bluuebunny/crossref_metadata_2025 huggingface dataset:
Adipogenic differentiation was inhibited by downregulation of PPARγ signaling pathway in aging tendon stem/progenitor cells
Authors: Lai Fan , Wang Jingjing , Tang Hong , Bian Xuting , Lu Kang , He Gang , Huang Pan , Liu Juan , Zhou Mei , Liu Jian , Tao Xu , Tang Kang-lai
Published: October 2021

Background

Tendon stem/progenitor cells (TSPCs) play a vital role in tendon repair and regeneration. Previously we found more adipocytes accumulated in the patellar tendon injury sites in aging rats compared with the young ones, of which the mechanism is still unknown. Here, we want to identify whether erroneous differentiation of TSPCs by aging accounts for the adipocyte accumulation.

Methods

TSPCs from young and aging rats were isolated and propagated. Both young and aging TSPCs were induced to differentiate into adipocytes, and Oil red O staining, quantitative real-time polymerase chain reaction (qRT-PCR), western-blot and immunofluorescent staining were used to evaluate the capability of TSPCs. RNA sequencing was utilized to screen out different genes and signaling pathways related to adipogenesis between young and aging TSPCs.

Results

The Oil red O staining showed there were more adipocytes formed in young TSPCs. Besides, adipogenic markers perilipin, peroxisome proliferator-activated receptor γ (PPARγ), CCAAT/enhancer-binding proteins alpha (C/EBPα) and Fatty acid-binding protein 4 (FABP4) were elevated both at gene and protein level. PPARγ signaling pathway was selected as our target via RNA sequencing. After adding the signaling activators, Rosiglitazone maleate (RM), inhibited adipogenesis of aging TSCs was reversed.

Conclusions

In conclusion, aging inhibited adipogenesis of TSPCs by down‐regulating PPARγ signaling. It is not likely that the adipocyte accumulation in aging tendon during repair was due to the aging of TSPCs. This may provide new targets for curing aging tendon injuries or tendinopathies.
MiR-4303 relieves chondrocyte inflammation by targeting ASPN in osteoarthritis
Authors: Wang Chunyu , Wang Li , Guan Xingfa , Yue Changfeng
Published: October 2021

Background

Osteoarthritis (OA) is a severe articular cartilage disease whose pathogenesis involves the inflammation of chondrocytes. MicroRNAs (miRNAs) are considered to be effective inflammation regulators. However, the regulatory mechanism of miRNAs in osteoarthritis needs to be further elucidated. In this paper, we aim to investigate the underlying mechanisms by which miR-4303 regulates osteoarthritis.

Methods

RT-qPCR is performed to detect the mRNA expression levels of miR-4303, ASPN, PDIA3, PIK3CA, and TRAF3. CCK-8 assay and EdU assay are carried to assess chondrocyte viability. The protein expression levels of ASPN, PCNA, Ki-67, CyclinA1, CyclinB1, CyclinD2, p27, Bax, Bcl-2, cleaved caspase-3, and Cleaved caspase-9 were measured by western blot. FACs is performed to detect the cell cycle and apoptosis of chondrocyte. ELISA is conducted to assess the levels of TNF-β, IL-1β and IL-6 in the supernatant of chondrocytes. The potential binding sites of miR-4303 and ASPN are predicted by the miRDB database and confirmed by the dual-luciferase reporter gene assay.

Results

Our findings illustrated that miR-4303 was down-regulated in arthritic tissues and LPS-induced chondrocytes; miR-4303 overexpression rescued the decrease in cell viability, cell cycle arrest and apoptosis induced by LPS. Furthermore, miR-4303 overexpression inhibited the release of inflammatory factors in LPS-induced chondrocytes, miR-4303 relieved chondrocyte inflammation via targeting ASPN.

Conclusion

MiR-4303 serves as a prognostic biomarker and relieves chondrocyte inflammation via targeting ASPN. Our findings provide novel prognostic biomarkers in predicting the progression and prognosis of osteoarthritis.
LIPUS inhibits inflammation and catabolism through the NF‐κB pathway in human degenerative nucleus pulposus cells
Authors: Yi Weiwei , Chen Qing , Liu Chuan , Li Kaiting , Tao Bailong , Tian Guihua , Zhou Lu , Li Xiaohong , Shen Jieliang , Liu Bo , Hu Zhenming , Wang Dawu , Bai Dingqun
Published: October 2021

Background

Low-intensity pulsed ultrasound (LIPUS) is a safe and noninvasive rehabilitative physical therapy with anti-inflammatory effects. The current study investigated the effect of LIPUS on the inflammation of nucleus pulposus (NP) cells and its underlying mechanism.

Methods

Human NP cells were acquired from lumbar disc herniation tissue samples and cultured for experiments. Human NP cells were treated with LPS and then exposed to LIPUS (15 mW/cm2, 30 mW/cm2 and 60 mW/cm2) for 20 min daily for 3 days to determine the appropriate intensity to inhibit the expression of the inflammatory factors TNF-α and IL-1β. The gene and protein expression of aggrecan, collagen II, MMP-3 and MMP-9 was measured by real‐time PCR and western blotting, respectively. The activity of the nuclear factor‐kappa B (NF‐κB) pathway was examined by western blotting and immunofluorescence. After pretreatment with the NF-κB inhibitor PDTC, the expression of TNF-α, IL-1β, MMP-3 and MMP-9 was measured by real‐time PCR.

