Microdroplet digital PCR: detection and quantitation of biomarkers in archived tissue and serial plasma samples in patients with lung cancer.

INTRODUCTION: There is much interest in the use of noninvasive biomarkers in the management of lung cancer, particularly with respect to early diagnosis and monitoring the response to intervention. Cell-free tumor DNA in patients with cancer has been shown to hold potential as a noninvasive biomarker, in which the response to treatment may be evaluated using a blood test only. Multiple technologies have been suggested as being appropriate to measure cell-free tumor DNA. Microdroplet digital polymerase chain reaction (mdPCR) has a number of attributes that suggest it may be a useful tool for detecting clinically relevant genetic events. It offers precise and accurate quantitation of mutant alleles, including rare variants. METHODS: We evaluate the performance of mdPCR in the analysis of DNA extracted from reference standards, tumor biopsies, and patient plasma. RESULTS: The potential of mdPCR to detect clinically relevant mutations is demonstrated, in both formalin-fixed paraffin-embedded material and plasma. Furthermore, we show that mdPCR can be used to track changes in peripheral blood biomarkers in response to treatment and to detect the emergence of drug-resistant clones. CONCLUSIONS: MdPCR has potential as a tool to detect and quantify tumor-derived mutational events in cell-free DNA from patients with lung cancer.

The kinetics of relapse in DEK-NUP214-positive acute myeloid leukemia patients.

Preemptive treatment of relapse of acute myeloid leukemia (AML) holds the promise to improve the prognosis of this currently highly lethal condition. Proposed treatment modalities applicable in preemptive cytoreduction (e.g., demethylating agents or standard chemotherapy) differ substantially in interval from administration to antileukemic effect. The t(6;9) balanced translocation, producing the DEK-NUP214 fusion protein, is seen in only 1% of patients with AML. We hypothesized that in these patients, who relapse with a very high frequency, a more detailed knowledge of leukemic relapse growth kinetics would improve the personalized decision-making regarding re-administration of chemotherapy. Based on standardized quantitative PCR data, we therefore delineated the relapse kinetics in a cohort of 27 relapsing DEK-NUP214-positive patients treated in four different European countries. The prerelapse leukemic burden increased with a median doubling time of 13 d (range: 5-51 d, median: 0.71 logs/month, range: 0.18-1.91 logs/month), with FLT3-ITD-positive patients relapsing significantly faster than FLT3-ITD-negative ones (median: 0.9 vs. 0.6 logs/month, Wilcoxon rank sum test, P = 0.041). Peripheral blood and bone marrow were equally useful for minimal residual disease (MRD) detection, and thus, we found that with sampling intervals of 2 months, 94% of relapses would be detected with a median time from MRD detection to hematological relapse of 64 d. In conclusion, this data provide algorithms for handling the rare patients with DEK-NUP214-positive AML allowing for planning of both MRD follow-up and, upon molecular relapse, the timing of cytoreduction or possibly transplant procedures.

EGFR-mutated lung cancer in Li-Fraumeni syndrome.

This is a revised case report of a 52 year old Caucasian female with Li-Fraumeni syndrome with a rare TP53 mutation, who was treated for breast cancer and later developed epidermal growth factor receptor (EGFR) mutated non-small cell lung cancer.

Hepatocellular adenoma in glycogen storage disorder type I: a clinicopathological and molecular study.

AIMS: Glycogen storage disease type I is a metabolic disorder resulting from deficiency of the glucose-6-phosphate complex. Long-term complications include the development of hepatocellular adenoma (HCA). In this retrospective study, our aim was to reclassify according to geno-phenotypic characteristics nodular lesions identified in hepatectomy specimens of such patients transplanted between 1998 and 2008 at our institution. METHODS AND RESULTS: Clinicopathological data of seven consecutive transplanted patients with glycogen storage disease type I were reviewed. Liver nodules were re-examined histologically and by immunohistochemistry. Molecular analysis was performed additionally in a case with specific features. Four patients had multiple tumours. We concluded that 26 of 38 nodules available for study had features of inflammatory hepatocellular adenomas, seven comprised adenomas not otherwise specified and five were found to be focal nodular hyperplasia. CONCLUSIONS: Further studies are needed to clarify the pathogenesis of hepatocellular adenomas in glycogen storage disease; in particular to determine whether they share abnormal metabolic pathways with inflammatory adenomas in the general population. Testing for acute phase proteins may be a helpful tool in the early detection of HCA in such patients. Finally, there is a need to further define their risk of malignant transformation, in relation to age and possible cofactors.

