bluuebunny/crossref_metadata_2025_split huggingface dataset:
A catalogue of resistance gene homologs and a chromosome-scale reference sequence support resistance gene mapping in winter wheat
Authors: Kale Sandip M. , Schulthess Albert W. , Padmarasu Sudharsan , Boeven Philipp H. G. , Schacht Johannes , Himmelbach Axel , Steuernagel Burkhard , Wulff Brande B. H. , Reif Jochen C. , Stein Nils , Mascher Martin 
Published: January 2022

AbstractA resistance gene atlas is an integral component of the breeder’s arsenal in the fight against evolving pathogens. Thanks to high-throughput sequencing, catalogues of resistance genes can be assembled even in crop species with large and polyploid genomes. Here, we report on capture sequencing and assembly of resistance gene homologs in a diversity panel of 907 winter wheat genotypes comprising ex situ genebank accessions and current elite cultivars. In addition, we use accurate long-read sequencing and chromosome conformation capture sequencing to construct a chromosome-scale genome sequence assembly of cv. Attraktion, an elite variety representative of European winter wheat. We illustrate the value of our resource for breeders and geneticists by (i) comparing the resistance gene complements in plant genetic resources and elite varieties and (ii) conducting genome-wide associations scans (GWAS) for the fungal diseases yellow rust and leaf rust using reference-based and reference-free GWAS approaches. The gene content under GWAS peaks was scrutinized in the assembly of cv. Attraktion.
Robust and reproducible neuronal differentiation of human embryonic stem cells for neurotoxicology
Authors: Samara Athina , Falck Martin , Spildrejorde Mari , Leithaug Magnus , Acharya Ganesh , Lyle Robert , Eskeland Ragnhild 
Published: January 2022

AbstractNeuronal differentiation from pluripotent cells is commonly used to recapitulate events in early brain development. Neuronal precursors and developing neurons cultured in vivo, rely on attachment, density and cell-to-cell communication, and cell-passaging steps should be minimised to avert disruption of network cross-connectivity. This is crucial both for viability and maturation, and the former also applies to human embryonic stem cells (hESCs). Neuronal differentiation protocols from hESCs for neurotoxicology assessment studies should therefore provide standardized cell density requirements, and optimised coating matrix conditions. The effect of drug treatments may be masked by compound instability and degradation in cell culture medium but performing daily media changes can circumvent these issues. Here, we describe a robust neuronal differentiation protocol using dual SMAD/WNT signalling inhibitors LDN193189, SB431542 and XAV939 (LSX) for neural induction of hESCs, followed by self-patterning and cell maturation stages, for the generation of ventral telencephalic progenitors and neurons. We provide critical information on the optimized cell culture parameters and standardized methods of stage-specific validation. Using cell counts, immunofluorescence, qRT-PCR, and a proof of principle treatment with valproic acid to showcase issues with drug-induced cell toxicity, we facilitate reproducibility of the protocol.Graphical abstract
The CIC-ERF co-deletion underlies fusion independent activation of ETS family member, ETV1, to drive prostate cancer progression
Authors: Gupta Nehal , Song Hanbing , Wu Wei , Ponce Rovingaile Kriska , Lin Yone Kawe , Kim Ji Won , Small Eric J , Feng Felix Y. , Huang Franklin W. , Okimoto Ross A. 
Published: January 2022

AbstractThe dysregulation of ETS family transcription factors drives human prostate cancer. The majority of prostate cancer is the result of chromosomal rearrangements that lead to aberrant ETS gene expression. The mechanisms that lead to fusion independent ETS factor upregulation and prostate oncogenesis remain unknown. Here, we show that two neighboring transcription factors, Capicua (CIC) and ETS2 repressor factor (ERF), which are co-deleted in human prostate tumors can drive prostate oncogenesis. Concurrent CIC and ERF loss commonly occurs through focal genomic deletions at chromosome 19q13.2. Mechanistically, CIC and ERF co-bind the proximal regulatory element and mutually repress the ETS transcription factor, ETV1. Targeting ETV1 in CIC and ERF deficient prostate cancer limits tumor growth. Thus, we have uncovered a fusion independent mode of ETS transcriptional activation defined by concurrent loss of CIC and ERF.
Mindin is essential for cutaneous fibrogenesis in a new mouse model of systemic sclerosis
Authors: Rana Isha , Kataria Sunny , Tan Tuan Lin , Hajam Edries Yousaf , Kashyap Deepak Kumar , Saha Dyuti , Ajnabi Johan , Paul Sayan , Jayappa Shashank , Ananthan Akhil SHP , Kumar Pankaj , Zaarour Rania F. , J Haarshaadri , Samuel Rekha , George Renu , Danda Debashish , Jacob Paul Mazhuvanchary , Dey Rakesh , Dhandapany Perundurai S , He You-Wen , Varga John , Varghese Shyni , Jamora Colin 
Published: January 2022

