Migrating to Long-Read Sequencing for Clinical Routine BCR-ABL1 TKI Resistance Mutation Screening

Objective

The aim of this project was to implement long-read sequencing for BCR-ABL1 TKI resistance mutation screening in a clinical setting for patients undergoing treatment for chronic myeloid leukemia.

Materials and Methods

Processes were established for registering and transferring samples from the clinic to an academic sequencing facility for long-read sequencing. An automated analysis pipeline for detecting mutations was established, and an information system was implemented comprising features for data management, analysis and visualization. Clinical validation was performed by identifying BCR-ABL1 TKI resistance mutations by Sanger and long-read sequencing in parallel. The developed software is available as open source via GitHub at https://github.com/pharmbio/clamp.

Results

The information system enabled traceable transfer of samples from the clinic to the sequencing facility, robust and automated analysis of the long-read sequence data, and communication of results from sequence analysis in a reporting format that could be easily interpreted and acted upon by clinical experts. In a validation study, all 17 resistance mutations found by Sanger sequencing were also detected by long-read sequencing. An additional 16 mutations were found only by long-read sequencing, all of them with frequencies below the limit of detection for Sanger sequencing. The clonal distributions of co-existing mutations were automatically resolved through the long-read data analysis. After the implementation and validation, the clinical laboratory switched their routine protocol from using Sanger to long-read sequencing for this application.

Conclusions

Long-read sequencing delivers results with higher sensitivity compared to Sanger sequencing and enables earlier detection of emerging TKI resistance mutations. The developed processes, analysis workflow, and software components lower barriers for adoption and could be extended to other applications.

Inter- and intra-rater reliability of the head-shaft angle in children with cerebral palsy

PURPOSE

Children with cerebral palsy (CP) are at increased risk for hip dislocation. This can be prevented in most cases using surveillance programmes that include radiographic examinations. Known risk factors for hip dislocation include young age, high Gross Motor Function Classification System (GMFCS) level and high migration percentage (MP). The head-shaft angle (HSA) has recently been described as an additional risk factor. The study aim was to determine inter- and intra-rater reliability of the HSA in a surveillance programme for children with CP.

METHODS

We included hip radiographs from the CP surveillance programme CPUP in southern Sweden during the first half of 2016. Fifty radiographs were included from children at GMFCS levels II-V, with a mean age of 6.6 (SD 3.2) years. Three raters measured the HSA of one hip (left or right) at baseline and four weeks later; intraclass correlation coefficient (ICC) was used to estimate inter- and intra-rater reliability.

RESULTS

Inter- and intra-rater reliability were excellent for the HSA, with ICC 0.92 (95% CI 0.87-0.96) and ICC 0.99 (95% CI 0.98-0.99), respectively.

CONCLUSION

The HSA showed excellent inter- and intra-rater reliability for children with CP, providing further evidence for use of the HSA as an additional factor for identifying risk for further hip displacement or dislocation.

Prediction of hip displacement in children with cerebral palsy

Hip displacement, defined in this study as a migration percentage (MP) of more than 40%, is a common, debilitating complication of cerebral palsy (CP). In this prospective study we analysed the risk of developing hip displacement within five years of the first pelvic radiograph.

All children with CP in southern and western Sweden are invited to register in the hip surveillance programme CPUP. Inclusion criteria for the two groups in this study were children from the CPUP database born between 1994 and 2009 with Gross Motor Function Classification System (GMFCS) III to V. Group 1 included children who developed hip displacement, group 2 included children who did not develop hip displacement over a minimum follow-up of five years. A total of 145 children were included with a mean age at their initial pelvic radiograph of 3.5 years (0.6 to 9.7).

The odds ratio for hip displacement was calculated for GMFCS-level, age and initial MP and head-shaft angle. A risk score was constructed with these variables using multiple logistic regression analysis. The predictive ability of the risk score was evaluated using the area under the receiver operating characteristics curve (AUC).

All variables had a significant effect on the risk of a MP > 40%. The discriminatory accuracy of the CPUP hip score is high (AUC = 0.87), indicating a high ability to differentiate between high- and low-risk individuals for hip displacement. The CPUP hip score may be useful in deciding on further follow-up and treatment in children with CP.

Cite this article: Bone Joint J 2015;97-B:1441–4.

