bluuebunny/crossref_metadata_2025 huggingface dataset:
A Pilot Quality Improvement Project to Reduce Intraoperative MRI Hypothermia in Neurosurgical Patients
Authors: Wong Becky J. , Rama Asheen , Caruso Thomas J. , Lee Charles K. , Wang Ellen , Chen Michael
Published: March 2022

Introduction:

Intraoperative hypothermia increases patient morbidity, including bleeding and infection risk. Neurosurgical intraoperative magnetic resonance imaging (iMRI) can lead to hypothermia from patient exposure and low ambient temperature in the MRI suite. This quality improvement project aimed to reduce the risk of hypothermia during pediatric neurosurgery laser ablation procedures with iMRI. The primary aim was to increase the mean lowest core temperature in pediatric patients with epilepsy during iMRI procedures by 1 °C from a baseline mean lowest core temperature of 34.2 ± 1.2 °C within 10 months and sustain for 10 months.

Methods:

This report is a single-institution quality improvement project from March 2019 to June 2021, with 21 patients treated at a pediatric hospital. After identifying key drivers, temperature-warming interventions were instituted to decrease hypothermia among patients undergoing iMRI during neurosurgery procedures. A multidisciplinary team of physicians, nurses, and MRI technologists convened for huddles before each case. Interventions included prewarmed operating rooms (ORs), blanket coverings, MRI table and room; forced-air blanket warming, temperature monitoring in the OR and iMRI environments; and the MRI fan turned off.

Results:

Data were analyzed for five patients before and nine patients after the institution of the temperature-warming elements. The sustainment period included 15 patients. The mean lowest intraoperative temperature rose from 34.2 ± 1.3 °C in the preintervention period to 35.5 ± 0.6 °C in sustainment (P = 0.004).

Conclusion:

Hybrid OR and MRI procedures increase hypothermia risk, which increases patient morbidity. Implementation of a multidisciplinary, multi-item strategy for patient warming mitigates the risk.
A Recanalized Umbilical Vein Hypermetabolic Thrombosis Mimicked an Hepatocellular Carcinoma Recurrence
Authors: Fidani Thibault , Desmarets Guillaume , Goupil Jean , Pouget Jean-Pierre , Boudousq Vincent
Published: March 2022

A transarterial left hepatic artery radioembolization involving 90Y microspheres was performed on a cirrhotic man with hypermetabolic 18F-FDG segment III hepatocellular carcinoma. During the 18F-FDG PET/CT follow-up, the disappearance of the hypermetabolic lesion was initially observed. Then, a focal segment III hypermetabolism reappeared mimicking a recurrence before disappearing without any treatment. Finally, the hepatic MRI demonstrated that the transitory segment III hypermetabolism matched a thrombus of the dilated recanalized umbilical vein.
Orbital Metastasis
Authors: Morland David , Jallet Lucas , Deguelte Sophie , Cadiot Guillaume , Papathanassiou Dimitri
Published: March 2022

Orbital foci of increased uptake are sometimes visualized on 18F-FDOPA PET/CT, but the literature remains poor as to their nature. The orbit is indeed a rare site of metastatic involvement. Given this low probability of metastatic location, the question of an incidental benign finding may arise. We reviewed all 18F-FDOPA PET/CT examinations performed at our institution between January 2015 and May 2021: 4/149 patients presented at least 1 orbital focus of increased uptake, all of them presented a metastatic small intestine neuroendocrine tumor. Somatostatin receptor expression was confirmed using 68Ga-DOTATOC PET/CT supporting the hypothesis of genuine metastases.
Galectin-3 ablation does not affect infarct size or inflammatory cytokines after experimental stroke in 24-month-old female mice
Authors: Manouchehrian Oscar , Andersson Emelie , Eriksson-Hallberg Björn , Deierborg Tomas
Published: March 2022

Background

The tissue damage following a focal stroke causes an inflammatory response that is thought to aggravate the disease state. Galectin-3 is a proinflammatory molecule that has been shown to play a significant role in the inflammatory responses in brain diseases and following experimental stroke. In most animal experiments, young animals are used, although attempts are often made to model diseases that affect the elderly. Therefore, in this project, we intended to investigate the role of Galectin-3 in experimental stroke in older mice.

Methods

In this project, 24-month-old (aged) female mice were subjected to an experimental stroke (permanent middle cerebral artery occlusion) 7 days before sacrifice. We wanted to investigate whether the absence of the inflammatory protein Galectin-3 could affect motor phenotype, neuroinflammation and infarct size. Number of mice without Galectin-3 (Galectin-3 KO) = 9, number of wildtype controls of the same age = 6.

Results

In our aged female mice, we could not observe any significant differences between Galectin-3 KO and wildtype regarding the inclined plane test or cylinder test. We could not observe different infarct sizes between the two genotypes. In brain homogenates, we measured levels of 10 inflammatory cytokines, but we could not see any significant differences in any of them.

