bluuebunny/crossref_metadata_2025 huggingface dataset:
Severe acute respiratory syndrome coronavirus-2-associated cholangiopathies
Authors: Bartoli Alessandra , Cursaro Carmela , Andreone Pietro
Published: December 2021

Purpose of review

SARS-CoV2 is a β-coronavirus, isolated for the first time in Wuhan in December 2019. Bilateral interstitial pneumonia is the hallmark of this disease. Liver is the second viral target for frequency and AST and ALT elevation is a common finding. From February 2020, two different cholangiopathies have been reported in COVID-19 patients. The aim of this article is to review the cases so far described in order to share information and awareness about these new clinical entities.

Recent findings

SARS-CoV2 seems to trigger autoimmunity and two cases of primary biliary cholangitis (PBC) have been developed after viral infection while more than 30 patients have showed a rapidly progressing cholangiopathy with features of secondary sclerosing cholangitis (SSC). For what concerns SSC pathogenesis, a theory combining multiple hits is the most recognized.

Two different cholangiopathies have been reported in patients after severe-COVID-19. Attention should be paid to the development of cholestasis in ICU setting but above all after discharge and liver function tests should be, therefore, periodically performed. No treatment strategies are available and liver transplantation remains the last option in individuals with liver failure because of SSC. Other efforts are necessary to better understand the pathogenesis and to expand therapeutic options.
Dysregulated lipid metabolism in colorectal cancer
Authors: Coleman Olivia , Ecker Miriam , Haller Dirk
Published: December 2021

Purpose of review

Lipid metabolism presents a targetable metabolic vulnerability in colorectal cancer (CRC). Lipid signatures and cancer-cell lipid requirements may serve as noninvasive diagnostic and prognostic biomarkers and as a therapeutic target, respectively.

Recent findings

A growing body of new studies highlight the complexity of lipid metabolism in CRC. Cancer cells are able to utilize an alternative fatty acid desaturation pathway, underlining the metabolic plasticity of tumors. CRC tissue shows a robust triglyceride-species signature with prognostic value in CRC patients. Lipidomic analyses in germfree and colonized mice identify a unique lipid signature and suggest that bacteria inhibit metabolism of polyunsaturated fatty acids by blocking desaturase and elongase activities. Cellular stress responses, particularly the well characterized unfolded protein response, are involved in regulating lipid synthesis and homeostasis, and contribute to adaptation of the lipid environment. Together, lipid metabolism, the intestinal microbiota and cellular stress responses unarguably play crucial roles in CRC.

A number of recent advances in our understanding of dysregulated lipid metabolism in CRC underline the importance of this research field. An improved knowledge of the complex interplay between lipid metabolism, cellular stress and the intestinal microbiota in the context of CRC may lead to novel therapeutic strategies.
Macrophages in cholangiopathies
Authors: Bruneau Alix , Guillot Adrien , Tacke Frank
Published: December 2021

Purpose of review

Cholangiopathies are a heterogeneous class of liver diseases where cholangiocytes are the main targets of liver injury. Although available and emerging therapies mainly target bile acids (ursodeoxycholic acid/UDCA, 24-Norursodeoxycholic acid/norUDCA) and related signaling pathways (obeticholic acid, fibrates, FXR, and PPAR agonists), the mechanisms underlying inflammation, ductular reaction and fibrosis in cholestatic liver diseases remain poorly understood.

Recent findings

Data from patients with cholestatic diseases, such as primary biliary cholangitis (PBC) or primary sclerosing cholangitis (PSC) as well as mouse models of biliary injury emphasize the role of immune cells in the pathogenesis of cholestatic disorders and indicate diverse functions of hepatic macrophages. Their versatile polarization phenotypes and their capacity to interact with other cell types (e.g. cholangiocytes, other immune cells) make macrophages central actors in the progression of cholangiopathies.

In this review, we summarize recent findings on the response of hepatic macrophages to cholestasis and biliary injury and their involvement in the progression of cholangiopathies. Furthermore, we discuss how recent discoveries may foster the development of innovative therapies to treat patients suffering from cholestatic liver diseases, in particular, treatments targeting macrophages to limit hepatic inflammation.
Management of long-term cardiovascular risk factors post organ transplant
Authors: de la Fuente-Mancera Juan Carlos , Forado-Bentar Ilana , Farrero Marta
Published: December 2021

Purpose of review

Cardiovascular disease is one of the leading causes of death in solid organ transplant (SOT) recipients. Early identification of cardiovascular risk factors and their adequate management in this population is key for prevention and improved outcomes.

Recent findings

Approximately 80% of SOT present one or more cardiovascular risk factors, with increasing prevalence with time posttransplantation. They are due to the interplay of pretransplant conditions and metabolic consequences of immunosuppressive agents, mainly corticosteroids and calcineurin inhibitors. Among the pharmacological management strategies, statins have shown an important protective effect in SOT.

