Empirical Bayesian elastic net for multiple quantitative trait locus mapping

In multiple quantitative trait locus (QTL) mapping, a high-dimensional sparse regression model is usually employed to account for possible multiple linked QTLs. The QTL model may include closely linked and thus highly correlated genetic markers, especially when high-density marker maps are used in QTL mapping because of the advancement in sequencing technology. Although existing algorithms, such as Lasso, empirical Bayesian Lasso (EBlasso) and elastic net (EN) are available to infer such QTL models, more powerful methods are highly desirable to detect more QTLs in the presence of correlated QTLs. We developed a novel empirical Bayesian EN (EBEN) algorithm for multiple QTL mapping that inherits the efficiency of our previously developed EBlasso algorithm. Simulation results demonstrated that EBEN provided higher power of detection and almost the same false discovery rate compared with EN and EBlasso. Particularly, EBEN can identify correlated QTLs that the other two algorithms may fail to identify. When analyzing a real dataset, EBEN detected more effects than EN and EBlasso. EBEN provides a useful tool for inferring high-dimensional sparse model in multiple QTL mapping and other applications. An R software package 'EBEN' implementing the EBEN algorithm is available on the Comprehensive R Archive Network (CRAN).

Benzylidene acylhydrazides inhibit chlamydial growth in a type III secretion- and iron chelation-independent manner

Chlamydiae are widespread Gram-negative pathogens of humans and animals. Salicylidene acylhydrazides, developed as inhibitors of type III secretion system (T3SS) in Yersinia spp., have an inhibitory effect on chlamydial infection. However, these inhibitors also have the capacity to chelate iron, and it is possible that their antichlamydial effects are caused by iron starvation. Therefore, we have explored the modification of salicylidene acylhydrazides with the goal to uncouple the antichlamydial effect from iron starvation. We discovered that benzylidene acylhydrazides, which cannot chelate iron, inhibit chlamydial growth. Biochemical and genetic analyses suggest that the derivative compounds inhibit chlamydiae through a T3SS-independent mechanism. Four single nucleotide polymorphisms were identified in a Chlamydia muridarum variant resistant to benzylidene acylhydrazides, but it may be necessary to segregate the mutations to differentiate their roles in the resistance phenotype. Benzylidene acylhydrazides are well tolerated by host cells and probiotic vaginal Lactobacillus species and are therefore of potential therapeutic value.

BMI1 attenuates etoposide-induced G2/M checkpoints via reducing ATM activation

The BMI1 protein contributes to stem cell pluripotency and oncogenesis via multiple functions, including its newly identified role in DNA damage response (DDR). Although evidence clearly demonstrates that BMI1 facilitates the repair of double-stranded breaks via homologous recombination (HR), it remains unclear how BMI1 regulates checkpoint activation during DDR. We report here that BMI1 has a role in G2/M checkpoint activation in response to etoposide (ETOP) treatment. Ectopic expression of BMI1 in MCF7 breast cancer and DU145 prostate cancer cells significantly reduced ETOP-induced G2/M arrest. Conversely, knockdown of BMI1 in both lines enhanced the arrest. Consistent with ETOP-induced activation of the G2/M checkpoints via the ATM pathway, overexpression and knockdown of BMI1, respectively, reduced and enhanced ETOP-induced phosphorylation of ATM at serine 1981 (ATM pS1981). Furthermore, the phosphorylation of ATM targets, including γH2AX, threonine 68 (T68) on CHK2 (CHK2 pT68) and serine 15 (S15) on p53 were decreased in overexpression and increased in knockdown BMI1 cells in response to ETOP. In line with the requirement of NBS1 in ATM activation, we were able to show that BMI1 associates with NBS1 and that this interaction altered the binding of NBS1 with ATM. BMI1 consists of a ring finger (RF), helix-turn-helix-turn-helix-turn (HT), proline/serine (PS) domain and two nuclear localization signals (NLS). Although deletion of either RF or HT did not affect the association of BMI1 with NBS1, the individual deletions of PS and one NLS (KRMK) robustly reduced the interaction. Stable expression of these BMI1 mutants decreased ETOP-induced ATM pS1981 and CHK2 pT68, but not ETOP-elicited γH2AX in MCF7 cells. Furthermore, ectopic expression of BMI1 in non-transformed breast epithelial MCF10A cells also compromised ETOP-initiated ATM pS1981 and γH2AX. Taken together, we provide compelling evidence that BMI1 decreases ETOP-induced G2/M checkpoint activation via reducing NBS1-mediated ATM activation.

Cloquet's node trumps imaging modalities in the prediction of pelvic nodal involvement in patients with lower limb melanomas in Asian patients with palpable groin nodes

Patients with clinically palpable lymph node metastases to the groin are treated with groin dissection to control local disease and stage the malignancy. However, the extent of nodal dissection required to optimize survival rate is controversial.

AIM

To evaluate the approach to the extent of nodal dissection in advanced lower limb melanomas with clinically palpable inguinal nodes; to review survival outcomes based on the extent of nodal dissection and nodal disease.

MATERIALS AND METHODS

A prospectively maintained database of 12 patients with lower limb melanoma was analyzed. Cloquet's node was assessed based on the frozen section result which guided the decision to proceed to iliac-obturator dissection. The correlation of the results of the Cloquet's nodes and radiological imaging to the final histological outcome of groin nodal dissection were compared.