Conclusion

In summary, it can be said that the absence of the inflammatory mediator Galectin-3 does not seem to have a strong poststroke effect in aged females. Unfortunately, we could not analyze these mice with immunohistochemistry, which limited our study.
Neuroimaging within the Dominantly Inherited Alzheimer’s Network (DIAN): PET and MRI
Authors: McKay Nicole S. , Gordon Brian A. , Hornbeck Russ C. , Jack Clifford R. , Koeppe Robert , Flores Shaney , Keefe Sarah , Hobbs Diana A. , Joseph-Mathurin Nelly , Wang Qing , Rahmani Farzaneh , Chen Charles D. , McCullough Austin , Koudelis Deborah , Chua Jasmin , Ances Beau M. , Millar Peter R. , Nickels Mike , Perrin Richard J. , Allegri Ricardo F. , Berman Sarah B. , Brooks William S. , Cash David M. , Chhatwal Jasmeer P. , Farlow Martin R. , Fox Nick C. , Fulham Michael , Ghetti Berhadino , Graff-Radford Neill , Ikeuchi Takeshi , Day Gregg , Klunk William , Levin Johannes , Lee Jae-Hong , Martins Ralph , Masters Colin L. , McConathy Jonathan , Mori Hiroshi , Noble James M. , Rowe Christopher , Salloway Stephen , Sanchez-Valle Raquel , Schofield Peter R. , Shimada Hiroyuki , Shoji Mikio , Su Yi , Suzuki Kazushi , Vöglein Jonathan , Yakushev Igor , Swisher Laura , Cruchaga Carlos , Hassenstab Jason , Karch Celeste , McDade Eric , Xiong Chengjie , Morris John C. , Bateman Randall J. , Benzinger Tammie L.S. ,   Dominantly Inherited Alzheimer Network
Published: March 2022

The Dominantly Inherited Alzheimer Network (DIAN) Observational Study is an international collaboration studying autosomal dominant Alzheimer disease (ADAD). This rare form of Alzheimer disease (AD) is caused by mutations in the presenilin 1 (PSEN1), presenilin 2 (PSEN2), or amyloid precursor protein (APP) genes. As individuals from these families have a 50% chance of inheriting the familial mutation, this provides researchers with a well-matched cohort of carriers vs non-carriers for case-control studies. An important trait of ADAD is that the age at symptom onset is highly predictable and consistent for each specific mutation, allowing researchers to estimate an individual’s point in their disease time course prior to symptom onset. Although ADAD represents only a small proportion (approximately 0.1%) of all AD cases, studying this form of AD allows researchers to investigate preclinical AD and the progression of changes that occur within the brain prior to AD symptom onset. Furthermore, the young age at symptom onset (typically 30-60 years) means age-related comorbidities are much less prevalent than in sporadic AD, thereby allowing AD pathophysiology to be studied independent of these confounds. A major goal of the DIAN Observational Study is to create a global resource for AD researchers. To that end, the current manuscript provides an overview of the DIAN magnetic resonance imaging (MRI) and positron emission tomography (PET) protocols and highlights the key imaging results of this study to date.
Right Anterior Theta Connectivity Predicts Autistic Social Traits in Neurotypical Children
Authors: Hill Aron T. , Van Der Elst Jodie , Bigelow Felicity J. , Lum Jarrad A. G. , Enticott Peter G.
Published: March 2022

Growing evidence supports functional network alterations in autism spectrum disorder, however much less is known about the neural mechanisms underlying autistic traits in typically developing children. Using resting-state electroencephalographic (EEG) recordings, we examined whether functional connectivity could predict autistic trait expression in 127 children aged between 4-12 years. Regression models showed that right anterior theta connectivity was a significant predictor of autistic traits (p = 0.013), with increased connectivity in this region associated with greater autistic trait expression. These results corroborate similar recent findings in adults, extending this observation to a cohort of children spanning early-to-middle childhood. These findings further highlight EEG-derived functional connectivity as a sensitive physiological correlate of autistic trait expression in neurotypical children.
Costimulation of TLR8 responses by CXCL4 in Human Monocytes Mediated by TBK1-IRF5 Signaling and Epigenomic Remodeling
Authors: Yang Chao , Bachu Mahesh , Du Yong , Brauner Caroline , Yuan Ruoxi , Ah Kioon Marie Dominique , Chesi Giancarlo , Barrat Franck J. , Ivashkiv Lionel B.
Published: March 2022

Regulation of endosomal TLR responses by the chemokine CXCL4 is implicated in inflammatory and fibrotic diseases. The current paradigm is that CXCL4 potentiates TLR responses by binding and facilitating endosomal delivery of nucleic acid TLR ligands. We report that in human monocytes/macrophages, CXCL4 initiates signaling cascades and downstream epigenomic reprogramming that change the profile of the TLR8 response by selectively and dramatically amplifying inflammatory gene transcription and IL-1β production, while partially attenuating the IFN response. Mechanistically, costimulation by CXCL4 and TLR8 synergistically activated TBK1/IKKε and repurposed these kinases towards an inflammatory response via coupling with IRF5, and by activating the NLRP3 inflammasome without the need for an exogenous activator of a second signal for IL-1β maturation. CXCL4 signaling strongly induced chromatin remodeling and de novo enhancers associated with inflammatory genes in a cooperative and synergistic manner with TLR8. These findings identify new mechanisms of regulation of TLR responses relevant for cytokine storm, and suggest targeting the TBK1/IKKε-IRF5 axis may be beneficial in inflammatory diseases.
Post-activation depression produces extensor H-reflex suppression following flexor afferent conditioning
Authors: Metz K. , Concha-Matos I. , Hari K. , Bseis O. , Afsharipour B. , Lin S. , Li Y. , Singla R. , Fenrich K , Bennett DJ. , Gorassini MA.
Published: March 2022

