bluuebunny/crossref_metadata_2025 huggingface dataset:
Combined General and Epidural Anesthesia is Associated With Decreased Opioid Consumption and Enhanced Pain Control After Penile Inversion Vaginoplasty in Transwomen
Authors: Salgado Christopher J. , Gonzalez Daisy I. , Wolfe Erin M. , Balise Raymond R. , Gebhard Ralf E. , Kamisetti Seema , Ovadia Steven
Published: August 2019

Background

Penile skin inversion vaginoplasty is a gender-affirming surgical procedure for transwomen with limited surgical analgesic protocol. This study compares the postoperative pain and opioid use in patients managed for surgery with general anesthesia (GA) with patients who were given combined epidural and general anesthesia (E/GA) with continuing postoperative epidural analgesia.

Methods

All patients who underwent penile inversion vaginoplasty between May of 2016 and May of 2018 under the care of single surgeon were identified retrospectively, 18 patients of which met the inclusion criteria. A retrospective chart review was conducted. Outcome measures were postoperative pain using visual analog scale, type and dosage of postoperatively administered intravenous or oral opioids (converted to morphine milligram equivalents, duration of inpatient admission, and time to ambulation.

Results

Patients who received combined E/GA reported significantly less pain and used less opioids during the first 4 postoperative days in comparison with patients who received GA alone. The reduction in mean pain associated with the use of an epidural was found to be statistically significant (P < 0.0005) as was the difference in opioid used in the 2 groups (P < 0.005) over the first 4 days postoperatively. Differences in day 5 pain suggest that postoperative pain is significantly lower even after the epidural has been removed (P < 0.005). There was no significant difference in length of hospital stay and time to ambulation (P > 0.05).

Conclusions

Combined E/GA was associated with decreased inpatient opioid consumption after surgery and provided superior pain control than administration of GA alone. Based on these findings, combined E/GA should be strongly considered for patients undergoing penile inversion vaginoplasty.
SIRT1 Mediates Septic Cardiomyopathy in a Murine Model of Polymicrobial Sepsis
Authors: Smith Lane M. , Yoza Barbara K. , Hoth J. Jason , McCall Charles E. , Vachharajani Vidula
Published: August 2019

Background:

Cardiac dysfunction, a common complication from severe sepsis, is associated with increased morbidity and mortality. However, the molecular mechanisms of septic cardiac dysfunction are poorly understood. SIRT1, a member of the sirtuin family of NAD+-dependent protein deacetylases, is an important immunometabolic regulator of sepsis, and sustained SIRT1 elevation is associated with worse outcomes and organ dysfunction in severe sepsis. Herein, we explore the role of SIRT1 in septic cardiac dysfunction using a murine model of sepsis.

Methods:

An in vitro model of inflammation in isolated H9c2 cardiomyocytes was used to confirm SIRT1 response to stimulation with lipopolysaccharide (LPS), followed by a murine model of cecal ligation and puncture (CLP) to investigate the molecular and echocardiographic response to sepsis. A selective SIRT1 inhibitor, EX-527, was employed to test for SIRT1 participation in septic cardiac dysfunction.

Results:

SIRT1 mRNA and protein levels in cultured H9c2 cardiomyocytes were significantly elevated at later time points after stimulation with LPS. Similarly, cardiac tissue harvested from C57BL/6 mice 36 h after CLP demonstrated increased expression of SIRT1 mRNA and protein compared with sham controls. Administration of EX-527 18 h after CLP reduced SIRT1 protein expression in cardiac tissue at 36 h. Moreover, treatment with EX-527 improved cardiac performance with increased global longitudinal strain and longitudinal strain rate.

Conclusions:

Our findings reveal that SIRT1 expression increases in isolated cardiomyocytes and cardiac tissue after sepsis inflammation. Moreover, rebalancing SIRT1 excess in late sepsis improves cardiac performance, suggesting that SIRT1 may serve as a therapeutic target for septic cardiomyopathy.
From cachexia to obesity: the role of host metabolism in cancer immunotherapy
Authors: Brocco Davide , Di Marino Pietro , Grassandonia Antonino
Published: August 2019

Purpose of review

Currently, several clinical trials in cancer therapy have demonstrated the success of immunomodulatory therapies. However, only a variable fraction of patients actually benefit from these treatments. The understanding of key mechanisms behind this response heterogeneity is one of the major unmet need and intense research field in immuno-oncology. This review will discuss the host metabolic dysfunctions derived from cachexia or obesity that can affect the response to cancer immunotherapy.

Recent findings

Preclinical studies demonstrated that chronic inflammation, nutritional intake impairment and endocrine dysfunction may affect anticancer innate and adaptive immunity, both in cachexia and obesity. New emerging clinical findings have highlighted the impact of metabolic biomarkers in predicting response to immune checkpoint inhibitors in cancer patients.

Patient's weight and inflammatory status could be relevant in the clinical decision-making process before starting cancer immunotherapy and for an effective patient selection and stratification in future clinical trials employing this class of anticancer agents.
It's About Time: Transfusion effects on postinjury platelet aggregation over time
Authors: Kornblith Lucy Z. , Decker Anna , Conroy Amanda S. , Hendrickson Carolyn M. , Fields Alexander T. , Robles Anamaria J. , Callcut Rachael A. , Cohen Mitchell J.
Published: August 2019

BACKGROUND

Impaired postinjury platelet aggregation is common, but the effect of transfusion on this remains unclear. Data suggest that following injury platelet transfusion may not correct impaired platelet aggregation, and impaired platelet aggregation may not predict the need for platelet transfusion. We sought to further investigate platelet aggregation responses to transfusions, using regression statistics to isolate the independent effects of transfusions given in discrete time intervals from injury on both immediate and longitudinal platelet aggregation. We hypothesized that platelet aggregation response to platelet transfusion increases over time from injury.