Strict surveillance of cardiovascular risk factors is recommended in SOT due to their high prevalence and prognostic implications. Further studies on the best managements strategies in this population are needed.
Spontaneous Multiple Arterial Dissection in a COVID-19–Positive Decedent
Authors: James Christine , Peterson Diane C.
Published: December 2021

Spontaneous multiple arterial dissection (SMAD) is a rarely reported phenomenon and has been previously linked to connective tissue diseases and specifically the genetic mutations in SMAD3 and COL3A1. Herein we describe a case of SMAD with scattered thrombi in a COVID-19–positive patient with a history of unspecified mitochondrial myopathy. Vasculopathy involved the splenic artery, inferior mesenteric artery, internal mammary arteries, omental arteries, mesenteric arteries, and small renal arteries. Dissections were confirmed by histology in the splenic artery, inferior mesenteric artery, and bilateral renal medullary arteries. Genetic studies were done to rule out SMAD3 and COL3A1 mutations. Because the Smad3 protein has been previously implicated in COVID-19–associated tissue fibrosis, it may play a role in endothelial dysfunction as well.
Cervical Epidural Abscess
Authors: McCarthy Sinead , Milne David , O'Connor Kate , Tse Rexson , Garland Jack
Published: December 2021

Spinal epidural abscess is an uncommon condition, which may have serious complications, including neurological sequelae and death. Classical symptoms include spinal pain, fever, and neurological deficit; however, diagnosis is difficult and requires a high degree of clinical suspicion. Antemortem magnetic resonance imaging (MRI) scanning is the gold-standard diagnostic tool. Computed tomography (CT) is less sensitive and as such, postmortem CT may miss the diagnosis. We report a case of Staphylococcus aureus cervical epidural abscess presenting as neck pain and causing flaccid paralysis and subsequently death. Antemortem MRI showed a small epidural collection, spinal cord edema, and fluid in the adjacent cervical disc and facet joints; however, these findings could not be appreciated on postmortem CT. Postmortem examination, guided by the antemortem imaging, was able to confirm a cervical spinal epidural abscess; however, similar deaths may occur before medical presentation. This case demonstrates a limitation of postmortem imaging in diagnosing spinal epidural abscess and highlights that such cases may be missed.
Intubation During Pediatric Cardiac Arrest in the Emergency Department Is Associated With Reduced First-Pass Success
Authors: Pacheco Garrett S. , Patanwala Asad E. , Leetch Aaron N. , Mendelson Jenny S. , Hurst Nicholas B. , Sakles John C.
Published: December 2021

Background

Airway compromise and respiratory failure are leading causes of pediatric cardiac arrest making advanced airway management central to pediatric resuscitation. Previous literature has demonstrated that achieving first-pass success (FPS) is associated with fewer adverse events. In cardiac arrest for adult patients, increasing number of intubation attempts is associated with lower likelihood of return of spontaneous circulation (ROSC) and favorable neurologic outcome. There is limited evidence regarding advanced airway management for pediatric out-of-hospital cardiac arrest (OHCA) in the emergency department (ED). The purpose of this study was to compare FPS in pediatric OHCA and non–cardiac arrest patients in the ED.

Methods

This is an analysis of pediatric intubations prospectively recorded into a continuous quality improvement database in an academic pediatric ED over a 12-year period. Between July 1, 2007, and June 30, 2019, physicians recorded all intubations performed in the pediatric ED. The database included patient demographics and detailed information about each intubation such as age of the patient, reason for intubation, number of intubation attempts, and outcome of each attempt. All patients younger than 18 years who underwent intubation in the ED were eligible for inclusion in the study. The primary outcome was FPS for pediatric patients in cardiac arrest compared with those not in cardiac arrest. A logistic regressions analysis was performed to identify characteristics associated with FPS in OHCA patients.

Results

Six hundred eight pediatric patients were intubated during the study period. One hundred three pediatric patients had OHCA compared with 459 non–cardiac arrest patients who underwent rapid sequence intubation. In patients with OHCA, 47.6% had FPS (95% confidence interval [CI], 38.2%–57.1%), 33% required 2 attempts (95% CI, 24.7%–42.6%), and 19.4% required 3 or more attempts (95% CI, 12.9%–28.2%). In patients without OHCA, 75.4% had FPS (95% CI, 75.4%–79.1%), 15% required 2 attempts (95% CI, 12.0%–18.6%), and 9.6% required 3 or more attempts (95% CI, 7.2%–12.6%). Cardiac arrest was associated with a reduction in FPS adjusted odds ratio 0.44 (95% CI, 0.26–0.77).

Conclusions

In this study, we found that pediatric OHCA is associated with reduced FPS in the ED. Although additional studies are needed, rescuers should prioritize restoring effective oxygenation and ventilation and optimizing intubation conditions before an advanced airway attempt.
Histopathological Changes In The Intestine Of Infected Pigeons (Columba Livia Domestica) Caused By Helminthes Infection From Al-Qassim, Saudi Arabia
Authors: Aldamigh Mashael A. , Hassan Amaal H. , Alahmadi Ahlam A.
Published: December 2021

Helminthes infection causes extensive harm to the pigeon host. The purpose of this study was to observe histopathological changes caused by helminths infection. Thirty-five pigeons (C.L. domestica) were purchased weekly from a bird’s market from Al-Qassim region, Saudi Arabia. Out of the 35 pigeons examined, 9 pigeons (25.71%) were found infected with helminth parasites, which were identified as one cestode (Raillietina sp.), and one nematode (Ascaridia columbae). The infected pigeons suffered from growth retardation, emaciation, weakness, droopiness, and diarrhea. A lot of histopathological changes were seen in the intestine of infected pigeons including atrophy and distortion of villi, infiltration of inflammatory lymphocytic cells, erosion, and loss of the typical structure of the intestine, necrosis in villi, and blood vessels congestion. This study concludes, for the first time in AL-Qassim region-Saudi Arabia, that the infection with helminth parasites caused significant histopathological changes in the intestines of the infected pigeons, and this could lead to increased mortality to the infected pigeons. Further work is necessary in Saudi Arabia to determine the prevalence and biological factors that have a significant impact on the helminth parasites community.
High-fidelity Cas13 variants for targeted RNA degradation with minimal collateral effect
Authors: Tong Huawei , Huang Jia , Xiao Qingquan , He Bingbing , Dong Xue , Liu Yuanhua , Yang Xiali , Han Dingyi , Wang Zikang , Ying Wenqin , Zhang Runze , Wei Yu , Wang Xuchen , Xu Chunlong , Zhou Yingsi , Li Yanfei , Cai Minqing , Wang Qifang , Xue Mingxing , Li Guoling , Fang Kailun , Zhang Hainan , Yang Hui
Published: December 2021