Suppression of the extensor H-reflex by flexor afferent conditioning is thought to be produced by a long-lasting inhibition of extensor Ia-afferent terminals via primary afferent depolarization (PAD) activated by GABAAreceptors. Considering the recent finding that PAD does not produce presynaptic inhibition of Ia-afferent terminals, we examined if H-reflex suppression is instead mediated by post-activation depression of the test extensor Ia-afferents triggered by PAD-evoked spikes and/or by a long-lasting inhibition of the extensor motoneurons. A brief conditioning vibration of the flexor tendon suppressed both the extensor soleus H-reflex and the tonic discharge of soleus motor units for 300 ms, indicating that part of the H-reflex suppression was mediated by a long-lasting inhibition of the extensor motoneurons. When activating the flexor afferents electrically to produce conditioning, the soleus H-reflex was also suppressed for 300 ms, but only when a short-latency reflex was evoked in the soleus muscle by the conditioning input itself. In mice, a similar short-latency reflex was evoked when optogenetic or afferent activation of GABAergic (GAD2+) neurons produced PAD large enough to evoke orthodromic spikes in the test Ia-afferents, causing post-activation depression of subsequent monosynaptic excitatory-post-synaptic potentials. The time course of this post-activation depression and related H-reflex suppression (lasting 2 s) was like rate-dependent depression that is also due to post-activation depression. We conclude that extensor H-reflex inhibition by brief flexor afferent conditioning is produced by both post-activation depression of extensor Ia-afferents and long-lasting inhibition of extensor motoneurons, rather than from PAD directly inhibiting Ia afferent terminals.
Slc9a6 mutation causes Purkinje cell loss and ataxia in the shaker rat
Authors: Figueroa Karla , Anderson Collin J. , Paul Sharan , Dansithong Warunee , Gandelman Mandi , Scoles Daniel R. , Pulst Stefan M.
Published: March 2022

Background

The shaker rat carries a naturally occurring mutation leading to progressive ataxia characterized by Purkinje cell (PC) loss. We previously reported on fine-mapping the shaker locus to the long arm of the rat X chromosome. In this work, we sought to identify the mutated gene underlying the shaker phenotype and confirm its identity by functional complementation.

Methods

We fine-mapped the candidate region and analyzed cerebellar transcriptomes to identify deleterious variants. We generated an adeno-associated virus (AAV) targeting solute carrier family 9, member A6 (Slc9a6) expression to PCs using a mouse L7-6 (L7) promoter, as well as a control green fluorescent protein (GFP)-expressing virus. We administered AAVs prior to the onset of PC degeneration through intracerebroventricular injection and evaluated the molecular, cellular, and motor phenotypes.

Results

We identified a XM_217630.9 (Slc9a6):c.[191_195delinsA] variant in the Slc9a6 gene that segregated with disease. This mutation is predicted to generate a truncated sodium-hydrogen exchanger 6 (NHE6) protein, p.(Ala64Glufs*23). Administration of AAV9-PHP.eB expressing rat Slc9a6 prior to symptom onset reduced the shaker motor, molecular, and cellular phenotypes.

Interpretation

Slc9a6 is mutated in shaker and also in human Christianson syndrome, an epileptic encephalopathy. AAV-based gene therapy may be a viable therapeutic strategy for Christianson syndrome, and the shaker rat model may aid in therapeutic development.
Mutated Tumor Suppressors Follow Oncogenes Profile by the Gene Hypermethylation of Partners in the Protein Interaction Networks
Authors: Tagore Somnath , Frenkel-Morgenstern Milana
Published: March 2022

As a result of current advances in the analysis of patient sequencing data, many tumors have been characterized in a personalized manner. Such data can also be used to characterize genes that act as either oncogenes or tumor suppressors. These include “defective” tumor suppressor genes which may function as driver oncogenes that play a key role in cancer proliferation due to various genetic alterations, specifically, chromosomal translocations. In this study, we considered protein networks, mutations, methylation data and cancer fusions to classify tumor suppressors that may convert into oncogenes. Moreover, we developed a novel network-based parameter called the ‘preferential attachment score’ to categorize genes as oncogenes and/or tumor suppressors. Such classification was achieved using a naïve Bayes computation approach. We used an ABC-MCMC method for selecting features for training our classification algorithm. We then performed a survey of tumor suppressors and oncogenes from the perspective of somatic mutations and network properties for 691 TCGA cases. For comparative purposes, we chose currently well-established methods, such as MutSigCV, OncodriveCLUST, Oncodrive-FM, 20/20+, ActiveDriver, MuSiC, TUSON, OncodriveFML, and found that our algorithm outperformed these other tolls, with 93.3% efficiency. Based on 691 TCGA cohorts, we found that tumor suppressors presented the highest mutation frequency in most tumor types, relative to oncogenes. Using protein-protein interaction data, we found that essential proteins, tumor suppressors and oncogenes had higher degrees of connectivity and betweenness centrality, relative to normal proteins. Similarly, tumor suppressors and oncogenes had lower clustering coefficients, as well as shortest path distances (FDR < 0.05). Finally, most mutated tumor suppressors integrate hyper-methylated partners in the protein interaction networks of 3091 fusions, following the patterns of oncogenes (43%). Thus, these results further characterize cancer oncogenes and tumor suppressors in the context of deep analysis of cancer network alterations.

