Identification, mapping, and phylogenomic analysis of four new human members of the T-box gene family: EOMES, TBX6, TBX18, and TBX19

Molecular Basis of Müllerian Agenesis Causing Congenital Uterine Factor Infertility-A Systematic Review

Infertility affects around 1 in 5 couples in the world. Congenital absence of the uterus results in absolute infertility in females. Müllerian agenesis is the nondevelopment of the uterus. Mayer-Rokitansky-Küster-Hauser (MRKH) syndrome is a condition of uterovaginal agenesis in the presence of normal ovaries and the 46 XX Karyotype. With advancements in reproductive techniques, women with MA having biological offspring is possible. The exact etiology of MA is unknown, although several genes and mechanisms affect the development of Müllerian ducts. Through this systematic review of the available literature, we searched for the genetic basis of MA. The aims included identification of the genes, chromosomal locations, changes responsible for MA, and fertility options, in order to offer proper management and counseling to these women with MA. A total of 85 studies were identified through searches. Most of the studies identified multiple genes at various locations, although the commonest involved chromosomes 1, 17, and 22. There is also conflicting evidence of the involvement of various candidate genes in the studies. The etiology of MA seems to be multifactorial and complex, involving multiple genes and mechanisms including various mutations and mosaicism.

Mutations in the TBX15-ADAMTS2 pathway associate with a novel soft palate dysplasia

We reported de novo variants in specific exons of the TBX15 and ADAMTS2 genes in a hitherto undescribed class of patients with unique craniofacial developmental defects. The nine unrelated patients represent unilateral soft palate hypoplasia, lost part of the sphenoid bone in the pterygoid process, but the uvula developed completely. Interestingly, these clinical features are contrary to the palate's anterior-posterior (A-P) developmental direction. Based on developmental characteristics, we suggested that these cases correspond to a novel craniofacial birth defect different from cleft palate, and we named it soft palate dysplasia (SPD). However, little is known about the molecular mechanism of the ADAMTS2 and TBX15 genes in the regulation of soft palate development. Phylogenetic analysis showed that the sequences around these de novo mutation sites are conserved between species. Through cellular co-transfections and chromatin immunoprecipitation assays, we demonstrate that TBX15 binds to the promoter regions of the ADAMTS2 gene and activates the promoter activity. Furthermore, we show that TBX15 and ADAMTS2 are colocalization in the posterior palatal mesenchymal cells during soft palate development in E13.5 mice embryos. Based on these data, we propose that the disruption of the TBX15-ADAMTS2 signaling pathway during embryogenesis leads to a novel SPD.

Influence of Genetic Polymorphisms on Clinical Outcomes of Glatiramer Acetate in Multiple Sclerosis Patients

Multiple sclerosis (MS) is a chronic, inflammatory, demyelinating disease of autoimmune origin, in which inflammation and demyelination lead to neurodegeneration and progressive disability. Treatment is aimed at slowing down the course of the disease and mitigating its symptoms. One of the first-line treatments used in patients with MS is glatiramer acetate (GA). However, in clinical practice, a response rate of between 30% and 55% is observed. This variability in the effectiveness of the medication may be influenced by genetic factors such as polymorphisms in the genes involved in the pathogenesis of MS. Therefore, this review assesses the impact of genetic variants on the response to GA therapy in patients diagnosed with MS. The results suggest that a relationship exists between the effectiveness of the treatment with GA and the presence of polymorphisms in the following genes: CD86, CLEC16A, CTSS, EOMES, MBP, FAS, TRBC1, IL1R1, IL12RB2, IL22RA2, PTPRT, PVT1, ALOX5AP, MAGI2, ZAK, RFPL3, UVRAG, SLC1A4, and HLA-DRB1*1501. Consequently, the identification of polymorphisms in these genes can be used in the future as a predictive marker of the response to GA treatment in patients diagnosed with MS. Nevertheless, there is a lack of evidence for this and more validation studies need to be conducted to apply this information to clinical practice.

Gene Expression Profiles Analyzed Using Integrating RNA Sequencing, and Microarray Reveals Increased Inflammatory Response, Proliferation, and Osteoclastogenesis in Pigmented Villonodular Synovitis

Background

Pigmented villonodular synovitis (PVNS) is a rare condition that involves benign proliferation of the synovial tissue and is characterized by severe joint destruction and high recurrence even after surgical resection. However, poor understanding of the pathogenesis limits its effective therapy.

Method

In this study, gene expression profiles of six patients with PVNS, 11 patients with osteoarthritis (OA), nine patients with rheumatoid arthritis (RA) (E-MTAB-6141), and three healthy subjects (GSE143514) were analyzed using integrating RNA sequencing (RNA-seq) and microarray to investigate the PVNS transcriptome. Gene ontology, string, and cytoscape were used to determine the gene functional enrichment. Cell functional molecules were detected using flow cytometry or immunohistochemical test to identify the cell subset and function. CD14⁺ cells were isolated and induced to osteoclast to evaluate the monocyte/macrophage function.

Results

The most obvious local manifestations of PVNS were inflammation, including increased immune cells infiltration and cytokine secretion, and tumor phenotypes. High proportion of inflammatory cells, including T cells, natural killer (NK) cells, NKT cells, and B cells were recruited from the blood. Th17 and monocytes, especially classical monocytes but not nonclassical monocytes, increased in PVNS synovium. An obvious increase in osteoclastogenesis and macrophage activation was observed locally. Elevated expression of MMP9, SIGLEC 15, and RANK were observed in myeloid cell of PVNS than OA. When compared with RA, osteoclast differentiation and myeloid cell activation are PVNS-specific characters, whereas T cell activation is shared by PVNS and RA.

Conclusion

The transcriptional expression characteristics of PVNS showed increased immune response, cell migration, and osteoclastogenesis. Osteoclast differentiation is only observed in PVNS but not RA, whereas T-cell activation is common in inflammatory arthritis.