METHODS

Serial (0–96 hours) blood samples were collected from 248 trauma patients. Platelet aggregation was assessed in vitro with impedance aggregometry stimulated by adenosine diphosphate, collagen, and thrombin receptor-activating peptide-6. Using regression, transfusion exposure was modeled against platelet aggregation at each subsequent timepoint and adjusted for confounders (Injury Severity Score, international normalized ratio (INR), base deficit, platelet count, and interval transfusions). The expected change in platelet aggregation at each timepoint under the intervention of transfusion exposure was calculated and compared with the observed platelet aggregation.

RESULTS

The 248 patients analyzed were severely injured (Injury Severity Score, 21 ± 19), with normal platelet counts (mean, 268 × 109/L ± 90), and 62% were transfused in 24 hours. The independent effect of transfusions on subsequent platelet aggregation over time was modeled with observed platelet aggregation under hypothetical treatment of one unit transfusion of blood, plasma, or platelets. Platelet transfusions had increasing expected effects on subsequent platelet aggregation over time, with the maximal expected effect occurring late (4–5 days from injury).

CONCLUSION

Controversy exists on whether transfusions improve impaired postinjury platelet aggregation. Using regression modeling, we identified that expected transfusion effects on subsequent platelet aggregation are maximal with platelet transfusion given late after injury. This is critical for tailored resuscitation, identifying a potential early period of resistance to platelet transfusion that resolves by 96 hours.

LEVEL OF EVIDENCE

Therapeutic, level V.
Cold-stored whole blood: A better method of trauma resuscitation?
Authors: Hazelton Joshua Paul , Cannon Jeremy W. , Zatorski Catherine , Roman Janika San , Moore Sarah A. , Young Andrew J. , Subramanian Madhu , Guzman Jessica F. , Fogt Franz , Moran Anna , Gaughan John , Seamon Mark J. , Porter John
Published: August 2019

BACKGROUND

Cold-stored whole blood (CWB) provides a balance of red blood cells, plasma, and platelets in less anticoagulant volume than standard blood component therapy (BCT). We hypothesize that patients receiving CWB along with BCT have improved survival compared with patients receiving only BCT.

METHODS

We performed a dual-center case-match study of trauma patients who received CWB and BCT at two urban, Level-I Trauma Centers. Criteria to receive CWB included boys 16 years of older, women older than 50 years, SBP less than 90 mm Hg, and identifiable source of hemorrhage. We performed a 2:1 propensity match against any trauma patient who received 1 unit or greater of packed red cells during their initial trauma bay resuscitation. Endpoints included trauma bay mortality, 30-day mortality, laboratory values at 4 hours and 24 hours, and overall blood product utilization. Comparisons were made with Wilcoxon-ranked sum and Fisher's exact test, p less than 0.05 was significant.

RESULTS

Between both institutions, a total of 107 patients received CWB during the study period with 91 being matched to 182 BCT patients for analysis. Hemodynamic parameters of the patients in both groups at the time of presentation were similar. The CWB patients had higher mean hemoglobin (10 ± 2 g/dL vs. 11 ± 2 g/dL; p < 0.001) and hematocrit (29.2 ± 6.1% vs. 32.1 ± 5.8%; p < 0.001) at 24 hours. Importantly, trauma bay mortality was less in CWB patients (8.8% vs. 2.2%;p = 0.039). Thirty-day mortality was not different in CWB patients, and there were no differences in the total amount of blood products transfused at the 4-hour and 24-hour periods.

CONCLUSION

Cold-stored whole blood offers the benefit of a balanced resuscitation with improved trauma bay survival and higher mean hemoglobin at 24 hours. A larger, prospective study is needed to determine whether it has a longer-term survival benefit for severely injured patients.

LEVEL OF EVIDENCE

Therapeutic, level III.
Differential expression of Ormdl genes in the islets of mice and humans with obesity
Authors: Fenske Rachel , Lee Hugo , Akcan Tugce , Domask Elliot , Davis Dawn Belt , Kimple Michelle , Engin Feyza
Published: August 2019

The orosomucoid-like proteins (Ormdl1-3) are emerging as the critical regulators of sphingolipid homeostasis, inflammation and ER stress. However, their roles in β-cells and obesity remain unknown. Here, we showed that islets isolated from overweight/obese human donors displayed marginally reduced ORMDL1-2 expression while ORMDL3 expression was significantly reduced as compared to islets from lean donors. In contrast, Ormdl3 expression was significantly upregulated in the islets of leptin-deficient obese (ob/ob) mice compared to lean mice. We identified that the difference in expression of Ormdl3 between mouse and human islets was leptin-dependent, as treatment of ob/ob mice with leptin significantly reduced Ormld3 expression. Furthermore, Ormdl1-3 were significantly upregulated upon chemically-induced ER stress, but they showed differential responsiveness to cytokines in a β-cell line. Knockdown of Ormdl3 substantially increased expression of apoptotic markers, which was rescued by a pharmacological inhibitor of ceramide synthase. Taken together we demonstrate leptin-dependent regulation of Ormdl3 expression in ob/ob islets, highlight the possible importance of β-cell stress conditions in differential Ormdl expression and identify a critical role for Ormdl3 in β-cell survival.
Altered brain-wide auditory networks in fmr1-mutant larval zebrafish
Authors: Constantin Lena , Poulsen Rebecca E. , Favre-Bulle Itia A. , Taylor Michael A. , Sun Biao , Goodhill Geoffrey J. , Vanwalleghem Gilles C. , Scott Ethan K.
Published: August 2019

