SIX1 Research Articles

Chronological Expression of PITX2 and SIX1 Genes and the Association between Their Polymorphisms and Chicken Meat Quality Traits.

Simple SummaryThe production of chickens plays an increasingly important role in people’s daily life because of the high nutritional quality and relatively low cost. Meanwhile, with the improvement of living standards, the requirements for meat quality have also increased significantly. Thus, the improvement of meat quality is becoming more and more important in chicken breeding. Studies have shown that meat quality is closely related to the development of skeletal muscle, which is a complex process regulated by many genes. Paired-like homeodomain transcription factor 2 (PITX2) and SIX homeobox 1 (SIX1) genes are involved in skeletal muscle development, and their polymorphisms were significantly associated with the carcass and body size traits of chickens in our previous studies. The objective of the present study was to detect the chronological expression of them on the pectoral muscles, and evaluate whether their single nucleotide polymorphisms (SNPs) are associated with the meat quality traits in chickens. Our results could provide useful information for the functional research of regulatory mechanisms of meat quality and marker assisted-selection for chicken production and quality.Meat quality is closely related to the development of skeletal muscle, in which PITX2 and SIX1 genes play important regulatory roles. The present study firstly provided the data of chronological expression files of PITX2 and SIX1 genes in the post-hatching pectoral muscle and analyzed the association of their polymorphisms with the meat quality traits of Wuliang Mountain Black-bone (WLMB) chickens. The results showed that both PITX2 and SIX1 genes were weakly expressed in the second and third weeks, and then increased significantly from the third week to the fourth week. Furthermore, there was a significant positive correlation between the expression levels of the two genes. Twelve and one SNPs were detected in the chicken PITX2 and SIX1 genes, respectively, of which four SNPs (g.9830C > T, g.10073C > T, g.13335G > A, g.13726A > G) of the PITX2 gene and one SNP (g.564G > A) of the SIX1 gene were significantly associated with chicken meat quality traits. For the PITX2 gene, chickens with the CT genotype of g.9830C > T showed the highest meat color L*, shear force (SF), pH, and the lowest electrical conductivity (EC), and drip loss (DL) (p < 0.05 or p < 0.01); chickens with the CC genotype of g.10073C > T had the lowest L*, pH, and the highest DL (p < 0.01). For the SIX1 gene, chickens with the GG genotype of g.564G > A had the highest (p < 0.05) SF and pH. Furthermore, pH had a significant correlation with all the other meat quality traits. The current study could contribute to the research of regulatory mechanisms of meat quality and lay the foundation for improving meat quality based on marker-assisted selection in chickens.

Nuclear TEAD4 with SIX1 Overexpression is an Independent Prognostic Marker in the Stage I-III Colorectal Cancer.

IntroductionStage I–III colorectal cancer patients are under risk of tumor recurrence and metachronous metastasis after radical surgery. An increased expression of transcription factor TEAD4 is associated with epithelial-mesenchymal transition, metastasis and poor prognosis in colorectal cancer. However, the mechanistic role of TEAD4 in driving colon cancer progression and its prognostic value in early stage of CRC remains unclear.MethodsIn this study, the regulation, function and prognostic significance of TEAD4 and its new direct target gene SIX1 in CRC progression were evaluated using human tissues, molecular and cell biology.ResultsWe show that TEAD4 directly upregulates the expression of SIX1 at transcriptional level in CRC cells, establishing that SIX1 is a new direct target gene of TEAD4. TEAD4 promotes EMT and cell migration of CRC cells, while SIX1 knockdown attenuates this effect and SIX1 overexpression enhances this effect, indicating that SIX1 mediates the function of TEAD4 in promoting cell migration in CRC cells. Clinically, nuclear TEAD4, overexpression of SIX1 and nuclear TEAD4 with SIX1 overexpression predict poor prognosis in CRC patients.DiscussionOur study identifies TEAD4-SIX1-CDH1 form a novel signaling axis, which contributes to CRC progression, and its aberrant expression and activation predicts poor prognostic for CRC patients in stage I–III.

Diagnostic Outcomes for Genetic Testing of 54 Genes in Pregnancy Loss Using Array CGH Method: A Two-Year Retrospective Study

