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author:("Li, shiba")
1.  Primary intracranial Ewing’s sarcoma with unusual features 
Pediatric primary “small round blue cell” tumors in the CNS represent several entities, some more common than others. Ewing sarcoma/peripheral primitive neuroectodermal tumor (ES/pPNET) is rare and must be distinguished from other tumors such as medulloblastoma [1, 2], atypical rhabdoid/teratoid tumor, ependymomal tumors, metastatic sarcomas, hematologic malignancies, and other mimics. Although therapy for ES/pPNET is effective, it brings severe side effects, including cardiac toxicity, making correct recognition important [3]. As small blue cell tumors look similar, diagnosis often depends on special stains, immunohistochemistry, and molecular techniques. While the combination of membranous immunohistochemical reactivity for CD99 with cytoplasmic glycogen provides effective screening, demonstration of characteristic translocations of EWSR1 (chromosome 22) or FUS (chromosome 16) by fluorescent in situ hybridization (FISH) can confirm the diagnosis. We are reporting three primary ES/pPNET of the CNS, two of which occurred in children. While the adult case demonstrates the classic histopathology, the two pediatric cases have histopathology that significantly deviates from the usual. One is suggestive of a primary sarcoma, and the other mimics an ependymoma, but all three cases are confirmed with FISH. These observations suggest that primary ES in the CNS may have histology different from the classic morphology and a high index of suspicion should be maintained in order to make the correct diagnosis. A search of the literature suggests that these tumors are most frequently seen in children and young adults. Imaging often shows a supratentorial enhancing mass that touches the leptomeninges. Survival over three years is good but long term prognosis is unknown [3, 4].
PMCID: PMC4348914  PMID: 25755713
Ewing sarcoma; peripheral primitive neuroectodermal tumor; diagnosis
2.  16p13.3 duplication associated with non-syndromic pierre robin sequence with incomplete penetrance 
Pierre Robin sequence (PRS) is a condition present at birth. It is characterized by micrognathia, cleft palate, upper airway obstruction, and feeding problems. Multiple etiologies including genetic defects have been documented in patients with syndromic, non-syndromic, and isolated PRS.
Case presentation
We report a 4-year-old boy with a complex small supernumerary marker chromosome (sSMC) who had non-syndromic Pierre Robin sequence (PRS). The complex marker chromosome, der(14)t(14;16)(q11.2;p13.13), was initially identified by routine chromosomal analysis and subsequently characterized by array-comparative genomic hybridization (array CGH) and confirmed by fluorescence in situ hybridization (FISH). Clinical manifestations included micrognathia, U-type cleft palate, bilateral congenital ptosis, upslanted and small eyes, bilateral inguinal hernias, umbilical hernia, bilateral clubfoot, and short fingers and toes. To our best knowledge, this was the first case diagnosed with non-syndromic PRS associated with a complex sSMC, which involved a 3.8 Mb gain in the 14q11.2 region and an 11.8 Mb gain in the 16p13.13-pter region.
We suggest that the duplicated chromosome segment 16p13.3 possibly may be responsible for the phenotypes of our case and also may be a candidate locus of non-syndromic PRS. The duplicated CREBBP gene within chromosome 16p13.3 is associated with incomplete penetrance regarding the mandible development anomalies. Further studies of similar cases are needed to support our findings.
PMCID: PMC4260201  PMID: 25493098
Small supernumerary marker chromosome; Pierre robin sequence; Array CGH; FISH; 16p13.3
3.  A Case of Acute Myeloid Leukemia with a Previously Unreported Translocation (14; 15) (q32; q13) 
Case Reports in Genetics  2014;2014:921240.
Background. We hereby describe what we believe to be the first reported case of t (14; 15) (q32; q13) associated with acute myeloid leukemia (AML). Methods. PubMed, Embase, and OVID search engines were used to review the related literature and similar published cases. Case. A47-year-old female presented in December 2011 with AML (acute myelomonocytic leukemia) with normal cytogenetics; molecular testing revealed FLT-3 internal tandem duplication (ITD) mutation, while no mutations involving FLT3 D385/I836, NPM1 exon 12, or KIT exons 8 and 17 were detected. She was induced with 7 + 3 (cytarabine + idarubicin) and achieved complete remission after a second induction with high-dose cytarabine (HiDAC) followed by uneventful consolidation. She presented 19 months after diagnosis with relapsed disease. Of note, at relapse cytogenetic analysis revealed t (14; 15) (q32; q13), while FLT-3 analysis showed a codon D835 mutation (no ITD mutation was detected). She proved refractory to the initial clofarabine-based regimen, so FLAG-idarubicin then was used. She continued to have persistent disease, and she was discharged on best supportive care. Conclusion. Based on this single case of AML with t (14; 15) (q32; q13), this newly reported translocation may be associated with refractory disease.
