Glioblastomas with copy number gains in EGFR and RNF139 show increased expressions of carbonic anhydrase genes transformed by ENO1.

BACKGROUND: Prominence of glycolysis in glioblastomas may be non-specific or a feature of oncogene-related subgroups (i.e. amplified EGFR, etc.). Relationships between amplified oncogenes and expressions of metabolic genes associated with glycolysis, directly or indirectly via pH, were therefore investigated. METHODS: Using multiplex ligation-dependent probe amplification, copy numbers (CN) of 78 oncogenes were quantified in 24 glioblastomas. Related expressions of metabolic genes encoding lactate dehydrogenases (LDHA, LDHC), carbonic anhydrases (CA3, CA12), monocarboxylate transporters (SLC16A3 or MCT4, SLC16A4 or MCT5), ATP citrate lyase (ACLY), glycogen synthase1 (GYS1), hypoxia inducible factor-1A (HIF1A), and enolase1 (ENO1) were determined in 22 by RT-qPCR. To obtain supra-glycolytic levels and adjust for heterogeneity, concurrent ENO1 expression was used to mathematically transform the expression levels of metabolic genes already normalized with delta-delta crossing threshold methodology. RESULTS: Positive correlations with EGFR occurred for all metabolic genes. Significant differences (Wilcoxon Rank Sum) for oncogene CN gains in tumors of at least 2.00-fold versus less than 2.00-fold occurred for EGFR with CA3's expression (p < 0.03) and for RNF139 with CA12 (p < 0.004). Increased CN of XIAP associated negatively. Tumors with less than 2.00-fold CN gains differed from those with gains for XIAP with CA12 (p < 0.05). Male gender associated with CA12 (p < 0.05). CONCLUSIONS: Glioblastomas with CN increases in EGFR had elevated CA3 expression. Similarly, tumors with RNF149 CN gains had elevated CA12 expression. GENERAL SIGNIFICANCE: In larger studies, subgroups of glioblastomas may emerge according to oncogene-related effects on glycolysis, such as control of pH via effects on carbonic anhydrases, with prognostic and treatment implications.

Low-level amplification of oncogenes correlates inversely with age for patients with nontypical meningiomas.

BACKGROUND: This study sought to identify genes in nontypical meningiomas with gains in copy number (CN) that correlate with earlier age of onset, an indicator of aggressiveness. METHODS: Among 94 adult patients, 91 had 105 meningiomas that were histologically confirmed. World Health Organization grades I (typical), II (atypical), and III (anaplastic) were assigned to tumors in 76, 14, and 1 patient, respectively. Brain invasion indicated that two World Health Organization grade I meningiomas were biologically atypical. DNA from 15 invasive/atypical/anaplastic meningiomas and commercial normal DNA were analyzed with multiplex ligation dependent probe amplification. The CN ratios (fold differences from normal) for 78 genes were determined. The CN ratio was defined as [tumor CN]/[normal CN] for each gene to normalize results. RESULTS: Characteristic gene losses (CN ratio < 0.75) occurred in >50% of the invasive/atypical/anaplastic meningiomas at 22q11, 1p34.2, and 1p22.1 loci. Gains (CN ratio ≥ 2.0) occurred in each tumor for 2 or more of 19 genes. Each of the 19 genes' CN ratio was ≥ 2.0 in multiple tumors, and their collective sums (up to 49.1) correlated inversely with age (r = -0.72), minus an outlier. In patients ≤ 55 versus >55 years, 5 genes (BIRC2, BRAF, MET, NRAS, and PIK3CA) individually exhibited significantly higher CN ratios (P < 0.05) or a trend for them (P < 0.09), with corrections for multiple comparisons, and their sums correlated inversely with age (r = -0.74). CONCLUSIONS: Low levels of amplification for selected oncogenes in invasive/atypical/anaplastic meningiomas were higher in younger adults, with the CN gains potentially underlying biological aggressiveness associated with early tumor development.

Rapid detection of high-level oncogene amplifications in ultrasonic surgical aspirations of brain tumors.