Altered sensory processing is characteristic of several psychiatric conditions, including autism and fragile X syndrome (FXS). Here, we use whole-brain calcium imaging at cellular resolution to map sensory processing in wild type larval zebrafish and mutants for fmr1, which causes FXS in humans. Using functional analyses and graph theory, we describe increased transmission and reduced filtering of auditory information, resulting in network-wide hypersensitivity analogous to the auditory phenotypes seen in FXS.
Complete structure of the core signalling unit of theE. colichemosensory array in an optimised minicell strain
Authors: Burt Alister , Cassidy C. Keith , Ames Peter , Bacia-Verloop Maria , Baulard Megghane , Huard Karine , Luthey-Schulten Zaida , Desfosses Ambroise , Stansfeld Phillip J. , Margolin William , Parkinson John S. , Gutsche Irina
Published: August 2019

Motile bacteria sense chemical gradients with transmembrane receptors organised in supramolecular signalling arrays.1,2Understanding stimulus detection and transmission at the molecular level requires precise structural characterisation of the array building block known as a core signalling unit (CSU). Here we introduce a novelE. colistrain that forms small minicells possessing extended and highly ordered chemosensory arrays. We provide a three-dimensional (3D) map of a complete CSU at ~16 Å resolution by cryo-electron tomography (cryo-ET) and subtomogram averaging. This map, combined with previously determined high resolution structures and molecular dynamics simulations, yields an atomistic model of the membrane-bound CSU and enables spatial localisation of its signalling domains. Our work thus offers a solid structural basis for interpretation of existing data and design of new experiments to elucidate signalling mechanisms within the CSU and larger array.
Residual feed intake in dairy ewes: an evidence of intraflock variability
Authors: González-García E. , Santos J. P. Dos , Hassoun P.
Published: August 2019

This study examined the intraflock variability of feed efficiency in dairy ewes, through monitoring residual feed intakes (RFI). Primiparous lactating ewes (n=43; 57.7±0.91 kg body weight [BW] at lambing), representative of a French Lacaune dairy flock, were allocated in an equilibrated 2 × 2 factorial design experiment, lasting for 63 days during mid-lactation and combining 2 litter sizes (singletons, SING or twins, TWIN) and 2 daily milking frequencies (once, ONE or twice, TWO). Ewes were individually fed a diet based on ryegrass silage, local hay and supplements. Individual DMI was recorded daily and further used to evaluate (and compare) differences in RFI between ewes at 35, 42, 49, 56, 63, 70, 77, 84, 91 and 98 days relative to lambing (DIM). Total (BW) and metabolic (BW0.75) body weight, BCS, milk yield and plasma NEFA were monitored weekly. Differences in DMI were mainly due to the lactation stage and litter size and were 11% higher in ewes with TWIN compared to SING. This was positively correlated to milk yield and consistent with differences in RFI which varied due to litter size and to the milking frequency × lactation stage interaction. Ewes that lambed SING showed higher feed efficiency (□0.13±0.020 vs. 0.08±0.015 kg DM/ewe/d of RFI in SING vs. TWIN, respectively), whereas there was no differences in BW or BCS. Milking frequency did not affect DMI but milk yields were higher in TWO, which was related to a higher feed efficiency in this group (0.04±0.017 vs. □0.10±0.018 kg DM/ewe/d of RFI in ONE vs. TWO, respectively). Average RFI was affected (P <0.0001) by the ewe, thus allowing a ranking among individuals to be established. High (n=22) or low (n=21) feed efficiency ewes averaged □0.17±0.09 or 0.18±0.09 kg DM/d RFI, respectively. Estimates of RFI were not correlated to the individual milk production potential. Even if no differences in BW, BW0.75 or BCS were detected, high efficiency ewes mobilised almost two-fold their body reserves when compared to the low efficiency group. The observed intraflock variability in feed efficiency of this dairy ewes flock was affected by litter size and milking frequency but also by evident differences between individuals’ physiologies.
Short-, medium- and long-term metabolic responses of adult ewes submitted to nutritional and β-adrenergic challenges
Authors: González-García Eliel , Alhamada Moutaz , Debus Nathalie , Menassol Jean-Baptiste , Tesnière Anne , Vero Jéssica Gonçalves , Barboza Bruna , Bocquier François
Published: August 2019

Background

In order to maintain homeostasis, ruminants submitted to alternating shortage and refeeding situations manifest switches in metabolic pathways induced by undernutrition and body reserves (BR) replenishment cycles. The objective of this experiment was to study adaptive regulatory mechanisms present during subsequent feeding transition periods and the inherent lipolytic activity of the adipose tissue in individuals with contrasted BR. Three diets containing different levels of energy were offered to 36 mature, dry, non-pregnant Mérinos d’Arles ewes in an experiment lasting 122 days. Ewes were selected with similar body weight (BW), body condition score (BCS) and were allocated into three equivalent treatments according to the plane of nutrition: normally fed (Control); underfed (Under) or overfed (Over). The BW, BCS and individual energy metabolism were monitored. At the end of the experiment, lipolytic activity of adipose tissue was studied through a ß-adrenergic challenge to the same ewes, with body conditions according to the offered diet (Normal, Leans and Fat, respectively).

