bluuebunny/crossref_metadata_2025 huggingface dataset:
BET inhibition sensitizes immunologically-cold Rb-deficient prostate cancer to immune checkpoint blockade
Authors: Olson Brian , Chaudagar Kiranj , Bao Riyue , Saha Sweta Sharma , Hong Christina , Rameshbabu Srikrishnan , Chen Raymond , Thomas Alison , Patnaik Akash
Published: March 2022

Purpose

Non-T cell-inflamed immunologically “cold” tumor microenvironments (TME) are associated with poor responsiveness to immune checkpoint blockade (ICB), and can be sculpted by tumor cell genomics. Here we evaluated how Retinoblastoma (Rb) tumor suppressor loss of function (LOF), one of the most frequent alterations in human cancer and associated with lineage plasticity, poor prognosis and therapeutic outcomes, alters the TME, and whether therapeutic strategies targeting the molecular consequences of Rb loss enhance ICB efficacy.

Experimental Design

We performed bioinformatics analysis to elucidate the impact of endogenous Rb LOF on the immune TME in human primary and metastatic tumors. Next, we utilized isogenic murine models of Rb-deficient prostate cancer (PC) for in vitro and in vivo mechanistic studies to examine how Rb loss and bromodomain and extraterminal (BET) domain inhibition (BETi) reprograms the immune landscape, and evaluated in vivo therapeutic efficacy of BETi, singly and in combination with ICB and androgen deprivation therapy.

Results

Rb loss was enriched in non-T cell-inflamed tumors, and Rb-deficient murine tumors demonstrated decreased immune infiltration in vivo. The BETi JQ1 increased immune infiltration into the TME through enhanced tumor cell STING/NF-κB activation and type I interferon (IFN) signaling within tumor cells, resulting in differential macrophage and T cell-mediated tumor growth inhibition and sensitization of Rb-deficient PC to ICB.

Conclusions

BETi can reprogram the immunologically cold Rb-deficient TME via STING/NF-κB/IFN signaling to sensitize Rb-deficient PC to ICB. These data provide the mechanistic rationale to test combinations of BETi and ICB in clinical trials of Rb-deficient PC.

STATEMENT OF TRANSLATIONAL RELEVANCE

Rb LOF is one of the most common genomic alterations in human cancer, occurring in approximately 1/3 of advanced malignancies, Furthermore, loss of Rb correlates with enhanced aggressiveness and poor therapeutic outcomes. In this study, we demonstrate that loss of Rb is also associated with an immunosuppressive tumor microenvironment and lack of responsiveness to immune checkpoint blockade (ICB). As a strategy to overcome Rb LOF induced immunosuppression, we have demonstrated that BETi treatment drives STING/NF-κB signaling and type I interferon production within tumor cells, resulting in immune-mediated tumor control in Rb-deficient PC, which is accentuated by the combination with ICB and ADT. These findings provide a roadmap for maximizing the clinical translation of BET inhibitors into the clinic to treat aggressive-variant Rb-deficient PC.
Sub-cellular dynamic investigation of the multi-component drug on the gastric cancer cell BGC823 using Raman spectroscopy
Authors: Shang Wenhao , Fang Teng , Ye Anpei
Published: March 2022

The potential of Raman spectroscopy in anticancer drug study has been demonstrated, yet its ability to character systematic cellular changes caused by multi-component drugs has not been explored. Here we used micro-Raman spectroscopy combined with bright field imaging to study Compound Kushen injection (CKI) at a sub-cellular level including intracellular vesicles(IVs). In our report, CKI caused dysfunction of DNA replication and repair was displayed by Raman spectrum (RS) from the cell nucleus. Meanwhile, the dynamics of CKI induced intracellular vesicles and cell component deconstruction was delineated by RS from the cytoplasm and IVs. The lipids-related biomolecular changes were also presented by the cytoplasm RS: the lipids level in the cytoplasm first descended then uprising. In conclusion, this study validated the mechanism and displayed the dynamics of CKI in treating cancer cells. We proved the capability of subcellular micro-Raman spectroscopy for detecting systematic cellular changes and its application for multi-component drug evaluation.
Strategies for sampling pseudo-absences for species distribution models in complex mountainous terrain
Authors: Descombes Patrice , Chauvier Yohann , Brun Philipp , Righetti Damiano , Wüest Rafael O. , Karger Dirk N. , Zurell Damaris , Zimmermann Niklaus E.
Published: March 2022

Predictions from species distribution models (SDMs) that rely on presence-only data are strongly influenced by how pseudo-absences are derived. However, which strategies to generate pseudo-absences give rise to faithful SDMs in complex mountainous terrain, and whether species-specific or generic strategies perform better remain open questions.

Here, across 500 plant species, we investigated comprehensively how predictions of SDMs at a 93 m spatial resolution are influenced by pseudo-absence strategies, using the complex topography of the Swiss mountains as a model system. We used five generic (random, equal-stratified, proportional-stratified, target, density) and three species-specific (target specific, density specific and geographic specific) approaches to derive pseudo-absence data. We conducted performance tests for each of our eight strategies in combination with (a) spatial bias, generated within our occurrence dataset on sites with highest sampling density, to investigate how this common bias problem influences the performance of pseudo-absence sampling strategies, and (b) a new approach to reduce model extrapolation in environmental space by including background data from all environmental conditions of the study area. SDMs were evaluated against an independent and well-sampled dataset of true presences and absences.

The random, the density (generic), and the geographic specific (species-specific) strategies consistently performed best, even in cases of strong spatial sampling bias in the occurrence data. Including a background of environmentally stratified pseudo-absences improved predictions of species distributions towards environmental extremes, and significantly reduced spatial extrapolations of model predictions in environmental space.

