Genes Frequently Coexpressed with Hoxc8 Pro-vide Insight into the Discovery of Target Genes

Myoung Hee Kim,Ruthala Kalyani,Ji-Yeon Lee,민혜현,Heejei Yoon 한국분자세포생물학회 2016 Molecules and cells Vol.39 No.5

Identifying Hoxc8 target genes is at the crux of under-standing the Hoxc8-mediated regulatory networks underlying its roles during development. However, identification of these genes remains difficult due to intrinsic factors of Hoxc8, such as low DNA binding specificity, context-dependent regulation, and unknown cofactors. Therefore, as an alternative, the present study attempted to test whether the roles of Hoxc8 could be inferred by simply analyzing genes frequently coexpressed with Hoxc8, and whether these genes include putative target genes. Using archived gene expression datasets in which Hoxc8 was differentially expressed, we identified a total of 567 genes that were positively coexpressed with Hoxc8 in at least four out of eight datasets. Among these, 23 genes were coexpressed in six datasets. Gene sets associated with extracellular matrix and cell adhesion were most significantly enriched, followed by gene sets for skeletal system development, morphogenesis, cell motility, and transcriptional regulation. In particular, transcriptional regulators, including paralogs of Hoxc8, known Hox co-factors, and transcriptional remodeling factors were enriched. We randomly selected Adam19, Ptpn13, Prkd1, Tgfbi, and Aldh1a3, and validated their coexpression in mouse embryonic tissues and cell lines following TGF-2 treatment or ectopic Hoxc8 expression. Except for Aldh1a3, all genes showed concordant expression with that of Hoxc8, suggesting that the coexpressed genes might include direct or indirect target genes. Collectively, we suggest that the coexpressed genes provide a resource for constructing Hoxc8-mediated regulatory networks.

Differential Expression of Hox Genes during Murine Liver Regeneration

Boyeon Youn,Hyoung Woo Park,Sung Goo Park,Myoung Hee Kim 한국유전학회 2007 Genes & Genomics Vol.29 No.4

In order to infer the Hox code during liver regeneration, Hox gene expression pattern was analyzed during liver regeneration after partial hepatectomy in mice. Total RNAs and proteins have been prepared from the liver tissues at various times after regeneration (0 h, 4 h, and 3 d) following partial hepatectomy. Using degenerate RT-PCR, cloning, and sequencing technique, expressed Hox genes were analyzed. The Hox genes belonging to the paralogous groups VIII, IX and X manifested themselves in a peculiar way during regeneration process with stage specific characteristics: Hox genes belonging to the paralogous groups IX and X were almost exclusively expressed during regeneration whereas the paralogous group VIII, especially Hoxb8 and -c8 were strongly expressed in normal liver. The proteom analysis revealed that almost 21% of the differentially expressed proteins (6 out of 29 differentially expressed protein spots) during liver regeneration turned out to be Hox genes. Furthermore, Hoxa10 and- d10 belonging to the AbdB type paralogous group X were upregulated during regeneration. These results altogether indicate that Hox genes seemed to be differentially expressed during murine liver regeneration at the transcriptional as well as translational level. Especially the Hox genes belonging to the paralogous group X such as Hoxa10 and Hoxd10 seemed to be a part of Hox code for the murine liver regeneration.

Genes Frequently Coexpressed with Hoxc8 Provide Insight into the Discovery of Target Genes

Kalyani, Ruthala,Lee, Ji-Yeon,Min, Hyehyun,Yoon, Heejei,Kim, Myoung Hee Korean Society for Molecular and Cellular Biology 2016 Molecules and cells Vol.39 No.5

Identifying Hoxc8 target genes is at the crux of understanding the Hoxc8-mediated regulatory networks underlying its roles during development. However, identification of these genes remains difficult due to intrinsic factors of Hoxc8, such as low DNA binding specificity, context-dependent regulation, and unknown cofactors. Therefore, as an alternative, the present study attempted to test whether the roles of Hoxc8 could be inferred by simply analyzing genes frequently coexpressed with Hoxc8, and whether these genes include putative target genes. Using archived gene expression datasets in which Hoxc8 was differentially expressed, we identified a total of 567 genes that were positively coexpressed with Hoxc8 in at least four out of eight datasets. Among these, 23 genes were coexpressed in six datasets. Gene sets associated with extracellular matrix and cell adhesion were most significantly enriched, followed by gene sets for skeletal system development, morphogenesis, cell motility, and transcriptional regulation. In particular, transcriptional regulators, including paralogs of Hoxc8, known Hox co-factors, and transcriptional remodeling factors were enriched. We randomly selected Adam19, Ptpn13, Prkd1, Tgfbi, and Aldh1a3, and validated their coexpression in mouse embryonic tissues and cell lines following $TGF-{\beta}2$ treatment or ectopic Hoxc8 expression. Except for Aldh1a3, all genes showed concordant expression with that of Hoxc8, suggesting that the coexpressed genes might include direct or indirect target genes. Collectively, we suggest that the coexpressed genes provide a resource for constructing Hoxc8-mediated regulatory networks.

