Liver regulatory mechanisms of noncoding variants at lipid and metabolic trait loci

Genome-wide association studies (GWASs) have identified hundreds of risk loci for liver disease and lipid-related metabolic traits, although identifying their target genes and molecular mechanisms remains challenging. We predicted target genes at GWAS signals by integrating them with molecular quantitative trait loci for liver gene expression (eQTL) and liver chromatin accessibility QTL (caQTL). We predicted specific regulatory caQTL variants at four GWAS signals located near EFHD1, LITAF, ZNF329, and GPR180. Using transcriptional reporter assays, we determined that caQTL variants rs13395911, rs11644920, rs34003091, and rs9556404 exhibit allelic differences in regulatory activity. We also performed a protein binding assay for rs13395911 and found that FOXA2 differentially interacts with the alleles of rs13395911. For variants rs13395911 and rs11644920 in putative enhancer regulatory elements, we used CRISPRi to demonstrate that repression of the enhancers altered the expression of the predicted target and/or nearby genes. Repression of the element at rs13395911 reduced the expression of EFHD1, and repression of the element at rs11644920 reduced the expression of LITAF, SNN, and TXNDC11. Finally, we showed that EFHD1 is a metabolically active gene in HepG2 cells. Together, these results provide key steps to connect genetic variants with cellular mechanisms and help elucidate the causes of liver disease.

Chromatin accessibility and gene expression during adipocyte differentiation identify context-dependent effects at cardiometabolic GWAS loci

Chromatin accessibility and gene expression in relevant cell contexts can guide identification of regulatory elements and mechanisms at genome-wide association study (GWAS) loci. To identify regulatory elements that display differential activity across adipocyte differentiation, we performed ATAC-seq and RNA-seq in a human cell model of preadipocytes and adipocytes at days 4 and 14 of differentiation. For comparison, we created a consensus map of ATAC-seq peaks in 11 human subcutaneous adipose tissue samples. We identified 58,387 context-dependent chromatin accessibility peaks and 3,090 context-dependent genes between all timepoint comparisons (log2 fold change>1, FDR<5%) with 15,919 adipocyte- and 18,244 preadipocyte-dependent peaks. Adipocyte-dependent peaks showed increased overlap (60.1%) with Roadmap Epigenomics adipocyte nuclei enhancers compared to preadipocyte-dependent peaks (11.5%). We linked context-dependent peaks to genes based on adipocyte promoter capture Hi-C data, overlap with adipose eQTL variants, and context-dependent gene expression. Of 16,167 context-dependent peaks linked to a gene, 5,145 were linked by two or more strategies to 1,670 genes. Among GWAS loci for cardiometabolic traits, adipocyte-dependent peaks, but not preadipocyte-dependent peaks, showed significant enrichment (LD score regression P<0.005) for waist-to-hip ratio and modest enrichment (P < 0.05) for HDL-cholesterol. We identified 659 peaks linked to 503 genes by two or more approaches and overlapping a GWAS signal, suggesting a regulatory mechanism at these loci. To identify variants that may alter chromatin accessibility between timepoints, we identified 582 variants in 454 context-dependent peaks that demonstrated allelic imbalance in accessibility (FDR<5%), of which 55 peaks also overlapped GWAS variants. At one GWAS locus for palmitoleic acid, rs603424 was located in an adipocyte-dependent peak linked to SCD and exhibited allelic differences in transcriptional activity in adipocytes (P = 0.003) but not preadipocytes (P = 0.09). These results demonstrate that context-dependent peaks and genes can guide discovery of regulatory variants at GWAS loci and aid identification of regulatory mechanisms.

Cardiovascular and metabolic diseases are widespread, and an increased understanding of genetic mechanisms behind these diseases could improve treatment. Chromatin accessibility and gene expression in relevant cell contexts can guide identification of regulatory elements and genetic mechanisms for disease traits. A relevant context for cardiovascular and metabolic disease traits is adipocyte differentiation. To identify regulatory elements and genes that display differences in activity during adipocyte differentiation, we profiled chromatin accessibility and gene expression in a human cell model of preadipocytes and adipocytes. We identified chromatin regions that change accessibility during differentiation and predicted genes they may affect. We also linked these chromatin regions to genetic variants associated with risk of disease. At one genomic region linked to fatty acids, a chromatin region more accessible in adipocytes linked to a fatty acid synthesis gene and exhibited allelic differences in transcriptional activity in adipocytes but not preadipocytes. These results demonstrate that chromatin regions and genes that change during cell context can guide discovery of regulatory variants and aid identification of disease mechanisms.

