bioRxiv Science⌕ Search

Biology subjects

Russo, L.

Publications and source records attributed to Russo, L..

13 recordsLinked to original sources

Diversifying stocking practices within rangelands supports diverse plant-pollinator communities and interactions

Understanding how management alters species' biodiversity and interactions is critical for sustainable agriculture. This can be especially important for rangelands, grasslands used for livestock grazing that cover 30% of land worldwide. In rangelands, ranchers need to maximize livestock production while supporting healthy ecosystems. Grazing management can alter the impact of livestock by varying grazing timing and intensity, but its ecological impacts remain poorly understood. One critical function that may be supported in these systems is pollination; how rangeland management may alter this ecosystem service is not systematically understood. We investigated how rotational stocking, where livestock are rotated among pastures, affected plant and pollinator communities and plant-pollinator interactions using working ranches in the Southern Great Plains. Sites were managed through continuous stocking or rotation with low or high frequency. We found that high-frequency livestock rotation supported greater flower abundance, and consequently greater pollinator abundance. Pollinator orders varied in their responses to management with Hymenoptera directly responding to management, and Coleoptera and Lepidoptera responding indirectly via changes in flower abundance. Community-level changes produced more specialized interaction networks and higher interaction diversity. These community changes, and resulting species turnover, led to high interaction turnover across rangeland sites. This suggests that a mosaic of management strategies likely diversifies habitat and helps support plant and pollinator biodiversity at the landscape scale. This study demonstrates that rangelands can support plants, pollinators, and their interactions, particularly when managed with high-frequency rotational stocking.

ecology↗

Engineering a PD-L1-sensing synthetic receptor for programmable macrophage-mediated phagocytosis

Macrophages are abundant immune cells within the tumor microenvironment with intrinsic phagocytic capabilities, yet their antitumor functions are frequently suppressed by inhibitory signals. Synthetic biology enables the rational design of ligand-responsive genetic circuits to reprogram immune cell behavior. Here, we report the engineering of a synthetic Notch-based receptor that detects PD-L1, an immune-checkpoint broadly expressed by cancer cells. Upon PD-L1 engagement, the circuit triggers programmable outputs, including expression of a fluorescent reporter or CV1-Fc, that locally blocks the CD47 "dont eat me" signal. We show that circuit activation scales with PD-L1 levels, partially attenuates PD-1/PD-L1 signaling, and that conditional CV1-Fc expression enhances engulfment of SKOV-3 ovarian cancer cells by THP-1-derived macrophages in vitro. Collectively, this work reframes PD-L1 from an end-point therapeutic target to a primary input signal for synthetic circuit activation and establishes a modular framework for engineering macrophage behaviour through spatially confined, ligand-responsive control. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/700810v1_ufig1.gif" ALT="Figure 1"> View larger version (60K): org.highwire.dtl.DTLVardef@1cbb391org.highwire.dtl.DTLVardef@7a0900org.highwire.dtl.DTLVardef@1e4f6d6org.highwire.dtl.DTLVardef@109838d_HPS_FORMAT_FIGEXP M_FIG Graphical abstract. A novel -PDL1 SNIPR receptor to program macrophage outputs. PD-L1 expressed on cancer cells is detected by -PD-L1 SNIPR-engineered macrophages, triggering release of the GAL4-VP64 transcription factor and activation of a programmable actuator. Circuit activation leads to customized outputs, including biosensing and enhanced macrophage phagocytosis via CD47 blockade, as well as immunomodulatory effects through interference with the PD-1/PD-L1 checkpoint axis. This sensor-actuator framework enables spatially confined and ligand-dependent reprogramming of macrophage function. C_FIG

synthetic biology↗

Defective insulin clearance plays a primary role in the pathogenesis of chronic kidney disease in mice with null deletion of Ceacam2 gene

