Mass Spectrometry Acquisition and Fractionation Recommendations for TMT11 and TMT16 Labeled Samples.

Proteome coverage and accurate protein quantification are both important for evaluating biological systems; however, compromises between quantification, coverage, and mass spectrometry (MS) resources are often necessary. Consequently, experimental parameters that impact coverage and quantification must be adjusted, depending on experimental goals. Among these parameters is offline prefractionation, which is utilized in MS-based proteomics to decrease sample complexity resulting in higher overall proteome coverage upon MS analysis. Prefractionation leads to increases in required MS analysis time, although this is often mitigated by isobaric labeling using tandem-mass tags (TMT), which allow samples to be multiplexed. Here we evaluate common prefractionation schemes, TMT variants, and MS acquisition methods and their impact on protein quantification and coverage. Furthermore, we provide recommendations for experimental design depending on the experimental goals.

[Research advances on the mechanism of Wnt/ß-catenin signaling pathway in body surface wound healing].

Wound healing is a slow and complex biological process, including inflammatory reaction, cell proliferation, cell differentiation, cell migration, angiogenesis, extracellular matrix deposition, tissue remodeling, and so on. Wnt signaling pathway can be divided into classical pathway and non-classical pathway. Wnt classical pathway, also known as Wnt/ß-catenin signaling pathway, plays an important role in cell differentiation, cell migration, and maintenance of tissue homeostasis. Many inflammatory factors and growth factors are involved in the upstream regulation of this pathway. The activation of Wnt/ß-catenin signaling pathway plays an important role in the occurrence, development, regeneration, repair and related treatment of skin wounds. This article review the relationship between Wnt/ß-catenin signaling pathway and wound healing, meanwhile summarizes its effects on important processes of wound healing, such as inflammation, cell proliferation, angiogenesis, hair follicle regeneration, and skin fibrosis, as well as the role of inhibitors of Wnt signaling pathway in wound healing.

The Pathognomonic FOXL2 C134W Mutation Alters DNA-Binding Specificity.

The somatic missense point mutation c.402C>G (p.C134W) in the FOXL2 transcription factor is pathognomonic for adult-type granulosa cell tumors (AGCT) and a diagnostic marker for this tumor type. However, the molecular consequences of this mutation and its contribution to the mechanisms of AGCT pathogenesis remain unclear. To explore these mechanisms, we engineered V5-FOXL2WT- and V5-FOXL2C134W-inducible isogenic cell lines and performed chromatin immunoprecipitation sequencing and transcriptome profiling. FOXL2C134W associated with the majority of the FOXL2 wild-type DNA elements as well as a large collection of unique elements genome wide. This model enabled confirmation of altered DNA-binding specificity for FOXL2C134W and identification of unique targets of FOXL2C134W including SLC35F2, whose expression increased sensitivity to YM155. Our results suggest FOXL2C134W drives AGCT by altering the binding affinity of FOXL2-containing complexes to engage an oncogenic transcriptional program. SIGNIFICANCE: A mechanistic understanding of FOXL2C134W-induced regulatory state alterations drives discovery of a rationally designed therapeutic strategy.

Methods and clinical outcomes of in situ fenestration for aortic arch revascularization during thoracic endovascular aortic repair.