CRISPR-Cas13 systems have recently been employed for targeted RNA degradation in various organisms. However, collateral degradation of bystander RNAs has imposed a major barrier for their in vivo applications. We designed a dual-fluorescent reporter system for detecting collateral effects and screening Cas13 variants in mammalian cells. Among over 200 engineered variants, several Cas13 variants (including Cas13d and Cas13X) exhibit efficient on-target activity but markedly reduced collateral activity. Furthermore, transcriptome-wide off-targets and cell growth arrest induced by Cas13 are absent for these variants. Importantly, high-fidelity Cas13 variants show comparable RNA knockdown activity with wild-type Cas13 but no detectable collateral damage in transgenic mice and adeno-associated virus-mediated somatic cell targeting. Thus, high-fidelity Cas13 variants with minimal collateral effect are now available for targeted degradation of RNAs in basic research and therapeutic applications.
Pyrethroid insecticides susceptibility of Stomoxys calcitrans (Linnaeus) and Stomoxys indicus Picard (Diptera: Muscidae) from cattle farms in southern Thailand
Authors: Lorn Sokchan , Tainchum Krajana , Nusen Pitunart , Sumarnrote Anchana , Chareonviriyaphap Theeraphap
Published: December 2021

The susceptibility to six pyrethroid insecticides (permethrin, deltamethrin, alpha-cypermethrin, cypermethrin, lambda-cyhalothrin and bifenthrin), each at the recommended concentration, was evaluated for the two stable fly species Stomoxys calcitrans (Linnaeus) and Stomoxys indicus Picard, through tarsal contact using a World Health Organization (WHO) cone bioassay procedure. The field populations of stable flies were collected from three study sites (Songkhla, Phattalung and Satun provinces) in Thailand. The stable flies were exposed to insecticide-treated filter paper for 30 min and their knockdown counts at 30 min and 60 min and mortality counts at 12 hr and 24 hr were recorded. The S. calcitrans and S. indicus in Songkhla and Phattalung populations were moderately susceptible to pyrethroids for 24-hr mortality. Nonetheless, the Satun population of S. indicus was completely susceptible to permethrin with 100% mortality and the lowest susceptible to deltamethrin and bifenthrin. The results indicate a generally low susceptibility of stable flies to pyrethroids in the southern provinces of Thailand.
ePat: extended PROVEAN annotation tool
Authors: Ito Takumi , Yoshitake Kazutoshi , Iwata Takeshi
Published: December 2021

The ‘ePat’ (extended PROVEAN annotation tool) is a software tool that extends the functionality of PROVEAN: a software tool for predicting whether amino acid substitutions and indels will affect the biological function of proteins. The ‘ePat’ extends the conventional PROVEAN to enable the following two things, which the conventional PROVEAN could not calculate the pathogenicity of these variants. First is to calculate and score the pathogenicity of indel mutations with frameshift and variants near splice junctions. Second is to use batch processing to calculate the pathogenicity of multiple variants into a variants list (VCF file) in a single step. ePat can help extract variants that affect biological functions by utilizing not only point mutations, and indel mutations that does not cause frameshift, but also frameshift, stop gain, and splice variants. These extended features will increase detection rate and improve diagnostic of inherited diseases or associate specific variant to phenotype.
Long-term non-invasive drug treatments for adult zebrafish
Authors: Lu Yuting , Patton E. Elizabeth
Published: December 2021

Zebrafish embryos are widely used for drug-discovery however administering drugs to adult zebrafish is limited by current protocols that can cause stress. Here, we develop a drug formulation and administration method for adult zebrafish by producing food-based drug pellets which are consumed voluntarily. We apply this to zebrafish with BRAF-mutant melanoma, a model that has significantly advanced our understanding of melanoma progression, but not of drug resistance due to the limitations of current treatment methods. Short-term, precise, and daily dosing with drug-pellets made with the BRAFV600E inhibitor, vemurafenib, led to tumour regression. On-target drug efficacy was determined by phospho-ERK staining. Continued drug treatment led to the emergence, for the first time in zebrafish, of acquired drug resistance and melanoma relapse, modelling the responses seen in melanoma patients. This method presents a controlled, non-invasive approach that permits long-term drug studies, and can be widely applied to any adult zebrafish model.

SUMMARY STATEMENT

This drug-pellet approach is a precise dosing method to administer short or long-term drug treatments to adult zebrafish, that is stress-free for the fish and requires minimal animal handling. We use this method to develop new drug-resistant models of melanoma in zebrafish, opening new doors for modelling and screening drug treatments in adult zebrafish.
CSF1R inhibition by small molecule affects T-helper cell differentiation independently of microglia depletion
Authors: Lei Fengyang , Cui Naiwen , Zhou Chengxin , Chodosh James , Vavvas Demetrios G. , Paschalis Eleftherios I.
Published: December 2021

Colony-stimulating factor 1 receptor (CSF1R) inhibition has been proposed as a specific method for microglia depletion. However, recent work revealed that in addition to microglia, CSF1R inhibition also affects other innate immune cells, such as peripheral monocytes and tissueresident macrophages of the lung, liver, spleen, and peritoneum. Here, we show that this effect is not restricted to innate immune cells only, but extends to the adaptive immune compartment. CSF1R inhibition alters the transcriptional profile of bone marrow cells that control T helper cell activation. In vivo or ex vivo inhibition of CSF1R profoundly changes the transcriptional profile of CD4+ cells and suppresses Th1 and Th2 differentiation in directionally stimulated and unstimulated cells and independently of microglia depletion. Given that T cells also contribute in CNS pathology, these effects may have practical implications in the interpretation of relevant experimental data.