Screening for EGFR and KRAS mutations in endobronchial ultrasound derived transbronchial needle aspirates in non-small cell lung cancer using COLD-PCR.

EGFR mutations correlate with improved clinical outcome whereas KRAS mutations are associated with lack of response to tyrosine kinase inhibitors in patients with non-small cell lung cancer (NSCLC). Endobronchial ultrasound (EBUS)-transbronchial needle aspiration (TBNA) is being increasingly used in the management of NSCLC. Co-amplification at lower denaturation temperature (COLD)-polymerase chain reaction (PCR) (COLD-PCR) is a sensitive assay for the detection of genetic mutations in solid tumours. This study assessed the feasibility of using COLD-PCR to screen for EGFR and KRAS mutations in cytology samples obtained by EBUS-TBNA in routine clinical practice. Samples obtained from NSCLC patients undergoing EBUS-TBNA were evaluated according to our standard clinical protocols. DNA extracted from these samples was subjected to COLD-PCR to amplify exons 18-21 of EGFR and exons two and three of KRAS followed by direct sequencing. Mutation analysis was performed in 131 of 132 (99.3%) NSCLC patients (70F/62M) with confirmed lymph node metastases (94/132 (71.2%) adenocarcinoma; 17/132 (12.8%) squamous cell; 2/132 (0.15%) large cell neuroendocrine; 1/132 (0.07%) large cell carcinoma; 18/132 (13.6%) NSCL-not otherwise specified (NOS)). Molecular analysis of all EGFR and KRAS target sequences was achieved in 126 of 132 (95.5%) and 130 of 132 (98.4%) of cases respectively. EGFR mutations were identified in 13 (10.5%) of fully evaluated cases (11 in adenocarcinoma and two in NSCLC-NOS) including two novel mutations. KRAS mutations were identified in 23 (17.5%) of fully analysed patient samples (18 adenocarcinoma and five NSCLC-NOS). We conclude that EBUS-TBNA of lymph nodes infiltrated by NSCLC can provide sufficient tumour material for EGFR and KRAS mutation analysis in most patients, and that COLD-PCR and sequencing is a robust screening assay for EGFR and KRAS mutation analysis in this clinical context.

New monoallelic (partial tandem duplication) mutation of HNF1a gene in steatotic hepatocellular adenoma.

Hepatocellular adenomas (HCAs) containing inactivating HNF1a mutations correspond to a homogenous group of tumors with marked steatosis and no cytological abnormalities or inflammatory infiltrates. We report a case of a 60-year-old woman who was referred with a 13-cm mass in the left lobe of the liver with no history of oral contraception use and no family history of note. Histology revealed a severely steatotic HCA. Immunohistochemistry showed no nuclear staining for ß-catenin, limited glutamine synthetase positivity, and slightly attenuated liver-fatty acid binding protein staining. Serum amyloid A2 antibodies produced a coarse granular staining. Mutational screening detected monoallelic partial tandem duplication within exon 4 of TCF1 in tumoral tissue. No mutations in the ß-catenin and IL6ST genes were detected. Quantitative reverse transcription PCR showed lower expression levels of FABP1 and uridine glycosyltransferase 2B7 and higher levels of serum amyloid A2 in tumor than in normal hepatocytes. Clinicopathological and molecular investigation of HCA cases with unique features could result in a better understanding of HCAs pathogenesis.

Effects on erythropoiesis of alemtuzumab-containing reduced intensity and standard conditioning regimens.

Haemopoietic cell transplantation (HCT) with reduced-intensity conditioning (RIC) has been associated with delayed disappearance of host anti-A and anti-B isohaemaglutinins and hindrance of donor erythropoiesis in major ABO mismatched transplants. Erythroid recovery, disappearance of recipient type and appearance of donor-type isohaemaglutinins was compared in 84 patients undergoing RIC and 50 patients with standard-conditioning (SCo) HCT. All patients received alemtuzumab as part of their conditioning. The incidence of immune-mediated anaemia and red cell transfusion usage were also compared. Immune factors affecting post-transplant erythroid kinetics showed little variance between different conditioning regimens. Disappearance of recipient isohaemaglutinins and emergence of donor red cells proceeded at similar rates in RIC and SCo transplants; the effects of ABO mismatch were marginal. Pure red cell aplasia, alloimmune haemolysis and autoimmune haemolytic anaemia were not more common in RIC transplants. We believe that alemtuzumab played a critical role in dampening immune reactions of both the host and the donor. Patients in both conditioning groups had similar post-transplant erythroid burst-forming unit (BFU-E) counts; BFU-E chimaerism analysis showed that 90-100% progenitors were of donor origin. However, transfusion requirements were significantly higher in the SCo group, due at least partly to earlier onset of bone marrow hypoplasia.