Our results indicate that both generic and species-specific pseudo-absence strategies allow estimating robust SDMs and we provide clear recommendations which strategies to choose in complex terrain and when presence data are prone to high sampling bias. In datasets with strong sampling bias, most pseudo-absence strategies produce extrapolation problems and we additionally recommend environmentally stratified pseudo-absences in these cases. Overall, in species rich datasets the use of complex and computationally demanding, species-specific pseudo-absence strategies may not always be justified compared to simpler generic approaches.
HPCA1 is required for systemic ROS and calcium cell-to-cell signaling and plant acclimation to stress
Authors: Fichman Yosef , Zandalinas Sara I , Peck Scott , Luan Sheng , Mittler Ron
Published: March 2022

As multicellular organisms, plants constantly balance and coordinate many metabolic, physiological, and molecular responses between different cell types and tissues. This process is essential for plant development, growth, and response to different environmental cues. Because plants lack a nervous system, they transmit different signals over long distances via cell-to-cell signaling. Recent studies revealed that reactive oxygen species (ROS), produced by respiratory burst oxidase homologs (RBOHs) at the apoplast play a key role in cell-to-cell signaling. A state of enhanced ROS production by one cell is thereby sensed by a neighboring cell, causing it to produce ROS, creating a continuous chain of cell-to-cell ROS accumulation termed the ‘ROS wave’. This process was found to mediate systemic signals throughout the plant and is required for plant acclimation to different stresses. Although RBOHs were found to produce ROS essential for this process, the identity of the receptor(s) perceiving the apoplastic ROS signal is currently unknow. Here we reveal that the leucine-rich-repeat receptor-like kinase HPCA1 (H2O2-induced Ca2+increases 1) acts as a central ROS receptor required for the propagation of cell-to-cell ROS signals, systemic signaling in response to different biotic and abiotic stresses, and plant acclimation to stress. We further report that HPCA1 is required for systemic calcium signals, but not systemic membrane depolarization responses, and identify key calcium-dependent signal transduction proteins involved in this process. Our findings reveal that HPCA1 plays a key role in mediating and coordinating systemic cell-to-cell ROS and calcium signals that are required for plant acclimation to stress.
A chromosome-level assembly of the “Cascade” hop (Humulus lupulus) genome uncovers signatures of molecular evolution and improves time of divergence estimates for the Cannabaceae family
Authors: Padgitt-Cobb Lillian K , Pitra Nicholi J , Matthews Paul D , Henning John A , Hendrix David A
Published: March 2022

We present a chromosome-level assembly of the Cascade hop (Humulus lupulus L. var. lupulus) genome. The hop genome is large (2.8 Gb) and complex, and early attempts at assembly resulted in fragmented assemblies. Recent advances have made assembly of the hop genome more tractable, transforming the extent of investigation that can occur.

The chromosome-level assembly of Cascade was developed by scaffolding the previously-reported Cascade assembly generated with PacBio long-read sequencing, and polishing with Illumina short-read DNA sequencing. We developed gene models and repeat annotations, and used a controlled bi-parental mapping population to identify significant sex-associated markers. We assess molecular evolution in gene sequences, gene family expansion and contraction, and time divergence using Bayesian inference.

We identified the putative sex chromosome in the female genome based on significant sex-associated markers from the bi-parental mapping population. While the estimate of repeat content (~64%) is similar to the hemp genome, syntenic blocks in hop contain a greater percentage of LTRs. Hop is enriched for disease resistance-associated genes in syntenic gene blocks and expanded gene families.

The Cascade chromosome-level assembly will inform cultivation strategies and serve to deepen our understanding of the hop genomic landscape, benefiting hop researchers and the Cannabaceae genomics community.
Zinc as a non-hormonal contraceptive: a better alternative to the copper intrauterine device (IUD)
Authors: Shankie-Williams Kirsten , Lindsay Laura , Murphy Chris , Dowland Samson
Published: March 2022

Long-acting and reversible contraceptives (LARC) are the most widely used form of female contraception worldwide, however they have significant side-effects that often result in early removal. Most LARCs are hormonal, but the use of exogenous hormones is not suitable for all women and causes side-effects in many others. The copper IUD (CuIUD) is the only non-hormonal LARC, but a large proportion of users suffer severe side effects. This study proposes the use of zinc as a suitable alternative to the CuIUD.

A rat intrauterine device (IUD) model was established to test the efficacy of a zinc IUD (ZnIUD) against a CuIUD, and a control nylon IUD. The IUD was surgically implanted into one uterine horn while the other remained untreated. Both the ZnIUD and CuIUD resulted in significantly fewer implantation sites compared to untreated horns. There was no significant difference between treated and untreated horns in the control nylon IUD group. Histological assessment revealed damage and inflammation in the endometrium of CuIUD treated horns, but only minor epithelial damage in ZnIUD treated horns, closely resembling the normal appearance of the control horns. This suggests ZnIUDs may not share the side-effect profile of the CuIUD. To test the long-term efficacy of the ZnIUD, rats had a ZnIUD surgically implanted into both horns and cohoused with males for 3 months. These rats mated regularly but did not get pregnant, confirming the long-term effectiveness of the ZnIUD. Reversibility of the ZnIUD was also established, as removal of the ZnIUD after 3 months resulted in no significant difference in the number of implantation sites between treated and untreated horns.