Endogenous insulin clearance occurs primarily in hepatocytes and to a lower extent in kidneys proximal tubule cells (KPTCs). CEACAM1 promotes receptor-mediated insulin uptake to be degraded in hepatocytes in a phosphorylation-dependent manner. Its deletion/inactivation causes hyperinsulinemia-driven insulin resistance, steatohepatitis and liver fibrosis. CEACAM2, the dominant CEACAM protein in murine KPTCs, shares a high homology with CEACAM1. Thus, we examined whether it regulates renal insulin disposal to maintain renal homeostasis. KPTCs derived from Ceacam2 null mice (Cc2-/-) exhibited lower receptor-mediated insulin uptake. Combined with the gradual decline in CEACAM1-dependent hepatic insulin clearance, impaired renal insulin clearance contributed to chronic hyperinsulinemia and insulin resistance starting at 10 months of age in Cc2-/-males. This was followed by proteinuria and reduced glomerular filtration rate in association with glomerulosclerosis and tubulointerstitial damage. Increased collagen deposition in Cc2-/- kidneys could be mediated in part, by hyperinsulinemia-driven activation of the 5{beta}1 integrin-focal adhesion kinase (FAK) signaling pathways. Together, the data demonstrated that loss of CEACAM2 impaired renal insulin clearance that contributed to hyperinsulinemia and resultant insulin resistance, followed by kidney dysfunction and renal fibrosis. This study provided an in vivo demonstration of the regulation of kidney function by insulin clearance along the liver-kidney axis.

physiology↗

LncRNA LINC00941 Links Oncogenic KRAS Signaling to Aggressiveness and Chemoresistance in Pancreatic Cancer

Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest cancers, driven largely by oncogenic KRAS, yet effective targeted therapies remain unavailable. Long noncoding RNAs (lncRNAs) are emerging as key regulators of tumor biology, but their role in KRAS-driven PDAC is not well defined. To address this gap, we integrated RNA sequencing, exome, and clinical data from The Cancer Genome Atlas (TCGA) and identified 49 long intergenic noncoding RNAs (lincRNAs) differentially expressed according to KRAS status. Among the ten most abundant, LINC00941 and AC006262.5 showed the strongest differential expression in an independent PDAC cohort from the International Cancer Genome Consortium (ICGC). Experimental validation in KRAS-mutant PDAC cell lines and isogenic pancreatic epithelial models confirmed KRAS-dependent regulation of LINC00941, which was consistently upregulated in patient tumors and correlated with poor prognosis in both TCGA and ICGC datasets. Single-cell transcriptomic analysis further demonstrated that LINC00941 is enriched in malignant epithelial populations. Functional assays revealed that LINC00941 silencing impaired migration and invasion, reduced DNA repair capacity, and sensitized PDAC cells to gemcitabine, while having little effect on viability. Supporting these findings, co-expression and enrichment analyses linked LINC00941 to pathways regulating cell adhesion, motility, extracellular matrix organization, and DNA repair. Together, these findings demonstrate that oncogenic KRAS reshapes the lncRNA landscape in PDAC and identify LINC00941 as a KRAS-regulated oncogenic lncRNA that promotes aggressiveness and chemoresistance, highlighting its prognostic value and potential as a therapeutic target.

cancer biology↗

Ablation of the evolutionarily acquired functions of the Atp1b4 gene in mice protects against obesity and increases metabolic capacity

The co-option of vertebrate orthologous ATP1B4 genes in placental mammals has radically altered the properties of the encoded BetaM proteins, which are genuine {beta}-subunits of Na,K-ATPases in lower vertebrates. Eutherian BetaM acquired an extended Glu-rich N-terminal domain resulting in complete loss of its ancestral function and became skeletal and cardiac muscle-specific component of the inner nuclear membrane. BetaM is expressed at the highest level during perinatal development and is implicated in gene regulation (Pestov et al., Proc Natl Acad Sci U S A. 2007). Here we report the long-term consequences of the Atp1b4 ablation on metabolic parameters in adult mice. BetaM deficient (Atp1b4-/Y) mice have significantly lower body weight and remarkably low adiposity. They exhibit lower fasting blood glucose, enhanced insulin sensitivity, and improved glucose tolerance as compared to their wild type littermates. Knockout mice display higher heat production, increased food intake, elevated oxygen consumption especially in darkness, and higher locomotor activity. The lower respiratory exchange ratio of knockout mice indicates that fat from the diet is metabolized rather than deposited as storage. These robust changes in mouse metabolic parameters induced by Atp1b4 disruption clearly demonstrate that eutherian BetaM plays an important role in the regulation of adult mouse metabolism. Ablation of Atp1b4, leading to the loss of evolutionarily acquired BetaM functions, serves as a model for a potential alternative pathway in mammalian evolution. Essentially, Atp1b4 ablation simulates a scenario where a specific stage in mammalian evolution is bypassed. Our results suggest that bypassing the co-option of Atp1b4 potentially reduces susceptibility to obesity.