개불에서 Hox 유전자의 동정 및 계통분석

신길상,이대희 순천향대학교 기초과학연구소 2004 순천향자연과학연구 논문집 Vol.10 No.2

An echiuriod species, Urechis unicinctus, was surveyed for Homeobox(Hox) genes using PCR with Homeobox-specific degenerate primers. We were able to identify five Hox genes. The results revealed that the five Hox genes were belonged to central group of body plan-genes in the echiuroid. Analyses in this work made it able to classify the five Hox genes comparatively and phylogenetically, and came to the conclusion that the echiuroid can be classified one of lophotrochozoan. The result may be the first report regarding sequence information and phylogenetic analysis of Hox genes in the echiuroid species.

Up-regulation of HOXB cluster genes are epigenetically regulated in tamoxifen-resistant MCF7 breast cancer cells

( Seoyeon Yang ),( Ji-yeon Lee ),( Ho Hur ),( Ji Hoon Oh ),( Myoung Hee Kim ) 생화학분자생물학회(구 한국생화학분자생물학회) 2018 BMB Reports Vol.51 No.9

Tamoxifen (TAM) is commonly used to treat estrogen receptor (ER)-positive breast cancer. Despite the remarkable benefits, resistance to TAM presents a serious therapeutic challenge. Since several HOX transcription factors have been proposed as strong candidates in the development of resistance to TAM therapy in breast cancer, we generated an in vitro model of acquired TAM resistance using ER-positive MCF7 breast cancer cells (MCF7-TAMR), and analyzed the expression pattern and epigenetic states of HOX genes. HOXB cluster genes were uniquely up-regulated in MCF7-TAMR cells. Survival analysis of in slico data showed the correlation of high expression of HOXB genes with poor response to TAM in ER-positive breast cancer patients treated with TAM. Gain- and loss-of-function experiments showed that the overexpression of multi HOXB genes in MCF7 renders cancer cells more resistant to TAM, whereas the knockdown restores TAM sensitivity. Furthermore, activation of HOXB genes in MCF7-TAMR was associated with histone modifications, particularly the gain of H3K9ac. These findings imply that the activation of HOXB genes mediate the development of TAM resistance, and represent a target for development of new strategies to prevent or reverse TAM resistance. [BMB Reports 2018; 51(9): 450-455]

흰쥐에서 임신 중 레티노산이 입천장 형태발생에 미치는 영향

정명섭(Meang Sub Cheng),유병기(Byoung Ki Yoo),박형우(Hyoung Woo Park),김명희(Myoung Hee Kim) 대한해부학회 2006 Anatomy & Cell Biology Vol.39 No.4