This study demonstrated the contraceptive efficacy of zinc and its potential as a LARC. The ZnIUD had minimal histological impact on the endometrium compared to the current copper standard, indicating that IUDs containing zinc may offer highly effective contraception while causing fewer side effects.
Leaf nitrogen does not explain changes in soybean radiation-use efficiency in vegetative and early reproductive stages
Authors: La Menza Nicolás Cafaro , Arkebauer Timothy J. , Lindquist John L. , Monzon Juan Pablo , Knops Johannes M.H. , Graef George , Scoby David , Howard Réka , Rees Jennifer , Specht James E. , Grassini Patricio
Published: March 2022

Ontogenic changes in soybean radiation-use efficiency (RUE) have been attributed to variation in specific leaf nitrogen (SLN) based only on data collected during seed filling. We evaluated this hypothesis using data on leaf area, absorbed photosynthetically active radiation (APAR), aboveground dry matter (ADM), and plant nitrogen (N) concentration collected during the entire crop season from seven field experiments conducted in a stress-free environment. Each experiment included a full N treatment that received ample N fertilizer and a zero N treatment that relied on N fixation and soil N mineralization. We estimated RUE based on changes in ADM between sampling times and associated APAR, accounting for changes in biomass composition. The SLN and RUE exhibited different seasonal patterns: a bell-shaped pattern with a peak around the beginning of seed filling, and a convex pattern followed by an abrupt decline during late seed filling, respectively. The level of N supply influenced SLN more than RUEviachanges in leaf N concentration, with small changes in specific leaf weight. Changes in SLN explained the decline in RUE during seed filling but failed to predict changes in RUE in earlier stages. A simple approach based on phenological stages may give more realistic estimates of RUE before seed filling, improving crop growth and yield predictionviacrop models and remote sensing.

Highlight

Changes in radiation-use efficiency during soybean vegetative and early reproductive stages are not related to specific leaf nitrogen.
Multi-omic integrated curvature study on pan-cancer genomic data
Authors: Zhu Jiening , Tran Anh Phong , Deasy Joseph O. , Tannenbaum Allen
Published: March 2022

In this work, we introduce a new mathematical framework based on network curvature to extract significant cancer subtypes from multi-omics data. This extends our previous work that was based on analyzing a fixed single-omics data class (e,g, CNA, gene expression, etc.). Notably, we are able to show that this new methodology provided us with significant survival differences on Kaplan-Meier curves across almost every cancer that we considered. Moreover, the variances in Ollivier-Ricci curvature was explored to investigate its usefulness in network topology analysis as this curvature may be capturing subtle functional changes between various cancer subtypes.
Utilisation of Oxford Nanopore sequencing to generate six complete gastropod mitochondrial genomes as part of a biodiversity curriculum
Authors: De Vivo Mattia , Lee Hsin-Han , Huang Yu-Sin , Dreyer Niklas , Fong Chia-ling , de Mattos Felipe Monteiro Gomes , Jain Dharmesh , Wen Yung-Hui Victoria , Mwihaki John Karichu , Wang Tzi-Yuan , Machida Ryuji J. , Wang John , Chan Benny K. K. , Tsai Isheng Jason
Published: March 2022

High-throughput sequencing has enabled genome skimming approaches to produce complete mitochondrial genomes (mitogenomes) for species identification and phylogenomics purposes. In particular, the portable sequencing device from Oxford Nanopore Technologies (ONT) has the potential to facilitate hands-on training from sampling to sequencing and interpretation of mitogenomes. In this study, we present the results from sampling and sequencing six gastropod mitogenomes (Aplysia argus, Cellana orientalis, Cellana toreuma, Conus ebraeus, Conus miles and Tylothais aculeata) from a graduate level biodiversity course. The students were able to produce mitochondrial genomes from sampling to annotation using existing protocols and programs. Approximately 4Gb of sequence was produced from 15 Flongle and two R9.4 Flowcells, averaging 235Mb and N50=4.4kb per Flowcell. Five of the six 14.1-18kb mitogenomes were circlised containing all 13 core protein coding genes. Additional Illumina sequencing reveal that the ONT assemblies were able to span over highly AT rich sequence in the control region that was otherwise missing in Illumina-assembled mitogenomes, but still contained a base error of one every 70.8-346.7bp with the majority occurring at homopolymer regions. Our findings suggest that ONT are portable and can be used to rapidly produce mitogenomes at low cost and tailored to genomics-based training in biodiversity research.
Study of aging using circuit tests and parametric analysis
Authors: Konishi Tomokazu , Yanai Shuichi , Endo Shogo
Published: March 2022

Mouse development and aging were investigated in 11 tests. The test data were parametrically analysed, normalized, and integrated using principal component analysis (PCA). Changes in the indexing items displayed two trends: power and accuracy in the trials. Power decreased monotonically with age, whereas accuracy peaked at 6 months. Features, such as fear or anxiety, could not have been measured. The noise level and sensitivity of each test were determined. In an open field test that involved a video recording of movement, the noise level was the lowest and the sensitivity was high. This test contributed the most to the PCA axes, and reproduced the two main directions.

