-positive) from dorsal (OCAM/mamFas II-negative), we find that explants maintain protein expression levels in vitro that are characteristic of the phenotype at the original location in vivo. At least some neurons are born in culture, suggesting that any cues that direct differential expression are also maintained in vitro. Finally, high OCAM/mamFas II expression correlates with increased growth and fasciculation of olfactory axons in vitro. These data and the similarity between OCAM/mamFas II, on the one hand, and fasciclin II and NCAM, on the other, suggest that OCAM/mamFas II might play a role in growth and fasciculation of primary olfactory axons during development of the projection.

Animals↗

Differential expression of insulin-like growth factor binding protein 1 and ferritin light polypeptide in gestational trophoblastic neoplasia: combined cDNA suppression subtractive hybridization and microarray study.

BACKGROUND: Hydatidiform mole (HM), the most common type of gestational trophoblastic diseases, can be considered as placenta with abnormal chromosome composition with potential of malignant transformation. Few biologic markers can predict subsequent development of persistent gestational trophoblastic neoplasia (GTN) requiring chemotherapy. METHODS: Suppression subtractive hybridization (SSH) combined with cDNA microarray was used to compare the differential expression pattern of HM that spontaneously regressed and that subsequently developed metastatic GTN. Tissue-specific chips were constructed from the subtracted cDNA libraries, followed by cDNA microarray analysis. Verification by quantitative RNA analysis by real-time polymerase chain reaction (PCR) and immunohistochemical analysis was performed in 23 genotyped complete HM. RESULTS: Sixteen differentially expressed transcripts were identified. Quantitative RNA analysis confirmed down-regulation of ferritin light polypeptide (FTL) (P = 0.037) and insulin-like growth factor binding protein 1 (IGFBP1) (P = 0.037) in HM that subsequently developed GTN when compared with those HM that regressed. Immunohistochemical analysis further confirmed reduced IGFBP1 protein (P = 0.03) expression in HM that developed GTN. CONCLUSIONS: Findings showed that reduced expression of genes related to cell invasion and immunosuppression, especially FTL and IGFBP1, were associated with development of GTN, and this finding may provide a better understanding of the pathogenesis of GTN. The potential application of FTL and IGFBP1 in management of patients with HM should be explored.

Adolescent↗

Identification of differentially expressed cDNA clones from gerbil cochlear outer hair cells.

In order to identify genes that are associated with outer hair cell(OHC)-specific function, a plasmid library enriched with OHC-specific gene products was constructed using single cell-type-specific complementary DNA (cDNA) and a PCR subtractive hybridization strategy. As a first step, we created separate OHC and inner hair cell (IHC) cDNA pools from individually collected cells using a nonspecific reverse transcription polymerase chain reaction. Next, the OHC cDNA was subtracted against IHC cDNA using a PCR-based subtractive technique. IHCs and OHCs share many common features, making IHC cDNA an ideal 'driver' to 'subtract away' common hair cell gene products and enrich differentially expressed cDNAs, including OHC-specific genes. The subtracted OHC cDNAs were then cloned to generate an OHC - IHC subtracted cDNA plasmid library. Finally, a differential screening procedure was performed, resulting in 477 differentially positive clones. After analysis of these 477 clones, 50 known genes were identified, including two previously known OHC-specific proteins: oncomodulin and the recently described motor protein prestin. An additional 84 novel clones were also found. As this library of cDNA fragments represents differentially expressed genes in OHCs, it can be used as starting material for isolation and characterization of a complete set of OHC gene products, an important step in investigating normal and abnormal cochlear function.

Animals↗

Inverse labeling-mass spectrometry for the rapid identification of differentially expressed protein markers/targets.