흰쥐 입천장발생은 배자 발생 14일에서 17일까지 입천장선반 (palatal shelves)이 아래쪽으로 성장하고 16일에 혀 위쪽으로 이동하여 중앙을 중심으로 병합하여 17일에는 완전한 입천장이 형성된다. 레티노산은 비타민 A의 생체 내 활성 대사산물로써 발생에서 배자의 앞뒤축 형성 등에 관여하는데, 이런 레티노산에 과다히 노출∙결핍 시에는 기형이 유발되고, 배자 축 형성에 관여하는 Hox 유전자의 발현 또한 조절한다고 알려져 있다. 본 연구는 임신중 레티노산이 입천장 형태발생에 미치는 영향을 보기위하여 임신 11일째 흰쥐에 레티노산을 복강내주사로 주입하고 발생 13일부터 17일까지의 배자를 분리한 후 배자의 형태를 분석하고 또 형태형성에 관여하는 Hox와 Bcl-2 family 유전자를 포함하여 레티노산에 의해 차등 발현하는 유전자를 (DD) RT-PCR방법을 이용하여 분석하였다. 실험 결과 레티노산에 노출된 실험군 배자의 경우 정상군에 비해 머리 발생 지연을 포함하여 머리-엉덩 길이와 사지 등의 길이가 짧았다. 또 발생 17일째에는 정상군에서는 완전한 입천장이 형성되었으나 실험군에서는 총 52예의 배자 중 36예에서 입천장갈림증이 관찰되었으며, 입천장갈림증 간격은 약 0.80±0.36 mm이었다. DDRT-PCR 결과 레티노산 투여로 인해 차등발현하는 유전자들이 많이 존재함이 관찰되었다. Hoxa7 유전자는 정상군에서는 발생 13일째에 그러나 레티노산 투여군에서는 발생 15일째에 강하게 발현한 후 점차 감소한 반면 Hoxc8은 발현이 거의 감지되지 않았으나 정상군에서는 발생 16일째에서 그리고 레티노산 투여군에서는 15일째에서 아주 약한 발현이 감지되었다. Bcl-2 family 유전자의 경우 정상군에서는 발생 13일에서 17일까지 Bclxl과 Bcl-2 유전자, 그리고 Bax 유전자 모두 강하게 발현하였으나, 실험군의 경우 Bcl-xl과 Bcl-2의 발현이 발생 16일 이후에는 감소한 반면 Bax의 경우는 발생 13일에서 15일까지 매우 저하되었다. 이상의 결과로 임신중 레티노산 노출이 배자 발생과정 중 입천장갈림증을 포함한 형태적 기형유발을 가능하게 하는 물질임을 알 수 있었으며, 또 배자의 형태 발생에 관련된 Hox 유전자와 세포사멸 관련 유전자인 Bcl-xl, Bcl-2, 그리고 Bax 유전자의 발현을 조절하여 배자, 특히 입천장의 형태 기형 유발에 관여한 것으로 유추된다. In order to understand the effect of retinoic acid (RA) on the craniofacial pattern formation during embryogenesis, we injected RA intraperitoneally into the pregnant female rat on day 11 post coitum (p.c.) and then embryos of day 13 to day 17 p.c. were isolated consequently. The overall morphology and the differential gene expression patterns were analyzed by the microscopic and (DD) RT-PCR methods, respectively. For the morphological study, the retardation of craniofacial region, the shortage of crown rump length and limbs were analyzed in the RA-treated embryos. In the RA-treated embryos of day 17, it was observed that the palatogenesis was completely finished just like in the normal embryos. However, the cleft plate was observed in 36 out of 52 total samples with the distance of cleft palate being 0.80±0.36 mm in average. The temporal expression pattern of Hox genes through RT-PCR revealed that the expression of Hoxa7 reached its peak on day 13 then slowly declined in the normal embryos. Whereas in the RA-treated embryos, the expression peak was observed on day 15, then declined subsequently. With the Hoxc8 gene, its expression was low in all stages until the day 16 of normal embryogenesis. On the other hand, Hoxc8 gene expression was detected slightly early on day 15 in the RA-treated embryos. In the study of Bcl-2 family genes, uniformly strong expression of anti-apoptotic and pro-apoptotic genes was observed from day 13 to day 17 of normal embryos, whereas anti-apoptotic gene expressions were decreased after day 16 in the RAtreated embryos. Additionally, a dramatic decline of pro-apoptotic gene expression was observed from day 13 to day 15 of the RA-treated embryos. Therefore, we believe that RA is a potential factor that is actively involved in the cleft palate formation. Moreover, it is profoundly linked with the regulation of Hox and Bcl-2 family gene expression pattern that leads to the embryonic malformation.

A Study of Hox Gene Expression Profile During Murine Liver Regeneration

Youn, Boyeon,Kim, Byung-Gyu,Kim, Myoung Hee 대한의생명과학회 2003 Biomedical Science Letters Vol.9 No.1

Liver is an organ having an ability to regenerate by itself when it is damaged or removed. Since the research on the liver regeneration so far was regarding on the cellular multiplications not the formation of the shape, we intended to analyze the expression pattern of Hox genes during liver regeneration. RNA samples isolated from liver at the time of partial hepatectomy, 4 hours as well as 3 days later following regeneration were used to perform RT-PCR with Hox-specific degenerate primers. The PCR products were cloned, sequenced and analyzed through BLAST program, Genes belonging to the AbdB type Hox genes (paralogous groups IX-XIII)expressed predominantly during regeneration, while the other group (I-VII), especially Hoxal and b1 seemed to be expressed continuously before and after regeneration. These data altogether imply that paralogous group IX and X genes including Hoxa10 and d10 seemed to be regeneration specific genes of liver.

