Theoretical and Computational Analysis of the Thermal Quasi-Geostrophic Model

This work involves theoretical and numerical analysis of the thermal quasi-geostrophic (TQG) model of submesoscale geophysical fluid dynamics (GFD). Physically, the TQG model involves thermal geostrophic balance, in which the Rossby number, the Froude number and the stratification parameter are all of the same asymptotic order. The main analytical contribution of this paper is to construct local-in-time unique strong solutions for the TQG model. For this, we show that solutions of its regularised version α -TQG converge to solutions of TQG as its smoothing parameter α → 0 and we obtain blow-up criteria for the α -TQG model. The main contribution of the computational analysis is to verify the rate of convergence of α -TQG solutions to TQG solutions as α → 0 , for example, simulations in appropriate GFD regimes.

Semi-martingale driven variational principles

Spearheaded by the recent efforts to derive stochastic geophysical fluid dynamics models, we present a general framework for introducing stochasticity into variational principles through the concept of a semi-martingale driven variational principle and constraining the component variables to be compatible with the driving semi-martingale. Within this framework and the corresponding choice of constraints, the Euler–Poincaré equation can be easily deduced. We show that the deterministic theory is a special case of this class of stochastic variational principles. Moreover, this is a natural framework that enables us to correctly characterize the pressure term in incompressible stochastic fluid models. Other general constraints can also be incorporated as long as they are compatible with the driving semi-martingale.

Association between PNPLA3[G]/I148M variant, steatosis and fibrosis stage in hepatitis C virus - genetic matters

There is an established correlation between the PNPLA3 rs738409 C > G single nucleotide polymorphism (SNP) and hepatic steatosis and fibrosis in hepatitis C virus (HCV) infected patients. However not all data is convergent regarding the exact impact of this SNP on the pattern of disease progression in different clinical settings. In this study, we aimed to further bridge the knowledge gap on this topic by investigating the role of the G allele in promoting steatosis, fibrosis and disease progression in relation to other metabolic and anthropometric host factors. Two hundred and fifty consecutive patients, previously diagnosed with chronic hepatitis C (CHC) underwent liver biopsy. Histology was assessed using the Metavir scoring system. Transient elastography was used for follow-up. Ninety-eight patients were genotyped for PNPLA3 rs738409 and followed up for fibrosis progression. PNPLA3 rs738409[G] allele was significantly correlated with severe steatosis (P = 0.04), severe fibrosis at the time of enrollment (P = 0.0005) and fibrosis progression with an OR of 10.31 (95% CI 1.06 - 99.59, P = 0.04), after a mean follow-up time of 62.85 (95%CI: 52.21 - 76.15) months. Severe steatosis at the time of enrollment had an OR of 11.02 (95% CI 1.48 - 82.09, P = 0.01) for the association with fibrosis progression. The HOMA-IR index was also positively correlated with severe fibrosis (P = 0.03) and fibrosis progression on univariate analysis (P = 0.02). PNPLA3 rs738409[G] allele is a reliable predictor for steatosis and fibrosis in CHC. The presence of G allele, along with severe steatosis and insulin resistance are significant predictors for fibrosis progression.

Pointwise gradient bounds for degenerate semigroups (of UFG type)

In this paper, we consider diffusion semigroups generated by second-order differential operators of degenerate type. The operators that we consider do not , in general, satisfy the Hörmander condition and are not hypoelliptic. In particular, instead of working under the Hörmander paradigm, we consider the so-called UFG (uniformly finitely generated) condition, introduced by Kusuoka and Strook in the 1980s. The UFG condition is weaker than the uniform Hörmander condition, the smoothing effect taking place only in certain directions (rather than in every direction, as it is the case when the Hörmander condition is assumed). Under the UFG condition, Kusuoka and Strook deduced sharp small time asymptotic bounds for the derivatives of the semigroup in the directions where smoothing occurs. In this paper, we study the large time asymptotics for the gradients of the diffusion semigroup in the same set of directions and under the same UFG condition. In particular, we identify conditions under which the derivatives of the diffusion semigroup in the smoothing directions decay exponentially in time. This paper constitutes, therefore, a stepping stone in the analysis of the long-time behaviour of diffusions which do not satisfy the Hörmander condition.

