bluuebunny/crossref_metadata_2025 huggingface dataset:
AMP-Kinase mediates regulation of glomerular volume and podocyte survival
Authors: Banu Khadija , Lin Qisheng , Basgen John M. , Planoutene Marina , Wei Chengguo , Reghuvaran Anand C. , Garzon Felipe , Garcia Aitor , Chun Nicholas , Cumpelik Arun , Shi Hongmei , Santaneusio Andrew , Zhang Weijia , Das Bhaskar , Salem Fadi , Li Li , Cantley Lloyd G , Ishibe Shuta , Kaufman Lewis , Lemley Kevin V. , Ni Zhaohui , He John C. , Murphy Barbara , Menon Madhav C.
Published: May 2021

We reported that Shroom3 knockdown, via Fyn inhibition, induced albuminuria with foot process effacement (FPE) without glomerulosclerosis (FSGS) or podocytopenia. Interestingly, knockdown mice had reduced podocyte volumes. Human minimal change disease, where podocyte Fyn inactivation was reported, also showed lower glomerular volumes than FSGS. We hypothesized that lower glomerular volume prevented the progression to podocytopenia. To test this hypothesis, we utilized unilateral- and 5/6thnephrectomy models in Shroom3 knockdown mice. Knockdown mice exhibited lower glomerular volume, and less glomerular and podocyte hypertrophy after nephrectomy. FYN-knockdown podocytes had similar reductions in podocyte volume, implying Fyn was downstream of Shroom3. Using SHROOM3- or FYN-knockdown, we confirmed reduced podocyte protein content, along with significantly increased phosphorylated AMP-kinase, a negative regulator of anabolism. AMP-Kinase activation resulted from increased cytoplasmic redistribution of LKB1 in podocytes. Inhibition of AMP-Kinase abolished the reduction in glomerular volume and induced podocytopenia in mice with FPE, suggesting a protective role for AMP-Kinase activation. In agreement with this, treatment of glomerular injury models with AMP-Kinase activators restricted glomerular volume, podocytopenia and progression to FSGS. In summary, we demonstrate the important role of AMP-Kinase in glomerular volume regulation and podocyte survival. Our data suggest that AMP-Kinase activation adaptively regulates glomerular volume to prevent podocytopenia in the context of podocyte injury.
Evolutionary puzzle: discussing the evolution of sentience in Metazoa through a phylogenetic perspective
Authors: Andrade Michaella P. , Santos Charles Morphy D.
Published: May 2021

Sentience is the capacity of organisms to feel and experience through subjective states. During the last years, several investigations have indicated that response mechanisms to harmful stimuli can be highly conserved among the Metazoa. However, there is a research bias towards vertebrates in the available studies. Here we discuss the evolution of the nervous and sensory system, pain and nociception in animals through a phylogenetic perspective testing the hypothesis of common ancestry of sentience. Our results indicate that characteristics related to sentience - morphological and molecular and behavioural -, were already present in the common ancestors of Metazoa, Eumetazoa and Bilateria. Our phylogenetic hypotheses positioned Porifera as the sister-group to all the other Metazoa, corroborating the hypothesis of a single origin of the nervous system. Our results also depict Urbilateria as the ancestor of the metazoan toolkit related to the sentience. These scenarios suggest that some attributes of the sensory system may have appeared even before the emergence of the nervous system, through possible cooptations of sensory modules of the first Metazoa.
Histone H3K27 methylation perturbs transcriptional robustness and underpins dispensability of highly conserved genes in fungi
Authors: Tralamazza Sabina Moser , Abraham Leen Nanchira , Corrêa Benedito , Croll Daniel
Published: May 2021

Epigenetic modifications are key regulators of gene expression and underpin genome integrity. Yet, how epigenetic changes affect the evolution and transcriptional robustness of genes remains largely unknown. Here, we show how the repressive histone mark H3K27me3 influences the trajectory of highly conserved genes in fungi. We first performed transcriptomic profiling on closely related species of the plant pathogen Fusarium graminearum species complex. We determined transcriptional responsiveness of genes across environmental conditions to determine expression robustness. To infer evolutionary conservation of coding sequences, we used a comparative genomics framework of 23 species across the Fusarium genus. We integrated histone methylation data from three Fusarium species across the phylogenetic breadth of the genus. Gene expression variation is negatively correlated with gene conservation confirming that highly conserved genes show higher expression robustness. Furthermore, we show that highly conserved genes marked by H3K27me3 deviate from the typical housekeeping gene archetype. Compared to the genomic background, H3K27me3 marked genes encode smaller proteins, exhibit lower GC content, weaker codon usage bias, higher levels of hydrophobicity and are enriched for functions related to regulation and membrane transport. The evolutionary age of conserved genes with H3K27me3 histone marks falls typically within the origins of the Fusarium genus. We show that highly conserved genes marked by H3K27me3 are more likely to be dispensable for survival. Lastly, we show that conserved genes exposed to repressive H3K27me3 marks across distantly related fungi predict transcriptional perturbation at the microevolutionary scale in Fusarium fungi. In conclusion, we establish how repressive histone marks determine the evolutionary fate of highly conserved genes across evolutionary timescales.
Meclizine and metabotropic glutamate receptor agonists attenuate severe pain and primary sensory neuron Ca2+activity in chemotherapy-induced peripheral neuropathy
Authors: Shannonhouse John , Bernabucci Matteo , Gomez Ruben , Son Hyeonwi , Zhang Yan , Ishida Hirotake , Kim Yu Shin
Published: May 2021