PMCID: PMC4243475  PMID: 25436161
4.  Feature Selection for the Automated Detection of Metaphase Chromosomes: Performance Comparison Using a Receiver Operating Characteristic Method 
Background. The purpose of this study is to identify a set of features for optimizing the performance of metaphase chromosome detection under high throughput scanning microscopy. In the development of computer-aided detection (CAD) scheme, feature selection is critically important, as it directly determines the accuracy of the scheme. Although many features have been examined previously, selecting optimal features is often application oriented. Methods. In this experiment, 200 bone marrow cells were first acquired by a high throughput scanning microscope. Then 9 different features were applied individually to group captured images into the clinically analyzable and unanalyzable classes. The performance of these different methods was assessed by a receiving operating characteristic (ROC) method. Results. The results show that using the number of labeled regions on each acquired image is suitable for the first on-line CAD scheme. For the second off-line CAD scheme, it would be suggested to combine four feature extraction methods including the number of labeled regions, average regions area, average region pixel value, and the standard deviation of either region distance or circularity. Conclusion. This study demonstrates an effective method of feature selection and comparison to facilitate the optimization of the CAD schemes for high throughput scanning microscope in the future.
PMCID: PMC4334018  PMID: 25763334
5.  Characterization of Severe Fever with Thrombocytopenia Syndrome in Rural Regions of Zhejiang, China 
PLoS ONE  2014;9(10):e111127.
Severe fever with thrombocytopenia syndrome virus (SFTSV) infections have recently been found in rural regions of Zhejiang. A severe fever with thrombocytopenia syndrome (SFTS) surveillance and sero-epidemiological investigation was conducted in the districts with outbreaks. During the study period of 2011–2014, a total of 51 SFTSV infection cases were identified and the case fatality rate was 12% (6/51). Ninety two percent of the patients (47/51) were over 50 years of age, and 63% (32/51) of laboratory confirmed cases occurred from May to July. Nine percent (11/120) of the serum samples from local healthy people without symptoms were found to be positive for antibodies to the SFTS virus. SFTSV strains were isolated by culture using Vero, and the whole genomic sequences of two SFTSV strains (01 and Zhao) were sequenced and submitted to the GenBank. Homology analysis showed that the similarity of the target nucleocapsid gene from the SFTSV strains from different geographic areas was 94.2–100%. From the constructed phylogenetic tree, it was found that all the SFTSV strains diverged into two main clusters. Only the SFTSV strains from the Zhejiang (Daishan) region of China and the Yamaguchi, Miyazakj regions of Japan, were clustered into lineage II, consistent with both of these regions being isolated areas with similar geographic features. Two out of eight predicted linear B cell epitopes from the nucleocapsid protein showed mutations between the SFTSV strains of different clusters, but did not contribute to the binding ability of the specific SFTSV antibodies. This study confirmed that SFTSV has been circulating naturally and can cause a seasonal prevalence in Daishan, China. The results also suggest that the molecular characteristics of SFTSV are associated with the geographic region and all SFTSV strains can be divided into two genotypes.
PMCID: PMC4214719  PMID: 25356556
6.  Coexistence of t(15;17) and t(15;16;17) detected by fluorescence in situ hybridization in a patient with acute promyelocytic leukemia: A case report and literature review 
Oncology Letters  2014;8(3):1001-1008.
Acute promyelocytic leukemia (APL) is characterized by the t(15;17)(q22;q21), which results in the fusion of the promyelocytic leukemia (PML) gene at 15q22 with the retinoic acid α-receptor (RARA) gene at 17q21. The current study presents the case of a 54-year-old female with APL carrying the atypical PML/RARA fusion signal due to a novel complex variant translocation t(15;16;17)(q22;q24;q21), as well as the classical PML/RARA fusion signal. Subsequent array comparative genomic hybridization revealed somatic, cryptic deletions on 3p25.3, 8q23.1 and 12p13.2-p13.1, and a duplication on 8q11.2; however, no genetic material loss or gain was observed in the breakpoint regions of chromosomes 15, 16 or 17. To the best of our knowledge, this is the first report of the coexistence of two abnormal clones, one classical and one variant, presenting simultaneously in addition to cryptic chromosome segmental imbalances in an adult APL patient.
