The Interlaboratory RObustness of Next-generation sequencing (IRON) study: a deep sequencing investigation of TET2, CBL and KRAS mutations by an international consortium involving 10 laboratories.

Massively parallel pyrosequencing allows sensitive deep sequencing to detect molecular aberrations. Thus far, data are limited on the technical performance in a clinical diagnostic setting. Here, we investigated as an international consortium the robustness, precision and reproducibility of amplicon next-generation deep sequencing across 10 laboratories in eight countries. In a cohort of 18 chronic myelomonocytic leukemia patients, mutational analyses were performed on TET2, a frequently mutated gene in myeloproliferative neoplasms. Additionally, hotspot regions of CBL and KRAS were investigated. The study was executed using GS FLX sequencing instruments and the small volume 454 Life Sciences Titanium emulsion PCR setup. We report a high concordance in mutation detection across all laboratories, including a robust detection of novel variants, which were undetected by standard Sanger sequencing. The sensitivity to detect low-level variants present with as low as 1-2% frequency, compared with the 20% threshold for Sanger-based sequencing is increased. Together with the output of high-quality long reads and fast run time, we demonstrate the utility of deep sequencing in clinical applications. In conclusion, this multicenter analysis demonstrated that amplicon-based deep sequencing is technically feasible, achieves high concordance across multiple laboratories and allows a broad and in-depth molecular characterization of cancer specimens with high diagnostic sensitivity.

AIDS-related sinonasal Burkitt lymphoma successfully treated with intensive chemotherapy regimen and high active antiretroviral therapy.

Burkitt lymphoma (BL) is the second most common AIDS-related lymphoma. Primary sinonasal BL in HIV patients is extremely rare and treatment data in this subset of patients is almost nonexistent. Recently, a few studies reported promising results treating HIV-associate BL with an intensive chemotherapy regimen. The use of highly active antiretroviral therapy (HAARTHAART) concomitantly with chemotherapy seems to improve patient outcomes, but this topic is still controversial due to potential drug interactions. We report a case of a 29-year old woman diagnosed with AIDS presenting with symptoms of chronic sinusitis. Subsequent investigation by CT scan and endoscopic biopsy discovered a sinonasal BL in an early stage. The patient was treated with intensive chemotherapy and HAARTHAART and achieved a complete remission and long-term immunologic recovery. This case report describes a rare entity whose natural history, treatment and prognosis is infrequently characterized in the medical literature.

Is there any association between TACSTD2, KIAA1253, Ku70 and mutant KRAS gene expression and clinical-pathological features of colorectal cancer?

AIM: To determine the quantitative gene expression of KRAS codon 12 mutant, TACSTD2, Ku70 and SERIN1 in samples of tumor tissue and to relate them with clinical-pathological characteristics of colorectal cancer. METHODS: Samples of tumor and normal tissue of patients surgically treated for colorectal cancer between July 2005 and July 2009 were stored in a tissue bank. These samples were studied with the technique of real-time polymerase chain reaction in respect to expression of the following genes: KRAS codon 12 mutation, TACSTD2, Ku70, and SERIN1. RESULTS: Tumor samples of 37 patients were studied. The mean age was 65.5 years. Twenty one patients (56.8%) were male. Nine patients (24.3%) were classified as TNM stage I, 11 patients (29.8%) as TNM stage II, eight patients (21.6%) as TNM stage III and nine patients (24.3%) as TNM stage IV. The Ku70 expression in poorly-differentiated tumors is significantly higher than in well and moderately-differentiated tumors (2.76 vs. 1.13; p < 0.05). SERIN1, TACSTD2 and KRAS codon 12 mutation are not associated with clinical-pathological characteristics of colorectal cancer. CONCLUSION: Ku70 expression in poorly-differentiated tumors is significantly higher than in well and moderately-differentiated colorectal tumors.

Can local supply of bone marrow mononuclear cells improve the outcome from late tubular repair of human median and ulnar nerves?

The purpose of this non-randomised retrospective study was to compare nerve regeneration after reconnection with silicone tubes with two different strategies. A total of 44 patients with injured median or ulnar nerves in the forearm were surgically treated. In one group of patients, a silicone tube alone was placed in the nerve gap. In a second group, the silicone tube was filled with autologous bone marrow mononuclear cells obtained by aspiration from the iliac crest. Motor function, sensation and the effect of pain on function were assessed 1 year after surgery. The tubes filled with bone marrow cells showed better recovery than the empty tubes. The use of bone marrow mononuclear cells in addition to tube re-connection may promote better nerve regeneration than conventional tubular repair.