Eomesodermin in CD4+T cells is essential for Ginkgolide K ameliorating disease progression in experimental autoimmune encephalomyelitis

Eomesodermin (Eomes), a transcription factor, could suppress the Th17 cell differentiation and proliferation through directly binding to the promoter zone of the Rorc and Il17a gene, meanwhile the expression of Eomes is suppressed when c-Jun directly binds to its promoter zone. Ginkgolide K (1,10-dihydroxy-3,14-didehydroginkgolide, GK) is a diterpene lactone isolated from the leaves of Ginkgo biloba. A previous study indicated that GK could decrease the level of phospho JNK (c-Jun N-terminal kinase). Here, we reported the therapeutic potential of Ginkgolide K (GK) treatment to ameliorate experimental autoimmune encephalomyelitis (EAE) disease progression. Methods: EAE was induced in both wildtype and CD4-Eomes conditional knockout mice. GK was injected intraperitoneally. Disease severity, inflammation, and tissue damage were assessed by clinical evaluation, flow cytometry of mononuclear cells (MNCs), and histopathological evaluation. Dual-luciferase reporter assays were performed to measure Eomes transcription activity in vitro. The potency of GK (IC50) was determined using JNK1 Kinase Enzyme System. Results: We revealed that GK could ameliorate EAE disease progression by the inhibition of the Th17 cells. Further mechanism studies demonstrated that the level of phospho JNK was decreased and the level of Eomes in CD4+T cells was dramatically increased. This therapeutic effect of GK was almost completely interrupted in CD4-Eomes conditional knockout mice. Conclusions: These results provided the therapeutic potential of GK treatment in EAE, and further suggested that Eomes expression in CD4+T cells might be essential in this process.

Inherited variants at 3q13.33 and 3p24.1 are associated with risk of diffuse large B-cell lymphoma and implicate immune pathways

We previously identified five single nucleotide polymorphisms (SNPs) at four susceptibility loci for diffuse large B-cell lymphoma (DLBCL) in individuals of European ancestry through a large genome-wide association study (GWAS). To further elucidate genetic susceptibility to DLBCL, we sought to validate two loci at 3q13.33 and 3p24.1 that were suggestive in the original GWAS with additional genotyping. In the meta-analysis (5662 cases and 9237 controls) of the four original GWAS discovery scans and three replication studies, the 3q13.33 locus (rs9831894; minor allele frequency [MAF] = 0.40) was associated with DLBCL risk [odds ratio (OR) = 0.83, P = 3.62 × 10-13]. rs9831894 is in linkage disequilibrium (LD) with additional variants that are part of a super-enhancer that physically interacts with promoters of CD86 and ILDR1. In the meta-analysis (5510 cases and 12 817 controls) of the four GWAS discovery scans and four replication studies, the 3p24.1 locus (rs6773363; MAF = 0.45) was also associated with DLBCL risk (OR = 1.20, P = 2.31 × 10-12). This SNP is 29 426-bp upstream of the nearest gene EOMES and in LD with additional SNPs that are part of a highly lineage-specific and tumor-acquired super-enhancer that shows long-range interaction with AZI2 promoter. These loci provide additional evidence for the role of immune function in the etiology of DLBCL, the most common lymphoma subtype.

TBX2 overexpression promotes proliferation and invasion through epithelial-mesenchymal transition and ERK signaling pathway

The present study aimed to clarify the clinical significance and biological effects of T-box (TBX)2 and its potential mechanism in gastric cancer (GC). TBX2 protein expression levels in human GC tissues were investigated using immunohistochemistry, and it was demonstrated that TBX2 was overexpressed in 55.9% (90/161) GC samples. TBX2 overexpression correlated with tumor invasion, advanced tumor node metastasis stage and presence of lymph node metastasis. In addition, TBX2 correlated with poor patient survival. To investigate the effect of TBX2 on biological behaviors, TBX2 plasmid transfection was performed in SGC-7901 cells and TBX2 small interfering RNA knockdown was carried out in BGC-823 cells. MTT and matrigel invasion assays demonstrated that TBX2 overexpression promoted proliferation and invasion, whereas TBX2 depletion inhibited proliferation and invasion. TBX2 overexpression also promoted epithelial-mesenchymal transition by downregulating E-cadherin and upregulating N-cadherin. TBX2 overexpression also upregulated matrix metalloproteinase (MMP)2, MMP9, cyclin E and phosphorylated-extracellular signal regulated kinase levels, however downregulated p21. In conclusion, TBX2 may serve as an effective predictor and therapeutic target in human GC.

TBX19 is overexpressed in colorectal cancer and associated with lymph node metastasis

The T-box 19 (TBX19) gene encodes a transcription factor characterized by a highly conserved DNA-binding motif (T-box). Recent studies have revealed that TBX19 has been identified as one of the genes activated by KRAS mutations, and is upregulated in colon adenoma. These results indicate that TBX19 may work as an oncogene in colorectal cancer (CRC). However, the expression and role of TBX19 have yet to be investigated. Here, we investigated TBX19 mRNA and protein expressions in colon cancer cells or surgically resected CRC. We found that TBX19 mRNA expression was significantly increased in tumorous tissues compared to that in non-tumorous tissues, and increased TBX19 mRNA expression was associated with positive lymph node metastasis in our cohort. The expression of TBX19 mRNA was not correlated with that of TBX19 protein in tissue sample taken from the CRC patients. Moreover, TBX19 showed positive staining even in the normal colonic tissues and the adjacent non-tumorous tissues. These results suggest that the expression of TBX19 protein is not correlated with the expression of TBX19 mRNA. In addition, our results promote further investigations into the impact of TBX19 upregulation on colorectal carcinogenesis, as well as the underlying mechanisms.