A novel pathophysiological-based panel of biomarkers for the diagnosis of nonalcoholic steatohepatitis

Non-invasive biochemical markers are useful to distinguish between nonalcoholic steatohepatitis (NASH) and simple steatosis. The aim of this study was to test the diagnostic value of a panel of biomarkers derived from the pathophysiological events involved in the development of NASH. A total of 79 patients: 20 not-NASH and 59 NASH were included in the study. Definitive NASH was defined according to Kleiner's classification. In all subjects, parameters of the metabolic syndrome, insulin resistance (HOMA-IR), adiponectin, interleukin-6 (IL-6) and total cytokeratin-18 (M65 antigen) were determined. Univariate and multivariate analysis were used to identify independent predictors of NASH. In multivariate analysis three markers were independently predictors of NASH: adiponectin, IL-6 and M65 levels. In decreasing order, the independent predictors of NASH (NAS≥5) were M65 with an AUROC of 0.791, IL-6 with an AUROC of 0.727 and adiponectin with an AUROC of 0.709. The combination of two biomarkers yelded an AUROC of 0.828 for M65 and IL-6, 0.841 for adiponectin and M65 and 0.852 for adiponectin and IL-6. The best value was obtained by triple combination: adiponectin, M65 and IL-6 with and AUROC of 0.903, Sp=85.7% (PPV=94.2%) and Se=84.5% (NPV=66.7%). In conclusion, a novel pathophysiological - based panel of biomarkers combining total CK-18, IL-6 and adiponectin may be useful to predict NASH.

Hepatosplenic gamma/delta T-cell lymphoma in immunocompromised patients. Report of two cases and review of literature

We describe 2 male patients in whom hepatosplenic gamma/delta T-cell lymphoma (HSTL) developed 6 and 10 years after renal transplantation. The onset was abrupt with systemic symptoms, cytopenia, and hepatosplenomegaly. The histologic examination of the spleen (case 1), liver, and bone marrow revealed sinusoidal infiltrates of markedly abnormal lymphocytes. The neoplastic cells in these cases were CD2+, CD3+, CD4-, CD5-, CD7+, CD8+, CD16+, CD56+, beta F1-negative, and TIA-1-negative. Both cases displayed clonal rearrangement of the T-cell receptor (TCR) delta gene and the TCR beta gene. The spleen in case 1 was positive for Epstein-Barr virus genome and showed TCR-gamma gene rearrangement by polymerase chain reaction. Isochromosome 7 [i(7)(q10)] was found in each case. Both patients died within 4 months of diagnosis. HSTL has been reported in only 5 renal transplant recipients. HSTL may be relatively more frequent in immunocompromised patients compared with the general population.

Combined factor V Leiden and prothrombin genotyping in patients presenting with thromboembolic episodes

BACKGROUND

Several genetic defects are associated with increased risk of venous thrombosis. The factor V Leiden (FVL) and prothrombin G20210A mutations are the most frequent causes of inherited thrombophilia.

OBJECTIVES

To evaluate combined genotyping for these 2 mutations in patients presenting with thromboembolic episodes and to correlate genotypic findings with clinical characteristics.

RESULTS

Blood specimens were collected from 401 patients presenting with thromboembolic disease between January 1998 and September 1998, and genotyping for both FVL and prothrombin mutations was performed. Thirty-two patients (8%) were heterozygous for FVL, 4 (1%) were homozygous for FVL, and 20 (5%) were heterozygous for the prothrombin mutation. Two cases (0.5%) were identified with combined FVL and prothrombin mutations. The most common clinical presentation was lower-extremity deep vein thrombosis with or without pulmonary embolism. Arterial events were rare. The thromboembolic episodes were often precipitated by additional risk factors. Recurrent disease was found in 73.9% of FVL carriers and 52.9% of prothrombin mutation carriers; 52% of the patients with FVL and 50% of prothrombin mutation carriers had a first thrombotic episode before age 45 years. The 2 cases with combined genetic defects demonstrate amplified thrombotic risk. In the first case this was effected in thrombosis at a young age, and recurrence of thrombotic events even in the absence of precipitating factors. A complex interplay between genetic and additional risk factors was seen in the second case.

