bluuebunny/crossref_metadata_2025 huggingface dataset:
New trends in congenital syphilis: epidemiology, testing in pregnancy, and management
Authors: Thean Lijun , Moore Aoife , Nourse Clare
Published: September 2022

Purpose of review

In light of alarming increases in the incidence of congenital syphilis in many middle and higher income countries across the globe, this review summarizes recent changes in the epidemiology of syphilis, highlights recommended changes to testing in pregnancy and provides an update for the management of syphilis infection in pregnancy (SIP) and of the infant born to a mother with SIP.

Recent findings

The re-emergence of congenital syphilis is a result of increasing infectious syphilis in women of childbearing age, which is in turn a result of increasing syphilis in the general population particularly in Indigenous and marginalized populations. Potential reasons for the increase include changing sexual practices and increased travel and migration, as well as factors that limit healthcare access, particularly access to antenatal care and limited awareness and education amongst mothers and maternity services. A single antenatal test for syphilis is insufficient; more frequent testing in pregnancy is necessary even for women deemed to be low risk. The management of SIP and of the newborn is complex and guidelines should be readily available with clear recommendations.

Congenital syphilis is preventable. The current crisis calls for a global and national multipronged, co-ordinated approach involving public health and hospital systems which includes education of individuals and healthcare workers, availability of updated guidelines for prevention and treatment, prioritization of antenatal testing, assurance of accessible and prompt treatment and appropriate assessment and follow-up of infants.
Posterior Reversible Encephalopathy Syndrome Occurred During the Use of Pseudoephedrine: A Case Report
Authors: Gunduz Zahide Betul
Published: September 2022

Introduction

Posterior reversible encephalopathy syndrome (PRES) is a syndrome that is manifested by a variety of clinical findings, like headache, seizure, loss of vision and change in consciousness, and characterized by bilateral vasogenic edema, which is usually located in the posterior part of the hemispheres, but sometimes located in atypical localization.

Case Presentation

A 56-year-old man with no known systemic disease with generalized tonic clonic seizure was evaluated. He had oral paracetamol + pseudoephedrine HCl for runny nose, sore throat, and headache. After the second dosage, he had a seizure during sleeping. In flair sequence of magnetic resonance imaging, bilateral cortical and subcortical hyperintensities were observed in the posterior parts of the hemispheres and the cerebellar hemispheres, which demonstrated PRES.

Conclusion

We presented a PRES case with seizures after using 2 doses of pseudoephedrine. In addition to hypertension, several factors have been blamed, such as eclampsia-preeclampsia, some immunosuppressive and chemotherapeutic drugs, some kidney diseases. Although the patient had no known risk factors for PRES, he was diagnosed with hypertension and diabetes mellitus during follow-up.
Pten regulates endocytic trafficking of cell adhesion and signaling molecules to pattern the retina
Authors: Touahri Yacine , Hanna Joseph , Tachibana Nobuhiko , David Luke Ajay , Olender Thomas , Okawa Satoshi , Chinchalongporn Vorapin , Balakrishnan Anjali , Cantrup Robert , Dixit Rajiv , Mattar Pierre , Saleh Fermisk , Ilnytskyy Yaroslav , Murshed Monzur , Mains Paul E. , Kovalchuk Igor , Lefebvre Julie L , Cayouette Michel , del Sol Antonio , Brand Marjorie , Reese Benjamin E , Schuurmans Carol
Published: September 2022

The retina is an exquisitely patterned tissue, with neuronal somata positioned at regular intervals to completely sample the visual field. Cholinergic amacrine cells are spectacular exemplars of precision, distributing in two radial layers and tangentially, forming regular mosaics. Here, we investigated how the intracellular phosphatase Pten and the cell adhesion molecule Dscam cooperate to regulate amacrine cell patterning. Using double mutants to test epistasis, we found that Pten and Dscam function in parallel pathways to regulate amacrine cell positioning. Mechanistically, Pten regulates endocytic remodeling of cell adhesion molecules (Dscam, Megf10, Fat3), which are aberrantly redistributed in Pten conditional-knock-out (cKO) amacrine cells. Furthermore, extracellular vesicles derived from multivesicular endosomes have altered proteomes in PtencKO retinas. Consequently, Wnt signaling is elevated in PtencKO retinal amacrine cells, the pharmacological disruption of which phenocopies PtencKO patterning defects. Pten thus controls endocytic trafficking of critical cell adhesion/signaling molecules to control amacrine cell spacing.

HIGHLIGHTS

Pten and Dscam act in parallel pathways to regulate amacrine cell spacing

Endocytic remodeling of cell adhesion molecules is perturbed in PtencKO retinas

Extracellular vesicle content is altered in PtencKO retinas

Perturbation of Wnt signaling phenocopies defects in amacrine cell positioning

eTOC BLURB

Patterns in nature range from stereotyped distributions of colored patches on butterfly wings to precise neuronal spacing in the nervous system. Waddington proposed that built-in constraints canalize developmental patterns. Touahri et al. identified Pten-mediated endocytic trafficking of cell adhesion/signaling molecules as a novel constraint measure controlling retinal amacrine cell patterning.
The Entorhinal-DG/CA3 Pathway in the Medial Temporal Lobe Retains Visual Working Memory of a Simple Surface Feature
Authors: Xie Weizhen , Cappiello Marcus , Yassa Michael A. , Ester Edward , Zaghloul Kareem , Zhang Weiwei
Published: September 2022