Plant Stress Responses Mediated by CBL-CIPK Phosphorylation Network

At any given time and location, plants encounter a flood of environmental stimuli. Diverse signal transduction pathways sense these stimuli and generate a diverse array of responses. Calcium (Ca²⁺) is generated as a second messenger due to these stimuli and is responsible for transducing the signals downstream in the pathway. A large number of Ca²⁺ sensor-responder components are responsible for Ca²⁺ signaling in plants. The sensor-responder complexes calcineurin B-like protein (CBL) and CBL-interacting protein kinases (CIPKs) are pivotal players in Ca²⁺-mediated signaling. The CIPKs are the protein kinases and hence mediate signal transduction mainly by the process of protein phosphorylation. Elaborate studies conducted in Arabidopsis have shown the involvement of CBL-CIPK complexes in abiotic and biotic stresses, and nutrient deficiency. Additionally, studies in crop plants have also indicated their role in the similar responses. In this chapter, we review the current literature on the CBL and CIPK network, shedding light into the enzymatic property and mechanism of action of CBL-CIPK complexes. We also summarize various reports on the functional modulation of the downstream targets by the CBL-CIPK modules across all plant species.

Histopathological Pattern of Salivary Gland Tumors

Background: The tumors of the salivary glands are uncommon head and neck neoplasms. The aim of this study was to evaluate the relative frequencies, types, site distribution and the histopathological features of salivary gland tumors. Materials and Methods: This was a retrospective study of 176 cases of salivary gland tumors collected from medical record section and department of pathology at B.P.Koirala Memorial Cancer Hospital from Jan. 2005 to Dec. 2010. Tumors were analyzed based on demographics, anatomic location and histopathological type. Results: Out of 176 cases, 66 (37.5 %) were benign and 110 (62.5 %) were malignant with M:F ratio of 1.7:1. The mean age observed was 44.76 years with age range of 12 to 75 years. Pleomorphic adenoma was found to be the commonest benign tumor (72.7 %), followed by Warthin tumor (15.1%), monomorphic adenoma (3.0 %) and basal cell adenoma (3.0 %). The mucoepidermoid carcinoma was the most common malignant tumor (38.1 %), followed by adenoid cystic carcinoma (25.4%), acinic cell carcinoma (10.9%), adenocarcinoma NOS (6.3%), carcinoma ex pleomorphic adenoma (5.4%) and unclassified malignant tumor (4.5 %). Parotid was the most common site for the location of tumors (70.4%) followed by submandibular (19.3%) and minor salivary glands (10.2 %). Conclusion: Pleomorphic adenoma was the commonest salivary gland tumor observed in both sexes. Mucoepidermoid carcinoma was the most common malignant salivary gland tumor. The parotid gland was the most common site of origin in both benign and malignant tumors. DOI: http://dx.doi.org/10.3126/jpn.v4i7.10291 Journal of Pathology of Nepal (2014) Vol. 4, 520-524

Partner and relationship factors in domestic violence: perspectives of women from a slum in Calcutta, India

A cross-sectional study in a representative sample of 751 women, living in slums, examined their perspectives on partner and relationship factors of domestic violence. More than 17% of women experienced physical violence in the past year. Individual factors related to the husband-namely, poor socioeconomic status, use of alcohol, extramarital relations, and visiting red light districts-increased the risk of violence. The following relationship factors were associated with a higher risk of violence: age difference of 5 years or less between spouses, husband's irregular contribution to family expenses, not sharing information about his personal expenses, manifestation of controlling behaviors, and longer duration of marriage. The study concludes that adverse socioeconomic conditions create low self-esteem and insecurity among men, who find expression in aberrant behaviors, and violence is used as a compensatory behavior. Interventions, therefore, need to go beyond the victim-centric approach and address partner and relationship issues for greater impact.

Teenage pregnancy: a socially inflicted health hazard

BACKGROUND

Early marriage and confinement are contributing factors to high maternal and perinatal mortality and morbidity.

OBJECTIVE

To assess the magnitude of the problem of teenage pregnancy and its complications.