Significance statement

Here we show that CSF1R inhibition affects not only innate immune cells and microglia, but also the adaptive immune compartment by suppressing Th1/Th2 differentiation of CD4+ cells, independently of microglia depletion.
Genomic diversity and biosynthetic capabilities of sponge-associated chlamydiae
Authors: Dharamshi Jennah E. , Gaarslev Natalia , Steffen Karin , Martin Tom , Sipkema Detmer , Ettema Thijs J. G.
Published: December 2021

Sponge microbiomes contribute to host health, nutrition, and defense through the production of secondary metabolites. Chlamydiae, a phylum of obligate intracellular bacteria ranging from animal pathogens to endosymbionts of microbial eukaryotes, are frequently found associated with sponges. However, sponge-associated chlamydial diversity has not yet been investigated at the genomic level and host-interactions remain thus far unexplored. Here, we sequenced the microbiomes of three sponge species and found high, though variable, Chlamydiae relative abundances of up to 21.2% of bacterial diversity. Using genome-resolved metagenomics 18 high-quality sponge-associated chlamydial genomes were reconstructed, covering four chlamydial families. Among these, Sorochlamydiaceae shares a common ancestor with Chlamydiaceae animal pathogens, suggesting long-term co-evolution with animals. Sponge-associated chlamydiae genomes mostly resembled environmental chlamydial endosymbionts, but not pathogens, and encoded genes for degrading diverse compounds associated with sponges, such as taurine. Unexpectedly, we identified widespread genetic potential for secondary metabolite biosynthesis across Chlamydiae, which may represent an explored reservoir of novel natural products. This finding suggests that chlamydiae may partake in defensive symbioses and that secondary metabolites play a wider role in mediating intracellular interactions. Furthermore, sponge-associated chlamydiae relatives were found in other marine invertebrates, pointing towards wider impacts of this phylum on marine ecosystems.
Estimating cell-type-specific gene co-expression networks from bulk gene expression data with an application to Alzheimer’s disease
Authors: Su Chang , Zhang Jingfei , Zhao Hongyu
Published: December 2021

Inferring and characterizing gene co-expression networks has led to important insights on the molecular mechanisms of complex diseases. Most co-expression analyses to date have been performed on gene expression data collected from bulk tissues with different cell type compositions across samples. As a result, the co-expression estimates only offer an aggregate view of the underlying gene regulations and can be confounded by heterogeneity in cell type compositions, failing to reveal gene coordination that may be distinct across different cell types. In this paper, we describe a flexible framework for estimating cell-type-specific gene co-expression networks from bulk sample data, without making specific assumptions on the distributions of gene expression profiles in different cell types. We develop a novel sparse least squares estimator, referred to as CSNet, that is efficient to implement and has good theoretical properties. Using CSNet, we analyzed the bulk gene expression data from a cohort study on Alzheimer’s disease and identified previously unknown cell-type-specific co-expressions among Alzheimer’s disease risk genes, suggesting cell-type-specific disease pathology for Alzheimer’s disease.
Correlated STORM-homoFRET Imaging: Applications to the Study of Membrane Receptor Self-Association and Clustering
Authors: Driouchi Amine , Gray-Owen Scott D. , Yip Christopher M.
Published: December 2021

Mapping the self-organization and spatial distribution of membrane proteins is key to understanding their function. We report here on a correlated STORM/homoFRET imaging approach for resolving the nanoscale distribution and oligomeric state of membrane proteins. Live cell homoFRET imaging of CEACAM1, a cell-surface receptor known to exist in a complex equilibrium between monomer and dimer/oligomer states, revealed highly heterogenous diffraction-limited structures on the surface of HeLa cells. Correlated super-resolved STORM imaging revealed that these structures comprised a complex mixture and spatial distribution of self-associated CEACAM1 molecules. This correlated approach provides a compelling strategy for addressing challenging questions about the interplay between membrane protein concentration, distribution, interaction, clustering, and function.
From mass spectral features to molecules in molecular networks: a novel workflow for untargeted metabolomics
Authors: Olivier-Jimenez Damien , Bouchouireb Zakaria , Ollivier Simon , Mocquard Julia , Allard Pierre-Marie , Bernadat Guillaume , Chollet-Krugler Marylène , Rondeau David , Boustie Joël , van der Hooft Justin J.J. , Wolfender Jean-Luc
Published: December 2021

In the context of untargeted metabolomics, molecular networking is a popular and efficient tool which organizes and simplifies mass spectrometry fragmentation data (LC-MS/MS), by clustering ions based on a cosine similarity score. However, the nature of the ion species is rarely taken into account, causing redundancy as a single compound may be present in different forms throughout the network. Taking advantage of the presence of such redundant ions, we developed a new method named MolNotator. Using the different ion species produced by a molecule during ionization (adducts, dimers, trimers, in-source fragments), a predicted molecule node (or neutral node) is created by triangulation, and ultimately computing the associated molecule’s calculated mass. These neutral nodes provide researchers with several advantages. Firstly, each molecule is then represented in its ionization context, connected to all produced ions and indirectly to some coeluted compounds, thereby also highlighting unexpected widely present adduct species. Secondly, the predicted neutrals serve as anchors to merge the complementary positive and negative ionization modes into a single network. Lastly, the dereplication is improved by the use of all available ions connected to the neutral nodes, and the computed molecular masses can be used for exact mass dereplication. MolNotator is available as a Python library and was validated using the lichen database spectra acquired on an Orbitrap, computing neutral molecules for >90% of the 156 molecules in the dataset. By focusing on actual molecules instead of ions, MolNotator greatly facilitates the selection of molecules of interest.

