Application of counter-selectable marker PIGA in engineering designer deletion cell lines and characterization of CRISPR deletion efficiency.

The CRISPR/Cas9 system is a technology for genome engineering, which has been applied to indel mutations in genes as well as targeted gene deletion and replacement. Here, we describe paired gRNA deletions along the PIGA locus on the human X chromosome ranging from 17 kb to 2 Mb. We found no compelling linear correlation between deletion size and the deletion efficiency, and there is no substantial impact of topologically associating domains on deletion frequency. Using this precise deletion technique, we have engineered a series of designer deletion cell lines, including one with deletions of two X-chromosomal counterselectable (negative selection) markers, PIGA and HPRT1, and additional cell lines bearing each individual deletion. PIGA encodes a component of the glycosylphosphatidylinositol (GPI) anchor biosynthetic apparatus. The PIGA gene counterselectable marker has unique features, including existing single cell level assays for both function and loss of function of PIGA and the existence of a potent counterselectable agent, proaerolysin, which we use routinely for selection against cells expressing PIGA. These designer cell lines may serve as a general platform with multiple selection markers and may be particularly useful for large scale genome engineering projects such as Genome Project-Write (GP-write).

Rapid and robust reversion to essential thrombocythemia on treatment with Decitabine in a case of hydroxyurea-induced t-MDS/AML.

Rapid remission of MDS/AML may be induced with Decitabine; however, significant megakaryocyte expansion and subsequent thrombocytosis may occur. Decitabine-mediated reversion of the MDS to benign ET via hypomethylation of JAK/STAT pathway repressors is one potential mechanism to explain this observed phenomenon.

Clear cell sarcoma of the penis: a case report.

Clear cell sarcoma of the penis is exceedingly rare with only one prior case involving the penis reported in the literature. We present the case of a 32 year old male who presented with an infiltrative neoplasm at the base of the penis as well as extensive metastatic disease to the lymph nodes and bone. Morphologic, immunohistochemical and cytogenetic findings established the diagnosis of clear cell sarcoma. Despite chemotherapy the patient's disease was rapidly progressive and the patient died of disease within 8 months of diagnosis.

Trisomy 8 in myeloid leukemia cutis confirmed by fluorescence in situ hybridization analysis.

We present a case of a 64-year-old man with refractory acute myeloid leukemia and trisomy 8 who developed leukemia cutis. Interphase fluorescence in situ hybridization (FISH) was performed on a paraffin-embedded skin section. FISH confirmed a population of cells with trisomy 8 in the blastic infiltrates involving the skin. This case illustrates a novel application of interphase FISH to confirm the diagnosis of leukemia cutis.

Characteristics of chromosomal abnormalities diagnosed after spontaneous abortions in an infertile population.

PURPOSE: To estimate the prevalence of chromosomally abnormal related miscarriages in an infertile population. METHODS: Retrospective analysis of cytogenetics obtained by chorionic villi harvesting of the first miscarriage cycle of infertile patients at our center from 2001-2010 were reviewed. Abnormal results were characterized as trisomy, monosomy X, structural, or other. Age, # of eggs, #2PN, # embryos transferred, day of transfer, and performance of intracytoplasmic sperm injection (ICSI) were recorded. RESULTS: In a study population of 299 patients with a mean age of 38.0 ± 4.5 y, 276(92 %) patients had some form of assisted reproductive technologies (ART), and 244(82 %) had IVF. Of all results, 71.6 % had an abnormal karyotype. Patients with abnormal cytogenetics were older (38.6 ± 4.1 vs. 36.3 ± 4.9, p < 0.001), and more likely to have a day 3 transfer (age < 38 ( 20.7 %) vs. age 38 (46.3 %), p = <0.001) with more embryos transferred (3.0 ± 1.2, vs. 2.3 ± 0.9, p < 0.001). The performance of ICSI did not affect the rate of cytogenetically abnormal products of conception (ICSI 68.3 % vs. no ICSI 70.7 %). In comparing patients, monosomy X was more common in <38 y. Rates of trisomy, although not statistically significant, were higher in older patients. CONCLUSIONS: The classic associations between advancing age and chromosomal abnormalities, and younger age and monosomy X, are affirmed in our infertile population. There was no increase in chromosomal abnormalities in cycles where ICSI was performed. Older patients are more likely to have day 3 transfers and more embryos transferred. Our chromosomal abnormality rates are higher than classic estimates but comparable to recent studies. The limitation of this study was a lack in uniformity among practitioners in recommending all patients have a Dilation and Curettage (D&C) at time of diagnosis. Such information may serve to improve the counseling of patients after miscarriage.