CONCLUSIONS

Identification of both FVL and prothrombin mutations is important in the overall assessment and management of patients with thrombophilia. Detection of these mutations can identify patients at high risk and help evaluate the interaction of genetic and acquired risk factors.

Detection of circulating epithelial cells after surgery for benign breast disease

BACKGROUND

Cytokeratins are predominantly expressed in epithelial cells and their malignant counterparts. Ultrasensitive methods for cytokeratin messenger RNAs (mRNAs) can detect rare circulating tumor cells consistent with hematogenous dissemination in epithelial-derived malignancies, including breast carcinomas. Intraoperative tumor-cell shedding may contribute to this process; this hypothesis is based on the assumption that only tumor cells can be mobilized during surgical manipulation.

METHODS AND RESULTS

The present study addresses this issue by using cytokeratin 19 mRNA detection by reverse transcription-polymerase chain reaction (RT-PCR) in preoperative and postoperative blood samples from 54 patients undergoing excisional biopsy for benign breast disease; 22 healthy volunteers represented the control group. No cytokeratin RT-PCR positivity was found in the control or preoperative samples. Cytokeratin RT-PCR positivity was found in 21 postoperative samples (39%).

CONCLUSIONS

This finding shows that benign epithelial cells can be mobilized during breast surgery; this effect of surgical manipulation warrants caution in the interpretation of RT-PCR positivity for cytokeratin mRNA in the peripheral blood of patients undergoing surgery for breast cancer.

Molecular mechanisms in myelodysplastic syndromes and implications for evolution to acute leukemias

This article reviews the molecular lesions that occur in the clonal hematopoietic disorders classified as myelodysplastic syndromes (MDS). A systematization of these molecular lesions is attempted based on the types of molecular abnormalities. Characteristically, these molecular lesions affect pluripotent hematopoietic progenitors and therefore affect myeloid, monocytic, erythroid, and megakaryocytic lineages. Progression of MDS to acute myelogenous leukemia is common; transformation is considered the final stage in the multi-step process of accumulation of molecular lesions over a prolonged latency period of MDS evolution. Although no molecular lesion is MDS specific, multiple combinations of molecular lesions are common and a systematic approach based on the type of molecular abnormality may offer a better understanding of MDS pathogenesis and the basis for new therapeutic strategies.

Lymphoma of the breast. A clinicopathologic study of primary and secondary cases

BACKGROUND

Primary lymphomas of the breast are rare, accounting for 1.7% to 2.2% of extranodal lymphomas and 0.38% to 0.7% of all non-Hodgkin lymphomas. Although secondary breast lymphomas are also rare, they represent the largest group of metastatic tumors of the breast.

OBJECTIVES

To investigate the clinicopathologic and immunophenotypic characteristics of breast lymphomas, the relative frequency of primary and secondary mammary lymphomas, and in selected cases, the role of gene rearrangement analysis in diagnosis and staging of these lymphomas.

RESULTS

We conducted a retrospective review of 22 cases of breast lymphoma diagnosed at William Beaumont Hospital, Royal Oak, Mich, during a 30-year period (1963-1994). Eleven of the 22 cases fulfilled the criteria for primary breast lymphoma; these cases represented 0.6% of all non-Hodgkin lymphomas seen in our hospital. Of the 11 cases, 5 were diffuse large B-cell lymphomas, 2 were follicle center lymphomas, 2 were marginal zone B-cell lymphomas (mucosa-associated lymphoid tissue type), 1 was a lymphoplasmacytoid lymphoma, and 1 was a peripheral B-cell neoplasm, unclassified. Using a panel of immunohistochemical stains (CD45RO, CD45RA, CD43, CD3, CD20, CD30, CD68, and HLA-DR), 8 cases demonstrated unequivocal B-cell phenotype and 3 cases had equivocal or weak staining patterns for B-cell markers. We identified no cases of T-cell lymphoma. Of 7 cases that had bone marrow biopsies for staging, 3 were positive morphologically for bone marrow involvement. Molecular analysis of B- and T-cell gene rearrangement was used to exclude bone marrow involvement in one case with bone marrow lymphoid aggregates and to confirm negativity in a case that was morphologically negative. Of the 11 secondary breast lymphomas, 5 were diffuse large B-cell lymphomas; 1 was diffuse large B-cell, primary mediastinal subtype; and 5 were follicle center lymphomas.

