Sry-box (Sox) transcription factors in gastrointestinal physiology and disease

Highlighting the role of long non-coding RNA (LncRNA) in multiple myeloma (MM) pathogenesis and response to therapy

Transcripts longer than 200 nucleotides that are not translated into proteins are known as long non-coding RNAs, or lncRNAs. Now, they are becoming more significant as important regulators of gene expression, and as a result, of many biological processes in both healthy and pathological circumstances, such as blood malignancies. Through controlling alternative splicing, transcription, and translation at the post-transcriptional level, lncRNAs have an impact on the expression of genes. In multiple myeloma (MM), the majority of lncRNAs is elevated and promotes the proliferation, adhesion, drug resistance and invasion of MM cells by blocking apoptosis and altering the tumor microenvironment (TME). To control mRNA splicing, stability, and translation, they either directly attach to the target mRNA or transfer RNA-binding proteins (RBPs). By expressing certain miRNA-binding sites that function as competitive endogenous RNAs (ceRNAs), most lncRNAs mimic the actions of miRNAs. Here, we highlight lncRNAs role in the MM pathogenesis with emphasize on their capacity to control the molecular mechanisms known as "hallmarks of cancer," which permit earlier tumor initiation and progression and malignant cell transformation.

Resolution of Acinar Dedifferentiation Regulates Tissue Remodeling in Pancreatic Injury and Cancer Initiation

BACKGROUND & AIMS

Acinar-to-ductal metaplasia (ADM) is crucial in the development of pancreatic ductal adenocarcinoma. However, our understanding of the induction and resolution of ADM remains limited. We conducted comparative transcriptome analyses to identify conserved mechanisms of ADM in mouse and human.

METHODS

We identified Sox4 among the top up-regulated genes. We validated the analysis by RNA in situ hybridization. We performed experiments in mice with acinar-specific deletion of Sox4 (Ptf1a: CreER; Rosa26-LSL-YFPLSL-YFP; Sox4fl/fl) with and without an activating mutation in Kras (KrasLSL-G12D/+). Mice were given caerulein to induce pancreatitis. We performed phenotypic analysis by immunohistochemistry, tissue decellularization, and single-cell RNA sequencing.

RESULTS

We demonstrated that Sox4 is reactivated in ADM and pancreatic intraepithelial neoplasias. Contrary to findings in other tissues, Sox4 actually counteracts cellular dedifferentiation and helps maintain tissue homeostasis. Moreover, our investigations unveiled the indispensable role of Sox4 in the specification of mucin-producing cells and tuft-like cells from acinar cells. We identified Sox4-dependent non-cell-autonomous mechanisms regulating the stromal reaction during disease progression. Notably, Sox4-inferred targets are activated upon KRAS inactivation and tumor regression.

CONCLUSIONS

Our results indicate that our transcriptome analysis can be used to investigate conserved mechanisms of tissue injury. We demonstrate that Sox4 restrains acinar dedifferentiation and is necessary for the specification of acinar-derived metaplastic cells in pancreatic injury and cancer initiation and is activated upon Kras ablation and tumor regression in mice. By uncovering novel potential strategies to promote tissue homeostasis, our findings offer new avenues for preventing the development of pancreatic ductal adenocarcinoma.

ROR2 deficit may induce the tetralogy of Fallot via down-regulating of β-catenin/SOX3/HSPA6 in vitro and in vivo

Tetralogy of Fallot (TOF) is the highly conventional appearance of cyanotic congenital heart disease. Our study aimed to assess the involvement of receptor tyrosine kinase-like orphan receptor 2 (ROR2) in TOF and elucidate the specific mechanism. Upon investigation of human tissue samples, we observed a decrease in ROR2 expression in TOF patients compared to healthy control individuals. Transcriptome analysis revealed diminished ROR2 expression in TOF pathological samples relative to normal tissues. Of the 2246 genes that exhibited altered expression, 886 were upregulated, while 1360 were down-regulated. KEGG analysis and GO analysis of the differentially expressed genes indicated that these genes were significantly enriched in the Wnt signalling pathway, apoptosis and cardiac development function. Importantly, ROR2 was the only gene shared among the three pathways. Furthermore, interference with ROR2 promotes apoptosis and curtails cell proliferation in vitro. The knockdown of the ROR2 gene in AC16 cells resulted in a significant decrease in Edu-positive cells. Flow cytometry studies indicated an increase in the percentage of cells in the S phase. In contrast, the G2/M cell cycle transition was blocked in the ROR2-knockdown group, leading to a significant increase in apoptosis. Moreover, the CCK-8 cell viability assay demonstrated a reduced proliferation in the ROR2-knockdown group. Furthermore, both in vivo and in vitro data indicated that the expression of HSPA6 (Recombinant Heat Shock 70 kDa Protein6), an essential gene enriched in cardiac tissue and associated with apoptosis, was down-regulated following ROR2 knockdown mediated by the β-catenin/SOX3 signalling pathway. In conclusion, low expression of ROR2 plays a crucial role in the occurrence and development of TOF, which may be related to the downregulation of HSPA6 through the β-catenin/SOX3 signalling pathway.