Association between TERT promoter polymorphisms and acute myeloid leukemia risk and prognosis

Telomerase reverse transcriptase gene (TERT) promoter mutations are identified in many malignancies but not in hematological malignancies. Here we analyzed TERT and protection of telomeres 1 gene (POT1) mutations, and four different TERT SNVs in 226 acute myeloid leukemia (AML) patients and 806 healthy individuals in a case referent design, where also overall survival was assessed. A significant association for increased risk of AML was found for TERT SNVs, rs2853669 (OR = 2.45, p = 0.00015) and rs2736100 (OR = 1.5, p = 0.03). The overall survival for patients with CC genotype of rs2853669 was significantly shorter compared to those with TT or TC genotypes (p = 0.036 and 0.029 respectively). The influence of TERT rs2853669 CC on survival was confirmed in multivariable Cox regression analysis as an independent risk biomarker in addition to high risk group, higher age and treatment. No hot spot TERT promoter mutations at -228C > T or -250C > T or POT1 mutations could be identified in this AML cohort. We show that rs2853669 CC may be a risk factor for the development of AML that may also be used as a prognostic marker to identify high risk normal karyotype-AML (NK-AML) patients, for treatment guidance.

Abstract 5275: Association of TERT polymorphism with acute myeloid leukemia risk and prognosis

Telomerase reverse transcriptase gene (TERT) promoter mutations are identified in many malignancies but not in hematological malignancies. Here we analyzed TERT and protection of telomeres 1 gene (POT1) mutations, and four different TERT SNPs in 256 acute myeloid leukemia (AML) patients. A significant association for increased risk of AML was found for TERT SNPs, rs2853669 (OR = 2.45, p = 0.00006) and rs2736100 (OR = 1.52, p = 0.02). The overall survival for patients with CC genotype of rs2853669 was significantly shorter compared to those with TT or TC genotypes (p = 0.036 and 0.029 (respectively). The influence of TERT rs2853669 CC on survival was confirmed in multivariable Cox regression analysis as an independent risk biomarker in addition to high risk group, age and treatment. No hot spot TERT promoter mutations at -228C>T or -250C>T or POT1 mutations could be identified in this AML cohort. We show for the first time that rs2853669 CC may be a risk factor for the development of AML that may also be used as a prognostic marker to identify relative high risk NK-AML patients, for treatment guidance.

Note: This abstract was not presented at the meeting.

Citation Format: Kourosh Lotfi, Mohamed Ali Mosrati, Kerstin Willander, Ingrid Jakobsen Falk, Monica Hermanson, Martin Höglund, Dick Stockelberg, Yuan Wei, Peter Söderkvist. Association of TERT polymorphism with acute myeloid leukemia risk and prognosis. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 5275. doi:10.1158/1538-7445.AM2015-5275

Ecological conditions of ponds situated on blast furnace slag deposits located in South Gare Site of Special Scientific Interest (SSSI), Teesside, UK

Slag, a by-product from the iron and steel industry, has a range of applications within construction and is used in wastewater treatment. Historically considered a waste material, little consideration was given to the environmental impacts of its disposal. South Gare (a Site of Special Scientific Interest) located at the mouth of the Tees estuary, UK, formed on slag deposits used to create a sea wall and make the land behind permanent. Over time, ponds formed in depressions with the water chemistry, being significantly impacted by the slag deposits. Calcium levels reached 504 mg/L, nitrate 49.0 mg/L and sulphate 1,698 mg/L. These levels were also reflected in the composition of the sediment. pH (5.10-9.90) and electrical conductivity (2,710-3,598 µS/cm) were variable but often notably high. Pb, Cu and Cd were not present within the water, whilst Zn ranged from 0.027 to 0.37 mg/L. Heavy metal levels were higher in surface sediments. Zinc was most dominant (174.3-1,310.2 mg/L) followed by Pb (9.9-431 mg/L), Cu (8.4-41.8 mg/L) and Cd (0.4-1.1 mg/L). A sediment core provided a historical overview of the ponds. The ponds were unfavourable for aquatic biodiversity and unsuitable for drinking water abstraction.

Clonal distribution of BCR-ABL1 mutations and splice isoforms by single-molecule long-read RNA sequencing

Background

The evolution of mutations in the BCR-ABL1 fusion gene transcript renders CML patients resistant to tyrosine kinase inhibitor (TKI) based therapy. Thus screening for BCR-ABL1 mutations is recommended particularly in patients experiencing poor response to treatment. Herein we describe a novel approach for the detection and surveillance of BCR-ABL1 mutations in CML patients.

