The role of chromodomain helicase DNA binding protein 1 (CHD1) in promoting an invasive prostate cancer phenotype.

BACKGROUND: Prostate cancer (PCa) phenotypes vary from indolent to aggressive. Molecular subtyping may be useful in predicting aggressive cancers and directing therapy. One such subtype involving deletions of chromodomain helicase DNA binding protein 1 (CHD1), a tumor suppressor gene, are found in 10-26% of PCa tumors. In this study, we evaluate the functional cellular effects that follow CHD1 deletion. METHODS: CHD1 was knocked out (KO) in the non-tumorigenic, human papillomavirus 16 (HPV16)-immortalized prostate epithelial cell line, RWPE-1, using CRISPR/Cas9. In vitro assays such as T7 endonuclease assay, western blot, and sequencing were undertaken to characterize the CHD1 KO clones. Morphologic and functional assays for cell adhesion and viability were performed. To study expression of extracellular matrix (ECM) and adhesion molecules, a real-time (RT) profiler assay was performed using RWPE-1 parental, non-target cells (NT2) and CHD1 KO cells. RESULT: Compared to parental RWPE-1 and non-target cells (NT2), the CHD1 KO cells had a smaller, rounder morphology and were less adherent under routine culture conditions. Compared to parental cells, CHD1 KO cells showed a reduction in ECM and adhesion molecules as well as a greater proportion of viable suspension cells when cultured on standard tissue culture plates and on plates coated with laminin, fibronectin or collagen I. CHD1 KO cells showed a decrease in the expression of secreted protein acidic and rich in cysteine (SPARC), matrix metalloproteinase 2 (MMP2), integrin subunit alpha 2 (ITGA2), integrin subunit alpha 5 (ITGA5), integrin subunit alpha 6 (ITGA6), fibronectin (FN1), laminin subunit beta-3 precursor (LAMB3), collagen, tenascin and vitronectin as compared to parental and NT2 cells. CONCLUSION: These data suggest that in erythroblast transformation specific (ETS) fusion-negative, phosphatase and tensin homolog (PTEN) wildtype PCa, deletion of CHD1 alters cell-cell and cell-matrix adhesion dynamics, suggesting an important role for CHD1 in the development and progression of PCa.

Recurring Translocations in Barrett's Esophageal Adenocarcinoma.

Barrett's esophagus (BE) is a premalignant metaplasia in patients with chronic gastroesophageal reflux disease (GERD). BE can progress to esophageal adenocarcinoma (EA) with less than 15% 5-year survival. Chromosomal aneuploidy, deletions, and duplication are early events in BE progression to EA, but reliable diagnostic assays to detect chromosomal markers in premalignant stages of EA arising from BE are lacking. Previously, we investigated chromosomal changes in an in vitro model of acid and bile exposure-induced Barrett's epithelial carcinogenesis (BEC). In addition to detecting changes already known to occur in BE and EA, we also reported a novel recurring chromosomal translocation t(10:16) in the BE cells at an earlier time point before they undergo malignant transformation. In this study, we refine the chromosomal event with the help of fluorescence microscopy techniques as a three-way translocation between chromosomes 2, 10, and 16, t(2:10;16) (p22;q22;q22). We also designed an exclusive fluorescent in situ hybridization for esophageal adenocarcinoma (FISH-EA) assay that detects these chromosomal breakpoints and fusions. We validate the feasibility of the FISH-EA assay to objectively detect these chromosome events in primary tissues by confirming the presence of one of the fusions in paraffin-embedded formalin-fixed human EA tumors. Clinical validation in a larger cohort of BE progressors and non-progressors will confirm the specificity and sensitivity of the FISH-EA assay in identifying malignant potential in the early stages of EA.

A rare case of primary dermal clear cell sarcoma with focal epidermotropism: An entity difficult to distinguish from melanoma.