Availability

Source scripts are available at https://github.com/somnathtagore/NBC and the resource is available at http://ontum.md.biu.ac.il/index.html
Xanthomonas infection transforms the apoplast into an accessible and habitable niche for Salmonella enterica
Authors: Dixon Megan H. , Cowles Kimberly N. , Zaacks Sonia C. , Marciniak Isabel N. , Barak Jeri D.
Published: March 2022

The physiology of plant hosts can be dramatically altered by phytopathogens. Xanthomonas hortorum pv. gardneri is one such pathogen that creates an aqueous niche within the leaf apoplast by manipulating the plant via the transcription activator-like effector AvrHah1. Simultaneous immigration of X. gardneri and Salmonella enterica to healthy tomato leaves results in increased survival of S. enterica as Xanthomonas infection progresses. However, the fate of S. enterica following arrival on actively infected leaves has not been examined. We hypothesized that the water-soaking caused by X. gardneri could facilitate the ingression of S. enterica into the apoplast, and that this environment would be conducive for growth. We found that a water-soaked apoplast, abiotically or Xanthomonas-infected, enabled surface S. enterica to passively localize to the protective apoplast and facilitated migration of S. enterica to distal sites within the aqueous apoplast. AvrHah1 contributed to the protection and migration of S. enterica early in X. gardneri infection. Xanthomonas-infected apoplasts facilitated prolonged survival and promoted S. enterica replication compared to healthy apoplasts. Access to an aqueous apoplast in general protects S. enterica from immediate exposure to irradiation whereas, the altered environment created by Xanthomonas infection provides growth-conducive conditions for S. enterica. Overall, we have characterized an ecological relationship in which host infection converts an unreachable niche to a habitable environment.

Importance

Bacterial spot disease caused by Xanthomonas species devastates tomato production worldwide. Salmonellosis outbreaks from consumption of raw produce have been linked to the arrival of Salmonella enterica on crop plants in the field via contaminated irrigation water. Considering that Xanthomonas is difficult to eradicate, it is highly likely that S. enterica arrives on leaves pre-colonized by Xanthomonas with infection underway. Our study demonstrates that infection and disease fundamentally alter the leaf, resulting in redistribution and change in abundance of a phyllosphere bacterial member. These findings contribute to our understanding of how S. enterica manages to persist on leaf tissue despite lacking the ability to liberate nutrients from plant cells. More broadly, this study reveals a mechanism by which physiochemical changes to a host environment imposed by a plant pathogen can convert an uninhabitable leaf environment into a hospitable niche for select epiphytic microbes.
An atypical ABC transporter is involved in antifungal resistance and host interactions in the pathogenic fungus Cryptococcus neoformans
Authors: Winski Christopher J. , Qian Yuanyuan , Mobashery Shahriar , Santiago-Tirado Felipe H.
Published: March 2022

ATP-binding cassette (ABC) transporters represent one of the largest protein superfamilies. Functionally diverse, ABC transporters have been implicated in many aspects of microbial physiology. The genome of the human fungal pathogen Cryptococcus neoformans encodes 54 putative ABC transporters and the majority of them remain uncharacterized. In a previous genetic screen for fungal regulators of phagocytosis, we identified an uncharacterized gene, CNAG_06909, that modulates host interactions. This gene encodes a half-size ABC transporter of the PDR-type, and phenotypic studies of a strain with this gene deleted revealed an altered antifungal susceptibility profile, including hypersensitivity to fluconazole (FLC). This gene, which we have named PDR6, localizes to the endoplasmic reticulum (ER) and plasma membrane (PM), and when absent, less ergosterol is observed in the PM. Additionally, we observed that the pdr6Δ strain displays a reduction in secreted polysaccharide capsular material. These changes to the cellular surface may explain the observed increased uptake by macrophages and the reduced intracellular survival. Finally, studies in mice demonstrate that Pdr6 function is required for normal progression of cryptococcal infection. Taken together, this study demonstrates a novel dual role for PDR transporters in C. neoformans, which could represent a potential target for antifungal therapeutics. Furthermore, the atypical half-size transporter encoded by PDR6 is conserved in many fungal pathogens, but absent in model non-pathogenic fungi. Hence, this study provides for the first time, a function for this unique group of fungal half-size PDR transporters that, although conserved, remain largely understudied.

IMPORTANCE

Conserved across all kingdoms of life, ABC transporters comprise one of the largest protein families. They are associated with multidrug resistance, affecting aspects such as resistance to antimicrobials or anti-cancer drugs. Despite their importance, they are understudied in fungal pathogens. In the environmental fungus Cryptococcus neoformans, a leading cause of fungal infections, only a few ABC transporters have been studied. Here we characterize an atypical, half-size, ABC transporter of the PDR-type, that affects both antifungal resistance and host-pathogen interactions. PDR-type transporters are only present in fungi and plants, and this subgroup of half-size transporters is conserved in fungal pathogens, yet their function was completely unknown. Because the current treatments for cryptococcal infection are suboptimal, understanding the mechanisms of antifungal resistance and the host interactions that drive the infection is critical to improve the management of this disease. Here we provide insights into these important aspects of cryptococcal pathogenesis.
Nectar compounds impact bacterial and fungal growth and shift community dynamics in a nectar analog
Authors: Mueller Tobias G. , Francis Jacob S. , Vannette Rachel L.
Published: March 2022

Floral nectar is frequently colonized by fungi and bacteria. However, within individual flowers, nectar microbial communities are typically species-poor and dominated by few cosmopolitan genera. One hypothesis is that nectar constituents may act as a strong environmental filter. Non-sugar constituents in nectar could affect species composition via broad antimicrobial activity or differential effects on nectar microbial species. Here, we tested how five non-sugar nectar compounds as well as elevated sugar impacted the growth of 12 fungal and bacterial species isolated from flowers, pollinators, and the environment. We hypothesized that microbes isolated from nectar would be better able to grow in the presence of these compounds. Additionally, to test if nectar compounds could affect the outcome of competition among microbial taxa, we grew a subset of microbes in co-culture assays across a subset of treatments.