Classic models consider working memory (WM) and long-term memory as distinct mental faculties that are supported by different neural mechanisms. Yet, there are significant parallels in the computation that both types of memory require. For instance, the representation of precise item-specific memory requires the separation of overlapping neural representations of similar information. This computation has been referred to as pattern separation, which can be mediated by the entorhinal-DG/CA3 pathway of the medial temporal lobe (MTL) in service of long-term episodic memory. However, although recent evidence has suggested that the MTL is involved in WM, the extent to which the entorhinal-DG/CA3 pathway supports precise item-specific WM has remained elusive. Here, we combine an established orientation WM task with high-resolution fMRI to test the hypothesis that the entorhinal-DG/CA3 pathway retains visual WM of a simple surface feature. Participants were retrospectively cued to retain one of the two studied orientation gratings during a brief delay period and then tried to reproduce the cued orientation as precisely as possible. By modeling the delay-period activity to reconstruct the retained WM content, we found that the anterior-lateral entorhinal cortex (aLEC) and the hippocampal DG/CA3 subfield both contain item-specific WM information that is associated with subsequent recall fidelity. Together, these results highlight the contribution of MTL circuitry to item-specific WM representation.
Female Friendships: Social Network Analysis as a tool to understand intra-group affiliation in semi-commensal lion-tailed macaques
Authors: Dhawale Ashni Kumar , Sinha Anindya
Published: September 2022

The lion-tailed macaque is a gregarious, rainforest-adapted species, that has, in certain locations across its natural distribution, recently begun to explore and utilise surrounding human-dominated habitats. In many primate species, exposure to novel human-use food resources and potential provisioning has previously been associated with changes in intra-group social structure, often categorised by increased aggression and, more importantly, increased affiliation, possibly as a means of reconciliation. Here we quantify the changing affiliative relationships among the female members of two groups with varying degrees of habituation, using social network analysis. We examine frequencies of pair-wise affiliation between the female members of each group, ranked within the prevailing linear hierarchy, to measure individual attributes or the local importance of individuals in a network, and group attributes or the global role of all individuals in the whole network. We found that the subordinate individuals in the less habituated group maintained a higher number of connections with group members, an expected outcome, as key affiliative behaviours such as grooming are known to be directed upwards in the hierarchy. This pattern was observed to be inverse in the highly habituated group, with dominant individuals maintaining more connections, suggesting that under the conditions of increased competition for the novel food resource, dominance rank was highly contested. In support of this theory, we also found multiple fluctuations in dominance rank over time for this highly habituated group, with nearly no fluctuations in the less habituated group. This study demonstrates that varied intensities of human presence and dependence on human-use foods have differential effects on the intra-group sociality of lion-tailed macaques.
Efficacy and safety of glycosphingolipid SSEA-4 targeting CAR-T cells in an ovarian carcinoma model
Authors: Monzo HJ , Hyytiäinen M , Elbasani E , Kalander K , Wall J , Moyano-Galceran L , Tanjore-Ramanathan J , Jukonen J , Laakkonen P , Ristimäki A , Carlson JW , Lehti K , Salehi S , Puolakkainen P , Haglund C , Seppänen H , Leppä S , Ojala PM
Published: September 2022

Chimeric antigen receptor (CAR) T-cell immunotherapies for solid tumors face critical challenges such as heterogeneous antigen expression. We characterized SSEA-4 cell-surface glycolipid as a target for CAR-T cell therapy. SSEA-4 is mainly expressed during embryogenesis but is also found in several cancer types making it an attractive tumor-associated antigen. Anti-SSEA-4 CAR-T cells were generated and assessed pre-clinicallyin vitroandin vivofor anti-tumor response and safety. SSEA-4 CAR-T cells effectively eliminated SSEA-4 positive cells in all tested cancer cell lines whereas SSEA-4 negative cells lines were not targeted.In vivoefficacy and safety studies using NSG mice and the high-grade serous ovarian cancer cell line OVCAR4 demonstrated a remarkable and specific anti-tumor response at all CAR-T cell doses used. At high T cell doses, CAR-T cell-treated mice showed signs of health deterioration after a follow-up period. However, severity of toxicity was reduced with delayed onset when lower CAR-T cell doses were used. Our data demonstrate the efficacy of anti-SSEA-4 CAR-T therapy; however, safety strategies, such as dose-limiting and/or equipping CAR-T cells with combinatorial antigen recognition should be implemented for its potential clinical translation.
CRISPR-Analytics (CRISPR-A): a platform for precise analytics and simulations for gene editing
Authors: Sanvicente-García Marta , García-Valiente Albert , Jouide Socayna , Jabara-Wallace Jessica , Bautista Èric , Escobosa Marc , Sánchez-Mejías Avencia , Güell Marc
Published: September 2022