Abstract Figure
Biofilm matrix proteome of clinical strain of P. aeruginosa
Authors: Egorova Daria A. , Solovyev Andrey I. , Polyakov Nikita B. , Danilova Ksenya V. , Scherbakova Anastasya A. , Kravtsov Ivan N. , Dmitrieva Maria A. , Rykova Valentina S. , Tutykhina Irina L. , Romanova Yulia M. , Gintsburg Alexander L.
Published: December 2021

Extracellular matrix plays a pivotal role in biofilm biology and proposed as a potential target for therapeutics development. As matrix is responsible for some extracellular functions and influence bacterial cytotoxicity against eukaryotic cells, it must have unique protein composition. P. aeruginosa is one of the most important pathogens with emerging antibiotic resistance, but only a few studies were devoted to matrix proteomes and there are no studies describing matrix proteome for any clinical isolates. Here we report the first biofilm matrix proteome of P. aeruginosa isolated from bronchoalveolar lavage of patient in intensive care unit. We have identified the largest number of proteins in the matrix among all published studies devoted to P. aeruginosa biofilms. Comparison of matrix proteome with proteome from embedded cells let us to identify several enriched bioprocess groups. Bioprocess groups with the largest number of overrepresented in matrix proteins were oxidation-reduction processes, proteolysis, and transmembrane transport. The top three represented in matrix bioprocesses concerning the size of the GO annotated database were cell redox homeostasis, nucleoside metabolism, and fatty acid synthesis. Finally, we discuss the obtained data in a prism of antibiofilm therapeutics development.
L-type calcium channel blocker increases VEGF concentrations in retinal cells and human serum
Authors: Kumar Anmol , Mutter Stefan , Parente Erika B. , Harjutsalo Valma , Lithovius Raija , Mathavan Sinnakaruppan , Forsblom Carol , Lehto Markku , Hiltunen Timo P. , Kontula Kimmo K. , Groop Per-Henrik
Published: December 2021

Objective

Vascular endothelial growth factor (VEGF) plays a key role in diabetic retinopathy (DR). L-type calcium channel blockers (LTCCBs) have been widely used as antihypertensive medication (AHM), but their association with VEGF and DR is still unclear. Therefore, we explored the effect of LTCCBs compared to other AHMs on VEGF concentrations in retinal cells and human serum. Furthermore, we evaluated the association between the use of LTCCBs and the risk of severe diabetic eye disease (SDED).

Research design and methods

Müller cells (MIO-M1) were cultured as per recommended protocol and treated with LTCCBs and other AHMs. VEGF secreted from cells were collected at 24 hours intervals. In an interventional study, 39 individuals received LTCCBs or other AHM for four weeks with a four-week wash-out placebo period between treatments. VEGF was measured during the medication and placebo periods. Finally, we evaluated the risk of SDED associated with LTCCB usage in 192 individuals from the FinnDiane Study in an oberservational setting.

Results

In the cell cultures, medium VEGF concentration increased time-dependently after amlodipine (p<0.01) treatment, but not after losartan (p>0.01), or lisinopril (p>0.01). Amlodipine, but no other AHM, increased serum VEGF concentration (p<0.05) during the interventional clinical study. The usage of LTCCB was not associated with the risk of SDED in the observational study.

Conclusions

LTCCB increases VEGF concentrations in retinal cells and human serum. However, the usage of LTCCBs does not appear to be associated with SDED in adults with type 1 diabetes.
Engineered High-Affinity ACE2 Peptide Mitigates ARDS and Death Induced by Multiple SARS-CoV-2 Variants
Authors: Zhang Lianghui , Dutta Soumajit , Xiong Shiqin , Chan Matthew , Chan Kui K. , Fan Timothy M. , Bailey Keith L. , Lindeblad Matthew , Cooper Laura M. , Rong Lijun , Gugliuzza Anthony F. , Shukla Diwakar , Procko Erik , Rehman Jalees , Malik Asrar B.
Published: December 2021

Vaccine hesitancy and continuing emergence of SARS-CoV-2 variants of concern that may escape vaccine-induced immune responses highlight the urgent need for effective COVID-19 therapeutics. Monoclonal antibodies used in the clinic have varying efficacies against distinct SARS-CoV-2 variants; thus, there is considerable interest in engineered ACE2 peptides with augmented binding affinities for SARS-CoV-2 Spike protein. These could have therapeutic benefit against multiple viral variants. Using molecular dynamics simulations, we show how three amino acid substitutions in an engineered soluble ACE2 peptide (sACE22.v2.4-IgG1) markedly increase affinity for the SARS-CoV-2 Spike (S) protein. We demonstrate high binding affinity to S protein of the early SARS-CoV-2 WA-1/2020 isolate and also to multiple variants of concern: B.1.1.7 (Alpha), B.1.351 (Beta), P.1 (Gamma), and B.1.617.2 (Delta) SARS-CoV-2 variants. In humanized K18-hACE2 mice, prophylactic and therapeutic administration of sACE22.v2.4-IgG1 peptide prevented acute lung vascular endothelial injury and lung edema (essential features of ARDS) and significantly improved survival after infection by SARS-CoV-2 WA-1/2020 as well as P.1 variant of concern. These studies demonstrate for the first time broad efficacy in vivo of an ACE2 decoy peptide against multiple SARS-CoV-2 variants and point to its therapeutic potential.
A DNA-based optical force sensor for live-cell applications
Authors: Jayachandran Christina , Ghosh Arindam , Prabhune Meenakshi , Bath Jonathan , Turberfield Andrew J. , Hauke Lara , Enderlein Jörg , Rehfeldt Florian , Schmidt Christoph F.
Published: December 2021