We found that some compounds such as H2O2broadly suppressed microbial growth across many but not all microbes tested. Other tested compounds were more specialized in the microbes they impacted. As hypothesized, the nectar specialistMetschnikowia reukaufiiwas unaffected by most nectar compounds assayed. However, many non-nectar specialist microbes remained unaffected by compounds thought to reduce microbial growth in nectar. Our results show that nectar chemistry can influence nectar microbial communities but that microbe-specific responses to nectar compounds are common. Nectar chemistry also affected the outcome of species interactions among microbial taxa, suggesting that non-sugar compounds in nectar can affect microbial community assembly and abundance in flowers.
Base editing screens map mutations affecting IFNγ signalling in cancer
Authors: Coelho Matthew A. , Karakoc Emre , Bhosle Shriram , Gonçalves Emanuel , Burgold Thomas , Cooper Sarah , Cattaneo Chiara M. , Veninga Vivien , Consonni Sarah , Dinçer Cansu , Vieira Sara F. , Gibson Freddy , Barthorpe Syd , Hardy Claire , Rein Joel , Thomas Mark , Voest Emile , Bassett Andrew , Garnett Mathew J.
Published: March 2022

IFNγsignalling underpins host responses to infection, inflammation and anti-tumour immunity. Mutations in the IFNγsignalling pathway cause immunological disorders, haematological malignancies, and resistance to immune checkpoint blockade (ICB) in cancer, however the function of most clinically observed variants remain unknown. Here, we systematically investigate the genetic determinants of IFNγresponse in colorectal cancer cells using CRISPR-Cas9 screens and base editing mutagenesis. Deep mutagenesis of JAK1 with cytidine and adenine base editors, combined with pathway-wide screens, reveal loss-of-function and gain-of-function mutations with clinical precedence, including causal variants in haematological malignancies and mutations detected in patients refractory to ICB. We functionally validate variants of uncertain significance in primary tumour organoids, where engineering missense mutations in JAK1 enhanced or reduced sensitivity to autologous tumour-reactive T cells. By classifying > 300 missense variants altering IFNγ pathway activity, we demonstrate the utility of base editing for mutagenesis at scale, and generate a resource to inform genetic diagnosis.
The human placenta shapes the phenotype of decidual macrophages
Authors: Vondra Sigrid , Höbler Anna-Lena , Lackner Andreas Ian , Raffetseder Johanna , Mihalic Zala Nikita , Vogel Andrea , Saleh Leila , Kunihs Victoria , Haslinger Peter , Wahrmann Markus , Husslein Heinrich , Oberle Raimund , Kargl Julia , Haider Sandra , Latos Paulina , Schabbauer Gernot , Knöfler Martin , Ernerudh Jan , Pollheimer Jürgen
Published: March 2022

During human pregnancy, placenta-derived extravillous trophoblasts (EVT) invade the decidua and communicate with maternal immune cells. The decidua can be distinguished into basalis (decB) and parietalis (decP), the latter being unaffected by placentation. By defining a novel gating strategy, we report accumulation of myeloid cells in decB. We identified a decidua basalis-associated macrophage (decBAM) population with a differential transcriptome and secretome when compared to decidua parietalis-associated macrophages (decPAMs). decBAMs are CD11chiand efficient inducers of Tregs, proliferatein situand secrete high levels of CXCL1, CXCL5, M-CSF, and IL-10. In contrast, decPAMs exert a dendritic cell-like, motile phenotype characterized by induced expression of HLA class II molecules, enhanced phagocytosis, and the ability to activate T cells. Strikingly, EVT-conditioned media are able to convert decPAMs into a decBAM phenotype. Cumulatively, these findings assign distinct macrophage phenotypes to decidual areas depending on placentation and further highlight a critical role for EVTs in the induction of pregnancy-tolerant macrophage polarization.

Graphical Abstract

Highlights

In this study, we identified so far unrecognized, placenta-induced immune responses at the maternal-fetal interface. Altogether, we imply that placenta-derived trophoblasts induce a pregnancy-tolerant phenotype by suppressing antigen-presenting cell-like functions in maternal tissue macrophages.
Lifting the ban on nuclear import activates Gdown1-mediated modulation of global transcription and facilitates adaptation to cellular stresses
Authors: Zhu Zhanwu , Liu Jingjing , Feng Huan , Zhang Yanning , Huang Ruiqi , Pan Qiaochu , Nan Jing , Miao Ruidong , Cheng Bo
Published: March 2022

Dynamic regulation of transcription is crucial for cellular response to various environmental or developmental cues. Gdown1 is a ubiquitously expressed, RNA polymerase II (Pol II) interacting protein, essential for embryonic development. It tightly binds Pol IIin vitroand competitively blocks binding of TFIIF and other transcriptional regulatory factors, yet its cellular functions and regulatory circuits remain unclear. Here, we show that Gdown1 strictly localizes in the cytoplasm of mammalian somatic cells and exhibits potent resistance to the imposed driving force for nuclear localization. Combined with genetic and microscope-based approaches, two types of functionally coupled and evolutionally conserved localization regulatory motifs are identified, including the CRM1-dependent nucleus export signal (NES) and a novel Cytoplasm Anchoring Signal (CAS) which mediates nuclear pore retention. Mutagenesis of CAS alleviates the cytoplasmic retention activity thus unlocks its nucleocytoplasmic shuttling properties, and increased nuclear import of Gdown1 causes drastic reduction of Pol II levels and global transcription. Importantly, nuclear translocation of Gdown1 occurs in a stress-responsive manner and ablation ofGDOWN1significantly weakens cellular tolerance. Collectively, our work uncovers the molecular basis of the localization of Gdown1 and highlights that its controlled nuclear translocation serves as a key strategy in modulating global transcription and stress-adaptation.
2-deoxyglucose transiently inhibits yeast AMPK signaling and triggers glucose transporter endocytosis, potentiating the drug toxicity
Authors: Laussel Clotilde , Albanèse Véronique , García-Rodríguez Francisco Javier , Ballin Alberto , Defenouillère Quentin , Léon Sébastien
Published: March 2022