Delayed attainment of full donor chimaerism following alemtuzumab-based reduced-intensity conditioning haematopoeitic stem cell transplantation for acute myeloid leukaemia and myelodysplastic syndromes is associated with improved outcomes.

This prospective study evaluated the kinetics of lymphoid (CD3) engraftment in 110 patients with acute myeloid leukaemia (AML) and myelodysplastic syndromes (MDS) after allogeneic transplantation and conditioning with fludarabine, busulphan and alemtuzumab, using ciclosporin for post-transplant immunosuppression. Declining donor CD3 chimaerism beyond day+100 was treated with pre-emptive donor lymphocyte infusion (pDLI). The median age of patients was 53.0 years (range: 19-72 years), and the median follow-up was 690 d (range:168-1470 d). Patients achieving full CD3 donor chimaerism (FDC, n = 46) by day+100 had a significantly inferior disease-free survival (DFS) and overall survival (OS) compared to patients with mixed donor chimaerism (MDC, n = 59). Twenty patients had stable MDC and did not require pDLI. Patients attaining early FDC had a higher transplant-related mortality compared to those who maintained stable levels of MDC (P = 0.02), with no difference between the FDC and pDLI groups (P = 0.07). There was no difference in relapse between all three groups (P = 0.21). On multivariate analysis, only CD3 chimaerism status at day+100 and disease status at transplantation had a significant effect on DFS and OS. In patients with AML/MDS undergoing alemetuzumab based-RIC HSCT, prolonged MDC beyond day+100 is associated with an improved OS. Future studies need to be directed towards establishing the underlying factors that dictate T-cell engraftment, expansion and homing post-transplantation.

Diagnosis and monitoring of AML1-MTG8 (ETO)-positive acute myeloid leukemia by qualitative and real-time quantitative RT-PCR.

Assessing the level of residual disease in leukemia is vital for evaluating patients' response to treatment and for identifying those at high risk of relapse. This should enable early preemptive intervention to prevent the onset of hematological relapse in those patients. One of the most common translocations in acute myeloid leukemia (AML) is the t(8;21). t(8;21) AML is characterized by a relatively good prognosis. This chapter discusses both qualitative and quantitative (real-time quantitative reverse-transcription polymerase chain reaction [RQ-PCR]) protocols for the diagnosis and minimal residual disease (MRD) monitoring in t(8;21) AML. It also discusses the importance of choosing appropriate controls for each assay. The chapter provides a simple equation for assessing the sensitivity/reliability of RQ-PCR assays, which enables scientists to assess the accuracy and reliability of their data.

Humoral detection of leukaemia-associated antigens in presentation acute myeloid leukaemia.

The serological analysis of recombinant cDNA expression libraries (SEREX) technique was used to immunoscreen a testes cDNA expression library with sera from newly diagnosed acute myeloid leukaemia (AML) patients. We used a testis cDNA library to aid our identification of cancer-testis (CT) antigens. We identified 44 antigens which we further immunoscreened with sera from AML, chronic myeloid leukaemia (CML), and normal donors. Eight antigens were solely recognised by patient sera including the recently described CT antigen, PASD1, and the cancer-related SSX2 interacting protein, SSX2IP. RT-PCR analysis indicated that we had identified three antigens which were expressed in patient bone marrow (BM) and peripheral blood (PB) but not in normal donor samples (PASD1, SSX2IP, and GRINL1A). Real-time PCR (RQ-PCR) confirmed the restricted expression of PASD1 in normal donor organs. Antigen presentation assays using monocyte-derived dendritic cells (mo-DCs) showed that PASD1 could stimulate autologous T-cell responses, suggesting that PASD1 could be a promising target for future immunotherapy clinical trials.