Genome-wide association studies of human and rat BMI converge on synapse, epigenome, and hormone signaling networks

A vexing observation in genome-wide association studies (GWASs) is that parallel analyses in different species may not identify orthologous genes. Here, we demonstrate that cross-species translation of GWASs can be greatly improved by an analysis of co-localization within molecular networks. Using body mass index (BMI) as an example, we show that the genes associated with BMI in humans lack significant agreement with those identified in rats. However, the networks interconnecting these genes show substantial overlap, highlighting common mechanisms including synaptic signaling, epigenetic modification, and hormonal regulation. Genetic perturbations within these networks cause abnormal BMI phenotypes in mice, too, supporting their broad conservation across mammals. Other mechanisms appear species specific, including carbohydrate biosynthesis (humans) and glycerolipid metabolism (rodents). Finally, network co-localization also identifies cross-species convergence for height/body length. This study advances a general paradigm for determining whether and how phenotypes measured in model species recapitulate human biology.

Kolon adenokarsinomlarında ve adenomatöz poliplerinde Beta-Catenin ve Sox2 ekspresyonu ve klinikopatolojik parametreler ile ilişkileri

Objective: Our aim was to investigate the immunohistochemical expression of β-catenin and Sox-2 in adenomatous polyps and adenocarcinoma of colon and also to evaluate the effects of these markers in adenoma-carcinoma sequence and their association with clinicopathological parameters. Methods: Fifty-six tubular adenomas with low grade dysplasia (TALGD), 53 tubular adenomas with high grade dysplasia (TAHGD), 44 tubulovillous adenomas (TVA), 29 villous adenomas (VA) and 60 adenocarcinomas were included in the study. The nuclear staining of Sox2 was evaluated as well as both nuclear and cytoplasmic stainings of β-catenin. A semiquantitative scoring was performed. The results were compared between the groups and the relationship of the results with clinicopathological parameters was evaluated. Results: Nuclear and cytoplasmic β-catenin expressions of the adenocarcinomas were higher than polyps. The expressions in the VA and TVA polyp groups were higher than the expressions in TAHGD and TALGD, respectively. Membranous β-catenin expression in the adenocarcinoma was higher than the polyps except VA. The evaluation between polyp groups with respect to membranous β-catenin staining revealed a statistically significantly difference in favor of VA compared with TVA, TAHGD and TALGD; in favor of TAHGD compared with TVA, in favor of TVA compared with TALGD while it was found statistically significantly higher in TAHGD than TALGD. Conclusion: The results regarding β-catenin expression of the polyp groups were consistent with the literature. There was a positive correlation between β-catenin expression (nuclear and cytoplasmic) and malignancy. High Sox2 expressions were found correlated with malignancy potential. Large sampling size investigations to be supported by further molecular studies are needed to clarify the effect of Sox2 expression in the sequence of adenoma-carcinoma comprehensively.

Follow the Metaplasia: Characteristics and Oncogenic Implications of Metaplasia's Pattern of Spread Throughout the Stomach

The human stomach functions as both a digestive and innate immune organ. Its main product, acid, rapidly breaks down ingested products and equally serves as a highly effective microbial filter. The gastric epithelium has evolved mechanisms to appropriately handle the myriad of injurious substances, both exogenous and endogenous, to maintain the epithelial barrier and restore homeostasis. The most significant chronic insult that the stomach must face is Helicobacter pylori (Hp), a stomach-adapted bacterium that can colonize the stomach and induce chronic inflammatory and pre-neoplastic changes. The progression from chronic inflammation to dysplasia relies on the decades-long interplay between this oncobacterium and its gastric host. This review summarizes the functional and molecular regionalization of the stomach at homeostasis and details how chronic inflammation can lead to characteristic alterations in these developmental demarcations, both at the topographic and glandular levels. More importantly, this review illustrates our current understanding of the epithelial mechanisms that underlie the pre-malignant gastric landscape, how Hp adapts to and exploits these changes, and the clinical implications of identifying these changes in order to stratify patients at risk of developing gastric cancer, a leading cause of cancer-related deaths worldwide.

Genome wide identification, phylogeny, and synteny analysis of sox gene family in common carp (Cyprinus carpio)

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27 SOX (high-mobility group HMG-box) genes were identified in the C. carp genome.

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SOX genes ranging from 3496 (SOX6) to 924bp (SOX17b) which coded with putative protein series from 307 to 509 amino acids.

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Gene ontology revealed SOX proteins maximum involvement is in metabolic process 49.796 %.

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Chromosomal location and synteny analysis display all SOX gene are located on different chromosomes.