Clear cell sarcoma (CCS) is an uncommon soft-tissue sarcoma that only rarely arises within the dermis. It is challenging to distinguish dermal CCS from nodular, primary dermal, or metastatic melanoma, as they share morphologic features and immunoprofiles. We describe a dermal CCS in a 25-year-old man with a cutaneous groin mass. The lesion was initially diagnosed as melanoma, likely metastatic. On consultation, in addition to a melanoma-like tumor in the dermis, we identified focal infiltration of tumor cells into the overlying epidermis (epidermotropism), resembling primary nodular or metastatic melanoma. Given the patient's age and absence of a history of primary melanoma, fluorescence in situ hybridization (FISH) was performed, which revealed separation of the 5' and 3' EWSR1 probe signals on chromosome 22q12, prompting a diagnosis of CCS. Our case highlights the histopathological, immunohistochemical, and ultrastructural similarities between CCS and melanoma, and the consequent potential for major diagnostic confusion. In such cases, FISH analysis remains the key to diagnosis. CCS should be considered in patients with a melanoma-like tumor in the dermis or subcutaneous tissue without epidermal (or with minimal) involvement, or prior to diagnosing metastatic melanoma in the absence of a known history of primary melanoma, especially in young individuals.

The Genomic Landscape of Renal Oncocytoma Identifies a Metabolic Barrier to Tumorigenesis.

Oncocytomas are predominantly benign neoplasms possessing pathogenic mitochondrial mutations and accumulation of respiration-defective mitochondria, characteristics of unknown significance. Using exome and transcriptome sequencing, we identified two main subtypes of renal oncocytoma. Type 1 is diploid with CCND1 rearrangements, whereas type 2 is aneuploid with recurrent loss of chromosome 1, X or Y, and/or 14 and 21, which may proceed to more aggressive eosinophilic chromophobe renal cell carcinoma (ChRCC). Oncocytomas activate 5' adenosine monophosphate-activated protein kinase (AMPK) and Tp53 (p53) and display disruption of Golgi and autophagy/lysosome trafficking, events attributed to defective mitochondrial function. This suggests that the genetic defects in mitochondria activate a metabolic checkpoint, producing autophagy impairment and mitochondrial accumulation that limit tumor progression, revealing a novel tumor-suppressive mechanism for mitochondrial inhibition with metformin. Alleviation of this metabolic checkpoint in type 2 by p53 mutations may allow progression to eosinophilic ChRCC, indicating that they represent higher risk.

Cobblestone-area forming cells derived from patients with mantle cell lymphoma are enriched for CD133+ tumor-initiating cells.

Mantle cell lymphoma (MCL) is associated with a significant risk of therapeutic failure and disease relapse, but the biological origin of relapse is poorly understood. Here, we prospectively identify subpopulations of primary MCL cells with different biologic and immunophenotypic features. Using a simple culture system, we demonstrate that a subset of primary MCL cells co-cultured with either primary human mesenchymal stromal cells (hMSC) or murine MS-5 cells form in cobblestone-areas consisting of cells with a primitive immunophenotype (CD19-CD133+) containing the chromosomal translocation t (11;14)(q13;q32) characteristic of MCL. Limiting dilution serial transplantation experiments utilizing immunodeficient mice revealed that primary MCL engraftment was only observed when either unsorted or CD19-CD133+ cells were utilized. No engraftment was seen using the CD19+CD133- subpopulation. Our results establish that primary CD19-CD133+ MCL cells are a functionally distinct subpopulation of primary MCL cells enriched for MCL-initiating activity in immunodeficient mice. This rare subpopulation of MCL-initiating cells may play an important role in the pathogenesis of MCL.

Prolonged exposure to acid and bile induces chromosome abnormalities that precede malignant transformation of benign Barrett's epithelium.