CONCLUSIONS

Breast lymphomas represented 1.2% of all non-Hodgkin lymphomas in this study; the frequency of primary and secondary cases was equal. In both groups, right breast lesions were predominant, and the most frequent morphologic type was diffuse large B-cell lymphoma. Gene rearrangement analysis is helpful in selected cases to rule out bone marrow involvement, especially in older patients, in whom lymphoid aggregates are common.

Myeloperoxidase mRNA analysis in acute lymphoblastic leukemia

Expression of the myeloperoxidase (MPO) gene at the mRNA level is a better lineage marker than enzymatic activity in early myeloid precursors and their leukemic counterparts. Its diagnostic use depends on the specificity of expression for myeloblasts and its absence in blasts of lymphoid lineage. The present study investigates MPO mRNA expression in adult acute lymphoblastic leukemia (ALL), using reverse transcription-polymerase chain reaction. Of a total of 13 cases, six were found to have blasts positive for MPO mRNA; in all of these cases, the blasts were cytochemically negative for MPO. This unexpected finding of MPO mRNA positivity in six of 13 cases was further investigated at the molecular level. Bcr gene rearrangement analysis was positive in all six cases for the bcr breakpoint diagnostic of chronic myelogenous leukemia (CML). Only three of these six cases were cytogenetically positive for a Philadelphia (Ph) chromosome. Based on molecular analysis, these cases are considered as CML presenting in blast crisis of lymphoid lineage, as opposed to de novo ALL. The remaining seven cases were Ph negative at the cytogenetic and molecular levels; the leukemic blasts were MPO mRNA negative, confirming the lack of MPO gene expression in de novo ALL.

Specimen stability for DNA-based diagnostic testing

The use of molecular diagnostic testing is increasing in the clinical setting; therefore, data regarding DNA stability in clinical specimens are essential for correct test performance and interpretation. This study was designed to determine DNA stability in peripheral blood and solid tissue under different storage conditions. DNA quality and yield were assayed by spectrophotometric absorbance, gel electrophoresis, and suitability for Southern hybridization and polymerase chain reaction (PCR), the most widely employed clinical DNA analyses. A second goal of the study was to evaluate DNA stability during storage at 4 degrees C for 1 month to 3 years. The data show that freezing or refrigeration of separated leukocytes is preferable for short- to intermediate-term storage and freezing is preferable for solid tissue. DNA degradation varying from slight to severe is seen inconsistently with such specimens, probably due to sampling of unevenly frozen-tissue areas. Depending on the degree of DNA degradation, analysis may still be possible by PCR and in some cases even by Southern hybridization. Once isolated, DNA was stable at 4 degrees C for at least 3 years. These results suggest a more flexible approach to specimen requirements for molecular pathology, as some samples that would routinely be rejected gave interpretable results.

Use of myeloperoxidase mRNA as a marker for myeloid lineage in acute leukemias

BACKGROUND

Positivity for myeloperoxidase is considered the diagnostic hallmark of myeloid lineage and is the major criterion in the classification of acute leukemias. Early myeloid precursors, however, may be cytochemically negative for myeloperoxidase enzymatic activity or protein, but positive for myeloperoxidase mRNA.

OBJECTIVE

To evaluate the expression of the myeloperoxidase gene in leukemic blasts at the mRNA level and correlate the expression with blast cytochemistry and immunophenotyping.

PATIENTS AND METHODS

Sixteen cases of acute myelogenous leukemia and six cases of acute lymphoblastic leukemia were studied retrospectively using cellular material from Wright-stained and unstained archival smears of peripheral blood and bone marrow aspirate and a reverse-transcription polymerase chain reaction procedure for detection of myeloperoxidase mRNA.

RESULTS

Positivity in leukemic blasts was found in all acute myelogenous leukemia cases, including cases of M0, M1, and M5 that were cytochemically negative, equivocal, or weakly positive for the enzyme. None of the acute lymphoblastic leukemia cases showed positivity for myeloperoxidase mRNA.