Recent advances in the molecular mechanisms of Mayer-Rokitansky-Küster-Hauser syndrome

Mayer-Rokitansky-Küster-Hauser syndrome (MRKHS) is a disease caused by congenital absence of the uterus and two-thirds of the upper vagina. The pathogenic mechanism of MRKHS may involve gene abnormalities, and there are various case reports associating MRKHS with the Wnt family member 4 (Wnt4) mutation. Analysis of genes mapped to regions in which deletion and duplication are frequently detected in patients with MRKHS has shown involvement of LIM homeobox 1 (LHX1), HNF1 homeobox B (HNF1B) and T-box 6 (TBX6). In addition, there are case reports of MRKHS caused by chromosomal translocation and epigenetic function may be involved in MRKHS onset. Overexpression of HOXA and overexposure to estrogen may contribute to the onset and regulation of expression by methylation as a pathogenic mechanism. Determination of the molecular basis of MRKHS is in progress, but current treatment only includes vaginal enlargement and vaginoplasty for improved quality of life. Clinical application of uterine transplantation to allow childbearing by MRKHS patients is under investigation and clinical trials are underway around the world.

Genomic analysis reveals selection in Chinese native black pig

Identification of genomic signatures that help reveal mechanisms underlying desirable traits in domesticated pigs is of significant biological, agricultural and medical importance. To identify the genomic footprints left by selection during domestication of the Enshi black pig, a typical native and meat-lard breed in China, we generated about 72-fold coverage of the pig genome using pools of genomic DNA representing three different populations of Enshi black pigs from three different locations. Combining this data with the available whole genomes of 13 Chinese wild boars, we identified 417 protein-coding genes embedded in the selected regions of Enshi black pigs. These genes are mainly involved in developmental and metabolic processes, response to stimulus, and other biological processes. Signatures of selection were detected in genes involved in body size and immunity (RPS10 and VASN), lipid metabolism (GSK3), male fertility (INSL6) and developmental processes (TBX19). These findings provide a window into the potential genetic mechanism underlying development of desirable phenotypes in Enshi black pigs during domestication and subsequent artificial selection. Thus, our results illustrate how domestication has shaped patterns of genetic variation in Enshi black pigs and provide valuable genetic resources that enable effective use of pigs in agricultural production.

T-Box Genes in Human Development and Disease

T-box genes are important development regulators in vertebrates with specific patterns of expression and precise roles during embryogenesis. They encode transcription factors that regulate gene transcription, often in the early stages of development. The hallmark of this family of proteins is the presence of a conserved DNA binding motif, the "T-domain." Mutations in T-box genes can cause developmental disorders in humans, mostly due to functional deficiency of the relevant proteins. Recent studies have also highlighted the role of some T-box genes in cancer and in cardiomyopathy, extending their role in human disease. In this review, we focus on ten T-box genes with a special emphasis on their roles in human disease.

T-Box Genes in the Kidney and Urinary Tract

T-box (Tbx) genes encode an ancient group of transcription factors that play important roles in patterning, specification, proliferation, and differentiation programs in vertebrate organogenesis. This is testified by severe organ malformation syndromes in mice homozygous for engineered null alleles of specific T-box genes and by the large number of human inherited organ-specific diseases that have been linked to mutations in these genes. One of the organ systems that has not been associated with loss of specific T-box gene function in human disease for long is the excretory system. However, this has changed with the finding that mutations in TBX18, a member of a vertebrate-specific subgroup within the Tbx1-subfamily of T-box transcription factor genes, cause congenital anomalies of the kidney and urinary tract, predominantly hydroureter and ureteropelvic junction obstruction. Gene expression analyses, loss-of-function studies, and lineage tracing in the mouse suggest a primary role for this transcription factor in specifying the ureteric mesenchyme in the common anlage of the kidney, the ureter, and the bladder. We review the function of Tbx18 in ureterogenesis and discuss the body of evidence that Tbx18 and other members of the T-box gene family, namely, Tbx1, Tbx2, Tbx3, and Tbx20, play additional roles in development and homeostasis of other components of the excretory system in vertebrates.

TBX6, LHX1 and copy number variations in the complex genetics of Müllerian aplasia

Background

Müllerian aplasia (MA) is a congenital disorder of the female reproductive tract with absence of uterus and vagina with paramount impact on a woman’s life. Despite intense research, no major genes have been found to explain the complex genetic etiology.

Methods and Results

We have used several genetic methods to study 112 patients with MA. aCGH identified CNVs in 8/50 patients (16%), including 16p11.2 and 17q12 deletions previously associated with MA. Subsequently, another four patients were shown to carry the ~0.53 Mb deletion in 16p11.2. More importantly, sequencing of TBX6, residing within 16p11.2, revealed two patients carrying a splice site mutation. Two previously reported TBX6 variants in exon 4 and 6 were shown to have a significantly higher frequency in patients (8% and 5%, respectively) than in controls (2% each). We also sequenced LHX1 and found three apparently pathogenic missense variants in 5/112 patients. Altogether, we identified either CNVs or variations in TBX6 or LHX1 in 30/112 (26.8%) MA patients. CNVs were found in 12/112 (10.7%), patients, novel variants in TBX6 or LHX1 in 7/112 (6.3%), and rare variants in TBX6 in 15/112 (13.4%) patients. Furthermore, four of our patients (4/112, 3.6%) were shown to carry variants in both TBX6 and LHX1 or a CNV in combination with TBX6 variants lending support to the complex genetic etiology of MA.

Conclusions

We have identified TBX6 as a new gene associated with MA. Our results also support the relevance of LHX1 and CNVs in the development of this congenital malformation.