evolutionary biology↗

Characterization of BoHV-4 ORF45

Bovine herpesvirus 4 (BoHV-4) is a Gammaherpesvirus of the genus Rhadinovirus, his natural host is the bovine whereas the African Buffalo the natural reservoir. Anyhow, BoHV-4 infection is not associated to a specific disease. Genome structure and genes are well conserved in Gammaherpesvirus, and orf45 gene and its product, ORF45, is one of those. BoHV-4 ORF45 has been suggested to be a tegument protein, however, BoHV-4 ORF45 structure and function have not yet been experimentally characterized. In the present study, it is shown that BoHV-4 ORF45, despite its poor homology with other characterized Rhadinovirus ORF45s, is structurally related to Kaposis sarcoma-associated herpesvirus (KSHV), is a phosphoprotein and localizes in the host cell nuclei. Through the generation of an ORF45-null mutant BoHV-4 and its pararevertant, it was possible to demonstrate that ORF45 is essential for BoHV-4 lytic replication and is associated to the viral particles, as for the other characterized Rhadinovirus ORF45s. Finally, the impact of BoHV-4 ORF45 on cellular transcriptome was investigated, an aspect poorly explored or not at all for other Gammaherpesvirus. Many cellular transcriptional pathways were found to be alterate, mainly those involving p90 ribosomal S6 kinase (RSK) and signal-regulated kinase (ERK) complex (RSK/ERK), thus highlighting the authentic character of BoHV-4 ORF45 and paving the way to further investigations.

microbiology↗

MAP4K4 determines cancer cell phenotype by controlling the plasma membrane-associated proteome

The composition of the plasma membrane (PM)-associated proteome of tumor cells determines cell-cell and cell-matrix interactions and the response to environmental cues. Whether the PM-associated proteome impacts the phenotype of Medulloblastoma (MB) tumor cells and how it adapts in response to growth factor cues is poorly understood. Using a spatial proteomics approach, we observed that hepatocyte growth factor (HGF)-induced activation of the receptor tyrosine kinase c-MET in MB cells changes the abundance of transmembrane and membrane-associated proteins. The depletion of MAP4K4, a pro-migratory effector kinase downstream of c-MET, leads to a specific decrease of the adhesion and immunomodulatory receptor CD155 and of components of the fast-endophilin-mediated endocytosis (FEME) machinery in the PM-associated proteome of HGF-activated MB cells. The decreased surface expression of CD155 or of the FEME effector Endophilin A1 reduces growth and invasiveness of MB tumor cells in the tissue context. These data thus describe a novel function of MAP4K4 in the control of the PM-associated proteome of tumor cells and identified two downstream effector mechanisms controlling proliferation and invasiveness of MB cells. Graphical abstractc-MET activation upon HGF stimulation induces c-MET internalization and induces downstream MAP4K4 activity. (1) MAP4K4 is required downstream of activated c-MET for the maintenance of surface presentation of CD155 in activated cells. CD155 expression is required for MB cell migration, invasion and proliferation in the tissue context. (2) MAP4K4 is required downstream of activated c-MET to maintain membrane depolarization, possibly by regulating the surface localization of several ion channels and transporters. (3) MAP4K4 is required downstream of activated c-MET cause PM-proximal localization of FEME effector CIP4, FBP17 and CIN85. The FEME effector endophilin A is necessary for MB cell migration, invasion and dissemination.

cell biology↗

Doxycycline inhibition of a pseudotyped virus transduction does not translate to inhibition of SARS-CoV-2 infectivity