Gene editing characterization with currently available tools does not always give precise relative proportions among the different types of gene edits present in an edited bulk of cells. We have developed CRISPR-Analytics, CRISPR-A, which is a comprehensive and versatile genome editing web application tool and a nextflow pipeline to give support to gene editing experimental design and analysis. CRISPR-A provides a robust gene editing analysis pipeline composed of data analysis tools and simulation. It achieves higher accuracy than current tools and expands the functionality. The analysis includes mock-based noise correction, spike-in calibrated amplification bias reduction, and advanced interactive graphics. This expanded robustness makes this tool ideal for analyzing highly sensitive cases such as clinical samples or experiments with low editing efficiencies. It also provides an assessment of experimental design through the simulation of gene editing results. Therefore, CRISPR-A is ideal to support multiple kinds of experiments such as double-stranded DNA break-based engineering, base editing (BE), primer editing (PE), and homology-directed repair (HDR), without the need of specifying the used experimental approach.
Impact of sensitive circulating tumor DNA monitoring on CT scan intervals during postoperative colorectal cancer surveillance
Authors: Sasaki Tomoko , Iwaya Takeshi , Yaegashi Mizunori , Idogawa Masashi , Hiraki Hayato , Abe Masakazu , Koizumi Yuka , Sasaki Noriyuki , Yashima-Abo Akiko , Fujisawa Ryosuke , Endo Fumitaka , Tange Shoichiro , Hirano Tomomi , Otsuka Koki , Sasaki Akira , Masuda Mari , Fujita Masashi , Nakagawa Hidewaki , Takahashi Fumiaki , Sasaki Yasushi , Tokino Takashi , Nishizuka Satoshi S.
Published: September 2022

Objective

This study investigated whether digital PCR (dPCR)-based circulating tumor DNA (ctDNA) monitoringcan allow longer intervals between computed tomography (CT) scans during postoperative surveillance of colorectal cancer (CRC).

Design

The longitudinal dynamics of ctDNA for 52 patients with CRC as measured by dPCR using probes targeting 87 individual tumor-specific mutations (1-5 per patient) were compared with results from conventional (i.e., clinical) surveillance using serum tumor markers and CT. A total of 382 CT procedures were carried out for the patient cohort (3.3/year per patient) and the median lead time from ctDNA relapse to clinical relapse was 182 days (range 0-376 days). If the CT interval was annual, potential delays in detection of clinical relapse would have occurred for 7 of the 10 patients who experienced clinical relapse (9 of 13 events), with a median delay of 164 days (range, 0-267 days). If annual CT surveillance was performed together with ctDNA monitoring, 218 (57.1%) CTs would not have been needed to detect the first clinical relapse. Nonetheless, ctDNA monitoring would still have provided a lead time of 339 days for detection of clinical relapse (range, 42-533 days).

Conclusion

Our findings suggest that the ctDNA monitoring as part of post-operative surveillance and clinical relapse detection for patients with CRC could allow the CT interval to be lengthened.
Statistical learning of large-scale genetic data: How to run a genome-wide association study of gene-expression data using the 1000 Genomes Project data
Authors: Sugolov Anton , Emmenegger Eric , Paterson Andrew D. , Sun Lei
Published: September 2022

Teaching statistics through engaging applications to contemporary large-scale datasets is essential to attracting students to the field. To this end, we developed a hands-on, week-long workshop for senior high-school or junior undergraduate students, without prior knowledge in statistical genetics but with some basic knowledge in data science, to conduct their own genome-wide association studies (GWAS). The GWAS was performed for open source gene expression data, using publicly-available human genetics data. Assisted by a detailed instruction manual, students were able to obtain ∼1.4 million p-values from a real scientific study, within several days. This early motivation kept students engaged in learning the theories that support their results, including regression, data visualization, results interpretation, and large-scale multiple hypothesis testing. To further their learning motivation by emphasizing the personal connection to this type of data analysis, students were encouraged to make short presentations about how GWAS has provided insights into the genetic basis of diseases that are present in their friends and/or families. The appended open source, step-by-step instruction manual includes descriptions of the datasets used, the software needed, and results from the workshop. Additionally, scripts used in the workshop are archived on Zenodo to further enhance reproducible research and training.
Survival rate of dental implants installed by residents attending an implantology Program in Brazil: a 52-month retrospective analysis
Authors: Kang Myungjin , Neto Henrique Smanio , Pelegrine André Antonio , Turssi Cecilia Pedroso , Clemente-Napimoga Juliana Trindade , Napimoga Marcelo Henrique
Published: September 2022

The aim of this study was to identify any associations between predictor variables, mainly risk factors and dental implant outcome. Dental records were reviewed from January 1, 2018, to December 31, 2020. The inclusion criteria was all implant surgery made using Intraoss brand. Data collected from the patients’ medical charts included: implant loss, gender, diabetes, smoking, continuous use of medication, type of implant connection system, implant position (maxilla or mandible), previous bone grafting and type of prosthetic provisioning (temporary prosthesis, immediate prosthesis or permanent prosthesis). It was evaluated the cumulative survival rate of 1,164 dental implants made by residents attending an implantology residency in a university setting. One thousand forty-eight dental implants were placed on 471 patients seen by residents. The cumulative survival rate was 2.5%. Furthemore, the association of implant losses to the variables tested using the chi-square and G tests showed no statistically significant association. Based on Kaplan-Meier curve analysis, with a 95% confidence interval up to 52 months of implant placement, it revealed that the overall survival rate was 90.5%. Therefore, this study showed high survival rates of implants installed by residents of implantology at Faculdade São Leopoldo Mandic using Intraoss implants. The implant failure was not correlated with any of the variables tested.
An Unexpected Single-step Glycosylation Enables the Construction of Antibody-Biomacromolecule Conjugates as Therapeutics
Authors: Yang Yang , Song Zhentao , Tian Tian , Zhao Zihan , Chen Ji , Hu Jiangping , Jiang Xin , Yang Guoli , Xue Qi , Zhao Xinlu , Sha Wanxing , Yang Yi , Li Jie P.
Published: September 2022