PMCID: PMC4114661  PMID: 25120648
promyelocytic leukemia/retinoic acid α-receptor; array comparative genomic hybridization; variant translocation; acute promyelocytic leukemia; fluorescence in situ hybridization
7.  Fifty-four novel mutations in the NF1 gene and integrated analyses of the mutations that modulate splicing 
Neurofibromatosis type 1 (NF1) is a common autosomal dominant genetic disorder caused by mutations in the NF1 gene. One of the hallmarks of NF1 is the high mutation rate in this gene. In this study, we present 127 different NF1 mutations and 54 novel mutations detected at both the genomic DNA and mRNA level using a retrospective case series review. We found that 25.2% of these different mutations induced aberrant splicing. Of note, 40.6% of these splicing errors were caused by exonic variants. In addition, one mutation produced mosaicism in the post-transcriptional profile. However, studies investigating these splicing aberrations are limited. In order to better understand the pathogenicity of NF1 and to provide a more accurate interpretation in molecular diagnostic testing, combined computational analyses were employed to elucidate the underlying mechanisms of the variants modulating NF1 gene splicing.
PMCID: PMC4072343  PMID: 24789688
neurofibromatosis 1 gene; mutation; splicing error
8.  Identification of Novel Genomic Aberrations in AML-M5 in a Level of Array CGH 
PLoS ONE  2014;9(4):e87637.
To assess the possible existence of unbalanced chromosomal abnormalities and delineate the characterization of copy number alterations (CNAs) of acute myeloid leukemia-M5 (AML-M5), R-banding karyotype, oligonucelotide array CGH and FISH were performed in 24 patients with AML-M5. A total of 117 CNAs with size ranging from 0.004 to 146.263 Mb was recognized in 12 of 24 cases, involving all chromosomes other than chromosome 1, 4, X and Y. Cryptic CNAs with size less than 5 Mb accounted for 59.8% of all the CNAs. 12 recurrent chromosomal alterations were mapped. Seven out of them were described in the previous AML studies and five were new candidate AML-M5 associated CNAs, including gains of 3q26.2-qter and 13q31.3 as well as losses of 2q24.2, 8p12 and 14q32. Amplication of 3q26.2-qter was the sole large recurrent chromosomal anomaly and the pathogenic mechanism in AML-M5 was possibly different from the classical recurrent 3q21q26 abnormality in AML. As a tumor suppressor gene, FOXN3, was singled out from the small recurrent CNA of 14q32, however, it is proved that deletion of FOXN3 is a common marker of myeloid leukemia rather than a specific marker for AML-M5 subtype. Moreover, the concurrent amplication of MLL and deletion of CDKN2A were noted and it might be associated with AML-M5. The number of CNA did not show a significant association with clinico-biological parameters and CR number of the 22 patients received chemotherapy. This study provided the evidence that array CGH served as a complementary platform for routine cytogenetic analysis to identify those cryptic alterations in the patients with AML-M5. As a subtype of AML, AML-M5 carries both common recurrent CNAs and unique CNAs, which may harbor novel oncogenes or tumor suppressor genes. Clarifying the role of these genes will contribute to the understanding of leukemogenic network of AML-M5.
PMCID: PMC3984075  PMID: 24727659
9.  The impact of the condenser on cytogenetic image quality in digital microscope system 
Optimizing operational parameters of the digital microscope system is an important technique to acquire high quality cytogenetic images and facilitate the process of karyotyping so that the efficiency and accuracy of diagnosis can be improved.
This study investigated the impact of the condenser on cytogenetic image quality and system working performance using a prototype digital microscope image scanning system.
Both theoretical analysis and experimental validations through objectively evaluating a resolution test chart and subjectively observing large numbers of specimen were conducted.
The results show that the optimal image quality and large depth of field (DOF) are simultaneously obtained when the numerical aperture of condenser is set as 60%~70% of the corresponding objective. Under this condition, more analyzable chromosomes and diagnostic information are obtained. As a result, the system shows higher working stability and less restriction for the implementation of algorithms such as autofocusing especially when the system is designed to achieve high throughput continuous image scanning.
Although the above quantitative results were obtained using a specific prototype system under the experimental conditions reported in this paper, the presented evaluation methodologies can provide valuable guidelines for optimizing operational parameters in cytogenetic imaging using the high throughput continuous scanning microscopes in clinical practice.