Results

Anabolic or catabolic responses to energy dietary manipulation were accompanied by synchronised metabolic regulation, leading to contrasting metabolic and BR profiles. Average BW and BCS were higher and lower in Over and Under ewes, respectively. The higher and lower BR variations were observed for Under and Over ewes. Higher plasma non-esterified fatty acids (NEFA) concentrations were accompanied by lower insulin, leptin and glucose. Differences in leptin were consistent with the dietary energy load (Over > Control > Under). After refeeding, a rebound in BW and BCS was observed for the three groups whereas NEFA was drastically reduced in Under ewes. No differences among treatments were detected in NEFA profiles at the end of the study but lipolytic activity responses to the ß - adrenergic challenge were different and coherent with the adipose tissue mass (Fat > Normal > Lean) and, importantly, was also different between ewes from the same group or BR status, thus evidencing diversity among individual adaptive capacities.

Conclusions

The ability of ewes to quickly overcome undernutrition situations by efficiently using their BR was confirmed. There is potential for a simplified ß-adrenergic challenge protocol helping to identify differences in adaptive capacity among individuals.
Sensory information from a slipping object elicits a rapid and automatic shoulder response
Authors: Hernandez-Castillo Carlos R. , Maeda Rodrigo S. , Pruszynski J. Andrew , Diedrichsen Jörn
Published: August 2019

Humans have the remarkable ability to hold, grasp, and manipulate objects. Previous work has reported rapid and coordinated reactions in hand and shoulder muscles in response to external perturbations to the arm during object manipulation; however, little is known about how somatosensory feedback of an object slipping in the hand influences responses of the arm. We built a hand-held device to stimulate the sensation of slipping at all five fingertips. The device was integrated into an exoskeleton robot that supported it against gravity. The setup allowed us to decouple somatosensory stimulation in the fingers from forces applied to the arm— two variables that are highly interdependent in real-world scenarios. Fourteen participants performed three experiments in which we measured their arm feedback responses during slip stimulation. Slip stimulations were applied horizontally, in one of two directions, and participants were either instructed to follow the slip direction, or to move the arm in the opposite direction. Participants showed responses within ∼67 ms of slip onset when following the direction of slip, but significantly slower responses when instructed to move in the opposite direction. Arm responses were modulated by the speed but not the distance of the slip. Finally, when slip stimulation was combined with mechanical perturbations to the arm, we found that sensory information from the fingertips significantly modulated the shoulder feedback response. Overall, the results demonstrate the existence of a rapid feedback system that stabilizes hand-held objects.

NEW & NOTHEWORTHY

We tested whether the sensation of an object slipping from the fingers modulates shoulder feedback responses. We found rapid shoulder feedback responses when participants were instructed to follow the slip direction with the arm. Shoulder responses following mechanical joint perturbations were also potentiated when combined with slipping. These results demonstrate the existence of fast and automatic feedback responses in the arm in reaction to sensory input to the fingertips that maintain grip on hand-held objects.
Brown adipose expansion and remission of glycemic dysfunction in obese SM/J mice
Authors: Carson Caryn , Macias-Velasco Juan F , Gunawardana Subhadra , Miranda Mario A , Oyama Sakura , Schmidt Heather , Wayhart Jessica P , Lawson Heather A
Published: August 2019

Disruption of glucose homeostasis increases the risk of type II diabetes, cardiovascular disease, stroke, and cancer. We leverage a novel rodent model, the SM/J mouse, to understand glycemic control in obesity. On a high fat diet, obese SM/J mice initially develop impaired glucose tolerance and elevated fasting glucose. Strikingly, their glycemic dysfunction resolves by 30 weeks of age despite persistence of obesity. A prominent phenotype is that they dramatically expand their brown adipose depots as they resolve glycemic dysfunction. This occurs naturally and spontaneously on a high fat diet, with no temperature or genetic manipulation. When the brown adipose depot is removed from normoglycemic obese mice, fasting blood glucose and glucose tolerance revert to unhealthy levels, and animals become insulin resistant. We identified 267 genes whose expression changes in the brown adipose when the mice resolve their unhealthy glycemic parameters, and find the expanded tissue has a ‘healthier’ expression profile of cytokines and extracellular matrix genes. We describe morphological, physiological, and transcriptomic changes that occur during the unique brown adipose expansion and remission of glycemic dysfunction in obese SM/J mice. Understanding this phenomenon in mice will open the door for innovative therapies aimed at improving glycemic control in obesity.

