Systematic validation of variants of unknown significance in APP, PSEN1 and PSEN2.

Alzheimer's disease (AD) is a neurodegenerative disease that is clinically characterized by progressive cognitive decline. More than 200 pathogenic mutations have been identified in amyloid-ß precursor protein (APP), presenilin 1 (PSEN1) and presenilin 2 (PSEN2). Additionally, common and rare variants occur within APP, PSEN1, and PSEN2 that may be risk factors, protective factors, or benign, non-pathogenic polymorphisms. Yet, to date, no single study has carefully examined the effect of all of the variants of unknown significance reported in APP, PSEN1 and PSEN2 on Aß isoform levels in vitro. In this study, we analyzed Aß isoform levels by ELISA in a cell-based system in which each reported pathogenic and risk variant in APP, PSEN1, and PSEN2 was expressed individually. In order to classify variants for which limited family history data is available, we have implemented an algorithm for determining pathogenicity using available information from multiple domains, including genetic, bioinformatic, and in vitro analyses. We identified 90 variants of unknown significance and classified 19 as likely pathogenic mutations. We also propose that five variants are possibly protective. In defining a subset of these variants as pathogenic, individuals from these families may eligible to enroll in observational studies and clinical trials.

Imatinib mesylate resistance through BCR-ABL independence in chronic myelogenous leukemia.

Imatinib mesylate (IM) binds to the BCR-ABL protein, inhibiting its kinase activity and effectively controlling diseases driven by this kinase. IM resistance has been associated with kinase mutations or increased BCR-ABL expression. However, disease progression may be mediated by other mechanisms that render tumor cells independent of BCR-ABL. To demonstrate this potential, IM-resistant cells were found in chronic myelogenous leukemia patients with continuous BCR-ABL gene expression but undetectable BCR-ABL protein expression. These cells were unresponsive to IM and acquired BCR-ABL-independent signaling characteristics. IM resistance in some patients may be mediated through loss of kinase target dependence.

A genetically defined model for human ovarian cancer.

Disruptions of the p53, retinoblastoma (Rb), and RAS signaling pathways and activation of human telomerase reverse transcriptase (hTERT) are common in human ovarian cancer; however, their precise role in ovarian cancer development is not clear. We thus introduced the catalytic subunit of hTERT, the SV40 early genomic region, and the oncogenic alleles of human HRAS or KRAS into human ovarian surface epithelial cells and examined the phenotype and gene expression profile of those cells. Disruption of p53 and Rb pathway by SV40 early genomic region and hTERT immortalized but did not transform the cells. Introduction of HRAS(V12) or KRAS(V12) into the immortalized cells, however, allowed them to form s.c. tumors after injection into immunocompromised mice. Peritoneal injection of the transformed cells produced undifferentiated carcinoma or malignant mixed Mullerian tumor and developed ascites; the tumor cells are focally positive for CA125 and mesothelin. Gene expression profile analysis of transformed cells revealed elevated expression of several cytokines, including interleukin (IL)-1beta, IL-6, and IL-8, that are up-regulated by the nuclear factor-kappaB pathway, which is known to contribute to the tumor growth of naturally ovarian cancer cells. Incubation with antibodies to IL-1beta or IL-8 led to apoptosis in the ras-transformed cells and ovarian cancer cells but not in immortalized cells that had not been transformed. Thus, the transformed human ovarian surface epithelial cells recapitulated many features of natural ovarian cancer including a subtype of ovarian cancer histology, formation of ascites, CA125 expression, and nuclear factor-kappaB-mediated cytokine activation. These cells provide a novel model system to study human ovarian cancer.

A missense mutation in KIT kinase domain 1 correlates with imatinib resistance in gastrointestinal stromal tumors.