ABSTRACTFibrosis is a result of chronically activated fibroblasts leading to the overproduction of extracellular matrix (ECM), causing tissue hardening and loss of organ function. Systemic sclerosis (SSc) is a fibrotic skin disease marked by inflammation, autoimmunity and vasculopathy along with progressive fibrosis of the skin and internal organs. A major bottleneck in understanding the etiology of SSc has been the lack of a holistic animal model that can mimic the human SSc disease. We found that the transcription factor Snail is overexpressed in the epidermis of SSc patients and a transgenic mouse recapitulating this expression pattern is sufficient to induce hallmark clinical features of the human disease. Using this mouse model as a discovery platform, we have uncovered a critical role for the matricellular protein Mindin in fibrogenesis. Mindin is produced by Snail transgenic skin keratinocytes and aids fibrogenesis by inducing inflammatory cytokine and collagen production in resident dermal fibroblasts. Given the dispensability of Mindin in normal tissue physiology, targeting this protein holds promise as an effective therapy for fibrosis.
Existence of blood circulating immune-cell clusters (CICs) comprising antigen-presenting cells and B cells
Authors: Bae Sangwook , Lee Yonghee , Kang MyeongHo , Noh Jinsung , Seo Dongyup , Seo Hanna , Lee Sumin , Kwon Sunghoon 
Published: January 2022

AbstractCell-to-cell physical interactions are involved in almost every physiological processes in multicellular organisms. Although the dynamics of these interactions could be highly diverse and complex in many circumstances, certain cell-to-cell interactions among immune cells have been well studied due importance in understanding disease pathogenesis and immune therapy development1. Dendritic cells (DCs) and B cells are directly involved in adaptive immune response against pathogens. Interaction mechanism between these two celltypes is well-known to occur in germinal centers either indirectly via helper T (Th) cells or directly via cell contact. However, there are animalin vitroandin vivoevidence that such direct DC-to-B cell contact can occur outside germinal centers like in peripheral blood or collagen matrix and display antiviral immune-related activity2,3. Here, we provide evidence that certain types of antigen presenting cells (APCs) can form robust cell clusters with B cells and circulate in blood. From healthy human blood immune single cell RNA-seq datasets, we detected APC subpopulations (0.34±0.19% of total PBMCs) that were also enriched with well-known naïve B cell markers. We visually observed DC:B doublets and multiplets (∼0.69% of total live PBMCs) in wildtype mouse blood using flow cytometry and microscopic imaging, thus proving the existence of circulating immune-cell clusters (CICs) composed of APCs and B cells. BCR repertoire of these healthy mouse CICs were similar to circulating B cells. Noticeably, frequency of these APC:B CICs were higher COVID-19 patients than healthy donors and their B cell subtype composition (e.g. naïve, plasmablast, IgM+, IgG+) varied with disease severity.
In silico transcriptomics identifies FDA-approved drugs and biological pathways for protection against cisplatin-induced hearing loss
Authors: Salehi Pezhman , Zallocchi Marisa , Vijayakumar Sarath , Urbanek Madeleine , Giffen Kimberlee P. , Li Yuju , Hati Santanu , Zuo Jian 
Published: January 2022