Comparative proteomic studies can lead to the identification of protein markers for disease diagnostics and protein targets for potential disease interventions. An inverse labeling strategy based on the principle of protein stable isotope labeling and mass spectrometric detection has been successfully applied to three general protein labeling methods. In contrast to the conventional single experiment approach, two labeling experiments are performed in which the initial labeling is reversed in the second experiment. Signals from differentially expressed proteins will distinguish themselves by exhibiting a characteristic pattern of isotope intensity profile reversal that will lead to the rapid identification of these proteins. Application of the inverse labeling method is demonstrated using model systems for protein chemical labeling, protein proteolytic labeling, and protein metabolic labeling. The methodology has clear advantages which are illustrated in the various studies. The inverse labeling strategy permits quick focus on signals from differentially expressed proteins (markers/targets) and eliminates ambiguities caused by the dynamic range of detection. In addition, the inverse labeling approach enables the unambiguous detection of covalent changes of proteins responding to a perturbation.

Chromatography, Liquid↗

Differential expression and subcellular localization for subunits of cAMP-dependent protein kinase during ram spermatogenesis.

The expression of mRNAs for the RI alpha, RII alpha, and C alpha subunits of cAMP-dependent protein kinase has been studied in different ram germ cells. The sizes of the specific RI alpha, RII alpha, and C alpha mRNAs, observed in germ cells were 1.6, 2.0, and 2.6 kb, respectively. RI alpha and C alpha mRNAs were mainly expressed in primary spermatocytes. A postmeiotic expression predominating in early spermatids was unique to RII alpha mRNA. The location of RI, RII alpha, and C subunits in well-defined organelles of ram spermatids and epididymal sperm was assessed by immunogold electron microscopy. In spermatids, RI, RII alpha, and C were essentially present in the forming acrosome and, to a lesser extent, in the nucleus. During sperm epididymal maturation, the protein kinases disappeared from the acrosome and were detected in a variety of sperm functional areas, such as the tip of the acrosome, the motility apparatus, and the membrane network. The present study on subunits of cAMP-dependent protein kinase supports the concept that specific functions are attached to the different subunits in that it shows differential expression and differential subcellular localization in germ cells.

Animals↗

Cloning of differentially expressed genes in skin fibroblasts from centenarians.

Normal human fibroblasts undergoing serial passaging have been extensively used to identify genes linked with aging. Most of the isolated genes relate to growth retardation signals and the failure of homeostasis that accompanies aging and senescence. In contrast, there is still limited knowledge regarding the nature of the genes that influence positively the rate of aging and longevity. Healthy centenarians represent the best example of successful aging and longevity. Studies using samples from these individuals have proved very valuable for identifying a variety of factors that contribute to successful aging. The aim of the current work was to take advantage of skin fibroblast cultures established from healthy donors including centenarians in order to clone differentially expressed genes in centenarians. First, we demonstrate that centenarian derived cultures follow the typical Hayflick curve and they enter senescence after serial passaging. Application of differential screening techniques in minimally passaged cultures of four control donors of different ages (18-80 years old) and four centenarians has resulted in the cloning of six differentially expressed genes in centenarians. Four of the cloned genes, namely adlican, KBL, EST 38 and EST 39, were over-expressed in centenarians, while VDUP1 and OCIF were down-regulated in the same samples. We have also compared the expression levels of two representative cloned genes in cultures of human embryonic and adult fibroblasts to establish potential links with replicative senescence. Interestingly, VDUP1 was found over-expressed in late passage cells, while EST 39 was down-regulated in the same cultures. Thus our work demonstrates that a combination of the use of both biopsies derived cells and classical in vitro cells passaging will facilitate the better understanding of the biology of aging and longevity.

Adult↗

Application of SELDI-TOF mass spectrometry for the identification of differentially expressed proteins in transformed follicular lymphoma.