PMCID: PMC3748598  PMID: 23676284
Optimizing operational parameters; microscope condenser; image sharpness; resolution; depth of field (DOF); cytogenetic imaging
10.  Evaluations of auto-focusing methods under a microscopic imaging modality for metaphase chromosome image analysis 
Auto focusing is an important operation in high throughput imaging scanning. Although many autofocus methods have been developed and tested for a variety of imaging modalities, few investigations have been performed on the selection of an optimal auto-focusing method that is suitable for the pathological metaphase chromosome analysis under a high resolution scanning microscopic system.
The purpose of this study is to investigate and identify an optimal auto-focusing method for the pathological metaphase chromosome analysis.
In this study, five auto-focusing methods were applied and tested using metaphase chromosome images acquired from bone marrow and blood specimens. These methods were assessed by measuring a number of indices including execution time, accuracy, number of false maxima, and full width at half maximum (FWHM).
For the specific condition investigated in this study, the results showed that the Brenner gradient and threshold pixel counting methods were the optimal methods for acquiring high quality metaphase chromosome images from the bone marrow and blood specimens, respectively.
Selecting an optimal auto-focusing method depends on the specific clinical tasks. This study also provides useful information for the design and implementation of the high throughput microscopic image scanning systems in the future digital pathology.
PMCID: PMC3748595  PMID: 23629477
metaphase chromosome; autofocus technique
11.  Comparative genomic hybridization in a case of melanoma that loses expression of S100, HMB45, Melan A and tyrosinase in metastasis 
We recently reported three cases of metastatic melanoma that does not express S100, HMB45, Melan A and Tyrosinase. A concurrent cutaneous scalp primary melanoma was identified later in one of the cases, which showed strong expression of these markers. The difference in immunophenotype between the primary melanoma and its metastasis in the parotid gland in this case raised the question of the biological significance of the expression of these markers and metastatic potential. To address this question, we utilized microarray comparative genomic hybridization (aCGH) to compare the cytogenetic features between the primary and metastatic melanoma. We observed chromosomal gains including 6p, entire chromosome 7, and 8q11.1-q24.3 in both primary and metastatic tumors. However, the metastatic lesion showed unique additional copy of chromosomal 7q, and loss of chromosome 9p24.3-q13 and chromosome 4, which included Melan A encoding gene region in 9p24.1. The above findings suggest the unique cytogenetic changes in the parotid lesion are most likely related to the metastatic behavior, as well as responsible for loss of multiple melanocytic marker expression in the metastatic melanoma for this case.
PMCID: PMC3885509  PMID: 24427375
Melanoma; metastasis; cytogenetics; comparative genomic hybridization
12.  Potential clinical impact of three-dimensional visualization for fluorescent in situ hybridization image analysis 
Journal of Biomedical Optics  2012;17(5):050501.
Chromosomal translocation is strong indication of cancers. Fluorescent in situ hybridization (FISH) can effectively detect this translocation and achieve high accuracy in disease diagnosis and prognosis assessment. For this purpose, whole chromosome paint probes are utilized to image the configuration of DNA fragments. Although two-dimensional (2-D) microscopic images are typically used in FISH signal analysis, we present a case where the translocation occurs in the depth direction where two probed FISH signals are overlapped in the projected image plane. Thus, the translocation cannot be identified. However, when imaging the whole specimen with a confocal microscope at 27 focal planes with 0.5-μm step interval, the translocation can be clearly identified due to the free rotation capability by the three-dimensional (3-D) visualization. Such a translocation detection error of using 2-D images might be critical in detecting and diagnosing early or subtle disease cases where detecting a small number of abnormal cells can make diagnostic difference. Hence, the underlying implication of this report suggests that utilizing 3-D visualization may improve the overall accuracy of FISH analysis for some clinical cases. However, the clinical efficiency and cost of using 3-D versus 2-D imaging methods are also to be assessed carefully.
PMCID: PMC3381014  PMID: 22612116
fluorescent in situ hybridization; chromosome translocation; 3-D image visualization
13.  Sex chromosome Aneuploides among Men with Systemic Lupus Erythematosus 
Journal of Autoimmunity  2011;38(2-3):J129-J134.
