Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation.

Higher-order chromosomal organization for transcription regulation is poorly understood in eukaryotes. Using genome-wide Chromatin Interaction Analysis with Paired-End-Tag sequencing (ChIA-PET), we mapped long-range chromatin interactions associated with RNA polymerase II in human cells and uncovered widespread promoter-centered intragenic, extragenic, and intergenic interactions. These interactions further aggregated into higher-order clusters, wherein proximal and distal genes were engaged through promoter-promoter interactions. Most genes with promoter-promoter interactions were active and transcribed cooperatively, and some interacting promoters could influence each other implying combinatorial complexity of transcriptional controls. Comparative analyses of different cell lines showed that cell-specific chromatin interactions could provide structural frameworks for cell-specific transcription, and suggested significant enrichment of enhancer-promoter interactions for cell-specific functions. Furthermore, genetically-identified disease-associated noncoding elements were found to be spatially engaged with corresponding genes through long-range interactions. Overall, our study provides insights into transcription regulation by three-dimensional chromatin interactions for both housekeeping and cell-specific genes in human cells.

KLF4 and PBX1 directly regulate NANOG expression in human embryonic stem cells.

Insight into the regulation of core transcription factors is important for a better understanding of the molecular mechanisms that control self-renewal and pluripotency of human ESCs (hESCs). However, the transcriptional regulation of NANOG itself in hESCs has largely been elusive. We established a NANOG promoter luciferase reporter assay as a fast read-out for indicating the pluripotent status of hESCs. From the functional cDNA screens and NANOG promoter characterization, we successfully identified a zinc finger transcription factor KLF4 and a homeodomain transcription factor PBX1 as two novel transcriptional regulators that maintain the pluripotent and undifferentiated state of hESCs. We showed that both KLF4 and PBX1 mRNA and protein expression were downregulated during hESC differentiation. In addition, overexpression of KLF4 and PBX1 upregulated NANOG promoter activity and also the endogenous NANOG protein expression in hESCs. Direct binding of KLF4 on NANOG proximal promoter and PBX1 on a new upstream enhancer and proximal promoter were confirmed by chromatin immunoprecipitation and electrophoretic mobility shift assay. Knockdown of KLF4/PBX1 or mutation of KLF4/PBX1 binding motifs significantly downregulated NANOG promoter activity. We also showed that specific members of the SP/KLF and PBX family are functionally redundant at the NANOG promoter and that KLF4 and PBX1 cooperated with OCT4 and SOX2, and transactivated synergistically the NANOG promoter activity. Our results show two novel upstream transcription activators of NANOG that are functionally important for the self-renewal of hESC and provide new insights into the expanded regulatory circuitry that maintains hESC pluripotency.

A Randomized, Controlled Treatment Trial of Eyelid-Warming Therapies in Meibomian Gland Dysfunction.

AIM: The main treatment for meibomian gland dysfunction (MGD), a major cause of dry eye, is eyelid warming. Lack of compliance is the main reason for treatment failure. This has led to the development of eyelid-warming devices that are safe, effective and convenient. To obtain robust evidence demonstrating their efficacy, the authors conducted a 3-arm randomized clinical study. METHODS: The authors conducted a 3-month assessor-blinded, randomized, controlled trial of patients from the Singapore National Eye Centre experiencing at least one of eight dry eye symptoms 'often' or 'all the time'. Patients who wore contact lenses, had an active infection or known diagnosis of thyroid dysfunction and rheumatoid arthritis were excluded from the study. MGD participants were randomly assigned to warm towel (n = 25), EyeGiene(®) (Eyedetec Medical Inc., Danville, CA, USA) (n = 25) and Blephasteam(®) (Spectrum Thea Pharmaceuticals LTD, Macclesfield, UK) (n = 25) treatments. The primary efficacy and safety outcomes included the proportions of participants with improved symptoms and changes in best corrected visual acuity (BCVA), respectively. Other outcomes included tear break up time (TBUT), Schirmer test, corneal fluorescein dye staining and number of visibly occluded meibomian gland (MG) orifices. RESULTS: The study population was 53.5 ± 11.1 years old and predominantly Chinese. For severity of symptom after 3 months of treatment, 78.3% Blephasteam(®) participants reported improvement compared to 45.5% warm towel participants (p = 0.023). The corresponding proportions for improvement in the frequency of symptoms were 82.6% and 50.0%, respectively (p = 0.020). The proportions of improvement of symptoms in EyeGiene(®) patients were not significantly different from warm towel intervention. At 1 month of treatment, the crude odds ratio of improvement of severity of irritation for Blephasteam(®) compared to control was 3.0 (95% CI 0.88-10.18). However, the odds ratio adjusted by age was 5.67 (1.30-24.66). The lid-warming treatments did not significantly change the TBUT, Schirmer test results or number of visibly occluded MGs in the study period. All treatment modalities did not worsen BCVA after 3 months. CONCLUSION: Blephasteam(®) is more effective than warm towel for MGD treatment, with warm towel and EyeGiene(®) being comparable effective. Older age might predict for treatment efficacy. All studied therapies were safe for visual acuity (VA) for 3 months of treatment.