Objective: The current study aimed to retrospectively evaluate different diag- nostic approaches for the array genetic analysis of the cases from all trimester fetal loss in the medical genetics clinic between 2016 and 2017. The Quantitati- ve Fluorescent Polymerase Chain Reaction(QFPCR) test was performed on 50 samples, and aneuploidy was detected in 11 samples as a result of the test, and the array-CGH was performed when 39 QF-PCR resulted in normal test results. Under this purpose, we aimed to analyze and determine the possible copy num- ber variation(CNV), gene deletions, and/or duplications involved in embryonic cell division, tissue differentiation, intended.Materials and methods: DNA isolation from cases of this retrospective study was completed using the PureLink Genomic DNA isolation kit. DNA samples were then genoty - ped for molecular etiological reasons by oligonücleotid microarray -CGH method (aCGH , 60 K ISCA design , Agilent , Germany ). Hybridized probe correlations of the case and reference DNAs were evaluated with databases (Database of Genomic Variants Analysis ) used in genomic variation analysis in terms of 54 functional genes CNVs associated with intrauterine losses.Results: CNV was detected in 30 (77%) of 39 fetal samples analyzed within the scope of the research. Fifty-five percent of CNVs were found to be duplication (55%) and forty-five percent were deletions (45%). As a result of the evaluation, deletion was detected in 19 (35%) of 54 genes, duplication was detected in 26 (48%), while in 3 (6%) both deletion and duplication were detected. Although CNV detected in autosomal chromosomes (chromosome 1, 2, 3, 4, 5, 7, 8, 10, 12, 13, 14, 15 and 20), CNV was established the most common in X chromosome. In our study, CNVs associated with COX7B, ZIC1, MECP2, FMR1, HOXD13, JAG1, MSX2, NEXN, and SIX3 genes were found to be more frequent in terms of fetal loss etiology.Conclusions: Based on our experience, the array-CGH method can be used to investigate the etiology of the normal results of QF-PCR in cases of fetal loss. The array CGH method will be preferred more and more due to the ease of application and the data obtained. When we look at the literature, it is seen that there is not enough research on array CGH about fetal loss and more studies are needed to increase the experience in this field.

The SIX1 homeobox Gene Is a Novel Therapeutic Target in CALM-AF10 Leukemogenesis

Background : The CALM-AF10 translocation is found 5-10% of T-cell acute lymphoblastic leukemias (T-ALL), and a subset of acute myeloid leukemias (AML). CALM-AF10 leukemias are characterized by elevated expression of proleukemic HOXA genes. Since HOXA genes are difficult to target, we hypothesized that identification of non-HOXA CALM-AF10 effector genes could potentially yield novel therapeutic targets. To discover novel CALM-AF10-regulated genes, we took advantage of our prior observation that the nuclear export factor CRM1/XPO1 tethers CALM-AF10 to HOXA genes by interacting with a nuclear export signal within CALM. Using microarrays, we identified a set of genes that showed decreased expression in response to the CRM1 inhibitor, Leptomycin B (LMB), similar to Hoxa genes, in murine CALM-AF10 leukemia cells. Then using RNA-sequencing, we discovered a set of genes increased in murine hematopoietic stem cells transduced with CALM-AF10. There were 11 genes that were both decreased in response to LMB and increased in response to CALM-AF10, which included the Hoxa gene cluster, as well as Six1. Similar to HOXA genes, SIX1 is a homeobox gene that is associated with embryogenesis and is quiescent post-embryologically. Additionally, SIX1 and its cofactor EYA2 have been found to be overexpressed in numerous solid tumors, and inhibitor of the SIX1/EYA2 complex has recently been described. While there is evidence of a role for SIX1 in solid tumors, its role in leukemias has not been explored. Objective: To evaluate the role of SIX1 in CALM-AF10 leukemias. Design/Methods: RT-qPCR and Chromatin Immunoprecipitation (ChIP) were performed using bone marrow progenitors transduced with CALM-AF10 or an empty vector, with and without LMB. Methylcellulose colony assays assessed the ability of SIX1 to enhance self-renewal of hematopoietic progenitors. An inhibitor of the Six1/Eya2 interaction (compound 8430) was used to evaluate cell proliferation. Downstream targets of Six1 were evaluated using RT-qPCR in CALM-AF10 cells treated with Six1/Eya2 inhibitor (8430). Results: RT-qPCR confirmed overexpression of SIX1 in CALM-AF10 leukemia cells, and showed decreased SIX1 expression in the presence of LMB. Furthermore, ChIP revealed that CALM-AF10 binds to the SIX1 gene locus. Overexpression of SIX1 in fetal liver progenitors was sufficient to increase self-renewal potential. The 8430 Six1/Eya2 inhibitor slowed cell growth in CALM-AF10 cells compared to cells treated with DMSO alone. Finally, downstream targets such as Slc2a1, Cdk2, and Cyclina2 were decreased in 8430-treated CALM-AF10 leukemia cells. Conclusions: The SIX1 homeobox gene is highly expressed during embryogenesis, and its expression is silenced post-embryogenesis. Through an initial unbiased screen, we discovered that Six1 may play a role in CALM-AF10 leukemogenesis. We have determined that Six1 expression is upregulated in the presence of CALM-AF10. Further, we have shown a potential oncogenic role for Six1, as it was able to increase the self-renewal potential of hematopoietic progenitors. The role of Six1 in CALM-AF10 leukemia is further supported by the ability of a SIX1/EYA2 inhibitor to slow the growth of CALM-AF10 leukemia cells and decrease the expression of downstream targets of SIX1. These observations suggest that Six1 plays a pathogenic role in leukemogenesis, and may be a novel therapeutic target in CALM-AF10 leukemias. Disclosures No relevant conflicts of interest to declare.