KIT gain of function mutations play an important role in the pathogenesis of gastrointestinal stromal tumors (GISTs). Imatinib is a selective tyrosine kinase inhibitor of ABL, platelet-derived growth factor receptor (PDGFR), and KIT and represents a new paradigm of targeted therapy against GISTs. Here we report for the first time that, after imatinib treatment, an additional specific and novel KIT mutation occurs in GISTs as they develop resistance to the drug. We studied 12 GIST patients with initial near-complete response to imatinib. Seven harbored mutations in KIT exon 11, and 5 harbored mutations in exon 9. Within 31 months, six imatinib-resistant rapidly progressive peritoneal implants (metastatic foci) developed in five patients. Quiescent residual GISTs persisted in seven patients. All six rapidly progressive imatinib-resistant implants from five patients show an identical novel KIT missense mutation, 1982T-->C, that resulted in Val654Ala in KIT tyrosine kinase domain 1. This novel mutation has never been reported before, is not present in pre-imatinib or post-imatinib residual quiescent GISTs, and is strongly correlated with imatinib resistance. Allelic-specific sequencing data show that this new mutation occurs in the allele that harbors original activation mutation of KIT.

Preventing hospital-acquired venous thromboembolism: Improving patient safety with interdisciplinary teamwork, quality improvement analytics, and data transparency.

BACKGROUND: Hospital-acquired venous thromboembolism (HA-VTE) is a potentially preventable cause of morbidity and mortality. Despite high rates of venous thromboembolism (VTE) prophylaxis in accordance with an institutional guideline, VTE remains the most common hospital-acquired condition in our institution. OBJECTIVE: To improve the safety of all hospitalized patients, examine current VTE prevention practices, identify opportunities for improvement, and decrease rates of HA-VTE. DESIGN: Pre/post assessment. SETTING/PATIENTS: Urban academic tertiary referral center, level 1 trauma center, safety net hospital; all patients. INTERVENTION: We formed a multidisciplinary VTE task force to review all HA-VTE events, assess prevention practices relative to evidence-based institutional guidelines, and identify improvement opportunities. The task force developed an electronic tool to facilitate efficient VTE event review and designed decision-support and reporting tools, now integrated into the electronic health record, to bring optimal VTE prevention practices to the point of care. Performance is shared transparently across the institution. MEASUREMENTS: Harborview benchmarks process and outcome performance, including patient safety indicators and core measures, against hospitals nationally using Hospital Compare and Vizient data. RESULTS: Our program has resulted in >90% guideline-adherent VTE prevention and zero preventable HA-VTEs. Initiatives have resulted in a 15% decrease in HA-VTE and a 21% reduction in postoperative VTE. CONCLUSIONS: Keys to success include the multidisciplinary approach, clinical roles of task force members, senior leadership support, and use of quality improvement analytics for retrospective review, prospective reporting, and performance transparency. Ongoing task force collaboration with frontline providers is critical to sustained improvements. Journal of Hospital Medicine 2016;11:S38-S43. © 2016 Society of Hospital Medicine.

The value of fluorescence in situ hybridization in the diagnosis and prognosis of chronic lymphocytic leukemia.

Chronic lymphocytic leukemia (CLL) is the most common adult leukemia. Prognosis is related to clinical staging and cytogenetic findings. Conventional cytogenetic analysis of CLL reveals abnormalities in approximately one third of patients. Fluorescence in situ hybridization (FISH) is analytically more sensitive than conventional cytogenetics for specific chromosomal abnormalities. To evaluate the usefulness of FISH in CLL, a study of 100 CLL patients comparing conventional cytogenetics and a commercially available multiprobe FISH kit was undertaken. One hundred consecutive CLL patients (67 males, 33 females) were studied. The male-female patient ratio was approximately 2.0 to 1. Twenty-eight percent (28/98) of patients had abnormal karyotypes by conventional cytogenetics (one patient had no specimen for conventional cytogenetics and one had an unanalyzable karyotype), and of those 19/100 (19%) had more than one chromosomal abnormality. Sixty-four percent (64/100) of the patients were positive for at least one abnormality by the FISH probes used. The following abnormalities were noted with FISH: 11q22 ATM, 23/100 (23%); trisomy 12, 11/100 (11%); 13q14.3, 40/100 (40%); 13q34.3, 4/100 (4%); 17p13.1, 12/100 (12%). Conventional karyotypes revealed 2 patients with abnormalities of chromosome 6 (which FISH did not address); 11 with abnormalities of 11 or 11q; 6 with trisomy 12; and 4 with abnormalities of 17. Aberrations of 11q and 17p are reported to have a poor prognosis in CLL. FISH can identify abnormalities missed with conventional cytogenetics and is helpful in diagnosis, prognosis, and evaluation of therapy for CLL. Additional chromosomal changes are identified with conventional cytogenetics that are not addressed by the multiprobe FISH kit.