Chemotherapy-induced peripheral neuropathy (CIPN) affects about 68% of patients undergoing chemotherapy and causes severe neuropathic pain which is debilitating health problem and greatly reduces quality of life. Cisplatin is a commonly used platinum-based chemotherapeutic drug known to cause CIPN, possibly by causing oxidative stress damage to primary sensory neurons. Metabotropic glutamate receptors (mGluRs) are widely hypothesized to be involved in pain processing. Meclizine is an H1 histamine receptor antagonist which is known to have neuroprotective effects including anti-oxidative effect. Here, we used a mouse model of cisplatin-induced CIPN to test agonists of mGluR8 and group II mGluR as well as meclizine as interventions to reduce cisplatin-induced pain. We performed behavioral pain tests andin vivoentire DRG neurons Ca2+imaging using genetically-encoded Ca2+indicator, Pirt-GCaMP3 to monitor different drug interventions on a populational ensemble level. CIPN induced increased spontaneous Ca2+activity in DRG neurons, increased Ca2+transient amplitudes, and hyperresponses to mechanical, thermal, and chemical stimuli. We found mGluR8 agonist, DCPG, group II mGluR agonist, LY379268, and Histamine1 receptor antagonist, meclizine all significantly attenuated mechanical and thermal pain caused by CIPN. LY379268 and meclizine, but not DCPG, attenuated DRG neuronal Ca2+activity elevated by CIPN. Furthermore, meclizine attenuated cisplatin-induced weight loss. These results suggest group II mGluR agonist, mGluR8 agonist, and meclizine are excellent candidates to study for mechanisms and new treatment option for CIPN.
Stromal HIF2 Regulates Immune Suppression in the Pancreatic Cancer Microenvironment
Authors: Huang Yanqing , Garcia Garcia Carolina J. , Lin Daniel , Nguyen Nicholas D. , Fujimoto Tara N. , Zhao Jun , Lee Jaewon J. , Bernard Vincent , Yu Meifang , Delahoussaye Abagail M. , Phan Jae L. , Deorukhkar Amit , Molkentine Jessica M. , Fuentes Natividad R. , Turner Madeleine C. , Saur Dieter , Maitra Anirban , Taniguchi Cullen M.
Published: May 2021

Background & Aims

Pancreatic ductal adenocarcinoma (PDAC) has a hypoxic, immunosuppressive stroma, which contributes to its resistance to immune checkpoint blockade therapies. The hypoxia-inducible factors (HIFs) mediate the cellular response to hypoxia, but their role within the PDAC tumor microenvironment remains unknown.

Methods

We used a dual recombinase mouse model to delete Hif1α or Hif2α in α-smooth muscle actin (αSMA)-expressing cancer-associated fibroblasts (CAFs) arising within spontaneous pancreatic tumors. The effects of CAF-Hif2α expression on tumor progression and composition of the tumor microenvironment were evaluated by Kaplan-Meier analysis, quantitative real-time polymerase chain reaction, histology, immunostaining, and by both bulk and single-cell RNA sequencing. CAF-macrophage crosstalk was modeled ex vivo using conditioned media from CAFs after treatment with hypoxia and PT2399, a HIF2 inhibitor currently in clinical trials. Syngeneic flank and orthotopic PDAC models were used to assess whether HIF2 inhibition improves response to immune checkpoint blockade.

Results

CAF-specific deletion of HIF2, but not HIF1, suppressed PDAC tumor progression and growth, and improved survival of mice by 50% (n = 21-23 mice/group, Log-rank P = 0.0009). Deletion of CAF-HIF2 modestly reduced tumor fibrosis and significantly decreased the intratumoral recruitment of immunosuppressive M2 macrophages and regulatory T cells. Treatment with the clinical HIF2 inhibitor PT2399 significantly reduced in vitro macrophage chemotaxis and M2 polarization, and improved tumor responses to immunotherapy in both syngeneic PDAC mouse models.

Conclusions

Together, these data suggest that stromal HIF2 is an essential component of PDAC pathobiology and is a druggable therapeutic target that could relieve tumor microenvironment immunosuppression and enhance immune responses in this disease.
Capsaicin pretreatment alleviates postoperative pain and reduces primary sensory neuron Ca2+ activity
Authors: Ishida Hirotake , Zhang Yan , Gomez Ruben , Shannonhouse John , Son Hyeonwi , Kim Yu Shin
Published: May 2021

After surgeries, especially thoracotomy incision, patients develop unbearable pain. Opioids are used for reducing pain but often cause serious side effects. Previously, we found that capsaicin pretreatment of the incision area alleviated spontaneous and thermal pain in a postoperative pain animal model. In the present study, we aimed to monitor primary sensory neuron Ca2+ activity in in vivo dorsal root ganglia (DRG) in a postoperative pain model using Pirt-GCaMP3 treated with capsaicin or controls. Intraplantar injection of capsaicin (0.05%) alleviated spontaneous, mechanical, and thermal postoperative pain. The Ca2+ response in in vivo DRG and in in situ spinal cord was significantly enhanced in the ipsilateral side compared to contralateral side or naive control. Primary sensory nerve fiber length was significantly decreased in the incision skin area in capsaicin-pretreated animals detected by immunohistochemistry and placental alkaline phosphatase (PLAP) staining. Thus, capsaicin pretreatment alleviates postoperative pain by suppressing Ca2+ response due to degeneration of primary sensory nerve fibers in the skin.
Imaging sensory transmission and neuronal plasticity in primary sensory neurons with genetically-encoded voltage indicator, ASAP4.4-Kv
Authors: Zhang Yan , Shannonhouse John , Gomez Ruben , Son Hyeonwi , Ishida Hirotake , Evans Stephen , Chavarha Mariya , Shi Dongqing , Zhang Guofeng , Lin Michael Z , Kim Yu Shin
Published: May 2021