SIX1 ve Kanser Kök Hücre Belirteçlerinin Hepatoselluler Karsinomada Kapsamlı Analizi

Objective: Transcription factor SIX1 aberrant expression has been shown in various mammalian tumors, and also recent studies indicated that SIX1 has a role in cancer stem cell properties. However, its roles in HCC cancer stem cell characteristics remain unclear. The aim of the study, to evaluate the EMT-inducer SIX1 and cancer stem cell markers expression profile in-vitro and in-vivo analyses.&#x0D; Material and Methods: SIX1 expression was suppressed by short hairpin RNA transduction in the SNU398 HCC cell line. Tumorsphere formation assay is a golden useful assay for cancer stem cell analysis. SIX1-dependent cancer stem cell markers PROM1, EPCAM, and OCT4 differential gene expression profiles were assessed in tumorsphere formation assay by RT-qPCR. Differential expression and correlation analyses were performed in transcriptome data in cirrhosis and HCC tissue samples.&#x0D; Results: Assessment of SIX1-knockdown expression of target genes in tumorsphere formation assay revealed PROM1, EPCAM expressions were significantly up-regulated but OCT4 gene expression was significantly down-regulated. Conformably, PROM1 and EPCAM expressions were inversely but OCT4 expression was positively correlated in transcriptome arrays in HCC tissues. Interestingly, to the evaluation of the same gene expressions were shown different patterns except, OCT4 in cirrhosis samples. The mRNA expression profiles did not change between cirrhosis and HCC samples in the SIX1, EPCAM, PROM1, and OCT4 gene expression profiles.&#x0D; Conclusion: Cancer stem cells are self‐renewable cell types and are responsible for cancer progression. Findings from this study highlight the SIX1 and cancer stemness-related genes expression correlations to improve our knowledge for HCC molecular signatures.

Abstract 9: Histone Deacetylases 1 And 2 Regulate Six2 Function To Maintain Nephron Progenitor Cells During Nephrogenesis

Low nephron endowment is strongly associated with cardiovascular disease, especially hypertension. Sine oculis homeobox 2 (Six2) is the master transcriptional regulator in balancing self-renewal and differentiation of nephron progenitor cells (NPCs) for appropriate nephron endowment. Loss of Six2 in mice causes early-onset loss of self-renewal and premature differentiation of NPCs. However, it is unclear how Six2 is functionally regulated during nephrogenesis. In vivo interaction of histone deacetylase1 and 2 (Hdac1/2) to Six2 was detected in developing kidney by co-immunoprecipitation and proximity ligation assay. Chromatin immunoprecipitation and DNA sequencing experiments in isolated E16.5 NPCs revealed 1,180 (84.58%) of the Six2 peaks overlapped with Hdac2 peaks, implying the involvement of Hdac1/2 in Six2 DNA binding and its function in NPCs. To test whether Hdac1/2 are required for Six2 function to regulate nephron formation, we employed Six2 GC mouse line, in which the eGFP and Cre fusion gene (GC) replaces and fully recapitulates the endogenous Six2 gene expression pattern. Analysis of kidneys at embryonic day (E) 19.5 and newborn (P0) showed that Six2 heterozygous (Six2 GC ) together with three alleles knockout of Hdac1/2 resulted in severely hypoplastic kidneys, while three alleles knockout of Hdac1/2 by transgenic Six2-Cre only led to very subtle phenotypes. Immunostaining at E 19.5 and P0 revealed about 50% reduction of Six2 level in the kidney of Six2 GC only and Six2 GC together with three alleles knockout of Hdac1/2 mice. In the kidneys of Six2 heterozygous mice, no change was observed for most of the NPC identity makers for self-renewal, including the three Six2 targets, Pax2, Sall1 and WT1. However, sequential removal of three alleles of Hdac1/2 of Six2 GC mice did not change Six2 protein level but significantly decreased the expression of Pax2, Sall1 and WT1, suggesting the requirement of Hdac1/2 for Six2’s function to transcriptionally activate the expression of its target genes. We also observed the premature differentiation and decreased nephron formation in mutant kidneys. Therefore, we conclude that Hdac1/2 are required for Six2’s function to promote NPC self-renewal and repress premature differentiation during nephrogenesis.

Steelhead (Oncorhynchus mykiss) lineages and sexes show variable patterns of association of adult migration timing and age-at-maturity traits with two genomic regions.

As life history diversity plays a critical role in supporting the resilience of exploited populations, understanding the genetic basis of those life history variations is important for conservation management. However, effective application requires a robust understanding of the strength and universality of genetic associations. Here, we examine genetic variation of single nucleotide polymorphisms in genomic regions previously associated with migration phenology and age‐at‐maturity in steelhead (Oncorhynchus mykiss) from the Columbia River. We found chromosome 28 markers (GREB1L, ROCK1 genes) explained significant variance in migration timing in both coastal and inland steelhead. However, strength of association was much greater in coastal than inland steelhead (R 2 0.51 vs. 0.08), suggesting that genomic background and challenging inland migration pathways may act to moderate effects of this region. Further, we found that chromosome 25 candidate markers (SIX6 gene) were significantly associated with age and size at first return migration for inland steelhead, and this pattern was mediated by sex in a predictable pattern (males R 2 = 0.139–0.170; females R 2 = 0.096–0.111). While this encourages using these candidate regions in predicting life history characteristics, we suggest that stock‐specific associations and haplotype frequencies will be useful in guiding implementation of genetic assays to inform management.