Imatinib mesylate for Philadelphia chromosome-positive, chronic-phase myeloid leukemia after failure of interferon-alpha: follow-up results.

We treated 261 patients with Philadelphia chromosome (Ph)-positive chronic myeloid leukemia (CML) in chronic phase after failure of IFN-alpha with the Bcr-Abl tyrosine kinase inhibitor imatinib mesylate (400 mg/day given p.o.) and analyzed hematological and cytogenetic responses, long-term prognosis, factors associated with achievement of major cytogenetic response and survival, and comparative survival in similar patients treated with other regimens. Median patient age was 55 years; 34% were 60 years or older, and median chronic-phase duration was 33 months. Overall, 94% achieved a complete hematological response, and 71% had a cytogenetic response [major (Ph+ cells <35%) in 62% and complete in 45%]. At a median follow-up of 17 months, 241 patients (92%) were still taking imatinib mesylate; estimated 18-month freedom from progression and survival rates were 93 and 96%. Multivariate analysis of factors associated with major cytogenetic response identified long chronic phase, marrow basophilia, high percentage of Ph+ cells before therapy, and prior hematological resistance to IFN-alpha as being adverse factors. This model was used to generate good-, intermediate- and poor-risk subgroups who had estimated major cytogenetic response rates of 93, 53, and 34%, respectively. Univariate analysis in terms of survival identified leukocytosis, high percentages of peripheral and marrow blasts, marrow basophilia, and the presence of cytogenetic clonal evolution as being adverse factors. Achieving a cytogenetic response at 3 or 6 months of therapy was associated with prolonged survival. In a subset analysis, survival rates among 161 patients with Ph-positive CML after hematological or cytogenetic failure after IFN-alpha who had been treated with imatinib mesylate were better than those for similar patients treated previously with other regimens. In summary, imatinib mesylate is highly effective in chronic-phase CML after IFN-alpha failure. We identified pretreatment and treatment-associated factors that were associated with higher major cytogenetic response rates and with improved survival.

Cytogenetic findings in blastoid mantle cell lymphoma.

A subset of mantle cell lymphoma (MCL) tumors has blastoid morphology, and a number of morphologic variants of blastoid MCL have been described in the literature. In this report, we document the cytogenetic findings in 27 cases of blastoid MCL. Conventional cytogenetic analyses were performed on bone marrow aspirates involved by MCL from 27 patients. There were 14 men and 13 women with a median age of 63 years (range, 40-79 years). Diagnostic tissue biopsy and bone marrow specimens were reviewed, and cases were divided into 2 morphologic groups: classic (12 cases) and pleomorphic (15 cases), as defined in the World Health Organization classification. All tumors had an immunophenotype compatible with MCL, were positive for cyclin D1, and carried the t(11;14). Twenty-four cases had complex karyotypes with 3 or more chromosomal abnormalities in addition to the t(11;14). In classic blastoid MCL, abnormalities of chromosomes 13, 18, and 8 were most common. In pleomorphic blastoid MCL, abnormalities of chromosomes 13, 17, and 3 were most frequent. Chromosome 22 abnormalities were detected exclusively in the pleomorphic group. Tumors in which the neoplastic cells showed prominent nucleoli had a significantly higher frequency of chromosome 17 abnormalities (P = 0.03). We conclude that blastoid MCL tumors often show complex cytogenetic aberrations. Some abnormalities correlate with morphologic features, suggesting that morphologic variants of blastoid MCL may arise via different molecular pathways.