Significance Statement

The mathematical aspect may have been neglected in behavioural tests. Here, the circuit test data were objectively analysed by focusing on the data distributions during the aging of mice. The test results revealed two clear directions for the data: power, which was gradually reduced, and accuracy, which peaked at sixth months old. Compared with the open field test evaluated using video recordings, the other tests had higher noise levels and weaker signals. Other tests can be improved by using movie recordings and identifying appropriate items.
The role of hepatitis B virus surface protein in inducing Sertoli cell ferroptosis
Authors: Pan Chengshuang , xiangbin Kong , zhigang Wu , Fei Qianjin
Published: March 2022

Hepatitis B virus infection could result in male infertility by inhibiting sperm function and viability. Sertoli cell death contributes to spermatogenesis impairment, which is associated with sperm defects and dysfunction. Ferroptosis-mediated cell death of Sertoli cells was found to contribute to spermatogenesis disorder and poor sperm quality. However, the effects of hepatitis B virus infection on ferroptosis of Sertoli cells remain to be elucidated. Human Sertoli cells were cultured in vitro with 25, 50, and 100 mg/mL of hepatitis B virus surface protein for 48 hours. Cell viability was measured with CCK-8. Levels of glutathione, malondialdehyde, iron, and m6A in human Sertoli cells were determined. Lipid peroxidation was assessed using C11-BODIPY. Luminescence analysis was performed to detect the binding of METTL3 and 3¢-UTR of TRIM37 containing the m6A motifs. Immunoprecipitation was applied to determine the relationship between TRIM37 and GPX4. qPCR and immunoblotting were performed to measure mRNA and protein levels. Hepatitis B virus surface protein exposure significantly increased TRIM37 expression, malondialdehyde level, and ferroptosis, and decreased cell viability and glutathione level of human Sertoli cells. TRIM37 silencing inhibits the effect of HBs exposure-regulated cell viability and ferroptosis in human Sertoli cells. TRIM37 inhibits GPX4 expression through ubiquitination. GPX4 overexpression inhibits the effect of TRIM37 on cell viability and ferroptosis in human Sertoli cells.

Administration of ferroptosis inhibitor recovers the cell viability decreased by TRIM37. Mechanism study showed HBs increases the level of TRIM37 3’-UTR m6A by promoting the expression of METTL3, and the binding of m6A reader IGF2BP2 and TRIM37 3’-UTR promotes the stability of TRIM37 mRNA.HBs inhibit Sertoli cell viability by promoting ferroptosis of Sertoli cells through TRIM37-mediated ubiquitination of GPX4. The findings highlight the importance of TRIM37/GPX4 signaling in the ferroptosis of Sertoli cells.
Patterns of presentations of children to emergency departments across Europe and the impact of the COVID-19 pandemic: retrospective observational multinational study
Authors: Nijman Ruud G. , Honeyford Kate , Farrugia Ruth , Rose Katy , Bognar Zsolt , Buonsenso Danilo , Da Dalt Liviana , De Tisham , Maconochie Ian K. , Parri Niccolo , Roland Damian , Alfven Tobias , Aupiais Camille , Barrett Michael , Basmaci Romain , Borensztajn Dorine , Castanhinha Susana , Corrine Vasilico , Durnin Sheena , Fitzpatrick Paddy , Fodor Laszlo , Gomez Borja , Greber-Platzer Susanne , Guedj Romain , Hartshorn Stuart , Hey Florian , Jankauskaite Lina , Kohlfuerst Daniela , Kolnik Mojca , Lyttle Mark D , Mação Patrícia , Mascarenhas Maria Inês , Messahel Shrouk , Özkan Esra Akyüz , Pučuka Zanda , Reis Sofia , Rybak Alexis , Rinder Malin Ryd , Teksam Ozlem , Turan Caner , Thors Valtýr Stefánsson , Velasco Roberto , Bressan Silvia , Moll Henriette A , Oostenbrink Rianne , Titomanlio Luigi ,   in association with the REPEM network (Research in European Pediatric Emergency Medicine) as part of the EPISODES study group
Published: March 2022

Background

To investigate the impact of the COVID-19 pandemic and infection prevention measures on children visiting emergency departments across Europe.

Methods

Routine health data were extracted retrospectively from electronic patient records of children aged <16 years, presenting to 38 emergency departments (ED) in 16 European countries for the period January 2018 – May 2020, using predefined and standardized data domains. Observed and predicted numbers of ED attendances were calculated for the period February 2020 to May 2020. Poisson models and incidence rate ratios (IRR) were used to compare age groups, diagnoses and outcomes.

Findings

Reductions in pediatric ED attendances, hospital admissions and high triage urgencies were seen in all participating sites. ED attendances were relatively higher in countries with lower SARS-CoV-2 prevalence (incidence rate ratio (IRR) 2·62, 95% CI 2·19 to 3·13) and in children aged >12 months (12-<24 months IRR 0·89, 95% CI 0·86 to 0·92; 2-<5years IRR 0·84, 95% CI 0·82 to 0·87; 5-<12 years IRR 0·74, 95% CI 0·72 to 0·76; 12-<16 years IRR 0·74, 95% CI 0·71 to 0·77; vs. age <12 months as reference group). The impact on pediatric intensive care admissions (IRR 1·30, 95% CI 1·16 to 1·45) was not as great as the impact on general admissions. Lower triage urgencies were reduced more than higher triage urgencies (urgent triage IRR 1·10, 95% CI 1·08 to 1·12; emergent and very urgent triage IRR 1·53, 95% CI 1·49 to 1·57; vs. non-urgent triage category). Reductions were highest and sustained throughout the study period for children with communicable infectious diseases.

Interpretation:

Reductions in ED attendances were seen across Europe during the first COVID-19 lockdown period. More severely ill children continued to attend hospital more frequently compared to those with minor injuries and illnesses, although absolute numbers fell.

Funding:

RGN was supported by National Institute of Health Research, award number ACL-2018-021-007.