About 90% of patients with systemic lupus erythematosus (SLE) are female. We hypothesize that the number of X chromosomes, not sex, is a determinate of risk of SLE. Number of X chromosomes was determined by single nucleotide typing and then confirmed by karyotype or fluorescent in situ hybridization in a large group of men with SLE. Presence of an sry gene was assessed by rtPCR. We calculated 96% confidence intervals using the Adjusted Wald method, and used Bayes’ theorem to estimate the prevalence of SLE among 47,XXY and 46,XX men. Among 316 men with SLE, 7 had 47,XXY and 1 had 46,XX. The rate of Klinefelter’s syndrome (47,XXY) was statistically different from that found in control men and from the known prevalence in the population. The 46,XX man had an sry gene, which encodes the testes determining factor, on an X chromosome as a result of an abnormal crossover during meiosis. In the case of 46,XX, 1 of 316 was statistically different from the known population prevalence of 1 in 20,000 live male births. A previously reported 46,XX man with SLE had a different molecular mechanism in which there were no common gene copy number abnormalities with our patient. Thus, men with SLE are enriched for conditions with additional X chromosomes. Especially since 46,XX men are generally normal males, except for infertility, these data suggest the number of X chromosomes, not phenotypic sex, is responsible for the sex bias of SLE.
PMCID: PMC3309073  PMID: 22154021
Systemic lupus erythematosus; Klinefelter’s syndrome; male 46; XX; female bias; X chromosome
14.  Hypogonadotropic hypogonadism presenting with arhinia: a case report 
Arhinia, congenital absence of the nose, is a rare malformation. We present the third reported case of arhinia accompanied by hypogonadism and demonstrate that this is due to gonadotropin deficiency.
Case presentation
A 13-year-old Caucasian boy with congenital arhinia presented for evaluation of delayed puberty and micropenis. We examined genes known to be associated with hypogonadotropic hypogonadism for mutations and performed a chromosomal microarray to assess copy number variation.
No mutations in KAL1, FGFR1, PROK2, PROKR2, FGF8, CHD7 and GnRHR were identified in our patient and there were no copy number variations observed that would explain the phenotype. Though studies are limited in such patients, we suggest that hypogonadotropic hypogonadism is associated with arhinia and that the two entities likely result from a common genetic cause that affects early nasal development and gonadotropin-releasing hormone neuron formation or migration.
PMCID: PMC3599766  PMID: 23432817
15.  Trisomy 8: a common finding in mouse embryonic stem (ES) cell lines 
Obtaining a germ cell line is one of the most important steps in developing a transgenic or knockout mouse with a targeted mutated gene of interest. A common problem with this technology is that embryonic stem (ES) cells often lack, or are extremely inefficient at, germ line transmission.
To determine whether chromosomal anomalies are correlated with inefficient ES cell germ line transmission, we examined 97 constructed ES cell lines using conventional cytogenetic analysis, and fluorescence in situ hybridization (FISH). Chromosomal abnormalities occurred in 44 (45%) out of the 97 specimens analyzed: 31 specimens had trisomy 8 or mosaic trisomy 8, eight specimens had partial trisomy 8 resulting from unbalanced translocations, and five specimens had other chromosomal anomalies.
Our data suggest that chromosomal analysis is an important tool for improving the yield and quality of gene targeting experiments.
PMCID: PMC3564830  PMID: 23320952
Mouse ES cells; Chromosomal aberrations; FISH; Mosaicism
16.  Fluorescence in situ hybridization (FISH) signal analysis using automated generated projection images 
Fluorescence in situ hybridization (FISH) tests provide promising molecular imaging biomarkers to more accurately and reliably detect and diagnose cancers and genetic disorders. Since current manual FISH signal analysis is low-efficient and inconsistent, which limits its clinical utility, developing automated FISH image scanning systems and computer-aided detection (CAD) schemes has been attracting research interests. To acquire high-resolution FISH images in a multi-spectral scanning mode, a huge amount of image data with the stack of the multiple three-dimensional (3-D) image slices is generated from a single specimen. Automated preprocessing these scanned images to eliminate the non-useful and redundant data is important to make the automated FISH tests acceptable in clinical applications. In this study, a dual-detector fluorescence image scanning system was applied to scan four specimen slides with FISH-probed chromosome X. A CAD scheme was developed to detect analyzable interphase cells and map the multiple imaging slices recorded FISH-probed signals into the 2-D projection images. CAD scheme was then applied to each projection image to detect analyzable interphase cells using an adaptive multiple-threshold algorithm, identify FISH-probed signals using a top-hat transform, and compute the ratios between the normal and abnormal cells. To assess CAD performance, the FISH-probed signals were also independently visually detected by an observer. The Kappa coefficients for agreement between CAD and observer ranged from 0.69 to 1.0 in detecting/counting FISH signal spots in four testing samples. The study demonstrated the feasibility of automated FISH signal analysis applying a CAD scheme to the automated generated 2-D projection images.