Common carp (Cyprinus carpio) is a commercial fish species valuable for nutritious components and plays a vital role in human healthy nutrition. The SOX (SRY-related genes systematically characterized by a high-mobility group HMG-box) encoded important gene regulatory proteins, a family of transcription factors found in a broad range of animal taxa and extensively known for its contribution in multiple developmental processes including contribution in sex determination across phyla. In our current study, we initially accomplished a genome-wide analysis to report the SOX gene family in common carp fish based on available genomic sequences of zebrafish retrieved from gene repository databases, we focused on the global identification of the Sox gene family in Common carp among wide range of vertebrates and teleosts based on bioinformatics tools and techniques and explore the evolutionary relationships. In our results, a total of 27 SOX (high-mobility group HMG-box) domain genes were identified in the C. carp genome. The full length sequences of SOX genes ranging from 3496 (SOX6) to 924bp (SOX17b) which coded with putative proteins series from 307 to 509 amino acids and all gene having exon number expect SOX9 and SOX13. All the SOX proteins contained at least one conserved DNA-binding HMG-box domain and two (SOX7 and SOX18) were found C terminal. The Gene ontology revealed SOX proteins maximum involvement is in metabolic process 49.796 %, average in biological regulation 45.188 %, biosynthetic process (19.992 %), regulation of cellular process 39.68, 45.508 % organic substance metabolic process, multicellular organismal process 23.23 %,developmental process 21.74 %, system development 16.59 %, gene expression 16.05 % and 14.337 % of RNA metabolic process. Chromosomal location and syntanic analysis show all SOX gene are located on different chromosomes and apparently does not fallow the unique pattern. The maximum linkage of chromosome is (2) on Unplaced Scaffold region. Finally, our results provide important genomic suggestion for upcoming studies of biochemical, physiological, and phylogenetic understanding on SOX genes among teleost.

LncRNA SNHG1 contributes to the regulation of acute myeloid leukemia cell growth by modulating miR-489-3p/SOX12/Wnt/β-catenin signaling

The long noncoding RNA (lncRNA) small nucleolar RNA host gene 1 (SNHG1) is a critical regulator for the development and progression of multiple tumors. Yet, the role of SNHG1 in acute myeloid leukemia (AML) is unknown. The present study demonstrated that SNHG1 expression was upregulated in AML. SNHG1 silencing markedly repressed AML cell growth, whereas SNHG1 overexpression had the opposite effect. MicroRNA-489-3p (miR-489-3p) was identified as a SNHG1-targeting miRNA. SNHG1 knockdown increased miR-489-3p expression. Low expression of miR-489-3p was correlated with high expression of SNHG1 in AML tissues. miR-489-3p overexpression restricted AML cell growth, and SRY-related high-mobility-group box 12 (SOX12) was identified as a miR-489-3p-targeting gene. SNHG1 inhibition or miR-489-3p overexpression inactivated Wnt/β-catenin signaling through downregulation of SOX12. SOX12 overexpression partially reversed the SNHG1 knockdown- or miR-489-3p overexpression-mediated effects. Taken together, these data indicate that suppression of SNHG1 downregulates AML cell growth by inactivating SOX12/Wnt/β-catenin signaling via upregulating miR-489-3p.

Associations between body condition score at parturition and microRNA profile in colostrum of dairy cows as evaluated by paired mapping programs

MicroRNA (miRNA) are abundant in milk, and likely have regulatory activity involving lactation and immunity. The objective of this study was to determine the miRNA profile in colostrum of overconditioned cows compared with cows of more moderate body condition score (BCS) at calving. Multiparous cows with either high (≥4.0 on a scale of 1 to 5; n = 7) or moderate BCS (2.75 to 3.50; n = 9) in the week before parturition were selected from a commercial dairy herd. Blood and colostrum were sampled within 24 h after calving. Blood serum was analyzed for free fatty acid (FFA) concentration. MicroRNA was isolated from colostrum samples after removing milk fat and cells. MicroRNA were sequenced, and reads were mapped to the bovine genome and to the existing database of miRNA at miRBase.org. Two programs, Oasis 2.0 and miRDeep2, were employed in parallel for read alignment, and analysis of miRNA count data was performed using DESeq2. Identification of differentially expressed miRNA from DESeq2 was not affected by the differences in miRNA detected by the 2 mapping programs. Most abundant miRNA included miR-30a, miR-148a, miR-181a, let-7f, miR-26a, miR-21, miR-22, and miR-92a. Large-scale shifts in miRNA profile were not observed; however, colostrum of cows with high BCS contained less miR-486, which has been linked with altered glucose metabolism. Colostrum from cows with elevated serum FFA contained less miR-885, which may be connected to hepatic function during the transition period. Potential functions of abundant miRNA suggest involvement in development and maintenance of cellular function in the mammary gland, with the additional possibility of influencing neonatal tissue and immune system development.

Sox4 Promotes Atoh1-Independent Intestinal Secretory Differentiation Toward Tuft and Enteroendocrine Fates

BACKGROUND & AIMS

The intestinal epithelium is maintained by intestinal stem cells (ISCs), which produce postmitotic absorptive and secretory epithelial cells. Initial fate specification toward enteroendocrine, goblet, and Paneth cell lineages requires the transcription factor Atoh1, which regulates differentiation of the secretory cell lineage. However, less is known about the origin of tuft cells, which participate in type II immune responses to parasite infections and appear to differentiate independently of Atoh1. We investigated the role of Sox4 in ISC differentiation.

