Objectives: To determine whether the fraction of CD177+ neutrophils might be altered in clonal myeloid disorders, similar to the skewed kappa/lambda. ratio for B-cell lymphomas, and could be used to identify myeloid neoplasms. Methods: Blood and bone marrow samples were evaluated for the fraction of CD177+ neutrophils by flow cytometry. Results: Skewed high neutrophil CD177(%) was not associated with neoplasia, but skewed low neutrophil CD177(%) was highly correlated with clonal myeloid disorders at values less than 40%. Specificity of low neutrophil CD177(%) for clonal myeloid disorders was 87% with a 40% cutoff and 95% with a 30% cutoff Findings were most pronounced for myelodysplasia, with 52% (11/21) containing fewer than 40% CD177+ neutrophils. Specificity was also suggested by normalization of neutrophil CD177(%) in four patients who reached morphologic remission after therapy for myelodysplasia or acute leukemia. Conclusions: Skewed low neutrophil CD177(%) is highly associated with clonal myeloid disorders, particularly myelodysplasia, and may be useful for detecting clonal myeloid disorders.
The information on candidate cancer driver alterations available from public databases is often descriptive and of limited mechanistic insight, which poses difficulties for reliable distinction between true driver and passenger events. To address this challenge, we performed in-depth analysis of whole-exome sequencing data from cell lines generated by a barrier bypass-clonal expansion (BBCE) protocol. The employed strategy is based on carcinogen-driven immortalization of primary mouse embryonic fibroblasts and recapitulates early steps of cell transformation. Among the mutated genes were almost 200 COSMIC Cancer Gene Census genes, many of which were recurrently affected in the set of 25 immortalized cell lines. The alterations affected pathways regulating DNA damage response and repair, transcription and chromatin structure, cell cycle and cell death, as well as developmental pathways. The functional impact of the mutations was strongly supported by the manifestation of several known cancer hotspot mutations among the identified alterations. We identified a new set of genes encoding subunits of the BAF chromatin remodeling complex that exhibited Ras-mediated dependence on PRC2 histone methyltransferase activity, a finding that is similar to what has been observed for other BAF subunits in cancer cells. Among the affected BAF complex subunits, we determined Smarcd2 and Smarcc1 as putative driver candidates not yet fully identified by large-scale cancer genome sequencing projects. In addition, Ep400 displayed characteristics of a driver gene in that it showed a mutually exclusive mutation pattern when compared with mutations in the Trrap subunit of the TIP60 complex, both in the cell line panel and in a human tumor data set. We propose that the information generated by deep sequencing of the BBCE cell lines coupled with phenotypic analysis of the mutant cells can yield mechanistic insights into driver events relevant to human cancer development.
Purpose To analyze the progression in patients with a morphological diagnosis of intraductal proliferative lesions by PCR-based clonal assay. Materials and methods An X-chromosome inactivation assay was applied to explore clonal relationships in human intraductal proliferative lesions of the breast. Four groups samples, including 40 cases of usual ductal hyperplasia (UDH), 40 cases of atypical ductal hyperplasia (ADH), 29 cases of flat epithelia atypia (FEA), and 40 cases of ductal carcinoma in situ (DCIS) were selected for analysis. Thirty specimens of normal breast tissue were used as a control group. Microdissection was performed to collect the tissue samples for extraction of genomic DNA from paraffin-embedded tissues. The DNA was subjected to PCR amplification of the CAG repeats in androgen receptor (AR) gene exon I with and without prior digestion of methylation-sensitive restriction enzyme HhaI. Gel electrophoresis was used to detect the clonal nature of these four groups samples. Results The clonal analysis confirmed monoclonality in all informative samples of DCIS cells. Normal tissues and the majority (97.1%) of UDH were shown to be polyclonal. Monoclonality was revealed in 20/39 (51.3%) cases of ADH. Among 26 cases of FEA, 20 were shown to be polyclonal, while six displayed monoclonal alterations which accounted for 23.1%. Conclusion These findings reinforce recent suggestions that clonal analysis with AR gene polymerase chain reaction may be used to define the genetic relationships among the human tumor and the breast intraductal proliferative lesions. Furthermore, our observations demonstrate nearly a half ADH and the smaller part of FEA have clonal alterations, which may be neoplastic lesions. This method would shed light on genetic abnormalities that play a role in early tumorigenesis of the breast, and thus might be an adjunct in predicting the probability of breast tumor occurrence and in guiding the management of these cases.