BACKGROUND: Genomic tumor information, such as identification of amplified oncogenes, can be used to plan treatment. The two sources of a brain tumor that are commonly available include formalin-fixed, paraffin-embedded (FFPE) sections from the small diagnostic biopsy and the ultrasonic surgical aspiration that contains the bulk of the tumor. In research centers, frozen tissue of a brain tumor may also be available. This study compared ultrasonic surgical aspiration and FFPE specimens from the same brain tumors for retrieval of DNA and molecular assessment of amplified oncogenes. METHODS: Surgical aspirations were centrifuged to separate erythrocytes from the tumor cells that predominantly formed large, overlying buffy coats. These were sampled to harvest nuclear pellets for DNA purification. Four glioblastomas, 2 lung carcinoma metastases, and an ependymoma were tested. An inexpensive PCR technique, multiplex ligation-dependent probe amplification (MLPA), quantified 79 oncogenes using 3 kits. Copy number (CN) results were normalized to DNA from non-neoplastic brain (NB) in calculated ratios, [tumor DNA]/[NB DNA]. Bland-Altman and Spearman rank correlative comparisons were determined. Regression analysis identified outliers. RESULTS: Purification of DNA from ultrasonic surgical aspirations was rapid (<3 days) versus FFPE (weeks) and yielded greater amounts in 6 of 7 tumors. Gene amplifications up to 15-fold corresponded closely between ultrasonic aspiration and FFPE assays in Bland-Altman analysis. Correlation coefficients ranged from 0.71 to 0.99 using 3 kit assays per tumor. Although normalized CN ratios greater than 2.0 were more numerous in FFPE specimens, some were found only in the ultrasonic surgical aspirations, consistent with tumor heterogeneity. Additionally, CN ratios revealed 9 high-level (≥ 6.0) gene amplifications in FFPE of which 8 were also detected in the ultrasonic aspirations at increased levels. The ultrasonic aspiration levels of these amplified genes were also greater than 6.0 CN ratio, except in one case (3.53 CN ratio). Ten of 17 mid-level (≥3.0 & <6.0 CN ratio) amplifications detected in FFPE were also detected as being increased (≥ 2.0 CN ratio) in the aspirations. CONCLUSIONS: Buffy coats of centrifuged ultrasonic aspirations contained abundant tumor cells whose DNA permitted rapid, multiplex detection of high-level oncogene amplifications that were confirmed in FFPE. VIRTUAL SLIDES: http://www.diagnosticpathology.diagnomx.eu/vs/1883718801686466.

Potential roles of cell-derived microparticles in ischemic brain disease.

PURPOSE: The objective of this study is to review the role of cell-derived microparticles in ischemic cerebrovascular diseases. MATERIALS AND METHODS: An extensive PubMed search of literature pertaining to this study was performed in April 2009 using specific keyword search terms related to cell-derived microparticles and ischemic stroke. Some references are not cited here as it is not possible to be all inclusive or due to space limitation. DISCUSSION: Cell-derived microparticles are small membranous vesicles released from the plasma membranes of platelets, leukocytes, red cells and endothelial cells in response to diverse biochemical agents or mechanical stresses. They are the main carriers of circulating tissue factor, the principal initiator of intravascular thrombosis, and are implicated in a variety of thrombotic and inflammatory disorders. This review outlines evidence suggesting that cell-derived microparticles are involved predominantly with microvascular, as opposed to macrovascular, thrombosis. More specifically, cell-derived microparticles may substantially contribute to ischemic brain disease in several settings, as well as to neuroinflammatory conditions. CONCLUSION: If further work confirms this hypothesis, novel therapeutic strategies for minimizing cell-derived microparticles-mediated ischemia are available or can be developed, as discussed.

EGFR expression as an ancillary tool for diagnosing lung cancer in cytology specimens.