Trial registry:

ISRCTN91495258
Plasma cell-free DNA as a prognostic biomarker in small cell lung cancer patients
Authors: Mondelo-Macía Patricia , García-González Jorge , Abalo Alicia , Mosquera-Presedo Manuel , López-López Rafael , León-Mateos Luis , Muinelo-Romay Laura , Díaz-Peña Roberto
Published: March 2022

Background

Lack of biomarkers for treatment selection and monitoring in small-cell lung cancer (SCLC) patients with the limited therapeutic options, result in poor outcomes. Therefore, new prognostic biomarkers are needed to improve their management. The prognostic value of cell-free DNA (cfDNA) and circulating tumor cells (CTCs) have been less explored in SCLC.

Methods

We quantified cfDNA in 46 SCLC patients at different times during therapy. Moreover, CTCs were analyzed in 21 patients before therapy onset using CellSearch® system. Both biomarkers were associated with patients’ outcomes and a prognostic model was developed.

Results

High cfDNA levels before therapy were associated with shorter progression-free survival and overall survival. Furthermore, changes in cfDNA levels between baseline and 3 weeks and cfDNA levels at progression disease were also associated with patients’ outcomes. Multivariate analyses confirmed the independence of cfDNA levels as a prognostic biomarker. Finally, the three-risk category prognostic model developed included ECOG Performance Status, gender and baseline cfDNA levels was associated with a higher risk of progression and death.

Conclusions

We confirmed the prognostic utility of cfDNA in SCLC patients before and during therapy. Our novel risk prognostic model in clinical practice will allow to identify patients who could benefit with actual therapies.
Structural visualization of the tubulin folding pathway directed by eukaryotic chaperonin TRiC
Authors: Gestaut Daniel , Zhao Yanyan , Park Junsun , Ma Boxue , Leitner Alexander , Collier Miranda , Pintilie Grigore , Roh Soung-Hun , Chiu Wah , Frydman Judith
Published: March 2022

The ATP-dependent ring-shaped chaperonin TRiC/CCT is essential for cellular proteostasis. To uncover why some eukaryotic proteins can only fold with TRiC assistance, we reconstituted the folding of β-tubulin using human Prefoldin and TRiC. We find unstructured β-tubulin is delivered by Prefoldin to the open TRiC chamber followed by ATP-dependent chamber closure. CryoEM resolves four near-atomic resolution structures containing progressively folded β-tubulin intermediates within the closed TRiC chamber, culminating in native tubulin. This substrate folding pathway appears closely guided by site-specific interactions with conserved regions in the TRiC chamber. Initial electrostatic interactions between the TRiC interior wall and both the folded tubulin N-domain and its C-terminal E-hook tail establish the native substrate topology, thus enabling C-domain folding. Disordered CCT C-termini within the chamber promote subsequent folding of tubulin Core and Middle domains and GTP-binding. Thus, TRiC’s chamber provides chemical and topological directives that shape the folding landscape of its obligate substrates.
Domestication in dry-cured meatPenicilliumfungi: convergent specific phenotypes and horizontal gene transfers without strong genetic subdivision
Authors: Lo Ying-Chu , Bruxaux Jade , Rodríguez de la Vega Ricardo C. , O’Donnell Samuel , Snirc Alodie , Coton Monika , Le Piver Mélanie , Le Prieur Stéphanie , Roueyre Daniel , Dupont Joëlle , Houbraken Jos , Debuchy Robert , Ropars Jeanne , Giraud Tatiana , Branca Antoine
Published: March 2022

Some fungi have been domesticated for food production, with genetic differentiation between populations from food and wild environments, and food populations often acquiring beneficial traits through horizontal gene transfers (HGTs). Studying their adaptation to human-made substrates are of fundamental and applied importance, for understanding adaptation processes and for further strain improvement. We studied here the population structures and phenotypes of two distantly relatedPenicilliumspecies used for dry-cured meat production,P. nalgiovense, the most common species in the dry-cured meat food industry, andP. salamii, used locally by farms. Both species displayed low genetic diversity, lacking differentiation between strains isolated from dry-cured meat and those from other environments. Nevertheless, the strains collected from dry-cured meat within each species displayed slower proteolysis and lipolysis than their wild conspecifics, and those ofP. nalgiovensewere whiter. Phenotypically, the non-dry-cured meat strains were more similar to their sister species than to their conspecific dry-cured meat strains, indicating an evolution of specific phenotypes in dry-cured meat strains. A comparison of availablePenicilliumgenomes from various environments revealed HGTs, particularly betweenP. nalgiovenseandP. salamii(representing almost 1.5 Mb of cumulative length). HGTs additionally involvedP. biforme, also found in dry-cured meat products. We further detected positive selection based on amino-acid changes. Our findings suggest that selection by humans has shaped theP. salamiiandP. nalgiovensepopulations used for dry-cured meat production, which constitutes domestication. Several genetic and phenotypic changes were similar inP. salamii,P. nalgiovense,andP. biforme, indicating convergent adaptation to the same human-made environment. Our findings have implications for fundamental knowledge on adaptation and for the food industry: the discovery of different phenotypes and of two mating types paves the way for strain improvement by conventional breeding, to elucidate the genomic bases of beneficial phenotypes and to generate diversity.
Multiplexed microfluidic chip for cell co-culture
Authors: Watson Craig , Liu Chao , Ansari Ali , Miranda Helen C. , Somoza Rodrigo A , Senyo Samuel E.
Published: March 2022