AbstractAcquired hearing loss is a major health problem that affects 5-10% of the world population. However, there are no FDA-approved drugs for the treatment or prevention of hearing loss. Employing the Connectivity Map (CMap) that contains >54,000 compounds, we performed an unbiased in silico screen using the transcriptomic profiles of cisplatin-resistant and -sensitive cancer cell lines. Pathway enrichment analysis identified gene-drug targets for which 30 candidate drugs were selected with potential to confer protection against cisplatin-induced ototoxicity. In parallel, transcriptomic analysis of a cisplatin-treated cochlear-derived cell line identified common enriched pathway targets. We subsequently tested these top 30 candidate compounds, 15 (50%) of which are FDA-approved for other indications, and 26 (87%) of which were validated for their protective effects in either a cochlear-derived cell line or zebrafish lateral line neuromasts, thus confirming our in silico transcriptomic approach. Among these top compounds, niclosamide, a salicyanilide drug approved by the FDA for treating tapeworm infections for decades, protected from cisplatin- and noise-induced hearing loss in mice. Finally, niclosamide and ezetimibe (an Nrf2 agonist) exerted synergistic protection against cisplatin-ototoxicity in zebrafish, validating the Nrf2 pathway as part of niclosamide’s mechanism of action. Taken together, employing the CMap, we identified multiple pathways and drugs against cisplatin ototoxicity and confirmed that niclosamide can effectively be repurposed as an otoprotectant for future clinical trials against cisplatin- and noise-induced hearing loss.Significant StatementEmploying the Connectivity Map as our in silico transcriptomic screening strategy we identified FDA-approved drugs and biological pathways for protection against cisplatin-induced hearing loss.
Inactivity and Ca2+ signaling regulate synaptic compensation in motoneurons following hibernation in American bullfrogs
Authors: Zubov Tanya , do Amaral-Silva Lara , Santin Joseph M. 
Published: January 2022

AbstractNeural networks tune synaptic and cellular properties to produce stable activity. One form of homeostatic regulation involves scaling the strength of synapses up or down in a global and multiplicative manner to oppose activity disturbances. In American bullfrogs, excitatory synapses scale up to regulate breathing motor function after inactivity in hibernation, connecting homeostatic compensation to motor behavior. In traditional models of homeostatic synaptic plasticity, inactivity is thought to increase synaptic strength via mechanisms that involve reduced Ca2+ influx through voltagegated channels. Therefore, we tested whether pharmacological inactivity and inhibition of voltage-gated Ca2+ channels are sufficient to drive synaptic compensation in this system. For this, we chronically exposed ex vivo brainstem preparations containing the intact respiratory network to tetrodotoxin (TTX) to stop activity and nimodipine to block L-type Ca2+ channels. We show that hibernation and TTX similarly increased motoneuron synaptic strength and that hibernation occluded the response to TTX. In contrast, block of L-type Ca2+ channels did not alter mean synaptic strength but disrupted the apparent multiplicative scaling of synaptic compensation typically observed in response to hibernation. Thus, inactivity drives up synaptic strength through mechanisms that do not rely on reduced L-type channel function, while Ca2+ signaling associated with the hibernation environment independently regulates the balance of synaptic weights. Altogether, these results point to multiple feedback signals for shaping synaptic compensation that gives rise to proper network function during environmental challenges in vivo.
Bio-inspired artificial printed bioelectronic cardio-3D-cellular constructs
Authors: Sanjuan-Alberte Paola , Whitehead Charlie , Jones Joshua N. , Silva João C. , Carter Nathan , Kellaway Simon , Hague Richard J.M. , Cabral Joaquim M.S. , Ferreira Frederico C. , White Lisa J. , Rawson Frankie J. 
Published: January 2022