Mechanical forces are relevant for many biological processes, from wound healing or tumour formation to cell migration and differentiation. Cytoskeletal actin is largely responsible for responding to forces and transmitting them in cells, while also maintaining cell shape and integrity. Here, we describe a novel approach to employ a FRET-based DNA force sensor in vitro and in cellulo for non-invasive optical monitoring of intracellular mechanical forces. We use fluorescence lifetime imaging to determine the FRET efficiency of the sensor, which makes the measurement robust against intensity variations. We demonstrate the applicability of the sensor by monitoring cross-linking activity in in vitro actin networks by bulk rheology and confocal microscopy. We further demonstrate that the sensor readily attaches to stress fibers in living cells which opens up the possibility of live-cell force measurements.
Induction of flight via midbrain projections to the cuneiform nucleus
Authors: Tsang Emmy , Orlandini Camilla , Sureka Rahul , Crevenna Alvaro H. , Perlas Emerald , Prankerd Izzie , Masferrer Maria E. , Gross Cornelius T.
Published: December 2021

The dorsal periaqueductal gray is a midbrain structure implicated in the control of defensive behaviors and the processing of painful stimuli. Electrical stimulation or optogenetic activation of excitatory neurons in dorsal periaqueductal gray results in freezing or flight behavior at low or high intensity, respectively. However, the output structures that mediate these defensive behaviors remain unconfirmed. Here we carried out a targeted classification of neuron types in dorsal periaqueductal gray using multiplex in situ sequencing and then applied cell-type and projection-specific optogenetic stimulation to identify projections from dorsal periaqueductal grey to the cuneiform nucleus that promoted goal-directed flight behavior. These data confirmed that descending outputs from dorsal periaqueductal gray serve as a trigger for directed escape behavior.
PAR recognition by PARP1 regulates DNA-dependent activities and independently stimulates catalytic activity of PARP1
Authors: Deeksha Waghela , Abhishek Suman , Rajakumara Eerappa
Published: December 2021

Poly(ADP-ribosyl)ation is predominantly catalyzed by Poly(ADP-ribose) polymerase 1 (PARP1) in response to DNA damage, mediating the DNA repair process to maintain genomic integrity. Single strand (SSB) and double strand (DSB) DNA breaks are bonafide stimulators of PARP1 activity. However, PAR mediated PARP1 regulation remains unexplored. Here, we report ZnF3, BRCT and WGR, hitherto uncharacterized, as PAR reader domains of PARP1. Surprisingly, these domains recognize PARylated protein with a higher affinity compared to PAR but bind with weak or no affinity to DNA breaks as standalone domains. Conversely, ZnF1 and ZnF2 of PARP1 recognize DNA breaks but weakly to PAR. In addition, PAR reader domains, together, exhibit a synergy to recognize PAR or PARylated protein. Further competition binding studies suggest that PAR binding releases DNA from PARP1, and WGR domain facilitates the DNA release. Unexpectedly, PAR showed catalytic stimulation of PARP1 but hampers the DNA-dependent stimulation. Altogether, our work discovers dedicated high-affinity PAR reader domains of PARP1 and uncovers a novel mechanism of allosteric stimulation, but retardation of DNA-dependent activities of PARP1 by its catalytic product PAR. Therefore, our studies can be used as a model to understand the effect of one or more allosteric activators on the regulation of receptors or modular enzyme activities by another allosteric activator.
Targeting BRPF3 moderately reverses olaparib resistance in high grade serous ovarian carcinoma
Authors: Bitler Benjamin G. , Yamamoto Tomomi M. , McMellen Alexandra , Kim Hyunmin , Watson Zachary L.
Published: December 2021

Background

PARP inhibitors (PARPi) kill cancer cells by stalling DNA replication and preventing DNA repair, resulting in a critical accumulation of DNA damage. Resistance to PARPi is a growing clinical problem in the treatment of high grade serous ovarian carcinoma (HGSOC). Acetylation of histone H3 lysine 14 (H3K14ac) and associated histone acetyltransferases (HATs) and epigenetic readers have known functions in DNA repair and replication. Our objectives are to examine their expression and activities in the context of PARPi-resistant HGSOC, and to determine if targeting H3K14ac or associated proteins has therapeutic potential.

Results

Using mass spectrometry profiling of histone modifications, we observed increased H3K14ac enrichment in PARPi-resistant HGSOC cells relative to isogenic PARPi-sensitive lines. By RT-qPCR and RNA-Seq, we also observed altered expression of numerous HATs in PARPi-resistant HGSOC cells and a PARPi-resistant PDX model. Knockdown of HATs only modestly altered PARPi response, although knockdown and inhibition of PCAF significantly increased resistance. Pharmacologic inhibition of HBO1 severely depleted H3K14ac but did not affect PARPi response. However, knockdown and inhibition of BRPF3, which is known to interact in a complex with HBO1, did reduce PARPi resistance.