The pandemic caused by the SARS-CoV-2 has created the need of compounds able to interfere with the biological processes exploited by the virus. Doxycycline, with its pleiotropic effects, including anti-viral activity, has been proposed as a therapeutic candidate for COVID-19 and about twenty clinical trials have started since the beginning of the pandemic. To gain information on the activity of doxycycline against SARS-CoV-2 infection and clarify some of the conflicting clinical data published, we designed in vitro binding tests and infection studies with a pseudotyped virus expressing the spike protein, as well as a clinically isolated SARS-CoV-2 strain. Doxycycline inhibited the transduction of the pseudotyped virus in Vero E6 and HEK-293 T cells stably expressing human receptor angiotensin-converting enzyme 2 but did not affect the entry and replication of SARS-CoV-2. Although this conclusion is apparently disappointing, it is paradigmatic of an experimental approach aimed at developing an integrated multidisciplinary platform. To avoid wasting precious time and resources we believe very stringent experimental criteria are needed in the preclinical phase, including infectious studies with SARS-CoV-2 in the platform before moving on to [failed] clinical trials. Author SummaryThe pandemic caused by the SARS-CoV-2 virus has created a completely unusual situation in rapidly searching for compounds able to interfere with the biological processes exploited by the virus. This new scenario has substantially changed the timing of drug development which has also resulted in the generation of controversial results, proving that the transition from computational screening to the clinical application requires great caution and careful studies. It is therefore necessary to establish new paradigms for evaluating the efficacy of a potential active molecule. We set up a preclinical platform aimed at identifying molecules active against SARS-CoV-2 infection developing a multidisciplinary approach based on very stringent experimental criteria, comprising in-silico studies, in vitro binding tests and infection studies with pseudovirus expressing the spike protein as well as clinically isolated SARS-CoV-2 strains. We focused our attention on doxycycline which has been suggested as potential therapeutic candidate for treating COVID-19 and is currently employed in about twenty clinical trials. Doxycycline resulted effective in inhibiting the transduction of pseudovirus but it did not affect the entry and replication of SARS-CoV-2. The results obtained underline the need to define more stringent and controlled pharmacological approaches before wasting precious time and resources with clinical trials.

pharmacology and toxicology↗

The molecular logic of the self-organization of primitive streak and neuroectoderm fates

The formation of the primitive streak (PS) and the subsequent induction of neuroectoderm are hallmarks of gastrulation. Combining an in vitro reconstitution of this process based on mouse embryonic stem cells (mESCs) with a collection of knockouts in reporter mESC lines, we reassessed the contribution of retinoic acid (RA) signaling at early stages of neural commitment and its cross-talk with TGF{beta} and Wnt signaling inhibition. Single-cell RNA sequencing analysis captured the temporal unfolding of cell type diversification from epiblast and primitive streak-like cells up to the emergence of anterior and posterior neural fates. In conditions thought to lack RA synthesis, we discovered a hitherto unidentified residual RA production via a sensitive RA reporter. Genetic perturbations proved that the RA-degrading enzyme Cyp26a1 safeguard the developmental capabilities of the PS-like cells, limiting neural differentiation in wild type and in Chrd-/-Nog-/- or Dkk1-/- cells. Finally, the knockout of the three RAR receptors highlighted their function as negative regulators of loci critical for neural induction. Overall, we identified two mechanisms whereby components of the RA pathway can control the formation of neural progenitors in our PS-like context: a RA-dependent neural induction gated by RARs, and a receptor-mediated repression in the absence of ligand.

developmental biology↗

Role of misfolded tau in the onset and progression of brain toxicity after trauma

Traumatic brain injury (TBI) is associated with widespread tau pathology in about one third of patients. We previously found that TBI induces a transmissible tau pathology (tauTBI), with late cognitive decline and synaptic dysfunction. To understand whether tauTBI is a marker of ongoing neurodegeneration or a driver of functional decline, we employed C. elegans. Brain homogenates from chronic TBI mice, or from mice in which tauTBI had been transmitted by intracerebral inoculation, impaired C. elegans motility and neuromuscular synaptic transmission. Brain homogenates from tau P301L transgenic mice, or pre-aggregated recombinant tau, induced a similar toxic response. Protease digestion or pre-incubation of homogenates with anti-tau antibodies abolished toxicity, and TBI brain homogenates from tau knock-out mice had no toxic effect. These results support a vital role of abnormal tau species in chronic neurodegeneration after TBI and set the groundwork for the development of a C. elegans-based platform for screening anti-tau compounds.