Detection of somatosensory inputs requires conversion of external stimuli into electrical signals by activation of primary sensory neurons. The mechanisms by which heterogeneous primary sensory neurons encode different somatosensory inputs remains unclear. In vivo dorsal root ganglia (DRG) imaging using genetically-encoded Ca2+ indicators (GECIs) is currently the best technique for this purpose by providing an unprecedented spatial and populational resolution. It permits the simultaneous imaging of >1800 neurons/DRG in live mice. However, this approach is not ideal given that Ca2+ is a second messenger and has inherently slow response kinetics. In contrast, genetically-encoded voltage indicators (GEVIs) have the potential to track voltage changes in multiple neurons in real time but often lack the brightness and dynamic range required for in vivo use. Here, we used soma-targeted ASAP4.4-Kv, a novel GEVI, to dissect the temporal dynamics of noxious and non-noxious neuronal signals during mechanical, thermal, or chemical stimulation in DRG of live mice. ASAP4.4-Kv is sufficiently bright and fast enough to optically characterize individual neuron coding dynamics. Notably, using ASAP4.4-Kv, we uncovered cell-to-cell electrical synchronization between adjacent DRG neurons and robust dynamic transformations in sensory coding following tissue injury. Finally, we found that a combination of GEVI and GECI imaging empowered in vivo optical studies of sensory signal processing and integration mechanisms with optimal spatiotemporal analysis.

Highlights

In vivo ultra fast and sensitive dynamic voltage imaging of peripheral primary sensory neurons by a newly generated genetically-encoded voltage indicator.

Identification of mechanical, thermal, or chemical stimuli-evoked voltage signals with superior temporal resolution.

Single-cell detection of changes in sub- and suprathreshold voltage dynamics across different disease conditions.

Combination of voltage (by ASAP4.4-Kv) and Ca2+ (by Pirt-GCaMP3) signals to facilitate the understanding of signal processing and integration of primary sensory neurons, especially for noxious versus non-noxious sensation.
Noninvasive genetic surveys before and after a megafire detect displacement of migratory mule deer
Authors: Brazeal Jennifer L. , Sollmann Rahel , Sacks Benjamin N.
Published: May 2021

Due to climate change and past logging and fire suppression, the western US are experiencing increasingly large and frequent wildfires. Understanding how wildlife respond to these mega-fires is becoming increasingly relevant to protect and manage these populations. However, the lack of predictability inherent in such events makes studies difficult to plan. We took advantage of a large high-severity wildfire that burned adjacent to an ongoing study of mule deer (Odocoileus hemionus) on their summer range upslope of the fire to investigate their displacement onto our study area both immediately and upon their return to summer range the following year. We used spatial capture-recapture models in conjunction with noninvasive fecal DNA sampling to estimate density and non-spatial Pradel robust-design models to estimate apparent survival and recruitment rates. Compared to density before the fire, we observed an increase in deer density and an increase in per-capita recruitment rates one month after the fire. These findings suggest that the immediate response of at least some deer was to flee the fire upslope onto the study area rather than to downslope toward their winter range. These changes did not carry over into the following year, however, suggesting that deer formerly using the burned area as summer range may have returned there despite the high severity of the fire, or may have chosen new areas for their summer range. This suggests that, at least in the short term, the fire did not negatively affect the deer population.
Intrapopulation adaptive variance supports selective breeding in a reef-building coral
Authors: Drury Crawford , Bean Nina , Harris Casey , Hancock Josh , Hucekba Joel , Christian Martin H. , Roach Ty , Quinn Robert , Gates Ruth D.
Published: May 2021

The long-term persistence of coral reefs under climate change requires heritable drivers of thermal tolerance which support adaptation. The genomic basis of thermal tolerance has been evaluated across strong spatial and environmental gradients, but this variation also exists within populations due to neutral evolutionary processes. Small scale heterogeneity in coral bleaching is ubiquitous, so we used corals from a single reef to examine genomic signatures of bleaching performance, their biochemical correlates and the downstream consequences of selective breeding. In the absence of directional selection due to environmental differences, adult corals from a single population exhibit strong genomic patterns related to natural bleaching tolerance and symbiosis state, including functional differentiation in signaling pathways, protein and amino acid modification and metabolism. Conversely, growth, development and innate immune responses did not distinguish bleaching tolerance in adult corals. The genomic signatures of these gene ontologies influence biochemical patterns in healthy corals, primarily via cell-signaling pathway impacts on peptides and amino acids. Thermal tolerance in this population is highly heritable, with significantly higher survivorship under temperature stress in larvae and juveniles reared from thermally tolerant parents than those from sensitive parents. Using a select and re-sequence approach, certain gene ontologies were reproducibly impacted, while antioxidant activity and cell signaling ontologies were disproportionately selected in thermally tolerant corals, demonstrating the genomic drivers of successful selective breeding. These data show that intrapopulation variance in the absence of historical selection supports the adaptive capacity of coral reefs under climate change.
Leveraging a founder population to identify novel rare-population genetic determinants of lipidome
Authors: Montasser May E. , Aslibekyan Stella , Srinivasasainagendra Vinodh , Tiwari Hemant K. , Patki Amit , Bagheri Minoo , Kind Tobias , Barupal Dinesh Kumar , Fan Sili , Perry James , Ryan Kathleen A. , Arnett Donna K. , Beitelshees Amber L. , Irvin Marguerite Ryan , O’Connell Jeffrey R.
Published: May 2021