Glycoengineering has been demonstrated to be a powerful tool to construct site-specific antibody conjugates. However, with most glycoengineering strategies, several hours to days are needed to complete the reaction, and the payloads are limited to small molecules. Herein, we show that reducing the complexity of Fc glycan could dramatically boost the enzymatic glycoengineering of IgG molecules to achieve unexpectedly high efficiency and payload capacity. Notably, antibodies with the modified Fc glycan were successfully conjugated with biomacromolecules, e.g., oligonucleotides and nanobodies, in one step by an engineered fucosyltransferase. Moreover, the conversion of this chemoenzymatic engineering could be finished in minutes, or up to hours, affording homogeneous products. The trisaccharide linker of these antibody conjugates exhibits excellent hydrophilicity and stability and reduced ADCC activity. Using this platform, we successfully synthesized an antibody-conjugate-based HER2/CD3 bispecific antibody and applied it to selectively destroy patient-derived cancer organoids by reactivating endogenous T cells inside the organoid. These results suggest that this bispecific antibody format has a high translational value.
Savanna chimpanzees (Pan troglodytes verus) in Senegal react to deadly snakes and other reptiles: Testing the snake detection hypothesis
Authors: Pruetz Jill D. , LaDuke Thomas C. , Dobson K.
Published: September 2022

The hypothesis that dangerous snakes served as evolutionary selective pressures on traits characterizing the Order Primates (Snake Detection Hypothesis, SDH), specifically vision and aspects of the brain, has received recent attention. We provide data on 52 encounters between chimpanzees (Pan troglodytes verus) in a savanna landscape and snakes and other large reptiles at the Fongoli site in Senegal, over the course of eight years. These encounters yielded data on 178 interactions between identified individual chimpanzees and reptiles. The majority of encounters with identified reptiles (62%) involved potentially deadly snakes. Constrictors of the family Pythonidae were encountered more frequently than any other reptile. Chimpanzees exhibited a variety of reactions to reptiles, ranging from attacking with objects to ignoring them. Even reptiles other than snakes were met with some degree of alarm when they were in water or moving quickly. We assessed variables that may affect apes’ reactions, as well as the age-sex class of chimpanzees. As a test of Isbell’s snake detection hypothesis, we examined chimpanzees’ reaction intensity to venomous versus constricting snakes but found no difference. We did find significant age-sex differences in chimpanzees’ reactions to snakes, with adolescent males exhibiting higher-intensity reactions than adult males and females and adolescent female chimpanzees. Chimpanzees reacted at significantly higher intensities when snakes were arboreal in location, but reptile species, size, and activity did not significantly influence individuals’ reactions to snakes. We also report one inferred encounter between an adult female chimpanzee and a venomous snake, which led to her death. Our data suggest that snakes are significant threats to chimpanzees in savanna environments and support the hypothesis that danger from snakes could have exerted significant evolutionary pressure on the Order Primates.
Sea lamprey nests promote the diversity of benthic macroinvertebrate assemblages
Authors: Dhamelincourt Marius , Rives Jacques , Pons Marie , Larrañaga Aitor , Tentelier Cédric , Elosegi Arturo
Published: September 2022

The habitat heterogeneity hypothesis states that increased habitat heterogeneity promotes species diversity through increased availability of ecological niches. We aimed at describing the local-scale effects of nests of the sea lamprey (Petromyzon marinus L.) as ecosystem engineer on macroinvertebrate assemblages. We hypothesized that increased streambed physical heterogeneity caused by sea lamprey spawning would modify invertebrate assemblages and specific biologic traits and promote reach-scale diversity. We sampled thirty lamprey nests of the Nive River in three zones: the unmodified riverbed (control) and zones corresponding to the nest: the area excavated (pit) and the downstream accumulation of pebbles and cobbles (mound). The increased habitat heterogeneity created by lamprey was traduced by biological heterogeneity with a reduced density of invertebrates (1160 to 6540 individuals per m2 in control, 680 to 6460 individuals per m2 in pit and 1980 to 6240 individuals per m2 in mound) and number of taxa (23.5 ± 3.9 taxa for control, 18.6 ± 3.9 taxa in pit and 21.2 ± 4.5 taxa for mound) in the pit compared to other zones. However the overall taxa diversity in nest increased with 82 ± 14 taxa compared to the 69 ± 8 taxa estimated in control zone. Diversity indices were consistent with the previous results indicating a loss of α diversity in pit but a higher β diversity between a pit and a mound than between two control zones, especially considering Morisita index accounting for taxa abundance. Trait analysis showed high functional diversity within zones with a reduced proportion of collectors, scrapers, shredders, litter/mud preference and small invertebrates in mound, while the proportion of “slabs, blocks, stones and pebbles” preference and largest invertebrates increased. Pit presented the opposite trend, while control had globally intermediate trait proportions. Our results highlight important effects on species and functional diversity due to habitat heterogeneity created by a nest-building species, what can ultimately influence food webs and nutrient processes in river ecosystems.
Advanced Care Planning (ACP) in the early phase of COVID-19: A rapid review of the practice and policy lessons learned
Authors: Younan Sarah , Cardona Magnolia , Sahay Ashlyn , Willis Eileen , Chroinin Danielle Ni
Published: September 2022