PMCID: PMC3496037  PMID: 22935778
Fluorescence in situ hybridization (FISH); Automated FISH signal analysis; Computer-aided detection (CAD); Molecular imaging biomarker
17.  Characterization of novel RS1 exonic deletions in juvenile X-linked retinoschisis 
Molecular Vision  2013;19:2209-2216.
X-linked juvenile retinoschisis (XLRS) is a vitreoretinal dystrophy characterized by schisis (splitting) of the inner layers of the neuroretina. Mutations within the retinoschisis (RS1) gene are responsible for this disease. The mutation spectrum consists of amino acid substitutions, splice site variations, small indels, and larger genomic deletions. Clinically, genomic deletions are rarely reported. Here, we characterize two novel full exonic deletions: one encompassing exon 1 and the other spanning exons 4–5 of the RS1 gene. We also report the clinical findings in these patients with XLRS with two different exonic deletions.
Unrelated XLRS men and boys and their mothers (if available) were enrolled for molecular genetics evaluation. The patients also underwent ophthalmologic examination and in some cases electroretinogram (ERG) recording. All the exons and the flanking intronic regions of the RS1 gene were analyzed with direct sequencing. Two patients with exonic deletions were further evaluated with array comparative genomic hybridization to define the scope of the genomic aberrations. After the deleted genomic region was identified, primer walking followed by direct sequencing was used to determine the exact breakpoints.
Two novel exonic deletions of the RS1 gene were identified: one including exon 1 and the other spanning exons 4 and 5. The exon 1 deletion extends from the 5′ region of the RS1 gene (including the promoter) through intron 1 (c.(−35)-1723_c.51+2664del4472). The exon 4–5 deletion spans introns 3 to intron 5 (c.185–1020_c.522+1844del5764).
Here we report two novel exonic deletions within the RS1 gene locus. We have also described the clinical presentations and hypothesized the genomic mechanisms underlying these schisis phenotypes.
PMCID: PMC3820431  PMID: 24227916
18.  Development and Assessment of an Integrated Computer-Aided Detection Scheme for Digital Microscopic Images of Metaphase Chromosomes 
Journal of electronic imaging  2008;17(4):043008.
The authors developed an integrated computer-aided detection (CAD) scheme for detecting and classifying metaphase chromosomes as well as assessing its performance and robustness. This scheme includes an automatic metaphase-finding module and a karyotyping module and it was applied to a testing database with 200 digital microscopic images. The automatic metaphase-finding module detects analyzable metaphase cells using a feature-based artificial neural network (ANN). The ANN-generated outputs are analyzed by a receiver operating characteristics (ROC) method and an area under the ROC curve is 0.966. Then, the automatic karyotyping module classifies individual chromosomes of this cell into 24 types. In this module, a two-layer decision tree-based classifier with eight ANNs established in its connection nodes was optimized by a genetic algorithm. Chromosomes are first classified into seven groups by the ANN in the first layer. The chromosomes in these groups are then separately classified by seven ANNs into 24 types in the second layer. The classification accuracy is 94.5% in the first layer. Six ANNs achieved the accuracy above 95% and only one had lessened performance (80.6%) in the second layer. The overall classification accuracy is 91.5% as compared to 86.7% in the previous study using two independent datasets randomly acquired from our genetic laboratory. The results demonstrate that our automated scheme achieves high and robust performance in identification and classification of metaphase chromosomes.
PMCID: PMC3475421  PMID: 23087585
Metaphase chromosome; Karyotype; Computer-aided detection; Artificial neural network; Receiver operating characteristics
19.  Loss of fragile histidine triad and amplification of 1p36.22 and 11p15.5 in primary gastric adenocarcinomas 
AIM: To investigate the genomic copy number alterations that may harbor key driver genes in gastric tumorigenesis.
METHODS: Using high-resolution array comparative genomic hybridization (CGH), we investigated the genomic alterations of 20 advanced primary gastric adenocarcinomas (seventeen tubular and three mucinous) of Chinese patients from the Jilin province. Ten matching adjacent normal regions from the same patients were also studied.
RESULTS: The most frequent imbalances detected in these cancer samples were gains of 3q26.31-q27.2, 5p, 8q, 11p, 18p, 19q and 20q and losses of 3p, 4p, 18q and 21q. The use of high-resolution array CGH increased the resolution and sensitivity of the observed genomic changes and identified focal genetic imbalances, which included 54 gains and 16 losses that were smaller than 1 Mb in size. The most interesting focal imbalances were the intergenic loss/homozygous deletion of the fragile histidine triad gene and the amplicons 11q13, 18q11.2 and 19q12, as well as the novel amplicons 1p36.22 and 11p15.5.