Conclusions

This study demonstrates that severe depletion of H3K14ac does not affect PARPi response in HGSOC. Our data suggest that bromodomain functions of HAT proteins, such as PCAF, or accessory proteins, such as BRPF3, may play a more direct role compared to direct histone acetyltransferase functions in PARPi response.
Young APPKINL-G-F/NL-G-Fmice display high-fat diet-induced metabolic disturbances and specific disorders associated with brain energy homeostasis
Authors: Wang Wei , Tanokashira Daisuke , Maruyama Megumi , Kuroiwa Chiemi , Saito Takashi , Saido Takaomi C. , Taguchi Akiko
Published: December 2021

Aim

Type 2 diabetes mellitus (T2DM) is an increased risk factor for Alzheimer’s disease (AD); however, the relationship between the two conditions is controversial. High-fat diet (HFD) causes cognitive impairment with/without Aβ accumulation in middle-aged or aged transgenic (Tg) and knock-in (KI) AD mouse models, except for metabolic disorders, which commonly occur in all mice types. Alternatively, whether HFD in early life impacts energy metabolism and neurological phenotypes in young AD mouse models remains unknown. In the present study, we examined the effects of HFD on young APPKINL-G-F/NL-G-Fmice, one of the novel knock-in (KI)-AD mouse models.

Methods

The mice were categorized by diet into two experimental groups, normal diet (ND) and HFD. Four-week-old WT and APPKINL-G-F/NL-G-Fmice were fed ND or HFD for nine weeks. Both types of mice on ND and HFD were examined during young adulthood.

Results

HFD causes T2DM-related metabolic disturbances in young WT and APPKINL-G-F/NL-G-Fmice and specific impairment of brain energy homeostasis only in young APPKINL-G-F/NL-G-Fmice. However, HFD-induced metabolic dysfunctions had no impact on behaviors, Aβ levels, and specific IRS1 modifications in both young APPKINL-G-F/NL-G-Fmice and young WT mice.

Conclusion

HFD in early life is effective in causing metabolic disturbances in young WT and APPKINL-G-F/NL-G-Fmice but is ineffective in inducing neurological disorders in young mice, which suggests that the aging effects along with long-term HFD cause neurological alterations.
Goal-directed motor actions drive acetylcholine dynamics in sensory cortex
Authors: Zou Jing , Willem de Gee Jan , Mridha Zakir , Trinh Simon , Erskine Andrew , Jing Miao , Yao Jennifer , Walker Stefanie , Li Yulong , McGinley Matthew , Hires Samuel Andrew
Published: December 2021

Numerous cognitive functions including attention and learning are influenced by the dynamic patterns of acetylcholine release across the brain. How acetylcholine mediates these functions in cortex remains unclear, as the relationship between cortical acetylcholine and behavioral events has not been precisely measured across task learning. To dissect this relationship, we quantified motor behavior and sub-second acetylcholine dynamics in primary somatosensory and auditory cortex during rewarded sensory detection and discrimination tasks. We found that acetylcholine dynamics were directly attributable to goal-directed actions (whisker motion and licking), rather than delivery of sensory cues or rewards. As task performance improved across training, acetylcholine release associated with the first lick in a trial was strongly and specifically potentiated. These results show that acetylcholine dynamics in sensory cortex are driven by directed motor actions to gather information and act upon it.
Meta analysis of variant predictions in congenital adrenal hyperplasia caused by mutations in CYP21A2
Authors: Prado Mayara J. , Ligabue-Braun Rodrigo , Zaha Arnaldo , Rosa Rossetti Maria Lucia , Pandey Amit V.
Published: December 2021

Context

CYP21A2 deficiency represents 95% of congenital adrenal hyperplasia cases (CAH), a group of genetic disorders that affect steroid biosynthesis. The genetic and functional analysis provides critical tools to elucidate complex CAH cases. One of the most accessible tools to infer the pathogenicity of new variants is in silico prediction.

Objective

Analyze the performance of in silico prediction tools to categorize missense single nucleotide variants (SNVs) of the CYP21A2.

Methods

SNVs of the CYP21A2 characterized in vitro by functional assays were selected to assess the performance of online single and meta predictors. SNVs were tested separately or in combination with the related phenotype (severe or mild CAH form). In total, 103 SNVs of the CYP21A2 (90 pathogenic and 13 neutral) were used to test the performance of 13 single-predictors and four meta-predictors.

Results

SNVs associated with the severe phenotypes were well categorized by all tools, with an accuracy between 0.69 (PredictSNP2) and 0.97 (CADD), and Matthews’ correlation coefficient (MCC) between 0.49 (PoredicSNP2) and 0.90 (CADD). However, SNVs related to the mild phenotype had more variation, with the accuracy between 0.47 (S3Ds&GO and MAPP) and 0.88 (CADD), and MCC between 0.18 (MAPP) and 0.71 (CADD).