CONCLUSIONS

The procedure is a highly specific and sensitive method for diagnosis of myeloid lineage in leukemic blasts.

BCL-2 gene rearrangements in lymphoid malignancies

Chromosomal translocations consistently associated with lymphoid malignancies result in gene rearrangements and activation of cellular oncogenes. The bcl-2 gene rearrangement is one of the most thoroughly studied and clinically useful in the diagnosis and monitoring of patients with lymphoma. The molecular analysis of this gene rearrangement has led to the discovery of the first member of a new class of oncogenes, the regulators of programmed cell death.

Discordant morphologic features in bone marrow involvement by malignant lymphomas: use of gene rearrangement patterns for diagnosis

Discordant morphology between lymph node or extra-nodal site and bone marrow (BM) involvement by non-Hodgkin's malignant lymphoma (NHL) is a common occurrence, causing diagnostic difficulties. Additional diagnostic problems are posed by lymphoid aggregates commonly found in the BM of elderly patients, the age group with the highest incidence of lymphoma. Morphologic features are used to distinguish between benign and malignant lesions but no feature is diagnostic and exceptions are numerous. Immunophenotyping is helpful for detecting B cell monoclonality, but it cannot detect T cell monoclonality. Unique B and T cell gene rearrangement patterns, the molecular "signature" of the lymphoma, can be used to detect monoclonal lymphoid populations. Finding the same rearrangement pattern in the BM as in the primary mass is proof of BM involvement by the same clone of malignant cells. We used B/T and Bcl-2 gene rearrangements to help diagnose cases with discordant morphology between primary site and BM. One hundred and seventy-five specimens, obtained from patients undergoing staging or restaging for NHL, were analyzed for B/T cell and Bcl-2 gene rearrangements by multiple restriction endonuclease digestion and Southern hybridization with 32P labeled JH, JK, CT beta, and Bcl-2 probes. Forty-two specimens (24%) from 24 patients showed discordant morphology: of 13 specimens with atypical lymphoid aggregates, only one had B cell gene rearrangement; of 15 specimens with morphologically benign lymphoid aggregates, one demonstrated B cell gene rearrangement; and of 14 specimens positive for NHL with different morphology than the lymph node, 13 were positive for B cell gene rearrangements. Molecular analysis can aid in the diagnosis of NHL, can establish a "baseline" for detection of recurrence, and is useful in monitoring therapy. These data suggest that it is also a tool for the pathologist in cases of discordant morphology between the primary tumor and BM, and should be strongly considered for each site.

Myeloperoxidase mRNA detection for lineage determination of leukemic blasts: retrospective analysis

Myeloperoxidase (MPO) mRNA is an early myeloid marker; its detection in the morphologically and immunophenotypically primitive blasts of acute undifferentiated leukemia (AUL) establishes myeloid lineage and allows reclassification as acute myelogenous leukemia with minimal differentiation (AML-MO). We have previously reported a procedure for MPO mRNA detection by RT-PCR (reverse transcription-polymerase chain reaction) and an adaptation for use of routine hematology smears. This variant procedure allows retrospective analysis of mRNA and is used in the present study to evaluate the lineage of leukemic blasts in seven cases with morphology and cytochemistry consistent with AUL. All hematology smears used in this study were air-dried, unstained or Wright-stained and stored at room temperature for periods varying between 3 days and 2 years. MPO mRNA was detected in six cases, establishing the myeloid lineage of the blasts and the diagnosis of AML-MO. In the remaining case, the blasts were MPO mRNA negative, confirming the diagnosis of AUL. The RT-PCR procedure for retrospective mRNA analysis is useful in the clinical setting, due to its high specificity and sensitivity, speed (less than 24 h), safety (no radioactivity) and convenient use of routine hematology smears; it is particularly attractive in clinical situations when fresh or frozen specimens are no longer available at the time when the need for molecular diagnostics becomes apparent.