Significance Statement

Some obese individuals maintain normal glycemic control. Despite being obese, these individuals have low risk for metabolic complications, including type-II diabetes. If we better understood why some obese people maintain normoglycemia then we might develop new approaches for treating metabolic complications associated with obesity. However, the causative factors underlying glycemic control in obesity remain unknown. We discovered that, despite persistence of the obese state, SM/J mice enter into diabetic remission: returning to normoglycemia and reestablishing glucose tolerance and improving insulin sensitivity. A prominent phenotype is that they dramatically expand their brown adipose depots as they resolve glycemic dysfunction. Understanding this phenomenon in mice will open the door for innovative therapies aimed at improving glycemic control in obesity.
High Resolution Genome Wide Expression Analysis of Single Myofibers Using SMART-Seq
Authors: Blackburn Darren M. , Lazure Felicia , Corchado Aldo H. , Perkins Theodore J. , Najafabadi Hamed S. , Soleimani Vahab D.
Published: August 2019

Skeletal muscle is a heterogeneous tissue. Individual myofibers that make up muscle tissue exhibit variation in their metabolic and contractile properties. Although there are biochemical and histological assays to study myofiber heterogeneity, efficient methods to analyze the whole transcriptome of individual myofibers are lacking. We have developed single myofiber RNA-Seq (smfRNA-Seq) to analyze the whole transcriptome of individual myofibers by combining single fiber isolation with Switching Mechanisms at 5’ end of RNA Template (SMART) technology. Our method provides high-resolution genome wide expression profiles of single myofibers. Using smfRNA-Seq, we have analyzed the differences in the transcriptome of young and old myofibers to validate the effectiveness of this new method. Using smfRNA-Seq, we performed comparative gene expression analysis between single myofibers from young and old mice. Our data suggests that aging leads to significant changes in the expression of metabolic and structural genes in myofibers. Our data suggests that smfRNA-Seq is a powerful tool to study developmental, disease and age-related dynamics in the composition of skeletal muscle.
Establishment of a Reverse Genetics System for Influenza D Virus
Authors: Ishida Hiroho , Murakami Shin , Kamiki Haruhiko , Matsugo Hiromichi , Takenaka-Uema Akiko , Horimoto Taisuke
Published: August 2019

Influenza D virus (IDV) was initially isolated in the USA in 2011. IDV is distributed worldwide and is one of the causative agents of bovine respiratory disease complex (BRDC), which exhibits high morbidity and mortality in feedlot cattle. Molecular mechanisms of IDV pathogenicity are still unknown. Reverse genetics systems are vital tools not only for studying the biology of viruses, but also for use in applications such as recombinant vaccine viruses. Here, we report the establishment of a plasmid-based reverse genetics system for IDV. We first verified that the 3′-terminal nucleotide of each 7-segmented genomic RNA contained uracil in contrary to the previous report, and were then able to successfully generate recombinant IDV by co-transfecting 7 plasmids containing these genomic RNAs along with 4 plasmids expressing polymerase proteins and NP into HRT-18G cells. The recombinant virus had a growth deficit compared to the wild-type virus, and we determined the reason for this growth difference by examining the genomic RNA content of the viral particles. We found that recombinant virus incorporated an unbalanced ratio of viral RNA segments into particles as compared to the wild-type virus, and thus we adjusted the amount of each plasmid used in transfection to obtain recombinant virus with the same replicative capacity as wild-type virus. Our work here in establishing a reverse genetics system for IDV will have a broad range of applications, including uses in studies focused on better understanding IDV replication and pathogenicity as well as those contributing to the development of BRDC countermeasures.

IMPORTANCE

Bovine respiratory disease complex (BRDC) exhibits high mortality and morbidity in cattle, causing economic losses worldwide. Influenza D virus (IDV) is considered to be a causative agent of BRDC. Here, we developed a reverse genetics system that allows for the generation of IDV from cloned cDNAs, and the introduction of mutations into the IDV genome. This reverse genetics system will become a powerful tool for use in studies related to understanding the molecular mechanisms of viral replication and pathogenicity, and will also lead to the development of new countermeasures against BRDC.
Sequential transcriptional waves and NF-κB-driven chromatin remodeling direct drug-induced dedifferentiation in cancer
Authors: Su Yapeng , Liu Chunmei , Lu Xiang , Li Guideng , Shao Shiqun , Kong Yan , Lee Jihoon W. , Ng Rachel H. , Wong Stephanie , Robert Lidia , Warden Charles , Liu Victoria , Chen Jie , Wang Zhuo , Qin Guangrong , Tang Yin , Cheng Hanjun , Ng Alphonsus H. C. , Peng Songming , Xue Min , Johnson Dazy , Xu Yu , Wang Jinhui , Wu Xiwei , Shmulevich Ilya , Shi Qihui , Levine Raphael , Ribas Antoni , Baltimore David , Guo Jun , Heath James R. , Wei Wei
Published: August 2019

Drug-induced dedifferentiation towards a drug-tolerant persister state is a common mechanism cancer cells exploit to escape therapies, posing a significant obstacle to sustained therapeutic efficacy. The dynamic coordination of epigenomic and transcriptomic programs at the early-stage of drug exposure, which initiates and orchestrates these reversible dedifferentiation events, remains largely unexplored. Here we employ high-temporal-resolution multi-omics profiling, information-theoretic approaches, and dynamic system modeling to probe these processes inBRAF-mutant melanoma models and patient specimens. We uncover a hysteretic transition trajectory of melanoma cells in response to oncogene inhibition and subsequent release, driven by the sequential operation of two tightly coupled transcriptional waves, which orchestrate genome-scale chromatin state reconfiguration. Modeling of the transcriptional wave interactions predicts NF-κB/RelA-driven chromatin remodeling as the underlying mechanism of cell-state dedifferentiation, a finding we validate experimentally. Our results identify critical RelA-target genes that are epigenetically modulated to drive this process, establishing a quantitative epigenome gauge to measure cell-state plasticity in melanomas, which supports the potential use of drugs targeting epigenetic machineries to potentiate oncogene inhibition. Extending our investigation to other cancer models, we identify oxidative stress-mediated NF-κB/RelA activation as a common mechanism driving cellular transitions towards drug-tolerant persister states, revealing a novel and pivotal role for the NF-κB signaling axis in linking cellular oxidative stress to cancer progression.
Diversification of DNA-binding specificity via permissive and specificity-switching mutations in the ParB/Noc protein family
Authors: Jalal Adam S. B. , Tran Ngat T. , Stevenson Clare E. , Chan Elliot W. , Lo Rebecca , Tan Xiao , Noy Agnes , Lawson David M. , Le Tung B. K.
Published: August 2019