This rapid review of quantitative and qualitative publications of any design indexed in PUBMED between January 2020-April 2021 investigates barriers and enablers of advancecare planning (ACP) worldwide in the early stages of the life-threatening COVID-19 pandemic. Seventy-four papers were included: 35 primary research studies (cohorts, reviews, case studies, and cross-sectional designs) and 39 commentaries. Publications from hospitals, outpatient services, aged care and community indicated widespread interest in accelerating ACP documentation to facilitate management decisions and goal-aligned care. Enablers of ACP included targeted public awareness, availability of telehealth, access to online tools and a person-centered approaches. Barriers included uncertainty regarding clinical outcomes, cultural or communication difficulties, legal and ethical considerations, infection control restrictions, lack of time, and limited resources and support systems. The opportunities for rapid implementation of ACP offered by the social distancing restrictions and high demand for health services are valuable in informing future policy and practice.

What this paper adds

Our study adds to existing evidence by identifying emerging barriers and creative ways of overcoming them in response to a global crisis

Discussions on death prospects and care of the dying were feasible and a step towards normalisation of advance care planning

Despite new and overwhelming challenges, policies and practices could be rapidly implemented to satisfy clinicians and families in need of advance care planning

Applications of study findings

The lessons learnt can be incorporated in future health service planning since the threat of other pandemics is real

A formal evaluation of effectiveness of some of the emerging strategies would be a valuable addition to the evidence
AHoJ: rapid, tailored search and retrieval of apo and holo protein structures for user-defined ligands
Authors: Feidakis Christos P. , Krivak Radoslav , Hoksza David , Novotny Marian
Published: September 2022

Understanding the mechanism of action of a protein or designing better ligands for it often requires access to a bound (holo) and an unbound (apo) state of the protein. Resources for the quick and easy retrieval of such conformations are severely limited.

Apo-Holo Juxtaposition (AHoJ) is a web application for retrieving apo-holo structure pairs for user-defined ligands. Given a query structure and one or more defined ligands, it retrieves all other structures of the same protein that feature the same binding sites(s), aligns them, and examines the superimposed binding sites to determine whether each structure is apo or holo, in reference to the query. The resulting superimposed datasets of apo-holo pairs can be visualized and downloaded for further analysis. AHoJ accepts multiple input queries, allowing the creation of customized apo-holo datasets. To demonstrate AHoJ’s functionality, we present a newly constructed dataset of apo-holo pairs featuring 13 ion ligands, by complimenting an existing database of biologically relevant holo interactions (BioLiP).

Availability and Implementation

Freely available for non-commercial use at http://apoholo.cz.

Graphical abstract
The cytidine deaminase APOBEC3G drives cancer mutagenesis and clonal evolution in bladder cancer
Authors: Liu Weisi , Newhall Kevin P. , Khani Francesca , Barlow LaMont , Nguyen Duy , Gu Lilly , Eng Ken , Bhinder Bhavneet , Uppal Manik , Récapet Charlotte , Sboner Andrea , Ross Susan R. , Elemento Olivier , Chelico Linda , Faltas Bishoy M.
Published: September 2022

Mutagenic processes leave distinct signatures in cancer genomes. The mutational signatures attributed to APOBEC3 cytidine deaminases are pervasive in human cancers. However, data linking individual APOBEC3 proteins to cancer mutagenesis in vivo are limited. Here, we show that transgenic expression of human APOBEC3G promotes mutagenesis, genomic instability, and kataegis, leading to shorter survival in a murine bladder cancer model. Acting as mutagenic fuel, APOBEC3G increases the clonal diversity of bladder cancers, driving divergent cancer evolution. We characterize the single base substitution signature induced by APOBEC3G in vivo, showing the induction of a mutational signature different from that caused by APOBEC3A and APOBEC3B. Analysis of thousands of human cancers reveals the contribution of APOBEC3G to the mutational profiles of multiple cancer types, including bladder cancer. Our findings define the role of APOBEC3G in cancer mutagenesis and clonal heterogeneity. These results potentially inform future therapeutic efforts that restrict tumor evolution.
Acquisition of hybrid E/M phenotype associated with increased migration, drug resistance and stemness is mediated by reduced miR-18a levels in ER-negative breast cancer
Authors: Nair Madhumathy G , Apoorva D , Chandrakala M , Snijesh VP , Anupama CE , Rajarajan Savitha , Sahoo Sarthak , Mohan Gayathri , Jayakumar Vishnu Sunil , Ramesh Rakesh S , Srinath BS , Jolly Mohit Kumar , Maliekal Tessy Thomas , Prabhu Jyothi S
Published: September 2022