Monoclonality of asynchronous bilateral lymphoma of the testis.

OBJECTIVES: Lymphoma is the most frequent testicular malignancy in men over 60 years of age. Even though patients present initially with localized disease, the high incidence of bilateral involvement, synchronous or not, and early systemic dissemination are characteristic of these neoplasms. Sometimes the interval between tumor involvement of both testes is long. The question is raised whether either the patient has a predisposition to present new clones of transformed lymphocytes, or the same disease using the same pathway from a systemic reservoir infiltrates the contralateral testis. METHOD: Polymerase chain reaction and DNA sequencing were used to detect immunoglobulin heavy chain (IgH) rearrangement in paraffin-embedded specimens from asynchronous tumors affecting the right and left testis of a 85-year-old man with an interval period of 13 months. RESULTS: Both tumors showed the same IgH rearrangement. CONCLUSIONS: The lymphoma affecting the left and right testis derived from the same clone. It makes a strong case that lymphoma of the testis is the first manifestation of a systemic disease and should be treated aggressively early at the beginning of the disease.

ATIC-ALK: A novel variant ALK gene fusion in anaplastic large cell lymphoma resulting from the recurrent cryptic chromosomal inversion, inv(2)(p23q35).

The subset of CD30-positive anaplastic large cell lymphomas (ALCL) with the NPM-ALK gene fusion arising from the t(2;5)(p23;q35) forms a distinct clinical and prognostic entity. Recently, various cytogenetic, molecular, and protein studies have provided evidence for the existence of several types of variant ALK fusions in up to 20% of ALK+ ALCL, of which only one, a TPM3-ALK fusion resulting from a t(1;2)(q25;p23), has so far been cloned. A cryptic inv(2)(p23q35) has been described as another recurrent cytogenetic alteration involving ALK and an unidentified fusion partner in some ALCL. In a screen for variant ALK gene fusions, we identified two ALCL that were negative for NPM-ALK by reverse transcriptase-polymerase chain reaction, but were positive for cytoplasmic ALK with both polyclonal and monoclonal antibodies to the ALK tyrosine kinase domain, consistent with ALK deregulation by an alteration other than the t(2;5) Case 1 was a T-lineage nodal and cutaneous ALCL in a 52-year-old woman, and Case 2 was a T-lineage nodal ALCL in a 12-year-old girl. FISH analysis confirmed ALK rearrangement in both cases. An inverse polymerase chain reaction approach was then used to identify the ALK translocation partner in Case 1. We found an in-frame fusion of ALK to ATIC, a gene previously mapped to 2q34-q35. We then confirmed by DNA polymerase chain reaction the localization of ATIC to yeast artificial chromosome (YAC) 914E7 previously reported to span the 2q35 break in the inv(2)(p23q35). FISH analysis in Case 1 confirmed rearrangement of YAC 914E7 and fusion to ALK. The ATIC-ALK fusion was confirmed in Case 1 and also identified in Case 2 by conventional reverse transcriptase-polymerase chain reaction using ATIC forward and ALK reverse primers. ATIC encodes an enzyme involved in purine biosynthesis which, like other fusion partners of ALK, is constitutively expressed and appears to contain a dimerization domain. ATIC-ALK fusion resulting from the inv(2)(p23q35) thus provides a third mechanism of ALK activation in ALK+ ALCL.

Mutational analysis of N-RAS and GAP-related domain of the neurofibromatosis type 1 gene in chronic myelogenous leukemia.