Quantification of DEK-CAN fusion transcript by real-time reverse transcription polymerase reaction in patients with t(6;9) acute myeloid leukemia.

Real-time reverse transcription polymerase reaction (RT-PCR) was used to examine DEK-CAN transcript levels in serial samples from three patients with t(6;9) acute myeloid leukemia treated with intensive chemotherapy. All three patients achieved short first clinical remission, but without achieving RT-PCR negativity. DEK-CAN level significantly increased in two patients before relapse, while in the third a level of 2x10(-3) in remission bone marrow preceded relapse by 2 months.

Targeting PML/RARalpha transcript with DNAzymes results in reduction of proliferation and induction of apoptosis in APL cells.

DNAzymes are nucleic acid enzymes that can recognise specific RNA substrate via Watson-Crick base pairing and cleave it with multiple turnovers. We have designed and examined the effects of DNAzymes targeting the PML/RARalpha fusion gene in acute promyelocytic leukaemia (APL). The DNAzymes (DZ1 and DZ3) were designed to cleave the PML/RARalpha transcript at the GC nucleotides at the fusion point and three nucleotides upstream of that respectively. Disabled DNAzymes were synthesised and used as controls. Cell-free cleavage reactions were performed on total RNA from NB4 cell line and PML/RARalpha and RARalpha-amplified RNA fragments (aRNA). Postcleavage examination showed that DZ1 and DZ3 cleave PML/RARalpha efficiently and specifically. NB4 APL cells transfected with DZ1 or DZ3 showed a significant suppression of PML/RARalpha protein expression. These DNAzymes also inhibited the proliferation of NB4 cells, reduced the viability rate, and induced apoptosis in these cells. The disabled DNAzymes showed no effect on NB4 cells. The two DNAzymes did not produce any significant effect on K562 cells, which were used as control cells. DNAzymes are more resistant to serum than ribozymes. These data show that targeting the PML/RARalpha fusion gene with DNAzymes can induce apoptosis in APL cells and may have a role in the treatment of APL. They also show DNAzymes are promising tools for targeting specific genes in leukaemia.

Prognostic significance of quantitative analysis of WT1 gene transcripts by competitive reverse transcription polymerase chain reaction in acute leukaemia.

We have developed a sensitive, competitive, nested reverse transcription polymerase chain reaction (RT-PCR) titration assay that quantifies the number of Wilm's tumour (WT1) gene transcripts in bone marrow (BM) and peripheral blood (PB), coupled with a competitive RT-PCR protocol for the ABL gene as control. We studied BM/PB samples from 107 acute myeloid leukaemia (AML) patients and 22 acute lymphoblastic leukaemia (ALL) patients at presentation and detected the WT1 gene in > 90% of patients by a qualitative assay. Quantitative analysis of WT1 transcript at presentation in 66 patients (52 AML, 14 ALL) correlated significantly with remission rate, disease-free survival (DFS) and overall survival (OS) (P = 0.003). WT1 levels were normalized to 105ABL transcripts. Within good and standard cytogenetic risk groups, high WT1 levels correlated with poorer outcome. Serial quantification was performed in 35 patients (28 AML, seven ALL); those with less than 103 copies of WT1 after induction and second consolidation chemotherapy had significantly better DFS and OS. Fourteen patients have relapsed with a median complete remission duration of 12 (range 4-49) months. We detected a rise in WT1 levels in nine out of 14 patients, 2-4 months before the onset of haematological relapse, whereas in the remaining five patients, WT1 levels remained persistently high during the disease course. WT1 levels were lower in PB than in BM, but mirrored changes in the BM samples and were equally informative. We suggest that WT1 is a useful molecular target to monitor minimal residual disease in acute leukaemia, especially in cases without a specific fusion gene.

Prognostic significance of FLT3 ITD and D835 mutations in AML patients.