Results

LIPUS at intensities of 15 mW/cm2, 30 mW/cm2 and 60 mW/cm2 inhibited LPS-induced NP cell expression of the inflammatory factors TNF-α and IL-1β, especially at 30 mW/cm2. LIPUS significantly upregulated the gene and protein expression of aggrecan and collagen II and downregulated the gene and protein expression of MMP-3 and MMP-9 in LPS-induced NP cells. The NF‐κB signaling pathway was inhibited by LIPUS through inhibiting the protein expression of p-P65 and the translocation of P65 into the nucleus in LPS-induced NP cells. In addition, LIPUS had similar effects as the NF-κB inhibitor PDTC by inhibiting the NF-κB signaling pathway, inflammation and catabolism in LPS-induced human degenerative nucleus pulposus cells.

Conclusion

LIPUS inhibited inflammation and catabolism through the NF‐κB pathway in human degenerative nucleus pulposus cells.
Three-dimensional morphological study of the proximal femur in Crowe type IV developmental dysplasia of the hip
Authors: Yang Yuhui , Liao Weihong , Yi Weiqun , Jiang Hai , Fu Guangtao , Ma Yuanchen , Zheng Qiujian
Published: October 2021

Background

When performing femoral reconstruction in patients with Crowe type IV developmental dysplasia of the hip (DDH), anatomical deformity presents many technical challenges to orthopedic surgeons. The false acetabulum is suggested to influence load transmission and femoral development. The aim of this study was to describe the morphological features of dysplastic femurs in Crowe type IV DDH and further evaluate the potential effect of the false acetabulum on morphological features and medullary canal of Crowe type IV femurs.

Methods

We analyzed preoperative computed tomography scans from 45 patients with 51 hips (25 hips without false acetabulum in the IVa group and 26 hips with false acetabulum in the IVb group) who were diagnosed with Crowe type IV DDH and 30 normal hips in our hospital between January 2009 and January 2019. Three-dimensional reconstruction was performed using Mimics software, and the coronal femoral plane was determined to evaluate the following parameters: dislocation height, dislocation ratio, height of the femoral head (FH), height of the greater trochanter (GT), GT–FH height discrepancy, height of the isthmus, neck-shaft angle, femoral offset and anteversion of the femoral neck. The mediolateral (ML) width, anterolateral (AP) width and diameter of medullary canal of the proximal femur were measured on the axial sections. Further, canal flare index (CFI), metaphyseal-CFI and diaphyseal-CFI were also calculated.

Results

Compared with the normal femurs, the Crowe type IV DDH femurs had a higher femoral head, larger GT–FH height discrepancy, larger femoral neck anteversion, higher isthmus position and smaller femoral offset. Dislocation height and dislocation rate were significantly larger in the IVa DDH group (65.34 ± 9.83 mm vs. 52.24 ± 11.42 mm). Further, the IVb femurs had a significantly lower isthmus position, larger neck-shaft angle and smaller femoral neck anteversion than IVa femurs. The ML, AP canal widths and the diameter of medullary canal in both DDH groups were significantly smaller than the normal group. Dimensional parameters of IVa femurs were also narrower than IVb femurs in most sections, but with no difference at the level of isthmus. According to the CFIs, the variation of proximal medullary canal in IVb femurs was mainly located in the diaphyseal region, while that in IVa femurs was located in the whole proximal femur.

Conclusions

High dislocated femurs are associated with more anteverted femoral neck, smaller femoral offset and narrower medullary canal. Without stimulation of the false acetabulum, IVa DDH femurs were associated with higher dislocation and notably narrower medullary canal, whose variation of medullary canal was located in the whole proximal femur.
Multiple bronchiolar adenomas with malignant transformation and CCNE1 mutation: a case report and literature review
Authors: Li Xiaojun , Wu Yonghui , Hui Dayang , Luo Xiaoxuan , Wu Weibin , Zhang Jian , Chen Huiguo
Published: October 2021

Background

Bronchiolar adenoma (BA) is a recently proposed diagnostic terminology, which is considered as the expansion of the concept of ciliated muconodular papillary tumors. BA is considered to be a benign neoplasm, but a few previous cases have been reported with the possibility of malignant transformation. Therefore, the genetic and histological nature of BA is controversial so far. We describe a rare case of multiple BAs with malignant transformation and CCNE1 (cyclin E1) mutation to increase the understanding of this disease.

Case description

A 56-year-old woman was admitted to our hospital due to two ground-glass nodules (GGNs) in the left lung detected by chest CT without symptom. The pure GGN located in the upper lingual segment about 6 mm in diameter and another mixed GGN located in the dorsal segment about 7 mm. The two GGNs have been found a year ago without treatment, and the mixed GGN become larger to 8 mm with vacuole sign in the next year health checkup. We performed a wedge resection of the two nodules completely by video-assisted thoracoscopy (VATS). Postoperative pathology indicated that the pure GGN was atypical bronchial adenoma, while the mixed GGN was atypical bronchial adenoma with malignant transformation which was missed in frozen section. Gene mutations analysis by next-generation sequencing (NGS) showed CCNE1 gene mutation in both lesions, and her-2 mutation was identified in the mixed GGN. The programmed cell death 1 ligand 1 (PD-L1) expression analysis of tumor cells showed 0% and less than 1% in the pure GGN and the mixed GGN, respectively.