Identifying the genetic determinants of inter-individual variation in lipid species (lipidome) may provide deeper understanding and new insight into the mechanistic effect of complex lipidomic pathways in CVD risk and progression beyond simple traditional lipids. Previous studies have been largely population based and thus only powered to discover associations with common genetic variants. Founder populations represent a powerful resource to accelerate discovery of novel biology associated with rare population alleles that have risen to higher frequency due to genetic drift. We performed a GWAS of 355 lipid species in 650 individuals from the Old Order Amish founder population including 127 lipid species not previously tested. We report for the first time the lipid species associated with two rare-population but Amish-enriched lipid variants:APOB_rs5742904 andAPOC3_rs76353203. We also identified novel associations for 3 rare-population Amish-enriched loci with several sphingolipids and with proposed potential functional/causal variant in each locus includingGLPTD2_rs536055318,CERS5_rs771033566, andAKNA_rs531892793. We replicated 7 previously known common loci including novel associations with two sterols: androstenediol withUGTlocus on chromosome 2 and estriol withSLC22A8/A24locus on chromosome 11. Our results show the power of founder populations to discover novel biology due to genetic drift that can increase the frequency of an allele from only few copies in large sample cohorts such as the UK Biobank to dozens of copies in sample size as small as 650.
Design and modular assembly of synthetic intramembrane proteolysis receptors for custom gene regulation in therapeutic cells
Authors: Zhu Iowis , Liu Raymond , Hyrenius-Wittsten Axel , Piraner Dan I. , Alavi Josef , Israni Divya V. , Khalil Ahmad S. , Roybal Kole T.
Published: May 2021

Synthetic biology has established powerful tools to precisely control cell function. Engineering these systems to meet clinical requirements has enormous medical implications. Here, we adopted a clinically driven design process to build receptors for the autonomous control of therapeutic cells. We examined the function of key domains involved in regulated intramembrane proteolysis and showed that systematic modular engineering can generate a class of receptors we call SyNthetic Intramembrane Proteolysis Receptors (SNIPRs) that have tunable sensing and transcriptional response abilities. We demonstrate the potential transformative utility of the receptor platform by engineering human primary T cells for multi-antigen recognition and production of dosed, bioactive payloads relevant to the treatment of disease. Our design framework enables the development of fully humanized and customizable transcriptional receptors for the programming of therapeutic cells suitable for clinical translation.
Demuxalot: scaled up genetic demultiplexing for single-cell sequencing
Authors: Rogozhnikov Alex , Ramkumar Pavan , Shah Kevan , Bedi Rishi , Kato Saul , Escola G. Sean
Published: May 2021

Demultiplexing methods have facilitated the widespread use of single-cell RNA sequencing (scRNAseq) experiments by lowering costs and reducing technical variations. Here, we present demuxalot: a method for probabilistic genotype inference from aligned reads, with no assumptions about allele ratios and efficient incorporation of prior genotype information from historical experiments in a multi-batch setting. Our method efficiently incorporates additional information across reads originating from the same transcript, enabling up to 3x more calls per read relative to naive approaches. We also propose a novel and highly performant tradeoff between methods that rely on reference genotypes and methods that learn variants from the data, by selecting a small number of highly informative variants that maximize the marginal information with respect to reference single nucleotide variants (SNVs). Our resulting improved SNV-based demultiplex method is up to 3x faster, 3x more data efficient, and achieves significantly more accurate doublet discrimination than previously published methods. This approach renders scRNAseq feasible for the kind of large multi-batch, multi-donor studies that are required to prosecute diseases with heterogeneous genetic backgrounds.
Co-option of immune effectors by the hormonal signalling system triggering metamorphosis inDrosophila melanogaster
Authors: Nunes Catarina , Koyama Takashi , Sucena Élio
Published: May 2021

Insect metamorphosis is regulated by the production, secretion and degradation of two peripheral hormones: 20-hydroxyecdysone (ecdysone) and juvenile hormone (JH). In addition to their roles in developmental regulation, increasing evidence suggests that these hormones are involved in innate immunity processes, such as phagocytosis and the induction of antimicrobial peptide (AMP) production. AMP regulation includes systemic responses as well as local responses at surface epithelia that contact with the external environment. At pupariation,Drosophila melanogasterincreases dramatically the expression of three AMP genes,drosomycin (drs), drosomycin-like 2 (drsl2)anddrosomycin-like 5 (drsl5). We show that the systemic action ofdrsat pupariation is dependent on ecdysone signalling in the fat body and operates via the ecdysone downstream target, Broad-Z4. In parallel, ecdysone also regulates local responses, specifically through the activation ofdrsl2expression in the gut. Finally, we confirm the relevance of this ecdysone dependent AMP expression for the control of bacterial persistence by showing that flies lackingdrsexpression in the fat body have higher bacterial persistence over metamorphosis. Together, our data emphasize the importance of the association between ecdysone signalling and immunity usingin vivostudies and establish a new role for ecdysone at pupariation, which impacts developmental success by regulating the immune system in a stage-dependent manner. We speculate that this co-option of immune effectors by the hormonal system may constitute a pre-emptive mechanism to control bacterial numbers in the pupa at the core of metamorphosis evolution.
Fast processing of environmental DNA metabarcoding sequence data using convolutional neural networks
Authors: Flück Benjamin , Mathon Laëtitia , Manel Stéphanie , Valentini Alice , Dejean Tony , Albouy Camille , Mouillot David , Thuiller Wilfried , Murienne Jérôme , Brosse Sébastien , Pellissier Loïc
Published: May 2021