The complexity of the ER-negative subtype of breast cancer arises due to the heterogeneous nature of the disease rendering them more aggressive and this poses a challenge to effective treatment and eventually the prognosis of the patients. We have explored the miRNA regulation of altered molecular signatures and the effect on tumour progression in ER-negative breast cancer. Using breast tumour specimens, gene expression data from public datasets and in-vitro and in-vivo model systems we have shown that low-levels of miR-18a in ER-negative tumours drives enrichment of hybrid Epithelial/Mesenchymal (E/M) cells with luminal attributes. On inhibition of miR-18a in ER-negative breast cancer cell lines, the cells showed traits of increased migration, stemness and drug-resistance. miR-18a/low tumours were also associated with increased expression of genes associated with EMT, stemness, drug resistance and immune-suppression. Further analysis of the miR-18a targets pointed out at a possible HIF-1α mediated signalling in these tumours. HIF-1α inhibition reduced the enrichment of the hybrid E/M cells and decreased the migratory ability of miR-18a/low cells. Our study reports for the first time a dual role of miR-18a in breast cancer that is subtype specific based on hormone receptor expression and a novel association of low miR-18a levels and enrichment of hybrid E/M cells. The results highlight the possibility of stratifying the ER-negative disease into clinically relevant groups by analysing epigenetic signatures.
BBB-on-a-chip with Integrated micro-TEER for permeability evaluation of multi-functionalized gold nanorods against Alzheimer’s disease
Authors: Palma-Florez Sujey , López-Canosa Adrián , Morales-Zavala Francisco , Castaño Oscar , Kogan M.J. , Samitier Josep , Lagunas Anna , Mir Mónica
Published: September 2022

Background

The lack of predictive models that mimic the blood-brain barrier (BBB) hinders the development of effective drugs for neurodegenerative diseases. Animal models behave differently from humans, are expensive and have ethical constraints. Organ-on-a-chip (OoC) platforms offer several advantages to resembling physiological and pathological conditions in a versatile, reproducible, and animal-free manner. In addition, OoC give us the possibility to incorporate sensors to determine cell culture features such as trans-endothelial electrical resistance (TEER). Here, we developed a BBB-on-a-chip (BBB-oC) platform with a TEER measurement system in close distance to the barrier used for the first time for the evaluation of the permeability performance of GNR-PEG-Ang2/D1 for Alzheimer’s disease. GNR-PEG-Ang2/D1 is a therapeutic nanosystem previously developed by us consisting of gold nanorods (GNR) functionalized with polyethylene glycol (PEG), angiopep-2 peptide (Ang2) to overcome the BBB and the D1 peptide as beta amyloid fibrillation inhibitor, finally obtaining GNR-PEG-Ang2/D1 which showed to be useful for disaggregation of the amyloid inin vitroandin vivomodels. In this work, we evaluated its cytotoxicity, permeability, and some indications of its impact on the brain endothelium by employing an animal-free device based on neurovascular human cells.

Results

In this work, we fabricated a BBB-oC with human astrocytes, pericytes and endothelial cells and a TEER measuring system (TEER-BBB-oC) integrated at a micrometric distance of the endothelial barrier. The characterization displayed a neurovascular network and the expression of tight junctions in the endothelium. We produced GNR-PEG-Ang2/D1 and determined its non-cytotoxic range (0,05–0,4 nM) for plated cells included in the BBB-oC and confirmed its harmless effect at the highest concentration (0.4 nM) in the microfluidic device. The permeability assays revealed that GNR-PEG-Ang2/D1 cross the BBB and this entry is facilitated by Ang2 peptide. Parallel to the permeability analysis of GNR-PEG-Ang2/D1, an interesting behavior of the TJs expression was observed after its administration probably related to the ligands on the nanoparticle surface.

Conclusion

BBB-oC with TEER integrated setup was proven as a functional and throughput platform to evaluate the brain permeability performance of nanotherapeutics in a physiological environment with human cells, putting forward a viable alternative to animal experimentation.
Membrane Targeted Azobenzene Drives Optical Modulation of Bacterial Membrane Potential
Authors: de Souza-Guerreiro Tailise Carlina , Bondelli Gaia , Grobas Iago , Donini Stefano , Sesti Valentina , Bertarelli Chiara , Lanzani Guglielmo , Asally Munehiro , Paternò Giuseppe Maria
Published: September 2022

Recent studies have shown that bacterial membrane potential is dynamic and plays signalling roles. Yet, little is still known about the mechanisms of bacterial membrane potential regulation –owing in part to a scarcity of appropriate research tools. Optical modulation of bacterial membrane potential could fill this gap and provide a new approach to studying and controlling bacterial physiology and electrical signalling. Here, we show that a membrane-targeted azobenzene (Ziapin2) can be used to photo-modulate the membrane potential in cells of the Gram-positive bacterium Bacillus subtilis. We found that upon exposure to blue-green light (λ = 470 nm), isomerization of Ziapin2 in the bacteria membrane induces hyperpolarisation of the potential. In order to investigate the origin of this phenomenon we examined ion-channel-deletion strains and ion channel blockers. We found that in presence of the chloride channel blocker idanyloxyacetic acid-94 (IAA-94) or in absence of KtrAB potassium transporter, the hyperpolarisation response is attenuated. These results reveal that the Ziapin2 isomerization can induce ion channel opening in the bacterial membrane, and suggest that Ziapin2 can be used for studying and controlling bacterial electrical signalling. This new optical tool can contribute to better understand microbial phenomena, such as biofilm electric signalling and antimicrobial resistance.
The Tripod neuron: a minimal structural reduction of the dendritic tree
Authors: Quaresima Alessio , Fitz Hartmut , Duarte Renato , van den Broek Dick , Hagoort Peter , Petersson Karl Magnus
Published: September 2022