METHODS

We performed experiments in mice with intestinal epithelial-specific disruption of Sox4 (Sox4fl/fl:vilCre; SOX4 conditional knockout [cKO]) and mice without disruption of Sox4 (control mice). Crypt- and single-cell-derived organoids were used in assays to measure proliferation and ISC potency. Lineage allocation and gene expression changes were studied by immunofluorescence, real-time quantitative polymerase chain reaction, and RNA-seq analyses. Intestinal organoids were incubated with the type 2 cytokine interleukin 13 and gene expression was analyzed. Mice were infected with the helminth Nippostrongylus brasiliensis and intestinal tissues were collected 7 days later for analysis. Intestinal tissues collected from mice that express green fluorescent protein regulated by the Atoh1 promoter (Atoh1GFP mice) and single-cell RNA-seq analysis were used to identify cells that coexpress Sox4 and Atoh1. We generated SOX4-inducible intestinal organoids derived from Atoh1fl/fl:vilCreER (ATOH1 inducible knockout) mice and assessed differentiation.

RESULTS

Sox4cKO mice had impaired ISC function and secretory differentiation, resulting in decreased numbers of tuft and enteroendocrine cells. In control mice, numbers of SOX4+ cells increased significantly after helminth infection, coincident with tuft cell hyperplasia. Sox4 was activated by interleukin 13 in control organoids; SOX4cKO mice had impaired tuft cell hyperplasia and parasite clearance after infection with helminths. In single-cell RNA-seq analysis, Sox4+/Atoh1- cells were enriched for ISC, progenitor, and tuft cell genes; 12.5% of Sox4-expressing cells coexpressed Atoh1 and were enriched for enteroendocrine genes. In organoids, overexpression of Sox4 was sufficient to induce differentiation of tuft and enteroendocrine cells-even in the absence of Atoh1.

CONCLUSIONS

We found Sox4 promoted tuft and enteroendocrine cell lineage allocation independently of Atoh1. These results challenge the longstanding model in which Atoh1 is the sole regulator of secretory differentiation in the intestine and are relevant for understanding epithelial responses to parasitic infection.

Reserve Stem Cells in Intestinal Homeostasis and Injury

Renewal of the intestinal epithelium occurs approximately every week and requires a careful balance between cell proliferation and differentiation to maintain proper lineage ratios and support absorptive, secretory, and barrier functions. We review models used to study the mechanisms by which intestinal stem cells (ISCs) fuel the rapid turnover of the epithelium during homeostasis and might support epithelial regeneration after injury. In anatomically defined zones of the crypt stem cell niche, phenotypically distinct active and reserve ISC populations are believed to support homeostatic epithelial renewal and injury-induced regeneration, respectively. However, other cell types previously thought to be committed to differentiated states might also have ISC activity and participate in regeneration. Efforts are underway to reconcile the proposed relatively strict hierarchical relationships between reserve and active ISC pools and their differentiated progeny; findings from models provide evidence for phenotypic plasticity that is common among many if not all crypt-resident intestinal epithelial cells. We discuss the challenges to consensus on ISC nomenclature, technical considerations, and limitations inherent to methodologies used to define reserve ISCs, and the need for standardized metrics to quantify and compare the relative contributions of different epithelial cell types to homeostatic turnover and post-injury regeneration. Increasing our understanding of the high-resolution genetic and epigenetic mechanisms that regulate reserve ISC function and cell plasticity will help refine these models and could affect approaches to promote tissue regeneration after intestinal injury.

The Sox transcriptional factors: Functions during intestinal development in vertebrates

The intestine has long been studied as a model for adult stem cells due to the life-long self-renewal of the intestinal epithelium through the proliferation of the adult intestinal stem cells. Recent evidence suggests that the formation of adult intestinal stem cells in mammals takes place during the thyroid hormone-dependent neonatal period, also known as postembryonic development, which resembles intestinal remodeling during frog metamorphosis. Studies on the metamorphosis in Xenopus laevis have revealed that many members of the Sox family, a large family of DNA binding transcription factors, are upregulated in the intestinal epithelium during the formation and/or proliferation of the intestinal stem cells. Similarly, a number of Sox genes have been implicated in intestinal development and pathogenesis in mammals. Futures studies are needed to determine the expression and potential involvement of this important gene family in the development of the adult intestinal stem cells. These include the analyses of the expression and regulation of these and other Sox genes during postembryonic development in mammals as well as functional investigations in both mammals and amphibians by using the recently developed gene knockout technologies.

PlGF knockdown inhibited tumor survival and migration in gastric cancer cell via PI3K/Akt and p38MAPK pathways

The molecular signalling of placental growth factor (PlGF), a member of the vascular endothelial growth factor family, was not uncovered in human adenocarcinoma gastric cell line (AGS). The purpose of this study was to examine the inhibitory effects of PlGF knockdown on cell proliferation, apoptosis and migration through p38 mitogen-activated protein kinase (p38MAPK) and PI3K pathways in human adenocarcinoma gastric cell line (AGS). To study PlGF knockdown effect, AGS cells were treated with 40 pmol of small interfering RNA (siRNA) related to PlGF gene and also a scrambled siRNA as control. Trypan Blue and Anexin V staining of AGS cells treated with PlGF-specific siRNA showed induction of apoptosis. Wound healing assay and zymography indicated that cellular migration and matrix metalloproteinases activities were reduced in response to PlGF knockdown. Phosphorylation of Akt and p38MAPK was reduced in AGS cells treated with PlGF-specific siRNA. PlGF knockdown decreased transcripts of PI3K, Akt, p38MAPK, PCNA, Caspase-3, OCT3/OCT4 and CD44, but elevated p53 and SOX2 transcripts. Our results indicated that PlGF knockdown decreased migration and induced apoptosis through PI3K/Akt1 and p38MAPK signal transduction in AGS cells.