OBJECTIVE: Despite endovascular advances in fenestrated and branched devices, thoracic endovascular aortic repair (TEVAR) for arch pathologies remains challenging. The aim of this study was to provide a contemporary review on the current evidence for in situ fenestration during TEVAR and to evaluate its short- and mid-term clinical outcome in the management of arch pathology. METHODS: A systematic literature review on in situ fenestration of thoracic aortic stent-graft from January 2003 to September 2018 was performed under the instruction of Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) Statement. RESULTS: Our initial search yielded 169 studies, of which 21 articles were relevant to the topic and were finally included. One hundred and forty-five in situ fenestration procedures in 99 patients were reviewed, involving 25 innominate arteries (17%), 33 left common carotid arteries (23%) and 87 left subclavian arteries (60%). Twelve patients (12/99, 12%) had two-vessel fenestration and three-vessel fenestration was performed in 17 patients (17/99, 17%). Technical success was achieved in 136 arteries (136/145, 93%). Talent/Valiant with monofilament twill woven polyester fabric was the most common (50/99, 51%) stent-graft used for fenestration. Three methods reported for in situ fenestration were needle, laser and radiofrequency. Needle was the most frequently used device for fenestration, which was performed in 60 patients (60/99, 61%). Three patients (3/99, 3%) died with 30 days, none were in situ fenestration TEVAR procedure-related. Perioperative complications including one (1%) retrograde type A aortic dissection, two (2%) type II endoleaks, and three (3%) strokes were reported. The pooled estimate for overall technical success, perioperative mortality and stroke was 88.3% (95% CI, 78.6%-93.9%), 5.9% (95% CI, 2.5%-13.4%) and 9.5% (95% CI, 4.1%-20.6%), respectively. Four patients (4/96, 4%) died during follow-up, none were aortic-related. All the fenestration bridging stents were reportedly patent, with only 1 (1/96, 1%) asymptomatic left subclavian stent stenosis. Two patients (2/96, 2%) with type II endoleak from left subclavian artery required secondary intervention. CONCLUSION: In situ fenestration appeared to be a feasible and effective method to extend proximal landing zone during TEVAR. It had an acceptable short-term result with high technical success and low fenestration related morbidity. Long-term durability data were lacking, and there was no high level evidence to recommend the routine use of in situ fenestration TEVAR for the management of arch pathology.

Percutaneous mechanical thrombectomy in the treatment of acute iliofemoral deep vein thrombosis: a systematic review.

BACKGROUND: Conventional treatment of deep vein thrombosis (DVT) of the lower extremities by anticoagulation alone has been proven to be insufficient to prevent recurrence and post-thrombotic syndrome (PTS). Early restoration of venous patency and preservation of valvular function by endovascular surgery has been advocated. The aim of this study was to review the efficacy and safety of percutaneous mechanical thrombectomy (PMT) against catheter-directed thrombolysis (CDT) in the treatment of acute iliofemoral DVT. METHODS: Three hundred sixty-nine articles were identified through screening of the PubMed, EMBASE, and Cochrane databases from January 2006 to December 2016. RESULTS: Fifteen retrospective studies and one prospective registry, totalling 1170 patients, were recruited for qualitative synthesis. The venous patency rate ranged from 75% to 100% with mean follow-up of 12.3 months. The rates of PTS and recurrent DVT were less than 17% and 15%, respectively. The overall mortality rate was 0.26%. Compared with CDT, PMT was shown to reduce PTS at 1 year (Villalta score: 2.1 ± 3.0 in the PMT group and 5.1 ± 4.1 in the CDT group, P=0.03) and bleeding complications (packed cells transfused: 0.2 ± 0.3 units in the pharmacomechanical thrombectomy group and 1.2 ± 0.7 units in the CDT group, P<0.05). CONCLUSION: Percutaneous mechanical thrombectomy is a safe and effective treatment for acute iliofemoral DVT in terms of restoration of venous patency, prevention of DVT recurrence, and PTS. Compared with CDT alone, PMT offers a lower risk of PTS and bleeding complications.

Arch branch endografts for arch aneurysms associated with bovine anomaly.

Bovine aortic arch is known to be associated with an increased rate of aortic arch expansion. The most frequently observed human variant of bovine aortic arch is a common origin of the innominate trunk and left common carotid artery. This is a report of two patients who had successful custom-made arch branch endograft treatment for an arch aneurysm associated with bovine arch anomaly. Modular endovascular repair of aortic arch aneurysms using an inner-branched device adds to the armamentarium of treatment options, and is a minimally invasive management modality without the need for sternotomy or intraoperative extracorporeal bypass.

Delayed open conversion after endovascular aortic repair.