Germline mutation analysis of Tpit in Poodle dogs with ACTH-dependent hyperadrenocorticism

There is a high incidence of pituitary-dependent hyperadrenocorticism (PDH) in Poodle dogs, with family members being affected by the disease, suggesting a genetic involvement. Tpit is an obligate transcription factor for the expression of pro-opiomelanocortingene and for corticotroph terminal differentiation. The aim of the present study was to screen the Tpit gene for germline mutations in Poodles with PDH. Fifty Poodle dogs (33 female, 8.71±2.8 years) with PDH and 50 healthy Poodle dogs (32 females, 9.4241 2.8 years) were studied. Genomic DNA was isolated from peripheral blood, amplified by PCR and submitted to automatic sequence. No mutation in the coding region of Tpit was found, whereas the new single nucleotide polymorphism p.S343G, in heterozygous state, was found in the same frequency in both PDH and control groups. We concluded that Tpit gain-of-function mutations are not involved in the etiology of PDH in Poodle dogs.

Transcription factor Smad-independent T helper 17 cell induction by transforming-growth factor-β is mediated by suppression of eomesodermin

Transforming growth factor-β (TGF-β) has been shown to be required for Th17 cell differentiation via Smad-independent mechanisms. The molecular mechanism underlying this pathway remains to be clarified, however. We searched for genes regulated by TGF-β through the Smad-independent pathway by using Smad2 and Smad3 double-deficient T cells and identified the transcription factor Eomesodermin (Eomes), whose expression was suppressed by TGF-β via the c-Jun N-terminal kinase (JNK)-c-Jun signaling pathway. Inhibition of JNK strongly suppressed disease in an in vivo EAE model as well as in vitro Th17 cell induction. Overexpression of Eomes substantially suppressed Th17 cell differentiation, whereas ablation of Eomes expression could substitute for TGF-β in Th17 cell induction in primary T cells. Eomes suppressed Rorc and Il17a promoters by directly binding to the proximal region of these promoters. In conclusion, the suppression of Eomes by TGF-β via the JNK pathway is an important mechanism for Smad-independent Th17 cell differentiation.

In vitro generated anti-tumor T lymphocytes exhibit distinct subsets mimicking in vivo antigen-experienced cells

The T-lymphocyte pool can be subdivided into naïve (Tn), effector memory (Tem), and central memory (Tcm) T cells. In this study, we characterized in vitro short-term cultured anti-tumor human T lymphocytes generated by lentiviral transduction with an anti-tumor antigen TCR vector. Within 2 weeks of in vitro culture, the cultured T cells showed a Tcm-like phenotype illustrated by a high percentage of CD62L and CD45RO cells. When the cells were sorted into populations that were CD45RO+/CD62L-(Tem), CD45RO+/CD62L+(Tcm), or CD45RO(low)/CD62L+(Tn) and co-cultured with antigen-matched tumor lines, the magnitude of cytokine release from these populations for IFNγ (Tn < Tcm < Tem) and IL-2 (Tn > Tcm > Tem) mimicked the types of immune cell responses observed in vivo. In comparing cell-mediated effector function, Tn were found to be deficient (relative to Tcm and Tem) in the ability to form conjugates with tumor cells and subsequent lytic activity. Moreover, analysis of the gene expression profiles of the in vitro cultured and sorted T-cell populations also demonstrated patterns consistent with their in vivo counterparts. When Tcm and Tem were tested for the ability to survive in vivo, Tcm displayed significantly increased engraftment and persistence in NOD/SCID/γc(-/-) mice. In general, a large percentage of in vitro generated anti-tumor T lymphocytes mimic a Tcm-like phenotype (based on phenotype, effector function, and increased persistence in vivo), which suggests that these Tcm-like cultured T cells may be optimal for adoptive immunotherapy.

Inhibitors of histone deacetylases as potential therapeutic tools for high-risk embryonal tumors of the nervous system of childhood

The origin of malignant embryonal tumors is incompletely understood and certain risk groups remain difficult to treat. The epigenetic structure of DNA and its lesions play a role in the origin of these neoplasms. Manipulation of the epigenome may offer novel treatment options. The authors evaluated the cytotoxicity of histone deacetylase inhibitors (HDI) [MS-275, SAHA, TSA, M344, M360, D85, SW55, SW187 and valproic acid (VPA)] on 13 embryonal tumor cell lines [4 medulloblastomas, 5 neuroblastomas, 2 atypical teratoid/rhabdoid tumors (AT/RT), and 2 malignant rhabdoid tumors of the kidney (RTK)] in MTT assay. In addition, HDI effects on hyperacetylation, reexpression of growth regulatory genes and apoptosis were characterized by Western analysis, RT-PCR and annexin-V staining. All HDI inhibited cell proliferation in a time- and dose-dependent manner. VPA was least cytotoxic with GI50 values after 72 hr ranging from 53.6 to 332.9 microM, while TSA was most efficient with GI50 values after 72 hr ranging from 0.01 to 8.8 microM. M344 and M360 were also highly effective. Western blot revealed hyperacetylation of histone H4 after HDI treatment. Reactivation of several genes including the proapoptotic CASP8 was identified by RT-PCR. Annexin-V staining demonstrated a dose and time dependent induction of apoptosis. HDI inhibited the growth of medulloblastoma, neuroblastoma and rhabdoid tumors in vitro. Treatment with HDI induced the reactivation of growth regulatory genes and consequently apoptosis. Our results warrant further studies and may help in the design of new protocols geared at the treatment of high risk embryonal tumors.

