Yun-Fai Chris Lau

[20] Suppression subtractive hybridization: A versatile method for identifying differentially expressed genes

Abstract A new and highly effective method, termed suppression subtractive hybridization (SSH), has been developed for the generation of subtracted cDNA libraries. It is based primarily on a technique called suppression PCR and combines normalization and subtraction in a single procedure. The normalization step equalizes the abundance of cDNAs within the target population and the subtraction step excludes the common sequences between the target and driver populations. As a result only one round of subtractive hybridization is needed and the subtracted library is normalized in terms of abundance of different cDNAs. It dramatically increases the probability of obtaining low-abundance differentially expressed cDNA and simplifies analysis of the subtracted library. The SSH technique is applicable to many molecular genetic and positional cloning studies for the identification of disease, developmental, tissue-specific, or other differentially expressed genes. This chapter provides detailed protocols for the generation of subtracted cDNA and differential screening of subtracted cDNA libraries. As a representative example we demonstrate the usefulness of the method by constructing a testis-specific cDNA library as well as using the subtracted cDNA mixture as a hybridization probe. Finally, we discuss the characteristics of subtracted libraries, the nature and level of background nondifferentially expressed clones in the libraries, as well as a procedure for the rapid identification of truly differentially expressed cDNA clones.

Pathobiological implications of the expression of markers of testicular carcinoma in situ by fetal germ cells

Several proteins, such as the placental/germ cell alkaline phosphatases (PLAPs), the stem cell factor receptor c‐KIT, and the transcriptional regulator and marker of pluripotency OCT3/4, have been found in both normal immature and malignant germ cells, known as carcinoma in situ/intratubular germ cell neoplasia unclassified (CIS/ITGCNU). In the present study, immunohistochemical methods were used to evaluate the expression of these markers in a series of male gonads from fetuses from the second and third trimesters, and neonates. In addition to these markers, the presence of VASA (a protein specific for the germ cell lineage), TSPY (the testis‐specific protein, Y‐encoded), and the proliferation index (Ki‐67 antigen) was analysed. All these proteins are reported to be present both during spermatogenesis and in CIS/ITGCNU. Positive staining for VASA with varying intensity was found in all germ cells, while TSPY was predominantly located in the prespermatogonial cells at all developmental ages. In contrast, the markers PLAP, c‐KIT, OCT3/4, and Ki‐67 were more frequent at earlier developmental stages and decreased gradually with time, although they could occasionally be detected in germ cells of neonates. These findings are in line with a declining number of gonocytes during fetal development, concomitant with an increase in the number of prespermatogonia. The latter have lost the immature germ cell phenotype. These findings are compatible with the hypothesis that CIS/ITGCNU arises from developmentally arrested germ cells, most likely primordial germ cells/gonocytes, at an early time point during intrauterine development. Copyright

Gonadoblastoma, Testicular and Prostate Cancers, and the TSPY Gene

The role of the Y chromosome in oncogenesis of human cancers has been somewhat controversial. Both gain and loss of the Y chromosome in different leukemia, lymphoma, and solid tumors have been reported (Abeliovich et al. 1994; Brothman 1997; Dave et al. 1996; Geburek et al. 1997; Jackson-Cook et al. 1996; Kirk et al. 1994; Konig et al. 1994; Mertens et al. 1997; Riske et al. 1994; Watanabe et al. 1996). Conceivably, both oncogenes and tumor-suppressor genes exist on this chromosome, and they may act at different points during tumorigenesis, particularly for cancers of male-specific organs, such as the testis and the prostate.

Expression of a candidate gene for the gonadoblastoma locus in gonadoblastoma and testicular seminoma

The gonadoblastoma locus on the Y chromosome (GBY) predisposes the dysgenetic gonads of XY females to develop in situ tumors. It has been mapped to a critical interval on the short arm and adjacent centromeric region on the Y chromosome. Currently there are five functional genes identified on the GBY critical region, thereby providing likely candidates for this cancer predisposition locus. To evaluate the candidacy of one of these five genes, testis-specific protein Y-encoded (TSPY), as the gene for GBY, expression patterns of TSPY in four gonadoblastoma from three patients were analyzed by immunohistochemistry using a TSPY specific antibody. Results from this study showed that TSPY was preferentially expressed in tumor germ cells of all gonadoblastoma specimens. Additional study on two cases of testicular seminoma demonstrated that TSPY was also abundantly expressed in all stages of these germ cell tumors. The present observations suggest that TSPY may either be involved in the oncogenesis of or be a useful marker for both types of germ cell tumors.