Conclusion

BA is generally considered to be a benign tumor. The present study indicated that BA may be carcinogenic in atypical cases with some driver genes mutation and we should be vigilant for its potentiality of malignant transformation in clinical practice.
Scutellarin ameliorates neonatal hypoxic-ischemic encephalopathy associated with GAP43-dependent signaling pathway
Authors: Niu Rui-Ze , Xiong Liu-Lin , Zhou Hao-Li , Xue Lu-Lu , Xia Qing-Jie , Ma Zheng , Jin Yuan , Chen Li , Jiang Ya , Wang Ting-Hua , Liu Jia
Published: October 2021

Background

Neonatal hypoxic-ischemic encephalopathy (HIE) refers to the perinatal asphyxia caused by the cerebral hypoxic-ischemic injury. The current study was aimed at investigating the therapeutic efficacy of Scutellarin (Scu) administration on neurological impairments induced by hypoxic-ischemic injury and exploring the underlying mechanisms.

Methods

Primary cortical neurons were cultured and subjected to oxygen–glucose deprivation (OGD), and then treated with Scu administration. The growth status of neurons was observed by immunofluorescence staining of TUJ1 and TUNEL. Besides, the mRNA level of growth-associated protein 43 (GAP43) in OGD neurons with Scu treatment was detected by quantitative real-time polymerase chain reaction (qRT-PCR). To further verify the role of GAP43 in Scu treatment, GAP43 siRNA and knockout were applied in vitro and in vivo. Moreover, behavioral evaluations were performed to elucidate the function of GAP43 in the Scu-ameliorated long-term neurological impairments caused by HI insult. The underlying biological mechanism of Scu treatment was further elucidated via network pharmacological analysis. Finally, the interactive genes with GAP43 were identified by Gene MANIA and further validated by qRT-PCR.

Results

Our data demonstrated that Scu treatment increased the number of neurons and axon growth, and suppressed cell apoptosis in vitro. And the expression of GAP43 was downregulated after OGD, but reversed by Scu administration. Besides, GAP43 silencing aggravated the Scu-ameliorated neuronal death and axonal damage. Meanwhile, GAP43 knockout enlarged brain infarct area and deteriorated the cognitive and motor dysfunctions of HI rats. Further, network pharmacological analysis revealed the drug targets of Scu participated in such biological processes as neuronal death and regulation of neuronal death, and apoptosis-related pathways. GAP43 exhibited close relationship with PTN, JAK2 and STAT3, and GAP43 silencing upregulated the levels of PTN, JAK2 and STAT3.

Conclusions

Collectively, our findings revealed Scu treatment attenuated long-term neurological impairments after HI by suppressing neuronal death and enhancing neurite elongation through GAP43-dependent pathway. The crucial role of Scutellarin in neuroprotection provided a novel possible therapeutic agent for the treatment of neonatal HIE.

Graphic abstract
Eat, breathe, sleep with Osteogenesis Imperfecta
Authors: LoMauro Antonella , Landoni Carlo Vittorio , Fraschini Paolo , Molteni Franco , Aliverti Andrea , Bertoli Simona , De Amicis Ramona
Published: October 2021

Background

Although Osteogenesis Imperfecta (OI) affects the connective tissue causing extremely brittle bones with consequent skeletal deformities, it is important to go beyond bones. Indeed, the quality of life in OI does not only depend on bones status, as OI might affect also other important functions. We have therefore implemented a multidisciplinary study to assess lung function, breathing pattern, sleep quality and nutritional status in 27 adult OI type III and IV patients (median age: 34.6 years; 19 women; 14 type III).

Results

According to nocturnal oxygen desaturation, two groups were identified: 13 patients with (OI_OSA, incidence: 48.2%) and 14 without (no_OSA) obstructive sleep apnea. The former was characterized by higher spinal and ribcage deformity, by more restrictive lung function, by paradoxical thoracic breathing in supine position, by rapid and shallow breathing, by higher body mass index, by longer neck and waist circumferences; by higher abdominal volume and by greater percentage of body fat mass, particularly localized in the trunk.

The best predictor of OI_OSA was the negative value of the supine ribcage contribution to tidal volume, followed by the ratio between the neck and the waist circumferences with body height and the supine thoraco-abdominal volumes phase shift angle.

Conclusions

The pathophysiology of OI ensued a dangerous vicious circle, in which breathing, sleep and nutritional status are tightly linked, and they might all end up in negatively affecting the quality of life. The vicious circle is fed by some intrinsic characteristics of the disease (thoracic, cranial and mandibular deformities) and some bad daily habits of the patients (i.e. physical inactivity and low dietary quality). The former impacts on restricting the respiratory function, the latter makes Olers more prone to experience overweight or obesity. The main consequence is a high incidence of obstructive sleep apnea, which remains an underdiagnosed disorder in individuals with severe OI who are obese, with a neck to height ratio over than 31.6%, and characterized by paradoxical breathing in supine position. A multidisciplinary approach, including evaluations of breathing, sleep and nutrition, is required to better manage the disease and fulfil the maximizing well-being of OI patients.
Impaired antioxidant KEAP1-NRF2 system in amyotrophic lateral sclerosis: NRF2 activation as a potential therapeutic strategy
Authors: Bono Silvia , Feligioni Marco , Corbo Massimo
Published: October 2021

Background

Oxidative stress (OS) is an imbalance between oxidant and antioxidant species and, together with other numerous pathological mechanisms, leads to the degeneration and death of motor neurons (MNs) in amyotrophic lateral sclerosis (ALS).

Main body

Two of the main players in the molecular and cellular response to OS are NRF2, the transcription nuclear factor erythroid 2-related factor 2, and its principal negative regulator, KEAP1, Kelch-like ECH (erythroid cell-derived protein with CNC homology)-associated protein 1. Here we first provide an overview of the structural organization, regulation, and critical role of the KEAP1-NRF2 system in counteracting OS, with a focus on its alteration in ALS. We then examine several compounds capable of promoting NRF2 activity thereby inducing cytoprotective effects, and which are currently in different stages of clinical development for many pathologies, including neurodegenerative diseases.