RAS mutations can be detected in a variable number of patients with myeloproliferative disorders such as myelodysplastic syndromes and acute myeloid leukemia, but are rare events in chronic myelogenous leukemia in chronic phase. However, there is good evidence supporting the involvement of RAS signalling pathway in CML and this could be due to alterations in RAS activity regulatory proteins. The neurofibromatosis (NF1) gene down-regulates the RAS signal transduction pathway through the inhibitory function of its GAP-related domain (GRD) on RAS protein. The loss or alteration of neurofibromin (the NF1 protein) may produce a disfunction similar to point mutations in the RAS gene resulting in the permanent stimulation of the RAS signal transduction pathway. Mutations involving the GRD region of the NF1 gene (GRD-NF1) have been described in a variety of tumors such as colon carcinoma and astrocytoma. Germline mutations and deletions in the NF1 gene, as seen in neurofibromatosis type 1, are also associated with certain myeloid disorders. In the present work, we sought to identify mutations in the codons 12/13 and 61 of RAS gene and in the Lys-1423 codon of GRD-NF1, which are well known hot spots in these genes, in a group of 36 adults and ten children with chronic myelogenous leukemia in chronic phase and blast crisis. Using the PCR-SSCP and the allele-specific restriction assay (ASRA) techniques, we were not able to observe any RAS or NF1 detectable mutation. These findings suggest that RAS and GRD-NF1 mutations are not involved either in chronic phase or in the progression to blast crisis in chronic myelogenous leukemia in adults and children.

Reverse transcriptase-polymerase chain reaction analysis of cytokeratin 19 expression in the peripheral blood mononuclear cells of normal female blood donors.

BACKGROUND: Early detection of haematogenous dissemination of epithelial tumours afforded by the analysis of epithelial antigen expression in the peripheral blood mononuclear fraction (PBMN) and bone marrow may confer a worse prognosis to patients with carcinoma. Cytokeratin 19 is a protein normally expressed by epithelial cells including normal and malignant mammary cells. Previous studies have demonstrated that analysis of cytokeratin 19 expression by the reverse transcriptase-polymerase chain reaction (RT-PCR) can detect one epithelial cell in as many as 10(5)-10(7) haematopoetic cells. Despite its sensitivity concern has been voiced recently about the specificity of this technique owing to the detection of cytokeratin 19 expression in the PBMN of normal volunteers and the bone marrow of patients with haematological malignancies. AIMS: To assess the sensitivity and specificity of RT-PCR detection of cytokeratin 19 in PBMN of normal female blood donors. METHODS: Blood was taken from 52 normal female blood donors and PBMN separated through Fycol gradient centrifugation. Cytokeratin 19 was measured using a two step nested RT-PCR assay. RESULTS: No amplification was found in the first step for any of the samples studied, whereas in the second step amplification was observed in 10 of the 52 samples. Both steps could detect one MCF-7 cell (the cytokeratin 19 positive control) in 10(6) CEM (cytokeratin 19 negative control) cells. CONCLUSIONS: As both PCR steps are sensitive to the 10(-6) level, performing only the first amplification step may decrease the non-specificity of this method. Further studies are needed to define the specificity and sensitivity of this technique in blood and bone marrow specimens of women with breast cancer.

Leptomeningeal involvement in chronic lymphocytic leukemia identified by polymerase chain reaction in stored slides: a case report.

The use of polymerase chain reaction (PCR) for routine detection of clonal immunoglobulin heavy-chain (IgH) gene rearrangements represents an attractive alternative to Southern hybridization analysis not only because PCR protocols are quicker and simpler, but also because of the ability to analyze very small population of cells in search of minimal residual disease. This can be especially important for the detection of clonal malignant cells in locations other than bone marrow or peripheral blood. We describe a case in which central nervous system involvement, a very rare complication of chronic lymphocytic leukemia, was confirmed by PCR analysis for IgH genes rearrangement of the lymphocytes found in cerebrospinal fluid. The cerebrospinal fluid and the peripheral blood lymphocytes (obtained from archival cytospins stored at the time of diagnosis, 5 years before) presented an identical IgH gene rearrangement, as shown by sequence analysis. Thus, the use of PCR for IgH genes rearrangement can be very useful in the detection of monoclonality in samples with a small number of cells and in the confirmation of the common origin of B cells in different specimens of the same patient.

Aplasia after donor lymphocyte infusion (DLI) for CML in relapse after sex-mismatched BMT: recovery of donor-type haemopoiesis predicted by non-isotopic in situ hybridization (ISH).

We report a patient with CML in relapse after a sex-mismatch bone marrow transplant who was treated with donor lymphocyte infusions and developed severe marrow aplasia 3 months later. As cytogenetic analysis at this point was not possible because of the very low number of marrow cells available, we used in situ hybridization (ISH) for sex chromosomes and the BCR/ABL gene together with quantitative PCR to monitor the patient's response. The results suggest that recovering haemopoiesis was derived from donor cells and contributed to the decision not to transfuse donor marrow cells on a second occasion.