Completion of the human genome project has focused scientific attention on the development of methods that permit rapid characterization of proteins that are encoded by the genome. Recent improvements in two-dimensional separation techniques in combination with protein identification software/databases and mass spectrometry (MS) now permit rapid comprehensive large-scale analysis of individual proteins within complex protein mixtures. We have performed pairwise comparisons of low-grade and transformed follicular lymphomas (FLs) in order to identify proteins that may be involved in FL progression using surface-enhanced laser desorption/ionization time-of-flight (SELDI-TOF) mass spectrometer (ProteinChip, Ciphergen Biosystems). This system utilizes preactivated differential binding surfaces to achieve multidimensional chromatography. The protein-bound chips were then analyzed by a SELDI-TOF mass spectrometer to generate protein profiles. In preliminary experiments, we established that the MS data obtained from SELDI-TOF MS were reproducible, and that reduction in sample complexity improved the ability to detect lower abundance proteins. With specific regard to FL transformation, we rapidly identified a number of potential candidate proteins involved in this process. These included an upregulated 32 kDa protein and a down-regulated 11.8 kDa protein. Protein database searches revealed several candidates, among them cyclin D3 (32.5 kDa) and caspase 3 (11.8 kDa) whose differential expression were confirmed by immunoblotting and/or immunohistochemical analysis on the primary tissue specimens. Our studies demonstrate the utility of SELDI-TOF-MS for the rapid discovery of differentially expressed proteins using femtomolar quantities of crude protein derived from biopsy material. The versatility of this methodology supports its application to the rapid discovery of potential biomarkers in a variety of cellular systems.

Antigens, CD20↗

Differentially expressed genes in rat dorsal root ganglia following peripheral nerve injury.

Ordered differential display PCR was used to identify differentially expressed genes in rat dorsal root ganglia at 7 days following chronic constriction injury (CCI) of the sciatic nerve. Fourteen differentially displayed cDNA bands were isolated, cloned and verified by RT-PCR. The four mRNAs were increased, which included mRNAs encoding heat shock protein 27, fatty acid binding protein, apolipoprotein D and one novel gene. Six down-regulated clones were microtubule-associated protein 1B, protein tyrosine phosphatase alpha, Kv1.2 channel, myelin protein SR13, medium-sized neurofilament protein, and one novel gene. Our results show that many differentially regulated genes after CCI may play a role in nerve degeneration and/or regeneration and provide a molecular framework for understanding the peripheral mechanism underlying neuropathic pain.

Animals↗

Differential expression of CD11b/CD18 (Mo1) and myeloperoxidase genes during myeloid differentiation.

During the course of differentiation of early human myeloid cells toward monocytes and granulocytes, cell surface expression of the cell adhesion molecule, CD11b/CD18 (Mo1) increases dramatically and expression of myeloperoxidase (MPO), a bacteriocidal enzyme, decreases markedly. Using the inducible promyelocytic cell line HL-60 as a model, we studied the mRNA expression of these genes. Differentiation of these cells along both a monocytic and a granulocytic pathway demonstrated that the mRNA levels of the two subunits of CD11b/CD18 increased in a pattern temporally and quantitatively similar to the increase in cell surface expression of this heterodimer. In contrast, the expression of MPO mRNA decreased in a temporal and quantitative pattern similar to the known decrease in MPO protein during differentiation, suggesting that regulation of these myeloid-specific proteins may occur at the level of mRNA expression. These findings have important implications with regard to the nature of the block in differentiation in acute nonlymphocytic leukemia and the regulation of myeloid gene expression.

Antigens, Differentiation↗

Differential expression of hyperpolarization-activated currents reveals distinct classes of visual cortical projection neurons.

Combining in vivo retrograde labeling and in vitro electrophysiological recording techniques, we examined the distributions, densities, and biophysical properties of hyperpolarization-activated inward currents in two types of isolated, identified visual cortical projection neurons, superior colliculus-projecting (SCP) and callosal-projecting (CP) cells. In SCP cells, two kinetically distinct time-dependent hyperpolarization-activated inward current components are present. We have termed these Ih,f and Ih,s to denote the fast and slow components, respectively, of Ih activation. In CP cells, in contrast, Ih,f and Ih,s are differentially expressed. In 59% of the CP cells examined, for example, both Ih,f and Ih,s were present. The properties of the currents are indistinguishable from those recorded from SCP cells, although both Ih,f and Ih,s are expressed at significantly lower densities in this subset of CP cells (as compared to the current densities in SCP cells). Of the remaining 41% of the CP cells studied, 26% were found to express only Ih,s, and 12% of the cells expressed neither Ih,f nor Ih,s. Taken together, these results reveal that the electrical properties of CP visual cortical neurons are considerably more heterogeneous than those of SCP cells. The differential expression of Ih,f and Ih,s is expected to influence the integrated responses of different types of cortical projection neurons to excitatory and inhibitory synaptic inputs.

