bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Divergence of Mean Phenotypes Under Persistent Directional Selection
Authors: Devi Archana , Speyer Gil , Lynch Michael 
Published: September 2022

AbstractNumerous organismal traits, particularly at the cellular level, are likely to be under persistent directional selection across phylogenetic lineages. For such traits, unless all mutations affecting such traits have large enough effects to be efficiently selected in all species, gradients in mean phenotypes are expected to arise as a consequence of differences in the power of random genetic drift, which varies by approximately five orders of magnitude across the Tree of Life. Prior theoretical work examining the conditions under which such gradients can arise focused on the simple situation in which all genomic sites affecting the trait have identical and constant mutational effects. Here, we extend this theory to incorporate the more biologically realistic situation in which mutational effects on a trait differ among nucleotide sites. Pursuit of such modifications lead to the development of semi-analytic expressions for the ways in which selective interference arises via linkage effects in single-effect models, which then extend to more complex scenarios. The theory developed clarifies the conditions under which mutations of different selective effects mutually interfere with each others’ fixation, and shows how variance in effects among sites can substantially modify and extend the expected scaling relationships between mean phenotypes and effective population sizes.
FAM237A, rather than peptide PEN and proCCK56-63, is a ligand of the orphan receptor GPR83
Authors: Li Hao-Zheng , Wang Ya-Fen , Shao Xiao-Xia , Liu Ya-Li , Xu Zeng-Guang , Wang Shi-Long , Guo Zhan-Yun 
Published: September 2022

ABSTRACTG protein-coupled receptor 83 (GPR83) is primarily expressed in the brain and is implicated in the regulation of energy metabolism and some behaviors. Recently, the PCSK1N/proSAAS-derived peptide PEN, the procholecystokinin-derived peptide proCCK56-63, and family with sequence similarity 237 member A (FAM237A) were all reported as agonists of GPR83. However, these results have not yet been reproduced by other laboratories and thus GPR83 is still officially an orphan receptor. The PEN and proCCK56-63 share sequence similarity; however, they are completely different from FAM237A, raising doubts that all of them are ligands of GPR83. To identify its actual ligand(s), in the present study we developed a NanoLuc Binary Technology (NanoBiT)-based ligand-binding assay, fluorescent ligand-based visualization, and a NanoBiT-based β-arrestin recruitment assay for human GPR83. Using these assays, we demonstrated that mature human FAM237A could bind to GPR83 with nanomolar range affinity, which activated this receptor and induced its internalization in transfected human embryonic kidney 293T cells. However, we did not detect any interaction of PEN and proCCK56-63 with GPR83 using these assays. Thus, the results confirmed that FAM237A is an agonist of GPR83, but did not support PEN and proCCK56-63 as ligands of this receptor. Clarification of its actual endogenous agonist will pave the way for further functional studies of this brain-specific receptor. The present study also provided an efficient approach for the preparation of mature FAM237A, which would facilitate further functional studies of this difficult-to-make peptide in the future.
CD26-negative and CD26-positive tissue-resident fibroblasts contribute to functionally distinct CAF subpopulations in breast cancer
Authors: Houthuijzen Julia M. , de Bruijn Roebi , van der Burg Eline , Drenth Anne Paulien , Wientjens Ellen , Filipovic Tamara , Bullock Esme , Brambillasca Chiara S. , Nieuwland Marja , de Rink Iris , van Diepen Frank , Klarenbeek Sjoerd , Kerkhoven Ron , Brunton Valerie G. , Scheele Colinda L.G.J. , Boelens Mirjam C. , Jonkers Jos 
Published: September 2022

AbstractCancer-associated fibroblasts (CAFs) are abundantly present in the microenvironment of virtually all tumors and strongly impact tumor progression. Despite increasing insight into their function and heterogeneity, little is known regarding the origin of CAFs. Understanding the origin of CAF heterogeneity is needed to develop successful CAF-based targeted therapies. Through various transplantation studies in mice we determined that CAFs in both invasive lobular breast cancer and triple negative breast cancer originate from mammary tissue-resident normal fibroblasts (NFs). Single-cell transcriptomics, in vivo tracing and in vitro studies revealed the transition of CD26+ and CD26- NF populations into inflammatory CAFs (iCAFs) and myofibroblastic CAFs (myCAFs), respectively. In vitro functional assays showed that CD26+ NFs transition into pro-tumorigenic iCAFs which recruit myeloid cells in a CXCL12-dependent manner and enhance tumor cell invasion via matrix-metalloproteinase (MMP) activity. Together, our data show that CD26+ and CD26- NFs transform into distinct CAF subpopulations in breast cancer.
Adjusting for genetic confounders in transcriptome-wide association studies leads to reliable detection of causal genes
Authors: Zhao Siming , Crouse Wesley , Qian Sheng , Luo Kaixuan , Stephens Matthew , He Xin 
Published: September 2022