Paracrine signaling is challenging to study in vitro, as conventional culture tools dilute soluble factors and offer little to no spatiotemporal control over signaling. Microfluidic chips offer potential to address both of these issues. However, few solutions offer both control over onset and duration of cell-cell communication, and high throughput. We have developed a microfluidic chip designed to culture cells in adjacent chambers, separated by valves to selectively allow or prevent exchange of paracrine signals. The chip features 16 fluidic inputs and 128 individuallyaddressable chambers arranged in 32 sets of 4 chambers. Media can be continuously perfused or delivered by diffusion, which we model under different culture conditions to ensure normal cell viability. Immunocytochemistry assays can be performed in the chip, which we modeled and fine-tuned to reduce total assay time to 1h. Finally, we validate the use of the chip for co-culture studies by showing that HEK293Ta cells respond to signals secreted by RAW 264.7 immune cells in adjacent chambers, only when the valve between the chambers is opened.
Integrative single cell and spatial transcriptomic analysis reveal reciprocal microglia-plasma cell crosstalk in the mouse brain during chronicTrypanosoma bruceiinfection
Authors: Quintana Juan F. , Chandrasegaran Praveena , Sinton Matthew C. , Briggs Emma , Otto Thomas D. , Heslop Rhiannon , Bentley-Abbot Calum , Loney Colin , de Lecea Luis , Mabbott Neil A. , MacLeod Annette
Published: March 2022

Human African trypanosomiasis, or sleeping sickness, is caused by the protozoan parasiteTrypanosoma bruceiand induces profound reactivity of glial cells and neuroinflammation when the parasites colonise the central nervous system. However, the transcriptional and functional responses of the brain to chronicT. bruceiinfection remain poorly understood. By integrating single cell and spatial transcriptomics of the mouse brain, we identified that glial responses triggered by infection are readily detected in the proximity to the circumventricular organs, including the lateral and 3rdventricle. This coincides with the spatial localisation of both slender and stumpy forms ofT. brucei. Furthermore,in silicopredictions and functional validations led us to identify a previously unknown crosstalk between homeostaticCx3cr1+microglia andCd138+plasma cells mediated by IL-10 and B cell activating factor (BAFF) signalling. This study provides important insights and resources to improve understanding of the molecular and cellular responses in the brain during infection with African trypanosomes.
Cuticle and cuticular sensilla in Agnostina
Authors: Naimark Elena B. , Chaika Stanislav Yu.
Published: March 2022

The microstructure of the cuticle of several Agnostina species is described. For the first time, it has been shown that their cuticle consists of three layers: thick outer and transitional layers and a thin inner layer. The layers are made up of stacks of laminae: the laminae in the outer layer are thicker than in the transitional and inner ones. The evolution of the agnostoid cuticle proceeded, apparently, in the direction of decreasing the thickness of the inner layer which in contrast to all other arthropods, is thinner than the outer layer. Apparently, the inner layer was mineralized to a lesser extent than the outer one. In the structure of the cuticle, Agnostina are close to horseshoe crabs and trilobites. On the outer and inner layers, a set of sensilla was revealed; they can be attributed to trichoid, campaniform, and digitiform sensilla (with mechanoreceptor function) and celoconic sensilla (with chemoreceptor function). Also, unique sensorial ensembles were found on cephalons and pygidia; the function of the former is probably mechanosensorial, and the purpose of the latter cannot be assumed on this material.
CHA1: A New Combinatorial Therapy That Reciprocally Regulates Wnt and JAK/STAT/Interferon Signaling to Re-program Breast Tumors and the Tumor-Resident Landscape
Authors: Alamoudi Mariam K. , Chipman Mollie , Deieso-Frechette Francesca , Bogis Ahlam Mukhtar , Alqurashi Roaya S. , Li Kaiqi , Zhang Rui , Castañer Maricel , Triafallou George , Herbosa Christopher G. , Carland Corinne , Lee AJ. Jaehoon , Gillani Kyle , Paulson K. Eric , Yee Amy S.
Published: March 2022

Triple negative breast cancers (TNBC) pose exceptional challenges with fatal brain metastases as a clear and unmet need. Immune checkpoint inhibitors (ICIs) are promising therapeutic strategies, but most TNBC are resistant, or “cold” tumors, due to lack of tumor-resident immune engagement. No FDA-approved therapies exist which promote a “cold-to-hot” transition or induce the important biomarker PD-L1, often used for ICI clinical decision-making. Maximal ICI susceptibility, or a full “cold-to-hot” transition, requires reciprocal Wnt signaling inhibition and Jak/STAT/interferon signaling activation. We report a new compound combination (CHA1) that fits the above criteria. CHA1 is comprised of EGCG (epigallocatechin-3-gallate; green-tea compound) and decitabine (DNA-methyltransferase (DNMT1) inhibitor; 5’deaza-cytidine; FDA-approved for hematologic malignancies). We used immune-compromised and syngeneic TNBC pre-clinical models to investigate tumor-intrinsic and tumor-resident T-cell effects, respectively. All results required CHA1 (but not EGCG or decitabine alone) and utilized attainable human dose equivalences with manageable safety profiles. CHA1 triggered efficient Wnt signaling inhibition by elevating Wnt pathway inhibitors (HBP1 and SFRP1) and traversed the blood-brain barrier to reduce both tumor and brain metastatic growth. Transcriptomic and expression analyses revealed that CHA1 treatment effectuated a robust tumor-intrinsic JAK/STAT/IFN response 1) to induce PDL1 and 2) to induce antigen presentation and processing genes, including MHC-1, MHC-2 and numerous genes attributed to professional antigen-presenting cells; 3) to induce CD8+-T-cell infiltration and activation. Additionally, CHA1 pre-treatment improved anti-PDL1 efficacy in a syngeneic setting. Lastly, we derived a composite gene signature emblematic of CHA1 treatment and of a favorable clinical prognosis in-silico. Together, our work supports a model in which CHA1 influences epigenetics, Wnt and Jak/STAT/IFN signaling mechanisms—all to reprogram an epithelial-mesenchymal TNBC tumor to express antigen-presenting properties and to recruit and activate tumor-resident CD8+-T-cells. We discuss our findings in the context of cancer biology and immunity with implications for improving ICI susceptibility for TNBC.
Combinatorial interactions of Hox genes establish appendage diversity of the amphipod crustacean Parhyale hawaiensis
Authors: Alberstat Erin Jarvis , Chung Kevin , Sun Dennis A , Ray Shagnik , Patel Nipam H.
Published: March 2022

