Integrated genomic analysis reveals regulatory pathways and dynamic landscapes of the tRNA transcriptome

tRNAs and tRNA-derived RNA fragments (tRFs) play various roles in many cellular processes outside of protein synthesis. However, comprehensive investigations of tRNA/tRF regulation are rare. In this study, we used new algorithms to extensively analyze the publicly available data from 1332 ChIP-Seq and 42 small-RNA-Seq experiments in human cell lines and tissues to investigate the transcriptional and posttranscriptional regulatory mechanisms of tRNAs. We found that histone acetylation, cAMP, and pluripotency pathways play important roles in the regulation of the tRNA gene transcription in a cell-specific manner. Analysis of RNA-Seq data identified 950 high-confidence tRFs, and the results suggested that tRNA pools are dramatically distinct across the samples in terms of expression profiles and tRF composition. The mismatch analysis identified new potential modification sites and specific modification patterns in tRNA families. The results also show that RNA library preparation technologies have a considerable impact on tRNA profiling and need to be optimized in the future.

Diversity of Avian leukosis virus subgroup J in local chickens, Jiangxi, China

Avian leukosis caused by avian leukosis virus (ALV) is one of the most severe diseases endangering the poultry industry. When the eradication measures performed in commercial broilers and layers have achieved excellent results, ALV in some local chickens has gradually attracted attention. Since late 2018, following the re-outbreak of ALV-J in white feather broilers in China, AL-like symptoms also suddenly broke out in some local flocks, leading to great economic losses. In this study, a systematic epidemiological survey was carried out in eight local chicken flocks in Jiangxi Province, China, and 71 strains were finally isolated from 560 samples, with the env sequences of them being successfully sequenced. All of those new isolates belong to subgroup J but they have different molecular features and were very different from the strains that emerged in white feature broilers recently, with some strains being highly consistent with those previously isolated from commercial broilers, layers and other flocks or even isolated from USA and Russian, suggesting these local chickens have been acted as reservoirs to accumulate various ALV-J strains for a long time. More seriously, phylogenetic analysis shows that there were also many novel strains emerging and in a separate evolutionary branch, indicating several new mutated ALVs are being bred in local chickens. Besides, ALV-J strains isolated in this study can be further divided into ten groups, while there were more or fewer groups in different chickens, revealing that ALV may cross propagate in those flocks. The above analyses explain the complex background and future evolution trend of ALV-J in Chinese local chickens, providing theoretical support for the establishment of corresponding prevention and control measures.

How can we help? Medical students' views on their role in the COVID-19 pandemic

Background

The ongoing COVID-19 pandemic has resulted in a sharp rise in demand for healthcare workers worldwide. This has been coupled with reduced numbers of available medical professionals due to confirmed or suspected infections with SARS-CoV-2. To counteract these shortages, governments of several countries have considered the enrolment of medical students into the workforce in order to help to tackle the ongoing crisis.

Methods

Questionnaire-based study assessing the perceived role of medical students in assisting in the COVID-19 pandemic. The primary aim was to determine factors contributing to the willingness of medical students to actively assist in the pandemic. The secondary aim was to evaluate their perspectives regarding the associated changes in medical education.

Results

Out of 760 responses, 71.18% of medical students were willing to assist the medical workforce during the pandemic. Clinical year students were more likely to help in a medical capacity than pre-clinical students (OR = 0.384, 95%CI [0.167, 0.883, P < 0.05)]. Respondents concerned about their own well-being were less likely to engage in clinical work (OR = 0.680, 95%CI [0.491, 0.941], P < 0.020). Students who agreed that online lectures will negatively impact their education were inclined to think that the academic year should be extended (95%CI [0.065, 0.271], P = 0.001).

Conclusions

Most students are willing to help in both a medical and non-medical capacity. Their primary concerns when working in a medical setting are the risk of infecting their relatives and patients, lack of protective equipment and necessary knowledge as well as legal uncertainty whilst working without a medical qualification.