AbstractExpression Quantitative Trait Loci (eQTLs), provide valuable information on the effects of genetic variants. Many methods have been developed to leverage eQTLs to nominate candidate genes of complex traits, including colocalization analysis, transcriptome-wide association studies (TWAS), and Mendelian Randomization (MR)-based methods. All these methods, however, suffer from a key problem: when using the eQTLs of a gene to assess its role in a trait, nearby variants and nearby genetic components of expression of other genes can be correlated with the eQTLs of the test gene, while affecting the trait directly. These “genetic confounders” often lead to false discoveries. We introduced a novel statistical framework to address this challenge. Our method, causal-TWAS (cTWAS), borrowed ideas from statistical fine-mapping, and allowed us to adjust all genetic confounders. In our simulations, we found that existing methods based on TWAS, colocalization or MR all suffered from high false positive rates, often greater than 50%. In contrast, cTWAS showed calibrated false positive rates while maintaining power. Application of cTWAS on several common traits highlighted the weakness of existing methods and discovered novel candidate genes. In conclusion, cTWAS is a novel statistical framework to integrate eQTL and GWAS data, enabling reliable gene discoveries.
Zinc-based Ultrasensitive Microscopic Barrier Assay (ZnUMBA): a live-imaging method for detecting epithelial barrier breaches with spatiotemporal precision
Authors: Higashi Tomohito , Stephenson Rachel E. , Schwayer Cornelia , Huljev Karla , Heisenberg Carl-Philipp , Chiba Hideki , Miller Ann L. 
Published: September 2022

AbstractEpithelial barrier function is commonly analyzed using transepithelial electrical resistance (TER), which measures the ion flux across epithelia, or by adding traceable macromolecules to one side of the epithelium and monitoring their passage to the other side. While these methods effectively measure changes to global barrier function, they are not sensitive enough to detect local or transient disruptions in the barrier, and they do not reveal the location of barrier breaches within the context of cell or tissue morphology. Therefore, we developed a method that we named Zinc-based Ultrasensitive Microscopic Barrier Assay (ZnUMBA), which overcomes these limitations, allowing for detection of local tight junction (TJ) leaks with high spatial and temporal resolution (Stephenson et al., 2019; Varadarajan et al., 2021). Here, we present expanded applications for ZnUMBA. First, we show that ZnUMBA can be used in Xenopus embryos to measure the dynamics of barrier restoration and actin dynamics following laser injury of the junction. We also demonstrate that ZnUMBA can be effectively utilized in developing zebrafish embryos as well as cultured monolayers of Madin-Darby Canine Kidney II (MDCK II) epithelial cells. ZnUMBA is a powerful and flexible method that, with some optimization, can be applied to multiple systems to measure dynamic changes in barrier function with spatiotemporal precision.
Down the Penrose stairs: How selection for fewer recombination hotspots maintains their existence
Authors: Baker Zachary , Przeworski Molly , Sella Guy 
Published: September 2022