Specific interactions between proteins and DNA are essential to many biological processes. Yet it remains unclear how the diversification in DNA-binding specificity was brought about, and what were the mutational paths that led to changes in specificity. Using a pair of evolutionarily related DNA-binding proteins, each with a different DNA preference (ParB and Noc: both having roles in bacterial chromosome maintenance), we show that specificity is encoded by a set of four residues at the protein-DNA interface. Combining X-ray crystallography and deep mutational scanning of the interface, we suggest that permissive mutations must be introduced before specificity-switching mutations to reprogram specificity, and that mutational paths to a new specificity do not necessarily involve dual-specificity intermediates. Overall, our results provide insight into the possible evolutionary history of ParB and Noc, and in a broader context, might be useful in understanding the evolution of other classes of DNA-binding proteins.
SORBS2is a susceptibility gene to arrhythmogenic right ventricular cardiomyopathy
Authors: Ding Yonghe , Yang Jingchun , Chen Peng , Lu Tong , Jiao Kunli , Tester David , Jiang Kai , Ackerman Michael J , Li Yigang , Wang Dao Wu , Wang Dao Wen , Lee Hon-Chi , Xu Xiaolei
Published: August 2019

BACKGROUND

Arrhythogenic right ventricular cardiomyopathy (ARVC) is an inherited cardiomyopathy characterized by right ventricular remodeling and ventricular arrhythmia. To date, 16 ARVC causative genes have been identified from human genetic studies, accounting for about 60% of ARVC probands. Genetic basis for the remaining 40% ARVC probands remain elusive.

METHODS

Prompted by a zebrafish mutagenesis screen that suggested theSorbin and SH3 domain-containing 2 (SORBS2)ortholog as a candidate cardiomyopathy gene, we conducted detailed expressionl analysis of Sorbs2 in mice, as well as phenotypic characterization in the Sorbs2 knock-out (KO) mice. The intercalated disc (ICD) expression pattern and ARVC-like phenotypes further prompted us to conduct targeted sequencing of human patients with ARVC to search for rare variants in theSORBS2gene.

RESULTS

Sorbs2is robustly expressed in the mouse heart, encoding an adhesion junction/desmosome protein that is mainly localized to the ICD. A mutation with near complete depletion of the Sorbs2 protein in mouse results in phenotypes characteristic of human ARVC, such as dilated right ventricle (RV), RV dysfunction, spontaneous ventricular tachycardia (VT), and premature death. Sorbs2 is required to maintain the structural integrity of ICD. Its absence resulted in profound cardiac electrical remodeling with impaired impulse conduction and action potential derangements. Five rare variants were identified from a cohort of 59 ARVC patients, among which two variants affect splicing.

CONCLUSIONS

Sorbs2 KO mouse is an ARVC model andSORBS2is a new ARVC susceptibility gene.
Extraordinary diversity of HLA class I gene expression in single cells contribute to the plasticity and adaptability of human immune system
Authors: Tian Rui , Zhu Hao , Pang Zhiying , Tian Yi , Liang Chao
Published: August 2019

HLA, the coding genes of human major histocompatibility (MHC) proteins, play a crucial role in the human adaptive immune system by presenting antigenic peptides to T cell receptors on T cells. HLA-A, HLA-B and HLA-C, these 3 Class I HLA genes are one of the most polymorphic loci in the human genome. For decades, HLA typing has been performed prior to tissue and stem cell transplantation. However, beyond the role in tissue matching, HLA has also been implicated in a wide array of autoimmune diseases and HLA genotypes and expression levels are closely associated with cancer patients prognosis as recent studies have revealed. Recently methods have been developed to perform HLA typing and HLA expression quantification together by using RNA-seq techniques. However, these bulk RNA-seq experiments are measuring an averaged signal of cell populations. Single-cell RNA-seq (scRNA-seq) has regained its popularity due to its power to reliably resolve single RNA transcriptomes at large scales. In our present study, we did HLA typing using three independent scRNA-seq datasets. Interestingly, we found that single cells from the same donor could be classified into different groups where each group has a distinct expressed HLA genotype (e.g., HLA-A, heterozygous or homozygous); in other words, HLA class I genes show abundant allele specific expression in single cells. This phenomenon has been repeatedly observed in a total of 14 donors from 3 independent datasets (one is breast epithelium, another two are multiple myeloma). Our systematic analysis of HLA class I gene expression using multiple scRNA-seq datasets has uncovered a putative mechanism, where by fine tuning HLA class I expressions both at the quantity and allele levels, our immune system is able to handle various internal challenges through single cells equipped with extraordinary diverse HLA expression patterns.
Positively selected variants in functionally important regions of TLR7 inAlouatta guariba clamitanswith yellow fever virus exposure in Northern Argentina
Authors: Torosin Nicole S. , Webster Timothy H. , Argibay Hernan , Ferreyra Hebe , Uhart Marcela , Agostini Ilaria , Knapp Leslie A.
Published: August 2019