1

The intensification of anthropogenic pressures have increased consequences on biodiversity and ultimately on the functioning of ecosystems. To monitor and better understand biodiversity responses to environmental changes using standardized and reproducible methods, novel high-throughput DNA sequencing is becoming a major tool. Indeed, organisms shed DNA traces in their environment and this “environmental DNA” (eDNA) can be collected and sequenced using eDNA metabarcoding. The processing of large volumes of eDNA metabarcoding data remains challenging, especially its transformation to relevant taxonomic lists that can be interpreted by experts. Speed and accuracy are two major bottlenecks in this critical step. Here, we investigate whether convolutional neural networks (CNN) can optimize the processing of short eDNA sequences. We tested whether the speed and accuracy of a CNN are comparable to that of the frequently used OBITools bioinformatic pipeline. We applied the methodology on a massive eDNA dataset collected in Tropical South America (French Guiana), where freshwater fishes were targeted using a small region (60pb) of the 12S ribosomal RNA mitochondrial gene. We found that the taxonomic assignments from the CNN were comparable to those of OBITools, with high correlation levels and a similar match to the regional fish fauna. The CNN allowed the processing of raw fastq files at a rate of approximately 1 million sequences per minute which was 150 times faster than with OBITools. Once trained, the application of CNN to new eDNA metabarcoding data can be automated, which promises fast and easy deployment on the cloud for future eDNA analyses.
Predicting behavior through dynamic modes in resting-state fMRI data
Authors: Ikeda Shigeyuki , Kawano Koki , Watanabe Soichi , Yamashita Okito , Kawahara Yoshinobu
Published: May 2021

Dynamic properties of resting-state functional connectivity (FC) provide rich information on brainbehavior relationships. Dynamic mode decomposition (DMD) has been used as a method to characterize FC dynamics. However, it remains unclear whether dynamic modes (DMs), spatial-temporal coherent patterns computed by DMD, provide information about individual behavioral differences. This study established a methodological approach to predict individual differences in behavior using DMs. Furthermore, we investigated the contribution of DMs within each of seven specific frequency bands (0-0.1,…,0.6–0.7 Hz) for prediction. To validate our approach, we confirmed whether each of 59 behavioral measures could be predicted by performing multivariate pattern analysis on a gram matrix, which was created using subject-specific DMs computed from resting-state functional magnetic resonance imaging (rs-fMRI) data of individuals. The prediction was successful, and DMD outperformed temporal independent component analysis, a conventional data decomposition method for extracting spatial activity patterns. Most of the behavioral measures that showed significant prediction accuracies in a permutation test were cognitive-behavioral measures. Our results suggested that DMs within frequency bands <0.2 Hz primarily contributed to prediction. In addition, we found that DMs <0.2 Hz had spatial structures similar to several common resting-state networks. We demonstrated the effectiveness of DMs, indicating that DMD is a key approach for extracting spatiotemporal features from rs-fMRI data.
Gains of 12p13.31 delay WNT-mediated initiation of hPSC differentiation and promote residual pluripotency in a cell cycle dependent manner
Authors: Keller Alexander , Lei Yingnan , Krivec Nuša , de Deckersberg Edouard Couvreu , Dziedzicka Dominika , Markouli Christina , Sermon Karen , Geens Mieke , Spits Claudia
Published: May 2021

Though gains of chromosome 12p13.31 are highly recurrent in hPSC, their impact on differentiation is poorly understood. We identify a reduction in differentiation capacity towards all three germ layers and a subpopulation of residual pluripotent cells that appear during hepatic specification. These cells form as a result of the overexpression of NANOG and GDF3, whereby NANOG as the primary driver delays activation of WNT signaling, partly as a result of a direct physical interaction with TCF7. Entry into the residual state is determined by cell cycle position at the onset of differentiation and is maintained by a feedback loop between NANOG and GDF3. These findings highlight the ability of genetically abnormal hPSC to escape correct differentiation and to form residual pluripotent cells, an important risk in the safe clinical translation of hPSC. Our results further refine the molecular mechanisms that underpin the exit from pluripotency and onset of differentiation.
Structural basis of the interaction between SETD2 methyltransferase and hnRNP L paralogs for governing co-transcriptional splicing
Authors: Bhattacharya Saikat , Wang Suman , Reddy Divya , Shen Siyuan , Zhang Ying , Zhang Ning , Li Hua , Washburn Michael P. , Florens Laurence , Shi Yunyu , Li Fudong , Workman Jerry L.
Published: May 2021

The RNA recognition motif (RRM) binds to nucleic acids as well as proteins. More than one such domain is found in the pre-mRNA processing hnRNP proteins. While the mode of RNA recognition by RRMs is known, the molecular basis of their protein interaction remains obscure. Here we describe the mode of interaction between hnRNP L and LL with the methyltransferase SETD2. We demonstrate that for the interaction to occur, a leucine pair within a highly conserved stretch of SETD2 insert their side chains in hydrophobic pockets formed by hnRNP L RRM2. Notably, the structure also highlights that RRM2 can form a ternary complex with SETD2 and RNA. Remarkably, mutating the leucine pair in SETD2 also results in its reduced interaction with other hnRNPs. Importantly, the similarity that the mode of SETD2-hnRNP L interaction shares with other related protein-protein interactions reveals a conserved design by which splicing regulators interact with one another.
Comparison of human and mouse tissues with focus on genes with no 1-to-1 homology
Authors: Jeong Jieun , Kellis Manolis
Published: May 2021

We assembled a panel of 28 tissue pairs of human and mouse with RNA-Seq data on gene expression. We focused on genes with no 1-to-1 homology, because they pose special challenges. In this way, we identified expression patterns that identify and explain differences between the two species and suggest target genes for therapeutic applications. Here we mention three examples.