Methods

To detect mutations in the BCR-ABL1 transcript we developed an assay based on the Pacific Biosciences (PacBio) sequencing technology, which allows for single-molecule long-read sequencing of BCR-ABL1 fusion transcript molecules. Samples from six patients with poor response to therapy were analyzed both at diagnosis and follow-up. cDNA was generated from total RNA and a 1,6 kb fragment encompassing the BCR-ABL1 transcript was amplified using long range PCR. To estimate the sensitivity of the assay, a serial dilution experiment was performed.

Results

Over 10,000 full-length BCR-ABL1 sequences were obtained for all samples studied. Through the serial dilution analysis, mutations in CML patient samples could be detected down to a level of at least 1%. Notably, the assay was determined to be sufficiently sensitive even in patients harboring a low abundance of BCR-ABL1 levels. The PacBio sequencing successfully identified all mutations seen by standard methods. Importantly, we identified several mutations that escaped detection by the clinical routine analysis. Resistance mutations were found in all but one of the patients. Due to the long reads afforded by PacBio sequencing, compound mutations present in the same molecule were readily distinguished from independent alterations arising in different molecules. Moreover, several transcript isoforms of the BCR-ABL1 transcript were identified in two of the CML patients. Finally, our assay allowed for a quick turn around time allowing samples to be reported upon within 2 days.

Conclusions

In summary the PacBio sequencing assay can be applied to detect BCR-ABL1 resistance mutations in both diagnostic and follow-up CML patient samples using a simple protocol applicable to routine diagnosis. The method besides its sensitivity, gives a complete view of the clonal distribution of mutations, which is of importance when making therapy decisions.

Abstract 3518: TP53 mutations and MDM2 single nucleotide polymorphism 309T-G predicts outcome and treatment resistance in acute myeloid leukemia

The tumor-suppressor gene TP53, encoding the p53 protein, is vital for normal cellular processes including cell cycle regulation, apoptosis and senescence. Mutations in TP53 are frequent in many cancers, and have been associated with treatment resistance and inferior prognosis in acute myeloid leukemia (AML). Altered expression of MDM2 (mouse double minute 2), a negative regulator of p53, may also attenuate normal p53 signaling, thereby enhancing tumor transformation and resistance to apoptosis. The single nucleotide polymorphism (SNP) 309 (T>G, rs2279744) has been reported to increase MDM2 expression and impair normal p53 response. We investigated the frequency and impact of TP53 mutations (TP53mut) and MDM2SNP309 on treatment response and overall survival (OS) in 207 Swedish AML patients. To detect the TP53mut in exons 5-8, the single strand conformation analysis (SSCA) was performed. Samples with mobility shift were sequenced to determine the exact nucleotide sequence and compared to the corresponding TP53 reference sequence (NM_000546.4). MDM2SNP309 was analyzed using Pyrosequencing. We found a high frequency (22%) of TP53mut in patients with cytogenetic aberrations, with strong association to high risk cytogenetics (p<0.001). TP53mut patients had markedly lower response rates compared to TP53 wild-type (wt) patients (21% and 76% CR, respectively, p<0.001) and a significantly reduced OS (5 and 21 months, respectively, p<0.001). In TP53wt patients with abnormal karyotype, the MDM2SNP309 conferred an impaired outcome, with patients carrying the alternative G allele having shorter OS compared to T/T patients (13 and 29 months, p=0.031). This effect was neither observed in OS analysis of the entire group, nor in the normal karyotype patients, suggesting that the SNP G-allele carriers may suppress function of wild-type p53 in cytogenetically altered tumors. Allo-SCT in first complete remission improves the prognosis in AML patients with intermediate or high risk. However, some patients, including those with monosomal karyotype, and, as seen in our study, patients with TP53mut, are unlikely to reach CR with standard treatment. These patients may be considered for clinical trials with emerging novel therapies targeting the p53 signaling pathway. In conclusion, our results show that TP53mut identifies a subgroup of AML patients with dramatically impaired outcome. TP53 analysis, and potentially also MDM2SNP309 genotyping, should be implemented in prognostication, risk stratification and selection of patients most likely to benefit from new drugs such as the nutlins (MDM2-inhibitors) and PRIMA-1 (“p53 Reactivation and Induction of Massive Apoptosis”).