A quantitative analysis of genomic instability in lymphoid and plasma cell neoplasms based on the PIG-A gene.

It has been proposed that hypermutability is necessary to account for the high frequency of mutations in cancer. However, historically, the mutation rate (mu) has been difficult to measure directly, and increased cell turnover or selection could provide an alternative explanation. We recently developed an assay for mu using PIG-A as a sentinel gene and estimated that its average value is 10.6 x 10(-7) mutations per cell division in B-lymphoblastoid cell lines (BLCLs) from normal donors. Here we have measured mu in human malignancies and found that it was elevated in cell lines derived from T cell acute lymphoblastic leukemia, mantle cell lymphoma, follicular lymphoma in transformed phase, and 2 plasma cell neoplasms. In contrast, mu was much lower in a marginal zone lymphoma cell line and 5 other plasma cell neoplasms. The highest mu value that we measured, 3286 x 10(-7), is 2 orders of magnitude above the range we have observed in non-malignant human cells. We conclude that the type of genomic instability detected in this assay is a common but not universal feature of hematologic malignancies.

De novo 12;17 translocation upstream of SOX9 resulting in 46,XX testicular disorder of sex development.

Individuals with rare cytogenetic variants have contributed to our understanding of the genetics of sex development and its disorders. Here, we report on a child with a de novo 12;17 translocation, 46,XX,t(12;17)(q14.3;q24.3) chromosome complement, resulting in SRY-negative 46,XX testicular disorder of sex development (46,XX DSD without campomelic dysplasia). The chromosome 12 breakpoint was mapped via array comparative genomic hybridization (aCGH) of a hybrid somatic cell line to 64.2-64.6 Mb (from the p arm telomere). The chromosome 17 breakpoint was mapped to 66.4-67.1 Mb, that is, upstream of SOX9. The location of the chromosome 17 breakpoint was refined by fluorescence in situ hybridization (FISH) at > or =776 kb upstream of SOX9. Thus, the 12;17 translocation removed part of the SOX9 cis-regulatory region and replaced it with a regulatory element from pseudogene LOC204010 or the next gene, Deynar, of chromosome 12, potentially causing up-regulation of the testis-determining SOX9 gene during gonadal development and the phenotype of 46,XX testicular DSD.

Let-7 repression leads to HMGA2 overexpression in uterine leiomyosarcoma.

Overexpression of HMGA2 is common in uterine leiomyomas (ULM). The expression of HMGA2 in its malignant counterpart - uterine leiomyosarcomas (ULMS) remains undetermined. Recently it has been shown that repression of HMGA2 by microRNA let-7s is a critical molecular regulatory mechanism associated with tumour growth in many tumours and cell types, including leiomyomas. To test whether HMGA2 and let-7s play a role in ULMS, we examined the levels of endogenous HMGA2 and let-7 expression and found a significant correlation between these two molecules in a case-matched cohort of human ULMS. We found that overexpression of HMGA2 and let-7-mediated HMGA2 repression is a relevant molecular alteration in ULMS. Disrupting the control of HMGA2 and let-7 pairs promotes ULMS cell growth in vitro.

Primary Ewing sarcoma/PNET of the kidney: fine-needle aspiration, histology, and dual color break apart FISH Assay.