Influences of Extracellular Matrix and of Conditioned Media on Differentiation and Invasiveness of Trophoblast Stem Cells

Embryo implantation in the human and rodents relies on the trophoblast's ability to invade into the uterine stroma, partly depending on proteinases degrading components of basement membrane and underlying extracellular matrix (ECM). We have utilized mouse trophoblast stem (TS) cells (Science, 1998, 282:2072) to study trophoblast invasion and trophoblast-ECM interactions in vitro. On plastic in fibroblast-conditioned medium containing fibroblast growth factor (FGF)-4 and heparin, the cells remain proliferative but display increased differentiation in media without these components. Marker gene expression (Eomes, Pl-1, Tpbp) and invasion assays showed that TS cells exhibit increased invasive capacity when differentiating into giant cells and spongiotrophoblasts in unconditioned media without FGF-4 and heparin. Concomitantly, an up-regulation of matrix metalloproteinases (MMP)-9 and -14 was observed. Culture on gels of the basement membrane-like Matrigel resulted in striking changes in morphology and gene expression. Differentiating TS cells invaded into this ECM in a three-dimensional culture, while in turn ECM contact enhanced differentiation of TS cells and up-regulated the expression of MMP-9 and its tissue inhibitor (TIMP)-3. These findings implicate that the TS cell culture system used in this study can be utilized as a model for studying the regulation of trophoblast-ECM interactions, differentiation, and invasion in vitro.

IL-21 inhibits IFN-gamma production in developing Th1 cells through the repression of Eomesodermin expression

Exposure of naive Th cell precursors (Thp) to IL-21 inhibits IFN-gamma production from developing Th1 cells. The inhibition of IFN-gamma seen in IL-21-treated Thp cells is specific as the expression of other Th1 cytokines is unaffected. Recently, it has been reported that Eomesodermin (Eomes), a member of the T-box gene family, is expressed in developing CD8+ T cells and plays an important role in regulating IFN-gamma production and cytolytic effector function. In this study, we show that Eomes mRNA and protein are also expressed in developing Th1 cells, and exposure of naive Thp cells to IL-21 results in a decrease in Eomes expression. Moreover, the repression of Eomes expression by IL-21 is not due to an indirect effect of IL-21 on the expression of IFN-gamma or STAT4 and is independent of STAT1 and T-bet expression. Finally, we show that ectopic expression of Eomes prevents the inhibition of IFN-gamma production from IL-21-treated Thp cells. Taken together, these results demonstrate that Eomes plays a role in regulating IFN-gamma production in CD4+ T cells and IL-21 inhibits IFN-gamma production in developing Th1 cells through the repression of Eomes expression.

T-box genes in vertebrate development

The myriad developmental roles served by the T-box family of transcription factor genes defy easy categorization. Present in all metazoans, the T-box genes are involved in early embryonic cell fate decisions, regulation of the development of extraembryonic structures, embryonic patterning, and many aspects of organogenesis. They are unusual in displaying dosage sensitivity in most instances. In humans, mutations in T-box genes are responsible for developmental dysmorphic syndromes, and several T-box genes have been implicated in neoplastic processes. T-box transcription factors function in many different signaling pathways, notably bone morphogenetic protein and fibroblast growth factor pathways. The few downstream target genes that have been identified indicate a wide range of downstream effectors.

Genetic control of pituitary development and hypopituitarism

The pituitary gland functions as a relay between the hypothalamus and peripheral target organs that regulate basic physiological functions, including growth, the stress response, reproduction, metabolism and lactation. The development of the pituitary gland has been studied extensively in mice, and has begun to be explored in zebrafish, an animal model system amenable to forward genetics. Multiple signaling molecules and transcription factors, expressed in overlapping but distinct spatial and temporal patterns, are required at various stages of pituitary development. Defects in this precisely regulated genetic program lead to diverse pituitary dysfunction. The animal models have greatly enhanced our understanding of molecular mechanisms underlying pituitary development in addition to congenital pituitary disorders in humans.

Gene expression profile of the mouse organ of Corti at the onset of hearing

We describe the generation of an expressed sequence tag (EST) database of the mouse organ of Corti (OC). Over 20,000 independent clones were isolated, analyzed, and grouped into 8690 unique gene clusters. A large pool of novel genes unique to the OC was identified. Sequence alignments frequently revealed alternatively spliced forms of known genes potentially relevant in the OC function. We have also electronically mapped a subset of OC mouse ESTs to several syntenic regions associated with human autosomal and recessive deafness, which may prove useful for the identification of new positional candidates for these human diseases. The EST dataset is available as an interactive Web-based public database at. This resource provides both a view of the profile of gene expression in the OC at the onset of hearing and a tool to identify novel genes of importance in hearing.

Transcript map of the candidate region for HSNI with cough and gastroesophageal reflux on chromosome 3p and exclusion of candidate genes

Dominantly inherited sensory neuropathy (HSNI) is a degenerative disorder of sensory neurons characterized predominantly by sensory loss with mild motor impairment. Recently our group identified a locus on chromosome 3p for a new form of HSNI associated with cough and gastroesophageal reflux (GER). Haplotype analysis in a second family refined the interval to a 3.4-cM region that includes the candidate genes TOP2B and SLC4A7. The genes TOP2B and SLC4A7 and five other characterized genes that map within the critical interval have been investigated and excluded from having a pathogenic role in HSNI with cough and GER. Two novel single nucleotide polymorphisms were identified; however both changes were observed in affected and non-affected individuals, suggesting that they have no relation to the disease. We have used the resources of the Human Genome Project to report a transcript map of the region on chromosome 3p24 containing the HSNI with cough and GER locus.

Control of effector CD8+ T cell function by the transcription factor Eomesodermin

Activated CD8+ T cells play a critical role in host defense against viruses, intracellular microbes, and tumors. It is not clear if a key regulatory transcription factor unites the effector functions of CD8+ T cells. We now show that Eomesodermin (Eomes), a paralogue of T-bet, is induced in effector CD8+ T cells in vitro and in vivo. Ectopic expression of Eomes was sufficient to invoke attributes of effector CD8+ T cells, including interferon-gamma (IFN-gamma), perforin, and granzyme B. Loss-of-function analysis suggests Eomes may also be necessary for full effector differentiation of CD8+ T cells. We suggest that Eomesodermin is likely to complement the actions of T-bet and act as a key regulatory gene in the development of cell-mediated immunity.