Separate clones in concomitant multiple myeloma and a second B-cell neoplasm demonstrated by molecular and immunophenotypic analysis

The occurrence of multiple myeloma (MM) and a second B-cell neoplasm in the same patient is a rare event. We present 2 such patients, and provide evidence to support the presence of separate clones in these coexisting neoplasms. In the first case, MM became evident 14 months after the diagnosis of chronic lymphocytic leukemia (CLL). In past reports, most occurrences of this association, when investigated, have been regarded to be biclonal disease processes; however, with few exceptions, most were documented by immunologic studies alone. To establish the clonality in our case of CLL with MM, we examined both immunophenotypic data obtained by standard two-color flow cytometric analysis, and patterns of immunoglobulin gene rearrangement, using standard Southern analysis and hybridization with 32P-labelled JH and JK probes. This provided evidence for the presence in this patient of two separate monoclonal populations of B cells, manifested as light chain restrictions and gene rearrangements which differed in blood (CLL) and bone marrow (MM) samples. In the second case, MM presented simultaneously with bone marrow lymphocytosis and abnormal peripheral lymphocytes. Clonality studies on blood were not done. Bone marrow B-cell gene rearrangement studies, however, revealed the presence of three bands in the JK blot of significantly different intensities, suggestive of two monoclonal populations. A monoclonal population of small cells with surface B markers and surface IgM was demonstrated by flow cytometry, while a second population of larger cells with intracytoplasmic IgG matching the patient's serum monoclonal protein was detected by immunofluorescence microscopy. The results in these 2 cases expand previous findings of the rare association of MM with a second B-cell neoplasm, and demonstrate the usefulness of molecular diagnostic investigation.

Polymerase chain reaction in the diagnosis of chromosomal breakpoints

Polymerase chain reaction-based methods for the detection of translocation-induced gene rearrangements are now widely used for diagnostics and patient monitoring. This article concentrates on two of the best studied chromosome translocations resulting in specific gene rearrangements and oncogene activation: the Philadelphia translocation of chronic myelogenous leukemia and acute leukemias, and the t(14;18) translocation of follicular lymphomas.

Molecular diagnostic testing for determination of myeloid lineage in acute leukemias

Determination of myeloid vs. lymphoid cell lineage in acute leukemias is essential for diagnosis, prognosis, and treatment. However, some leukemic cells are too primitive to be identified based on conventional morphology, cytochemistry, and immunophenotype criteria. The gene for myeloperoxidase (MPO) is central to the lineage designation of myeloid cells and their function. Expression of MPO messenger ribonucleic acid (mRNA) may serve to determine the myeloid lineage of primitive leukemic cells that do not express the final product, MPO. Recently, a procedure has been developed for detection of MPO mRNA in leukemic cells, based on message amplification by reverse transcription-polymerase chain reaction (RT-PCR). Three variant polymerase chain reaction (PCR) methods, developed in view of future diagnostic applications of the RT-PCR procedure are reported: (A) nested PCR, using a second pair of internal primers for reamplification of the first PCR product; (B) multiplex PCR for concomitant amplification of up to seven sequences encompassing all regions of MPO mRNA; (C) adaptation of the standard PCR procedure and the two variant methods for use of cellular material from air-dried unstained or Wright stained smears. These variant procedures developed on the HL-60 cell line make the RT-PCR detection of MPO mRNA easily applicable as a new diagnostic test in acute leukemias and confer the versatility needed in the clinical setting. The advantages of our new procedure for MPO mRNA detection are: high sensitivity and specificity, speed, simplicity, and safety. Myeloid lineage of leukemic blasts can be established, confirmed, or ruled out in 6 to 10 hours, making results available at the time of bone marrow sign-out.(ABSTRACT TRUNCATED AT 250 WORDS)

Bone marrow biopsy imprint preparations: use for molecular diagnostics in leukemias

Bone marrow (BM) biopsies occasionally fail to yield aspirate specimens; such "dry taps" pose diagnostic difficulties. In the absence of a BM aspirate, morphological evaluation and cytochemistry rely on core biopsy imprint preparations (IP) and other analyses, e.g., molecular pathology studies, become impossible. The use of imprint preparations (IPs) for molecular diagnostics based on messenger ribonucleic acid (mRNA) analysis by reverse transcription-polymerase chain reaction (RT-PCR) for detection of breakpoint cluster region (bcr) gene rearrangements in chronic myelogenous leukemia (CML) and myeloperoxidase (MPO) mRNA in acute leukemias (AL) is described. Fifteen IPs from five core biopsies (three CML and two AL) were used. Analysis of bcr was positive in all nine IPs from the three cases of CML and was confirmed on peripheral blood samples. Detection of MPO mRNA established the myeloid lineage of the blasts in two cases of AL, when cytochemistry and flow cytometry failed to reveal myeloid markers. These tests are useful when fresh BM aspirate is unobtainable, since multiple imprints of the biopsy are easily prepared at the bedside.