One pattern is observed by defining the aggregate expression of immunoglobulin genes (which have no homology) as a measure of different levels of an immune response. In Lung, we used this statistic to find genes that have significantly higher expression in low/moderate response, and thus they may be therapy targets: increasing their expression or mimicking their function with medications may help in recovery from inflammation in the lungs. Some of the observed associations are common to human and mouse; other associations involve genes involved in cell-to-cell signaling or in regeneration but were not known to be important in Lung.

Second pattern is that in the Small Intestine, mouse expresses much less antimicrobial defensins, while it has much higher expression of enzymes that are found to improve adaptive immune response. Such enzymes may be tested if they improve probiotic supplements that help in gut inflammation and other diseases.

Another pattern involves a many-to-many homology group of defensins that did not have a described function. In human tissues, expression of its genes was found only in a study of a disease of hair covered skin, but several of its genes are highly expressed in two tissues of our panel: mouse Skin and to a lesser degree mouse Vagina. This suggests that those genes or their homologs in other species may provide non-antibiotic medications for hair covered skin and other tissues with microbiome that includes fungi.
Ebola virus glycoprotein domains associated with protective efficacy
Authors: Bhatia Bharti , Furuyama Wakako , Hoenen Thomas , Feldmann Heinz , Marzi Andrea
Published: May 2021

Ebola virus (EBOV) is the cause of sporadic outbreaks of human hemorrhagic disease in Africa, and the best-characterized virus in the filovirus family. The West Africa epidemic accelerated the clinical development of vaccines and therapeutics leading to licensure of vaccines and antibody-based therapeutics for human use in recent years. The most widely used vaccine is based on vesicular stomatitis virus (VSV) expressing the EBOV glycoprotein (GP)(VSV-EBOV). Due to its favorable immune cell targeting, this vaccine has also been used as base-vector for the development of second generation VSV-based vaccines against Influenza, Nipah, and Zika viruses. However, in these situations it may be beneficial if the immunogenicity against EBOV GP is minimized to induce a better protective immune response against the other foreign immunogen. Here, we analyzed if EBOV GP can be truncated to be less immunogenic yet still able to drive replication of the vaccine vector. We found that the EBOV GP glycan cap and the mucin-like domain are both dispensable for VSV-EBOV replication. The glycan cap domain, however, appears critical for mediating a protective immune response against lethal EBOV challenge in mice.
Reactive/Non-cooperative individuals advance Population’s Synchronization: Modeling ofDictyostelium discoideumConcerted Signaling during Aggregation Phase
Authors: Eidi Zahra , Khorasani Najme , Sadeghi Mehdi
Published: May 2021

Orchestrated chemical signaling of single cells sounds to be a linchpin of emerging organization and multicellular life form. The social amoebaDictiostelium discoiudiumis a well-studied model organism to explore overall pictures of grouped behavior in developmental biology. The chemical waves secreted by aggregatingDictiosteliumis a superb example of pattern formation. The waves are either circular or spiral in shape, according to the incremental population density of a self-aggregating community of individuals. Here, we revisit the spatiotemporal patterns that appear in an excitable medium due to synchronization of randomly firing individuals, but with a more parsimonies attitude. According to our model, a fraction of these individuals is refusal to amplify external stimulants. Our simulations indicate that the cells enhance the system’s asymmetry and as a result, nucleate early sustainable spiral territory zones, provided that their relative population does not exceed a tolerable threshold.
Non-coding NFKBIZ 3′ UTR mutations promote cell growth and resistance to targeted therapeutics in diffuse large B-cell lymphoma
Authors: Arthur Sarah E. , Gao Jie , Healy Shannon , Rushton Christopher K. , Thomas Nicole , Hilton Laura K. , Dreval Kostiantyn , Tang Jeffrey , Alcaide Miguel , Cojocaru Razvan , Mottok Anja , Telenius Adèle , Unrau Peter , Wilson Wyndham H. , Staudt Louis M. , Scott David W. , Hodson Daniel J , Steidl Christian , Morin Ryan D.
Published: May 2021

Amplifications and non-coding 3′ UTR mutations affecting NFKBIZ have been identified as recurrent genetic events in diffuse large B-cell lymphoma (DLBCL). We confirm the prevalence and pattern of NFKBIZ 3′ UTR mutations in independent cohorts and determine they are enriched in the ABC subtype as well as the recently described novel BN2/C1/NOTCH2 classes of DLBCL. Presently, the effects of and mechanism by which non-coding mutations can act as cancer drivers has been relatively unexplored. Here, we provide a functional characterization of these non-coding NFKBIZ 3′ UTR mutations. We demonstrate that the resulting elevated expression of IκB-ζ confers growth advantage in DLBCL cell lines and primary germinal center B-cells as well as nominate novel IκB-ζ target genes with potential therapeutic implications. The limited responses to targeted treatments in DLBCL, particularly those targeting the NF-κB axis, led us to investigate and confirm that NFKBIZ 3′ UTR mutations affect response to therapeutics and suggest it may be a useful predictive biomarker.