Pathogenomics Characterization of an Emerging Fungal Pathogen, Fusarium oxysporum f. sp. lycopersici in Greenhouse Tomato Production Systems.

In recent years, greenhouse-grown tomato (Solanum lycopersicum) plants showing vascular wilt and yellowing symptoms have been observed between 2015 and 2018 in North Carolina (NC) and considered as an emerging threat to profitability. In total, 38 putative isolates were collected from symptomatic tomatoes in 12 grower greenhouses and characterized to infer pathogenic and genomic diversity, and mating-type (MAT) idiomorphs distribution. Morphology and polymerase chain reaction (PCR) markers confirmed that all isolates were Fusarium oxysporum f. sp. lycopersici (FOL) and most of them were race 3. Virulence analysis on four different tomato cultivars revealed that virulence among isolates, resistance in tomato cultivars, and the interaction between the isolates and cultivars differed significantly (P < 0.001). Cultivar ‘Happy Root’ (I-1, I-2, and I-3 genes for resistance) was highly resistant to FOL isolates tested. We sequenced and examined for the presence of 15 pathogenicity genes from different classes (Fmk1, Fow1, Ftf1, Orx1, Pda1, PelA, PelD, Pep1, Pep2, eIF-3, Rho1, Scd1, Snf1, Ste12, and Sge1), and 14 Secreted In Xylem (SIX) genes to use as genetic markers to identify and differentiate pathogenic isolates of FOL. Sequence data analysis showed that five pathogenicity genes, Fmk1, PelA, Rho1, Sge1, and Ste12 were present in all isolates while Fow1, Ftf1, Orx1, Peda1, Pep1, eIF-3, Scd1, and Snf1 genes were dispersed among isolates. Two genes, Pep2 and PelD, were absent in all isolates. Of the 14 SIX genes assessed, SIX1, SIX3, SIX5, SIX6, SIX7, SIX8, SIX12, and SIX14 were identified in most isolates while the remaining SIX genes varied among isolates. All isolates harbored one of the two mating-type (MAT-1 or MAT-2) idiomorphs, but not both. The SIX4 gene was present only in race 1 isolates. Diversity assessments based on sequences of the effector SIX3- and the translation elongation factor 1-α encoding genes SIX3 and tef1-α, respectively were the most informative to differentiate pathogenic races of FOL and resulted in race 1, forming a monophyletic clade while race 3 comprised multiple clades. Furthermore, phylogeny-based on SIX3- and tef1-α gene sequences showed that the predominant race 3 from greenhouse production systems significantly overlapped with previously designated race 3 isolates from various regions of the globe.

SIX6 is a TAL1-regulated transcription factor in T-ALL and associated with inferior outcome

T-cell acute lymphoblastic leukemia (T-ALL) is a hematological malignancy driven by abnormal activity of transcription factors. Here we report an aberrant expression of the developmental transcription factor SIX6 in the TAL1-subtype of T-ALL. Our results demonstrate that the binding of TAL1 and GATA3 transcription factors into an upstream enhancer element directly regulates SIX6 expression. High expression of SIX6 was associated with inferior event-free survival within three independent patient cohorts. At a functional level, CRISPR-Cas9-mediated knockout of the SIX6 gene in TAL1 positive Jurkat cells induced changes in genes associated with the mTOR-, K-RAS-, and TNFα-related molecular signatures but did not impair cell proliferation or viability. There was also no acceleration of T-ALL development within a Myc driven zebrafish tumor model in vivo. Taken together, our results show that SIX6 belongs to the TAL1 regulatory gene network in T-ALL but is alone insufficient to influence the development or maintenance of T-ALL.

New Insights Into Cranial Synchondrosis Development: A Mini Review.

The synchondroses formed via endochondral ossification in the cranial base are an important growth center for the neurocranium. Abnormalities in the synchondroses affect cranial base elongation and the development of adjacent regions, including the craniofacial bones. In the central region of the cranial base, there are two synchondroses present—the intersphenoid synchondrosis and the spheno-occipital synchondrosis. These synchondroses consist of mirror image bipolar growth plates. The cross-talk of several signaling pathways, including the parathyroid hormone-like hormone (PTHLH)/parathyroid hormone-related protein (PTHrP), Indian hedgehog (Ihh), Wnt/β-catenin, and fibroblast growth factor (FGF) pathways, as well as regulation by cilium assembly and the transcription factors encoded by the RUNX2, SIX1, SIX2, SIX4, and TBX1 genes, play critical roles in synchondrosis development. Deletions or activation of these gene products in mice causes the abnormal ossification of cranial synchondrosis and skeletal elements. Gene disruption leads to both similar and markedly different abnormalities in the development of intersphenoid synchondrosis and spheno-occipital synchondrosis, as well as in the phenotypes of synchondroses and skeletal bones. This paper reviews the development of cranial synchondroses, along with its regulation by the signaling pathways and transcription factors, highlighting the differences between intersphenoid synchondrosis and spheno-occipital synchondrosis.

Copy Number Variants Contributing to Combined Pituitary Hormone Deficiency.