The maternally expressed zebrafish T-box geneeomesoderminregulates organizer formation

Early embryonic development in many organisms relies upon maternal molecules deposited into the egg prior to fertilization. We have cloned and characterized a maternal T-box gene in the zebrafish, eomesodermin(eomes). During oogenesis, the eomes transcript becomes localized to the cortex of the oocyte. After fertilization during early cleavage stages, eomes is expressed in a vegetal to animal gradient in the embryo, whereas Eomesodermin protein (Eom) is distributed cytoplasmically throughout the blastoderm. Strikingly, following midblastula transition, nuclear-localized Eomesodermin is detected on the dorsal side of the embryo only. Overexpression of eomes results in Nodal-dependent and nieuwkoid/dharma (nwk/dhm) independent ectopic expression of the organizer markers goosecoid (gsc), chordin (chd) and floating head (flh) and in the formation of secondary axes. The same phenotypes are observed when a VP16-activator construct is injected into early embryos, indicating that eomes acts as a transcriptional activator. In addition, a dominant-negative construct and antisense morpholino oligonucleotides led to a reduction in gsc and flh expression. Together these data indicate that eomes plays a role in specifying the organizer.

Differential regulation of proopiomelanocortin and pituitary-restricted transcription factor (TPIT), a new marker of normal and adenomatous human corticotrophs

Since the identification of the pituitary-restricted transcription factor Tpit, a novel T-box factor that is only present in mouse in the two pituitary proopiomelanocortin (POMC)-expressing lineages, no information was available on its pattern of expression in human pituitary. We investigated by immunohistochemistry and in situ hybridization the expression of TPIT in normal human anterior pituitary tissue and in several types of human pituitary adenomas (n = 52). TPIT expression was restricted to the nucleus of normal or adenomatous human corticotroph cells. No specific TPIT immunostaining was detectable in all prolactin (PRL)-, GH-, or gonadotropin-secreting adenomas. In situ hybridization studies demonstrated that TPIT transcripts were coexpressed with POMC mRNA in both secreting and silent corticotroph adenomas, and in normal corticotrophs, whereas TPIT mRNA was not detectable in other types of pituitary adenomas. Unlike POMC, TPIT was not up-regulated by adrenalectomy in rats and did not seem down-regulated in the normal pituitary adjacent to human corticotroph microadenomas. TPIT is the only currently known transcription factor selectively expressed in human normal and adenomatous corticotrophs. In human and experimental models, TPIT and its target gene POMC were thus differentially regulated by glucocorticoids. Moreover, TPIT represents a new marker of POMC-expressing pituitary cells.

Human squamous cell carcinomas lose a mortality gene from chromosome 6q14.3 to q15

Normal human keratinocytes possess a finite replicative lifespan. Most advanced squamous cell carcinomas (SCCs), however, are immortal, a phenotype that is associated with p53 and INK4A dysfunction, high levels of telomerase and loss of heterozygosity (LOH) at several genetic loci, suggestive of the dysfunction of other mortality genes. We show here that human chromosome 6 specifically reduces the proliferation or viability of a human SCC line, BICR31, possessing LOH across the chromosome. This was determined by an 88% reduction in colony yield (P<0.001), following the reintroduction of an intact normal chromosome 6 by monochromosome transfer. Deletion analysis of immortal segregants using polymorphic markers revealed the loss of a 2.9 Mbp interval, centred on marker D6S1045 at 6q14.3-q15, in 6/19 segregants. Crucially, allelic losses of this region were not identified in control hybrids constructed between chromosome 6 and the BICR6 SCC cell line that is heterozygous for chromosome 6 and which showed no reduction in colony formation relative to the control chromosome transfers. This indicates that the minimally deleted region at D6S1045 is not the result of fragile sites, a recombination hot spot, or a feature of the monochromosome transfer technique. LOH of D6S1045 was found in 2/9 immortal SCC lines and was part of a minimally deleted region of line BICR19. Furthermore, allelic imbalance, consistent with LOH, was detected in 3/17 advanced SCCs of the tongue. These results suggest the existence of a suppressor of SCC immortality and tumour development at chromosome 6q14.3-q15, which is important to a subset of human SCCs.

Evolution of developmental functions by the Eomesodermin, T-brain-1, Tbx21 subfamily of T-box genes: insights from amphioxus

We have identified an amphioxus T-box gene that is orthologous to the Eomesodermin, T-brain-1, and Tbx21 genes of vertebrates, and we have characterized its expression pattern during embryonic and larval development. AmphiEomes/Tbr1/Tbx21 is maternally expressed in oocytes and cleavage stage embryos. After the onset of zygotic transcription at the blastula stage, it is expressed in invaginating mesendoderm cells during gastrulation, but it is downregulated in presumptive ectoderm and neurectoderm. Expression is seen in both axial and paraxial mesendoderm in neurulae and early larvae, but it is not detected in differentiated endoderm, somites, or notochord. Expression persists in mesendoderm cells of the tail bud in early larvae, but it disappears between 1 to 1.5 days post fertilization. Unlike orthologous genes in basal deuterostomes or vertebrates, no anterior neural expression domain is detected at any stage of development. Integrating phylogenetic and developmental data, we have reconstructed the evolutionary history of the Eomesodermin/Tbr1/Tbx21 subfamily of T-box genes from a single ancestral locus that originated very early in metazoan evolution, before the evolution of triploblasts from their diploblast ancestor.

Cloning of zebrafish T-box genes tbx15 and tbx18 and their expression during embryonic development

Members of the T-box (tbx) gene family encode developmentally regulated transcription factors, several of which are implicated in human hereditary diseases. We have cloned the paralogous genes tbx15 and tbx18 in zebrafish and have characterised their expression in detail. tbx15 is expressed in paraxial head mesenchyme and its derivatives, the extraocular and jaw musculature and the posterior neurocranium. Further areas of tbx15 expression are in the anterior somitic mesoderm, in periocular mesenchyme and in the pectoral fin mesenchyme throughout larval development. Areas of strong tbx18 expression are found in the developing somitic and presomitic mesoderm, in the heart and in pectoral fin mesenchyme, as well as the ventral neuroectoderm and the developing palate. Both genes exhibit particular differences in expression compared to their murine orthologs.