Genome-Wide Identification and Transcriptome-Based Expression Profiling of the Sox Gene Family in the Nile Tilapia (Oreochromis niloticus)

The Sox transcription factor family is characterized with the presence of a Sry-related high-mobility group (HMG) box and plays important roles in various biological processes in animals, including sex determination and differentiation, and the development of multiple organs. In this study, 27 Sox genes were identified in the genome of the Nile tilapia (Oreochromis niloticus), and were classified into seven groups. The members of each group of the tilapia Sox genes exhibited a relatively conserved exon-intron structure. Comparative analysis showed that the Sox gene family has undergone an expansion in tilapia and other teleost fishes following their whole genome duplication, and group K only exists in teleosts. Transcriptome-based analysis demonstrated that most of the tilapia Sox genes presented stage-specific and/or sex-dimorphic expressions during gonadal development, and six of the group B Sox genes were specifically expressed in the adult brain. Our results provide a better understanding of gene structure and spatio-temporal expression of the Sox gene family in tilapia, and will be useful for further deciphering the roles of the Sox genes during sex determination and gonadal development in teleosts.

A Sox Transcription Factor Is a Critical Regulator of Adult Stem Cell Proliferation in the Drosophila Intestine

Adult organs and their resident stem cells are constantly facing the challenge of adapting cell proliferation to tissue demand, particularly in response to environmental stresses. Whereas most stress-signaling pathways are conserved between progenitors and differentiated cells, stem cells have the specific ability to respond by increasing their proliferative rate, using largely unknown mechanisms. Here, we show that a member of the Sox family of transcription factors in Drosophila, Sox21a, is expressed in intestinal stem cells (ISCs) in the adult gut. Sox21a is essential for the proliferation of these cells during both normal epithelium turnover and repair. Its expression is induced in response to tissue damage, downstream of the Jun N-terminal kinase (JNK) and extracellular signal-regulated kinase (ERK) pathways, to promote ISC proliferation. Although short-lived, Sox21a mutant flies show no developmental defects, supporting the notion that this factor is a specific regulator of adult stem cell proliferation.

miR-21 promotes the differentiation of hair follicle-derived neural crest stem cells into Schwann cells

Hair follicle-derived neural crest stem cells can be induced to differentiate into Schwann cells in vivo and in vitro. However, the underlying regulatory mechanism during cell differentiation remains poorly understood. This study isolated neural crest stem cells from human hair follicles and induced them to differentiate into Schwann cells. Quantitative RT-PCR showed that microRNA (miR)-21 expression was gradually increased during the differentiation of neural crest stem cells into Schwann cells. After transfection with the miR-21 agonist (agomir-21), the differentiation capacity of neural crest stem cells was enhanced. By contrast, after transfection with the miR-21 antagonist (antagomir-21), the differentiation capacity was attenuated. Further study results showed that SOX-2 was an effective target of miR-21. Without compromising SOX2 mRNA expression, miR-21 can down-regulate SOX protein expression by binding to the 3′-UTR of miR-21 mRNA. Knocking out the SOX2 gene from the neural crest stem cells significantly reversed the antagomir-21 inhibition of neural crest stem cells differentiating into Schwann cells. The results suggest that miR-21 expression was increased during the differentiation of neural crest stem cells into Schwann cells and miR-21 promoted the differentiation through down-regulating SOX protein expression by binding to the 3′-UTR of SOX2 mRNA.

Peroxisome proliferator-activated receptor γ-mediated induction of microRNA-145 opposes tumor phenotype in colorectal cancer

MicroRNAs (miRNAs) regulate diverse biological processes by inhibiting translation or inducing degradation of target mRNAs. miR-145 is a candidate tumor suppressor in colorectal carcinoma (CRC). Colorectal carcinogenesis involves deregulation of cellular processes controlled by a number of intertwined chief transcription factors, such as PPARγ and SOX9. Since PPAR family members are able to modulate complex miRNAs networks, we hypothesized a role of miRNA-145 in the interaction between PPARγ and SOX9 in colorectal carcinogenesis. To address this issue, we evaluated gene expression in tissue specimens of CRC patients and we took advantage of invitro models represented by CRC derived cell lines (CaCo2, SW480, HCT116, and HT-29), employing PPARγ activation and/or miRNA-145 ectopic overexpression to analyze how their interplay impact the expression of SOX9 and the development of a malignant phenotype.

RESULTS

PPARγ regulates the expression of miR-145 by directly binding to a PPAR response element (PPRE) in its promoter at -1207/-1194bp from the transcription start site. The binding is essential for miR-145 upregulation by PPARγ upon rosiglitazone treatment. Ectopic expression of miR-145, in turn, regulates SOX9 expression through the binding to specific seed motifs. The PPARγ-miR-145-SOX9 axis overarches cell cycle progression, invasiveness and differentiation of CRC derived cell lines. Together, these results suggest that miR-145 is a novel target of PPARγ, acts as a tumor suppressor in CRC cell lines and is a key regulator of intestinal cell differentiation by directly targeting SOX9, a marker of undifferentiated progenitors in the colonic crypts.