AbstractIn many species, meiotic recombination events tend to occur in narrow intervals of the genome, known as hotspots. In humans and mice, double strand break (DSB) hotspot locations are determined by the DNA-binding specificity of the zinc finger array of the PRDM9 protein, which is rapidly evolving at residues in contact with DNA. Previous models explained this rapid evolution in terms of the need to restore PRDM9 binding sites lost to gene conversion over time, under the assumption that more PRDM9 binding always leads to more DSBs. In recent experimental work, however, it has become apparent that PRDM9 binding on both homologs facilitates DSB repair, and moreover that, in the absence of enough symmetric binding, meiosis no longer progresses reliably. We therefore consider the possibility that the benefit of PRDM9 stems from its role in coupling DSB formation and efficient repair. To this end, we model the evolution of PRDM9 from first principles: from its binding dynamics to the population processes that govern the evolution of the zinc finger array and its binding sites in the genome. As we show, the loss of a small number of strong binding sites leads to the use of a greater number of weaker ones, resulting in a sharp reduction in symmetric binding and favoring new PRDM9 alleles that restore the use of a smaller set of strong binding sites. This decrease in PRDM9 binding symmetry and in its ability to promote DSB repair drive the rapid zinc finger turnover. These results imply that the advantage of new PRDM9 alleles is in limiting the number of binding sites used effectively, rather than in increasing net PRDM9 binding, as previously believed. By extension, our model suggests that the evolutionary advantage of hotspots may have been to increase the efficiency of DSB repair and/or homolog pairing.
PINK1 supports colorectal cancer growth by regulating the labile iron pool
Authors: Chen Brandon , Das Nupur K. , Talukdar Indrani , Singhal Rashi , Castillo Cristina , Andren Anthony , Mancias Joseph D. , Lyssiotis Costas A. , Shah Yatrik M. 
Published: September 2022

AbstractMitophagy is a cargo-specific autophagic process that recycles damaged mitochondria to promote mitochondrial turnover. PTEN-induced putative kinase 1 (PINK1) mediates the canonical mitophagic pathway. We show that PINK1 expression is positively correlated with decreased colon cancer survival, and mitophagy is required for colon cancer growth following nutrient stress. However, the mechanism by which PINK1 maintains colon cancer growth remains equivocal. Inducible knockdown (KD) of PINK1 in a panel of colon cancer cell lines inhibited colon cancer cell proliferation, whereas disruption of other mitophagy receptors did not similarly impact cellular proliferation. Mechanistically, we observed a decrease in mitochondrial respiration, membrane hyperpolarization, accumulation of mitochondrial DNA, and depletion of antioxidant glutathione following PINK1 KD. Mitochondria are important hubs for storing iron and synthesizing iron-dependent cofactors such as heme and iron sulfur clusters. An increase iron storage protein ferritin and a decrease labile iron pool was observed in PINK1 KD cells. However, neither total cellular iron nor markers of iron starvation/overload were affected. Cellular iron storage and the labile iron pool are maintained via autophagic degradation of ferritin (ferritinophagy). Overexpressing nuclear receptor coactivator 4 (NCOA4), a key adaptor for ferritinophagy, rescued cell growth and the labile iron pool in PINK1 KD cells. We demonstrate that PINK1 regulates intracellular iron availability by integrating mitophagy to ferritinophagy. In conclusion, these results indicate that PINK1 is essential for maintaining intracellular iron homeostasis to support survival and growth in colorectal cancer cells.
Phylogenetic inference from single-cell RNA-seq data
Authors: Liu Xuan , Griffiths Jason , Bishara Isaac , Liu Jiayi , Bild Andrea H. , Chang Jeffrey T. 
Published: September 2022

AbstractTumors are comprised of subpopulations of cancer cells that harbor distinct genetic profiles and phenotypes that evolve over time and during treatment. By reconstructing the course of cancer evolution, we can understand the acquisition of the malignant properties that drive tumor progression. Unfortunately, recovering the evolutionary relationship of individual cancer cells linked to their phenotypes remains a difficult challenge. To address this issue, we have developed PhylinSic, a method that reconstructs the phylogenetic relationships among cells linked to their gene expression profiles from single cell RNA-sequencing (scRNA-Seq) data, and showed that it was robust to the low read depth, drop-out, and noisiness of scRNA-Seq data. This method called nucleotide bases from scRNA-Seq reads using a probabilistic smoothing approach, and then estimated a phylogenetic tree using a Bayesian modeling algorithm. We evaluated PhylinSic and showed that it identified evolutionary relationships resulting from selective events such as drug selection and metastasis and was sensitive enough to identify subclones from genetic drift. Finally, we applied methods of phylogenetic inference and found that breast tumors resistant to chemotherapies harbored two genetic lineages that independently manifested high predicted activity of K-Ras and β-catenin, potentially acquired by distinct mechanisms through convergent evolution. This suggested that therapeutic strategies may need to target multiple lineages to be durable. Taken together, these results demonstrated that PhylinSic provides a framework to model the evolution and link the genotypes and phenotypes of cells within a tumor or cohort of monophyletic tumors using scRNA-Seq.
Diet-induced obesity alters intestinal monocyte-derived and tissue-resident macrophages in female mice independent of TNF
Authors: Breznik Jessica A. , Jury Jennifer , Verdú Elena F. , Sloboda Deborah M. , Bowdish Dawn M. E. 
Published: September 2022