MATERIALS AND METHODS

A hospital-based cohort study was undertaken over 4 months among women admitted to a rural hospital in West Bengal. The study cohort comprised of teenage mothers between 15-19 years old and a control cohort of mothers between 20-24 years old. Data included demographic variables, available medical records, and complications viz. anemia, preterm delivery, and low birth weight. Anemia was defined as a hemoglobin level below 10 gm% during the last trimester of pregnancy, preterm delivery was defined as occurring within 37 weeks of gestation, and low birth weight was defined as babies weighing less than 2500 grams at birth.

RESULT

Teenage pregnancy comprised 24.17% of total pregnancies occurring in the hospital during the study period. The study group had 58 subjects and the control group had 91 subjects. The prevalence of anemia was significantly higher (P<0.05) in the women in the teenage group (62.96%) than in the women in the control group (43.59%). However, severe anemia with a hemoglobin level below 8 gm% was only found in the control group. Preterm delivery occurred significantly more (P<0.001) in the study group (51.72%) than in the control group (25.88%). The incidence of low birth weight was significantly higher (P<0.0001) among the group of teenagers (65.52%) than among the women in the control group (26.37%). Not a single newborn was above 3 kg in the study group, while none were below 1.5 kg in the control group. The mean birth weight was 2.36 kg in the study group and 2.74 kg in the control group; the difference was strongly significant (P<0.001).

CONCLUSION

The study shows that anemia, preterm delivery, and low birth weight were more prevalent among teenagers than among women who were 20-24 years old. This indicates the need for enhancing family welfare measures to delay the age at first pregnancy, thereby reducing the multiple complications that may occur in the young mother and her newborn baby.

Evaluation of gross anatomical features of cervix of tropical sheep using cervical silicone moulds

The lambing rate obtained following cervical artificial insemination (AI) with frozen semen in sheep is low mainly due to the inability of frozen-thawed sperm to traverse the tortuous nature of the cervical canal. Although acceptable fertility has been attained by circumventing the cervical barrier through laparoscope aided intrauterine AI, the emphasis is currently given on the development of alternate non-invasive transcervical AI procedures. The complex anatomy of the cervix does not facilitate easy transcervical passage for an insemination catheter. The aim of the present study was: (i) to examine the gross anatomy of the cervix in slaughtered ewe lambs and adult ewes of the native Malpura and Kheri breeds raised under semi-arid tropical environment; and (ii) to cast silicone moulds of the reproductive tracts for measuring the dimensions of the cervix. Eighty reproductive tracts were excised immediately from carcass of Malpura and Kheri ewes and the external os of each one was classified depending on their appearance as duckbill, spiral, rosette or flap. The cervical canal of each tract was filled with a silicone sealant for casting the mould. Fifty complete silicone moulds were obtained representing 25 from ewe lambs and 25 from adult ewes. The mean lengths of the cervical mould of ewe lambs and adult ewes were 3.8+/-0.12 and 5.3+/-0.15 cm, respectively. The average number of funnel shaped folds in the cervical mould of ewe lambs and adult ewes were 3.2+/-0.19 and 3.4+/-0.22. However, the second and third-folds from the os were observed to be accentric in both ewe lambs and adult ewes. The information generated in this study would be useful for increasing the success rate of penetration in ewes exhibiting estrus in order to improve the lambing rate of tropical ewes following transcervical AI.

Rabbit model of non-cirrhotic portal fibrosis with repeated immunosensitization by rabbit splenic extract

BACKGROUND

Non-cirrhotic portal fibrosis (NCPF) or idiopathic portal hypertension, a disease of unknown etiology, is a common cause of portal hypertension in developing countries. Attempts to understand the etiopathogenesis of NCPF by developing animal models have been made. We describe a novel approach using repeated injections of rabbit splenic extract that were obtained from a previously primed rabbit, to develop a model of NCPF.

METHODS

Twenty-eight rabbits (1.5-2.0 kg) were divided into the control (group I, n = 13) and the experimental (group II, n = 15) groups. The supernatant obtained after centrifugation of a 20% splenic homogenate, containing 6 mg protein/mL, was mixed with Freund's complete adjuvant (1:1 ratio) and injected intramuscularly to the recipient rabbits every 2 weeks for 3 months. Portal pressure was measured by inserting a cannula into the gastrosplenic vein.