Plasma kinetics and biodistribution of a lipid emulsion resembling low-density lipoprotein in patients with acute leukemia.

Low-density lipoprotein (LDL) could be used as a carrier of chemotherapeutic agents to neoplastic cells that overexpress LDL receptors (rLDL), but LDL is difficult to obtain and handle. Recently, it was observed that a protein-free emulsion resembling the lipid portion of LDL (LDE) behave like native LDL when injected into the bloodstream. In this study, the evidence that LDE is taken up by rLDL was expanded by comparing LDL and LDE plasma decay curves in rabbits and by competition experiments with lymphocytes. To verify whether LDE could be removed from the plasma by neoplastic cells with increased rLDL, LDE labeled with 14Ccholesteryl ester was injected into 14 patients with acute myeloid leukemia (AML) and into 7 with acute lymphocytic leukemia (ALL). In AML rLDL expression is increased but in ALL it is normal. LDE plasma fractional clearance rate (FCR, in h-1) was calculated from the remaining radioactivity measured in plasma samples collected during 24 h following injection. LDE FCR was 3-fold greater in AML than in ALL patients 0.192 +/- 0.210 (SD) and 0.066 +/- 0.033 h-1, respectively, P < 0.035. When LDE injection was repeated in 9 AML patients in hematological remission, LDE FCR diminished 66% compared to the pretreatment values (from 0.192 +/- 0.210 to 0.065 +/- 0.038 h-1, P < 0.02), so that it could be estimated that nearly 66% of the emulsion was taken up by AML cells and only 34% by the normal tissues. As expected, LDE FCR was unchanged in 4 patients with ALL in hematological remission (0.069 +/- 0.044 h-1). Gamma camera images obtained 6 h after the injection of 99mTc-label LDE into one patient with ALL showed biodistribution similar to that of LDL. In one AML patient LDE was comparatively more concentrated over the areas corresponding to the bone marrow infiltrated by AML cells. Our results indicate that LDE FCR is increased in a disease known to contain malignant cells that overexpress rLDL, suggesting that LDE is taken up by malignant cells with increased rLDL.

T lymphocytes in chronic myelogenous leukaemia (CML): no evidence of the BCR/ABL fusion gene detected by fluorescence in situ hybridization in 14 patients.

Previous studies designed to identify the Ph chromosome in T lymphocytes from patients with chronic myelogenous leukaemia (CML) were mostly based on small numbers of patients. To examine the possibility that the occasional CML patient might have major penetration of the T-cell compartment by the leukaemic clone, we studied interphase T cells from the blood of 11 CML patients conventionally treated in chronic phase and three in relapse after allogeneic bone marrow transplant (BMT) by fluorescence in situ hybridization using BCR and ABL cosmid probes. Granulocytes from the same patient and cells from the SD-1 CML cell line served as positive controls. Cells with juxtaposition of BCR and ABL signals or with the two signals up to one signal diameter apart were scored as positive. In each CML patient the incidence of 'positive' T cells was much less than in positive controls and similar to that found in negative controls (mean values +/- 1 SD: 7.7 +/- 3.6; 91.2 +/- 3.1, and 5.6 +/- 2.2, respectively). We conclude that none of the patients studied by this technique had any appreciable proportion of BCR/ABL-positive T cells in the circulation.

Relapse of chronic myeloid leukemia after allogeneic bone marrow transplant: the case for giving donor leukocyte transfusions before the onset of hematologic relapse.

Fourteen patients with chronic myeloid leukemia (CML) relapsing after allogeneic bone marrow transplant (BMT) were treated with leukocyte transfusions from the original marrow donor (sibling, n = 9; volunteer unrelated, n = 5). The relapse was defined at the molecular level in two cases, cytogenetically in five cases and hematologically in seven cases. Ten patients responded, seven of seven patients with cytogenetic/molecular relapse compared with three of seven with hematologic relapse (P < .03). All five recipients of cells from unrelated donors responded. Eight of the 10 responders have achieved polymerase chain reaction-negative status and this persisted in three patients for more than 2 years; no responder has shown sign of relapse. Reversible marrow aplasia occurred in two patients, both treated in hematologic relapse. Severe graft-versus-host disease occurred in four patients and was fatal in one. We confirm previous reports that donor leukocyte transfusions are effective in the management of CML in relapse after BMT. In this series, therapeutic intervention before the onset of hematologic relapse was associated with an increased likelihood of response and no marrow aplasia.