Neuron models with explicit dendritic dynamics have shed light on mechanisms for coincidence detection, pathway selection, and temporal filtering. However, it is still unclear which morphological and physiological features are required to capture these phenomena. In this work, we introduce the Tripod neuron model and propose a minimal structural reduction of the dendritic tree that is able to reproduce these dendritic computations. The Tripod is a three-compartment model consisting of two segregated passive dendrites and a somatic compartment modeled as an adaptive, exponential integrate-and-fire neuron. It incorporates dendritic geometry, membrane physiology, and receptor dynamics as measured in human pyramidal cells. We characterize the response of the Tripod to glutamatergic and GABAergic inputs and identify parameters that support supra-linear integration, coincidence-detection, and pathway-specific gating through shunting inhibition. Following NMDA spikes, the Tripod neuron generates plateau potentials whose duration depends on the dendritic length and the strength of synaptic input. When fitted with distal compartments, the Tripod neuron encodes previous activity into a dendritic depolarized state. This dendritic memory allows the neuron to perform temporal binding and we show that the neuron solves transition and sequence detection tasks on which a single-compartment model fails. Thus, the Tripod neuron can account for dendritic computations previously explained only with more detailed neuron models or neural networks. Due to its simplicity, the Tripod model can be used efficiently in simulations of larger cortical circuits.
Drug specificity and affinity are encoded in the probability of cryptic pocket opening in myosin motor domains
Authors: Meller Artur , Lotthammer Jeffrey M. , Smith Louis G. , Novak Borna , Lee Lindsey A. , Kuhn Catherine C. , Greenberg Lina , Leinwand Leslie A. , Greenberg Michael J. , Bowman Gregory R.
Published: September 2022

The design of compounds that can discriminate between closely related target proteins remains a central challenge in drug discovery. Specific therapeutics targeting the highly conserved myosin motor family are urgently needed as mutations in at least 6 of its members cause numerous diseases. Allosteric modulators, like the myosin-II inhibitor blebbistatin, are a promising means to achieve specificity. However, it remains unclear why blebbistatin inhibits myosin-II motors with different potencies given that it binds at a highly conserved pocket that is always closed in blebbistatin-free experimental structures. We hypothesized that the probability of pocket opening is an important determinant of the potency of compounds like blebbistatin. To test this hypothesis, we used Markov state models (MSMs) built from over 2 milliseconds of aggregate molecular dynamics simulations with explicit solvent. We find that blebbistatin’s binding pocket readily opens in simulations of blebbistatin-sensitive myosin isoforms. Comparing these conformational ensembles reveals that the probability of pocket opening correctly identifies which isoforms are most sensitive to blebbistatin inhibition and that docking against MSMs quantitatively predicts blebbistatin binding affinities (R2=0.82). To test our ability to make blind predictions, we predicted blebbistatin’s binding affinity for an isoform (Myh7b) whose blebbistatin sensitivity was unknown. Encouragingly, we find good agreement between the predicted and measured IC50 (0.67 µM vs. 0.36 µM). Therefore, we expect this framework to be useful for the development of novel specific drugs across numerous protein targets.

Significance

Drug development requires the discovery of compounds which specifically target one member of a protein family without triggering side effects that arise from interactions with other related proteins. Myosins are a family of motor proteins that are drug targets for heart diseases, cancer, and parasitic infections. Here, we investigate why the compound blebbistatin specifically inhibits some myosins more potently than others, even though its binding site is closed in all known experimental structures. We find that the blebbistatin binding pocket opens in molecular dynamics simulations of certain myosin motors, and that the probability of opening predicts how potently blebbistatin inhibits a particular motor. Our work suggests that differences in cryptic pocket formation can be exploited to develop specific therapeutics.
4.1N and SAP97 regulate different phases of AMPA receptor intracellular transport
Authors: Bonnet Caroline , Charpentier Justine , Retailleau Natacha , Choquet Daniel , Coussen Françoise
Published: September 2022

Changes in the number of synaptic AMPA subtypes of glutamate receptors (AMPAR) underlie many forms of synaptic plasticity. These variations are controlled by a complex interplay between their intracellular transport (IT), export to the plasma membrane, stabilization at synaptic sites, and recycling. The differential molecular mechanisms involved in these various trafficking pathways and their regulation remains partly unknown. We have recently reported the visualization of AMPAR IT in cultured hippocampal neurons and demonstrated its regulation during synaptic plasticity inducing protocols (Hangen, Cordelieres et al., 2018), opening the path to the differential analysis of the mechanisms controlling AMPAR transport and exocytosis.

The cytosolic C-terminal (C-ter.) domain of AMPAR GluA1 subunit is specifically associated with cytoplasmic proteins that could be implicated in the regulation of their IT such as 4.1N and SAP97. Here we analyze how interactions between GluA1 and 4.1N or SAP97 regulate IT and exocytosis at the plasma membrane in basal condition and after cLTP induction. We use sh-RNA against 4.1N and SAP97 and specific mutations and deletions of GluA1 C-ter. domain to characterize how these interactions are involved in coupling AMPAR to the transport machinery.