Hox genes establish regional identity along the anterior-posterior axis in diverse animals. Changes in Hox expression can induce striking homeotic transformations, where one region of the body is transformed into another. Previous work in Drosophila has demonstrated that Hox cross-regulatory interactions are crucial for maintaining proper Hox expression. One major mechanism is the phenomenon of “posterior prevalence”, wherein anterior Hox genes are repressed by more posterior Hox genes. Loss of posterior Hox expression under this model would predict posterior-to-anterior transformations, as is frequently observed in Drosophila. While posterior prevalence is thought to occur in many animals, studies of such Hox cross-regulation have focused on a limited number of organisms. In this paper, we examine the cross-regulatory interactions of three Hox genes, Ultrabithorax (Ubx), abdominal-A (abd-A), and Abdominal-B (Abd-B) in patterning thoracic and abdominal appendages in the amphipod crustacean Parhyale hawaiensis. Studies of Hox function in Parhyale have previously revealed two striking phenotypes which differed markedly from what a “posterior prevalence” model would predict, including non-contiguous and anterior-to-posterior transformations. We probe the logic of Parhyale Hox cross-regulation by using CRISPR/Cas9 to systematically examine all combinations of Ubx, abd-A, and Abd-B loss of function in Parhyale. By analyzing homeotic phenotypes and examining the expression of additional Hox genes, we reveal Hox cross-regulatory interactions in Parhyale. From these data, we also demonstrate that some Parhyale Hox genes function combinatorially to specify posterior limb identity, rather than abiding by a posterior prevalence mechanism. These results provide evidence that combinatorial Hox interactions may be responsible for the tremendous body plan diversity of crustaceans.

Graphical Abstract
Mobile elements in human population-specific genome and phenotype divergence
Authors: Kojima Shohei , Koyama Satoshi , Ka Mirei , Saito Yuka , Parrish Erica H. , Endo Mikiko , Takata Sadaaki , Mizukoshi Misaki , Hikino Keiko , Takeda Atsushi , Gelinas Asami F. , Heaton Steven M. , Koide Rie , Kamada Anselmo J. , Noguchi Michiya , Hamada Michiaki ,   Biobank Japan Project Consortium, Kamatani Yoichiro , Murakawa Yasuhiro , Ishigaki Kazuyoshi , Nakamura Yukio , Ito Kaoru , Terao Chikashi , Momozawa Yukihide , Parrish Nicholas F.
Published: March 2022

Mobile genetic elements (MEs) are heritable mutagens that contribute to divergence between lineages by recursively generating structural variants. ME variants (MEVs) are difficult to genotype, obscuring their impact on recent genome and trait diversification. We developed a tool that uses short-read sequence data to accurately genotype MEVs, enabling us to study them using statistical genetics methods in global human genomes. We observe population-specific differences in the distribution of Alu insertions that distinguish Japanese from other populations. We integrated MEVs with epigenomic and expression quantitative trait loci (eQTL) maps to determine how they impact traits. This reveals coherent patterns by which specific MEs regulate tissue-specific gene expression, including creating or attenuating enhancers and recruiting post-transcriptional regulators. We pinpoint MEVs as genetic causes of disease risk, including a LINE-1 insertion linked to keloid and other diseases of fibroblast inflammation, by introducing MEVs into the genome-wide association study (GWAS) framework. In addition to nominating previously-hidden MEVs as causes of human diseases, this work highlights MEs as accelerators of human population divergence and begins to decipher the semantics of MEs.
DiSiR: a software framework to identify ligand-receptor interactions at subunit level from single-cell RNA-sequencing data
Authors: Vahid Milad R. , Kurlovs Andre , Auge Franck , Olfati-Saber Reza , de Rinaldis Emanuele , Rapaport Franck , Savova Virginia
Published: March 2022

Most of cell-cell interactions and crosstalks are mediated by ligand-receptor interactions. The advent of single-cell RNA-sequencing (scRNA-seq) techniques has enabled characterizing tissue heterogeneity at single-cell level. Over the past recent years, several methods have been developed to study ligand-receptor interactions at cell type level using scRNA-seq data. However, there is still no easy way to query the activity of a specific user-defined signaling pathway in a targeted way or map the interactions of the same subunit with different ligands as part of different receptor complexes. Here, we present DiSiR, a fast and easy-to-use permutation-based software framework to investigate how individual cells are interacting with each other by analyzing signaling pathways of multi-subunit ligand-activated receptors from scRNA-seq data, not only for available curated databases of ligand-receptor interactions, but also for interactions that are not listed in these databases. We show that, when utilized to infer melanoma disease map on a gold-standard dataset, DiSiR outperforms other well-known permutation-based methods, e.g., CellPhoneDB and ICELLNET. To demonstrate DiSiR’s utility in exploring data and generating biologically relevant hypotheses, we apply it to COVID lung and rheumatoid arthritis (RA) synovium scRNA-seq data and highlight potential differences between inflammatory pathways at cell type level for control vs. disease samples.
Synthetic torpor triggers a neuroprotective and regulated mechanism in the rat brain, favoring the reversibility of Tau protein hyperphosphorylation
Authors: Squarcio Fabio , Hitrec Timna , Piscitiello Emiliana , Cerri Matteo , Giovannini Catia , Martelli Davide , Occhinegro Alessandra , Taddei Ludovico , Tupone Domenico , Amici Roberto , Luppi Marco
Published: March 2022