Independent prognostic significance of day 21 cytogenetic findings in newly-diagnosed acute myeloid leukemia or refractory anemia with excess blasts.

BACKGROUND AND OBJECTIVES: We investigated whether cytogenetic findings (CG) on day 21 (D21) of the first course of chemotherapy predicted subsequent outcome in patients who presented with CG abnormalities. DESIGN AND METHODS: D21 CG analysis was performed in 197 patients. RESULTS: Nineteen percent of the patients had exclusively abnormal metaphases (AA), 31% had only normal metaphases (NN), 39% had normal and abnormal metaphases (AN), and 11% had insufficient metaphases (0/0) on D21. A complete response was achieved in 79% of patients with NN, 60% with AN, 27% of those with AA, and 32% of those with 0/0. INTERPRETATIONS AND CONCLUSIONS: Disease-free survival in CR was longest in patients who had > or =1 normal metaphase on D21, with this finding being independent of D21 marrow and initial CG results. D21 CG can be used in therapeutic decision-making.

Detection of a novel reciprocal t(16;22)(q11.2;q12) in a Ewing sarcoma.

Several structural and numerical chromosomal abnormalities have been identified as primary and secondary chromosomal aberrations in Ewing sarcoma (ES). The majority of these are t(11;22) and trisomies, especially of chromosome 8. Specific chromosomal abnormalities often correlate with particular morphologic or phenotypic subtypes of tumor and play an important role in prognosis. The objective of this report is the cytogenetic evaluation of a case of ES using G-banding, fluorescence in situ hybridization, and spectral karyotyping techniques. Multiple chromosomal aberrations were identified including a novel reciprocal t(16;22)(q11.2;q12).

Establishment and characterization of a new mantle cell lymphoma cell line M-1.

A new mantle cell lymphoma cell line, M-1, was established from peripheral blood mononuclear cells of a patient with a diagnosis of blastoid variant of mantle cell lymphoma in leukemic phase. This cell line showed cell surface antigens identical to the original tumor and demonstrated the profile of a mature B-cell phenotype typical of mantle cell lymphoma: positive for CD5, CD19, CD20, sIgM and FMC7, and negative for CD3, CD10 and CD23. Cytogenetically, the M-1 cell line showed chromosomal alterations similar to the initial clinical specimen, among which a translocation t(11;14) (q13;q32) resulting in the overexpression of cyclin D1 as well as additional abnormalities involving chromosomes 3, 9 and 10. This cell line was used as a model to investigate the activity of the three drugs doxorubicin, cyclophosphamide and vincristine, commonly used in the treatment of mantle cell lymphoma patients. The effect of the drugs was evaluated by a 24 h cytotoxicity test and a 7-days anti-proliferation test using a microculture tetrazolium-based assay (MTT). Both assays indicated a higher sensitivity of the cell line to vincristine when compared to doxorubicin and cyclophosphamide. The characterization of a new mantle cell lymphoma cell line is a unique tool for studying the biology of this subtype of lymphoma for which only a few cell lines have been established.

Translocation (11;16)(q23;p13) acute myelogenous leukemia and myelodysplastic syndrome.

The purpose of this study is to examine the relationship of t(11;16)(q23;p13) to the type of myeloproliferative disorder noted by hematopathology. Previously, t(11;16) has been reported in fewer than 20 patients, all with the diagnosis of therapy-related (secondary) acute myelogenous leukemia (sAML) or myelodysplastic syndrome (MDS). Putative involved genes are the MLL on 11q23 and CBP at 16p13. Data from The University of Texas M. D. Anderson Cancer Center (UTMDACC) Cytogenetics Laboratory revealed 3 patients with t(11;16) observed during the past 5 years. Two of the patients had a prior diagnosis of non-Hodgkin lymphoma (NHL) and had been treated with chemotherapy, which included cyclophosphamide. The other patient presented with de novo AML and no history of cancer or chemotherapy. Two of the 3 patients had t(11;16) as the sole cytogenetic abnormality. One patient had a t(11;16) clone that included t(9;21) and t(10;21) as additional changes. Translocation (11;16) has previously been reported only as being therapy-related. In this study, the t(11;16) was seen in 2 patients with previous lymphomas treated with cyclophosphamide, doxorubicin, vincristine, and prednisone (CHOP). A single patient with apparently de novo AML constitutes the first reported instance of non-treatment associated t(11;16) AML.

t(3;21)(q26;q22) in myeloid leukemia: an aggressive syndrome of blast transformation associated with hydroxyurea or antimetabolite therapy.