Statement of Significance

Through functional characterization we reveal that non-coding NFKBIZ 3′ UTR mutations are a common driver in DLBCL, and mutation status may be a relevant biomarker to predict poor response to therapeutics targeting the NF-κB pathway.
The endoplasmic reticulum associated degradation adaptor Sel1L regulates T cell homeostasis and function
Authors: Dils Alexander T. , Correa Luis O. , Gronevelt J. Paige , Liu Lu , Kadiyala Padma , Li Qing , Carty Shannon A.
Published: May 2021

Suppressor/Enhancer of Lin-12-like (Sel1L) is a critical adaptor for endoplasmic reticulum-associated degradation (ERAD), a process that maintains cellular protein quality control through degradation of misfolded proteins. Here we investigate the role of Sel1L in T cell homeostasis and function. T cell-specific deletion of Sel1L profoundly impairs peripheral T cell survival and promotes apoptotic cell death. Furthermore, Sel1L is required to maintain naïve CD8+ T cell homeostasis in a cell-intrinsic manner with loss of quiescence as evidenced by increased proliferation. Sel1L-deficient T cells exhibit enhanced activation of the mammalian target of rapamycin (mTOR) pathway and altered cellular metabolism, including increased cellular reactive oxygen species, mitochondrial mass and mitochondrial membrane potential in the naïve CD8+ T cell compartment. Furthermore, loss of Sel1L impaired CD8+ T cell immune responses following bacterial infection. These results demonstrate a novel role for Sel1L/ERAD in T cell homeostasis and function.
A novel SERPINE1-FOSB fusion gene in a case of pseudomyogenic hemangioendothelioma results in activation of intact FOSB and the PI3K-AKT-mTOR signaling pathway and responsiveness to sirolimus
Authors: Ren Jun , Wang Xiaohui , Zhou Yulin , Yue Xin , Chen Shouhui , Ding Xin , Jiang Xiaoyong , Liu Xiaokun , Guo Qiwei
Published: May 2021

Pseudomyogenic hemangioendothelioma (PHE) is an extremely rare disease that affects mainly the young and more men than women. PHE are multicentric, locally aggressive, have low metastatic potential, and affect multiple tissue planes. Genetic aberrations are frequently detected in PHE and may play important roles in the occurrence, development, and treatment of this disease. In this study, we report a case of PHE with a novel SERPINE1-FOSB fusion gene. The fusion introduced a strong promoter near the coding region of FOSB, resulting in overexpression of intact FOSB. Immunohistochemical analysis showed overexpression of pAKT and mTOR in tumor cells, suggesting activation of the PI3K-AKT-mTOR signaling pathway. The patient responded well to targeted therapy with sirolimus, an mTOR inhibitor. Our study correlated dysregulation of a specific signaling pathway and the effectiveness of a targeted therapy to a specific genetic aberration. This information may be useful for future investigations of targeted therapeutics and provide a potential predictive biomarker for therapeutic effectiveness in cases of PHE with this genetic aberration.
Tmem138, a photoreceptor connecting cilium (CC) protein, is required for rhodopsin transport across the cilium and outer segment (OS) biogenesis
Authors: Guo Dianlei , Ru Jiali , Xie Lijing , Wu Mingjuan , Su Yingchun , Zhu Shiyong , Xu Shujuan , Wei Yanhong , Liu Xialin , Liu Yizhi , Liu Chunqiao
Published: May 2021

Photoreceptor connecting cilium (CC) is structurally analogous to the transition zone (TZ) of primary cilia and gates the molecular trafficking between the inner and the outer segment (OS). Retinal dystrophies with underlying CC defects are manifested in a broad array of syndromic conditions known as ciliopathies as well as non-syndromic retinal degenerations. Despite extensive studies, protein trafficking across the photoreceptor CC is largely unknown. Here we genetically inactivated mouse Tmem138, a gene encoding a ciliary membrane protein localized to the ciliary TZ and linked to Joubert syndrome (JBTS). Germline deletion of Tmem138 abolished OS morphogenesis followed by rapid photoreceptor degeneration. Tmem138 was found localized to the photoreceptor CC and, accordingly, the molecular compartments of the CC and axoneme of the mutant photoreceptors were altered despite ciliogenesis proceeding normally at the early stage of photoreceptor development. To gain further insights into Tmem138 function in OS biogenesis, we focused on trafficking of rhodopsin, the most abundant protein of the OS. Mislocalization of rhodopsin was readily observed as early as P5 in the mutant photoreceptors prior to growth of the OS. Ablation of Tmem138 in mature rods recapitulated the molecular changes in the germline mutants, causing well-formed outer segment discs to disintegrate accompanied by mislocalization of rhodopsin in the cell body. Furthermore, Tmem138 interacted with rhodopsin, and two additional CC compartment proteins Ahi1 and Tmem231, which were both altered in the mutant photoreceptors. Taken together, these results suggest that Tmem138 has a distinct role in gating the transport of rhodopsin and likely other OS bound proteins through formation of CC transport complex(es).
The spatial landscape of progression and immunoediting in primary melanoma at single cell resolution
Authors: Nirmal Ajit J. , Maliga Zoltan , Vallius Tuulia , Quattrochi Brian , Chen Alyce A. , Jacobson Connor A. , Pelletier Roxanne J. , Yapp Clarence , Arias-Camison Raquel , Chen Yu-An , Lian Christine G. , Murphy George F. , Santagata Sandro , Sorger Peter K.
Published: May 2021