Conclusions

Although challenges associated with some of these compounds remain, important advances have been made in the development of safer and more effective drugs that could actually represent a breakthrough for fatal degenerative diseases such as ALS.
Fusion versus fixation in complex comminuted C3-type tibial pilon fractures: a systematic review
Authors: Chaudhry Yash P. , Papadelis Efstratios , Hayes Hunter , Stahel Philip F. , Hasenboehler Erik A.
Published: October 2021

Background

Comminuted intra-articular tibial pilon fractures can be challenging to manage, with high revision rates and poor functional outcomes. This study reviewed [1] treatment, complications, and clinical outcomes in studies of complex comminuted tibial pilon fractures (type AO43-C3); and [2] primary ankle arthrodesis as a management option for these types of complex injuries.

Methods

A systematic literature search was performed on PubMed from 1990 to 2020 to determine complications and outcomes after staged fracture fixation and primary ankle joint arthrodesis for comminuted C3-type tibial pilon fractures.

The search was conducted in compliance with the PRISMA guidelines, using the following MeSH terms: “tibial pilon”/“pilon fracture”/“plafond fracture”/“distal tibial”/“43-C3”/“ankle fracture”/“ankle fusion”/“primary ankle arthrodesis”/“pilon fracture staged”/“pilon external fixation” and “pilon open reduction internal fixation.” Inclusion criteria were restricted to original articles in English language on adult patients ≥18 years of age. Eligibility criteria for retrieved publications were determined using a “PICO” approach (population, intervention/exposure, comparison, outcomes). Weighted analysis was used to compare treatment groups on time to definitive treatment, follow-up time, range of motion, fracture classification, and complications.

Results

The systematic literature review using the defined MeSH terms yielded 72 original articles. Of these, 13 articles met the eligibility criteria based on the PICO statements, of which 8 publications investigated the outcomes of a staged fixation approach in 308 cumulative patients, and 5 articles focused on primary ankle arthrodesis in 69 cumulative patients. For staged treatment, the mean wound complication rate was 14.6%, and the malunion/nonunion rate was 9.9%. For primary arthrodesis, the mean wound complication rate was 2.9%, and the malunion/nonunion rate was 2.9%. After risk stratification for fracture type and severity, the small cumulative cohort of patients included in the primary arthrodesis publications did not provide sufficient power to determine a clinically relevant difference in complications and long-term patient outcomes compared to the staged surgical fixation group.

Conclusions

At present, there is insufficient evidence in the published literature to provide guidance towards consideration of ankle arthrodesis for complex comminuted C3-type tibial pilon fractures, compared to the standard treatment by staged surgical fracture fixation.
Resistance to anti-EGFR therapies in metastatic colorectal cancer: underlying mechanisms and reversal strategies
Authors: Zhou Jing , Ji Qing , Li Qi
Published: October 2021

Cetuximab and panitumumab are monoclonal antibodies (mAbs) against epidermal growth factor receptor (EGFR) that are effective agents for metastatic colorectal cancer (mCRC). Cetuximab can prolong survival by 8.2 months inRASwild-type (WT) mCRC patients. Unfortunately, resistance to targeted therapy impairs clinical use and efficiency. The mechanisms of resistance refer to intrinsic and extrinsic alterations of tumours. Multiple therapeutic strategies have been investigated extensively to overcome resistance to anti-EGFR mAbs. The intrinsic mechanisms include EGFR ligand overexpression, EGFR alteration,RAS/RAF/PI3Kgene mutations, ERBB2/MET/IGF-1R activation, metabolic remodelling, microsatellite instability and autophagy. For intrinsic mechanisms, therapies mainly cover the following: new EGFR-targeted inhibitors, a combination of multitargeted inhibitors, and metabolic regulators. In addition, new cytotoxic drugs and small molecule compounds increase the efficiency of cetuximab. Extrinsic alterations mainly disrupt the tumour microenvironment, specifically immune cells, cancer-associated fibroblasts (CAFs) and angiogenesis. The directions include the modification or activation of immune cells and suppression of CAFs and anti-VEGFR agents. In this review, we focus on the mechanisms of resistance to anti-EGFR monoclonal antibodies (anti-EGFR mAbs) and discuss diverse approaches to reverse resistance to this therapy in hopes of identifying more mCRC treatment possibilities.
The lockdown effects on a pediatric obese population in the COVID-19 era
Authors: Valenzise M. , D’Amico F. , Cucinotta U. , Lugarà C. , Zirilli G. , Zema A. , Wasniewska M. , Pajno G. B.
Published: October 2021

Background

The social consequences of COVID-19 pandemic are universally known. In particular, the pediatric population is dealing with a radical lifestyle change. For some risk categories, such as overweight or obese children, the impact of home confinement has been greater than for others. The increased sedentary life, the wrong diet and social distancing have stopped the chance of losing weight.

The aims of this study were to analyse the impact of COVID-19 lockdown on the behavior changes in a obese pediatric population and to explore the correlation between the new lifestyle and the level of parental instruction.

Methods

Data show features of 40 obese and overweight pediatric patients of our Clinic in Messina (Italy). We evaluated weight, height, BMI and other biochemical parameters: total cholesterol, HDL, LDL, triglyceride, transaminases, glycemia and insulinemia. After the lockdown, we contacted all patients in order to get some information about diet, physical activity and sedentary lifestyle changes in correlation to the level of their parents’ instruction. Additionally, we also evaluated 20 children twice from a clinical and laboratory perspective.