Underlying liver disease influences volumetric changes in the spared hemiliver after selective internal radiation therapy with 90Y in patients with hepatocellular carcinoma.

OBJECTIVE: Hypertrophy of the contralateral liver lobe after treatment with yttrium-90 ((90)Y) microspheres has recently been reported. This study aimed to quantify left hepatic lobe hypertrophy after right-sided radioembolization for hepatocellular carcinoma (HCC) and to identify pretreatment predictive factors of hypertrophy in an Asian population. METHODS: A retrospective review of patients with inoperable HCC undergoing selective internal radiation treatment (SIRT) with (90)Y microspheres at a single institution from January 2008 to January 2012 was performed. Only patients who had treatment delivered via the right hepatic artery alone were included. RESULTS: In all, 17 patients fulfilling the study criteria were identified. The mean percentage of left-lobe hypertrophy was 34.2% ± 34.9% (range 19.0-106.5%) during a median of 5-month follow-up. Patients with hepatitis B were found to experience a significantly greater degree of hypertrophy than those with hepatitis C or alcoholic liver cirrhosis. There were no cases of acute liver failure after the administration of SIRT in this study and none of the patients developed disease in the contralateral lobe over the study period. CONCLUSIONS: Administration of unilobar SIRT to the right liver lobe in patients with HCC resulted in a significant degree of contralateral left lobe hypertrophy. Patients with hepatitis B experienced a greater degree of hypertrophy than those with hepatitis C or alcoholic liver cirrhosis.

Conjunctivochalasis is the precursor to pterygium.

Pterygium is a fibrovascular proliferative condition of the ocular surface with no known pathological mechanism. This condition affects vision due to dry eyes, astigmatism or physical occlusion of the visual axis for severe cases. The only definitive treatment for this condition is surgical excision. Interestingly, it is a lesion that may be related to UV radiation and elaboration of proteases. Conjunctivochalasis is a dry eye related condition that is exemplified by excessive conjunctiva or the mucous membrane of the front of the eye around the cornea. Both pterygium and conjunctivochalasis are associated with elaboration of matrix metalloproteinases as well as inflammatory cytokines. We propose that under specific conditions, conjunctivochalasis in the nasal part of the conjunctiva can progress to pterygium. The progression of conjunctivochalasis to pterygium may be related to special kinds of oxidative or inflammatory damage that affects only the part of the loose conjunctival tissue adjacent to the cornea. Protease expressed may then breakdown the conjunctival and corneal epithelium causing the head of pterygium to be very adherent to the cornea. This explains the fact that surgically excised pterygium tissue has stromal tissue enclosed by epithelia on both surfaces. In addition, it explains the existence of a surgical plane when an instrument is passed under the neck of the pterygium tissue but not at the apex. The implications of this hypothesis are first, treatment should be directed to the protection of conjunctivochalasis before it transforms to pterygium. This may be achieved by anti-inflammatory measures, anti-protease treatment, or preventing the triggering of the changes at the head of pterygium, such as avoidance of sunlight. Second, during resection of pterygium, it may not be necessary to resect the pterygium too extensively away from the cornea, since this effectively removes relatively normal conjunctiva.