UNLABELLED: Barrett's esophagus (BE) is an asymptomatic, pre-malignant condition of the esophagus that can progress to esophageal adenocarcinoma (EAC). BE arises typically in individuals with long-standing gastroesophageal reflux disease (GERD). The neoplastic progression of BE has been extensively studied histologically and defined as a metaplasia- dyplasia- carcinoma sequence. However the genetic basis of this process is poorly understood. It is conceived that preclinical models of BE may facilitate discovery of molecular markers due to ease of longitudinal sampling. Clinical markers to stratify the patients at higher risk are vital to institute appropriate therapeutic intervention since EAC has very poor prognosis. We developed a dynamic in-vitro BE carcinogenesis (BEC) model by exposing naïve Barrett's epithelium cell line (BAR-T) to acid and bile at pH4 (B4), 5min/day for a year. The BEC model acquired malignant characteristics after chronic repeated exposure to B4 similar to the sequential progression of BE to EAC in vivo. AIM: To study cytogenetic changes during progressive transformation in the BEC model. RESULTS: We observed that the BAR-T cells progressively acquired several chromosomal abnormalities in the BEC model. Evidence of chromosomal loss (-Y) rearrangements [t(10;16) and dup (11q)] and clonal selection appeared during the early stages of the BEC model. Clonal selection resulted in a stabilized monoclonal population of cells that had a changed morphology and formed colony in soft agar. BAR-T cells grown in parallel without any exposure did not show any of these abnormalities. CONCLUSIONS: Prolonged acid and bile exposure induced chromosomal aberrations and clonal selection in benign BAR-T cells. Since aneuploidy preceded morphological/dysplastic changes in the BEC model, chromosomal aberrations may be an early predictor of BE progression. The [t(10;16) and dup(11q)] aberrations identified in this study harbor several genes associated with cancer and may be responsible for neoplastic behavior of cells. After further validation, in-vivo, they may be clinically useful for diagnosis of BE, progressing to dysplasia/esophageal adenocarcinoma.

Duplication of chromosome 1 [dup(1)(q21q32)] as the sole cytogenetic abnormality in a patient previously treated for AML.

A nonrandom structural gain of 1q may be seen in myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML), and often it is due to an unbalanced translocation. Dup(1)(q21q32) as the sole abnormality has only rarely been reported. Reports have suggested that the dup(1)(q21q32) is predictive of a poor prognosis. We describe a case report of a 55 year old male who presented in 2002 with AML-M2, t(8;21)(q22;q22). He underwent induction with "7+3" followed by consolidation chemotherapy resulting in a complete remission. Two years later, his bone marrow revealed a dup(1)(q21q32) as an isolated aberration for the first time. In 2010, cytogenetic analysis of the bone marrow again confirmed this finding and FISH for AML1/ETO t(8;21) remained negative. Dup(1q) developed as an isolated abnormality two years after AML treatment, and to date, there is no evidence of progression to MDS. This is the first report of an acquired dup(1)(q21q32) as the sole abnormality in a patient treated for AML. This suggests that the dup(1q) may not be exclusively associated with a poor prognosis.

A new translocation between chromosomes 6 and 9 helps to establish diagnosis of renal oncocytoma.

Renal oncocytomas are benign epithelial tumors of the kidney. Histologically, they resemble certain malignant renal tumors, such as chromophobe renal cell carcinoma and the eosinophilic or granular form of clear cell renal carcinoma. It is, therefore, important to be able to differentiate among these tumors. Cytogenetic analysis is an important adjunct to the diagnosis of renal tumors, as the various subtypes have specific acquired chromosome abnormalities. Oncocytomas present either with loss of chromosome 1 and a sex chromosome, or with recurring translocations involving chromosome 11. We describe 2 patients with renal oncocytoma and a new translocation between chromosomes 6 and 9. The tumors in both patients were histologically virtually identical. The t(6;9)(p21;p23) may be a new translocation associated with renal oncocytomas.

Deficiency of the dual ubiquitin/SUMO ligase Topors results in genetic instability and an increased rate of malignancy in mice.

BACKGROUND: Topors is a nuclear protein that co-localizes with promyelocytic leukemia bodies and has both ubiquitin and SUMO E3 ligase activity. Expression studies implicated Topors as a tumor suppressor in various malignancies. To gain insight into the function of Topors, we generated a Topors-deficient mouse strain. RESULTS: Mice homozygous for a mutant Topors allele exhibited a high rate of perinatal mortality and decreased lifespan. In addition, heterozygotes were found to have an increased incidence of malignancy, involving a variety of tissues. Consistent with this finding, primary embryonic fibroblasts lacking Topors exhibited an increased rate of malignant transformation, associated with aneuploidy and defective chromosomal segregation. While loss of Topors did not alter sensitivity to DNA-damaging or microtubule-targeting agents, cells lacking Topors exhibited altered pericentric heterochromatin, manifested by mislocalization of HP1alpha and an increase in transcription from pericentric major satellite DNA. Topors-deficient cells exhibited a transcriptional profile similar to that of cells treated with histone deacetylase inhibitors, and were resistant to the anti-proliferative effects of the histone deacetylase inhibitor trichostatin A. CONCLUSION: These results indicate a unique role for Topors in the maintenance of genomic stability and pericentric heterochromatin, as well as in cellular sensitivity to histone deacetylase inhibitors.