Results

The study showed an increase of daily meals during COVID-19 lockdown (3.2 ± 0.4 vs 5 ± 1, P < 0.001). In particular, children whose parents have primary school diploma ate a greater significant number of meals during the lockdown, compared to those who have parents with secondary school diploma (P = 0.0019). In addition, the 95% of patients did low physical activity during the lockdown and the 97.5% spent more time in sedentary activity. Even if BMI’s values don’t show significant differences, they have increased after the lockdown. We didn’t find any correlation between biochemical parameters before and after the lockdown.

Conclusion

The lockdown has had bad consequences on good style of life’s maintenance in overweight and obese children. The absence of a significant correlation between the worsening of biochemical parameters and the lockdown doesn’t allow to exclude any long-term consequences. It’s safe to assume that, if the hours spent in sedentary activity and the number of meals don’t diminish, there will probably repercussion on the biochemical parameters.
Evaluation of zinc sulfate as an adjunctive therapy in COVID-19 critically ill patients: a two center propensity-score matched study
Authors: Al Sulaiman Khalid , Aljuhani Ohoud , Al Shaya Abdulrahman I. , Kharbosh Abdullah , Kensara Raed , Al Guwairy Alhomaidi , Alharbi Aisha , Algarni Rahmah , Al Harbi Shmeylan , Vishwakarma Ramesh , Korayem Ghazwa B.
Published: October 2021

Background

Zinc is a trace element that plays a role in stimulating innate and acquired immunity. The role of zinc in critically ill patients with COVID-19 remains unclear. This study aims to evaluate the efficacy and safety of zinc sulfate as adjunctive therapy in critically ill patients with COVID-19.

Methods

Patients aged ≥ 18 years with COVID-19 who were admitted to the intensive care unit (ICU) in two tertiary hospitals in Saudi Arabia were retrospectively assessed for zinc use from March 1, 2020 until March 31, 2021. After propensity score matching (1:1 ratio) based on the selected criteria, we assessed the association of zinc used as adjunctive therapy with the 30-day mortality. Secondary outcomes included the in-hospital mortality, ventilator free days, ICU length of stay (LOS), hospital LOS, and complication (s) during ICU stay.

Results

A total of 164 patients were included, 82 patients received zinc. Patients who received zinc sulfate as adjunctive therapy have a lower 30-day mortality (HR 0.52, CI 0.29, 0.92; p = 0.03). On the other hand, the in-hospital mortality was not statistically significant between the two groups (HR 0.64, CI 0.37–1.10; p = 0.11). Zinc sulfate use was associated with a lower odds of acute kidney injury development during ICU stay (OR 0.46 CI 0.19–1.06; p = 0.07); however, it did not reach statistical significance.

Conclusion

The use of zinc sulfate as an additional treatment in critically ill COVID-19 patients may improve survival. Furthermore, zinc supplementation may have a protective effect on the kidneys.
Lean mass as a risk factor for intensive care unit admission: an observational study
Authors: Thackeray Matthew , Mohebbi Mohammadreza , Orford Neil , Kotowicz Mark A. , Pasco Julie A.
Published: October 2021

Purpose

Intensive care unit (ICU) survivors have reduced physical function likely due to skeletal muscle wasting and weakness acquired during critical illness. However, the contribution of pre-morbid muscle mass has not been elucidated. We aimed to examine the association between pre-ICU muscle mass and ICU admission risk. Secondary outcomes include the relationship between muscle mass and ICU outcomes.

Methods

ICU admissions between June 1, 1998, and February 1, 2019, were identified among participants of Geelong Osteoporosis Study (GOS), a population-based cohort study. Cox proportional hazard regression models estimated hazard ratios (HR) for ICU admission across T-score strata and continuous values of DXA-derived lean mass measures of skeletal mass index (SMI, lean mass/body mass %) and appendicular lean mass corrected for height (ALM/h2, kg/m2). Multivariable regression was used to determine the relationship between lean mass and ICU outcomes.

Results

One hundred and eighty-six of 3126 participants enrolled in GOS were admitted to the ICU during the follow-up period. In adjusted models, lean mass was not predictive of ICU admission (SMI: HR 0.99 95%CI 0.97–1.01, p = 0.32; ALM/h2: HR 1.11 95%CI 0.94–1.31, p = 0.23), while greater appendicular lean mass was related to reduced 28-day mortality (ALM/h2 adjOR: 0.25, 95%CI 0.10–0.63, p = 0.003, SMI adjOR: 0.91, 95%CI 0.82–1.02, p = 0.09).

Conclusion

Lean mass was not associated with ICU admission in this population-based cohort study; however, greater appendicular lean mass was associated with reduced mortality. This suggests pre-ICU muscle status may not predict development of critical illness but is associated with better survival after critical illness occurs.
The chromatin remodeler Ino80 mediates RNAPII pausing site determination
Authors: Cheon Youngseo , Han Sungwook , Kim Taemook , Hwang Daehee , Lee Daeyoup
Published: October 2021

Background

Promoter-proximal pausing of RNA polymerase II (RNAPII) is a critical step for the precise regulation of gene expression. Despite the apparent close relationship between promoter-proximal pausing and nucleosome, the role of chromatin remodeler governing this step has mainly remained elusive.