2-deoxyglucose is a glucose analog that impacts many aspects of cellular physiology. After its uptake and its phosphorylation into 2-deoxyglucose-6-phosphate (2DG6P), it interferes with several metabolic pathways including glycolysis and protein N-glycosylation. Despite this systemic effect, resistance can arise through strategies that are only partially understood. In yeast, 2DG resistance is often associated with mutations causing increased activity of the yeast 5’-AMP activated protein kinase (AMPK), Snf1. Here we focus on the contribution of a Snf1 substrate in 2DG resistance, namely the alpha-arrestin Rod1 involved in nutrient transporter endocytosis. We report that 2DG triggers the endocytosis of many plasma membrane proteins, mostly in a Rod1-dependent manner. Rod1 participates in 2DG-induced endocytosis because 2DG, following its phosphorylation by hexokinase Hxk2, triggers changes in Rod1 post-translational modifications and promotes its function in endocytosis. Mechanistically, this is explained by a transient, 2DG-induced inactivation of Snf1/AMPK by protein phosphatase 1 (PP1). We show that 2DG-induced endocytosis is detrimental to cells, and the lack of Rod1 counteracts this process by stabilizing glucose transporters at the plasma membrane. This facilitates glucose uptake, which may help override the metabolic blockade caused by 2DG, and 2DG export - thus terminating the process of 2DG detoxification. Altogether, these results shed a new light on the regulation of AMPK signaling in yeast and highlight a remarkable strategy to bypass 2DG toxicity involving glucose transporter regulation.

Author summary

In this article, we study the resistance to a drug named 2-deoxyglucose (2DG). 2DG is an efficient inhibitor of several metabolic pathways, particularly glycolysis which is of prime importance for tumor cell proliferation. Cancer cells but also cells from other organisms can develop various resistance strategies that only being unraveled. Here, using baker’s yeast as a model organism, we document the resistance mechanism of a mutant lacking the arrestin gene ROD1, known to regulate nutrient transporter endocytosis. First, we show that 2DG triggers the endocytosis of many nutrient transporters. Mechanistically, 2DG leads to a transient inhibition of the AMPK signaling pathway, which in turn promotes the activation of Rod1, a pre-requisite for 2DG-induced endocytosis. Consequently, cells lacking Rod1 maintain various proteins at the plasma membrane including hexose transporters, the latter being essential for 2DG resistance. Hexose transporter stabilization at the cell surface may sustain glucose import and help cells cope with the 2DG-induced metabolic blockade, while also allowing 2DG detoxication.
Regulation of EBNA1 Protein Stability by PLOD1 Lysine Hydroxylase
Authors: Dheekollu Jayaraju , Wiedmer Andreas , Soldan Samantha S. , Castro Muñoz Leonardo Josué , Tang Hsin-Yao , Speicher David W. , Lieberman Paul M.
Published: March 2022

Epstein-Barr virus (EBV) is a ubiquitous human γ-herpesvirus that is causally associated with various malignancies and autoimmune disease. Epstein-Barr Nuclear Antigen 1 (EBNA1) is the viral-encoded DNA binding protein required for viral episome maintenance and DNA replication during latent infection in proliferating cells. EBNA1 is known to be a highly stable protein, but its mechanism of protein stability is not completely understood. Proteomic analysis of EBNA1 revealed interaction with Procollagen Lysine-2 Oxoglutarate 5 Dioxygenase (PLOD) family of proteins. Depletion of PLOD1 by shRNA or inhibition with small molecule inhibitors 2,-2’ dipyridyl resulted in the loss of EBNA1 protein levels, along with a selective growth inhibition of EBV-positive lymphoid cells. PLOD1 depletion also caused a loss of EBV episomes from latently infected cells and inhibited oriP-dependent DNA replication. We used mass spectrometry to identify EBNA1 peptides with lysine hydroxylation at K460 or K461. Mutation of K460 to alanine or arginine abrogates EBNA1-driven DNA replication of oriP, while K461 mutations enhanced replication. These findings suggest that PLOD1 is a novel post-translational regulator of EBNA1 protein stability and function in viral plasmid replication, episome maintenance and host cell survival.