Combined pituitary hormone deficiency represents a disorder with complex etiology. For many patients, causes of the disease remain unexplained, despite usage of advanced genetic testing. Although major and common transcription factors were identified two decades ago, we still struggle with identification of rare inborn factors contributing to pituitary function. In this report, we follow up genomic screening of CPHD patient cohort that were previously tested for changes in a coding sequences of genes with the use of the whole exome. We aimed to find contribution of rare copy number variations (CNVs). As a result, we identified genomic imbalances in 7 regions among 12 CPHD patients. Five out of seven regions showed copy gains whereas two presented losses of genomic fragment. Three regions with detected gains encompassed known CPHD genes namely LHX4, HESX1, and OTX2. Among new CPHD loci, the most interesting seem to be the region covering SIX3 gene, that is abundantly expressed in developing brain, and together with HESX1 contributes to pituitary organogenesis as it was evidenced before in functional studies. In conclusion, with the use of broadened genomic approach we identified copy number imbalances for 12 CPHD patients. Although further functional studies are required in order to estimate its true impact on expression pattern during pituitary organogenesis and CPHD etiology.

SAT-288 Pituitary Developmental Defects Caused by Haploinsufficiency for the Transcription Factor SIX3 Are Worsened by POU1F1 Deficiency

Advances in genomic technologies are revolutionizing the practice of medicine by delivering molecular diagnoses that can be informative for prognosis and treatment of genetic disorders. Most of the known genetic causes of multiple pituitary hormone deficiency have been investigated as monogenic disorders. It can be challenging to predict clinical features from genetic data, as loss of function mutations in some genes can present with a spectrum of phenotypes ranging from craniofacial abnormalities, intellectual disability, and neurosensory and neuroendocrine defects to pituitary hormone deficiency with no other abnormalities. Although maternal exposures could be contributing factors, the contribution of rare, deleterious variation in other genes is a likely contributor. In humans, loss of function mutations in the transcription factor SIX3 cause variable, autosomal dominant holoprosencephaly with incomplete penetrance, and mouse models recapitulate some of the clinical features. Because Six3 and Pou1f1 gene expression patterns overlap in pituitary development, we hypothesized that doubly heterozygous mice (Six3+/-; Pou1f1+/dw) might have pituitary anomalies not present in singly heterozygous mice. We intercrossed Six3+/- and Pou1f1+/dw mice to produce doubly heterozygous animals. At e11.5, both Six3+/- and Six3+/-; Pou1f1+/dw exhibited abnormal morphology of the developing infundibulum and Rathke’s pouch, although ventral diencephalon expression of Tle4, Fgf10, and Nkx2.1 appeared normal. Both newborn Six3+/- and Six3+/-; Pou1f1+/dw littermates had abnormal pituitary gland morphology that resembled that of Aes-/-. AES is a co-repressor that interacts with SIX3. Specification of vasopressin neurons and anterior lobe hormone cell types appeared normal. Mice of all genotypes were born in expected Mendelian ratios (N=144, p=0.49), and there were no significant differences in body weight at 3 wks. A portion of the Six3+/- and doubly heterozygous mice developed hydrocephalus, exhibited failure to thrive, and died (6-9% of N=82, 85, respectively). At 6 wks, 25% (N=61) of the Six3+/-; Pou1f1+/dw animals exhibited striking pituitary dysmorphology in which the rostral aspect of the pituitary penetrated the palate. This was not observed in single heterozygotes. These results reveal that haploinsufficiency for Six3 affects Rathke’s pouch formation, resulting in pituitary gland dysmorphology in and around the stem cell niche. A significant portion of the Six3+/-; Pou1f1+/dw doubly heterozygous mice have a more pronounced pituitary phenotype than Six3+/-, supporting the possibility of digenic pituitary disease and highlighting phenotypic variability. Genetically engineered mice provide an excellent tool for assessing the possibility of gene-gene interactions that could enhance the severity of hypopituitarism and associated craniofacial development.

Molecular characterization of Fusarium oxysporum f. sp. cubense Tropical Race 4 (Foc-TR4) isolates from Malaysian banana using secreted in Xylem (SIX) effector genes

Fusarium wilt of banana, caused by Fusarium oxysporum f. sp. cubense (Foc), is a major factor limiting banana production in Malaysia. To date, SSR, ISSR, AFLP and RAPD markers are widely used in PCR-based molecular characterization of Foc. Although these markers are effective in characterizing Foc, they all have their own limitations. An effector gene known as Secreted in Xylem (SIX) has been explored to broaden the molecular diagnostic toolbox for Foc. This study aims to investigate the diversity of Foc-TR4 in Peninsular Malaysia based on the phylogenetic analysis of SIX sequences. The virulence potential of twenty-seven Fusarium wilt of banana based on pathogenicity test and the presence of SIX1, SIX7 and SIX8 genes were determined. All of twenty-seven Foc ‘Tropical Race 4’ (TR4) (VCG 01213/160) isolates were obtained from Biological Control Laboratory, Department of Plant Protection, Universiti Putra Malaysia (UPM). The results showed that all Foc-TR4 isolates were pathogenic towards banana plantlets at different severity levels under greenhouse condition. Pathogenicity assays showed that the level of aggressiveness differs between isolates. The Foc-TR4 isolates were screened for the presence of three SIX genes (SIX1, SIX7 and SIX8) and the genetic differentiation of Foc-TR4 was evaluated by PCR analysis using three specific primers. Among these three SIX genes, SIX1 and SIX8 genes were detected in all twenty-seven Foc-TR4 isolates from Peninsular Malaysia. Phylogenetic analysis using SIX1 and SIX8 sequences showed that they were related to TR4 isolates (VCG 01213/16) from Australia and Indonesian with bootstrap values of 94% and 100% respectively. No variation was observed in the SIX1 and SIX8 sequences since all 27 isolates were clustered into the same clade. Virulence level also did not correlate with the existence or lack of these genes. Since Foc could hamper the local banana production in Malaysia, characterization of these isolates through SIX genes provides a great understanding of pathogenicity in Foc and could potentially improve the diagnostic and control of Fusarium wilt in the future.