Results

Here, we report highly confined RNAPII enrichments downstream of the transcriptional start site in Saccharomyces cerevisiae using PRO-seq experiments. This non-uniform distribution of RNAPII exhibits both similar and different characteristics with promoter-proximal pausing in Schizosaccharomyces pombe and metazoans. Interestingly, we find that Ino80p knockdown causes a significant upstream transition of promoter-proximal RNAPII for a subset of genes, relocating RNAPII from the main pausing site to the alternative pausing site. The proper positioning of RNAPII is largely dependent on nucleosome context. We reveal that the alternative pausing site is closely associated with the + 1 nucleosome, and nucleosome architecture around the main pausing site of these genes is highly phased. In addition, Ino80p knockdown results in an increase in fuzziness and a decrease in stability of the + 1 nucleosome. Furthermore, the loss of INO80 also leads to the shift of promoter-proximal RNAPII toward the alternative pausing site in mouse embryonic stem cells.

Conclusions

Based on our collective results, we hypothesize that the highly conserved chromatin remodeler Ino80p is essential in establishing intact RNAPII pausing during early transcription elongation in various organisms, from budding yeast to mouse.
Effects of sequence motifs in the yeast 3′ untranslated region determined from massively parallel assays of random sequences
Authors: Savinov Andrew , Brandsen Benjamin M. , Angell Brooke E. , Cuperus Josh T. , Fields Stanley
Published: October 2021

Background

The 3′ untranslated region (UTR) plays critical roles in determining the level of gene expression through effects on activities such as mRNA stability and translation. Functional elements within this region have largely been identified through analyses of native genes, which contain multiple co-evolved sequence features.

Results

To explore the effects of 3′ UTR sequence elements outside of native sequence contexts, we analyze hundreds of thousands of random 50-mers inserted into the 3′ UTR of a reporter gene in the yeast Saccharomyces cerevisiae. We determine relative protein expression levels from the fitness of transformants in a growth selection. We find that the consensus 3′ UTR efficiency element significantly boosts expression, independent of sequence context; on the other hand, the consensus positioning element has only a small effect on expression. Some sequence motifs that are binding sites for Puf proteins substantially increase expression in the library, despite these proteins generally being associated with post-transcriptional downregulation of native mRNAs. Our measurements also allow a systematic examination of the effects of point mutations within efficiency element motifs across diverse sequence backgrounds. These mutational scans reveal the relative in vivo importance of individual bases in the efficiency element, which likely reflects their roles in binding the Hrp1 protein involved in cleavage and polyadenylation.

Conclusions

The regulatory effects of some 3′ UTR sequence features, like the efficiency element, are consistent regardless of sequence context. In contrast, the consequences of other 3′ UTR features appear to be strongly dependent on their evolved context within native genes.
Orientia tsutsugamushi dynamics in vectors and hosts: ecology and risk factors for foci of scrub typhus transmission in northern Thailand
Authors: Elliott Ivo , Thangnimitchok Neeranuch , Chaisiri Kittipong , Wangrangsimakul Tri , Jaiboon Piangnet , Day Nicholas P. J. , Paris Daniel H. , Newton Paul N. , Morand Serge
Published: October 2021

Background

Scrub typhus is an important neglected vector-borne zoonotic disease across the Asia–Pacific region, with an expanding known distribution. The disease ecology is poorly understood, despite the large global burden of disease. The key determinants of high-risk areas of transmission to humans are unknown.

Methods

Small mammals and chiggers were collected over an 18-month period at three sites of differing ecological profiles with high scrub typhus transmission in Chiang Rai Province, northern Thailand. Field samples were identified and tested for Orientia tsutsugamushi by real-time PCR. The rates and dynamics of infection were recorded, and positive and negative individuals were mapped over time at the scale of single villages. Ecological analyses were performed to describe the species richness, community structure and interactions between infected and uninfected species and habitats. Generalised linear modelling (GLM) was applied to examine these interactions.

Results

The site with the highest rates of human infection was associated with the highest number of infected chigger pools (41%), individual chiggers (16%), proportion of the known vector species Leptotrombidium deliense (71%) and chigger index (151). Chigger species diversity was lowest (Shannon diversity index H′: 1.77) and rodent density appeared to be high. There were no consistent discrete foci of infection identified at any of the study sites. The small mammals Rattus tanezumi and Bandicota indica and the chiggers L. deliense and Walchia kritochaeta emerged as central nodes in the network analysis. In the GLM, the end of the dry season, and to a lesser extent the end of the wet season, was associated with O. tsutsugamushi-infected small mammals and chiggers. A clear positive association was seen between O. tsutsugamushi-positive chigger pools and the combination of O. tsutsugamushi-positive chigger pools and O. tsutsugamushi-positive small mammals with lowland habitats.

Conclusions

These findings begin to reveal some of the factors that may determine high-risk foci of scrub typhus at a fine local scale. Understanding these factors may allow practical public health interventions to reduce disease risk. Further studies are needed in areas with diverse ecology.

Graphical abstract
Comprehensive multi-omics integration identifies differentially active enhancers during human brain development with clinical relevance
Authors: Yousefi Soheil , Deng Ruizhi , Lanko Kristina , Salsench Eva Medico , Nikoncuk Anita , van der Linde Herma C. , Perenthaler Elena , van Ham Tjakko J. , Mulugeta Eskeatnaf , Barakat Tahsin Stefan
Published: October 2021

Background

Non-coding regulatory elements (NCREs), such as enhancers, play a crucial role in gene regulation, and genetic aberrations in NCREs can lead to human disease, including brain disorders. The human brain is a complex organ that is susceptible to numerous disorders; many of these are caused by genetic changes, but a multitude remain currently unexplained. Understanding NCREs acting during brain development has the potential to shed light on previously unrecognized genetic causes of human brain disease. Despite immense community-wide efforts to understand the role of the non-coding genome and NCREs, annotating functional NCREs remains challenging.