Lack of reciprocal translocation in BCR-ABL positive Ph-negative chronic myeloid leukaemia.

We used fluorescence in situ hybridization (FISH) to metaphase chromosomes with BCR and ABL cosmid probes in conjunction with the polymerase chain reaction (PCR) to study the mechanism by which the ABL proto-oncogene is inserted into a morphologically normal chromosome 22 in patients with Ph-negative chronic myeloid leukaemia characterized by the BCR-ABL chimeric gene. In control patients with Ph-positive CML the ABL probe localized to 22q- and the 3' BCR probe localized to 9q+. In nine Ph-negative CML patients the ABL probe localized to one normal chromosome 9 and to one 'normal' chromosome 22. Both 5' and 3' BCR probes localized exclusively to the chromosomes 22. By PCR all had evidence of BCR-ABL transcripts, but none had evidence of the reciprocal ABL-BCR gene product that is seen in 70% of the Ph-positive CML patients. These data confirm the view that Ph-negative CML results from insertion of ABL-containing DNA sequences into a normal-appearing chromosome 22 without reciprocal translocation of sequences from chromosome 22 to chromosome 9.

Increased plasma removal of microemulsions resembling the lipid phase of low-density lipoproteins (LDL) in patients with acute myeloid leukemia: a possible new strategy for the treatment of the disease.

A microemulsion of lipid composition resembling low-density lipoprotein (LDL), but devoid of apolipoproteins and labeled with [14C]-cholesteryl oleate was injected into 16 healthy subjects and into 15 patients with acute myeloid leukemia (AML). Removal from plasma of the lipid label was higher in the leukemic group compared to healthy subjects in terms of fractional clearance rate (0.185 +/- 0.205 and 0.080 +/- 0.030 h-1, respectively, P < 0.03). When the emulsion was again injected into 10 of the AML patients after complete hematological remission, the fractional clearance rate of cholesteryl ester was reduced to one third of the value observed prior to treatment (0.061 +/- 0.038 h-1) and was not different from that obtained for the healthy subjects. Also, in untreated AML patients, serum LDL-cholesterol levels inversely correlated with the values of fractional clearance rate of the microemulsion. This correlation was no longer observed after treatment. These data suggest that the LDL-like microemulsion was selectively taken up by the neoplastic cells presumably by interaction with LDL receptors. Therefore, microemulsions may function as potential carriers for anticancer drugs that are targeted to tumor cells for patients with acute myeloid leukemia. Unlike native LDL, microemulsions are suitable for utilization in routine clinical practice.

Increased plasma removal of microemulsions resembling the lipid phase of low-density lipoproteins (LDL) in patients with acute myeloid leukemia: a possible new strategy for the treatment of the disease

A microemulsion of lipid composition resembling low-density lipoprotein (LDL), but devoid of apolipoproteins and labeled with [14C]-cholesteryl oleate was injected into 16 healthy subjects and into 15 patients with acute myeloid leukemia (AML). Removal from plasma of the lipid label was higher in the leukemic group compared to healthy subjects in terms of fractional clearance rate (0.185 +/- 0.205 and 0.080 +/- 0.030 h-1, respectively, P < 0.03). When the emulsion was again injected into 10 of the AML patients after complete hematological remission, the fractional clearance rate of cholesteryl ester was reduced to one third of the value observed prior to treatment (0.061 +/- 0.038 h-1) and was not different from that obtained for the healthy subjects. Also, in untreated AML patients, serum LDL-cholesterol levels inversely correlated with the values of fractional clearance rate of the microemulsion. This correlation was no longer observed after treatment. These data suggest that the LDL-like microemulsion was selectively taken up by the neoplastic cells presumably by interaction with LDL receptors. Therefore, microemulsions may function as potential carriers for anticancer drugs that are targeted to tumor cells for patients with acute myeloid leukemia. Unlike native LDL, microemulsions are suitable for utilization in routine clinical practice