Retrospective DNA analysis using fixed tissue specimens

The recent explosion of scientific and technical knowledge in the field of molecular biology has allowed us to make important advances in our understanding of the molecular basis of many human diseases. This technology has now entered the clinical laboratory where identification of specific genetic sequences can aid in the precise diagnosis of hematologic and other malignancies, inherited diseases, specific infectious agents, and inherited predisposition to disease. In addition, it can be applied to prenatal diagnosis, paternity testing, identification of minimal residual disease following treatment, and assessment of drug sensitivity or resistance. In many cases in diagnostic pathology, the need for molecular analysis often is not realized until after a critical tissue specimen has been fixed, embedded, and examined microscopically. Thus, there is a clear need for development of techniques that would allow the retrospective study of archival tissues that have been fixed and embedded in paraffin. This review examines in depth those factors which influence the quality of the DNA available from fixed embedded tissues and discusses the usefulness of polymerase chain reaction amplification in obtaining sufficient diagnostically useful DNA from archival specimens. It is hoped that this review will aid the diagnostic pathologist interested in the application of molecular techniques in the retrospective study of fixed embedded tissues.

A new procedure for cell lineage determination in acute leukemias. Myeloperoxidase mRNA detection

Determination of cell lineage in acute leukemias is essential for diagnosis and treatment. Detection of myeloperoxidase (MPO) mRNA establishes myeloid lineage of leukemic blasts that may be too primitive to be identified as myeloblasts based on morphology, cytochemistry, or immunophenotype. A highly specific and sensitive new procedure for MPO mRNA detection has been developed using HL-60 cells. It involves a microprocedure for total cellular RNA extraction, reverse transcription, and specific amplification of target sequences in the resulting MPO cDNA, by the polymerase chain reaction. Specific primers are designed to amplify an 89-base pair (bp) sequence from the signal peptide, 179 and 318-bp sequences from the start and end, respectively, of the heavy-chain sequence, and a 255-bp sequence overlapping the proregion and light chain. The correct-size amplification products, detected electrophoretically, demonstrate MPO mRNA expression in the leukemic cells analyzed. The sensitivity of this new procedure was evaluated on serial concentrations of HL-60 cells and was found to be 10-10(4) cells depending on the MPO cDNA amplified sequence. No amplification products were obtained using peripheral blood lymphocytes as a negative cellular control. The specificity of the procedure is demonstrated by Southern blotting and hybridization with 32P-labeled oligonucleotide probes specific for each of the amplified sequences. An additional advantage of this procedure is availability of results in 8-24 h, compared with 1-2 weeks for conventional RNA methods.

Amplification of intermediate-size DNA sequences from formalin and B-5 fixed tissue by polymerase chain reaction

Retrospective analysis of DNA from paraffin-embedded fixed bone marrow biopsy specimens is possible if preceded by amplification of the DNA sequences of interest by the polymerase chain reaction (PCR). These fixed specimens yield degraded DNA that may not be suitable for direct analysis by conventional digestion and hybridization methods. This limitation is circumvented by PCR amplification and subsequent analysis of the amplified products. The model used in this study is the amplification of a 725 base-pair (bp) beta-globin gene sequence encompassing the sickle-cell anemia point mutation, followed by Cvn I digestion. The beta A beta A, beta A beta S, and beta S beta S genotypes are derived from analysis of the allele-specific digestion patterns. Two fixatives were compared: neutral-buffered formalin and a mercury-based fixative (B-5) routinely used for bone marrow biopsies. DNA extracted from B-5-fixed bone marrow specimens was found to be more degraded than DNA from neutral-buffered, formalin-fixed bone marrow aliquots from the same specimens. PCR amplification of the 725 bp beta-globin gene sequence was successful with DNA from formalin-fixed bone marrow specimens, but not with DNA from B-5-fixed identical specimens. Analysis of the amplified product by Cvn I digestion resulted in correct genotype derivation for all patients, normal controls and positive controls (patients diagnosed with sickle-cell anemia or trait). These results indicate that intermediate-size DNA sequences can be amplified and analyzed when DNA is extracted from formalin-fixed bone marrow specimens.(ABSTRACT TRUNCATED AT 250 WORDS)