Citation Format: Ingrid Jakobsen Falk, Kerstin Willander, Roza Chaireti, Johan Lund, Monica Hermanson, Henrik Greén, Peter Söderkvist, Kourosh Lotfi. TP53 mutations and MDM2 single nucleotide polymorphism 309T-G predicts outcome and treatment resistance in acute myeloid leukemia. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3518. doi:10.1158/1538-7445.AM2014-3518

Impact of ABCB1 single nucleotide polymorphisms 1236C>T and 2677G>T on overall survival in FLT3 wild-type de novo AML patients with normal karyotype

Drug resistance is a clinically relevant problem in the treatment of acute myeloid leukaemia (AML). We have previously reported a relationship between single nucleotide polymorphisms (SNPs) of ABCB1, encoding the multi-drug transporter P-glycoprotein, and overall survival (OS) in normal karyotype (NK)-AML. Here we extended this material, enabling subgroup analysis based on FLT3 and NPM1 status, to further elucidate the influence of ABCB1 SNPs. De novo NK-AML patients (n = 201) were analysed for 1199G>A, 1236C>T, 2677G>T/A and 3435C>T, and correlations to outcome were investigated. FLT3 wild-type 1236C/C patients have significantly shorter OS compared to patients carrying the variant allele; medians 20 vs. 49 months, respectively, P = 0·017. There was also an inferior outcome in FLT3 wild-type 2677G/G patients compared to patients carrying the variant allele, median OS 20 vs. 35 months, respectively, P = 0·039. This was confirmed in Cox regression analysis. Our results indicate that ABCB1 1236C>T and 2677G>T may be used as prognostic markers to distinguish relatively high risk patients in the intermediate risk FLT3 wild-type group, which may contribute to future individualizing of treatment strategies.

Decreased survival in normal karyotype AML with single-nucleotide polymorphisms in genes encoding the AraC metabolizing enzymes cytidine deaminase and 5'-nucleotidase

De novo acute myeloid leukemia with normal karyotype (NK-AML) comprises a large group of patients with no common cytogenetic alterations and with a large variation in treatment response. Single-nucleotide polymorphisms (SNPs) in genes related to the metabolism of the nucleoside analogue AraC, the backbone in AML treatment, might affect drug sensitivity and treatment outcome. Therefore, SNPs may serve as prognostic biomarkers aiding clinicians in individualized treatment decisions, with the aim of improving patient outcomes. We analyzed polymorphisms in genes encoding cytidine deaminase (CDA 79A>C rs2072671 and -451C>T rs532545), 5'-nucleotidase (cN-II 7A>G rs10883841), and deoxycytidine kinase (DCK 3'UTR 948T>C rs4643786) in 205 de novo NK-AML patients. In FLT3-internal tandem duplication (ITD)-positive patients, the CDA 79C/C and -451T/T genotypes were associated with shorter overall survival compared to other genotypes (5 vs. 24 months, P < 0.001 and 5 vs. 23 months, P = 0.015, respectively), and this was most pronounced in FLT3-ITD-positive/NPM1-positive patients. We observed altered in vitro sensitivity to topoisomerase inhibitory drugs, but not to nucleoside analogues, and a decrease in global DNA methylation in cells carrying both CDA variant alleles. A shorter survival was also observed for the cN-II variant allele, but only in FLT3-ITD-negative patients (25 vs. 31 months, P = 0.075). Our results indicate that polymorphisms in genes related to nucleoside analog drug metabolism may serve as prognostic markers in de novo NK-AML.

Abstract 1170: Correlation between cytidine deaminase single nucleotide polymorphisms and in vitro drug sensitivity, DNA methylation and outcome in normal karyotype acute myelogenous leukemia