RESULTS

The mean portal pressure in group II was significantly (P < 0.05) higher than group I at 1 (19.4 +/- 2.9 vs 10.4 +/- 2.2 mmHg), 3 (16.7 +/- 1.1 vs 7.2 +/- 3.6 mmHg), and 6 (20.3 +/- 5.4 vs 10.3 +/- 4.8 mmHg) months. The mean splenic weight in group II was significantly (P < 0.05) greater than group I at 1, 3 and 6 months. Histopathology of spleen showed medullary congestion, hemosidrin laden macrophages and mild fibrosis. Liver showed normal hepatocytes with mild portal lymphocytic infiltrates and Kupffer cell hyperplasia. No significant anomalies were observed in the tests of liver function at 1 and 6 months.

CONCLUSIONS

This animal model showed significant splenomegaly, with persistent rise in portal pressure without hepatic parenchymal injury, quite akin to NCPF seen in humans. This study also proposes that repeated immunostimulation may have an important role in the pathogenesis of NCPF.

Patterns of tobacco use amongst school teachers

Indulgence in tobacco is a known health risk. The example of school teachers in this regard is likely to have far reaching influence on their pupils and the community. A cross sectional study among 257 teachers from 30 schools revealed that as high as 51.0% teachers consumed tobacco in one form or the other. Smoking was the most popular form of tobacco use (72%). Marked gender differences were noted with 73.9%. Male teachers hooked to tobacco habit in comparison to 13.9% of female teachers. Educational qualification had paradoxical effect on tobacco habit as fewer (20.0%) graduate teachers used tobacco in comparison to non graduate teachers (55.7%). However proportion of Post graduate teachers consuming tobacco was still higher (64.2%). Initiation to tobacco habit in majority began at age 21 years and beyond. Common reasons given for tobacco consumption were curiosity (37.9%), to be social (22.0%), enjoyment (21.2%), to relieve stress (8.17%) and improving performance (5.8%). 21.9% smokers consumed more than 20 cigarettes a day. More than four fifth teachers consciously avoided tobacco use in school premises. Nearly half (45.3%) of tobacco users reported reduction in tobacco use in preceding two years. By and large teachers (92.4%) were aware of harmful consequences of tobacco on health. But only in 29.6% it was a cause for concern. 71.2% respondents intended to give up tobacco habit. 33.7% smokers were aware of hazards of passive smoking to others.

A novel protein kinase from Brassica juncea stimulated by a protozoan calcium binding protein. Purification and partial characterization

A novel protein kinase (BjCCaBPk) from etiolated Brassica juncea seedlings has been purified and partially characterized. The purified enzyme migrated on SDS/PAGE as a single band with an apparent molecular mass of 43 kDa. The optimum pH for the kinase activity was 8.0. It was stimulated more than sixfold by the protozoa Entamoeba histolytica calcium binding protein EhCaBP (10.5 nM) but not by calmodulin (CaM) when used at equimolar concentration. Moreover the kinase also did not bind CaM-Sepharose. There was neither inhibition of the kinase activity in the presence of W-7 (a CaM antagonist), KN-62 (a specific calcium/CaM kinase inhibitor) and anti-CaM Ig, nor any effect on BjCCaBPk activity of staurosporine (a protein kinase C inhibitor). Furthermore a CaM-kinase specific substrate, syntide-2, proved to be a poor substrate for the BjCCaBPk compared with histone III-S. The phosphorylation of histone III-S involved serine residues. Southern and Northern blot analysis showed the presence of EhCaBP homologues in Brassica. The data suggest that BjCCaBPk may be a novel protein kinase with an affinity towards a calcium binding protein like EhCaBP.

Gastrointestinal leiomyomas in a developing country

Twenty one consecutive patients with leiomyoma of the gastrointestinal tract were studied. Recurrent gastrointestinal bleeding was found in 18 (85.7%) and recurrent intestinal obstruction in 3 (14.3%) patients. The commonest site of the lesion was the stomach followed by ileum, jejunum and duodenum. Barium meal examination and gastrointestinal endoscopy were suggestive of the diagnosis in 8 and angiography in 2 patients. The remaining patients were diagnosed peroperatively. All patients underwent excision and remained asymptomatic on follow up except two patients who had a recurrence of the tumor as leiomyosarcoma.