AbstractBioelectronics is a growing field where novel smart materials are required to interface biology with electronic components. Conductive hydrogels have recently emerged as a promising material for biosensing/actuating applications as they can provide a wet, nanostructured and electrically conductive environment, minimising the mismatch between biological and electronic systems. In this work, we propose a strategy to develop conductive bioinks compatible with the freeform reversible embedding of suspended hydrogels (FRESH) extrusion bioprinting method. These bioinks are based on decellularized extracellular matrix (dECM), extracted from three different tissues (small intestine submucosa, liver and bone) and were characterised. 3D structures were manufactured containing human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs), exhibiting cell viabilities >80%. Multi-walled carbon nanotubes (MWCNTs) were selected as an additional component of the bioinks. The addition of the MWCNTs enhanced the conductive features of the hydrogels and the morphology of the dECM fibres. Electrical stimulation (ES) through alternating currents was applied to hPSC-CMs encapsulated in 3D structures manufactured with the previous material and our results indicated two main findings: (1) in the absence of external ES, the conductive properties of the materials can improve the contractile behaviour of the hPSC-CMs and (2) this effect is significantly enhanced under the application of external ES. Genetic markers analysed showed a trend towards a more mature state of the cells evaluated by the TNNI3/TNNI1 ratio, with upregulated SERCA2 and RYR2 calcium handling proteins when compared to controls and downregulation of calcium channels involved in the generation of pacemaking currents (CACNA1H). These results demonstrate the potential of our strategy to manufacture conductive hydrogels in complex geometries for bioactuating purposes. However, further development of the 3D bioprinting techniques is required to achieve higher control over the nano- and microarchitectures of the structures to improve their biomimicry.
Autolysis affects the iron cargo of ferritins in neurons and glial cells at different rates in the human brain
Authors: Sunkara Sowmya , Radulović Snježana , Lipovšek Saška , Birkl Christoph , Eggenreich Stefan , Birkl-Toeglhofer Anna Maria , Schinagl Maximilian , Funk Daniel , Stöger-Pollach Michael , Haybaeck Johannes , Goessler Walter , Ropele Stefan , Leitinger Gerd 
Published: January 2022

AbstractIron is known to accumulate in neurological disorders, so a careful balance of the iron concentration is essential for healthy brain functioning. An imbalance in iron homeostasis could arise due to the dysfunction of the proteins involved in iron homeostasis. Here, we focus on ferritin – the primary iron storage protein of the brain. Though it is known that glial cells and neurons differ in their concentration of ferritin, the change in the number of iron-filled ferritin cores or their distribution between different cell types during autolysis has not been revealed yet. Here, we show the cellular and region-wide distribution of ferritin in the human brain using state-of-the-art analytical electron microscopy. We validated the concentration of iron-filled ferritin cores to the absolute iron concentration measured by quantitative MRI and inductively coupled plasma mass spectrometry. We show that ferritins lost iron from their cores with progressing autolysis whereas the overall iron concentrations were unaffected. Though the highest concentration of ferritins was found in glial cells, we found that as the total ferritin concentration increased in a patient, ferritin accumulated more in neurons than in glial cells. Collectively our findings point out the unique behaviour of neurons in storing iron during autolysis and explain the differences between the absolute iron concentrations and iron-filled ferritin in a cell-type-dependent fashion in the human brain.Significance statementBalance of the iron load of the brain is crucial to preventing neurodegenerative disorders. Our study establishes a relation between autolysis, iron, and ferritin in the human brain with emphasis on the role of different cells in ferritin storage. We demonstrate that the iron load of ferritins does not correlate with mean iron concentrations during autolysis. Neurons retain more iron-loaded ferritin than glial cells with increasing ferritin count, which may make neurons more susceptible and exacerbate neuronal loss during iron overload. Neurons are also depleted of iron-loaded ferritin cores faster than glial cells during autolysis, demonstrating their unique role in iron storage. This paves the way to understanding the respective roles of neurons and glial cells in preventing or promoting neurodegeneration.
Upregulation ofTrem2expression occurs exclusively on microglial contact with plaques
Authors: Wood Jack , Wong Eugenia , Joghee Ridwaan , Balbaa Aya , Vitanova Karina S. , Vanshoiack Alison , Phelan Stefan-Laural J. , Launchbury Francesca , Desai Sneha , Tripathi Takshashila , Hanrieder Jörg , Cummings Damian M. , Hardy John , Edwards Frances A. 
Published: January 2022