Background: De novo AML with normal karyotype (NK-AML) comprise a large group of patients without common cytogenetic alterations but with a large variation in treatment response. New tools such as the analysis of nucleophosmine 1 (NPM1), FMS-like tyrosine kinase 3 (FLT3) and CCAAT/enhancer binding protein (CEBPA) mutations has emerged as clinical markers of prognosis, but there is still a need for additional tools to explain the variation in outcome. Cytarabine (Ara-C), a cornerstone in AML chemotherapy, is activated intracellularly by deoxycytidine kinase (dCK), and deactivated by cytidine deaminase (CDA) and poor treatment outcome or development of chemotherapy resistance can be due to altered activity of these enzymes. Single nucleotide polymorphisms (SNPs) of CDA genes have previously been reported to result in lower CDA allelic expression and to affect the outcome of treatment. In addition, pharmacological inhibition of CDA has been shown to reduce the degree of DNA methylation. DNA methylation may be an important regulatory mechanism for the expression of genes related to drug effect, and we therefore aimed to investigate the relationship between CDA polymorphisms and outcome in NK-AML, DNA methylation, and in vitro drug cytotoxicity. Method: 207 Swedish NK-AML patients were genotyped for the CDA SNPs 79A&gt;C (rs2072671) and -451C&gt;T (rs532545) and the results were correlated to treatment response and overall survival (OS) in the material as a whole as well as stratified based on FLT3 and NPM1 status. Cells from a subset of the patients were also investigated for genotype association with in vitro drug cytotoxicity (n=56) and global DNA methylation (n=82). Results: CDA 79C/C or -451T/T genotype was associated to a shorter OS compared to other genotypes (0.44 vs. 1.86 years, p=0.004; and 0.45 vs. 1.79 years, p=0.051) for FLT3-ITD+ patients, and this was even more pronounced in the FLT3-ITD+/NPM1+ cases. There was significantly less DNA methylation in cells heterozygous for both polymorphisms (A/C+C/T) compared to homozygous A/A+C/C cells (p=0.018). There was also a lower degree of methylation in homozygous C/C+T/T cells, but due to the small number of samples in this group significance was not reached. An altered in vitro sensitivity towards topoisomerase inhibitory drugs, but not towards nucleoside analogues was seen for both CDA SNPs with homozygous C/C or T/T cells being more sensitive. Conclusions: We found a significant correlation between CDA genotype and OS in NK-AML, the degree of DNA methylation in AML cells, and in vitro drug sensitivity. The change in methylation related to CDA genotype may be associated with differences in drug activation and subsequent sensitivity, making these polymorphisms potential markers of use for future individual chemotherapy decisions such as dose adjustments.

Citation Format: Ingrid Jakobsen Falk, Anna Fyrberg, Monica Hermanson, Martin Höglund, Hareth Nahi, Lars Palmqvist, Christer Paul, Esbjörn Paul, Richard Rosenquist, Dick Stockelberg, Yuan Wei, Henrik Green, Kourosh Lotfi. Correlation between cytidine deaminase single nucleotide polymorphisms and in vitro drug sensitivity, DNA methylation and outcome in normal karyotype acute myelogenous leukemia. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1170. doi:10.1158/1538-7445.AM2013-1170

The novel tyrosine kinase inhibitor AKN-028 has significant antileukemic activity in cell lines and primary cultures of acute myeloid leukemia

Aberrantly expressed tyrosine kinases have emerged as promising targets for drug development in acute myeloid leukemia (AML). We report that AKN-028, a novel tyrosine kinase inhibitor (TKI), is a potent FMS-like receptor tyrosine kinase 3 (FLT3) inhibitor (IC₅₀=6 nℳ), causing dose-dependent inhibition of FLT3 autophosphorylation. Inhibition of KIT autophosphorylation was shown in a human megakaryoblastic leukemia cell line overexpressing KIT. In a panel of 17 cell lines, AKN-028 showed cytotoxic activity in all five AML cell lines included. AKN-028 triggered apoptosis in MV4-11 by activation of caspase 3. In primary AML samples (n=15), AKN-028 induced a clear dose-dependent cytotoxic response (mean IC₅₀ 1 μℳ). However, no correlation between antileukemic activity and FLT3 mutation status, or to the quantitative expression of FLT3, was observed. Combination studies showed synergistic activity when cytarabine or daunorubicin was added simultaneously or 24 h before AKN-028. In mice, AKN-028 demonstrated high oral bioavailability and antileukemic effect in primary AML and MV4-11 cells, with no major toxicity observed in the experiment. In conclusion, AKN-028 is a novel TKI with significant preclinical antileukemic activity in AML. Possible sequence-dependent synergy with standard AML drugs and good oral bioavailability has made it a candidate drug for clinical trials (ongoing).