AIM: We present the clinical outcomes of patients who underwent delayed (>30 days) open surgical repair after endovascular aortic aneurysm repair. METHODS: All patients receiving delayed open repair of infrarenal and juxtarenal aortic aneurysms after endovascular repair from July 2001 to December 2017 were retrospectively reviewed. Patients' baseline characteristics, indications for delayed open conversion, and time between endovascular repair and open conversion are described. Early outcomes included operative approach, morbidity, and mortality. Midterm outcomes included survival. RESULTS: Twenty-two (3.3%) of 667 patients with prior infrarenal endovascular aortic aneurysm repair had delayed open conversion (20 elective and 2 emergency). The time from endovascular repair to open conversion was 60 ± 36 months. The indications were 6 (27%) type Ia endoleaks, 6 (27%) type II endoleaks with enlarging sac size, 2 (9%) endotensions, 7 (32%) unknown types of endoleak, and 1 (5%) graft infection. The 7 minutes unknown endoleaks were confirmed as lumbar leaks in 4 cases and fabric leaks in 3. Operative time was 222 ± 48 min with blood loss of 2211 ± 2057 mL. Hospital stay after conversion was 12 ± 8 days. There was no 30-day mortality. Estimated survival rates were 96%, 91%, 86%, 79% and 57% at 1, 2, 3, 4, and 5 years postoperatively. CONCLUSION: Delayed conversion to open surgery after endovascular aortic aneurysm repair by endograft explantation appears to be safe with good short- and mid-term outcomes. With careful preoperative assessment, open conversion remained a realistic and viable option in patients with failed endovascular treatment.

A report of three families with FBN1-related acromelic dysplasias and review of literature for genotype-phenotype correlation in geleophysic dysplasia.

Acromelic dysplasia is a heterogeneous group of rare skeletal dysplasias characterized by distal limb shortening. Weill-Marchesani syndrome (WMS), Geleophysic dysplasia (GD) and Acromicric dysplasia (AD) are clinically distinct entities within this group of disorders and are characterized by short stature, short hands, stiff joints, skin thickening, facial anomalies, normal intelligence and skeletal abnormalities. Mutations of the Fibrillin-1 (FBN1) gene have been reported to cause AD, GD and related phenotypes. We reported three families with acromelic short stature. FBN1 analysis showed that all affected individuals carry a heterozygous missense mutation c.5284G > A (p.Gly1762Ser) in exon 42 of the FBN1 gene. This mutation was previously reported to be associated with GD. We reviewed the literature and compared the clinical features of the patients with FBN1 mutations to those with A Distintegrin And Metalloproteinase with Thrombospondin repeats-like 2 gene (ADAMTSL2) mutations. We found that tip-toeing gait, long flat philtrum and thin upper upper lip were more consistently found in GD patients with ADAMTSL2 mutations than in those with FBN1 mutations. The results have shed some light on the phenotype-genotype correlation in this group of skeletal disorders. A large scale study involving multidisciplinary collaboration would be needed to consolidate our findings.

Predictors of early operative mortality and long-term survival in octogenarians undergoing open and endovascular repair of abdominal aortic aneurysm.

BACKGROUND: The study aims to report outcomes of open repair (OR) and endovascular aneurysm repair (EVAR) in octogenarians. METHODS: Consecutive patients aged between 80 and 89 who underwent OR or EVAR were identified from a prospectively collected departmental database. Short-term outcomes included 30 days mortalities and perioperative complications; long-term outcomes included overall survival and re-intervention using the Kaplan-Meier method. Logistic regression was used to identify predictors for operative mortality and Cox regression analysis was used to identify predictors for long-term survival. RESULTS: From January 1999 to December 2013, 53 underwent open repairs (23 emergency and 30 elective) and 115 underwent endovascular repairs (11 emergency and 104 elective). For elective procedures, 30 days operative mortalities were 6.7% and 0% in OR and EVAR respectively (Chi square test, p = 0.049). For emergency procedures, 30 days mortalities were 39.1% and 27.2% respectively (Chi square test, p = 0.705). Overall 5 years survival rates were 40.4% and 36.7% after OR and EVAR respectively. Rupture of aneurysm (Odd ratio 18.8, 95% CI 3.4-104.5, p = 0.001) was the only predictor for 30 days mortality. Rupture of aneurysm (Hazard ratio 2.0, 95% CI 1.3-3.3, p = 0.003), history of lung disease (Hazard ratio 1.7, 95% CI 1.0-2.9, p = 0.039) and history of renal disease (Hazard ratio 2.1, 95% CI 1.4-3.1, p < 0.001) were independent predictors for long-term overall survival. CONCLUSION: Decision of AAA repair in octogenarians should not be based on age alone. Both elective OR and EVAR had acceptable perioperative risk, but emergency repair, lung disease and renal impairment predicted poor long-term survival.

Pseudoepitheliomatous keratotic and micaceous balanitis treated with topical 5-fluorouracil and liquid nitrogen.