1

In 2007-2009, a ma jor yellow fever virus (YFV) outbreak in Northern Argentina decimated the local howler monkey (Alouatta) population. We explored the relationship between Toll-like receptor (TLR) 7 and TLR8 gene variation and YFV susceptibility using samples fromAlouattaindividuals alive before the YFV outbreak, individuals that died during the outbreak, and individuals that survived the outbreak and are alive today. We measured genetic divergence betweenAlouattaYFV exposure groups and evaluatedAlouatta-specific substitutions for functional consequences. We did not find different allele frequencies in the post-YFV exposureAlouattagroup compared to the pre-exposure group. However, we identified three nonsynonymous variants in TLR7 inA. guariba clamitans. Two of these substitutions are under positive selection in functionally important regions of the gene. These unique coding differences inA. guariba clamitansmay affect YFV resistance, but more work is necessary to fully explore this hypothesis.
Crif1 Promotes Osteoporosis in Mice after Radiation
Authors: Xiang Lixin , Chen Li , Xiang Yang , Li Fengjie , Zhang Xiaomei , Xiao Yanni , Zou Lingyun , Zhong Jiang F. , Li Shengwen Calvin , Ran Qian , Li Zhongjun
Published: August 2019

Radiation induces rapid bone loss and enhances bone resorption and RANKL expression. RANKL provides the crucial signal to induce osteoclast differentiation and plays an important role in bone resorption. However, the mechanisms of radiation-induced osteoporosis are not fully understood. Here, we show that Crif1 expression increases in bone marrow cells after radiation. Conditional Crif1 deletion in bone marrow cells causes decreases in RANKL expression and the RANKL/OPG ratio, and relieves bone loss after radiation in mice. We further demonstrated in vitro that Crif1 promotes RANKL secretion via the cAMP/PKA pathway. Moreover, protein-protein docking screening identified five compounds as Crif1 inhibitors; these compounds dramatically suppressed RANKL secretion and CREB phosphorylation when cells were exposed to forskolin. This study enriches current knowledge of the pathogenesis of osteoporosis and provides insights into potential therapeutic strategies for osteoporosis treatment.
Incorporating Randomness into DNA Steganography to Realize Secondary Secret key, Self-destruction, and Quantum Key Distribution-like Function
Authors: Cui Meiying , Zhang Yixin
Published: August 2019

DNA has become a promising candidate as future data storage medium, which makes DNA steganography indispensable in DNA data security. While PCR primers are conventional secret keys in DNA steganography, the information can be read once the primers are intercepted. New steganography approach is needed to make the DNA-encoded information safer, if not unhackable. Herein, by mixing information-carrying DNA with partially degenerated DNA library containing single or multiple restriction sites, we build an additional protective layer, which can be removed by desired restriction enzymes as secondary secret keys. As PCR is inevitable for reading DNA-encrypted information, heating will cause reshuffling and generate endonuclease-resistant mismatched duplexes, especially for DNA with high sequence diversity. Consequently, with the incorporation of randomness, the DNA steganography possesses both quantum key distribution (QKD)-like function for detecting PCR by an interceptor and self-destructive property. With a DNA-ink incorporating the steganography, the authenticity of a writing can be confirmed only by authorized person with the knowledge of all embedded keys.
Arabidopsis ERF109 regulates auxin transport-related genes in root development
Authors: Liu Rui , Cai Xiao-Teng , Zhao Ping-Xia , Xu Ping , Xiang Cheng-Bin
Published: August 2019

The transcription factor ERF109 acts as a crosstalk node between jasmonic acid signaling and auxin biosynthesis by directly regulatingYUC2andASA1during lateral root formation in Arabidopsis. However, whether ERF109 regulates the auxin transport remains unclear. Here we report a mechanism of ERF109-mediated auxin transport in root system. Through root transcriptome comparison betweenerf109, wild type, and35S:ERF109, we found that the genesPIN2andPIN4, encoding the major membrane-based efflux carriers of auxin, were enriched in the overexpression line. In the promoters of these auxin transport genes, GCC-box cis elements were found and potentially bound by ERF109. Moreover,PID, encoding a key regulator in polar auxin transport, was found upregulated in35S:ERF109and down regulated inerf109. Yeast-one-hybrid and chromatin immunoprecipitation assays showed that ERF109 directly bound to the GCC-box ofPIN2,PIN4, andPID. Genetic analyses with double mutants confirmed the function of ERF109 in the regulation of auxin transport in Arabidopsis roots. Taken together, our results show that ERF109 modulates auxin transport by directly regulatingPIN2,PIN4andPID. This ERF109-mediated auxin transport likely works together with ERF109-mediated auxin synthesis to establish auxin maxima for lateral root initiation.
Pairwise common variant meta-analyses of schizophrenia with other psychiatric disorders reveals shared and distinct gene and gene-set associations
Authors: Reay William R. , Cairns Murray J.
Published: August 2019