A simple transcriptomic signature able to predict drug-induced hepatic steatosis

It is estimated that only a few marketed drugs are able to directly induce liver steatosis. However, many other drugs may exacerbate or precipitate fatty liver in the presence of other risk factors or in patients prone to non-alcoholic fatty liver disease. On the other hand, current in vitro tests for drug-induced steatosis in preclinical research are scarce and not very sensitive or reproducible. In the present study, we have investigated the effect of well-characterized steatotic drugs on the expression profile of 47 transcription factors (TFs) in human hepatoma HepG2 cells and found that these drugs are able to up- and down-regulate a substantial number of these factors. Multivariate data analysis revealed a common TF signature for steatotic drugs, which consistently and significantly repressed FOXA1, HEX and SREBP1C in cultured cells. This signature was also observed in the livers of rats and in cultured human hepatocytes. Therefore, we selected these three TFs as predictive biomarkers for iatrogenic steatosis. With these biomarkers, a logistic regression analysis yielded a predictive model, which was able to correctly classify 92 % of drugs. The developed algorithm also predicted that ibuprofen, nifedipine and irinotecan are potential steatotic drugs, whereas troglitazone is not. In summary, this is a sensitive, specific and simple RT-PCR test that can be easily implemented in preclinical drug development to predict drug-induced steatosis. Our results also indicate that steatotic drugs affect expression of both common and specific subsets of TF and lipid metabolism genes, thus generating complex transcriptomic responses that cause or contribute to steatosis in hepatocytes.

Combined overexpression of HIVEP3 and SOX9 predicts unfavorable biochemical recurrence-free survival in patients with prostate cancer

BACKGROUND

To clarify the involvement of HIVEP3 and SOX9 coexpression in prostate cancer (PCa).

METHODS

A small interfering RNA was used to knockdown SOX9 expression in a PCa cell line and to analyze the effects of SOX9 inhibition on the expression of HIVEP3 in vitro. Then, HIVEP3 and SOX9 expression patterns in the human PCa tissues were detected using quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis and immunohistochemistry.

RESULTS

We found that the downregulation of SOX9 could inhibit the expression of HIVEP3 in the PCa cells in vitro. In addition, both HIVEP3 and SOX9 messenger RNA expression levels in the PCa tissues were significantly higher than those in the noncancerous prostate tissues (P=0.006 and P<0.001, respectively). Moreover, the immunohistochemical staining scores of HIVEP3 in the PCa tissues with PSA failure were significantly higher than those without (P=0.042); the increased SOX9 protein expression was more frequently found in the PCa tissues with a high Gleason score (P=0.045) and a high clinical stage (P=0.012). The tumors showing the HIVEP3-high/SOX9-high expression more frequently had PSA failure (P=0.024). When the patients with an HIVEP3 overexpression combined with the SOX9 overexpression, this group had a worse biochemical recurrence-free survival (P<0.001). Furthermore, the multivariate analysis showed that the HIVEP3/SOX9 coexpression was an independent predictor of an unfavorable biochemical recurrence-free survival.

CONCLUSION

Our data offer the convincing evidence for the first time that a combined analysis of HIVEP3 and SOX9 may help to predict the tumor progression and prognosis of PCa patients. In particular, the overexpression of HIVEP3 in PCa might partly explain the poor prognosis of patients with an upregulation of SOX9.

Inducible intestine-specific deletion of Krüppel-like factor 5 is characterized by a regenerative response in adult mouse colon

Krüppel-like factor 5 (KLF5) is a pro-proliferative transcriptional regulator primarily expressed in the intestinal crypt epithelial cells. Constitutive intestine-specific deletion of Klf5 is neonatal lethal suggesting a crucial role for KLF5 in intestinal development and homeostasis. We have previously shown Klf5 to play an active role regulating intestinal tumorigenesis. Here we examine the effect of inducible intestine-specific deletion of Klf5 in adult mice. Klf5 is lost from the intestine beginning at day 3 after the start of a 5-day treatment with the inducer tamoxifen. Although the mice have no significant weight loss or lethality, the colonic tissue shows signs of epithelial distress starting at day 3 following induction. Accompanying the morphological changes is a significant loss of proliferative crypt epithelial cells as revealed by BrdU or Ki67 staining at days 3 and 5 after start of tamoxifen. We also observed a loss of goblet cells from the colon and Paneth cells from the small intestine upon induced deletion of Klf5. In addition, loss of Klf5 from the colonic epithelium is accompanied by a regenerative response that coincides with an expansion in the zone of Sox9 expression along the crypt axis. At day 11, both proliferation and Sox9 expression return to baseline levels. Microarray and quantitative PCR analyses reveal an up-regulation of several regeneration-associated genes (Reg1A, Reg3G and Reg3B) and down-regulation of many Klf5 targets (Ki-67, cyclin B, Cdc2 and cyclin D1). Sox9 and Reg1A protein levels are also increased upon Klf5 loss. Lentiviral-mediated knockdown of KLF5 and exogenous expression of KLF5 in colorectal cancer cell lines confirm that Sox9 expression is negatively regulated by KLF5. Furthermore, ChIP assays reveal a direct association of KLF5 with both the Sox9 and Reg1A promoters. We have shown that disruption of epithelial homeostasis due to Klf5 loss from the adult colon is followed by a regenerative response led by Sox9 and the Reg family of proteins. Our study demonstrates that adult mouse colonic tissue undergoes acute physiological changes to accommodate the loss of Klf5 withstanding epithelial damage further signifying importance of Klf5 in colonic homeostasis.