Lung cancer evolves in a multistep process, and its early detection portends a better prognosis. Bronchial washings/brushings and fine-needle aspirations are often used as early screening and cytological diagnosis of lung cancer. In some cases, it is difficult to differentiate morphologically malignant from reactive cells. Epidermal growth factor receptor (EGFR) is a transmembrane receptor overexpressed in high percentage lung cancers, and contributes to tumor growth. Assessing EGFR expression levels by fluorescence in situ hybridization (FISH) and immunohistochemistry (IHC) may provide critical information of tumor marker abnormalities, assist in the cytological diagnosis, and stratify patients for EGFR inhibitor therapy. Fifty patients with bronchial washings/brushings or fine-needle aspiration specimens, and corresponding histologically confirmed lung biopsies, were studied for EGFR expression with FISH and IHC. Copy numbers of the EGFR gene locus were analyzed with those of chromosome 7 by FISH. EGFR and FISH results were compared to our FISH data with combined EGFR, c-myc, 5p15.2, and chromosome 6 probes in selected cases. Cell blocks, if available, and tissue biopsy sections were used for EGFR IHC. The intensity of IHC was scored, and quantified. Only balanced aneuploidy of EGFR was identified by FISH. Gene amplification was not detected. The chromosomal abnormalities of EGFR were often accompanied by other chromosomal aneuploidies demonstrated in c-myc (8q24), 5p15.2 or 6p, indicating a general genomic instability. About half of the specimens with confirmed malignancy showed EGFR balanced aneuploidy by FISH, and gene copy number was not coupled with protein expression in many cases. The benign or reactive cytology specimens confirmed by biopsies had high specificity by FISH (96%) and IHC (88%). FISH and IHC analysis of EGFR, possibly along with other tumor markers, may be a useful ancillary tool to classify difficult cytology cases and inform clinicians arranging targeted chemotherapy.

Comparative gene expression analysis of a chronic myelogenous leukemia cell line resistant to cyclophosphamide using oligonucleotide arrays and response to tyrosine kinase inhibitors.

Acquired imatinib resistance in chronic myelogenous leukemia (CML) can be the consequence of mutations in the kinase domain of BCR-ABL or increased protein levels. However, as in other malignancies, acquired resistance to cytostatic drugs is a common reason for treatment failure or disease progression. As a model for drug resistance, we developed a CML cell line resistant to cyclophosphamide (CP). Using oligonucleotide arrays, we examined changes in global gene expression. Selected genes were also examined by real-time PCR and flow cytometry. Neither the parent nor the resistant lines had mutations in their ATP binding domain. Filtering genes with a low-base line expression, a total of 239 genes showed significant changes (162 up- and 77 down-regulated) in the resistant clone. Most of the up-regulated genes were associated with metabolism, signal transduction, or encoded enzymes. The gene for aldehyde dehydrogenase 1 was over-expressed more than 2000-fold in the resistant clone. BCR-ABL was expressed in both cell lines to a comparable extent. When exposed to the tyrosine kinase inhibitors imatinib and nilotinib, both lines were sensitive. In conclusion, we found multiple genetic changes in a CML cell line resistant to CP related to metabolism, signal transduction or apoptosis. Despite these changes, the resistant cells retained sensitivity to tyrosine kinase inhibitors.

Primary plasma cell leukemia: report of 17 new cases treated with autologous or allogeneic stem-cell transplantation and review of the literature.

Primary plasma cell leukemia (PPCL) is a rare hematologic malignancy characterized by the proliferation of plasma cells in blood, bone marrow, and other organs in the absence of established multiple myeloma. PPCL has a poor prognosis when treated with conventional therapy for multiple myeloma. We describe here 17 new cases of PPCL who underwent stem-cell transplantation (SCT) (2 cases observed by the authors and 15 cases from the International Bone Marrow Transplant Registry [IBMTR]). The first case was diagnosed in a 21-year-old male who presented with leukocytosis and acute renal failure. He was treated with hyper-CVAD, entered complete remission, and then proceeded to high-dose chemotherapy with peripheral stem-cell support. He is currently in complete remission 23 months after initial diagnosis and 19 months after autologous SCT. The second case was observed in a 31-year-old male who presented with leukocytosis and hepatic infiltration with plasma cells. He was treated with VAD chemotherapy and underwent allogeneic bone marrow transplantation from his HLA-identical sister. He remained in complete remission for 3 years and then developed progressive refractory disease, dying 7 years after the initial diagnosis. In addition to these 2 cases, 15 further unpublished cases of PPCL from the IBMTR are reported here (treated between 1993 and 2001, 6 by autologous and 9 by allogeneic transplantation). Finally, the features of PPCL, the outcome, published data of SCT for PPCL, and indications for treatment are discussed.

Evaluation of fluorescence in situ hybridization as an ancillary tool to urine cytology in diagnosing urothelial carcinoma.