Generation and characterization of Six2 conditional mice

Heterozygous deletion of Six2, which encodes a member of sine oculis homeobox family transcription factors, has recently been associated with the frontonasal dysplasia syndrome FND4. Previous studies showed that Six2 is expressed in multiple tissues during craniofacial development in mice, including embryonic head mesoderm, postmigratory frontonasal neural crest cells, and epithelial and mesenchymal cells of the developing palate and nasal structures. Whereas Six2 -/- mice exhibited cranial base defects but did not recapitulate frontonasal phenotypes of FND4 patients, Six1 -/- Six2 -/- double mutant mice showed severe craniofacial defects including midline facial clefting. The complex phenotypes of FND4 patients and of Six1 -/- Six2 -/- mutant mice indicate that Six2 plays crucial roles in distinct cell types at multiple stages of craniofacial morphogenesis. Here we report generation of mice carrying insertions of a pair of loxP sites flanking exon-1 of the Six2 gene (Six2 f allele) using CRISPR/Cas9-mediated genome editing. We show that the Six2 f allele functions normally and is effectively inactivated by Cre-mediated recombination in vivo. Furthermore, we show that Six2 f/f ;Wnt1-Cre mice recapitulated cranial base defects but not neonatal lethality of Six2 -/- mice. These results indicate that Six2 f/f mice enable systematic investigation of cell type- and stage-specific Six2 function in development and disease.

Beyond large-effect loci: large-scale GWAS reveals a mixed large-effect and polygenic architecture for age at maturity of Atlantic salmon

BackgroundUnderstanding genetic architecture is essential for determining how traits will change in response to evolutionary processes such as selection, genetic drift and/or gene flow. In Atlantic salmon, age at maturity is an important life history trait that affects factors such as survival, reproductive success, and growth. Furthermore, age at maturity can seriously impact aquaculture production. Therefore, characterizing the genetic architecture that underlies variation in age at maturity is of key interest.ResultsHere, we refine our understanding of the genetic architecture for age at maturity of male Atlantic salmon using a genome-wide association study of 11,166 males from a single aquaculture strain, using imputed genotypes at 512,397 single nucleotide polymorphisms (SNPs). All individuals were genotyped with a 50K SNP array and imputed to higher density using parents genotyped with a 930K SNP array and pedigree information. We found significant association signals on 28 of 29 chromosomes (P-values: 8.7 × 10−133–9.8 × 10−8), including two very strong signals spanning the six6 and vgll3 gene regions on chromosomes 9 and 25, respectively. Furthermore, we identified 116 independent signals that tagged 120 candidate genes with varying effect sizes. Five of the candidate genes found here were previously associated with age at maturity in other vertebrates, including humans.DiscussionThese results reveal a mixed architecture of large-effect loci and a polygenic component that consists of multiple smaller-effect loci, suggesting a more complex genetic architecture of Atlantic salmon age at maturity than previously thought. This more complex architecture will have implications for selection on this key trait in aquaculture and for management of wild salmon populations.

Characterization of Pathogenic and Nonpathogenic Fusarium oxysporum Isolates Associated with Commercial Tomato Crops in the Andean Region of Colombia.

In Colombia, tomato production under protected conditions represents an important economic contribution to the agricultural sector. Fusarium wilt diseases, caused by pathogenic formae speciales of the soil-borne fungus Fusarium oxysporum Schltdl., cause significant yield losses in tomatoes throughout the world. Investigation of the F. oxysporum–tomato pathosystem in Colombia is required to develop appropriate alternative disease management. In this study, 120 fungal isolates were obtained from four different departments in the Central Andean Region in Colombia from tomato crops with symptoms of wilt disease. A molecular characterization of the fungal isolates was performed using the SIX1, SIX3, and SIX4 effector genes of Fusarium oxysporum f. sp. lycopersici W.C. Snyder & H.N. Hansen (Fol). Additionally, we developed a new specific marker to distinguish between Fusarium oxysporum f. sp. radicis-lycopersici Jarvis & Shoemaker (Forl) and Fol isolates. Furthermore, a phylogenetic analysis using the Translation Elongation Factor 1-alpha (EF1a) gene was performed with the collected isolates. Two isolates (named Fol59 and Fol-UDC10) were identified as Fol race 2, four isolates were identified as Forl, six isolates were identified as F. solani, and most of the isolates were grouped within the F. oxysporum species complex. The phylogenetic tree of EF1a showed that most of the isolates could potentially correspond to nonpathogenic strains of F. oxysporum. Additional pathogenicity assays carried out with Fol59 and Fol-UDC10 confirmed that both isolates were highly virulent strains. This study represents a contribution to the understanding of the local interaction between tomatoes and F. oxysporum in Colombia.