AbstractMacrophages are essential for homeostatic maintenance of the anti-inflammatory and tolerogenic intestinal environment, yet monocyte-derived macrophages can promote local inflammation. Pro-inflammatory macrophage accumulation within the intestines may contribute to the development of systemic chronic inflammation and immunometabolic dysfunction in obesity. Using a model of high fat diet-induced obesity in C57BL/6J female mice, we assessed intestinal permeability by in vitro and in vivo assays, and quantitated intestinal macrophages in ileum and colon tissues by multicolour flow cytometry after short (6 weeks), intermediate (12 weeks), and prolonged (18 weeks) diet allocation. We characterized monocyte-derived CD4−TIM4− and CD4+TIM4− macrophages, as well as tissue-resident CD4+TIM4+ macrophages. Diet-induced obesity had tissue and time-dependent effects on intestinal permeability, as well as monocyte and macrophage numbers, surface phenotype, and intracellular production of the cytokines IL-10 and TNF. We found that obese mice had increased paracellular permeability, in particular within the ileum, but this did not elicit recruitment of monocytes, nor a local pro-inflammatory response by monocyte-derived or tissue-resident macrophages, in either the ileum or colon. Proliferation of monocyte-derived and tissue-resident macrophages was also unchanged. Wildtype and TNF−/- littermate mice had similar intestinal permeability and macrophage population characteristics in response to diet-induced obesity. These data are unique from reported effects of diet-induced obesity on macrophages in metabolic tissues, as well as outcomes of acute inflammation within the intestines, and collectively indicate that TNF does not mediate effects of diet-induced obesity on intestinal monocyte-derived and tissue-resident intestinal macrophages in young female mice.Abstract Figure
Acclimating to degraded environments: The social rationale for swift action on restoration
Authors: Karatayev Vadim A. , Wilson Robyn S. , Webster D.G. , Axelrod Mark , Bauch Chris T. , Anand Madhur 
Published: September 2022

As environmental degradation progresses, economies and societies adapt to the loss of ecosystem services and public attention to degradation subsides. In systems experiencing such societal acclimation to degradation, net incentives for stakeholder mitigation peak during early degradation phases and subside over time. Using harmful algae blooms in western Lake Erie as a case study, we illustrate how declines in public attention and societal reliance on lake recreation (i.e., finding recreation alternatives) reduce the incentives for stakeholders to reduce pollution runoff (i.e., mitigation efforts throughout the watershed). We then analyze how acclimation can affect a broad array of conservation challenges by developing a general socio-ecological model of societal response to degradation. We find that delays in initiating stakeholder-driven mitigation efforts can exponentially prolong restoration projects. Furthermore, when alleviating intense degradation relies upon voluntary commitments by many individuals, windows of opportunity for mitigation can be very limited because feedback loops of societal adaptation doom late restoration efforts to failure and lock human-environment systems into degraded states. These windows of opportunity can be particularly narrow when a) stakeholder mitigation requires supportive public opinion or b) even modestly valuable alternative services are available in degraded ecosystems. In such cases, maintaining undegraded human-environment regimes may hinge on quickly initiating stakeholder mitigation movements and allocating limited government conservation funds soon after degradation begins instead of spreading mitigation efforts out over decades. Such initiatives, regardless of whether acclimation is slow or rapid in a given system, also greatly accelerate the pace of environmental restoration.Significance StatementAs societies acclimate to degraded environments, mitigation efforts that hinge on action by many stakeholders can erode. Developing a socio-ecological model of acclimation, we reveal how social and environmental processes intertwine to create alternative stable socio-ecological regimes, with either: 1) undegraded ecosystem states sustained by widespread mitigation adoption, or 2) degraded states where societies neither maintain nor continue relying on traditional, local ecosystem services. This dynamic places a premium on prompt mitigation efforts, which may face narrow opportunity windows to get started and avert degraded regimes in systems that rely on stakeholder-driven mitigation. Moreover, in any system requiring stakeholder action, societal acclimation will increase the importance of early action because decaying mitigation incentives exponentially lengthen restoration efforts.
Adaptive structural and functional evolution of the placenta protects fetal growth in high elevation deer mice
Authors: Wilsterman Kathryn , Moore Emily C. , Schweizer Rena M. , Cunningham Kirksey , Good Jeffrey M. , Cheviron Zachary A. 
Published: September 2022