Importance

EBNA1 is essential for EBV latent infection and implicated in viral pathogenesis. We found that EBNA1 interacts with PLOD family of lysine hydroxylases and that this interaction is required for EBNA1 protein stability and function in viral persistence during viral latent infection. Identification of PLOD1 regulation of EBNA1 protein stability provide new opportunity to target EBNA1 for degradation in EBV associated disease.
Quantifying the capacity for assisted migration to achieve conservation and forestry goals under climate change
Authors: Zou Yibiao , Backus Gregory A. , Safford Hugh D. , Sawyer Sarah , Baskett Marissa L.
Published: March 2022

Many tree species might be threatened with extinction because they cannot disperse or adapt quickly enough to keep pace with climate change. One potential, and potentially risky, strategy to mitigate this threat is assisted migration, the intentional movement of species to facilitate population range shifts to more climatically suitable locations under climate change. The ability for assisted migration to minimize risk and maximize conservation and forestry outcomes depends on a multi-faceted decision process for determining, what, where, and how much to move. To quantify how the benefits and risks of assisted migration could affect the decision-making process, we used a dynamical vegetation model parameterized with 23 tree species in the western United States. We found that most of the modeled species are likely to experience a substantial decline in biomass, potentially facing regional extinction by 2100 under the high-emission SSP5-85 climate-change scenario. Though simulations show assisted migration had little effect on the forestry goal of total biomass across all species, its effects on the conservation goal of promoting individual species’ persistence were far more substantial. Among eight assisted migration strategies we tested that differ in terms of life cycle stage of movement and target destination selection criteria, the approach that conserved the highest biomass for individual species involved relocating target seedlings to areas with the highest canopy openness. Although this strategy significantly reduced extinction risk for six at-risk species compared to no action, it also slightly reduced biomass of four species, due to increasing competition. Species with relatively weak tolerance to drought, fire or high temperature were the most likely candidate groups for assisted migration. This model framework could be applied to other forest ecosystems to evaluate the efficacy of assisted migration globally.
spongEffects: ceRNA modules offer patient-specific insights into the miRNA regulatory landscape
Authors: Boniolo Fabio , Hoffmann Markus , Roggendorf Norman , Tercan Bahar , Baumbach Jan , Castro Mauro A. A. , Robertson A. Gordon , Saur Dieter , List Markus
Published: March 2022

Motivation

Cancer is one of the leading causes of death worldwide. Despite significant improvements in prevention and treatment, mortality remains high for many cancer types. Hence, innovative methods that use molecular data to stratify patients and identify biomarkers are needed. Promising biomarkers can also be inferred from competing endogenous RNA (ceRNA) networks that capture the gene-miRNA gene regulatory landscape. Thus far, the role of these biomarkers could only be studied globally but not in a sample-specific manner. To mitigate this, we introduce spongEffects, a novel method that infers subnetworks (or modules) from ceRNA networks and calculates patient- or sample-specific scores related to their regulatory activity.

Results

We show how spongEffects can be used for downstream interpretation and machine learning tasks such as tumor classification and for identifying subtype-specific regulatory interactions. In a concrete example of breast cancer subtype classification, we prioritize modules impacting the biology of the different subtypes. In summary, spongEffects prioritizes ceRNA modules as biomarkers and offers insights into the miRNA regulatory landscape. Notably, these module scores can be inferred from gene expression data alone and can thus be applied to cohorts where miRNA expression information is lacking.

Availability

https://bioconductor.org/packages/devel/bioc/html/SPONGE.html

Contact

markus.daniel.hoffmann@tum.de;markus.list@tum.de

Supplementary information

Supplementary data are available at Bioinformatics online.
Tuberculosis treatment failure associated with evolution of antibiotic resilience
Authors: Liu Qingyun , Zhu Junhao , Dulberger Charles L. , Stanley Sydney , Wilson Sean , Chung Eun Seon , Wang Xin , Culviner Peter , Liu Yue J. , Hicks Nathan D. , Babunovic Gregory H. , Giffen Samantha R. , Aldridge Bree B. , Garner Ethan C. , Rubin Eric J. , Chao Michael C. , Fortune Sarah M.
Published: March 2022

Antibiotics are a cornerstone of medicine, placing bacterial pathogens under intense pressure to evolve new survival mechanisms. Analysis of 51,229 Mycobacterium tuberculosis (Mtb) clinical isolates identified an essential transcriptional regulator, Rv1830 (here named resR) as a frequent target of positive (adaptive) selection. resR mutants do not demonstrate canonical drug resistance or drug tolerance but instead have significantly faster recovery after drug treatment across all antibiotics and combinations tested, a phenotype which we term antibiotic resilience. ResR acts in a regulatory cascade with other growth-controlling transcriptional regulators WhiB2 and WhiA, which are also under positive selection in Mtb clinical isolates. Mutations of these genes are associated with treatment failure and the acquisition of canonical drug resistance.
Driving Forces underlying Selectivity Filter Gating in the MthK Potassium Channel
Authors: Kopec Wojciech , Thomson Andrew S. , de Groot Bert L. , Rothberg Brad S.
Published: March 2022

K+channel activity can be limited by C-type inactivation, which is likely initiated in part by dissociation of K+ions from the selectivity filter, and modulated by side chains surrounding the selectivity filter. Whereas crystallographic and computational studies have linked inactivation to a ‘collapsed’ selectivity filter conformation in the KcsA channel, the structural basis for selectivity filter gating in other K+channels has been less clear. Here, we combined electrophysiological recordings with molecular dynamics based,in silicoelectrophysiology simulations, to study selectivity filter gating in the model potassium channel MthK and its V55E mutant (analogous to KcsA E71) in the pore-helix. Experimentally, we find that MthK V55E has a lower open probability than the WT channel, due to decreased stability of the open state, as well as a lower unitary conductance. Simulations account for both aspects of these observations on the atomistic scale, showing that ion permeation in V55E is altered by two distinct orientations of the E55 side chain. In the ‘vertical’ orientation of E55, in which E55 forms a hydrogen bond with D64 (as observed with KcsA WT channels), the filter displays reduced conductance compared to MthK WT. In contrast, with ‘horizontal’ orientation, K+conductance is closer to MthK WT; however the selectivity filter stability in the conducting conformation is lowered, and the filter more readily transitions to the inactivated conformation. Surprisingly, these transitions of MthK WT and V55E channels to the non-conducting (inactivated) state observed in simulations are associated with a widening selectivity filter, unlike its narrowing seen in KcsA, and reminisce the recent structures of stably-inactivated, voltage-gated potassium channels:ShakerW434F and Kv1.2 W362F mutants, as well as WT Kv1.3 channels.
Mesoscopic oblique plane microscopy (Meso-OPM) with a diffractive light sheet- enabling large-scale 4D cellular resolution imaging
Authors: Shao Wenjun , Chang Minzi , Emmerich Kevin , Kanold Patrick O , Mumm Jeff S , Yi Ji
Published: March 2022