RESULTS

The positive predictive value (PPV) of radiological imaging in identifying pelvic nodal disease was 60%. PPV of a positive or indeterminate frozen section result of Cloquet's node was 71.4%. Notably, all patients with a positive frozen section result for the Cloquet's node had positive pelvic nodal disease. Median DFS for all patients is 26 months (range 3-68 months) and the median OS for all patients is 28.5 months (range 5-68 months). Median DFS for node negative patients was 28 months (range 24-68 months). Median DFS for node positive patients was 20 months (range 3-36 months).

CONCLUSION

Cloquet's node was shown to be superior to radiological imaging and should be preferentially used to decide on the extent of nodal dissection.

Decreased levels of circulating sex hormones as a biomarker of lung cancer in male patients with solitary pulmonary nodules

BACKGROUND

An early differentiation of malignant from benign solitary pulmonary nodules (SPNs) is essential for management and prognosis of lung cancer.

OBJECTIVES

Here we investigated whether measurement of circulating sex hormones could be useful for an early detection of malignancy among patients with SPNs.

METHODS

We recruited 47 patients with malignant SPNs 45 patients with benign SPNs, and 32 healthy persons. Testosterone, estradiol, and progesterone were measured. Carcinoembryonic antigen (CEA) as well as TNF-α, IL-1 and IL-6 were also measured.

RESULTS

We found that sex hormones were decreased significantly in patients with malignant SPNs, as compared to patients with benign SPNs and healthy controls (P<0.05). Sex hormones levels showed a trend to decline in patients with benign SPNs as compared to normal controls, but the difference was not statistically significant (P>0.05). CEA levels were only abnormally elevated in eight patients with lung adenocarcinoma. The inflammatory cytokines were remarkably higher in both patients than in normal controls. However, there was no statistical difference in these cytokines among patients.

CONCLUSIONS

The reduced sex hormones levels seemed to be uniquely associated with lung cancer. Therefore, measurement of sex hormones may have clinical potential in the diagnosis of malignancy in patients with SPNs.

Determination of visual prognosis in children with open globe injuries

AIMS

To determine the predictive factors of visual outcomes in children with open globe injury and to give guidance to reduce the incidence of open globe injury.

METHODS

One hundred and forty eyes of 137 consecutive open globe injury patients, who were treated at the Eye Center of Second Bethune Hospital affiliated with Jilin University between August 2005 and August 2012, were retrospectively analyzed. Data recorded included demographic characteristics, causes of injury, location and extent of injury, presenting visual acuity, detailed ocular anterior and posterior segment evaluations, details of primary and subsequent surgeries, and postoperative complications and outcomes. The follow-up data included the most recent best-corrected visual acuity, complications, and the duration of follow-up.

RESULTS

Of the 137 patients, there were 116 (84.7%) boys and 21 (15.3%) girls. Their ages ranged between 3 and 17 years old (mean=11.57±4.19 years old). Sixty (43.8%) children had a right eye injury, whereas 74 (54.0%) had a left eye injury. Only three (2.2%) children suffered bilateral eye injury. Living utensils, industrial tools, and fireworks contributed to the most common causes of open globe injury. Eighty-one (59.1%) had sharp force injuries, 23 (16.8%) had blunt injuries, and 33 (24.1%) had missile injuries.

CONCLUSIONS

Unfavorable visual outcomes were related to a younger age at presentation, poor presenting visual acuity, injuries caused by blunt or missile objects, posterior wound location, hyphema, vitreous hemorrhage, and surgical intervention of pars plana vitrectomy.

Inner gorges cut by subglacial meltwater during Fennoscandian ice sheet decay

The century-long debate over the origins of inner gorges that were repeatedly covered by Quaternary glaciers hinges upon whether the gorges are fluvial forms eroded by subaerial rivers, or subglacial forms cut beneath ice. Here we apply cosmogenic nuclide exposure dating to seven inner gorges along ~500 km of the former Fennoscandian ice sheet margin in combination with a new deglaciation map. We show that the timing of exposure matches the advent of ice-free conditions, strongly suggesting that gorges were cut by channelized subglacial meltwater while simultaneously being shielded from cosmic rays by overlying ice. Given the exceptional hydraulic efficiency required for meltwater channels to erode bedrock and evacuate debris, we deduce that inner gorges are the product of ice sheets undergoing intense surface melting. The lack of postglacial river erosion in our seven gorges implicates subglacial meltwater as a key driver of valley deepening on the Baltic Shield over multiple glacial cycles.

Cab45S inhibits the ER stress-induced IRE1-JNK pathway and apoptosis via GRP78/BiP

Disturbance of endoplasmic reticulum (ER) homeostasis causes ER stress and leads to activation of the unfolded protein response, which reduces the stress and promotes cell survival at the early stage of stress, or triggers cell death and apoptosis when homeostasis is not restored under prolonged ER stress. Here, we report that Cab45S, a member of the CREC family, inhibits ER stress-induced apoptosis. Depletion of Cab45S increases inositol-requiring kinase 1 (IRE1) activity, thus producing more spliced forms of X-box-binding protein 1 mRNA at the early stage of stress and leads to phosphorylation of c-Jun N-terminal kinase, which finally induces apoptosis. Furthermore, we find that Cab45S specifically interacts with 78-kDa glucose-regulated protein/immunoglobulin heavy chain binding protein (GRP78/BiP) on its nucleotide-binding domain. Cab45S enhances GRP78/BiP protein level and stabilizes the interaction of GRP78/BiP with IRE1 to inhibit ER stress-induced IRE1 activation and apoptosis. Together, Cab45S, a novel regulator of GRP78/BiP, suppresses ER stress-induced IRE1 activation and apoptosis by binding to and elevating GRP78/BiP, and has a role in the inhibition of ER stress-induced apoptosis.