BACKGROUND: The t(3;21)(q26;q22) translocation is associated with myeloid leukemias and results in a chimeric oncoprotein containing AML1/RUNX1 variably fused to EAP, MDS1, and/or EVI1. METHODS: The current study describes what to the authors' knowledge is the first large case series reported to date of 26 t(3;21)(q26;q22)-associated leukemias, in which 24 cases arose after chemotherapy. Conventional G-band karyotyping and flow cytometry immunophenotyping were performed. Reverse transcriptase-polymerase chain reaction (RT-PCR) was performed to detect fusion transcripts between AML1 and EAP, MDS1, or EVI1, followed by DNA sequencing. RESULTS: In all 16 patients with chronic myeloproliferative disorders, including 14 with chronic myelogenous leukemia (CML), the occurrence of t(3;21) heralded myeloid blast transformation. Fifteen (93%) patients had been previously treated with hydroxyurea. Eight patients with chronic myeloproliferative disorders (CMPD) were found to have t(3;21) with t(9;22) as the sole cytogenetic abnormality; in 5 other patients this was accompanied by trisomy 8. Among 10 cases of t(3;21)-associated acute myeloid leukemia, 8 were secondary tumors after chemotherapy for other neoplasms that had been treated with regimens including fludarabine and 5-fluorouracil in 3 patients each and etoposide in 2 patients. The immunophenotype of the blasts in all 22 tested cases was similar, with uniform expression of myeloid markers and CD34 and variable expression of CD7 and CD9, but minimal morphological myeloid maturation. Dysplastic micromegakaryocytes and bone marrow fibrosis were observed predominantly in CMPD cases. RT-PCR followed by DNA sequencing showed that the AML1-/MDS1-/EVI1 (AME) fusion transcript was detected in all 5 cases assessed. Among the patients with CMPD, 8 died of disease (at a median of 6.5 mos) and 5 achieved disease remission with bone marrow transplantation. Among patients with acute myeloid leukemia/myelodysplastic syndrome, 7 died of disease (at a median of 2 mos) and 2 had persistent leukemia with short follow-up. CONCLUSIONS: Activation of AME through t(3;21) defines a highly aggressive, therapy-related leukemic blast syndrome. Prior treatment with hydroxyurea or other antimetabolites is implicated as a contributory cause.

Myelodysplasia and acute myeloid leukemia following therapy for indolent lymphoma with fludarabine, mitoxantrone, and dexamethasone (FND) plus rituximab and interferon alpha.

Treatment-related myelodysplasia (t-MDS) occurs less frequently with the nucleoside analogs than with DNA-damaging agents such as alkylators or topoisomerase II inhibitors. In a chemoimmunotherapy trial conducted between 1997 and 2003 in patients with stage IV indolent lymphoma, 202 patients were treated and 8 have developed MDS between 1 and 5 years after therapy, including 4 who received only fludarabine, mitoxantrone, and dexamethasone (FND) for 6 to 8 courses, with or without rituximab, followed by interferon alpha (IFN-alpha). Complex cytogenetic abnormalities were present in all patients. Abnormalities of chromosome 7 were present in 6 of the 8 patients, 3 of whom received only FND +/- rituximab and IFN-alpha. The abnormalities of chromosome 7 were monosomy 7 in 4 patients (1 of which had add 7p in the remaining chromosome); 1 del 7q; and 1 der 7. MDS with features classically associated with DNA-damaging agents can occur following therapy with FND, with or without rituximab, and IFN-alpha.