Methods

Here we performed an integrative computational analysis of virtually all currently available epigenome data sets related to human fetal brain.

Results

Our in-depth analysis unravels 39,709 differentially active enhancers (DAEs) that show dynamic epigenomic rearrangement during early stages of human brain development, indicating likely biological function. Many of these DAEs are linked to clinically relevant genes, and functional validation of selected DAEs in cell models and zebrafish confirms their role in gene regulation. Compared to enhancers without dynamic epigenomic rearrangement, DAEs are subjected to higher sequence constraints in humans, have distinct sequence characteristics and are bound by a distinct transcription factor landscape. DAEs are enriched for GWAS loci for brain-related traits and for genetic variation found in individuals with neurodevelopmental disorders, including autism.

Conclusion

This compendium of high-confidence enhancers will assist in deciphering the mechanism behind developmental genetics of human brain and will be relevant to uncover missing heritability in human genetic brain disorders.
A global cancer data integrator reveals principles of synthetic lethality, sex disparity and immunotherapy
Authors: Yogodzinski Christopher , Arab Abolfazl , Pritchard Justin R. , Goodarzi Hani , Gilbert Luke A.
Published: October 2021

Background

Advances in cancer biology are increasingly dependent on integration of heterogeneous datasets. Large-scale efforts have systematically mapped many aspects of cancer cell biology; however, it remains challenging for individual scientists to effectively integrate and understand this data.

Results

We have developed a new data retrieval and indexing framework that allows us to integrate publicly available data from different sources and to combine publicly available data with new or bespoke datasets. Our approach, which we have named the cancer data integrator (CanDI), is straightforward to implement, is well documented, and is continuously updated which should enable individual users to take full advantage of efforts to map cancer cell biology. We show that CanDI empowered testable hypotheses of new synthetic lethal gene pairs, genes associated with sex disparity, and immunotherapy targets in cancer.

Conclusions

CanDI provides a flexible approach for large-scale data integration in cancer research enabling rapid generation of hypotheses. The CanDI data integrator is available athttps://github.com/GilbertLabUCSF/CanDI.
Genomic approaches to trace the history of human brain evolution with an emerging opportunity for transposon profiling of ancient humans
Authors: Wang Yilan , Zhao Boxun , Choi Jaejoon , Lee Eunjung Alice
Published: October 2021

Transposable elements (TEs) significantly contribute to shaping the diversity of the human genome, and lines of evidence suggest TEs as one of driving forces of human brain evolution. Existing computational approaches, including cross-species comparative genomics and population genetic modeling, can be adapted for the study of the role of TEs in evolution. In particular, diverse ancient and archaic human genome sequences are increasingly available, allowing reconstruction of past human migration events and holding the promise of identifying and tracking TEs among other evolutionarily important genetic variants at an unprecedented spatiotemporal resolution. However, highly degraded short DNA templates and other unique challenges presented by ancient human DNA call for major changes in current experimental and computational procedures to enable the identification of evolutionarily important TEs. Ancient human genomes are valuable resources for investigating TEs in the evolutionary context, and efforts to explore ancient human genomes will potentially provide a novel perspective on the genetic mechanism of human brain evolution and inspire a variety of technological and methodological advances. In this review, we summarize computational and experimental approaches that can be adapted to identify and validate evolutionarily important TEs, especially for human brain evolution. We also highlight strategies that leverage ancient genomic data and discuss unique challenges in ancient transposon genomics.
SETD2-mediated epigenetic regulation of noncanonical Wnt5A during osteoclastogenesis
Authors: Deb Moonmoon , Laha Dipranjan , Maity Jyotirindra , Das Hiranmoy
Published: October 2021

To define the role of SETD2 in the WNT5a signaling in the context of osteoclastogenesis, we exploited two different models: in vitro osteoclast differentiation, and K/BxN serum-induced arthritis model. We found that SETD2 and WNT5a were upregulated during osteoclast differentiation and after induction of arthritis. Using gain- and loss-of-function approaches in the myeloid cell, we confirmed that SETD2 regulated the osteoclast markers, and WNT5a via modulating active histone marks by enriching H3K36me3, and by reducing repressive H3K27me3 mark. Additionally, during osteoclastic differentiation, the transcription ofWnt5awas also associated with the active histone H3K9 and H4K8 acetylations. Mechanistically, SETD2 directed induction of NF-κβ expression facilitated the recruitment of H3K9Ac and H4K8Ac around the TSS region of theWnt5agene, thereby, assisting osteoclast differentiation. Together these findings for the first time revealed that SETD2 mediated epigenetic regulation ofWnt5aplays a critical role in osteoclastogenesis and induced arthritis.

Graphic abstract

Model for the Role of SETD2 dependent regulation of osteoclastic differentiation.AIn monocyte cells SETD2-dependent H3K36 trimethylation help to create open chromatin region along with active enhancer mark, H3K27Ac. This chromatin state facilitated the loss of a suppressive H3K27me3 mark.BAdditionally, SETD2 mediated induction of NF-κβ expression leads to the recruitment of histone acetyl transferases, P300/PCAF, to the Wnt5a gene and establish H3K9Ac and H4K8Ac marks. Along with other activation marks, these acetylation marks help in Wnt5a transcription which leads to osteoclastogenesis.
Antifungal activity, identification and biosynthetic potential analysis of fungi against Rhizoctonia cerealis
Authors: Zhao Xingli , Song Peng , Hou Dianyun , Li Ziliang , Hu Zhenjie
Published: October 2021

Purpose

Wheat sheath blight mainly infected by Rhizoctonia cerealis is one of the soil-borne fungal diseases of wheat worldwide and prevalent in major wheat growing areas in China at present. This study aimed to evaluate the antifungal activity of 163 endophytic fungi on R. cerealis. Antifungal strains were identified and their biosynthetic potential was analysed.