Chromatin organization and transcriptional activation of Hox genes

Ji-Yeon Lee,Hyehyun Min,Xinnan Wang,Abdul Aziz Khan,Myoung Hee Kim 대한해부학회 2010 Anatomy & Cell Biology Vol.43 No.1

Spatially and temporally programmed expression of the Hox genes along the antero-posterior (A-P) axis is essential for correct pattern formation during embryonic development. An accumulating body of evidence indicates the pivotal role of spatial chromatin organization for the coordination of gene regulation. Recently, chromosome conformation capture (3C) technique has been developed and opened a new way to study chromosomal interactions in the nucleus. In this study, we describe 3C method we applied in F9 embryonic teratocarcinoma cells and demonstrate that the chromosomal interactions at Hox loci are successfully detected. Interestingly, at Hoxc loci, the abundance of intrachromosomal interactions with neighboring fragments was drastically decreased when the genes are expressed. These results indicate the possibility of the dynamic pattern of chromosomal interaction in association with the transcriptional regulation of Hox genes.

HOXA9 is Underexpressed in Cervical Cancer Cells and its Restoration Decreases Proliferation, Migration and Expression of Epithelial-to-Mesenchymal Transition Genes

Alvarado-Ruiz, Liliana,Martinez-Silva, Maria Guadalupe,Torres-Reyes, Luis Alberto,Pina-Sanchez, Patricia,Ortiz-Lazareno, Pablo,Bravo-Cuellar, Alejandro,Aguilar-Lemarroy, Adriana,Jave-Suarez, Luis Feli Asian Pacific Journal of Cancer Prevention 2016 Asian Pacific journal of cancer prevention Vol.17 No.3

HOX transcription factors are evolutionarily conserved in many different species and are involved in important cellular processes such as morphogenesis, differentiation, and proliferation. They have also recently been implicated in carcinogenesis, but their precise role in cancer, especially in cervical cancer (CC), remains unclear. In this work, using microarray assays followed by the quantitative polymerase chain reaction (qPCR), we found that the expression of 25 HOX genes was downregulated in CC derived cell lines compared with non-tumorigenic keratinocytes. In particular, the expression of HOXA9 was observed as down-modulated in CC-derived cell lines. The expression of HOXA9 has not been previously reported in CC, or in normal keratinocytes of the cervix. We found that normal CC from women without cervical lesions express HOXA9; in contrast, CC cell lines and samples of biopsies from women with CC showed significantly diminished HOXA9 expression. Furthermore, we found that methylation at the first exon of HOXA9 could play an important role in modulating the expression of this gene. Exogenous restoration of HOXA9 expression in CC cell lines decreased cell proliferation and migration, and induced an epithelial-like phenotype. Interestingly, the silencing of human papilloma virus (HPV) E6 and E7 oncogenes induced expression of HOXA9. In conclusion, controlling HOXA9 expression appears to be a necessary step during CC development. Further studies are needed to delineate the role of HOXA9 during malignant progression and to afford more insights into the relationship between downmodulation of HOXA9 and viral HPV oncoprotein expression during cercical cancer development.

Effects of Dexamethasone on Embryo Development and Hox Gene Expression Patterns in Mice

Sang Hoon Kim,Ji-Yeon Lee,Sung Joo Park,Myoung Hee Kim 대한의생명과학회 2011 Biomedical Science Letters Vol.17 No.3

During pregnancy, stress induces maternal glucocorticoid secretion, which in turn is known to affect structural malformation, retardation of growth, reduced birth weight of the fetus. As Hox genes are master transcription factors which fulfill critical roles in embryonic development, we aimed to explore the possibility that alterations of the Hox gene expression might be involved in stress-induced malformation. The pregnant mice were injected with dexamethasone at a dose of 1 mg/kg or 10 mg/kg on day 7.5, 8.5 and 9.5 p.c. (post coitum), as well as saline as control. Embryos of E11.5 and E18.5 were obtained by sacrificing pregnant animals. Weight and crown-rump length (CRL) were measured. RT-PCR was performed to examine the Hox gene expression levels. Embryos given dexamethasone at day 7.5~9.5 p.c. had small CRL and weighed less both in E11.5 and E18.5. The percentage of embryos showing abnormalities was high in groups received high dose of dexamethasone. To define the molecular basis for abnormal embryonic development, we analyzed the Hox gene expression pattern and found that many Hox genes display altered expression. Effects of prenatal dexamethasone treatment on embryonic development might be associated with the aberrant Hox gene expression.