SETDB1 Mediated H3K9 Methylation Suppresses MLL-Fusion Target Expression and Leukemic Transformation

Genes encoding epigenetic proteins are mutated in about 70% of Acute Myeloid Leukemia patients underscoring their role in leukemic transformation. Epigenetic deregulation of the HOXA gene cluster drives transformation of about 50% of acute myeloid leukemia (AML), such as those harboring MLL rearrangements, NPM mutations and others. Indeed, expression of Hoxa9 and its co-factor Meis1 is sufficient to transform bone marrow cells into a lethal AML. We have shown that epigenetic regulation of Hoxa9 and Meis1 is mediated through the Polymerase Associated Factor 1 complex (PAF1c). The PAF1c binds to RNA polymerase II and recruits enzymes that alter epigenetic landscapes and influence gene transcription. We and others have shown that the PAF1c directly binds and recruits MLL and MLL fusion proteins to target genes such as Hoxa9 and Meis1 to deliver H3K4 methylation or H3K79 methylation activity respectively. Importantly, the PAF1c-MLL1 interaction is necessary for the growth of MLL-fusion leukemia cells but appears dispensable for normal hematopoietic stem and progenitor cells (HSPCs) function. This suggests the PAF1c is differentially required in leukemic cells compared to its normal counterparts. Thus, we aimed to 1) define the role of the PAF1c in normal hematopoiesis, and 2) identify mechanisms regulating PAF1c function that may be deregulated in leukemia. To understand the role of the PAF1c in hematopoiesis, we conditionally deleted the PAF1c subunit Cdc73 in HSPCs in hematopoietic cells. Conditional hematopoietic deletion of Cdc73 leads to lethality within a week due to a depletion of c-kit+ cells. Characterization revealed a cell autonomous requirement for Cdc73 to prevent apoptosis in HSPCs. Gene expression profiling on both c-kit+ hematopoietic cells and AML cells revealed that Hoxa9/Meis1 gene programs are differentially responsive to loss of Cdc73. This work revealed an essential role for the PAF1c subunit in maintaining viability of HSPCs and points to AML specific functions for the PAF1c. Thus, we utilized immunoprecipitation followed by mass spectroscopy to identify novel PAF1c interactions in AML cells. We found a novel interaction with several H3K9 methyltransferases including SETDB1. We demonstrate that the PAF1c-SETDB1 interaction reduces expression of Hoxa9 and Meis1 by promoting deposition of H3K9me3. These findings mirrored human AML patient samples that showed SETDB1 expression was inversely correlated with HOXA9 and MEIS1 expression. Further, SETDB1 expression is correlated to disease status and overall survival in AML patients. We recapitulated these findings in mice, where high expression of SETDB1 delayed MLL-AF9 mediated disease progression by promoting differentiation of AML cells. We also explored the biological impact of treating normal and malignant hematopoietic cells with an H3K9 methyltransferase inhibitor, UNC0638. While AML cells demonstrate cytotoxicity to UNC0638 treatment, normal bone marrow cells exhibit an expansion of HSPCs. Consistent with these data, we show that bone marrow treated with UNC0638 is more amenable to transformation by MLL-AF9. Next generation sequencing of AML cells shows that high expression of SETDB1 induces repressive changes to the promoter epigenome and downregulation of genes linked with AML, including Dock1 and the MLL-AF9 target genes Hoxa9, Six1, and others. These data reveal novel targets of SETDB1 in AML that point to a role for SETDB1 in negatively regulating pro-leukemic target genes and suppressing AML. Disclosures Maillard: Genentech: Consultancy; Regeneron: Consultancy.