Chronic granulocytic leukemia: reassessment of morphologic and cytogenetic characteristics in Ph1-positive and Ph1-negative cases

33 cases of chronic granulocytic leukemia (CGL) were reassessed to determine if, by strict morphologic criteria. Philadelphia chromosome (Ph1)-negative CGL exists as a diagnostic entity and if Ph1-positive CGL could be distinguished from Ph1-negative CGL. Cases were reassessed using published criteria and, of 11 Ph1-negative cases, only 4 could be reclassified as myelodysplastic syndromes or undifferentiated chronic myeloproliferative disorder. Of the morphologic parameters evaluated, peripheral blood basophilia and bicytopenia proved to be good discriminators between Ph1-positive and Ph1-negative cases. As a group, Ph1-negative cases were more heterogeneous and tended to have lower hemoglobin, WBC, platelet count and absolute eosinophilia. Chromosomal abnormalities other than Ph1 were seen only in the Ph1-positive cases. Based on these findings, we conclude that Ph1-negative CGL constitutes a heterogeneous group, a subgroup of which is morphologically identical with the Ph1-positive CGL. The parameters that best discriminate between Ph1-positive and Ph1-negative cases are peripheral blood absolute basophilia and bicytopenia.

Digoxin-like immunoreactivity in serum from neonates and infants reduced by centrifugal ultrafiltration and fluorescence polarization immunoassay

We evaluated the TDx Digoxin II (Abbott) modified procedure for interference from digoxin-like immunoreactive factors (DLIF) in pediatric patients. The effectiveness of centrifugal ultrafiltration as a means of removing DLIF interference from the serum of such patients was assessed. We used sera from 40 patients who had not received digoxin, whom we divided into two age groups: 30 neonates (less than 34 days postpartum) and 10 infants (younger than six months). Digoxin-like immunoreactivity was detected in 34 of 41 (83%) neonatal specimens (range 0.2-1.0 micrograms/L) and 16 of 25 (60%) infants' specimens (range 0.2-1.3 micrograms/L). Centrifugal ultrafiltration of serum specimens from these patients reduced but did not eliminate the DLIF interference in some specimens. A comparison of concentrations of DLIF in serum with various other patients' characteristics demonstrated a strong correlation (r = 0.915; P = 0.0001) between DLIF and serum bilirubin in the infants. Apparent digoxin concentrations from 19 serum and serum ultrafiltrate samples collected from 13 patients (four neonates and nine infants) who were treated with digoxin showed a good correlation (r = 0.97); however, the serum samples showed a positive bias of 0.39 microgram/L. We conclude that the TDx Digoxin II modified procedure is still subject to considerable DLIF interference in these two pediatric populations. This interference can be reduced in some serum specimens, but cannot be eliminated completely as others reported.

Polymerase chain reaction: amplification of DNA from fixed tissue

The polymerase chain reaction (PCR) allows the analysis of DNA from biologic samples containing only nanogram quantities of DNA. We used DNA purified from fresh or frozen peripheral blood (PB) leukocytes and formalin, or B-5 fixed bone marrow aspirate clots (BM). A sequence of the beta-globin gene was amplified via the PCR then hybridized with allele specific oligonucleotide probes for hemoglobin A, S, and C. All DNA preparations, including formalin and B-5 fixed BMs, were successfully amplified; the hybridization of the amplified products resulted in patterns consistent with the hemoglobin phenotype for all patients. PCR can be used on DNA from many sources; retrospective studies using paraffin embedded fixed tissue are possible because extremely small amounts of DNA present in fixed tissue can be successfully amplified.