The T-box family

SUMMARY

Transcription factors of the T-box family are required both for early cell-fate decisions, such as those necessary for formation of the basic vertebrate body plan, and for differentiation and organogenesis. When mutated, T-box genes give dramatic phenotypes in mouse and zebrafish, and they have been implicated both in fundamentals of limb patterning and in a number of human congenital malformations such as Holt-Oram, ulnar-mammary and DiGeorge syndromes, as well as being amplified in a subset of cancers. Genes encoding members of the T-box family have recently been shown to comprise approximately 0.1% of genomes as diverse as those of nematodes and humans and have been identified in a wide variety of animals from ctenophores (comb jellies) to mammals; they are, however, completely absent from genomes from other organisms (such as the model plant Arabidopsis thaliana).

Tbx19, a tissue-selective regulator of POMC gene expression

Pituitary cell types arise in a temporally and spatially specific fashion, in response to combinatorial actions of transcription factors induced by transient signaling gradients. The critical transcriptional determinants of the two pituitary cell types that express the pro-opiomelanocortin (POMC) gene, the anterior lobe corticotropes, producing adrenocorticotropin, and the intermediate lobe melanotropes, producing melanocyte-stimulating hormone (MSH alpha), have remained unknown. Here, we report that a member of the T-box gene family, Tbx19, which is expressed only in the rostral ventral diencephalon and pituitary gland, commencing on e11.5, marks pituitary cells that will subsequently express the POMC gene and is capable of altering progression of ventral cell types and inducing adrenocorticotropin in rostral tip cells. It is suggested that Tbx19, depending on the presence of synergizing transcription factors, can activate POMC gene expression and repress the alpha glycoprotein subunit and thyroid-stimulating hormone beta promoters.

T-box genes in development: from hydra to humans

The T-box gene family was uncovered less than a decade ago but has been recognized as important in controlling many and varied aspects of development in metazoans from hydra to humans. Extensive screening and database searching has revealed several subfamilies of genes with orthologs in species as diverse as Caenorhabditis elegans and humans. The defining feature of the family is a conserved sequence coding for a DNA-binding motif known as the T-box, named after the first-discovered T-box gene, T or Brachyury. Although several T-box proteins have been shown to function as transcriptional regulators, to date only a handful of downstream target genes have been discovered. Similarly, little is known about regulation of the T-box genes themselves. Although not limited to the embryo, expression of T-box genes is characteristically seen in dynamic and highly specific patterns in many tissues and organs during embryogenesis and organogenesis. The essential role of several T-box genes has been demonstrated by the developmental phenotypes of mutant animals.

Cloning and expression analysis of the mouse T-box gene Tbx18

T-box genes encode transcription factors that regulate a variety of developmental processes. In this report, we describe the cloning and expression analysis of the novel mouse T-box gene Tbx18. During development expression is most prominent in the proepicardial organ and in the epicardium of the heart. Other sites of expression include the cranial paraxial mesoderm, the presomitic mesoderm, the anterior somite half, the genital ridge, and the developing limb buds.

Differential DNA binding and transcription modulation by three T-box proteins, T, TBX1 and TBX2

T-box genes encode a family of phylogenetically conserved DNA-binding proteins that regulate gene expression during embryogenesis. While the developmental importance of many T-box genes has been well documented, little is known about how family members differ in their DNA binding properties and ability to modulate transcription. Here we show that although TBX1, TBX2 and the Xenopus T protein (Xbra) share only 50-60% identity within their DNA-binding domains they can bind the same DNA sequence in vitro. However, the proteins differ in three important respects. While TBX1 protein binds a palindromic T oligonucleotide as a dimer, as had been previously reported for Xbra, TBX2 appears to bind the same DNA sequence as a monomer. Also, T protein/DNA complexes are stabilized in vitro by the addition of specific antibodies, whereas TBX2/DNA complexes are not stabilized by antibodies. Most importantly, TBX2 represses while Xbra activates transcription of the same chimeric reporter plasmid. TBX1, although capable of binding to the chimeric promoter, has no effect on transcription. Thus, while the DNA binding domains of T-box proteins share substantial homology, these proteins differ in both their DNA binding and transcriptional modulation properties. These results suggest that the various T-box proteins, while highly conserved, likely use different mechanisms to modulate transcription and may have different targets in vivo.

Phylogenetic analysis of T-Box genes demonstrates the importance of amphioxus for understanding evolution of the vertebrate genome

The duplication of preexisting genes has played a major role in evolution. To understand the evolution of genetic complexity it is important to reconstruct the phylogenetic history of the genome. A widely held view suggests that the vertebrate genome evolved via two successive rounds of whole-genome duplication. To test this model we have isolated seven new T-box genes from the primitive chordate amphioxus. We find that each amphioxus gene generally corresponds to two or three vertebrate counterparts. A phylogenetic analysis of these genes supports the idea that a single whole-genome duplication took place early in vertebrate evolution, but cannot exclude the possibility that a second duplication later took place. The origin of additional paralogs evident in this and other gene families could be the result of subsequent, smaller-scale chromosomal duplications. Our findings highlight the importance of amphioxus as a key organism for understanding evolution of the vertebrate genome.