neuroscience↗

Pollinator size and its consequences: Predictive allometry for pollinating insects

O_LIBody size is an integral functional trait that underlies pollination-related ecological processes, yet it is often impractical to measure directly. Allometric scaling laws have been used to overcome this problem. However, most existing models rely upon small sample sizes, geographically restricted sampling and have limited applicability for non-bee taxa. Predictive allometric models that consider biogeography, phylogenetic relatedness and intraspecific variation are urgently required to ensure greater accuracy.\nC_LIO_LIHere, we measured body size, as dry weight, and intertegular distance (ITD) of 391 bee species (4035 specimens) and 103 hoverfly species (399 specimens) across four biogeographic regions: Australia, Europe, North America and South America. We updated existing models within a Bayesian mixed-model framework to test the power of ITD to predict interspecific variation in pollinator dry weight in interaction with different co-variates: phylogeny or taxonomy, sexual dimorphism and biogeographic region. In addition, we used ordinary least squares (OLS) regression to assess intraspecific dry weight - ITD relationships for 10 bee and five hoverfly species.\nC_LIO_LIIncluding co-variates led to more robust interspecific body size predictions for both bees (Bayesian R2: 0.946; {Delta}R2 0.047) and hoverflies (Bayesian R2: 0.821; {Delta}R2 0.058) relative to models with ITD alone. In contrast, at the intraspecific level, our results demonstrate that ITD is an inconsistent predictor of body size for bees (R2: 0.02 - 0.66) and hoverflies (R2: -0.11 - 0.44).\nC_LIO_LITherefore, predictive allometry is more suitable for interspecific comparative analyses than assessing intraspecific variation. Collectively, these models form the basis of the dynamic R package, pollimetry, which provides a comprehensive resource for allometric research concerning insect pollinators worldwide.\nC_LI

ecology↗

Quantification of gene expression patterns to reveal the origins of abnormal morphogenesis

The earliest developmental origins of dysmorphologies are poorly understood in many congenital diseases. They often remain elusive because the first signs of genetic misregulation may initiate as subtle changes in gene expression, which can be obscured later in development due to secondary phenotypic effects. We here develop a method to trace back the origins of phenotypic abnormalities by accurately quantifying the 3D spatial distribution of gene expression domains in developing organs. By applying geometric morphometrics to 3D gene expression data obtained by Optical Projection Tomography, our approach is sensitive enough to find regulatory abnormalities never previously detected. We identified subtle but significant differences in gene expression of a downstream target of the Fgfr2 mutation associated with Apert syndrome. Challenging previous reports, we demonstrate that Apert syndrome mouse models can further our understanding of limb defects in the human condition. Our method can be applied to other organ systems and models to investigate the etiology of malformations.

developmental biology↗

Human-specific NOTCH-like genes in a region linked to neurodevelopmental disorders affect cortical neurogenesis

Genetic changes causing dramatic brain size expansion in human evolution have remained elusive. Notch signaling is essential for radial glia stem cell proliferation and a determinant of neuronal number in the mammalian cortex. We find three paralogs of human-specific NOTCH2NL are highly expressed in radial glia cells. Functional analysis reveals different alleles of NOTCH2NL have varying potencies to enhance Notch signaling by interacting directly with NOTCH receptors. Consistent with a role in Notch signaling, NOTCH2NL ectopic expression delays differentiation of neuronal progenitors, while deletion accelerates differentiation. NOTCH2NL genes provide the breakpoints in typical cases of 1q21.1 distal deletion/duplication syndrome, where duplications are associated with macrocephaly and autism, and deletions with microcephaly and schizophrenia. Thus, the emergence of hominin-specific NOTCH2NL genes may have contributed to the rapid evolution of the larger hominin neocortex accompanied by loss of genomic stability at the 1q21. 1 locus and a resulting recurrent neurodevelopmental disorder.

neuroscience↗