Animals↗

Direct cloning of cell differential expression genes with full-length by a new strategy based on the multiple rounds of 'long distance' polymerase chain reaction and magnetic beads mediated subtraction.

The paper described a new cDNA subtractive cloning strategy. This strategy was based on the 'cap-finder' method, 'long distance' polymerase chain reaction (PCR), streptavidin magnetic beads mediated subtraction, and spin column chromatography. When PCR products were resolved on agarose gel after three rounds of subtraction, the 'single gene difference' group displayed a predominantly enriched band, but the 'multiple gene difference' group did not display any apparent difference. Of 200 clones inserted with 0.7-2 kb fragments from the 'multiple gene difference' group, 50% were identified to be new sequences and 35% were known. Of 100 new sequences, 35% contained coding regions and 75% were confirmed by dot-blotting to be differentially expressed by genes of the target cell. The results suggested that this strategy might be very efficient for full-length cloning of differentially expressed genes of the cell.

Cloning, Molecular↗

Differential expression of p53, p63 and p73 protein and mRNA for DMBA-induced hamster buccal-pouch squamous-cell carcinomas.

Abnormalities in the p53 gene are regarded as the most consistent of the genetic abnormalities associated with oral squamous-cell carcinoma. Two related members of the p53 gene family, p73 and p63, have shown remarkable structural similarity to p53, suggesting possible functional and biological interactions. The purpose of this study was to investigate the differential expression of p73, p63 and p53 genes for DMBA-induced hamster buccal-pouch squamous-cell carcinoma. Immunohistochemical analysis for protein expression and reverse transcriptase-polymerase chain reaction (RT-PCR) for mRNA expression were performed for 40 samples of hamster buccal pouches, the total being separated into one experimental group (15-week DMBA-treated; 20 animals) and two control groups (untreated and mineral oil-treated; 10 animals each). Using immunohistochemical techniques, nuclear staining of p53 and p73 proteins was detected in a subset of hamster buccal-pouch tissue specimens treated with DMBA for a period of 15 weeks, whereas p63 proteins were noted for all of the 20 hamster buccal-pouch tissue specimens treated with DMBA for 15 weeks as well as for all of the untreated and mineral oil-treated hamster buccal-pouch tissue specimens. Differential expression of p63, p73 and p53 protein for the experimental group was as follows: p63+/p73+/p53+ (n = 14; 70%); p63+/p73+/p53- (n = 2; 10%); p63+/p73-/p53- (n = 4; 20%) and p63+/p73-/p53- (untreated [n = 10] and mineral oil-treated mucosa [n = 10]; 100% each). Upon RT-PCR, DeltaNp63mRNA was detected within all of the 20 hamster buccal-pouch tissue specimens treated with DMBA for 15 weeks, whereas expression of TAp63 was not detected. Furthermore, p73 mRNA was identified for 16 of the hamster buccal-pouch tissue specimens treated with DMBA for 15 weeks, whereas p53 mRNA was noted for 14 15-week DMBA-treated pouches. The proportional (percentage) expression of DeltaNp63, p73 and p53 mRNA for the hamster buccal-pouch tissue specimens treated with DMBA for 15 weeks was noted to be consistent with the findings using immunohistochemical techniques. A significant correlation between p53, p63 and p73 expression (protein and mRNA) was demonstrated for the hamster buccal-pouch carcinoma samples. Our results indicate that both p73 and p63 may be involved in the development of chemically induced hamster buccal-pouch carcinomas, perhaps in concert with p53.

9,10-Dimethyl-1,2-benzanthracene↗