Hyperphosphorylated Tau protein (PPTau) is the hallmark of tauopathic neurodegeneration. During “synthetic torpor” (ST), a transient hypothermic state which can be induced in rats by the local pharmacological inhibition of the Raphe Pallidus, a reversible brain Tau hyperphosphorylation occurs. The aim of the present study was to elucidate the – as yet unknown – molecular mechanisms underlying this process, at both a cellular and systemic level. Different phosphorylated forms of Tau and the main cellular factors involved in Tau phospho-regulation were assessed by western blot in the parietal cortex and hippocampus of rats induced in ST, at either the hypothermic nadir or after the recovery of euthermia. Pro- and anti-apoptotic markers, as well as different systemic factors which are involved in natural torpor, were also assessed. Finally, the degree of microglia activation was determined through morphometry. Overall, the results show that ST triggers a regulated biochemical process which can counteract PPTau formation starting, unexpectedly even for a non-hibernator, from the hypothermic nadir. In particular, at the nadir, the glycogen synthase kinase-β was largely inhibited in both regions, the antiapoptotic factor AKT was significantly activated in the hippocampus, and melatonin plasma levels were significantly increased, while a transient neuroinflammation was observed during the recovery period. Together, the present data suggest that ST can trigger a previously undescribed latent and regulated physiological process, that is able to cope with brain PPTau formation.

Graphical abstract
qad: An R-package to detect asymmetric and directed dependence in bivariate samples
Authors: Griessenberger Florian , Trutschnig Wolfgang , Junker Robert R.
Published: March 2022

Correlations belong to the standard repertoire of ecologists for quantifying the strength of dependence between two random variables. Classical dependence measures are usually not capable of detecting non-monotonic or non-functional dependencies. Furthermore, they completely fail to detect asymmetry and direction in dependence, which exist in many situations and should not be ignored. In this paper, we present qad (short for quantification of asymmetric dependence), a non-parametric statistical method to quantify directed and asymmetric dependence of bivariate samples. qad is applicable in general situations, is sensitive to noise in data, exhibits a good small sample performance, detects asymmetry in dependence, shows high power in testing for independence, requires no assumptions regarding the underlying distribution of the data, and reliably quantifies the information gain/predictability of quantity Y given knowledge of quantity X, and vice versa (i.e. q(X,Y) ≠ q(Y, X)). Here, we briefly recall the methodology underlying qad, introduce the functions of the R-package qad, which returns estimates for the measures q(X, Y) denoting the directed dependence of Y on X (or, equivalently, the influence of X on Y), q(Y, X) the directed dependence of X on Y, a(X, Y) ≔ q(X, Y) − q(Y, X) the asymmetry in dependence. Furthermore, qad can be used to predict Y given knowledge of X, and vice versa. Additionally, we compare empirical performance of qad with that of seven other well established measures and demonstrate the applicability of qad on ecological datasets. We illustrate that direction and asymmetry in dependence are universal properties of bivariate associations. qad thus provides additional information gain and the avoidance of model bias and will therefore advance and facilitate the understanding of ecological systems.
Subjective cognitive decline predicts lower cingulo-opercular network functional connectivity in individuals with lower neurite density in the forceps minor
Authors: Ruiz-Rizzo Adriana L. , Viviano Raymond P. , Daugherty Ana M. , Finke Kathrin , Müller Hermann J. , Damoiseaux Jessica S.
Published: March 2022

Cognitive complaints of attention/concentration problems are highly frequent in older adults with subjective cognitive decline (SCD). Functional connectivity in the cingulo-opercular network (CON-FC) supports cognitive control, tonic alertness, and visual processing speed. Thus, those complaints in SCD may reflect a decrease in CON-FC. Frontal white-matter tracts such as the forceps minor exhibit age- and SCD-related alterations and, therefore, might influence the CON-FC decrease in SCD. Here, we aimed to determine whether SCD predicts an impairment in CON-FC and whether neurite density in the forceps minor modulates that effect. To do so, we integrated cross-sectional and longitudinal analyses of multimodal data in a latent growth curve modeling approach. Sixty-nine healthy older adults (13 males; 68.33 ± 7.95 years old) underwent resting-state functional and diffusion-weighted magnetic resonance imaging, and the degree of SCD was assessed at baseline with the memory functioning questionnaire (greater score indicating more SCD). Forty-nine of the participants were further enrolled in two follow-ups, each about 18 months apart. Baseline SCD did not predict CON-FC after three years or its rate of change (p-values > 0.092). Notably, however, the forceps minor neurite density did modulate the relation between SCD and CON-FC (intercept; b = 0.21, 95% confidence interval, CI, [0.03, 0.39], p = 0.021), so that SCD predicted a greater CON-FC decrease in older adults with relatively lower neurite density in the forceps minor. The neurite density of the forceps minor, in turn, negatively correlated with age. These results suggest that CON-FC alterations in SCD are dependent upon the forceps minor neurite density. Accordingly, these results imply modifiable age-related factors that could help delay or mitigate both age and SCD-related effects on brain connectivity.