CONCLUSION: These regions, especially the focal amplicons, may harbor key driver genes that will serve as biomarkers for either the diagnosis or the prognosis of gastric cancer, and therefore, a large-scale investigation is recommended.
PMCID: PMC3435777  PMID: 22969225
Array comparative genomic hybridization; Amplicon; Gastric adenocarcinoma; Oncogene; Fragile histidine triad
20.  Generation and characterization of a highly effective protein substrate for analysis of FLT3 activity 
Gain-of-function mutations of tyrosine kinase FLT3 are frequently found in acute myeloid leukemia (AML). This has made FLT3 an important marker for disease diagnosis and a highly attractive target for therapeutic drug development. This study is intended to generate a sensitive substrate for assays of the FLT3 enzymatic activity.
We expressed in Escherichia coli cells a glutathione S-transferase (GST) fusion protein designated GST-FLT3S, which contains a peptide sequence derived from an autophosphorylation site of FLT3. The protein was used to analyze tyrosine kinase activity of baculovirus-expressed FLT3 and crude cell extracts of bone marrow cells from AML patients. It was also employed to perform FLT3 kinase assays for FLT3 inhibitor screening.
GST-FLT3S in solution or on beads was strongly phosphorylated by recombinant proteins carrying the catalytic domain of wild type FLT3 and FLT3D835 mutants, with the latter exhibiting much higher activity and efficiency. GST-FLT3S was also able to detect elevated tyrosine kinase activity in bone marrow cell extracts from AML patients. A small-scale inhibitor screening led to identification of several potent inhibitors of wild type and mutant forms of FLT3.
GST-FLT3S is a sensitive protein substrate for FLT3 assays. It may find applications in diagnosis of diseases related to abnormal FLT3 activity and in inhibitor screening for drug development.
PMCID: PMC3419602  PMID: 22800464
Tyrosine kinase; FLT3; Activity assay; Inhibitor screening; Acute myeloid leukemia
21.  Intravascular large B-cell lymphoma with hemophagocytic syndrome (Asian variant) in a Caucasian Patient 
Intravascular lymphoma is an aggressive and extremely rare extranodal lymphoma with neoplastic lymphoid cells confined exclusively within intravascular spaces. The histopathologic findings are subtle due to the rarity of the neoplastic cells in blood vessels. Clinical presentations are non-specific and focal space-occupying lesions or lymphoadenopathy are always lacking. It is a diagnostic challenge. Secondary hemophagocytic syndrome is uncommon and is typically associated with infection, malignancy, and suppressed immune states. Intravascular lymphoma has a strong association with hemophagocytic syndrome in Asian patients, the so-called "Asian variant", but not in Western patients. We report a case of intravascular B-cell lymphoma in a Caucasian patient associated with secondary hemophagocytic syndrome. The patient was diagnosed by core liver biopsy and successfully treated. This case demonstrates the importance of high index of suspicion and astute histopathologic examination in recognition of this unusual clinical and pathologic combination.
PMCID: PMC3396055  PMID: 22808298
Intravascular lymphoma; hemophagocytic syndrome; liver; Asian variant; hepatosplenomegaly
22.  Molecular cytogenetic characterization of undifferentiated embryonal sarcoma of the liver: a case report and literature review 
Undifferentiated embryonal sarcoma of the liver (UESL) represents a heterogeneous group of tumors derived from mesenchymal tissues. Earlier cytogenetic studies in limited cases demonstrated that UESL is associated with a recurrent translocation t(11;19)(q11;q13.3-q13.4) or add(19)(q13.4). In this report, we present our array comparative genomic hybridization (aCGH), fluorescence in situ hybridization (FISH) findings, and a missense mutation of TP53 gene by DNA sequencing in a 19-year-old patient with UESL. The data were compared to laboratory findings reported by previous studies.
PMCID: PMC3478990  PMID: 22551002
Undifferentiated embryonal sarcoma of the liver (UESL); Cytogenetic anomalies; FISH; aCGH; TP53 mutation
23.  Heterogeneity of primary glioblastoma cells in the expression of caspase-8 and the response to TRAIL-induced apoptosis 
Apoptosis  2011;16(11):1150-1164.