The down-regulation of both 4.1N or SAP97 by shRNAs decrease GluA1 containing vesicle number, modify their transport properties and decrease GluA1 export to the PM, indicating their role in GluA1 IT. The total deletion of the C-ter. domain of GluA1 fully suppresses its IT. Disruption of GluA1 binding to 4.1N decreases the number of GluA1 containing transport vesicles, inhibits GluA1 externalization but does not affect the transport properties of the remaining GluA1 containing vesicles. This indicates a role of the 4.1N-GluA1 interaction during exocytosis of the receptor in basal transmission. In contrast, disrupting the binding between SAP97 and GluA1 modifies the basal transport properties of GluA1 containing vesicles and decreases GluA1 export to the plasma membrane. Importantly, disrupting GluA1 interaction with either 4.1N or SAP97 prevents both the cLTP induced increase in the number of GluA1 containing vesicles observed in control and GluA1 externalization. Our results demonstrate that specific interactions between 4.1N or SAP97 with GluA1 have different roles in GluA1 IT and exocytosis. During basal transmission, the binding of 4.1N to GluA1 allows the fusion/fission membrane exocytosis whereas the interaction with SAP97 is essential for GluA1 IT. During cLTP the interaction of 4.1N with GluA1 allows both IT and exocytosis of the receptor in hippocampal cultured neurons. Altogether, our results identify the differential roles of 4.1N and SAP97 in the control of various phases of GluA1 IT.
Hunter-gatherer admixture facilitated natural selection in Neolithic European farmers
Authors: Davy Tom , Ju Dan , Mathieson Iain , Skoglund Pontus
Published: September 2022

Ancient DNA has revealed multiple episodes of admixture in human prehistory during geographic expansions associated with cultural innovations. One important example is the expansion of Neolithic agricultural groups out of the Near East into Europe, and their consequent admixture with Mesolithic hunter-gatherers. Ancient genomes from this period provide an opportunity to study the role of admixture in providing new genetic variation for selection to act upon, and also to identify genomic regions that resisted hunter-gatherer introgression and may thus contribute to agricultural adaptations. We used genome-wide DNA from 728 individuals spanning Mesolithic and Neolithic Europe to infer ancestry deviations in the genomes of admixed individuals, and to test for natural selection after admixture using a new method based on testing for deviations from a genome-wide null distribution. We find that the region around the pigmentation-associated gene SLC24A5 shows the greatest overrepresentation of Neolithic ancestry in the genome (|Z| = 3.45). In contrast, we find the greatest overrepresentation of Mesolithic local ancestry across the key immunity locus that is the Major Histocompatibility Complex (MHC; |Z| > 4) which also shows allele frequency deviations indicative of a selective sweep following admixture (p =1×10−29). This could reflect negative frequency dependent selection on MHC alleles common in Neolithic populations, or that Mesolithic alleles were positively selected for and facilitated adaptation by Neolithic populations to pathogens, new diets, or other environmental factors. Our results extend previous results that highlight immune function and pigmentation as targets of adaptation in more recent populations to selection processes in the Stone Age, and demonstrate that admixture facilitated selection by contributing new genetic variation.
EzMechanism: An Automated Tool to Propose Catalytic Mechanisms of Enzyme Reactions
Authors: Ribeiro Antonio J. M. , Riziotis Ioannis G. , Tyzack Jonathan D. , Borkakoti Neera , Thornton Janet M.
Published: September 2022

A rich literature dedicated to understanding the reaction mechanisms of hundreds of enzymes has emerged over time from the works of experimental and computational researchers. This body of information can now be the starting point for an entirely novel approach to studying enzyme mechanisms using knowledge-based prediction methods. Here, we present such a method, EzMechanism, (pronounced as “Easy Mechanism”) which is able to automatically generate mechanism proposals for a given active site. It works by searching the chemical reaction space available to the enzyme using a set of newly created biocatalytic rules based on knowledge from the literature. EzMechanism aims to complement existing methods for studying enzyme mechanisms by facilitating and improving the hypotheses generating step. We show that EzMechanism works by validating it against 56 enzymes with a known mechanism and identify the limited coverage of the current ruleset as the main target for further improvement.
Efficient repair of human homozygous genetic mutation by CRISPR/Cas9 mediated interlocus gene conversion
Authors: Yang Fei , Pang Jingtao , Liu Guolong , Yang Yang , Qin Shenguang , Zhang Ying , Lai Yongrong , Liang Dan , Wu Yuxuan
Published: September 2022

DNA double-strand breaks (DSBs) induced by gene editing tools are primarily resolved either by non-homologous end joining (NHEJ) or homology-directed repair (HDR) using exogenous synthetic DNA templates. Repaired by error-prone NHEJ may lead to unexpected indels at the targeted site. In the case of most genetic disorders, HDR-mediated precise correction using an exogenous homologous sequence is ideal. However, the therapeutic application of HDR might be especially challenging given the requirement for the codelivery of exogenous DNA templates with toxicity into cells, and the low efficiency of HDR could also limit its clinical application. Here, we used hematopoietic stem cells (HSCs) with genetic mutations to cause β-thalassemia in HBB coding regions and discovered that many cells are actually repaired by CRISPR/Cas9-mediated gene conversion (GC) independent of exogenous synthetic DNA templates. We show that pathogenic mutations in the HBB coding regions of HSCs can be repaired efficiently through CRISPR/GC using the paralog gene HBD as the internal template. Electroporations of Cas9 for ribonucleoprotein with sgRNA into haematopoietic stem and progenitor cells (HSPCs) with a variety of pathogenic gene mutations also resulted in effective conversion of mutations to normal wild-type sequences without exogenous DNA template. Moreover, the edited HSCs can repopulate the haematopoietic system and generate erythroid cells with a greatly reduced propensity for thalassemia after transplantations. Thus, CRISPR/GC, independent of exogenous DNA templates, holds great promise for gene therapy of genetic diseases.