Assessing hematopoietic chimerism after allogeneic stem cell transplantation by multiplexed SNP genotyping using microarrays and quantitative analysis of SNP alleles

Single-nucleotide polymorphisms (SNPs) have the potential to be particularly useful as markers for monitoring of chimerism after stem cell transplantation (SCT) because they can be analyzed by accurate and robust methods. We used a two-phased minisequencing strategy for monitoring chimerism after SCT. First, informative SNPs with alleles differing between donor and recipient were identified using a multiplex microarray-based minisequencing system screening 51 SNPs to ensure that multiple informative SNPs were detected in each donor-recipient pair. Secondly, the development of chimerism was followed up after SCT by sensitive, quantitative analysis of individual informative SNPs by applying the minisequencing method in a microtiter plate format. Using this panel of SNPs, we identified multiple informative SNPs in nine unrelated and in 16 related donor-recipient pairs. Samples from nine of the donor-recipient pairs taken at time points ranging from 1 month to 8 years after transplantation were available for analysis. In these samples, we monitored the allelic ratios of two or three informative SNPs in individual minisequencing reactions. The results agreed well with the data obtained by microsatellite analysis. Thus, we conclude that the two-phased minisequencing strategy is a useful approach in the following up of patients after SCT.

Phosphorylation of Shc by Src family kinases is necessary for stem cell factor receptor/c-kit mediated activation of the Ras/MAP kinase pathway and c-fos induction

In this report we show that Tyr568 and Tyr570 are phosphorylated in vivo in the Kit/stem cell factor receptor (Kit/SCFR) following ligand-stimulation. By mutation of Tyr568 and Tyr570 to phenylalanine residues and expression of the mutated receptors in porcine aortic endothelial (PAE) cells, we could demonstrate a loss of activation of members of the Src family of tyrosine kinases when Tyr568 was mutated, while mutation of Tyr570 only led to a minor decrease in activation of Src family members. Mutation of both tyrosine residues led to a complete loss of Src family kinase activation. Phosphorylation of the adapter protein Shc by growth factor receptors provides association sites for Grb2-Sos, thereby activating the Ras/MAP kinase pathway. A much lowered degree of Shc phosphorylation, Ras and Erk2 activation and c-fos induction was seen in the Y568F mutant, while in the Y570F mutant these responses were less affected. In contrast, the mitogenic response was only slightly reduced. In a mutant receptor with both Tyr568 and Tyr570 mutated to phenylalanine residues, no phosphorylation of Shc and no activation of Ras and Erk2 was seen in response to stem cell factor stimulation, very weak induction of c-fos was seen and the mitogenic response was severely depressed. These data show that Ras/MAP kinase activation and c-fos induction by Kit/SCFR are mediated by members of the Src family kinases. However, the mitogenic response is only to a minor extent dependent on Src kinase activity.

Association of loss of heterozygosity on chromosome 17p with high platelet-derived growth factor alpha receptor expression in human malignant gliomas

The aim of this study was to examine platelet-derived growth factor alpha receptor (PDGFR-alpha) expression in gliomas of various degrees of malignancy and to correlate the findings with genetic alterations present in the same tumor samples. We analyzed 83 tumors by in situ hybridization using a PDGFR-alpha cRNA probe. Increased PDGFR-alpha mRNA expression was observed in astrocytic tumors of all stages of malignancy, although the highest levels were found in glioblastoma multiforme. To evaluate the frequency of PDGFR-alpha gene amplification, differential PCR requiring less DNA than Southern analysis was used with fluorescence-labeled primers corresponding to the kinase insert region of the PDGFR-alpha. Only 7 of 43 glioblastomas and none of the other tumors tested showed amplification of the PDGFR-alpha gene, suggesting that a mechanism other than gene amplification is responsible for the overexpression of PDGFR-alpha in glial brain tumors. Comparison of the in situ hybridization data with genetic alterations in the same tumor material showed a significant correlation of loss of heterozygosity on chromosome 17p (Fisher's exact, P < 0.0002) with high expression levels of PDGFR-alpha. Because that was the case in both low- and high-grade astrocytomas, our data imply that PDGFR-alpha is actively involved in tumor cell proliferation in early and late stages of glioma development. The association of PDGFR-alpha expression with a distinct subset of glioblastomas characterized by loss of heterozygosity 17p further supports the differentiation of these tumors into molecular variants.