A 34-year-old previously healthy Hispanic man presented with lower back pain. CT scan revealed an 8-cm space-occupying lesion in the superior pole of the left kidney with numerous small lytic lesions in the skull, vertebrae, ribs, and pelvic bones. CT-guided fine-needle aspiration biopsy revealed a high-grade primitive small round cell tumor with the tumor cells being strongly positive for CD99 and vimentin. The patient subsequently underwent a left nephrectomy. Fluorescence in situ hybridization analysis using a DNA probe for the Ewing Sarcoma breakpoint region 1 (EWSR1) on chromosome 22g12 revealed a rearrangement of the EWSR1 locus. The diagnosis of primary Ewing sarcoma/primitive neuroectodermal tumor of the kidney was established.

Isolated echogenic intracardiac foci in patients with low-risk triple screen results: assessing the risk of trisomy 21.

OBJECTIVE: While an echogenic intracardiac focus (EIF) is associated with an increased risk of trisomy 21 (T21), the magnitude of that risk remains controversial, particularly in the setting of a low-risk triple screen (TS). The objective of this study is to define the risk of T21 in patients with a low-risk TS and an isolated EIF. STUDY DESIGN: A retrospective analysis was performed on patients presenting prior to 22 6/7 weeks of gestation. Patients met criteria for inclusion if an EIF was noted, a TS had been drawn, the anatomic survey was complete and was determined to be normal, and karyotyping or delivery occurred at Bellevue Hospital. A high-risk TS was defined as a risk of <1:500, assuming a 2-fold increased risk in the setting of an isolated EIF. A low-risk TS was defined as a risk of >1:500. Statistical analysis was performed using chi-square, with p values of <0.05 considered significant. RESULTS: 7,318 anatomic surveys were performed. An EIF was identified in 584 patients (7.98%), of which 391 met the criteria for inclusion. Of the 391, 51% were Asian and 38% were Hispanic; 348 had a low-risk TS and 43 had a high-risk TS. Patients with an EIF and a low-risk TS had a significantly lower risk of having a T21 pregnancy compared to those with a high-risk TS and an EIF (0 vs. 2.3%; p = 0.004). CONCLUSION: An isolated EIF with a low risk TS is not associated with an increased risk of T21.

Giant cell tumor of soft tissue with pulmonary metastases: pathologic and cytogenetic study.

Giant cell tumor of soft tissue (GCTST) has gained general acceptance as an uncommon but distinct primary soft tissue tumor since it was first described in 1972. GCTST is predominantly seen in adults and typically shows uniformly dispersed osteoclast-like giant cells admixed with oval to polygonal mononuclear cells. It usually follows a benign clinical course, although the malignant variant has been described in cases in which the mononuclear cells demonstrate obvious dysplastic features. It is still not clear whether the two variants belong to the spectrum of the same tumor. No cytogenetic chromosomal abnormalities have been reported in the literature of GCTST. Interestingly, the osseous counterpart of giant cell tumor, which shares similar histologic features, quite often displays a telomeric association at the cytogenetic level, a finding that has never been reported in GCTST. We report the case of a 12-year-old girl with GCTST of the right leg that metastasized to the lung. Cytogenetic studies from the primary tumor showed the phenomenon of telomeric association involving multiple chromosomes.

Differential amplification and overexpression of HER-2/neu, p53, MIB1, and estrogen receptor/progesterone receptor among medullary carcinoma, atypical medullary carcinoma, and high-grade invasive ductal carcinoma of breast.