Characterization of the human TBX20 gene, a new member of the T-Box gene family closely related to the Drosophila H15 gene

T-box transcription factors contain a novel type of DNA-binding domain, the T-box domain, and are encoded by an ancient gene family. Four T-box genes, omb, Trg, org-1, and H15, have been identified in Drosophila, whereas in mammals the T-box gene family has expanded, and 12 human T-box genes have been isolated. We have identified a new human T-box gene, TBX20, and its mouse homologue Tbx20, which are more closely related to the Drosophila H15 gene than to any known vertebrate gene. H15 expression in leg imaginal discs correlates with commitment to a ventral fate, implicating this gene in early patterning events. We find that TBX20 is expressed in the fetal heart, eye, and limb, and during embryogenesis in the mouse, Tbx20 is expressed in the developing heart, eye, ventral neural tube, and limbs, indicating a possible role in regulating development of these tissues. The TBX20 gene maps to chromosome 7p14-p15. An association between TBX20 and loci for retinitis pigmentosa, RP9, and blepharophimosis syndrome, BPES, have been excluded.

The gene encoding the T-box factor Tbx2 is a target for the microphthalmia-associated transcription factor in melanocytes

Commitment to the melanocyte lineage is characterized by the onset of microphthalmia-associated transcription factor (Mitf) expression. Mitf plays a fundamental role in melanocyte development, with mice lacking Mitf being entirely devoid of pigment cells. In the absence of functional Mitf protein, melanoblasts expressing Mitf mRNA disappear around 2 days after their first appearance either by apoptosis or by losing their identity and adopting an alternative cell fate. The role of Mitf must therefore be to regulate genes required for melanoblast survival, proliferation, or the maintenance of melanoblast identity. Yet to date, Mitf has been shown to regulate genes such as Tyrosinase, Tyrp-1, and Dct, which are required for pigmentation, a differentiation-specific process. Because expression of these genes cannot account for the complete absence of pigment cells in Mitf-negative mice, Mitf must regulate the expression of other as yet uncharacterized genes. Here we provide several lines of evidence to suggest that Mitf may regulate the expression of the Tbx2 transcription factor, a member of the T-box family of proteins implicated in the maintenance of cell identity. First, isolation and sequencing of the entire murine Tbx2 gene revealed that the Tbx2 promoter contains a full consensus Mitf recognition element; second, Mitf could bind the promoter in vitro and activate Tbx2 expression in vivo in an E box-dependent fashion; and third, Tbx2 is expressed in melanoma cell lines expressing Mitf, but not in a line in which Mitf expression was not detectable. Taken together, with the fact that Tbx2 is expressed in Mitf-positive melanoblasts and melanocytes, but not in Mitf-negative melanoblast precursor cells, the evidence suggests that the Tbx2 gene may represent one of the first known targets for Mitf that is not a gene involved directly in the manufacture of pigment.

Virtual cloning and physical mapping of a human T-box gene, TBX4

The Tbx2/3/4/5 subfamily is one of the largest subgroupings within the T-box gene family, the members of which encode developmentally critical transcription factors. TBX4, a human member of the Tbx2/3/4/5 subfamily, has been identified and characterized from a high-throughput genomic sequence. The genomic organization of TBX4 was elucidated by computational sequence analysis, and the putative cDNA sequence was assembled. The genomic organization of TBX4 is very similar to that of TBX5, as is the situation for TBX2 and TBX3. The physical configuration of the TBX4-TBX2 cluster on human chromosome 17q21-q22 is similar to that of the TBX5-TBX3 cluster on chromosome 12q23-q24. The assembled TBX4 cDNA sequence was searched against the EST databases, and a TBX4 EST was identified.

A starfish homolog of mouse T-brain-1 is expressed in the archenteron of Asterina pectinifera embryos: possible involvement of two T-box genes in starfish gastrulation

A cDNA clone for a starfish T-box gene (Ap-Tbr) was isolated and characterized. Molecular phylogenetic analysis showed that the Ap-Tbr gene was a member of the T-brain subfamily, which includes mouse T-brain-1 and Xenopus Eomesodermin. Ap-Tbr was expressed as early as in late blastulae, and the transcript was evident in a disc-like region at the vegetal end or the vegetal plate. In early gastrulae, the gene was expressed in the cells of the invaginated archenteron, from which the majority of mesodermal cells as well as some endodermal cells are derived. The Ap-Tbr expression disappeared by the end of gastrulation, and was not detected in early bipinnaria larvae. This expression pattern of Ap-Tbr suggests its role in an early step of archenteron invagination, associated with mesoderm and endoderm formation. Furthermore, double staining of late blastulae and early gastrulae with a probe specific for Ap-Tbr and one for ApBra (the starfish Brachyury gene) demonstrated that the regions of Ap-Tbr and ApBra expression at the vegetal/posterior end of the embryo did not overlap, the region with Ap-Tbr expression being encircled by a ring-shaped region of ApBra expression. A gap without expression of the two genes was located between them, and the gap was seen around the blastoporal lip in the early gastrula. These observations suggest implication of the two T-box genes, with different roles, in starfish gastrulation.

Chamber-specific cardiac expression of Tbx5 and heart defects in Holt-Oram syndrome

To further define the role of a T-box transcription factor, Tbx5, in cardiac development, we have examined its expression in the developing mouse and chick heart and correlated this pattern with cardiac defects caused by human TBX5 mutations in Holt-Oram syndrome. Early in the developing heart, Tbx5 is uniformly expressed throughout the entire cardiac crescent. Upon formation of the linear heart tube, Tbx5 is expressed in a graded fashion, stronger near the posterior end and weaker at the anterior end. As the heart tube loops, asymmetric Tbx5 expression continues; Tbx5 is expressed in the presumptive left ventricle, but not the right ventricle or outflow tract. This pattern of expression is maintained in more mature hearts. Expression in the ventricular septum is restricted to the left side and is contiguous with left ventricular free wall expression. Trabeculae, vena cavae (inferior and superior), and the atrial aspect of the atrioventricular valves also express high levels of Tbx5. These patterns of Tbx5 expression provide an embryologic basis for the prevalence of atrial septal defects (ostium primum and secundum), ventricular muscular septal defects, and left-sided malformations (endocardial cushion defects, hypoplastic left heart, and aberrant trabeculation) observed in patients with Holt-Oram syndrome.