Conclusion

From our analysis, we identified four predictors of CYP21A2 pathogenicity with good performance. These results can be used for future analysis to infer the impact of uncharacterized SNVs’ in CYP21A2.
Deep Learning-powered Bessel-beam Multi-parametric Photoacoustic Microscopy
Authors: Zhou Yifeng , Sun Naidi , Hu Song
Published: December 2021

Enabling simultaneous and high-resolution quantification of the total concentration of hemoglobin (CHb), oxygen saturation of hemoglobin (sO2), and cerebral blood flow (CBF), multi-parametric photoacoustic microscopy (PAM) has emerged as a promising tool for functional and metabolic imaging of the live mouse brain. However, due to the limited depth of focus imposed by the Gaussian-beam excitation, the quantitative measurements become inaccurate when the imaging object is out of focus. To address this problem, we have developed a hardware-software combined approach by integrating Bessel-beam excitation and conditional generative adversarial network (cGAN)-based deep learning. Side-by-side comparison of the new cGAN-powered Bessel-beam multi-parametric PAM against the conventional Gaussian-beam multi-parametric PAM shows that the new system enables high-resolution, quantitative imaging of CHb, sO2, and CBF over a depth range of ∼600 μm in the live mouse brain, with errors 13–58 times lower than those of the conventional system. Better fulfilling the rigid requirement of light focusing for accurate hemodynamic measurements, the deep learning-powered Bessel-beam multi-parametric PAM may find applications in large-field functional recording across the uneven brain surface and beyond (e.g., tumor imaging).
How synaptic strength, short-term plasticity, and input synchrony contribute to neuronal spike output
Authors: Guilabert Alexandra Gastone , Buchholz Moritz O. , Ehret Benjamin , Schuhknecht Gregor F.P.
Published: December 2021

Neurons integrate from thousands of synapses whose strengths span an order of magnitude. Intriguingly, in mouse neocortex, the few ‘strong’ synapses are formed between similarly tuned cells, suggesting they determine neuronal spiking output. This raises the question of how other computational primitives, including ‘background’ activity from the many ‘weak’ synapses, short-term plasticity, and temporal factors contribute to spiking. We combined extracellular stimulation and whole-cell recordings in mouse barrel cortex to map excitatory postsynaptic potential (EPSP) amplitudes and paired-pulse ratios of excitatory synaptic connections converging onto individual layer 2/3 (L2/3) neurons. While net short-term plasticity was weak, connections with EPSPs > 2 mV were exclusively depressing. There was no evidence for clustering of synaptic properties on individual neurons. Instead, EPSPs and paired-pulse ratios of connections converging onto the same cells spanned the full range observed across L2/3, which critically constrains theoretical models of cortical filtering. To investigate how different computational primitives of synaptic information processing interact to shape spiking, we developed a computational model of a pyramidal neuron in the rodent L2/3 circuitry, which was constrained by our own experiments and published in vivo data. We found that the ability of strong inputs to evoke spiking depended on their high temporal synchrony and high firing rates observed in vivo and on synaptic background activity – and not primarily on synaptic strength, which further amplified information transfer. Our results provide a framework of how cortical neurons exploit complex synergies between temporal coding, synaptic properties, and noise to transform synaptic inputs into output firing.
Using synthetic activity to design ultra-potent antibody cocktails
Authors: Zhao Hui , Dodds Michael , Tasch Michael , Gewe Mesfin , Martinez Anissa , Hutton Melanie , Keeney Kristie , Pollock Alex , Jester Benjamin W. , Khuong Nhi , Zhang Mia , Ertel Stacey , Brady Colin , Heinnickel Mark , Tabakh Hannah , Sanjaya Nathan , Cruickshank Kendra , Paddock Troy , Struyvenberg Sarah , Dang Jason , Saveria Tracy , Shanitta Chelsea , Fletcher David , Sigmar Kristjan , Goetsch Lauren , Gamble Caitlin , Mileto Steven J. , Heselpoth Ryan , Lyras Dena , Behnke Craig A. , Fischetti Vincent , Finrow Brian , Roberts James M.
Published: December 2021

Drugs which independently inhibit a shared target or pathway can have synthetic activities that result in multiplicative instead of merely additive potencies. This characteristic of drug combinations can be quantified by expressing the potency of the combination as if it were a single agent. We show that by optimizing this quantity we can prospectively design drug cocktails with apparent potencies that far exceed any of its individual components. We illustrate the power of this approach, which is based on statistical design of experiments to select optimal drug combinations, and response surface methodology to determine optimal drug ratios, by building a drug cocktail comprised of three antibodies for treating C. difficile infection that is almost 1000-fold more potent than the current, clinically approved antibody monotherapy. High synthetic activities do not require unusual drug interactions, and therefore may be achievable much more readily than generally appreciated.

One-Sentence Summary

A development pathway is described for designing antibody cocktails with potencies that far exceed what is achievable with single antibodies
Stabilized COre gene and Pathway Election uncovers pan-cancer shared pathways and a cancer specific driver
Authors: Kossinna Pathum , Cai Weijia , Lu Xuewen , Shemanko Carrie S , Zhang Qingrun
Published: December 2021

Approaches systematically characterizing interactions via transcriptomic data usually follow two systems: (1) co-expression network analyses focusing on correlations between genes; (2) linear regressions (usually regularized) to select multiple genes jointly. Both suffer from the problem of stability: a slight change of parameterization or dataset could lead to dramatic alternations of outcomes. Here, we proposeStabilizedCore gene andPathwayElection, orSCOPE, a tool integrating bootstrapped LASSO and co-expression analysis, leading to robust outcomes insensitive to variations in data. By applying SCOPE to six cancer expression datasets (BRCA, COAD, KIRC, LUAD, PRAD and THCA) in The Cancer Genome Atlas, we identified core genes capturing interaction effects in crucial pan-cancer pathways related to genome instability and DNA damage response. Moreover, we highlighted the pivotal role of CD63 as an oncogenic driver and a potential therapeutic target in kidney cancer. SCOPE enables stabilized investigations towards complex interactions using transcriptome data.

Availability

https://github.com/QingrunZhangLab/SCOPE