Regulation of monoamine oxidase A by the SRY gene on the Y chromosome

Monoamine oxidase A (MAO A), encoded by the X chromosome, catalyzes the oxidative deamination of monoamine neurotransmitters, such as serotonin, and plays a critically important role in brain development and functions. Abnormal MAO A activity has been implicated in several neuropsychiatric disorders, such as depression, autism, and attention deficit hyperactivity disorder, which show sexual dimorphism. However, the molecular basis for these disease processes is unclear. Recently, we found that MAO A was a putative target gene directly regulated by a transcription factor encoded by the sex‐determining region Y (SRY) gene located on the Y chromosome. We demonstrated that SRY activates both MAO A‐promoter and catalytic activities in a human male neuroblastoma BE(2)C cell line. A functional SRY‐binding site in the MAO A core promoter was identified and validated by electrophoretic mobility shift and chromatin immuno‐precipitation (ChIP) analyses. Coimmunoprecipitation and ChIP assays showed that SRY and Spl form a transcriptional complex and synergistically activate MAO A transcription. This is the first study demonstrating that the Y‐encoded transcription factor SRY is capable of regulating an X‐located gene, suggesting a novel molecular mechanism for sexual dimorphism in neural development, brain functions, and initiation/ progression of neural disorders associated with MAO A dysfunction.—Wu, J. B., Chen, K., Li, Y., Lau, Y.‐F. C., Shih, J. C. Regulation of monoamine oxidase A by the SRY gene on the Y chromosome. FASEB J. 23, 4029–4038 (2009). www.fasebj.org

Expression analysis of thirty one Y chromosome genes in human prostate cancer

Rapid advances in positional cloning studies have identified most of the genes on the human Y chromosome, thereby providing resources for studying the expression of its genes in prostate cancer. Using a semiquantitative reverse transcription–polymerase chain reaction (RT–PCR) procedure, we had examined the expression of the Y chromosome genes in a panel of prostate samples diagnosed with benign prostatic hyperplasia (BPH), low and/or high grade carcinoma, and the prostatic cell line, LNCaP, stimulated by androgen treatment. Results from this expression analysis of 31 of the 33 genes, isolated so far from the Y chromosome, revealed three types of expression patterns: i) specific expression in other tissues (e.g., AMELY, BPY1, BPY2, CDY, and RBM); ii) ubiquitous expression among prostate and control testis samples, similar to those of house‐keeping genes (e.g., ANT3, XE7,ASMTL, IL3RA, SYBL1, TRAMP, MIC2, DBY, RPS4Y, and SMCY); iii) differential expression in prostate and testis samples. The last group includes X‐Y homologous (e.g., ZFY, PRKY, DFFRY, TB4Y, EIF1AY, and UTY) and Y‐specific genes (e.g., SRY, TSPY, PRY, and XKRY). Androgen stimulation of the LNCaP cells resulted in up‐regulation of PGPL, CSFR2A, IL3RA, TSPY, and IL9R and down regulation of SRY, ZFY, and DFFRY. The heterogeneous and differential expression patterns of the Y chromosome genes raise the possibility that some of these genes are either involved in or are affected by the oncogenic processes of the prostate. The up‐ and down‐regulation of several Y chromosome genes by androgen suggest that they may play a role(s) in the hormonally stimulated proliferation of the responsive LNCaP cells. Mol. Carcinog. 27:308–321, 2000.

TSPY potentiates cell proliferation and tumorigenesis by promoting cell cycle progression in HeLa and NIH3T3 cells

BackgroundTSPY is a repeated gene mapped to the critical region harboring the gonadoblastoma locus on the Y chromosome (GBY), the only oncogenic locus on this male-specific chromosome. Elevated levels of TSPY have been observed in gonadoblastoma specimens and a variety of other tumor tissues, including testicular germ cell tumors, prostate cancer, melanoma, and liver cancer. TSPY contains a SET/NAP domain that is present in a family of cyclin B and/or histone binding proteins represented by the oncoprotein SET and the nucleosome assembly protein 1 (NAP1), involved in cell cycle regulation and replication.MethodsTo determine a possible cellular function for TSPY, we manipulated the TSPY expression in HeLa and NIH3T3 cells using the Tet-off system. Cell proliferation, colony formation assays and tumor growth in nude mice were utilized to determine the TSPY effects on cell growth and tumorigenesis. Cell cycle analysis and cell synchronization techniques were used to determine cell cycle profiles. Microarray and RT-PCR were used to investigate gene expression in TSPY expressing cells.ResultsOur findings suggest that TSPY expression increases cell proliferation in vitro and tumorigenesis in vivo. Ectopic expression of TSPY results in a smaller population of the host cells in the G2/M phase of the cell cycle. Using cell synchronization techniques, we show that TSPY is capable of mediating a rapid transition of the cells through the G2/M phase. Microarray analysis demonstrates that numerous genes involved in the cell cycle and apoptosis are affected by TSPY expression in the HeLa cells.ConclusionThese data, taken together, have provided important insights on the probable functions of TSPY in cell cycle progression, cell proliferation, and tumorigenesis.