Both ITD and D835 mutations of the fms-like tyrosine kinase (FLT3) gene cause constitutive activation of the receptor, in the absence of ligand. We have examined a cohort of 91 patients, AML (80) and MDS (11), to determine the prevalence of these mutations and any correlations between the two mutations and disease prognosis. FLT3/ITD (ITD+) or D835 mutations (D835+) were not detected in MDS patients examined. However, 10% (8/80) and 7.5% (6/80) of AML patients were ITD+ and D835+, respectively. ITD+ patients have a higher rate of relapse than patients with wild-type (WT) FLT3. Median overall survival was 4.6 months (range 0.6-36.2) for ITD+ and 19.85 months (range 0.2-197.5) for WT patients (P=0.0066), and disease-free survival (DFS) was also worse for ITD+ patients than FLT3/WT patients (P=0.047). FLT3/ITD is also a significant prognostic marker for overall survival (OS) and DFS in patients in the standard karyotype group (P=0.0040, 0.0365, respectively). ITD is more prevalent in patients in the standard karyotype category (7/41, 17.1%) as compared to patients in the poor-risk category (1/32, 3.1%). Similar to ITD, D835 mutations were found to be more frequent in patients with standard-risk rather than poor-risk cytogenetic category. WBC count (mean 63.8 x 10(9)/l) was significantly higher in ITD+ patients than patients with D835 mutations (mean 34.8 x 10(9)/l) and WT patients (mean 26.4 x 10(9)/l) (P=0.004). D835 mutants did not appear to have a worse median OS or DFS compared with the WT group. We conclude that FLT3/ITD mutations may be an important prognostic marker in AML, especially in the standard/good risk karyotype groups, where it may allow risk-directed therapy.

High level of microsatellite instability but not hypermethylation of mismatch repair genes in therapy-related and secondary acute myeloid leukaemia and myelodysplastic syndrome.

Microsatellite instability (MSI) is associated with defects in the DNA mismatch repair (MMR) system, such as mutation or epigenetic silencing of the genes by promoter hypermethylation. We investigated the presence of MSI and promoter hypermethylation of hMLH1 and hMSH2 genes in 82 patients (68 acute myeloid leukaemia, AML; 14 myelodysplastic syndromes, MDS). Twelve separate microsatellite loci, including three mononucleotide repeat markers, were used. Mutator phenotype (RER+) was detected in 20 AML (29.4%) and 3 MDS (21.4%) patients. RER+ rate was much higher in the therapy-related and secondary cases compared with the de novo cases. Three out of 7 (42.9%) secondary (s-AML) and 8 out of 17 (47.1%) therapy-related (t-AML) showed RER+ in comparison with 9 out of 44 (20.5%) de novo cases. Similar rates were detected in MDS patients (2/2 therapy-related and 1/12 de novo). The promoter hypermethylation was found in three hMLH1 (3.7%) and two hMSH2 (2.4%) genes. All these five patients had AML and were older than 60 years of age. Two of them had s-AML and one had t-AML. RER+ was detected in three of these five patients. Our data suggest that genetic instability is associated with AML and MDS, especially t-AML and s-AML. In addition, our results indicate that the hMSH2 and hMLH1 promoter hypermethylation is not a common event in these malignancies, but may play a role in the development of AML in elderly patients.

Cellular src Gene Expression Associated with Lentoidogenesis in Transdifferentiating Cultures.: (pp60c-src /retina, tapetum/transdifferentiation/lens).

We have shown (9) that elevated pp60c-src kinase activity accompanies the transdifferentiation of chick embryo neuroretinal (NR) cells into lens in vitro; moreover, most immunologically-detectable pp60c-src protein is confined to lentoid bodies in permissive cultures (FH; 6). By contrast, pp60c-src expression is low in non-permissive cultures where lentoid formation is blocked by high glucose (FHG; 6) or medium 199 (11). We now extend these findings in several respects. Firstly, glial-enriched cultures in both FH and FHG media form small but sparse lentoid bodies at around 20 days, accompanied by increases in both δ crystallin and pp60c-src expression. In later FHG cultures, these lentoids increase neither in number/size nor in δ/pp60c-src expression, in contrast to permissive (FH) cultures. Thus the high glucose block on transdifferentiation is only partly mediated by neuronal influences (19). Secondly, transdifferentiating cultures of tapetal cells show higher levels of pp60c-src relative to redifferentiated or dedifferentiated (16, 17) cultures of these cells. Thirdly, we find no evidence that c-src oncogene expression directly signals transdifferentiation. Thus v-src expression in RSV-transformed NR cells inhibits δ crystallin accumulation (29; this study), while a c-src-substituted RSV variant has little effect on NR transdifferentiation. Late cultures of NR cells in medium 199 fail to accumulate pp60c-src protein or c-src transcripts, even though previous studies (2) showed that δ crystallin transcripts are localised within the nuclei of many cells in such cultures.