Recent studies suggest that cancer stem cells (CSCs) are responsible for cancer resistance to therapies. We therefore investigated how glioblastoma-derived CSCs respond to the treatment of tumor necrosis factor-related apoptosis-inducing ligand (TRAIL). Neurospheres were generated from glioblastomas, characterized for CSC properties including self-renewal, cell differentiation and xenograft formation capacity, and analyzed for TRAIL-induced apoptosis, CASP8 genomic status, and caspase-8 protein expression. The neurosphere NSC326 was sensitive to TRAIL-induced apoptosis as evidenced by cell death and caspase-8, -3, and -7 enzymatic activities. In contrast, however, the neurosphere NSC189 was TRAIL-resistant. G-banding analysis identified five chromosomally distinguishable cell populations in the neurospheres. Fluorescence in situ hybridization revealed the variation of chromosome 2 copy number in these populations and the loss of CASP8 locus in 2q33-34 region in a small set of cell populations in the neurosphere. Immunohistochemistry of NSC189 cell blocks revealed the lack of caspase-8 protein in a subset of neurosphere cells. Western blotting and immunohistochemistry of human glioblastoma tumors demonstrated the expression of caspase-8 protein in the vast majority of the tumors as compared to normal human brain tissues that lack the caspase-8 expression. This study shows heterogeneity of glioblastomas and derived CSCs in the genomic status of CASP8, expression of caspase-8, and thus responsiveness to TRAIL-induced apoptosis. Clinic trials may consider genomic analysis of the cancer tissue to identify the genomic loss of CASP8 and use it as a genomic marker to predict the resistance of glioblastomas to TRAIL apoptosis pathway-targeted therapies.
PMCID: PMC3257579  PMID: 21877214
Apoptosis; cancer stem cells; caspase-8; glioblastoma; TRAIL
24.  Expression of HPV16 E5 Produces Enlarged Nuclei and Polyploidy through Endoreplication 
Virology  2010;405(2):342-351.
Anogenital cancers and head and neck cancers are causally-associated with infection by high-risk human papillomavirus (HPV). The mechanism by which high-risk HPVs contribute to oncogenesis is poorly understood. HPV16 encodes three genes (HPV16 E5, E6, and E7) that can transform cells when expressed independently. HPV16 E6 and E7 have well-described roles causing genomic instability and unregulated cell cycle progression. The role of HPV16 E5 in cell transformation remains to be elucidated. Expression of HPV16 E5 results in enlarged, polyploid nuclei that are dependent on the level and duration of HPV16 E5 expression. Live-cell imaging data indicate these changes do not arise from cell-cell fusion or failed cytokinesis. The increase in nuclear size is a continual process that requires DNA synthesis. We conclude HPV16 E5 produces polyploid cells by endoreplication. These findings provide insight into how HPV16 E5 can contribute to cell transformation.
PMCID: PMC2923234  PMID: 20605566
25.  Trisomy chromosome 5 is a recurrent cytogenetic lesion in mammary tumors from parous MMTV-erbB-2 transgenic mice 
Oncology Letters  2011;2(6):1077-1081.
erbB-2 is amplified or overexpressed in approximately 30% of human breast cancers, and has been associated with poor prognosis and therapeutic resistance. Previous studies have suggested that erbB-2 overexpression in transgenic mice induces genomic instability; however, the patterns of genetic lesions vary with individual model systems. The development of mammary tumors in multiparous murine mammary tumor virus (MMTV)-erbB-2 transgenic mice is accelerated due to hormonal interactions which induce the overexpression of MMTV-mediated erbB-2. However, whether or not accelerated tumor development is associated with modified cytogenetic patterns remains to be determined. In this study, chromosomal changes were characterized in mammary tumor cells derived from multiparous MMTV-erbB-2 transgenic mice, and compared with tumor cells derived from control virgin mice. Immunohistochemistry and Western blotting were used to detect erbB-2 overexpression in mammary tissues. Each of the five tumors from the multiparous MMTV-erbB-2 transgenic mice was found to exhibit a marked chromosomal imbalance, compared with only one tumor with aberrant chromosomes among the five tumors from the control virgin mice. In particular, trisomy 5 and loss of the X chromosome were recurrent cytogenetic lesions in tumors from the parous mice, which is a novel pattern compared with previous studies. The elevated number of genetic lesions in tumors from parous mice, which were characterized by enhanced erbB-2 overexpression and increased receptor tyrosine kinase activation in the mammary glands, suggest a causal role for erbB-2 in the genomic instability present in these tumors. These data advance our understanding of erbB-2-mediated pathogenesis and underscore the role of cytogenetic alteration in this process.
PMCID: PMC3406573  PMID: 22848270
erbB-2/Neu; genomic instability; breast cancer; transgenic mouse model

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