Convergent Validity of Suffering and Quality of Life as Measured by The Hidradenitis Suppurativa Quality of Life

BACKGROUND

Hidradenitis suppurativa (HS) is a painful chronic, recurrent inflammatory skin disease with great impact on health-related quality of life (HRQOL). Recently, Hidradenitis SuppuraTiva cORe outcomes set International Collaboration (HISTORIC) established HRQOL as a core domain set for HS clinical trials and developed the Hidradenitis Suppurativa Quality of Life (HiSQOL) as a validated outcome measurement instrument.

OBJECTIVES

To provide further convergent validity of HiSQOL by comparing it to Dermatology Life Quality Index (DLQI) and Pictorial Representation of Illness and Self Measure-Revised 2 (PRISM-R2).

METHODS

In this cross-sectional study, 103 participants completed HiSQOL, PRISM-R2 and DLQI. PRISM-R2 is an instrument designed to measure suffering and reports the two measures, Illness Perception Measure (IPM) and Self-Illness Separation (SIS). Correlation analyses were performed including a sub-analysis for a subgroup of patients with high scores in the HS-specific domains of HiSQOL.

RESULTS

A very strong correlation was found between HiSQOL and DLQI (ρ = 0.93, P < 2.2 × 10^-16 , (95% CI: 0.89;0.95)), and moderately strong correlations were found between HiSQOL and SIS (ρ = -0.73, P < 2.2 × 10^-16 , (95% CI: -0.81; -0.62)) and DLQI and SIS (ρ = -0.70, P < 2.2 × 10^-16 , (95% CI: -0.79; -0.59)). IPM was positively associated with HiSQOL and DLQI and negatively with SIS.

CONCLUSIONS

HiSQOL is a valid measure of quality of life for HS patients, and we suggest that HiSQOL can be used as a measure of suffering as well.

SCARA5 suppresses the proliferation and migration, and promotes the apoptosis of human retinoblastoma cells by inhibiting the PI3K/AKT pathway

Retinoblastoma (RB) is the most common ocular malignancy that occurs during childhood. Scavenger receptor class A member 5 (SCARA5) is considered to function as an anti-oncogene in several types of malignant tumor. The present study investigated the functional role and underlying mechanism of SCARA5 in human RB cells. Reverse transcription-quantitative PCR and western blotting were used to detect the relative expression levels of SCARA5 in four human RB cell lines. In addition, transfection was performed to either knockdown or induce overexpression of SCARA5 in human RB Y79 cells. The proliferation, migration and apoptosis of RB cells was then measured by Cell Counting Kit 8 assay, 5-ethynyl-2′-deoxyuridine assay, clone formation assay, Transwell assay, Hoechst staining and TUNEL staining, respectively. Western blotting was performed to detect changes in the expression levels of key proteins involved in the PI3K/AKT and apoptotic pathways. The present study revealed that SCARA5 was expressed at lower levels in four tumorigenic human RB cell lines compared with in a human retinal pigment non-tumorigenic cell line. Functional analysis demonstrated that overexpression of SCARA5 decreased the proliferation and migration, and promoted the apoptosis of human RB cells in vitro, whereas in vivo experiments revealed a decrease in RB progression following SCARA5 overexpression. In addition, overexpression of SCARA5 inhibited phosphorylated (p)-PI3K and p-AKT expression, and knockdown of SCARA5 increased p-PI3K and p-AKT expression; however, no changes in total PI3K and AKT expression were observed. Bcl-2 exhibited similar changes in expression to those displayed by p-PI3K and p-AKT, whereas Bax and cleaved caspase-3 exhibited trends in expression that were the opposite to those shown by p-PI3K and p-AKT. In conclusion, the present results demonstrated that SCARA5 could inhibit the proliferation and promote the apoptosis of RB cell lines by suppressing the PI3K/AKT signaling pathway, thus suggesting a novel strategy for treating RB.

Application of computed tomography angiography-assisted classification of arterial branches in the first web space of the foot for thumb reconstruction

BACKGROUND

Computed tomography angiography (CTA) has become a widely used imaging modality in vascular surgery. The first web arterial branches of the foot are significant for surgical planning of the donor site for thumb reconstruction.