Imatinib mesylate therapy may overcome the poor prognostic significance of deletions of derivative chromosome 9 in patients with chronic myelogenous leukemia.

Deletions of derivative chromosome 9 [der(9)] can be identified by fluorescence in situ hybridization (FISH) in 10% to 15% of patients with chronic myeloid leukemia (CML). Patients with der(9) deletions have been reported to have an adverse outcome when treated with chemotherapy, interferon, and possibly imatinib mesylate. We investigated the frequency and prognostic significance of der(9) deletions among 352 patients with CML treated with imatinib mesylate at our institution, in whom a deletion status of der(9) was determined. Thirty-three patients (9%; 95% CI 0.07, 0.13) (30 in chronic phase, 3 in accelerated phase) had der(9) deletions. The rates of major (82% vs 79%, P = 0.82) and complete cytogenetic response (76% vs 66%, P = .33) with imatinib mesylate therapy were similar in patients with and without der(9) deletions, respectively. After a median follow-up of 28 months, there was no difference in overall survival (P = .30) or response duration (P = .49) in patients with and without deletions. In a multivariate analysis, der(9) deletions had no significant impact on response, survival, or response duration. We conclude that treatment with imatinib mesylate overcomes the adverse prognostic significance of der(9) deletions in patients with CML.

Molecular monitoring of cerebrospinal fluid can predict clinical relapse in acute lymphoblastic leukemia with eosinophilia.

In a patient with precursor B-cell acute lymphoblastic leukemia (ALL) associated with eosinophilia that completely responded to induction chemotherapy, we assayed serial remission cerebrospinal fluid and bone marrow specimens for minimal residual disease using a quantitative polymerase chain reaction assay to assess for clone-specific immunoglobulin heavy-chain gene cluster (IGH) gene rearrangement. Cerebrospinal fluid eosinophilia and minimal residual disease were detected on day 406, preceding the morphologic diagnosis of central nervous system relapse on day 578. By day 841, the bone marrow had 35% blasts. Despite aggressive therapy, including unrelated umbilical cord blood transplantation, the patient developed testicular and bone marrow relapses and died of disease. We conclude that increasing levels of minimal residual disease in cerebrospinal fluid can predict recurrence of ALL prior to clinical and morphologic relapse. Furthermore, we demonstrate a novel translocation in this tumor, the t(5;9)(q31;p24), that possibly led to fusion of the interleukin-3 (IL3) (5q31) and JAK2 (9p24) genes and may explain the concomitant appearance of eosinophilia and ALL.

Feasibility and utility of using chromosomal aneusomy to further define the cytologic categories in nipple aspirate fluid specimens: a preliminary study.

BACKGROUND: There is renewed interest in using the cytologic changes in the epithelial cells obtained from specimens such as nipple aspiration fluid (NAF) and ductal lavage for risk stratification of women at increased risk for developing breast carcinoma. METHODS: Molecular tests such as fluorescence in situ hybridization (FISH) have the potential to be used as adjuncts to conventional cytology for more accurately categorizing cells in these types of specimens. The current study investigated the feasibility and utility of FISH analysis of aneusomy in chromosomes 1, 8, 11 and 17 as an adjunct to conventional cytology in the classification of NAF specimens. RESULTS: The authors found chromosomal aneusomy for at least one chromosome in all three malignant and both markedly atypical cases. Of the five cases classified as being mildy atypical on cytology, four were disomic, and only one showed aneusomy in chromosomes 8 and 11. CONCLUSIONS: The current study established the possibilities, limitations, and feasibility of using FISH in conjunction with routine cytology for a more accurate classification of ductal epithelial cells in NAF specimens. FISH-based detection of chromosomal aneusomy helped to define mild atypia, thereby aiding in the selection of the truly atypical cases for appropriate therapeutic intervention. In addition, FISH-based detection of chromosomal aneusomy can also be a valuable adjunct to conventional cytology in selected cases for confirming a benign, suspicious, or malignant diagnosis.