CONTEXT: Medullary carcinoma (MC) is a special type of breast cancer that has a better prognosis than atypical medullary carcinoma (AMC) and high-grade invasive ductal carcinoma (HGIDC) with prominent lymphocytic infiltrates. What accounts for the different clinical courses of these carcinomas, despite their similar histology, is unknown. To address this issue, we performed a comparative study of amplification and overexpression of HER-2/neu and expression of several other important biochemical markers (p53, MIB1, and estrogen receptor [ER]/progesterone receptor [PR]) in these 3 cancer groups. OBJECTIVE: To evaluate HER-2/neu, p53, MIB1, and ER/PR as markers in the differential diagnosis of MC, AMC, and HGIDC.Design.-Nine cases of MC, 13 cases of AMC, and 16 cases of HGIDC with prominent lymphocytic infiltrates were identified according to strict histologic criteria. All tests were performed on formalin-fixed, paraffin-embedded archival tissues. HER-2/neu gene amplification was examined by fluorescence in situ hybridization using PathVysion HER-2 DNA probes. Expression of HER-2/neu, p53, MIB1, and ER/PR was detected by immunohistochemistry. chi2 and Student t tests were applied for statistical analyses. RESULTS: None of 9 cases of MC examined had either amplification or overexpression of HER-2/neu (0%). In contrast, HER-2/neu amplification was observed in AMC (46%, P <.025) and HGIDC (56%, P <.005). All 3 categories of tumors had similar percentages of expression of p53 (78% of MC, 77% of AMC, and 69% of HGIDC) and MIB1 (89% of MC, 92% of AMC, and 94% of HGIDC). Immunostaining for ER/PR was rarely positive in either MC or AMC, and there were no significant differences of expression of ER/PR between these 2 lesions (P >.05). However, the expression rate of ER/PR (31%/44%) in HGIDC is higher than in both MC (P =.05) and AMC (P =.01). CONCLUSIONS: Medullary carcinoma of breast is distinct from AMC and HGIDC with prominent lymphocytic infiltrates in amplification and overexpression of HER-2/neu. This difference may account for its different clinical and biological behavior, and may potentially aid in diagnosis and management of these groups of patients.

Parachordoma or chordoma periphericum? Case report of a tumor of the thoracic wall.

We report the findings from an aspiration biopsy and resection of a chordoma-like tumorous mass in the wall of the thorax of a 36-yr-old man with immunohistochemical, ultrastructural, and cytogenetic studies. The 4-cm oval tumor was an incidental finding on physical examination, and no other lesions were identified after comprehensive radiologic studies. The aspirate was composed of sheets and nests of cells with distinct borders in a myxoid and fibrillary extracellular matrix. The neoplastic cells were uniform and round or polygonal with abundant pale blue vacuolated cytoplasm and small round, central or eccentric nuclei. On electron microscopy, mitochondrial rough endoplasmic reticulum complexes were seen in neoplastic cells. These features were similar to those of a conventional chordoma. However, the cytogenetic pattern, 43, XY ,-1, -2, der (5)t(1p;5q), -6, add(8p) ,add(10q), was not typical. In addition, the neoplastic cells were positive for vimentin, S-100, AE1/AE3, CAM 5.2, and CK 19; were focally positive for EMA and smooth muscle actin; and were negative for cytokeratin 1 and 10 (34 beta E12), CK 7, CK 8 (35H 11B), CK 17, and CK 20. The cytogenetic and immunohistochemical patterns were different from conventional chordoma and its peripheral counterpart, chordoma periphericum, suggesting the diagnosis of parachordoma. To the best of our knowledge, this is the first report of fine-needle aspiration of this newly defined and rare entity.

T-cell clonality and myelodysplasia without chromosomal fragility in a patient with features of Seckel syndrome.

Seckel syndrome is a rare autosomal recessive disorder with characteristic craniofacial dysmorphism, skeletal defects, mental and prenatal growth retardation. About 50 cases have been reported in the literature. Hematologic abnormalities with associated chromosomal fragility have been noted in about 15% of the reported cases. We report a patient with Seckel syndrome with myelodysplastic features and clonal T-cells in the bone marrow but no evidence of chromosomal fragility. After 5 years of follow-up, this patient remains asymptomatic without any treatment and with stable peripheral blood counts.

Amplification of Her-2/neu gene in Her-2/neu-overexpressing and -nonexpressing breast carcinomas and their synchronous benign, premalignant, and metastatic lesions detected by FISH in archival material.