Enterocyte-specific regulation of the apical nutrient transporter SLC6A19 (B(0)AT1) by transcriptional and epigenetic networks

Enterocytes are specialized to absorb nutrients from the lumen of the small intestine by expressing a select set of genes to maximize the uptake of nutrients. They develop from stem cells in the crypt and differentiate into mature enterocytes while moving along the crypt-villus axis. Using the Slc6a19 gene as an example, encoding the neutral amino acid transporter B(0)AT1, we studied regulation of the gene by transcription factors and epigenetic factors in the intestine. To investigate this question, we used a fractionation method to separate mature enterocytes from crypt cells and analyzed gene expression. Transcription factors HNF1a and HNF4a activate transcription of the Slc6a19 gene in villus enterocytes, whereas high levels of SOX9 repress expression in the crypts. CpG dinucleotides in the proximal promoter were highly methylated in the crypt and fully de-methylated in the villus. Furthermore, histone modification H3K27Ac, indicating an active promoter, was prevalent in villus cells but barely detectable in crypt cells. The results suggest that Slc6a19 expression in the intestine is regulated at three different levels involving promoter methylation, histone modification, and opposing transcription factors.

Decreased expression of SOX6 confers a poor prognosis in hepatocellular carcinoma

BACKGROUND AND AIM

SOX6, a member of the D subfamily of sex determining region y-related transcription factors, plays critical roles in cell fate determination, differentiation and proliferation. It has been identified as a tumor suppressor or an oncogene in different human cancers. However, the role of SOX6 in the development and progression of hepatocellular carcinoma (HCC) has not been explored. The aim of this study was to investigate the expression of SOX6 in HCC and determine its correlation with tumor progression and prognosis.

METHODS

130 HCC patients who had undergone curative liver resection were selected and immunohistochemistry, Western blotting, and quantitative real time polymerase chain reaction (Q-PCR) were performed to analyze SOX6 expression in the respective tumors.

RESULTS

Q-PCR, immunohistochemistry and Western blotting consistently confirmed the decreased expression of SOX6 at both mRNA and protein levels in HCC tissues compared with their adjacent nonneoplastic tissues (P<0.01). Additionally, the expression of SOX6, determined by immunohistochemistry, was negatively correlated with the tumor stage (P=0.003) and serum AFP (P=0.02). Moreover, HCC patients with lower SOX6 expression had worse 5-year disease-free survival and 5-year overall survival than those with high SOX6 expression (P=0.006 and 0.001, respectively). Furthermore, the Cox proportional hazards model showed that the decreased expression of SOX6 was an independent poor prognostic factor for both 5-year disease-free survival (hazards ratio [HR]=2.398, 95% confidence interval [CI]=1.601-5.993, P=0.01) and 5-year overall survival (HR=3.569, CI=1.381-7.290, P=0.008) in HCC.

CONCLUSION

These findings provide evidence for the first time that SOX6 expression was decreased in HCC, which correlated with poor prognosis, suggesting that SOX6 may be a novel and potential prognostic marker for HCC.

Interplay between SOX9, β-catenin and PPARγ activation in colorectal cancer

Colorectal carcinogenesis relies on loss of homeostasic mechanisms regulating cell proliferation, differentiation and survival. These cell processes have been reported to be influenced independently by transcription factors activated downstream of the Wnt pathway, such as SOX9 and β-catenin, and by the nuclear receptor PPARγ. The purpose of this study was to explore the expression levels and functional link between SOX9, β-catenin and PPARγ in the pathogenesis of colorectal cancer (CRC). We evaluated SOX9, β-catenin and PPARγ expression levels on human CRC specimens by qPCR and immunoblot detection. We tested the hypothesis that PPARγ activation might affect SOX9 and β-catenin expression using four colon cancer cell lines (CaCo2, SW480, HCT116, and HT29 cells). In CRC tissues SOX9 resulted up-regulated at both mRNA and protein levels when compared to matched normal mucosa, β-catenin resulted up-regulated at protein levels, while PPARG mRNA and PPARγ protein levels were down-regulated. A significant relationship was observed between high PPARG and SOX9 expression levels in the tumor tissue and female gender (p=0.005 and p=0.04, respectively), and between high SOX9 expression in the tumor tissue and age (p=0.04) and microsatellite instability (MSI), in particular with MSI-H (p=0.0002). Moreover, treatment with the synthetic PPARγ ligand rosiglitazone induced different changes of SOX9 and β-catenin expression and subcellular localization in the colon cancer cell lines examined. In conclusion, SOX9, β-catenin and PPARγ expression levels are deregulated in the CRC tissue, and in colon cancer cell lines ligand-dependent PPARγ activation unevenly influences SOX9 and β-catenin expression and subcellular localization, suggesting a variable mechanistic role in colon carcinogenesis.