13q deletions in lymphoid malignancies

Previous studies have indicated that a candidate tumor suppressor gene resides telomeric of the RB1 gene at 13q14, a region that is commonly deleted in B-cell chronic lymphocytic leukemia (B-CLL). In this study, we have evaluated the frequency and minimal region of overlap for 13q deletions in malignant cells from various lymphoid neoplasms. We observed losses at 13q14 in 33/75 (44%) B-CLL cases, four of 16 (25%) non-Hodgkin's lymphoma (NHL) cases, eight of 29 (28%) patients with acute lymphocytic leukemia (ALL), and one of 15 T-cell lines. In some ALL cases, inactivation of the RB1 gene is suggested as the important event in the 13q deletions. The most commonly deleted marker in CLL and NHL was D13S319, between RBkpt and the D13S25 loci. Homozygous deletions of this marker were observed in 10 of 75 B-CLL cases, in six of which the homozygous deletions included only the D13S319 locus. Our data suggest that 13q deletions are common in lymphoid neoplasms, and that deletion of a candidate tumor suppressor gene(s) in the vicinity of the D13S319 marker is a tumorigenic event in these diseases.

PDGF and its receptors following facial nerve axotomy in rats: expression in neurons and surrounding glia

We investigated the expression of platelet-derived growth factor (PDGF) and its receptors in rat facial nuclei following axotomy by in situ hybridization and immunohistochemistry. Facial nuclei were examined on days 3, 6, 12, 19 and 26 postoperatively (p.o.). Strong immunoreactivity for PDGF was found in facial neurons and surrounding astrocytes on the ipsilateral side of the brainstem already after 3 days p.o. and persisted at a high level until day 26 p.o. in rats with a facial nerve cut injury. After crushing of the facial nerve, a similar increase was seen in PDGF immunoreactivity which, however, decreased after day 19 p.o., when reinnervation had occurred. Reactive gliosis appeared on the operated side and was confirmed by an increase in intensity of GFAP staining. The kinetics of PDGF A-chain mRNA expression corresponded to the PDGF immunoreactivity, whereas the B-chain mRNA was present only in the neurons. The PDGF alpha-receptor immunoreactivity as well as the mRNA were detected in scattered glial cells. The density of the PDGF alpha-receptor mRNA expressing glial cells was higher on the injured side, but the intensity of the expression per cell did not change after axotomy. An increase in PDGF beta-receptor immunoreactivity was seen in the ipsilateral facial nuclei after 3-6 days p.o., however, the increase in the mRNA could not be detected. The staining persisted until day 26 p.o., when transected facial neurons showed heavier staining than those that had been crushed.(ABSTRACT TRUNCATED AT 250 WORDS)

Platelet-derived growth factor and its receptors in human glioma tissue: expression of messenger RNA and protein suggests the presence of autocrine and paracrine loops

The expression of platelet-derived growth factor (PDGF) and its receptors was analyzed in 14 gliomas of various degrees of malignancy and compared with three gliosis cases by in situ hybridization and immunohistochemistry techniques. Expression of both PDGF A- and B-chains was higher in glioblastomas than in astrocytomas. The PDGF A-chain mRNA was predominantly found in cell-rich areas in glioblastomas. The cognate PDGF-alpha receptor (PDGFR-alpha) mRNA was heterogeneously distributed in gliomas of all grades, and PDGFR-alpha expression was higher in gliomas than in gliosis. Within some glioblastomas probed with PDGFR-alpha complementary RNA, cells heavily loaded with grains were intermingled with others containing low or moderate signals. The heavily labeled cells were often found in the vicinity of proliferating capillaries. Immunostaining with an anti-PDGF antibody and an affinity-purified antiserum against the PDGFR-alpha showed strong staining of most tumor cells with both antibodies in glioblastoma. In addition, the PDGFR-alpha antibodies yielded a strong staining of scattered cells, and the anti-PDGF antibody yielded staining of a few cells within the astrocytoma. Furthermore, high levels of the PDGF-beta receptor (PDGFR-beta) and PDGF B-chain mRNA as well as the beta receptor protein were found in hyperplastic capillaries. These results suggest the presence of autocrine and paracrine loops in glioma, activating the PDGFR-alpha in glioma cells and the PDGFR-beta in endothelial cells.