The complex aetiology of schizophrenia is postulated to share factors with other psychiatric disorders. Recently, this has been supported by genome-wide association studies, with several psychiatric phenotypes displaying high genomic correlation with schizophrenia. We sought to investigate pleiotropy amongst the common variant genomics of schizophrenia and seven other psychiatric disorders using a multimarker test of association. Gene-based analysis of common variation revealed over 50 schizophrenia-associated genes shared with other psychiatric phenotypes; including bipolar disorder, major depressive disorder, ADHD, and autism spectrum disorder. In addition, we uncovered 78 genes significantly enriched with common variant associations for schizophrenia that were not linked to any of these seven disorders (P > 0.05). Transcriptomic imputation was then leveraged to investigate the functional significance of variation mapped to these genes, prioritising several interesting functional candidates. Pairwise meta-analysis of schizophrenia and each psychiatric phenotype further revealed 330 significantly associated genes (PMeta < 2.7 × 10−6) that were only nominally associated with each disorder individually (P < 0.05). Multivariable gene-set association suggested that common variation enrichment within biologically constrained genes observed for schizophrenia also occurs across several psychiatric phenotypes. These analyses consolidate the overlap between the genomic architecture of schizophrenia and other psychiatric disorders and uncovered several pleiotropic genes which warrant further investigation.

AUTHOR SUMMARY

Schizophrenia and other psychiatric disorders have many similarities, and this includes features of their overall genetic risk. Here, we investigate genes which may play a role in schizophrenia as well one or more of seven other psychiatric phenotypes and demonstrate that a number of them are pleiotropic and influence at least one other disorder. We also identify genes amongst the psychiatric disorders studied here which only show association with schizophrenia. Furthermore, we find a number of genes which were only significant when combining genetic association data from schizophrenia and one of the other seven disorders, suggesting there are shared genetic influences that are revealed through the power of joint analysis. This study identifies interesting novel shared (pleiotropic) genes in psychiatry which warrant future study.
Conformational sensors and domain-swapping reveal structural and functional differences between β-arrestin isoforms
Authors: Ghosh Eshan , Dwivedi Hemlata , Baidya Mithu , Srivastava Ashish , Kumari Punita , Stepniewski Tomek , Kim Hee Ryung , Lee Mi-Hye , van Gastel Jaana , Chaturvedi Madhu , Roy Debarati , Pandey Shubhi , Maharana Jagannath , Guixà-Gonzàlez Ramon , Luttrell Louis M. , Chung Ka Young , Dutta Somnath , Selent Jana , Shukla Arun K.
Published: August 2019

Desensitization, signaling and trafficking of G protein-coupled receptors (GPCRs) are critically regulated by multifunctional adaptor proteins, β-arrestins (βarrs). The two isoforms of βarrs (βarr1 and 2) share a high degree of sequence and structural similarity, still however, they often mediate distinct functional outcomes in the context of GPCR signaling and regulation. A mechanistic basis for such a functional divergence of βarr isoforms is still lacking. Using a set of complementary approaches including antibody fragment based conformational sensors, we discover structural differences between βarr1 and 2 upon their interaction with activated and phosphorylated receptors. Interestingly, domain swapped chimeras of βarrs display robust complementation in functional assays thereby, linking the structural differences between the receptor-bound βarr1 and 2 with their divergent functional outcomes. Our findings reveal important insights into the ability of βarr isoforms to drive distinct functional outcomes, and underscore the importance of integrating this aspect in the current framework of biased agonism.
Hippocampal-amygdala interactions mediate uncertainty-dependent resistance to extinction following fear conditioning
Authors: Morris John , Windels Francois , Sah Pankaj
Published: August 2019

The partial reinforcement extinction effect (PREE) is a paradoxical learning phenomenon in which omission of reinforcement during acquisition results in more persistent conditioned responding in extinction. Here, we report a significant PREE with an inverted-U, entropy-like distribution against reinforcement probability following tone foot shock fear conditioning in rats, which was associated with increased neural activity in hippocampus and amygdala as indexed by p-ERK and c-fos immunolabelling. In vivo electrophysiological recordings of local field potentials (LFPs) showed that 50% reinforcement was associated with increases in the frequency and power of tone-evoked theta oscillations in both the subiculum region of hippocampus and in basolateral amygdala (BLA) during both acquisition (Day 1) and extinction (Day 2) sessions. Tone-evoked LFPs in 50% reinforced animals also showed increases in coherence and bidirectional Granger Causality between hippocampus and amygdala. The results support a Bayesian interpretation of the PREE, in which the phenomenon is driven by increases in the entropy or uncertainty of stimulus contingencies, and indicate a crucial role for hippocampus in mediating this uncertainty-dependent effect.
Extinction and the temporal distribution of macroevolutionary bursts
Authors: De Lisle Stephen P. , Punzalan David , Rollinson Njal , Rowe Locke
Published: August 2019

Phenotypic evolution through deep time is slower than expected from microevolutionary rates. This is the paradox of stasis. Previous models suggest stasis occurs because populations track adaptive peaks that typically move on million-year intervals, raising the equally perplexing question of why peaks shifts are so rare. Here, we consider the possibility that peaks can move more rapidly than populations can adapt, resulting in extinction. We model peak movement with explicit population dynamics, parameterized with published microevolutionary parameters. Allowing extinction greatly increases the parameter space of peak movements that yield the appearance of stasis observed in real data through deep time. Our work highlights population ecology as an important contributor to macroevolutionary dynamics, presenting an alternative perspective on the paradox of stasis where apparent constraint on phenotypic evolution in deep time reflects our restricted view of the subset of earth’s lineages that were fortunate enough to reside on relatively stable peaks.