Methods

The antifungal activity of the strains was evaluated via dual-culture antagonism assay. The antifungal strains were identified on the basis of morphological characteristics and internal transcribed spacer gene sequencing. The polyketide synthases (PKSs) and nonribosomal peptide synthetase (NRPS) genes in antifungal strains were detected via specific amplification of chromosomal DNA.

Result

Twelve out of 163 fungal strains, including seven strains with matrix competition and five strains with antibiosis, were obtained. The twelve antifungal strains belonged to four genera: Alternaria, Ascochyta, Botryosphaeria, and Talaromyces. The inhibition rate of the seven strains with matrix competition was greater than 50%, with that of Botryosphaeria dothidea S2-33 being the highest at 84.6%. The inhibition zone of Talaromyces assiutensis R-03 amongst the five strains with antibiosis was the widest at up to 7 mm. Among the twelve antifungal strains, the strain S2-16 contained all the genes tested, five B. dothidea strains contained PKS-II and NRPS genes, two Alternaria alternata strains only contained PKS-II gene and the remaining four strains did not contain any.

Conclusion

Results demonstrated twelve potential strains for the biocontrol of wheat sheath blight. In particular, T. assiutensis R-03 was determined as a promising agent. The active substances secreted by antifungal strains may be produced by other biosynthetic pathways.
Co-administration of vitamin D3 and Lacticaseibacillus paracasei DG increase 25-hydroxyvitamin D serum levels in mice
Authors: Castagliuolo Ignazio , Scarpa Melania , Brun Paola , Bernabe Giulia , Sagheddu Valeria , Elli Marina , Fiore Walter , De Vitis Valerio , Guglielmetti Simone
Published: October 2021

Purpose

Subclinical vitamin D (vitD) deficiency enhances the predisposition to a myriad of acute and chronic pathologies in many people worldwide. Due to the scarcity of vitD-rich foods, the consumption of supplements or fortified foods can be required to maintain healthy serum levels of 25-hydroxyvitamin D [25(OH)D], and the major circulating form of vitD that is commonly measured in serum to determine the vitD status. Since the vitD absorption seems to resemble that of lipids, improved emulsification in the gut could favor vitD permeation through the enterocyte membrane. Contextually, we hypothesized that a microorganism with cholecalciferol (vitD3)-solubilization properties may potentially result in enhanced serum vitD levels.

Methods and results

Six probiotic strains were screened for their ability to create a stable suspension of vitD3 in water: Lacticaseibacillus paracasei DG, L. paracasei LPC-S01, L. paracasei Shirota, L. rhamnosus GG, Limosilactobacillus reuteri DSM 17938, and Lactobacillus acidophilus LA5. The DG strain displayed the strongest vitD3 solubilization ability and, consequently, were used in an in vivo trial where a commercial preparation of vitD3 in refined olive oil was administered by gavage to CD-1 mice with or without the concurrent administration of L. paracasei DG. ELISA measurements showed that the DG strain significantly increased the serum levels of 25(OH) D when administered once a day for 1 week in association with the vitD3 supplement.

Conclusion

This preliminary pre-clinical study suggests that the combined administration of L. paracasei DG with an oil-based cholecalciferol supplement could contribute to the maintenance of the adequate 25(OH) D serum levels in people at risk of vitD deficiency.
Duplication of spiralian-specific TALE genes and evolution of the blastomere specification mechanism in the bivalve lineage
Authors: Phuangphong Supanat , Tsunoda Jumpei , Wada Hiroshi , Morino Yoshiaki
Published: October 2021

Background

Despite the conserved pattern of the cell-fate map among spiralians, bivalves display several modified characteristics during their early development, including early specification of the D blastomere by the cytoplasmic content, as well as the distinctive fate of the 2d blastomere. However, it is unclear what changes in gene regulatory mechanisms led to such changes in cell specification patterns. Spiralian-TALE (SPILE) genes are a group of spiralian-specific transcription factors that play a role in specifying blastomere cell fates during early development in limpets. We hypothesised that the expansion of SPILE gene repertoires influenced the evolution of the specification pattern of blastomere cell fates.

Results

We performed a transcriptome analysis of early development in the purplish bifurcate mussel and identified 13 SPILE genes. Phylogenetic analysis of the SPILE gene in molluscs suggested that duplications of SPILE genes occurred in the bivalve lineage. We examined the expression patterns of the SPILE gene in mussels and found that some SPILE genes were expressed in quartet-specific patterns, as observed in limpets. Furthermore, we found that several SPILE genes that had undergone gene duplication were specifically expressed in the D quadrant, C and D quadrants or the 2d blastomere. These expression patterns were distinct from the expression patterns of SPILE in their limpet counterparts.

Conclusions

These results suggest that, in addition to their ancestral role in quartet specification, certain SPILE genes in mussels contribute to the specification of the C and D quadrants. We suggest that the expansion of SPILE genes in the bivalve lineage contributed to the evolution of a unique cell fate specification pattern in bivalves.