Fundamental understanding of large-scale dynamic connectivity within a living organism requires volumetric imaging over a large field of view (FOV) at biologically relevant speed and resolution. However, most microscopy methods make trade-offs between FOV and depth resolution, making it challenging to observe highly dynamic processes at cellular resolution in 3D across mesoscopic scales (e.g., whole zebrafish larva). To overcome this limitation, we have developed mesoscopic oblique plane microscopy (Meso-OPM) with a diffractive light sheet. By augmenting the illumination angle of the light sheet with a transmission grating, the axial resolution was improved ~6-fold over existing methods and ~2-fold beyond the diffraction limitation of the primary objective lens. We demonstrated an unprecedented FOV up to 5.4 × 3.3 mm with resolution of 2.5× 3 × 6 μm, allowing volumetric imaging of 3D cellular structures with a single scan. Applying Meso-OPM for in vivo imaging of zebrafish larvae, we report here the first in toto whole body volumetric recordings of neuronal activity at 2 Hz volume rate and the first example of whole body volumetric recordings of blood flow dynamics at 5 Hz with 3D cellular resolution.
A multidisciplinary analysis of the as-isolated Escherichia coli SufBC2D complex reveals the presence of two new iron-sulfur clusters
Authors: Veronesi Giulia , Pérard Julien , Clémancey Martin , Gerez Catherine , Duverger Yohann , Kieffer Isabelle , Barras Frédéric , Gambarelli Serge , Blondin Geneviève , de Choudens Sandrine Ollagnier
Published: March 2022

Iron-sulfur (Fe-S) clusters are essential inorganic cofactors dedicated to a wide range of biological functions including electron transfer and catalysis. Specialized multi-protein machineries present in all types of organisms support their biosynthesis. These machineries encompass a scaffold protein on which Fe-S clusters are assembled before being transferred to cellular targets. Here, we describe the first characterization of the native Fe-S cluster of the anaerobically purified SufBC2D scaffold from Escherichia coli by XAS, Mössbauer, UV-visible absorption and EPR spectroscopy. Interestingly, we propose that SufBC2D harbors two types of Fe-S cluster, a [2Fe-2S] cluster with an unprecedented usual coordination and a previously unreported [3Fe-3S] cluster. These data combined with mutagenesis and biochemistry allow to propose ligands for these clusters. These results support the hypothesis that both SufB and SufD are involved in Fe-S cluster ligation and are discussed in the context of Fe-S cluster biogenesis where both [2Fe-2S] and [4Fe-4S] clusters need to mature cellular Fe-S protein targets.
Focal Non-invasive Deep-brain Stimulation with Temporal Interference for the Suppression of Epileptic Biomarkers
Authors: Acerbo Emma , Jegou Aude , Luff Charlotte , Dzialecka Patrycja , Botzanowski Boris , Missey Florian , Ngom Ibrahima , Lagarde Stanislas , Bartolomei Fabrice , Cassara Antonino , Neufeld Esra , Jirsa Viktor , Carron Romain , Grossman Nir , Williamson Adam
Published: March 2022

Neurostimulation applied from deep brain stimulation (DBS) electrodes is an effective therapeutic intervention in patients suffering from intractable drug-resistant epilepsy when resective surgery is contraindicated or failed. Inhibitory DBS to suppress seizures and associated epileptogenic biomarkers could be performed with high-frequency stimulation (HFS), typically between 100 –165Hz, to various deep-seated targets such as for instance the Mesio-temporal lobe (MTL) which leads to changes in brain rhythms, specifically in the hippocampus. The most prominent alterations concern high-frequency oscillations (HFOs), namely increase in ripples, a reduction in pathological Fast Ripples (FRs), and a decrease in pathological interictal epileptiform discharges (IEDs). In the current study, we use Temporal Interference stimulation to provide a non-invasive focal DBS (130 Hz) of the MTL, specifically the hippocampus, which increases physiological ripples, and decreases the number of FRs and IEDs in a mouse model of epilepsy. Similarly, we show the inability of 130 Hz transcranial current stimulation (TCS) to achieve similar results. The method could potentially revolutionize how DBS, certainly in epilepsy, is performed, and we therefore further demonstrate the translatability to human subjects via measurements of the TI stimulation vs TCS in human cadavers. Results show the better penetration of TI fields into the human hippocampus as compared with TCS. Finally, we provide evidence of the efficacy of the specific form of Pulse-width Modulated TI (PWM-TI), implemented with square waves, which is used in this study.

One Sentence Summary

A non-invasive deep brain stimulation applied via temporal interference achieves the suppression of biomarkers of epilepsy in mice and is scaled to humans.