Pseudoepitheliomatous keratotic and micaceous balanitis (PKMB) is an uncommon premalignant condition involving the glans penis. We report the case of an 86-year-old man who presented with phimosis and pain on retracting his foreskin. He had previously undergone circumcision, which revealed a hyperkeratotic plaque with thin mica-like scales involving his glans penis. Histology of the lesion showed hyperkeratosis, parakeratosis, epidermal acanthosis and papillomatosis with no evidence of dysplasia. Immunohistochemistry for human papillomavirus was negative. The patient was treated with topical 5-fluorouracil and liquid nitrogen with clinical improvement. He is now under long-term surveillance for verrucous carcinoma and squamous cell carcinoma.

CDK12 regulates alternative last exon mRNA splicing and promotes breast cancer cell invasion.

CDK12 (cyclin-dependent kinase 12) is a regulatory kinase with evolutionarily conserved roles in modulating transcription elongation. Recent tumor genome studies of breast and ovarian cancers highlighted recurrent CDK12 mutations, which have been shown to disrupt DNA repair in cell-based assays. In breast cancers, CDK12 is also frequently co-amplified with the HER2 (ERBB2) oncogene. The mechanisms underlying functions of CDK12 in general and in cancer remain poorly defined. Based on global analysis of mRNA transcripts in normal and breast cancer cell lines with and without CDK12 amplification, we demonstrate that CDK12 primarily regulates alternative last exon (ALE) splicing, a specialized subtype of alternative mRNA splicing, that is both gene- and cell type-specific. These are unusual properties for spliceosome regulatory factors, which typically regulate multiple forms of alternative splicing in a global manner. In breast cancer cells, regulation by CDK12 modulates ALE splicing of the DNA damage response activator ATM and a DNAJB6 isoform that influences cell invasion and tumorigenesis in xenografts. We found that there is a direct correlation between CDK12 levels, DNAJB6 isoform levels and the migration capacity and invasiveness of breast tumor cells. This suggests that CDK12 gene amplification can contribute to the pathogenesis of the cancer.

CLK-dependent exon recognition and conjoined gene formation revealed with a novel small molecule inhibitor.

CDC-like kinase phosphorylation of serine/arginine-rich proteins is central to RNA splicing reactions. Yet, the genomic network of CDC-like kinase-dependent RNA processing events remains poorly defined. Here, we explore the connectivity of genomic CDC-like kinase splicing functions by applying graduated, short-exposure, pharmacological CDC-like kinase inhibition using a novel small molecule (T3) with very high potency, selectivity, and cell-based stability. Using RNA-Seq, we define CDC-like kinase-responsive alternative splicing events, the large majority of which monotonically increase or decrease with increasing CDC-like kinase inhibition. We show that distinct RNA-binding motifs are associated with T3 response in skipped exons. Unexpectedly, we observe dose-dependent conjoined gene transcription, which is associated with motif enrichment in the last and second exons of upstream and downstream partners, respectively. siRNA knockdown of CLK2-associated genes significantly increases conjoined gene formation. Collectively, our results reveal an unexpected role for CDC-like kinase in conjoined gene formation, via regulation of 3'-end processing and associated splicing factors.The phosphorylation of serine/arginine-rich proteins by CDC-like kinase is a central regulatory mechanism for RNA splicing reactions. Here, the authors synthesize a novel small molecule CLK inhibitor and map CLK-responsive alternative splicing events and discover an effect on conjoined gene transcription.

Influence of meteorological factors on acute aortic events in a subtropical territory.