AbstractUsing spatial cell-type-enriched transcriptomics, we compare plaque-induced gene (PIG) expression in microglia touching plaques, neighboring plaques, and far from plaques in 18-month-oldAPPNLF/NLFknock-in mice with and without the Alzheimer’s disease risk mutationTrem2R47H/R47H. We report that, inAppNLF/NLFmice, expression of 35/55 PIGs, is exclusively upregulated in microglia that are touching plaques. In 7 PIGs includingTrem2this upregulation is prevented by theTrem2R47H/R47Hmutation. Unlike in young mice, knockin of theTrem2R47H/R47Hmutation does not significantly decrease theTrem2expression but decreases protein levels by 20% in the absence of plaques. On plaques, despite the mutation preventing increased gene expression, TREM2 protein levels increased by 1.6-fold (compared to 3-fold withTrem2WT/WT) and microglial density increased 20-fold compared to 30-fold. Hence microglia must touch plaques beforeTrem2gene expression is increased but small changes in protein expression can increase microglia density without a change in gene expression.
Inhibitor of the nuclear transport protein XPO1 enhances the anticancer efficacy of KRAS G12C inhibitors in preclinical models of KRAS G12C mutant cancers
Authors: Khan Husain Yar , Nagasaka Misako , Li Yiwei , Aboukameel Amro , Uddin Md. Hafiz , Sexton Rachel , Bannoura Sahar , Mzannar Yousef , Al-Hallak Mohammed Najeeb , Kim Steve , Beydoun Rafic , Landesman Yosef , Mamdani Hirva , Uprety Dipesh , Philip Philip A. , Mohammad Ramzi M. , Shields Anthony F. , Azmi Asfar S. 
Published: January 2022

ABSTRACTThe identification of molecules that can bind covalently to KRAS G12C and lock it in an inactive GDP-bound conformation has opened the door to targeting KRAS G12C selectively. These agents have shown promise in preclinical tumor models and clinical trials. FDA has recently granted approval to sotorasib for KRAS G12C mutated non-small cell lung cancer (NSCLC). However, patients receiving these agents as monotherapy may not respond and generally develop drug resistance over time. This necessitates the development of multi-targeted approaches that can potentially sensitize tumors to KRAS inhibitors. We generated KRAS G12C inhibitor-resistant cell lines and observed that they exhibit sensitivity toward selinexor, a selective inhibitor of nuclear export protein exportin1 (XPO1), as a single agent. KRAS G12C inhibitor MRTX1257 in combination with selinexor suppressed the proliferation of KRAS G12C mutant cancer cell lines MiaPaCa-2 and NCI-H2122 in a synergistic manner. Moreover, combined treatment of selinexor with KRAS G12C inhibitors resulted in enhanced spheroid disintegration, reduction in the number and size of colonies formed by G12C mutant cancer cells. A combination of selinexor with KRAS G12C inhibitors potentiated the inhibition of KRAS expression in MiaPaCa-2 cells. NF-kB protein expression was also markedly reduced by selinexor and MRTX1257 combination. In an in vivo KRAS G12C cell-derived xenograft model, oral administration of a combination of selinexor and sotorasib was demonstrated to reduce tumor burden and enhance survival. In conclusion, we have shown that the nuclear transport protein XPO1 inhibitor can enhance the anticancer activity of KRAS G12C inhibitors in preclinical cancer models.SignificanceIn this study, combining nuclear transport inhibitor selinexor with KRAS G12C inhibitors has resulted in potent antitumor effects in preclinical cancer models. This can be an effective combination therapy for cancer patients that do not respond or develop resistance to KRAS G12C inhibitor treatment.
Recombination, selection and the evolution of tandem gene arrays
Authors: Otto Moritz , Zheng Yichen , Wiehe Thomas 
Published: January 2022

AbstractMulti-gene families – immunity genes or sensory receptors, for instance – are often subject to diversifying selection. Allelic diversity may be favoured not only through balancing or frequency dependent selection at individual loci, but also by associating different alleles in multi copy gene families. Using a combination of analytical calculations and simulations, we explored a population genetic model of epistatic selection and unequal recombination, where a trade-off exists between the benefit of allelic diversity and the cost of copy abundance. Starting from the neutral case, where we showed that gene copy number is Gamma-distributed at equilibrium, we derived also mean and shape of the limiting distribution under selection. Considering a more general model which includes variable population size and population substructure, we explored by simulations mean fitness and some summary statistics of the copy number distribution. We determined the relative effects of selection, recombination and demographic parameters in maintaining allelic diversity and shaping mean fitness of a population. One way to control the variance of copy number is by lowering the rate of unequal recombination. Indeed, when encoding recombination by a rate modifier locus, we observe exactly this prediction. Finally, we analyzed the empirical copy number distribution of three genes in human and estimated recombination and selection parameters of our model.