Our purpose was to evaluate the feasibility of performing fluorescence in situ hybridization (FISH) on routine urine samples and to compare the relative sensitivities of urine cytology and FISH for detecting urothelial carcinoma. Light microscopy (LM) using cytologic evaluation and FISH were used to study 121 consecutive urine samples. A mixture of fluorescent probes to chromosomes 3, 7, 17, and the 9p21 locus were used for detection of numerical chromosomal abnormalities (UroVysion, Vysis/Abbott). Biopsy specimens from patients in the study were reviewed if available. FISH analysis was performed without knowledge of cytology or biopsy findings. The urine cytology of 121 samples was interpreted as 59 negative, 41 reactive, 16 atypical, 2 suspicious and 3 insufficient cells for diagnosis. 85 samples were successfully analyzed by FISH. Thirty-one of these showed chromosomal abnormalities and these samples were initially regarded on the original cytology reading as follows: 10 negative, 10 reactive, 9 atypical, and 2 suspicious. FISH demonstrated chromosomal abnormalities in a significant number of cases (67%) that were initially diagnosed as normal or reactive by LM. Twenty-five patients were identified who had biopsy-proven TCC and successful FISH. Thirteen of the 25 patients (52%) were abnormal by FISH (cytology: 2 suspicious, 6 atypical, 4 reactive, 1 negative). One patient was atypical by cytology with normal FISH results but had TCC on biopsy. Hyperdiploidy for chromosomes 3 (77%) and 7 (67%) were seen consistently. Multiple chromosomal abnormalities were seen in 67% of these cases. We conclude that FISH has a greater sensitivity in detecting urothelial carcinoma when coupled with urine cytology. It is not entirely clear at this time whether a positive FISH may indicate frank neoplastic urothelial transformation or merely be an indicator of unstable urothelium capable of or primed for malignant transformation thus detecting patients at significant risk. The use of FISH in conjunction with urine cytology can potentially reduce urothelial carcinoma morbidity and mortality by diagnosing these tumors earlier.

Histiocytic sarcoma involving the central nervous system: clinical, immunohistochemical, and molecular genetic studies of a case with review of the literature.

Histiocytic sarcoma (HS) is a rare disease, and there has been much confusion concerning the diagnostic criteria for this entity. Since immunohistochemical and cytogenetic techniques have become more universally available, many cases initially diagnosed as histiocytic sarcoma have been reclassified as other diseases. We describe a case of HS that presented as a single mass lesion in left occipital lobe. At autopsy the tumor also involved the meninges as a thick exudate. Histologic examination showed numerous large pleomorphic malignant cells with areas of necrosis, numerous neutrophils, and phagocytosis by tumor cells. Immunohistochemically, the tumor cells stained positively with antibodies directed against most histiocytic markers and did not stain with antibodies directed against myeloid markers, dendritic markers, CD30, ALK1, or other lymphoid markers. Molecular cytogenetic analysis showed no rearrangement [i.e. t(2;5) translocation or other variant] by fluorescence in situ hybridization. The T-cell receptor-gamma chain by multiplex polymerase chain reaction showed a polyclonal pattern. No heavy or light chain gene rearrangements were found. To our knowledge, this is the first reported autopsy case of this rare entity primarily involving the brain and meninges.

CD23 negative chronic lymphocytic leukemia of the tonsil: report of a case.

We present the case of atypical chronic lymphocytic leukemia presenting as a tonsillar mass in an elderly man. Histological examination of the tumor revealed diffuse submucosal infiltration by small lymphocytes. On flow cytometry, a monoclonal B lymphocytic population expressing CD5, CD19, lambda light chain, but not expressing CD10, CD23, or FMC7 activities, was observed. A diagnostic conundrum occurred with the demonstration on molecular cytogenetic analysis of the chromosomal translocation abnormality, t(11;14)(q13;q32). The diagnosis of CD23 negative chronic lymphocytic leukemia was made after further molecular studies failed to detect the bcl-1 gene rearrangement.

Pathology case of the month. Abdominal pain and weight loss in a young adult. Anaplastic large cell lymphoma.

A 34-year-old black man presented with a three-month history of abdominal pain, anorexia, and weight loss. Physical examination and radiologic studies revealed diffuse lymphadenopathy. Ascites and bilateral pleural effusions were also evident. The patient's condition deteriorated after admission, and he died prior to initiation of therapy. Histologic sections and special studies performed on a cervical lymph node biopsy performed shortly before the patient's death are shown in Figures 1-4. A bone marrow aspirate and biopsy were also performed and revealed no evidence of disease.