METHODS

We retrospectively analysed 30 thumb reconstructions with free second toe/great toe wrap-around flap transfer, performed between January 2016 and January 2019. The mean patient age was 30 (2-45) years. The causes of hand injury were: 20 machine strangulation injuries, 6 heavy weight smash injuries, and 4 crush injuries. Patients with iodine allergy were excluded preoperatively. We evaluated the effectiveness of CTA in visualizing first web arterial branches and compared it with intraoperative findings. Surgical plan for donor sites was prepared based on the classification of the first web arterial branches.

RESULTS

The arterial branches of the patients were classified based on CTA findings as follows: (1) fork type: 24 patients (48 feet, 80%); (2) main trunk type: four patients (8 feet, 13.33%); and (3) side branch type: one patient (2 feet, 3.33%). One case of poor vascular continuity and artifacts in CTA underwent thumb reconstruction with free great toe wrap-around flap transfer. Tissue survival was achieved in all reconstructed thumbs. During the follow-up period (average, 12 months), all reconstructed thumbs exhibited good outcomes. The donor sites on the feet of all patients recovered well.

CONCLUSION

CTA allows preoperative assessment of blood supply and planning of donor site. Our results can serve as a reference for surgical planning of the donor site while reducing the occurrence of adverse events.

Scurvy presenting as lower limb ecchymoses in the setting of metastatic colorectal cancer

A 58-year-old woman presented with a 1-week history of lower limb bruising. She had a medical history of recurrent metastatic colon cancer with a sigmoid colectomy and complete pelvic exenteration leading to colostomy and urostomy formation. She had malignant sacral mass encroaching on the spinal cord. This caused a left-sided foot drop for which she used an ankle-foot orthosis. She was on cetuximab and had received radiotherapy to the sacral mass 1 month ago. On examination, there were macular ecchymoses with petechiae on the lower limbs. There was sparing of areas that had been compressed by the ankle-foot orthosis. Bloods showed mild thrombocytopaenia and anaemia with markedly raised inflammatory markers. Coagulation studies consistent with inflammation rather than disseminated intravascular coagulation. She was found to have Klebsiella bacteraemia secondary to urinary source. Skin biopsy showed dermal haemorrhage without vessel inflammation. Vitamin C levels were low confirming the diagnosis of scurvy.

Identifying and appraising patient-reported outcome measures on treatment satisfaction in acne: a systematic review

BACKGROUND

After dermatitis, acne is the next skin disease to contribute most to the burden of skin diseases worldwide. Recently, seven core outcome domains have been identified, which together form an Acne Core Outcome Set (ACORN). One of these was satisfaction with acne treatment.

OBJECTIVES

To identify studies that described the development of patient-reported outcome measures (PROMS), evaluated one or more measurement properties of a PROM, or evaluated the interpretability of a PROM in patients with acne regarding treatment satisfaction.

METHODS

The COnsensus-based Standards for the selection of health Measurement INstruments (COSMIN) search strategy for identifying PROMS on acne treatment satisfaction was used. We searched PubMed, MEDLINE, Embase, LILACS, Web of Science, Cochrane Library, Emcare, PsycINFO and Academic Search premier (June 2020). Study selection, data extraction and assessment of methodological quality according to COSMIN guidance were carried out independently by two authors.

RESULTS

Only one study could be included, describing the development of a treatment satisfaction measure in patients with acne. The development was assessed as inadequate and data on measurement properties were lacking. Additionally, we found 188 studies reporting treatment satisfaction solely as an outcome, using a wide variety of methods, none of them standardized or validated.

CONCLUSIONS

We could not find a PROM on treatment satisfaction to recommend for a core outcome set in acne. There is an unmet need for a PROM on treatment satisfaction in acne that is robustly developed, designed and validated.

Gastric cancer nodal tumour-stroma ratios influence prognosis

This study showed that nodal tumour-stroma ratio (NTSR) is an independent prognostic factor for overall and disease-free survival of patients with gastric cancer. Both relative stroma-rich primary tumour-stroma ratio (PTSR) and NTSR were independent negative prognostic factors for overall survival in gastric cancer. This study supports assessment of tumour-stroma ratio in the routine pathological diagnosis of gastric cancer. validated in node-positive disease.