Cutaneous melanoma is a highly immunogenic malignancy, surgically curable at early stages, but life- threatening when metastatic. Here we integrate high-plex imaging, 3D high-resolution microscopy, and spatially-resolved micro-region transcriptomics to study immune evasion and immunoediting in primary melanoma. We find that recurrent cellular neighborhoods involving tumor, immune, and stromal cells change significantly along a progression axis involving precursor states, melanomain situ,and invasive tumor. Hallmarks of immunosuppression are already detectable in precursor regions. When tumors become locally invasive, a consolidated and spatially restricted suppressive environment forms along the tumor-stromal boundary. This environment is established by cytokine gradients that promote expression of MHC-II and IDO1, and by PD1-PDL1 mediated cell contacts involving macrophages, dendritic cells, and T cells. A few millimeters away, cytotoxic T cells synapse with melanoma cells in fields of tumor regression. Thus, invasion and immunoediting can co-exist within a few millimeters of each other in a single specimen.

STATEMENT OF SIGNIFICANCE

The reorganization of the tumor ecosystem in primary melanoma is an excellent setting in which to study immunoediting and immune evasion. Guided by classical histopathology, spatial profiling of proteins and mRNA reveals recurrent morphological and molecular features of tumor evolution that involve localized paracrine cytokine signaling and direct cell-cell contact.
Biomechanics and Myofibrillar Alignment Enhance Contractile Development and Reproducibility in Stem Cell Derived Cardiac Muscle
Authors: Tsan Yao-Chang , Zhao Yan-Ting , DePalma Samuel J. , Capilnasiu Adela , Wu Yu-Wei , Elder Brynn , Panse Isabella , Friedline Sabrina , O’Leary Thomas S. , Wubshet Nadab , Ho Kenneth K. Y. , Previs Michael J. , Nordsletten David , Baker Brendon M. , Isom Lori L. , Liu Allen P. , Helms Adam S.
Published: May 2021

Human pluripotent stem cell derived cardiomyocytes (hPSC-CMs) allow novel investigations of human cardiac disease, but disorganized mechanics and immaturity of hPSC-CMs on two-dimensional (2D) surfaces have been hurdles for efficient and reproducible study of these cells. Here, we developed a platform of micron-scale 2D cardiac tissues (M2DCTs) to precisely control biomechanics in arrays of thousands of purified, independently contracting cardiac muscle strips in 2D. By defining geometry and workload in M2DCTs in this reductionist platform that does not incorporate other cell types, we show that myofibrillar alignment and auxotonic contractions at physiologic workload critically drive maturation of cardiac contractile function, calcium handling, and electrophysiology. Additionally, the organized biomechanics in this system facilitates rapid and automated extraction of contractile kinetic parameters from brightfield microscopy images, increasing the reproducibility and throughput of pharmacologic testing. Finally, we show that M2DCTs enable precise and efficient dissection of contractile kinetics in cardiomyopathy disease models.
Resource levelling in projects considering different activity execution modes and splitting
Authors: Khalilzadeh Mohammad
Published: May 2021

Purpose

This study aims to develop a mathematical programming model for preemptive multi-mode resource-constrained project scheduling problems in construction with the objective of levelling resources considering renewable and non-renewable resources.

Design/methodology/approach

The proposed model was solved by the exact method and the genetic algorithm integrated with the solution modification procedure coded with MATLAB software. The Taguchi method was applied for setting the parameters of the genetic algorithm. Different numerical examples were used to show the validation of the proposed model and the capability of the genetic algorithm in solving large-sized problems. In addition, the sensitivity analysis of two parameters, including resource factor and order strength, was conducted to investigate their impact on computational time.

Findings

The results showed that preemptive activities obtained better results than non-preemptive activities. In addition, the validity of the genetic algorithm was evaluated by comparing its solutions to the ones of the exact methods. Although the exact method could not find the optimal solution for large-scale problems, the genetic algorithm obtained close to optimal solutions within a short computational time. Moreover, the findings demonstrated that the genetic algorithm was capable of achieving optimal solutions for small-sized problems. The proposed model assists construction project practitioners with developing a realistic project schedule to better estimate the project completion time and minimize fluctuations in resource usage during the entire project horizon.

Originality/value

There has been no study considering the interruption of multi-mode activities with fluctuations in resource usage over an entire project horizon. In this regard, fluctuations in resource consumption are an important issue that needs the attention of project planners.
Technology options to help people with dementia or acquired cognitive impairment perform multistep daily tasks: a scoping review
Authors: Lancioni Giulio , Desideri Lorenzo , Singh Nirbhay , O'Reilly Mark , Sigafoos Jeff
Published: May 2021

Purpose

The purpose of this paper is to review studies that evaluated technology-based prompting systems for supporting participants with dementia or acquired cognitive impairment in their performance of multistep daily tasks.

Design/methodology/approach

A scoping review was conducted to identify eligible studies through a search of four electronic databases, that is, PubMed, PsycINFO, Web of Science and Institute of Electrical and Electronics Engineers.

Findings

The search, which covered the 2010–2020 period, led to the identification of 1,311 articles, 30 of which were included in the review. These articles evaluated six different types of prompting systems: context-aware, automatic computer prompting, context-aware, mediated computer prompting, teleoperated robot prompting, self-operated augmented reality prompting, self-operated computer or tablet prompting and time-based (preset) computer, tablet or smartphone prompting.

Originality/value

Technology-aided prompting to help people with dementia or acquired cognitive impairment perform relevant multistep daily tasks is considered increasingly important. This review provides a picture of the different prompting options available and of their level of readiness for application in daily contexts.