SIX1 Is a Novel Effector Gene in CALM-AF10 Leukemia

Background: The CALM-AF10 translocation is detected in ~10% of T-cell acute lymphoblastic leukemias (T-ALLs), and in some acute myeloid leukemias (AMLs). CALM-AF10 leukemias are characterized by high expression of proleukemic HOXA genes, which serve a critical role in hematopoiesis. We hypothesized that identification of novel CALM-AF10 effector genes may yield new therapeutic targets in this difficult to treat leukemia. We took advantage of our prior observation that the nuclear export factor CRM1/XPO1 tethers CALM-AF10 to HOXA genes by interacting with a nuclear export signal (NES) in CALM. Using next generation sequencing, we determined that, SIX1, similar to HOXA genes, is increased in CALM-AF10 leukemias and decreased in response to CRM1 inhibition with Leptomycin B (LMB). Design/Methods: RT-qPCR and Chromatin Immunoprecipitation were performed using both bone marrow progenitors and murine embryonic fibroblasts (MEFs) transduced with CALM-AF10 or an empty vector, with and without LMB. The ability of SIX1 to enhance self-renewal of hematopoietic progenitors was examined by measuring the colony-forming ability of transduced fetal liver hematopoietic progenitor cells. CRISPR-Cas9 was used to silence SIX1 in Human Embryonic Kidney 293 (HEK293) cells. Results: RT-qPCR confirmed overexpression of SIX1 in both CALM-AF10 transduced MEFs and CALM-AF10 leukemias, with decreased SIX1 expression observed in the presence of LMB. ChIP analysis showed that CALM-AF10 binds to the SIX1 gene locus. Overexpression of SIX1 in fetal liver cells was sufficient to increase the self-renewal potential of colony-forming progenitors. SIX1 was successfully knocked out in HEK293 cells without a significant effect on HEK293 proliferation. Conclusions: The SIX1 homeobox gene is highly expressed during development and its expression is silenced post-embryogenesis. Increased SIX1 expression has been reported in numerous solid tumors. We have determined that SIX1 is upregulated in CALM-AF10 leukemias, and increases the self-renewal potential of hematopoietic progenitors. Using CRISPR-Cas9 to silence SIX1, we have demonstrated that SIX1 is not essential for cell survival, and that its inhibition may impair CALM-AF10 leukemia cell proliferation. Thus, SIX1 may play a pathogenic role in leukemogenesis and is a potential therapeutic target in CALM-AF10 leukemias. Disclosures No relevant conflicts of interest to declare.

SETDB1 mediated histone H3 lysine 9 methylation suppresses MLL-fusion target expression and leukemic transformation.

Epigenetic regulators play a critical role in normal and malignant hematopoiesis. Deregulation, including epigenetic deregulation, of the HOXA gene cluster drives transformation of about 50% of acute myeloid leukemia (AML). We recently showed that the histone 3 lysine 9 methyltransferase SETDB1 negatively regulates the expression of the proleukemic genes Hoxa9 and its cofactor Meis1 through deposition of promoter H3K9 trimethylation in MLL-AF9 leukemia cells. Here, we investigated the biological impact of altered SETDB1 expression and changes in H3K9 methylation on AML. We demonstrate that SETDB1 expression is correlated to disease status and overall survival in AML patients. We recapitulated these findings in mice, where high expression of SETDB1 delayed MLL-AF9 mediated disease progression by promoting differentiation of leukemia cells. We also explored the biological impact of treating normal and malignant hematopoietic cells with an H3K9 methyltransferase inhibitor, UNC0638. While myeloid leukemia cells demonstrate cytotoxicity to UNC0638 treatment, normal bone marrow cells exhibit an expansion of cKit+ hematopoietic stem and progenitor cells. Consistent with these data, we show that bone marrow treated with UNC0638 is more amenable to transformation by MLL-AF9. Next generation sequencing of leukemia cells shows that high expression of SETDB1 induces repressive changes to the promoter epigenome and downregulation of genes linked with AML, including Dock1 and the MLL-AF9 target genes Hoxa9, Six1, and others. These data reveal novel targets of SETDB1 in leukemia that point to a role for SETDB1 in negatively regulating pro-leukemic target genes and suppressing AML.

LncRNA FOXD2-AS1 confers cisplatin resistance of non-small-cell lung cancer via regulation of miR185-5p-SIX1 axis.

Background: Chemoresistance is a major obstacle for chemotherapy failure in non-small-cell lung cancer (NSCLC). lncRNAs are a class of pivotal regulators in various cancers, and the lncRNA FOXD2-AS1 is implicated in the progression of NSCLC. However, it is still unclear whether it regulates chemosensitivity.Methods: Expression levels of FOXD2-AS1, miR185-5p, and SIX1 mRNA were identified by reverse-transcription qPCR. CCK8 assay was performed to assess cell proliferation and chemosensitivity of cisplatin-resistant A549/DDP and H1299/DDP cells. Colony-forming assay was utilized to detect colony numbers. Cell migration and invasion ability were measured by transwell assay. The protein levels of LRP, Pgp, MRP1, and SIX1 were examined by Western blot assay. The correlation between FOXD2-AS1 and miR185-5p or miR185-5p and SIX1 were validated by bioinformatic, dual-luciferase, and RNA immunoprecipitation assays. Tumor xenografts were constructed to confirm the function and mechanism of FOXD2-AS1 in chemosensitivity of DDP-resistant NSCLC.Results: FOXD2-AS1 and SIX1 were upregulated and miR185-5p downregulated in DDP-resistant NSCLC. Absence of FOXD2-AS1 enhanced drug sensitivity of A549/DDP and H1299/DDP cells, reflected by the reduced colony formation, cell proliferation, migration, invasion, and drug resistance–associated protein expression. FOXD2-AS1 acted as a molecular sponge for miR185-5p and relieved the binding of miR185-5p and its target gene SIX1, leading to the derepression of SIX1 in A549/DDP and H1299/DDP cells. Rescue experiments validated the functional interaction among FOXD2-AS1, miR185-5p, and SIX1. Moreover, FOXD2-AS1 interference receded the growth of DDP-resistant NSCLC tumors in vivo.Conclusion: FOXD2-AS1/miR185-5p/SIX1 regulates the progression and chemosensitivity of DDP-resistant NSCLC, suggesting a potential therapeutic target for cisplatin-resistant NSCLC patients.