Major signaling pathways in intestinal stem cells

BACKGROUND

The discovery of markers to identify the intestinal stem cell population and the generation of powerful transgenic mouse models to study stem cell physiology have led to seminal discoveries in stem cell biology.

SCOPE OF REVIEW

In this review we give an overview of the current knowledge in the field of intestinal stem cells (ISCs) highlighting the most recent progress on markers defining the ISC population and pathways governing intestinal stem cell maintenance and differentiation. Furthermore we review their interaction with other stem cell related pathways. Finally we give an overview of alteration of these pathways in human inflammatory gastrointestinal diseases.

MAJOR CONCLUSIONS

We highlight the complex network of interactions occurring among different pathways and put in perspective the many layers of regulation that occur in maintaining the intestinal homeostasis.

GENERAL SIGNIFICANCE

Understanding the involvement of ISCs in inflammatory diseases can potentially lead to new therapeutic approaches to treat inflammatory GI pathologies such as IBD and celiac disease and could reveal the molecular mechanisms leading to the pathogenesis of dysplasia and cancer in inflammatory chronic conditions. This article is part of a Special Issue entitled Biochemistry of Stem Cells.

SOXs in human prostate cancer: implication as progression and prognosis factors

Background

SOX genes play an important role in a number of developmental processes. Potential roles of SOXs have been demonstrated in various neoplastic tissues as tumor suppressors or promoters depending on tumor status and types. The aim of this study was to investigate the involvement of SOXs in the progression and prognosis of human prostate cancer (PCa).

Methods

The gene expression changes of SOXs in human PCa tissues compared with non-cancerous prostate tissues was detected using gene expression microarray, and confirmed by real-time quantitative reverse transcriptase-polymerase chain reaction (QRT-PCR) analysis and immunohositochemistry. The roles of these genes in castration resistance were investigated in LNCaP xenograft model of PCa.

Results

The microarray analysis identified three genes (SOX7, SOX9 and SOX10) of SOX family that were significantly dis-regulated in common among four PCa specimens. Consistent with the results of the microarray, differential mRNA and protein levels of three selected genes were found in PCa tissues by QRT-PCR analysis and immunohistochemistry. Additionally, we found that the immunohistochemical staining scores of SOX7 in PCa tissues with higher serum PSA level (P = 0.02) and metastasis (P = 0.03) were significantly lower than those with lower serum PSA level and without metastasis; the increased SOX9 protein expression was frequently found in PCa tissues with higher Gleason score (P = 0.02) and higher clinical stage (P < 0.0001); the down-regulation of SOX10 tend to be found in PCa tissues with higher serum PSA levels (P = 0.03) and advanced pathological stage (P = 0.01). Moreover, both univariate and multivariate analyses showed that the down-regulation of SOX7 and the up-regulation of SOX9 were independent predictors of shorter biochemical recurrence-free survival. Furthermore, we discovered that SOX7 was significantly down-regulated and SOX9 was significantly up-regulated during the progression to castration resistance.

Conclusions

Our data offer the convince evidence that the dis-regulation of SOX7, SOX9 and SOX10 may be associated with the aggressive progression of PCa. SOX7 and SOX9 may be potential markers for prognosis in PCa patients. Interestingly, the down-regulation of SOX7 and the up-regulation of SOX9 may be important mechanisms for castration-resistant progression of PCa.

Significance of expression of Sox2 and Cdx2 in gastric intestinal metaplasia

AIM: To investigate the significance of expression of sex determining region Y-box 2 (Sox2) and caudal type homeobox transcription factor 2 (Cdx2) in gastric intestinal metaplasia (IM).

METHODS: The expression of SOX2 and CDX2 proteins in 80 paraffin-embedded specimens of gastritis and mild/moderate/severe IM was detected by immunohistochemistry. The mRNA levels of Sox2 and Cdx2 in 40 endoscopic biopsy specimens of gastritis and mild/moderate/severe IM were quantified by real-time Q-PCR.

RESULTS: Both SOX2 and CDX2 proteins were located in the nuclei of normal gastric and normal intestinal epithelial cells. The positive rates of SOX2 and CDX2 protein expression in gastritis and mild/moderate/severe IM were 94.4% and 5.6%, 75.0% and 50.0%, 23.5% and 85.7%, and 9.5% and 90.5%, respectively (all P < 0.05). The relative expression levels of Sox2 and Cdx2 mRNAs in gastritis and mild/moderate/severe IM were 0.5778 ± 0.0778 and 0.0517 ± 0.0218, 0.1496 ± 0.0384 and 0.1402 ± 0.0300, and 0.1131 ± 0.0384 and 0.3453 ± 0.0537, respectively (all P < 0.05). The levels of Sox2 transcripts decreased but those of Cdx2 transcripts increased with the progression of IM. There is an inverse correlation between the expression levels of Sox2 and Cdx2 (r < 0).

CONCLUSION: Down-regulation of Sox2 and ectopic expression of Cdx2 were found in the progression of gastric IM.