BACKGROUND/OBJECTIVE: This study aims to examine the relationship between weather changes and acute aortic events in a subtropical territory. METHODS: A linear regression analysis was performed in a pan-territory epidemiological survey for a period of 10 years on the impacts of meteorological factors (ambient temperature, atmospheric pressure, relative humidity, amount of cloud, rainfall, number of lightning strikes, presence of typhoon, and thunderstorm warning) on the daily incidences of acute aortic dissections and ruptured aortic aneurysms. Meteorological variables were retrieved on a daily basis from a well-established observatory, and the daily incidences of aortic dissections and rupture of aortic aneurysms were retrieved from the Clinical Data Analysis and Reporting System. RESULTS: During the study period (January 2005 to December 2014), 3878 patients were identified as having acute aortic dissections, and 1174 patients had ruptured aortic aneurysms. Corresponding averaged daily incidences were 1.06 and 0.32, respectively. The incidences of aortic dissection and ruptured aortic aneurysm in a day could be predicted by ambient temperature in degrees Celsius using the following linear regression models: (1) incidence of aortic dissection = 1.548 - 0.021 × temperature; (2) incidence of ruptured aortic aneurysm = 0.564 - 0.010 × temperature. In addition, both high atmospheric pressure and absence of thunderstorm warning are positively associated with more aortic dissections. For rupture of aortic aneurysms, high atmospheric pressure and low relative humidity were positive predictors. In multiple regression analysis, however, ambient temperature was the only significant predictor for both acute aortic dissections and ruptured aortic aneurysms. CONCLUSION: This is the first pan-territory study to show an attributable effect of ambient temperature on acute aortic events. This paper confirms that even in a subtropical country, meteorological variables were important factors influencing acute aortic events.

Surgical management of carotid body tumor - Is Shamblin classification sufficient to predict surgical outcome?

Background The study aims to conduct a review of the surgical management of carotid body tumor. Methods Consecutive patients with CBT who received surgical interventions from January 1994 to January 2014 at our institution were reviewed. Clinical, operative, pathological and follow up information were reported. Results Twenty patients (four males; median age was 36) with 21 CBT operations were recorded during the period. One patient undertook sequential operations for bilateral CBTs. Patients had 19 neck mass, 1 incidental finding and 1 facial nerve palsy. Six CBTs (28.6%) were Shamblin class I, ten (47.6%) were class II and five (23.8%) were class III. Nine CBTs had preoperative conjunctive embolization. Two operations required internal carotid artery resection and reconstruction. Four patients received subtotal resections, while 17 achieved complete resection. Complications included two major strokes, three hoarse voice and two Horner's syndrome. Shamblin class was significant predictor of operative time, blood loss, and whether complete resection accomplished, but could not predict postoperative complication. With median follow up period of 94 months, there was no tumor recurrence found in those had complete resection. Conclusions This small cohort showed that Shamblin class was significant in predicting technical difficulties but could not predict occurrence of complications.

Haemodynamic Variations of Flow to Renal Arteries in Custom-Made and Pivot Branch Fenestrated Endografting.

OBJECTIVE: This study aimed to investigate variation of blood flow to renal arteries in custom-made and pivot branch (p-branch) fenestrated endografting, using a computational fluid dynamics (CFD) technique. METHODS: Idealised models of custom-made and p-branch fenestrated grafting were constructed on a basis of a 26 mm stent graft. The custom-made fenestration was designed with a 6 mm diameter, while the 5 mm depth renal p-branch was created with a 6 mm inner and 15 mm outer fenestration. Two configurations (option A and option B) were constructed with different locations of p-branches. Option A had both renal p-branches at the same level, whereas option B contained two staggered p-branches at lower positions. The longitudinal stent orientation in both custom-made and p-branch models was represented by a takeoff angle (ToA) between the renal stent and distal stent graft centreline, varying from 55° to 125°. Computational simulations were performed with realistic boundary conditions governing the blood flow. RESULTS: In both custom-made and p-branch fenestrated models, the flow rate and wall shear stress (WSS) were generally higher and recirculation zones were smaller when the renal stent faced caudally. In custom-made models, the highest flow rate (0.390 L/min) was detected at 70° ToA and maximum WSS on vessel segment (16.8 Pa) was attained at 55° ToA. In p-branch models, option A and option B displayed no haemodynamic differences when having the same ToA. The highest flow rate (0.378 L/min) and maximum WSS on vessel segment (16.7 Pa) were both calculated at 55° ToA. The largest and smallest recirculation zones occurred at 90° and 55° ToA respectively in both custom-made and p-branch models. Custom-made fenestrated models exhibited consistently higher flow rate and shear stress and smaller recirculation zones in renal arteries than p-branch models at the same ToA. CONCLUSIONS: Navigating the renal stents towards caudal orientation can achieve better haemodynamic outcomes in both fenestrated devices. Custom-made fenestrated stent grafts are the preferred choice for elective patients. Further clinical evidence is required to validate the computational simulations.