Sry Associates with the Heterochromatin Protein 1 Complex by Interacting with a KRAB Domain Protein

Abstract In mammals, the SRY/Sry gene on the Y chromosome is necessary and sufficient for a bipotential gonad to develop into a testis, regardless of its chromosomal sex. The SRY/Sry gene encodes a protein that belongs to a high-mobility-group (HMG) box protein family and that has been postulated to modulate the expression of genes necessary for male gonadal differentiation. Using a yeast two-hybrid screen, we identified a novel protein containing only a Krüppel-associated box (KRAB) domain, which is hereafter named KRAB-O (KRAB Only), as an SRY-interacting protein. The KRAB-O protein is encoded by an alternatively spliced transcript from the Zfp208 locus that also produces another transcript coding for a KRAB-zinc finger protein, ZFP208. The interaction of the mouse SRY with KRAB-O was further confirmed by glutathione S-transferase pull-down assay and coimmunoprecipitation in transfected COS7 cells. The KRAB-O interaction domain in both the human and mouse SRY was mapped to the bridge region outside the HMG box. Indirect immunofluorescence and confocal microscopy show that the mouse SRY colocalizes with KRAB-O in nuclear dots in transiently transfected COS7 cells and primary fetal mouse gonadal cells. Using similar approaches, we demonstrate that KRAB-O interacts directly with KAP1 (KRAB-associated protein 1), the obligatory corepressor for KRAB domain proteins. Furthermore, we show that the mouse SRY is associated indirectly with KAP1 and heterochromatin protein 1 (HP1) through its interaction with KRAB-O, suggesting that the mouse SRY could use the KRAB-KAP1-HP1 organized transcriptional regulatory complex to regulate its yet-to-be-identified downstream target genes.

Gonadoblastoma locus and the TSPY gene on the human Y chromosome

The gonadoblastoma (GBY) locus is the only oncogenic locus on the human Y chromosome. It is postulated to serve a normal function in the testis, but could exert oncogenic effects in dysgenetic gonads of individuals with intersex and/or dysfunctional testicular phenotypes. Recent studies establish the testis-specific protein Y-encoded (TSPY) gene to be the putative gene for GBY. TSPY serves normal functions in male stem germ cell proliferation and differentiation, but is ectopically expressed in early and late stages of gonadoblastomas, testicular carcinoma in situ (the premalignant precursor for all testicular germ cell tumors), seminomas, and selected nonseminomas. Aberrant TSPY expression stimulates protein synthetic activities, accelerates cell proliferation, and promotes tumorigenicity in athymic mice. TSPY binds to type B cyclins, enhances an activated cyclin B-CDK1 kinase activity, and propels a rapid G(2)/M transition in the cell cycle. TSPY also counteracts the normal functions of its X-homologue, TSPX, which also binds to cyclin B and modulates the cyclin B-CDK1 activity to insure a proper G(2)/M transition in the cell cycle. Hence, ectopic expression and actions of the Y-located TSPY gene in incompatible germ cells, such as those in dysgenetic or ovarian environments and dysfunctional testis, disrupt the normal cell cycle regulation and predispose the host cells to tumorigenesis. The contrasting properties of TSPY and TSPX suggest that somatic cancers, such as intracranial germ cell tumors, melanoma, and hepatocellular carcinoma, with detectable TSPY expression could exhibit sexual dimorphisms in the initiation and/or progression of the respective oncogenesis.

Expression pattern of a gonadoblastoma candidate gene suggests a role of the Y chromosome in prostate cancer

The contribution of specific genes on the Y chromosome in the etiology of prostate cancer has been undefined. Genetic mapping studies have identified a gonadoblastoma locus on the human Y chromosome (GBY) that predisposes the dysgenetic gonads of XY sex-reversed patients to tumorigenesis. Recently a candidate gene, the testis-specific protein Y-encoded (TSPY) that resides on the GBY critical region, has been demonstrated to express preferentially in tumor cells in gonadoblastoma and testicular germ cell tumors. TSPY shares high homology to a family of cyclin B binding proteins and has been considered to possibly play a role in cell cycle regulation or cell division. To address the possible involvement of the TSPY gene in prostate cancer, both in situ mRNA hybridization and immunohistochemistry techniques were used to study the expression of this putative GBY gene in prostate specimens. Our results demonstrated that TSPY was expressed at low levels in normal epithelial cells and benign prostatic hyperplasia (BPH), but at elevated levels in tumor cells of prostate cancers at various degrees of malignancy. Sequence analysis of RT-PCR products obtained from both prostatic and testicular tissues using specific primers flanking the open reading frame of the TSPY mRNA revealed a complex pattern of RNA processing of the TSPY transcripts involving cryptic intron splicing and/or intron skipping. The variant transcripts encode a variety of polymorphic isoforms or shortened versions of the TSPY protein, some of which might possess different biochemical and/or functional properties. The abbreviated transcripts were more abundant in prostatic cancer tissues than the testicular ones. Although the exact nature of such variant TSPY transcripts and proteins is still unclear, their differential expression suggests that the TSPY gene may also be involved in the multi-step prostatic oncogenesis besides its putative role in gonadoblastoma and testicular seminoma.