Thymolipoma: clues to pathogenesis revealed by cytogenetics.

The pathogenesis of thymolipoma is controversial and unclear despite numerous reports. A case report of thymolipoma with cytogenetic analysis is herein presented. The lesion demonstrated a translocation involving the HMGA2 gene on chromosome 12q15, which is seen in two thirds of solitary lipomas. This finding supports the theory that this case of thymolipoma is a neoplasm of thymic fat.

p16 immunohistochemistry as an alternative marker to distinguish atypical lipomatous tumor from deep-seated lipoma.

Atypical lipomatous tumor (ALT)/well-differentiated liposarcoma (WDLPS) is a locally aggressive malignant mesenchymal neoplasm, resembling ordinary lipoma in many clinical aspects. This study investigates the value of expression of p16, an important cell cycle regulator, alone or in combination with MDM2, to distinguish the 2 entities. Fifty cases of lipomatous neoplasms, with cytogenetic results, from 45 patients were collected from the archives in Department of Pathology, University of Medicine and Dentistry of New Jersey/New Jersey Medical School during 1998 to 2006. These include 18 cases of deep-seated lipoma, 1 hibernoma, 1 lipoblastoma, and 30 cases of ALT/WDLPS. p16 was detected in 25/30 (83.3%) of ALT/WDLPS, and none (0/18) of the deep-seated lipomas (P<0.0000001, Fisher exact test). MDM2 was detected in 18/30 (60%) of ALT/WDLPS, and was negative in 0/18 of the deep-seated lipomas (P<0.0001, Fisher exact test). Combined together, 27/30 (90%) of ALT/WDLPS showed positive staining of either p16, MDM2, or both, whereas no staining was observed in all the deep-seated lipomas (P<0.0000001, Fisher exact test). The single case of hibernoma and lipoblastoma revealed p16+MDM2- phenotype. These results indicated that p16 is yet another marker which seems to be a valuable marker to differentiate ALT/WDLPS from deep-seated lipomas.

Further delineation of interstitial chromosome 6 deletion syndrome and review of the literature.

Interstitial deletions of chromosome 6q are a relatively rare finding. Deletions have ranged from the loss of a single band to larger deletions spanning multiple bands. The clinical phenotype varies, but some features commonly seen include cardiac anomalies, hypotonia, facial dysmorphism and mental retardation. To further delineate the syndrome, we report an infant with facial dysmorphism, ectrodactyly and tetralogy of Fallot owing to interstitial deletion 6q16.1-6q22.32. On array comparative genomic hybridization analysis, the deletion spanned from the 93 377 323rd base to the 127 650 582nd base on chromosome 6 [coordinates are based on Human Mar. 2006 (hg18) assembly of International Human Genome Sequencing Consortium]. A literature review identified 16 additional cases with overlapping interstitial deletions of chromosome 6q between q13 and q23.1. Genotype-phenotype correlations are considered.

Simultaneous appearance of trisomy 8 and trisomy 12 in different cell populations in a patient with untreated B-cell chronic lymphocytic leukemia and myelodysplasia.

The co-existence of spontaneously arising myeloid and lymphoid malignancies in the same patient is rare, and is thought to be mainly due to chance. We describe a patient presenting simultaneously with chronic lymphocytic leukemia (CLL) and myelodysplasia (MDS). Histological, flow cytometric, chromosomal and fluorescent in situ hybridization (FISH) studies show that both cell populations possess different sets of markers consistent with the myeloid and lymphoid differentiation pathways. The question of whether these arose from a single or two separate progenitor cells is explored.

HER-2/neu and p53 in osteosarcoma: an immunohistochemical and fluorescence in situ hybridization analysis.