Amplification of Her-2/neu in breast carcinoma is associated with poor prognosis, short disease-free interval, and short survival time in both node-negative and -positive patients. Little is known about the starting point of amplification of Her-2/neu and how it progresses from benign to malignant breast lesions. We attempted to address these questions by evaluating amplification of Her-2/neu in benign, premalignant, and malignant lesions using fluorescence in situ hybridization (FISH). Twenty-six patients with Her-2/neu-overexpressing invasive ductal carcinomas (as judged by strong immunoreactivity with Her-2/neu antibody) and coexisting lesions of ductal hyperplasia (DH), atypical ductal hyperplasia (ADH), ductal carcinoma in situ (DCIS) in the vicinity of the invasive tumor (as judged by review of the hematoxylin and eosin-stained sections), as well as metastatic carcinoma in axillary lymph nodes (mets) were selected for this study. In the primary carcinomas, a close relationship was present between overexpression as detected by immunohistochemistry (IHC) and amplification as demonstrated by FISH (85% concordance). Among these patients, amplification of Her-2/neu in ADH was demonstrated in 7 of 13 cases with ADH, and in DCIS, in 21 of 22 cases with DCIS. There was no amplification in DH or normal ductal epithelium. Significantly, in all 12 patients with synchronous positive axillary lymph nodes, there was concordant amplification of Her-2/neu in the primary and metastatic carcinoma. Amplification was consistent in multifocal metastases, despite morphological heterogeneity in some patients. Amplification ratios increased from ADH to DCIS to invasive carcinoma (P <.01, ADH versus DCIS; P <.05, DCIS versus invasive cancer), but there was no difference in amplification ratios between primary cancers and synchronous axillary metastases (P >.05). We also evaluated Her-2/neu amplification in 21 patients without Her-2/neu overexpression in their primary carcinomas (as judged by absent immunoreactivity with Her-2/neu antibody). Three showed amplification in both primary and metastatic lesions, with a low amplification ratio (approximately 2). One patient had amplification in the primary tumor but not in an axillary metastasis. Two patients exhibited slight amplification in the metastatic carcinoma (ratios 1.6 and 2), but not in their primary cancers. This FISH study indicates that amplification of Her-2/neu can emerge de novo in any stage of the disease process, from ADH to metastatic lesions, but most often appears first in ADH or DCIS. The degree of Her-2/neu amplification increases with progression to invasive carcinoma, there being no further increase in synchronous metastasis. Our data suggest that amplification of Her-2/neu appears to be mainly involved in initiation of breast oncogenesis and that its role in progression of breast cancers is uncertain.

Bone abnormalities in latent TGF-[beta] binding protein (Ltbp)-3-null mice indicate a role for Ltbp-3 in modulating TGF-[beta] bioavailability.

The TGF-betas are multifunctional proteins whose activities are believed to be controlled by interaction with the latent TGF-beta binding proteins (LTBPs). In spite of substantial effort, the precise in vivo significance of this interaction remains unknown. To examine the role of the Ltbp-3, we made an Ltbp-3-null mutation in the mouse by gene targeting. Homozygous mutant animals develop cranio-facial malformations by day 10. At 2 mo, there is a pronounced rounding of the cranial vault, extension of the mandible beyond the maxilla, and kyphosis. Histological examination of the skulls from null animals revealed ossification of the synchondroses within 2 wk of birth, in contrast to the wild-type synchondroses, which never ossify. Between 6 and 9 mo of age, mutant animals also develop osteosclerosis and osteoarthritis. The pathological changes of the Ltbp-3-null mice are consistent with perturbed TGF-beta signaling in the skull and long bones. These observations give support to the notion that LTBP-3 is important for the control of TGF-beta action. Moreover, the results provide the first in vivo indication for a role of LTBP in modulating TGF-beta bioavailability.

Wilms' tumor in adults: aspiration cytology and cytogenetics.

The fine-needle aspiration cytologic findings of Wilms' tumor occurring in a 20-yr-old female patient and a 35-yr-old male patient showing blastemal, spindled sarcomatous and rare epithelial components are reported. The male patient had the typical presentation of renal mass with metastasis to lung and pleura, whereas the female patient had an unusual presentation with the tumor originated from the subcapsular nephrogenic zone of the kidney, extending into the liver without invasion into the renal cortex. Cytogenetic analysis of this case identified: 90, XXXX, +2x3-4, -5, -15, -16, -17, -17, i (17)(q10) x2. This finding may represent a genetic change associated with Wilms' tumor of older pediatric and young adult patients. To the best of our knowledge, this case is the sixth case with cytogenetic study and the first case revealing isochromosome 17q of an adult Wilms' tumor.