Environmental hypoxia challenges female reproductive physiology in placental mammals, increasing rates of gestational complications. Adaptation to high elevation has limited many of these effects in humans and other mammals, offering potential insight into the developmental processes that lead to and protect against hypoxia-related gestational complications. However, our understanding of these adaptations has been hampered by a lack of experimental work linking the functional, regulatory, and genetic underpinnings of gestational development in locally-adapted populations. Here, we dissect high-elevation adaptation in the reproductive physiology of deer mice, (Peromyscus maniculatus), a rodent species with an exceptionally broad elevational distribution that has emerged as a model for hypoxia adaptation. Using experimental acclimations, we show that lowland mice experience pronounced fetal growth restriction when challenged with gestational hypoxia, while highland mice maintain normal growth by expanding the compartment of the placenta that facilitates nutrient and gas exchange between dam and fetus. We then use compartmentspecific transcriptome analyses to show that adaptive structural remodeling of the placenta is coincident with widespread changes in gene expression within this same compartment. Genes associated with fetal growth in deer mice significantly overlap with genes involved in human placental development, pointing to conserved or convergent pathways underlying these processes. Finally, we overlay our results with genetic data from natural populations to identify can-didate genes and genomic features that contribute to these placental adaptations. Collectively, these experiments advance our understanding of adaptation to hypoxic environments by revealing physiological and genetic mechanisms that shape fetal growth trajectories under maternal hypoxia.Significance StatementResidence at high elevations is associated with higher risk pregnancies and low birth weight, yet the causal mechanisms remain poorly understood. Using a high elevation-adapted rodent model, we investigated the physiological traits that explain fetal growth trajectories in low oxygen environments, and how evolutionary adaptation has modified these traits. We showed that high- and low-elevation populations of deer mice differ in their susceptibility to fetal growth restriction during gestational hypoxia and that these population-level differences are associated with structural and transcriptomic changes in the placenta. We further link placental gene expression to genomic features under selection at high elevation. Our findings identify adaptations that are likely relevant to offsetting the effects of hypoxia on fetal and placental development across mammals.
Mis-regulation of Zn and Mn homeostasis is a key phenotype of Cu stress inStreptococcus pyogenes
Authors: Hong YoungJin , Mackenzie Eilidh S , Firth Samantha J , Bolton Jack RF , Stewart Louisa J , Waldron Kevin J , Djoko Karrera Y 
Published: September 2022

ABSTRACTAll bacteria possess homeostastic mechanisms that control the availability of micronutrient metals within the cell. Cross-talks between different metal homeostasis pathways within the same bacterial organism have been reported widely. In addition, there have been previous suggestions that some metal uptake transporters can promote adventitious uptake of the wrong metal. This work describes the cross-talk between Cu and the Zn and Mn homeostasis pathways in Group A Streptococcus (GAS). Using a ΔcopAmutant strain that lacks the primary Cu efflux pump and thus traps excess Cu in the cytoplasm, we show that growth in the presence of supplemental Cu promotes downregulation of genes that contribute to Zn or Mn uptake. This effect is not associated with changes in cellular Zn or Mn levels. Co-supplementation of the culture medium with Zn or, to a lesser extent, Mn alleviates key Cu stress phenotypes, namely bacterial growth and secretion of the fermentation end-product lactate. However, neither co-supplemental Zn nor Mn influences cellular Cu levels or Cu availability in Cu-stressed cells. In addition, we provide evidence that the Zn or Mn uptake transporters in GAS do not promote Cu uptake. Together, the results from this study strengthen and extend our previous proposal that mis-regulation of Zn and Mn homeostasis is a key phenotype of Cu stress in GAS.GRAPHICAL ABSTRACT