The Role of Technology and the Continuum of Care for Youth Suicidality: Systematic Review

Background

Youth suicide is a global public health issue, and using technology is one strategy to increase participation in preventive interventions. However, there is minimal knowledge on how technology-enhanced interventions for youth correspond to the stages of care, from illness or risk recognition to treatment follow-up.

Objective

This systematic review aims to examine the efficacy of technology-enhanced youth suicide prevention and interventions across the continuum of care.

Methods

Four electronic databases were searched up to spring 2019 for youth suicide preventive interventions that used technology. The review was not restricted by study design and eligible studies could report outcomes on suicidality or related behaviors, such as formal treatment initiation. An adapted version of the Methodological Quality Ratings Scale was used to assess study quality.

Results

A total of 26 studies were identified. The findings support the emerging efficacy of technology-enhanced interventions, including a decline in suicidality and an increase in proactive behaviors. However, evidence suggests that there are gaps in the continuum of care and recent study samples do not represent the diverse identities of vulnerable youth.

Conclusions

The majority of identified studies were conducted in school settings and were universal interventions that aligned with the illness and risk recognition and help-seeking stages of the continuum of care. This field could be strengthened by having future studies target the stages of assessment and treatment initiation, include diverse youth demographics, and examine the varying roles of providers and technological components in emerging interventions.

Research Note: A putative novel subtype of the avian hepatitis E virus of genotype 3, Jiangxi province, China

In recent years, the avian hepatitis E virus (HEV) has been widely spread in China, causing huge economic losses. Several studies have carried out detailed epidemiologic investigations of the avian HEV, but no data were from Jiangxi province. Since early April 2020, diseases similar to hepatic rupture hemorrhage syndrome caused by the avian HEV occurred in a Roman Brown layer farm in Jiangxi province, indicating this virus may also be epidemic there. To make this assumption clear, 20 liver samples were collected from the sick flock and then analyzed by detailed viral detection, which confirmed that the avian HEV should be responsible for the aforementioned disease (6 of 20). Then, the capsid gene of the virus was sequenced to show the molecular characteristics of the strain circulating in the aforementioned flock. Sequence comparison showed that it shared 80.7 to 94.7% identities with 12 published strains, while phylogenetic analysis confirmed that it belongs to a new subtype of genotype 3. Moreover, basing on a 242 bp fragment, the novel also shared high similarities to reference strains identified as genotypes before, revealing the genotype 3 maybe very popular in China and even can be divided into several subgroups. In conclusion, a novel avian HEV strain was identified in this study, which belongs to a new subtype of genotype 3. The analysis makes up for the molecular epidemiologic data of avian HEV and provides a basis for further understanding the spread of avian HEV in China.

Long noncoding RNA LINC00052 suppressed the proliferation, migration and invasion of glioma cells by upregulating KLF6

OBJECTIVE

Recent studies have discovered a class of dysregulated long noncoding RNAs (lncRNAs) related to carcinogenesis. This study aims to uncover the molecular functions of lncRNA LINC00052 in the tumorigenesis of glioma.

PATIENTS AND METHODS

Quantitative Real-time polymerase chain reaction (qRT-PCR) was performed to detect LINC00052 expression in 40 glioma samples and 4 glioma cell lines. Besides, regulatory effects of LINC00052 on the in vitro behaviors of glioma cells were evaluated by the proliferation assay, transwell assay and wound healing assay. Furthermore, the interaction between LINC00052 and kruppel-like factor 6 (KLF6) in mediating the progression of glioma was studied by performing qRT-PCR and Western blot.

RESULTS

LINC00052 expression was remarkably downregulated in glioma samples compared with that in adjacent samples. Moreover, cell proliferation, invasion, and migration of glioma were inhibited after overexpression of LINC00052 in vitro. Besides, LINC00052 overexpression upregulated mRNA and protein level of KLF6. Besides, the expression of KLF6 in tumor tissues was positively correlated to the expression of LINC00052.

CONCLUSIONS

These results suggested that LINC00052 could repress cell migration, invasion and proliferation in glioma through upregulating KLF6, which may offer a new therapeutic intervention for glioma patients.