The overexpression of HER-2/neu and p53 has been associated with poor outcome in many neoplasms. Their role in patients with osteosarcoma is unclear. We studied the expression of HER-2/neu and p53 in 22 osteosarcoma samples (from 20 patients--2 had locally recurrent disease) biopsied at the University of Medicine and Dentistry of New Jersey (UMDNJ) from 1996-2000 using both immunohistochemical (IHC) and fluorescence in situ hybridization (FISH) analysis. Fourteen patients (14 samples) presented with Stage II and 6 patients (8 samples) presented with Stage III disease. Median follow-up is two years (range one year to five years). Four of 22 (18%) samples showed focal membranous or cytoplasmic positivity for HER-2/neu and six of 22 samples (27%) showed nuclear positivity for p53 by IHC analysis. In contrast, none of 22 tested samples showed gene amplification for HER-2/neu by FISH analysis. Seven of 13 HER-2/neu and p53 negative patients (54%) are currently disease free (between one year to five years). In this sample of patients, the HER-2/neu oncogene is not overexpressed or amplified in osteosarcoma; six of 22 samples (27%) showed overexpression of p53 by IHC analysis. By FISH, none of the samples demonstrated deletion of p53. Neither HER2/neu nor p53 expression was important for the biology of osteosarcoma in this population.

Comprehensive genome-wide comparison of DNA and RNA level scan using microarray technology for identification of candidate cancer-related genes in the HL-60 cell line.

Genome-wide scans for DNA and RNA changes in the HL-60 cell line relative to normal leukocytes were conducted. Microarray-based comparative genome hybridization (CGH) studies were performed with the Spectral Genomics Human Bacterial Artificial Chromosome (BAC) 3MB system. Transcriptional measurements of approximately 12,500 human genes were monitored using Affymetrix U95A GeneChips. In HL-60, genomic DNA amplification of the 8q24 locus, trisomy 18, and deletions at loci 5q11.2 approximately q31, 6q12, 9p21.3 approximately p22, 10p12 approximately p15, 14q22 approximately q31, 17p12 approximately p13.3, and monosomy X were detected. After obtaining locus information about the RNA transcripts from the Affymetrix database, 4368 genes were stratified both according to status of RNA expression and the DNA copy number of their designated loci. The expression level of 2326 (53.25%) of 4368 transcripts is concordant with DNA copy number. Examples of specific, highly expressed, cancer-associated genes in amplified loci include SERPINB10, MYC, TYMS, HEC, and EPB41L3, while CD14, GZMK, TCF7, FOS, MLH3, CTNNA1, IRF1, VIM, CRK, MAP3K1, STAM, MAX, SFRG5, ENC1, PURA, MNT, RASA1, GLRX, UBE2B, NR3C1, PTENP1, BS69, COPEB, SKIP, PIM2, and MIC2 represent cancer-associated genes in deleted loci with decreased expression. The complementary usage of genome-wide DNA and RNA scans should enhance the identification of candidate genes in the neoplastic process.

Veto-like activity of mesenchymal stem cells: functional discrimination between cellular responses to alloantigens and recall antigens.

Trans-differentiation of stem cells shows promise for use in tissue repair medicine. Although poorly defined, mesenchymal stem cells (MSC) appear useful for applications in repair medicine. Despite the low frequency of MSC, they are relatively easy to expand. The expression of MHC class II on MSC, however, could deter their use in repair medicine, since these molecules could stimulate an allogeneic host response. This study sought to compare the immune stimulatory and suppressive effects of MSC. Primary human MSC were cultured from bone marrow aspirates and then passaged at least three times before use in assays. Morphologically, MSC were symmetrical; were SH2(+), MHC class II(+), CD45(-), CD44(+), CD31(-), CD14(-), proly-4-hydroxylase(-); and showed normal karyotype patterns and elevated telomerase activities. MSC elicited significant stimulatory responses when cocultured with allogeneic PBMC. Despite the production of different types of growth factors, allogeneic effects of MSC could not be explained by the production of these growth factors. One-way MLR reactions were significantly blunted by third-party MSC. Similar suppression was not observed for responses to three different recall Ags. Based on these functional differences by MSC in responses to allo- and recall Ags, we examined whether MSC could exert veto-like functions. We showed that MSC could blunt the cytotoxic effects of allogeneic-induced effectors to mitogen-activated targets. The results showed that although MSC elicited allogeneic responses in a model that mimics a graft-vs-host reaction, they also exerted veto-like activity, but caused no effect on responses to recall Ags.